bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of developing sorghum grains to detect genes related to cell wall biosynthesis and remodelling
Authors: Costes Camille , Navarro Sanz Sergi , Calatayud Caroline , Soriano Alexandre , Mameri Hamza , Terrier Nancy , Francin-Allami Mathilde 
Published: February 2024

Abstract
Objective
Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important grain produced in the world. Interest for cultivating sorghum is increasing all over the world in the context of climate change, due to its low input and water requirements. Like other cultivated cereals, sorghum has significant nutritional value thanks to its protein, carbohydrate and dietary fiber content, these latter mainly consisting of cell wall polysaccharides. This work describes for the first time a transcriptomic analysis dedicated to identify the genes involved in the biosynthesis and remodelling of cell walls both in the endosperm and outer layers of sorghum grain during its development. Further analysis of these transcriptomic data will improve our understanding of cell wall assembly, which is a key component of grain quality.

Data description
This research delineates the steps of our analysis, starting with the cultivation conditions and the grain harvest at different stages of development, followed by the laser microdissection applied to separate the endosperm from the outer layers. It also describes the procedures implemented to generate RNA libraries and to obtain a normalized and filtered table of transcript counts, and finally determine the number of putative cell wall-related genes already listed in literature.
Single-cell RNA sequencing of mid-to-late stage spider embryos: new insights into spider development
Authors: Medina-Jiménez Brenda I. , Budd Graham E. , Janssen Ralf 
Published: February 2024

AbstractBackgroundThe common house spiderParasteatoda tepidariorumrepresents an emerging new model organism of arthropod evolutionary and developmental (EvoDevo) studies. Recent technical advances have resulted in the first single-cell sequencing (SCS) data on this species allowing deeper insights to be gained into itsearlydevelopment, but mid-to-late stage embryos were not included in these pioneering studies.ResultsTherefore, we performed SCS on mid-to-late stage embryos ofParasteatodaand characterized resulting cell clusters by means ofin-silicoanalysis (comparison of key markers of each cluster with previously published information on these genes).In-silicoprediction of the nature of each cluster was then tested/verified by means of additionalin-situhybridization experiments with additional markers of each cluster.ConclusionsOur data show that SCS data reliably group cells with similar genetic fingerprints into more or less distinct clusters, and thus allows identification of developing cell types on a broader level, such as the distinction of ectodermal, mesodermal and endodermal cell lineages, as well as the identification of distinct developing tissues such as subtypes of nervous tissue cells, the developing heart, or the ventral sulcus (VS). In comparison with recent other SCS studies on the same species, our data represent later developmental stages, and thus provide insights into different stages of developing cell types and tissues such as differentiating neurons and the VS that are only present at these later stages.
Unified mRNA Subcellular Localization Predictor based on machine learning techniques
Authors: Musleh Saleh , Arif Muhammad , Alajez Nehad M. , Alam Tanvir 
Published: February 2024

Abstract
Background
The mRNA subcellular localization bears substantial impact in the regulation of gene expression, cellular migration, and adaptation. However, the methods employed for experimental determination of this localization are arduous, time-intensive, and come with a high cost.

Methods
In this research article, we tackle the essential challenge of predicting the subcellular location of messenger RNAs (mRNAs) through Unified mRNA Subcellular Localization Predictor (UMSLP), a machine learning (ML) based approach. We embrace an in silico strategy that incorporate four distinct feature sets: kmer, pseudo k-tuple nucleotide composition, nucleotide physicochemical attributes, and the 3D sequence depiction achieved via Z-curve transformation for predicting subcellular localization in benchmark dataset across five distinct subcellular locales, encompassing nucleus, cytoplasm, extracellular region (ExR), mitochondria, and endoplasmic reticulum (ER).

Results
The proposed ML model UMSLP attains cutting-edge outcomes in predicting mRNA subcellular localization. On independent testing dataset, UMSLP ahcieved over 87% precision, 94% specificity, and 94% accuracy. Compared to other existing tools, UMSLP outperformed mRNALocator, mRNALoc, and SubLocEP by 11%, 21%, and 32%, respectively on average prediction accuracy for all five locales. SHapley Additive exPlanations analysis highlights the dominance of k-mer features in predicting cytoplasm, nucleus, ER, and ExR localizations, while Z-curve based features play pivotal roles in mitochondria subcellular localization detection.

Availability
We have shared datasets, code, Docker API for users in GitHub at: https://github.com/smusleh/UMSLP.
Meat and meat products as potential sources of emerging MDR Bacillus cereus: groEL gene sequencing, toxigenic and antimicrobial resistance
Authors: Algammal Abdelazeem M. , Eid Hamza M. , Alghamdi Saad , Ghabban Hanaa , Alatawy Roba , Almanzalawi Enas A. , Alqahtani Tahani M. , Elfouly Sabreen G. , Mohammed Gihan M. , Hetta Helal F. , El-Tarabili Reham M. 
Published: February 2024

Abstract
Background
Bacillus cereus is implicated in severe foodborne infection in humans. This study intended to assess the occurrence, groEL gene sequencing, biofilm production, and resistance profiles of emerged multidrug resistant (MDR) B. cereus in meat and meat product samples. Moreover, this work highlights the virulence and toxigenic genes (hblABCD complex, nheABC complex, cytK, ces, and pc-plc) and antimicrobial resistance genes (bla1, tetA, bla2, tetB, and ermA).

Methods
Consequently, 200 samples (sausage, minced meat, luncheon, beef meat, and liver; n = 40 for each) were indiscriminately collected from commercial supermarkets in Port Said Province, Egypt, from March to May 2021. Subsequently, food samples were bacteriologically examined. The obtained isolates were tested for groEL gene sequence analysis, antibiotic susceptibility, biofilm production, and PCR screening of toxigenic and resistance genes.

Results
The overall prevalence of B. cereus among the inspected food samples was 21%, where the highest predominance was detected in minced meat (42.5%), followed by beef meat (30%). The phylogenetic analysis of the groEL gene exposed that the examined B. cereus strain disclosed a notable genetic identity with other strains from the USA and China. Moreover, the obtained B. cereus strains revealed β-hemolytic activity, and 88.1% of the recovered strains tested positive for biofilm production. PCR evidenced that the obtained B. cereus strains usually inherited the nhe complex genes (nheA and nheC: 100%, and nheB: 83.3%), followed by cytK (76.2%), hbl complex (hblC and hblD: 59.5%, hblB: 16.6%, and hblA: 11.9%), ces (54.7%), and pc-plc (30.9%) virulence genes. Likewise, 42.9% of the examined B. cereus strains were MDR to six antimicrobial classes and encoded bla1, bla2, ermA, and tetA genes.

Conclusion
In summary, this study highlights the presence of MDR B. cereus in meat and meat products, posing a significant public health risk. The contamination by B. cereus is common in minced meat and beef meat. The molecular assay is a reliable fundamental tool for screening emerging MDR B. cereus strains in meat and meat products.
Is atrial fibrillation in HFpEF a distinct phenotype? Insights from multiparametric MRI and circulating biomarkers
Authors: Dattani Abhishek , Brady Emer M. , Kanagala Prathap , Stoma Svetlana , Parke Kelly S. , Marsh Anna-Marie , Singh Anvesha , Arnold Jayanth R. , Moss Alastair J. , Zhao Lei , Cvijic Mary Ellen , Fronheiser Matthew , Du Shuyan , Costet Philippe , Schafer Peter , Carayannopoulos Leon , Chang Ching-Pin , Gordon David , Ramirez-Valle Francisco , Jerosch-Herold Michael , Nelson Christopher P. , Squire Iain B. , Ng Leong L. , Gulsin Gaurav S. , McCann Gerry P. 
Published: February 2024

Abstract
Background
Heart failure with preserved ejection fraction (HFpEF) and atrial fibrillation (AF) frequently co-exist. There is a limited understanding on whether this coexistence is associated with distinct alterations in myocardial remodelling and mechanics. We aimed to determine if patients with atrial fibrillation (AF) and heart failure with preserved ejection fraction (HFpEF) represent a distinct phenotype.

Methods
In this secondary analysis of adults with HFpEF (NCT03050593), participants were comprehensively phenotyped with stress cardiac MRI, echocardiography and plasma fibroinflammatory biomarkers, and were followed for the composite endpoint (HF hospitalisation or death) at a median of 8.5 years. Those with AF were compared to sinus rhythm (SR) and unsupervised cluster analysis was performed to explore possible phenotypes.

Results
136 subjects were included (SR = 75, AF = 61). The AF group was older (76 ± 8 vs. 70 ± 10 years) with less diabetes (36% vs. 61%) compared to the SR group and had higher left atrial (LA) volumes (61 ± 30 vs. 39 ± 15 mL/m2, p < 0.001), lower LA ejection fraction (EF) (31 ± 15 vs. 51 ± 12%, p < 0.001), worse left ventricular (LV) systolic function (LVEF 63 ± 8 vs. 68 ± 8%, p = 0.002; global longitudinal strain 13.6 ± 2.9 vs. 14.7 ± 2.4%, p = 0.003) but higher LV peak early diastolic strain rates (0.73 ± 0.28 vs. 0.53 ± 0.17 1/s, p < 0.001). The AF group had higher levels of syndecan-1, matrix metalloproteinase-2, proBNP, angiopoietin-2 and pentraxin-3, but lower level of interleukin-8. No difference in clinical outcomes was observed between the groups. Three distinct clusters were identified with the poorest outcomes (Log-rank p = 0.029) in cluster 2 (hypertensive and fibroinflammatory) which had equal representation of SR and AF.

Conclusions
Presence of AF in HFpEF is associated with cardiac structural and functional changes together with altered expression of several fibro-inflammatory biomarkers. Distinct phenotypes exist in HFpEF which may have differing clinical outcomes.
‘Why do we have to be the gatekeepers?’ Australian general practitioners’ knowledge, attitudes and prescribing intentions on e-cigarettes as a smoking cessation aid
Authors: Selamoglu Melis , Erbas Bircan , Wilson Hester , Barton Chris 
Published: February 2024

Abstract
Background
A significant policy change impacting the availability of nicotine for use in electronic cigarettes (e-cigarettes) in Australia took effect from October 1, 2021. This change meant that nicotine containing liquids for use with e-cigarettes would only be available by prescription from a medical practitioner as part of a smoking cessation plan. This study aimed to explore general practitioners (GPs) perceptions about the role of e-cigarettes, and understand factors informing their intentions to prescribe e-cigarettes as part of a smoking cessation plan.

Methods
In-depth semi-structured interviews were conducted with thirteen GPs. Purposeful sampling was used to recruit participants. Interviews were audio recorded and transcribed verbatim. Thematic analysis was used to classify, describe and report themes in the data. QSR NVivo was used to aid coding, thematic analysis and retrieval of quotes.

Results
Participants had diverse views on recommending and prescribing e-cigarettes as smoking cessation aids to patients. Some participants were willing to prescribe e-cigarettes to patients if other methods of smoking cessation had not worked but there were concerns, and uncertainty, about the safety and efficacy of e-cigarettes for smoking cessation. There was poor understanding of the current policy and legislation about e-cigarettes in Australia. Mostly the participants in this sample did not feel confident or comfortable to prescribe, or have discussions about e-cigarettes with patients.

Conclusion
The participants of this study held diverse attitudes on recommending and prescribing e-cigarettes for smoking cessation. Clarity in guidelines and consumer product information are required to enable GPs to provide consistent and accurate advice to patients that wish to use e-cigarettes as a smoking cessation aid.
Attitudes toward active aging and their association with social determinants and views on older adults in Japan: a cross-sectional study
Authors: Osawa Eri , Sasaki Yuri , Hsu Hui-Chuan , Miura Hiroko 
Published: February 2024

Abstract
Background
Globally, the population of older adults has greatly increased, and active aging—whereby older adults can live healthy and fulfilling lives—is considered crucial for a sustainable society. However, the concept and practice of active aging are highly debated because it is unclear how people perceive active aging. This study explored Japanese people’s attitudes toward active aging (ATAA) and examined the associations between ATAA scores and sociodemographic variables, views on older adults, and self-rated life and health.

Methods
This study used data obtained from an online survey that originally targeted adults of all generations in Taiwan, South Korea, and Japan. In this study, we used only data from Japanese participants to elaborate on factors associated with ATAA in Japan. We conducted a one-way analysis of variance test and multiple linear regression analysis to evaluate the associations between the ATAA scores of 506 Japanese individuals and sociodemographic variables, views on older adults, and self-rated life and health.

Results
The sample comprised 171 females and 335 males. The mean (± SD) ATAA score of the 506 respondents was 138.8 (± 20.80). Females had a significantly higher ATAA score than males (144.02 versus 136.13, F = 26.29, p < 0.001). The respondents with higher education attainment, religious beliefs, better views on older adults, and better self-rated health were more likely to have a positive ATAA score (B: 3.83, 95% CI: 0.11, 7.56; B: 4.31, 95% CI: 0.93, 7.69; B: 2.07, 95% CI: 1.61, 2.53; B: 2.87, 95% CI: 0.92, 4.82, respectively). Being male, single (i.e., never married, divorced, or widowed) and other non-married marital statuses, and satisfied with one’s financial condition were negatively associated with ATAA (B: -8.73, 95% CI: -12.49, -4.96; B: -5.47, 95% CI: -9.07, -1.86; B: -2.04, 95% CI: -3.99, -0.09, respectively).

Conclusions
This study identified that females have more positive ATAA than males. Better views on older adults are a possible contributing factor that promotes ATAA among Japanese people. Our findings provide useful evidence that an approach towards those who are male, single, and economically satisfied is needed so that they have a positive attitude toward aging in Japan. It is necessary to address ageism and develop an environment in which individuals can expect to age actively.
Ocular syphilis masquerading as refractory retinal diseases
Authors: Park Sung Who , Kim Kye-Hyung , Kwon Han Jo , Byon Ik Soo , Khan Youan Hasan , Nguyen Quan Dong 
Published: February 2024

Abstract
Purpose
To report two cases of syphilis masquerading as chronic refractory macular diseases.

Case descriptions
Two patients had been diagnosed with neovascular age-related macular degeneration (neovascular AMD) and diabetic macular edema (DME), respectively. The disease worsened despite repeated intravitreal injections of anti-vascular endothelial growth factor (VEGF) and also surgical treatment (in suspected case of DME). Systemic evaluations were positive for syphilis. Intravenous penicillin was started, and the macular diseases improved. The lesions were well controlled afterward.

Conclusions
The current two cases demonstrated that ocular syphilis can masquerade as refractory chronic retinal diseases such as DME and neovascular AMD. Laboratory evaluations for syphilis may be needed, not only for uveitis but also for refractory retinal diseases. Indocyanine green angiography may be helpful to reveal occult syphilis.
Diagnosis of human leptospirosis: systematic review and meta-analysis of the diagnostic accuracy of the Leptospira microscopic agglutination test, PCR targeting Lfb1, and IgM ELISA to Leptospira fainei serovar Hurstbridge
Authors: Valente Marta , Bramugy Justina , Keddie Suzanne H. , Hopkins Heidi , Bassat Quique , Baerenbold Oliver , Bradley John , Falconer Jane , Keogh Ruth H. , Newton Paul N. , Picardeau Mathieu , Crump John A. 
Published: February 2024

Abstract
Background
Leptospirosis is an underdiagnosed infectious disease with non-specific clinical presentation that requires laboratory confirmation for diagnosis. The serologic reference standard remains the microscopic agglutination test (MAT) on paired serum samples. However, reported estimates of MAT’s sensitivity vary. We evaluated the accuracy of four index tests, MAT on paired samples as well as alternative standards for leptospirosis diagnosis: MAT on single acute-phase samples, polymerase chain reaction (PCR) with the target gene Lfb1, and ELISA IgM with Leptospira fainei serovar Hurstbridge as an antigen.

Methods
We performed a systematic review of studies reporting results of leptospirosis diagnostic tests. We searched eight electronic databases and selected studies that tested human blood samples and compared index tests with blood culture and/or PCR and/or MAT (comparator tests). For MAT selection criteria we defined a threshold for single acute-phase samples according to a national classification of leptospirosis endemicity. We used a Bayesian random-effect meta-analysis to estimate the sensitivity and specificity of MAT in single acute-phase and paired samples separately, and assessed risk of bias using the Quality Assessment of Studies of Diagnostic Accuracy Approach- 2 (QUADAS-2) tool.

Results
For the MAT accuracy evaluation, 15 studies were included, 11 with single acute-phase serum, and 12 with paired sera. Two included studies used PCR targeting the Lfb1 gene, and one included study used IgM ELISA with Leptospira fainei serovar Hurstbridge as antigen. For MAT in single acute-phase samples, the pooled sensitivity and specificity were 14% (95% credible interval [CrI] 3–38%) and 86% (95% CrI 59–96%), respectively, and the predicted sensitivity and specificity were 14% (95% CrI 0–90%) and 86% (95% CrI 9–100%). Among paired MAT samples, the pooled sensitivity and specificity were 68% (95% CrI 32–92%) and 75% (95% CrI 45–93%) respectively, and the predicted sensitivity and specificity were 69% (95% CrI 2–100%) and 75% (2–100%).

Conclusions
Based on our analysis, the accuracy of MAT in paired samples was not high, but it remains the reference standard until a more accurate diagnostic test is developed. Future studies that include larger numbers of participants with paired samples will improve the certainty of accuracy estimates.
Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance
Authors: Mohtar Jad , Mallah Hiba , Mardirossian Jean Marc , El-Bikai Rana , Jisr Tamima El , Soussi Shatha , Naoufal Rania , Alam Gabriella , Chaar Mira El 
Published: February 2024

Abstract
Background
Syndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers.

Methods
A multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens.

Results
Overall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons.

Conclusions
The adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.
Liver fat volume fraction measurements based on multi-material decomposition algorithm in patients with nonalcoholic fatty liver disease: the influences of blood vessel, location, and iodine contrast
Authors: Zhu Liuhong , Wang Funan , Wang Heqing , Zhang Jinhui , Xie Anjie , Pei Jinkui , Zhou Jianjun , Liu Hao 
Published: February 2024

Abstract
Background
In recent years, spectral CT-derived liver fat quantification method named multi-material decomposition (MMD) is playing an increasingly important role as an imaging biomarker of hepatic steatosis. However, there are various measurement ways with various results among different researches, and the impact of measurement methods on the research results is unknown. The aim of this study is to evaluate the reproducibility of liver fat volume fraction (FVF) using MMD algorithm in nonalcoholic fatty liver disease (NAFLD) patients when taking blood vessel, location, and iodine contrast into account during measurement.

Methods
This retrospective study was approved by the institutional ethics committee, and the requirement for informed consent was waived because of the retrospective nature of the study. 101 patients with NAFLD were enrolled in this study. Participants underwent non-contrast phase (NCP) and two-phase enhanced CT scanning (late arterial phase (LAP) and portal vein phase (PVP)) with spectral mode. Regions of interest (ROIs) were placed at right posterior lobe (RPL), right anterior lobe (RAL) and left lateral lobe (LLL) to obtain FVF values on liver fat images without and with the reference of enhanced CT images. The differences of FVF values measured under different conditions (ROI locations, with/without enhancement reference, NCP and enhanced phases) were compared. Friedman test was used to compare FVF values among three phases for each lobe, while the consistency of FVF values was assessed between each two phases using Bland–Altman analysis.

Results
Significant difference was found between FVF values obtained without and with the reference of enhanced CT images. There was no significant difference about FVF values obtained from NCP images under the reference of enhanced CT images between any two lobes or among three lobes. The FVF value increased after the contrast injection, and there were significant differences in the FVF values among three scanning phases. Poor consistencies of FVF values between each two phases were found in each lobe by Bland–Altman analysis.

Conclusion
MMD algorithm quantifying hepatic fat was reproducible among different lobes, while was influenced by blood vessel and iodine contrast.