bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Risk Factors of Premature Coronary Artery Disease in Patients From North India: A Rising Epidemic
Authors: Bunker Gautam Kumar , Patidar Manoj , Atal Devendra , Meena Ratti Lal 
Published: October 2022

Background: The incidence of premature coronary artery disease (PCAD) is on rising trend in low- and middle-income countries. Considering the limited reports, the current study was conducted to evaluate the prevalence, various predisposing factors, and coronary angiographic findings of PCAD in North India. Methods: Study design—hospital-based analytical cross-sectional study. Setting: Outpatient and inpatient units of a tertiary cardiac center in North India. Two hundred sequential patients (170 males and 30 females) with acute coronary syndrome were evaluated for history of risk factors, measurement of anthropometric parameters, biochemical blood examination, electrocardiogram, complete dental examination, and angiographic assessment of coronary artery lesion. Patients with acute infection or chronic inflammatory disorders were excluded. Patients were divided into PCAD (age ≤45 years) and mature CAD. Results: The prevalence of PCAD was 15% (N = 30). PCAD had higher rates of family history of CAD ( P < 0.001), tobacco consumption ( P = 0.01), smoking ( P = 0.004), and single-vessel disease (SVD) ( P < 0.001). Premature CAD group had significantly lower mean fasting blood glucose (105 ± 41 mg/dL vs 127 ± 45 mg/dL) levels. Conclusion: Family history of CAD, smoking, and tobacco consumption are important risk factors of PCAD. SVD is more common in PCAD. Screening the susceptible population at risk and controlling the cardiovascular risk factors will help reduce the epidemic and consequences of PCAD.
Genome-edited allogeneic donor “universal” chimeric antigen receptor T cells
Authors: Qasim Waseem 
Published: October 2022

Abstract
αβ T cell receptor (TCRαβ) T cells modified to express chimeric antigen receptors (CAR), are now available as authorized therapies for certain B-cell malignancies. However the process of autologous harvest and generation of patient-specific products is costly, with complex logistics and infrastructure requirements. Premanufactured banks of allogeneic donor–derived CAR T cells could help widen applicability if the challenges of HLA-mismatched T-cell therapy can be addressed. Genome editing is being applied to overcome allogeneic barriers, most notably, by disrupting TCRαβ to prevent graft-versus-host disease, and multiple competing editing technologies, including CRISPR/Cas9 and base editing, have reached clinical phase testing. Improvements in accuracy and efficiency have unlocked applications for a wider range of blood malignancies, with multiplexed editing incorporated to target HLA molecules, shared antigens and checkpoint pathways. Clinical trials will help establish safety profiles and determine the durability of responses as well as the role of consolidation with allogeneic transplantation.
Human genetic defects in SRP19 and SRPRA cause severe congenital neutropenia with distinctive proteome changes
Authors: Linder Monika I. , Mizoguchi Yoko , Hesse Sebastian , Csaba Gergely , Tatematsu Megumi , Łyszkiewicz Marcin , Ziȩtara Natalia , Jeske Tim , Hastreiter Maximilian , Rohlfs Meino , Liu Yanshan , Grabowski Piotr , Ahomaa Kaarin , Maier-Begandt Daniela , Schwestka Marko , Pazhakh Vahid , Isiaku Abdulsalam I. , Briones Miranda Brenda , Blombery Piers , Saito Megumu K. , Rusha Ejona , Alizadeh Zahra , Pourpak Zahra , Kobayashi Masao , Rezaei Nima , Unal Ekrem , Hauck Fabian , Drukker Micha , Walzog Barbara , Rappsilber Juri , Zimmer Ralf , Lieschke Graham J. , Klein Christoph 
Published: October 2022

Abstract
The mechanisms of coordinated changes in proteome composition and their relevance for the differentiation of neutrophil granulocytes are not well studied. Here, we discover 2 novel human genetic defects in signal recognition particle receptor alpha (SRPRA) and SRP19, constituents of the mammalian cotranslational targeting machinery, and characterize their roles in neutrophil granulocyte differentiation. We systematically study the proteome of neutrophil granulocytes from patients with variants in the SRP genes, HAX1, and ELANE, and identify global as well as specific proteome aberrations. Using in vitro differentiation of human induced pluripotent stem cells and in vivo zebrafish models, we study the effects of SRP deficiency on neutrophil granulocyte development. In a heterologous cell–based inducible protein expression system, we validate the effects conferred by SRP dysfunction for selected proteins that we identified in our proteome screen. Thus, SRP-dependent protein processing, intracellular trafficking, and homeostasis are critically important for the differentiation of neutrophil granulocytes.
Design and Analysis of a Novel Compliant Mechanism with RPR Degrees of Freedom
Authors: Zhang Shuang , Liu Jingfang , Ding Huafeng 
Published: October 2022

AbstractA novel compliant mechanism with RPR degrees of freedom (DOF) is proposed where R and P represent rotation and translation DOFs, respectively. The proposed compliant mechanism is obtained from dimension synthesizing a 2-RPU-UPR rigid parallel mechanism with the method of optimization of motion/force transfer characteristic. R, P and U represent rotation, translation and universal pairs, respectively. Firstly, inverse kinematics and Jacobian matrix are analyzed for the dimensional synthesis. Then, output transmission indexes of branches in the parallel mechanism are given. Dimensional synthesis is completed based on the normalized design parameter. And optimization of flexure joints based on constrained energy is carried out. Afterwards, the novel compliant mechanism is obtained by direct replacing method. Mechanical model of the compliant mechanism including static stiffness and input stiffness is built based on the pseudo-rigid body modeling method and virtual work principle. Finally, FEA simulation by Ansys Workbench is carried out to verify DOF, effectiveness of the dimension synthesis, and compliant model. Optimization of motion/force transfer characteristic is first applied for the design of compliant mechanisms to suppress drift of rotation axis in the paper.
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
Authors: Espinoza Josh L. , Dupont Chris L. 
Published: October 2022

AbstractBackgroundWith the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth’s natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ,however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes.ResultsIn this study, we introduce theViral Eukaryotic Bacterial Archaeal(VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge,VEBAis the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes.VEBAimplements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone.VEBAincludes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification.VEBAalso provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally,VEBAis the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments.VEBA’s capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives.ConclusionsTheVEBAsoftware suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways.VEBAfully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions ofVEBAto the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks.VEBAallows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.
Comparison of meiotic transcriptomes of three maize inbreds with different origins reveals differences in cell cycle and recombination
Authors: Garcia Nelson , Yin Lu , Dukowic-Schulze Stefanie , Milsted Claire , Kianian Penny M. A. , Kianian Shahryar , Pawlowski Wojciech P. , Chen Changbin 
Published: October 2022

Abstract
Background
Cellular events during meiosis can differ between inbred lines in maize. Substantial differences in the average numbers of chiasmata and double-strand breaks (DSBs) per meiotic cell have been documented among diverse inbred lines of maize: CML228, a tropical maize inbred line, B73 and Mo17, temperate maize lines. To determine if gene expression might explain these observed differences, an RNA-Seq experiment was performed on CML228 male meiocytes which was compared to B73 and Mo17 male meiocytes, where plants were grown in the same controlled environment.

Results
We found that a few DSB-repair/meiotic genes which promote class I crossovers (COs) and the Zyp1 gene which limits newly formed class I COs were up-regulated, whereas Mus81 homolog 2 which promotes class II COs was down-regulated in CML228. Although we did not find enriched gene ontology (GO) categories directly related to meiosis, we found that GO categories in membrane, localization, proteolysis, energy processes were up-regulated in CML228, while chromatin remodeling, epigenetic regulation, and cell cycle related processes including meiosis related cell cycle processes were down-regulated in CML228. The degree of similarity in expression patterns between the three maize lines reflect their genetic relatedness: B73 and Mo17 had similar meiotic expressions and CML228 had a more distinct expression profile.

Conclusions
We found that meiotic related genes were mostly conserved among the three maize inbreds except for a few DSB-repair/meiotic genes. The findings that the molecular players in limiting class I CO formation (once CO assurance is achieved) were up-regulated and those involved in promoting class II CO formation were down-regulated in CML228 agree with the lower chiasmata number observed in CML228 previously. In addition, epigenetics such as chromatin remodeling and histone modification might play a role. Transport and energy-related processes was up-regulated and Cyclin13 was down-regulated in CML228. The direction of gene expression of these processes agree with that previously found in meiotic tissues compared with vegetative tissues. In summary, we used different natural maize inbred lines from different climatic conditions and have shown their differences in expression landscape in male meiocytes.
Analysis of antibiotic use and clinical outcomes in adults with known and suspected pleural empyema
Authors: Avner Benjamin S. , Ginosyan Anush , Le James , Mak Justin , Qiryaqoz Zeena , Huffman Cuyler 
Published: October 2022

Abstract
Background
There is not a prevailing consensus on appropriate antibiotic choice, route, and duration in the treatment of bacterial pleural empyema after appropriate source control. Professional society guidelines note the lack of comparative trials with which to guide recommendations. We assessed clinical outcomes in the treatment of known and suspected empyema based upon three aspects of antibiotic use: (1) total duration, (2) duration of intravenous (IV) antibiotics, and (3) duration of anti-anaerobic antibiotics.

Methods
We performed a hypothesis-generating retrospective chart review analysis of 355 adult inpatients who had pleural drainage, via either chest tube or surgical intervention, for known or suspected empyema. The primary outcome variable was clinician assessment of resolution or lack thereof. The secondary outcomes were death within 90 days, hospital readmission within 30 days for empyema, and all-cause hospital readmission within 30 days. Mann-Whitney U test was used to compare outcomes with regard to these variables.

Results
None of the independent variables was significantly associated with a difference in clinical resolution rate despite trends for total antibiotic duration and anti-anaerobic antibiotic duration. None of the independent variables was associated with mortality. Longer total antibiotic duration was associated with lower readmission rate for empyema (median 17 [interquartile range 11–28] antibiotic days in non-readmission group vs. 13 [6-15] days in readmission group), with a non-significant trend for all-cause readmission rate (17 [11–28] days vs. 14 [9–21] days). IV antibiotic duration was not associated with a difference in any of the defined outcomes. Longer duration of anti-anaerobic antibiotics was associated with both lower all-cause readmission (8.5 [0–17] vs. 2 [0–11]) and lower readmission rate for empyema (8 [0–17] vs. 2 [0–3]).

Conclusion
Our data support the premise that routine use of anti-anaerobic antibiotics is indicated in the treatment of pleural empyema. However, our study casts doubt on the benefits of extended IV rather than oral antibiotics in the treatment of empyema. This represents a target for future investigation that could potentially limit complications associated with the excessive use of IV antibiotics.
Sex differences in determinants of COVID-19 severe outcomes – findings from the National COVID Cohort Collaborative (N3C)
Authors: Yoshida Yilin , Chu San , Fox Sarah , Zu Yuanhao , Lovre Dragana , Denson Joshua L. , Miele Lucio , Mauvais-Jarvis Franck 
Published: October 2022

Abstract
Objective
The impact of comorbidities and biomarkers on COVID-19 severity vary by sex but have not yet been verified in population-based studies. We examined the association of comorbidities, inflammatory biomarkers, and severe outcomes in men and women hospitalized for COVID-19.

Design
This is a retrospective cohort analysis based on the National COVID Cohort Collaborative (N3C). We included 574,391 adult patients admitted for COVID-19 at hospitals or emergency rooms between 01/01/2020 and 12/31/2021.

Methods
We defined comorbidities at or before the first admission for COVID-19 by Charlson Comorbidity Index (CCI) and CCI components. We used the averaged lab values taken within 15 days before or after the admission date to measure biomarkers including c-reactive protein (CRP), ferritin, procalcitonin, N-terminal pro b-type natriuretic peptide (NT proBNP), d-dimer, absolute lymphocyte counts, absolute neutrophil counts, and platelets. Our primary outcome was all-cause mortality; secondary outcomes were invasive mechanical ventilation (IMV) and hospital length of stay (LOS). We used logistic regression adjusted for age, race, ethnicity, visit type, and medications to assess the association of comorbidities, biomarkers, and mortality disaggregating by sex.

Results
Moderate to severe liver disease, renal disease, metastatic solid tumor, and myocardial infarction were the top four fatal comorbidities among patients who were hospitalized for COVID-19 (adjusted odds ratio [aOR] > 2). These four comorbid conditions remained the most lethal in both sexes, with a higher magnitude of risk in women than in men (p-interaction < 0.05). Abnormal elevations of CRP, ferritin, procalcitonin, NT proBNP, neutrophil, and platelet counts, and lymphocytopenia were significantly associated with the risk of death, with procalcitonin and NT proBNP as the strongest predictors (aOR > 2). The association between the abnormal biomarkers and death was stronger in women than in men (p-interaction < 0.05).

Conclusion
There are sex differences in inpatient mortality associated with comorbidities and biomarkers. The significant impact of these clinical determinants in women with COVID-19 may be underappreciated as previous studies stressed the increased death rate in male patients that is related to comorbidities or inflammation. Our study highlights the importance and the need for sex-disaggregated research to understand the risk factors of poor outcomes and health disparities in COVID-19.
Correlation study between multiplanar reconstruction trigeminal nerve angulation and trigeminal neuralgia
Authors: Sun Tao , Huang Qinghao , Li Chuangfeng , Yang Wensheng , Wang Wentao , He Longshuang , Liu Jinlong , Yang Chao 
Published: October 2022

Abstract
Objectives
Neurovascular compression (NVC) produces morphological changes on the trigeminal nerve root is considered the cause of trigeminal neuralgia (TN), but there were some patients with TN found no NVC, and also NVC was found in asymptomatic individuals. Many studies found tight relationships of TN and morphological structures of trigeminal nerve. We designed this study to explore the correlation between multiplanar reconstruction (MPR) trigeminal nerve angulation (TNA) and TN.

Methods
Patients with classical symptoms of TN were recruited as observation group (OG) in this study, 50 healthy controls were enrolled as control group (CG), the OG was further subtyped into young patients (YP), middle-aged patients (MP) and old patients (OP) based to the onset age of symptoms, and also divided into patients with or without trigger maneuvers (TM) based on the presence of TM or not. All the participants underwent magnetic resonance (MR) examinations in same device, bilateral TNA measurements were carried out in OG and CG, then TNA was compared between different groups or subgroups. All images were interpreted by two radiologists who were blinded to the study, diagnosis of TN was made by two senior neurosurgery professors.

Result
Ultimately, 95 patients with primary TN were recruited in OG, aged from 25 to 84 (61.15 ± 12.70) years with a course of 0.5 to 30 (5.03 ± 5.41) years, their onset age ranged from 24 to 82 (56.13 ± 11.98) years. There were 34 males and 61 females in OG, and 58 cases involved right side. The CG aged from 22 to 85 (61.86 ± 13.03) years. No statistical difference was found between the age of OG and CG(p = 0.76), and also the bilateral TNA of CG (154.92 ± 16.90° vs 155.55 ± 17.03°, p > 0.05), while TNA of OG was significantly smaller than CG (150.78 ± 11.29° vs 155.24 ± 16.88°, p = 0.019). In OG, TNA on the affected side was significantly smaller than the unaffected side (149.29 ± 12.44° vs 152.27 ± 9.85°, p = 0.014). TNA showed a positive correlation with onset age of patients with TN, as TNA on the affected side of YP was significantly smaller than MP and OP (139.00 ± 11.64° vs 148.86 ± 11.54°, 139.00 ± 11.64° vs 152.18 ± 12.61°, p = 0.004 and 0.026). Furthermore, patients with TM showed smaller TNA than those without TM (147.05 ± 11.30° vs 164.75 ± 8.39°, p < 0.001).

Conclusions
This study suggested that TNA might play a role in TN, small TNA could be a risk factor of TN. Furthermore, patients with small TNA are more likely to combine with TM, but more studies are needed to explore the exact role of TNA in TN.
Doula support among brazilian women who attended the senses of birth health education intervention – a cross sectional analysis
Authors: Fernandes Luísa M M , Mishkin Kathryn E , Lansky Sônia 
Published: October 2022

Abstract
Background
While maternal health is a priority in international goals, maternal health outcomes remain poor in many regions of the world. In Brazil, maternal mortality has decreased over the past decades, but the country’s maternal mortality ratio is higher than over half of all countries at 59 deaths per 100,000 live births. The Brazilian maternal health care model facilitates high rates of medical interventions during labor and childbirth; 56% of births are by cesarean birth. Doula support is considered a potential strategy to reduce medically unnecessary interventions during childbirth that contribute to maternal mortality.

Methods
The cross-sectional study analyses associations with use of doula support and normal birth among Brazilian women who participated in a health education intervention named the Senses of Birth (SoB). The SoB intervention, implemented in five cities from 2015 to 2017, was developed to educate about normal birth and to evidence-based practices (EBP) reduce medically in childbirth. Chi-Square tests were performed to identify the relationship between doula support during childbirth and sociodemographic characteristics, childbirth information, perceived knowledge, and use of EBPs during labor. Logistic regression was performed to identify associations in adjusted analysis.

Results
Controlling for covariates, doula support was associated with vaginal delivery (OR 2.47, 95% CI: 1.37–4.45.) Findings also suggest that women who had doula support were more likely to use non-pharmacological pain relief methods during labor (OR 9.68, 95% CI: 2.67–34.61), deliver in a public hospital (OR 2.02, 95% CI: 1.09–3.72), and be low and mid-level income compared to women with high income.

Conclusion
This study’s findings suggest that doula support is significantly associated with vaginal birth. The results may be useful for advocating for changes to the childbirth care model in Brazil. Incorporating EBPs, such as doula support, for all women who desire may improve maternal and child outcomes.