bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spiking network model of A1 learns temporal filters with frequency preferences
Authors: Roedel Danielle , Brinkman Braden A. W. 
Published: July 2023

AbstractThe sparse coding hypothesis has successfully predicted neural response properties of several sensory brain areas. For example, sparse basis representations of natural images match edge-detecting receptive fields observed in simple cells of primary visual cortex (V1), and sparse representations of natural sounds mimic auditory nerve waveforms. SAILnet, a leaky integrate-and-fire network model (“Sparse and Independently Local network”) has previously been shown to learn simple V1 receptive fields when trained on natural images. Experimental work rewiring visual input to auditory cortex found that auditory neurons developed visual response properties, suggesting that developmental rules may be shared across sensory cortices.In this work we adapt SAILnet to train it on waveforms of auditory sounds and learn temporal receptive fields (filters), in contrast with previous work that trained SAILnet or other network models on spectrograms. In our model network of primary auditory cortex (A1) neurons receive synaptic current from input neurons who temporally filter the direct sound waveforms. To show the network learns frequency-dependent filters naturally, we do not parametrize the temporal filters, and only restrict the total number of time points in the filters. To make training feasible, we simplify the model to a single input neuron and 768 A1 neurons, and we train the network on “lo-fi” music, whose spectral power is limited to frequencies of∼10, 000 Hz or less, giving a manageable temporal resolution of the stimulus and filters. The learned filters develop distinct frequency preferences, and reconstruction of novel stimuli captures the low-frequency content of signals in reasonable detail, with audio playback capturing clear aspects of the original stimulus. Lastly, our work also has a pedagogical benefit: the learned stimulus features can be played as sounds, which aids in teaching sensory coding to learners with visual impairments who cannot perceive stimulus features learned by V1 models.
Second-order boundaries segment more easily when they are density-defined rather than feature-defined
Authors: DiMattina Christopher 
Published: July 2023

ABSTRACTPrevious studies have demonstrated that density is an important perceptual aspect of textural appearance to which the visual system is highly attuned. Furthermore, it is known that density cues not only influence texture segmentation, but can enable segmentation by themselves, in the absence of other cues. A popular computational model of texture segmentation known as the “Filter-Rectify-Filter” (FRF) model predicts that density should be a second-order cue enabling segmentation. For a compound texture boundary defined by superimposing two single-micropattern density boundaries, a version of the FRF model in which different micropattern-specific channels are analyzed separately by different second-stage filters makes the prediction that segmentation thresholds should be identical in two cases: (1) Compound boundaries with an equal number of micropatterns on each side but different relative proportions of each variety (compound feature boundaries) and (2) Compound boundaries with different numbers of micropatterns on each side, but with each side having an identical number of each variety (compound density boundaries). We directly tested this prediction by comparing segmentation thresholds for second-order compound feature and density boundaries, comprised of two superimposed single-micropattern density boundaries comprised of complementary micropattern pairs differing either in orientation or contrast polarity. In both cases, we observed lower segmentation thresholds for compound density boundaries than compound feature boundaries, with identical results when the compound density boundaries were equated for RMS contrast. In a second experiment, we considered how two varieties of micropatterns summate for compound boundary segmentation. In the case where two single micro-pattern density boundaries are superimposed to form a compound density boundary, we find that the two channels combine via probability summation. By contrast, when they are superimposed to form a compound feature boundary, segmentation performance is worse than for either channel alone. From these findings, we conclude that density segmentation may rely on neural mechanisms different from those which underlie feature segmentation, consistent with recent findings suggesting that density comprises a separate psychophysical ‘channel’.
Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams
Authors: Campbell Bronwyn C. , Greenfield Paul , Gong Se , Midgley David J. , Paulsen Ian T. , George Simon C. 
Published: July 2023

ABSTRACTBiogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study used coal seam metagenomes to reconstruct important metagenome-assembled genomes (MAGs) using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene (bcrABCD). Three taxa were identified with this genetic potential. The first was a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota sp. contained a full set of genes for benzoyl-CoA dearomatisation, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common within this phylum, and thus they may be important organisms for the liberation of recalcitrant carbon on a global scale. Further, two taxa from the Deltaproteobacteria class were also implicated in monoaromatic degradation; two geographically unrelatedSyntrophorhabdus aromaticivoransMAGs, and a Syntrophaceae sp. MAG. Each of these three taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides an understanding of their function within the coal seam microbiome, and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic carbon cycling and emissions.ImportanceSubsurface coal seams are highly anoxic and oligotrophic environments, where the main source of carbon is “locked away” within aromatic rings. Despite these challenges, biogenic methane accumulates within many of these coal seams, which implies that the coal seam microbiome can “unlock” this carbon sourcein situ. For over two decades, researchers have been working to understand which organisms are responsible for these processes. This study provides the first descriptions of these organisms. Here, we report metagenomic insights into the liberation of carbon from aromatic molecules typically found within coal, the degradation pathways involved, and descriptions of the Krumholzibacteriota sp.,Syntrophorhabdus aromaticivorans, and Syntrophaceae sp. that contain this genetic potential. Additionally, this is the first time that the Krumholzibacteriota phylum has been implicated in anaerobic dearomatisation of aromatic hydrocarbons. This potential is identified here in numerous taxa within the phylum from other subsurface environments, implicating Krumholzibacteriota in global-scale carbon-cycling processes.
The Role of Attention in Immersion: The Two–Competitor Model
Authors: Strauss Daniel J. , Francis Alexander L. , Vibell Jonas , Corona–Strauss Farah I. 
Published: July 2023

AbstractCurrently, we face an exponentially increasing interest in immersion, especially sensory–driven immersion, mainly due to the rapid development of ideas and business models centered around a digital virtual universe as well as the increasing availability of affordable immersive technologies for education, communication, and entertainment. However, a clear definition of ‘immersion’, in terms of established neurocognitive concepts and measurable properties, remains elusive, slowing research on the human side of immersive interfaces.To address this problem, we propose a conceptual, taxonomic model of attention in immersion. We argue (a) modeling immersion theoretically as well as studying immersion experimentally requires a detailed characterization of the role of attention in immersion, even though (b) attention, while necessary, cannot be a sufficient condition for defining immersion. Our broader goal is to characterize immersion in terms that will be compatible with established psychophysiolgical measures that could then in principle be used for the assessment and eventually the optimization of an immersive experience. We start from the perspective that immersion requires the projection of attention to an induced reality, and build on accepted taxonomies of different modes of attention for the development of our two–competitor model. The two–competitor model allows for a quantitative implementation and has an easy graphical interpretation. It helps to highlight the important link between different modes of attention and affect in studying immersion.
What explains the high island endemicity of PhilippineRafflesia? A species distribution modeling analysis of three threatened parasitic plant species and their hosts
Authors: Obico Jasper J.A. , Lapuz R. Sedricke C. , Barcelona Julie F. , Pelser Pieter B. 
Published: July 2023

ABSTRACTPremiseRafflesiaare rare holoparasitic plants. In the Philippines, all but one species are found only on single islands. This study aimed to better understand the factors contributing to this distribution pattern. Specifically, we sought to determine whether narrow environmental tolerances of host and/or parasite species might explain their island endemicity.MethodsWe used Maxent species distribution modeling to identify areas with suitable habitat forR. lagascae,R. lobata, andR. speciosaand theirTetrastigmahost species. These analyses were carried out for current climate conditions as well as two future climate change scenarios.Key resultsWhereas species distribution models indicated suitable environmental conditions for theTetrastigmahost species in many parts of the Philippines, considerably fewer areas have suitable conditions for the threeRafflesiaspecies. Some of these areas are found on islands from which they have not been reported. All three species will face significant threats as a result of climate change.ConclusionsOur results suggest that limited inter-island dispersal abilities and/or specific environmental requirements are likely responsible for the current pattern of island endemicity of the threeRafflesiaspecies, rather than the environmental requirements of theirTetrastigmahost species.
Latent EBV impairs immune cell signaling and enhances the efficacy of anti-CD3 mAb in Type 1 Diabetes
Authors: Delgado Ana Lledo , Preston-Hurlburt Paula , Lim Noha , Sumida Tomokazu S. , Long S. Alice , McNamara James , Serti Elisavet , Higdon Lauren , Herold Kevan C. 
Published: July 2023

SummaryTeplizumab has been approved for the delay of the onset of type 1 diabetes and may modulate new onset disease. We found that patients who were EBV positive at baseline had a more robust response to drug in two clinical trials and therefore postulated that latent virus has general effects in modifying immune responses. We compared the phenotypes, transcriptomes, and development of peripheral blood cells before and after teplizumab treatment. Higher number of Tregs and partially exhausted CD8+T cells were found in EBV seropositive individuals at the baseline in the TN10 trial and AbATE trial. Single cell transcriptomics and functional assays identified downregulation of the T cell receptor and other signaling pathways before treatment. Impairments in function of adaptive immune cells were enhanced by teplizumab treatment in EBV seropositive individuals. Our data indicate that EBV can impair signaling pathways generally in immune cells, that broadly redirect cell differentiation.
Healthcare Stakeholder Perspectives on a Value Assessment Approach for Duchenne Muscular Dystrophy Therapies
Authors: Fischer Ryan , Furlong Pat , Kennedy Annie , Maynard Kelly , Penrod Marissa , Miller Debra , Laverty Chamindra G. , Lowes Linda , Kuntz Nancy L. , Shieh Perry B. , Kondejewski Jane , Neumann Peter J. , Shafrin Jason , Willke Richard J. 
Published: July 2023

ABSTRACTBACKGROUNDTraditional value assessment frameworks are challenged in comprehensively assessing the societal value new therapies bring to individuals with rare, progressive, genetic, fatal, neuromuscular diseases such as Duchenne muscular dystrophy (DMD).OBJECTIVETo identify how value assessment frameworks may need to be adapted to measure the value to society of DMD therapies.METHODSThree groups of stakeholders (patient advocates, clinicians, health economists) participated in semi-structured interviews around the International Society for Pharmacoeconomics and Outcomes Research’s Value Flower, which includes elements of value that can be considered within value assessments of healthcare technologies.RESULTSAll stakeholders agreed that traditional value assessment frameworks based on the quality-adjusted life year (QALY) are narrow and will undervalue new DMD therapies. All stakeholders expressed some level of concern that use of the QALY as a key metric of value discriminates against patients with severe progressive diseases and disabilities. Some stakeholders saw value in using the QALY for cross-disease comparisons in resource-constrained environments if the methodology was appropriate. All stakeholders recommended considering additional elements of value in decision-making around new DMD therapies. These elements reflect: the economic and humanistic costs incurred by patients, caregivers, and families with Duchenne, such as indirect out-of-pocket costs, lost productivity, and family spillovers; the attributes that are meaningful for individuals with disabilities and high unmet need, such as severity of disease, value of hope, and real option value; and factors that contribute to improvements in population health, such as insurance value, equity, and scientific spillovers.CONCLUSIONSThese findings highlight the need to expand traditional value assessment frameworks and take a holistic approach that incorporates the perspectives of individuals with Duchenne, caregivers, clinicians, and heath economists when assessing the societal value of new DMD therapies. Broadening value assessment will prevent restricted or delayed access to therapies for individuals with Duchenne.
Unleashing the Power of Language Models in Clinical Settings: A Trailblazing Evaluation Unveiling Novel Test Design
Authors: Li Qian , Tang Kang , Li Sen , Zhang Kaihua , Li Zhantao , Chang Lufan , Li Wenxue , Shen Bingzhi , Ding Jia , Min Xianjun 
Published: July 2023

AbstractThe realm of clinical medicine stands on the brink of a revolutionary breakthrough as large language models (LLMs) emerge as formidable allies, propelled by the prowess of deep learning and a wealth of clinical data. Yet, amidst the disquieting specter of misdiagnoses haunting the halls of medical treatment, LLMs offer a glimmer of hope, poised to reshape the landscape. However, their mettle and medical acumen, particularly in the crucible of real-world professional scenarios replete with intricate logical interconnections, re-main shrouded in uncertainty. To illuminate this uncharted territory, we present an audacious quantitative evaluation method, harnessing the ingenuity of tho-racic surgery questions as the litmus test for LLMs’ medical prowess. These clinical questions covering various diseases were collected, and a test format consisting of multi-choice questions and case analysis was designed based on the Chinese National Senior Health Professional Technical Qualification Examination. Five LLMs of different scales and sources were utilized to answer these questions, and evaluation and feedback were provided by professional thoracic surgeons. Among these models, GPT-4 demonstrated the highest performance with a score of 48.67 out of 100, achieving accuracies of 0.62, 0.27, and 0.63 in single-choice, multi-choice, and case-analysis questions, respectively. However, further improvement is still necessary to meet the passing threshold of the examination. Additionally, this paper analyzes the performance, advantages, disadvantages, and risks of LLMs, and proposes suggestions for improvement, providing valuable insights into the capabilities and limitations of LLMs in the specialized medical domain.
Exploring the use of preprints in dentistry
Authors: Sarkis-Onofre Rafael , Girotto Carolina , Agostini Bernardo Antonio 
Published: July 2023

AbstractObjective:This study aims to assess the use, impact, and dissemination of preprints in dentistry.Methods:This is a meta-research study with a cross-sectional design. We included preprints published in dentistry, regardless of the year of publication. Searches were performed in themedRxiv.organdPreprints.orgplatforms and restricted to English. One researcher extracted the data, and another researcher verified data consistency. The following data were extracted: year of publication, country of the corresponding author, number of abstract and full-text views and downloads, Altmetric attention score, whether the preprint was mentioned in other servers such as Twitter and Publons, number of mentions in other servers, number of citations in the Dimensions database, and whether the preprint had already been published in a peer-reviewed journal. If already published, we extracted the journal’s impact factor (JCR 2021) and the number of citations in the Dimensions database. We conducted a descriptive analysis of the extracted characteristics and explored relationships between metrics using the Spearman correlation.Results:We identified 276 preprints. Most of the studies were published between 2020 and 2022 (n= 229), especially those from ten countries. The most-cited preprint and published article are the same study. Only the correlation between the number of preprint citations and peer-reviewed article citations in the Dimensions database showed a large positive association (Spearman’s rho = 0.5809).Conclusion:Preprints gained popularity over the last several years due to the COVID-19 pandemic and reached a larger audience, especially on platforms such as Twitter.Clinical Significance:Preprint publishing allows faster dissemination of science for the benefit of society.
Changes in Masking Policies in US Healthcare Facilities in the First Quarter of 2023: Do COVID-19 Cases, Hospitalizations, or Local Political Preferences Predict Loosening Restrictions?
Authors: Miller Sarah L. , Prasad Vinay 
Published: July 2023

AbstractIntroductionIn the first half of 2023, many US healthcare facilities updated their policies on the required use of face masks by patients and employees. Despite statewide lifts of mask mandates in healthcare settings, the decisions by individual healthcare facilities have remained controversial and inconsistent. We sought to understand these decisions by examining COVID-19 case rates, hospitalization rates, and political affiliation, among counties where hospitals reported updated masking policies in news or social media posts.MethodsWe searched Twitter, Facebook, and Google for news stories related to changes in US healthcare facility masking policies between February 1st and April 30th, 2023. We extracted county-level COVID-19 cases and hospitalizations using data from the CDC and political affiliation was measured using the 2020 presidential election results. We performed logistic regression using COVID-19 cases, hospitalizations, and political affiliation as predictors and a complete lifting of masking requirements as the outcome.ResultsWe found that the odds of lifting the mask requirement was not associated with COVID-19 cases (OR 1.00, 95% CI 0.97 - 1.02, p-value = 0.54), or hospitalizations (OR 1.06 95% CI 0.88-1.27, p-value = 0.33). We found that for every 10% increase in Republican votes in the 2020 presidential election, there was a 1.33 (95% CI 1.07 - 1.64, p-value = 0.01) increase in odds of having lifted masking requirements completely.DiscussionWe found that the odds of lifting the face mask requirement in healthcare facilities was not associated with COVID-19 cases or hospitalizations but was associated with county-level political affiliation. Our results raise the concern that public health measures may be increasingly seen as political gestures or a response to local political factors.
Implementation of risk triaging in primary healthcare facilities in Sub-Saharan Africa: A systematic review
Authors: Maskew Mhairi , Sande Linda Alinafe , Benade Mariet , Ntjiekelane Vinolia , Scott Nancy , Flynn David , Rosen Sydney 
Published: July 2023

ABSTRACTBackgroundOne challenge facing treatment programs for HIV and other chronic conditions in sub-Saharan Africa (SSA) is how to target interventions to optimize retention in care and other outcomes. Most efforts to target interventions have identified predictive features among high risk patients after negative outcomes have already been observed. An alternative for identifying patients at high risk of negative outcomes is “risk triaging,” or identifying vulnerable or higher risk patients before they experience an interruption in care or other negative outcome. We conducted a systematic review of the use of risk triaging tools at the primary healthcare (PHC) level in SSA.MethodsWe searched PubMed and other databases for publications after 1 January 2012 that reported development or implementation of risk triaging tools for PHC use in SSA. We extracted information on three outcomes: 1) characterization of the risk triaging tools; 2) tool performance metrics (sensitivity, specificity, positive and negative predictive value, area under the curve); and 3) health system effects (efficiency, acceptability, resource utilization, cost). We report outcomes for each eligible study and identify lessons for use of risk triaging.ResultsOf 1,876 articles identified, 28 were eligible for our review. Thirteen addressed HIV, 10 TB, 1 TB/HIV, and 4 other conditions. Approximately 60% used existing, retrospective data to identify important risk factors for an outcome and then construct a scoring system, but no implementation of these tools was reported. The remaining 40% designed a tool using existing data or experience and reported implementation results. More than half (16/28, 58%) of the tools achieved sensitivities >80%; specificity was much lower. Only one tool, the World Health Organization’s 4-symptom screen for tuberculosis, had been scaled up widely. While most studies claimed that their tools could increase the efficiency of healthcare delivery, none of the studies provided examples of tangible health system impacts.ConclusionMost of the tools identified were at least somewhat successful in identifying potential risks but uptake by health systems has been minimal. Although well-designed risk triaging tools have the potential to improve health outcomes, implementation will require commitment at the policy, operational, and funding levels.