bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of Change in Nucleotide Diversity Over Gene Length
Authors: Ali Farhan 
Published: April 2024

Abstract
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site of a gene. The degree of reduction in diversity at the translation initiation site and the length of this region of reduced diversity can be quantified as “Effect Size” and “Effect Length” respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of translation-associated traits such as the avoidance of mRNA secondary structure around translation initiation site, the number of rRNAs, and relative codon usage of ribosomal genes. Evolutionary simulations under purifying selection reproduce the observed patterns and diversity–length correlation and highlight that selective constraints on the 5′-region of a gene may be more extensive than previously believed. These results have implications for the estimation of effective population size, and relative mutation rates, and for genome scans of genes under positive selection based on “silent-site” diversity.
Evaluating the potential impacts of grey seal predation and fishery bycatch/discards on cod productivity on the Western Scotian Shelf and in the Bay of Fundy
Authors: Rossi Steven P , Wang Yanjun , den Heyer Cornelia E , Benoît Hugues P 
Published: April 2024

Abstract
The recovery of many groundfish stocks in the Northwest Atlantic has been impeded by elevated mortality among older/larger individuals. The sources of groundfish mortality are generally uncertain, though predation by growing grey seal herds and unreported fishing are thought to be drivers of mortality for Atlantic cod (Gadus morhua) on the Western Scotian Shelf and Bay of Fundy (4X5Y), as well as in nearby ecosystems. We developed a statistical catch-at-age model for 4X5Y cod that accounted for grey seal predation and bycatch/discards and tested the model across a broad range of consumption and discard scenarios. We found that most cod mortality was unexplained by seal predation and fishing when cod comprised a small to moderate portion of the grey seal diet. Predation and fishing accounted for slightly more than half of recent cod mortality when cod was highly prevalent in the seal diet (45% by weight) but explained little historical mortality. Bycatch was a minor source of mortality prior to 2019 and accounted for 0.%1–8.1% of recent mortality. Increased sampling of seal diets and monitoring of emerging seal colonies is necessary for reducing uncertainties around seal predation effects in the Northwest Atlantic.
Respiratory Syncytial Virus Prefusion F Vaccination: Antibody Persistence and Revaccination
Authors: Walsh Edward E , Falsey Ann R , Zareba Agnieszka M , Jiang Qin , Gurtman Alejandra , Radley David , Gomme Emily , Cooper David , Jansen Kathrin U , Gruber William C , Swanson Kena A , Schmoele-Thoma Beate 
Published: April 2024

Abstract

Background
Respiratory syncytial virus (RSV) causes substantial respiratory disease. Bivalent RSV prefusion F (RSVpreF) vaccine is licensed in ≥60-year-olds. RSVpreF was well tolerated and immunogenic in a phase 1/2 study. We evaluated antibody persistence after initial vaccination and safety and immunogenicity after revaccination from this study.

Methods
Healthy adults were randomized to receive initial vaccination and revaccination 12 months later with either placebo or RSVpreF (240 µg with or without aluminum hydroxide). RSV-A and RSV-B geometric mean neutralizing titers (GMTs) were measured through 12 months after both vaccinations. Tolerability and safety were assessed.

Results
There were 263 participants revaccinated (18–49 years old, n = 134; 65–85 years old, n = 129). Among 18- to 49-year-olds and 65- to 85-year-olds, geometric mean fold rises (GMFRs) for both RSV subgroups (RSV-A, RSV-B) 1 month after initial RSVpreF vaccination were 13.3 to 20.4 and 8.9 to 15.5, respectively, as compared with levels before initial vaccination; corresponding GMFRs 12 months after initial vaccination were 4.1 to 5.0 and 2.6 to 4.1. GMFRs 1 month after revaccination vs levels before revaccination were 1.4 to 2.3 and 1.4 to 2.2 for 18- to 49-year-olds and 65- to 85-year-olds. Peak GMTs after revaccination were lower than those after initial vaccination. GMTs 12 months after initial vaccination and revaccination were similar, with GMFRs ranging from 0.7 to 1.6. No safety signals occurred.

Conclusions
RSVpreF revaccination was immunogenic and well tolerated among adults.
Clinical Trials Registration. NCT03529773 (ClinicalTrials.gov).
Impact of deoxynivalenol in a calcium depletion and repletion nutritional strategy in piglets
Authors: Sauvé Béatrice , Guay Frédéric , Létourneau Montminy Marie-Pierre 
Published: April 2024

Abstract
This study evaluated the effect of dietary calcium (Ca) levels and deoxynivalenol (DON) contamination on Ca and phosphorus (P) utilization and bone mineralization in piglets. During an initial 13-d depletion phase, 64 piglets (15.7 ± 0.7 kg) received a control (DON−) or DON-contaminated treatment (DON+, 2.7 mg DON/kg) with either a low Ca (Ca−, 0.39%) or normal Ca level (Ca+, 0.65%) with a constant digestible P level (0.40%). A second group of 16 piglets received DON− or DON+ treatments for 9 d for gene expression analysis. During the subsequent 14-d repletion phase, all piglets were fed a Ca+ DON− diet containing 0.65% Ca and 0.35% digestible P without DON. After 5 d of the depletion phase, the absorption of P (DON × Ca; P &lt; 0.05) and Ca was increased by the Ca− (P &lt; 0.01) and DON+ (P &lt; 0.01) diet. After 13 d, feed conversion ratio (P &lt; 0.01) and average daily feed intake (P = 0.06) tended to decrease with the Ca− diet. The bone mineral content (BMC) gain was decreased by Ca, especially with Ca− DON + (DON × Ca, P &lt; 0.05). The P absorption was increased by Ca− DON + (DON × Ca, P &lt; 0.01), although the P retention efficiency was only increased by Ca+ DON + (DON × Ca, P &lt; 0.001). The absorption of Ca was increased by DON+ (P &lt; 0.001), and the Ca efficiency was increased by Ca− DON− (DON × Ca, P &lt; 0.01). After 9 d, the gene expression of intestinal claudin 12 (P &lt; 0.01) and CYP24A1 (P &lt; 0.05), femur cortical RANKL (P &lt; 0.05) and OPG (P = 0.06), and renal calbindin D9K (P &lt; 0.05) and Klotho (P = 0.07) were decreased by DON+. The Ca (P = 0.06) and magnesium (P &lt; 0.01) concentrations were decreased by DON+, and the Ca (P = 0.06) and P digestibility (P &lt; 0.01) were increased. After the repletion phase, Ca− piglets recovered their BMC deficit, but not those receiving DON+ (DON × Ca; P = 0.06). The Ca (P &lt; 0.05) and P (P = 0.06) retention efficiency tended to increase with Ca−. The absorption of Ca and P was increased by Ca− and DON+ (DON × Ca, P &lt; 0.05). The results show that piglets increased their Ca and P utilization efficiency, allowing them to recover the BMC deficit caused by Ca−, but not when the piglets were exposed to DON. Pigs previously receiving Ca-deficient diet with DON still have lower body Ca and P, leading to elevated calcitriol concentrations and enhanced Ca and P intestinal absorption. The fact that DON decreased the expression of genes implicated in Ca intestinal and renal transport and P excretion after 9 d can potentially explain the reduced plasma Ca concentration.
Paratrypaea Komai & Tachikawa, 2008 (Decapoda: Axiidea: Callianassidae): more than two or three species
Authors: Poore Gary C B , Kou Qi 
Published: April 2024

Abstract
Paratrypaea Komai & Tachikawa, 2008 has for more than a decade been thought to contain only two species, both widespread throughout the Indo-West Pacific, or briefly three species. Molecular studies using mitochondrial 16S rRNA and 12S rRNA plus nuclear H3 and 18S rRNA genes, repeated here with samples from more individuals, have shown well separated clades within the genus. Morphological examination has found differences, especially in the form of the adult male cheliped, between the clades leading to the conclusion that Paratrypaea comprises at least eight species of which four are new and described herein. Not all closely related clades could be morphologically distinguished. Some species are narrowly and others widely distributed. The species are: P. baliensissp. nov. from Indonesia; P. bouvieri (Nobili, 1904) from the Red Sea and Indian Ocean; P. chichijimaensis (Sakai, 2015) comb. nov. from Japan; P. dworschakisp. nov. from the Hawaiian Islands; P. maldivensis (Borradaile, 1904) from the eastern Indian Ocean, Papua New Guinea, and possibly western Pacific; P. niuginiensissp. nov. from Papua New Guinea; P. rectangularis (Ngoc-Ho, 1991) from French Polynesia to the Red Sea; and P. rempiensissp. nov. from Papua New Guinea. A published partial 16S sequence from Japan has provided evidence of one more species than those proposed here. Paratrypaea cristata (Borradaile, 1910) comb. nov. remains a species inquirenda.
Natural genetic variation in dynamic photosynthesis is correlated with stomatal anatomical traits in diverse tomato species across geographical habitats
Authors: Yoshiyama Yugo , Wakabayashi Yu , Mercer Kristin L , Kawabata Saneyuki , Kobayashi Takayuki , Tabuchi Toshihito , Yamori Wataru 
Published: April 2024

Abstract
Plants grown under field conditions experience fluctuating light. Understanding the natural genetic variations for a similarly dynamic photosynthetic response among untapped germplasm resources, as well as the underlying mechanisms, may offer breeding strategies to improve production using molecular approaches. Here, we measured gas exchange under fluctuating light, along with stomatal density and size, in eight wild tomato species and two tomato cultivars. The photosynthetic induction response showed significant diversity, with some wild species having faster induction rates than the two cultivars. Species with faster photosynthetic induction rates had higher daily integrated photosynthesis, but lower average water use efficiency because of high stomatal conductance under natural fluctuating light. The variation in photosynthetic induction was closely associated with the speed of stomatal responses, highlighting its critical role in maximizing photosynthesis under fluctuating light conditions. Moreover, stomatal size was negatively correlated with stomatal density within a species, and plants with smaller stomata at a higher density had a quicker photosynthetic response than those with larger stomata at lower density. Our findings show that the response of stomatal conductance plays a pivotal role in photosynthetic induction, with smaller stomata at higher density proving advantageous for photosynthesis under fluctuating light in tomato species. The interspecific variation in the rate of stomatal responses could offer an untapped resource for optimizing dynamic photosynthetic responses under field conditions.
‘Border Country’: health law in a devolved UK
Authors: Harrington John , Hampton Abbie-Rose 
Published: April 2024

Abstract
How are we to understand and research health law under devolution in the UK? Building on work in law and geography, we argue that the figure of the border is key to the production and implementation of devolved health law and the variety of forms that this takes. The utility of border thinking in this context is shown through a review of thematic areas, including infectious disease control, access to health care, and abortion, each instantiating a distinct bordering process. In each, we consider recent developments in policy and legislation, framed with reference to constitutional change, and the politics of devolution in the UK. Taking Wales as an exemplary site, we argue that health law produces borders in traditional and non-traditional places. It creates and blurs territories. It is equally constituted by pluralistic bordering practices. On the basis of this theoretically informed review, we conclude by proposing a cross-disciplinary legal, ethical, and socio-legal research agenda for future research.
Predicting conditional probability distributions of redshifts of Active Galactic Nuclei using Hierarchical Correlation Reconstruction
Authors: Duda Jaroslaw , Bhatta Gopal 
Published: April 2024

ABSTRACT
The Large Area Telescope (LAT) onboard the Fermi gamma-ray observatory continuously scans the sky in an energy range from 50 MeV to 1 TeV. The telescope has identified over 6000 gamma-ray emitting sources, approximately half of which are classified as active galactic nuclei (AGN). However, not all of these gamma-ray sources have known redshift values for the reason that redshift estimation following traditional methods can be an expensive, challenging task. Alternatively, as an effort to robustly predict the AGN redshift values, many researchers have recently turned to machine learning methods. However, while the focus has primarily been on predicting specific values, real-world data often allows us only to predict conditional probability distributions, constrained by conditional entropy [H(Y|X)]. In our study, we employ the Hierarchical Correlation Reconstruction approach to inexpensively predict complex conditional probability distributions, including multimodal ones. This is achieved through independent Mean Squared Error estimation of multiple moment-like parameters, combined into reconstruction of the conditional distribution. By employing linear regression for this purpose, we can develop interpretable models where coefficients describe the contributions of features to conditional moments. This article extends the original approach by incorporating Canonical Correlation Analysis for feature optimization and l1 ‘lasso’ regularization. Our primary focus is on the practical problem of predicting the redshift of AGN using data from the Fourth Fermi-LAT Data Release 3 (4LAC-DR3) data set.
Constraining the coronal properties of AB Dor in the radio regime
Authors: Brasseur C E , Jardine M M , Hussain G A J 
Published: April 2024

ABSTRACT
We present a multiwavelength study of AB Doradus, combining modelling that incorporates a spectropolarimetric magnetic field map with 8.4 GHz radio interferometry to measure the coronal extent and density of this young star. We use the surface magnetic field map to produce a 3D extrapolation of AB Dor’s coronal magnetic field. From this model we create synthetic radio images throughout the stellar rotation period which we can compare with the interferometric radio observations. Our models reproduce the two-lobe structure seen in the radio observations. We successfully fit the observed flux magnitude and lobe separation with our model. We conclude that that the features seen in the radio images are a result of centrifugal containment of hot gas at the peak of closed magnetic loops, and that the corona of AB Dor extends to about 8–10 stellar radii, making it much more extended than the present-day solar corona.
Combating multidrug-resistance in S. pneumoniae: a G-quadruplex binding inhibitor of efflux pump and its bio-orthogonal assembly
Authors: Chaudhuri Ritapa , Prasanth Thumpati , Biswas Debasmita , Mandal Subhranshu , Dash Jyotirmayee 
Published: April 2024

Abstract
Antibiotic resistance poses a significant global health threat, necessitating innovative strategies to combat multidrug-resistant bacterial infections. Streptococcus pneumoniae, a pathogen responsible for various infections, harbors highly conserved DNA quadruplexes in genes linked to its pathogenesis. In this study, we introduce a novel approach to counter antibiotic resistance by stabilizing G-quadruplex structures within the open reading frames of key resistance-associated genes (pmrA, recD and hsdS). We synthesized An4, a bis-anthracene derivative, using Cu(I)-catalyzed azide-alkyne cycloaddition, which exhibited remarkable binding and stabilization of the G-quadruplex in the pmrA gene responsible for drug efflux. An4 effectively permeated multidrug-resistant S. pneumoniae strains, leading to a substantial 12.5-fold reduction in ciprofloxacin resistance. Furthermore, An4 downregulated pmrA gene expression, enhancing drug retention within bacterial cells. Remarkably, the pmrA G-quadruplex cloned into the pET28a(+) plasmid transformed into Escherichia coli BL21 cells can template Cu-free bio-orthogonal synthesis of An4 from its corresponding alkyne and azide fragments. This study presents a pioneering strategy to combat antibiotic resistance by genetically reducing drug efflux pump expression through G-quadruplex stabilization, offering promising avenues for addressing antibiotic resistance.
Choline in pregnant women: a systematic review and meta-analysis
Authors: Nguyen Hoan Thi , Oktayani Pande Putu Ida , Lee Shin-Da , Huang Li-Chi 
Published: April 2024

Abstract

Context: Choline is a critical nutrient. Inadequate choline intake during pregnancy increases the risk of adverse maternal and offspring health.

Objective
A systematic review and meta-analysis were conducted to examine the current recommendations for choline intake by pregnant women, estimate the overall prevalence of pregnant women with adequate choline intake, and explore associations between maternal choline level and adverse pregnancy outcomes (APOs).

Methods
Choline recommendations for pregnant women were assessed from eight nutrient guidelines of the United States, United Kingdom, Canada, Australia, Asia, International Federation of Gynecology and Obstetrics, and World Health Organization. Data on the prevalence of pregnant women with adequate choline intake and the association between maternal choline level and APOs were collected from 5 databases up to May 2023. Meta-analyses with random effects and subgroup analyses were performed for the pooled estimate of prevalence and association.

Results
Five recent nutrition guidelines from the United States (United States Department of Agriculture), United States (Food and Drug Administration), Canada, Australia, and the International Federation of Gynecology and Obstetrics have emphasized the importance of adequate choline intake for pregnant women. Of 27 publications, 19 articles explored the prevalence and 8 articles explored the association. Meta-analysis of 12 prevalence studies revealed a concerning 11.24% (95% confidence interval, 6.34–17.26) prevalence of pregnant women with adequate choline intake recommendations. A meta-analysis of 6 studies indicated a significant association between high maternal choline levels and a reduced risk of developing APOs, with an odds ratio of 0.51 (95% confidence interval, 0.40–0.65).

Conclusion
The existing guidelines highlight the importance of choline in supporting maternal health and fetal development during pregnancy. Furthermore, a high maternal choline level was likely to be associated with a lower risk of APOs. However, 88.76% of pregnant women do not achieve the optimal choline intake. Therefore, specific policies and actions may be necessary to improve choline intake in pregnant women’s care and support the well-being of pregnant women.

Systematic Review Registration
PROSPERO registration no. CDR42023410561.
BIG enhances Arg/N-degron pathway-mediated protein degradation to regulate Arabidopsis hypoxia responses and suberin deposition
Authors: Zhang Hongtao , Rundle Chelsea , Winter Nikola , Miricescu Alexandra , Mooney Brian C , Bachmair Andreas , Graciet Emmanuelle , Theodoulou Frederica L 
Published: April 2024

Abstract
BIG/DARK OVEREXPRESSION OF CAB1/TRANSPORT INHIBITOR RESPONSE3 is a 0.5 MDa protein associated with multiple functions in Arabidopsis (Arabidopsis thaliana) signaling and development. However, the biochemical functions of BIG are unknown. We investigated a role for BIG in the Arg/N-degron pathways, in which substrate protein fate is influenced by the N-terminal residue. We crossed a big loss-of-function allele to 2 N-degron pathway E3 ligase mutants, proteolysis6 (prt6) and prt1, and examined the stability of protein substrates. Stability of model substrates was enhanced in prt6-1 big-2 and prt1-1 big-2 relative to the respective single mutants, and the abundance of the PRT6 physiological substrates, HYPOXIA-RESPONSIVE ERF2 (HRE2) and VERNALIZATION2 (VRN2), was similarly increased in prt6 big double mutants. Hypoxia marker expression was enhanced in prt6 big double mutants; this constitutive response required arginyl transferase activity and RAP-type Group VII ethylene response factor (ERFVII) transcription factors. Transcriptomic analysis of roots not only demonstrated increased expression of multiple hypoxia-responsive genes in the double mutant relative to prt6, but also revealed other roles for PRT6 and BIG, including regulation of suberin deposition through both ERFVII-dependent and independent mechanisms, respectively. Our results show that BIG acts together with PRT6 to regulate the hypoxia-response and broader processes in Arabidopsis.
Effectiveness of intravenous methylprednisolone pulse in patients with severe microscopic polyangiitis and granulomatosis with polyangiitis
Authors: Omura Satoshi , Kida Takashi , Noma Hisashi , Inoue Hironori , Sofue Hideaki , Sakashita Aki , Kadoya Masatoshi , Nakagomi Daiki , Abe Yoshiyuki , Takizawa Naoho , Nomura Atsushi , Kukida Yuji , Kondo Naoya , Yamano Yasuhiko , Yanagida Takuya , Endo Koji , Hirata Shintaro , Matsui Kiyoshi , Takeuchi Tohru , Ichinose Kunihiro , Kato Masaru , Yanai Ryo , Matsuo Yusuke , Shimojima Yasuhiro , Nishioka Ryo , Okazaki Ryota , Takata Tomoaki , Ito Takafumi , Moriyama Mayuko , Takatani Ayuko , Miyawaki Yoshia , Ito-Ihara Toshiko , Yajima Nobuyuki , Kawaguchi Takashi , Hirano Aiko , Fujioka Kazuki , Fujii Wataru , Seno Takahiro , Wada Makoto , Kohno Masataka , Kawahito Yutaka 
Published: April 2024

Abstract

Objectives
To evaluate the effectiveness and safety of two different intravenous methylprednisolone (IVMP) pulse doses in patients with severe microscopic polyangiitis (MPA) and granulomatosis with polyangiitis (GPA).

Methods
We emulated a target trial using observational data from the nationwide registry in Japan. Patients with severe glomerulonephritis or diffuse alveolar haemorrhage were selected and pseudo-randomized into three groups using propensity score-based overlap weighting as follows: non-IVMP, IVMP 0.5 g/day and IVMP 1.0 g/day. The primary outcome was all-cause mortality, and the secondary outcomes were composite all-cause mortality and kidney failure, severe relapse and serious infection from 2 to 48 weeks after treatment initiation. To estimate the treatment effects, the Cox proportional hazard model and Fine–Gray subdistribution hazard model were used.

Results
In this emulated target trial, of 201 eligible patients (MPA, 175; GPA, 26), 6 (3%) died, 4 (2.0%) had kidney failure, 11 (5.5%) had severe relapse, and 40 (19.9%) had severe infections. Hazard ratios (HR) for IVMP 0.5 g/day and IVMP 1.0 g/day pulse groups compared with non-IVMP pulse were as follows: all-cause mortality 0.46 (95% CI: 0.07, 2.81) and 0.07 (95% CI: 0.01, 0.41), respectively; all-cause mortality/kidney failure 1.18 (95% CI: 0.26, 5.31) and 0.59 (95% CI: 0.08, 4.52), respectively; subdistribution HRs for severe relapse were 1.26 (95% CI: 0.12, 13.70) and 3.36 (95% CI: 0.49, 23.29), respectively; and for serious infection 1.88 (95% CI: 0.76, 4.65) and 0.94 (95% CI: 0.28, 3.13), respectively.

Conclusion
IVMP 1.0 g/day pulse may improve 48-week mortality in patients with severe MPA/GPA.