bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification ofStaphylococcus aureusand prevalence ofStaphylococcus aureusresistant to mithicillin and other patterns of resistance to antibiotics in clinical isolates of diabetic foot
Authors: Ramon Edder Guadalupe Segura , Gonzalez Gabriel Martinez , Almeida Jorge 
Published: July 2024

AbstractObjectiveTo determine the prevalence of methicillin-resistantStaphylococcus aureus(MRSA) in diabetic foot wounds and analyze antibiotic resistance patterns.IntroductionThe global incidence of diabetes mellitus, particularly type II, has significantly increased, leading to complications such as diabetic foot ulcers. These ulcers often become infected, with MRSA being a common and challenging pathogen. Understanding the prevalence and resistance patterns of MRSA in diabetic foot infections is crucial for effective treatment.MethodologyDiabetic foot wound samples were collected from 65 patients in the Valley of Toluca, Mexico. Samples were cultured and analyzed using chromogenic agar, BHI, salt and mannitol, calf blood, EMB, and MacConkey agars. Strain identification and antibiotic sensitivity testing were performed using the Vytek automated system. Oxacillin and cefoxitin were used to detect methicillin resistance. Statistical analyses, including Kolmogorov-Smirnov, Shapiro-Wilk tests, and Spearman correlation, were conducted to evaluate relationships between clinical factors and antibiotic resistance.ResultsOf the 65 samples, 56.9% were from men and 43.1% from women, with 97.1% having type II diabetes. MRSA prevalence was 63%. Resistance rates were highest for ampicillin (100%), clindamycin (89%), erythromycin (87%), and gentamicin (73%). Statistical analysis showed no significant correlation between oxacillin resistance and glycemic control, erythromycin resistance (MLS resistance), hypertension, or gender.ConclusionThe high prevalence of MRSA in diabetic foot wounds underscores the need for targeted infection control and appropriate antibiotic therapy. The lack of correlation between resistance and clinical factors suggests a multifactorial nature of antibiotic resistance, necessitating broader clinical and microbiological considerations for future studies.
UCS: a unified approach to cell segmentation for subcellular spatial transcriptomics
Authors: Chen Yuheng , Xu Xin , Wan Xiaomeng , Xiao Jiashun , Yang Can 
Published: July 2024

AbstractSubcellular Spatial Transcriptomics (SST) represents an innovative technology enabling researchers to investigate gene expression at the subcellular level within tissues. To comprehend the spatial architecture of a given tissue, cell segmentation plays a crucial role in attributing the measured transcripts to individual cells. However, existing cell segmentation methods for SST datasets still face challenges in accurately distinguishing cell boundaries due to the varying characteristics of SST technologies. In this study, we propose a unified approach to cell segmentation (UCS) specifically designed for SST data obtained from diverse platforms, including 10X Xenium, NanoString CosMx, MERSCOPE, and Stereo-seq. UCS leverages deep learning techniques to achieve high accuracy in cell segmentation by integrating nuclei segmentation from nuclei staining and transcript data. Compared to current methods, UCS not only provides more precise transcript assignment to individual cells but also offers computational advantages for large-scale SST data analysis. The analysis output of UCS further supports versatile downstream analyses, such as subcellular gene classification and missing cell detection. By employing UCS, researchers gain the ability to characterize gene expression patterns at both the cellular and subcellular levels, leading to a deeper understanding of tissue architecture and function.
Spectral algal fingerprinting and long sequencing in synthetic algal-microbial communities
Authors: Meirkhanova Ayagoz , Marks Sabina , Feja Nicole , Vorobjev Ivan A. , Barteneva Natasha S. 
Published: July 2024

AbstractSynthetic biology has made progress in creating artificial microbial and algal communities, but technical and evolutionary complexities still pose significant challenges.Traditional methods for studying microbial and algal communities, such as microscopy and pigment analysis, are limited in throughput and resolution. In contrast, advancements in full-spectrum cytometry enabled high-throughput, multidimensional analysis of single cells based on their size, complexity, and spectral fingerprints, offering more precise and comprehensive analysis than conventional flow cytometry.This study demonstrates the use of full-spectrum cytometry for analyzing synthetic algal-microbial communities, facilitating rapid species identification and enumeration. The workflow involves recording individual spectral signatures from monocultures, utilizing autofluorescence to distinguish them from noise, and subsequent creation of a spectral library for further analysis. The obtained library is used then to analyze mixtures of unicellular cyanobacteria and synthetic phytoplankton communities, revealing differences in spectral signatures. The synthetic consortium experiment monitored algal growth, comparing results from different instruments and highlighting the advantages of the spectral virtual filter system for precise population separation and abundance tracking. This approach demonstrated higher flexibility and accuracy in analyzing multi-component algal-microbial assemblages and tracking temporal changes in community composition.By capturing the complete emission spectrum of each cell, this method enhances the understanding of algal-microbial community dynamics and responses to environmental stressors. With development of standardized spectral libraries, our work demonstrates an improved characterization of algal communities, advancing research in synthetic biology and phytoplankton ecology.
Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways
Authors: Nawrocka Wioletta I. , Cheng Shouqiang , Hao Bingjie , Rosen Matthew C. , Cortés Elena , Baltrusaitis Elana E. , Aziz Zainab , Kovács István A. , Özkan Engin 
Published: July 2024

ABSTRACTMulticellularity was accompanied by the emergence of new classes of cell surface and secreted proteins. The nematodeC. elegansis a favorable model to study cell surface interactomes, given its well-defined and stereotyped cell types and intercellular contacts. Here we report ourC. elegansextracellular interactome dataset, the largest yet for an invertebrate. Most of these interactions were unknown, despite recent datasets for flies and humans, as our collection contains a larger selection of protein families. We uncover new interactions for all four major axon guidance pathways, including ectodomain interactions between three of the pathways. We demonstrate that a protein family known to maintain axon locations are secreted receptors for insulins. We reveal novel interactions of cystine-knot proteins with putative signaling receptors, which may extend the study of neurotrophins and growth-factor-mediated functions to nematodes. Finally, our dataset provides insights into human disease mechanisms and how extracellular interactions may help establish connectomes.
GPT-3 reveals selective insensitivity to globalvs.local linguistic context in speech produced by treatment-naïve patients with positive thought disorder
Authors: Sharpe Victoria , Mackinley Michael , Eddine Samer Nour , Wang Lin , Palaniyappan Lena , Kuperberg Gina R. 
Published: July 2024

AbstractBackgroundEarly psychopathologists proposed that certain features of positive thought disorder, the disorganized language output produced by some people with schizophrenia, suggest an insensitivity to global, relative to local, discourse context. This idea has received support from carefully controlled psycholinguistic studies in language comprehension. In language production, researchers have so far remained reliant on subjective qualitative rating scales to assess and understand speech disorganization. Now, however, recent advances in large language models mean that it is possible to quantify sensitivity to global and local context objectively by probing lexical probability (the predictability of a word given its preceding context) during natural language production.MethodsFor each word in speech produced by 60 first-episode psychosis patients and 35 healthy, demographically-matched controls, we extracted lexical probabilities from GPT-3 based on contexts that ranged from very local— a single preceding word: P(Wn | Wn-1)—to global— up to 50 preceding words: P(Wn|Wn-50, Wn-49, …, Wn-1).ResultsWe show, for the first time, that disorganized speech is characterized by disproportionate insensitivity to global, versus local, linguistic context. Critically, this global-versus-local insensitivity selectively predicted clinical ratings of positive thought disorder, above and beyond overall symptom severity. There was no evidence of a relationship with negative thought disorder (impoverishment).ConclusionsWe provide an automated, interpretable measure that can potentially be used to quantify speech disorganization in schizophrenia. Our findings directly link the clinical phenomenology of thought disorder to neurocognitive constructs that are grounded in psycholinguistic theory and neurobiology.
Mechanistic Insights into MinD Regulation and Pattern Formation inBacillus subtilis
Authors: Feddersen Helge , Bramkamp Marc 
Published: July 2024

AbstractBacteria precisely regulate the place and timing of their cell division. One of the best-understood systems for division site selection is the Min system inEscherichia coli. InE. coli, the Min system displays remarkable pole-to-pole oscillation, creating a time-averaged minimum at the cell’s geometric center, which marks the future division site. Interestingly, the Gram-positive model speciesBacillus subtilisalso encodes homologous proteins: the cell division inhibitor MinC and the Walker-ATPase MinD. However,B. subtilislacks the activating protein MinE, which is essential for Min dynamics inE. coli. We have shown before that theB. subtilisMin system is highly dynamic and quickly relocalizes to active sites of division. This raised questions about how Min protein dynamics are regulated on a molecular level inB. subtilis. Here, we show with a combination ofin vitroexperiments andin vivosingle-molecule imaging that the ATPase activity ofB. subtilisMinD is activated solely by membrane binding. Additionally, both monomeric and dimeric MinD bind to the membrane, and binding of ATP to MinD is a prerequisite for fast membrane detachment. Single-molecule localization microscopy data confirm membrane binding of monomeric MinD variants. However, only wild type MinD enriches at cell poles and sites of ongoing division, likely due to interaction with MinJ. Monomeric MinD variants and locked dimers remain distributed along the membrane and lack the characteristic pattern formation. Single-molecule tracking data further support that MinD has a freely diffusive population, which is increased in the monomeric variants and a membrane binding defective mutant. Thus, MinD dynamics inB. subtilisdo not require any unknown protein component and can be fully explained by MinD’s binding and unbinding kinetics with the membrane. The generation of MinD patterns relies on the short-lived temporal residence of MinD dimers at the membrane.
Plasmid2MC: Efficient cell-free recombination of plasmids into high-purity minicircle DNA for use in genome editing applications
Authors: Oliynyk Roman Teo , Mahas Ahmed , Karpinski Emil , Church George M. 
Published: July 2024

AbstractDNA plasmids are commonly used for delivering proteins and RNA in genome editing. However, their bacterial components can lead to inactivation, cell toxicity, and reduced efficiency compared to minicircle DNA (mcDNA) lacking such bacterial sequences. Existing commercial kits that recombine plasmids into mcDNA within proprietary bacterial strains are labor-intensive, yield inconsistent results, and often produce low-quality mcDNA. To address this, we developed Plasmid2MC, a cell-free method using ΦC31 recombination to efficiently excise the bacterial backbone from conventionally prepared plasmids, while mcDNA purification steps digest all DNA impurities and reduce endotoxin levels. We demonstrated application of mcDNA to express CRISPR-dCas9 for base editing in HEK293T cells and mouse embryonic stem cells, as well as for homology-independent targeted insertion (HITI) genome editing. The method’s ease of preparation, efficiency and mcDNA purity make it a valuable alternative for applications requiring bacterial backbone-free circular DNA.
Biological tick control: modeling the potential impact of entomopathogenic fungi on the transmission of East Coast fever in cattle
Authors: Oundo Joseph Wang’ang’a , Hartemink Nienke , de Jong Mart C.M , Koenraadt Constantianus J.M. , Kalayou Shewit , Masiga Daniel , ten Bosch Quirine 
Published: July 2024

AbstractBiological control of ticks using entomopathogenic fungi (EPF) is a highly desired alternative to chemical acaricides for the control of tick-borne pathogens. ForMetarhizium anisopliaeisolate ICIPE 7, one of these EPFs, efficacy against multiple tick species has been demonstrated in laboratory and field settings. However, we currently have little quantitative understanding of how EPFs can impact transmission. We developed a deterministic model of tick–host–pathogen interactions to explore how the effects of EPF onRhipicephalus appendiculatusticks may impact the transmission dynamics of East Coast fever (ECF) in cattle populations. We parameterized the multi-faceted effects of EPFs on tick dynamics using experimental data on Tickoff® biopesticide (a novel formulation ofM. anisopliaeICIPE 7) and related EPFs. The epidemiological impact of EPF was evaluated across a range of product profiles and implementation strategies. Model results indicate that, for the explored product profiles, EPF derives most of its epidemiological impact through the delayed mortality effect. This EPF-induced mortality could not only reduce the onwardTheileria parvatransmission to cattle (both treated and untreated) but could also cause a reduction in the tick-to-host ratio and thus cattle exposure to ticks. The effects of EPF on reproduction fitness and engorgement of ticks elicit negligible impact. High levels of population coverage and treatment frequency are needed to reduce the tick population size and reach meaningful epidemiological impact in cattle populations. Additionally, increasing the persistence time of fungal conidia on cattle skin – through technological improvements to the EPF formulation – can substantially reduce acute infections when combined with appreciable population coverage levels, treatment frequency, and efficient spraying techniques. Our model analysis provides insights into the potential impact of EPF when deployed at a population level, and lends support to further research and development of this biological tick control tool.
Discordance in Genotypic and Phenotypic anti-tuberculosis drug susceptibility results: time to reconsider critical concentration
Authors: Shrivas Arti , Singh Sarman , Singh Jitendra , Shankar Prem , Soni Payal , Rufai Syed Beenish , Maurya Anand , Purwar Shashank 
Published: July 2024

AbstractObjectiveTo correlaterpoBmutations found on the sanger sequencing inMycobacterium tuberculosis(MTB) isolates with Minimum Inhibitory Concentrations (MICs) to the rifampicin.MethodsWe assessed the minimum inhibitory concentrations (MICs) for 151 archived clinical MTB isolates that were determined phenotypically susceptible to RIF (101;66.89%) and remaining fifty (50;33.11%) were resistant to RIF by BACTEC MGIT SIRE DST. MIC values were determined using colorimetric redox indicator (Resazurin/REMA) method and results were correlated withrpoBgene mutations associate with rifampicin resistance found.ResultsComparing the MIC and critical concentration, we found that 15 of these 101 (14.85%) isolates were misclassified by MGIT-960 as sensitive at standard critical concentration (1.0µg/mL) though these were found to have low-level RIF resistance by CRI assay (MIC 0.50µg/mL to 1.0µg/mL) and sanger sequencing. We found that all of 15 isolates contained non-synonymous mutations, the commonest being theIle572Phe(7, 46.66%), followed byLeu533Pro(3, 20.0%),His526Leu(2, 13.33%),His526Asn+Ile572Phe(1),Asp516Tyr(1), andLeu533Pro+Pro564Arg(1). These mutations are reported to confer low-level RIF resistance. But we did not find any mutation at MIC<0.25μg/mL.ConclusionWe found that a significant number of MTB isolates have phenotypic and genotypic discordance. Taking 1.0µg/mL of rifampicin as critical concentration, isolates from approximately 15% patients are misidentified as susceptible to rifampicin, even when these strains carry low level drug resistance conferring mutations and have potential to develop clinical MDR-TB.
Physiological Roles of anAcinetobacter-specific σ Factor
Authors: Bacon Emily E. , Myers Kevin S. , Iruegas-López Rubén , Banta Amy B. , Place Michael , Ebersberger Ingo , Peters Jason M. 
Published: July 2024

AbstractThe Gram-negative pathogenAcinetobacter baumanniiis considered an “urgent threat” to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used byA. baumanniito mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress.Acinetobacterspecies contain the poorly characterized ECF “SigAb;” however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique toAcinetobacterspecies and distinct from RpoE. We combine promoter mutagenesis, motif scanning, and ChIP-seq to define the direct SigAb regulon, which consists ofsigAbitself, the stringent response mediator,relA, and the uncharacterized small RNA, “sabS.” However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown ofsigAborsabSresulted in increased copper sensitivity and excess copper induced SigAb-dependent transcription. Further, we found that two uncharacterized genes in thesigAboperon, “aabA” and “aabB”, have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show thatsigAb,aabA, andaabBare important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture ofA. baumannii.ImportanceAcinetobacter baumanniiis a hospital-acquired pathogen, and many strains are resistant to multiple antibiotics. Understanding howA. baumanniisenses and responds to stress may uncover novel routes to treat infections. Here, we examine how theAcinetobacter-specific transcription factor, SigAb, mitigates stress. We find that SigAb directly regulates only a small number of genes, but indirectly controls hundreds of genes that have substantial impacts on cell physiology. We show that SigAb is required for maximal growth, even during optimal conditions, and is acutely required during growth in the presence of elevated copper. Given that copper toxicity plays roles in pathogenesis and on copper-containing surfaces in hospitals, we speculate that SigAb function may be important in clinically-relevant contexts.
Kidney ‘pathway-orphan’ genes as a potential overlooked source of novel insights into kidney health and disease
Authors: Acoba Dianne , Gunnarsson Sophie , Reznichenko Anna 
Published: July 2024

ABSTRACTHundreds of protein-coding genes still have unknown functions and no biological pathway annotations. Mechanistic studies typically investigate well-known genes, despite growing evidence of associations between disease and some understudied genes. We hypothesized that examining these overlooked genes lacking pathway annotation could lead to new insights on chronic kidney disease (CKD) pathogenesis. Human protein-coding genes (N=19,258) from HGNC were annotated with pathway membership using a comprehensive collection of pathway databases (including but not limited to GO, KEGG, MSigDB, Reactome, WikiPathways) to reveal ‘pathway-orphan genes’— genes that are not members of any biological pathways. Expression and enrichment of pathway-orphan genes in healthy kidneys were established using GTEx data. Kidney-expressed pathway-orphan genes were tested for differential case-control expression using publicly available CKD datasets with kidney tissue RNA-seq transcriptomics profiling (GSE98422, GSE142025, GSE175759, GSE197307, Levin et al., 2020). A total of 286 genes in the human genome currently lack any biological pathway membership and are identified as pathway-orphan genes. We have determined 97 of these pathway-orphan genes are expressed in healthy kidneys, with several showing kidney-specific enrichment. Furthermore, 34 pathway-orphan genes show significant modulation of expression (FDR < 0.05) in CKD kidney, out of which 10 robustly demonstrate concordant directionality of change in more than one RNA-seq study. Through interrogating multiple lines of evidence, we showed how possible physiological functions of the pathway-orphan genes in kidney health and disease can be inferred. A substantial number of kidney-expressed genes remain ‘pathway-orphan’ while displaying clear signals of kidney relevance, such as enrichment of expression in the kidney, significant modulation in CKD, and genetic associations with kidney function. Directing mechanistic studies into this overlooked gene group might broaden our biological understanding of kidney physiology and highlight novel disease drivers.
Clathrin-associated carriers enable recycling through a kiss-and-run mechanism
Authors: Xu Jiachao , Liang Yu , Li Nan , Dang Song , Jiang Amin , Liu Yiqun , Guo Yuting , Yang Xiaoyu , Yuan Yi , Zhang Xinyi , Yang Yaran , Du Yongtao , Shi Anbing , Liu Xiaoyun , Li Dong , He Kangmin 
Published: July 2024

AbstractEndocytosis and recycling control the uptake and retrieval of various materials, including membrane proteins and lipids, in all eukaryotic cells. These processes are crucial for cell growth, organization, function, and environmental communication. However, the mechanisms underlying efficient, fast endocytic recycling remain poorly understood. Here, by utilizing a biosensor and imaged-based screening, we uncover a novel recycling mechanism that couples endocytosis and fast recycling, which we name the clathrin-associated fast endosomal recycling pathway (CARP). Clathrin-associated tubulovesicular carriers containing clathrin, AP1, Arf1, Rab1, and Rab11, while lacking the multimeric retrieval complexes, are generated at subdomains of early endosomes, and then transported along actin to cell surfaces. Unexpectedly, the clathrin-associated recycling carriers undergo partial fusion with the plasma membrane. Subsequently, they are released from the membrane by dynamin and reenter cells. Multiple receptors utilize and modulate CARP for fast recycling following endocytosis. Thus, CARP represents a novel endocytic recycling mechanism with kiss-and-run membrane fusion.
Picobiinae mites (Acariformes: Syringophilidae) parasitising the Starlings (Passeriformes: Sturnidae) in the Afrotropical region
Authors: Patan Milena , Skoracki Maciej , Marcisova Iva , Hromada Martin , Sikora Bozena 
Published: July 2024

AbstractIn the present paper, we continue our studies on quill mites of the family Syringophilidae parasitising birds of the family Sturnidae. Herein, we describe a new species,Picobia wisniewskiisp. nov., collected from the red-winged starlingOnychognathus morio(Linnaeus) in Tanzania. Additionally, we provide an emended diagnosis and new host records forPicobia lamprotornisKlimovicova et al., 2014 andPicobia sturniSkorackiet al. 2004.