bluuebunny/crossref_metadata_2025_split huggingface dataset:
Searching for the extra-tidal stars of globular clusters using high-dimensional analysis and a core particle spray code
Authors: Grondin Steffani M , Webb Jeremy J , Leigh Nathan W C , Speagle(沈佳士) Joshua S , Khalifeh Reem J 
Published: November 2022

ABSTRACT
Three-body interactions can eject stars from the core of a globular cluster, causing them to enter the Galactic halo as extra-tidal stars. While finding extra-tidal stars is imperative for understanding cluster evolution, connecting isolated extra-tidal field stars back to their birth cluster is extremely difficult. In this work, we present a new methodology consisting of high-dimensional data analysis and a particle spray code to identify extra-tidal stars of any Galactic globular cluster using M3 as a case study. Using the t-Stochastic Neighbour Embedding and Uniform Manifold Approximation and Projection machine learning dimensionality reduction algorithms, we first identify a set of 103 extra-tidal candidates in the APOGEE DR17 data catalogue with chemical abundances similar to M3 stars. To confirm each candidate’s extra-tidal nature, we introduce corespray – a new python-based three-body particle spray code that simulates extra-tidal stars for any Galactic globular cluster. Using Gaia EDR3 proper motions and APOGEE DR17 radial velocities, we apply multivariate Gaussian modelling and an extreme deconvolution to identify the extra-tidal candidates that are more likely to be associated with a distribution of corespray-simulated M3 extra-tidal stars than the field. Through these methods, we identify 10 new high-probability extra-tidal stars produced via three-body interactions in M3. We also explore whether any of our extra-tidal candidates are consistent with being ejected from M3 through different dynamical processes. Future applications of corespray will yield better understandings of core dynamics, star formation histories, and binary fractions in globular clusters.
The white dwarf binary pathways survey - IX. Three long period white dwarf plus subgiant binaries
Authors: Parsons S G , Hernandez M S , Toloza O , Zorotovic M , Schreiber M R , Gänsicke B T , Lagos F , Raddi R , Rebassa-Mansergas A , Ren J J , Koester D 
Published: November 2022

ABSTRACT
Virtually all binaries consisting of a white dwarf with a non-degenerate companion can be classified as either close post-interaction systems (with orbital periods of a few days or less), or wide systems (with periods longer than decades), in which both components have effectively evolved as single stars. Binaries with periods between these two extremes can help constrain common envelope efficiency, or highlight alternative pathways towards the creation of compact binaries. To date such binaries have remained mostly elusive. Here we present three white dwarfs in binaries with evolved subgiant stars with orbital periods of 41, 52, and 461 d. Using Hubble Space Telescope spectroscopy we find that all three systems contain low mass white dwarfs (≤0.4 M⊙). One system, TYC 8394−1331−1, is the inner binary of a hierarchical triple, where the white dwarf plus subgiant binary is orbited by a more distant companion star. These binaries were likely formed from a phase of stable but non-conservative mass transfer, as opposed to common envelope evolution. All three systems will undergo a common envelope phase in the future, but the two shorter period systems are expected to merge during this event, while the longest period system is likely to survive and create a close binary with two low mass white dwarfs.
Markhor-derived Introgression of a Genomic Region EncompassingPAPSS2Confers High-altitude Adaptability in Tibetan Goats
Authors: Li Chao , Wu Yujiang , Chen Bingchun , Cai Yudong , Guo Jiazhong , Leonard Alexander S , Kalds Peter , Zhou Shiwei , Zhang Jingchen , Zhou Ping , Gan Shangqu , Jia Ting , Pu Tianchun , Suo Langda , Li Yan , Zhang Ke , Li Lan , Purevdorj Myagmarsuren , Wang Xihong , Li Ming , Wang Yu , Liu Yao , Huang Shuhong , Sonstegard Tad , Wang Ming-Shan , Kemp Stephen , Pausch Hubert , Chen Yulin , Han Jian-Lin , Jiang Yu , Wang Xiaolong 
Published: November 2022

AbstractUnderstanding the genetic mechanism of how animals adapt to extreme conditions is fundamental to determine the relationship between molecular evolution and changing environments. Goat is one of the first domesticated species and has evolved rapidly to adapt to diverse environments, including harsh high-altitude conditions with low temperature and poor oxygen supply but strong ultraviolet radiation. Here, we analyzed 331 genomes of domestic goats and wild caprid species living at varying altitudes (high &gt; 3000 m above sea level and low &lt; 1200 m), along with a reference-guided chromosome-scale assembly (contig-N50: 90.4 Mb) of a female Tibetan goat genome based on PacBio HiFi long reads, to dissect the genetic determinants underlying their adaptation to harsh conditions on the Qinghai-Tibetan Plateau (QTP). Population genomic analyses combined with genome-wide association studies (GWAS) revealed a genomic region harboring the 3′-phosphoadenosine 5′-phosphosulfate synthase 2 (PAPSS2) gene showing strong association with high-altitude adaptability (PGWAS = 3.62 × 10−25) in Tibetan goats. Transcriptomic data from 13 tissues revealed that PAPSS2 was implicated in hypoxia-related pathways in Tibetan goats. We further verified potential functional role of PAPSS2 in response to hypoxia in PAPSS2-deficient cells. Introgression analyses suggested that the PAPSS2 haplotype conferring the high-altitude adaptability in Tibetan goats originated from a recent hybridization between goats and a wild caprid species, the markhor (Capra falconeri). In conclusion, our results uncover a hitherto unknown contribution of PAPSS2 to high-altitude adaptability in Tibetan goats on QTP, following interspecific introgression and natural selection.
Socioeconomic status does not change decision-making in the treatment of distal radius fractures at a level 1 trauma center
Authors: Verlinsky Luke , Ulmer Clinton J. , Griffin Leah P. , Brady Christina I. , Rose Ryan A. 
Published: November 2022

Abstract

Objectives:
To compare operative rates, total hospital charges, and length of stay between different socioeconomic cohorts in treating distal radius fractures (DRFs).

Design:
A retrospective cohort study.

Setting:
Large public level 1 trauma center.

Patients:
A retrospective search of all trauma activations over a 7-year period (2013–2020) yielded 816 adult patients diagnosed with DRF. Patients were separated into cohorts of socioeconomic status based on 2010 US Census data and insurance status.

Intervention:
DRFs were treated either nonoperatively using closed reduction and splinting or operatively using open reduction and internal fixation, closed reduction percutaneous pinning, or external fixator application.

Main Outcome Measurements:
Operative rates of DRF, total hospital charges, and length of stay.

Results:
Patients who were uninsured or in the low-income socioeconomic cohort had no significant difference in operative rates, total hospital costs, or length of stay when compared with their respective insured or standard income groups. Younger patients and those with OTA/AO type C, bilateral, or open DRFs were more likely to undergo operative intervention.

Conclusions:
This study demonstrates that low socioeconomic status based on annual household income and insurance status was not associated with differences in operative rates on DRFs, length of stay, or total hospital charges. These results suggest that outcome disparities between groups may be caused by postoperative differences rather than treatment decision-making. Although this study investigates access to surgical care at a publicly funded level 1 trauma center, disparities may still exist in other models of care.

Level of Evidence:
Prognostic Level III.
Activating de novo monoallelic variants causing inborn errors of immunity in two unrelated children born of HIV-seroconcordant couples
Authors: Lugo Reyes Saul O. , Solórzano Suárez Andrea , Scheffler Mendoza Selma C. , Xóchihua Díaz Luis , González Serrano M. Edith , López Herrera Gabriela , Medina-Torres Edgar Alejandro , Cruz Ugalde Claudia I. , Olguín-Calderón Diana , Berrón Ruiz Laura , Espinosa-Padilla Sara E. , Yamazaki-Nakashimada Marco Antonio , Murata Chiharu 
Published: November 2022

Introduction:
Around 20% of all inborn errors of immunity (IEI) are autosomal dominant or monoallelic, either by haploinsufficiency, negative dominance, or gain of function (GOF). GOF phenotypes usually include autoinflammation, autoimmunity, lymphoproliferation, allergies, and some infections.

Case series:
We describe the cases of two unrelated patients born of HIV-seroconcordant parents. Both patients are HIV-negative but carry de novo GOF missense variants that resulted in inflammatory lymphoproliferative IEI diseases: signal transducer and activator of transcription 3 (STAT3)-GOF and phosphatidylinositol 3-kinase, catalytic delta (PIK3CD)-GOF. Both variants were found through whole-exome sequencing and confirmed by Sanger.
An 11-year-old male with recurrent sinopulmonary infections, dysmorphism, growth delay, bronchiectasis, and mild mental retardation, as well as lymphopenia, thrombocytopenia, and high immunoglobulin M. Both his parents were known to be HIV-positive under anti-retroviral treatment. HIV infection was repeatedly ruled out in the patient, whom through whole-exome sequencing was found to have a heterozygous missense variant in exon 24 of PIK3CD, a hotspot transition, and the most reported variant in PIK3CD-GOF patients.
A 6-year-old male with autoimmune hemolytic anemia, lymphoproliferation, short stature, and intractable diarrhea. Both his parents were found to be HIV-positive. HIV was repeatedly ruled out in the patient by ELISA and viral load. He was found to have a heterozygous missense/splice variant in exon 22 of STAT3, a hotspot transition, and the most reported variant in STAT3-GOF patients.

Discussion:
The AID/APOBEC3 A-H family of proteins are cytidine deaminases that induce G>A hypermutation in both the invading viral DNA and the host genome, which results in stop codons inside the endogenized retroviral sequence. Both variants found in our patients are G to A transitions. Retroviral infection might thus have resulted in host genome instability, and our patients’ rare congenital diseases are the unfortunate consequence of somatic hypermutation in one of their parents’ gametes.
Using conditional Generative Adversarial Networks (GAN) to generatede novosynthetic cell nuclei for training machine learning-based image segmentation
Authors: Cosacak Mehmet Ilyas , Kizil Caghan 
Published: November 2022

ABSTRACTGenerating masks on training data for augmenting machine learning is one of the challenges as it is time-consuming when performed manually. While variable random images can be generated by Generative Adversarial Networks, an image-to-image translation is needed to generate both images and ground truth data. To generate cells and their corresponding masks, we used a new approach to prepare the training data by adding masks on 4 different channels preventing any overlapping between masks on the same channel at an exactly 2-pixel distance. We used GAN to generate nuclei from only two images (415 and 435 nuclei) and tested different GANs with alternating activation functions and kernel sizes. Here, we provide the proof-of-principle application of GAN for image-to-image translation for cell nuclei and tested variable parameters such as kernel and filter sizes and alternating activation functions, which played important roles in GAN learning with small datasets. This approach will decrease the time required to generate versatile training datasets for various cell types and shapes with their corresponding masks for augmenting machine learning-based image segmentation.
Personalized Deep Learning based Source Imaging Framework Improves the Imaging of Epileptic Sources from MEG Interictal Spikes
Authors: Sun Rui , Zhang Wenbo , Bagić Anto , He Bin 
Published: November 2022

AbstractElectromagnetic source imaging (ESI) has been widely used to image brain activities for research and clinical applications from MEG and EEG. It is a challenging task due to the ill-posedness of the problem and the complexity of modeling the underlying brain dynamics. Deep learning has gained attention in the ESI field for its ability to model complex distributions and has successfully demonstrated improved imaging performance for ESI. In this work, we investigated the capability of imaging epileptic sources from MEG interictal spikes using deep learning-based source imaging framework (DeepSIF). A generic DeepSIF model was first trained with a generic head model using a template MRI. A fine-tuning procedure was proposed to introduce personalized head model information into the neural network for a personalized DeepSIF model. Two models were evaluated and compared in extensive computer simulations. The MEG-DeepSIF approach was further rigorously validated for imaging epileptogenic regions from interictal spike recordings in focal epilepsy patients. We demonstrated that DeepSIF can be successfully applied to MEG recordings and the additional fine-tuning step for personalized DeepSIF can alleviate the impact of head model variations and further improve the performance significantly. In a cohort of 29 drug-resistant focal epilepsy patients, the personalized DeepSIF model provided a sublobar concordance of 93%, sublobar sensitivity of 77% and specificity of 99%, respectively. When compared to the seizure-onset-zone defined by intracranial recordings, the localization error is 15.78 ± 5.54 mm; and when compared with resection volume in seizure free patients, the spatial dispersion is 8.19 ± 8.14 mm. DeepSIF enables an accurate and robust imaging of spatiotemporal brain dynamics from MEG recordings, suggesting its unique value to neuroscience research and clinical applications.
Towards One Health surveillance of antibiotic resistance, use and residues of antibiotics in France: characterisation and mapping of existing programmes in humans, animals, food and the environment
Authors: Collineau L. , Bourély C. , Rousset L. , Berger-Carbonne A. , Ploy MC. , Pulcini C. , Colomb-Cotinat M. 
Published: November 2022

AbstractInternational organizations are calling for One Health approaches to tackle antibiotic resistance (ABR). In France, the diversity of surveillance programmes makes it difficult to get an overview of the current surveillance system and its level of integration. This study aimed to map and characterise all French surveillance programmes for ABR, antibiotic use (ABU) and antibiotic residues in humans, animals, food and the environment, to identify integration points, gaps and overlaps.A literature review and interviews with 36 programme coordinators were conducted to identify and characterise programmes using a standardized grid (28 variables). Forty-eight programmes were included. They targeted the human (n=35), animal (n=12), food (n=3) and/or the environment (n=1); 35 programmes focused on ABR, 14 on ABU and two on antibiotic residues. Two programmes were cross-sectoral. Among the 35 ABR programmes, 23 collected bacterial isolates. Bacteria most targeted wereEscherichia coli(n=17 programmes),Klebsiella pneumoniae(n=13), andStaphylococcus aureus(n=12). ESBL-producingE. coliwas monitored by the majority of ABR programmes in humans, animals and food, and is a good candidate for integrated data analysis. ABU indicators were highly variable. Areas poorly covered were the environmental sector, overseas territories, ABR colonisation in humans and ABU in companion animals.The French surveillance system appears rich and extensive, but with gaps and only few integration points. We believe this mapping will be of high interest to policy makers and surveillance stakeholders, and that our methodology may inspire other countries willing to progress towards One Health surveillance of ABR.
Establishing Internationally Accepted Conceptual and Operational Definitions of Social Prescribing Through Expert Consensus: A Delphi Study
Authors: Muhl Caitlin , Mulligan Kate , Bayoumi Imaan , Ashcroft Rachelle , Godfrey Christina 
Published: November 2022

ABSTRACTIntroductionWith the social prescribing movement gaining traction globally, there is a need for an agreed definition of social prescribing. There are two types of definitions – conceptual and operational, meaning agreement on both types of definitions is needed.ObjectiveThe aim of this study was to establish internationally accepted conceptual and operational definitions of social prescribing.DesignA three-round Delphi study was conducted.MethodsConsensus was defineda priorias ≥80% agreement. In Round 1, participants were asked to list key elements that are essential to the conceptual definition of social prescribing and to provide corresponding statements that operationalize each of the key elements. In Round 2, participants were asked to rate their agreement with items from the first round for inclusion in the conceptual and/or operational definitions of social prescribing. Based on the findings from this round, the conceptual and operational definitions of social prescribing were developed, including long and short versions of the conceptual definition. In Round 3, participants were asked to rate their agreement with the conceptual and operational definitions of social prescribing.ParticipantsThis study involved an international, multidisciplinary panel of experts. The expert panel (n=48) represented 26 different countries across five continents, numerous expert groups, and a variety of years of experience with social prescribing, with the average being 5 years (range = 1-20 years).ResultsAfter three rounds, internationally accepted conceptual and operational definitions of social prescribing were established. The definitions were transformed into the Common Understanding of Social Prescribing (CUSP) conceptual framework.ConclusionThis foundational work offers a common thread – a shared sense of what social prescribing is, which may be woven into social prescribing research, policy, and practice to foster common understanding of this concept.STRENGTHS AND LIMITATIONS OF THIS STUDYStrengths of this study include the consensus method that was chosen, the diversity and size of the expert panel, and the fact that consensus was defineda priorias ≥80% agreementLimitations of this study include the fact that only those who could speak, read, and write English were eligible to participate in this study, the attrition of the expert panel, and the fact that the expert panel did not reach 100% agreement on the definitions
A new chapter of the Japanese beetle invasion saga: predicting suitability from long-infested areas to inform surveillance strategies in Europe
Authors: Borner Leyli , Martinetti Davide , Poggi Sylvain 
Published: November 2022

AbstractThe Japanese beetle (Popillia japonica) is a polyphagous pest that spreads rapidly and is estimated to cost more than 460 M$/year in damage and control in the USA alone. This study provides risk maps to inform surveillance strategies in Continental Europe, following the beetle’s introduction and successive spread in the last decade. We developed a species distribution model using a machine-learning algorithm, considering factors relevant to the beetle’s biology, climate, land use and human-related variables. This analysis was performed using presence-only data from native and invaded ranges (Japan, North America, Azores archipelago - Portugal). We gathered more than 30 000 presence data from citizen science platforms and standardized surveys, and generated pseudo-absences using the target-group method. We used the environmental structure of data to randomly sample pseudo-absences, and evaluate model performanceviaa block cross-validation strategy. Our results show that climate, in particular seasonal trends, and human-related variables, are major drivers of the Japanese beetle distribution at the global scale. Risk maps show that Central Europe can be considered as suitable, whereas Southern and Northern European countries are at lower risk. The region currently occupied is among the most suitable according to our predictions, and represents less than 1% of the highest suitable area in Europe. A major cluster of high suitability areas is located near the currently infested zone, whereas others are scattered across the continent. This highlights the importance of designing surveillance strategies considering both active insect dispersal and the possibility of hitchhiking to reach distant areas.
An adaptive interaction between cell type and metabolism drives ploidy evolution in a wild yeast
Authors: Crandall Johnathan G. , Fisher Kaitlin J. , Sato Trey K. , Hittinger Chris Todd 
Published: November 2022

ABSTRACTPloidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here we report an unusual recurrent ploidy reduction in replicate populations of the budding yeastSaccharomyces eubayanusexperimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment-cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.
Nanopore sequencing enables multigenic family reconstruction despite highly frequent PCR-induced recombination
Authors: Namias Alice , Sahlin Kristoffer , Makoundou Patrick , Bonnici Iago , Sicard Mathieu , Belkhir Khalid , Weill Mylène 
Published: November 2022

AbstractThis study developed a new bioinformatics pipeline to acquire all the different copies of multi-copy gene families based on Oxford Nanopore Technologies sequencing of PCR products. We used this pipeline to acquire the sequences of highly similar copies of thecidAandcidBgenes present in the genomes ofWolbachia pipientis(wPip) bacteria infecting the cells ofCulex pipiensmosquitoes. The approach is based on read mapping, SNP calling and haplotyping, using our already wide existing reference database for thecidgenes obtained by cloning and Sanger sequencing. We addressed problems commonly faced when using mapping approaches for multi-copy gene families with highly similar variants (or haplotypes). In addition, we confirmed that PCR amplification causes frequent chimeras which have to be carefully considered when working on families of recombinant genes. We tested the robustness of the pipeline through a combination of analyses of simulated reads and of gene sequence acquisitions through cloning and Sanger sequencing. For genes of which the haplotype cannot be reconstructed from short reads sequencing, this pipeline confers a high throughput acquisition, gives reliable results as well as insights of the relative copy numbers of the different variants.