bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fission and fusion of heavy nuclei induced by the passage of a radiation-mediated shock in BNS mergers
Authors: Granot Alon , Levinson Amir , Nakar Ehud 
Published: August 2024

ABSTRACT
We compute the structure of a Newtonian, multi-ion radiation-mediated shock (RMS) for different compositions anticipated in various stellar explosions. We use a multifluid RMS model that incorporates electrostatic coupling between the different plasma constituents as well as Coulomb friction in a self-consistent manner, and approximates the effect of pair creation and the presence of free neutrons in the shock upstream on the shock structure. We find that under certain conditions a significant velocity separation is developed between different ions in the shock downstream and demonstrate that in fast enough shocks ion–ion collisions may trigger fusion and fission events at a relatively high rate. Our analysis ignores anomalous coupling through plasma microturbulence, which might reduce the velocity spread downstream below the activation energy for nuclear reactions. A rough estimate of the scale separation in RMS suggests that for shocks propagating in binary neutron star (BNS) merger ejecta, the anomalous coupling length may exceed the radiation length, allowing a considerable composition change behind the shock via inelastic collisions of $\alpha$ particles with heavy elements at shock velocities $\beta _\mathrm{ u}\gtrsim 0.25$. A sufficient abundance of free neutrons in the shock upstream, as expected during the first second after the merger, is also expected to alter the ejecta composition through neutron capture downstream. The resultant change in the composition profile may affect the properties of the early kilonova emission. The generation of microturbulence due to velocity separation can also give rise to particle acceleration that might alter the breakout signal in supernovae and other systems.
Blind QSO reconstruction challenge: exploring methods to reconstruct the Ly α emission line of QSOs
Authors: Greig Bradley , Bosman S E I , Davies F B , Ďurovčíková D , Fathivavsari H , Liu B , Meyer R A , Sun Z , D’Odorico V , Gallerani S , Mesinger A , Ting Y -S 
Published: August 2024

ABSTRACT
Reconstructing the intrinsic Ly $\alpha$ line flux from high-z QSOs can place constraints on the neutral hydrogen content of the intergalactic medium during reionization. There are now $\gtrsim 10$ different Ly $\alpha$ reconstruction pipelines using different methodologies to predict the Ly $\alpha$ line flux from correlations with the spectral information redwards of Ly $\alpha$. However, there have been few attempts to directly compare the performance of these pipelines. Therefore, we devised a blind QSO challenge to compare these reconstruction pipelines on a uniform set of objects. Each author was provided de-identified, observed rest-frame QSO spectra with spectral information only redwards of 1260 Å rest-frame to ensure unbiased reconstruction. We constructed two samples of 30 QSOs, from X-Shooter and Sloan Digital Sky Survey (SDSS) both spanning $3.5\lt z\lt 4.5$. Importantly, the purpose of this comparison study was not to champion a single, best-performing reconstruction pipeline but rather to explore the relative performance of these pipelines over a range of QSOs with broad observational characteristics to infer general trends. In summary, we find machine-learning approaches in general provide the strongest ‘best guesses’ but underestimate the accompanying statistical uncertainty, although these can be recalibrated, while pipelines that decompose the spectral information, for example principal component or factor analysis, generally perform better at predicting the Ly $\alpha$ profile. Further, we found that reconstruction pipelines trained on SDSS QSOs performed similarly on average for both the X-Shooter and SDSS samples indicating no discernible biases owing to differences in the observational characteristics of the training set or QSO being reconstructed, although the recovered distributions of reconstructions for X-Shooter were broader likely due to an increased fraction of outliers.
Rational design of base, sugar and backbone modifications improves ADAR-mediated RNA editing
Authors: Lu Genliang , Shivalila Chikdu , Monian Prashant , Yu Hui , Harding Ian , Briem Stearne , Byrne Michael , Faraone Alyse , Friend Stephen , Huth Olivia , Iwamoto Naoki , Kawamoto Tomomi , Kumarasamy Jayakanthan , Lamattina Anthony , Longo Kenneth , McCarthy Leah , McGlynn Andrew , Molski Allison , Pan Qianli , Pu Tom , Purcell-Estabrook Erin , Rossi Jeff , Standley Stephany , Thomas Carina , Walen Alexandra , Yang Hailin , Kandasamy Pachamuthu , Vargeese Chandra 
Published: August 2024

Abstract
AIMers are short, chemically modified oligonucleotides that induce A-to-I RNA editing through interaction with endogenous adenosine deaminases acting on RNA (ADAR) enzymes. Here, we describe the development of new AIMer designs with base, sugar and backbone modifications that improve RNA editing efficiency over our previous design. AIMers incorporating a novel pattern of backbone and 2′ sugar modifications support enhanced editing efficiency across multiple sequences. Further efficiency gains were achieved through incorporation of an N-3-uridine (N3U), in place of cytidine (C), in the ‘orphan base’ position opposite the edit site. Molecular modeling suggests that N3U might enhance ADAR catalytic activity by stabilizing the AIMer-ADAR interaction and potentially reducing the energy required to flip the target base into the active site. Supporting this hypothesis, AIMers containing N3U consistently enhanced RNA editing over those containing C across multiple target sequences and multiple nearest neighbor sequence combinations. AIMers combining N3U and the novel pattern of 2′ sugar chemistry and backbone modifications improved RNA editing both in vitro and in vivo. We provide detailed N3U synthesis methods and, for the first time, explore the impact of N3U and its analogs on ADAR-mediated RNA editing efficiency and targetable sequence space.
A new perspective on microRNA-guided gene regulation specificity, and its potential generalization to transcription factors and RNA-binding proteins
Authors: Seitz Hervé 
Published: August 2024

Abstract
Our conception of gene regulation specificity has undergone profound changes over the last 20 years. Previously, regulators were considered to control few genes, recognized with exquisite specificity by a ‘lock and key’ mechanism. However, recently genome-wide exploration of regulator binding site occupancy (whether on DNA or RNA targets) revealed extensive lists of molecular targets for every studied regulator. Such poor biochemical specificity suggested that each regulator controls many genes, collectively contributing to biological phenotypes. Here, I propose a third model, whereby regulators’ biological specificity is only partially due to ‘lock and key’ biochemistry. Rather, regulators affect many genes at the microscopic scale, but biological consequences for most interactions are attenuated at the mesoscopic scale: only a few regulatory events propagate from microscopic to macroscopic scale; others are made inconsequential by homeostatic mechanisms. This model is well supported by the microRNA literature, and data suggest that it extends to other regulators. It reconciles contradicting observations from biochemistry and comparative genomics on one hand and in vivo genetics on the other hand, but this conceptual unification is obscured by common misconceptions and counter-intuitive modes of graphical display. Profound understanding of gene regulation requires conceptual clarification, and better suited statistical analyses and graphical representation.
Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch
Authors: Hicks Chad W , Rahman Sanim , Gloor Susan L , Fields James K , Husby Natalia Ledo , Vaidya Anup , Maier Keith E , Morgan Michael , Keogh Michael-Christopher , Wolberger Cynthia 
Published: August 2024

Abstract
Monoubiquitination of histones H2B-K120 (H2BK120ub) and H2A-K119 (H2AK119ub) play opposing roles in regulating transcription and chromatin compaction. H2BK120ub is a hallmark of actively transcribed euchromatin, while H2AK119ub is highly enriched in transcriptionally repressed heterochromatin. Whereas H2BK120ub is known to stimulate the binding or activity of various chromatin-modifying enzymes, this post-translational modification (PTM) also interferes with the binding of several proteins to the nucleosome H2A/H2B acidic patch via an unknown mechanism. Here, we report cryoEM structures of an H2BK120ub nucleosome showing that ubiquitin adopts discrete positions that occlude the acidic patch. Molecular dynamics simulations show that ubiquitin remains stably positioned over this nucleosome region. By contrast, our cryoEM structures of H2AK119ub nucleosomes show ubiquitin adopting discrete positions that minimally occlude the acidic patch. Consistent with these observations, H2BK120ub, but not H2AK119ub, abrogates nucleosome interactions with acidic patch-binding proteins RCC1 and LANA, and single-domain antibodies specific to this region. Our results suggest a mechanism by which H2BK120ub serves as a gatekeeper to the acidic patch and point to distinct roles for histone H2AK119 and H2BK120 ubiquitination in regulating protein binding to nucleosomes.
GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations
Authors: Degalez Fabien , Bardou Philippe , Lagarrigue Sandrine 
Published: August 2024

Abstract
GEGA is a user-friendly tool designed to navigate through various genomic and functional information related to an enriched gene atlas in chicken that integrates the gene catalogues from the two reference databases, NCBI-RefSeq and EMBL-Ensembl/GENCODE, along with four additional rich resources such as FAANG and NONCODE. Using the latest GRCg7b genome assembly, GEGA encompasses a total of 78 323 genes, including 24 102 protein-coding genes (PCGs) and 44 428 long non-coding RNAs (lncRNAs), significantly increasing the number of genes provided by each resource independently. However, GEGA is more than just a gene database. It offers a range of features that allow us to go deeper into the functional aspects of these genes. Users can explore gene expression and co-expression profiles across 47 tissues from 36 datasets and 1400 samples, discover tissue-specific variations and their expression as a function of sex or age and extract orthologous genes or their genomic configuration relative to the closest gene. For the communities interested in a specific gene, a list of genes or a quantitative trait locus region in chicken, GEGA’s user-friendly interface facilitates efficient gene analysis, easy downloading of results and a multitude of graphical representations, from genomic information to detailed visualization of expression levels.
SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects
Authors: Ferrer Florensa Alfred , Almagro Armenteros Jose Juan , Nielsen Henrik , Aarestrup Frank Møller , Clausen Philip Thomas Lanken Conradsen 
Published: August 2024

Abstract
The use of deep learning models in computational biology has increased massively in recent years, and it is expected to continue with the current advances in the fields such as Natural Language Processing. These models, although able to draw complex relations between input and target, are also inclined to learn noisy deviations from the pool of data used during their development. In order to assess their performance on unseen data (their capacity to generalize), it is common to split the available data randomly into development (train/validation) and test sets. This procedure, although standard, has been shown to produce dubious assessments of generalization due to the existing similarity between samples in the databases used. In this work, we present SpanSeq, a database partition method for machine learning that can scale to most biological sequences (genes, proteins and genomes) in order to avoid data leakage between sets. We also explore the effect of not restraining similarity between sets by reproducing the development of two state-of-the-art models on bioinformatics, not only confirming the consequences of randomly splitting databases on the model assessment, but expanding those repercussions to the model development. SpanSeq is available at https://github.com/genomicepidemiology/SpanSeq.
Defining the Landscape of Educational Experiences in Transplant Infectious Diseases: A National Survey of Infectious Diseases Fellows in the United States
Authors: Phadke Varun K , Nematollahi Saman , Steinbrink Julie M , Bartash Rachel , Morales Megan K , Roberts Scott C , Ardura Monica I , Theodoropoulos Nicole M 
Published: August 2024

Abstract

Background
Transplant infectious diseases (TID) is a growing area of expertise within infectious diseases (ID), but TID training is not standardized. Previous surveys of fellows identified opportunities to improve TID education resources but did not explore didactic, clinical, and nonclinical experiences comprehensively.

Methods
The American Society of Transplantation ID Community of Practice surveyed adult and pediatric fellows in US-based general ID or dedicated TID training programs to explore their didactic exposure, clinical experiences, and non–direct patient care activities in TID.

Results
A total of 234 fellows initiated the survey, and 195 (83%) (190 general ID and 19 TID fellows, including 125 adult, 76 pediatric, and 8 combined adult-pediatric fellows) completed the entire survey. More than half of the fellows described receiving no formal curricular content on most foundational topics in transplant medicine. Almost all respondents (&gt;90%) had some inpatient TID experience, but for &gt;60% of fellows this was &lt;12 weeks annually. Clinical exposure varied by fellow and patient type—in an average month rotating on an inpatient TID service, more than half of adult fellows had evaluated ≥10 kidney, liver, or hematopoietic stem cell transplant recipients but &lt;10 heart, lung, pancreas, or intestinal recipients; pediatric fellows saw &lt;10 of all patient types. Nearly half (46%) of general ID fellows had not spent any time in the dedicated TID clinic at their program. Few fellows had participated in protocol development, organ selection meetings, or donor evaluations.

Conclusions
This survey highlights important gaps in TID training. Given the increasing need for TID specialists, updated curricula and educational resources are needed.
Inflammatory cytokine signalling in vulvovaginal candidiasis: a hot mess driving immunopathology
Authors: Cheng Kar On , Montaño Dolly E , Zelante Teresa , Dietschmann Axel , Gresnigt Mark S 
Published: August 2024

Abstract
Protective immunity to opportunistic fungal infections consists of tightly regulated innate and adaptive immune responses that clear the infection. Immune responses to infections of the vaginal mucosa by Candida species are, however, an exception. In the case of vulvovaginal candidiasis (VVC), the inflammatory response is associated with symptomatic disease, rather than that it results in pathogen clearance. As such VVC can be considered an inflammatory disease, which is a significant public health problem due to its predominance as a female-specific fungal infection. Particularly, women with recurrent VVC (RVVC) suffer from a significant negative impact on their quality of life and mental health. Knowledge of the inflammatory pathogenesis of (R)VVC may guide more effective diagnostic and therapeutic options to improve the quality of life of women with (R)VVC. Here, we review the immunopathogenesis of (R)VVC describing several elements that induce an inflammatory arson, starting with the activation threshold established by vaginal epithelial cells that prevent unnecessary ignition of inflammatory responses, epithelial and inflammasome-dependent immune responses. These inflammatory responses will drive neutrophil recruitment and dysfunctional neutrophil-mediated inflammation. We also review the, sometimes controversial, findings on the involvement of adaptive and systemic responses. Finally, we provide future perspectives on the potential of some unexplored cytokine axes and discuss whether VVC needs to be subdivided into subgroups to improve diagnosis and treatment.
Long-term spectral variations of V Sagittae: Two spectroscopic states with red- or blue-shifted emission wings of H i and He ii
Authors: Iijima Takashi , Naito Hiroyuki , Narusawa Sin-ya 
Published: August 2024

Abstract
The spectral variation in the optical region of a peculiar variable star V Sagittae was monitored in the recent three decades. The main aim of this article is to report several interesting phenomena discovered in the monitoring; we briefly discuss interpretations of them. Emission lines of H i and He ii were decomposed into narrow components and wide wings. The radial velocities of the wings were related to the orbital motion of the hot primary, but did not reflect it directly. Widely red-shifted sinusoidal variations according to the orbital period were detected in 1993–2005 (e.g., $K = 195$ km s$^{-1}$ and $\gamma = +252$ km s$^{-1}$ for He ii 4686). Sporadic blue-shifts were also observed. The mode of the radial velocity variation drastically changed between 2005 and 2007. Red-shifted sinusoidal variations ($K = 224$ km s$^{-1}$ and $\gamma = +260$ km s$^{-1}$ idem) or blue-shifted ones ($K =206$ km s$^{-1}$ and $\gamma = -289$ km s$^{-1}$ idem) appeared alternately in 2007–2019. One red- or blue-shift state lasted several years. The radial velocities of O iii 5592 and the doublet C iv 5805 exhibited sinusoidal variations without large red- or blue-shifts (e.g., $K =215$ km s$^{-1}$ and $\gamma = -18$ km s$^{-1}$ for C iv 5805). The widths of emission lines He ii 5412 and C iv in the doublet 5805 suggest that helium and carbon ions contained nearly the same kinetic energy, because the former line was wider than the latter by a factor of about $\surd {3}$ on most spectra. It is probable that there was no large-scale mass motion in such a thermal-equilibrium-like condition. The C iv lines and He ii 5412 had roughly same widths, like the spectra of Wolf–Rayet stars, only three times in 2007–2019 on which there were likely large-scale mass outflows.
Informed Voting
Authors: Gao Meng , Huang Jiekun 
Published: August 2024

Abstract
Information production by shareholders is essential for proxy voting to produce efficient outcomes. We propose a stock return-based measure to capture informed voting. Our measure, the vote alpha, quantifies the extent to which a shareholder votes in the direction that the market perceives as value increasing. Using data on mutual funds’ proxy voting records, we find that the vote alpha exhibits persistence. Our main result shows that the voting pattern of high vote alpha funds positively predicts long-run abnormal stock returns following contentious votes, suggesting that these funds possess information about the shareholder value implication of contentious governance proposals.
A Transdiagnostic Network Analysis of Childhood Trauma and Psychopathology
Authors: Huang Yi-hang , Liu Chao , Zhang Jian-biao , Li Shuai-biao , Wang Ling-ling , Hu Hui-xin , Cai Yuan , Zhu Zhenhua , Chu Min-yi , Wang Yi , Lv Qin-yu , Lui Simon S Y , Yi Zheng-hui , Hui Li , Chan Raymond C K 
Published: August 2024

Abstract

Background and Hypothesis
Psychiatric comorbidities suggest that symptoms overlap across different diagnoses; the transdiagnostic network approach is valuable for studying psychopathology. Childhood trauma is a common transdiagnostic risk factor for psychiatric disorders, but the complex relationship between childhood trauma and psychopathology has seldom been investigated using a large cross-sectional transdiagnostic sample.

Study Design
This study recruited 869 patients with different diagnoses, including 418 schizophrenia, 215 bipolar disorder, and 236 major depressive disorder. Participants completed psychiatric interviews and self-report questionnaires. We constructed dimension- and item-level Least Absolute Shrinkage and Selection Operator-based (LASSO) networks to explore the relationship between childhood trauma, psychopathology, and duration of illness. Moreover, we constructed directed acyclic graphs (DAGs) to tentatively clarify the potential directions of associations among these variables. Network Comparison Tests (NCTs) were conducted for different diagnostic groups and gender-stratified groups.

Study Results
The transdiagnostic LASSO networks showed that different types of childhood trauma exerted distinct impacts on various psychopathological dimensions. Emotional abuse was linked to depressive symptoms, physical abuse to excited symptoms, sexual abuse to positive and disorganized symptoms, emotional neglect to depressive symptoms and motivation and pleasure (MAP) deficits factor of negative symptoms, and physical neglect to MAP factor. The DAG findings generally concurred with the LASSO network. The NCT showed comparable networks.

Conclusions
Our findings suggest that childhood trauma is significantly associated with the development of psychopathology across different diagnostic groups. The affective pathway model suggests that early identification and tailored interventions would be needed for people with a history of childhood trauma.
Governance by Gaslight: The Reproductive Politics of the Two-Child Limit
Authors: Hewer Rebecca 
Published: August 2024

Abstract
In 2017, the UK government limited the number of children for a whom a low-income family could claim a means tested benefit (the “child element” of “Universal Credit”) to two. Since then, over 400,000 families—including 1.5 million children—have been affected by the “two-child limit.” Emerging research indicates that the limit has done little to influence fertility rates, nothing to influence workforce participation, and a great deal to increase financial hardship and poverty. Via a synthesis of existing research, and a critical analysis of formal policy dialogue, I explore the specifically reproductive politics of the two-child limit. I cast the limit as “successful” reproductive governance, a “technology of discipline” with complementary effects and rationales, which works by further marginalizing intersectionally marginalized women. In concluding, I argue that the state justifies this abject outcome via what has been termed “cultural gaslighting.”