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Abstract The blue bottle genus Physalia is one of the well-known siphonophore belonging to the Cnidaria, Hydrozoa. Physalia is also known as a ferocious predator, occasionally stinging and fatally wounding humans, but key details of its life cycle and reproductive biology are unclear. Physalia have separate sexes, and sexual reproduction occurs through the release of complex structures called gonodendra that contain many gonophores that will release either eggs or sperm. It is not known how mature the gonophores are when the gonodendra are released. In this study, we aim to characterize germ cell maturation by conducting histological, cytological, and gene expression analyses of the gonodendron of Physalia utriculus from Japan. We found a layered structure of the gonophore, consistent with other studies; however, gametes were not found even in gonophores that were within the released gonodendra. Moreover, haploid cells were not detected by flow cytometry. Analysis of the expression of putative germ cell marker and meiosis related genes showed high expression in the gonophore. These results strongly suggest that germ cells do not mature until after gonodendra are released. These findings provide valuable insights into the reproductive ecology and life cycle of Physalia.

Antlers are genetically coded to have bilateral symmetry. However, environmental stressors cause asymmetries between antlers. Previous studies have investigated fluctuating asymmetries on harvested white-tailed deer (Odocoileus virginianus Zimmermann, 1780). Cast antlers provide underutilized metrics that are not available prior to shedding. The objectives of this study were to quantify relative fluctuating asymmetry (RFA) between age groups and identify the best age-specific pre- and post-cast antler metrics to confirm an antler pair. We hypothesized lower RFA values for post-cast measurements than pre-cast measurements due to a lessened chance for damage when atop the head. Additionally, younger individuals were hypothesized to have higher RFA values due to greater susceptibility to environmental stressors. Cast antler pairs from 196 white-tailed deer were collected in Nebraska. We measured 14 available antler metrics per cast antler side classified by age group. The most symmetric measurements between antler sides included pedicle seal area, main beam length, and circumference. Antlers of older deer were consistently more symmetric than younger deer. When combining the top metrics and testing against random antler pairs, we found an 81.9–92.3% match rate for 1.5 and ≥2.5-year-olds, respectively. Our findings provided a quantifiable method to assign antler pair classifications more confidently while documenting decreased symmetry in younger individuals.

Studying the factors that influence the quality of physics Ph.D. students’ doctoral experiences, especially those that motivate them to stay or leave their programs, is critical for providing them with more holistic and equitable support. Prior literature on doctoral attrition has found that students with clear research interests who establish an advisor-advisee relationship early in their graduate careers are most likely to persist. However, these trends have not been investigated in the context of physics, and the underlying reasons for why these characteristics are associated with leaving remain unstudied. Using semistructured interviews with 40 first and second year physics Ph.D. students, we construct a model describing the characteristic pathways that physics Ph.D. students take while evaluating the interest congruence of prospective research groups. We show how access to undergraduate research and other formative experiences helped some students narrow their interests and look for research groups before arriving at graduate school. In turn, these students reported fewer difficulties finding a group than students whose search for an advisor took place during the first year of their Ph.D. Finally, we identify two characteristic types of students at a higher risk of leaving their programs: students who enter graduate school with broad interests and struggle to find a group and students who join a research group early based on research interest alone and subsequently encounter issues with a negative mentoring relationship. This work serves as a major step toward creating a comprehensive model of how Ph.D. students find a research group and opens the door for future work to investigate how factors such as group culture and working environment impact the search process.

ABSTRACT: The increasing demand for cage-free (CF) poultry farming raises concern regarding air pollutant emissions in these housing systems. Previous studies have indicated that air pollutants such as particulate matter (PM) and ammonia (NH3) pose substantial risks to the health of birds and workers. This study aimed to evaluate the efficacy of electrostatic particle ionization (EPI) technology with different lengths of ion precipitators in reducing air pollutants and investigate the relationship between PM reduction and electricity consumption. Four identical CF rooms were utilized, each accommodating 175 hens of 77 wk of age (WOA). A Latin Square Design method was employed, with 4 treatment lengths: T1 = control (0 m), T2 = 12 ft (3.7 m), T3 = 24 ft (7.3 m), and T4 = 36 ft (11.0 m), where room and WOA are considered as blocking factors. Daily PM concentrations, temperature, and humidity measurements were conducted over 24 h, while NH3 levels, litter moisture content (LMC), and ventilation were measured twice a week in each treatment room. Statistical analysis involved ANOVA, and mean comparisons were performed using the Tukey HSD method with a significance level of P ≤ 0.05. This study found that the EPI system with longer wires reduced PM2.5 concentrations (P ≤ 0.01). Treatment T2, T3, and T4 led to reductions in PM2.5 by 12.1%, 19.3%, and 31.7%, respectively, and in small particle concentrations (particle size >0.5 μm) by 18.0%, 21.1%, and 32.4%, respectively. However, no significant differences were observed for PM10 and large particles (particle size >2.5 μm) (P < 0.10), though the data suggests potential reductions in PM10 (32.7%) and large particles (33.3%) by the T4 treatment. Similarly, there was no significant impact of treatment on NH3 reduction (P = 0.712), possibly due to low NH3 concentration (

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Cage-free (CF) layer houses tend to have high particulate matter (PM) levels because of bedding/litter floor and the birds’ activities, such as perching, dustbathing, and foraging on it. It has been reported that optimizing bedding management can potentially suppress PM levels in CF houses. The objectives of this study were to (1) test the effect of the top application of new bedding materials (BMs) on PM levels and (2) compare different BM PM reduction efficiencies. Small flake shavings (SFS), large flake shavings (LFS), and aspen wood chips (AWC) were top-dressed on the surface of the original litter (33-week-old litter) evenly in each of the BM treatment rooms at 20% volume of the original litter floor. The initial litter depths in the control, SFS, LFS, and AWC rooms were 4.6 ± 0.6, 4.8 ± 0.8 cm, 4.8 ± 0.8 cm, and 4.6 ± 0.9 cm, respectively. One room was used as a control without adding new BM. The results indicate that the top application of new bedding suppressed PM levels in all treatment rooms (p < 0.01). The PM2.5 reductions in the SFS, AWC, and LFS treatment rooms were 36.5%, 34.6%, and 28.9% greater than in the control room, respectively. The mitigation efficiencies were different between PM sizes. For instance, PM2.5, PM10, and TSP in the SFS room were lower than in the control room by 36.5%, 39.4%, and 38.7%, respectively. For litter quality, the moisture content was 18.0 ± 2.8, 20.0 ± 3.1, 20.6 ± 2.4, and 19.7 ± 4.2% in the control, SFS, LFS, and AWC rooms, respectively. Treatment rooms with 20% new BM had 10% higher litter moisture than the control room. The findings of this study reveal that the top application of new bedding on old litter is a potential strategy for reducing PM generation in CF houses. Further studies are warranted, such as regarding the effect of different ratios of new bedding on PM reduction, cost analysis, and verification tests in commercial CF houses.

In the past five years, the number of virtual American Sign Language (ASL) classes has dramatically increased from being a novel option to being a common course delivery mode across the country. Yet, little is known regarding virtual ASL course design and the implementation of evidence-based practices. Overarchingly, this programmatic case study sought insight from a small population of experienced virtual ASL teachers who had been teaching ASL online prior to the crisis teaching phenomenon that has laid the foundation for virtual ASL as it stands today. More specifically, the qualitative design utilized questionnaires, semi-structured interviews, member checks, and document reviews of five teachers who had been teaching ASL virtually to K-12 students prior to the onset of the COVID-19 pandemic. Rich qualitative data, analyzed through directed and summative content analysis, revealed many themes specific to virtual ASL education, including differences from traditional ASL instruction, specific job responsibilities, limitations, advantages, disadvantages, and suggestions for improvement. Additionally, aligning with previous literature, we explored teacher, student, and programmatic characteristics that were perceived to be conducive to virtual students’ success. Finally, all participants expressed broader concerns that continue to exist in the field of ASL education. Implications for stakeholders, including K-12 ASL students, their families, teachers, administrators, and teacher training programs are addressed, followed by suggestions for future research.

The welfare of laying hens in conventional caged houses has become an increased public concern, leading primary food chains, restaurants, and grocers in the United States to pledge to source only cage-free (CF) eggs by 2025 or 2030. Cage-free housing systems have been considered as a more humane alternative; however, they still come with certain challenges. One of the primary challenges with CF housing is the poor indoor air quality due to the high levels of ammonia (NH3) and particulate matter (PM). Despite the importance of air quality in animal welfare, most studies have focused on the egg-laying stage, thereby leaving a significant knowledge gap in the pullet phase. Addressing this gap is essential to ensure the well-being of laying hens in CF housing and to help producers and researchers identify effective strategies to mitigate the impact of poor indoor air quality on the bird’s health and welfare. Therefore, the objective of this study was to (a) examine the effect of the pullets’ age on NH3 and PM levels, and (b) find the effect of housing, litter moisture content (LMC), and relative humidity (RH) on air pollutant concentrations. The results show that the PM levels of PM2.5, PM10, and total suspended particles (TSP) increased significantly with the growth of birds from 1 to 16 weeks of age (WOA) (p < 0.01). For instance, PM2.5, PM10, and TSP levels were measured at 0.023 ± 0.003, 0.031 ± 0.004, and 0.058 ± 0.013 mg m−3 in the first week, and these levels increased to 1.44 ± 0.58, 2.723 ± 1.094, and 6.39 ± 2.96 mg m−3, respectively, by 16 WOA. In addition, PM levels measured near the perch were found to be three times higher than other locations inside the rooms (e.g., between the feeder and drinker or near the exhaust fan) (p < 0.01), as perching is one of the primary reasons for dust generation. Furthermore, a significant interaction between the age of the pullets and PM levels was found (p < 0.01), as the litter quality and the behaviors of birds were changing over time. For NH3 levels, average daily concentrations were lower than 1 ppm at 16 WOA for all rooms due to dry litter conditions (i.e., 9–10% LMC). Additionally, RH has been shown to have a significant effect on air pollutant concentration. Overall, the results indicate that the bird’s age significantly affects PM generation and PM variation within the rooms. The variation of PM was directly affected by RH inside the house. Therefore, this research will provide valuable information for both researchers and producers to control air pollutant emissions from the pullet stage in CF housing to ultimately improve the health and welfare of hens.

Abstract The magnetic properties of permalloy-based trilayers of the form Py0.8Cu0.2/Py0.4Cu0.6/Py/IrMn were studied as the spacer layer undergoes a paramagnetic to ferromagnetic phase transition. We find the coupling between the free Py0.8Cu0.2 layer and the exchange bias pinned Py to be strongly temperature-dependent: there is negligible coupling above the Curie temperature of the Py0.4Cu0.6 spacer layer, strong ferromagnetic coupling below that temperature, and a tunable coupling between these extremes. Polarized neutron reflectometry was used to measure the depth profile of the magnetic order in the system, allowing us to correlate the order parameter with the coupling strength. The thickness dependence shows that these are interface effects with an inverse relationship to thickness, and that there is a magnetic proximity effect that enhances the Curie temperature of the spacer layer with characteristic length scale of about 7 nm. As a demonstration of potential functionality of such a system, the structure is shown to spontaneously flip from the antiparallel to parallel magnetic configuration once the spacer layer has developed long-range magnetic order.

Category: Trauma; Arthroscopy Introduction/Purpose: Deltoid ligament rupture is a common occurrence in the setting of acute ankle fractures. The indications for surgical restoration of the deltoid ligament complex vary considerably throughout the literature. If medial ankle instability exists after ankle fracture fixation, repair or reconstruction of the deltoid ligament complex may be performed, which is traditionally done via an open approach. While the superficial deltoid is easily accessed with an open approach, the deep deltoid ligament is extremely difficult to visualize. We present a novel technique for reconstruction of the deep deltoid ligament complex utilizing suture augmentation via an arthroscopically-assisted approach and present our outcomes. With this method, the deep deltoid ligament disruption is easily visualized and reconstructed in a minimally invasive manner through an accessory anteromedial arthroscopy portal. Methods: This is a technique guide and retrospective case series. Data was obtained via chart review including pre-operative, intraoperative, and post-operative follow ups. Variables such as age, weight, body mass index (BMI), sex, side, history of previous ankle surgery, preoperative ambulatory status, length of hospital stay, as well as disposition were documented. Radiographs were reviewed for evidence of restoration of the medial clear space as well as hardware position and bony union. In addition, a technique guide was developed using expert surgeon experience and opinion while using this novel technique. Results: 7 patients who underwent this novel technique were reviewed with an average follow up time of six months (3-8 months). All patients suffered bimalleolar or trimalleolar equivalent fractures. Patients were indicated for deep deltoid ligament reconstruction if medial ankle instability existed intraoperatively with valgus stress testing under fluoroscopy. Medial clear space decreased from a mean 11mm preoperatively to 3.3mm postoperatively. 6 patients returned to ambulation without brace by three months postoperatively. One patient demonstrated increased medial clear space measured at 6.6mm postoperatively and residual pain on follow up, but was treated conservatively and able to progress to weight bearing as tolerated by 6 months. One patient developed a keloid scar that required a steroid injection. No postoperative infections occurred. Conclusion: Deep deltoid ligament reconstruction utilizing suture augmentation via an arthroscopically-assisted approach should be considered in patients who have residual medial ankle instability after ankle fracture fixation. This novel technique allows visualization of the deep deltoid ligament complex and reconstruction in a minimally invasive manner via an accessory anteromedial arthroscopy portal. Our short term outcomes demonstrate success in restoring ankle function and radiographic parameters of the medial clear space. Further studies are needed to evaluate long term postoperative functional outcomes, stability, and development of post-traumatic arthritis.

Abstract Background Young onset dementia (YOD) is a major diagnostic and management problem. Methods We set out to explore if electroencephalography (EEG) might be useful in the diagnosis of young onset Alzheimer’s disease (YOAD) and young onset frontotemporal dementia (YOFTD). The ARTEMIS project is a 25-year prospective study of YOD based in Perth, Western Australia. 231 participants were included: YOAD: n = 103, YOFTD: n = 28, controls: n = 100. EEGs were performed prospectively, with 30-minute recording time for each subject, without knowledge of diagnosis or other diagnostic data. Results 80.9% of patients with YOD had abnormal EEGs (P

Perching is one of the essential natural behaviors for avian species. Providing an optimal perching design (e.g., shape, dimension, and materials) for commercial poultry production is critical for maintaining bird health, welfare, and production efficiency. This review paper summarized poultry perching studies and discussed the relationship between perch design, bird welfare, and production efficiency. Providing perches at an early stage may ensure optimum use during adulthood, reduce perching accidents, and lower the risk of floor eggs in cage-free (CF) hen houses. Therefore, a perch space of 15 cm per bird is recommended for the CF hen house. Similarly, rectangular perches are preferred to circular perches as the rectangular perch provides hens with an excellent tendon-locking mechanism to prevent slipping. In addition, perches with softer materials such as polyurethane and rubber coverings are recommended to increase the contact surface on the chicken’s toes. Perching behavior (PB) promotes a musculocutaneous system and reduces the incidences of footpad dermatitis and lesions. Generally, providing perching may reduce aggression and stress in birds and improve welfare and production efficiency. In the case of broilers, it is found that the broiler perches less during the latter stage of their lives because they are comparatively heavier and exhibit a more inactive lifestyle. Studies have investigated the effect of the surface temperature of the perch on broilers’ welfare. Perches with lower temperatures help improve performance and welfare by relieving heat stress and leg issues. Overall, PB is required to improve bird health and welfare.

Abstract Siphonophores are a clade of understudied colonial hydrozoans (Cnidaria) that are abundant predators in oceanic ecosystems, with species present across the water column. We (1) synthesize current knowledge about siphonophore trophic ecology and predator–prey interactions, (2) analyze siphonophore‐prey networks to compare food‐web topology between shallow and deep‐pelagic habitats, (3) discuss contemporary techniques that will allow for more integrative studies of siphonophore feeding ecology, and (4) and present a vision for future research. We found distinct diet differences between siphonophore species, indicating that siphonophores occupy multiple trophic niches and prey on a diversity of taxa. Our results suggest that siphonophore‐prey networks may be more specialized in the deep pelagic than in the epipelagic, suggesting potential trophic differences between depth habitats. This study highlights niche differentiation and trophic complexity among siphonophores and demonstrates the importance of gelatinous zooplankton in shaping food web structure in pelagic ecosystems.

Computed Tomography (CT) is a standard clinical tool utilized to diagnose known lung pathologies based on established grading methods. However, for preclinical trials and toxicity investigations in animal models, more comprehensive datasets are typically needed to determine discriminative features between experimental treatments, which oftentimes require analysis of multiple images and their associated differential quantification using manual segmentation methods. Furthermore, for manual segmentation of image data, three or more readers is the gold standard of analysis, but this requirement can be time-consuming and inefficient, depending on variability due to reader bias. In previous papers, microCT image manual segmentation was a valuable tool for assessment of lung pathology in several animal models; however, the manual segmentation approach and the commercial software used was typically a major rate-limiting step. To improve the efficiency, the semi-manual segmentation method was streamlined, and a semi-automated segmentation process was developed to produce: • Quantifiable segmentations: using manual and semi-automated analysis methods for assessing experimental injury and toxicity models, • Deterministic results and efficiency through automation in an unbiased and parameter free process, thereby reducing reader variance, user time, and increases throughput in data analysis, • Cost-Effectiveness: portable with low computational resource demand, based on a cross-platform open-source ImageJ program.

With detailed data on gene expression accessible from an increasingly broad array of species, we can test the extent to which our developmental genetic knowledge from model organisms predicts expression patterns and variation across species. But to know when differences in gene expression across species are significant, we first need to know how much evolutionary variation in gene expression we expect to observe. Here we provide an answer by analyzing RNAseq data across twelve species of Hawaiian Drosophilidae flies, focusing on gene expression differences between the ovary and other tissues. We show that over evolutionary time, there exists a cohort of ovary specific genes that is stable and that largely corresponds to described expression patterns from laboratory model Drosophila species. Our results also provide a demonstration of the prediction that, as phylogenetic distance increases, variation between species overwhelms variation between tissue types. Using ancestral state reconstruction of expression, we describe the distribution of evolutionary changes in tissue-biased expression, and use this to identify gains and losses of ovary-biased expression across these twelve species. We then use this distribution to calculate the evolutionary correlation in expression changes between genes, and demonstrate that genes with known interactions in D. melanogaster are significantly more correlated in their evolution than genes with no or unknown interactions. Finally, we use this correlation matrix to infer new networks of genes that share evolutionary trajectories, and we present these results as a dataset of new testable hypotheses about genetic roles and interactions in the function and evolution of the Drosophila ovary.

Category: Arthroscopy; Ankle; Sports; Trauma Introduction/Purpose: The deltoid ligament complex is the main stabilizing structure of the ankle mortise and is often disrupted in rotational ankle injuries. Current treatment involves open techniques for the acute repair of the superficial deltoid layer, however, repair or reconstruction of the deep deltoid ligament (DDL) has proven to be challenging using open techniques. Our described arthroscopically-assisted technique allows for better intra-articular visualization and durable reconstruction of the ruptured DDL with suture and knotless bone anchors. The goal of this new, minimally invasive approach is to facilitate a faster and more reliable recovery and prevent long-term dysfunction and degeneration from medial and rotational ankle instability. We believe it has the potential to provide improved immediate ankle stability and decrease overall surgical morbidity compared to open treatments. Methods: Case of a 48-year-old male with ligamentous-equivalent Massioneuve fracture with medial clear space (MCS) measuring 11 millimeters. Arthroscopy revealed unstable syndesmosis and rupture of the DDL. After syndesmotic fixation, there was persistent MCS widening on stress exam. Arthroscopically-assisted DDL reconstruction was performed using an accessory anteromedial (AAM) portal between the tibialis anterior tendon and posterior tibial tendon. Needle localization identified the sagittal midpoint of the medial wall of the talus, inferior to articular cartilage. Anchor sites at both the medial talar wall and midportion of the distal medial malleolus (insertion and origin of the DDL, respectively) were then drilled via the AAM portal under arthroscopic and fluoroscopic guidance respectively at the isometric point. A suture anchor was placed into the talus and tails were loaded and secured to the medial malleolus with a bioabsorbable anchor. Ankle mortise was stable to stress exam and there were no restraints to physiologic motion. Results: The patient was kept non-weight bearing on his right lower extremity for a total of 6 weeks postoperatively and was seen in the clinic for routine follow-up visits at 2 weeks, 6 weeks, and 3 months post-procedure. Sutures were removed at 2 weeks, without any wound complications, and he was transitioned from splint to a short leg cast. He required only three days of oral narcotic analgesia. Weight-bearing in a controlled ankle motion (CAM) boot and physical therapy were both initiated at 6 weeks post-op. Radiographs at each follow-up visit were without abnormalities. At 3 months post-op, he was graduated from the CAM boot into a lace-up ankle brace, without any complaints of ankle pain or instability. The patient progressed well with full weight-bearing and physical therapy and was seen for a final visit at 5 months post-op with stable MCS. No complications were encountered. Conclusion: Acute DDL rupture is a common occurrence in ankle fractures and can be diagnosed radiographically and by arthroscopy. Known sequelae of untreated DDL disruption include medial instability and late valgus collapse. This case report demonstrates a novel, minimally invasive technique to successfully reconstruct the DDL, which may minimize the surgical morbidity compared to open dissection methods and allow for decreased recovery time postoperatively. This approach may also be utilized for cases of chronic instability. Future work includes larger case series with long-term follow-up and refinement of the technique as instrumentation advances.

Category: Sports; Ankle; Trauma Introduction/Purpose: Chronic achilles tendon injuries present several technical considerations. A reported 20-25% of acute ruptures may be missed and lead to late diagnosis. A commonly faced problem with chronic ruptures is the amount of tendon retraction that occurs, leading to the inability to perform a direct end-to-end repair. Previous studies have demonstrated that central turndown lengthening with addition of flexor hallucis longus (FHL) augmentation can be performed with good results, although it has been associated with post-surgical wound complications and infection. The following description is a turndown technique with FHL tendon transfer augmentation for chronic achilles rupture that allows increased fixation with a tendon to bone construct, accomplished with a minimally invasive approach. Methods: Dissection is made down to the Achilles rupture site. Scar tissue is debrided down to two stable ends. The residual gap is then measured and 2cm is added. This distance is then used to make a proximal incision. Dissection is performed to gastrocnemius tendinous raphe. The central third of this segment is incised perpendicularly. A quadriceps tendon harvester (Arthrex, Naples, FL) is utilized to cut in an antegrade fashion down the tendon portion percutaneously, leaving a 1-1.5cm of tendon spared distally. The tendon is pulled under and through the distal incision. A percutaneous achilles repair system (PARS, Arthrex, Naples, FL) Jig is used to span proximal tendon. FHL tendon transfer is then completed in usual fashion. Suture tails from proximal tendon are then passed through the distal end. Tension is pulled through the sutures, approximating repair. The suture is loaded onto anchors and secured into the calcaneus under tension. Results: Favorable outcomes have been observed following the 2 patients that have had chronic achilles repair with utilization of this minimally invasive turn-down technique with FHL transfer. At a follow up of at least 6 months, no patient has demonstrated wound dehiscence or breakdown. There have been no reports of re-rupture. All patients have been satisfied with the procedure and their level of returned function. Conclusion: Our method of repair with combination of central turndown procedure and FHL tendon transfer provides a suitable option for improved functional outcomes in the treatment of chronic achilles ruptures while providing a minimally invasive approach and avoiding the need for allograft tissue. By using the quadricep tendon harvester in a subcutaneous fashion, incision length can be reduced by nearly 50%. This technique can be performed with existing technologies and is readily reproducible. Using the tendon to bone fixation along with intra-tendinous shuttling, allows for excellent fixation strength, a knotless construct, and almost complete intra-substance suture placement.

Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.

BackgroundPhylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, obtained from Sanger or next-generation sequencing (NGS). There is growing recognition that this approach discards potentially important information about within-host sequence variation, which can impact phylogenetic inference. However, whether alternative summary methods that incorporate intra-host variation impact phylogenetic inference of transmission network features is unknown.MethodsWe introduce profile sampling, a method to incorporate within-host NGS sequence diversity into phylogenetic HIV cluster inference. We compare this approach to Sanger- and NGS-derived pol and near-whole-genome consensus sequences and evaluate its potential benefits in identifying molecular clusters among all newly-HIV-diagnosed individuals over six months at the largest HIV center in Rhode Island.ResultsProfile sampling cluster inference demonstrated that within-host viral diversity impacts phylogenetic inference across individuals, and that consensus sequence approaches can obscure both magnitude and effect of these impacts. Clustering differed between Sanger- and NGS-derived consensus and profile sampling sequences, and across gene regions.DiscussionProfile sampling can incorporate within-host HIV diversity captured by NGS into phylogenetic analyses. This additional information can improve robustness of cluster detection.

Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species' diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the 'jelly-web', and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems.

The ontogenetic diet shift to piscivory can be energetically beneficial for fish growth and allows larger, more energetically profitable prey to be consumed. A shift to piscivory may be easier for longer individuals within a cohort due to larger gape size, and an early shift is likely advantageous, potentially leading to increased growth rates and survival. Such length-dependent ontogenetic diet shifts may explain the intracohort variability in length that is common for age-0 walleye (Sander vitreus). The objectives of this study were to describe seasonal intracohort variability in length, identify the timing of the shift to piscivory and determine if the onset of piscivory was length-dependent in age-0 walleye. Walleye initially fed on zooplankton, but shifted to piscivory during July of 2010 and June of 2011. The onset of piscivory in age-0 walleye was associated with length-dependent differences during both years, in which longer individuals within the cohort became piscivorous earlier than shorter individuals within the same cohort. Intracohort variability in length was detected and increased postontogenetic diet shift. Age-0 walleye that experience a growth advantage could benefit from increased survival and feeding opportunities.

Understanding consumption patterns and preferences of particular life stages for fish species can clarify potential dietary overlap and identify energy flow within aquatic communities. Age-0 white bass (Morone chrysops) have been documented to consume a variety of prey items and zooplankton are a common occurrence. The importance of particular zooplankton taxa and available sizes will likely impact prey selectivity, which is not understood for age-0 white bass. The objectives of this study were to evaluate food habits, prey electivity, and size selectivity of age-0 white bass in an irrigation reservoir from July to September 2015 and 2016. By number, age-0 white bass consumed mostly zooplankton from July to September. Consumption of fish become an important component of the diet for 22% of fish starting at 80 mm TL. Calanoida were the primary zooplankton taxa consumed and selected for by age-0 white bass. In relation to other zooplankton taxa, Calanoida were one of the most abundant taxa groups available and age-0 white bass displayed size selective feeding by consuming the larger Calanoida available in the environment. While Calanoida are not the largest taxa available, their high density appears to result in higher consumption by age-0 white bass compared to other available taxa.

A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as clades of tips from the same species with improbably short branch lengths. treeinform is a method that uses phylogenetic information across species to refine transcriptome assemblies within species. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene. The treeinform method is implemented in Agalma, available at https://bitbucket.org/caseywdunn/agalma, and the general approach is relevant in a variety of other contexts.

Background: Hematologic toxicity is a critical problem limiting treatment delivery in cancer patients undergoing concurrent chemoradiotherapy. However, the extent to which anatomic variations in radiation dose limit chemotherapy delivery is poorly understood. A unique natural experiment arises in patients with head and neck and cervical cancer, who frequently undergo identical chemotherapy but receive radiation to different regions of the body. Comparing these cohorts can help elucidate to what extent hematologic toxicity is attributable to marrow radiation as opposed to chemotherapy.Methods: In this longitudinal cohort study, we compared hematologic toxicity and bone marrow compensatory response in 148 patients (90 cervix, 58 head/neck) undergoing chemoradiotherapy with concurrent weekly cisplatin 40 mg/m2. We used linear mixed effect models to compare baseline and time-varying peripheral cell counts and hemoglobin levels between cohorts. To assess bone marrow compensatory response, we measured the change in metabolically active bone marrow (ABM) volume on 18F-fluorodeoxyglucose positron emission tomography/computed tomography.Results: We observed greater reductions in log-transformed lymphocyte, platelet, and absolute neutrophil counts (ANC) for cervix compared to head/neck cancer patients (fixed effects for time-cohort interaction [95% CI]: lymphocytes, −0.06 [−0.09, −0.031]; platelets,−0.028 [-0.051, −0.0047]; ANC, −0.043 [−0.075, −0.011]). Mean ANC nadirs were also lower for cervical vs. head/neck cancer cohorts (2.20 vs. 2.85 × 103 per μL, p < 0.01). Both cohorts exhibited reductions in ABM volume within the radiation field, and increases in ABM volume in out-of-field areas, indicating varying compensatory response to radiation injury.Conclusions: Cervical cancer patients had faster decreases in ANC, lymphocyte, and platelet counts, and lower ANC nadirs, indicating a significant effect of pelvic irradiation on acute peripheral blood cell counts. Both cohorts exhibited a compensatory response with increased out-of-field bone marrow activity.

Fluid flow in the subsurface is fundamental in a variety of geological processes including volcanism, metamorphism, and mineral dissolution and precipitation. It is also of economic and societal significance given its relevance, for example, within groundwater and contaminant transport, hydrocarbon migration, and precipitation of ore-forming minerals. In this example-based overview, we use the distribution of iron oxide precipitates as a proxy for palaeofluid flow to investigate the relationship between fluid flow, geological structures, and depositional architecture in sedimentary rocks. We analyse and discuss a number of outcrop examples from sandstones and carbonate rocks in New Zealand, Malta, and Utah (USA), showing controls on fluid flow ranging from simple geological heterogeneities to more complex networks of structures. Based on our observations and review of a wide range of the published literature, we conclude that flow within structures and networks is primarily controlled by structure type (e.g., joint and deformation band), geometry (e.g., length and orientation), connectivity (i.e., number of connections in a network), kinematics (e.g., dilation and compaction), and interactions (e.g., relays and intersections) within the network. Additionally, host rock properties and depositional architecture represent important controls on flow and may interfere to create hybrid networks, which are networks of combined structural and stratal conduits for flow.

We evaluated the prey electivity of lotic slimy sculpin (Cottus cognatus) within the Lake Superior-North Watershed, an area characterized by high gradient streams and lacking the preferred prey of Gammarus. Fish and macroinvertebrates were sampled at 67 sites within 52 rivers and streams during 2013 in the Lake Superior-North Watershed by the Minnesota Pollution Control Agency. Fish sampling was conducted with the use of backpack and stream tote barge electrofishers, and macroinvertebrates were collected using qualitative multi-habitat sampling within D-Frame kick nets. Feeding electivity was calculated using Strauss’ modified feeding electivity model for three rivers. In total we sampled 174 slimy sculpins within the Lake Superior-North Watershed and found sculpins positively selected for Hydropsychidae (47.3% of total taxa consumed) and Perlidae (11% of total taxa consumed) instead of abundant Chironomidae (20% of total taxa sampled).

Gizzard shad (Dorosoma cepedianum) are an influential forage fish and driver of zooplankton resources in many reservoirs. The ability to identify the biotic and abiotic factors that influence the timing of elevated gizzard shad densities can be important to better utilize this forage fish and manage sport fish. The objective of this study was to investigate which biotic and abiotic factors influence larval gizzard shad annual peak density. We used combinations of six variables (CPUE of adult gizzard shad from the prior fall, mean zooplankton density, turbidity, chlorophyll a, relative reservoir elevation, and water temperature) from a long-term (2003–2014) monitoring program to create 28 a-priori candidate models to assess the relative support of explanatory variables using Akaike's information criterion (AIC). During the course of our study, larval gizzard shad annual peak densities were best explained by zooplankton density and relative reservoir elevation. Zooplankton density provides greater food availability which has been shown to increase larval gizzard shad growth. Relative reservoir elevation was negatively associated with higher densities of larval gizzard shad. This study describes two important factors that may result in greater larval gizzard shad densities, which can assist managers in anticipating available forage for sport fish and identify strategies to improve system management.

An analysis of 1955 physics graduate students from 19 Ph.D. programs shows that undergraduate grade point average predicts graduate grades and Ph.D. completion more effectively than GRE scores. Students’ undergraduate GPA (UGPA) and GRE Physics (GRE-P) scores are small but statistically significant predictors of graduate course grades, while GRE quantitative and GRE verbal scores are not. We also find that males and females score equally well in their graduate coursework despite a statistically significant 18 percentile point gap in median GRE-P scores between genders. A counterfactual mediation analysis demonstrates that among admission metrics tested only UGPA is a significant predictor of overall Ph.D. completion, and that UGPA predicts Ph.D. completion indirectly through graduate grades. Thus UGPA measures traits linked to graduate course grades, which in turn predict graduate completion. Although GRE-P scores are not significantly associated with Ph.D. completion, our results suggest that any predictive effect they may have is also linked indirectly through graduate GPA. Overall our results indicate that among commonly used quantitative admissions metrics, UGPA offers the most insight into two important measures of graduate school success, while posing fewer concerns for equitable admissions practices.

Joining a research group is one of the most important events on a graduate student's path to becoming an independent physics researcher and earning a Ph.D. However, graduate students' perspectives on the experience of finding a research group are not well documented in the literature. Understanding these perspectives is crucial for evaluating whether departments are providing students with adequate support while they search for a research group, and how difficulties during this process contribute to attrition. Semistructured interviews with N=20 first and second year physics Ph.D. students reveal that incoming graduate students see joining a research group as a significant decision, and recognize that it may impact whether they will be able to complete the program. We found that students who struggled to find a group felt isolated and worried about falling behind their peers, whereas students who were able to immerse themselves in a positive group environment reported increased sense of belonging in their programs. The process of finding a research group often held differential importance for students identifying as women and nonbinary, who at times reported having to deprioritize their preferred research topic in order to be part of a more inclusive working environment. Although incoming graduate students characterized joining a research group as a significant decision, they often felt unprepared to make it. Moreover, they perceived an overall lack of guidance and structure from their departments, and characterized coursework as a barrier to searching for a group. Our findings suggest that providing students with better support during their group search process could help improve retention, particularly for traditionally underrepresented students, and improve students' overall satisfaction in their graduate programs.

Carbapenem-resistant Enterobacteriaceae (CRE) and vancomycin-resistant Enterococci (VRE) have emerged as multidrug-resistant (MDR) pathogens associated with periprosthetic joint infections (PJI). In this study, we evaluated the efficacy of antibiotic-loaded calcium sulfate beads (ALCSB) in inhibiting bacterial growth, encouraging biofilm formation and killing preformed biofilms of CRE and VRE. Three strains of Klebsiella pneumoniae (KP) and a strain of Enterococcus faecalis (EF) were used. ALCSB of 4.8-mm diameter were loaded with vancomycin (V) and gentamicin (G), V and rifampicin (R), V and tobramycin (T) or R and meropenem (M), and placed onto tryptic soy agar (TSA), spread with one of the test strains and incubated for 24 h at 37 °C. Beads were transferred daily onto fresh TSA spread plates and the zone of inhibition (ZOI) was recorded until no inhibition was observed. ALCSB containing R + M or R + V produced the most extensive ZOI up to 5 weeks. Biofilm prevention efficacy was investigated by challenging ALCSB daily with 5 × 105 CFU/mL bacterial cells and analyzing for biofilm formation at challenges 1, 2 and 3. In the biofilm killing experiments, ALCSB were added to pre-grown 3-day biofilms of KP and EF strains, which were then analyzed at days 1 and 3 post-exposure. The CFU counts and confocal images of the attached cells showed that ALCSB treatment reduced colonization and biofilm formation significantly (5–7 logs) with combinations of R + M or R + V, compared to unloaded beads. This study provides evidence that the local release of antibiotics from ALCSB may be useful in treating the biofilms of multidrug-resistant strains of CRE and VRE.

This article explores the use of telehealth and the ability to provide health care to patients through interactive technology and telecommunication tools. The use of telehealth continues to grow, reaching multiple medical specialties and providing care to a greater population of patients. The purpose of this article is to increase the knowledge of telehealth, identify positive outcomes associated with telehealth as well as potential barriers, and evaluate the benefits against the downfalls to determine whether the positive outcomes outweigh the barriers.

New sequence data from choanoflagellates improves our understanding of the genetic changes that occurred along the branch of the evolutionary tree that gave rise to animals.

Multiple primary malignancies (MPMs) are present when a patient is diagnosed with more than one primary malignancy and when each tumor is histologically unrelated to the others. MPMs are considered synchronous when they present within 6 months of one another. Here, we report the case of a 57-year-old woman with a past medical history significant for melanoma in 1988, who presented in 2014 with 5 distinct tumors within 4 months: malignant melanoma of the right popliteal fossa, invasive lobular breast carcinoma, diffuse large B cell lymphoma, nodular lymphocyte predominant Hodgkin lymphoma, and a giant cell tumor of tendon sheath/pigmented villonodular synovitis. We discuss her treatment and also present a brief review of the literature. The incidence of MPMs appears to be on the rise, which demands an interdisciplinary, multimodal, and personalized approach to care.

Although proteins in the green fluorescent protein family (GFPs) have been discovered in a wide array of taxa, their ecological functions in these organisms remain unclear. Many hypothesized roles are related to modifying bioluminescence spectra or modulating the light regime for algal symbionts, but these do not explain the presence of GFPs in animals that are non-luminous and non-symbiotic. Other hypothesized functions are unrelated to the visual signals themselves, including stress responses and antioxidant roles, but these cannot explain the localization of fluorescence in particular structures on the animals. Here we tested the hypothesis that fluorescence might serve to attract prey. In laboratory experiments, the predator was the hydromedusa Olindias formosus (previously known as O. formosa), which has fluorescent and pigmented patches on the tips of its tentacles. The prey, juvenile rockfishes in the genus Sebastes, were significantly more attracted (P

Many animals go through one or more metamorphoses during their lives, however, the molecular underpinnings of metamorphosis across diverse species are not well understood. Medusozoa (Cnidaria) is a clade of animals with complex life cycles, these life cycles can include a polyp stage that metamorphoses into a medusa (jellyfish). Medusae are produced through a variety of different developmental mechanisms-in some species polyps bud medusae (Hydrozoa), in others medusae are formed through polyp fission (Scyphozoa), while in others medusae are formed through direct transformation of the polyp (Cubozoa). To better understand the molecular mechanisms that may coordinate these different forms of metamorphosis, we tested two compounds first identified to induce metamorphosis in the moon jellyfish Aurelia aurita (indomethacin and 5-methoxy-2-methylindole) on a broad diversity of medusozoan polyps. We discovered that indole-containing compounds trigger metamorphosis across a broad diversity of species. All tested discomedusan polyps metamorphosed in the presence of both compounds, including species representatives of several major lineages within the clade (Pelagiidae, Cyaneidae, both clades of Rhizostomeae). In a cubozoan, low levels of 5-methoxy-2-methylindole reliably induced complete and healthy metamorphosis. In contrast, neither compound induced medusa metamorphosis in a coronate scyphozoan, or medusa production in either hydrozoan tested. Our results support the hypothesis that metamorphosis is mediated by a conserved induction pathway within discomedusan scyphozoans, and possibly cubozoans. However, failure of these compounds to induce metamorphosis in a coronate suggests this induction mechanism may have been lost in this clade, or is convergent between Scyphozoa and Cubozoa.

Ferromagnetic alloy materials with designed composition depth profiles provide an efficient route for the control of magnetism at the nanometer length scale. In this regard, cobalt-chromium and cobalt-ruthenium alloys constitute powerful model systems. They exhibit easy-to-tune magnetic properties such as saturation magnetization MS and Curie temperature TC while preserving their crystalline structure over a wide composition range. In order to demonstrate this materials design potential, we have grown a series of graded Co1−xCrx and Co1−wRuw (10 1 ¯ 0) epitaxial thin films, with x and w following predefined concentration profiles. Structural analysis measurements verify the epitaxial nature and crystallographic quality of our entire sample sets, which were designed to exhibit in-plane c-axis orientation and thus a magnetic in-plane easy axis to achieve suppression of magnetostatic domain generation. Temperature and field-dependent magnetic depth profiles have been measured by means of polarized neutron reflectometry. In both investigated structures, TC and MS are found to vary as a function of depth in accordance with the predefined compositional depth profiles. Our Co1−wRuw sample structures, which exhibit very steep material gradients, allow us to determine the localization limit for compositionally graded materials, which we find to be of the order of 1 nm. The Co1−xCrx systems show the expected U-shaped TC and MS depth profiles, for which these specific samples were designed. The corresponding temperature dependent magnetization profile is then utilized to control the coupling along the film depth, which even allows for a sharp onset of decoupling of top and bottom sample parts at elevated temperatures.

Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations.

Acute heat shock can induce apoptosis through a canonical pathway involving the upstream activation of caspase-2, followed by BID cleavage and stimulation of the intrinsic pathway. Herein, we report that the BH3-only protein BIM, rather than BID, is essential to heat shock-induced cell death. We observed that BIM-deficient cells were highly resistant to heat shock, exhibiting short and long-term survival equivalent to Bax(-/-)Bak(-/-) cells and better than either Bid(-/-) or dominant-negative caspase-9-expressing cells. Only Bim(-/-) and Bax(-/-)Bak(-/-) cells exhibited resistance to mitochondrial outer membrane permeabilization and loss of mitochondrial inner membrane potential. Moreover, while dimerized caspase-2 failed to induce apoptosis in Bid(-/-) cells, it readily did so in Bim(-/-) cells, implying that caspase-2 kills exclusively through BID, not BIM. Finally, BIM reportedly associates with MCL-1 following heat shock, and Mcl-1(-/-) cells were indeed sensitized to heat shock-induced apoptosis. However, pharmacological inhibition of BCL-2 and BCL-X(L) with ABT-737 also sensitized cells to heat shock, most likely through liberation of BIM. Thus, BIM mediates heat shock-induced apoptosis through a BAX/BAK-dependent pathway that is antagonized by antiapoptotic BCL-2 family members.

Most genome assemblers construct point estimates, choosing only a single genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. We implement this approach in a prototype assembler, called Genome Assembly by Bayesian Inference (GABI), and illustrate its application to the bacteriophage [Formula: see text]X174. Our sampling strategy achieves both good mixing and convergence on Illumina test data for [Formula: see text]X174, demonstrating the feasibility of our approach. We summarize the posterior distribution of assembly hypotheses generated by GABI as a majority-rule consensus assembly. Then we compare the posterior distribution to external assemblies of the same test data, and annotate those assemblies by assigning posterior probabilities to features that are in common with GABI's assembly graph. GABI is freely available under a GPL license from https://bitbucket.org/mhowison/gabi.