866 results on '"J Morin"'
Search Results
2. Integrated Pockels laser
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Mingxiao Li, Lin Chang, Lue Wu, Jeremy Staffa, Jingwei Ling, Usman A. Javid, Shixin Xue, Yang He, Raymond Lopez-rios, Theodore J. Morin, Heming Wang, Boqiang Shen, Siwei Zeng, Lin Zhu, Kerry J. Vahala, John E. Bowers, and Qiang Lin
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Science - Abstract
On-Chip integration of laser systems led to impressive development in many field of application like LIDAR or AR/VR to cite a few. Here the authors harness Pockels effect in an integrated semiconductor platform achieving fast on-chip configurability of a narrow linewidth laser.
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- 2022
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3. Oral susceptibility to ivermectin is over fifty times greater in a wild population of Anopheles albimanus mosquitoes from Belize than the STECLA laboratory reference strain of this mosquito
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Staci M. Dreyer, Kelsey J. Morin, Marla Magaña, Marie Pott, Donovan Leiva, Nicole L. Achee, John P. Grieco, and Jefferson A. Vaughan
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Anopheles albimanus ,Ivermectin ,STECLA ,Belize ,Arctic medicine. Tropical medicine ,RC955-962 ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background The STECLA strain of Anopheles albimanus has been in continuous colony for many years and is the reference strain on which genomic studies for the species are based. Recently, the STECLA strain was demonstrated to be much less susceptible to ivermectin ingested in a blood meal (4-day LC50 of 1468 ng/ml) than all other Anopheles species tested to-date (LC50 values range from 7 to 56 ng/ml). The ability of An. albimanus to survive ingestion of ivermectin at concentrations far beyond that typically found in the blood of ivermectin-treated people or livestock (i.e., 30–70 ng/ml) could invalidate the use of ivermectin as a malaria vector control strategy in areas where An. albimanus is a primary vector. Methods To investigate this, host-seeking An. albimanus were captured in northern Belize and used in membrane feeding bioassays of ivermectin, employing the same methods as described earlier with the STECLA strain. Results Field-collected An. albimanus in Belize were 55 times more susceptible to ingested ivermectin than were the STECLA reference strain. Oral susceptibility to ivermectin in wild An. albimanus from Belize (4-day LC50 of 26 ng/ml) was equivalent to that of other Anopheles species tested. Conclusions Contrary to initial assessments using a highly inbred strain of mosquito, laboratory studies using a field population indicate that ivermectin treatment of livestock could reduce An. albimanus populations in areas of Central America and the Caribbean where malaria transmission may occur. Toxicity screening of ivermectin and other systemic parasiticides for malaria control should examine wild populations of the vector species being targeted.
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- 2022
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4. Asymmetrical intraguild interactions with coyotes, red foxes, and domestic dogs may contribute to competitive exclusion of declining gray foxes
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Dana J. Morin, Damon B. Lesmeister, Clayton K. Nielsen, and Eric M. Schauber
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biotic homogenization ,co‐occurrence ,interspecific competition ,niche partitioning ,trophic downgrading ,Ecology ,QH540-549.5 - Abstract
Abstract Species coexistence is governed by availability of resources and intraguild interactions including strategies to reduce ecological overlap. Gray foxes are dietary generalist mesopredators expected to benefit from anthropogenic disturbance, but populations have declined across the midwestern USA, including severe local extirpation rates coinciding with high coyote and domestic dog occurrence and low red fox occurrence. We used data from a large‐scale camera trap survey in southern Illinois, USA to quantify intraguild spatial and temporal interactions among the canid guild including domestic dogs. We used a two‐species co‐occurrence model to make pairwise assessments of conditional occupancy and detection rates. We also estimated temporal activity overlap among species and fit a fixed‐effects hierarchical community occupancy model with the four canid species. We partitioned the posterior distributions to compare gray fox occupancy probabilities conditional on estimated state of combinations of other species to assess support for hypothesized interactions. We found no evidence of broadscale avoidance among native canids and conclude that spatial and temporal segregation were limited by ubiquitous human disturbance. Mean guild richness was two canid species at a site and gray fox occupancy was greater when any combination of sympatric canids was also present, setting the stage for competitive exclusion over time. Domestic dogs may amplify competitive interactions by increasing canid guild size to the detriment of gray foxes. Our results suggest that while human activities can benefit some mesopredators, other species such as gray foxes may serve as bellwethers for habitat degradation with trophic downgrading and continued anthropogenic homogenization.
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- 2022
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5. Comparison of methods for estimating density and population trends for low-density Asian bears
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Dana J. Morin, John Boulanger, Richard Bischof, David C. Lee, Dusit Ngoprasert, Angela K. Fuller, Bruce McLellan, Robert Steinmetz, Sandeep Sharma, Dave Garshelis, Arjun Gopalaswamy, Muhammad Ali Nawaz, and Ullas Karanth
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Abundance estimation ,Camera trap ,IUCN Red List criteria ,Population monitoring ,Power analysis ,Spatial capture recapture ,Ecology ,QH540-549.5 - Abstract
Populations of bears in Asia are vulnerable to extinction and effective monitoring is critical to measure and direct conservation efforts. Population abundance (local density) or growth (λ) are the most sensitive metrics to change. We discuss the value in implementing spatially explicit capture-recapture (SCR), the current gold standard for density estimation, and open population SCR (OPSCR) to monitor changes in density over time. We provide guidance for designing studies to provide estimates with sufficient power to detect changes. Because of the wide availability of camera traps and interest in their use, we consider six density estimation methods and their extensions developed for use with camera traps, with specific consideration of assumptions and applications for monitoring Asian bears. We conducted a power analysis to calculate the precision in estimates needed to detect changes in populations with reference to IUCN Red List criteria. We performed a systematic review of empirical studies implementing camera trap abundance estimation methods and considered sample sizes, effort, and model assumptions required to achieve adequate precision for population monitoring. We found SCR and OPSCR, reliant on “marked” individuals, are currently the only methods with enough power to reliably detect even moderate to major (20–80%) declines. Camera trap methods with unmarked individuals rarely achieved precision sufficient to detect even large declines (80–90%), although with some exceptions (e.g., situations with moderate population densities, large number of sampling sites, or inclusion of ancillary local telemetry data. We describe additional estimation options including line transects, direct observations, monitoring age-specific survival and reproductive rates, and hybrid/integrated methodologies that may have potential to work for some Asian bear populations. We conclude monitoring changes in abundance or density is possible for most Asian bear populations but will require collaboration among researchers over broad spatial extents and extensive financial investment to overcome biological and logistical constraints. We strongly encourage practitioners to consider study design and sampling effort required to meet objectives by conducting simulations, power analyses, and assumption checks prior to implementing monitoring efforts, and reporting standardized dispersion measures such as coefficients of variation to allow for assessment of precision. Our guidance is relevant to other low-density and wide-ranging species.
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- 2022
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6. Is the delineation of range maps useful for monitoring Asian bears?
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William J. McShea, Mei-Hsiu Hwang, Fang Liu, Sheng Li, Clayton Lamb, Bruce McLellan, Dana J. Morin, Karine Pigeon, Michael F. Proctor, Haydee Hernandez-Yanez, Taylor Frerichs, and David L. Garshelis
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Conservation metrics ,Asiatic black bears ,Giant pandas ,Field surveys ,Expert opinion ,Ecology ,QH540-549.5 - Abstract
Changes in the distribution of a species can be used to as a metric of conservation status and to identify the loss or gain of isolated populations. This mapping process is a primary tool of the IUCN SSC Red List assessment. Most distribution maps are based on expert opinion or species distribution models based on a combination of species detection records and known habitat and landscape affiliations for that species. However, modeling the distribution for some species is difficult due to low levels of sampling, low detectability, and loose or uncertain associations with landscape attributes. These issues may be particularly prevalent for Asian bears that have generalist habitat requirements and are heavily poached across their range. Presently the range of all bear species in Asia is delineated primarily using expert opinion. Members of the IUCN SSC Bear Specialist Group attempted to create a rule set to combine current detections with known habitat and home range preferences to improve distribution maps for the purpose of conservation metrics and monitoring. The results of applying this rule set for giant pandas (Ailuropoda melanoleuca) closely matched the current IUCN mapped range, but the results for Asiatic black bears (Ursus thibetanus) did not corroborate the IUCN map based solely on expert opinion. We present a list of recommended actions for improving distribution mapping for bears in Asia and possibly any species whose current distribution is heavily influenced by poorly measured metrics such as poaching.
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- 2022
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7. The occupancy-abundance relationship and sampling designs using occupancy to monitor populations of Asian bears
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Angela K. Fuller, Ben C. Augustine, Dana J. Morin, Karine Pigeon, John Boulanger, David C. Lee, Francesco Bisi, and David L. Garshelis
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Abundance ,Detection-non-detection ,Density ,Species occurrence ,Population trend ,False positive detection ,Ecology ,QH540-549.5 - Abstract
Designing a population monitoring program for Asian bears presents challenges associated with their low densities and detectability, generally large home ranges, and logistical or resource constraints. The use of an occupancy-based method to monitor bear populations can be appropriate under certain conditions given the mechanistic relationship between occupancy and abundance. The form of the occupancy–abundance relationship is dependent on species-specific characteristics such as home range size and population density, as well as study area size. To assess the statistical power of tests to detect population change of Asian bears, we conducted a study using a range of scenarios by simulating spatially explicit individual-based capture-recapture data from a demographically open model. Simulations assessed the power to detect changes in population density via changes in site-level occupancy or abundance through time, estimated using a standard occupancy model or a Royle-Nichols model, both with point detectors (representing camera traps). We used IUCN Red List criteria as a guide in selection of two population decline scenarios (20% and 50%), but we chose a shorter time horizon (10 years = 1 bear generation), meaning that declines were steeper than used for IUCN criteria (3 generations). Our simulations detected population declines of 50% with high power (>0.80) and low false positive rates (FPR: incorrectly detecting a decline) ( 0.67 times the home range diameter (home-range spacing ratio: HRSR, a measure of spatial correlation), such that bears would tend to overlap no more than two detectors. There was high (0.85) correlation between realized occupancy and N in these scenarios. The FPR increased as the HRSR decreased because of spatial correlation in the occupancy process induced when individual home ranges overlap multiple detectors. The mean statistical power to detect more gradual population declines (20% in 10 years) with HRSR > 0.67 was low for occupancy models 0.22 (maximum power 0.67) and Royle-Nichols models (0.24; maximum power 0.67), suggesting that declines of this magnitude may not be described reliably with 10 years of monitoring. Our results demonstrated that under many realistic scenarios that we explored, false positive rates were unacceptably high. We highlight that when designing occupancy studies, the spacing between point detectors be at least 0.67 times the diameter of the home range size of the larger sex (e.g., males) when the assumptions of the spatial capture-recapture model used for simulation are met.
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- 2022
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8. The need to step-up monitoring of Asian bears
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David L. Garshelis, Karine Pigeon, Mei-hsiu Hwang, Michael Proctor, William J. McShea, Angela K. Fuller, and Dana J. Morin
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Distribution ,Occupancy ,Population estimation ,Population density ,Population trend ,Presence data ,Ecology ,QH540-549.5 - Abstract
Many wildlife species are threatened in Asia, including the five species of terrestrial bears (Asiatic black, Ursus thibetanus; brown, U. arctos; sloth, Melursus ursinus; sun, Helarctos malayanus; giant panda, Ailuropoda melanoleuca): many populations of these bears are thought to be declining or imperiled by small population size. Here our aim is to document how population assessments have been conducted for bears in Asia. We searched the literature and identified 102 studies published during 1999–2021 that investigated the status of an Asian bear population; these occurred in 24 of the 32 bear range countries in Asia. At the most basic level, 11% of studies verified presence of bears in places where they were not known to exist. The most common objective (53% of papers) was a distribution map, often derived from presence locations in a habitat-based model. Occupancy studies (15%) used temporal (time stamps on images from cameras) or spatial (transect segments) replicates, but tended to focus on “use”, so detector spacing was sometimes not appropriate for occupancy. Purported population indices, such as sign density or camera trap encounter rates, were reported in 16% of studies. One third of studies provided a population estimate, but only 10 studies in two decades used a rigorous method (e.g., mark–recapture). Sign surveys and interviews were the most common methods for determining bear presence, and local interviews were heavily relied upon for assessing population trend. Camera trapping has become increasingly prevalent, but only one study obtained a population estimate using photographs to distinguish natural individual markings. Only three studies used hair traps to obtain DNA-based population estimates, and three other studies obtained population estimates from DNA in scats. Just three studies quantitatively measured change in population size or occupancy over time, and none of these showed a decline. Unique rangewide sign surveys of giant pandas showed significant geographic expansion. The opinions of experts and local people, now heavily relied upon for population assessments, are not reliable or sensitive enough for monitoring. Quantitative population assessments are desirable to direct conservation actions toward the most perilous situations, and provide a means to gauge the effectiveness of conservation actions. This paper demonstrates the paucity of rigorous monitoring of Asian bears, and leads off a series of papers that propose improved methods for assessing distribution, occupancy, and density.
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- 2022
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9. On the importance of atmospheric loss of organic nitrates by aqueous-phase ⚫OH oxidation
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J. M. González-Sánchez, N. Brun, J. Wu, J. Morin, B. Temime-Roussel, S. Ravier, C. Mouchel-Vallon, J.-L. Clément, and A. Monod
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Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
Organic nitrates are secondary species in the atmosphere. Their fate is related to the chemical transport of pollutants from polluted areas to more distant zones. While their gas-phase chemistry has been studied, their reactivity in condensed phases is far from being understood. However, these compounds represent an important fraction of organic matter in condensed phases. In particular, their partition to the aqueous phase may be especially important for oxidized organic nitrates for which water solubility increases with functionalization. This work has studied for the first time the aqueous-phase ⚫OH-oxidation kinetics of four alkyl nitrates (isopropyl nitrate, isobutyl nitrate, 1-pentyl nitrate, and isopentyl nitrate) and three functionalized organic nitrates (α-nitrooxyacetone, 1-nitrooxy-2-propanol, and isosorbide 5-mononitrate) by developing a novel and accurate competition kinetic method. Low reactivity was observed, with kOH ranging from 8×107 to 3.1×109 L mol−1 s−1 at 296±2 K. Using these results, a previously developed aqueous-phase structure–activity relationship (SAR) was extended, and the resulting parameters confirmed the extreme deactivating effect of the nitrate group, up to two adjacent carbon atoms. The achieved extended SAR was then used to determine the ⚫OH-oxidation rate constants of 49 organic nitrates, including hydroxy nitrates, ketonitrates, aldehyde nitrates, nitrooxy carboxylic acids, and more functionalized organic nitrates such as isoprene and terpene nitrates. Their multiphase atmospheric lifetimes towards ⚫OH oxidation were calculated using these rate constants, and they were compared to their gas-phase lifetimes. Large differences were observed, especially for polyfunctional organic nitrates: for 50 % of the proposed organic nitrates for which the ⚫OH reaction occurs mainly in the aqueous phase (more than 50 % of the overall removal), their ⚫OH-oxidation lifetimes increased by 20 % to 155 % under cloud/fog conditions (liquid water content LWC = 0.35 g m−3). In particular, for 83 % of the proposed terpene nitrates, the reactivity towards ⚫OH occurred mostly (>98 %) in the aqueous phase, while for 60 % of these terpene nitrates, their lifetimes increased by 25 % to 140 % compared to their gas-phase reactivity. We demonstrate that these effects are of importance under cloud/fog conditions but also under wet aerosol conditions, especially for the terpene nitrates. These results suggest that considering aqueous-phase ⚫OH-oxidation reactivity of biogenic nitrates is necessary to improve the predictions of their atmospheric fate.
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- 2021
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10. Fine‐scale habitat selection by sympatric Canada lynx and bobcat
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Samantha J. Morin, Jeff Bowman, Robby R. Marrotte, and Marie‐Josée Fortin
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bobcat ,Canada lynx ,habitat selection ,Lynx canadensis ,Lynx rufus ,snow tracking ,Ecology ,QH540-549.5 - Abstract
Abstract The Canada lynx (Lynx canadensis) and the bobcat (Lynx rufus) are closely related species with overlap at their range peripheries, but the factors that limit each species and the interactions between them are not well understood. Habitat selection is a hierarchical process, in which selection at higher orders (geographic range, home range) may constrain selection at lower orders (within the home range). Habitat selection at a very fine scale within the home range has been less studied for both lynx and bobcat compared to selection at broader spatiotemporal scales. To compare this fourth‐order habitat selection by the two species in an area of sympatry, we tracked lynx and bobcat during the winters of 2017 and 2018 on the north shore of Lake Huron, Ontario. We found that both lynx and bobcat selected shallower snow, higher snowshoe hare abundance, and higher amounts of coniferous forest at the fourth order. However, the two species were spatially segregated at the second order, and lynx were found in areas with deeper snow, more snowshoe hare, and more coniferous forest. Taken together, our findings demonstrate that the lynx and bobcat select different resources at the second order, assorting along an environmental gradient in the study area, and that competition is unlikely to be occurring between the two species at finer scales.
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- 2020
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11. Spatial segregation and habitat partitioning of bobcat and Canada lynx
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Robby R. Marrotte, Jeff Bowman, and Samantha J. Morin
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spatial segregation ,habitat partitioning ,lynx rufus ,lynx canadensis ,occupancy ,competition ,Education ,Science - Abstract
Harvest records suggest that the abundance of bobcats (Lynx rufus) has increased and the leading edge of their distribution has spread northward, while the trailing edge of the Canada lynx (Lynx canadensis) range has contracted in Ontario, Canada. There has been a debate about whether these closely related felids might compete in areas of sympatry, but there is little research on sympatric populations of bobcat and lynx. Both species are found on the north shore of Lake Huron in Ontario, Canada, which provided an opportunity to investigate their spatial patterns and habitat use. We surveyed snowmobile routes for snow tracks over three winters and estimated probability of occupancy for the two felid species while accounting for detectability. Bobcat and lynx tracks were never found on the same survey route. Bobcat occupancy increased with habitat heterogeneity, whereas lynx occupancy increased with homogeneity. Our results fit with the common assumption of the generalist and specialist natures of bobcat and lynx, respectively. Our findings suggest that bobcats invaded former lynx territory after these areas became vacant. The story of the bobcat and the lynx is one of the loss of a unique, boreal specialist due to anthropogenic change, and eventual replacement by an adaptable generalist.
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- 2020
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12. Unbiased interrogation of memory B cells from convalescent COVID-19 patients reveals a broad antiviral humoral response targeting SARS-CoV-2 antigens beyond the spike protein
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Jillian M. DiMuzio, Baron C. Heimbach, Raymond J. Howanski, John P. Dowling, Nirja B. Patel, Noeleya Henriquez, Chris Nicolescu, Mitchell Nath, Antonio Polley, Jamie L. Bingaman, Todd Smith, Benjamin C. Harman, Matthew K. Robinson, Michael J. Morin, and Pavel A. Nikitin
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Convalescent plasma ,COVID-19 ,Antibody response ,B cell repertoire ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Patients who recover from SARS-CoV-2 infections produce antibodies and antigen-specific T cells against multiple viral proteins. Here, an unbiased interrogation of the anti-viral memory B cell repertoire of convalescent patients has been performed by generating large, stable hybridoma libraries and screening thousands of monoclonal antibodies to identify specific, high-affinity immunoglobulins (Igs) directed at distinct viral components. As expected, a significant number of antibodies were directed at the Spike (S) protein, a majority of which recognized the full-length protein. These full-length Spike specific antibodies included a group of somatically hypermutated IgMs. Further, all but one of the six COVID-19 convalescent patients produced class-switched antibodies to a soluble form of the receptor-binding domain (RBD) of S protein. Functional properties of anti-Spike antibodies were confirmed in a pseudovirus neutralization assay. Importantly, more than half of all of the antibodies generated were directed at non-S viral proteins, including structural nucleocapsid (N) and membrane (M) proteins, as well as auxiliary open reading frame-encoded (ORF) proteins. The antibodies were generally characterized as having variable levels of somatic hypermutations (SHM) in all Ig classes and sub-types, and a diversity of VL and VH gene usage. These findings demonstrated that an unbiased, function-based approach towards interrogating the COVID-19 patient memory B cell response may have distinct advantages relative to genomics-based approaches when identifying highly effective anti-viral antibodies directed at SARS-CoV-2.
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- 2021
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13. Long‐term monitoring using DNA sampling reveals the dire demographic status of the critically endangered Gobi bear
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Odbayar Tumendemberel, Joel M. Tebbenkamp, Andreas Zedrosser, Michael F. Proctor, Erik J. Blomberg, Dana J. Morin, Frank Rosell, Harry V. Reynolds, Jennifer R. Adams, and Lisette P. Waits
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brown bear ,genetic sampling ,Gobi Desert ,population abundance and density ,spatial capture–recapture ,survival ,Ecology ,QH540-549.5 - Abstract
Abstract Information about population demography is crucial for developing and implementing conservation measures. The brown bear in the Gobi desert of southwestern Mongolia (referred to as the Gobi bear) is one of the smallest and most isolated brown bear populations in the world. We conducted genetic sampling (n = 2660 samples collected) using hair corrals around feeding sites at 13 water sources during 2009, 2013, and 2017 to evaluate population size, survival, and population trend. Bears were identified using 13 microsatellite loci and one sex marker. We detected 51 unique individuals (15F and 36M) from our targeted surveys in 2009, 2013, and 2017. Based on capture–mark–recapture robust design, population estimates were 23 (95% CI: 21–32) in 2009, 28 (95% CI: 25–35) in 2013, and 31 (95% CI: 29‐38) individuals in 2017. Spatial capture–recapture analysis suggested abundance was very low (N^ = 27; 95% CI: 22–35), and there was no significant change from 2009 to 2017. The population density was 0.93 bears/1000 km2 (95% CI: 0.74–1.17). Our population estimates suggested a stable population trend. However, the population is still very small, and the sex ratio is skewed toward males, raising concerns for future persistence. Annual survival based on Robust design CMR was 0.85. Low abundance and apparent survival for both sexes in this unhunted population coupled with a skewed sex ratio highlight the need for on‐the‐ground conservation action to conserve this isolated population of bears.
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- 2021
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14. The magnetic field and stellar wind of the mature late-F star χ Draconis A
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S C Marsden, D Evensberget, E L Brown, C Neiner, J M Seach, J Morin, P Petit, S V Jeffers, and C P Folsom
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Space and Planetary Science ,Astronomy and Astrophysics - Abstract
F stars lie in the transition region between cool stars with dynamo generated fields and hot star fossil fields and offer an interesting window into the generation of magnetic fields in shallow convection zones. In this paper, we investigate the magnetic field of the mature F7V primary of the bright χ Draconis system. χ Dra was observed in circularly polarized light at four epochs from 2014 through to 2019 using the NARVAL spectropolarimeter at the Téléscope Bernard Lyot. Using the technique of least-squares deconvolution, we created high signal-to-noise line profiles from which we were able to measure the radial velocity of both the primary and secondary and use these to improve the orbital parameters of the system. Additionally, we used the technique of Zeeman Doppler imaging to reconstruct the large-scale magnetic field geometry of the primary at the four epochs. The magnetic maps show that χ Dra A has a predominately dipolar poloidal magnetic field at all epochs with the magnetic axis well aligned with the stellar rotation axis. The large-scale features of the magnetic field appear to be relatively stable over the ∼5 yr time base of our observations, with no evidence of any polarity reversals. We used the magnetic field maps to model the wind from χ Dra A at all epochs, showing that the mass-loss from the stellar wind of χ Dra A is 3–6 times the current solar value, while the angular momentum loss from the wind is around 3–4 times the solar value.
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- 2023
15. Clinical and Scientific Challenges to Effectiveness Studies Under Coverage with Evidence Development in Alzheimer’s Disease
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Peter J. Morin, Quanwu Zhang, Weiming Xia, Donald Miller, Henry Querfurth, and Amir Abbas Tahami Monfared
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Neurology ,Neurology (clinical) - Published
- 2023
16. Is your ad hoc model selection strategy affecting your multimodel inference?
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Dana J. Morin, Charles B. Yackulic, Jay E. Diffendorfer, Damon B. Lesmeister, Clayton K. Nielsen, Janice Reid, and Eric M. Schauber
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AIC ,information criterion ,model selection ,multimodel inference ,occupancy models ,parameter estimation ,Ecology ,QH540-549.5 - Abstract
Abstract Ecologists routinely fit complex models with multiple parameters of interest, where hundreds or more competing models are plausible. To limit the number of fitted models, ecologists often define a model selection strategy composed of a series of stages in which certain features of a model are compared while other features are held constant. Defining these multi‐stage strategies requires making a series of decisions, which may potentially impact inferences, but have not been critically evaluated. We begin by identifying key features of strategies, introducing descriptive terms when they did not already exist in the literature. Strategies differ in how they define and order model building stages. Sequential‐by‐sub‐model strategies focus on one sub‐model (parameter) at a time with modeling of subsequent sub‐models dependent on the selected sub‐model structures from the previous stages. Secondary candidate set strategies model sub‐models independently and combine the top set of models from each sub‐model for selection in a final stage. Build‐up approaches define stages across sub‐models and increase in complexity at each stage. Strategies also differ in how the top set of models is selected in each stage and whether they use null or more complex sub‐model structures for non‐target sub‐models. We tested the performance of different model selection strategies using four data sets and three model types. For each data set, we determined the "true" distribution of AIC weights by fitting all plausible models. Then, we calculated the number of models that would have been fitted and the portion of "true" AIC weight we recovered under different model selection strategies. Sequential‐by‐sub‐model strategies often performed poorly. Based on our results, we recommend using a build‐up or secondary candidate sets, which were more reliable and carrying all models within 5–10 AIC of the top model forward to subsequent stages. The structure of non‐target sub‐models was less important. Multi‐stage approaches cannot compensate for a lack of critical thought in selecting covariates and building models to represent competing a priori hypotheses. However, even when competing hypotheses for different sub‐models are limited, thousands or more models may be possible so strategies to explore candidate model space reliably and efficiently will be necessary.
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- 2020
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17. A handheld platform for target protein detection and quantification using disposable nanopore strips
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Trevor J. Morin, William L. McKenna, Tyler D. Shropshire, Dustin A. Wride, Joshua D. Deschamps, Xu Liu, Reto Stamm, Hongyun Wang, and William B. Dunbar
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Tetanus Toxin ,Point-of-care Technology ,Detection Reagents ,Nanopore Experiments ,Lateral Flow Immunoassay (LFAs) ,Medicine ,Science - Abstract
Abstract Accessible point-of-care technologies that can provide immunoassay and molecular modalities could dramatically enhance diagnostics, particularly for infectious disease control in low-resource settings. Solid-state nanopores are simple and durable sensors with low-energy instrumentation requirements. While nanopore sensors have demonstrated efficacy for nucleic acid targets, selective detection and quantification of target proteins from sample background has not been demonstrated. We present a simple approach for electronic detection and quantification of target proteins that combines novel biomolecular engineering methods, a portable reader device and disposable nanopore test strips. The target of interest can be varied by swapping the binding domain on our engineered detection reagent, which eficiently binds in the bulk-phase to the target and subsequently generates a unique signature when passing through the pore. We show modularity of the detection reagent for two HIV antibodies, TNFα and tetanus toxin as targets. A saliva swab-to-result is demonstrated for clinically relevant HIV antibody levels (0.4–20 mg/liter) in under 60 seconds. While other strip-like assays are qualitative, the presented method is quantitative and sets the stage for simultaneous immunoassay and molecular diagnostic functionality within a single portable platform.
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- 2018
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18. Structural delineation of potent transmission-blocking epitope I on malaria antigen Pfs48/45
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Prasun Kundu, Anthony Semesi, Matthijs M. Jore, Merribeth J. Morin, Virginia L. Price, Alice Liang, Jingxing Li, Kazutoyo Miura, Robert W. Sauerwein, C. Richter King, and Jean-Philippe Julien
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Science - Abstract
Malaria protein Pfs48/45 is a promising transmission-blocking antigen targeted by antibodies. Here, the authors determine the structure of its transmission-blocking epitope I, and generate a humanized monoclonal antibody that binds Pfs48/45 with high affinity.
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- 2018
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19. Extending the spectrum of fully integrated photonics to submicrometre wavelengths
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Minh A. Tran, Chong Zhang, Theodore J. Morin, Lin Chang, Sabyasachi Barik, Zhiquan Yuan, Woonghee Lee, Glenn Kim, Aditya Malik, Zeyu Zhang, Joel Guo, Heming Wang, Boqiang Shen, Lue Wu, Kerry Vahala, John E. Bowers, Hyundai Park, and Tin Komljenovic
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Multidisciplinary ,Affordable and Clean Energy ,General Science & Technology ,Generic health relevance - Abstract
Integrated photonics has profoundly affected a wide range of technologies underpinning modern society1–4. The ability to fabricate a complete optical system on a chip offers unrivalled scalability, weight, cost and power efficiency5,6. Over the last decade, the progression from pure III–V materials platforms to silicon photonics has significantly broadened the scope of integrated photonics, by combining integrated lasers with the high-volume, advanced fabrication capabilities of the commercial electronics industry7,8. Yet, despite remarkable manufacturing advantages, reliance on silicon-based waveguides currently limits the spectral window available to photonic integrated circuits (PICs). Here, we present a new generation of integrated photonics by directly uniting III–V materials with silicon nitride waveguides on Si wafers. Using this technology, we present a fully integrated PIC at photon energies greater than the bandgap of silicon, demonstrating essential photonic building blocks, including lasers, amplifiers, photodetectors, modulators and passives, all operating at submicrometre wavelengths. Using this platform, we achieve unprecedented coherence and tunability in an integrated laser at short wavelength. Furthermore, by making use of this higher photon energy, we demonstrate superb high-temperature performance and kHz-level fundamental linewidths at elevated temperatures. Given the many potential applications at short wavelengths, the success of this integration strategy unlocks a broad range of new integrated photonics applications.
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- 2022
20. Human adenoviruses associated with severe acute respiratory infections in the Philippines
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C. Calzado, V.L. Arguelles, J. Morin, M.T. Quimpo, H. Base, F.M. Abing, J.L. Foronda, and M. Lumandas
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Infectious and parasitic diseases ,RC109-216 - Published
- 2020
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21. Comparative assessment of An. gambiae and An. stephensi mosquitoes to determine transmission-reducing activity of antibodies against P. falciparum sexual stage antigens
- Author
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Maarten Eldering, Anaïs Bompard, Kazutoyo Miura, Will Stone, Isabelle Morlais, Anna Cohuet, Geert-Jan van Gemert, Patrick M. Brock, Sanna R. Rijpma, Marga van de Vegte-Bolmer, Wouter Graumans, Rianne Siebelink-Stoter, Dari F. Da, Carole A. Long, Merribeth J. Morin, Robert W. Sauerwein, Thomas S. Churcher, and Teun Bousema
- Subjects
Malaria ,Anopheles ,Transmission ,Vaccine ,Immunity ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background With the increasing interest in vaccines to interrupt malaria transmission, there is a demand for harmonization of current methods to assess Plasmodium transmission in laboratory settings. Potential vaccine candidates are currently tested in the standard membrane feeding assay (SMFA) that commonly relies on Anopheles stephensi mosquitoes. Other mosquito species including Anopheles gambiae are the dominant malaria vectors for Plasmodium falciparum in sub-Saharan Africa. Methods Using human serum and monoclonal pre-fertilization (anti-Pfs48/45) and post-fertilization (anti-Pfs25) antibodies known to effectively inhibit sporogony, we directly compared SMFA based estimates of transmission-reducing activity (TRA) for An. stephensi and An. gambiae mosquitoes. Results In the absence of transmission-reducing antibodies, average numbers of oocysts were similar between An. gambiae and An. stephensi. Antibody-mediated TRA was strongly correlated between both mosquito species, and absolute TRA estimates for pre-fertilisation monoclonal antibodies (mAb) showed no significant difference between the two species. TRA estimates for IgG of naturally exposed individuals and partially effective concentrations of anti-Pfs25 mAb were higher for An. stephensi than for An. gambiae. Conclusion Our findings support the use of An. stephensi in the SMFA for target prioritization. As a vaccine moves through product development, better estimates of TRA and transmission-blocking activity (TBA) may need to be obtained in epidemiologically relevant parasite-species combination.
- Published
- 2017
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22. Fast and accurate quantification of insertion-site specific transgene levels from raw seed samples using solid-state nanopore technology.
- Author
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Michael D Pearson, Leslee Nguyen, Yanan Zhao, William L McKenna, Trevor J Morin, and William B Dunbar
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Medicine ,Science - Abstract
Many modern crop varieties contain patented biotechnology traits, and an increasing number of these crops have multiple (stacked) traits. Fast and accurate determination of transgene levels is advantageous for a variety of use cases across the food, feed and fuel value chain. With the growing number of new transgenic crops, any technology used to quantify them should have robust assays that are simple to design and optimize, thereby facilitating the addition of new traits to an assay. Here we describe a PCR-based method that is simple to design, starts from whole seeds, and can be run to end-point in less than 5 minutes. Subsequent relative quantification (trait vs. non-trait) using capillary electrophoresis performed in 5% increments across the 0-100% range showed a mean absolute error of 1.9% (s.d. = 1.1%). We also show that the PCR assay can be coupled to non-optical solid-state nanopore sensors to give seed-to-trait quantification results with a mean absolute error of 2.3% (s.d. = 1.6%). In concert, the fast PCR and nanopore sensing stages demonstrated here can be fully integrated to produce seed-to-trait quantification results in less than 10 minutes, with high accuracy across the full dynamic range.
- Published
- 2019
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23. IL-38 blockade induces anti-tumor immunity by abrogating tumor-mediated suppression of early immune activation
- Author
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John P. Dowling, Pavel A. Nikitin, Fang Shen, Halley Shukla, James P. Finn, Nirja Patel, Cezary Swider, Jamie L. Bingaman-Steele, Chris Nicolescu, Eden L Sikorski, Evan J. Greenawalt, Michael J. Morin, Matthew K. Robinson, Karen Lundgren, and Benjamin C. Harman
- Subjects
Immunology ,Immunology and Allergy - Published
- 2023
24. Balancing Tradeoffs in Climate-Smart Agriculture: Will Selling Carbon Credits Offset Potential Losses in the Net Yield Income of Small-Scale Soybean (Glycine max L.) Producers in the Mid-Southern United States?
- Author
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Adrienne L. Contasti, Alexandra G. Firth, Beth H. Baker, John P. Brooks, Martin A. Locke, and Dana J. Morin
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General Decision Sciences - Abstract
There is a need to achieve sustainable agricultural production to secure food, fiber, and fuel for a growing global population. Climate-smart (CS) actions (no-till and cover crops) can reduce carbon emissions and promote soil organic carbon (SOC) storage. Contemporary voluntary carbon markets provide producers with a monetary incentive to adopt CS actions. However, SOC–yield dynamics under CS actions are not well known, making it difficult for producers to judge whether additional income from carbon credits will offset potential losses to yield income. We designed a SOC–yield framework that captures SOC–yield–income dynamics under traditional (reduced tillage, no cover crops) and CS actions. Using a modified structured decision-making approach, we applied the framework to a case study in which producers aim to increase income by selling carbon credits after adopting CS actions. Specifically, we demonstrated how to balance tradeoffs between yield and carbon credit income that arise from tillage and winter cover crop actions (cereal rye, Secale cereale L. and crimson clover, Trifolium incarnatum L.) in a soybean (Glycine max L.) production system in Mississippi. Results indicated that a producer could minimize losses to net yield income by adopting no-till if already using cover crops. There was also evidence that carbon credit income could offset losses to yield income when adopting CS in place of traditional actions. Identifying risks to yield income and SOC storage can help design carbon neutrality policies that have minimum impact on a producer’s income. History: This paper has been accepted for the Decision Analysis Special Issue on Further Environmental Sustainability. Funding: This work was supported by the USDA-ARS [Grants 58-0200-0-002 (Advancing Agricultural Research) and 58-6001-8-003] and the USDA National Institute of Food and Agriculture [McIntire Stennis Project 1020959]. Supplemental Material: The online appendix is available at https://doi.org/10.1287/deca.2023.0478 .
- Published
- 2023
25. Data from Unraveling the Mysteries of PAX8 in Reproductive Tract Cancers
- Author
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Ronny Drapkin, Patrice J. Morin, and Daniele Chaves-Moreira
- Abstract
Paired Box 8 (PAX8) is a lineage-specific transcription factor that has essential roles during embryogenesis and tumorigenesis. The importance of PAX8 in the development of the reproductive system is highlighted by abnormalities observed upon the loss or mutation of this PAX family member. In cancer, PAX8 expression is deregulated in a key set of neoplasms, including those arising from the Müllerian ducts. The roles of PAX8 in oncogenesis are diverse and include epigenetic remodeling, stimulation of proliferation, inhibition of apoptosis, and regulation of angiogenesis. PAX8 can interact with different protein partners during cancer progression and may exhibit significant function-altering alternative splicing. Moreover, expression of PAX8 in cancer can also serve as a biomarker for diagnostic and prognostic purposes. In this review, we focus on the roles of PAX8 in cancers of the reproductive system. Understanding the diverse mechanisms of action of PAX8 in development and oncogenesis may identify new vulnerabilities in malignancies that currently lack effective therapies.
- Published
- 2023
26. Supplementary Figure 1 from Unraveling the Mysteries of PAX8 in Reproductive Tract Cancers
- Author
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Ronny Drapkin, Patrice J. Morin, and Daniele Chaves-Moreira
- Abstract
Supplementary Figure 1 from Unraveling the Mysteries of PAX8 in Reproductive Tract Cancers
- Published
- 2023
27. Supplementary Table 1, Figures 1-7 from Jagged-1 and Notch3 Juxtacrine Loop Regulates Ovarian Tumor Growth and Adhesion
- Author
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Tian-Li Wang, Ie-Ming Shih, Patrice J. Morin, Ben Davidson, Joon T. Park, and Jung-Hye Choi
- Abstract
Supplementary Table 1, Figures 1-7 from Jagged-1 and Notch3 Juxtacrine Loop Regulates Ovarian Tumor Growth and Adhesion
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- 2023
28. Data from Jagged-1 and Notch3 Juxtacrine Loop Regulates Ovarian Tumor Growth and Adhesion
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Tian-Li Wang, Ie-Ming Shih, Patrice J. Morin, Ben Davidson, Joon T. Park, and Jung-Hye Choi
- Abstract
Notch3 gene amplification and pathway activation have been reported in ovarian serous carcinoma. However, the primary Notch3 ligand that initiates signal transduction in ovarian cancer remains unclear. In this report, we identify Jagged-1 as the highest expressed Notch ligand in ovarian tumor cells as well as in peritoneal mesothelial cells that are in direct contact with disseminated ovarian cancer cells. Cell-cell adhesion and cellular proliferation were reduced in Notch3-expressing ovarian cancer cells that were cocultured with Jagged-1 knockdown mesothelial and tumor feeder cells. Interaction of Notch3-expressing ovarian cancer cells with Jagged-1–expressing feeder cells activated the promoter activity of candidate Notch3 target genes, and this activity was attenuated by Notch3 siRNA. Constitutive expression of the Notch3 intracellular domain significantly suppressed the Jagged-1 shRNA–mediated growth inhibitory effect. In Notch3-expressing ovarian cancer cells, Jagged-1–stimulating peptides enhanced cellular proliferation, which was suppressed by γ-secretase inhibitor and Notch3 siRNA. Taken together, our results show that Jagged-1 is the primary Notch3 ligand in ovarian carcinoma and Jagged-1/Notch3 interaction constitutes a juxtacrine loop promoting proliferation and dissemination of ovarian cancer cells within the intraperitoneal cavity. [Cancer Res 2008;68(14):5716–23]
- Published
- 2023
29. Acute mitral regurgitation and cardiogenic shock: Reverse takotsubo cardiomyopathy or acute coronary syndrome?
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Mohammed Essa, Scott J Morin, Augustin J. DeLago, Alireza Ghajar, and Kyle Pond
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medicine.medical_specialty ,Acute coronary syndrome ,Mitral regurgitation ,Ejection fraction ,biology ,business.industry ,Cardiogenic shock ,Cardiomyopathy ,Case Report ,medicine.disease ,Troponin ,Coronary artery disease ,Internal medicine ,Cardiology ,medicine ,biology.protein ,Transthoracic echocardiogram ,Cardiology and Cardiovascular Medicine ,business - Abstract
Reverse takotsubo cardiomyopathy (rTCM) is characterized by basal ballooning and accounts for approximately 1% of all TCM. To our knowledge, there have been no reports describing rTCM complicated by acute, severe, transient mitral regurgitation (MR). A 75-year-old woman with a medical history of hypertension, dyslipidemia, and anxiety presented to the hospital with 2 days of substernal chest pain, dyspnea, and nausea. Initial troponin was 0.203 ng/mL, and electrocardiography showed sinus tachycardia at 121 bpm, with inferior and anterolateral ST segment depressions. Transthoracic echocardiogram (TTE) found an ejection fraction of 30%, apical hyperkinesis, severe hypokinesis of the basal to mid segments of the left ventricle (LV), and a severe central MR jet. Cardiac angiography demonstrated non-obstructive coronary artery disease, and elevated left ventricular end diastolic pressures. Left ventriculography showed a hyperdynamic apex and severe basal hypokinesis. The patient was treated medically, clinical status improved, and was discharged on day 3. TTE four weeks later, showed an ejection fraction of 60–65%, mild MR, and normal LV function. rTCM is the rarest variant of TCM. Basal and mid-myocardial stunning can cause severe secondary MR leading to acute congestive heart failure, mimicking acute coronary syndrome with acute MR. rTCM with rapidly reversible severe MR has not previously been described. Learning Objectives Mitral regurgitation secondary to reverse takotsubo cardiomyopathy can mimic coronary flow obstruction syndromes and when recognized early, can improve with amelioration of cardiomyopathy. Acute severe mitral regurgitation in reverse takotsubo cardiomyopathy is likely secondary to basilar dilatation. Reverse takotsubo cardiomyopathy represents approximately 1% of all takotsubo cardiomyopathy cases.
- Published
- 2021
30. Soil bacterial community dynamics in plots managed with cover crops and no-till farming in the Lower Mississippi Alluvial Valley, USA
- Author
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A G Firth, J P Brooks, M A Locke, D J Morin, A Brown, and B H Baker
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General Medicine ,Applied Microbiology and Biotechnology ,Biotechnology - Abstract
AimsAssess bacterial community changes over time in soybean (Glycine max) crop fields following cover crop (CC) and no-till (NT) implementation under natural abiotic stressors.Method and resultsSoil bacterial community composition was obtained by amplifying, sequencing, and analysing the V4 region of the 16S rRNA gene. Generalized linear mixed models were used to assess the effects of tillage, CC, and time on bacterial community response. The most abundant phyla present were Acidobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Bacterial diversity increased in periods with abundant water. Reduced tillage (RT) increased overall bacterial diversity, but NT with a CC was not significantly different than RT treatments under drought conditions. CCs shifted abundances of Firmicutes and Bacteroidetes depending on abiotic conditions.ConclusionsIn the Lower Mississippi Alluvial Valley (LMAV), USA, NT practices lower diversity and influence long-term community changes while cover crops enact a seasonal response to environmental conditions. NT and RT management affect soil bacterial communities differently than found in other regions of the country.
- Published
- 2022
31. Synergy in anti-malarial pre-erythrocytic and transmission-blocking antibodies is achieved by reducing parasite density
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Ellie Sherrard-Smith, Katarzyna A Sala, Michael Betancourt, Leanna M Upton, Fiona Angrisano, Merribeth J Morin, Azra C Ghani, Thomas S Churcher, and Andrew M Blagborough
- Subjects
Anopheles stephensi ,Plasmodium berghei ,transmission-blocking vaccine ,synergy ,multigenerational population assay ,pre-erythrocytic vaccine ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Anti-malarial pre-erythrocytic vaccines (PEV) target transmission by inhibiting human infection but are currently partially protective. It has been posited, but never demonstrated, that co-administering transmission-blocking vaccines (TBV) would enhance malaria control. We hypothesized a mechanism that TBV could reduce parasite density in the mosquito salivary glands, thereby enhancing PEV efficacy. This was tested using a multigenerational population assay, passaging Plasmodium berghei to Anopheles stephensi mosquitoes. A combined efficacy of 90.8% (86.7–94.2%) was observed in the PEV +TBV antibody group, higher than the estimated efficacy of 83.3% (95% CrI 79.1–87.0%) if the two antibodies acted independently. Higher PEV efficacy at lower mosquito parasite loads was observed, comprising the first direct evidence that co-administering anti-sporozoite and anti-transmission interventions act synergistically, enhancing PEV efficacy across a range of TBV doses and transmission intensities. Combining partially effective vaccines of differing anti-parasitic classes is a pragmatic, powerful way to accelerate malaria elimination efforts.
- Published
- 2018
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32. Tocilizumab Induces Rapid, Sustained Improvement of Inflammatory Markers in COVID-19, With Clinical Improvement in Most Patients
- Author
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Arashdeep Rupal, Daniel L. Bourque, Scott J Morin, Chinmay Jani, Robert C. Colgrove, and Harpreet Singh
- Subjects
Pharmacology ,2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,SARS-CoV-2 ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,MEDLINE ,General Medicine ,Antibodies, Monoclonal, Humanized ,COVID-19 Drug Treatment ,chemistry.chemical_compound ,Tocilizumab ,chemistry ,Immunology ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,Humans ,Medicine ,Pharmacology (medical) ,Letters to the Editor ,business - Abstract
Supplemental Digital Content is Available in the Text.
- Published
- 2021
33. A no film slot blot for the detection of developing P. falciparum oocysts in mosquitoes.
- Author
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Bryan Grabias, Nitin Verma, Hong Zheng, Abhai K Tripathi, Godfree Mlambo, Merribeth J Morin, Emily Locke, and Sanjai Kumar
- Subjects
Medicine ,Science - Abstract
Non-microscopy-based assays for sensitive and rapid detection of Plasmodium infection in mosquitoes are needed to allow rapid and high throughput measurement of transmission intensity and malaria control program effectiveness. Here, we report on a modified enhanced chemiluminescence-based slot blot assay for detection of Plasmodium falciparum (Pf) circumsporozite protein (PfCSP) expressed on parasite oocysts developing inside the mosquito midgut. This modified assay has several novel features that include eliminating the need for exposure to autoradiography (AR) film, as well as utilizing a novel high affinity anti-CSP antibody, and optimizing assay procedures resulting in significant reduction in the time required to perform the assay. The chemiluminescent signal for the detection of PfCSP in mosquito samples was captured digitally utilizing the C-Digit blot scanner that, allowed the detection of 0.01 pg of recombinant P. falciparum CSP and as few as 0.02 P. falciparum oocysts in a little over two hours. The earlier ECL-SB detected rCSP and oocysts and took approximately 5 h to perform. Whole mosquito lysates from both high and low prevalence-infected mosquito populations were prepared and evaluated for PfCSP detection on the ECL-SB by both AR film and digital data capture and analysis. There was a 100% agreement between the AR film and the C-Digit scanner methods for PfCSP detection in randomly sampled mosquitoes. This novel "No Film" Slot Blot assay obviates the need for AR film exposure and development and significantly reduces the assay time enabling widespread use in field settings.
- Published
- 2017
- Full Text
- View/download PDF
34. Dynamics of Soil Organic Carbon and CO2 Flux under Cover Crop and No-Till Management in Soybean Cropping Systems of the Mid-South (USA)
- Author
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Alexandra G. Firth, John P. Brooks, Martin A. Locke, Dana J. Morin, Ashli Brown, and Beth H. Baker
- Subjects
Renewable Energy, Sustainability and the Environment ,carbon ,no-till ,cover crops ,soil carbon sequestration ,conservation agriculture ,carbon measurement ,Ecology, Evolution, Behavior and Systematics ,General Environmental Science - Abstract
The transition of natural landscapes to agricultural uses has resulted in severe loss of soil organic carbon, significantly contributing to CO2 emissions and rising global temperatures. However, soil has the largest store of terrestrial carbon (C), a considerable sink and effective strategy for climate change mitigation if managed properly. Cover crops (CC) and no-till (NT) management are two management strategies that are known to increase percent organic carbon (%OC); however, adoption of these practices has been low in the mid-South due to lack of region-specific research and resistance to unproven practices. Therefore, the purpose of this study was to evaluate the impacts of CC-NT treatments in soybean cropping systems on soil percent organic carbon (%OC) and CO2 flux following long-term implementation. Results showed significantly greater %OC in NT (1.27% ± 0.03) than reduced till (RT; 1.10% ± 0.03; p < 0.001) and greater in both CC (rye: 1.23% ± 0.03, rye + clover: 1.22% ± 0.03) than no cover (1.11% ± 0.03; p < 0.001). Bacterial abundance (p = 0.005) and pH (p = 0.006) were significant predictors of %OC. There was no overall significant difference in CO2 flux between tillage or CC treatments; however, there were significant differences between NT and RT in July of 2020 when %RH increased (p < 0.001). Bacterial abundance negatively impacted CO2 flux (p < 0.05), which contradicts most studies. The rate of proportional change and pattern of variability in C pools suggested loss of %OC in RT treatments that were not apparent when considering %OC alone. The results of this study provide valuable insight into C turnover and the effectiveness of CC use in the Mid-South to increase soil C stocks.
- Published
- 2022
- Full Text
- View/download PDF
35. Historical contingency and the role of post‐invasion evolution in alternative community states
- Author
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Cara A. Faillace, Rita L. Grunberg, and Peter J. Morin
- Subjects
Phenotype ,Humans ,Biological Evolution ,Ecosystem ,Ecology, Evolution, Behavior and Systematics - Abstract
Historical contingency has long figured prominently in the conceptual frameworks of evolutionary biology and community ecology. Evolutionary biologists typically consider the effects of chance mutation and historical contingency in driving divergence and convergence of traits in populations, whereas ecologists instead are often interested in the role of historical contingency in community assembly and succession. Although genetic differences among individuals in populations can influence community interactions, variability among populations of the same species has received relatively little attention for its potential role in community assembly and succession. We used a community-level study of experimental evolution in two compositionally different assemblages of protists and rotifers to explore whether initial differences in species abundances among communities attributed to differences in evolutionary history, persisted as species that continued to evolve over time. In each assemblage, we observed significant convergence between two invaded treatments initially differing in evolutionary history over an observation period equal to ~40-80 generations for most species. Nonetheless, community structure failed to converge completely across all invaded treatments within an assemblage to a single structure. This suggests that whereas the species in the assemblage represent a common selective regime, differences in populations reflecting their evolutionary history can produce long-lasting transient alternative community states. In one assemblage, we also observed increasing within-treatment variability among replicate communities over time, suggesting that ecological drift may be another factor contributing to community change. Although subtle, these transient alternative states, in which communities differed in the abundance of interacting species, could nonetheless have important functional consequences, suggesting that the role of evolution in driving these states deserves greater attention.
- Published
- 2022
36. Optical and near-infrared stellar activity characterization of the early M dwarf Gl 205 with SOPHIE and SPIRou
- Author
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P. Cortés-Zuleta, I. Boisse, B. Klein, E. Martioli, P. I. Cristofari, A. Antoniadis-Karnavas, J.-F. Donati, X. Delfosse, C. Cadieux, N. Heidari, É. Artigau, S. Bellotti, X. Bonfils, A. Carmona, N. J. Cook, R. F. Díaz, R. Doyon, P. Fouqué, C. Moutou, P. Petit, T. Vandal, L. Acuña, L. Arnold, N. Astudillo-Defru, V. Bourrier, F. Bouchy, R. Cloutier, S. Dalal, M. Deleuil, O. D. S. Demangeon, X. Dumusque, T. Forveille, J. Gomes da Silva, N. Hara, G. Hébrard, S. Hoyer, G. Hussain, F. Kiefer, J. Morin, A. Santerne, N. C. Santos, D. Segransan, M. Stalport, and S. Udry
- Subjects
Earth and Planetary Astrophysics (astro-ph.EP) ,Astrophysics - Solar and Stellar Astrophysics ,Space and Planetary Science ,FOS: Physical sciences ,Astronomy and Astrophysics ,Solar and Stellar Astrophysics (astro-ph.SR) ,Astrophysics - Earth and Planetary Astrophysics - Abstract
The stellar activity of M dwarfs is the main limitation for discovering and characterizing exoplanets orbiting them since it induces quasi-periodic RV variations. We aim to characterize the magnetic field and stellar activity of the early, moderately active, M dwarf Gl205 in the optical and nIR domains. We obtained high-precision quasi-simultaneous spectra in the optical and nIR with the SOPHIE spectrograph and SPIRou spectropolarimeter between 2019 and 2022. We computed the RVs from both instruments and the SPIRou Stokes V profiles. We used ZDI to map the large-scale magnetic field over the time span of the observations. We studied the temporal behavior of optical and nIR RVs and activity indicators with the Lomb-Scargle periodogram and a quasi-periodic GP regression. In the nIR, we studied the equivalent width of Al I, Ti I, K I, Fe I, and He I. We modeled the activity-induced RV jitter using a multi-dimensional GP regression with activity indicators as ancillary time series. The optical and nIR RVs have similar scatter but nIR shows a more complex temporal evolution. We observe an evolution of the magnetic field topology from a poloidal dipolar field in 2019 to a dominantly toroidal field in 2022. We measured a stellar rotation period of Prot=34.4$\pm$0.5 d in the longitudinal magnetic field. Using ZDI we measure the amount of latitudinal differential rotation (DR) shearing the stellar surface yielding rotation periods of Peq=32.0$\pm$1.8 d at the stellar equator and Ppol=45.5$\pm$0.3 d at the poles. We observed inconsistencies in the activity indicators' periodicities that could be explained by these DR values. The multi-dimensional GP modeling yields an RMS of the RV residuals down to the noise level of 3 m/s for both instruments, using as ancillary time series H$\alpha$ and the BIS in the optical, and the FWHM in the nIR., Comment: 41 pages, 24 figures. Accepted for publication in A&A. Improved quality of figures and reduced size of Appendix
- Published
- 2023
37. The SPIRou legacy survey
- Author
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P. Fouqué, E. Martioli, J.-F. Donati, L. T. Lehmann, B. Zaire, S. Bellotti, E. Gaidos, J. Morin, C. Moutou, P. Petit, S. H. P. Alencar, L. Arnold, É. Artigau, T.-Q. Cang, A. Carmona, N. J. Cook, P. Cortés-Zuleta, P. I. Cristofari, X. Delfosse, R. Doyon, G. Hébrard, L. Malo, C. Reylé, and C. Usher
- Subjects
Earth and Planetary Astrophysics (astro-ph.EP) ,Astrophysics - Solar and Stellar Astrophysics ,Space and Planetary Science ,FOS: Physical sciences ,Astronomy and Astrophysics ,Solar and Stellar Astrophysics (astro-ph.SR) ,Astrophysics - Earth and Planetary Astrophysics - Abstract
Context. The rotation period of stars is an important parameter together with mass, radius, and effective temperature. It is an essential parameter for any radial velocity monitoring, as stellar activity can mimic the presence of a planet at the stellar rotation period. Several methods exist to measure it, including long sequences of photometric measurements or temporal series of stellar activity indicators. Aims. Here, we use the circular polarization in near-infrared spectral lines for a sample of 43 quiet M dwarfs and compare the measured rotation periods to those obtained with other methods. Methods. From Stokes V spectropolarimetric sequences observed with SPIRou at the Canada-France-Hawaii Telescope and the data processed with the APERO pipeline, we computed the least-squares deconvolution profiles using different masks of atomic stellar lines with known Landé factor appropriate to the effective temperature of the star. We derived the longitudinal magnetic field to examine its possible variation in 50 to 200 observations of each star. To determine the stellar rotation period, we applied a Gaussian process regression, enabling us to determine the rotation period of stars with evolving longitudinal field. Results. We were able to measure a rotation period for 27 of the 43 stars of our sample. The rotation period was previously unknown for 8 of these stars. Our rotation periods agree well with periods found in the literature based on photometry and activity indicators, and we confirm that near-infrared spectropolarimetry is an important tool for measuring rotation periods, even for magnetically quiet stars. Furthermore, we computed the ages for 20 stars of our sample using gyrochronology.
- Published
- 2023
38. Unraveling the Mysteries of PAX8 in Reproductive Tract Cancers
- Author
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Patrice J. Morin, Ronny Drapkin, and Daniele Chaves-Moreira
- Subjects
Male ,0301 basic medicine ,Cancer Research ,Carcinogenesis ,Genital Neoplasms, Female ,Mullerian Ducts ,Biology ,medicine.disease_cause ,Article ,PAX8 Transcription Factor ,03 medical and health sciences ,0302 clinical medicine ,Biomarkers, Tumor ,medicine ,Animals ,Humans ,Molecular Targeted Therapy ,Epigenetics ,Transcription factor ,Alternative splicing ,Cancer ,Prognosis ,medicine.disease ,Biomarker (cell) ,030104 developmental biology ,Oncology ,030220 oncology & carcinogenesis ,Genital Neoplasms, Male ,Cancer research ,Female ,PAX8 - Abstract
Paired Box 8 (PAX8) is a lineage-specific transcription factor that has essential roles during embryogenesis and tumorigenesis. The importance of PAX8 in the development of the reproductive system is highlighted by abnormalities observed upon the loss or mutation of this PAX family member. In cancer, PAX8 expression is deregulated in a key set of neoplasms, including those arising from the Müllerian ducts. The roles of PAX8 in oncogenesis are diverse and include epigenetic remodeling, stimulation of proliferation, inhibition of apoptosis, and regulation of angiogenesis. PAX8 can interact with different protein partners during cancer progression and may exhibit significant function-altering alternative splicing. Moreover, expression of PAX8 in cancer can also serve as a biomarker for diagnostic and prognostic purposes. In this review, we focus on the roles of PAX8 in cancers of the reproductive system. Understanding the diverse mechanisms of action of PAX8 in development and oncogenesis may identify new vulnerabilities in malignancies that currently lack effective therapies.
- Published
- 2021
39. Decoupling salt- and polymer-dependent dynamics in polyelectrolyte complex coacervates via salt addition
- Author
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Frances J. Morin, Marissa L. Puppo, and Jennifer E. Laaser
- Subjects
chemistry.chemical_classification ,Coacervate ,Salt (chemistry) ,02 engineering and technology ,General Chemistry ,Polymer ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Polyelectrolyte ,0104 chemical sciences ,Styrene ,chemistry.chemical_compound ,Sulfonate ,Rheology ,chemistry ,Chemical engineering ,Volume fraction ,0210 nano-technology - Abstract
In polyelectrolyte complex coacervates, changes in salt concentration and changes in polymer concentration are typically strongly coupled, complicating interpretation of the salt- and polymer-concentration-dependent dynamics of these materials. To address this problem, we developed a “salt addition” method for preparation of complex coacervates that allows the salt concentration of a coacervate sample to be varied without changing its polymer concentration. This method was used to prepare coacervates of poly(styrene sulfonate) (PSS) with poly(diallyldimethylammonium chloride) (PDADMAC) with salt concentrations between 1.2 and 2 M and volume fractions of polymer between 0.1 and 0.25. Characterization of these samples by small-amplitude oscillatory shear rheology revealed that the relaxation times scale significantly more strongly with polymer volume fraction than has been previously assumed, highlighting the need to account for both salt and polymer-dependent contributions to the dynamics of these complex materials.
- Published
- 2021
40. Linking chromospheric activity and magnetic field properties for late-type dwarf stars
- Author
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E L Brown, S V Jeffers, S C Marsden, J Morin, S Boro Saikia, P Petit, M M Jardine, V See, A A Vidotto, M W Mengel, M N Dahlkemper, null the BCool Collaboration, Science & Technology Facilities Council, University of St Andrews. School of Physics and Astronomy, Laboratoire Univers et Particules de Montpellier (LUPM), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), and BCool
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stars ,Astrophysics and Astronomy ,astro-ph.SR ,FOS: Physical sciences ,magnetic field ,magnetic field, Astrophysics - Solar and Stellar Astrophysics ,late-type, stars ,stars: activity ,QB Astronomy ,late-type ,Solar and Stellar Astrophysics (astro-ph.SR) ,QC ,QB ,stars: activity, stars ,activity ,stars: late-type ,stars: magnetic field ,Astronomy and Astrophysics ,3rd-DAS ,magnetic field [Stars] ,QC Physics ,Astrophysics - Solar and Stellar Astrophysics ,Space and Planetary Science ,late-type [Stars] ,MCP ,[PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph] ,activity [Stars] - Abstract
Spectropolarimetric data allow for simultaneous monitoring of stellar chromospheric $\log{R^{\prime}_{\rm{HK}}}$ activity and the surface-averaged longitudinal magnetic field, $B_l$, giving the opportunity to probe the relationship between large-scale stellar magnetic fields and chromospheric manifestations of magnetism. We present $\log{R^{\prime}_{\rm{HK}}}$ and/or $B_l$ measurements for 954 mid-F to mid-M stars derived from spectropolarimetric observations contained within the PolarBase database. Our magnetically active sample complements previous stellar activity surveys that focus on inactive planet-search targets. We find a positive correlation between mean $\log{R^{\prime}_{\rm{HK}}}$ and mean $\log|B_l|$, but for G stars the relationship may undergo a change between $\log{R'_{\rm{HK}}}\sim-4.4$ and $-4.8$. The mean $\log{R^{\prime}_{\rm{HK}}}$ shows a similar change with respect to the $\log{R^{\prime}_{\rm{HK}}}$ variability amplitude for intermediately-active G stars. We also combine our results with archival chromospheric activity data and published observations of large-scale magnetic field geometries derived using Zeeman Doppler Imaging. The chromospheric activity data indicate a slight under-density of late-F to early-K stars with $-4.75\leq\log{R'_{\rm HK}}\leq-4.5$. This is not as prominent as the original Vaughan-Preston gap, and we do not detect similar under-populated regions in the distributions of the mean $|B_l|$, or the $B_l$ and $\log{R'_{\rm HK}}$ variability amplitudes. Chromospheric activity, activity variability and toroidal field strength decrease on the main sequence as rotation slows. For G stars, the disappearance of dominant toroidal fields occurs at a similar chromospheric activity level as the change in the relationships between chromospheric activity, activity variability and mean field strength., 20 pages, 15 figures, 3 tables
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- 2022
41. The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17
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Daniele Chaves-Moreira, Marilyn A. Mitchell, Cristina Arruza, Priyanka Rawat, Simone Sidoli, Robbin Nameki, Jessica Reddy, Rosario I. Corona, Lena K. Afeyan, Isaac A. Klein, Sisi Ma, Boris Winterhoff, Gottfried E. Konecny, Benjamin A. Garcia, Donita C. Brady, Kate Lawrenson, Patrice J. Morin, and Ronny Drapkin
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Ovarian Neoplasms ,Cell Biology ,Biochemistry ,Article ,Mice ,PAX8 Transcription Factor ,HMGB Proteins ,SOXF Transcription Factors ,Animals ,Humans ,Female ,Neoplasm Grading ,Molecular Biology ,Fallopian Tubes ,Transcription Factors - Abstract
PAX8 is a master transcription factor that is essential during embryogenesis and promotes neoplastic growth. It is expressed by the secretory cells lining the female reproductive tract, and its deletion during development results in atresia of reproductive tract organs. Nearly all ovarian carcinomas express PAX8, and its knockdown results in apoptosis of ovarian cancer cells. To explore the role of PAX8 in these tissues, we purified the PAX8 protein complex from nonmalignant fallopian tube cells and high-grade serous ovarian carcinoma cell lines. We found that PAX8 was a member of a large chromatin remodeling complex and preferentially interacted with SOX17, another developmental transcription factor. Depleting either PAX8 or SOX17 from cancer cells altered the expression of factors involved in angiogenesis and functionally disrupted tubule and capillary formation in cell culture and mouse models. PAX8 and SOX17 in ovarian cancer cells promoted the secretion of angiogenic factors by suppressing the expression of SERPINE1 , which encodes a proteinase inhibitor with anti a ngiogenic effects. The findings reveal a non–cell-autonomous function of these transcription factors in regulating angiogenesis in ovarian cancer.
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- 2022
42. Nanopore-Based Target Sequence Detection.
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Trevor J Morin, Tyler Shropshire, Xu Liu, Kyle Briggs, Cindy Huynh, Vincent Tabard-Cossa, Hongyun Wang, and William B Dunbar
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Medicine ,Science - Abstract
The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA. In contrast to methods that require precise geometries, we demonstrate detection using a range of pore geometries. As a result, our assay model tolerates any pore-forming method and in-situ pore enlargement. Using peptide nucleic acid (PNA) probes modified for conjugation with synthetic bulk-adding molecules, pores ranging 15-50 nm in diameter are shown to detect individual PNA-bound DNA. Detection of the CFTRΔF508 gene mutation, a codon deletion responsible for ∼66% of all cystic fibrosis chromosomes, is demonstrated with a 26-36 nm pore size range by using a size-enhanced PNA probe. A mathematical framework for assessing the statistical significance of detection is also presented.
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- 2016
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43. Young women with poor ovarian response exhibit epigenetic age acceleration based on evaluation of white blood cells using a DNA methylation-derived age prediction model
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Yiping Zhan, Emre Seli, Brent M. Hanson, Scott J. Morin, Richard T. Scott, Timothy G. Jenkins, and Xin Tao
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Oncology ,medicine.medical_specialty ,Acceleration ,Population ,Bisulfite sequencing ,Ovary ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,Ovulation Induction ,Biomarkers of aging ,Internal medicine ,Leukocytes ,medicine ,Humans ,Prospective Studies ,Epigenetics ,education ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,business.industry ,Rehabilitation ,Obstetrics and Gynecology ,DNA Methylation ,Polycystic ovary ,medicine.anatomical_structure ,Reproductive Medicine ,Private practice ,030220 oncology & carcinogenesis ,DNA methylation ,Female ,business - Abstract
STUDY QUESTION Is poor ovarian response associated with a change in predicted age based on a DNA methylation-derived age prediction model (the Horvath algorithm) in white blood cells (WBCs) or cumulus cells (CCs)? SUMMARY ANSWER In young women, poor ovarian response is associated with epigenetic age acceleration within WBC samples but is not associated with age-related changes in CC. WHAT IS KNOWN ALREADY The majority of human tissues follow predictable patterns of methylation which can be assessed throughout a person’s lifetime. DNA methylation patterns may serve as informative biomarkers of aging within various tissues. Horvath’s ‘epigenetic clock’, which is a DNA methylation-derived age prediction model, accurately predicts a subject’s true chronologic age when applied to WBC but not to CC. STUDY DESIGN, SIZE, DURATION A prospective cohort study was carried out involving 175 women undergoing ovarian stimulation between February 2017 and December 2018. Women were grouped according to a poor (≤5 oocytes retrieved) or good (>5 oocytes) response to ovarian stimulation. Those with polycystic ovary syndrome (PCOS) (n = 35) were placed in the good responder group. PARTICIPANTS/MATERIALS, SETTING, METHODS DNA methylation patterns from WBC and CC were assessed for infertile patients undergoing ovarian stimulation at a university-affiliated private practice. DNA was isolated from peripheral blood samples and CC. Bisulfite conversion was then performed and a DNA methylation array was utilized to measure DNA methylation levels throughout the genome. Likelihood ratio tests were utilized to assess the relationship between predicted age, chronologic age and ovarian response. MAIN RESULTS AND THE ROLE OF CHANCE The Horvath-predicted age for WBC samples was consistent with patients’ chronologic age. However, predicted age from analysis of CC was younger than chronologic age. In subgroup analysis of women less than 38 years of age, poor ovarian response was associated with an accelerated predicted age in WBC (P = 0.017). Poor ovarian response did not affect the Horvath-predicted age based on CC samples (P = 0.502). No alternative methylation-based calculation was identified to be predictive of age for CC. LIMITATIONS, REASONS FOR CAUTION To date, analyses of CC have failed to identify epigenetic changes that are predictive of the aging process within the ovary. Despite the poor predictive nature of both the Horvath model and the novel methylation-based age prediction model described here, it is possible that our efforts failed to identify appropriate sites which would result in a successful age-prediction model derived from the CC epigenome. Additionally, lower DNA input for CC samples compared to WBC samples was a methodological limitation. We acknowledge that a universally accepted definition of poor ovarian response is lacking. Furthermore, women with PCOS were included and therefore the group of good responders in the current study may not represent a population with entirely normal methylation profiles. WIDER IMPLICATIONS OF THE FINDINGS The process of ovarian and CC aging continues to be poorly understood. Women who demonstrate poor ovarian response to stimulation represent a common clinical challenge, so clarifying the exact biological changes that occur within the ovary over time is a worthwhile endeavor. The data from CC support a view that hormonally responsive tissues may possess distinct epigenetic aging patterns when compared with other tissue types. Future studies may be able to determine whether alternative DNA methylation sites can accurately predict chronologic age or ovarian response to stimulation from CC samples. Going forward, associations between epigenetic age acceleration and reproductive and general health consequences must also be clearly defined. STUDY FUNDING/COMPETING INTEREST(S) No external funding was obtained for the study and there are no conflicts of interest. TRIAL REGISTRATION NUMBER N/A.
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- 2020
44. Three‐dimensional ultrasound diagnosis of adenomyosis is not associated with adverse pregnancy outcome following single thawed euploid blastocyst transfer: prospective cohort study
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Paul Pirtea, N.-A. Gueye, Scott J. Morin, Linnea R. Goodman, Shelby A. Neal, Richard T. Scott, Marie D. Werner, and George Patounakis
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Adult ,medicine.medical_specialty ,Pregnancy Rate ,Population ,Fertilization in Vitro ,Miscarriage ,03 medical and health sciences ,Imaging, Three-Dimensional ,0302 clinical medicine ,Obstetrics and gynaecology ,Pregnancy ,Prevalence ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Adenomyosis ,Prospective Studies ,030212 general & internal medicine ,Birth Rate ,education ,Prospective cohort study ,Retrospective Studies ,Ultrasonography ,education.field_of_study ,030219 obstetrics & reproductive medicine ,Radiological and Ultrasound Technology ,business.industry ,Obstetrics ,Pregnancy Outcome ,Obstetrics and Gynecology ,General Medicine ,Embryo Transfer ,medicine.disease ,Embryo transfer ,Abortion, Spontaneous ,Logistic Models ,Reproductive Medicine ,Infertility ,Female ,business ,Live birth ,Live Birth - Abstract
Objectives The objectives of this study were (1) to assess the prevalence of ultrasound (US) features of adenomyosis in an infertile population undergoing in-vitro fertilization (IVF), (2) to define the inter- and intrarater agreement of three-dimensional (3D) US assessment of adenomyosis, and (3) to evaluate sonographic features of adenomyosis with respect to pregnancy outcome following transfer of a single thawed euploid blastocyst. Methods This was a prospective cohort study. Subjects scheduled to undergo a single thawed euploid blastocyst transfer between April and December 2017 at a large IVF center were eligible for inclusion. Enrolled subjects underwent endometrial preparation for frozen embryo transfer. 3D-US was performed on the day prior to embryo transfer, with images stored for subsequent evaluation. Subjects then underwent transfer of a single thawed euploid blastocyst, and pregnancy outcomes were collected. All 3D-US volumes were de-identified and reviewed independently by five reproductive endocrinologists/infertility specialists with expertise in gynecological US for the presence of seven sonographic features of adenomyosis: global uterine enlargement, myometrial wall asymmetry, heterogeneous echogenicity, irregular junctional zone, myometrial cysts, fan-shaped shadowing and ill-defined myometrial lesions. Adenomyosis was considered to be present if the majority of the reviewers noted at least one of the seven sonographic features. Inter- and intrarater agreement was evaluated using Fleiss's kappa. Clinical and cycle characteristics of subjects with and those without adenomyosis were compared. The primary outcome of interest was live birth rate. Secondary outcomes included clinical pregnancy rate and miscarriage rate. Logistic regression analysis was performed to account for potential confounders. Results A total of 648 subjects were included. The prevalence of adenomyosis on US was 15.3% (99/648). On retrospective chart review, very few patients with adenomyosis had symptoms. The inter- and intrarater agreement amongst five independent specialists conducting the 3D-US assessments of adenomyosis were poor (κ = 0.23) and moderate (κ = 0.58), respectively. Subjects with adenomyosis were older (37.1 vs 35.9 years, P = 0.02) and more likely to undergo a gonadotropin-releasing hormone agonist downregulation protocol when compared with those without adenomyosis (12.1% vs 5.1%, P = 0.02). Clinical pregnancy (80.0% vs 75.0%) and live birth (69.5% vs 66.5%) rates were similar between the groups. When adjusting for potential confounders, there was no difference in the rate of clinical pregnancy (adjusted odds ratio (aOR), 1.47 (95% CI, 0.85-2.56)), miscarriage (aOR, 1.3 (95% CI, 0.62-2.72)) or live birth (aOR, 1.28 (95% CI, 0.78-2.08)) between subjects with and those without adenomyosis. No individual sonographic marker of adenomyosis was predictive of pregnancy outcome. Conclusions The inter-rater agreement of 3D-US assessment of adenomyosis is poor. Furthermore, sonographic markers of adenomyosis in asymptomatic patients may not be associated with altered pregnancy outcome following transfer of a single thawed euploid blastocyst. These findings suggest that routine screening for asymptomatic adenomyosis in an unselected infertile patient population undergoing frozen embryo transfer may not be warranted. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
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- 2020
45. Zooming in on mechanistic predator–prey ecology: Integrating camera traps with experimental methods to reveal the drivers of ecological interactions
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Michael J. Cherry, Justine L. Atkins, Martijn J. A. Weterings, Sarah Huebner, Jennifer S. Hunter, Lydia Beaudrot, Lisa Teckentrup, Irene Castañeda, Justine A. Smith, Justin P. Suraci, Meredith S. Palmer, Patrick M. Garvey, Dana J. Morin, Kaitlyn M. Gaynor, and Carson B. Keller
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0106 biological sciences ,Computer science ,Ecology (disciplines) ,Foraging ,detection ,predator recognition ,010603 evolutionary biology ,01 natural sciences ,Predation ,landscape of fear ,antipredator behaviour ,Animals ,Zoom ,Ecology, Evolution, Behavior and Systematics ,prey selection ,camera trap ,Ecology ,010604 marine biology & hydrobiology ,experiments ,PE&RC ,Multiple species ,Wildlife Ecology and Conservation ,Predatory Behavior ,Risk allocation ,Camera trap ,Animal Science and Zoology ,Experimental methods ,Introduced Species - Abstract
Camera trap technology has galvanized the study of predator–prey ecology in wild animal communities by expanding the scale and diversity of predator–prey interactions that can be analysed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator–prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive predator and prey behaviour, incorporating environmental realism not possible in the laboratory while benefiting from the distinct capacity of camera traps to generate large datasets from multiple species with minimal observer interference. However, such pairings of camera traps with experimental methods remain underutilized. We review recent advances in the experimental application of camera traps to investigate fundamental mechanisms underlying predator–prey ecology and present a conceptual guide for designing experimental camera trap studies. Only 9% of camera trap studies on predator–prey ecology in our review use experimental methods, but the application of experimental approaches is increasing. To illustrate the utility of camera trap-based experiments using a case study, we propose a study design that integrates observational and experimental techniques to test a perennial question in predator–prey ecology: how prey balance foraging and safety, as formalized by the risk allocation hypothesis. We discuss applications of camera trap-based experiments to evaluate the diversity of anthropogenic influences on wildlife communities globally. Finally, we review challenges to conducting experimental camera trap studies. Experimental camera trap studies have already begun to play an important role in understanding the predator–prey ecology of free-living animals, and such methods will become increasingly critical to quantifying drivers of community interactions in a rapidly changing world. We recommend increased application of experimental methods in the study of predator and prey responses to humans, synanthropic and invasive species, and other anthropogenic disturbances.
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- 2020
46. Spatial segregation and habitat partitioning of bobcat and Canada lynx
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Jeff Bowman, Robby R. Marrotte, and Samantha J. Morin
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0106 biological sciences ,Leading edge ,Spatial segregation ,Occupancy ,media_common.quotation_subject ,010603 evolutionary biology ,01 natural sciences ,Competition (biology) ,spatial segregation ,Abundance (ecology) ,habitat partitioning ,Trailing edge ,lcsh:Science ,media_common ,occupancy ,Multidisciplinary ,Ecology ,010604 marine biology & hydrobiology ,Geography ,Habitat ,lynx rufus ,lynx canadensis ,lcsh:Q ,lcsh:L ,competition ,lcsh:Education - Abstract
Harvest records suggest that the abundance of bobcats ( Lynx rufus) has increased and the leading edge of their distribution has spread northward, while the trailing edge of the Canada lynx ( Lynx canadensis) range has contracted in Ontario, Canada. There has been a debate about whether these closely related felids might compete in areas of sympatry, but there is little research on sympatric populations of bobcat and lynx. Both species are found on the north shore of Lake Huron in Ontario, Canada, which provided an opportunity to investigate their spatial patterns and habitat use. We surveyed snowmobile routes for snow tracks over three winters and estimated probability of occupancy for the two felid species while accounting for detectability. Bobcat and lynx tracks were never found on the same survey route. Bobcat occupancy increased with habitat heterogeneity, whereas lynx occupancy increased with homogeneity. Our results fit with the common assumption of the generalist and specialist natures of bobcat and lynx, respectively. Our findings suggest that bobcats invaded former lynx territory after these areas became vacant. The story of the bobcat and the lynx is one of the loss of a unique, boreal specialist due to anthropogenic change, and eventual replacement by an adaptable generalist.
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- 2020
47. Development of an amphibian sperm biobanking protocol for genetic management and population sustainability
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Isabella J, Burger, Shaina S, Lampert, Carrie K, Kouba, Dana J, Morin, and Andrew J, Kouba
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Physiology ,Ecological Modeling ,Management, Monitoring, Policy and Law ,Nature and Landscape Conservation - Abstract
Sperm cryopreservation is a vital tool in amphibian assisted reproductive technologies that aids in genetic and population management, specifically for at-risk species. Significant advancements have been made in the cryopreservation of amphibian sperm, yet there is little information on how the cryopreservation process influences fertilization and embryonic development. In this study, we tested several cryoprotective agents (CPAs) and freezing rates on sperm recovery, fertilization potential and embryo development using Fowler’s toads (Anaxyrus fowleri) as a model amphibian species for application to at-risk anurans. Three cryoprotectant treatments were tested, which included 10% trehalose + 0.25% bovine serum albumin with (1) 5% N,N-dimethylformamide (DMFA); (2) 10% DMFA; or (3) 10% dimethyl sulfoxide (DMSO). Additionally, sperm in each cryoprotectant was frozen at two different rates, −32 to −45°C/min and −20 to −29°C/min. Post-thaw sperm analysis included motility, morphology, viability, fertilization success and embryo development. Results show that 10% DMFA produced significantly higher (P = 0.005) post-thaw sperm motility than 5% DMFA and was similar to 10% DMSO. Furthermore, sperm frozen at −32 to −45°C/min had significantly higher post-thaw motility (P
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- 2022
48. Transition from multipolar to dipolar dynamos in stratified systems
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B Zaire, L Jouve, T Gastine, J-F Donati, J Morin, N Landin, C P Folsom, Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire Univers et Particules de Montpellier (LUPM), and Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
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Astrophysics - Solar and Stellar Astrophysics ,Space and Planetary Science ,MHD ,[SDU]Sciences of the Universe [physics] ,turbulence ,FOS: Physical sciences ,Astronomy and Astrophysics ,magnetic fields ,dynamo ,Solar and Stellar Astrophysics (astro-ph.SR) ,convection ,methods: numerical - Abstract
Observations of surface magnetic fields of cool stars reveal a large diversity of configurations. Although there is now a consensus that these fields are generated through dynamo processes occurring within the convective zone, the physical mechanism driving such a variety of field topologies is still debated. This paper discusses the possible origins of dipole and multipole-dominated morphologies using three-dimensional numerical simulations of stratified systems where the magnetic feedback on the fluid motion is significant. Our main result is that dipolar solutions are found at Rossby numbers up to 0.4 in strongly stratified simulations, where previous works suggested that only multipolar fields should exist. We argue that these simulations are reminiscent of the outlier stars observed at Rossby numbers larger than 0.1, whose large-scale magnetic field is dominated by their axisymmetric poloidal component. As suggested in previous Boussinesq calculations, the relative importance of inertial over Lorentz forces is again controlling the dipolar to multipolar transition. Alternatively, we find that the ratio of kinetic to magnetic energies can equally well capture the transition in the field morphology. We test the ability of this new proxy to predict the magnetic morphology of a few M-dwarf stars whose internal structure matches that of our simulations and for which homogeneous magnetic field characterization is available. Finally, the magnitude of the differential rotation obtained in our simulations is compared to actual measurements reported in the literature for M-dwarfs. In our simulations, we find a clear relationship between anti-solar differential rotation and the emergence of dipolar fields., Comment: 15 pages, 15 figures, accepted for publication in MNRAS
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- 2022
49. TOI-1759 b: A transiting sub-Neptune around a low mass star characterized with SPIRou and TESS
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E. Martioli, G. Hébrard, P. Fouqué, É. Artigau, J.-F. Donati, C. Cadieux, S. Bellotti, A. Lecavelier des Etangs, R. Doyon, J.-D. do Nascimento, L. Arnold, A. Carmona, N. J. Cook, P. Cortes-Zuleta, L. de Almeida, X. Delfosse, C. P. Folsom, P.-C. König, C. Moutou, M. Ould-Elhkim, P. Petit, K. G. Stassun, A. A. Vidotto, T. Vandal, B. Benneke, I. Boisse, X. Bonfils, P. Boyd, C. Brasseur, D. Charbonneau, R. Cloutier, K. Collins, P. Cristofari, I. Crossfield, R. F. Díaz, M. Fausnaugh, P. Figueira, T. Forveille, E. Furlan, E. Girardin, C. L. Gnilka, J. Gomes da Silva, P.-G. Gu, P. Guerra, S. B. Howell, G. A. J. Hussain, J. M. Jenkins, F. Kiefer, D. W. Latham, R. A. Matson, E. C. Matthews, J. Morin, R. Naves, G. Ricker, S. Seager, M. Takami, J. D. Twicken, A. Vanderburg, R. Vanderspek, J. Winn, Institut d'Astrophysique de Paris (IAP), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université de Montréal (UdeM), Universidade Federal do Rio Grande do Norte [Natal] (UFRN), Canada-France-Hawaii Telescope Corporation (CFHT), National Research Council of Canada (NRC)-Centre National de la Recherche Scientifique (CNRS)-University of Hawai'i [Honolulu] (UH), Université Grenoble Alpes (UGA), Laboratoire d'Astrophysique de Marseille (LAM), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France, Vanderbilt University [Nashville], Universiteit Leiden, Département de Physique [Montréal], University of British Columbia (UBC), Space Telescope Science Institute (STSci), Center for Astrophysics (emeritus), Harvard-Smithsonian, Cambridge, MA, USA, Université du Québec à Rimouski (UQAR), SETI Institute, University of Kansas [Kansas City], International Center for Advanced Studies (ICAS) and ICIFI (CONICET), Massachusetts Institute of Technology (MIT), European Southern Observatory (ESO), NASA ExoPlanet Science Institute (NExScI), California Institute of Technology (CALTECH), Grand Pra Observatory, Universidade do Porto = University of Porto, Institute of Astronomy and Astrophysics, Academia Sinica, Taipei, Observatori Astronòmic Albanyà, NASA Ames Research Center (ARC), European Space Research and Technology Centre (ESTEC), Agence Spatiale Européenne = European Space Agency (ESA), U.S. Naval Observatory, Observatoire Astronomique de l'Université de Genève (ObsGE), Université de Genève = University of Geneva (UNIGE), Laboratoire Univers et Particules de Montpellier (LUPM), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Academia Sinica Institute of Astronomy and Astrophysics (ASIAA), Academia Sinica, Peyton Hall, ANR-15-IDEX-0002,UGA,IDEX UGA(2015), ANR-18-CE31-0019,SPlaSH,Recherche de planètes habitables avec SPIRou(2018), and European Project: 740651,New Worlds
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Earth and Planetary Astrophysics (astro-ph.EP) ,stars: individual: TOI-1759 ,stars: magnetic field ,FOS: Physical sciences ,Astronomy and Astrophysics ,Astrophysics::Cosmology and Extragalactic Astrophysics ,techniques: photometric ,Astrophysics - Solar and Stellar Astrophysics ,Space and Planetary Science ,techniques: radial velocities ,Astrophysics::Solar and Stellar Astrophysics ,Astrophysics::Earth and Planetary Astrophysics ,[PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph] ,planetary systems ,Solar and Stellar Astrophysics (astro-ph.SR) ,Astrophysics::Galaxy Astrophysics ,Astrophysics - Earth and Planetary Astrophysics - Abstract
We report the detection and characterization of the transiting sub-Neptune TOI-1759 b, using photometric time-series from TESS and near infrared spectropolarimetric data from SPIRou on the CFHT. TOI-1759 b orbits a moderately active M0V star with an orbital period of $18.849975\pm0.000006$ d, and we measure a planetary radius and mass of $3.06\pm0.22$ R$_\oplus$ and $6.8\pm2.0$ M$_\oplus$. Radial velocities were extracted from the SPIRou spectra using both the CCF and the LBL methods, optimizing the velocity measurements in the near infrared domain. We analyzed the broadband SED of the star and the high-resolution SPIRou spectra to constrain the stellar parameters and thus improve the accuracy of the derived planet parameters. A LSD analysis of the SPIRou Stokes $V$ polarized spectra detects Zeeman signatures in TOI-1759. We model the rotational modulation of the magnetic stellar activity using a GP regression with a quasi-periodic covariance function, and find a rotation period of $35.65^{+0.17}_{-0.15}$ d. We reconstruct the large-scale surface magnetic field of the star using ZDI, which gives a predominantly poloidal field with a mean strength of $18\pm4$ G. Finally, we perform a joint Bayesian MCMC analysis of the TESS photometry and SPIRou RVs to optimally constrain the system parameters. At $0.1176\pm0.0013$ au from the star, the planet receives $6.4$ times the bolometric flux incident on Earth, and its equilibrium temperature is estimated at $433\pm14$ K. TOI-1759 b is a likely gas-dominated sub-Neptune with an expected high rate of photoevaporation. Therefore, it is an interesting target to search for neutral hydrogen escape, which may provide important constraints on the planetary formation mechanisms responsible for the observed sub-Neptune radius desert., Accepted for publication in the 10. Planets and planetary systems section of Astronomy & Astrophysics
- Published
- 2022
50. Retromer disruption promotes amyloidogenic APP processing
- Author
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Christopher P. Sullivan, Anthony G. Jay, Edward C. Stack, Maria Pakaluk, Erin Wadlinger, Richard E. Fine, John M. Wells, and Peter J. Morin
- Subjects
Retromer ,Vps35 ,APP ,Aβ ,Exosome ,Endosome ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Retromer deficiency has been implicated in sporadic AD and animals deficient in retromer components exhibit pronounced neurodegeneration. Because retromer performs retrograde transport from the endosome to the Golgi apparatus and neuronal Aβ is found in late endosomal compartments, we speculated that retromer malfunction might enhance amyloidogenic APP processing by promoting interactions between APP and secretase enzymes in late endosomes. We have evaluated changes in amyloid precursor protein (APP) processing and trafficking as a result of disrupted retromer activity by knockdown of Vps35, a vacuolar sorting protein that is an essential component of the retromer complex. Knocking down retromer activity produced no change in the quantity or cellular distribution of total cellular APP and had no affect on internalization of cell-surface APP. Retromer deficiency did, however, increase the ratio of secreted Aβ42:Aβ40 in HEK-293 cells over-expressing APP695, due primarily to a decrease in Aβ40 secretion. Recent studies suggest that the retromer-trafficked protein, Wntless, is secreted at the synapse in exosome vesicles and that these same vesicles contain Aβ. We therefore hypothesized that retromer deficiency may be associated with altered exosomal secretion of APP and/or secretase fragments. Holo-APP, Presenilin and APP C-terminal fragments were detected in exosomal vesicles secreted from HEK-293 cells. Levels of total APP C-terminal fragments were significantly increased in exosomes secreted by retromer deficient cells. These data suggest that reduced retromer activity can mimic the effects of familial AD Presenilin mutations on APP processing and promote export of amyloidogenic APP derivatives.
- Published
- 2011
- Full Text
- View/download PDF
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