bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes
Authors: Altayb Hisham N. , Hosawi Salman , Baothman Othman , Kazmi Imran , Chaieb Kamel , Abu Zeid Isam M. , Elbadawi Hana S. , Lopes Bruno Silvester , Moglad Ehssan 
Published: January 2023

IntroductionThe emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of K. quasipneumoniae using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be K. pneumoniae.MethodsWhole-genome sequencing was performed using the Illumina platform, and the generated raw reads were de novo assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools.ResultsSix strains were identified as K. quasipneumoniae subsp similipneumoniae and one as K. quasipneumoniae subsp. quasipneumoniae. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the fosA, blaOKP types, oqxB, and oqxA genes. One isolate additionally harbored a gene cassettes consisting of blaSHV−1, blaOXA−1, aac(6′)-Ib-cr, catB genes. The aminoglycoside-modifying enzyme gene aph(3”)-Ia was bracketed by two insertion elements. Plasmid analyses showed that IncFIBK was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, adherence, and biofilm formation (mrkA, mrkB, mrkC, mrkD, mrkF, and mrkH).ConclusionOur study highlights the ecology and transmission of K. quasipneumoniae (which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.
Addressing institutional and community barriers to development and implementation of community-engaged research through competency-based academic and community training
Authors: Hallmark C. Claire , Bohn Krista , Hallberg Lance , Croisant Sharon A. 
Published: January 2023

IntroductionThe National Center for Advancing Translational Sciences (NCATS) focuses on reducing barriers to effective translational research that rapidly translates science to clinical and community interventions to improve individual and community health. Community-Engaged Research (CEnR) plays a crucial role in this process by bridging gaps between research and practice. It effectively generates bi-directional knowledge and communication by engaging patients and communities throughout the translation research process. Skills development, however, is critical to enable investigators and communities to establish successful partnerships in research. While there are many independent CEnR education programs nationally, few curricula are mapped to identified domains and competencies.Assessment of current community engagement educational frameworks and competenciesWe located three comprehensive efforts to identify CEnR domains and competencies that we aligned to inform development of our curriculum, which we then mapped to these competencies. The first, undertaken by the NCATS Joint Workgroup on Researcher Training and Education and Community Capacity Building (JWG) was developed to assess training opportunities for academic researchers and community partners to increase their capacity to meaningfully engage collaborators in translational research. The JWG identified curricula, resources, tools, strategies, and models for innovative training programs and community engagement in all stages of research. It also conducted a gap analysis of deficiencies in available resources. Using Competency Mapping, they developed a framework for curriculum mapping that included eight domains, each with two to five competencies of knowledge, attitudes, and skills. The second aligned community-engaged research competencies with online training resources across the CTSA consortium, while the third was focused on Dissemination and Implementation training.Actionable recommendationsFurther informed by a conceptual model to advance health equity, we have adapted and integrated these components into a set of modules designed to educate and empower investigators, trainees, students, and community partners to engage in effective CEnR.DiscussionThis curriculum fills an important gap in our workforce development and helps to meet needs of our community partners. Following program evaluation and validation, we will offer the curriculum for use and further evaluation by other groups interested in using or adapting it for their own programming.
Twenty-eight-day in-hospital mortality prediction for elderly patients with ischemic stroke in the intensive care unit: Interpretable machine learning models
Authors: Huang Jian , Jin Wanlin , Duan Xiangjie , Liu Xiaozhu , Shu Tingting , Fu Li , Deng Jiewen , Chen Huaqiao , Liu Guojing , Jiang Ying , Liu Ziru 
Published: January 2023

BackgroundRisk stratification of elderly patients with ischemic stroke (IS) who are admitted to the intensive care unit (ICU) remains a challenging task. This study aims to establish and validate predictive models that are based on novel machine learning (ML) algorithms for 28-day in-hospital mortality in elderly patients with IS who were admitted to the ICU.MethodsData of elderly patients with IS were extracted from the electronic intensive care unit (eICU) Collaborative Research Database (eICU-CRD) records of those elderly patients admitted between 2014 and 2015. All selected participants were randomly divided into two sets: a training set and a validation set in the ratio of 8:2. ML algorithms, such as Naïve Bayes (NB), eXtreme Gradient Boosting (xgboost), and logistic regression (LR), were applied for model construction utilizing 10-fold cross-validation. The performance of models was measured by the area under the receiver operating characteristic curve (AUC) analysis and accuracy. The present study uses interpretable ML methods to provide insight into the model's prediction and outcome using the SHapley Additive exPlanations (SHAP) method.ResultsAs regards the population demographics and clinical characteristics, the analysis in the present study included 1,236 elderly patients with IS in the ICU, of whom 164 (13.3%) died during hospitalization. As regards feature selection, a total of eight features were selected for model construction. In the training set, both the xgboost and NB models showed specificity values of 0.989 and 0.767, respectively. In the internal validation set, the xgboost model identified patients who died with an AUC value of 0.733 better than the LR model which identified patients who died with an AUC value of 0.627 or the NB model 0.672.ConclusionThe xgboost model shows the best predictive performance that predicts mortality in elderly patients with IS in the ICU. By making the ML model explainable, physicians would be able to understand better the reasoning behind the outcome.
Factors associated with prolonged viral shedding in older patients infected with Omicron BA.2.2
Authors: Zhong Weijie , Yang Xiaosheng , Jiang Xiufeng , Duan Zhixin , Wang Wei , Sun Zhaoliang , Chen Wanghao , Zhang Wenchuan , Xu Jie , Cheng Juan , Yuan Xiaoling , Li Yi 
Published: January 2023

BackgroundThis study explores the risk factors associated with viral shedding time in elderly Chinese patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron.MethodsParticipants infected with SARS-CoV-2 omicron were enrolled in a retrospective study, and divided into two groups according to shedding time (≥10 days, “late clearance group” and &lt;10 days, “early clearance group”).ResultsA total of 180 patients were enrolled in the study (88 early, 92 late), with a median viral shedding time of 10 days and a mean age of 77.02 years. Prolonged SARS-CoV-2 omicron shedding was associated with old age (p = 0.007), lack of vaccination (p = 0.001), delayed admission to hospital after onset of diagnosis (p = 0.001), D-dimer (p = 0.003), and methylprednisolone treatment (p = 0.048). In multivariate analysis, vaccination (OR, 0.319, 95% CI, 0.130–0.786, p = 0.013), Paxlovid (OR, 0.259, 95% CI, 0.104–0.643, p = 0.004), and time from onset of diagnosis to admission (OR, 1.802, 95% CI, 1.391–2.355, p = 0.000) were significantly associated with viral clearance.ConclusionsTime from onset of diagnosis to hospitalization, lack of treatment with Paxlovid, and lack of vaccination were independent risk factors in elderly Chinese patients infected with SARS-CoV-2 omicron for prolonged viral shedding.
Quantitative analysis of knowledge, attitude and practice of workers in chicken slaughter slabs toward food safety and hygiene in Ouagadougou, Burkina Faso
Authors: Assefa Ayalew , Dione Michel , Ilboudo Guy , Lallogo Valerie , Gemeda Biruk Alemu , Grace Delia , Knight-Jones Theodore J. D. 
Published: January 2023

IntroductionIn low- and middle-income countries, chicken serves as a cheap source of protein and an income source for many households. It is particularly important in the capital, Ouagadougou, Burkina Faso, where chicken is regularly consumed. However, hygiene standards are very low, posing a significant public health risk.MethodsTo better understand the food safety situation, we conducted a cross-sectional survey of the hygienic practices of 155 randomly selected chicken slaughter outlets and carcass shops with a semi-structured questionnaire.Results and discussionOf the outlets visited, 59% are not licensed, and 63% are not regularly inspected, operating in the dominant, largely unregulated informal sector. More than 80% of the chickens are sourced from village production systems, but around 6% of the birds die during transport. The monetary loss due to chicken death during transportation is around four million USD annually. Market hygiene is poor; 86% of the holding pens have no hard floor and are not washed regularly. Almost all (92%) chickens are slaughtered on bare earth floors; bleeding, plucking, and evisceration are done on a wooden table that is rarely washed. On average, the same scalding water is used for 33 birds, seven scalded at a time. Most respondents (49%) thought that plucking and evisceration were the major cause of contamination of carcasses with foodborne pathogens. Most operators only washed their hands and knives with tap water at the beginning of the slaughtering process. Some shops use refrigerators and freezers to store carcasses before selling. However, they store carcasses with other foods like fish, beef and vegetables, facilitating further cross-contamination. There were rats (26%), cats (39%) and dogs (30%) present at outlets, roaming for food, especially roadside outlets. Training schemes on hygienic food handling practices were favoured by outlets as an approach to improve matters; however, improvements in food safety will be limited without significant upgrades in infrastructure and facilities. Slaughter slabs need a standard house with stable energy, adequate airflow, clean water, toilets, detergents and freezers. Also, they need equipment like knives, tables and dishes made of high-quality, easy-to-clean materials.
Identification of the main genetic clusters of avian reoviruses from a global strain collection
Authors: Kovács Edit , Varga-Kugler Renáta , Mató Tamás , Homonnay Zalán , Tatár-Kis Tímea , Farkas Szilvia , Kiss István , Bányai Krisztián , Palya Vilmos 
Published: January 2023

IntroductionAvian reoviruses (ARV), an important pathogen of poultry, have received increasing interest lately due to their widespread occurrence, recognized genetic diversity, and association to defined disease conditions or being present as co-infecting agents. The efficient control measures require the characterization of the available virus strains.MethodsThe present study describes an ARV collection comprising over 200 isolates from diagnostic samples collected over a decade from 34 countries worldwide. One hundred and thirty-six ARV isolates were characterized based on σC sequences.Results and discussionThe samples represented not only arthritis/tenosynovitis and runting-stunting syndrome, but also respiratory symptoms, egg production problems, and undefined disease conditions accompanied with increased mortality, and were obtained from broiler, layer or breeder flocks. In 31 percent of the cases other viral or bacterial agents were demonstrated besides ARV. The most frequent co-infectious agent was infectious bronchitis virus followed by infectious bursal disease virus and adenoviruses. All isolates could be classified in one of the major genetic clusters, although we observed marked discrepancies in the genotyping systems currently in use, a finding that made genotype assignment challenging. Reovirus related clinical symptoms could not be unequivocally connected to any particular virus strains belonging to a specific genetic group, suggesting the lack of strict association between disease forms of ARV infection and the investigated genetic features of ARV strains. Also, large genetic differences were seen between field and vaccine strains. The presented findings reinforce the need to establish a uniform, widely accepted molecular classification scheme for ARV and further, highlight the need for ARV strain identification to support more efficient control measures.
Transcriptome Analysis Reveals the Defense Mechanism of Cotton against Verticillium dahliae Induced by Hypovirulent Fungus Gibellulopsis nigrescens CEF08111
Authors: Feng Zili , Wei Feng , Feng Hongjie , Zhang Yalin , Zhao Lihong , Zhou Jinglong , Xie Jiatao , Jiang Daohong , Zhu Heqin 
Published: January 2023

Verticillium wilt is a kind of plant vascular disease caused by the soilborne fungus Verticillium dahliae, which severely limits cotton production. Our previous studies showed that the endophytic fungus Gibellulopsis nigrescens CEF08111 can effectively control Verticillium wilt and induce a defense response in cotton plants. However, the comprehensive molecular mechanism governing this response is not yet clear. To study the signaling mechanism induced by strain CEF08111, the transcriptome of cotton seedlings pretreated with CEF08111 was sequenced. The results revealed 249, 3559 and 33 differentially expressed genes (DEGs) at 3, 12 and 48 h post inoculation with CEF08111, respectively. At 12 h post inoculation with CEF08111, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the DEGs were enriched mainly in the plant–pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway-plant, and plant hormone signal transduction pathways. Gene ontology (GO) analysis revealed that these DEGs were enriched mainly in the following terms: response to external stimulus, systemic acquired resistance, kinase activity, phosphotransferase activity, xyloglucan: xyloglucosyl transferase activity, xyloglucan metabolic process, cell wall polysaccharide metabolic process and hemicellulose metabolic process. Moreover, many genes, such as calcium-dependent protein kinase (CDPK), flagellin-sensing 2 (FLS2), resistance to Pseudomonas syringae pv. maculicola 1(RPM1) and myelocytomatosis protein 2 (MYC2), that regulate crucial points in defense-related pathways were identified and may contribute to V. dahliae resistance in cotton. Seven DEGs of the pathway phenylpropanoid biosynthesis were identified by weighted gene co-expression network analysis (WGCNA), and these genes are related to lignin synthesis. The above genes were compared and analyzed, a total of 710 candidate genes that may be related to the resistance of cotton to Verticillium wilt were identified. These results provide a basis for understanding the molecular mechanism by which the biocontrol fungus CEF08111 increases the resistance of cotton to Verticillium wilt.
Morphologic Characters of the Rostrum in Two Weevils, Eucryptorrhynchus scrobiculatus Motschulsky and E. brandti Harold (Coleoptera: Curculionidae: Cryptorrhychinae)
Authors: Zhang Ganyu , Sun Ruihong , Li Huijuan , Wen Junbao 
Published: January 2023

(1) Eucryptorrhynchus scrobiculatus and E. brandti (Coleoptera: Curculionidae: Cryptorrhychinae) are both pests of Ailanthus altissima, found in China. During ovipositing, gravid females of the two weevils need to excavate a cavity in the oviposition substrate with their rostrum, while their oviposition sites are different. (2) In this study, to explore the boring mechanism of E. scrobiculatus and E. brandti during ovipositing, the morphologic characters of the rostra of two weevils were studied in detail by scanning electron microscopy and micro-CT. (3) Their rostra appear similar, but the rostrum surface of E. scrobiculatus is rougher than that of E. brandti; their fine structures of rostrum and sensilla distribution are similar, but the sensilla twig basiconica 3 is distributed at the apex of labial palpus in E. brandti females, while not at the apex of labial palpus in E. scrobiculatus females; their rostra are hollow and their cuticle thickness is constantly changing, but the proportion of the whole rostrum tube cuticle in E. scrobiculatus is significantly larger than that of E. brandti. The above structural differences make E. scrobiculatus more conducive to oviposition in the soil and E. brandti more conducive to oviposition in the trunk of A. altissima. (4) Overall, this study not only plays an important role in exploring the excavating mechanism during the oviposition of the two weevils, but also provides new insights into the coexistence of two weevil species on the same host A. altissima.
Epiphytic and Endophytic Fungi Colonizing Seeds of Two Poaceae Weed Species and Fusarium spp. Seed Degradation Potential In Vitro
Authors: Ņečajeva Jevgenija , Borodušķe Anete , Nikolajeva Vizma , Seņkovs Māris , Kalniņa Ineta , Roga Ance , Skinderskis Edmunds , Fridmanis Dāvids 
Published: January 2023

Fungi colonizing the surface and endosphere of two widespread Poaceae weed species, Avena fatua and Echinochloa crus-galli, were isolated to compare the taxonomic composition between the plant species, location, and year of the seed collection. The seed-degrading potential of Fusarium isolated from the seeds was tested by inoculating seeds of E. crus-galli with spore suspension. Molecular identification of epiphytic and endophytic fungal genera was performed by sequencing the ITS region of rDNA. Endophytes comprised of significantly lower fungal richness compared to epiphytes. A significant taxonomic overlap was observed between the endosphere and seed surface. The most abundant genera were Alternaria, Fusarium, Cladosporium, and Sarocladium. Analysis of similarities and hierarchical clustering showed that microbial communities were more dissimilar between the two plant species than between the years. Fusarium isolates with a high potential to infect and degrade E. crus-galli seeds in laboratory conditions belong to F. sporotrichioides and F. culmorum.
Possible Third Step Preventing Conjugation between Different Species of Blepharisma
Authors: Sugino Ayu , Kobayashi Mayumi , Sugiura Mayumi , Harumoto Terue 
Published: January 2023

In the genus Blepharisma, reproductive isolation between different species appears to be established at least by two barriers: (1) a mating pheromone, i.e., gamone 1, and (2) a factor involved in pair formation. Using four species, we experimentally investigated other potential barriers to interspecific conjugation in Blepharisma, as well as the first and second barriers. Cell-free fluid from type I cells (CFF1) of B. americanum had no effect on B. undulans, B. japonicum, or B. stoltei. Type II cells of B. americanum responded to CFF1 from B. americanum but not to CFF1 from B. undulans, B. japonicum, or B. stoltei. Gamone 1, therefore, seems to be the first reproductive barrier (with the inclusion of B. americanum species [megakaryotype 3]) as reported previously. In pretreated cells with complementary gamones in B. undulans and B. americanum, inter-species pair formation was rare, but pair formation between B. americanum and B. japonicum and between B. americanum and B. stoltei occurred at relatively high frequency. Most of the inter-species B. americanum–B. stoltei pairs underwent nuclear changes specific to conjugation. No significant difference was observed between the intra- and inter-species pairs over the time course of the nuclear changes, but the percentage of abnormal cells was higher in inter-species pairs than in intra-species pairs, and no progenies were produced by inter-species pairs. These results suggest a third barrier or step, in addition to the first and second ones, in nuclear changes after pair formation that prevents interspecific conjugation in Blepharisma.
Triazine-Based Small Molecules: A Potential New Class of Compounds in the Antifungal Toolbox
Authors: Conrad Karen A. , Kim Hyunjeong , Qasim Mohammad , Djehal Amel , Hernday Aaron D. , Désaubry Laurent , Rauceo Jason M. 
Published: January 2023

Invasive fungal infections caused by Candida species remain a significant public health problem worldwide. The increasing prevalence of drug-resistant infections and a limited arsenal of antifungal drugs underscore the need for novel interventions. Here, we screened several classes of pharmacologically active compounds against mammalian diseases for antifungal activity. We found that the synthetic triazine-based compound melanogenin (Mel) 56 is fungicidal in Candida albicans laboratory and clinical strains with minimal inhibitory concentrations of 8–16 µg/mL. Furthermore, Mel56 has general antifungal activity in several non-albicans Candida species and the non-pathogenic yeast Saccharomyces cerevisiae. Surprisingly, Mel56 inhibited the yeast-to-hyphae transition at sublethal concentrations, revealing a new role for triazine-based compounds in fungi. In human cancer cell lines, Mel56 targets the inner mitochondrial integral membrane prohibitin proteins, PHB1 and PHB2. However, Mel56 treatment did not impact C. albicans mitochondrial activity, and antifungal activity was similar in prohibitin single, double, and triple homozygous mutant strains compared to the wild-type parental strain. These results suggests that Mel56 has a novel mechanism-of-action in C. albicans. Therefore, Mel56 is a promising antifungal candidate warranting further analyses.
Gestion des champs abandonnés pour le développement de l'élevage extensif dans les Pyrénées centrales espagnoles
Authors: Lasanta Martínez Teodoro 
Published: January 2023

Gestion de campos abandonados para el desarrollo de la ganadería extensiva en el Pirineo central español.
Los campos abandonados ocupan una superficie muy amplia en el Pirineo español. En la actualidad están cubiertos por matorral y aportan muy poco a la alimentación del ganado. Los objetivos de este trabajo son delimitar posibles campos abandonados que podrían desbrozarse y ser utilizados como prados con el fin de disminuir el actual desequilibrio estacional en pastos. A partir de un Sistema de Información Cartográfica (SIG) se han cartografiado los campos recuperables en función de factor-es topográficos y de accesibilidad. Por otro lado, se aporta información sobre el Valor Pastoral de dichos campos y se ha calculado en qué medida su cambio de uso (de campos abandonados a prados) repercutiría en la disminución del desequilibrio estacional de pastos. Finalmente se discute sobre las ventajas medioambientales y paisajísticas que tendría el desbroce del matorral.