bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of the angles between magnetic moments and rotation axes in radio pulsars
Authors: Ken’ko Z V , Malov I F 
Published: April 2023

ABSTRACT
Distribution of angles β between magnetic moments and rotation axes for radio pulsars with periods in the interval 0.1 s &lt; P &lt; 2 s has been obtained. This distribution is rather wide with a mean value of 23°. For the bulk of pulsars, the inclination of axes is characterized by moderate values of angles β. About 60 per cent of pulsars considered have angles in the interval from 20° to 45°. The useful correlation between kinematic tkin and characteristic ages τ has been detected. The relationship between tkin and τ can be used to make a conversion of catalogue values of τ to more real pulsar ages tkin. It will be important in further pulsar investigations. It is shown that inclination angles for pulsars with 0.1 s &lt; P &lt; 2 s decrease with their ages. This decrease is the best described by the power law. Values of angles β have been calculated for pulsars, which are at the moment in SNRs. These angles are not changed markedly during 105 yr. Their decrease begins much later.
Retrieval study of cool, directly imaged exoplanet 51 Eri b
Authors: Whiteford Niall , Glasse Alistair , Chubb Katy L , Kitzmann Daniel , Ray Shrishmoy , Phillips Mark W , Biller Beth A , Palmer Paul I , Rice Ken , Waldmann Ingo P , Changeat Quentin , Skaf Nour , Wang Jason , Edwards Billy , Al-Refaie Ahmed 
Published: April 2023

ABSTRACT
Retrieval methods are a powerful analysis technique for modelling exoplanetary atmospheres by estimating the bulk physical and chemical properties that combine in a forward model to best fit an observed spectrum, and they are increasingly being applied to observations of directly imaged exoplanets. We have adapted taurex3, the Bayesian retrieval suite, for the analysis of near-infrared spectrophotometry from directly imaged gas giant exoplanets and brown dwarfs. We demonstrate taurex3’s applicability to sub-stellar atmospheres by presenting results for brown dwarf benchmark GJ 570D which are consistent with previous retrieval studies, whilst also exhibiting systematic biases associated with the presence of alkali lines. We also present results for the cool exoplanet 51 Eri b, the first application of a free chemistry retrieval analysis to this object, using spectroscopic observations from GPI and SPHERE. While our retrieval analysis is able to explain spectroscopic and photometric observations without employing cloud extinction, we conclude this may be a result of employing a flexible temperature-pressure profile which is able to mimic the presence of clouds. We present Bayesian evidence for an ammonia detection with a 2.7σ confidence, the first indication of ammonia in a directly imaged exoplanetary atmosphere. This is consistent with this molecule being present in brown dwarfs of a similar spectral type. We demonstrate the chemical similarities between 51 Eri b and GJ 570D in relation to their retrieved molecular abundances. Finally, we show that overall retrieval conclusions for 51 Eri b can vary when employing different spectral data and modelling components, such as temperature–pressure and cloud structures.
Ferrocenoyl-substituted quinolinone and coumarin as organometallic inhibitors of SARS-CoV-2 3CLpro main protease
Authors: Graf Dominic , Farn Nikolas , Klopf Jonas , Hojjati Mahniya , Schatzschneider Ulrich 
Published: April 2023

Abstract
The 3-chymotrypsin-like protease 3CLpro from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a potential target for antiviral drug development. In this work, three organometallic ferrocene-modified quinolinones and coumarins were compared to their benzoic acid ester analogues with regard to inhibition of 3CLpro using an HPLC-based assay with a 15mer model peptide as the substrate. In contrast to FRET-based assays, this allows direct identification of interference of buffer constituents with the inhibitors, as demonstrated by the complete abolishment of ebselen inhibitory activity in the presence of dithiothreitol as a redox protectant. The presence of the organometallic ferrocene moiety significantly increased the stability of the title compounds towards hydrolysis. Among the studied compounds, 4-ferrocenyloxy-1-methyl-quinol-2-one was identified as the most stable and potent inhibitor candidate. IC50 values determined for ebselen and this sandwich complex compound are (0.40 ± 0.07) and (2.32 ± 0.21) μM, respectively.
Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs
Authors: Jennings Martin D , Srivastava Priya , Kershaw Christopher J , Talavera David , Grant Christopher M , Pavitt Graham D 
Published: April 2023

AbstractIn response to oxidative stress cells reprogram gene expression to enhance levels of antioxidant enzymes and promote survival. In Saccharomyces cerevisiae the polysome-interacting La-related proteins (LARPs) Slf1 and Sro9 aid adaptation of protein synthesis during stress by undetermined means. To gain insight in their mechanisms of action in stress responses, we determined LARP mRNA binding positions in stressed and unstressed cells. Both proteins bind within coding regions of stress-regulated antioxidant enzyme and other highly translated mRNAs in both optimal and stressed conditions. LARP interaction sites are framed and enriched with ribosome footprints suggesting ribosome–LARP–mRNA complexes are identified. Although stress-induced translation of antioxidant enzyme mRNAs is attenuated in slf1Δ, these mRNAs remain on polysomes. Focusing further on Slf1, we find it binds to both monosomes and disomes following RNase treatment. slf1Δ reduces disome enrichment during stress and alters programmed ribosome frameshifting rates. We propose that Slf1 is a ribosome-associated translational modulator that stabilises stalled/collided ribosomes, prevents ribosome frameshifting and so promotes translation of a set of highly-translated mRNAs that together facilitate cell survival and adaptation to stress.
A multidisciplinary approach to the identification of the protein–RNA connectome in double-stranded RNA virus capsids
Authors: Sung Po-yu , Zhou Yiyang , Kao C Cheng , Aburigh Ali A , Routh Andrew , Roy Polly 
Published: April 2023

Abstract
How multi-segmented double-stranded RNA (dsRNA) viruses correctly incorporate their genomes into their capsids remains unclear for many viruses, including Bluetongue virus (BTV), a Reoviridae member, with a genome of 10 segments. To address this, we used an RNA-cross-linking and peptide-fingerprinting assay (RCAP) to identify RNA binding sites of the inner capsid protein VP3, the viral polymerase VP1 and the capping enzyme VP4. Using a combination of mutagenesis, reverse genetics, recombinant proteins and in vitro assembly, we validated the importance of these regions in virus infectivity. Further, to identify which RNA segments and sequences interact with these proteins, we used viral photo-activatable ribonucleoside crosslinking (vPAR-CL) which revealed that the larger RNA segments (S1-S4) and the smallest segment (S10) have more interactions with viral proteins than the other smaller segments. Additionally, using a sequence enrichment analysis we identified an RNA motif of nine bases that is shared by the larger segments. The importance of this motif for virus replication was confirmed by mutagenesis followed by virus recovery. We further demonstrated that these approaches could be applied to a related Reoviridae member, rotavirus (RV), which has human epidemic impact, offering the possibility of novel intervention strategies for a human pathogen.
Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs
Authors: Fan Yu-Jie , Ding Zhan , Zhang Yu , Su Ruibao , Yue Jia-Le , Liang An-Min , Huang Qi-Wei , Meng Yan-Ran , Li Muwang , Xue Yuanchao , Xu Yong-Zhen 
Published: April 2023

Abstract
Conversely to canonical splicing, back-splicing connects the upstream 3' splice site (SS) with a downstream 5'SS and generates exonic circular RNAs (circRNAs) that are widely identified and have regulatory functions in eukaryotic gene expression. However, sex-specific back-splicing in Drosophila has not been investigated and its regulation remains unclear. Here, we performed multiple RNA analyses of a variety sex-specific Drosophila samples and identified over ten thousand circular RNAs, in which hundreds are sex-differentially and -specifically back-spliced. Intriguingly, we found that expression of SXL, an RNA-binding protein encoded by Sex-lethal (Sxl), the master Drosophila sex-determination gene that is only spliced into functional proteins in females, promoted back-splicing of many female-differential circRNAs in the male S2 cells, whereas expression of a SXL mutant (SXLRRM) did not promote those events. Using a monoclonal antibody, we further obtained the transcriptome-wide RNA-binding sites of SXL through PAR-CLIP. After splicing assay of mini-genes with mutations in the SXL-binding sites, we revealed that SXL-binding on flanking exons and introns of pre-mRNAs facilitates back-splicing, whereas SXL-binding on the circRNA exons inhibits back-splicing. This study provides strong evidence that SXL has a regulatory role in back-splicing to generate sex-specific and -differential circRNAs, as well as in the initiation of sex-determination cascade through canonical forward-splicing.
Haplogrep 3 - an interactive haplogroup classification and analysis platform
Authors: Schönherr Sebastian , Weissensteiner Hansi , Kronenberg Florian , Forer Lukas 
Published: April 2023

Abstract
Over the last decade, Haplogrep has become a standard tool for haplogroup classification in the field of human mitochondrial DNA and is widely used by medical, forensic, and evolutionary researchers. Haplogrep scales well for thousands of samples, supports many file formats and provides an intuitive graphical web interface. Nevertheless, the currently available version has limitations when applying it to large biobank-scale data. In this paper, we present a major upgrade to the software by adding (a) haplogroup summary statistics and variant annotations from various publicly available genome databases, (b) an interface to connect new phylogenetic trees, (c) a new state-of-the-art web framework managing large scale data, (d) algorithmic adaptions to improve FASTA classification using BWA-specific alignment rules and (e) a pre-classification quality control step for VCF samples. These improvements will give researchers the opportunity to classify thousands of samples as usual but providing additional ways to investigate the dataset directly in the browser. The web service and its documentation can be accessed freely without any registration at https://haplogrep.i-med.ac.at.
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
Authors: Avila Ricardo , Rubinetti Vincent , Zhou Xinghua , Hu Dongbo , Qian Zhongchao , Cano Marco Alvarado , Rodolpho Everaldo , Tsueng Ginger , Greene Casey , Wu Chunlei 
Published: April 2023

Abstract
Gene definitions and identifiers can be painful to manage–more so when trying to include gene function annotations as this can be highly context-dependent. Creating groups of genes or gene sets can help provide such context, but it compounds the issue as each gene within the gene set can map to multiple identifiers and have annotations derived from multiple sources. We developed MyGeneset.info to provide an API for integrated annotations for gene sets suitable for use in analytical pipelines or web servers. Leveraging our previous work with MyGene.info (a server that provides gene-centric annotations and identifiers), MyGeneset.info addresses the challenge of managing gene sets from multiple resources. With our API, users readily have read-only access to gene sets imported from commonly-used resources such as Wikipathways, CTD, Reactome, SMPDB, MSigDB, GO, and DO. In addition to supporting the access and reuse of approximately 180k gene sets from humans, common model organisms (mice, yeast, etc.), and less-common ones (e.g. black cottonwood tree), MyGeneset.info supports user-created gene sets, providing an important means for making gene sets more FAIR. User-created gene sets can serve as a way to store and manage collections for analysis or easy dissemination through a consistent API.
The 2000s Housing Cycle with 2020 Hindsight: A Neo-Kindlebergerian View
Authors: Chodorow-Reich Gabriel , Guren Adam M , McQuade Timothy J 
Published: April 2023

Abstract
With “2020 hindsight,” the 2000s housing cycle is not a boom–bust but a boom–bust–rebound. Using a spatial equilibrium regression in which house prices are determined by income, amenities, urbanization, and supply, we show that long-run city-level fundamentals predict not only 1997–2019 price and rent growth but also the amplitude of the boom–bust–rebound. This evidence motivates our model of a cycle rooted in fundamentals. Households learn about fundamentals by observing “dividends” but become over-optimistic in the boom due to diagnostic expectations. A bust ensues when beliefs start to correct, exacerbated by a price–foreclosure spiral that drives prices below their long-run level. The rebound follows as prices converge to a path commensurate with higher fundamental growth. The estimated model explains the boom–bust–rebound with a single shock and accounts quantitatively for the dynamics of prices, rents, and foreclosures in cities with the largest cycles. We draw implications for asset cycles more generally.
Vaginal dryness in women infected by human T-lymphotropic virus type 1: an exploratory study
Authors: Martins Adenilda Lima Lopes , de Aquino Firmino Alisson , Boa-Sorte Ney , Araújo Jean Paulo Lacerda , Paixão Taiane Silva , Viriato Adriele Ribeiro França , Galvão-Castro Bernardo , Grassi Maria Fernanda Rios 
Published: April 2023

AbstractBackgroundHuman T-lymphotropic virus type-1 (HTLV-1) causes a variety of sicca symptoms, including xeroderma, xerostomia, and xerophthalmia.AimWe sought to evaluate vaginal dryness via the degree of perceived vaginal lubrication, vaginal hormonal cytology, and direct measurements of vaginal wetting.MethodsThe research was designed as a cross-sectional study. Vaginal dryness was assessed by scores in the lubrication domain of the Female Sexual Function Index (FSFI) questionnaire and the Vaginal Maturation Index (VMI) determined by vaginal hormonal cytology, as well as the measurement of vaginal lubrication using Schirmer strips placed at the anterior vaginal wall. Medians (25th-75th percentiles) were calculated for each group and compared using a nonparametric Kruskal-Wallis test and the Dunn-Bonferroni post hoc method.OutcomesOutcomes were detection of the presence of vaginal dryness in women who were infected or noninfected with HTLV-1.ResultsHTLV-1–infected women (n = 72, 57 asymptomatic and 15 with HTLV-1–associated myelopathy/tropical spastic paraparesis [HAM/TSP]) and uninfected women (n = 49) were studied. Women with HAM/TSP had significantly lower FSFI lubrication scores than asymptomatic and uninfected women (P = .032). In addition, women with HAM/TSP had significantly lower VMI compared with the asymptomatic and uninfected groups (P = .027 and P = .039, respectively).Clinical ImplicationsThe results of this study show a reduction in vaginal lubrication in HTLV-1-infected women diagnosed with HAM/TSP compared with asymptomatic and uninfected women.Strengths and LimitationsThe lack of a gold standard test for the diagnosis of vaginal dryness and the fact that no assessment of vaginal pH was performed were limitations of this study. The strength of the study was the comprehensive assessment of vaginal dryness from several perspectives: subjective (perception of vaginal lubrication according to the vaginal lubrication domain of the FSFI), hormonal (vaginal hormonal cytology to assess local hormone status), and the degree of vaginal moisture (direct measurement of vaginal dryness with an instrument, the Schirmer strip, already used to measure the presence of dry eye).ConclusionHTLV-1-infected women with HAM/TSP have decreased vaginal lubrication compared with asymptomatic and uninfected women after adjusting for age.
Quantifying the number of US men with erectile dysfunction who are potential candidates for penile prosthesis implantation
Authors: Rojanasarot Sirikan , Williams Abimbola O , Edwards Natalie , Khera Mohit 
Published: April 2023

AbstractIntroductionPenile prosthesis implantation (PPI) is a treatment option recommended in clinical guidelines for erectile dysfunction (ED). However, a limited number of urologists perform PPI procedures in the United States.AimTo quantify the number of insured men with ED in the United States and project the number of potential candidates for PPI in 2022.MethodsAn Excel-based disease impact model was constructed using a top-down estimation approach. The starting US male population consisted of adult men from 2022 US Census data after exclusion of age-specific mortality rates from the National Vital Statistics Reports. Men with health insurance were included in the model based on insurance status data from the US Census database. ED prevalence and ED treatment rates were obtained from administrative claims data analyses—the Merative MarketScan Commercial Database (18-64 years) and the 5% Medicare Standard Analytical Files (≥65 years)—and literature-based estimates of patient-reported ED prevalence.OutcomesThe number of men with ED in the United States and the number of potential candidates for PPI were estimated.ResultsBy utilizing ED prevalence based on administrative claims, an estimated 8.3% of insured men (10,302,540 estimated men [8,882,548 aged 18-64 years and 1,419,992 aged ≥65 years]) had a diagnosis of ED and sought ED care, out of 124,318,519 eligible US men aged ≥18 years in 2022. An estimated 17.1% of men with an ED diagnosis claim could benefit from PPI in 2022 (1,759,248 men aged ≥18 years). Patient self-reported ED prevalence across all ages ranged from 5.1% to 70.2%. Scenario analyses applying the patient self-reported ED prevalence range revealed the number of men in the United States who could benefit from PPI could have been higher than 1.7 million if their ED symptoms were diagnosed by health care providers.Clinical ImplicationsMost men with ED in the United States are undertreated, and many could benefit from PPI.Strengths and LimitationsThis analysis is a US population–level estimation. However, given this study utilized a variety of assumptions, the results may vary if different model assumptions are applied.ConclusionsThis disease impact model estimated that approximately 10.3 million men were diagnosed with ED by their health care providers and sought ED care in the United States in 2022. Of those, 1.7 million men could be PPI candidates and benefit from the treatment option.
EptA of Riemerella anatipestifer mediates phenotypes involved in colistin resistance and virulence
Authors: Chen Qiwei , Quan Heng , Yu Yongfeng , Liu Donghui , Li Caiyu , Chu Yuefeng , Gong Xiaowei 
Published: April 2023

AbstractColistin (polymyxin E) is a group of cationic antimicrobial cyclic peptides and is recognized as a last‐resort defense against lethal infections with carbapenem‐resistant pathogens. In addition to the plasmid‐borne mobilized phosphoethanolamine (PEA) transferases, the functional expression of lipid A‐modifying enzymes encoded on chromosomes has been attributed to intrinsic bacterial colistin resistance. However, the mechanisms of colistin resistance in Riemerella anatipestifer remain unknown. Herein, the GE296_RS09715 gene‐encoded Lipid A PEA transferases (RaEptA) was identified in R. anatipestifer. Genetic and structural analyses revealed that the amino acid sequence of RaEptA shared 26.6%–33.1% similarities with the family of Lipid A PEA transferases (EptA) and MCR‐like proteins and have defined 12 residues that contribute to the formation of phosphatidylethanolamine (PE)‐recognizable cavities. Comparative analyses of colistin resistance in RA‐LZ01 and RA‐LZ01ΔRaEptA showed the level of colistin has fallen from 96 μg mL−1 down to 24 ~ 32 μg mL−1. Site‐directed mutagenesis assay of the PE‐binding cavity and expression of the mutants reveals that K309‐rRaEptA can remodel the surface of Escherichia coli and rendering it resistant to colistin, suggesting this point‐mutation of P309K is necessary for EptA‐mediated lipid A modification. Moreover, the virulence of RA‐LZ01ΔRaEptA was attenuated compared with RA‐LZ01 both in vivo and vitro. Taken together, the results represent the RaEptA involved in the colistin resistance and pathogenicity, and the P309K mutation might alter bacterial adaptation and increase the spread of colistin resistance from R. anatipestifer to other gram‐negative bacteria. The findings of this study suggest another scenario for the spread of colistin resistance genes and should be considered by a wide audience.
Phenobarbital-Based Protocol for Alcohol Withdrawal Syndrome in a Medical ICU: Pre-Post Implementation Study
Authors: Alwakeel Mahmoud , Alayan Dina , Saleem Talha , Afzal Saira , Immler Ellen , Wang Xiaofeng , Akbik Bassel , Duggal Abhijit 
Published: April 2023

OBJECTIVES:
We assessed the efficacy and safety of PB compared with benzodiazepine (BZD)-based protocols in treating AWS in MICU.

DESIGN:
Single-center, pre-post protocol implementation study.

SETTING:
The setting is a forty-bed MICU in a tertiary-level academic medical center.

PATIENTS:
We included all patients admitted to the MICU with a primary diagnosis of AWS.

INTERVENTIONS:
Intravenous PB 260 mg followed by 130-mg doses every 15–30 minutes as needed up to 15 mg/kg of ideal body weight versus escalating doses of BZD, to achieve a Clinical Institute Withdrawal Assessment Alcohol Scale-Revised score less than 10.

MEASUREMENTS AND MAIN RESULTS:
ICU and hospital length of stay (LOS), in addition to safety measures were the main outcomes of the study. A total of 102 patients were included, 51 in the PB arm and 51 in the BZD arm. There were no differences in baseline clinical characteristics. Half the patients in each group were admitted with delirium tremens. The use of PB-based protocol was associated with 35% reduction in median ICU LOS (1.5 d [interquartile range, 1.2–2.4 d] vs 2.3 d [1.4–4.8 d]; p = 0.009) and 50% reduction in hospital LOS (3 d [2.7–4 d] vs 6 d [4–10 d]; p < 0.001). After adjustment for comorbidities and clinical factors, PB protocol decreased ICU LOS days by 40% (95% CI; 25.8–53.5%). PB group required fewer adjunctive medications to control symptoms (0.7 [0.5–1] vs 2.5 [2–3]; p < 0.001), less need for intubation (1/51 [2%] vs 10/10 [19.6%]; p = 0.023) and less need for physical restraint (19/51 [37.3%] vs 29/51 [56.9%]; p = 0.047), compared with the BZD group.

CONCLUSIONS:
A protocol utilizing rapidly escalating doses of PB over a short period is an effective and safe alternative to BZD in treating AWS in MICU.