julilili42/papers huggingface dataset:
Age-Dependent Auditory Processing Deficits after Cochlear Synaptopathy Depend on Auditory Nerve Latency and the Ability of the Brain to Recruit LTP/BDNF
2020-10-06

Age-related decoupling of auditory nerve fibers from hair cells (cochlear synaptopathy) has been linked to temporal processing deficits and impaired speech recognition performance. The link between both is elusive. We have previously demonstrated that cochlear synaptopathy, if centrally compensated through enhanced input/output function (neural gain), can prevent age-dependent temporal discrimination loss. It was also found that central neural gain after acoustic trauma was linked to hippocampal long-term potentiation (LTP) and upregulation of brain-derived neurotrophic factor (BDNF). Using middle-aged and old BDNF-live-exon-visualization (BLEV) reporter mice we analyzed the specific recruitment of LTP and the activity-dependent usage of Bdnf exon-IV and -VI promoters relative to cochlear synaptopathy and central (temporal) processing. For both groups, specimens with higher or lower ability to centrally compensate diminished auditory nerve activity were found. Strikingly, low compensating mouse groups differed from high compensators by prolonged auditory nerve latency. Moreover, low compensators exhibited attenuated responses to amplitude-modulated tones, and a reduction of hippocampal LTP and Bdnf transcript levels in comparison to high compensators. These results suggest that latency of auditory nerve processing, recruitment of hippocampal LTP, and Bdnf transcription, are key factors for age-dependent auditory processing deficits, rather than cochlear synaptopathy or aging per se.
Faculty Opinions recommendation of Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases.
2020-10-06

Read the full review for this Faculty Opinions recommended article: Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases.
SARS-CoV2 (COVID-19) Pandemic Lockdown Influences Nature-Based Recreational Activity: The Case of Birders
2020-10-07

The new corona virus infection SARS-CoV2 which was later renamed COVID-19 is a pandemic affecting public health. The fear and the constraints imposed to control the pandemic may correspondingly influence leisure activities, such as birding, which is the practice of observing birds based on visual and acoustic cues. Birders are people who carry out birding observations around the globe and contribute to the massive data collection in citizen science projects. Contrasting to earlier COVID-19 studies, which have concentrated on clinical, pathological, and virological topics, this study focused on the behavioral changes of birders. A total of 4484 questionnaire survey responses from 97 countries were received. The questionnaire had an open-ended style. About 85% of respondents reported that COVID-19 has changed their birding behavior. The most significant change in birdwatchers’ behavior was related to the geographic coverage of birding activities, which became more local. People focused mostly on yard birding. In total, 12% of respondents (n = 542 cases) reported having more time for birding, whereas 8% (n = 356 cases) reported having less time for birding. Social interactions decreased since respondents, especially older people, changed their birding behavior toward birding alone or with their spouse. Women reported more often than men that they changed to birding alone or with their spouse, and women also reported more often about canceled fieldtrips or society meetings. Respondents from higher developed countries reported that they spend currently more time for birding, especially for birding alone or with their spouse, and birding at local hotspots. Our study suggests that long lockdowns with strict regulations may severely impact on leisure activities. In addition, a temporal and spatial shift in birding due to the pandemic may influence data quality in citizen science projects. As nature-based recreation will be directed more toward nearby sites, environmental management resources and actions need to be directed to sites that are located near the users, e.g., in urban and suburban areas. The results can be applied with caution to other nature-based recreational activities.
Generalization in data-driven models of primary visual cortex
2020-10-07

A bstract Deep neural networks (DNN) have set new standards at predicting responses of neural populations to visual input. Most such DNNs consist of a convolutional network (core) shared across all neurons which learns a representation of neural computation in visual cortex and a neuron-specific readout that linearly combines the relevant features in this representation. The goal of this paper is to test whether such a representation is indeed generally characteristic for visual cortex, i.e. gener-alizes between animals of a species, and what factors contribute to obtaining such a generalizing core. To push all non-linear computations into the core where the generalizing cortical features should be learned, we devise a novel readout that reduces the number of parameters per neuron in the readout by up to two orders of magnitude compared to the previous state-of-the-art. It does so by taking advantage of retinotopy and learns a Gaussian distribution over the neuron’s receptive field po-sition. With this new readout we train our network on neural responses from mouse primary visual cortex (V1) and obtain a gain in performance of 7% compared to the previous state-of-the-art network. We then investigate whether the convolutional core indeed captures general cortical features by using the core in transfer learning to a different animal. When transferring a core trained on thousands of neurons from various animals and scans we exceed the performance of training directly on that animal by 12%, and outperform a commonly used VGG16 core pre-trained on imagenet by 33%. In addition, transfer learning with our data-driven core is more data-efficient than direct training, achieving the same performance with only 40% of the data. Our model with its novel readout thus sets a new state-of-the-art for neural response prediction in mouse visual cortex from natural images, generalizes between animals, and captures better characteristic cortical features than current task-driven pre-training approaches such as VGG16.
UltraTrail: A Configurable Ultralow-Power TC-ResNet AI Accelerator for Efficient Keyword Spotting
2020-10-07

Recent advances in machine learning show the superior behavior of temporal convolutional networks (TCNs) and especially their combination with residual networks (TC-ResNet) for intelligent sensor signal processing in comparison to classical CNNs and LSTMs. In this article, we propose UltraTrail, a configurable, ultralow-power TC-ResNet AI accelerator for sensor signal processing and its application to efficient keyword spotting (KWS). Following a strict hardware/model co-design approach, we have derived an optimized low-power hardware architecture for generalized TC-ResNet topologies consisting of a configurable array of processing elements and a distributed memory with dynamic content reallocation. We additionally extend the network with conditional computing to reduce the number of operations during inference and to provide the possibility for power-gating. The final accelerator implementation in Globalfoundries' 22FDX technology achieves a power consumption of 8.2 μW for the task of always-on KWS meeting the real-time requirement of 100 ms per inference with an accuracy of 93% on the Google Speech Command Dataset.
On the interpretability of predictors in spatial data science: the information horizon
2020-10-07

Abstract Two important theories in spatial modelling relate to structural and spatial dependence. Structural dependence refers to environmental state-factor models, where an environmental property is modelled as a function of the states and interactions of environmental predictors, such as climate, parent material or relief. Commonly, the functions are regression or supervised classification algorithms. Spatial dependence is present in most environmental properties and forms the basis for spatial interpolation and geostatistics. In machine learning, modelling with geographic coordinates or Euclidean distance fields, which resemble linear variograms with infinite ranges, can produce similar interpolations. Interpolations do not lend themselves to causal interpretations. Conversely, with structural modeling, one can, potentially, extract knowledge from the modelling. Two important characteristics of such interpretable environmental modelling are scale and information content. Scale is relevant because very coarse scale predictors can show nearly infinite ranges, falling out of what we call the information horizon, i.e. interpretation using domain knowledge isn’t possible. Regarding information content, recent studies have shown that meaningless predictors, such as paintings or photographs of faces, can be used for spatial environmental modelling of ecological and soil properties, with accurate evaluation statistics. Here, we examine under which conditions modelling with such predictors can lead to accurate statistics and whether an information horizon can be derived for scale and information content.
Collagen and Endothelial Cell Coculture Improves β-Cell Functionality and Rescues Pancreatic Extracellular Matrix
2020-10-07

The use of biomaterials and biomaterial functionalization is a promising approach to support pancreatic islet viability posttransplantation in an effort to reduce insulin dependence for patients afflicted with diabetes mellitus type 1. Extracellular matrix (ECM) proteins are known to impact numerous reparative functions in the body. Assessing how endogenously expressed pancreatic ECM proteins are affected by posttransplant-like hypoxic conditions may provide significant insights toward the development of tissue-engineered therapeutic strategies to positively influence β-cell survival, proliferation, and functionality. Here, we investigated the expression of three relevant groups of pancreatic ECM proteins in human native tissue, including basement membrane (BM) proteins (collagen type 4 [COL4], laminins [LAM]), proteoglycans (decorin [DCN], nidogen-1 [NID1]), and fibril-forming proteins (fibronectin [FN], collagen type 1 [COL1]). In an <i>in vitro</i> hypoxia model, we identified that ECM proteins were differently affected by hypoxic conditions, contributing to an overall loss of β-cell functionality. The use of a COL1 hydrogel as carrier material demonstrated a protective effect on β-cells mitigating the effect of hypoxia on proteoglycans as well as fibril-forming protein expression, supporting β-cell functionality in hypoxia. We further showed that providing endothelial cells (ECs) into the COL1 hydrogel improves β-cell response as well as the expression of relevant BM proteins. Our data show that β-cells benefit from a microenvironment composed of structure-providing COL1 with the incorporation of ECs to withstand the harsh conditions of hypoxia. Such hydrogels support β-cell survival and can serve as an initial source of ECM proteins to allow cell engraftment while preserving cell functionality posttransplantation. Impact statement Expression analysis identifies hypoxia-induced pathological changes in extracellular matrix (ECM) homeostasis as potential targets to support β-cell transplants by encapsulation in biomaterials for the treatment of diabetes mellitus. A collagen-1 hydrogel is shown to attenuate the effect of hypoxia on β-cells and their ECM expression. The functionalization of the hydrogel with endothelial cells increases the β-cell response to glucose and rescues essential basement membrane proteins.
“I Trust in Staff's Creativity”—The Impact of COVID-19 Lockdowns on Physical Activity Promotion in Nursing Homes Through the Lenses of Organizational Sociology
2020-10-07

<b>Objectives:</b> The health-enhancing benefits or regular physical activity (PA) reach into old age. With the emergence of the coronavirus disease of 2019 (COVID-19) pandemic and the associated national lockdowns and restrictions, nursing home residents were restrained from being physically active. In our study, we aimed to assess the impact of the COVID-19-related restrictions on PA promotion in nursing homes from an organizational-sociological lens. <b>Methods:</b> We collected data in eight nursing homes in Germany. Data collection included (i) semistructured interviews focusing on COVID-19-related restrictions and their effects on nursing homes from the home administrators' perspectives; (ii) open-ended surveys with nursing home staff and relatives focusing on daily routines and contact restrictions; and (iii) collection of documents such as care concepts, mission statements, and weekly activity plans. We analyzed all data with a reflexive thematic analysis approach. <b>Results:</b> We identified three stages of COVID-19-related changes in nursing homes that impacted PA promotion, as follows: (1) external closure and search for emergency control, (2) organizational adaptations to create a livable daily life in the internal environment, and (3) slow reintegration of interactions with the external organizational environment. Document analysis revealed that PA promotion was not part of decision programs or internal staff work descriptions. Rather, PA promotion was delegated to external service providers. The assignment of PA promotion to external providers was not structurally anchored in decision programs, which makes PA promotion not sustainable, particularly during unforeseen events that limit access to the organization. During the pandemic, executive staff believed in internal staff to buffer competencies with regard to PA promotion. Thus, executive staff often considered PA promotion relevant, even during the pandemic, but thought that PA promotion is a task that can be fulfilled by unqualified but motivated internal staff. <b>Conclusion:</b> While our study participants showed a high level of coping-capacity belief, it remains unclear which long-term impacts of COVID-19 on PA promotion in nursing homes are to be expected. At the practice level, executive staff in nursing homes that aim to promote PA within their organization should become aware that PA promotion needs to be incorporated into organizational structures to be implemented and continued in challenging times such as in a pandemic.
Haploinsufficiency due to a novel ACO2 deletion causes mitochondrial dysfunction in fibroblasts from a patient with dominant optic nerve atrophy
2020-10-07

Abstract ACO2 is a mitochondrial protein, which is critically involved in the function of the tricarboxylic acid cycle (TCA), the maintenance of iron homeostasis, oxidative stress defense and the integrity of mitochondrial DNA (mtDNA). Mutations in the ACO2 gene were identified in patients suffering from a broad range of symptoms, including optic nerve atrophy, cortical atrophy, cerebellar atrophy, hypotonia, seizures and intellectual disabilities. In the present study, we identified a heterozygous 51 bp deletion (c.1699_1749del51) in ACO2 in a family with autosomal dominant inherited isolated optic atrophy. A complementation assay using aco1 -deficient yeast revealed a growth defect for the mutant ACO2 variant substantiating a pathogenic effect of the deletion. We used patient-derived fibroblasts to characterize cellular phenotypes and found a decrease of ACO2 protein levels, while ACO2 enzyme activity was not affected compared to two age- and gender-matched control lines. Several parameters of mitochondrial function, including mitochondrial morphology, mitochondrial membrane potential or mitochondrial superoxide production, were not changed under baseline conditions. However, basal respiration, maximal respiration, and spare respiratory capacity were reduced in mutant cells. Furthermore, we observed a reduction of mtDNA copy number and reduced mtDNA transcription levels in ACO2-mutant fibroblasts. Inducing oxidative stress led to an increased susceptibility for cell death in ACO2-mutant fibroblasts compared to controls. Our study reveals that a monoallelic mutation in ACO2 is sufficient to promote mitochondrial dysfunction and increased vulnerability to oxidative stress as main drivers of cell death related to optic nerve atrophy.
Fluorescence lifetime metabolic mapping of hypoxia‐induced damage in pancreatic pseudo‐islets
2020-10-07

Abstract Pancreatic islet isolation from donor pancreases is an essential step for the transplantation of insulin‐secreting β‐cells as a therapy to treat type 1 diabetes mellitus. This process however damages islet basement membranes, which can lead to islet dysfunction or death. Posttransplantation, islets are further stressed by a hypoxic environment and immune reactions that cause poor engraftment and graft failure. The current standards to assess islet quality before transplantation are destructive procedures, performed on a small islet population that does not reflect the heterogeneity of large isolated islet batches. In this study, we incorporated fluorescence lifetime imaging microscopy (FLIM) into a pancreas‐on‐chip system to establish a protocol to noninvasively assess the viability and functionality of pancreatic β‐cells in a three‐dimensional in vitro model (= pseudo‐islets). We demonstrate how (pre‐) hypoxic β‐cell‐composed pseudo‐islets can be discriminated from healthy functional pseudo‐islets according to their FLIM‐based metabolic profiles. The use of FLIM during the pretransplantation pancreatic islet selection process has the potential to improve the outcome of β‐cell islet transplantation.
Characterization of Hormone-Dependent Pathways in Six Human Prostate-Cancer Cell Lines: A Gene-Expression Study
2020-10-07

Prostate cancer (PCa), the most incident cancer in men, is tightly regulated by endocrine signals. A number of different PCa cell lines are commonly used for in vitro experiments, but these are of diverse origin, and have very different cell-proliferation rates and hormone-response capacities. By analyzing the gene-expression pattern of main hormone pathways, we systematically compared six PCa cell lines and parental primary cells. We compared these cell lines (i) with each other and (ii) with PCa tissue samples from 11 patients. We found major differences in the gene-expression levels of androgen, insulin, estrogen, and oxysterol signaling between PCa tissue and cell lines, and between different cell lines. Our systematic characterization gives researchers a solid basis to choose the appropriate PCa cell model for the hormone pathway of interest.
Pediatric COVID‐19 case with regard to the family infection chain and the psychosocial context
2020-10-07

Abstract The role of children in households, spreading SARS‐CoV‐2, may differ from measles or influenza, and therefore, these diseases are not directly comparable to COVID‐19. The psychosocial aspect of infection and quarantine for families and children suggests that fear of social stigmatization can lead to not disclosing the infection.
Island Migration, Resource Use, and Lithic Technology by Anatomically Modern Humans in Wallacea
2020-10-07

Island migration and adaptation including both marine and terrestrial resource use and technological development by anatomically modern humans (AMH) are among the most significant issues for Pleistocene archaeology in Southeast Asia and Oceania, and directly related to the behavioral and technological advancements by AMH. This paper discusses such cases in the Wallacean islands, located between the past Sundaland and the Sahul continent during the Pleistocene. The Pleistocene open sea gaps between the Wallacean islands and both landmasses are very likely the major factor for the relative scarcity of animal species originating from Asia and Oceania and the high diversity of endemic species in Wallacea. They were also a barrier for hominin migration into the Wallacean islands and Sahul continent. We summarize three recent excavation results on the Talaud Islands, Sulawesi Island and Mindoro Island in Wallacea region and discuss the evidence and timeline for migrations of early modern humans into the Wallacean islands and their adaptation to island environments during the Pleistocene.
Allopregnanolone Enhances GABAergic Inhibition in Spinal Motor Networks
2020-10-07

The neurosteroid allopregnanolone (ALLO) causes unconsciousness by allosteric modulation of γ-aminobutyric acid type A (GABAA) receptors, but its actions on the spinal motor networks are unknown. We are therefore testing the hypothesis that ALLO attenuates the action potential firing of spinal interneurons and motoneurons predominantly via enhancing tonic, but not synaptic GABAergic inhibition. We used video microscopy to assess motoneuron-evoked muscle activity in organotypic slice cultures prepared from the spinal cord and muscle tissue. Furthermore, we monitored GABAA receptor-mediated currents by performing whole-cell voltage-clamp recordings. We found that ALLO (100 nM) reduced the action potential firing of spinal interneurons by 27% and that of α-motoneurons by 33%. The inhibitory effects of the combination of propofol (1 μM) and ALLO on motoneuron-induced muscle contractions were additive. Moreover, ALLO evoked a tonic, GABAA receptor-mediated current (amplitude: 41 pA), without increasing phasic GABAergic transmission. Since we previously showed that at a clinically relevant concentration of 1 μM propofol enhanced phasic, but not tonic GABAergic inhibition, we conclude that ALLO and propofol target distinct subpopulations of GABAA receptors. These findings provide first evidence that the combined application of ALLO and propofol may help to reduce intraoperative movements and undesired side effects that are frequently observed under total intravenous anesthesia.
Optically and electrically driven nanoantennas
2020-10-07

Keywords: active plasmonics; electrically driven nanoantenna; gap antenna; nanoantenna; nanofabrication; nanospectroscopy; nano-photonics; optical antenna; second harmonic generation; sensing; scanning tip; surface-enhanced infrared absorption (SEIRA); surface-enhanced Raman spectroscopy (SERS); tip-enhanced Raman spectroscopy (TERS); tunnel junction
The distribution and host range of Thecaphora melandrii, with first records for Britain
2020-10-07

Summary Thecaphora melandrii (Syd.) Vánky &amp; M.Lutz infects species in the Caryophyllacaeae forming sori with spore balls in the floral organs. We report new finds from Britain, supported by phylogenetic analysis, that confirm its occurrence on Silene uniflora Roth. We review published and web accessible records and note the relatively few records of this smut, its sparse distribution, confined to Europe but scattered predominantly from central to eastern Europe. Analysis of the rDNA ITS and 28S sequences demonstrates little variability among specimens, even those parasitising different host genera, which suggests that the species has evolved relatively recently. Some Microbotryum species infect the same host plants, and we found two species, M. lagerheimii Denchev and M. silenes-inflatae (DC. ex Liro) G.Deml &amp; Oberw., in the same locations as T. melandrii , identified by morphology and molecular phylogenetic analysis. These species may form a stable multi-species community of parasites of Silene uniflora .
Comparison of Proteomic Responses as Global Approach to Antibiotic Mechanism of Action Elucidation
2020-10-08

New antibiotics are urgently needed to address the mounting resistance challenge. In early drug discovery, one of the bottlenecks is the elucidation of targets and mechanisms. To accelerate antibiotic research, we provide a proteomic approach for the rapid classification of compounds into those with precedented and unprecedented modes of action. We established a proteomic response library of Bacillus subtilis covering 91 antibiotics and comparator compounds, and a mathematical approach was developed to aid data analysis.