bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiwavelength study of the luminous GRB 210619B observed with Fermi and ASIM
Authors: Caballero-García M D , Gupta Rahul , Pandey S B , Oates S R , Marisaldi M , Ramsli A , Hu Y-D , Castro-Tirado A J , Sánchez-Ramírez R , Connell P H , Christiansen F , Ror A Kumar , Aryan A , Bai J-M , Castro-Tirado M A , Fan Y-F , Fernández-García E , Kumar A , Lindanger A , Mezentsev A , Navarro-González J , Neubert T , Østgaard N , Pérez-García I , Reglero V , Sarria D , Sun T R , Xiong D-R , Yang J , Yang Y-H , Zhang B-B 
Published: December 2022

ABSTRACT
We report on detailed multiwavelength observations and analysis of the very bright and long GRB 210619B, detected by the Atmosphere-Space Interactions Monitor installed on the International Space Station and the Gamma-ray Burst Monitor (GBM) on-board the Fermi mission. Our main goal is to understand the radiation mechanisms and jet composition of GRB 210619B. With a measured redshift of z = 1.937, we find that GRB 210619B falls within the 10 most luminous bursts observed by Fermi so far. The energy-resolved prompt emission light curve of GRB 210619B exhibits an extremely bright hard emission pulse followed by softer/longer emission pulses. The low-energy photon index (αpt) values obtained using the time-resolved spectral analysis of the burst suggest a transition between the thermal (during harder pulse) to non-thermal (during softer pulse) outflow. We examine the correlation between spectral parameters and find that both peak energy and αpt exhibit the flux tracking pattern. The late time broad-band photometric data set can be explained within the framework of the external forward shock model with νm &lt; νc &lt; νx (where νm, νc, and νx are the synchrotron peak, cooling-break, and X-ray frequencies, respectively) spectral regime supporting a rarely observed hard electron energy index (p &lt; 2). We find moderate values of host extinction of E(B − V) = 0.14 ± 0.01 mag for the small magellanic cloud extinction law. In addition, we also report late-time optical observations with the 10.4 m Gran Telescopio de Canarias placing deep upper limits for the host galaxy (z = 1.937), favouring a faint, dwarf host for the burst.
Optimizing the shape of photometric redshift distributions with clustering cross-correlations
Authors: Stölzner Benjamin , Joachimi Benjamin , Korn Andreas ,   the LSST Dark Energy Science Collaboration
Published: December 2022

ABSTRACT
We present an optimization method for the assignment of photometric galaxies to a chosen set of redshift bins. This is achieved by combining simulated annealing, an optimization algorithm inspired by solid-state physics, with an unsupervised machine learning method, a self-organizing map (SOM) of the observed colours of galaxies. Starting with a sample of galaxies that is divided into redshift bins based on a photometric redshift point estimate, the simulated annealing algorithm repeatedly reassigns SOM-selected subsamples of galaxies, which are close in colour, to alternative redshift bins. We optimize the clustering cross-correlation signal between photometric galaxies and a reference sample of galaxies with well-calibrated redshifts. Depending on the effect on the clustering signal, the reassignment is either accepted or rejected. By dynamically increasing the resolution of the SOM, the algorithm eventually converges to a solution that minimizes the number of mismatched galaxies in each tomographic redshift bin and thus improves the compactness of their corresponding redshift distribution. This method is demonstrated on the synthetic Legacy Survey of Space and Time cosmoDC2 catalogue. We find a significant decrease in the fraction of catastrophic outliers in the redshift distribution in all tomographic bins, most notably in the highest redshift bin with a decrease in the outlier fraction from 57 per cent to 16 per cent.
Shelterin reduces the accessibility of telomeric overhangs
Authors: Shiekh Sajad , Jack Amanda , Saurabh Ayush , Mustafa Golam , Kodikara Sineth G , Gyawali Prabesh , Hoque Mohammed Enamul , Pressé Steve , Yildiz Ahmet , Balci Hamza 
Published: December 2022

Abstract
Telomeres terminate with a 50–300 bases long single-stranded G-rich overhang, which can be misrecognized as a DNA damage repair site. Shelterin plays critical roles in maintaining and protecting telomere ends by regulating access of various physiological agents to telomeric DNA, but the underlying mechanism is not well understood. Here, we measure how shelterin affects the accessibility of long telomeric overhangs by monitoring transient binding events of a short complementary peptide nucleic acid (PNA) probe using FRET-PAINT in vitro. We observed that the POT1 subunit of shelterin reduces the accessibility of the PNA probe by ∼2.5-fold, indicating that POT1 effectively binds to and protects otherwise exposed telomeric sequences. In comparison, a four-component shelterin stabilizes POT1 binding to the overhang by tethering POT1 to the double-stranded telomeric DNA and reduces the accessibility of telomeric overhangs by ∼5-fold. This enhanced protection suggests shelterin restructures the junction between single and double-stranded telomere, which is otherwise the most accessible part of the telomeric overhang.
Temporal and Geographic Patterns of Documentation of Sexual Orientation and Gender Identity Keywords in Clinical Notes
Authors: Workman T. Elizabeth , Goulet Joseph L. , Brandt Cynthia A. , Lindemann Luke , Skanderson Melissa , Warren Allison R. , Eleazer Jacob R. , Kronk Clair , Gordon Kirsha S. , Pratt-Chapman Mandi , Zeng-Treitler Qing 
Published: December 2022

Objective:
Disclosure of sexual orientation and gender identity correlates with better outcomes, yet data may not be available in structured fields in electronic health record data. To gain greater insight into the care of sexual and gender-diverse patients in the Veterans Health Administration (VHA), we examined the documentation patterns of sexual orientation and gender identity through extraction and analyses of data contained in unstructured electronic health record clinical notes.

Methods:
Salient terms were identified through authoritative vocabularies, the research team’s expertise, and frequencies, and the use of consistency in VHA clinical notes. Term frequencies were extracted from VHA clinical notes recorded from 2000 to 2018. Temporal analyses assessed usage changes in normalized frequencies as compared with nonclinical use, relative growth rates, and geographic variations.

Results:
Over time most terms increased in use, similar to Google ngram data, especially after the repeal of the “Don’t Ask Don’t Tell” military policy in 2010. For most terms, the usage adoption consistency also increased by the study’s end. Aggregated use of all terms increased throughout the United States.

Conclusion:
Term usage trends may provide a view of evolving care in a temporal continuum of changing policy. These findings may be useful for policies and interventions geared toward sexual and gender-diverse individuals. Despite the lack of structured data, the documentation of sexual orientation and gender identity terms is increasing in clinical notes.
Liver transplantation for alcohol-associated hepatitis
Authors: Durkin Claire , Bittermann Therese 
Published: December 2022

Purpose of review
Early liver transplantation is emerging as a treatment option for severe alcohol-associated hepatitis refractory to pharmacotherapies. This review outlines the current status of transplantation for alcohol-associated hepatitis and the treatment of alcohol use disorder after liver transplantation.

Recent findings
Rates of early liver transplantation for alcohol-associated hepatitis are increasing with significant heterogeneity in practices across the Unites States. Recent studies have demonstrated a substantial survival benefit in patients transplanted for alcohol-associated hepatitis with improved outcomes in early vs. late transplantation, first vs. prior hepatic decompensation, and posttransplant abstinence/delayed relapse vs. early return to alcohol use. Several prediction algorithms have been developed to ascertain patients’ risk of alcohol relapse and aid in candidate selection, though data on treatment of alcohol use disorders in transplant recipients remains limited.

Summary
Although controversial, early liver transplantation for severe alcohol-associated hepatitis has shown to be a lifesaving intervention. Additional research is needed to evaluate its long-term outcomes, optimize candidate selection, and understand treatment of alcohol use disorder posttransplant.
Prevalence and risk factors of unsuppressed viral load among pregnant and breastfeeding women in sub-Saharan Africa: analysis from population-based surveys
Authors: Schrubbe Leah A. , Stöckl Heidi , Hatcher Abigail M. , Marston Milly , Kuchukhidze Salome , Calvert Clara 
Published: December 2022

Objective:
To examine the prevalence of viral suppression and risk factors for unsuppressed viral load among pregnant and breastfeeding women living with HIV (WLH).

Design:
Pooled analysis among pregnant and breastfeeding WLH from Population-Based HIV Impact Assessment (PHIA) cross-sectional surveys from 10 sub-Saharan African countries.

Methods:
Questionnaires included sociodemographic, relationship-related, and HIV-related items, while blood tests examined HIV serostatus and viral load (data collected 2015–2018). The weighted prevalence of viral suppression was calculated. Logistic regression was used to examine risk factors for unsuppressed viral load (≥1000 copies/ml).

Results:
Of 1685 pregnant or breastfeeding WLH with viral load results, 63.8% (95% confidence interval (CI): 60.8–66.7%) were virally suppressed at the study visit. Among all included women, adolescence (adjusted odds ratio (aOR): 4.85, 95% CI: 2.58–9.14, P < 0.001) and nondisclosure of HIV status to partner (aOR: 1.48, 95% CI: 1.02–2.14, P = 0.04) were associated with unsuppressed viral load. Among only partnered women, adolescence (aOR: 7.95, 95% CI: 3.32–19.06, P < 0.001), and lack of paid employment (aOR: 0.67, 95% CI: 0.47–0.94, P = 0.02) were associated with unsuppressed viral load. Examining only women on ART, nondisclosure of HIV status to partner (aOR: 1.85, 95% CI: 1.19–2.88, P = 0.006) was associated with unsuppressed viral load.

Conclusion:
Viral suppression among pregnant and breastfeeding WLH in sub-Saharan Africa remains suboptimal. Relationship dynamics around nondisclosure of HIV-positive status to partners was an important risk factor for unsuppressed viral load. Improving HIV care via sensitive discussions around partner dynamics in pregnant and breastfeeding women could improve maternal HIV outcomes and prevention of mother-to-child transmission of HIV (PMTCT).
Minimal theory of 3D vision: new approach to visual scale and visual shape
Authors: Linton Paul 
Published: December 2022

Since Kepler and Descartes in the early-1600s, vision science has been committed to a triangulation model of stereo vision. But in the early-1800s, we realized that disparities are responsible for stereo vision. And we have spent the past 200 years trying to shoe-horn disparities back into the triangulation account. The first part of this article argues that this is a mistake, and that stereo vision is a solution to a different problem: the eradication of rivalry between the two retinal images, rather than the triangulation of objects in space. This leads to a ‘minimal theory of 3D vision’, where 3D vision is no longer tied to estimating the scale, shape, and direction of objects in the world. The second part of this article then asks whether the other aspects of 3D vision, which go beyond stereo vision, really operate at the same level of visual experience as stereo vision? I argue they do not. Whilst we want a theory of real-world 3D vision, the literature risks giving us a theory of picture perception instead. And I argue for a two-stage theory, where our purely internal ‘minimal’ 3D percept (from stereo vision) is linked to the world through cognition.This article is part of a discussion meeting issue ‘New approaches to 3D vision’.
Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos
Authors: McCoy Rajiv C. , Summers Michael C. , McCollin Abeo , Ottolini Christian S. , Ahuja Kamal , Handyside Alan H. 
Published: December 2022

AbstractThe high incidence of aneuploidy in early human development, arising either from errors in meiosis or postzygotic mitosis, is the primary cause of pregnancy loss, miscarriage, and still birth following natural conception as well asin vitrofertilization (IVF). Preimplantation genetic testing for aneuploidy (PGT-A) has confirmed the prevalence of meiotic and mitotic aneuploidies among blastocyst-stage IVF embryos that are candidates for transfer. However, only about half of normally fertilized embryos develop to the blastocyst stagein vitro, while the others arrest at cleavage to late morula or early blastocyst stages. To achieve a more complete view of the impacts of aneuploidy, we applied a validated method of PGT-A to a large series (n = 909) of arrested embryos and trophectoderm biopsies. We then correlated observed aneuploidies with abnormalities of the first two cleavage divisions using time lapse imaging (n = 843). The combined incidence of meiotic and mitotic aneuploidies was strongly associated with blastocyst morphological grading, with the proportion ranging from 20% to 90% for the highest to lowest grades, respectively. In contrast, the incidence of aneuploidy among arrested embryos was exceptionally high (94%), dominated by mitotic aneuploidies affecting multiple chromosomes. In turn, these mitotic aneuploidies were strongly associated with abnormal cleavage divisions, such that 51% of abnormally dividing embryos possessed mitotic aneuploidies compared to only 23% of normally dividing embryos. We conclude that the combination of meiotic and mitotic aneuploidies drives arrest of human embryosin vitro, as development increasingly relies on embryonic gene expression at the blastocyst stage.
The Global Environment Facility approach for allocating biodiversity funding to countries
Authors: Mcowen Chris , Burgess Neil D. , Ash Neville , Baquero Andrea , Fonseca Gustavo , Harfoot Mike , Hilton-Taylor Craig , Kapos Val , Ravilious Corinna , Sayor Catherine , Tallowin Oliver , Teelucksingh Sonja Sabita , Weatherdon Lauren , Wyatt Sarah 
Published: December 2022

AbstractBiodiversity is not evenly distributed across the globe and some areas have greater potential to contribute to biodiversity conservation than others. Whilst there are multiple ways to determine priority areas for conservation, for a global institution like the Global Environment Facility (GEF), the funding mechanism for the Convention on Biological Diversity and the largest multilateral source of funding for developing countries focused on enhancing biodiversity outcomes and promoting sustainable use, it is important to fund the top-ranked countries whilst also ensuring that all eligible countries are able to undertake some biodiversity conservation actions in accordance with the Convention. To this end, the GEF uses the System for Transparent Allocation of Resources (STAR) to allocate funding in separate funding rounds to eligible countries. This country focus means that all prioritization analyses need to be undertaken within that political framework, while also considering the intrinsic patterns in biodiversity that don’t respect national borders. We present the 2018 update of the biodiversity component of GEF-STAR, investigate how the weighting system affects the ranking of countries. We show that top ranked and bottom ranked countries are robust to changes in the weighting of analytical elements, but the weighting can significantly alter the importance of middle ranking countries, affecting their funding allocation. This analysis has been used by the GEF, along with other data, to allocate over $1 billion in biodiversity funding (GEF-7 = $1.2 billion) to improve country and global prospects for conservation. However, this large funding allocation for conservation needs to be set against the vastly larger funding flows that decrease natural values around the world, and the need for systems level change remains evident across the entire planet.
IIIandMe: An Algorithm for Chromosome-scale Haplotype Determination Using Genome-wide Variants of Three Haploid Reproductive Cells
Authors: Qu Han , Li Ruidong , Yu Lei , Chen Weiming , Feng Yuanfa , Jia Qiong , Traband Ryan , Wang Xuesong , Wang Shibo , He Luoxian , Wang Zixian , Qu Meng , Ferrante Sergio Pietro , Zhu Jianguo , Zhong Weide , Roose Mikeal , Jia Zhenyu 
Published: December 2022

AbstractOur recent algorithm,Hapi, infers chromosome-scale haplotypes using genomic data of a small number of single gametes. Its advanced version,IIIandMe, is proposed here to achieve comparable phasing accuracy with as few as three gametes, pushing the analysis to its limit. The new method is validated with simulation and a citrus gamete dataset. The rapid advances in genotyping technologies promise a broad application ofIIIandMein disclosing important genetic information.
Use of clustering to improve estimation of epidemic model parameters under a Bayesian hierarchical framework
Authors: Alahakoon Punya , McCaw James M. , Taylor Peter G. 
Published: December 2022

AbstractWe study infectious disease outbreaks that have evolved in isolation without the influence of one another. If stochastic effects are identified within each outbreak, it is necessary to model the dynamics with stochastic epidemic models. However, the accuracy of the estimated model parameters depends on several factors including the statistical inference methodologies that are used. One approach to making inferences from multiple outbreak data is the use of a Bayesian hierarchical model. This statistical framework allows simultaneous inference for multiple outbreaks and the estimation of model parameters at a group level. A hierarchical model will generally provide improved estimates; however, we show that this is not always true when the variability among model parameter values of the outbreaks is high. We further show that subsets of outbreaks with similar parameter values can be identified prior to a hierarchical analysis using common clustering algorithms such as k-means. When hierarchical analyses are carried out for these pre-identified subsets of outbreaks, parameter estimates are improved compared to those estimated under a hierarchical analysis for the complete set of outbreaks. We have applied our estimation framework within a simulation-based experiment using synthetic data generated from stochasticSIRSmodels. The framework is generalizable to other biological data.
dgram2dmap: Extraction, visualisation and formatting of distance constraints from AlphaFold distograms
Authors: Wallner Björn , Amunts Alexey , Naschberger Andreas , Nystedt Björn , Mirabello Claudio 
Published: December 2022

AbstractDistograms are data structures output by AlphaFold, along with the predicted 3D coordinates of the target protein, that encode predictions about Euclidean distances between pairs of amino acids. Although distograms are often overlooked, they do provide information that is to some extent complementary to that of the final 3D model. Here, we introduce dgram2dmap, a simple tool to convert distograms into distance maps that can be visualised and used in external tools for further downstream analyses. dgram2dmap runs within seconds to minutes, is open source and available on GitHub:https://github.com/clami66/dgram2dmap.
The function of environmentally acquired perfume blends in male orchid bees
Authors: Henske Jonas , Saleh Nicholas W. , Chouvenc Thomas , Ramírez Santiago R. , Eltz Thomas 
Published: December 2022

AbstractPerfume making by male orchid bees is a remarkable behavior giving rise to an entire pollination syndrome in the neotropics. Male orchid bees concoct and store perfume mixtures in specialized hind-leg pockets using volatiles acquired from multiple environmental sources, including orchids. However, the precise function and ultimate causes of this behavior have remained elusive. We supplemented maleEuglossa dilemmareared from trap-nests with perfume loads harvested from wild conspecifics. In dual-choice experiments, males supplemented with perfumes mated with more females, and sired more offspring, than untreated, equal-aged, control males. Our results demonstrate that male-acquired perfumes function as chemical signals emitted during courtship and received by females when selecting mates. Sexual selection might be a key agent shaping the evolution of perfume signaling.One-Sentence SummaryThe possession of exogenous volatiles increase male mating success and paternity in orchid bees.
Cell composition inference and identification of layer-specific transcriptional profiles with POLARIS
Authors: Chen Jiawen , Luo Tianyou , Jiang Minzhi , Liu Jiandong , Gupta Gaorav P , Li Yun 
Published: December 2022

AbstractSpatial transcriptomics (ST) technology, providing spatially resolved transcriptional profiles, facilitates advanced understanding of key biological processes related to health and disease. Sequencing-based ST technologies provide whole-transcriptome profiles, but are limited by the non-single cell level resolution. Lack of knowledge in the number of cells or cell type composition at each spot can lead to invalid downstream analysis, which is a critical issue recognized in ST data analysis. Methods developed, however, tend to under-utilize histological images, which conceptually provide important and complementary information including anatomical structure and distribution of cells. To fill in the gaps, we present POLARIS, a versatile ST analysis method that can perform cell type deconvolution, identify anatomical or functional layer-wise differentially expressed (LDE) genes and enable cell composition inference from histology images. Applied to four tissues, POLARIS demonstrates high deconvolution accuracy, accurately predicts cell composition solely from images, and identifies LDE genes that are biologically relevant and meaningful.
Statistical inference reveals the role of length, breathing, and nucleotide identity in V(D)J nucleotide trimming
Authors: Russell Magdalena L , Simon Noah , Bradley Philip , Matsen Frederick A 
Published: December 2022

AbstractTo appropriately defend against a wide array of pathogens, humans somatically generate highly diverse repertoires of B cell and T cell receptors (BCRs and TCRs) through a random process called V(D)J recombination. Receptor diversity is achieved during this process through both the combinatorial assembly of V(D)J-genes and the junctional deletion and insertion of nucleotides. While the Artemis protein is often regarded as the main nuclease involved in V(D)J recombination, the exact mechanism of nucleotide trimming is not understood. Using a previously-published TCRβrepertoire sequencing data set, we have designed a flexible probabilistic model of nucleotide trimming that allows us to explore various mechanistically-interpretable sequence-level features. We show that local sequence context and the capacity for sequence-breathing, together, can most accurately predict the trimming probabilities of a given V-gene sequence. This model suggests that double-stranded DNA needs to be able to “breathe” for trimming to occur, and provides evidence of a sequence motif that appears to get preferentially trimmed, independent of breathing. Further, we find that the inferred mechanistic coefficients from this model provide accurate prediction for V- and J-gene sequences from other adaptive immune receptor loci. These results refine our understanding of how the Artemis nuclease may function to trim nucleotides during V(D)J recombination and provide another step towards understanding how V(D)J recombination generates diverse receptors and supports a powerful, unique immune response in healthy humans.