bluuebunny/crossref_metadata_2025_split huggingface dataset:
“I’m Not Going Home With a Catheter”: Patient-Perceived Outcomes Associated With Perioperative Intermittent Catheterization
Authors: Shinnick Julia K. , Raker Christina A. , Geller Elizabeth J. , Rardin Charles R. , Cooper Anne C. 
Published: July 2023

Importance
Indwelling catheters are a known source of dissatisfaction for postoperative patients. There is a paucity of data describing patient-perceived outcomes associated with the alternative of intermittent self-catheterization (ISC).

Objectives
The aim of this study was to describe patient satisfaction and outcomes associated with ISC after outpatient female pelvic reconstructive surgery.

Study Design
This was a secondary analysis of a prospective cohort study at an academic tertiary referral center from September 2018 to June 2021. Participants completed preoperative ISC instruction that included an instructional video, 1:1 demonstration with a health care provider, and provision of ISC supplies. Participants were instructed to perform ISC postoperatively until they had 2 consecutive outpatient PVRs less than one-half the voided volume. Participant satisfaction was assessed 2 weeks postprocedure, with adverse events evaluated at 6 weeks.

Results
One hundred sixty participants completed preoperative ISC instruction and were included in this analysis. Mean age was 52.1 (SD +/− 11.4) years, mean body mass index was 28.9 (SD +/− 5.8), and mean time from ISC instruction to surgery was 16.4 (SD +/− 15.7) days. Most participants reported no difficulty with ISC (124/160 [78%]) and had high levels of satisfaction (148/151 [98%]). Difficulty performing ISC was not associated with time since ISC instruction (P = 0.32), difficulty noted at ISC instruction by the health care provider (P = 0.24), or the duration of ISC instruction (P = 0.16). On multiple logistic regression, age, body mass index, and prolapse beyond the hymen did not predict difficulty learning or performing ISC. At 6 weeks postprocedure, 22 of 155 participants (14%) endorsed symptoms of a urinary tract infection, and 15 of 160 (9%) had a culture-proven urinary tract infection.

Conclusions
Women undergoing outpatient pelvic reconstructive surgery report ease and satisfaction with ISC.
Role of humanities in modern medical education
Authors: Isaac Mohan 
Published: July 2023

Purpose of review
The role and importance of integrating humanities into medical education has been recognized for a long time. However, to what extent humanities are included in the medical curricula and how and when they are taught during the medical training in medical schools across the world is unclear. The review was undertaken to study the current status and role of humanities in medical education

Recent findings
Humanities content in the medical curriculum and the teaching of humanities continue to remain unstandardized. What constitutes medical humanities is unclear as there are several understandings of medical humanities. The benefits and value – both short term and long term - of including humanities in training of doctors and other health professionals remain unresolved and continue to be debated. Although some surveys have shown that exposure to the humanities was significantly correlated with positive personal qualities, including empathy, tolerance for ambiguity, wisdom, emotional appraisal, self-efficacy, and spatial skills, and inversely correlated with some components of burnout, robust evidence from well conducted studies to support the benefits of integrating humanities into medical training is very limited. An overreaching conceptual or theoretical framework for the health humanities in health professionals’ education continue to be elusive.

Summary
The status, stature, profile, and role of humanities in medical education remain varied across medical schools and universities. There is a need for standardized curricula, uniform criteria and guidelines for teaching medical humanities, training modules / materials, methods of assessment and better integration of humanities in medical education.
Liebig’s law of the minimum in the TGF-β/SMAD pathway
Authors: Li Yuchao , Deng Difan , Höfer Chris Tina , Kim Jihye , Heo Won Do , Xu Quanbin , Liu Xuedong , Zi Zhike 
Published: July 2023

AbstractCells use signaling pathways to sense and respond to their environments. The transforming growth factor-β (TGF-β) pathway produces context-specific responses. Here, we combined modeling and experimental analysis to study the dependence of the output of the TGF-β pathway on the abundance of signaling molecules in the pathway. We showed that the TGF-β pathway processes the variation of TGF-β receptor abundance using Liebig’s law of the minimum, meaning that the output-modifying factor is the signaling protein that is most limited, to determine signaling responses across cell types and in single cells. We found that the abundance of either the type I (TGFBR1) or type II (TGFBR2) TGF-β receptor determined the responses of cancer cell lines, such that the receptor with relatively low abundance dictates the response. Furthermore, nuclear SMAD2 signaling correlated with the abundance of TGF-β receptor in single cells depending on the relative expression levels of TGFBR1 and TGFBR2. A similar control principle could govern the heterogeneity of signaling responses in other signaling pathways.One-sentence summaryHeterogeneous TGF-β signaling responses are dictated by the low abundance TGF-β receptor in different cell types and in single cells, resembling Liebig’s law of the minimum.
Indigenous probioticsLactobacillus reuteriandEnterococcus faeciumexhibit positive growth performance and disease prevention against extended-spectrum cephalosporin and fluoroquinolones resistantSalmonella entericain broiler chicks
Authors: Siddique Abubakar , Ali Roomana , Ali Amjad , Andleeb Saadia , Nimatullah  , Mohiuddin Mudassar , Akbar Samina , Imran Muhammad , Syoc Emily Van , Yue Min , Rahman Abdur , Ganda Erika 
Published: July 2023

ABSTRACTThe rapid increase in antibiotic resistance poses a global threat to public health, necessitating the development of effective antimicrobial alternatives. This study compared an indigenous probiotic mix containingLactobacillus reuteriand two strains ofEnterococcus faeciumto a commercial probiotic blend ProtexinRon the growth performance, mortality rate, histomorphology, serum immunoglobulins, and intestinal microflora of broiler chickens challenged with two multi drug resistantSalmonellaserovars, Typhimurium and Enteritidis. Two hundred and forty day-old broiler chicks were randomly assigned to six treatment groups for 4 weeks: the treatment groups were; birds continuously supplemented with only indigenous probiotic strains (108CFU/mL) (IPRO-); birds challenged withSalmonellaserovars 106(CFU/mL) (PC+); birds continuously supplemented with indigenous probiotic strains and challenged withSalmonellaserovars (IPRO+); birds supplemented with ProtexinRand challenged withSalmonellaserovars (CM+); birds supplemented with only ProtexinR(CM-); and birds with noSalmonellachallenge or probiotics (negative control; PC-). The results revealed that IPRO- diets significantly improved feed conversion ratio (FCR) and increased body weight (BW) (P≤ 0.05). No effect of probiotic treatments was observed on IPRO- and CM- on relative organ weights as compared to the negative control (PC-). TheSalmonella- challenged group PC+ had the highest (20%) mortality rate and lowest BW. The IPRO- had significantly lower FCR (1.55) compared to PC- (1.86) and PC+ (1.95). The broilers in the IPRO- group showed significantly increased serum concentrations of IgA and IgG relative to both control groups (P≤ 0.05). Morphological analysis of the ileum revealed significant increases (P≤ 0.05) in the villus height and villus height/crypt depth in birds fed IPRO- compared with the PC+. CecalLactobacillusandEnterococcuscounts were the highest (P≤ 0.05) andSalmonellacounts were the lowest (P≤ 0.05) in the IPRO- group compared to theSalmonellainfected group PC+. These results indicated that indigenous probiotic strainsLactobacillus reuteriandEnterococcus faeciumcan be an effective and low-cost alternative compared to commercial probiotics in the Pakistan poultry industry.
Chimeric oncolytic adenovirus evades neutralizing antibodies from human patients and exhibits enhanced anti-glioma efficacy in immunized mice
Authors: Shin Dong Ho , Jiang Hong , Gillard Andrew , Kim Debora , Fan Xuejun , Singh Sanjay , Nguyen Teresa T , Sohoni Sagar , Lopez-Rivas Andres , Parthasarathy Akhila , Ene Chibawanye I. , Gumin Joy , Lang Frederick , Alonso Marta M , Gomez-Manzano Candelaria , Fueyo Juan 
Published: July 2023

ABSTRACTBACKGROUNDOncolytic adenoviruses, such as Delta-24-RGD, show promise as a potential breakthrough in treating patients with high-grade gliomas. However, their effectiveness against gliomas can be hindered by the presence of neutralizing antibodies.METHODSProduction of human neutralizing antibodies against adenoviruses was assessed in two cohorts of patients with malignant gliomas treated with Delta-24-RGD in a phase 1 clinical trial. Sera containing neutralizing antibodies were also obtained from mice immunized with intramuscular injections of wild-type Ad5. Chimeric adenovirus was constructed using molecular cloning, and its activity was assessed in vitro using quantitative PCR, western blot, and transmission electron microscopy. The therapeutic efficacy of the chimeric virus was tested in vivo using sera from patients previously treated with Delta-24-RGD and immunocompetent murine models of glioma.RESULTSExamination of sera from patients with malignant gliomas treated with Delta-24-RGD revealed that in the cohort treated with multiple injections of this oncolytic adenovirus, a higher percentage of patients developed neutralizing antibodies when compared to the patients treated with a single injection of Delta-24-RGD. Of note, long-term survival was only observed in patients who received a single injection. Delta-24-RGD-H43m, a chimeric oncolytic adenovirus engineered to overcome virus neutralization, demonstrated a potent anti-glioma effect both in vitro and in vivo. This chimeric virus showed resilience against anti-Ad5 neutralizing antibodies and conferred better therapeutic efficacy compared to Delta-24-RGD in mice with immunity against Ad5. Of further clinical relevance, Delta-24-RGD-H43m also evaded the inhibitory effects of sera from human patients treated with Delta-24-RGD.CONCLUSIONSThe development of neutralizing antibodies due to multiple virus injections was associated with lower frequency of long-term survivors in a clinical trial. The new chimeric virus shows increased resilience to inactivation by the sera of human patients compared to the parental virus. These findings lay the foundation for a novel oncolytic virus treatment approach targeting a significant percentage of glioma patients with prior exposure to adenovirus.
Absence of CD47 in the tumor microenvironment modulates tumor metabolism and immunosuppressive signatures limiting breast cancer progression
Authors: Stirling Elizabeth R. , Tsai Yu-Ting , Bronson Steven M. , Wilson Adam , Westwood Brian , Thomas Alexandra , Triozzi Pierre L. , Furdui Cristina M. , Lesser Glenn J. , Cook Katherine L. , Soto-Pantoja David R. 
Published: July 2023

AbstractThe majority of breast cancers are generally considered immune-deprived tumors. This lack of immunogenicity severely hinders effectiveness of current immunotherapy approaches limiting therapeutic options to control disease. Therefore, we need new biomarkers to determine and enhance immune responses to improve the outcome of cancer patients experiencing invasive disease. Our data in matched human patient biopsies show that CD47 expression increases from primary to metastatic tumors. CD47 is an integral membrane protein that impairs antitumor immunosurveillance and influences normal tissue metabolism. However, whether CD47 plays a role in regulating tumor bioenergetics is unknown. A carcinogen-induced mouse mammary carcinogenesis model demonstrates that the absence of CD47 reduces tumor burden, which is associated with a distinct metabolic signature compared to WT tumors. Depletion of several lipid metabolites was observed in the absence of CD47, and metabolic dependency experiments suggest that anti-sense blockade of CD47 limits reliance on fatty acid oxidation as a fuel supporting cellular respiration on cancer cells. Our global metabolomics analysis also implicated the absence of CD47 in downregulation of immunosuppressive metabolites of the tryptophan and prostaglandin pathways. Spatial proteomic analysis revealed increased immune infiltrate and substantial reduction in immunosuppressive immune checkpoint proteins in the absence of CD47 with the highest reduction in intra-tumoral PD-L1 expression. Since anti-PD-L1 therapy is used in the current strategy to treat triple-negative breast cancer (TNBC), we targeted CD47 in an EMT-6 syngeneic TNBC model. Thein vivoknockdown of CD47 sensitized tumors to anti-PD-L1 therapy to decrease tumor burden and increase intratumoral cytotoxic T cells. Therefore, targeting CD47 may be a suitable immunotherapeutic option to limit immunosuppression and enhance the efficacy of immune checkpoint blockade.
Tutorial on MUedit: An open-source software for identifying and analysing the discharge timing of motor units from electromyographic signals
Authors: Avrillon Simon , Hug François , Gibbs Ciara , Farina Dario 
Published: July 2023

AbstractWe introduce the open-source software MUedit and we describe its use for identifying the discharge timing of motor units from all types of electromyographic (EMG) signals recorded with multi-channel systems. MUedit performs EMG decomposition using a blind-source separation approach. Following this, users can display the estimated motor unit pulse trains and inspect the accuracy of the automatic detection of discharge times. When necessary, users can correct the automatic detection of discharge times and recalculate the motor unit pulse train with an updated separation vector. Here, we provide an open-source software and a tutorial that guides the user through i) the parameters and steps of the decomposition algorithm, and ii) the manual editing of motor unit pulse trains. Further, we provide simulated and experimental EMG signals recorded with grids of surface electrodes and intramuscular electrode arrays to benchmark the performance of MUedit. Finally, we discuss advantages and limitations of the blind-source separation approach for the study of motor unit behaviour during muscle contractions in humans.
Single Cell Portal: an interactive home for single-cell genomics data
Authors: Tarhan Leyla , Bistline Jon , Chang Jean , Galloway Bryan , Hanna Emily , Weitz Eric 
Published: July 2023

ABSTRACTSingle-cell omics research has the power to leave a deep impact on modern healthcare. Sharing data widely and freely advances this progress in both the academic and clinical spheres. We developed the Single Cell Portal (SCP) to maximize the impact of this work. SCP enables data sharing, supports dynamic results visualization, and facilitates scientific exploration across a large repository of single-cell datasets. SCP’s data contributors maintain full control over how their data are shared and presented, without requiring web development expertise. Finally, SCP supports the entire lifecycle of a research project, from sparking an idea, to fine-tuning the data with collaborators, to sharing results in an accessible and interactive way. This paper highlights the most valuable ways in which SCP helps to advance single-cell research.
Development and Assessment of a Sustainable PhD Internship Program Supporting Diverse Biomedical Career Outcomes
Authors: Brandt Patrick D. , Whittington Dawayne , Wood Kimberley D. , Holmquist Chris , Nogueira Ana T. , Gaines Christiann H. , Brennwald Patrick J. , Layton Rebekah L. 
Published: July 2023

ABSTRACTA doctoral-level internship program was developed at the University of North Carolina at Chapel Hill with the intent to create customizable experiential learning opportunities for biomedical trainees to support career exploration, preparation, and transition into their post-graduate professional roles. We report the outcomes of this program over a five-year period. During that 5-year period, 123 internships took place at over 70 partner sites, representing at least 20 academic, for-profit, and non-profit career paths in the life sciences. A major goal of the program was to enhance trainees’ skill development and expertise in careers of interest. The benefits of the internship program for interns, host/employer, and supervisor/principal investigator were assessed using a mixed-methods approach, including surveys with closed- and open-ended responses as well as focus group interviews. Balancing stakeholder interests is key to creating a sustainable program with widespread support; hence, the level of support from internship hosts and faculty members were key metrics analyzed throughout. We hypothesized that once a successful internship program was implemented, faculty culture might shift to be more accepting of internships; indeed, the data quantifying faculty attitudes support this. Furthermore, host motivation and performance expectations of interns were compared with results achieved, and this data revealed both expected and surprising benefits to hosts. Data suggests a myriad of benefits for each stakeholder group, and themes are cataloged and discussed. Program outcomes, evaluation data, policies, resources, and best practices developed through the implementation of this program are shared to provide resources that facilitate the creation of similar internship programs at other institutions. Program development was initially spurred by National Institutes of Health pilot funding, thereafter, successfully transitioning from a grant-supported model, to an institutionally supported funding model to achieve long-term programmatic sustainability.
A Burst-dependent Thalamocortical Substrate for Perceptual Awareness
Authors: Whyte Christopher J. , Müller Eli J. , Aru Jaan , Larkum Matthew , John Yohan , Munn Brandon R. , Shine James M. 
Published: July 2023

AbstractContemporary models of perceptual awareness lack tractable neurobiological constraints. Inspired by recent cellular recordings in a mouse model of tactile threshold detection, we constructed a biophysical model of perceptual awareness that incorporated essential features of thalamocortical anatomy and cellular physiology. Our model reproduced, and mechanistically explains, the keyin vivoneural and behavioural signatures of perceptual awareness in the mouse model, as well as the response to a set of causal perturbations. We generalised the same model (with identical parameters) to a more complex task – visual rivalry – and found that the same thalamic-mediated mechanism of perceptual awareness determined perceptual dominance. This led to the generation of a set of novel, and directly testable, electrophysiological predictions. Analyses of the model based on dynamical systems theory show that perceptual awareness in simulations of both threshold detection and visual rivalry arises from the emergent systems-level dynamics of thalamocortical loops.
RNA Strain-Match: A tool for matching single-nucleus, single-cell, or bulk RNA-sequencing alignment data to its corresponding genotype
Authors: Willcox Jon A. L. , Telpoukhovskaia Maria A. , Hadad Niran , Boas Stephanie M. , Dunn Amy , Saul Michael C. , Ashbrook David G. , Williams Robert W. , O’Connell Kristen M. S. , Kaczorowski Catherine C. 
Published: July 2023

AbstractWhen next generation sequencing is performed in large batches, there are several stages at which samples can be swapped or mislabeled. It is therefore helpful, when possible, to integrate measures into analysis pipelines to confirm that samples match their assigned metadata. Here, we introduce RNA Strain-Match (GitHub:https://github.com/jon-willcox/RNA-strain-match), a quality control tool developed to match RNA data in the form of sequence alignment files (i.e. SAM or BAM files) to their corresponding genotype without the use of an RNA variant call format file. We successfully used RNA Strain-Match in tandem with assessment of markers for sex and transgene status to identify and correct sample mismatches in 50/379 samples (13%) from two distinct recombinant inbred mouse models (BXD and Collaborative Cross). We believe this tool will be beneficial to any research group working with similar data.
Fully automated and integrated proteomics sample preparation platform for high-throughput drug target identification
Authors: Wu Qiong , Zheng Jiangnan , Sui Xintong , Fu Changying , Cui Xiaozhen , Liao Bin , Ji Hongchao , Luo Yang , He An , Lu Xue , Tan Chris Soon Heng , Tian Ruijun 
Published: July 2023

AbstractWith the increased demand of large-cohort proteomic analysis, fast and reproducible sample preparation has become the critical issue that needs to be solved. Herein, we developed a fully automated and integrated proteomics sample preparation workflow (autoSISPROT), enabling the simultaneous processing of 96 samples in less than 2.5 hours. Benefiting from its 96-channel all-in-tip operation, protein digestion, peptide desalting, and TMT labeling could be achieved in a fully automated manner. The autoSISPROT demonstrated good sample preparation performances, including >94% of digestion efficiency, nearly 100% of alkylation efficiency, >98% of TMT labeling efficiency, and >0.9 of intra- and inter-batch Pearson correlation coefficients. Furthermore, by combining with cellular thermal shift assay-coupled to mass spectrometry (CETSA-MS), the autoSISPROT was able to process and TMT-label 40 samples automatically and accurately identify the known target of methotrexate. Importantly, taking advantage of the data independent acquisition and isothermal CETSA-MS, the autoSISPROT was well applied for identifying known targets and potential off-targets of 20 kinase inhibitors by automatedly processing 87 samples, affording over a 10-fold improvement in throughput when compared to classical CETSA-MS. Collectively, we developed a fully automated and integrated workflow for high-throughput proteomics sample preparation and drug target identification.
Short and Long-term Mortality of Pneumococcal Pneumonia in Adults and Children- A Detailed Scoping Review
Authors: Vijayan Rupalakshmi , Nagpal Shavy , Dissanayake Manthi , Masthan Shameera Shaik , Fatima Aiman , Ramirez Julio , Karkera Sahana , Dutta Ipshita , Karani Pavani , Chao Andrea Galecio 
Published: July 2023

AbstractStreptococcus pneumoniae is a common infectious agent responsible for pneumonia, which can result in serious complications such as meningitis, sepsis, morbidity, and mortality. The objective of this study is to examine the risk factors and complications associated with mortality caused by community-acquired pneumococcal pneumonia in both adults and children. To conduct this research, a thorough literature review was carried out by researchers between May 1, 2021, and August 1, 2021. Various databases, including PubMed, WHO,clinicaltrials.gov, Embase, Web of Science, Cochrane, and Google Scholar, were searched using specific keywords such as mortality, pneumococcal pneumonia, adults, children, and their combinations. The study encompassed patients of all age groups affected by pneumococcal pneumonia, while systematic reviews focusing on other types of pneumonia and non-pneumonia patients were excluded. After eliminating duplicate studies, the search yielded 1783 relevant articles, which underwent title and abstract screening. Ultimately, 8 studies were included in the final review. In conclusion, pneumococcal pneumonia is a significant contributor to mortality among both adults and children. This research emphasizes the importance of implementing effective management strategies to reduce long-term mortality