bluuebunny/crossref_metadata_2025_split huggingface dataset:
The virome of bats inhabiting Brazilian biomes: knowledge gaps and biases towards zoonotic viruses
Authors: Wallau Gabriel Luz , Barbier Eder , Tomazatos Alexandru , Schmidt-Chanasit Jonas , Bernard Enrico 
Published: October 2022

AbstractBats are hosts of a large variety of viruses including some that may infect other vertebrates and humans. Research on bat-borne viruses attracted significant attention in recent years mainly due to epizootics caused by viruses having bats as hosts. The characterization of the viral communities of bats was then prioritized, but despite increasing efforts, there are large disparities in the geographical ranges covered and the methodologies employed around the world. As a result, large gaps remain in our current understanding of bat viromes and their role in disease emergence. This is particularly true for megadiverse regions in Latin America. This review aims to summarize the current understanding about bat-viruses that inhabit Brazilian biomes, one of the most bat species-rich and diverse regions of the globe. Taking into account all known bat-associated viral families studied in Brazilian biomes, we found that almost half of all bat species (86/181 species) were not investigated for viruses at all. Moreover, only a small fraction of viral lineages or families have been studied more in depth, usually employing targeted methods with limited power to characterize a broad virus diversity. Additionally, these studies relied on limited spatio-temporal sampling and small sample sizes. Therefore, our current understanding of bat viral communities in the Brazilian biomes is limited and biased at different levels, limiting zoonotic risk assessments of bat-borne viruses. Considering these limitations, we propose strategies to bridge the existing gaps in the near future.
Long-range inhibitory neurons mediate cortical neurovascular coupling
Authors: Ruff Catherine F. , Anaya Fernanda Juarez , Dienel Samuel J. , Rakymzhan Adiya , Altamirano-Espinoza Alain , Couey Jay , Watson Alan M. , Fish Kenneth N. , Hooks Bryan M. , Rubio Maria E. , Su Aihua , Ross Sarah E. , Vazquez Alberto L. 
Published: October 2022

AbstractNeuronal activity evokes a vascular response that is essential to sustain brain function. We show that neurovascular coupling (NVC) is mediated by long-range projecting GABAergic neurons that express Tacr1. Whisker stimulation elicited Tacr1 neuron activity in the barrel cortex through feed-forward excitatory pathways. Optogenetic activation of Tacr1 neurons elicited vasodilation, whereas inhibition significantly reduced whisker-evoked hemodynamic responses. Moreover, vasodilation was preceded by capillary pericyte activity, demonstrating a mechanism for NVC.
Pre-saccadic neural enhancements in marmoset area MT
Authors: Coop Shanna H. , Yates Jacob L. , Mitchell Jude F 
Published: October 2022

AbstractEach time we make an eye movement, attention moves before the eyes, resulting in a perceptual enhancement at the target. Recent psychophysical studies suggest that this pre-saccadic attention enhances the visual features at the saccade target, whereas covert attention causes only spatially-selective enhancements. While previous non-human primate studies have found that pre-saccadic attention does enhance neural responses spatially, no studies have tested if changes in neural tuning reflects an automatic feature enhancement. Here we examined pre-saccadic attention using a saccade foraging task developed for marmoset monkeys. We recorded from neurons in the middle temporal (MT) area with peripheral receptive fields that contained a motion stimulus which would either be the target of a saccade or a distracter as a saccade was made to another location. We established that marmosets, like macaques, show enhanced pre-saccadic neural responses for saccades towards the receptive field, including increases in firing rate and motion information. We then examined if the specific changes in neural tuning might support feature enhancements for the target. Neurons exhibited diverse changes in tuning, but predominantly showed additive and multiplicative increases that were uniformly applied across motion directions. These findings confirm that marmoset monkeys, like macaques, exhibit pre-saccadic neural enhancements during saccade foraging tasks with minimal training requirements. However, at the level of individual neurons, the lack of feature-tuned enhancements is similar to neural effects reported during covert spatial attention.Significance StatementAttention leads eye movements producing perceptual enhancements at saccade targets. Recent psychophysical studies indicate that increases in pre-saccadic sensitivity are concentrated around features of the target. We tested at the neural level how pre-saccadic attention modulates the tuning curves of visual neurons in area MT of marmoset monkeys. While neurons exhibited clear pre-saccadic enhancements that were consistent with previous studies in macaques, the changes in tuning were uniform across tuning. These results show pre-saccadic enhancements are a general feature of visual processing, shared by New World monkeys, but at the level of individual neuron’s enhancements are uniform across features much like what has been reported previously for covert attention.
TopFD - A Proteoform Feature Detection Tool for Top-Down Proteomics
Authors: Basharat Abdul Rehman , Zang Yong , Sun Liangliang , Liu Xiaowen 
Published: October 2022

AbstractTop-down liquid chromatography-mass spectrometry (LC-MS) analyzes intact proteoforms and generates mass spectra containing peaks of proteoforms with various isotopic compositions, charge states, and retention times. An essential step in top-down MS data analysis is proteoform feature detection, which aims to group these peaks into peak sets (features), each containing all peaks of a proteoform. Accurate protein feature detection enhances the accuracy in MS-based proteoform identification and quantification. Here we present TopFD, a software tool for top-down MS feature detection that integrates algorithms for proteoform feature detection, feature boundary refinement, and machine learning models for proteoform feature evaluation. We performed extensive benchmarking of TopFD, Promex, FlashDeconv, and Xtract using five top-down MS data sets and demonstrated that TopFD outperforms other tools in feature accuracy, reproducibility, and feature abundance reproducibility.
A Parametric Blueprint for Optimum Cochlear Outer Hair Cell Design
Authors: Rabbitt Richard D. , Bidone Tamara C. 
Published: October 2022

AbstractThe present work examines the hypothesis that cochlear outer hair cell (OHC) properties vary in precise proportions along the tonotopic map to optimize electro-mechanical power conversion. We tested this hypothesis using a very simple model of a single isolated OHC driving a mechanical load. Results identify three nondimensional ratios that are predicted to optimize power conversion: the ratio of the resistive-capacitive (RC) corner to the characteristic frequency (CF), the ratio of nonlinear to linear capacitance, and the ratio of OHC stiffness to cochlear load stiffness. Optimum efficiency requires all three ratios to be universal constants, independent of CF and species. The same ratios are cardinal control parameters that maximize power output by positioning the OHC operating point on the edge of a dynamic instability. Results support the hypothesis that OHC properties evolved to optimize electro-mechanical power conversion. Identification of the RC corner frequency as a control parameter reveals a powerful mechanism used by medial olivocochlear efferent system to control OHC power output. Results indicate the upper frequency limit of OHC power output is not constrained by the speed of the motor itself, but instead is likely limited by the size of the nucleus and membrane surface area available for ion-channel expression.
Staphylococcus lugdunensisand Coagulase-Negative Staphylococci species characterisation in a tropical climate
Authors: Howes Matthew , Baird Rob 
Published: October 2022

AbstractCoagulase negative staphylococci (CoNS) are a heterogeneous group of colonising organisms that have historically been differentiated from Staphyloccocus aureus but are now known to cause invasive disease. We characterised the CoNS species from a single tropical centre to compare with previous studies. 1262 isolates were collected with 203 from blood stream samples over an 18 month period. S. lugdunensis was the second most isolated CoNS comprising 15.9% of isolates, much greater than comparative studies. A single blood stream infection with S. lugdunensis was identified over this time period, comprising a much lower ratio of blood to swab isolates than in previous studies.
Residential clustering of COVID-19 cases and efficiency of building-wide compulsory testing notices as a transmission control measure in Hong Kong
Authors: Young Benjamin R. , Yang Bingyi , Wu Peng , Adam Dillon C. , Wong Jessica Y. , Ho Faith , Gao Huizhi , Lau Eric H. Y. , Leung Gabriel M. , Cowling Benjamin J. 
Published: October 2022

ABSTRACTBackgroundDespite relatively few reports of residential case clusters of COVID-19, building-wide compulsory testing notices on residential apartment blocks are frequently applied in Hong Kong with the aim of identifying cases and reducing transmission.MethodsWe aimed to describe the frequency of residential case clusters and the efficiency of compulsory testing notices in identifying cases. The residences of locally infected COVID-19 cases in Hong Kong were grouped to quantify the number of cases per residence.Buildings targeted in compulsory testing notices were matched with the residence of cases to estimate the number of cases identified.ResultsWe found that most of the residential buildings (4246/7688, 55.2%) with a confirmed COVID-19 case had only one reported case. In the fourth and the fifth epidemic wave in Hong Kong, we estimated that compulsory testing notices detected 29 cases (95% confidence interval: 26, 32) and 46 cases (44, 48) from every 100 buildings tested (each with hundreds of residents), respectively. Approximately 13% of the daily reported cases were identified through compulsory testing notices.ConclusionsCompulsory testing notices can be an essential method when attempting to maintain local elimination (‘zero covid’) and most impactful early in an epidemic when the benefit remains of stemming a new wave. Compulsory testing therefore appears to be a relatively inefficient control measure in response to sustained community transmission in the community.
Enhancer/gene relationships: need for more reliable genome-wide reference sets
Authors: Hoellinger Tristan , Mestre Camille , Aschard Hugues , Goff Wilfried Le , Foissac Sylvain , Faraut Thomas , Djebali Sarah 
Published: October 2022

AbstractDifferences in cells’ functions arise from differential action of regulatory elements, in particular enhancers. Like promoters, enhancers are genomic regions bound by transcription factors (TF) that activate the expression of one or several genes by getting physically close to them in the 3D space of the nucleus. As there is increasing evidence that variants associated with common diseases are located in enhancers active in cell types relevant to these diseases, knowing the set of enhancers and more importantly the sets of genes activated by each enhancer (the so-called enhancer/gene or E/G relationships) in a cell type, will certainly help understanding these diseases.There are three broad approaches for the genome-wide identification of E/G relationships in a cell type: (1) genetic link methods or eQTL, (2) functional link methods based on 1D functional data such as open chromatin, histone mark and gene expression and (3) spatial link methods based on 3D data such as HiC. Since (1) and (3) are costly, there has been a focus on developing functional link methods and using data from (1) and (3) to evaluate them, however there is still no consensus on the best functional link method to date.For this reason we decided to start from the two latest benchmarks of the field, namely from the CRISPRi-FlowFISH (CRiFF) technique and from 3D and eQTL data inBENGI, and to evaluate the two methods claimed to be the best one on each of these benchmark studies, namely theABC modeland theAverage-Rankmethod respectively, on the other method’s reference data. Not only did we manage to reproduce the results of the two benchmarks but we also saw that none of the two methods performed best on the two reference data. WhileCRiFFreference data are very reliable, it is not genome-wide and is mostly available on a cancer cell type. On the other handBENGIis genome-wide but may contain many false positives. This study therefore calls for new reliable and genome-wide E/G reference data rather than new functional link E/G identification methods.
A Generalizable Nanopore Sensor for Highly Specific Protein Detection at Single-Molecule Precision
Authors: Ahmad Mohammad , Ha Jeung-Hoi , Mayse Lauren A. , Presti Maria F. , Wolfe Aaron J. , Moody Kelsey J. , Loh Stewart N. , Movileanu Liviu 
Published: October 2022

AbstractProtein detection and biomarker profiling have wide-ranging implications in many areas of basic research and molecular diagnostics. Substantial progress has been made in protein analytics using nanopores and the resistive-pulse technique. Yet, a long-standing challenge is implementing specific binding interfaces for detecting proteins without the steric hindrance of the pore interior. To overcome this technological difficulty, we formulate a new class of sensing elements made of a programmable antibody-mimetic binder fused to a monomeric protein nanopore. This way, such a modular design significantly expands the utility of nanopore sensors to numerous proteins while preserving their architecture, specificity, and sensitivity. We prove the power of this approach by developing and validating nanopore sensors for protein analytes that drastically vary in size, charge, and structural complexity. These analytes produce unique electrical signatures that depend on their identity and quantity and the binder-analyte assembly at the nanopore tip. From a practical point of view, our sensors unambiguously probe protein recognition events without the necessity of using any additional exogenous tag. The outcomes of this work will impact biomedical diagnostics by providing a fundamental basis and tools for protein biomarker detection in biofluids.
Protocol for the development of a meta-core outcome set for stillbirth prevention and bereavement care following stillbirth
Authors: Dube Kushupika , Ayebare Elizabeth , Bakhbakhi Danya , Bedwell Carol , Chandriah Savitha , Chaudhry Nasim , Chilinda Ides , Chimwaza Angela , Goshomi Unice , Laisser Rose , Lavender Tina , Mills Tracey A , Fattepur Sudhindrashayana , Vwalika Bellington , Wakasiaka Sabina , Kirkham Jamie J 
Published: October 2022

AbstractIntroductionA stillbirth is the death of a baby before or during birth and accounts for about 14 in every 1,000 births globally with the highest rates seen in Sub-Saharan Africa and South Asia. Stillbirth prevention and bereavement care following stillbirth remains a challenge, particularly in Low-Middle Income Countries (LMiC). One approach to improvement is the prioritisation of women/family-centred care. However, there are a large variety of outcomes measured in stillbirth studies and consensus on the outcomes that matter most to women and families is often lacking, which can impact on the ability to make informed decisions about improved care practices. To help mitigate this problem, a core outcome set (COS) has been developed for stillbirth prevention and another COS has recently been finalised for care after stillbirth. Despite the majority of stillbirths occurring in LMiC involvement in these studies is ‘tokenistic’ and therefore the outcomes may not reflect the needs of parents or communities in these settings. The aim is to develop standard sets of outcomes for use in all interventional studies for stillbirth prevention and bereavement care using participants from predominantly Sub-Saharan Africa and South Asia, where the burden of stillbirth is highest.Methods/DesignThis study will involve three stages in the development of the COS: (1) a list of outcomes will be identified from multiple sources, specifically existing reviews of outcomes and a targeted qualitative literature review of studies that have interviewed parents who have experienced stillbirth and healthcare professionals working in this field across Sub-Saharan Africa and South Asia. (2) The list of outcomes will first be reviewed by in-country leads and scored by multiple stakeholder groups in a real-time online Delphi survey. (3) The results of the Delphi will be summarised and discussed at a face-to-face or virtual consensus meeting with representation from all stakeholder groups.DiscussionAs well as improving the consistency of outcomes for future research in an LMiC setting, these COS will harmonise with the existing COS in this field developed in a high income setting. The final output will be a global ‘meta-COS’, a recommended set of outcomes that can be used in stillbirth research worldwide.
Ultrasound versus fluoroscopy as imaging guidance for percutaneous nephrolithotomy: A systematic review and meta-analysis
Authors: Bahri Razman Arabzadeh , maleki Saba , Shafiee Arman , Shobeiri Parnian 
Published: October 2022

AbstractObjectivesTo determine whether the outcomes of ultrasound-guided percutaneous nephrolithotomy (UG-PCNL), an alternative to traditional fluoroscopy-guided percutaneous nephrolithotomy (FG-PCNL), are comparable.MethodsA systematic search of PubMed, Embase, and the Cochrane Library was carried out to discover investigations comparing UG-PCNL to FG-PCNL, and accordingly, a meta-analysis of those studies was performed. The primary outcomes included the stone-free rate (SFR), overall complications based on Clavien-Dindo classification, duration of surgery, duration of patients’ hospitalization, and hemoglobin (Hb) drop during the surgery. All statistical analyses and visualizations were implemented utilizing R software.ResultsNineteen studies, including eight randomized clinical trials (RCTs) and eleven observational cohorts, comprising 3016 patients (1521 UG-PCNL patients) and comparing UG-PCNL with FG-PCNL met the inclusion criteria of the current study. Considering SFR, overall complications, duration of surgery, duration of hospitalization, and Hb drop, our meta-analysis revealed no statistically significant difference between UG-PCNL and FG-PCNL patients, with p-values of 0.29, 0.47, 0.98, 0.28, and 0.42, respectively. Significant differences were discovered between UG-PCNL and FG-PCNL patients in terms of the length of time they were exposed to radiation (p-value< 0.0001). Moreover, FG-PCNL had shorter access time than UG-PCNL (p-value= 0.04).ConclusionUG-PCNL provides the advantage of requiring less radiation exposure while being just as efficient as FG-PCNL; thus, this study suggests prioritizing the use of UG-PCNL.
WITHDRAWN: Molecular characterization of enolase fromHaemaphysalis longicornistick
Authors: Haque Md. Samiul , Rahman Md. Khalesur , Islam Mohammad Saiful , You Myungjo 
Published: October 2022

Withdrawal StatementThe authors have withdrawn their manuscript owing tofor more improvement in our research work and need to revise our manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
SARS-CoV-2 infection in domestic rats after transmission from their infected owner
Authors: Montagutelli Xavier , Decaudin Bérénice , Beretta Maxime , Mouquet Hugo , Simon-Lorière Etienne 
Published: October 2022

AbstractWe report the transmission of SARS-CoV-2 Omicron variant from a COVID-19 symptomatic individual to two domestic rats, one of which developed severe symptoms. Omicron carries several mutations which permit rodent infection. This report demonstrates that pet, and likely wild, rodents could therefore contribute to SARS-CoV-2 spread and evolution.
A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike
Authors: Dadonaite Bernadeta , Crawford Katharine H D , Radford Caelan E , Farrell Ariana G , Yu Timothy C , Hannon William W , Zhou Panpan , Andrabi Raiees , Burton Dennis R , Liu Lihong , Ho David D. , Neher Richard A. , Bloom Jesse D 
Published: October 2022

AbstractA major challenge in understanding SARS-CoV-2 evolution is interpreting the antigenic and functional effects of emerging mutations in the viral spike protein. Here we describe a new deep mutational scanning platform based on non-replicative pseudotyped lentiviruses that directly quantifies how large numbers of spike mutations impact antibody neutralization and pseudovirus infection. We demonstrate this new platform by making libraries of the Omicron BA.1 and Delta spikes. These libraries each contain ~7000 distinct amino-acid mutations in the context of up to ~135,000 unique mutation combinations. We use these libraries to map escape mutations from neutralizing antibodies targeting the receptor binding domain, N-terminal domain, and S2 subunit of spike. Overall, this work establishes a high-throughput and safe approach to measure how ~105combinations of mutations affect antibody neutralization and spike-mediated infection. Notably, the platform described here can be extended to the entry proteins of many other viruses.
In silicocharacterization of cysteine-stabilized αβ defensins from neglected unicellular microeukaryotes
Authors: Senra Marcus Vinicius Xavier 
Published: October 2022

AbstractBackgroundThe emergence of multi-resistant pathogens have increased dramatically in recent years, becoming a major public-health concern. Among other promising antimicrobial molecules with potential to assist in this worldwide struggle, cysteine-stabilized αβ (CS-αβ) defensins are attracting attention due their efficacy, stability, and broad spectrum against viruses, bacteria, fungi, and protists, including many known human pathogens.ResultsHere, 23 genomes of ciliated protists were screened and three CS-αβ defensins with a likely antifungal activity were identified and characterized using bioinformatics from two freshwater and culturable speciesLaurentiellasp. (LsAMP-1 and LsAMP-2) andEuplotes focardii(EfAMP-1). Although any potential cellular ligand could be predicted for LsAMP-2 and EfAMP-1; evidences from structural, molecular dynamics, and docking analyses suggest that LsAMP-1 may form stably associations with phosphatidylinositol 4,5-bisphosphates (PIP2), a phospholipid found on many eukaryotic cells, which could, in turn, represent an anchorage mechanism within plasma membrane of targeted cells.ConclusionThese data stress that more biotechnology-oriented studies should be conducted on neglected protists, such ciliates, which could become valuable sources of novel bioactive molecules for therapeutic uses.