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Abstract Background Functional genomics technologies that measure genome expression at a global scale are accelerating biological knowledge discovery. Generating these high throughput datasets is relatively easy compared to the downstream functional modelling necessary for elucidating the molecular mechanisms that govern the biology under investigation. A number of publicly available ‘discovery-based’ computational tools use the computationally amenable Gene Ontology (GO) for hypothesis generation. However, there are few tools that support hypothesis-based testing using the GO and none that support testing with user defined hypothesis terms. Here, we present GOModeler, a tool that enables researchers to conduct hypothesis-based testing of high throughput datasets using the GO. GOModeler summarizes the overall effect of a user defined gene/protein differential expression dataset on specific GO hypothesis terms selected by the user to describe a biological experiment. The design of the tool allows the user to complement the functional information in the GO with his/her domain specific expertise for comprehensive hypothesis testing. Results GOModeler tests the relevance of the hypothesis terms chosen by the user for the input gene dataset by providing the individual effects of the genes on the hypothesis terms and the overall effect of the entire dataset on each of the hypothesis terms. It matches the GO identifiers (ids) of the genes with the GO ids of the hypothesis terms and parses the names of those ids that match to assign effects. We demonstrate the capabilities of GOModeler with a dataset of nine differentially expressed cytokine genes and compare the results to those obtained through manual analysis of the dataset by an immunologist. The direction of overall effects on all hypothesis terms except one was consistent with the results obtained by manual analysis. The tool’s editing capability enables the user to augment the information extracted. GOModeler is available as a part of the AgBase tool suite (http://www.agbase.msstate.edu). Conclusions GOModeler allows hypothesis driven analysis of high throughput datasets using the GO. Using this tool, researchers can quickly evaluate the overall effect of quantitative expression changes of gene set on specific biological processes of interest. The results are provided in both tabular and graphical formats.

Measurements of atmospheric N//2O concentrations in and around Ann Arbor, Michigan, between August 1976 and September 1977 yielded 329. 5 ppb (parts per billion) (mole fraction in whole air samples) as the average with a standard deviation of 3. 3 ppb. No seasonal or overall trend is discernible. Small, marginally significant diurnal variations of N//2O concentrations in the lowest 0. 5 m of atmosphere can be seen in our data. Gas collectors applied to soils near our laboratory provided evidence that soils can consume atmospheric N//2O under some conditions. Soils were seen to be N//2O sources more often than sinks. Stronger source activity was evident in compost piles. Exhaust samples taken from several conventional vehicles showed less than ambient N//2O concentrations, while catalytic converter equipped autos produce N//2O. Samples of steaming volcanic vent air from Hawaii indicate that volcanoes are probably a source of atmospheric N//2O, although emissions at the Sulphur Bank contain much less than ambient values of N//2O. All measurements were made by electron capture-gas chromatography; techniques and equipment are described.

Psychedelics such as psilocybin show great promise for the treatment of depression and PTSD, but their long duration of action poses practical limitations for patient access. 4-OH-DiPT is a fast-acting and shorter-lasting derivative of psilocybin. Here we characterized the pharmacological profile of 4-OH-DiPT and examined its impact on fear extinction learning as well as a potential mechanism of action. First, we profiled 4-OH-DiPT at all 12 human 5-HT GPCRs. 4-OH-DiPT showed strongest agonist activity at all three 5-HT 2A/2B/2C receptors with near full agonist activity at 5-HT 2A . Notably, 4-OH-DiPT had comparable activity at mouse and human 5-HT 2A/2B/2C receptors. In a fear extinction paradigm, 4-OH-DiPT significantly reduced freezing responses to conditioned cues in a dose-dependent manner with a greater potency in female mice than male mice. Female mice that received 4-OH-DiPT before extinction training had reduced avoidance behaviors several days later in the light dark box, elevated plus maze and novelty-suppressed feeding test compared to controls, while male mice did not show significant differences. 4-OH-DiPT produced robust increases in spontaneous inhibitory postsynaptic currents (sIPSCs) in basolateral amygdala (BLA) principal neurons and action potential firing in BLA interneurons in a 5-HT 2A -dependent manner. RNAscope demonstrates that Htr2a mRNA is expressed predominantly in BLA GABA interneurons, Htr2c mRNA is expressed in both GABA interneurons and principal neurons, while Htr2b mRNA is absent in the BLA. Our findings suggest that 4-OH-DiPT activates BLA interneurons via the 5-HT 2A receptor to enhance GABAergic inhibition of BLA principal neurons, which provides a potential mechanism for suppressing learned fear., (© 2023. The Author(s), under exclusive licence to American College of Neuropsychopharmacology.)

Organisms from microbes to humans engage in a variety of social behaviors, which affect fitness in complex, often nonlinear ways. The question of how these behaviors evolve has consequences ranging from antibiotic resistance to human origins. However, evolution with nonlinear social interactions is challenging to model mathematically, especially in combination with spatial, group, and/or kin assortment. We derive a mathematical condition for natural selection with synergistic interactions among any number of individuals. This result applies to populations with arbitrary (but fixed) spatial or network structure, group subdivision, and/or mating patterns. In this condition, nonlinear fitness effects are ascribed to collectives, and weighted by a new measure of collective relatedness. For weak selection, this condition can be systematically evaluated by computing branch lengths of ancestral trees. We apply this condition to pairwise games between diploid relatives, and to dilemmas of collective help or harm among siblings and on spatial networks. Our work provides a rigorous basis for extending the notion of "actor", in the study of social evolution, from individuals to collectives., (© The Author(s) 2024. Published by Oxford University Press on behalf of National Academy of Sciences.)

Objective: To develop and clinically evaluate a customizable active upper extremity (UE) assistive system with integrated functional electrical stimulation (FES) that improves function and independence of individuals during activities of daily living (ADLs)., Design: Single-arm, prospective, open-label cohort feasibility trial., Setting: An academic research institution., Participants: Subjects were 5 adults with a medical history of stroke resulting in distal UE impairment (N=5). The subjects volunteered from recruitment materials that detailed information about the study., Interventions: A novel, wearable, lightweight, low-profile, and patient-tailored UE assistive system. It comprises a splint component and FES unit that may each be controlled by electromyography (EMG) signals, inertial measurement units (IMUs), manual control source (joystick), and/or voice control., Main Outcome Measures: Several occupational therapy outcome measures were used, including the Canadian Occupational Performance Measure (COPM), Action Research Arm Test (ARAT), The Box and Blocks Test (BBT), the ABILHAND-Manual Ability Measure, and Patient Reported Outcomes Measurement Information System (PROMIS) UE Short Form., Results: All participants learned to use our UE assistive system to perform ADLs and were able to use it independently at home. Most participants experienced a clinically meaningful improvement in both performance and satisfaction for the majority of their COPM goals while using the system. All participants experienced improvement in hand grip and release as shown by their baseline and post assessment scores for hand function (BBT, ARAT) and patient-reported outcomes (ABILHAND, PROMIS)., Conclusions: The clinical outcomes suggest that our UE assistive system improves functional performance in patients with UE impairment, allowing them to engage more actively in ADLs. Further innovation including elbow and shoulder components will allow users to have more degrees of freedom during tasks., (© 2023 The Authors.)

Chronic cocaine exposure induces enduring neuroadaptations that facilitate motivated drug taking. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are known to modulate neuronal firing and pacemaker activity in ventral tegmental area (VTA) dopamine neurons. However, it remained unknown whether cocaine self-administration affects HCN channel function and whether HCN channel activity modulates motivated drug taking. We report that rat VTA dopamine neurons predominantly express Hcn3-4 mRNA, while VTA GABA neurons express Hcn1-4 mRNA. Both neuronal types display similar hyperpolarization-activated currents (I h ), which are facilitated by acute increases in cAMP. Acute cocaine application decreases voltage-dependent activation of I h in VTA dopamine neurons, but not in GABA neurons. Unexpectedly, chronic cocaine self-administration results in enhanced I h selectively in VTA dopamine neurons. This differential modulation of I h currents is likely mediated by a D 2 autoreceptor-induced decrease in cAMP as D 2 (Drd2) mRNA is predominantly expressed in dopamine neurons, whereas D 1 (Drd1) mRNA is barely detectable in the VTA. Moreover, chronically decreased cAMP via Gi-DREADD stimulation leads to an increase in I h in VTA dopamine neurons and enhanced binding of HCN3/HCN4 with tetratricopeptide repeat-containing Rab8b-interacting protein (TRIP8b), an auxiliary subunit that is known to facilitate HCN channel surface trafficking. Finally, we show that systemic injection and intra-VTA infusion of the HCN blocker ivabradine reduces cocaine self-administration under a progressive ratio schedule and produces a downward shift of the cocaine dose-response curve. Our results suggest that cocaine self-administration induces an upregulation of I h in VTA dopamine neurons, while HCN inhibition reduces the motivation for cocaine intake., (© 2023. The Author(s).)

Synthetic design allowing predictive control of charge transfer and other optoelectronic properties of Lewis acid adducts remains elusive. This challenge must be addressed through complementary methods combining experimental with computational insights from first principles. Ab initio calculations for optoelectronic properties can be computationally expensive and less straightforward than those sufficient for simple ground-state properties, especially for adducts of large conjugated molecules and Lewis acids. In this contribution, we show that machine learning (ML) can accurately predict density functional theory (DFT)-calculated charge transfer and even properties associated with excited states of adducts from readily obtained molecular descriptors. Seven ML models, built from a dataset of over 1000 adducts, show exceptional performance in predicting charge transfer and other optoelectronic properties with a Pearson correlation coefficient of up to 0.99. More importantly, the influence of each molecular descriptor on predicted properties can be quantitatively evaluated from ML models. This contributes to the optimization of a priori design of Lewis adducts for future applications, especially in organic electronics., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

An open-loop control scheme of molecular fragmentation based on transient molecular alignment combined with single-photon ionization induced by a short-wavelength free electron laser (FEL) is demonstrated for the acetylene cation. Photoelectron spectra are recorded, complementing the ion yield measurements, to demonstrate that such control is the consequence of changes in the electronic response with molecular orientation relative to the ionizing field. We show that stable C 2 H 2 + cations are mainly produced when the molecules are parallel or nearly parallel to the FEL polarization, while the hydrogen fragmentation channel (C 2 H 2 + → C 2 H + + H) predominates when the molecule is perpendicular to that direction, thus allowing one to distinguish between the two photochemical processes. The experimental findings are supported by state-of-the art theoretical calculations.

Repeated exposure to drugs of abuse results in an upregulation of cAMP signaling in the mesolimbic dopamine system, a molecular adaptation thought to be critically involved in the development of drug dependence. Exchange protein directly activated by cAMP (Epac2) is a major cAMP effector abundantly expressed in the brain. However, it remains unknown whether Epac2 contributes to cocaine reinforcement. Here, we report that Epac2 in the mesolimbic dopamine system promotes cocaine reinforcement via enhancement of dopamine release. Conditional knockout of Epac2 from midbrain dopamine neurons (Epac2-cKO) and the selective Epac2 inhibitor ESI-05 decreased cocaine self-administration in mice under both fixed-ratio and progressive-ratio reinforcement schedules and across a broad range of cocaine doses. In addition, Epac2-cKO led to reduced evoked dopamine release, whereas Epac2 agonism robustly enhanced dopamine release in the nucleus accumbens in vitro. This mechanism is central to the behavioral effects of Epac2 disruption, as chemogenetic stimulation of ventral tegmental area (VTA) dopamine neurons via deschloroclozapine (DCZ)-induced activation of Gs-DREADD increased dopamine release and reversed the impairment of cocaine self-administration in Epac2-cKO mice. Conversely, chemogenetic inhibition of VTA dopamine neurons with Gi-DREADD reduced dopamine release and cocaine self-administration in wild-type mice. Epac2-mediated enhancement of dopamine release may therefore represent a novel and powerful mechanism that contributes to cocaine reinforcement., Competing Interests: XL, CV, HY, SL, SS, VF, LM, BC, TK, DB, QL No competing interests declared, (© 2022, Liu et al.)

In addition to motor dysfunction, patients with Parkinson's disease (PD) are often affected by neuropsychiatric disorders, such as anxiety and depression. In animal models, activation of the endocannabinoid (eCB) system produces anxiolytic and antidepressant-like behavioral effects. CB2 agonists have demonstrated neuroprotective effects against neurotoxin-induced dopamine neuron loss and deficits in motor function. However, it remains unknown whether CB2 agonism ameliorates anxiogenic- and depressive-like behaviors in PD models. Here, we report that the selective CB2 agonist GW842166x exerted neuroprotective effects against 6-hydroxydopamine (6-OHDA)-induced loss of dopaminergic terminals and dopamine release in the striatum, which were blocked by the CB2 antagonist AM630. We found that 6-OHDA-treated mice exhibited anxiogenic- and depressive-like behaviors in the open-field, sucrose preference, novelty-suppressed feeding, marble burying, and forced swim tests but did not show significant changes in the elevated plus-maze and light-dark box test. GW842166x treatments ameliorated 6-OHDA-induced anxiogenic- and depressive-like behaviors, but the effects were blocked by CB2 antagonism, suggesting a CB2-dependent mechanism. These results suggest that the CB2 agonist GW842166x not only reduces 6-OHDA-induced motor function deficits but also anxiogenic- and depressive-like behaviors in 6-OHDA mouse models of PD.

We developed a method to tag telomeres and measure telomere length by nanopore sequencing in the yeast S. cerevisiae Nanopore allows long-read sequencing through the telomere, through the subtelomere, and into unique chromosomal sequence, enabling assignment of telomere length to a specific chromosome end. We observed chromosome end-specific telomere lengths that were stable over 120 cell divisions. These stable chromosome-specific telomere lengths may be explained by slow clonal variation or may represent a new biological mechanism that maintains equilibrium unique to each chromosome end. We examined the role of RIF1 and TEL1 in telomere length regulation and found that TEL1 is epistatic to RIF1 at most telomeres, consistent with the literature. However, at telomeres that lack subtelomeric Y' sequences, tel1Δ rif1Δ double mutants had a very small, but significant, increase in telomere length compared with the tel1Δ single mutant, suggesting an influence of Y' elements on telomere length regulation. We sequenced telomeres in a telomerase-null mutant ( est2Δ ) and found the minimal telomere length to be ∼75 bp. In these est2Δ mutants, there were apparent telomere recombination events at individual telomeres before the generation of survivors, and these events were significantly reduced in est2Δ rad52Δ double mutants. The rate of telomere shortening in the absence of telomerase was similar across all chromosome ends at ∼5 bp per generation. This new method gives quantitative, high-resolution telomere length measurement at each individual chromosome end and suggests possible new biological mechanisms regulating telomere length., (© 2022 Sholes et al.; Published by Cold Spring Harbor Laboratory Press.)

Background & Aims: Excessive shedding of apoptotic enterocytes into the intestinal lumen is observed in inflammatory bowel disease and is correlated with disease relapse. Based on their cytolytic capacity and surveillance behavior, we investigated whether intraepithelial lymphocytes expressing the γδ T cell receptor (γδ IELs) are actively involved in the shedding of enterocytes into the lumen., Methods: Intravital microscopy was performed on GFP γδ T cell reporter mice treated with intraperitoneal lipopolysaccharide (10 mg/kg) for 90 minutes to induce tumor necrosis factor-mediated apoptosis. Cell shedding in various knockout or transgenic mice in the presence or absence of blocking antibody was quantified by immunostaining for ZO-1 funnels and cleaved caspase-3 (CC3). Granzyme A and granzyme B release from ex vivo-stimulated γδ IELs was quantified by enzyme-linked immunosorbent assay. Immunostaining for γδ T cell receptor and CC3 was performed on duodenal and ileal biopsies from controls and patients with Crohn's disease., Results: Intravital microscopy of lipopolysaccharide-treated mice revealed that γδ IELs make extended contact with shedding enterocytes. These prolonged interactions require CD103 engagement by E-cadherin, and CD103 knockout or blockade significantly reduced lipopolysaccharide-induced shedding. Furthermore, we found that granzymes A and B, but not perforin, are required for cell shedding. These extracellular granzymes are released by γδ IELs both constitutively and after CD103/E-cadherin ligation. Moreover, we found that the frequency of γδ IEL localization to CC3-positive enterocytes is increased in Crohn's disease biopsies compared with healthy controls., Conclusions: Our results uncover a previously unrecognized role for γδ IELs in facilitating tumor necrosis factor-mediated shedding of apoptotic enterocytes via CD103-mediated extracellular granzyme release., (Copyright © 2022 AGA Institute. Published by Elsevier Inc. All rights reserved.)

Parkinson's disease (PD) is a chronic neurodegenerative disorder associated with dopamine neuron loss and motor dysfunction. Neuroprotective agents that prevent dopamine neuron death hold great promise for slowing the disease's progression. The activation of cannabinoid (CB) receptors has shown neuroprotective effects in preclinical models of neurodegenerative disease, traumatic brain injury, and stroke, and may provide neuroprotection against PD. Here, we report that the selective CB2 agonist GW842166x exerted protective effects against the 6-hydroxydopamine (6-OHDA)-induced loss of dopamine neurons and its associated motor function deficits in mice, as shown by an improvement in balance beam walking, pole, grip strength, rotarod, and amphetamine-induced rotation tests. The neuroprotective effects of GW842166x were prevented by the CB2 receptor antagonist AM630, suggesting a CB2-dependent mechanism. To investigate potential mechanisms for the neuroprotective effects of GW842166x, we performed electrophysiological recordings from substantia nigra pars compacta (SNc) dopamine neurons in ex vivo midbrain slices prepared from drug-naïve mice. We found that the bath application of GW842166x led to a decrease in action potential firing, likely due to a decrease in hyperpolarization-activated currents (I h ) and a shift of the half-activation potential ( V 1/2 ) of I h to a more hyperpolarized level. Taken together, the CB2 agonist GW842166x may reduce the vulnerability of dopamine neurons to 6-OHDA by decreasing the action potential firing of these neurons and the associated calcium load.

Ibudilast is a non-selective phosphodiesterase (PDE) inhibitor and glial cell modulator which has shown great promise for the treatment of drug and alcohol use disorders in recent clinical studies. However, it is unknown whether and how ibudilast affects cocaine seeking behavior. Here we show that systemic administration of ibudilast dose-dependently reduced cocaine self-administration under fixed- and progressive-ratio reinforcement schedules in rats and shifted cocaine dose-response curves downward. In addition, ibudilast decreased cocaine prime- and cue-induced reinstatement of cocaine seeking. These results indicate that ibudilast was effective in reducing the reinforcing effects of cocaine and relapse to cocaine seeking. Chronic cocaine exposure induces cAMP-related neuroadaptations in the reward circuitry of the brain. To investigate potential mechanisms for ibudilast-induced attenuation of cocaine self-administration, we recorded from ventral tegmental area (VTA) dopamine neurons in ex vivo midbrain slices prepared from rats that had undergone saline and cocaine self-administration. We found cocaine self-administration led to a decrease in inhibitory postsynaptic currents (IPSCs), an increase in the AMPAR/NMDAR ratio, and an increase in the excitation to inhibition (E/I) ratio. Ibudilast pretreatments enhanced GABAergic inhibition and did not further change cocaine-induced potentiation of excitation, leading to normalization of the E/I ratio. Restoration of the balance between excitation and inhibition in VTA dopamine neurons may contribute to the attenuation of cocaine self-administration by ibudilast., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The frequency and duration of flooding events is increasing due to land-use changes increasing run-off of precipitation, and climate change causing more intense rainfall events. Floodplain soils situated downstream of urban or industrial catchments, which were traditionally considered a sink of potentially toxic elements (PTEs) arriving from the river reach, may now become a source of legacy pollution to the surrounding environment, if PTEs are mobilised by unprecedented flooding events. When a soil floods, the mobility of PTEs can increase or decrease due to the net effect of five key processes; (i) the soil redox potential decreases which can directly alter the speciation, and hence mobility, of redox sensitive PTEs (e.g. Cr, As), (ii) pH increases which usually decreases the mobility of metal cations (e.g. Cd 2+ , Cu 2+ , Ni 2+ , Pb 2+ , Zn 2+ ), (iii) dissolved organic matter (DOM) increases, which chelates and mobilises PTEs, (iv) Fe and Mn hydroxides undergo reductive dissolution, releasing adsorbed and co-precipitated PTEs, and (v) sulphate is reduced and PTEs are immobilised due to precipitation of metal sulphides. These factors may be independent mechanisms, but they interact with one another to affect the mobility of PTEs, meaning the effect of flooding on PTE mobility is not easy to predict. Many of the processes involved in mobilising PTEs are microbially mediated, temperature dependent and the kinetics are poorly understood. Soil mineralogy and texture are properties that change spatially and will affect how the mobility of PTEs in a specific soil may be impacted by flooding. As a result, knowledge based on one river catchment may not be particularly useful for predicting the impacts of flooding at another site. This review provides a critical discussion of the mechanisms controlling the mobility of PTEs in floodplain soils. It summarises current understanding, identifies limitations to existing knowledge, and highlights requirements for further research., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

In this work we investigate the effect of the confinement angle on self-colliding aluminium laser produced plasmas. More specifically, we apply V-shaped channel targets of different angles (90°, 60° and 30°) and report both broadband and filtered time-resolved fast imaging measurements on the formation of such plasmas in ambient air. Based on the broadband measurements we suggest that the plasmas formed on the two inner walls of the V-shaped channel expand normally to the surface, interact with each other and possibly stagnate. The spectrally filtered fast imaging reveals the presence of a spatial distribution of different species within the plasmas and signatures of forced recombination.

Floodplains downstream of urban catchments are sinks for potentially toxic trace elements. An intensification of the hydrological cycle and changing land use will result in floodplains becoming inundated for longer durations in the future. We collected intact soil cores from a floodplain meadow downstream of an urban catchment and subjected them to an inundation/drainage cycle in the laboratory to investigate the effect of flood duration on trace element concentrations in the soil porewater. The porewater concentrations of Ni, Cr, and Zn increased, whereas Cu and Pb decreased with flood duration. All the Cr present in porewaters was identified as Cr(III). Copper concentrations increased after drainage but Pb mobility remained suppressed. Both pH and dissolved organic carbon (DOC) increased with flood duration but were lower in treatments that were drained for the longest duration (which were also the treatments flooded for the shortest duration). The porewater concentrations of Cr and Ni decreased after drainage to levels below those observed before inundation, mirroring the DOC concentrations. We concluded that the duration of floodplain inundation does have an influence on the environmental fate of trace elements but that flooding does not influence all trace elements in the same way. The implications of an intensification of the hydrological cycle over the coming decades are that floodplains may become a source of some trace elements to aquatic and terrestrial ecosystems. Environ Toxicol Chem 2020;39:2124-2135. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC., (© 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.)

Action potential (AP) burst firing caused by the activation of low-voltage-activated T-type Ca 2+ channels is a unique mode of neuronal firing. T-type channels have been implicated in diverse physiological and pathophysiological processes, including epilepsy, autism, and mood regulation, but the brain structures involved remain incompletely understood. The medial habenula (MHb) is an epithalamic structure implicated in anxiety-like and withdrawal behavior. Previous studies have shown that MHb neurons fire tonic APs at a frequency of ∼2-10 Hz or display depolarized low-amplitude membrane oscillations. Here, we report in C57BL/6J mice that a subpopulation of MHb neurons are capable of firing transient, high-frequency AP bursts mediated by T-type channels. Burst firing was observed following rebounding from hyperpolarizing current injections or during depolarization from hyperpolarized membrane potentials in ∼20% of MHb neurons. It was rarely observed at baseline but could be evoked in MHb neurons displaying different initial activity states. Further, we show that T-type channel mRNA, in particular Ca v 3.1, is expressed in the MHb in both cholinergic and substance P-ergic neurons. Pharmacological Ca v 3 antagonism blocked both burst firing and evoked Ca 2+ currents in MHb neurons. Additionally, we observed high-frequency AP doublet firing at sustained depolarized membrane potentials that was independent of T-type channels. Thus, there is a greater diversity of AP firing patterns in MHb neurons than previously identified, including T-type channel-mediated burst firing, which may uniquely contribute to behaviors with relevance to neuropsychiatric disease., (Copyright © 2020 Vickstrom et al.)

Objectives: The aim of this study was to study the impact of a decision-making protocol for shunt type in the Norwood procedure for hypoplastic left heart syndrome. Our cohort extends from 2004 to 2016. In era 1 (pre-2008), there was no policy for the choice of Norwood shunt. In era 2 (post-2008), a standard protocol was implemented. The right ventricle (RV)-to-pulmonary artery conduit was utilized for low-birth weight patients (<2.5 kg). The right modified Blalock-Taussig Shunt (RBTS) was constructed for normal birth weight patients., Methods: The records of 133 consecutive operative patients with hypoplastic left heart syndrome anatomy between 2004 and 2016 were retrospectively reviewed. Survival risk factors were analysed using the Cox proportional hazards risk model., Results: The Norwood procedure was performed at a mean age of 2.9 ± 1.9 days. Bidirectional cavopulmonary shunt was performed at a median age of 99 days (interquartile range 91-107). In era 1, 38.6% (22/57) of patients received the RBTS and 61.4% (35/57) of patients received the RV-to-pulmonary artery conduit. In era 2, 86.8% (66/76) of patients received the RBTS and 13.2% (10/76) of patients received the RV-to-pulmonary artery conduit. The actuarial survival to Fontan was 72.2% (96/133). Era 1 patients were more likely to die within the 1st year (hazard ratio = 2.310, P = 0.025)., Conclusions: The shunt protocol may improve outcomes in high-risk patients, and we have demonstrated the reliability of the RBTS in low-risk patients. The short- and mid-term outcomes of our Norwood population justify the continued efforts to improve surgical and perioperative management., (© The Author(s) 2020. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.)

Aquaculture production continues to grow in West Bengal, where on average people consume 8.2 kg capita -1 of fish each year, and an extensive mosaic of aquaculture ponds has developed along the River Hugli as clay pits are repurposed. The adjacent brickworks and industry (especially tanneries) are a source of environmental pollution, with potential for bioaccumulation of potentially harmful elements (PHEs) in fish farmed in these ponds. Fish from aquaculture present an opportunity to meet food sufficiency in West Bengal; however, an investigation to assess their effectiveness for micronutrient supply balanced against food safety is required. Five ponds close to industrial brick manufacture (urban) and three from rural areas were assessed for the degree of pollution within their pond sediments and waters. Fish were also sampled from each location including a subset from the market in Kolkata to determine the concentrations of PHEs in their fish muscle tissue. Dietary intake and PHE loading were calculated for four fish species to evaluate their nutrient content with respect to recommended daily intakes for adults, e.g. calcium (Ca), potassium (K), magnesium (Mg), iron (Fe), zinc (Zn) and selenium (Se), and to establish whether the provisional maximum tolerable intakes (PMTIs) are exceeded for PHEs, e.g. aluminium (Al), arsenic (As), mercury (Hg), chromium (Cr), tin (Sn), copper (Cu) and lead (Pb). Preliminary results suggest that aquaculture is making an important contribution to nutrition, with fish being a good source of Se. However, in contrast to small wild-caught fish, aquaculture fish in the present study were poor sources of Fe, Ca and Zn. The fish also made substantial contributions (> 10%) to the PMTI of Hg and As. Therefore, there is an urgent need for ongoing monitoring and an expanded sampling programme, as well as research into approaches which might improve the nutritional quality of the farmed fish.

Although microRNAs (miRNAs) function in the control of embryonic stem cell (ESC) pluripotency, a systems-level understanding is still being developed. Through the analysis of progressive Argonaute (Ago)-miRNA depletion and rescue, including stable Ago knockout mouse ESCs, we uncover transforming growth factor beta (TGF-β) pathway activation as a direct and early response to ESC miRNA reduction. Mechanistically, we link the derepression of weaker miRNA targets, including TGF-β receptor 1 (Tgfbr1), to the sensitive TGF-β pathway activation. In contrast, stronger miRNA targets impart a more robust repression, which dampens concurrent transcriptional activation. We verify such dampened induction for TGF-β antagonist Lefty. We find that TGF-β pathway activation contributes to the G1 cell-cycle accumulation of miRNA-deficient ESCs. We propose that miRNA target affinity is a determinant of the temporal response to miRNA changes, which enables the coordination of gene network responses., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Argonaute (Ago) proteins interact with various binding partners and play a pivotal role in microRNA (miRNA)-mediated silencing pathways. By utilizing immunoprecipitation followed by mass spectrometry to determine cytoplasmic Ago2 protein complexes in mouse embryonic stem cells (mESCs), we identified a putative RNA-binding protein FAM120A (also known as OSSA/C9ORF10) as an Ago2 interacting protein. Individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP) analysis revealed that FAM120A binds to homopolymeric tracts in 3'-UTRs of about 2000 mRNAs, particularly poly(G) sequences. Comparison of FAM120A iCLIP and Ago2 iCLIP reveals that greater than one-third of mRNAs bound by Ago2 in mESCs are co-bound by FAM120A. Furthermore, such FAM120A-bound Ago2 target genes are not subject to Ago2-mediated target degradation. Reporter assays suggest that the 3'-UTRs of several FAM120A-bound miRNA target genes are less sensitive to Ago2-mediated target repression than those of FAM120A-unbound miRNA targets and FAM120A modulates them via its G-rich target sites. These findings suggest that Ago2 may exist in multiple protein complexes with varying degrees of functionality., (© 2019 Kelly et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)

Understanding and controlling the optoelectronic properties of organic semiconductors at the molecular level remains a challenge due to the complexity of chemical structures and intermolecular interactions. A common strategy to address this challenge is to utilize both experimental and computational approaches. In this contribution, we show that density functional theory (DFT) calculation is a useful tool to provide insights into the bonding, electron population distribution, and optical transitions of adducts between conjugated molecules and Lewis acids (CM-LA). Adduct formation leads to relevant modifications of key properties, including a red shift in optical transitions and an increase in charge carrier density and charge mobility, compared to the parent conjugated molecules. We show that electron density transfer from the CM to the LA, which was hypothesized to cause the experimental red shift in absorption spectra upon LA binding, can be quantified and interpreted by population analysis. Experimental red shifts in optical transitions for all molecular families can also be predicted by time-dependent DFT calculations with different density functionals. These detailed insights help to optimize a priori design guidelines for future applications.

To date there have only been two studies using testate amoebae as palaeoecological indicators in tropical peatlands. Here we present a new ∼500-year testate amoeba record from San Jorge, a domed peatland in Peruvian Amazonia, which has a well-constrained vegetation history based on pollen analysis. We observe a major shift from Hyalosphenia subflava to Cryptodifflugia oviformis-dominated communities at ∼50 cm depth (c. AD 1760), which suggests a change to drier conditions in the peatland. The application of a statistical transfer function also suggests a deepening of the water table at this time. The transition in the microbial assemblage occurs at a time when pollen and geochemical data indicate drier conditions (reduced influence of river flooding), leading to an ecosystem switch to more ombrotrophic-like conditions in the peatland. Our work illustrates the potential of testate amoebae as important tools in tropical peatland palaeoecology, and the power of multiproxy approaches for understanding the long-term development of tropical peatlands., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

Large, intact areas of tropical peatland are highly threatened at a global scale by the expansion of commercial agriculture and other forms of economic development. Conserving peatlands on a landscape scale, with their hydrology intact, is of international conservation importance to preserve their distinctive biodiversity and ecosystem services and maintain their resilience to future environmental change. We explored threats to and opportunities for conserving remaining intact tropical peatlands; thus, we excluded peatlands of Indonesia and Malaysia, where extensive deforestation, drainage, and conversion to plantations means conservation in this region can protect only small fragments of the original ecosystem. We focused on a case study, the Pastaza-Marañón Foreland Basin (PMFB) in Peru, which is among the largest known intact tropical peatland landscapes in the world and is representative of peatland vulnerability. Maintenance of the hydrological conditions critical for carbon storage and ecosystem function of peatlands is, in the PMFB, primarily threatened by expansion of commercial agriculture linked to new transport infrastructure that is facilitating access to remote areas. There remain opportunities in the PMFB and elsewhere to develop alternative, more sustainable land-use practices. Although some of the peatlands in the PMFB fall within existing legally protected areas, this protection does not include the most carbon-dense (domed pole forest) areas. New carbon-based conservation instruments (e.g., REDD+, Green Climate Fund), developing markets for sustainable peatland products, transferring land title to local communities, and expanding protected areas offer pathways to increased protection for intact tropical peatlands in Amazonia and elsewhere, such as those in New Guinea and Central Africa which remain, for the moment, broadly beyond the frontier of commercial development., (© 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.)

Herpes simplex virus (HSV) was originally implicated in the aetiology of cervical cancer, and although high-risk human papillomavirus (HPV) is now the accepted causative agent, the epidemiological link between HSV and HPV-associated cancers persists. The annexin A2 heterotetramer (A2t) has been shown to mediate infectious HPV type 16 (HPV16) uptake by human keratinocytes, and secretory leukocyte protease inhibitor (SLPI), an endogenous A2t ligand, inhibits HPV16 uptake and infection. Interestingly, HSV infection induces a sustained downregulation of SLPI in epithelial cells, which we hypothesized promotes HPV16 infection through A2t. Here, we show that in vitro infection of human keratinocytes with HSV-1 or HSV-2, but not with an HSV-1 ICP4 deletion mutant that does not downregulate SLPI, leads to a >70% reduction of SLPI mRNA and a >60% decrease in secreted SLPI protein. Consequently, we observed a significant increase in the uptake of HPV16 virus-like particles and gene transduction by HPV16 pseudovirions (two- and 2.5-fold, respectively) in HSV-1- and HSV-2-infected human keratinocyte cell cultures compared with uninfected cells, whereas exogenously added SLPI reversed this effect. Using a SiMPull (single-molecule pulldown) assay, we demonstrated that endogenously secreted SLPI interacts with A2t on epithelial cells in an autocrine/paracrine manner. These results suggested that ongoing HSV infection and resultant downregulation of local levels of SLPI may impart a greater susceptibility for keratinocytes to HPV16 infection through the host cell receptor A2t, providing a mechanism that may, in part, provide an explanation for the aetiological link between HSV and HPV-associated cancers.

DNA damage tolerance (DDT) mechanisms allow cells to synthesize a new DNA strand when the template is damaged. Many mutations resulting from DNA damage in eukaryotes are generated during DDT when cells use the mutagenic translesion polymerases, Rev1 and Polζ, rather than mechanisms with higher fidelity. The coordination among DDT mechanisms is not well understood. We used live-cell imaging to study the function of DDT mechanisms throughout the cell cycle of the fission yeast Schizosaccharomyces pombe. We report that checkpoint-dependent mitotic delay provides a cellular mechanism to ensure the completion of high fidelity DDT, largely by homology-directed repair (HDR). DDT by mutagenic polymerases is suppressed during the checkpoint delay by a mechanism dependent on Rad51 recombinase. When cells pass the G2/M checkpoint and can no longer delay mitosis, they completely lose the capacity for HDR and simultaneously exhibit a requirement for Rev1 and Polζ. Thus, DDT is coordinated with the checkpoint response so that the activity of mutagenic polymerases is confined to a vulnerable period of the cell cycle when checkpoint delay and HDR are not possible.

Organic rich sediments were obtained from seven core tops taken in Lake Quistococha, near the city of Iquitos in the Peruvian Amazon. Subsamples from 0 to 4cm depth in each core were analyzed under dissecting light microscopy to carry out the first investigation of Arcellinida (testate lobose amoebae) from a lacustrine environment in this ecologically important region. The fauna was characterized by a low diversity, low abundance community dominated by centropyxids. This fauna is similar to 'stressed' assemblages reported from temperate latitudes, except that test concentrations were two orders of magnitude lower than typical in temperate lakes. Principle arcellinidan stressors in Lake Quistococha likely include the low pH 4 conditions in the lake, and a general lack of suitable minerogenic material to construct tests in the organic rich lake substrate. The low pH conditions are the result of runoff and seepage of water high in dissolved organic carbon from the adjacent similarly low pH 4 terrestrial peatland. The dearth of minerogenic material is the result of the lake being isolated from riverine input for the past ∼2000 years, even during flooding events. Other limiting factors contributing to depressed arcellinidan populations may include nutrient supply, predation pressure, competition, and post-mortem taphonomic factors., (Copyright © 2015 Elsevier GmbH. All rights reserved.)

There is a lack of data for how the viability of biological agents may degrade over time in different environments. In this study, experiments were conducted to determine the persistence of Bacillus anthracis and Bacillus subtilis spores on outdoor materials with and without exposure to simulated sunlight, using ultraviolet (UV)-A/B radiation. Spores were inoculated onto glass, wood, concrete, and topsoil and recovered after periods of 2, 14, 28, and 56 days. Recovery and inactivation kinetics for the two species were assessed for each surface material and UV exposure condition. Results suggest that with exposure to UV, decay of spore viability for both Bacillus species occurs in two phases, with an initial rapid decay, followed by a slower inactivation period. The exception was with topsoil, in which there was minimal loss of spore viability in soil over 56 days, with or without UV exposure. The greatest loss in viable spore recovery occurred on glass with UV exposure, with nearly a four log10 reduction after just two days. In most cases, B. subtilis had a slower rate of decay than B. anthracis, although less B. subtilis was recovered initially.

Objective: To describe a quality improvement (QI) initiative that was associated with a dramatic reduction in neonatal central-line associated bloodstream infection (CLABSI) rate in a diverse group of 8 intensive care nurseries (Neonatal Services)., Study Design: A quasi-experimental time series QI initiative using the model for improvement and evidenced-based interventions., Results: The aggregate CLABSI rate for Nationwide Children's Hospital-associated Neonatal Services decreased from 6.0 CLABSI per 1000 catheter days to 1.43 CLABSI per 1000 catheter days in less than 2 years and has remained in control at 0.68 per 1000 catheter days for over 5 years. Each of 8 nurseries has had a 1 year or more CLABSI-free period, including the neonatal intensive care unit with the largest patient volume, acuity, and central line usage. Aggregate Neonatal Services has experienced 3 CLABSI-free quarters since 2007. Key success factors included: (1) engagement of senior executive leadership; (2) bedside "huddles" among clinical and epidemiology staffs conducted within 72 hours after a positive blood culture; (3) implementation of chlorhexidine antisepsis and the use of chlorhexidine-impregnated catheter site discs; and (4) and establishment of a dedicated team for percutaneously inserted central catheter insertion to serve units in which central lines are placed less frequently., Conclusions: Using the model for improvement and evidenced-based interventions, this QI project has been associated with reduction in the CLABSI rate by 89%, and over 430 CLABSIs likely have been avoided., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Many organic molecules have strong absorption bands which can be accessed by ultraviolet short pulse lasers to produce efficient ionization. This resonant multiphoton ionization scheme has already been exploited as an ionization source in time-of-flight mass spectrometers used for environmental trace analysis. In the present work we quantify the ultimate potential of this technique by measuring absolute ion yields produced from the interaction of 267 nm femtosecond laser pulses with the organic molecules indole and toluene, and gases Xe, N2 and O2. Using multiphoton ionization cross sections extracted from these results, we show that the laser pulse parameters required for real-time detection of aromatic molecules at concentrations of one part per trillion in air and a limit of detection of a few attomoles are achievable with presently available commercial laser systems. The potential applications for the analysis of human breath, blood and tissue samples are discussed.

Collective behaviour is a characteristic feature in many-body systems, important for developments in fields such as magnetism, superconductivity, photonics and electronics. Recently, there has been increasing interest in the optically nonlinear response of collective excitations. Here we demonstrate how the nonlinear interaction of a many-body system with intense XUV radiation can be used as an effective probe for characterizing otherwise unresolved features of its collective response. Resonant photoionization of atomic xenon was chosen as a case study. The excellent agreement between experiment and theory strongly supports the prediction that two distinct poles underlie the giant dipole resonance. Our results pave the way towards a deeper understanding of collective behaviour in atoms, molecules and solid-state systems using nonlinear spectroscopic techniques enabled by modern short-wavelength light sources.

Introduction: Pyoderma gangrenosum (PG) is a rare, inflammatory skin pathology frequently associated with systemic inflammatory disease. While rare after surgery, recognition of this disease in the post-surgical setting is important as it can mimic wound infection., Presentation of Case: We herein present a dramatic presentation of perianal PG four days after routine excision and fulguration of anal condyloma acuminatum. The affected area did not improve with broad spectrum antibiotics or surgical debridement. A diagnosis of PG was made from clinical suspicion and pathology findings, and further confirmed with rapid improvement after starting steroids. Diagnosis of this disease in the postoperative period requires high suspicion when the characteristic ulcerative or bullae lesions are seen diffusely and show minimal improvement with antibiotic treatment or debridement., Discussion: Our case highlights the importance of recognizing this disease in the post-operative period, to allow for early initiation of appropriate treatment and prevent unnecessary surgical debridement of a highly sensitive area. There have been 32 case reports of PG in the colorectal literature, mostly following stoma creation. There is one case report of idiopathic perianal pyoderma gangrenosum with no known prior trauma. To our knowledge there are no previously reported cases of perianal PG after routine elective anorectal surgery., Conclusion: This is the first reported case of perianal pyoderma gangrenosum in the post-surgical setting. Increased awareness of pyoderma gangrenosum in the surgical literature will aid in prompt diagnosis and proper medical management of this uncommon postoperative morbidity., (Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The initial step in initiation of eukaryotic DNA replication involves the assembly of pre-replicative complexes (pre-RCs) at origins of replication during the G1 phase of the cell cycle. In metazoans initiation is inhibited by the regulatory factor Geminin. We have purified the human pre-RC proteins, studied their interactions in vitro with each other and with origin DNA, and analyzed the effects of HsGeminin on formation of DNA-protein complexes. The formation of an initial complex containing the human origin recognition complex (HsORC), HsCdt1, HsCdc6, and origin DNA is cooperative, involving all possible binary interactions among the components. Maximal association of HsMCM2-7, a component of the replicative helicase, requires HsORC, HsCdc6, HsCdt1, and ATP, and is driven by interactions of HsCdt1 and HsCdc6 with multiple HsMCM2-7 subunits. Formation of stable complexes, resistant to high salt, requires ATP hydrolysis. In the absence of HsMCM proteins, HsGeminin inhibits the association of HsCdt1 with DNA or with HsORC-HsCdc6-DNA complexes. However, HsGeminin does not inhibit recruitment of HsMCM2-7 to DNA to form complexes containing all of the pre-RC proteins. In fact, HsGeminin itself is a component of such complexes, and interacts directly with the HsMcm3 and HsMcm5 subunits of HsMCM2-7, as well as with HsCdt1. Although HsGeminin does not prevent the initial formation of DNA-protein complexes containing the pre-RC proteins, it strongly inhibits the formation of stable pre-RCs that are resistant to high salt. We suggest that bound HsGeminin prevents transition of the pre-RC to a state that is competent for initiation of DNA replication., (© 2014 by The American Society for Biochemistry and Molecular Biology, Inc.)

Linear ubiquitination is a newly discovered posttranslational modification that is currently restricted to a small number of known protein substrates. The linear ubiquitination assembly complex (LUBAC), consisting of HOIL-1L, HOIP, and Sharpin, has been reported to activate NF-κB-mediated transcription in response to receptor signaling by ligating linear ubiquitin chains to Nemo and Rip1. Despite recent advances, the detailed roles of LUBAC in immune cells remain elusive. We demonstrate a novel HOIL-1L function as an essential regulator of the activation of the NLRP3/ASC inflammasome in primary bone marrow-derived macrophages (BMDMs) independently of NF-κB activation. Mechanistically, HOIL-1L is required for assembly of the NLRP3/ASC inflammasome and the linear ubiquitination of ASC, which we identify as a novel LUBAC substrate. Consequently, we find that HOIL-1L(-/-) mice have reduced IL-1β secretion in response to in vivo NLRP3 stimulation and survive lethal challenge with LPS. Together, these data demonstrate that linear ubiquitination is required for NLRP3 inflammasome activation, defining the molecular events of NLRP3 inflammasome activation and expanding the role of LUBAC as an innate immune regulator. Furthermore, our observation is clinically relevant because patients lacking HOIL-1L expression suffer from pyogenic bacterial immunodeficiency, providing a potential new therapeutic target for enhancing inflammation in immunodeficient patients., (© 2014 Rodgers et al.)

Argonaute (Ago) proteins mediate posttranscriptional gene repression by binding guide miRNAs to regulate targeted RNAs. To confidently assess Ago-bound small RNAs, we adapted a mouse embryonic stem cell system to express a single epitope-tagged Ago protein family member in an inducible manner. Here, we report the small RNA profile of Ago-deficient cells and show that Ago-dependent stability is a common feature of mammalian miRNAs. Using this criteria and immunopurification, we identified an Ago-dependent class of noncanonical miRNAs derived from protein-coding gene promoters, which we name transcriptional start site miRNAs (TSS-miRNAs). A subset of promoter-proximal RNA polymerase II (RNAPII) complexes produces hairpin RNAs that are processed in a DiGeorge syndrome critical region gene 8 (Dgcr8)/Drosha-independent but Dicer-dependent manner. TSS-miRNA activity is detectable from endogenous levels and following overexpression of mRNA constructs. Finally, we present evidence of differential expression and conservation in humans, suggesting important roles in gene regulation., (Copyright © 2014 Elsevier Inc. All rights reserved.)