bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of Lateral Extra-Articular Tenodesis With Improved Graft Maturity on MRI 2 Years After ACL Reconstruction With Quadriceps Tendon Autograft in Skeletally Immature Athletes
Authors: Retzky Julia S. , Chipman Danielle E. , Mintz Douglas N. , Cordasco Frank A. , Green Daniel W.
Published: January 2024

Background:

Quadriceps tendon autograft (QTA) has recently gained popularity in the treatment of anterior cruciate ligament (ACL) ruptures in pediatric patients. The addition of lateral extra-articular tenodesis (LET) to an ACL reconstruction (ACLR) has been found to reduce the risk of ACL retear in high-risk patients.

Purpose:

To (1) compare ACL graft maturity using signal intensity ratios (SIRs) on magnetic resonance imaging (MRI) scans in skeletally immature patients undergoing ACLR with QTA either with or without concomitant LET and (2) evaluate LET safety by calculating the physeal disturbance-related reoperation rate in the ACLR+LET group.

Study Design:

Cohort study; Level of evidence, 3.

Methods:

The records of patients aged ≤18 years who underwent ACLR between 2015 and 2021 were reviewed retrospectively. Patients undergoing ACLR with QTA who had open distal femoral and proximal tibial physes on MRI scans and a minimum 2-year follow-up data were included. SIR values were measured on sagittal MRI scans by averaging the signal at 3 regions of interest along the ACL graft and dividing by the signal of the posterior cruciate ligament at its insertion. Statistical analysis was performed to evaluate differences in SIR values at 6 months, 1 year, and 2 years postoperatively in patients who underwent ACLR alone versus ACLR+LET.

Results:

Overall, 29 patients were included in the study: 16 patients in the ACLR+LET group and 13 patients in the ACLR-only group. There were no significant differences in SIR values between groups at the 6-month or 1-year postoperative timepoints. At 2 years postoperatively, the median SIR of the ACLR+LET group was significantly lower than that of the ACLR-only group on both univariate (1.33 vs 1.86, respectively, P = .0012) and multivariate regression analyses adjusting for both sex and surgical technique (β = -0.49 [95% CI, -0.91 to -0.05]; P = .029). There were no cases of reoperation for physeal disturbance in patients who underwent ACLR+LET.

Conclusion:

The addition of LET to an ACLR with QTA was associated with lower average SIR values and thus improved graft maturity at 2 years postoperatively compared with ACLR alone in skeletally immature patients. The addition of LET to an ACLR was found to be safe in skeletally immature patients.
Effects of Vitamin D Supplementation in Elite Athletes: A Systematic Review
Authors: Wyatt Phillip B. , Reiter Charles R. , Satalich James R. , O’Neill Conor N. , Edge Carl , Cyrus John W. , O’Connell Robert S. , Vap Alexander R.
Published: January 2024

Background:

Deficiency in vitamin D has been shown to increase the risk of injury.

Purpose:

To synthesize current placebo-controlled randomized trials investigating the effect of vitamin D supplementation in elite athletes on (1) aerobic capacity; (2) anaerobic measures, such as strength, speed, and anaerobic power; (3) serum biomarkers of inflammation; and (4) bone health.

Study Design:

Systematic review; Level of evidence, 1.

Methods:

A literature search was conducted on November 30, 2022, according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Included were randomized, placebo-controlled studies of longer than 2 weeks on subjects with active participation in organized sport. Excluded were nonrandomized controlled trial study designs, vitamin D administration routes other than oral, studies that did not use vitamin D supplementation as the sole intervention, and studies with nonathletic or military populations.

Results:

Out of 2331 initial studies, 14 studies (482 athletes) were included. Of the 3 studies that assessed aerobic capacity, 2 demonstrated significantly greater improvements in maximal oxygen uptake and physical working capacity-170 ( P < .05) in supplemented versus nonsupplemented athletes. Measurements of anaerobic power and strength were consistently increased in supplemented groups compared with nonsupplemented groups in 5 out of the 7 studies that assessed this. Of the 6 studies that assessed sprint speed, 4 found no significant difference between supplemented and nonsupplemented groups. Aside from 1 study that found significantly lower interleukin-6 levels in supplemented athletes, measures of other inflammatory cytokines were not affected consistently by supplementation. The 4 studies that assessed markers of bone health were conflicting regarding benefits of supplementation. One study found demonstrated improvements in bone mineral density in response to supplementation ( P = .02) compared with control whereas another found no significant difference between supplemented and nonsupplemented groups. However, in 3 other studies, serum biomarkers of bone turnover such as bone-specific alkaline phosphatase, parathyroid hormone, and N-terminal telopeptide appeared to be higher in subjects with lower serum vitamin D levels ( P < .05).

Conclusion:

Results of this systematic review indicated that the greatest benefit of vitamin D supplementation in elite athletes may be improving aerobic endurance, anaerobic power, and strength. More research is needed to determine the effect of vitamin D supplementation on bone health and injury risk in this population.
Are Law Schools Cream-Skimming to Bolster Their Bar Exam Pass Rates? A Multilevel Regression Approach to Estimate How Attrition and Transfer Rates Affect Bar Passage
Authors: Scott Jason M. , Jackson Joshua L. , Pals Andrea M.
Published: January 2024

Law schools are held accountable on many fronts to achieve and maintain high bar passage rates. While the course of legal education itself, along with various interventions, is a key driver of bar exam performance, Bahadur et al. (2021) suggests that obscure institutional practices might be inflating institutional bar passage performance. Such practices could include recruitment and admission of transfer students and academic attrition. We examine this hypothesis to assess the influence of both attrition and transfer on law schools’ bar passage differential using fixed-effects and between-within models. We also utilize Poisson regression to explore the effect of geographical proximity to other law schools on transfer rates. We find that, on average, neither attrition nor transfer activity substantively affect bar passage performance, and that although geographic proximity to other schools is related to transfer rates, this relationship does not result in notable differences in bar passage.
Measuring the Interdisciplinarity and Collaboration Perceptions of U.S. Scientists, Engineers, and Educators
Authors: McCance Katherine R. , Blanchard Margaret
Published: January 2024

Interdisciplinarity has the potential to lead to more innovation and advances in knowledge than are possible from a single discipline. Yet, little is known about interdisciplinary collaborations and the perceptions of those involved. This quantitative study investigated the perceptions of U.S. faculty, staff, postdocs, and graduate students involved in education and science/engineering collaborations. Exploratory factor analysis was conducted for two modified scales, Collaboration Perceptions (CP; n = 117; 17 items; α = .923) and Interdisciplinarity Perceptions (IP; n = 119; 11 items; α = .852). Participants’ perceptions of collaboration and interdisciplinarity were strongly positive and did not significantly differ based on demographic factors (e.g., gender, discipline, role). Perceptions were influenced by collectivist orientation; the high collectivism group had significantly more positive perceptions of collaboration and interdisciplinarity, and collectivist orientation was positively and significantly correlated with CP and IP scores. Implications and recommendations for interdisciplinary collaborations will be discussed.
Filling in the Gaps. Making Sense of Living with Temporomandibular Disorders: A Reflexive Thematic Analysis
Authors: Penlington C. , Durham J. , O’Brien N. , Green R.
Published: January 2024

Introduction:

Persistent, painful temporomandibular disorders (TMDs) are challenging to manage and usually require the active engagement of patients. To achieve this, it is necessary to understand the complex and multifactorial nature of persistent pain. Many dental professionals have little education about persistent pain and may prefer to offer structural management and advice. This research aims to explore how people understand their persistent TMD and how this understanding has been influenced by their treatment providers.

Methods:

Twenty-one people were recruited to represent a diversity of experience with persistent TMD. Interviews followed a semistructured topic guide. Themes were constructed through reflexive thematic analysis to represent how people made sense of their symptoms and the messages that they had picked up through their treatment journey.

Results:

Participants described examples of conflicting opinions and inconsistent management recommendations. They rarely recalled collaborative discussions about the nature and complexity of their symptoms and different options for treatment. This experience is represented by a single theme, “a medical merry-go-round.” Subthemes of “a medical journey to nowhere—participants’ frustrated attempts to find medical management that will end their pain” and “is it me?—participants’ questioning their role in persisting pain” kept participants on the merry-go-round, while symptom resolution and participants’ emerging development of a holistic understanding of their TMD pain provided exit points. Understanding pain holistically tended to be helpful and typically occurred despite rather than because of the advice given in routine treatment settings.

Conclusion:

Participants in this study had not typically found their pain management within dental and medical settings to have helped them to construct meaning and understand their experiences of painful TMD. However, understanding symptoms holistically was experienced as beneficial. This study suggests that improved communication and signposting within services for persistent TMD may be beneficial to patients with TMD pain.

Knowledge Transfer Statement:

Results of this study confirm that being offered a series of anatomically based, singular-cause explanations for persisting pain symptoms had been experienced as unhelpful by the participants who had sought help for their TMD. Participants highlighted the importance of accurate and collaborative communication and of dental professionals explicitly adopting and communicating a biopsychosocial understanding of pain to their patients who have TMD. Results highlight that some people can struggle to manage persisting pain with minimal support. Signposting patients to appropriate services and resources may help them to understand more about the nature of persistent pain and methods of managing it.
Hydroxyurea reduces infections in children with sickle cell anemia in Uganda
Authors: Namazzi Ruth , Bond Caitlin , Conroy Andrea L. , Datta Dibyadyuti , Tagoola Abner , Goings Michael J. , Jang Jeong Hoon , Ware Russell E. , Opoka Robert , John Chandy C.
Published: January 2024

After starting hydroxyurea treatment, Ugandan children with sickle cell anemia had 60% fewer severe or invasive infections, including malaria, bacteremia, respiratory tract infections, and gastroenteritis, than before starting hydroxyurea treatment (incidence rate ratio, 0.40 [95% confidence interval, 0.29-0.54]; P < .001).
Key roles of autophagosome/endosome maturation mediated by Syntaxin17 in methamphetamine-induced neuronal damage in mice
Authors: Wang Xi , Hu Miaoyang , Chen Jingrong , Lou Xinyu , Zhang Hongchao , Li Muhan , Cheng Jie , Ma Tengfei , Xiong Jianping , Gao Rong , Chen Xufeng , Wang Jun
Published: January 2024

Background

Autophagic defects are involved in Methamphetamine (Meth)-induced neurotoxicity. Syntaxin 17 (Stx17), a member of the SNARE protein family, participating in several stages of autophagy, including autophagosome-late endosome/lysosome fusion. However, the role of Stx17 and potential mechanisms in autophagic defects induced by Meth remain poorly understood.

Methods

To address the mechanism of Meth-induced cognitive impairment, the adenovirus (AV) and adeno-associated virus (AAV) were injected into the hippocampus for stereotaxis to overexpress Stx17 in vivo to examine the cognitive ability via morris water maze and novel object recognition. In molecular level, the synaptic injury and autophagic defects were evaluated. To address the Meth induced neuronal damage, the epidermal growth factor receptor (EGFR) degradation assay was performed to evaluate the degradability of the “cargos” mediated by Meth, and mechanistically, the maturation of the vesicles, including autophagosomes and endosomes, were validated by the Co-IP and the GTP-agarose affinity isolation assays.

Results

Overexpression of Stx17 in the hippocampus markedly rescued the Meth-induced cognitive impairment and synaptic loss. For endosomes, Meth exposure upregulated Rab5 expression and its guanine-nucleotide exchange factor (GEF) (immature endosome), with a commensurate decreased active form of Rab7 (Rab7-GTP) and impeded the binding of Rab7 to CCZ1 (mature endosome); for autophagosomes, Meth treatment elicited a dramatic reduction in the overlap between Stx17 and autophagosomes but increased the colocalization of ATG5 and autophagosomes (immature autophagosomes). After Stx17 overexpression, the Rab7-GTP levels in purified late endosomes were substantially increased in parallel with the elevated mature autophagosomes, facilitating cargo (Aβ42, p-tau, and EGFR) degradation in the vesicles, which finally ameliorated Meth-induced synaptic loss and memory deficits in mice.

Conclusion

Stx17 decrease mediated by Meth contributes to vesicle fusion defects which may ascribe to the immature autophagosomes and endosomes, leading to autophagic dysfunction and finalizes neuronal damage and cognitive impairments. Therefore, targeting Stx17 may be a novel therapeutic strategy for Meth-induced neuronal injury.
A new physiological medium uncovers biochemical and cellular alterations in Lesch-Nyhan disease fibroblasts
Authors: Escudero-Ferruz Paula , Ontiveros Neus , Cano-Estrada Claudia , Sutcliffe Diane J. , Jinnah H. A. , Torres Rosa J. , López José M.
Published: January 2024

Background

Lesch-Nyhan disease (LND) is a severe neurological disorder caused by the genetic deficiency of hypoxanthine–guanine phosphoribosyltransferase (HGprt), an enzyme involved in the salvage synthesis of purines. To compensate this deficiency, there is an acceleration of the de novo purine biosynthetic pathway. Most studies have failed to find any consistent abnormalities of purine nucleotides in cultured cells obtained from the patients. Recently, it has been shown that 5-aminoimidazole-4-carboxamide riboside 5ʹ-monophosphate (ZMP), an intermediate of the de novo pathway, accumulates in LND fibroblasts maintained with RPMI containing physiological levels (25 nM) of folic acid (FA), which strongly differs from FA levels of regular cell culture media (2200 nM). However, RPMI and other standard media contain non-physiological levels of many nutrients, having a great impact in cell metabolism that does not precisely recapitulate the in vivo behavior of cells.

Methods

We prepared a new culture medium containing physiological levels of all nutrients, including vitamins (Plasmax-PV), to study the potential alterations of LND fibroblasts that may have been masked by the usage of non-physiological media. We quantified ZMP accumulation under different culture conditions and evaluated the activity of two known ZMP-target proteins (AMPK and ADSL), the mRNA expression of the folate carrier SLC19A1, possible mitochondrial alterations and functional consequences in LND fibroblasts.

Results

LND fibroblasts maintained with Plasmax-PV show metabolic adaptations such a higher glycolytic capacity, increased expression of the folate carrier SCL19A1, and functional alterations such a decreased mitochondrial potential and reduced cell migration compared to controls. These alterations can be reverted with high levels of folic acid, suggesting that folic acid supplements might be a potential treatment for LND.

Conclusions

A complete physiological cell culture medium reveals new alterations in Lesch-Nyhan disease. This work emphasizes the importance of using physiological cell culture conditions when studying a metabolic disorder.
MYCT1 inhibits hematopoiesis in diffuse large B-cell lymphoma by suppressing RUNX1 transcription
Authors: Liang Ying , Wei Xin , Yue Peng-Jie , Zhang He-Cheng , Li Zhen-Ning , Wang Xiao-Xue , Sun Yuan-Yuan , Fu Wei-Neng
Published: January 2024

Background

The abnormality of chromosomal karyotype is one factor causing poor prognosis of lymphoma. In the analysis of abnormal karyotype of lymphoma patients, three smallest overlap regions were found, in which MYCT1 was located. MYCT1 is the first tumor suppressor gene cloned by our research team, but its studies relating to the occurrence and development of lymphoma have not been reported.

Methods

R banding analyses were employed to screen the abnormality of chromosomal karyotype in clinical specimen and MYCT1 over-expression cell lines. FISH was to monitor MYCT1 copy number aberration. RT-PCR and Western blot were to detect the mRNA and protein levels of the MYCT1 and RUNX1 genes, respectively. The MYCT1 and RUNX1 protein levels in clinical specimen were evaluated by immunohistochemical DAB staining. The interaction between MYCT1 and MAX proteins was identified via Co-IP and IF. The binding of MAX on the promoter of the RUNX1 gene was detected by ChIP and Dual-luciferase reporter assay, respectively. Flow cytometry and CCK-8 assay were to explore the effects of MYCT1 and RUNX1 on the cell cycle and proliferation, respectively.

Results

MYCT1 was located in one of three smallest overlap regions of diffuse large B-cell lymphoma, it altered chromosomal instability of diffuse large B-cell lymphoma cells. MYCT1 negatively correlated with RUNX1 in lymphoma tissues of the patients. MAX directly promoted the RUNX1 gene transcription by binding to its promoter region. MYCT1 may represses RUNX1 transcription by binding MAX in diffuse large B-cell lymphoma cells. MYCT1 binding to MAX probably suppressed RUNX1 transcription, leading to the inhibition of proliferation and cell cycle of the diffuse large B-cell lymphoma cells.

Conclusion

This study finds that there is a MYCT1-MAX-RUNX1 signaling pathway in diffuse large B-cell lymphoma. And the study provides clues and basis for the in-depth studies of MYCT1 in the diagnosis, treatment and prognosis of lymphoma.
Nanomaterials: paving the way for the hydrogen energy frontier
Authors: Shaker Lina M. , Al-Amiery Ahmed A. , Al-Azzawi Waleed K.
Published: January 2024

This comprehensive review explores the transformative role of nanomaterials in advancing the frontier of hydrogen energy, specifically in the realms of storage, production, and transport. Focusing on key nanomaterials like metallic nanoparticles, metal–organic frameworks, carbon nanotubes, and graphene, the article delves into their unique properties. It scrutinizes the application of nanomaterials in hydrogen storage, elucidating both challenges and advantages. The review meticulously evaluates diverse strategies employed to overcome limitations in traditional storage methods and highlights recent breakthroughs in nanomaterial-centric hydrogen storage. Additionally, the article investigates the utilization of nanomaterials to enhance hydrogen production, emphasizing their role as efficient nanocatalysts in boosting hydrogen fuel cell efficiency. It provides a comprehensive overview of various nanocatalysts and their potential applications in fuel cells. The exploration extends to the realm of hydrogen transport and delivery, specifically in storage tanks and pipelines, offering insights into the nanomaterials investigated for this purpose and recent advancements in the field. In conclusion, the review underscores the immense potential of nanomaterials in propelling the hydrogen energy frontier. It emphasizes the imperative for continued research aimed at optimizing the properties and performance of existing nanomaterials while advocating for the development of novel nanomaterials with superior attributes for hydrogen storage, production, and transport. This article serves as a roadmap, shedding light on the pivotal role nanomaterials can play in advancing the development of clean and sustainable hydrogen energy technologies.
Quantification of putative ovarian cancer serum protein biomarkers using a multiplexed targeted mass spectrometry assay
Authors: Ryu Joohyun , Boylan Kristin L. M. , Twigg Carly A. I. , Evans Richard , Skubitz Amy P. N. , Thomas Stefani N.
Published: January 2024

Background

Ovarian cancer is the most lethal gynecologic malignancy in women, and high-grade serous ovarian cancer (HGSOC) is the most common subtype. Currently, no clinical test has been approved by the FDA to screen the general population for ovarian cancer. This underscores the critical need for the development of a robust methodology combined with novel technology to detect diagnostic biomarkers for HGSOC in the sera of women. Targeted mass spectrometry (MS) can be used to identify and quantify specific peptides/proteins in complex biological samples with high accuracy, sensitivity, and reproducibility. In this study, we sought to develop and conduct analytical validation of a multiplexed Tier 2 targeted MS parallel reaction monitoring (PRM) assay for the relative quantification of 23 putative ovarian cancer protein biomarkers in sera.

Methods

To develop a PRM method for our target peptides in sera, we followed nationally recognized consensus guidelines for validating fit-for-purpose Tier 2 targeted MS assays. The endogenous target peptide concentrations were calculated using the calibration curves in serum for each target peptide. Receiver operating characteristic (ROC) curves were analyzed to evaluate the diagnostic performance of the biomarker candidates.

Results

We describe an effort to develop and analytically validate a multiplexed Tier 2 targeted PRM MS assay to quantify candidate ovarian cancer protein biomarkers in sera. Among the 64 peptides corresponding to 23 proteins in our PRM assay, 24 peptides corresponding to 16 proteins passed the assay validation acceptability criteria. A total of 6 of these peptides from insulin-like growth factor-binding protein 2 (IBP2), sex hormone-binding globulin (SHBG), and TIMP metalloproteinase inhibitor 1 (TIMP1) were quantified in sera from a cohort of 69 patients with early-stage HGSOC, late-stage HGSOC, benign ovarian conditions, and healthy (non-cancer) controls. Confirming the results from previously published studies using orthogonal analytical approaches, IBP2 was identified as a diagnostic biomarker candidate based on its significantly increased abundance in the late-stage HGSOC patient sera compared to the healthy controls and patients with benign ovarian conditions.

Conclusions

A multiplexed targeted PRM MS assay was applied to detect candidate diagnostic biomarkers in HGSOC sera. To evaluate the clinical utility of the IBP2 PRM assay for HGSOC detection, further studies need to be performed using a larger patient cohort.
Estimating the heritability of nitrogen and carbon isotopes in the tail hair of beef cattle
Authors: Moradi Morteza , Warburton Christie L. , Porto-Neto Laercio Ribeiro , Silva Luis F. P.
Published: January 2024

Background

The natural abundance of nitrogen (δ15N) and carbon (δ13C) isotopes in animal tissues are used to estimate an animal’s efficiency in nitrogen utilization, and their feed conversion efficiency, especially in tropical grazing systems with prolonged protein restriction. It is postulated that selection for improving these two characteristics (δ15N and δ13C) would assist the optimisation of the adaptation in ever-changing environments, particularly in response to climate change. The aim of this study was to determine the heritability of δ15N and δ13C in the tail hair of tropically adapted beef cattle to validate their inclusion in genetic breeding programs.

Methods

In total, 492 steers from two breeds, Brahman (n = 268) and Droughtmaster (n = 224) were used in this study. These steers were managed in two mixed breed contemporary groups across two years (year of weaning): steers weaned in 2019 (n = 250) and 2020 (n = 242). Samples of tail switch hair representing hair segments grown during the dry season were collected and analysed for δ15N and δ13C with isotope-ratio mass spectrometry. Heritability and variance components were estimated in a univariate multibreed (and single breed) animal model in WOMBAT and ASReml using three generations of full pedigree.

Results

The estimated heritability of both traits was significantly different from 0, i.e. 0.43 ± 0.14 and 0.41 ± 0.15 for δ15N and δ13C, respectively. These traits had favourable moderate to high genetic and phenotypic correlations (− 0.78 ± 0.16 and − 0.40 ± 0.04, respectively). The study also provides informative single-breed results in spite of the limited sample size, with estimated heritability values of 0.37 ± 0.19 and 0.19 ± 0.17 for δ15N and δ13C in Brahman, and 0.36 ± 0.21 and 0.46 ± 0.22 for δ15N and δ13C in Droughtmaster, respectively.

Conclusions

The findings of this study show, for the first time, that the natural abundances of both nitrogen and carbon isotopes in the tail hair in cattle may be moderately heritable. With further research and validation, tail hair isotopes can become a practical tool for the large-scale selection of more efficient cattle.
cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data
Authors: Meyer Lasse , Eling Nils , Bodenmiller Bernd
Published: January 2024

Background

Highly multiplexed imaging enables single-cell-resolved detection of numerous biological molecules in their spatial tissue context. Interactive visualization of multiplexed imaging data is crucial at any step of data analysis to facilitate quality control and the spatial exploration of single cell features. However, tools for interactive visualization of multiplexed imaging data are not available in the statistical programming language R.

Results

Here, we describe cytoviewer, an R/Bioconductor package for interactive visualization and exploration of multi-channel images and segmentation masks. The cytoviewer package supports flexible generation of image composites, allows side-by-side visualization of single channels, and facilitates the spatial visualization of single-cell data in the form of segmentation masks. As such, cytoviewer improves image and segmentation quality control, the visualization of cell phenotyping results and qualitative validation of hypothesis at any step of data analysis. The package operates on standard data classes of the Bioconductor project and therefore integrates with an extensive framework for single-cell and image analysis. The graphical user interface allows intuitive navigation and little coding experience is required to use the package. We showcase the functionality and biological application of cytoviewer by analysis of an imaging mass cytometry dataset acquired from cancer samples.

Conclusions

The cytoviewer package offers a rich set of features for highly multiplexed imaging data visualization in R that seamlessly integrates with the workflow for image and single-cell data analysis.

It can be installed from Bioconductor via https://www.bioconductor.org/packages/release/bioc/html/cytoviewer.html. The development version and further instructions can be found on GitHub at https://github.com/BodenmillerGroup/cytoviewer.
ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management
Authors: Liu Qian , Hu Qiang , Liu Song , Hutson Alan , Morgan Martin
Published: January 2024

Background

The increasing volume and complexity of genomic data pose significant challenges for effective data management and reuse. Public genomic data often undergo similar preprocessing across projects, leading to redundant or inconsistent datasets and inefficient use of computing resources. This is especially pertinent for bioinformaticians engaged in multiple projects. Tools have been created to address challenges in managing and accessing curated genomic datasets, however, the practical utility of such tools becomes especially beneficial for users who seek to work with specific types of data or are technically inclined toward a particular programming language. Currently, there exists a gap in the availability of an R-specific solution for efficient data management and versatile data reuse.

Results

Here we presentReUseData, anRsoftware tool that overcomes some of the limitations of existing solutions and provides a versatile and reproducible approach to effective data management within R.ReUseDatafacilitates the transformation of ad hoc scripts for data preprocessing into Common Workflow Language (CWL)-based data recipes, allowing for the reproducible generation of curated data files in their generic formats. The data recipes are standardized and self-contained, enabling them to be easily portable and reproducible across various computing platforms.ReUseDataalso streamlines the reuse of curated data files and their integration into downstream analysis tools and workflows with different frameworks.

Conclusions

ReUseDataprovides a reliable and reproducible approach for genomic data management within theRenvironment to enhance the accessibility and reusability of genomic data. The package is available atBioconductor(https://bioconductor.org/packages/ReUseData/) with additional information on the project website (https://rcwl.org/dataRecipes/).
Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions
Authors: Choi Dae Gyu , Baek Ju Hye , Han Dong Min , Khan Shehzad Abid , Jeon Che Ok
Published: January 2024

Background

Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species.

Results

E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans.

Conclusions

Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.
PRMT2 silencing regulates macrophage polarization through activation of STAT1 or inhibition of STAT6
Authors: Liu Ting , Li Yinjiao , Xu Muqiu , Huang Hongjun , Luo Yan
Published: January 2024

Background

Macrophages play significant roles in innate immune responses and are heterogeneous cells that can be polarized into M1 or M2 phenotypes. PRMT2 is one of the type I protein arginine methyltransferases involved in inflammation. However, the role of PRMT2 in M1/M2 macrophage polarization remains unclear. Our study revealed the effect and mechanism of PRMT2 in macrophage polarization.

Methods

Bone marrow-derived macrophages (BMDMs) were polarized to M1 or M2 state by LPS plus murine recombinant interferon-γ (IFN-γ) or interleukin-4 (IL-4). Quantitative polymerase chain reaction (qPCR), western blot and flow cytometry (FCM) assay were performed and analyzed markers and signaling pathways of macrophage polarization.

Results

We found that PRMT2 was obviously upregulated in LPS/IFN-γ-induced M1 macrophages, but it was little changed in IL-4-induced M2 macrophages. Furthermore, PRMT2 konckdown increased the expression of M1 macrophages markers through activation of STAT1 and decreased the expression of M2 macrophages markers through inhibition of STAT6.

Conclusions

PRMT2 silencing modulates macrophage polarization by activating STAT1 to promote M1 and inhibiting STAT6 to attenuate the M2 state.
The zoonotic pathogen Wohlfahrtiimonas chitiniclastica – current findings from a clinical and genomic perspective
Authors: Kopf Anna , Bunk Boyke , Riedel Thomas , Schröttner Percy
Published: January 2024

The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.
Analysis of gut microbiota of ladybug beetle (Harmonia axyridis) after feeding on different artificial diets
Authors: Xie Bing-Hua , Chao Lei , Wan Si-Jing , Si Hui-Ru , Yu Wei-Dong , Huang Zhen , Wang Shi-Gui , Desneux Nicolas , Tang Bin , Sun Si-Si
Published: January 2024

Background

Harmonia axyridis is an effective natural enemy insect to a variety of phloem-sucking pests and Lepidopteran larvae, such as aphids, scabies, and phylloxera, while its industrial production is limited due to unmature artificial diet. Insect intestinal microbiota affect host development and reproduction. The aim of this study is to understand intestinal microbiota composition of H. axyridis and screen effective probiotics on artificial diet. Considering the role of the components and composition of the diet on the structure and composition of the intestinal microbiome, four kinds of diets were set up: (1) aphid; (2) basic diet; (3) basic diet + glucose; (4) basic diet + trehalose. The gut microbiota of H. axyridis was detected after feeding on different diets.

Results

Results showed that the gut microbiota between artificial diet group and aphid groups were far apart, while the basic and glucose groups were clearly clustered. Besides, the glucose group and trehalose group had one unique phylum, Cryptophyta and Candidatus Saccharibacteria, respectively. The highest abundance of Proteobacteria was found in the aphid diet. The highest abundance of Firmicutes was found in the basic diet. However, the addition of glucose or trehalose alleviated the change. In addition, the relative abundance of Enterobacter, Klebsiella, Enterobacteriaceae_unclassified, Enterobacteriales_unclassified and Serratia in the aphid group was higher than other groups. Moreover, the function of gut genes in each group also showed clear differences.

Conclusion

These results have offered a strong link between artificial diets and gut microbes, and also have provided a theoretical basis for the screening of synergistic probiotics in artificial diet.
Incidence of uterine infections, major bacteria and antimicrobial resistance in postpartum dairy cows in southern Ethiopia
Authors: Mekibib Berhanu , Belachew Mesfin , Asrade Biruhtesfa , Badada Girma , Abebe Rahmeto
Published: January 2024

Background

Uterine infections, primarily caused by bacterial pathogens, pose a significant problem for dairy farmers worldwide, leading to poor reproductive performance and economic losses. However, the bacteria responsible for uterine infections have not been adequately studied, nor has the antibiotic susceptibility of the causative bacteria been frequently tested in Ethiopia. This study aims to estimate the cumulative incidence of uterine infections in postpartum dairy cows, identify bacterial causes and determine antimicrobial susceptibility profile of the isolated bacteria.

Methods

A prospective cohort study was conducted in which 236 cows from 74 dairy farms were monitored biweekly from calving to 90 days postpartum for metritis, endometritis and other disorders. Aseptic uterine swab samples were collected from 40 cows with uterine infections. The samples were cultured, and the isolated bacteria were tested for antimicrobial susceptibility using the disk diffusion method.

Results

Out of 236 cows monitored during the postpartum phase, 45 (19.1%) were found to have contracted uterine infection. The cumulative incidence of metritis was 11.4% (n = 27), while the cumulative incidence of endometritis was 7.6% (n = 18). Of the 40 cultured swab samples, 29 (72.5%) had one or more bacteria isolated. The most commonly isolated bacteria were Escherichia coli (45%), coagulase-positive staphylococci (30%), and Klebsiella spp. (22.5%). Other bacterial spp, including Arcanobacterium pyogenes (12.5%), Fusobacterium spp. (12.5%), Enterobacter aerogenes (12.5%), coagulase-negative staphylococci (12.5%), Streptococcus spp. (7.5%), Salmonella spp, (5%) Proteus spp (5%) and Pasteurella spp (2.5%) were also isolated. All of the isolated bacteria demonstrated resistance to at least one of the antimicrobials tested. Multidrug resistance was observed in E. coli, Klebsiella spp., A. pyogenes, and Fusobacterium spp. Gentamicin was found to be the most effective antimicrobial against all bacteria tested, while tetracycline was the least effective of all.

Conclusion

The study found that a significant proportion of cows in the population were affected by uterine infections and the isolated bacteria developed resistance to several antimicrobials. The study emphasizes the need for responsible use of antimicrobials to prevent the emergence of antimicrobial resistance. It also highlights the importance of raising awareness among dairy farmers to avoid the indiscriminate use of antibiotics and its consequences.
A flexible approach to measure care coordination based on patient-sharing networks
Authors: Engels Alexander , Konnopka Claudia , Henken Espen , Härter Martin , König Hans-Helmut
Published: January 2024

Background

Effective care coordination may increase clinical efficiency, but its measurement remains difficult. The established metric “care density” (CD) measures care coordination based on patient-sharing among physicians, but it may be too rigid to generalize across disorders and countries. Therefore, we propose an extension called fragmented care density (FCD), which allows varying weights for connections between different types of providers. We compare both metrics in their ability to predict hospitalizations due to schizophrenia.

Methods

We conducted a longitudinal cohort study based on German claims data from 2014 through 2017 to predict quarterly hospital admissions. 21,016 patients with schizophrenia from the federal state Baden-Württemberg were included. CD and FCD were calculated based on patient-sharing networks. The weights of FCD were optimized to predict hospital admissions during the first year of a 24-month follow-up. Subsequently, we employed likelihood ratio tests to assess whether adding either CD or FCD improved a baseline model with control variables for the second follow-up year.

Results

The inclusion of FCD significantly improved the baseline model, Χ2(1) = 53.30, p < 0.001. We found that patients with lower percentiles in FCD had an up to 21% lower hospitalization risk than those with median or higher values, whereas CD did not affect the risk.

Conclusions

FCD is an adaptive metric that can weight provider relationships based on their relevance for predicting any outcome. We used it to better understand which medical specialties need to be involved to reduce hospitalization risk for patients with schizophrenia. As FCD can be modified for different health conditions and systems, it is broadly applicable and might help to identify barriers and promoting factors for effective collaboration.
Estimation of mortality rate ratios for chronic conditions with misclassification of disease status at death
Authors: Voß Sabrina , Hoyer Annika , Landwehr Sandra , Pavkov Meda E. , Gregg Edward , Brinks Ralph
Published: January 2024

Estimation of mortality rates and mortality rate ratios (MRR) of diseased and non-diseased individuals is a core metric of disease impact used in chronic disease epidemiology. Estimation of mortality rates is often conducted through retrospective linkage of information from nationwide surveys such as the National Health Interview Survey (NHIS) and death registries. These surveys usually collect information on disease status during only one study visit. This infrequency leads to missing disease information (with right censored survival times) for deceased individuals who were disease-free at study participation, and a possibly biased estimation of the MRR because of possible undetected disease onset after study participation. This occurrence is called “misclassification of disease status at death (MicDaD)” and it is a potentially common source of bias in epidemiologic studies. In this study, we conducted a simulation analysis with a high and a low incidence setting to assess the extent of MicDaD-bias in the estimated mortality. For the simulated populations, MRR for diseased and non-diseased individuals with and without MicDaD were calculated and compared. Magnitude of MicDaD-bias depends on and is driven by the incidence of the chronic disease under consideration; our analysis revealed a noticeable shift towards underestimation for high incidences when MicDaD is present. Impact of MicDaD was smaller for lower incidence (but associated with greater uncertainty in the estimation of MRR in general). Further research can consider the amount of missing information and potential influencers such as duration and risk factors of the disease.
The important role of whole-process computed tomography guidance for percutaneous gastrostomy in esophageal cancer patients who are unsuitable for or have had unsuccessful attempts with endoscopic and fluoroscopic gastrostomy
Authors: Geng Xiang , Zhao Qing , Yuan Hang , Li Hai-Liang , Guo Chen-Yang , Yang Ting , Fan Wei-Jun , Park Jung-Hoon , Zhao Xiao-Hui , Zhu Wen-Bo , Hu Hong-Tao
Published: January 2024

Purpose

To explore the value of clinical application with the whole process computed tomography (CT) guided percutaneous gastrostomy in esophageal tumor patients.

Materials and methods

A consecutive series of 32 esophageal tumor patients in whom endoscopic gastrostomy or fluoroscopy guided gastrostomy were considered too dangerous or impossible due to the esophagus complete obstruction, complicate esophageal mediastinal fistula, esophageal trachea fistula or severe heart disease. All of the 32 patients were included in this study from 2 medical center and underwent the gastrostomy under whole process CT guided.

Results

All of the gastrostomy procedure was finished successfully under whole process CT guided and the technical success rate was 100%. The average time for each operation was 27 min. No serious complications occurred and the minor complications occurred in 3 patients, including local infection, severe hyperplasia of granulation tissue and tube dislodgment. There were no procedure related deaths.

Conclusion

The technical success rate of whole process CT guided percutaneous gastrostomy is high and the complication is low. This technique can be used feasible and effectively in some special patients.
An imported malaria case with repeated episodes of neurological syndromes resulting from different Plasmodium species
Authors: Xiang Zheng , Zhou Longcan , Pan Maohua , Qin Yucheng , Bai Yao , Qin Pien , Zeng Weilin , Wei Xiaosheng , Lu Yuxin , Somboonwit Charurut , Menezes Lynette , Huang Yaming , Cui Liwang , Yang Zhaoqing
Published: January 2024

Background

Imported cerebral malaria (CM) cases in non-endemic areas are often misdiagnosed, which delays treatment. Post-malaria neurological syndrome (PMNS) after recovery from severe malaria can also complicate diagnosis.

Case

We report an imported malaria case from West Africa with two sequential episodes with neurological syndromes within about a month. The first episode was diagnosed as CM with microscopy-positive Plasmodium falciparum infection. The second episode, occurring a month after the recovery from the first CM episode, was consistent with PMNS, since malaria parasites were not detected by microscopy in peripheral blood smears. However, this diagnosis was complicated by the detection of Plasmodium vivax in peripheral blood by PCR, suggesting a potential cause of the second episode by P. vivax.

Conclusion

This study suggests that PMNS often occurs after severe falciparum malaria. Concurrent P. vivax infection with pathogenic biomass being predominantly extravascular further complicates accurate diagnosis.
Viability predictive factors of the daughter vesicles in hepatic cystic echinococcosis
Authors: Trigui Aymen , Khmekhem Nahed , Fendri Sami , Daoud Rahma , Akrout Amira , Trabelsi Jihene , Mzali Rafik , Cheikhrouhou Fatma , Ayadi Ali , Dziri Chadli , Amar Mohamed Ben , Boujelbene Saleh
Published: January 2024

Introduction

Management of cystic echinococcosis (CE) requires knowledge of certain aspects related to the survival of Echinococcus granulosus. The viability of daughter vesicles (DV) is a determining factor in guiding therapeutic indications, particularly for transiently active Cysts type CE3b.

Purpose

To determine the predictive factors of DV viability and its impact on the therapeutic management of CE3b type.

Materials and methods

This is a prospective pilot study with an analytical aim on patients with cystic echinococcosis of the liver type CE2 and CE3b, operated in the General Surgery Department of Habib-Bourguiba Academic Hospital, Sfax-Tunisia for 22 months from March 2018 until December 2019. The unit of the study is the DV. A parasitological study of the DV was done in the parasitology laboratory.

Results

During the study period, 27 (40.9%) of 66 operated CE Disease from 21 patients containing 248 DV were explored. The median viability of DV protoscoleces was 16.7%. In bivariate analysis, factors for viability of DV protoscoleces were: fever, acute cholangitis, hyperbilirubinemia, left liver location, rock water and bilious echinococcal fluid (EF), cyst size ≥ 43 mm, Intracystic pressure ≥ 35 mmHg, DV size ≥ 6.5 mm, volume, number of DV/cyst ≥ 5, and opaque wall (p < 0.05). Predictive factors for the Non-viability of DV were: CE3b type, purulent EF, gelatinous EF. In multivariate analysis, only CE2 type, cyst size ≥ 43 mm, number of DV/cyst ≥ 5 and DV size ≥ 6.5 mm were factors significantly associated with the viability of DV protoscoleces.

Conclusion

CE3b cysts without the criteria of viability of DV protoscoleces may become candidates for the ‘Wait-and-Watch’ procedure.