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Modern myoelectric prosthetic hands have multiple independently controllable degrees of freedom, but require constant visual attention to use effectively. Somatosensory feedback provides information not available through vision alone and is essential for fine motor control of our limbs. Similarly, stimulation of the nervous system can potentially provide artificial somatosensory feedback to reduce the reliance on visual cues to efficiently operate prosthetic devices. We have shown previously that epidural stimulation of the lateral cervical spinal cord can evoke tactile sensations perceived as emanating from the missing arm and hand in people with upper-limb amputation. In this case study, two subjects with upper-limb amputation used this somatotopically-matched tactile feedback to discriminate object size and compliance while controlling a prosthetic hand. With less than 30 min of practice each day, both subjects were able to use artificial somatosensory feedback to perform a subset of the discrimination tasks at a success level well above chance. Subject 1 was consistently more adept at determining object size (74% accuracy; chance: 33%) while Subject 2 achieved a higher accuracy level in determining object compliance (60% accuracy; chance 33%). In each subject, discrimination of the other object property was only slightly above or at chance level suggesting that the task design and stimulation encoding scheme are important determinants of which object property could be reliably identified. Our observations suggest that changes in the intensity of artificial somatosensory feedback provided via spinal cord stimulation can be readily used to infer information about object properties with minimal training.

SUMMARYIn the United States, over 1.5 million people live with lower-limb amputation. Existing prosthetic limbs do not restore somatosensory feedback from the limb, resulting in functional impairments including balance deficits and an increased risk of falls. Further, these prostheses do not alleviate the severe phantom limb pain that often follows amputation. Leveraging clinically available spinal cord stimulation electrodes, we designed a system that restores somatosensation in the missing limb, thereby improving balance and gait and reducing phantom limb pain. We show that spinal cord stimulation can evoke sensations in the missing foot and that we can control the location and intensity of those sensations. Further, by modulating stimulation intensity in real time based on signals from a wireless pressure-sensitive shoe insole, subjects exhibit improvements in functional measures of balance and gait stability. Finally, over the duration of the implant period, subjects experienced a clinically meaningful decrease in phantom limb pain. These combined results demonstrate that, with an electrode technology that is currently in widespread clinical use, our approach has the potential to become an important intervention for lower-limb amputation.

Floating life (obligate neuston) is a core component of the ocean surface food web. However, only 1 region of high neustonic abundance is known so far, the Sargasso Sea in the Subtropical North Atlantic gyre, where floating life provides critical habitat structure and ecosystem services. Here, we hypothesize that floating life is also concentrated in other gyres with converging surface currents. To test this hypothesis, we collected samples through the eastern North Pacific Subtropical Gyre in the area of the North Pacific “Garbage Patch” (NPGP) known to accumulate floating anthropogenic debris. We found that densities of floating life were higher inside the central NPGP than on its periphery and that there was a positive relationship between neuston abundance and plastic abundance for 3 out of 5 neuston taxa, Velella, Porpita, and Janthina. This work has implications for the ecology of subtropical oceanic gyre ecosystems.

Floating life (obligate neuston) is a core component of the ocean surface food web. However, only one region of high neustonic abundance is known so far, the Sargasso Sea in the Subtropical North Atlantic, where floating life provides critical habitat structure and ecosystem services. Here, we hypothesize that floating life is also concentrated in other gyres with converging surface currents. To test this hypothesis, we collected samples through the eastern North Pacific Subtropical Gyre in the area of the North Pacific “garbage patch” (NPGP) known to accumulate floating anthropogenic debris. We found that densities of floating life were significantly higher inside the central part of NPGP than on its periphery, and there was a significant positive relationship between neuston abundance and plastic abundance. This work has important implications for the ecology and human impact of subtropical oceanic gyre ecosystems.

Modern myoelectric prosthetic hands have multiple independently controllable degrees of freedom, but require constant visual attention to use effectively. As we know from motor control of our native limbs, somatosensory feedback is essential to control our movements and provides information not available through vision alone. Similarly, stimulation of the nervous system can potentially provide artificial somatosensory feedback to reduce the reliance on visual cues to efficiently operate prosthetic devices. We have shown previously that epidural stimulation of the lateral cervical spinal cord can evoke tactile sensations perceived as emanating from the missing arm and hand in people with upper-limb amputation. In this study, two subjects with upper-limb amputation used this somatotopically-matched tactile feedback to discriminate object size and compliance while controlling a prosthetic hand. With less than 30 minutes of training each day, both subjects were able to use artificial somatosensory feedback to perform a subset of the discrimination tasks at a success level well above chance. Subject 1 was consistently more adept at determining object size (74% accuracy; chance: 33%) while Subject 2 achieved a higher accuracy level in determining object compliance (60% accuracy; chance 33%). In each subject, discrimination of the other object property was only slightly above or at chance level suggesting that the task design and stimulation encoding scheme are important determinants of which object property could be reliably identified. Our observations suggest that artificial somatosensory feedback provided via spinal cord stimulation can be readily used to infer information about the real-world with minimal training, but that task design is critical and that performance improvements may not generalize across tasks.

The Sargasso Sea, located in the North Atlantic subtropical gyre, is one of the most well-known ocean surface ecosystems on the planet. It supports numerous ecologically and economically important fish species, juvenile turtles, and endemic species. However, in addition to the floating algaeSargassumfrom which the sea derives its name, numerous floating neustonic animals also live at the surface, yet their basic natural history remains poorly known. Without the basic knowledge of these species, understanding ecosystem function, food webs, and pollution impacts is impossible. This is especially problematic because pollutants like plastic are now increasing at the surface at alarming rates. This study examines the diet, reproduction, and behavior of four neustonic animal species:Velella velella,Janthina janthina,Janthina pallida, andGlaucus atlanticus. All mollusk species showed unique predatory preferences and behaviors, indicating possible methods of niche partitioning among these species. For example,Glaucus atlanticusshowed an equal preference for all prey but preyed primarily by crawling below to consume the underside of prey, while largeJ. janthinaoften preyed more on the margin ofV. velellaandP. physalis, in contrast,J. pallidaonly preyed onV. velella. Of the four species observed, two reproduced in the lab (G. atlanticusandV. velella), and the embryo cases ofJ. pallidawere examined from both collected snails and discarded bubble rafts. High fecundity rates were observed in all species, which may be an adaptation to high loss rates. This study lays the groundwork for future research on neustonic animals in the Sargasso Sea.

To fully utilize the power of single-cell RNA sequencing (scRNA-seq) technologies for identifying cell lineages and bona fide transcriptional signals, it is necessary to combine data from multiple experiments. We present BERMUDA (Batch Effect ReMoval Using Deep Autoencoders), a novel transfer-learning-based method for batch effect correction in scRNA-seq data. BERMUDA effectively combines different batches of scRNA-seq data with vastly different cell population compositions and amplifies biological signals by transferring information among batches. We demonstrate that BERMUDA outperforms existing methods for removing batch effects and distinguishing cell types in multiple simulated and real scRNA-seq datasets. Electronic supplementary material The online version of this article (10.1186/s13059-019-1764-6) contains supplementary material, which is available to authorized users.

The high seas—marine areas beyond national jurisdiction (1)—cover nearly half of Earth's surface (2). The high seas support our planet in countless ways, from regulating the climate, to feeding millions of people, to supporting industries that contribute billions of dollars to the global economy (3). Even so, less than 1% of the high seas are fully protected (4), and the current patchwork of management and lack of oversight leaves them vulnerable to abuse. In 2017, the United Nations resolved to develop an international treaty for the conservation and sustainable use of the high seas. Negotiations are set to end this year. We must ensure that the forthcoming framework conserves high-seas biodiversity and promotes sustainable and equitable use.

Variation in body size has important implications for physical performance and fitness. For insects, adult size and morphology are determined by larval growth and metamorphosis. Female blue orchard bees, Osmia lignaria, (Say) provision a finite quantity of food to their offspring. In this study, we asked how provision-dependent variation in size changes adult morphology. We performed a diet manipulation in which some larvae were starved in the final instar and some were given unlimited food. We examined the consequences on adult morphology in two ways. First, allometric relationships between major body regions (head, thorax, abdomen) and total body mass were measured to determine relative growth of these structures. Second, morphometrics that are critical for flight (wing area, wing loading, and extra flight power index) were quantified. Head and thorax mass had hyperallometric relationships with body size, indicating these parts become disproportionately large in adults when larvae are given copious provisions. However, abdominal mass and wing area increased hypoallometrically with body size. Thus, large adults had disproportionately lighter abdomens and smaller wing areas than smaller adults. Though both males and females followed these general patterns, allometric patterns were affected by sex. For flight metrics, small adults had reduced wing loading and an increased extra flight power index. These results suggest that diet quantity alters development in ways that affect the morphometric trait relationships in adult O. lignaria and may lead to functional differences in performance.

Life on the ocean’s surface connects worlds. From shallow waters to the deep sea, the open ocean to rivers and lakes, numerous terrestrial and marine species depend on the surface ecosystem and the organisms found therein. Organisms that live freely at the surface, termed “neuston,” include keystone organisms like the golden seaweed Sargassum that makes up the Sargasso Sea, floating barnacles, snails, nudibranchs, and cnidarians. Many ecologically and economically important fish species live as or rely upon neuston. Species at the surface are not distributed uniformly; the ocean’s surface harbors unique neustonic communities and ecoregions found at only certain latitudes and only in specific ocean basins. But the surface is also on the front line of climate change and pollution. Despite the diversity and importance of the ocean’s surface in connecting disparate habitats, and the risks it faces, we know very little about neustonic life. This Essay will introduce you to the neuston, their connections to diverse habitats, the threats they face, and new opportunities for research and discovery at the air-sea interface., The mysterious ’neuston’ ecosystem at the ocean’s surface includes keystone organisms like the golden seaweed Sargassum that makes up the Sargasso Sea, floating barnacles, snails, nudibranchs, and cnidarians; this Essay explores threats to its wellbeing and the importance of further research.

Sustainably managed wild fisheries support food and nutritional security, livelihoods, and cultures (1). Harmful fisheries subsidies—government payments that incentivize overcapacity and lead to overfishing—undermine these benefits yet are increasing globally (2). World Trade Organization (WTO) members have a unique opportunity at their ministerial meeting in November to reach an agreement that eliminates harmful subsidies (3). We—a group of scientists spanning 46 countries and 6 continents—urge the WTO to make this commitment...

Background and Hypothesis: The objective of this study was to analyze available whole genome sequencing from an adolescent male patient diagnosed with osteosarcoma (OS) in 2014. OS is a primary bone malignancy that most commonly affects the pediatric population. Precision medicine techniques provide new opportunities to improve treatment of OS patients. Pharmaceutical annotation tools such as PharmacoDB and DGIdb can help indicate chemotherapy agents that may benefit patients based on their molecular profiles. We hypothesize that these tools can indicate genome-specific chemotherapy agents for OS after genomic data has been aligned and analyzed. Project Methods: A PDX pipeline and retrospective study were performed that identified and compared pharmaceutical treatment options from software tools with the chemotherapy provided. Gene alignment and variant calling were used to process and analyze DNA sequencing data; germline and somatic mutations were also identified. Ensembl VEP was used for variant annotation. PharmacoDB and DGIdb were then applied to identify potentially beneficial medications. Results: Gene variant annotation indicated 54 potentially high impact mutations. Of these, DGIdb identified 15 drug-gene interactions. PharmacoDB identified no drugs that target any of the genes containing the 54 high impact mutations. For the entire mutated gene list, DGIdb identified 398 drug-gene interactions. After gene set enrichment, DGIdb identified medications targeting genes of pathways such as “O-glycan processing” and “Diseases of glycosylation”. Potentially harmful variants in the NPRL3 gene were identified. Because NPRL3 is a component of the Gator1 complex that serves as a negative regulator of mammalian target of rapamycin complex 1 (mTORC1), the identified variants in NPRL3 could have played a role in the patient’s OS. Potential Impact: This study will foster future collaborations to evaluate the pharmaceutical tool recommendations for this patient’s derived cell lines. These efforts will determine the efficacy of and identify improvements for computational treatment recommendation systems.

Restoring somatosensory feedback to people with limb amputations is crucial to improve prosthetic control. Multiple studies have demonstrated that peripheral nerve stimulation and targeted reinnervation can provide somatotopically relevant sensory feedback. While effective, the surgical procedures required for these techniques remain a major barrier to translatability. Here, we demonstrate in four people with upper-limb amputation that epidural spinal cord stimulation (SCS), a common clinical technique to treat pain, evoked somatosensory percepts that were perceived as emanating from the missing arm and hand. Over up to 29 days, stimulation evoked sensory percepts in consistent locations in the missing hand regardless of time since amputation or level of amputation. Evoked sensations were occasionally described as naturalistic (e.g. touch or pressure), but were often paresthesias. Increasing stimulus amplitude increased the perceived intensity linearly, without increasing area of the sensations. These results demonstrate the potential of SCS as a tool to restore somatosensation after amputations., eLife digest Even some of the most advanced prosthetic arms lack an important feature: the ability to relay information about touch or pressure to the wearer. In fact, many people prefer to use simpler prostheses whose cables and harnesses pass on information about tension. However, recent studies suggest that electrical stimulation might give prosthesis users more sensation and better control. After an amputation, the nerves that used to deliver sensory information from the hand still exist above the injury. Stimulating these nerves can help to recreate sensations in the missing limb and improve the control of the prosthesis. Still, this stimulation requires complicated surgical interventions to implant electrodes in or around the nerves. Spinal cord stimulation – a technique where a small electrical device is inserted near the spinal cord to stimulate nerves – may be an easier alternative. This approach only requires a simple outpatient procedure, and it is routinely used to treat chronic pain conditions. Now, Chandrasekaran, Nanivadekar et al. show that spinal cord stimulation can produce the feeling of sensations in a person’s missing hand or arm. In the experiments, four people who had an arm amputation underwent spinal cord stimulation over 29 days. During the stimulation, the participants reported feeling electrical buzzing, vibration, or pressure in their missing limb. Changing the strength of the electric signals delivered to the spinal cord altered the intensity of these sensations. The experiments are a step toward developing better prosthetics that restore some sensation. Further studies are now needed to determine whether spinal cord stimulation would allow people to perform sensory tasks with a prosthetic, for example handling an object that they cannot see.

Background Recent advances in kernel-based Deep Learning models have introduced a new era in medical research. Originally designed for pattern recognition and image processing, Deep Learning models are now applied to survival prognosis of cancer patients. Specifically, Deep Learning versions of the Cox proportional hazards models are trained with transcriptomic data to predict survival outcomes in cancer patients. Methods In this study, a broad analysis was performed on TCGA cancers using a variety of Deep Learning-based models, including Cox-nnet, DeepSurv, and a method proposed by our group named AECOX (AutoEncoder with Cox regression network). Concordance index and p-value of the log-rank test are used to evaluate the model performances. Results All models show competitive results across 12 cancer types. The last hidden layers of the Deep Learning approaches are lower dimensional representations of the input data that can be used for feature reduction and visualization. Furthermore, the prognosis performances reveal a negative correlation between model accuracy, overall survival time statistics, and tumor mutation burden (TMB), suggesting an association among overall survival time, TMB, and prognosis prediction accuracy. Conclusions Deep Learning based algorithms demonstrate superior performances than traditional machine learning based models. The cancer prognosis results measured in concordance index are indistinguishable across models while are highly variable across cancers. These findings shedding some light into the relationships between patient characteristics and survival learnability on a pan-cancer level.

Insect metamorphosis involves a complex change in form and function. In this study, we examined the development of the solitary bee, Megachile rotundata, using micro-computed tomography (μCT) and volume analysis. We describe volumetric changes of brain, tracheae, flight muscles, gut, and fat bodies in prepupal, pupal, and adult M. rotundata. We observed that individual organ systems have distinct patterns of developmental progression, which vary in their timing and duration. This has important implications for commercial management of this agriculturally relevant pollinator.

Structures such as nests and burrows are an essential component of many organisms' life-cycle and require a complex sequence of behaviours. Because behaviours can vary consistently among individuals and be correlated with one another, we hypothesized that these structures would (1) show evidence of among-individual variation, (2) be organized into distinct functional modules and (3) show evidence of trade-offs among functional modules due to limits on energy budgets. We tested these hypotheses using the alfalfa leafcutting bee, Megachile rotundata, a solitary bee and important crop pollinator. Megachile rotundata constructs complex nests by gathering leaf materials to form a linear series of cells in pre-existing cavities. In this study, we examined variation in the following nest construction traits: reproduction (number of cells per nest and nest length), nest protection (cap length and number of leaves per cap), cell construction (cell size and number of leaves per cell) and cell provisioning (cell mass) from 60 nests. We found a general decline in investment in cell construction and provisioning with each new cell built. In addition, we found evidence for both repeatability and plasticity in cell provisioning with little evidence for trade-offs among traits. Instead, most traits were positively, albeit weakly, correlated (r ~ 0.15), and traits were loosely organized into covarying modules. Our results show that individual differences in nest construction are detectable at a level similar to that of other behavioural traits and that these traits are only weakly integrated. This suggests that nest components are capable of independent evolutionary trajectories.

Species-specific biochemistry, morphology, and function of the Dufour’s gland have been investigated for social bees and some non-social bee families. Most of the solitary bees previously examined are ground-nesting bees that use Dufour’s gland secretions to line brood chambers. This study examines the chemistry of the cuticle and Dufour’s gland of cavity-nesting Megachile rotundata and Osmia lignaria, which are species managed for crop pollination. Glandular and cuticular lipid compositions were characterized and compared to each other and according to the nesting experience of adult females. Major lipid classes found were hydrocarbons, free fatty acids, and wax esters. Many components were common to the cuticle and Dufour’s glands of each species, yet not identical in number or relative composition. Wax esters and fatty acids were more prevalent in Dufour’s glands of M. rotundata than on cuticles. Wax esters were more abundant on cuticles of O. lignaria than in Dufour’s glands. In both species, fatty acids were more prevalent in glands of field-collected females compared to any other sample type. Chemical profiles of cuticles and glands were distinct from each other, and, for O. lignaria, profiles of laboratory-maintained bees could be distinguished from those of field-collected bees. Comparison of percentiles of individual components of cuticular and glandular profiles of the same bee showed that the proportions of some cuticular components were predictive of the proportion of the same glandular components, especially for nesting females. Lastly, evidence suggested that Dufour’s gland is the major source of nest-marking substances in M. rotundata, but evidence for this role in O. lignaria was less conclusive. Electronic supplementary material The online version of this article (doi:10.1007/s10886-017-0844-x) contains supplementary material, which is available to authorized users.

Single-cell RNA sequencing (scRNA-seq) resolves heterogenous cell populations in tissues and helps to reveal single-cell level function and dynamics. In neuroscience, the rarity of brain tissue is the bottleneck for such study. Evidence shows that, mouse and human share similar cell type gene markers. We hypothesized that the scRNA-seq data of mouse brain tissue can be used to complete human data to infer cell type composition in human samples. Here, we supplement cell type information of human scRNA-seq data, with mouse. The resulted data were used to infer the spatial cellular composition of 3702 human brain samples from Allen Human Brain Atlas. We then mapped the cell types back to corresponding brain regions. Most cell types were localized to the correct regions. We also compare the mapping results to those derived from neuronal nuclei locations. They were consistent after accounting for changes in neural connectivity between regions. Furthermore, we applied this approach on Alzheimer’s brain data and successfully captured cell pattern changes in AD brains. We believe this integrative approach can solve the sample rarity issue in the neuroscience.

Restoring somatosensory feedback to people with limb amputations is crucial for improving prosthesis acceptance and function. Epidural spinal cord stimulation is a commonly used clinical procedure that targets sensory neural pathways in the dorsal spinal cord to treat pain conditions. A similar approach could be developed as a clinically translatable means to restore somatosensation in amputees. We show that epidural stimulation of the dorsal spinal cord evoked sensory percepts, perceived as emanating from the amputated arm and hand, in four people with upper-limb amputation. After an initial caudal movement immediately following the implantation, the leads stabilized, exhibiting a median migration of

Rhabdomyosarcoma is subclassified by the presence or absence of a recurrent chromosome translocation that fuses the FOXO1 and PAX3 or PAX7 genes. The fusion protein (FOXO1-PAX3/7) retains both binding domains and becomes a novel and potent transcriptional regulator in rhabdomyosarcoma subtypes. Many studies have characterized and integrated genomic, transcriptomic, and epigenomic differences among rhabdomyosarcoma subtypes that contain the FOXO1-PAX3/7 gene fusion and those that do not, however, few investigations have investigated how gene co-expression networks are altered by FOXO1-PAX3/7. Although transcriptional data offer insight into one level of functional regulation, gene co-expression networks have the potential to identify biological interactions and pathways that underpin oncogenesis and tumorigenicity. Thus, we examined gene co-expression networks for rhabdomyosarcoma that were FOXO1-PAX3 positive, FOXO1-PAX7 positive, or fusion negative. Gene co-expression networks were mined using local maximum Quasi-Clique Merger (lmQCM) and analyzed for co-expression differences among rhabdomyosarcoma subtypes. This analysis observed 41 co-expression modules that were shared between fusion negative and positive samples, of which 17/41 showed significant up- or down-regulation in respect to fusion status. Fusion positive and negative rhabdomyosarcoma showed differing modularity of co-expression networks with fusion negative (n = 109) having significantly more individual modules than fusion positive (n = 53). Subsequent analysis of gene co-expression networks for PAX3 and PAX7 type fusions observed 17/53 were differentially expressed between the two subtypes. Gene list enrichment analysis found that gene ontology terms were poorly matched with biological processes and molecular function for most co-expression modules identified in this study, however, co-expressed modules were frequently localized to cytobands on chromosomes 8 and 11. Overall, we observed substantial restructuring of co-expression networks relative to fusion status and fusion type in rhabdomyosarcoma and identified previously overlooked genes and pathways that may be targeted in this pernicious disease.

Integrative and complementary non-pharmacological treatments have proven efficacious in treating both the physiological and psychological symptoms of chronic pain conditions but the potential of many combined therapies is unknown. This study examined the effects of a combined intervention of mindfulness meditation followed by aerobic walking exercise in chronic low back pain (cLBP) patients. We hypothesized that meditation before exercise would reduce disability and pain by increasing mindfulness prior to physical activity. Thirty-eight adults completed either meditation and exercise treatment (MedExT) (n=18) or an audiobook control condition (n=20). Over a 4-week period, participants in the MedExT group performed 12-17 minutes of guided meditation followed by 30 minutes of moderate intensity walking exercise 5 days per week. Measures of disability, pain, mindfulness and anxiety were taken at baseline and post-intervention. Ratings of pain were also assessed by participant self-report, before and after each intervention session. Following MedExT, participants showed significant improvement in our primary outcome of disability compared to the control group (p

Considerable advances in chronobiology have been made through controlled laboratory studies, but distinct temporal rhythms can emerge under natural environmental conditions. Lab-reared

Complex regional pain syndrome (CRPS) is a debilitating chronic pain disorder that is often resistant to traditional treatments and has long-term financial and emotional consequences. Spinal cord stimulation (SCS) has gained popularity over the last few decades for treating many types of chronic pain, and has been shown to significantly improve pain and quality of life in CRPS. Different variations of SCS, including burst and high-frequency stimulation, are equally as effective at reducing pain in patients with CRPS and can achieve this result at subsensory threshold levels. A promising new approach in neuromodulation is dorsal root ganglion stimulation, which is a technique that allows for more precise pain relief in areas that were previously difficult to reach. Advancements in both research and technology have helped make SCS a mainstay in the treatment of CRPS.

Technical advances have enabled the identification of high-resolution cell types within tissues based on single-cell transcriptomics. However, such analyses are restricted in human brain tissue due to the limited number of brain donors. In this study, we integrate mouse and human data to predict cell-type proportions in human brain tissue, and spatially map the resulting cellular composition. By applying feature selection and linear modeling, combinations of human and mouse brain single-cell transcriptomics profiles can be integrated to "fill in" missing information. These combined "in silico chimeric" datasets are used to model the composition of nine cell types in 3,702 human brain samples in six Allen Human Brain Atlas (AHBA) donors. Cell types were spatially consistent regardless of the scRNA-Seq dataset (91% significantly correlated) or AHBA donor (p-value = 4.43E-20 by t-test) used in the model. Importantly, neuron nuclei location and neuron mRNA location were correlated only after accounting for neural connectivity (p-value = 1.26E-10), which supports the notion that gene expression is a better indicator than nuclei location of cellular localization for cells with large and irregularly shaped cell bodies, such as neurons. These results advocate for the integration of mouse and human data in models of brain tissue heterogeneity.

Considerable advances in chronobiology have been made through controlled laboratory studies, but distinct temporal rhythms can emerge under natural environmental conditions. Lab-reared Nematostella vectensis sea anemones exhibit circadian behavioral and physiological rhythms. Given that these anemones inhabit shallow estuarine environments subject to tidal inputs, it was unclear whether circadian rhythmicity would persist following entrainment in natural conditions, or whether circatidal periodicity would predominate. Nematostella were conditioned within a marsh environment, where they experienced strong daily temperature cycles as well as brief tidal flooding around the full and new moons. Upon retrieval, anemones exhibited strong circadian (∼24 hour) activity rhythms under a light-dark cycle or continuous darkness, but reduced circadian rhythmicity under continuous light. However, some individuals in each light condition showed circadian rhythmicity, and a few individuals showed circatidal rhythmicity. Consistent with the behavioral studies, a large number of transcripts (1640) exhibited diurnal rhythmicity compared with very few (64) with semidiurnal rhythmicity. Diurnal transcripts included core circadian regulators, and 101 of 434 (23%) genes that were previously found to be up-regulated by exposure to ultraviolet radiation. Together the behavioral and transcriptional studies show that circadian rhythmicity predominates and suggest that solar radiation drives physiological cycles in this sediment-dwelling subtidal animal.

Tumors are heterogeneous tissues with different types of cells such as cancer cells, fibroblasts, and lymphocytes. Although the morphological features of tumors are critical for cancer diagnosis and prognosis, the underlying molecular events and genes for tumor morphology are far from being clear. With the advancement in computational pathology and accumulation of large amount of cancer samples with matched molecular and histopathology data, researchers can carry out integrative analysis to investigate this issue. In this study, we systematically examine the relationships between morphological features and various molecular data in breast cancers. Specifically, we identified 73 breast cancer patients from the TCGA and CPTAC projects matched whole slide images, RNA-seq, and proteomic data. By calculating 100 different morphological features and correlating them with the transcriptomic and proteomic data, we inferred four major biological processes associated with various interpretable morphological features. These processes include metabolism, cell cycle, immune response, and extracellular matrix development, which are all hallmarks of cancers and the associated morphological features are related to area, density, and shapes of epithelial cells, fibroblasts, and lymphocytes. In addition, protein specific biological processes were inferred solely from proteomic data, suggesting the importance of proteomic data in obtaining a holistic understanding of the molecular basis for tumor tissue morphology. Furthermore, survival analysis yielded specific morphological features related to patient prognosis, which have a strong association with important molecular events based on our analysis. Overall, our study demonstrated the power for integrating multiple types of biological data for cancer samples in generating new hypothesis as well as identifying potential biomarkers predicting patient outcome. Future work includes causal analysis to identify key regulators for cancer tissue development and validating the findings using more independent data sets.

Objectives: To investigate factors that predict speed of recovery and long-term CD4 cell count in HIV-1 seroconverters initiating combination antiretroviral therapy (cART), and to quantify the influence of very early treatment initiation. We make use of all pre-treatment CD4 counts, because analyses using only a single observation at initiation may be subject to biases. Methods: We used data from the CASCADE (Concerted Action on SeroConversion to AIDS and Death in Europe) multinational cohort collaboration of HIV-1 seroconverters. We analysed pre- and post-treatment data of patients with seroconversion dates estimated January 2003–March 2014 (n = 7600 for primary analysis) using a statistical model in which the characteristics of recovery in CD4 counts are determined by multiple predictive factors. Secondary analyses were performed incorporating uncertainty in the exact timing of seroconversion to allow more precise estimation of the benefit of very early treatment initiation. Results: ‘True’ CD4 count at cART initiation was the strongest predictor of CD4 count beyond 3 years on cART. Allowing for lack of complete certainty in the date of seroconversion, CD4 recovery was more rapid for patients in whom treatment was initiated within 4 months. For a given CD4 count, higher viral load (VL) at initiation was strongly associated with higher post-treatment CD4 recovery. For other patient and drug characteristics, associations with recovery were statistically significant but small in magnitude. Conclusions: CD4 count at cART initiation is the most important factor in predicting post-treatment recovery, but VL provides substantial additional information. If cART is initiated in the first 4 months following seroconversion, recovery of CD4 counts appears to be more rapid. © 2017 The Authors. HIV Medicine published by John Wiley & Sons Ltd on behalf of British HIV Association

Peroxiredoxins (PRXs) are a family of antioxidant enzymes present in all domains of life. To date, the diversity and function of peroxiredoxins within animals have only been studied in a few model species. Thus, we sought to characterize peroxiredoxin diversity in cnidarians and to gain insight into their function in one cnidarian-the sea anemone Nematostella vectensis. Phylogenetic analysis using all six known PRX subfamilies (PRX1-4, PRX5, PRX6, PRXQ/AHPE1, TPX, BCP-PRXQ) revealed that like bilaterians, cnidarians contain representatives from three subfamilies (PRX1-4, PRX5, PRX6). Within the PRX1-4 subfamily, cnidarian sequences fall into two clades: PRX4, and a cnidarian-specific clade, which we term CNID-PRX. This phylogenetic analysis demonstrates that the three PRX subfamilies present in Bilateria were also present in the last common ancestor of the Cnidaria and Bilateria, and further that diversification of the PRX1-4 subfamily has occurred within the cnidarian lineage. We next examined the impact of decreased salinity, increased temperature, and peroxide exposure on the expression of four prx genes in N. vectensis (cnid-prx, prx4, prx5, and prx6). These genes exhibited unique expression patterns in response to these environmental stressors. Expression of prx4 decreased with initial exposure to elevated temperature, cnid-prx increased with exposure to elevated temperatures as well as with hydrogen peroxide exposure, and expression of all prxs transiently decreased with reduced salinity. Predicted subcellular localization patterns also varied among PRX proteins. Together these results provide evidence that peroxiredoxins in N. vectensis serve distinct physiological roles and lay a groundwork for understanding how peroxiredoxins mediate cnidarian developmental processes and environmental responses.

Body size is an important phenotypic trait that correlates with performance and fitness. For determinate growing insects, body size variation is determined by growth rate and the mechanisms that stop growth at the end of juvenile growth. Endocrine mechanisms regulate growth cessation, and their relative timing along development shapes phenotypic variation in body size and development time. Larval insects are generally hypothesized to initiate metamorphosis once they attain a critical weight. However, the mechanisms underlying the critical weight have not been resolved even for well-studied insect species. More importantly, critical weights may or may not be generalizable across species. In this study, we characterized the developmental aspects of size regulation in the solitary bee, Osmia lignaria We demonstrate that starvation cues metamorphosis in O. lignaria and that a critical weight does not exist in this species. Larvae initiated pupation

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.

Luminal calcium released from secretory organelles has been suggested to play a regulatory role in vesicle transport at several steps in the secretory pathway; however, its functional roles and effector pathways have not been elucidated. Here we demonstrate for the first time that specific luminal calcium depletion leads to a significant decrease in endoplasmic reticulum (ER)-to-Golgi transport rates in intact cells. Ultrastructural analysis revealed that luminal calcium depletion is accompanied by increased accumulation of intermediate compartment proteins in COPII buds and clusters of unfused COPII vesicles at ER exit sites. Furthermore, we present several lines of evidence suggesting that luminal calcium affected transport at least in part through calcium-dependent interactions between apoptosis-linked gene-2 (ALG-2) and the Sec31A proline-rich region: 1) targeted disruption of ALG-2/Sec31A interactions caused severe defects in ER-to-Golgi transport in intact cells; 2) effects of luminal calcium and ALG-2/Sec31A interactions on transport mutually required each other; and 3) Sec31A function in transport required luminal calcium. Morphological phenotypes of disrupted ALG-2/Sec31A interactions were characterized. We found that ALG-2/Sec31A interactions were not required for the localization of Sec31A to ER exit sites per se but appeared to acutely regulate the stability and trafficking of the cargo receptor p24 and the distribution of the vesicle tether protein p115. These results represent the first outline of a mechanism that connects luminal calcium to specific protein interactions regulating vesicle trafficking machinery.

The scaling laws governing metabolism suggest that we can predict metabolic rates across taxonomic scales that span large differences in mass. Yet, scaling relationships can vary with development, body region, and environment. Within species, there is variation in metabolic rate that is independent of mass and which may be explained by genetic variation, the environment or their interaction (i.e., metabolic plasticity). Additionally, some structures, such as the insect tracheal respiratory system, change throughout development and in response to the environment to match the changing functional requirements of the organism. We discuss how study of the development of respiratory function meets multiple challenges set forth by the NSF Grand Challenges Workshop. Development of the structure and function of respiratory and metabolic systems (1) is inherently stable and yet can respond dynamically to change, (2) is plastic and exhibits sensitivity to environments, and (3) can be examined across multiple scales in time and space. Predicting respiratory performance and plasticity requires quantitative models that integrate information across scales of function from the expression of metabolic genes and mitochondrial biogenesis to the building of respiratory structures. We present insect models where data are available on the development of the tracheal respiratory system and of metabolic physiology and suggest what is needed to develop predictive models. Incorporating quantitative genetic data will enable mapping of genetic and genetic-by-environment variation onto phenotypes, which is necessary to understand the evolution of respiratory and metabolic systems and their ability to enable respiratory homeostasis as organisms walk the tightrope between stability and change.