bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRANSITION FROM CLINICAL PRACTITIONER TO ACADEMIC EDUCATOR: THE EXPERIENCES OF RADIOGRAPHY LECTURERS IN NIGERIA
Authors: Ogolodom Michael Promise , Chiegwu H.U. , Mbaba Awajimijan Nathaniel , Bakre Abdul Fatai K. , Balogun Elizabeth O. , Obasi Annmaris Chimebere , Ezechukwu Uchenna Norochukwunso , Ezugwu Emeka E. , Egop Egop Brownson 
Published: November 2023

AbstractBackgroundClinical educators are essential in radiography education programmes. Transitioning from clinical practicing radiographers to academic educators is a rewarding journey. This study was designed to examine the experience of Radiography Lecturers in the Nigerian universities that converted from radiography practitioners to academic educators.Materials and methods:A Google form questionnaire-based study design was conducted among 35 radiography lecturers in Nigeria. Only lecturers in Nigerian Universities who had worked as radiography clinical practitioners before transited to academics and consented to participate in this study were included. The questionnaire captured responses on socio-demographic variables, challenges, barriers, successes of transition from practitioners to academic educators.Results:The majority 17(48.6%) of the respondents earned income of above #251,000.00 as a practicing radiographers. Of the 35 respondents, the majority 12(34.3%) each respectively earned #101,000.00 −#150,000.00 and #151,000.00 - #200,000.00 as an academic radiographers. Majority 17(48.6%) of the respondents agreed that the main challenge they are encountering as an academic educator is rigorous research activities. Family issues affected smooth transition process as 23(65.7%) of the respondents agreed to that. Majority 18(51.4%) perceived mentorship as the key factor responsible for smooth transition from practice to academic. There was statistically significant relationship between gender and challenges encountered by the responders (χ2= 28.194, p = 0.00).Conclusion:The respondents experienced different challenges as they transited from clinical practice to academic. Mentorship is the key factor that militated against the smooth transition process. There was statistically significant relationship between gender and challenges encountered by the responders.
Statistical Analysis Plan for Dynamic HIV Choice Prevention delivered with Community Health Workers in Phase A of SEARCH-Sapphire
Authors: Balzer Laura B. , Kakande Elijah R. , Ayieko James , Kabami Jane , Chamie Gabriel , Kamya Moses R. , Havlir Diane V. , Petersen Maya L. ,   SEARCH Collaboration
Published: November 2023

AbstractThis document provides the statistical analytic plan (SAP) for a cluster randomized trial evaluating the effect of community-based Dynamic Choice HIV Prevention (DCP) intervention, delivered by community health workers in rural Uganda and Kenya (Clinicaltrials.gov:NCT04810650). The SAP was locked prior to unblinding and effect estimation.
Prevalence and risk factors of low back pain among nursing students
Authors: Liya Jin , Ya Zhu , Miaoye Hu , Chunmei Zhang 
Published: November 2023

AbstractStudy designRetrospective case-control studyObjectiveTo investigate the incidence of low back pain among nursing students and to analyze the factors contributing to low back pain among nursing students.MethodThis retrospective study was conducted in 78 nursing students who entered our hospital for internship from July 2022 to March 2023. Demographic data, including age, gender, height, weight, exercise habits, staying-up-late habits, smoking history, education level, mental status, working posture, menstrual pain, and other basic information were collected, and the number of interns experiencing low back pain in the past 1 month and 3 months was recorded to investigate the incidence of low back pain among nursing students. Relevant risk factors were also analyzed.ResultsThe incidence of low back pain among nursing students was 19.2% within 1 month and 25.6% within 3 months. Factors such as gender, age, height, weight, smoking history, exercise habits, staying-up-late habits, education level, mental status, working posture correctness, and menstrual pain showed no statistical significance between the pain and non-pain groups (P> 0.05), while BMI and exercise habits showed statistical differences between the two groups (P< 0.05). BMI (OR= 1.530; 95% confidence interval = 1.16 - 2.02;P= 0.003) was identified as a risk factor for low back pain. Exercise habits (OR= 0.232; 95% confidence interval = 0.07 - 0.81;P= 0.022) were identified as protective factors for low back pain.ConclusionThe incidence of low back pain among nursing students remains relatively high, and low back pain is associated with high BMI and lack of exercise. These results can provide a reference for developing preventive measures for low back pain among nursing students.
Bacterial assembly in the switchgrass rhizosphere is shaped by phylogeny, host genotype, and growing site
Authors: Sutherland Jeremy , Bell Terrence H. , Bonos Stacy , Tkach Christopher , Hansen Julie , Crawford Ryan , Carlson John E. , Lasky Jesse R. 
Published: November 2023

SummarySince microbial traits are conserved at different taxonomic levels, plant hosts may influence microbiome composition differently at different levels to broadly promote or resist microbiota with traits that impact host fitness. We tested this hypothesis by assessing signals of host genetic influence on bacterial composition in the switchgrass rhizosphere using 128 genotypes in dissimilar growing sites.We employed three common gardens, combined with host genetic mapping, 16S rRNA gene sequence analysis, hierarchical modeling, tests of phylogenetic conservation of host influence, and genome-wide association analyses to determine the contributions of host genetics in shaping rhizosphere bacterial composition at different taxonomic levels.Modeling bacterial assembly showed that growing site was a strong factor shaping bacterial composition in the rhizosphere, though host genetic influence played a significant role. The heritability of bacterial abundance was strongest at the genus level. Phylogenetic signal for heritability was detected within the bacterial phylogeny but conserved clades differed between common gardens. We identified shared host genetic variants associated with bacterial abundance and host traits related to plant metabolism.Our results suggest further investigation is required regarding the genotype-by-environment-by-microbiome relationship to elucidate the factors shaping rhizosphere microbiome composition and the agroecological dynamics shaping plant phenotype.
Active learning for medium optimization for selective bacterial culture
Authors: Zhang Shuyang , Aida Honoka , Ying Bei-Wen 
Published: November 2023

AbstractMedium optimization and development for selective bacterial culture are essential for isolating and functionalizing individual bacteria in microbial communities; nevertheless, it remains challenging due to the unknown mechanisms between bacterial growth and medium components. The present study first tried combining machine learning (ML) with active learning to finetune the medium components for the selective culture of two divergent bacteria, i.e.,Lactobacillus plantarumandEscherichia coli. ML models considering multiple growth parameters of the two bacterial strains were constructed to predict the finetuned medium combinations for higher specificity of bacterial growth. The growth parameters were designed as the exponential growth rate (r) and maximal growth yield (K), which were calculated according to the growth curves. The eleven chemical components in the commercially available medium MRS were subjected to medium optimization and specialization. High-throughput growth assays of both strains grown separately were performed to obtain thousands of growth curves in more than one hundred medium combinations, and the resultant datasets linking the growth parameters to the medium combinations were used for the ML training. Repeated rounds of active learning (i.e., ML model construction, medium prediction, and experimental verification) successfully improved the specific growth of a single strain out of the two. BothrandKshowed maximized differentiation between the two strains. Further analysis of all data accumulated in active learning identified the decision-making medium components for growth specificity and the differentiated determinative manner of growth decision of the two strains. In summary, this study demonstrated the efficiency and practicality of active learning in medium optimization for selective culture and offered novel insights into the contribution of the chemical components to specific bacterial growth.
Computationally Driven Design of Novel BACE-1 Inhibitors for Alzheimer’s Disease
Authors: Chinn Megan M. , Mateos Diego Lopez , Riley Mary A. , Siegel Justin B. 
Published: November 2023

ABSTRACTAlzheimer’s disease is the most common form of dementia affecting 35 million people globally. One of the major efforts in the development of a treatment for Alzheimer’s is to reduce the rate of plaque formation, the common hallmark of Alzheimer’s disease. The protease BACE-1 has been demonstrated to play a role in catalyzing plaque formation and is therefore a major drug target. Here we report potential new drug candidates building upon Verubecestat, developed through computationally driven molecular modeling methods. Both designed molecules have improved docking scores relative to Verubecestat when modeled in the BACE-1 active site, and therefore present potential new leads for more effective therapeutics to combat Alzheimer’s disease.
SAP expressing T peripheral helper cells identify systemic lupus erythematosus patients with lupus nephritis
Authors: Gartshteyn Yevgeniya , Geraldino-Pardilla Laura , Khalili Leila , Bukhari Shoiab , Lerrer Shalom , Askanase Anca D. , Mor Adam 
Published: November 2023

AbstractIntroductionT follicular (TFH) and peripheral helper (TPH) cells have been increasingly recognized as a pathogenic subset of CD4 T cells in systemic lupus erythematosus (SLE). The SLAM Associated Protein (SAP) regulates TFH and TPH function by binding to the co -stimulatory signaling lymphocyte activation molecule family (SLAMF) receptors that mediate T cell – B cell interactions. SAP and SLAMF are critical for TPH dependent B cell maturation into autoantibody-producing plasma cells that characterize SLE pathogenesis.MethodsPeripheral blood mononuclear cells (PBMCs) were isolated using density gradient separation from whole blood. Cells were stained for cell surface markers, followed by permeabilization and staining of intracellular SAP for spectral flow cytometry analysis. Additionally, we analyzed SAP expression from renal infiltrating lupus nephritis (LN) T cells using the publicly available single-cell RNA sequencing (sc-RNA seq) Accelerated Medicines Partnership (AMP) in SLE dataset.ResultsPBMCs from 30 patients with SLE (34±10 years old, 83% female), including 10 patients with LN, were analyzed. We found an increase in total SAP-positive CD4 and CD8 T cells in SLE compared with controls (55.5±2.6 vs. 41.3±3.4, p=0.007 and 52.5±3.0 vs. 39.2±2.8, p=0.007 respectively). In CD4 T cells, the highest SAP expression was in the TPH subset. The frequency of SAP+TPH in circulation correlated with disease activity, SLE patients with renal disease had higher levels of circulating SAP+TPH that remained significant after adjusting for age, sex, race, low complements, and elevated anti-dsDNA (p=0.014). scRNA-seq data of renal infiltrating T cells identified increased SAP from LN compared with control kidney biopsy samples (p=0.03), including an expansion of SAP-positive TFH-like subsets in the LN kidneys. Increased SAP expression in LN was associated with the differential expression of SLAMF3 and SLAMF7 as well as granzyme K and EOMES. The existence of two predominant SAP-expressing subsets, the TFH-like CD4 T cells and granzyme K positive effector CD8 T cells, was verified using scRNA-seq data from a human transcriptomic atlas of fifteen major organs.ConclusionThe expansion of SAP expressing T helper cells was associated with lupus nephritis in our cohort and verified using scRNA-seq data of renal infiltrating T cells. Improved understanding of SLAM/SAP signaling can identify new therapeutic targets in LN.
Exclusion of PD-1 from the immune synapse: a novel strategy to modulate T cell function
Authors: Hao Luke Yi , Lerrer Shalom , Song Ruijiang , Goeckeritz Michael , Hu Xizi , Mor Adam 
Published: November 2023

AbstractTargeting immune checkpoint receptors on T cells is a common cancer treatment strategy. Frequently, this is accomplished through antibodies targeting the ligand of inhibitory co-receptors. Blocking the immune checkpoint PD-1 binding to its ligands PD-L1 and PD-L2 prevents downstream signaling and enhances anti-tumor T cell responses. This approach improved cancer patients’ outcome. However, only one-third of the patients respond to these treatments. To better understand the mechanism of anti-PD-1 antibodies, we explored the location of PD-1 within the immune synapse. Surprisingly, we discovered that anti-PD-1 antibodies, besides blocking the interaction between PD-1 and its ligands, also removed PD-1 from the synapse. We demonstrated a correlation between removing PD-1 from the synapse by anti-PD-1 antibodies and the extent of T cell activation. Interestingly, a short version of the anti-PD-1 antibody, F(ab’)2, failed to remove PD-1 from the synapse and activate T cells. Using syngeneic tumor model, we showed a superior anti-tumor effect to anti-PD-1 antibody over the shorter version of the antibody. Our data indicates that anti-PD-1 antibodies activate T cells by removing PD-1 away from the synapse and changing the location of PD-1 or other immune receptors within immune synapse could serve as an alternative, efficient approach to treat cancer.
An automated archival single-nucleus total RNA sequencing platform mapping integrative and retrospective cell atlas of gliomas
Authors: Xu Ziye , Chen Lingchao , Lin Xin , Lyu Yuexiao , Zhou Mofei , Chen Haide , Zhang Heng , Zhang Tianyu , Chen Yu , Suo Yuanzhen , Liang Qian , Qin Zhiyong , Wang Yongcheng 
Published: November 2023

AbstractSingle-cell RNA sequencing (scRNA-seq) has dramatically transformed biomedical research within laboratory settings. It has been extensively employed to investigate the heterogeneity and plasticity of glioma, the most prevalent brain tumor. However, the clinical diagnosis and treatment of glioma remain complex and challenging, highlighting the need for comprehensive cancer research. Currently available scRNA-seq platforms are insufficient to fulfill the demands posed by large-scale clinical applications. Here, we present an automated high-throughput single-nucleus total RNA sequencing platform, known as AAsnRandom-seq. This platform integrates automated single-nucleus isolation and droplet barcoding systems with the random primer-based scRNA-seq chemistry, designed to accommodate a diverse range of sample types. The performance and versatility of AAsnRandom-seq are validated using over one hundred clinical FFPE and frozen samples. AAsnRandom-seq was applied to archival FFPE samples of various glioma subtypes, including rare clinical samples, and matched primary-recurrent glioblastomas (GBMs), delving into the comprehensive molecular characteristic of glioma at single-cell level. Abundant non-coding RNAs (ncRNAs) with distinct expression profiles within different glioma clusters are detected. Promising recurrence-related targets and pathways are identified from the matched primary-recurrent GBMs. AAsnRandom-seq holds significant application value on large-scale integrative and retrospective clinical research using archived specimens.
rNMPID: a database for riboNucleoside Mono-Phosphates In DNA
Authors: Yang Jingcheng , Sun Mo , Ran Zihan , Yang Taewhan , Kundnani Deepali L. , Storici Francesca , Xu Penghao 
Published: November 2023

AbstractMotivationRibonucleoside monophosphates (rNMPs) are the most abundant non-standard nucleotides embedded in genomic DNA. If the presence of rNMP in DNA cannot be controlled, it can lead to genome instability. The actual positive functions of rNMPs in DNA remain mainly unknown. Considering the association between rNMPs embedment and various diseases and cancer, the phenomenon of rNMPs embedment in DNA has become a prominent area of research in recent years.ResultsWe introduce the rNMPID database, which is the first database revealing rNMP-embedment characteristics, strand bias, and preferred incorporation patterns in the genomic DNA of samples from bacterial to human cells of different genetic backgrounds. The rNMPID database uses datasets generated by different rNMP-mapping techniques. It provides the researchers with a solid foundation to explore the features of rNMPs embedded in the genomic DNA of multiple sources, and their association with cellular functions, and, in future, disease. It also significantly benefits researchers in the fields of genetics and genomics who aim to integrate their studies with the rNMP-embedment data.AvailabilityrNMPID is freely accessible on the web athttps://www.rnmpid.org.Contactxph6113@gmail.comorstorici@gatech.edu
The bidirectional effects between cognitive ability and brain morphology: A life course Mendelian randomization analysis
Authors: Korologou-Linden Roxanna , Schuurmans Isabel K. , Cecil Charlotte A.M. , White Tonya , Banaschewski Tobias , Bokde Arun L.W. , Desrivières Sylvane , Grigis Antoine , Garavan Hugh , Gowland Penny , Heinz Andreas , Brühl Rüdiger , Martinot Jean-Luc , Martinot Marie-Laure Paillère , Artiges Eric , Nees Frauke , Orfanos Dimitri Papadopoulos , Paus Tomáš , Poustka Luise , Holz Nathalie , Fröhner Juliane H. , Smolka M , Walter Henrik , Winterer Jeanne , Whelan Robert , Schumann Gunter , Howe Laura D , Ben-Shlomo Yoav , Davies Neil M , Anderson Emma L 
Published: November 2023

AbstractIntroductionLittle is understood about the dynamic interplay between brain morphology and cognitive ability across the life course. Additionally, most existing research has focused on global morphology measures such as estimated total intracranial volume, mean thickness, and total surface area.MethodsMendelian randomization was used to estimate the bidirectional effects between cognitive ability, global and regional measures of cortical thickness and surface area, estimated total intracranial volume, total white matter, and the volume of subcortical structures (N=37,864). Analyses were stratified for developmental periods (childhood, early adulthood, mid-to-late adulthood; age range: 8-81 years).ResultsThe earliest effects were observed in childhood and early adulthood in the frontoparietal lobes. A bidirectional relationship was identified between higher cognitive ability, larger estimated total intracranial volume (childhood, mid-to-late adulthood) and total surface area (all life stages). A thicker posterior cingulate cortex and a larger surface area in the caudal middle frontal cortex and temporal pole were associated with greater cognitive ability. Contrary, a thicker temporal pole was associated with lower cognitive ability.DiscussionStable effects of cognitive ability on brain morphology across the life course suggests that childhood is potentially an important window for intervention.
A multi-task domain-adapted model to predict chemotherapy response from mutations in recurrently altered cancer genes
Authors: Jayagopal Aishwarya , Walsh Robert J. , Hariprasannan Krishna Kumar , Mariappan Ragunathan , Mahapatra Debabrata , Jaynes Patrick William , Lim Diana , Tan David Shao Peng , Tan Tuan Zea , Pitt Jason J. , Jeyasekharan Anand D. , Rajan Vaibhav 
Published: November 2023

AbstractNext generation sequencing (NGS) of tumours is increasingly utilised in oncological practice, however only a minority of patients harbour oncogenic driver mutations benefiting from targeted therapy. Development of a drug response prediction (DRP) model based on available genomic data is important for the ‘untargetable’ majority of cases. Prior DRP models typically rely on whole transcriptome and whole exome sequencing (WES), which is often unavailable in clinical practice. We therefore aim to develop a DRP model towards repurposing of standard chemotherapy, requiring only information available in clinical grade NGS (cNGS) panels of recurrently mutated genes in cancer. Such an approach is challenging due to the sparsity of data in a restricted gene set and limited availability of patient samples with documented drug response. We first show that an existing DRP performs equally well with whole exome data and a cNGS subset comprising ∼300 genes. We then develop Drug IDentifier (DruID), a DRP model specific for restricted gene sets, using a novel transfer learning-based approach combining variant annotations, domain-invariant representation learning and multi-task learning. Evaluation of DruID on pan-cancer data (TCGA) showed significant improvements over state-of-the-art response prediction methods. Validation on two real world - colorectal and ovarian cancer - clinical datasets showed robust response classification performance, suggesting DruID to be a significant step towards a clinically applicable DRP tool.
Riboswitch and small RNA modulatebtuBtranslation initiation inEscherichia coliand trigger distinct mRNA regulatory mechanisms
Authors: Bastet L. , Korepanov A.P. , Jagodnik J. , Grondin J.P. , Lamontagne A.M. , Guillier M. , Lafontaine D.A. 
Published: November 2023

AbstractSmall RNAs (sRNAs) and riboswitches represent distinct classes of RNA regulators that control gene expression upon sensing metabolic or environmental variations. While sRNAs and riboswitches regulate gene expression by affecting mRNA and protein levels, existing studies have been limited to the characterization of each regulatory system in isolation, suggesting that sRNAs and riboswitches target distinct mRNA populations. We report that the expression ofbtuBinEscherichia coli, which is regulated by an adenosylcobalamin (AdoCbl) riboswitch, is also controlled by the small RNAs OmrA and, to a lesser extent, OmrB. Strikingly, we find that the riboswitch and sRNAs reduce mRNA levels through distinct pathways. Our data show that while the riboswitch triggers Rho-dependent transcription termination, sRNAs rely on the degradosome to modulate mRNA levels. Importantly, OmrA pairs with thebtuBmRNA through its central region, which is not conserved in OmrB, indicating that these two sRNAs may have specific targets in addition to their common regulon. In contrast to canonical sRNA regulation, we find that OmrA repression ofbtuBis lost using an mRNA binding-deficient Hfq variant. Together, our study demonstrates that riboswitch and sRNAs modulatebtuBexpression, providing an example ofcis-andtrans-acting RNA-based regulatory systems maintaining cellular homeostasis.