bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information
Authors: Xu Liang , Zakem Emily , Weissman JL
Published: October 2024

Microbial maximum growth rates vary widely across species and are key parameters for ecosystem modeling. Measuring these rates is challenging, but genomic features like codon usage statistics provide useful signals for predicting growth rates for as-yet uncultivated organisms, though current predictors often show high variance. To improve accuracy, we integrate phylogenetic signals, leveraging the evolutionary relationships among species to refine trait predictions. We presentPhydon, which combines codon statistics and phylogenetic information to enhance the precision of maximum growth rate estimates, especially when a close relative with a known growth rate is available. We construct the largest and most taxonomically broad database of temperature-corrected growth rate estimates for 111,349 microbial species. The results reveal a bimodal distribution of maximum growth rates, resolving distinct groups of fast and slow growers. Our hybrid approach advances the accuracy of genome-based growth rate predictions and presents a new framework for accurate genome-based trait prediction.
Data-driven insights into the association between oxidative stress and calcium-regulating proteins in cardiovascular disease
Authors: Panday Namuna , Sigdel Dibakar , Adam Irsyad , Ramirez Joseph , Verma Aarushi , Eranki Anirudh , Wang Wei , Wang Ding , Ping Peipei
Published: October 2024

A growing body of biomedical literature suggests a bidirectional regulatory relationship between cardiac calcium (Ca2+)-regulating proteins and reactive oxygen species (ROS), which is integral to the pathogenesis of various cardiac disorders via oxidative stress signaling. To address the challenge of finding hidden connections within the growing volume of biomedical research, we developed a data science pipeline for efficient data extraction, transformation, and loading. Employing the CaseOLAP (Context-Aware Semantic Analytic Processing) algorithm, our pipeline quantifies interactions between 128 human cardiomyocyte Ca2+-regulating proteins and eight cardiovascular disease (CVD) categories. Our machine learning analysis of CaseOLAP scores reveals that the molecular interfaces of Ca2+-regulating proteins uniquely associate with cardiac arrhythmias and diseases of the cardiac conduction system, distinguishing them from other CVDs. Additionally, a knowledge graph analysis identified 59 of the 128 Ca2+-regulating proteins as involved in OS-related cardiac diseases, with cardiomyopathy emerging as the predominant category. By leveraging a link prediction algorithm, our research illuminates interactions between Ca2+-regulating proteins, OS, and CVDs. The insights gained from our study provide a deeper understanding of the molecular interplay between cardiac ROS and Ca2+-regulating proteins in the context of CVDs. Such understanding is essential for the innovation and development of targeted therapeutic strategies.
An integrated polygenic score stratifies risk of peripheral artery disease and adverse limb events in ancestrally diverse cohorts
Authors: Flores Alyssa M. , Ruan Yunfeng , Misra Anika , Selvaraj Margaret S. , Bellomo Tiffany R. , Nakao Tetsushi , Rosenfield Kenneth , Eagleton Matthew , Hornsby Whitney , Patel Aniruddh P. , Natarajan Pradeep
Published: October 2024

Background and Aims

Peripheral artery disease (PAD) is a heritable atherosclerotic condition that is underdiagnosed and undertreated. With growing knowledge of the genetic basis for PAD and related risk factors, this study sought to construct a new polygenic score for PAD (GPSPAD).

Methods

GPSPADwas constructed by integrating multi-ancestry summary statistics for PAD and related traits. GPSPADwas trained in a UK Biobank dataset of 96,239 individuals and validated in a holdout UK Biobank dataset (N=304,294) and All of Us (AoU; N=237,173) and Mass General Brigham Biobank (MGBB, N=37,017).

Results

GPSPADwas associated with an OR-per SD increase of 1.64 in the UK Biobank dataset (95% CI 1.60-1.68). Compared to previously published PAD polygenic scores, GPSPADwas more strongly associated with PAD in AoU and MGBB, including enhanced transferability to non-European subgroups. GPSPADimproved discrimination of incident PAD (1¢C-statistic 0.030) that was nearly equivalent to the additive performances of diabetes (1¢C-statistic 0.029) and smoking (1¢C-statistic 0.034). GPSPADwas associated with reduced ankle-brachial index in the MGBB with the top 8% of individuals having a mean ABI<0.90 when assessed. Among individuals with prevalent PAD, GPSPADconsistently identified individuals at high MALE-risk in the UK Biobank (HR 1.48; 95% CI 1.24-1.77), MGBB, (HR 1.34; 95% CI 1.12-1.60), and AoU (HR 1.33; 95% CI 1.12-1.58).

Conclusions

An integrated, multi-ancestry polygenic score for PAD predicts disease and adverse limb outcomes in three diverse cohorts. Incorporating polygenic risk into PAD care has the potential to guide screening and tailor management to prevent MALE.
Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer ofblaKPC
Authors: Gomez-Simmonds Angela , Annavajhala Medini K. , Seeram Dwayne , Hokunson Todd W. , Park Heekuk , Uhlemann Anne-Catrin
Published: October 2024

Transmission of carbapenem-resistant Enterobacterales (CRE) in hospitals has been shown to occur through complex, multifarious networks driven by both clonal spread and horizontal transfer mediated by plasmids and other mobile genetic elements. We performed nanopore long-read sequencing on CRE isolates from a large urban hospital system to determine the overall contribution of plasmids to CRE transmission and identify specific plasmids implicated in the spread ofblaKPC(theKlebsiella pneumoniaecarbapenemase [KPC] gene). Six hundred and five CRE isolates collected between 2009 and 2018 first underwent Illumina sequencing for genome-wide genotyping; 435blaKPC-positive isolates were then successfully nanopore sequenced to generate hybrid assemblies including circularizedblaKPC-harboring plasmids. Phylogenetic analysis and Mash clustering were used to define putative clonal and plasmid transmission clusters, respectively. Overall, CRE isolates belonged to 96 multilocus sequence types (STs) encodingblaKPCon 447 plasmids which formed 54 plasmid clusters. We found evidence for clonal transmission in 66% of CRE isolates, over half of which belonged to four clades comprisingK. pneumoniaeST258. Plasmid-mediated acquisition ofblaKPCoccurred in 23%–27% of isolates. While most plasmid clusters were small, several plasmids were identified in multiple different species and STs, including a highly promiscuous IncN plasmid and an IncF plasmid putatively spreadingblaKPCfrom ST258 to other clones. Overall, this points to both the continued dominance ofK. pneumoniaeST258 and the dissemination ofblaKPCacross clones and species by diverse plasmid backbones. These findings support integrating long-read sequencing into genomic surveillance approaches to detect the hitherto silent spread of carbapenem resistance driven by mobile plasmids.
Increased neutron reflectivity and polarization of neutron-optical engineered
Fe/B411CTi
multilayer optics
Authors: Zubayer A. , Ghafoor N. , Thorarinsdottir K. A. , Glavic A. , Stahn J. , Nagy G. , Vorobiev A. , Magnus F. , Birch J. , Eriksson F.
Published: October 2024

The concept of scattering length density tuning for improved polarization is investigated for Fe/B411CTi multilayers and compared to the commonly used Fe/Si system in polarizing multilayer neutron optics. X-ray and neutron reflectivity, magnetization, and neutron polarization were measured on such multilayers, highlighting differences from conventional Fe/Si multilayers. The multilayer systems were deposited with 25 Å period thickness, a layer thickness ratio of 0.35, and 20 periods using ion-assisted dc magnetron sputtering. Replacing Si with B411CTi for these multilayers showed an increase in reflectivity due to a reduction in interface width. Tuning the ratio between B411C and Ti in the nonmagnetic layers enabled a wide range of scattering length density contrasting and matching for spin-down neutrons, which in turn led to an improved polarization. These findings demonstrate the potential of Fe/B411CTi multilayers as a promising option for polarizing neutron optics and highlight the concept of scattering length density tuning in a large range using B411CTi.

Published by the American Physical Society
2024
Quark counting, Drell-Yan West, and the pion wave function
Authors: Alberg Mary , Miller Gerald A.
Published: October 2024

The relation between the pion's quark distribution function, q(x), its light-front wave function, and the elastic charge form factor, F(Δ2), is explored. The square of the leading-twist pion wave function at a special probe scale, ζH, is determined using models and Poincaré covariance from realistic results for q(x). This wave function is then used to compute form factors with the result that the Drell-Yan-West and quark counting relationships are not satisfied. A new relationship between q(x) and F(Δ2) is proposed.

Published by the American Physical Society
2024
Strong noninertial radiative shifts in atomic spectra at low accelerations
Authors: Arya Navdeep , Stargen D. Jaffino , Lochan Kinjalk , Goyal Sandeep K.
Published: October 2024

Despite numerous proposals investigating various properties of accelerated detectors in different settings, detecting the Unruh effect remains challenging due to the typically weak signal at achievable accelerations. For an atom with frequency gap ω0, accelerated in free space, significant acceleration-induced modification of properties like transition rates and radiative energy shifts requires accelerations of the order of ω0c. In this paper, we make the case for a suitably modified density of field states to be complemented by a judicious selection of the system property to be monitored. We study the radiative energy-level shift in inertial and uniformly accelerated atoms coupled to a massless quantum scalar field inside a cylindrical cavity. Uniformly accelerated atoms experience thermal correlations in the inertial vacuum, and the radiative shifts are expected to respond accordingly. We show that the noninertial contribution to the energy shift can be isolated and significantly enhanced relative to the inertial contribution by suitably modifying the density of field modes inside a cylindrical cavity. Moreover, we demonstrate that monitoring the radiative energy shift, as compared to transition rates, allows us to reap a stronger purely noninertial signal. We find that a purely noninertial radiative shift as large as 50 times the inertial energy shift can be obtained at small, experimentally achievable accelerations (a∼10−9ω0c) if the cavity’s radius R is specified with a relative precision of δR/R0∼10−7. Given that radiative shifts for inertial atoms have already been measured with high accuracy, we argue that the radiative energy-level shift is a promising observable for detecting Unruh thermality with current technology.

Published by the American Physical Society
2024
All-loop geometry for four-point correlation functions
Authors: He Song , Huang Yu-tin , Kuo Chia-Kai
Published: October 2024

In this letter, we consider a positive geometry conjectured to encode the loop integrand of four-point stress-energy correlators in planar N=4 super Yang-Mills. Beginning with four lines in twistor space, we characterize a positive subspace to which an ℓ-loop geometry is attached. The loop geometry then consists of ℓ lines in twistor space satisfying positivity conditions among themselves and with respect to the base. Consequently, the can be viewed as fibration over a . The fibration naturally dissects the base into chambers, in which the degree-4ℓ loop form is unique and distinct for each chamber. Interestingly, up to three loops, the chambers are simply organized by the six ordering of x1,22x3,42, x1,42x2,32, and x1,32x2,42. We explicitly verify our conjecture by computing the loop-forms in terms of a basis of planar conformal integrals up to

ℓ

=

3

, which indeed yield correct loop integrands for the four-point correlator.

Published by the American Physical Society
2024
Ultracold charged atom-dimer collisions: State-selective charge exchange and three-body recombination
Authors: Pandey A. , Vexiau R. , Marcassa L. G. , Dulieu O. , Bouloufa-Maafa N.
Published: October 2024

Based on an accurate determination of the potential energy surfaces of Rb3+ correlated to its first asymptotic limit Rb++Rb(5s)+Rb(5s), we identify the presence of intersections of a pair of singlet and triplet surfaces over all interparticle distances, leading to Jahn-Teller (JT) couplings. We elaborate scenarios for charge exchange between ultracold charged atom-dimer complex (Rb+Rb2+ or Rb++Rb2), predicting a strong selectivity on the preparation of the initial state of the dimer. We also demonstrate that the JT couplings must drive the three-body recombination (TBR) of Rb+, Rb, and Rb at ultracold energies. Using the current analysis, we provide a consistent picture of the TBR experiments performed in ion-atom hybrid Rb samples. We also demonstrate the presence of JT coupling as a general phenomenon in the singly charged homonuclear alkali triatomic systems.

Published by the American Physical Society
2024
Universal clusters in quasi-two-dimensional ultracold Fermi mixtures
Authors: Liu Ruijin , Shi Tingting , Zaccanti Matteo , Cui Xiaoling
Published: October 2024

We study universal clusters in quasi-two-dimensions (q2D) that consist of a light (L) atom interacting with two or three heavy (H) identical fermions, forming the trimer or tetramer bound state. The axial confinement in q2D is shown to lift the threefold degeneracy of three-dimensional trimer (tetramer) in p-wave channel and uniquely select the ground state with magnetic angular momentum |m|=1 (m=0). By varying the interaction or confinement strength, we explore the dimensional crossover of these clusters from 3D to 2D, characterized by a gradual change of critical H-L mass ratio for their emergence and momentum-space distribution. Importantly, we find that a finite effective range will not alter their critical mass ratios in the weak coupling regime. There, we establish an effective 2D model to quantitatively reproduce the properties of q2D clusters, and further identify the optimal interaction strengths for their detections in experiments. Our results suggest a promising prospect for observing universal clusters and associated high-order correlation effects in realistic q2D ultracold Fermi mixtures.

Published by the American Physical Society
2024
Structural insights into supramolecular interactions in isostructural salts of 2,4,6-triaminopyrimidinium with various heterocyclic carboxylates
Authors: Mohana Marimuthu , Gomathi Sundaramoorthy , Thomas Muthiah Packianathan , Butcher Ray J.
Published: October 2024

2,4,6-Triaminopyrimidine is an interesting and challenging molecule due to the presence of multiple hydrogen-bond donors and acceptors. Its noncovalent interactions with a variety of carboxylic acids provide several supramolecular aggregates with frequently occurring molecular synthons. The present work focuses on the supramolecular interactions of 2,4,6-triaminopyrimidinium 3-(indol-3-yl)propionate–3-(indol-3-yl)propionic acid (1/1), C4H8N5
+·C11H10NO2
−·C11H11NO2, (I), 2,4,6-triaminopyrimidinium 2-(indol-3-yl)acetate, C4H8N5
+·C10H8NO2
−, (II), 2,4,6-triaminopyrimidinium 5-bromothiophene-2-carboxylate, C4H8N5
+·C5H2BrO2S−, (III), and 2,4,6-triaminopyrimidinium 5-chlorothiophene-2-carboxylate, C4H8N5
+·C5H2ClO2S−, (IV). All four salts exhibit robust homomeric and heteromeric R
2
2(8) ring motifs. Salts (I) and (II) develop sextuple [in (I)] and quadruple [in (I) and (II)] hydrogen-bonded arrays through fused-ring motifs. Salt (II) exhibits a rosette-like architecture. Salt (IV) is isostructural and isomorphous with salt (III), exhibiting an identical crystal structure with a different composition and an identical supramolecular architecture. In salts (III) and (IV), a linear hetero-tetrameric motif is formed and, in addition, both salts exhibit halogen–π interactions which enhance the crystal stability. All four salts develop a supramolecular hydrogen-bonded pattern facilitated by several N—H...O and N—H...N hydrogen bonds with multiple furcated donors and acceptors.
Dinuclear zinc(II) acetate complexes derived from N,N′,S-tridentate Schiff bases: synthesis, structural study and Hirshfeld surface analysis
Authors: Anaya-Avila Odalys , Muñoz-Granados Oscar , Andrade-López Noemí , Alvarado-Rodríguez José G. , Martínez-Otero Diego
Published: October 2024

Three dinuclear zinc(II) acetate complexes of the general formula [Zn{L

n

}(AcO)]2, namely, di-μ-acetato-κ4
O:O′-bis[({2-[(pyridin-2-ylmethylidene)amino]phenyl}sulfanido-κ3
N,N′,S)zinc(II)], [Zn2(C12H9N2S)2(C2H3O2)2] (n = 1), 4, μ-acetato-1:2κ2
O:O′-acetato-2κO-[μ-(2-{[1-(pyridin-2-yl)ethylidene]amino}phenyl)sulfanido-1κS:2κ3
N,N′,S][(2-{[1-(pyridin-2-yl)ethylidene]amino}phenyl)sulfanido-1κ3
N,N′,S]dizinc(II), [Zn2(C13H11N2S)2(C2H3O2)2] (n = 2), 5, and μ-acetato-1:2κ2
O:O′-acetato-2κO-[μ-(2-{[phenyl(pyridin-2-yl)methylidene]amino}phenyl)sulfanido-1κS:2κ3
N,N′,S][(2-{[phenyl(pyridin-2-yl)methylidene]amino}phenyl)sulfanido-1κ3
N,N′,S]dizinc(II)–bis(2-aminophenyl) disulfide (2/1), [Zn2(C18H13N2S)2(C2H3O2)2]·0.5C12H12N2S2 (n = 3), 6·0.5(2-APS)2, were obtained from the reaction of 2-R-(pyridin-2-yl)benzothiazoline precursors (R = H, 1; R = Me, 2; R = Ph, 3) with zinc acetate dihydrate in a 1:1 ratio. All the complexes crystallized as dinuclear species and complex 6 cocrystallized with one molecule of bis(2-aminophenyl) disulfide (2-APS)2. The anionic Schiff base ligands {L

n

}− displayed a κ2
N,κS-tridentate coordination mode with the formation of two five-membered chelate rings. In 4, 5 and 6·0.5(2-APS)2, both ZnII ions are pentacoordinated and the coordination sphere of 4 was different with respect to those in 5 and 6·0.5(2-APS)2. For 4, the X-ray diffraction study showed a dinuclear complex containing two bridging acetate ligands linked to both ZnII ions. For 5 and 6·0.5(2-APS)2, the dinuclear complexes displayed one bridging acetate ligand linked to both ZnII ions, where the first ZnII ion includes a dative bond with one S atom from an adjacent anionic Schiff base {L

n

}−, while the second ZnII ion is coordinated to one terminal acetate ligand. In each dinuclear complex, the geometry is the same for both ZnII metal centres. The local geometry of the ZnII cation in 4 is halfway between trigonal bipyramidal and square pyramidal local geometries; in 5 and 6, the local geometries are described as distorted square pyramidal. Hirshfeld surface analysis of 5 and 6 showed the predominance of H...H interactions, as well as the contribution of C—H...C, C—H...O and C—H...S noncovalent interactions to the cohesion of the crystalline network of the ZnII complexes.
Personal reflection: Working in a social, emotional and mental health school in England
Authors: Kurawa Gwadabe
Published: October 2024

This paper draws on my experience working as a special needs support staff member in a special school in the UK for young people with social, emotional and mental health (SEMH) issues. The purpose of this paper is to share my understanding of practices that enable staff in an SEMH school to attend to the needs of their students. Although I have worked in mainstream schools, school practice in an SEMH setting was unfamiliar to me. Therefore, it was important to familiarise myself with the practices of the school. I also believe that sharing my experiences helps to support others who work in similar contexts. Through my visit(s), I was able to identify key features of effective pedagogical practice which enabled the learners to thrive. These included the establishment of mutually positive relationships between learners and staff and positively responding to behaviours.
Patient‐Reported Outcome Measures for Pelvic Organ Prolapse: A Systematic Review Using the COnsensus‐Based Standards for the Selection of Health Measurement Instruments (COSMIN) Checklist
Authors: Conrad Sarah J. , Bernard Stéphanie , Gross Douglas P. , McLean Linda
Published: October 2024

Background

Patient‐reported outcome measures (PROMs) are recommended to measure the impact of a health condition or intervention effectiveness as they aim to capture what is most meaningful to patients. Several PROMs are used to evaluate pelvic organ prolapse (POP)‐related domains, yet the measurement properties of these instruments have not been fully explored with a rigorous analysis of the methodological quality and quality of evidence.

Objective

To conduct a systematic review reporting on the measurement properties of PROMs used for the assessment of POP‐related domains in accordance with the COSMIN guidelines.

Search Strategy

Five databases were searched from inception to December 2023.

Selection Criteria

Studies were eligible if they involved (1) at least one group of female adults diagnosed with or presenting with symptoms of POP; (2) a self‐reported outcome measure (PROMs, questionnaires) to evaluate POP‐related domains; and (3) at least one measurement property.

Data Collection and Analysis

Methodological quality and measurement quality were assessed using the COSMIN risk of bias (ROB) checklist and the COSMIN criteria for good measurement properties.

Main Results

A total of 13 PROMs were included. The BIPOP had the lowest ROB for Content Validity. The POP‐SS was the only PROM with sufficient evidence of adequate construct validity and responsiveness to be used in both surgical and conservative management settings.

Conclusion

This original work identified a gap in evidence regarding the measurement qualities of identified PROMs used in the POP population.
Gut bacteria‐derived volatiles mediate Drosophila melanogaster attraction
Authors: Gou Xianwei , Feng Yilu , Yi Ge , Yang Nan , Zhang Shu‐Wen , Qi Xing‐Jiang , Zhou Wenwu , Mo Jianchu , Xu Rong , Li Hongjie
Published: October 2024

Bacteria‐originated volatile molecules play a crucial role in chemical communications between insects, representing their promising application as odor bait traps in pest control. In this study, we investigated the behavioral preferences of the fruit fly Drosophila melanogaster (Diptera: Drosophilidae) towards the fermentation broth of seven gut‐associated bacteria using trap choice assays. All seven bacterial fermentations significantly attracted adults and larvae compared to the medium control. We assessed the effects of bacterial fermentations on bayberry attractiveness to fly adults, and found that the bayberries sprayed with fermentation broth of seven bacteria were all significantly more attractive to adults than the non‐sprayed, following in increased total egg numbers. We also compared the attractive effect of bacterial fermentations with a sugar‐vinegar mixture and a commercial odor‐bait. The commercial odor bait proved more enticing than the unconcentrated 5‐day fermentation broths. However, out of the seven bacteria, 64‐fold concentrated bacterial fermentation of Corynebacterium (Actinomycetota phylum) was significantly more attractive than commercial bait. Finally, we chemically identified the predominant compounds 2‐methylpropanal and acetaldehyde, which are likely responsible for the behavioral preference of fruit flies. Our findings provide a deeper understanding of how gut microbes affect insect behavior and offer a potential bacteria‐originated odor bait for fly control in the orchard.
Fractionation of Boswellia serrata oleogum resin essential oil by short‐path molecular vacuum distillation: Unveiling potent biological activities and chemical composition
Authors: Ayub Muhammad Adnan , Ijaz Muhammad , Hanif Muhammad Asif , Hussain Amjad , Bahadur Ali
Published: October 2024

Boswellia serrata produces oleo gum resin, a rich source of essential oil (EO). EOs, produced as secondary metabolites by medicinal plants, are employed for medicinal and therapeutic purposes. The present study aimed to investigate the yield, chemical composition, antioxidant (AO), antimicrobial, and hemolytic activity of B. serrata EO and its fractions and sub‐fractions (SFs). The EO was extracted using the superheated steam extraction (SHSE) method at 140°C. Short‐path molecular vacuum distillation was used to separate the EO into fractions and SFs. Gas chromatography–mass spectrometry analysis showed α‐pinene, α‐thujene, trans verbenol, and linalool as major components of EO. The AO potential was evaluated using a 2,2‐diphenyl‐1‐picrylhydrazyl assay, % inhibition in a linoleic acid assay, H2O2 scavenging assay, and total AO content (TAOC) using a ferric reducing AO power assay. F2b SF exhibited the highest scavenging activity, with percentages of 95.77%, 96.20%, and 83.54%, respectively, whereas EO revealed the highest TAOC value of 115.94%. Antimicrobial activity was evaluated by disc diffusion, resazurin microtiter plate, and microdilution broth assays. F1c SF showed maximum antibacterial potential (high inhibition zone 17.65–38.28 mm and low minimum inhibitory concentration [MIC] 2.20–84.44 µg/mL). The EO showed the highest antifungal activity (high inhibition zone 12.58–25.81 mm and low MIC 35.18–225.17 µg/mL). Cytotoxicity was assessed by hemolytic assay, with the F1c SF showing the highest activity at 10.89%. It is concluded that SHSE is an effective technique for B. serrata EO extraction, and this EO can be utilized for various medicinal purposes.
Sodium butyrate alleviates T‐2 toxin–induced liver toxicity and renal toxicity in quails by modulating oxidative stress–related Nrf2 signaling pathway, inflammation, and CYP450 enzyme system
Authors: He Yihao , Zhu Xueyan , Song Huanni , Liu Yang , Cao Changyu
Published: October 2024

T‐2 toxin is a member of class A aspergilloides toxins, one of the most prevalent mycotoxins that contaminate feed and food. Direct ingestion of animals or feed contaminated by T‐2 toxin can cause various animal diseases. Butyrate is an organic fatty acid featuring a four‐carbon chain, which is commonly found in the form of sodium butyrate (NaB). NaB has several biological functions and pharmacological effects. However, the role of sodium butyrate in alleviating T‐2 toxin–induced hepatorenal toxicity has not been explored. In this study, 240 juvenile quails were evenly assigned into 4 groups. The experimental setup comprised four groups: The control group received a standard diet; the toxin group received a diet containing 0.9 mg/kg T‐2 toxin; the butyrate group received a diet containing 0.5 g/kg NaB; and the T‐2 treatment group received a diet containing both 0.9 mg/kg T‐2 toxin and 0.5 g/kg NaB. We evaluated the histopathological changes in the kidney and liver on Days 14 and 28 and explored the molecular mechanisms involving oxidative stress, inflammation, and expression of nuclear xenobiotic receptors (NXRs). Our results showed that T‐2 toxin exposure–induced inflammation in the liver and kidney by activating the oxidative stress pathway and modulating expression of NXRs to regulate related CYP450 isoforms, ultimately leading to histopathological injury in the liver and kidney, whereas sodium butyrate ameliorated this injury. These results offer novel insights into the molecular mechanisms underlying the protective effects of sodium butyrate in mitigating T‐2 toxin–induced hepatorenal injury in juvenile quails.

Practical Application

The mechanisms of T‐2 toxin toxicity have been well described in experimental animals, but studies in birds are limited. With the development of society, the market scale of quails farming has been expanding, and the value of quails meat and eggs is increasing; there is an urgent need to clarify the harm of T‐2 toxin to quails and its mechanism.
Disclosing α‐lactalbumin impact on the intestinal and vaginal microbiota of women suffering from polycystic ovary syndrome
Authors: Alessandri Giulia , Mancabelli Leonardo , Fontana Federico , Lepore Elisa , Forte Gianpiero , Burratti Moira , Ventura Marco , Turroni Francesca
Published: October 2024

Polycystic ovary syndrome (PCOS) is one of the most widespread endocrinopathy affecting women of reproductive age with detrimental effects on life quality and health. Among several mechanisms involved in its aetiopathogenesis, recent studies have also postulated the involvement of the vaginal and intestinal microbiota in the development of this disorder. In this study, an accurate insight into the microbial changes associated with PCOS was performed through a pooled‐analysis highlighting that this syndrome is characterized by intestinal and vaginal dysbiosis with a reduction of beneficial microorganisms and a higher proportion of potential pathogens. Based on this observation, we evaluated the ability of a milk‐derived protein exerting positive outcomes in the management of PCOS, that is, α‐lactalbumin (α‐LA), to recover PCOS‐related dysbiosis. In vitro experiments revealed that this protein improved the growth performances of members of two health‐promoting bacterial genera, that is, Bifidobacterium and Lactobacillus, depleted in both intestinal and vaginal microbiota of PCOS‐affected women. In addition, α‐LA modulated the taxonomic composition and growth performances of the microbial players of the complex intestinal and vaginal microbiota. Finally, an in vivo pilot study further corroborated these observations. The oral administration of α‐LA for 30 days to women with PCOS revealed that this protein may have a role in favouring the growth of health‐promoting bacteria yet limiting the proliferation of potential pathogens. Overall, our results could pave the way to the use of α‐LA as a valid compound with ‘prebiotic effects’ to limit/restore the PCOS‐related intestinal and vaginal dysbiosis.
Characterization and biological activity of selenium nanoparticles biosynthesized by Yarrowia lipolytica
Authors: Lashani Elham , Moghimi Hamid , Turner Raymond J. , Amoozegar Mohammad Ali
Published: October 2024

In this research, biogenic selenium nanoparticles were produced by the fungi Yarrowia lipolytica, and the biological activity of its nanoparticles was studied for the first time. The electron microscopy analyses showed the production of nanoparticles were intracellular and the resulting particles were extracted and characterized by XRD, zeta potential, FESEM, EDX, FTIR spectroscopy and DLS. These analyses showed amorphous spherical nanoparticles with an average size of 110 nm and a Zeta potential of −34.51 ± 2.41 mV. Signatures of lipids and proteins were present in the capping layer of biogenic selenium nanoparticles based on FTIR spectra. The antimicrobial properties of test strains showed that Serratia marcescens, Klebsiella pneumonia, Escherichia coli, Pseudomonas aeruginosa and Bacillus subtilis were inhibited at concentrations between 160 and 640 μg/mL, while the growth of Candida albicans was hindered by 80 μg/mL of biogenic selenium nanoparticles. At concentrations between 0.5 and 1.5 mg/mL of biogenic selenium nanoparticles inhibited up to 50% of biofilm formation of Klebsiella pneumonia, Acinetobacter baumannii, Staphylococcus aureus and Pseudomonas aeruginosa. Additionally, the concentration of 20–640 μg/mL of these bioSeNPs showed antioxidant activity. Evaluating the cytotoxicity of these nanoparticles on the HUVEC and HepG2 cell lines did not show any significant toxicity within MIC concentrations of SeNPs. This defines that Y. lipolytica synthesized SeNPs have strong potential to be exploited as antimicrobial agents against pathogens of WHO concern.
Strategies for the biocontrol Pseudomonas infections pre‐fruit harvest
Authors: Warring Suzanne L. , Sisson Hazel M. , Fineran Peter C. , Rabiey Mojgan
Published: October 2024

The efficiency of global crop production is under threat from microbial pathogens which is likely to be worsened by climate change. Major contributors to plant disease are Pseudomonas syringae (P. syringae) pathovars which affect a variety of important crops. This opinion piece focuses on P. syringae pathovars actinidiae and syringae, which affect kiwifruit and stone fruits, respectively. We discuss some of the current control strategies for these pathogens and highlight recent research developments in combined biocontrol agents such as bacteriophages and combinations of bacteriophages with known anti‐microbials such as antibiotics and bacteriocins.
Prevalence and influencing factors of malnutrition in diabetic patients: A systematic review and meta‐analysis
Authors: Zhang Tong , Qin Jiangxia , Guo Jiali , Dong Jianhui , Chen Junbo , Ma Yuxia , Han Lin
Published: October 2024

The prevalence of malnutrition in diabetic patients and its influencing factors remain poorly described. We aim to investigate the prevalence of malnutrition and the influencing factors in diabetic patients through meta‐analysis. Utilizing search terms, such as diabetes, malnutrition, and prevalence, we systematically searched eight databases, including Embase, PubMed, Web of Science, The Cochrane Library, China Knowledge Resource Integrated Database (CNKI), Wanfang Database, Chinese Biomedical Database (CBM), and VIP Database, from inception to May 4, 2023. The search aimed to identify studies related to the prevalence of malnutrition and its influencing factors in adult patients with diabetes. Cohort studies, case–control studies, and cross‐sectional studies that met the inclusion criteria were included in the analysis. Stata 16.0 software was used for meta‐analysis. Quality of the evidence was assessed using Grading of Recommendations, Assessment, Development and Evaluation (GRADE). The study protocol is registered with Prospective Register of Systematic Reviews (PROSPERO), CRD42023443649. A total of 46 studies were included, involving 18 062 patients with ages ranging from 18 to 95 years. The overall malnutrition prevalence was 33% (95% confidence interval [CI]: 0.25–0.40), compared with an at‐risk prevalence of 44% (95% CI: 0.34–0.54). Sixteen factors associated with malnutrition in diabetic patients were identified. This meta‐analysis provides insights into the prevalence of malnutrition and its risk factors in diabetic patients. Regular nutritional screening for patients with risk factors is essential for early detection and intervention.

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Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany
Authors: Buchner Dominik , Sinclair James S. , Ayasse Manfred , Beermann Arne J. , Buse Jörn , Dziock Frank , Enss Julian , Frenzel Mark , Hörren Thomas , Li Yuanheng , Monaghan Michael T. , Morkel Carsten , Müller Jörg , Pauls Steffen U. , Richter Ronny , Scharnweber Tobias , Sorg Martin , Stoll Stefan , Twietmeyer Sönke , Weisser Wolfgang W. , Wiggering Benedikt , Wilmking Martin , Zotz Gerhard , Gessner Mark O. , Haase Peter , Leese Florian
Published: October 2024

Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large‐scale and long‐term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost‐efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large‐scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU‐similarity among years) provides a blueprint for large‐scale biodiversity monitoring of insects and other biodiversity components in near real time.
Comparative analysis of amphibian genomes: An emerging resource for basic and applied research
Authors: Kosch Tiffany A. , Crawford Andrew J. , Lockridge Mueller Rachel , Wollenberg Valero Katharina C. , Power Megan L. , Rodríguez Ariel , O'Connell Lauren A. , Young Neil D. , Skerratt Lee F.
Published: October 2024

Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination and in some lineages, the ability to regenerate limbs and organs. Although genomic approaches would shed light on these unique traits and aid conservation, sequencing and assembly of amphibian genomes has lagged behind other taxa due to their comparatively large genome sizes. Fortunately, the development of long‐read sequencing technologies and initiatives has led to a recent burst of new amphibian genome assemblies. Although growing, the field of amphibian genomics suffers from the lack of annotation resources, tools for working with challenging genomes and lack of high‐quality assemblies in multiple clades of amphibians. Here, we analyse 51 publicly available amphibian genomes to evaluate their usefulness for functional genomics research. We report considerable variation in genome assembly quality and completeness and report some of the highest transposable element and repeat contents of any vertebrate. Additionally, we detected an association between transposable element content and climatic variables. Our analysis provides evidence of conserved genome synteny despite the long divergence times of this group, but we also highlight inconsistencies in chromosome naming and orientation across genome assemblies. We discuss sequencing gaps in the phylogeny and suggest key targets for future sequencing endeavours. Finally, we propose increased investment in amphibian genomics research to promote their conservation.
MhGeneS: An Analytical Pipeline to Allow for Robust Microhaplotype Genotyping
Authors: Geue Julia C. , Liu Peng , Keobouasone Sonesinh , Wilson Paul , Manseau Micheline
Published: October 2024

Microhaplotypes are small linked genomic regions comprising two or more single‐nucleotide polymorphisms (SNPs) that are being applied in forensics and are emerging in wildlife monitoring studies and genomic epidemiology. Typically, targeted in non‐coding regions, microhaplotypes in exonic regions can be designed with larger amplicons to capture functional non‐synonymous sites and minimise insertion/deletion (indel) polymorphisms. Quality control is an important first step for high‐confidence genotyping to counteract such false‐positive variants. As genetic markers with higher polymorphism compared to biallelic SNPs, it is critical to ensure sequencing errors across the microhaplotype amplicon are filtered out to avoid introducing false‐haplotypes. We developed the MhGeneS pipeline which works in tandem with Seq2Sat to help validate microhaplotype genotyping of the coding region of genes, with broader applicability to any microhaplotype profiling. We genotyped microhaplotype regions of the Zfx (≅ 160 bp) and Zfy (≅ 140 bp) genes, as well as an exon of the prion protein (Prnp) gene (≅ 370 bp) in caribou (Rangifer tarandus) using paired‐end Illumina technology. As important quality metrics affecting microhaplotype calling, we identified the sequencing error rate profile related to the overlap or non‐overlap of paired‐end reads as well as the read depth as significant. In the case of Prnp, we achieved confident microhaplotype calling through MhGeneS by removing small sections of the 5′ and 3′ amplicons and using a minimum read depth of 20. Read depth and sequence trimming may be locus‐specific, and validation of these parameters is recommended before the high‐throughput profiling of samples.
Conflicting signals: A study on firms announcing share repurchases soon after seasoned equity offerings
Authors: Wang Jin‐Ying
Published: October 2024

This study examines companies that announce open market share repurchases after seasoned equity offerings (SEO‐OMRs). This study finds that SEO‐OMRs have worse post‐OMR announcement returns, face a sharper decline in stock prices before OMR announcements, and have lower costs of buying back stocks. The study infers that firms announce an OMR soon after conducting an SEO to ensure market timing. The literature contains no evidence of SEO‐OMRs, and this study fills this gap. The findings of this study suggest that investors use SEOs as credible signals when deciding to purchase OMR stocks.
Morphometric Evaluation of the Thoracic and Lumbar Vertebral Canal and Spinal Cord Using Computed Tomography in Healthy Korean Shorthair Cats
Authors: Ahn Seunghyun , Lee Se‐eun , Kang Younjin , Choi Jihye , Yoon Junghee
Published: October 2024

This study aimed to evaluate the spinal morphometry of the thoracic and lumbar regions in normal Korean Shorthair cats using computed tomography (CT) and to investigate the relationship with variables such as sex, age and body weight. Fifteen clinically healthy Korean Shorthair cats (eight males, seven females) from Seoul National University Veterinary Medical Teaching Hospital were included in this retrospective study. Measurements of the height, width and area of the vertebral canal and spinal cord on CT images were taken at the cranial, middle and caudal points of the thoracic and lumbar vertebrae by three observers, and the ratios of the spinal cord area to the vertebral canal area were calculated. The significance of the differences in measurements between sexes and correlations with age and body weight were analysed. The mean age of the cats was 7 years (range: 2–12 years), with a mean weight of 5.27 kg (range: 2.6–8.3 kg). The height, width and area of the vertebral canal and spinal cord were significantly greater in males than in females (p < 0.05). The ratios of the spinal cord area to the vertebral canal area showed no significant difference between sexes (p > 0.05), and no significant correlations were found between the ratios of the spinal cord area to the vertebral canal area and age or body weight. This study provides useful reference intervals for spinal morphometry in the thoracic and lumbar regions of healthy Korean Shorthair cats and investigate the relationship with variables such as sex, age and body weight. This anatomical information may assist in the diagnosis and prognosis of thoracic, lumbar vertebral and spinal cord diseases using CT.
Community Structure and Species Diversity of Birds in Heterogenous Habitats of an East African Growing Agricultural Corridor
Authors: Lyimo Paulo J. , Kavana David J. , Shirima Deo D. , Bugingo Adili , Chidodo Simon , Bulenga George B. , Chilagane Nyemo , Kashaigili Japhet J. , Munishi Pantaleo K.
Published: October 2024

Species conservation mainly depends on the conservation of their habitats where an understanding of the role that habitats have in supporting species diversity and richness is important. This study aimed to determine how heterogeneous habitats in growing agriculture corridors support the biodiversity of birds in terms of their diversity and abundance. We assessed the diversity, richness and abundance of bird species in six different habitats: miombo woodland, montane forests, lowland forests, agro‐ecosystems, wetland and riverine in Tanzania's growing agriculture corridor. We assumed that heterogeneous habitats significantly influence species abundance, richness and diversity. We recorded 299 bird species which were categorised into 10 trophic guilds. Among the guilds, invertebrate‐eating (52%) was the species‐rich guild and nectarivore (1%), herbivore aquatic (0.67%), herbivore terrestrial (0.67%) and scavenger (0.34%) were the least guilds in terms of species richness, abundance and diversity. The six habitats differed in terms of bird species richness, abundance and diversity; miombo woodlands had the highest levels of diversity. There was an even distribution of birds, despite the fact that wetlands and agro‐ecosystems had few species reported there. A number of endangered bird species were recorded in habitats with minimum disturbance. These species include Gyps africanus (CR), Ardeola idea, Polemaetus bellicosus and Terathopius ecaudatus (EN). In order to implement effective conservation measures for corridors and heterogeneous habitats, we advocate proper land use, conservation‐friendly agriculture and the implementation of conservation connectivity on small and large scales.
PWWP3A deficiency accelerates testicular senescence in aged mice
Authors: Chen Zhen , Liu Cong , Qu Wei , Han Yan , Zhu Xiaoyu , Li Zejia , Ma Dupeng , Huang Mengya , Gong Weihao , Sun Qi , Lei Junhao , Guo Rui , Luo Mengcheng
Published: October 2024

Background

The PWWP domain‐containing proteins are involved in chromatin‐associated biological processes, including transcriptional regulation and DNA repair, and most of them are significant for gametogenesis and early embryonic development in mammals. PWWP3A, one of the PWWP domain proteins, is a reader of H3K36me2/H3K36me3 and a response factor to DNA damage. However, the physiological role of PWWP3A in spermatogenesis and fertility remains unclear.

Objective

The goal of this study was to explore the function and mechanism of PWWP3A in the process of spermatogenesis.

Materials and methods

We generated V5‐Pwwp3a KI mice and PWWP3A polyclonal antibody to observe the localization of PWWP3A in vivo. Meanwhile, Pwwp3a KO mice was used to explore the function in spermatogenesis.

Results

We reported that PWWP3A is a predominant expression in the testis of mice. During spermatogenesis, PWWP3A exhibits the temporal expression from early‐pachytene to the round spermatids. The results of spermatocyte spreading and immunostaining showed that PWWP3A aggregated on the XY body, which then diffused as the XY chromosome separated at late‐diplotene. Although the depletion of PWWP3A had no obvious reproductive defects in young male mice, there were observed morphological abnormalities in sperm heads. Immunoprecipitation demonstrated the interaction of PWWP3A with DNA repair proteins SMC5/6; however, PWWP3A deficiency did not result in any meiotic defects. Notably, the testes of aged male Pwwp3a KO mice displayed pronounced degeneration, and were characterized by the presence of vacuolated seminiferous tubules. Furthermore, RNA‐seq analysis revealed an upregulation in the expression of genes which may be involving in immunoregulatory and inflammatory response pathways in aged Pwwp3a KO mice with testicular degeneration.

Conclusions

Our study showed that PWWP3A was highly enriched in the mouse testis, and the Pwwp3a KO mice were fertile. However, the aged Pwwp3a KO male mice displayed testicular atrophy that may be due to changes in the immune micro‐environment or abnormal repair of DNA damage.