bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leveraging spiking deep neural networks to understand the neural mechanisms underlying selective attention
Authors: Sörensen Lynn K. A. , Zambrano Davide , Slagter Heleen A. , Bohté Sander M. , Scholte H. Steven 
Published: December 2020

AbstractSpatial attention enhances sensory processing of goal-relevant information and improves perceptual sensitivity. Yet, the specific neural mechanisms underlying the effects of spatial attention on performance are still contested. Here, we examine different attention mechanisms in spiking deep convolutional neural networks. We directly contrast effects of precision (internal noise suppression) and two different gain modulation mechanisms on performance on a visual search task with complex real-world images. Unlike standard artificial neurons, biological neurons have saturating activation functions, permitting implementation of attentional gain as gain on a neuron’s input or on its outgoing connection. We show that modulating the connection is most effective in selectively enhancing information processing by redistributing spiking activity, and by introducing additional task-relevant information, as shown by representational similarity analyses. Precision only produced minor attentional effects in performance. Our results, which mirror empirical findings, show that it is possible to adjudicate between attention mechanisms using more biologically realistic models and natural stimuli.
MiMeNet: Exploring Microbiome-Metabolome Relationships using Neural Networks
Authors: Reiman Derek , Layden Brian T. , Dai Yang 
Published: December 2020

AbstractThe advance in microbiome and metabolome studies has generated rich omics data revealing the involvement of the microbial community in host disease pathogenesis through interactions with their host at a metabolic level. However, the computational tools to uncover these relationships are just emerging. Here, we present MiMeNet, a neural network framework for modeling microbe-metabolite relationships. Using ten iterations of 10-fold cross-validation on three paired microbiome-metabolome datasets, we show that MiMeNet more accurately predicts metabolite abundances (mean Spearman correlation coefficients increase from 0.108 to 0.309, 0.276 to 0.457, and -0.272 to 0.264) and identifies more well-predicted metabolites (increase in the number of well-predicted metabolites from 198 to 366, 104 to 143, and 4 to 29) compared to state-of-art linear models for individual metabolite predictions. Additionally, we demonstrate that MiMeNet can group microbes and metabolites with similar interaction patterns and functions to illuminate the underlying structure of the microbe-metabolite interaction network, which could potentially shed light on uncharacterized metabolites through “Guilt by Association”. Our results demonstrated that MiMeNet is a powerful tool to provide insights into the causes of metabolic dysregulation in disease, facilitating future hypothesis generation at the interface of the microbiome and metabolomics.
A Guide to Pre-Processing High-Throughput Animal Tracking Data
Authors: Gupte Pratik Rajan , Beardsworth Christine E. , Spiegel Orr , Lourie Emmanuel , Toledo Sivan , Nathan Ran , Bijleveld Allert I. 
Published: December 2020

AbstractModern, high-throughput animal tracking studies collect increasingly large volumes of data at very fine temporal scales. At these scales, location error can exceed the animal’s step size, leading to mis-estimation of key movement metrics such as speed. ‘Cleaning’ the data to reduce location errors prior to analyses is one of the main ways movement ecologists deal with noisy data, and has the advantage of being more scalable to massive datasets than more complex methods. Though data cleaning is widely recommended, and ecologists routinely consider cleaned data to be the ground-truth, inclusive uniform guidance on this crucial step, and on how to organise the cleaning of massive datasets, is still rather scarce.A pipeline for cleaning massive high-throughput datasets must balance ease of use and computationally efficient signal vs. noise screening, in which location errors are rejected without discarding valid animal movements. Another useful feature of a pre-processing pipeline is efficiently segmenting and clustering location data for statistical methods, while also being scalable to large datasets and robust to imperfect sampling. Manual methods being prohibitively time consuming, and to boost reproducibility, a robust pre-processing pipeline must be automated.In this article we provide guidance on building pipelines for pre-processing high-throughput animal tracking data in order to prepare it for subsequent analysis. Our recommended pipeline, consisting of removing outliers, smoothing the filtered result, and thinning it to a uniform sampling interval, is applicable to many massive tracking datasets. We apply this pipeline to simulated movement data with location errors, and also show a case study of how large volumes of cleaned data can be transformed into biologically meaningful ‘residence patches’, for quick biological inference on animal space use. We use calibration data to illustrate how pre-processing improves its quality, and to verify that the residence patch synthesis accurately captures animal space use. Finally, turning to tracking data from Egyptian fruit bats (Rousettus aegyptiacus), we demonstrate the pre-processing pipeline and residence patch method in a fully worked out example.To help with fast implementation of standardised methods, we developed theRpackageatlastools, which we also introduce here. Our pre-processing pipeline andatlastoolscan be used with any high-throughput animal movement data in which the high data-volume combined with knowledge of the tracked individuals’ movement capacity can be used to reduce location errors. Theatlastoolsfunction is easy to use for beginners, while providing a template for further development. The use of common pre-processing steps that are simple yet robust promotes standardised methods in the field of movement ecology and leads to better inferences from data.
Bait-ER: a Bayesian method to detect targets of selection in Evolve-and-Resequence experiments
Authors: Barata Carolina , Borges Rui , Kosiol Carolin 
Published: December 2020

AbstractFor over a decade, experimental evolution has been combined with high-throughput sequencing techniques in so-called Evolve-and-Resequence (E&R) experiments. This allows testing for selection in populations kept in the laboratory under given experimental conditions. However, identifying signatures of adaptation in E&R datasets is far from trivial, and it is still necessary to develop more efficient and statistically sound methods for detecting selection in genome-wide data. Here, we present Bait-ER – a fully Bayesian approach based on the Moran model of allele evolution to estimate selection coefficients from E&R experiments. The model has overlapping generations, a feature that describes several experimental designs found in the literature. We tested our method under several different demographic and experimental conditions to assess its accuracy and precision, and it performs well in most scenarios. Nevertheless, some care must be taken when analysing trajectories where drift largely dominates and starting frequencies are low. We compare our method with other available software and report that ours has generally high accuracy even for trajectories whose complexity goes beyond a classical sweep model.Furthermore, our approach avoids the computational burden of simulating an empirical null distribution, outperforming available software in terms of computational time and facilitating its use on genome-wide data.We implemented and released our method in a new open-source software package that can be accessed athttps://github.com/mrborges23/Bait-ER.
Ruling the Roost: Avian Species Reclaim Urban Habitat During India’s COVID Lockdown
Authors: Madhok Raahil , Gulati Sumeet 
Published: December 2020

AbstractAs we retreated to our dwellings in the “anthropause” of spring 2020, did other species return to our urban centres? We leverage an increase in balcony birdwatching, a million eBird entries, and difference-in-difference techniques to test if avian species richness rose during India’s COVID lockdown. We find that birdwatchers in India’s 20 most populous cities observed 8-17% more species during the lockdown. Most additional observations occurred after a two-week lag, signaling greater abundance instead of improved detection. More frequent appearances of at-risk, rare, and common species were recorded, implying that making our cities more wildlife friendly can protect threatened species in addition to urban specialists. Our contributions are: 1) to isolate and estimate a causal impact of reducing human activity on avian diversity, 2) to improve the external validity of this literature in rapidly urbanizing bio-diverse developing countries, and, 3) to illustrate a method separating abundance from detection in observational avian surveys.
A vision prosthesis based on electrical stimulation of the primary visual cortex using epicortical microelectrodes
Authors: Oswalt Denise , Datta P. , Talbot N. , Mirzadeh Z. , Greger Bradley 
Published: December 2020

AbstractProstheses that can restore limited vision in the profoundly blind have been under investigation for several decades. Studies using epicortical macroelectrodes and intracortical microelectrodes have validated that electrical stimulation of primary visual cortical can serve as the basis for a vision prosthesis. However, neither of these approaches has resulted in a clinically viable vision prosthesis. Epicortical macroelectrodes required high levels of electrical current to evoke visual percepts, while intracortical microelectrodes faced challenges with longevity and stability. We hypothesized that epicortical microelectrodes could evoke visual percepts at lower currents than macroelectrodes and provide improved longevity and stability compared with intracortical microelectrodes. To test this hypotheses we implanted epicortical microelectrode arrays over the primary visual cortex of a nonhuman primate. Electrical stimulation via this array was used to evaluate the ability of epicortical microstimulation to evoke differentiable visual percepts. Visual percepts were evoked using the epicortical microelectrode array, and at electrical currents notably lower than those required to evoke visual percepts on macroelectrode arrays. The electrical current thresholds for evoking visual percepts on the epicortical microelectrode array were consistent across multiple array implants and over several months. Normal vision of light perception was not impaired by multiple array implants or chronic electrical stimulation, demonstrating that no gross visual deficit resulted from the experiments. We specifically demonstrate that epicortical microelectrode interfaces can serve as the basis for a vision prosthesis and more generally may provide an approach to evoking perception in multiple sensory modalities.One Sentence SummaryElectrical stimulation of the brain via microelectrodes resting on the surface of primary visual cortex can evoke multiple differentiable visual percepts.
Cooperative nest building in wild jackdaw pairs
Authors: Hahn Luca G. , Hooper Rebecca , McIvor Guillam E. , Thornton Alex 
Published: December 2020

AbstractAnimals create diverse structures, both individually and cooperatively, using materials from their environment. One striking example are the nests birds build for reproduction, which protect the offspring from external stressors such as predators and temperature, promoting reproductive success. To construct a nest successfully, birds need to make various decisions, for example regarding the nest material and their time budgets. To date, research has focused mainly on species where one sex is primarily responsible for building the nest. In contrast, the cooperative strategies of monogamous species in which both sexes contribute to nest building are poorly understood. Here we investigated the role of both sexes in nest building and fitness correlates of behaviour in wild, monogamous jackdaw pairs (Corvus monedula). We show that both partners contributed to nest building and behaved similarly, with females and males present in the nest box for a comparable duration and transporting material to the nest equally often. However, while females spent more time constructing the nest, males tended to invest more time in vigilance, potentially as a means of coping with competition for nest cavities. These findings suggest a moderate degree of division of labour, which may facilitate cooperation. Moreover, some aspects of behaviour were related to proxies of reproductive success (lay date and egg volume). Females that contributed relatively more to bringing material laid earlier clutches and pairs that spent less time together in the nest box had larger eggs. Thus, selection pressures may act on how nest building pairs spend their time and cooperatively divide the labour. We conclude that cooperative nest building in birds could be associated with monogamy and obligate biparental care, and provides a vital but relatively untapped context through which to study the evolution of cooperation.HighlightsIn wild monogamous jackdaws, mates behaved similarly and cooperated to build their nest.Females built more and called more frequently; males tended to be more vigilant.Females that contributed relatively more to transporting nest material laid earlier clutches.Pairs that spent more time together in the nest box had smaller eggs.Cooperation may be crucial in light of obligate biparental care and nest site competition.
Novel insights into potential therapeutic targets and biomarkers using integrated multi-omicsapproaches for dilated and ischemic cardiomyopathies
Authors: Kanapeckaitė Austė , Burokienė Neringa 
Published: December 2020

AbstractAt present heart failure treatment targets symptoms based on the left ventricle dysfunction severity; however, lack of systemic studies and available biological data to uncover heterogeneous underlying mechanisms on the scale of genomic, transcriptional and expressed protein level signifies the need to shift the analytical paradigm toward network centric and data mining approaches. This study, for the first time, aimed to investigate how bulk and single cell RNA-sequencing as well as the proteomics analysis of the human heart tissue can be integrated to uncover heart failure specific networks and potential therapeutic targets or biomarkers. Furthermore, it was demonstrated that transcriptomics data in combination with minded data from public databases can be used to elucidate specific gene expression profiles. This was achieved using machine learning algorithms to predict the likelihood of the therapeutic target or biomarker tractability based on a novel scoring system also introduced in this study. The described methodology could be very useful for the target selection and evaluation during the pre-clinical therapeutics development stage. Finally, the present study shed new light into the complex etiology of the heart failure differentiating between subtle changes in dilated and ischemic cardiomyopathy on the single cell, proteome and whole transcriptome level.HIGHLIGHTSFirst report of an integrated multi-omics analysis for dilated and ischemic cardiomyopathies.Identification of metabolic and regulatory network differences for the two types of cardiomyopathies.Introduction of a new scoring system to evaluate genes based on the size of their network and disease association.Two-step machine learning pipeline to uncover potential therapeutic target clusters.
Effect of artificial liver blood purification treatment on the survival of critical ill COVID‐19 patients
Authors: Dai Xiahong , Zhang Yimin , Yu Liang , Jiang Ying‐an , Chen Liang , Chen Ye , Li Ming , Gao Chunming , Shang Jia , Xiang Shulin , Li Yongguo , Li Jianzhou , Zhou Chenliang , Zhou Xiaoyang , Chen Nan , Liu Yuanchun , Liu Jing , Zhang Yuanyuan , Chen Xiaobei , Zhu Danhua , Gao Hainv , Tang Lingling , Zhu Mengfei , Li Lanjuan 
Published: December 2020

AbstractOur aim was to investigate the effect of artificial liver blood purification treatment on the survival of severe/critical patients with coronavirus disease 2019 (COVID‐19). A total of 101 severe and critical patients with coronavirus SARS‐CoV‐2 infection were enrolled in this open, case‐control, multicenter, prospective study. According to the patients’ and their families’ willingness, they were divided into two groups. One was named the treatment group, in which the patients received artificial liver therapy plus comprehensive treatment (n = 50), while the other was named the control group, in which the patients received only comprehensive treatment (n = 51). Clinical data and laboratory examinations, as well as the 28‐day mortality rate, were collected and analyzed. Baseline data comparisons on average age, sex, pre‐treatment morbidity, initial symptoms, vital signs, pneumonia severity index score, blood routine examination and biochemistry indices etc. showed no difference between the two groups. Cytokine storm was detected, with a significant increase of serum interleukin‐6 (IL‐6) level. The serum IL‐6 level decreased from 119.94 to 20.49 pg/mL in the treatment group and increased from 40.42 to 50.81 pg/mL in the control group (P < .05), indicating that artificial liver therapy significantly decreased serum IL‐6. The median duration of viral nucleic acid persistence was 19 days in the treatment group (ranging from 6 to 67 days) and 17 days in the control group (ranging from 3 to 68 days), no significant difference was observed (P = .36). As of 28‐day follow‐up,17 patients in the treatment group experienced a median weaning time of 24 days, while 11 patients in the control group experienced a median weaning time of 35 days, with no significant difference between the two groups (P = .33). The 28‐day mortality rates were 16% (8/50) in the treatment group and 50.98% (26/51) in the control group, with a significant difference (z = 3.70, P < .001). Cytokine storm is a key factor in the intensification of COVID‐19 pneumonia. The artificial liver therapy blocks the cytokine storm by clearing inflammatory mediators, thus preventing severe cases from progressing to critically ill stages and markedly reducing short‐term mortality.
Intravitreal anti‐vascular endothelial growth factors, panretinal photocoagulation and combined treatment for proliferative diabetic retinopathy: a systematic review and network meta‐analysis
Authors: Fallico Matteo , Maugeri Andrea , Lotery Andrew , Longo Antonio , Bonfiglio Vincenza , Russo Andrea , Avitabile Teresio , Pulvirenti Alfredo , Furino Claudio , Cennamo Gilda , Barchitta Martina , Agodi Antonella , Reibaldi Michele 
Published: December 2020

AbstractPurposeTo conduct a systematic review with network meta‐analysis (NMA) of randomized clinical trials (RCTs) comparing panretinal photocoagulation (PRP) versus anti‐vascular endothelial growth factor (VEGF) treatment alone or in combination with PRP, for proliferative diabetic retinopathy (PDR).MethodsPubMed, Medline and Embase databases were searched for RCTs comparing PRP versus intravitreal anti‐VEGF therapy and/or combined PRP and intravitreal anti‐VEGF for PDR. The primary outcome measures were the mean best corrected visual acuity (BCVA) change and the regression of neovascularization. Mean change of central macular thickness (CMT), the subgroup analyses of patients without diabetic macular oedema (DME) and the rate of vitreous haemorrhage and vitrectomy were secondary outcomes. Frequentist NMAs were performed.ResultsTwelve RCTs were included. For the 12‐month mean BCVA change, NMA showed a better visual outcome in both the anti‐VEGF group and combined group compared to PRP [anti‐VEGF vs PRP, mean difference (MD) = 3.42; standard error (SE) = 1.5; combined vs PRP, MD = 3.92; SE = 1.65], with no difference between combined group and anti‐VEGF (MD = −0.50; SE = 1.87). No difference in neovascularization regression was found between PRP and anti‐VEGF alone or in combination with PRP, but there was significant inconsistency (p = 0.016). Subgroup analyses in patients without DME yielded no difference for the 12‐month visual outcome between the three interventions, but with significant inconsistency (p = 0.005).ConclusionThis NMA showed limited evidence of comparable efficacy in terms of neovascularization regression between PRP and anti‐VEGF therapy alone or in combination with PRP, but better visual outcomes were associated with anti‐VEGF use. Intravitreal anti‐VEGF therapy could be a valid therapeutic option in association with PRP.
Insights into multiple sclerosis‐associated uveitis: a scoping review
Authors: Casselman Pauline , Cassiman Cathérine , Casteels Ingele , Schauwvlieghe Pieter‐Paul 
Published: December 2020

AbstractPurposeThis paper is a scoping review of research on multiple sclerosis (MS)‐associated uveitis to determine its epidemiology, pathophysiology, clinical features and treatment.MethodsA comprehensive search of the medical databases MEDLINE (PubMed), EMBASE, Web of Science and Cochrane was carried out on 25 November 2019, to identify papers published between 1980 and 2019 that focus on patients with MS‐associated uveitis.ResultsBased on large cohort studies (n ≥ 1000), the prevalence of uveitis in patients with MS is estimated to be 0.53–1.34% (mean = 0.83%), and MS is diagnosed in 0.52–3.20% (mean = 1.30%) of patients with uveitis. The condition is most frequent among middle‐aged women. Patients usually complain of floaters and/or blurred vision, with bilateral intermediate uveitis (with retinal vasculitis) as the most frequent ophthalmological finding. Both MS and intermediate uveitis are associated with HLA‐DRB1*15:01 and IL‐2RA gene polymorphism rs2104286 A > G, suggesting a common genetic background. T cells, and possibly B cells, play an important role in both autoimmune disorders. Multiple sclerosis (MS)‐related uveitis is classically treated as non‐infectious uveitis, with corticosteroids as the first treatment step. Other treatments include immunosuppressants, cryotherapy, laser photocoagulation and vitrectomy. These treatment options have a limited, if any, effect on the course of MS and can be complicated by side‐effects. As treatment strategies for MS have increased in the last decade, it would be interesting to evaluate the efficacy of these new treatments during the course of uveitis. Moreover, the correlation between retinal periphlebitis and MS could be established more accurately with the recently developed techniques of wide‐field fluorescein angiography in a large cohort of MS patients.ConclusionMS‐associated uveitis is a rare, highly discussed pathology about which much is still unknown. Large epidemiological studies and extrapolation of new MS treatments to this condition are warranted.