bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harmful Drinking Phenotype in a Large Dutch Community Sample
Authors: Hogenelst Koen , Snippe Almar , Martinic Marjana 
Published: August 2022

Abstract

Aims
Harmful drinking patterns are shaped by a broad complex interaction of factors, societal and individual, psychological and behavioral. Although previous studies have focused on a few variables at a time, the current study simultaneously examines a large number of variables in order to create a comprehensive view (i.e. phenotype) of harmful drinking, and to rank the main predictors of harmful and non-harmful drinking by order of importance.

Methods
We surveyed a large sample of Dutch adults about their habitual drinking characteristics and attitudes, perceptions and motives for drinking. We fed 45 variables into a random forest machine learning model to identify predictors for (1) drinking within and in excess of Dutch guideline recommendations and (2) harmful and non-harmful drinking.

Results
In both models, respondents’ subjective perceptions of ‘responsible drinking’, both per occasion and per week, showed the strongest predictive potential for different drinking phenotypes. The next strongest factors were respondents’ reason for drinking, motives for drinking and age. Other variables, such as drinking location, knowledge about alcohol-related health risks and consumption of different beverage types, were not strong predictors of drinking phenotypes.

Conclusions
Although the direction of the relationship is unclear from the findings, they suggest that interventions and policy measures aimed at individuals and social norms around drinking may offer promise for reducing harmful drinking. Messaging and promotion of drinking guidelines should be tailored with this in mind.
Ballad Poetics in the Era of Black Lives Matter
Authors: Ronda Margaret 
Published: August 2022

Abstract
This essay approaches ballads as a vital cultural form for dramatizing the histories and social meanings of racial conflict in the US, turning to a series of recent poems written alongside the rise of the Black Lives Matter movement. This archive of poems draws attention to recursive racial divisions as they emerge anew in a calamitous event, highlighting themes of anonymity and hypervisibility, motion and arrest, the violent imposition of carceral order, and the insurrectionary prospects of its refusal. Examining the ways a range of Black poets have been drawing on features associated with ballads, this essay considers how these writers recount the stories and scenes of Ferguson and other now-famous locales of anti-Black state violence and community uprising. With their narratives of common persons subjected to surveillance, exposure, and acts of violence, these poems further the social imaginaries and storytelling mode of the ballad to consider continuing forms of racial injustice and new eruptions of protest in the present.The archive of Black poetic works I consider pursues more oppositional orientations, keyed to the insurgent energy of the streets as well as to the layered practices of Black revisionary ballad and the material histories they encode.
Employment Precarity and Increased Risk of Hazardous Occupational Exposures Among Residents of High Socioeconomic Hardship Neighborhoods
Authors: Bonney Tessa , Rospenda Kathleen M , Forst Linda , Conroy Lorraine M , Castañeda Dolores , Avelar Sandra , Castañeda Yvette , Holloway Adlaide , Hebert-Beirne Jeni 
Published: August 2022

Abstract

Background
While there is evidence that workers in nonstandard employment arrangements are disproportionately exposed to recognized occupational hazards, existing studies have not comprehensively examined associations between employment precarity and exposure to occupational hazards for these workers in the USA. The aim of this study was to examine relationships between employment precarity and occupational hazards in two contiguous high socio-economic hardship neighborhoods in Chicago.

Methods
Using a community-based participatory research approach, community researchers administered a community-developed survey to 489 residents of Greater Lawndale who reported current or recent employment in a job that met at least one characteristic of precarious employment (e.g. unpredictable schedule, insecure work, no living wage/benefits). Employment precarity was calculated using a modified version of the Employment Precarity Index (EPI) developed by the Poverty and Employment Precarity in Southern Ontario group. We modeled the association between employment precarity and occupational exposures using logistic regression models.

Results
We identified a high prevalence of precarious employment in this sample, as well as a high prevalence of self-reported exposure to recognized occupational hazards. Increases in relative employment precarity were significantly associated with self-reported exposure to chemical and biological hazards, physical hazards, and slip, trip, strike, fall, trap or crush hazards at work.

Conclusions
Results highlight the importance of using community research approaches and robust measures of employment characteristics, such as the EPI, to evaluate associations between employment precarity and hazardous exposures. These results suggest that variability in employment situations and resultant relative employment precarity are important predictors of exposure to recognized occupational hazards. Findings also suggest that health inequities observed among precariously employed workers may be partly explained by increased risk for exposure to occupational hazards, which has implications for community health and should be investigated in future longitudinal research.
The Causal Relationship between Learner Motivation and Language Achievement: New Dynamic Perspective
Authors: Alamer Abdullah , Alrabai Fakieh 
Published: August 2022

Abstract
It is well known that successful second language (L2) learners are motivated individuals. Accordingly, L2 researchers have tested the predictive power of different motivational constructs on language learning outcomes. However, this perspective appears to neglect the assessment of achievement as a predictor of future motivation. To assess this possibility, we first employed the latent growth curve model (LGCM) to evaluate the initial values and growth rates of the two variables. We further applied a newly developed statistical method, the random-intercept cross-lagged panel model (RI-CLPM), to study the causal relationship. A total of 226 language students were monitored for 17 weeks at three time points. The analysis showed an increasing trend in the association between the growth levels of both variables. However, students’ autonomous motivation at Time 1 appears to affect achievement at Time 2. Further, the second wave of the RI-CLPM illustrated that achievement at Time 2 impacted autonomous motivation at Time 3, while motivation failed to predict scores on achievement at Time 3.
GTFtools: a software package for analyzing various features of gene models
Authors: Li Hong-Dong , Lin Cui-Xiang , Zheng Jiantao 
Published: August 2022

Abstract

Motivation
Gene-centric bioinformatics studies frequently involve the calculation or the extraction of various features of genes such as splice sites, promoters, independent introns and untranslated regions (UTRs) through manipulation of gene models. Gene models are often annotated in gene transfer format (GTF) files. The features are essential for subsequent analysis such as intron retention detection, DNA-binding site identification and computing splicing strength of splice sites. Some features such as independent introns and splice sites are not provided in existing resources including the commonly used BioMart database. A package that implements and integrates functions to analyze various features of genes will greatly ease routine analysis for related bioinformatics studies. However, to the best of our knowledge, such a package is not available yet.

Results
We introduce GTFtools, a stand-alone command-line software that provides a set of functions to calculate various gene features, including splice sites, independent introns, transcription start sites (TSS)-flanking regions, UTRs, isoform coordination and length, different types of gene lengths, etc. It takes the ENSEMBL or GENCODE GTF files as input and can be applied to both human and non-human gene models like the lab mouse. We compare the utilities of GTFtools with those of two related tools: Bedtools and BioMart. GTFtools is implemented in Python and not dependent on any third-party software, making it very easy to install and use.

Availability and implementation
GTFtools is freely available at www.genemine.org/gtftools.php as well as pyPI and Bioconda.
ntHash2: recursive spaced seed hashing for nucleotide sequences
Authors: Kazemi Parham , Wong Johnathan , Nikolić Vladimir , Mohamadi Hamid , Warren René L , Birol Inanç 
Published: August 2022

AbstractMotivationSpaced seeds are robust alternatives to k-mers in analyzing nucleotide sequences with high base mismatch rates. Hashing is also crucial for efficiently storing abundant sequence data. Here, we introduce ntHash2, a fast algorithm for spaced seed hashing that can be integrated into various bioinformatics tools for efficient sequence analysis with applications in genome research.ResultsntHash2 is up to 2.1× faster at hashing various spaced seeds than the previous version and 3.8× faster than conventional hashing algorithms with naïve adaptation. Additionally, we reduced the collision rate of ntHash for longer k-mer lengths and improved the uniformity of the hash distribution by modifying the canonical hashing mechanism.Availability and implementationntHash2 is freely available online at github.com/bcgsc/ntHash under an MIT license.Supplementary informationSupplementary data are available at Bioinformatics online.
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence
Authors: Kuipers Jack , Singer Jochen , Beerenwinkel Niko 
Published: August 2022

Abstract

Motivation
Tumours evolve as heterogeneous populations of cells, which may be distinguished by different genomic aberrations. The resulting intra-tumour heterogeneity plays an important role in cancer patient relapse and treatment failure, so that obtaining a clear understanding of each patient’s tumour composition and evolutionary history is key for personalized therapies. Single-cell sequencing (SCS) now provides the possibility to resolve tumour heterogeneity at the highest resolution of individual tumour cells, but brings with it challenges related to the particular noise profiles of the sequencing protocols as well as the complexity of the underlying evolutionary process.

Results
By modelling the noise processes and allowing mutations to be lost or to reoccur during tumour evolution, we present a method to jointly call mutations in each cell, reconstruct the phylogenetic relationship between cells, and determine the locations of mutational losses and recurrences. Our Bayesian approach allows us to accurately call mutations as well as to quantify our certainty in such predictions. We show the advantages of allowing mutational loss or recurrence with simulated data and present its application to tumour SCS data.

Availability and implementation
SCIΦN is available at https://github.com/cbg-ethz/SCIPhIN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python
Authors: Lubbock Alexander L R , Lopez Carlos F 
Published: August 2022

Abstract

Motivation
Computational systems biology analyses typically make use of multiple software and their dependencies, which are often run across heterogeneous compute environments. This can introduce differences in performance and reproducibility. Capturing metadata (e.g. package versions, GPU model) currently requires repetitious code and is difficult to store centrally for analysis. Even where virtual environments and containers are used, updates over time mean that versioning metadata should still be captured within analysis pipelines to guarantee reproducibility.

Results
Microbench is a simple and extensible Python package to automate metadata capture to a file or Redis database. Captured metadata can include execution time, software package versions, environment variables, hardware information, Python version and more, with plugins. We present three case studies demonstrating Microbench usage to benchmark code execution and examine environment metadata for reproducibility purposes.

Availability and implementation
Install from the Python Package Index using pip install microbench. Source code is available from https://github.com/alubbock/microbench.

Supplementary information
Supplementary data are available at Bioinformatics online.
What is consciousness? Artificial intelligence, real intelligence, quantum mind and qualia
Authors: Kauffman Stuart A , Roli Andrea 
Published: August 2022

AbstractWe approach the question ‘What is consciousness?’ in a new way, not as Descartes’ ‘systematic doubt’, but as how organisms find their way in their world. Finding one’s way involves finding possible uses of features of the world that might be beneficial or avoiding those that might be harmful. ‘Possible uses of X to accomplish Y’ are ‘affordances’. The number of uses of X is indefinite (or unknown), the different uses are unordered, are not listable, and are not deducible from one another. All biological adaptations are either affordances seized by heritable variation and selection or, far faster, by the organism acting in its world finding uses of X to accomplish Y. Based on this, we reach rather astonishing conclusions:1. Artificial general intelligence based on universal Turing machines (UTMs) is not possible, since UTMs cannot ‘find’ novel affordances.2. Brain-mind is not purely classical physics for no classical physics system can be an analogue computer whose dynamical behaviour can be isomorphic to ‘possible uses’.3. Brain-mind must be partly quantum—supported by increasing evidence at 6.0 to 7.3 sigma.4. Based on Heisenberg’s interpretation of the quantum state as ‘potentia’ converted to ‘actuals’ by measurement, where this interpretation is not a substance dualism, a natural hypothesis is that mind actualizes potentia. This is supported at 5.2 sigma. Then mind’s actualizations of entangled brain-mind-world states are experienced as qualia and allow ‘seeing’ or ‘perceiving’ of uses of X to accomplish Y. We can and do jury-rig. Computers cannot.5. Beyond familiar quantum computers, we discuss the potentialities of trans-Turing systems.
Linker histone H1FOO is required for bovine preimplantation development by regulating lineage specification and chromatin structure
Authors: Li Shuang , Shi Yan , Dang Yanna , Hu Bingjie , Xiao Lieying , Zhao Panpan , Wang Shaohua , Zhang Kun 
Published: August 2022

Abstract
Linker histone H1 binds to the nucleosome and is implicated in the regulation of the chromatin structure and function. The H1 variant H1FOO is heavily expressed in oocytes and early embryos. However, given the poor homology of H1FOO among mammals, the functional role of H1FOO during preimplantation embryonic development remains largely unknown, especially in domestic animals. Here, we find that H1FOO is not only expressed in oocytes and preimplantation embryos but granulosa cells and spermatids in cattle. We then demonstrate that the interference of H1FOO results in preimplantation embryonic developmental arrest in cattle using either RNA editing or Trim-Away approach. H1FOO depletion leads to a compromised expression of critical lineage-specific genes at the morula stage and affects the establishment of cell polarity. Interestingly, H1FOO depletion causes a significant increase in the expression of genes encoding other linker H1 and core histones. Concurrently, there is an increase of H3K9me3 and H3K27me3, two markers of repressive chromatin and a decrease of H4K16ac, a marker of open chromatin. Importantly, overexpression of bovine H1FOO results in severe embryonic developmental defects. In sum, we propose that H1FOO controls the proper chromatin structure that is crucial for the fidelity of cell polarization and lineage specification during bovine preimplantation development.
Aqp4 stop codon readthrough facilitates amyloid-β clearance from the brain
Authors: Sapkota Darshan , Florian Colin , Doherty Brookelyn M , White Kelli M , Reardon Kate M , Ge Xia , Garbow Joel R , Yuede Carla M , Cirrito John R , Dougherty Joseph D 
Published: August 2022

Abstract
Alzheimer’s disease is initiated by the toxic aggregation of amyloid-β. Immunotherapeutics aimed at reducing amyloid beta are in clinical trials but with very limited success to date. Identification of orthogonal approaches for clearing amyloid beta may complement these approaches for treating Alzheimer’s disease. In the brain, the astrocytic water channel Aquaporin 4 is involved in clearance of amyloid beta, and the fraction of Aquaporin 4 found perivascularly is decreased in Alzheimer’s disease. Further, an unusual stop codon readthrough event generates a conserved C-terminally elongated variant of Aquaporin 4 (AQP4X), which is exclusively perivascular. However, it is unclear whether the AQP4X variant specifically mediates amyloid beta clearance.
Here, using Aquaporin 4 readthrough-specific knockout mice that still express normal Aquaporin 4, we determine that this isoform indeed mediates amyloid beta clearance. Further, with high-throughput screening and counterscreening, we identify small molecule compounds that enhance readthrough of the Aquaporin 4 sequence and validate a subset on endogenous astrocyte Aquaporin 4. Finally, we demonstrate these compounds enhance brain amyloid-β clearance in vivo, which depends on AQP4X.
This suggests derivatives of these compounds may provide a viable pharmaceutical approach to enhance clearance of amyloid beta and potentially other aggregating proteins in neurodegenerative disease.
A demonstration of cone function plasticity after gene therapy in achromatopsia
Authors: Farahbakhsh Mahtab , Anderson Elaine J , Maimon-Mor Roni O , Rider Andy , Greenwood John A , Hirji Nashila , Zaman Serena , Jones Pete R , Schwarzkopf D Samuel , Rees Geraint , Michaelides Michel , Dekker Tessa M 
Published: August 2022

Abstract
Recent advances in regenerative therapy have placed the treatment of previously incurable eye diseases within arms’ reach. Achromatopsia is a severe monogenic heritable retinal disease that disrupts cone function from birth, leaving patients with complete colour blindness, low acuity, photosensitivity and nystagmus. While successful gene-replacement therapy in non-primate models of achromatopsia has raised widespread hopes for clinical treatment, it was yet to be determined if and how these therapies can induce new cone function in the human brain. Using a novel multimodal approach, we demonstrate for the first time that gene therapy can successfully activate dormant cone-mediated pathways in children with achromatopsia (CNGA3- and CNGB3-associated, 10–15 years). To test this, we combined functional MRI population receptive field mapping and psychophysics with stimuli that selectively measure cone photoreceptor signalling. We measured cortical and visual cone function before and after gene therapy in four paediatric patients, evaluating treatment-related change against benchmark data from untreated patients (n = 9) and normal-sighted participants (n = 28). After treatment, two of the four children displayed strong evidence for novel cone-mediated signals in visual cortex, with a retinotopic pattern that was not present in untreated achromatopsia and which is highly unlikely to emerge by chance. Importantly, this change was paired with a significant improvement in psychophysical measures of cone-mediated visual function. These improvements were specific to the treated eye, and provide strong evidence for successful read-out and use of new cone-mediated information. These data show for the first time that gene replacement therapy in achromatopsia within the plastic period of development can awaken dormant cone-signalling pathways after years of deprivation. This reveals unprecedented neural plasticity in the developing human nervous system and offers great promise for emerging regenerative therapies.
COVID-19 induces CNS cytokine expression and loss of hippocampal neurogenesis
Authors: Soung Allison L , Vanderheiden Abigail , Nordvig Anna S , Sissoko Cheick A , Canoll Peter , Mariani Madeline B , Jiang Xiaoping , Bricker Traci , Rosoklija Gorazd B , Arango Victoria , Underwood Mark , Mann J John , Dwork Andrew J , Goldman James E , Boon Adrianus C M , Boldrini Maura , Klein Robyn S 
Published: August 2022

Abstract
Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is associated with acute and postacute cognitive and neuropsychiatric symptoms including impaired memory, concentration, attention, sleep and affect. Mechanisms underlying these brain symptoms remain understudied. Here we report that SARS-CoV-2-infected hamsters exhibit a lack of viral neuroinvasion despite aberrant blood–brain barrier permeability. Hamsters and patients deceased from coronavirus disease 2019 (COVID-19) also exhibit microglial activation and expression of interleukin (IL)-1β and IL-6, especially within the hippocampus and the medulla oblongata, when compared with non-COVID control hamsters and humans who died from other infections, cardiovascular disease, uraemia or trauma. In the hippocampal dentate gyrus of both COVID-19 hamsters and humans, we observed fewer neuroblasts and immature neurons. Protracted inflammation, blood–brain barrier disruption and microglia activation may result in altered neurotransmission, neurogenesis and neuronal damage, explaining neuropsychiatric presentations of COVID-19. The involvement of the hippocampus may explain learning, memory and executive dysfunctions in COVID-19 patients.
Upregulated expression of substance P and NK1R in blood monocytes and B cells of patients with allergic rhinitis and asthma
Authors: Han Peixuan , Chen Liping , Chen Dong , Yang Ruiming , Wang Wei , Liu Jingyu , He Shaoheng , Zhang Huiyun 
Published: August 2022

Abstract
Increased expression of substance P (SP) and neurokinin-1 receptor (NK1R) has been noticed in patients with allergic rhinitis (AR) and allergic asthma (AA). However, little is known of the expression of SP and NK1R in monocytes and B cells of AR and AA. In the present study, the expression levels of SP and NK1R were determined by flow cytometry and mouse AR and AA models. The results showed that both percentages of SP+ monocytes and SP+ B cells, and mean fluorescence intensity (MFI) of SP in monocytes were elevated in the blood of AA and AR combined with AA (ARA) patients. Similarly, the percentages of NK1R+ monocytes were elevated in the blood of AR, AA, and ARA patients. Allergens Artemisia sieversiana wild allergen extract (ASWE), house dust mite extract (HDME), and Platanus pollen allergen extract (PPE) increased the expression density of SP molecules (determined by MFI) in an individual monocyte of AR patients. HDME and PPE appeared to enhance SP and NK1R expression in the B cells of ARA and AR patients. In the mouse AR and AA models, the percentages of NK1R+ monocytes and B cells were elevated in blood following OVA (ovalbumin) sensitization and challenge. Knocking out the FcεRI molecule completely abolished the OVA-induced upregulation of expression of NK1R in monocytes and B cells of AA mice. In conclusion, upregulated expressions of SP and NK1R may contribute to the pathogenesis of airway allergy.