bluuebunny/crossref_metadata_2025_split huggingface dataset:
SLEEP QUALITY AND CIRCADIAN RHYTHM DISRUPTION IN CRITICALLY ILL PATIENTS IN INTENSIVE CARE UNIT
Authors: Christina-Athanasia Sampani , Georgios Koukoulitsios , Athanasia Liveri , Papageorgiou Dimitrios 
Published: September 2024

AbstractAimThe aim of this study was to evaluate the quality of sleep in critically ill patients in the Intensive Care Unit (ICU).Method and MaterialThis study investigated the night-time sleep of 135 patients admitted to the general ICU of the General Hospital of Athens “G. Gennimatas” between January 2021 and December 2023. Data were collected using the Richards Campbell Sleep Questionnaire (RCSQ). Sensory stimuli, including noise, light, nursing activities, and invasive procedures, were reduced during the night to improve patients’ sleep. Measures to reduce light included implementing special lighting during nursing tasks and using bedside lamps during care. Noise reduction strategies involved closing doors, minimizing monitor alarms, and discouraging staff from speaking near patient beds. Grouping patient care activities was also promoted to limit sleep disturbances.ResultsPatients in the intervention group showed improved sleep quality compared to the control group, with a significant overall RCSQ score (p<0.05). Gender and age did not significantly affect sleep quality. However, hospital stay duration differed between groups, with the control group experiencing shorter stays. A negative correlation was observed between the duration of hospitalization and sleep quality, with longer stays linked to lower RCSQ scores. Additionally, extended mechanical ventilation was associated with poorer sleep quality.ConclusionPatients in the ICU often exhibit abnormal levels of alertness, poor quality of daytime sleep, disrupted nighttime sleep, and sleep patterns that lack both slow-wave and rapid eye movement (REM) sleep. Gaining a deeper understanding of the role circadian rhythms play in managing critical illness could pave the way for future chronotherapeutic strategies, enhancing clinical outcomes and promoting recovery for patients.
Revisiting the cytogenetics ofVelloziaVand.: immunolocalization of KLN1 elucidates the chromosome number for the genus
Authors: Braz Guilherme T. , Riboldi Lucas B. , Pinto Maísa S. , Forni-Martins Eliana R. , Yassitepe Juliana E. C. T. , Dante Ricardo A. , Gerhardt Isabel R. 
Published: September 2024

AbstractChromosome number is the most fundamental trait of a karyotype. Accurate chromosome counting is essential for further analyses including cytogenomics, taxonomic, evolutionary, and genomic studies. Despite its importance, miscounting is common, especially in early publications on species with small and morphologically similar chromosomes.VelloziaVand. is a genus mainly distributed throughout South America belonging to the angiosperm family Velloziaceae, a dominant taxon in the Brazilian “campos rupestres”. Cytogenetic studies within the group have been rare and have shown conflicting chromosome counts, even within the same species. These discrepancies are associated with the presence of a few small chromosome-like structures, which were previously classified as possible satellites. Here, to accurately determine the chromosome number of species belonging to the genus, we used different cytogenomics approaches, including the immunostaining of the KNL1 kinetochore protein combined with chromosome spread preparation using tissue culture-derived samples. Our results revealed 2n= 18 chromosomes for all six species studied. This finding suggests that the basic chromosome number forVelloziaisx= 9 and notx= 8, as previously proposed. The immunolocalization of functional centromeres was fundamental for undoubtedly identifying the smaller chromosome pair as real chromosomes and accurately determining the correct chromosome number of these species. This will provide substantial support for further studies, including investigations into karyotype evolution and the generation of reference genomes for the species of the family.
Morphology of softening and translucency in the stems of tomato and eggplant seedlings due to infection byRalstonia pseudosolanacearumF1C1
Authors: Bhuyan Shuvam , Boruah Lakhyajit , Jain Monika , Begum Shuhada , Giri Shubhra Jyoti , Dutta Lukapriya , Mandal Manabendra , Ray Suvendra Kumar 
Published: September 2024

AbstractRalstonia pseudosolanacearumF1C1 is a soil-borne phytopathogenic bacterium with a broad host range that infects several economically important crops. This study primarily focuses on the infection of this phytopathogen in two such important crop seedlings: tomato and eggplant. The observations of the study reveal a complex set of symptoms that include drooping and blackening of the seedling stem, as well as blackening, chlorosis, and curling of cotyledon leaves. Notably, the symptom of stem softening and translucency is seen primarily in the water-submerged stem regions of the root-inoculated seedlings. Furthermore, the morphology of stem softening and translucency is more frequent in root-inoculated eggplant seedlings, underscoring a difference between tomato and eggplant seedlings regarding the virulence of the bacterium. By investigating these unique pathological phenotypes in the infected seedlings, this study uncovers unique symptoms previously not reported in seedling inoculation experiments. Such findings deepen our understanding of the complex virulence mechanisms of the pathogen. The work also highlights the distinct escape mechanisms exhibited by seedlings, revealing how some of its host plants might resist wilting despite infection, offering new avenues for future research. These findings contribute to the understanding ofR. pseudosolanacearumpathogenesis, shedding light on its virulence and host response mechanisms.
Strategic targeting of Cas9 nickase expands tandem gene arrays
Authors: Takesue Hiroaki , Okada Satoshi , Doi Goro , Sugiyama Yuki , Kusumoto Emiko , Ito Takashi 
Published: September 2024

SUMMARYExpanding tandem gene arrays facilitates adaptation through dosage effects and gene family formation via sequence diversification. However, experimental induction of such expansions remains challenging. Here we introduce a method termed break-induced replication (BIR)-mediated tandem repeat expansion (BITREx) to address this challenge. BITREx strategically places Cas9 nickase adjacent to a tandem gene array to break the replication fork that has replicated the array, forming a single-end double-strand break. This break is subsequently end-resected to become single-stranded. Since there is no repeat unit downstream of the break, the single-stranded DNA often invades an upstream unit to initiate ectopic BIR, resulting in array expansion. BITREx has successfully expanded gene arrays in budding yeast, with theCUP1array reaching ∼1 Mb. Furthermore, appropriate splint DNA allows BITREx to generate tandem arrays de novo from single-copy genes. We have also demonstrated BITREx in mammalian cells. Therefore, BITREx will find various unique applications in genome engineering.
Targeted syndromic next-generation sequencing panel for simultaneous detection of pathogens associated with bovine reproductive failure
Authors: Periyasamy Dhinesh , Huang Yanyun , Hill Janet E. 
Published: September 2024

AbstractBovine reproductive failure, which includes infertility, abortion, and stillbirth in cattle, leads to significant economic losses for beef and milk producers. Diagnosing the infectious causes of bovine reproductive failure is challenging as there are multiple pathogens associated with it. The traditional stepwise approach to diagnostic testing is time-consuming and can cause significant delays. In this study, we have developed a syndromic next-generation sequencing panel (BovReproSeq), for the simultaneous detection of 17 pathogens (bacteria, virus and protozoa) associated with bovine reproductive failure. This targeted approach involves amplifying multiple pathogen-specific targets using ultra-multiplex PCR, followed by sequencing with the Oxford Nanopore platform and subsequent analysis of the data using a custom bioinformatic pipeline to determine the presence or absence of pathogens. We tested 116 clinical samples and found that BovReproSeq results matched with current diagnostic methods for 93% of the samples, and most of the disagreements occurring in samples with very low pathogen loads (Ct > 35). At the optimal read-count threshold of 10 reads (minimum number of reads to classify the sample as positive), the clinical sensitivity of the assay was approximately 82%, while clinical specificity was 100%. The overall accuracy of the assay was 98.8%. Matthew’s Correlation Coefficient (correlation coefficient of binary classification) was approximately 0.90 and F1 score (harmonic mean of Precision and Recall) was 0.90, indicating excellent overall performance. Our study presents a significant advancement in detecting the infectious agents associated with bovine reproductive failure and the BovReproSeq panel’s ability to detect 17 pathogens makes it a promising tool for veterinary diagnostics.ImportanceBovine reproductive failure causes substantial economic losses to beef and milk producers, and infectious disease contributes significantly to this syndrome. Etiologic diagnosis is complicated since multiple pathogens can be involved and infections with some pathogens are asymptomatic or cause similar clinical signs. A stepwise approach to diagnostic testing is time-consuming and increases the risk of missing the correct diagnosis. BovReproSeq is a next-generation sequencing based diagnostic panel that allows detection of 17 reproductive failure pathogens simultaneously.
Development of sensorimotor responses in larval zebrafish: a comparison between wild-type and GCaMP6s transgenic line
Authors: Caperaa Margaux , Roland-Caverivière Mathilde , Herdman Chelsea , Imloul Nesrine , Poulin Sandrine , Lemieux Mado , De Koninck Paul , Bossé Gabriel D 
Published: September 2024

AbstractDuring early development, zebrafish larvae exhibit stereotypical behaviors, which rapidly become more complex. Thus, the generation of mutant transgenic lines that maintain transparency throughout their larval stage and that can be used to record brain activity has offered strategic opportunities to investigate the underlying neural correlates of behavior establishment. However, few studies have documented the behavioral profile of these lines during larval development. Here, we set up a behavioral characterization using diverse stimuli (light and vibration) throughout larval development to compare the responses of a transgenic strain expressing a pan-neuronal calcium indicator (GCaMP6s) with that of a wild-type strain. Interestingly, we report a drastic switch in behavioral responses to light transitions at 11 days post-fertilization (dpf) and to vibration stimuli at 14 dpf in both lines. These data highlight a specific time window of behavioral complexification. Meanwhile, we found no major difference in the maturation of sensorimotor responses between GCaMP6s and wild-type strains. Thus, these results support using GCaMP6s strain in investigating the neural mechanisms underlying the developmental maturation of sensorimotor responses. We observed nevertheless some minor differences that suggest careful attention should be taken when using mutant/transgenic lines for behavioral studies.Highlights-Longitudinal investigation of sensorimotor responses by zebrafish during their larval development-During the second week of development, larval zebrafish switch their motor response to light transition-Pan-neuronal nuclear expression of GCaMP6s has little impact on larval fish response to various stimuli
Impacts of the COVID-19 pandemic on sepsis incidence, etiology and hospitalization costs in France: a retrospective observational study
Authors: Al Rahmoun Marie , Sabaté-Elabbadi Alexandre , Guillemot Didier , Brun-Buisson Christian , Watier Laurence 
Published: September 2024

AbstractBackgroundSepsis is a serious medical condition that causes long-term morbidity and high mortality, annually affecting millions of people worldwide. The COVID-19 pandemic may have impacted its burden.ObjectiveTo estimate the impact of the COVID-19 pandemic on sepsis incidence, etiology and associated hospitalization costs in metropolitan France.MethodsThis retrospective observational study used data drawn from a cohort of hospitalized sepsis patients in France’s national healthcare database. Sepsis was identified through both explicit ICD-10 codes (E-sepsis) and implicit codes (I-sepsis). Participants included all patients aged 15 years or older hospitalized with E-sepsis or I-sepsis in metropolitan France between January 1, 2018, and December 31, 2022. Patient and hospital stay characteristics were described by sepsis type (E-sepsis, I-sepsis) and overall. The distribution of sepsis etiology was estimated for each year. Annual incidence rates were estimated overall and by sepsis type and etiology. Total and median per-stay hospitalization costs were calculated.ResultsThe total age- and sex-standardized sepsis incidence rate per 100,000 increased slightly from 2018 (446, 95% CI 444.2 to 447.7) to 2020 (457, 95% CI 455.1 to 458.6) and then decreased in 2022 (382, 95% CI 380.2-383.7) (p <.0001). Incidence rates decreased for both E-sepsis and bacterial sepsis during the pandemic period, whereas I-sepsis incidence increased in 2020 and 2021, associated with a marked increase in viral sepsis and co-infections (p <.0001 for E- and I-sepsis). Viral sepsis represented about 10% of all sepsis cases during the pandemic, but only about 1% prior to the pandemic. Total sepsis-associated hospitalization costs and extra medication costs increased during the pandemic. Characteristics of patients and their hospital stays were overall stable over the five-year study period.ConclusionsThe COVID-19 pandemic led to a higher burden of sepsis in French hospitals and an increase in hospital stay costs. Critically, our study highlights the need for introducing explicit viral sepsis codes within the ICD-11 classification system and for achieving a consensus on its definition in order to robustly estimate sepsis incidence.
Three-Dimensional virtual reality-based visualization of fetal cardiac anatomy using spatio-temporal image correlation (STIC) ultrasound datasets of normal and abnormal hearts
Authors: Vaidyanathan Balu , Maya Harikrishnan Anil , Xavier Sarin , Kappanayil Mahesh 
Published: September 2024

AbstractThis case report demonstrates the feasibility of creating immersive 3D visualizations (3D Virtual reality and 3D printing) from fetal echocardiographic volume datasets for both normal heart and a heart with transposition of great arteries. Immersive 3D technologies could emerge as powerful tools in future for understanding fetal cardiac anatomy for clinical decision making as well as training and research.
Development and evaluation of codelists for identifying marginalised groups in primary care
Authors: Perchyk Tetyana , de Vere Hunt Isabella , Nicholson Brian D , Mounce Luke , Sykes Kate , Lyratzopoulos Yoryos , Lemanska Agnieszka , Whitaker Katriina L , Kerrison Robert S 
Published: September 2024

ABSTRACTBackgroundPrimary care electronic health records provide a rich source of information for inequalities research. However, the reliability and validity of the research derived from these records depends on the completeness and resolution of the codelists used to identify marginalised populations.AimThe aim of this project was to develop comprehensive codelists for identifying ethnic minorities, people with learning disabilities (LD), people with severe mental illness (SMI) and people who are transgender.Design and settingThis study was a codelist development project, conducted using primary care data from the United Kingdom.MethodGroups of interest were defined a priori. Relevant clinical codes were identified by searching Clinical Practice Research Datalink (CPRD) publications, codelist repositories and the CPRD code browser. Relevant codelists were downloaded and merged according to marginalised group. Duplicates were removed and remaining codes reviewed by two general practitioners. Comprehensiveness was assessed in a representative CPRD population of 10,966,759 people, by comparing the frequencies of individuals identified when using the curated codelists, compared to commonly used alternatives.ResultsA total of 52 codelists were identified. 1,420 unique codes were selected after removal of duplicates and GP review. Compared with comparator codelists, an additional 48,017 (76.6%), 52,953 (68.9%) and 508 (36.9%) people with a LD, SMI or transgender code were identified. The frequencies identified for ethnicity were consistent with expectations for the UK population.ConclusionThe codelists curated through this project will improve inequalities research by improving standards of identifying marginalised groups in primary care data.HOW THIS FITS INThe reliability and validity of primary care data for inequalities research depends on the comprehensiveness of the codes used to identify people from marginalised groups.This study set out to develop comprehensive codelists for the identification of four key groups, known to experience health inequalities.We developed comprehensive codelists for identifying ethnic minorities, learning disabilities, severe mental illness and people who are transgender, using a systematic approach.The codelists were validated by two general practitioners, assessed in a representative sample, and can now be used in primary care practice and research, both nationally and internationally.
Tuberculosis Infection Control in MDR-TB designated hospitals, Jiangsu Province of China
Authors: Song Honghuan , Li Guoli , Xu Zhuping , Wang Feixian , Wang Xiaoping , Dai Bing , Zhang Xing , Li Jincheng , Li Yan , Zhu Limei 
Published: September 2024

AbstractBackgroundHospital-acquired TB (Tuberculosis) infection among healthcare workers (HCWs) and patients is a severe problem due to the increased attributable risk of TB infection among these groups.MethodsA standardized tool was applied. The assessment was conducted by direct observation, document review, and interviews with the facility heads. Baseline evaluation of TBIC (Tuberculosis infection control) in TB outpatient, inpatient departments, and laboratories was completed by January 2019. Based on the results, we implemented a comprehensive package of interventions, including administrative, environmental engineering, and respiratory protection (PPE) three-level hierarchy of controls. Subsequent monitoring was finalized quarterly and improvement measures should be formulated accordingly. More than two years of follow-up data was collected until August 31, 2021, by hospitals, municipality CDCs, and Jiangsu provincial CDC.ResultsAt baseline, the implementation rate of administrative, environmental engineering and PPE IC was 57.29%, 59.21%, and 66.63%, respectively. After evaluation and implementation, priority way for cough patients was established, mechanical ventilation and the use of masks were improved, UV and UVGI lights were settled in need. The implementation rate of administrative, environmental and PPE IC were significantly increased to 86.27%, 87.41%, and 98.42%(P<0.05), respectively.ConclusionsAfter more than one and a half years of intervention, TBIC in the designated hospitals has significantly improved. However, the availability of separate TB wards remains suboptimal. TB IC measures must be strengthened to reduce TB transmission among HCWs and non-TB patients. This method was practical and suitable to be popularized in countries with high TB burden.
Pharmacist Impact on First-Line Antihypertensives in African American Patients
Authors: Reid Mia Y. , Coates Jamie E. , Yates Naomi Y. , McDonald Bennett 
Published: September 2024

AbstractIntroductionCurrent guidelines recommend thiazide/thiazide-type diuretics and dihydropyridine calcium channel blockers as first-line agents in treating African Americans with hypertension. The purpose of this study is to examine the impact that ambulatory care clinical pharmacy specialists (CPSs) had on initiation of first-line antihypertensives in the African American population within an integrated healthcare system.MethodsThis retrospective, matched, observational cohort analysis included African American patients with hypertension not receiving a first-line antihypertensive as of September 1, 2021. Patients followed by CPSs were matched up to 1:4 on age and sex to patients not followed by CPSs. The primary outcome was the percentage of patients started on first-line antihypertensive(s) after working with CPSs. Conditional logistic regression was used to analyze outcomes.ResultsA total of 865 patients followed by CPSs were matched to 3,192 patients not followed by CPSs. Patients followed by CPSs were initiated on first-line antihypertensives at a significantly higher rate (adjusted OR 1.98, 95% CI 1.63-2.41), and a clinically significant improvement in blood pressure was observed with systolic improving an average of 22 points and diastolic 13 points. 283 patients managed by CPSs achieved blood pressure less than 135/85 mmHg.ConclusionThe initiation of first-line antihypertensives in African American patients by CPSs led to clinically significant reductions in systolic and diastolic blood pressure which supports CPS involvement in hypertension management. The assessment of study outcomes provides guidance to clinical decision-making and contributes to the development of key practice standards across both physician and clinical pharmacy specialist services.
Stress-mediated growth determinesE. colidivision site morphogenesis
Authors: Pelech Petr , Navarro Paula P. , Vettiger Andrea , Chao Luke H. , Allolio Christoph 
Published: September 2024

AbstractIn order to proliferate, bacteria must remodel their cell wall at the division site. The division process is driven by the enzymatic activity of peptidoglycan (PG) synthases and hydrolases around the constricting Z-ring. PG remodelling is reg-ulated by de-and re-crosslinking enzymes, and the directing constrictive force of the Z-ring. We introduce a model that is able to reproduce correctly the shape of the division site during the constriction and septation phase ofE. coli. The model represents mechanochemical coupling within the mathematical framework of morphoelasticity. It contains only two parameters, associated with volumet-ric growth and PG remodelling, that are coupled to the mechanical stress in the bacterial wall. Different morphologies, corresponding either to mutant or wild type cells were recovered as a function of the remodeling parameter. In addition, a plausible range for the cell stiffness and turgor pressure was determined by comparing numerical simulations with bacterial cell lysis data.