bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signal processing basics applied to Ecoacoustics
Authors: Sanchez-Gendriz Ignacio 
Published: January 2021

AbstractEcoacoustics is a research field that has attracted attention of researchers from areas as diverse as ecology, biology, engineering, and human sciences, to cite a few. Ecoacoustics studies the sounds that emanates from the environments, by gaining insights of landscape dynamics from acoustic patterns and particularities at different places. With recent advance in technology, it is common to obtain sound datasets recorded 24-h a day for several months. The analysis of these long-term sound recordings represents several challenges. Investigators already involved in acoustic are familiar with signal processing methods, which are essential tools for sound analysis. However, in general beginners interested in Ecoacoustics do not share this background formation. The present work illustrates basic topics of digital signal processing in a comprehensible style, and an effective pipeline for long-term sound explorative data analysis (EDA) is presented. Finally, the described signal processing fundamentals are applied for EDA of 1-month underwater acoustic data recorded in a Brazilian marine protected area. The Matlab codes used for the analysis will be available as supplementary material.
Differential Gene Expression Pipeline for Whole Transcriptome RNA-Seq Data using Personal Computer
Authors: Saif Rashid , Ejaz Aniqa , Mahmood Tania , Zia Saeeda 
Published: January 2021

ABSTRACTAdvances in the next generation sequencing (NGS) technologies, their cost effectiveness and well-developed pipelines using computational tools/softwares has allowed researchers to reveal ground-breaking discoveries in multi-omics data analysis. However, there is still uncertainty due to massive upsurge in parallel tools and difficulty in choosing best practiced pipeline for expression profiling of RNA sequenced (RNA-seq) data. Here, we detail the optimized pipeline that works at a fast pace with enhanced accuracy on personal computer rather than using cloud or high-performance computing clusters (HPC). The steps include quality check, base filtration, quasi-mapping, quantification of samples, estimation and counting of transcript/gene expression abundances, identification and clustering of differentially expressed features and visualization of the data. The tools FastQC, Trimmomatic, Salmon and some other scripts in Trinity toolkit were applied on two paired-end datasets. An extension of this pipeline may also be formulated in future for the gene ontology enrichment analysis and functional annotation of the differential expression matrix to make this data biologically more significant.
ModifiedE. colistrains enhance baculovirus production by elimination of aberrant transposition events
Authors: Grose Carissa , Wright Chelsea , Mehalko Jennifer , Esposito Dominic 
Published: January 2021

AbstractBaculovirus technology has been the most commonly used expression system for insect cells both due to its potential to generate a large amount of recombinant protein as well as the benefit of post-translational modifications. The most commonly used system to generate recombinant baculoviruses is the Tn7 transposition-based technology known as Bac-to-Bac. Although improvements have been made to this system to further improve quality and reproducibility of baculovirus production, recent data suggests that improved strains still have potential issues with contamination of non-recombinant baculovirus caused by improper transposition into a Tn7 site in theE. colichromosome. Here we describe a new option for alteration of theE. coligenome to completely block the native Tn7 attachment site, leading to far fewer false positive bacmid colonies being selected and eliminating all risk of non-recombinant baculovirus production.
Graph Contextualized Attention Network for Predicting Synthetic Lethality in Human Cancers
Authors: Long Yahui , Wu Min , Liu Yong , Zheng Jie , Kwoh Chee Keong , Luo Jiawei , Li Xiaoli 
Published: January 2021

AbstractMotivationSynthetic Lethality (SL) plays an increasingly critical role in the targeted anticancer therapeutics. In addition, identifying SL interactions can create opportunities to selectively kill cancer cells without harming normal cells. Given the high cost of wet-lab experiments, in silico prediction of SL interactions as an alternative can be a rapid and cost-effective way to guide the experimental screening of candidate SL pairs. Several matrix factorization-based methods have recently been proposed for human SL prediction. However, they are limited in capturing the dependencies of neighbors. In addition, it is also highly challenging to make accurate predictions for new genes without any known SL partners.ResultsIn this work, we propose a novelgraph contextualized attention networknamed GCATSL to learn gene representations for SL prediction. First, we leverage different data sources to construct multiple feature graphs for genes, which serve as the feature inputs for our GCATSL method. Second, for each feature graph, we design node-level attention mechanism to effectively capture the importance of local and global neighbors and learn local and global representations for the nodes, respectively. We further exploit multi-layer perceptron (MLP) to aggregate the original features with the local and global representations and then derive the feature-specific representations. Third, to derive the final representations, we design feature-level attention to integrate feature-specific representations by taking the importance of different feature graphs into account. Extensive experimental results on three datasets under different settings demonstrate that our GCATSL model outperforms 14 state-of-the-art methods consistently. In addition, case studies further validate the effectiveness of our proposed model in identifying novel SL pairs.AvailabilityPython codes and dataset are available at:Contactluojiawei@hnu.edu.cnandxlli@i2r.a-star.edu.sg
A reservoir of stem-like CD8 T cells in the tumor-draining lymph node maintains the ongoing anti-tumor immune response
Authors: Connolly Kelli A. , Kuchroo Manik , Venkat Aarthi , Khatun Achia , Wang Jiawei , William Ivana , Hornick Noah , Fitzgerald Brittany , Damo Martina , Kasmani Moujtaba Y. , Cui Can , Fagerberg Eric , Monroy Isabel , Hutchins Amanda , Cheung Julie F , Foster Gena G. , Mariuzza Dylan L. , Zhao Hongyu , Cui Weiguo , Krishnaswamy Smita , Joshi Nikhil S. 
Published: January 2021

Abstract“Stem-like” TCF1+CD8+T cells (TSL) are necessary for long-term maintenance of T cell responses and the efficacy of immunotherapy but, as tumors contain signals that should drive T-cell terminal-differentiation, how these cells are maintained in tumors remains unclear. We found that a small number of TCF1+tumor-specific CD8+T cells were present in tumors throughout development. Yet, most intratumoral T cells differentiated as tumors progressed, corresponding with an immunologic shift in the tumor microenvironment (TME) from “hot” to “cold”. By contrast, most tumor-specific CD8+T cells in tumor-draining lymph nodes (dLNs) had functions and gene expression signatures similar to TSLfrom chronic LCMV infection and this population was stable over time, despite the changes in the TME. dLN T cells were the precursors of their more-differentiated intratumoral counterparts, and maintenance of TCF1 by intratumoral T cells required continuous migration from dLNs. Finally, TSLCD8 T cells were also present in LNs from lung adenocarcinoma patients, suggesting this population is also relevant in human disease. Thus, we propose that the dLN TSLreservoir has a critical function during tumor development in sustaining antitumor T cells during tumor development and protecting them from the terminal differentiation that occurs in the TME.
Transcriptome profiling of human pluripotent stem cell-derived cerebellar organoids reveals faster commitment under dynamic conditions
Authors: Silva Teresa P. , Sousa-Luís Rui , Fernandes Tiago G. , Bekman Evguenia P. , Rodrigues Carlos A. V. , Vaz Sandra H. , Moreira Leonilde M. , Hashimura Yas , Jung Sunghoon , Lee Brian , Carmo-Fonseca Maria , Cabral Joaquim M. S. 
Published: January 2021

AbstractHuman induced pluripotent stem cells (iPSCs) have great potential for disease modeling. However, generating iPSC-derived models to study brain diseases remains a challenge. In particular, the ability to recapitulate cerebellar developmentin vitrois still limited. We presented a reproducible and scalable production of cerebellar organoids by using the novel Vertical-Wheel single-use bioreactors, in which functional cerebellar neurons were obtained. Here, we evaluate the global gene expression profiles by RNA sequencing (RNA-seq) across cerebellar differentiation, demonstrating a faster cerebellar commitment in this novel dynamic differentiation protocol. Furthermore, transcriptomic profiles suggest a significant enrichment of extracellular matrix (ECM) in dynamic-derived cerebellar organoids, which can better mimic the neural microenvironment and support a consistent neuronal network. Thus, an efficient generation of organoids with cerebellar identity was achieved for the first time in a continuous process using a dynamic system without the need of organoids encapsulation in ECM-based hydrogels, allowing the possibility of large-scale production and application in high-throughput processes. The presence of factors that favors angiogenesis onset was also detected in dynamic condition, which can enhance functional maturation of cerebellar organoids. We anticipate that large-scale production of cerebellar organoids may help developing models for drug screening, toxicological tests and studying pathological pathways involved in cerebellar degeneration.
Stimulating human prefrontal cortex increases reward learning
Authors: Juliëtte Overman Margot , Sarrazin Verena , Browning Michael , O’Shea Jacinta 
Published: January 2021

AbstractWork in computational psychiatry suggests that mood disorders may stem from aberrant reinforcement learning processes. Specifically, it is proposed that depressed individuals believe that negative events are more informative than positive events, resulting in faster learning from negative outcomes (Pulcu & Browning, 2019). In this proof-of-concept study, we investigated whether learning rates for affective outcomes are malleable using transcranial direct current stimulation (tDCS). Healthy adults completed an established reinforcement learning task (Pulcu & Browning, 2017) in which the information content of reward and loss outcomes was manipulated by varying the volatility of stimulus-outcome associations. Learning rates on the tasks were quantified using computational models. Stimulation over dorsolateral prefrontal cortex (DLPFC) but not motor cortex (M1) specifically increased learning rates for reward outcomes. The effects of prefrontal tDCS were cognitive state-dependent: online stimulation increased learning rates for wins; offline stimulation decreased both win and loss learning rates. A replication study confirmed the key finding that online tDCS to DLPFC specifically increased learning rates for rewards relative to losses. Taken together, these findings demonstrate the potential of tDCS for modulating computational parameters of reinforcement learning relevant to mood disorders.Significance statementDisproportionate learning from negative relative to positive outcomes has been implicated in the development and maintenance of depression. The present work demonstrates that transcranial direct current stimulation (tDCS) to dorsolateral prefrontal cortex can specifically increase learning from positive events in healthy adults. Our results provide preliminary evidence that non-invasive brain stimulation can be used to shape reinforcement learning, indicating a potential novel cognitive neurostimulation intervention strategy for affective disorders.
Single-cell immune profiling reveals the impact of antiretroviral therapy on HIV-1-induced immune dysfunction, T cell clonal expansion, and HIV-1 persistencein vivo
Authors: Collora Jack A. , Pinto-Santini Delia , Pasalar Siavash , Ravindra Neal , Ganoza Carmela , Lama Javier , Alfaro Ricardo , Chiarella Jennifer , Spudich Serena , van Dijk David , Duerr Ann , Ho Ya-Chi 
Published: January 2021

AbstractDespite antiretroviral therapy (ART), HIV-1 persists in proliferating T cell clones that increase over time. To understand whether early ART affects HIV-1 persistencein vivo, we performed single-cell ECCITE-seq and profiled 89,279 CD4+T cells in paired samples during viremia and after immediate versus delayed ART in six people in the randomized interventional Sabes study. We found that immediate ART partially reverted TNF responses while delayed ART did not. Antigen and TNF responses persisted despite immediate ART and shaped the transcriptional landscape of CD4+T cells, HIV-1 RNA+cells, and T cell clones harboring them (cloneHIV-1). Some HIV-1 RNA+cells reside in the most clonally expanded cytotoxic T cell populations (GZMB and GZMK Th1 cells). CloneHIV-1+were larger in clone size, persisted despite ART, and exhibited transcriptional signatures of antigen, cytotoxic effector, and cytokine responses. Using machine-learning algorithms, we identified markers for HIV-1 RNA+cells and cloneHIV-1+as potential therapeutic targets. Overall, by combining single-cell immune profiling and T cell expansion dynamics tracking, we identified drivers of HIV-1 persistencein vivo.
High contrast, moving targets in an emerging target paradigm promote fast visuomotor responses during visually guided reaching
Authors: Kozak Rebecca A. , Corneil Brian D. 
Published: January 2021

AbstractHumans have a remarkable capacity to rapidly interact with the surrounding environment, often by transforming visual input into motor output on a moment-to-moment basis. But what visual features promote rapid reaching? High contrast, fast-moving targets elicit strong responses in the superior colliculus (SC), a structure associated with express saccades and implicated in rapid electromyographic (EMG) responses on upper limb muscles. To test the influence of stimulus properties on rapid reaches, we had human subjects perform visually guided reaches to moving targets varied by speed (experiment 1) or speed and contrast (experiment 2), in an emerging target paradigm which has recently been shown to robustly elicit fast visuomotor responses. Our analysis focused on stimulus-locked responses (SLRs) on upper limb muscles. SLRs appear within <100 ms of target presentation, and as the first wave of muscle recruitment, they have been hypothesized to arise from the SC. Across 32 subjects studied in both experiments, 97% expressed SLRs in the emerging target paradigm, whereas only 69% expressed SLRs in an immediate response paradigm towards static targets. Faster moving targets (experiment 1) evoked large magnitude SLRs, while high contrast fast moving targets (experiment 2) evoked short latency, large magnitude SLRs. In some instances, SLR magnitude exceeded the magnitude of movement aligned activity. Both large magnitude and short latency SLRs were correlated with short latency reach reaction times. Our results support the hypothesis that, in scenarios requiring expedited responses, a subcortical pathway originating in the SC elicits the earliest wave of muscle recruitment, expediting reaction times.New & NoteworthyHow does the brain rapidly transform vision into action? Here, by recording upper limb muscle activity, we find that high contrast and fast moving targets are highly effective at evoking rapid visually guided reaches. We surmise that a brainstem circuit originating in the superior colliculus contributes to the most rapid reaching responses. When time is of the essence, cortical areas may serve to prime this circuit, and elaborate subsequent phases of recruitment.
2.5D geophysical model of the Gällivare mining area: An integrated study to model the top 4 km of the subsurface and guide for future exploration activities
Authors: Tavakoli Saman , Sarlus Zmar , Kronsell Ida , Bauer Tobias E. 
Published: January 2021

ABSTRACTPotential field and Slingram data alongside rock physical properties, drill‐core information and results from geological field mapping were used to investigate the geometry of the geological structures in the Gällivare area in regional scale. The main purpose of this study was to delineate the vertical and lateral extension of the Malmberget felsic volcanic rocks, the Dundret and Vassaravaara units as well as geological structures related to the crustal‐scale Nautanen deformation zone. Furthermore, we aimed at identifying new magnetite‐hematite and sulphide mineralizations and lithologies related to the mineralizations based on the results from regional‐scale potential field modelling which are delineated with rock physical properties and borehole data. The study result indicated that the dome‐shaped Dundret gabbro extends downwards to ∼4 km depth and has its maximum depth at its centre. Hematite and magnetite assemblages occur within the top 2 km of the Dundret complex. Felsic volcanic rocks in the Malmberget area extend vertically down to a maximum depth of ∼3 km and get considerably thinner towards the west. The model for the known magnetite‐rich mineralizations in Malmberget was inferred from earlier drilling activities and was integrated into the profile models, which indicates a reasonable fit to the measured data, in particular on the magnetic anomaly; whereas the small dimensions of the modelled structures make them invisible on the Bouguer anomaly data. Additional magnetite‐rich mineralizations are suggested within the Malmberget felsic rocks. High real component and low imaginary response of the Slingram data suggests conductive zones within the Nautanen deformation zone towards the NE, which given the geology of the area in the high strain zone can indicate disseminated sulphide mineralizations. Drill‐hole data at the eastern parts of W‐E profiles agreed well with the suggested model inferred from potential field data, suggesting presence of mafic intrusions within the ∼top 1 km of the subsurface. The integrated model based on geophysical, petrophysical and geological data improved earlier understanding about the regional geometry of the key structures in the Gällivare area and indicates new magnetite‐rich and sulphide mineralization prospects which can be used as a guide for future exploration activities in the area.
Analytical chemistry, formation, mitigation, and risk assessment of polycyclic aromatic hydrocarbons: From food processing to in vivo metabolic transformation
Authors: Zhang Yiju , Chen Xiaoqian , Zhang Yu 
Published: January 2021

AbstractPolycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the air, oils, water, and food products we encounter every day. Among these exposures, food consumption is a major route of PAH exposure for nonsmokers. The PAH dietary exposure levels vary among different countries; however, many studies have shown PAH exposure to be highly concerning to human health. The levels of PAH contamination in food are mainly influenced by processing procedures and cooking methods, and they could be attenuated by modifying cooking procedures and adding antioxidant‐rich marinades. Several PAHs have toxic, mutagenic, and carcinogenic properties. The PAH benzo[a]pyrene (BaP) is particularly regarded as carcinogenic. There are three major metabolism pathways for PAHs, and the final products can bind to DNA, thus exerting mutagenic effects. Biological monitoring through the use of biomarkers is necessary for comprehensive and accurate risk assessments of human PAH exposure. It is important to reduce dietary PAH exposure and to implement reasonable and effective risk management strategies to reduce PAH levels in food to improve public health.
Specific oral and maxillofacial identifiers in panoramic radiographs used for human identification
Authors: Du Han , Li Min , Li Gang , Lyu Tu , Tian Xue‐mei 
Published: January 2021

AbstractRadiographically assisted dental identification is an important means for individual identification. Specific identifiers help to quickly filter some of the possible corresponding AM and PM images at the beginning. The study seeks specific oral and maxillofacial identifiers in panoramic radiographs. A total of 920 panoramic radiographs from 460 live patients were used. The most recent radiograph served as the surrogate post‐mortem (PM) record of an unidentified person, and the earliest radiograph served as the ante‐mortem (AM) record of the same person. We evaluated the following four groups of identifiers of the images: (1) dental morphology, tooth number, and position; (2) dental treatment and pathology; (3) morphological identifiers of the jaw; and (4) pathological identifiers of the jaw. The ratio of each identifier being identified simultaneously in the AM and PM databases was determined. Specific identifiers were defined as those that appeared at low frequency (ratio: 0%–0.250%). A total of 18 specific oral and maxillofacial identifiers were determined. The specific identifiers were a retained deciduous tooth (0.011%), S‐shaped deflection of a tooth root (0.012%), distal deflection of tooth root (0.017%), inverted impaction (0.018%), malposition (0.038%), supernumerary teeth (0.061%), mesial deflection of tooth root (0.092%), microdontia (0.136%), buccal/lingual impaction (0.188%), cementoma (0.002%), hypercementosis (0.002%), continuous crown (0.004%), pulp calcification (0.023%), attrition (0.030%), residual root (0.106%), root resorption (0.137%), implant (0.156%), and osteomyelitis (0.002%). Identifiers of the teeth and jaw can be used for human identification, and dental identifiers are more specific than identifiers of jaw.
Is waiver of consent for the use of health information for research acceptable to emergency department patients?
Authors: Schultz‐Swarthfigure Chase , Kelly Anne‐Maree 
Published: January 2021

AbstractSome emergency medicine research, especially retrospective studies using medical records review, rely on waiver of consent for use of personal health information (PHI) contained in clinical records. This is a secondary use of PHI and waiver of consent raises ethical, legal and practical issues. Granting of a waiver of consent is often (but not always) approved by a human research ethics committee and requires separate but inter‐related consideration of the legal and ethical issues. In part, this involves a balancing of the public interest versus the risk to privacy and an evaluation of whether subjects would, mostly likely, have agreed to the use of their PHI had they been asked. To date, there are no robust data about whether use of PHI without consent for research would be acceptable to people who attend Australasian EDs for care.