bluuebunny/crossref_metadata_2025 huggingface dataset:
Bactogram: Spatial Analysis of Bacterial Colonization in Epidermal Wounds
Authors: Wallblom Karl , Forsberg Fredrik , Lundgren Sigrid , Fisher Jane , Cardoso José , Petruk Ganna , Strömdahl Ann-Charlotte , Saleh Karim , Puthia Manoj , Schmidtchen Artur
Published: April 2024

Skin barrier damage and subsequent development of harmful microbiota contribute to conditions such as wound infections, atopic dermatitis, and chronic wounds, which impact millions of people globally and pose a significant economic burden on healthcare systems. Established microbial sampling methods, such as swabs and tissue biopsies, provide limited information on the spatial distribution of bacteria. We here describe a new method that produces a visual map of the distribution of cultivable bacteria, denoted “Bactogram”, across the whole wound and surrounding skin, suitable for image-based quantification. As part of an exploratory endpoint in a clinical trial (NCT05378997) we applied the Bactogram method to 48 suction blister wounds in 24 healthy volunteers. Bacteria developed in all wounds, predominantly on the skin under the dressing and near wound edges. Two quantification methods, based on visual scoring and image analysis, demonstrated high inter-, and intra-rater agreement and were used to characterize bacterial re-colonization during epidermal wound healing. We also demonstrated proof of concept that the method can be used with chromogenic agar to enable spatial identification of pathogenic bacterial species, such asStaphylococcus aureus. In conclusion, this study introduces a simple method for sampling bacteria over large areas and generating a bacterial map that can identify spatial variations in bacterial composition and abundance in skin and wound conditions.
BOADICEA model: updates to theBRCA2breast cancer risks for ages 60 years and older
Authors: Ficorella Lorenzo , Yang Xin , Easton Douglas F , Antoniou Antonis C
Published: April 2024

Breast cancer risks in olderBRCA2pathogenic variant carriers are understudied. Recent studies show a marked decline in the relative risk at older ages. We used data from two large studies to update the breast cancer risks in the BOADICEA model forBRCA2carriers 60 years and older.
Cognitive training reshapes functional lateralization of fronto-parietal network in patients with vascular cognitive impairment no dementia
Authors: Jin Xinhu , Xing Yi , Lyu Baihan , Wang Xiuyi , Tang Yi , Du Yi
Published: April 2024

Background and Objectives

Vascular cognitive impairment no dementia represents cognitive deficits due to vascular causes but falls short of a dementia diagnosis. Cognitive training has emerged as a safe and effective intervention for vascular cognitive impairment no dementia, though its underlying mechanisms remain obscure. This study investigates how subcortical vascular cognitive impairment no dementia and computerized cognitive training affect a brain fundamental organization feature named functional lateralization.

Methods

In a randomized, active-controlled trial, patients with subcortical vascular cognitive impairment no dementia were divided into training and control groups, and underwent neuropsychological assessments and resting-state functional magnetic resonance imaging at baseline, end of 7-week intervention, and 6-month follow-up. Additionally, a healthy older group provided baseline data. Two types of functional lateralization indices (LIs) were defined based on resting-state functional connectivity: LI of intrahemispheric functional connectivity (LI_intra) which represents the left-right difference of functional connectivity strength within the same hemisphere, and LI of interhemispheric heterotopic functional connectivity (LI_he) which represents the left-right difference of functional connectivity strength across bilateral hemispheres.

Results

Initially, patients (28 in training group and 28 in control group) showed a fronto-parietal network lateralization pattern akin to healthy older adults (N = 26). However, enhanced right-lateralized LI_he was associated with better memory solely in healthy adults. After the intervention, only the training group exhibited a reduction in LI_he in the fronto-parietal network, indicating a lateralization shift towards bilateral network connectivity. This shift, especially towards leftward lateralization, was linked with improved executive and memory functions in the training group. Notably, these changes disappeared at the 6-month follow-up.

Discussion

These findings suggest that subcortical vascular cognitive impairment no dementia modifies the relationship between fronto-parietal network lateralization and cognitive function, rather than altering the lateralization pattern itself. Through hemispherical reorganizing and balancing of the fronto-parietal network, short-term computerized cognitive training facilitates executive and memory functions by leveraging functional compensation by reorganization. This study illuminates the neural plasticity induced by cognitive training in vascular cognitive impairment no dementia, highlighting its potential to transform cognitive outcomes by tapping into the brain’s capacity for reorganization and adaptation.

Trial registration

The trial was registered underClinicalTrials.gov(NCT02640716) and conducted under both CONSORT statement and CONSORT statement for nonpharmacological interventions.
A program for real-time surveillance of SARS-CoV-2 genetics
Authors: Brochu Hayden N , Song Kuncheng , Zhang Qimin , Zeng Qiandong , Shafi Adib , Robinson Matthew , Humphrey Jake , Croy Bobbi , Peavy Lydia , Perera Minoli , Parker Scott , Pruitt John , Munroe Jason , Ghatti Rama , Urban Thomas J , Harris Ayla B , Alfego David , Norvell Brian , Levandoski Michael , Krueger Brian , Williams Jonathan D , Boles Deborah , Nye Melinda B , Dale Suzanne E , Sapeta Michael , Petropoulos Christos J , Meltzer Jonathan , Eisenberg Marcia , Cohen Oren , Letovsky Stanley , Iyer Lakshmanan K
Published: April 2024

The COVID-19 pandemic brought forth an urgent need for widespread genomic surveillance for rapid detection and monitoring of emerging SARS-CoV-2 variants. It necessitated design, development, and deployment of a nationwide infrastructure designed for sequestration, consolidation, and characterization of patient samples that disseminates de-identified information to public authorities in tight turnaround times. Here, we describe our development of such an infrastructure, which sequenced 594,832 high coverage SARS-CoV-2 genomes from isolates we collected in the U.S. from March 13th 2020 to July 3rd 2023. Our sequencing protocol ('Virseq') generates mutation-resistant sequencing of the entire SARS-CoV-2 genome, capturing all major lineages. We also characterize 379 clinically relevant SARS-CoV-2 multi-strain co-infections and ensure robust detection of emerging lineages via simulation. The modular infrastructure, sequencing, and analysis capabilities we describe support the U.S. Centers for Disease Control national surveillance program and serve as a model for rapid response to emerging pandemics at a national scale.
Mapping Global Research Trends in Digital Occupational Health: A Bibliometric Analysis Utilizing the Scopus Database
Authors: Er-Rays Youssef , M’dioud Meriem , Lemqeddem Hamid Ait
Published: April 2024

The 2019 health crisis has underscored the imperative role of information and communications technology (ICT) in bolstering employees’ health, well-being, and ameliorating health risks associated with artificial intelligence (AI) errors. Digital health technology facilitates remote healthcare delivery, employee health monitoring, and enhanced communication channels between workers and healthcare professionals. This paper conducts a comprehensive analysis of global trends in digital occupational health research over the past decade, with a specific focus on prolific authors, countries, academic institutions, and publications. Leveraging the PRISMA framework and VOSviewer software, relevant documents are extracted from the Scopus database. The findings underscore the significance of digital technology in the realm of occupational health and highlight the pressing need for further investigation, particularly encompassing emerging economies and employing robust methodologies to ensure the reliability of results. This study offers a valuable assessment of advancements in digital occupational health, serving as a foundation for future research endeavors aimed at optimizing workplace health and well-being on a global scale.
Re-defining how mRNA degradation is coordinated with transcription and translation in bacteria
Authors: Kim Seunghyeon , Wang Yu-Huan , Hassan Albur , Kim Sangjin
Published: April 2024

In eukaryotic cells, transcription, translation, and mRNA degradation occur in distinct subcellular regions. How these mRNA processes are organized in bacteria, without employing membrane-bound compartments, remains unclear. Here, we present generalizable principles underlying coordination between these processes in bacteria. InEscherichia coli, we found that co-transcriptional degradation is rare for mRNAs except for those encoding inner membrane proteins, due to membrane localization of the main ribonuclease, RNase E. We further found, by varying ribosome binding sequences, that translation affects mRNA stability not because ribosomes protect mRNA from degradation, but because low translation leads to premature transcription termination in the absence of transcription-translation coupling. Extending our analyses toBacillus subtilisandCaulobacter crescentus, we established subcellular localization of RNase E (or its homolog) and premature transcription termination in the absence of transcription-translation coupling as key determinants that explain differences in transcriptional and translational coupling to mRNA degradation across genes and species.
GPnotebook: A pan-cancer glycoproteomic database and toolkit for analysis of protein glycosylation changes associated with cancer phenotypes
Authors: Zhang Hui , Hu Yingwei
Published: April 2024

Protein glycosylation plays a pivotal role in various biological processes, and the analysis of intact glycopeptides (IGPs) has emerged as a powerful approach for characterizing alterations in protein glycosylation associated with diseases. Despite the critical insights gained from IGP analysis, there is an evident scarcity of intact glycopeptide database and specialized tools for a comprehensive glycoproteomic examination. In response to this deficiency, we have developed a Python package, "GPnotebook," which consolidates the intact glycopeptides identified from different cancer types by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and includes analytical tools for an in-depth characterization of glycopeptides. GPnotebook facilitates an array of functions including statistical profiling, differential expression analysis, glycosylation subtype categorization, investigation of glycosylation-phosphorylation interplay, survival analysis, and glycosylation enzyme assessment. We have deployed GPnotebook in a study of Pancreatic Ductal Adenocarcinoma (PDAC), thereby validating its application and demonstrating its capabilities. Our findings suggest that IGPs hold significant promise as cancer-specific changes and subtype differentiation. Consequently, GPnotebook stands out as a valuable resource for cancer researchers delving into the nuances of protein glycosylation and its correlation with cancer phenotypes.
Decoupled genetic and epigenetic variation in the montane endemicErodium cazorlanum(Geraniaceae) and a widespread congener
Authors: Martín-Blázquez Rubén , Medrano Mónica , Bazaga Pilar , Balao Francisco , Paun Ovidiu , Alonso Conchita
Published: April 2024

Epigenetic states offer an additional layer of variation besides genetic polymorphism that contribute to phenotypic variation and may arise either randomly or in response to environmental factors. We hypothesize that closely related species with different life-histories and habitat requirements could show distinct patterns of intraspecific epigenetic variation. We used Restriction-site Associated DNA sequencing (RADseq) and its bisulfite-converted variant (bsRADseq) to investigate in Sierra de Cazorla (SE Spain) the genetic and epigenetic population structure of two congeneric species, the endemic woody perennialErodium cazorlanumand the widely distributed annual herbE. cicutarium. Population genomics analyses revealed no structure in eitherE. cazorlanumandE. cicutarium,suggesting substantial gene flow between the study populations. In contrast, we found that the mean proportion of global DNA methylation was different between populations and species, withE. cazorlanumDNA showing higher methylation average and across-individuals variation. For each species, we searched for the loci with the strongest epigenetic differentiation between populations (differentially methylated cytosines, DMCs), and summarized them across regions (differentially methylated regions, DMRs). Multivariate analysis and hierarchical clustering of single cytosines’ methylation percentages did not group individuals by population, pointing to high epigenetic variation within populations. DMRs were enriched inCopiatransposable elements, putatively associated with stress response in plants. Our results suggest that variation at both genetic and epigenetic levels in our study area occur mainly within natural populations ofE. cazorlanumandE. cicutarium,with stronger population structure inE. cicutarium,and highlight the relevance of analyzing short distance spatial patterns.
Early-life scarcity adversity biases behavioral development toward a bipolar-like phenotype in mice heterozygous for CNTNAP2
Authors: Chelini Gabriele , Fortunato-Asquini Tommaso , Cerilli Enrica , Monsorno Katia , Catena Benedetta , Dall’O’ Ginevra Matilde , Paolicelli Rosa Chiara , Bozzi Yuri
Published: April 2024

The etiological complexity of psychiatric disorders arises from the dynamic interplay between genetic and environmental vulnerabilities. Among the environmental components, early-life adversities (ELA) are a major risk-factors for developing a psychiatric disorder. Yet, the mechanistic interaction between ELA and genetic vulnerability contributing to psychopathology is poorly understood. To fill this gap, we took advantage of the ideally controlled conditions of a pre-clinical approach. In this study we raised a mouse model with genetic predisposition to multiple psychiatric disorders (autism spectrum, schizophrenia, bipolar disorder), theCntnap2+/-mouse, with limited bedding and nesting (LBN), a well-established paradigm to induce early-life stress in rodents. These mice were compared to LBN-raisedCntnap2+/+littermates, as well as parallel groups ofCntnap2+/+andCntnap2+/-raised in standard conditions. Using a battery for behavioral phenotyping we show that ELA shapes non-overlapping phenotypic landscapes based on genetic predisposition. Specifically, we found that LBN-raisedCntnap2+/-mice develop a perseverative risk-taking behavior in the elevated plus maze and that this behavior is highly predictive of their success in the social interaction, assessed with the 3-chamber test. This finding suggests that the intrusion of anxiety into the social behavioral domain contributes to extreme gain- or loss-of function in social interaction, resembling a bipolar-like phenotype. Finally, we show that LBN promotes synaptic hypertrophy in the basolateral nucleus of the amygdala, but only inCntnap2+/-raised in LBN this condition was found in combination with microglia abnormalities. We conclude that the interplay between ELA andCntnap2haploinsufficiency exacerbates bipolar-like behaviors in mice, and that this may be consequence of deficient synaptic homeostasis in the basolateral amygdala.
Excitation Spillover from PSII to PSI Measured in Leaves at 77K
Authors: Terashima Ichiro , Oguchi Riichi , Atsuzawa Kimie , Kaneko Yasuko , Kono Masaru
Published: April 2024

Heterogeneous distribution of PSI and PSII in thick grana in shade chloroplasts is argued to hinder spillover of chlorophyll excitations from PSII to PSI. To examine this dogma, we measured fluorescence induction at 77K at 690 nm (PSII) and 760 nm (mainly PSI) in the leaf discs ofSpinacia oleracea,Cucumis sativusand shade tolerantAlocasia odora, grown at high and low light, and quantified their spillover capacities. PSI fluorescence (FI) consists of the intrinsic PSI fluorescence (FIα) and fluorescence caused by excitations spilt over from PSII (FIβ). WhenFIand FII parameters between State 1 and State 2, induced by weak far-red and blue light, were compared, PSII maximum fluorescence (FIIm) andFIβwere greater, andFIαwas smaller in State 1 and thereby the spillover ratio,FIβ/(FIα+FIβ) orFIβ/FIm, was greater in State 1. Since the leftoverFIImwas found to be about 10% of totalFmat 760 nm, all the data were corrected. Even after the correction, the spillover ratio inFImin State 1 ranged from 21 to 32%, and the spillover ratios were comparable irrespective of growth light conditions. Although extensive grana in low light grown plants would suggest that PSII and PSI are too separated for spillover, inA. odorachloroplasts, the ratio of non-appressed thylakoid membranes/total thylakoid membranes was little affected by growth light and more than 40%. Abundant non-appressed thylakoids would contribute to efficient spillover.
Rules of engagement for condensins and cohesins guide mitotic chromosome formation
Authors: Samejima Kumiko , Gibcus Johan H. , Abraham Sameer , Cisneros-Soberanis Fernanda , Samejima Itaru , Beckett Alison J. , Pučeková Nina , Abad Maria Alba , Medina-Pritchard Bethan , Paulson James R. , Xie Linfeng , Jeyaprakash A. Arockia , Prior Ian A. , Mirny Leonid A. , Dekker Job , Goloborodko Anton , Earnshaw William C.
Published: April 2024

During mitosis, interphase chromatin is rapidly converted into rod-shaped mitotic chromosomes. Using Hi-C, imaging, proteomics and polymer modeling, we determine how the activity and interplay between loop-extruding SMC motors accomplishes this dramatic transition. Our work reveals rules of engagement for SMC complexes that are critical for allowing cells to refold interphase chromatin into mitotic chromosomes. We find that condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. In contrast, condensin bypasses cohesive cohesins, thereby maintaining sister chromatid cohesion while separating the sisters. Studies of mitotic chromosomes formed by cohesin, condensin II and condensin I alone or in combination allow us to develop new models of mitotic chromosome conformation. In these models, loops are consecutive and not overlapping, implying that condensins do not freely pass one another but stall upon encountering each other. The dynamics of Hi-C interactions and chromosome morphology reveal that during prophase loops are extruded in vivo at ∼1-3 kb/sec by condensins as they form a disordered discontinuous helical scaffold within individual chromatids.
A natural ANI gap that can define intra-species units of bacteriophages and other viruses
Authors: Aldeguer-Riquelme Borja , Conrad Roth E , Antón Josefa , Rossello-Mora Ramon , Konstantinidis Konstantinos T.
Published: April 2024

Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A 95% whole-genome average nucleotide identity (ANI) gap is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage species revealed a region of low frequency of pairs around 99.2-99.8% ANI, showing 3-fold or fewer pairs than expected for an even or normal distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts, and from a variety of environments, although a few exceptions to this pattern were also observed (∼3.7% of the total species evaluated) and are likely attributed to cultivation biases. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled including SARS-CoV-2, whose ANI-based clusters matched well the WHO-defined Variants of Concern, indicating that they represent functionally and/or ecologically distinct units. The existence of sequence-discrete units appears to be predominantly driven by (high) ecological cohesiveness coupled to either recombination frequency for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2. These results indicate that fundamentally different underlying mechanisms could lead to similar diversity patterns. Based on these results, we propose the 99.5% ANI as a practical, standardized, and data-supported threshold for defining viral intra-species units of bacteriophages, for which we propose the term genomovars.

Importance

Viral species are composed of an ensemble of intra-species variants whose dynamic may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally-accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of viral bacteriophage genomes, we show that there is a nearly universal natural gap in whole-genome average nucleotide identities (ANI) among genomes at around 99.5%, which can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies.
Extended period of selection for antimicrobial resistance due to persistency of antimicrobials in broilers
Authors: Swinkels Aram F. , Berendsen Bjorn J.A. , Fischer Egil A.J. , Zomer Aldert L. , Wagenaar Jaap A.
Published: April 2024

Antimicrobials can select for antimicrobial resistant bacteria. After treatment the active compound is excreted through urine and faeces. As some antimicrobials are chemically stable and very persistent, recirculation of sub-inhibitory concentrations of antimicrobials may occur due to coprophagic behaviour of animals such as chickens.

The persistence of three antimicrobials over time and their potential effects on antimicrobial resistance were determined in four groups of broilers. Groups were left untreated (control) or were treated with amoxicillin (non-persistent), doxycycline or enrofloxacin (persistent). Antimicrobials were extracted from the faecal samples and concentrations were measured by LC-MS/MS. We determined the resistome genotypically using shotgun metagenomics and phenotypically by usingEscherichia colias indicator microorganism.

Up to 37 days after treatment, persistent antimicrobials (doxycycline and enrofloxacin) had concentrations in faeces equal to or higher than the minimal selective concentration (MSC), in contrast to the non-persistent (amoxicillin) treatment. The amoxicillin treatment showed a significant difference (p ≤ 0.01 and p ≤ 0.0001) in the genotypic resistance only directly after treatment. On the other hand, the doxycycline treatment showed approximately 52% increase in phenotypic and a significant difference (p ≤ 0.05 and p ≤ 0.0001) in genotypic resistance throughout the trial. Furthermore, the enrofloxacin treatment resulted in a complete enrofloxacin-resistantE. colipopulation but the quantity of resistance genes was similar to the control group, likely because resistance is mediated by point mutations.

Based on our findings, we suggest that persistency of antimicrobials should be taken into consideration in the assessment of priority classification of antimicrobials in livestock.
Toxicity assessment of 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl]-17β–marsdenin isolated fromGongronema latifoliumleaf on selected brain and kidney function indices in mice
Authors: Ani Onyedika Gabriel , Medayedupin Oluwatobi Ayodeji , Azeez Aminat Abike , Gyebi Gideon Ampoma , Boateng Isaac Duah , Adebayo Joseph Oluwatope
Published: April 2024

The safety of bioactive compounds, especially those isolated from medicinal plants, is a major concern for health authorities, pharmaceutical industries, and the public. Of recent, anti-tumor pregnane glycosides were isolated fromGongronema latifoliumleaf, of which the toxicity of one, 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl]-17β–marsdenin (3DMAOM), has not been evaluated. This study, therefore, evaluated the effects of 3DMAOM on selected brain and kidney function indices in mice. Female Swiss albino mice were randomly administered 5% dimethyl sulphoxide and different doses of 3DMAOM (0.5, 1, 2, and 4 mg/kg body weight) for fourteen (14) days, and their blood, brains, and kidneys were collected for biochemical analysis. There was no significant alteration in the activities of alkaline phosphatase (ALP), acetylcholinesterase, creatine kinase, Na+/K+-ATPase, Ca2+/Mg2+-ATPase, and Mg2+-ATPase in the brain of the treated groups compared to control. Also, no significant changes in the activities of ALP, gamma-glutamyltransferase, Na+/K+-ATPase, Ca2+/Mg2+-ATPase, and Mg2+-ATPase in the kidney of the treated groups compared to control. The plasma concentrations of Na+, K+, Cl-, PO43-, creatinine, and urea of mice were not significantly altered at all doses of the 3DMAOM compared to controls. However, the plasma concentration of Ca2+was significantly reduced (p<0.05) at all doses of the 3DMAOM, and the plasma concentration of uric acid was significantly reduced (p<0.05) at 2 mg/kg body weight of the 3DMAOM compared to controls. These findings suggest that 3DMAOM isolated fromGongronema latifoliumleaf may not adversely affect brain function but may affect calcium ion homeostasis in subjects.
Phosphorylation of KRP3, a KIP-related protein by MPK3 modulates rice tiller and seed number by fine-tuning cell division
Authors: Banerjee Gopal , Jonwal Sarvesh , Pal Uttam , Rengasamy Balakrishnan , Singh Dhanraj , Sinha Alok Krishna
Published: April 2024

During the cell cycle process, multiple inhibitors function as checkpoint regulators ensuring an impeccable duplication of genetic material. Kip-Related Proteins (KRPs) are a group of plant-specific cell cycle inhibitors and are known to regulate plant architecture and yield by differentially regulating cell division. KRPs, though functionally conserved, are dynamic in their amino acid composition. Interestingly, some KRPs are specific to dicots, and some are for monocots. In this study, we have identified that the presence of KRP3 and KRP6 is specific to the Poaceae family of monocots. An in-depth study ofKRP3showed a strict regulation of its expression in actively dividing cells during the G1-S phase progression of cell division. Our study identified KRP3 as a phosphorylation target of MPK3. The phosphorylation enhances KRP3 protein stability, which leads to strong inhibition of cell proliferation. By generating knock-out lines ofkrp3,mpk3and double knock-outkrp3mpk3, our study demonstrated that the MPK3-KRP3 module regulates rice root and shoot development as well as tiller and seed numbers. It was observed that KRP3 regulate the rate of cell division in a dose-dependent manner. The study, in a nutshell, establishes the role of KRP3 as an important regulator of rice vigor and yield.
Keetia gordoniisp. nov. (Rubiaceae - Vanguerieae) a new species of threatened forest liana from the littoral forest of Gabon
Authors: Cheek Martin , Bissiengou Pulchérie
Published: April 2024

Keetia gordoniisp. nov. (Rubiaceae - Vanguerieae) a new species of forest liana from the littoral forest of Gabon is formally described and illustrated as the first endemic species of the genus from that country. On current evidence, the species appears to have three locations and is threatened by forest clearance. It is provisionally assessed using the IUCN 2012 standard as Endangered (EN B2a,b(i-iv). The new species is extremely distinctive within the genus, showing several character states previously unrecorded inKeetia. Keetia gordoniiis currently unique in its genus for the massively thick, coriaceous leaf blades seen in the fruiting axillary branches (in this respect resembling aPsydraxGaertn., vs papery or rarely thinly coriaceous in otherKeetiaspecies), and also for the globose, smooth pyrenes (vs ovoid, colliculose in other species), in which the lid crest is so vestigial that it is almost imperceptible (vs lid crest conspicuous in other species). The tanniferous seed endosperm shows a new character state for the genus being present in a continuous, solid layer in the outer part of the seed, rather than being in radial bands or diffuse as in other species of the genus. However, there is no doubt that this taxon is best placed inKeetiaas opposed toPsydraxdue to the disc concealed deep inside the calyx tube (vs exposed), the presence of a pyrene cap (vs none) and the stipules that lack a well-developed keel (vs keel present). Further, the presence of tanniniferous seed endosperm is not recorded in any other genus of the tribe.Keetia gordoniiis currently assigned to theK. hispidaspecies group of Guineo-Congolian Africa.
A Sequential Binding Mechanism for 5’ Splice Site Recognition and Modulation for the Human U1 snRNP
Authors: White David S. , Dunyak Bryan M. , Vaillancourt Frédéric H. , Hoskins Aaron A.
Published: April 2024

Splice site recognition is essential for defining the transcriptome. Drugs like risdiplam and branaplam change how U1 snRNP recognizes particular 5’ splice sites (5’SS) and promote U1 snRNP binding and splicing at these locations. Despite the therapeutic potential of 5’SS modulators, the complexity of their interactions and snRNP substrates have precluded defining a mechanism for 5’SS modulation. We have determined a sequential binding mechanism for modulation of -1A bulged 5’SS by branaplam using a combination of ensemble kinetic measurements and colocalization single molecule spectroscopy (CoSMoS). Our mechanism establishes that U1-C protein binds reversibly to U1 snRNP, and branaplam binds to the U1 snRNP/U1-C complex only after it has engaged a -1A bulged 5’SS. Obligate orders of binding and unbinding explain how reversible branaplam interactions cause formation of long-lived U1 snRNP/5’SS complexes. Branaplam is a ribonucleoprotein, not RNA duplex alone, targeting drug whose action depends on fundamental properties of 5’SS recognition.
Comparative root transcriptome analysis suggests down-regulation of nitrogen assimilation in DJ123, a highly phosphorus-efficient rice genotype
Authors: Prodhan M. Asaduzzaman , Ueda Yoshiaki , Wissuwa Matthias
Published: April 2024

Many cultivable lands across the globe are characteristically low for plant-available phosphorus (P). This necessitates application of P fertilisers, but this increases farming costs beyond the affordability of marginal farmers. Thus, developing cultivars with high P-use efficiency (PUE) is necessary in high-yielding modern rice varieties, which are typically inefficient in P usage. However, the molecular and physiological bases to increase PUE in crops remain elusive. Here, we studied root transcriptomes of two breeding parents contrasting in PUE via RNA-seq to elucidate key physiological and molecular mechanisms that underlies efficient use of P in rice. Examination of transcriptome data obtained from plants grown under P-sufficient and P-deficient hydroponic conditions in DJ123 (an upland rice genotype adapted to low P soils) and IR64 (a modern rice variety less efficient in P use) revealed that the genes encoding nitrogen assimilation-related enzymes such as glutamine synthetase [EC. 6.3.1.2], glutamate synthase [EC. 1.4.1.13], and asparagine synthetase [EC. 6.3.5.4] were down-regulated only in DJ123 roots while it was not significantly affected in IR64 under low P conditions. In addition, DJ123 roots had a lower total nitrogen (N) concentration than IR64 irrespective of P conditions. Taken together, we surmise that the low level of N concentration together with down-regulation of the N assimilation-related genes allow DJ123 to operate at a low level of N, thus leading to formation of root tissues with lower metabolic investment and a greater PUE.
Periodic dietary restriction of animal products induces metabolic reprogramming in humans with effects on health
Authors: Rouskas Konstantinos , Bocher Ozvan , Simistiras Alexandros , Emmanouil Christina , Mantas Panagiotis , Skoulakis Anargyros , Park Y.C. , Dimopoulos Alexandros , Glentis Stavros , Kastenmüller Gabi , Zeggini Eleftheria , Dimas Antigone S.
Published: April 2024

Objectives

Dietary interventions can be a powerful tool for the prevention and treatment of diseases, but the molecular mechanisms through which diet affects health remain underexplored in humans. Generating robust evidence on the molecular impact of specific dietary patterns in humans will help us harness the power of dietary interventions to improve health.

Methods

Here, we compare plasma metabolomic and proteomic profiles between dietary states for a unique group of individuals (N=200) who alternate between omnivory and restriction of animal products for religious reasons. We also contrast findings to a control group of continuously omnivorous individuals (N=211).

Results

We find that short-term animal product restriction drives reductions in levels of lipid classes and of branched-chain amino acids, not detected in the control group, and results in metabolic profiles associated with decreased risk for all-cause mortality. We show that 23% of restriction-associated proteins are druggable targets and reveal that pro-longevity hormone FGF21 and seven additional proteins (FOLR2, SUMF2, HAVCR1, PLA2G1B, OXT, HPGDS, SPP1) display the greatest magnitude of change upon restriction. Through Mendelian randomization we demonstrate potentially causal effects of FGF21 and HAVCR1 on risk for type 2 diabetes, of HPGDS on BMI, and of OXT on risk for lacunar stroke.

Conclusions

We demonstrate that short-term restriction of animal products results in metabolic reprogramming with mostly positive effects on health and emphasise high-value targets for pharmacological intervention.
Conducting a survey of abortion-related knowledge, attitudes and practices amongst health professionals in Britain, strategies adopted and lessons learned: evidence from the SACHA Study
Authors: French RS , Palmer MJ , McCarthy O , Salaria N , Meiksin R , Shawe J , Lewandowska M , Scott R , Wellings K ,   the SACHA Study Team
Published: April 2024

Background

Most surveys examining health professionals’ knowledge, attitudes and practices around abortion have used convenience samples and have targeted doctors. Our goal in the SACHA Study, drawing on evidence-based strategies to maximise response rates, was to achieve a representative sample of a wider range of health professionals, working in general practice, maternity services, pharmacies, sexual and reproductive health (SRH) clinics and specialist abortion services in Britain, to explore the knowledge, attitudes and experience of abortion care and views on future models of delivery.

Methods

A cross-sectional questionnaire-based survey of midwives, doctors, nurses and pharmacists in England, Scotland and Wales was undertaken between November, 2021 and July, 2022. We used a stratified cluster sampling approach to select a random sample of sites and all eligible staff within those services were asked to respond to the survey. Evidence-based strategies to maximise completion rates were adopted, including postal delivery of the one-page questionnaire with personal letter of invitation and a stamped address envelope for return, inclusion of an unconditional voucher and follow-up.

Results

Overall, 147 of the 314 (46.8%) health service sites randomly selected took part in the survey. Reasons for non-participation included local Research and Development (R&D) Department non-response, lack of resources or insufficient time to support or approve the study, lack of interest in or perceived relevance of the topic and insufficient capacity to take part, exacerbated by work demands during the COVID epidemic. Of the 1370 questionnaires sent to eligible identified participants within these services, 771 were completed and returned (56.3%). At the service level the highest proportion of returns was from SRH clinics (81.0%) and the lowest from general practice (32.4%). In relation to profession, returns were highest amongst midwives (69.6%) and lowest amongst pharmacists (36.5%).

Conclusions

Obtaining information about health professional knowledge, attitudes and practices is key to guide service development and policy and to identify gaps in training and service provision in abortion. Despite our attempts to gain a representative sample of health professionals, the challenges we experienced limited the representativeness of the sample, despite the use of an evidence-based strategy.
The B-box protein BBX13/COL15 suppresses photoperiodic flowering by attenuating the action of CONSTANS in Arabidopsis
Authors: Rahul Puthan Valappil , Yadukrishnan Premachandran , Sasidharan Anagha , Datta Sourav
Published: April 2024

The optimal timing of transition from vegetative to floral reproductive phase is critical for plant productivity and agricultural yields. Light plays a decisive role in regulating this transition. The B-box (BBX) family of transcription factors regulates several light-mediated developmental processes in plants, including flowering. Here, we identify a previously uncharacterized group II member of the BBX family, BBX13/COL15, as a negative regulator of flowering under long-day conditions.BBX13is primarily expressed in the leaf vasculature, buds, and flowers. Its spatial expression pattern is similar to the major flowering time regulatorsCOandFT. bbx13mutants flower early, whileBBX13-overexpressors exhibit delayed flowering under long days. Genetic analyses showed thatBBX13acts upstream toCOandFTin the flowering pathway and negatively regulates their expression. We found that BBX13 physically interacts with CO and inhibits the CO-mediated transcriptional activation ofFT. In addition, BBX13 directly binds to theCORE2motif on theFTpromoter, a site where CO also binds. Furthermore, our ChIP data indicates that BBX13 reduces the in vivo binding of CO on theFTpromoter. Through luciferase assay, we found that BBX13 inhibits the CO-mediated transcriptional activation ofFT.All these data together suggest that BBX13/COL15 represses flowering in Arabidopsis by attenuating CO activity.

Summary statement

BBX13, a previously uncharacterized protein in the B-Box family of transcription factors, negatively regulates flowering time inArabidopsis thaliana. BBX13 physically and genetically interacts with CO and inhibits the CO-mediated transcriptional activation ofFT.
Filling-enforced obstructed atomic insulators
Authors: Xu Yuanfeng , Elcoro Luis , Song Zhi-Da , Vergniory M. G. , Felser Claudia , Parkin Stuart S. P. , Regnault Nicolas , Mañes Juan L. , Bernevig B. Andrei
Published: April 2024

Topological band theory has achieved great success in the high-throughput search for topological band structures both in paramagnetic and magnetic crystal materials. However, a significant proportion of materials are topologically trivial insulators at the Fermi level. In this paper, we show that, remarkably, for a subset of the topologically trivial insulators, knowing only their electron number and the Wyckoff positions of the atoms we can separate them into two groups: the obstructed atomic insulator (OAI) and the atomic insulator (AI). The interesting group, the OAI, have a center of charge not localized on the atoms. Using the theory of topological quantum chemistry, in this work we first derive the necessary and sufficient conditions for a topologically trivial insulator to be a filling enforced obstructed atomic insulator (feOAI) in the 1651 Shubnikov space groups. Remarkably, the filling enforced criteria enable the identification of obstructed atomic bands without knowing the representations of the band structures. Hence, no calculations are needed for the filling enforced criteria, although they are needed to obtain the band gaps. With the help of the Topological Quantum Chemistry website, we have performed a high-throughput search for feOAIs and have found that 957 ICSD entries (638 unique materials) are paramagnetic feOAIs, among which 738 (475) materials have an indirect gap. The metallic obstructed surface states of feOAIs are also showcased by several material examples.

Published by the American Physical Society
2024
Dependence of the Landau gauge ghost-gluon-vertex on the number of flavors
Authors: Zierler Fabian , Alkofer Reinhard
Published: April 2024

The gauge-boson, ghost and fermion propagators as well as the gauge-boson-ghost vertex function are studied for SU(N), Sp(2N), and SO(N) gauge groups. We solve a set of coupled Dyson-Schwinger equations in Landau gauge for a variable, fractional number Nf of massless fermions in the fundamental representation. For large Nf we find a phase transition from a chirally broken into a chirally symmetric phase that is consistent with the behavior expected inside the conformal window. Even in the presence of fermions the gauge-boson-ghost-vertex dressing remains small. In the conformal window this vertex shows the expected power law behavior. It does not assume its tree-level value in the far infrared, but the respective dressing function is a constant greater than 1.

Published by the American Physical Society
2024
Microresonator Brillouin laser and multi-Stokes generation at
2µm
Authors: Pathak Kanad , Puri Satyam , Pant Ravi
Published: April 2024

Brillouin scattering in microresonators has emerged as the driving process for developing high-coherence lasers for applications such as coherent optical communications, optical atomic clocks, microcomb solitons, and quantum communications. However, most of the demonstrations of microresonator Brillouin lasers have been limited to a 1550 nm wavelength regime, which benefits from the development of low-loss microresonator devices on different material platforms and the availability of tunable pump lasers. The development of wide bandwidth thulium-doped fiber amplifiers and low two-photon absorption in silicon around 2µm makes this wavelength region a potential candidate for applications in future optical communications, gravitation wave sensing, and atmospheric sensing. All these applications will benefit from the development of Brillouin lasers. However, there has not been much progress on microresonator-based 2µm Brillouin lasers. Here, we present a demonstration of a 2µm microresonator Brillouin laser. We use whispering gallery mode resonances in a ∼330µm silica microsphere to demonstrate a Brillouin lasing threshold of 35 mW. We achieve generation of second- and third-order Brillouin Stokes using pump powers of ∼60mW and 104 mW, respectively. By tuning the pump laser wavelength, we demonstrate high-resolution (∼10 pm) tuning of the Brillouin laser. From the beat signal of the first- and third-order Brillouin Stokes, we estimate a Brillouin laser linewidth of

∼

135

kHz

, which is 15 times smaller than the pump linewidth. This work may find applications in optical communications, soliton combs, and atmospheric sensing in the 2µm wavelength region.

Published by the American Physical Society
2024
Multidimensional relative poverty alleviation of the targeted microcredit in rural China: a gendered perspective
Authors: Wu Benjian , Niu Linyi , Tan Ruiqi , Zhu Haibo
Published: April 2024

Purpose

This study explores whether targeted microcredit can effectively alleviate households’ multidimensional relative poverty (MdRP) in rural China in the new era following the poverty elimination campaign and discusses it from a gendered perspective.

Design/methodology/approach

This study applies a fixed-effects model, propensity score matching (PSM) and two-stage instrumental variable method to two-period panel data collected from 611 households in rural western China in 2018 and 2021 to explore the effects, mechanisms and heterogenous performance of targeted microcredit on households’ MdRP in the new era.

Findings

(i) Targeted microcredit can alleviate MdRP among rural households in the new era, mainly by reducing income and opportunity inequality. (ii) Targeted microcredit can promote women’s empowerment, mainly by enhancing their social participation, thereby helping alleviate households’ MdRP. The effect of the targeted microcredit on MdRP is more significant in medium-educated women households and non-left-behind women households. (iii) The MdRP alleviation effect is stronger in villages with a high degree of digitalization.

Research limitations/implications

Learn from the experience of targeted microcredit. Accurately identify poor groups and integrate loan design into financial health and women empowerment. Particularly, pay attention to less-educated and left-behind women households and strengthen coordination between targeted microcredit and digital village strategies.

Originality/value

This study clarifies the effect of targeted microcredit on women’s empowerment and households’ MdRP alleviation in the new era. It also explores its various effects on households with different female characteristics and regional digitalization levels, providing ideas for optimizing microcredit.
Analysis of current distribution and termination conditions in 2D metasurfaces
Authors: Barmada Sami , Fontana Nunzia , Sandrolini Leonardo , Simonazzi Mattia
Published: April 2024

Purpose

The purpose of this paper is to gain a better understanding on how metasurfaces behave, in terms of currents in each unit cell. A better knowledge of their behavior could lead to an ad-hoc design for specific applications.

Design/methodology/approach

The methodology used is both theoretical and numerical; it is based on circuit theory and on an optimization procedure.

Findings

The results show that when the knowledge of the current in each unit cell of a metasurface is needed, the most common approximations currently used are often not accurate. Furthermore, a procedure for the termination of a metasurface, with application-driven goals, is given.

Originality/value

This paper investigates the distribution of the currents in a 2D metamaterial realized with magnetically coupled resonant coils. Different models for the analysis of these structures are illustrated, and the effects of the approximations they introduce on the current values are shown and discussed. Furthermore, proper terminations of the resonators on the boundaries have been investigated by implementing a numerical optimization procedure with the purpose of achieving a uniform distribution of the resonator currents. The results show that the behavior of a metasurface (in terms of currents in each single resonator) depends on different properties; as a consequence, their design is not a trivial task and is dependent on the specific applications they are designed for. A design strategy, with lumped impedance termination, is here proposed.