bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Between Markerless Motion Capture Screenings and Musculoskeletal Injury Risk for Military Trainees: A Large Cohort and Reliability Study
Authors: Hando Ben R. , Scott W. Casan , Bryant Jacob F. , Tchandja Juste N. , Scott Ryan M. , Angadi Siddhartha S. 
Published: October 2021

Background: Markerless motion capture (MMC) systems used to screen for musculoskeletal injury (MSKI) risk have become popular in military and collegiate athletic settings. However, little is known regarding the test-retest reliability or, more importantly, the ability of these systems to accurately identify individuals at risk for MSKI. Purpose: To determine the association between scores from a proprietary MMC movement screen test and the likelihood of suffering a subsequent MSKI and establish the test-retest reliability of the MMC system used. Study Design: Cohort study; Level of evidence, 3. Methods: Trainees for the Air Force Special Warfare program underwent MMC screenings immediately before entering the 8-week training course. MSKI data were extracted from a database for the surveillance period for each trainee. Logistic regression analyses were performed to identify associations between baseline MMC scores and the likelihood of suffering any MSKI or, specifically, a lower extremity MSKI. The test-retest portion of the study collected MMC scores from 10 separate participants performing 4 trials of the standard test procedures. Reliability was assessed using intraclass correlation coefficients by a single rater. Results: Overall, 1570 trainees, of whom 800 (51%) suffered an MSKI, were included in the analysis. MMC scores poorly predicted the likelihood of any or a lower extremity MSKI (odds ratio, 1.01-1.02). Further, receiver operating characteristic curve analyses demonstrated poor sensitivity and specificity for prediction of MSKI with MMC scores (area under the curve = 0.53). Finally, intraclass correlation coefficients from the test-retest analysis of MMC scores ranged from 0.157 to 0.602. Conclusion: This MMC system displayed poor to moderate test-retest reliability and did not demonstrate the ability to discriminate between individuals who were and were not likely to suffer an MSKI.
Centrality of drug targets in protein networks
Authors: Viacava Follis Ariele 
Published: October 2021

Abstract
Background
In the pharmaceutical industry, competing for few validated drug targets there is a drive to identify new ways of therapeutic intervention. Here, we attempted to define guidelines to evaluate a target’s ‘fitness’ based on its node characteristics within annotated protein functional networks to complement contingent therapeutic hypotheses.

Results
We observed that targets of approved, selective small molecule drugs exhibit high node centrality within protein networks relative to a broader set of investigational targets spanning various development stages. Targets of approved drugs also exhibit higher centrality than other proteins within their respective functional class. These findings expand on previous reports of drug targets’ network centrality by suggesting some centrality metrics such as low topological coefficient as inherent characteristics of a ‘good’ target, relative to other exploratory targets and regardless of its functional class. These centrality metrics could thus be indicators of an individual protein’s ‘fitness’ as potential drug target. Correlations between protein nodes’ network centrality and number of associated publications underscored the possibility of knowledge bias as an inherent limitation to such predictions.

Conclusions
Despite some entanglement with knowledge bias, like structure-oriented ‘druggability’ assessments of new protein targets, centrality metrics could assist early pharmaceutical discovery teams in evaluating potential targets with limited experimental proof of concept and help allocate resources for an effective drug discovery pipeline.
isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data
Authors: Barcelona-Cabeza Rosa , Sanseverino Walter , Aiese Cigliano Riccardo 
Published: October 2021

Abstract
Background
Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. To maximize the performance, the parameters of the CNV calling algorithms should be optimized for each specific dataset. This requires obtaining validated CNV information using either multiplex ligation-dependent probe amplification (MLPA) or array comparative genomic hybridization (aCGH). They are gold standard but time-consuming and costly approaches.

Results
We present isoCNV which optimizes the parameters of DECoN algorithm using only NGS data. The parameter optimization process is performed using an in silico CNV validated dataset obtained from the overlapping calls of three algorithms: CNVkit, panelcn.MOPS and DECoN. We evaluated the performance of our tool and showed that increases the sensitivity in both TS and WES real datasets.

Conclusions
isoCNV provides an easy-to-use pipeline to optimize DECoN that allows the detection of analysis-ready CNV from a set of DNA alignments obtained under the same conditions. It increases the sensitivity of DECoN without the need for orthogonal methods. isoCNV is available at https://gitlab.com/sequentiateampublic/isocnv.
Comparative transcriptome analysis uncovers cell wall reorganization and repressed cell division during cotton fiber initiation
Authors: Liu Wenyuan , Lv Yanjia , Li Xiaoyue , Feng Zongqin , Wang Lichen 
Published: October 2021

AbstractBackgroundTetraploid cotton plants serve as prime natural fiber source for the textile industry. Although various omics studies have revealed molecular basis for fiber development, a better understanding of transcriptional regulation mechanism regulating lint fiber initiation is necessary to meet global natural fiber demand.ResultsHere, we aimed to perform transcriptome sequencing to identify DEGs (differentially expressed genes) in ovules of the cotton variety Xu142 and its fibreless mutantXu142flduring early lint fiber initiation period. Totally, 5516 DEGs including 1840 upregulated and 3676 downregulated were identified. GO enrichment analysis revealed that the downregulated DEGs were mainly associated with biological processes such as transcription related biosynthesis and metabolism, organic cyclic compound biosynthesis and metabolism, photosynthesis, and plant cell wall organization, with molecular functions involving transcription related binding, organic cyclic compound binding, and dioxygenase activity, while the upregulated DEGs were associated with DNA replication and phospholipid biosynthetic related processes. Among the 490 DEGs annotated as transcription factor genes, 86.5% were downregulated in the mutant including theMalvaceae-specificMMLs, expression patterns of which were confirmed during the central period of lint fiber initiation. Investigation of the 16 genes enriched in the cell wall organization revealed that 15 were EXPA coding genes.ConclusionsOverall, our data indicate that lint fiber initiation is a complicated process involving cooperation of multiple transcription factor families, which might ultimately lead to the reorganization of the cell wall and terminated cell division of the differentiating fiber initials.
A linkage disequilibrium-based approach to position unmapped SNPs in crop species
Authors: Yadav Seema , Ross Elizabeth M. , Aitken Karen S. , Hickey Lee T. , Powell Owen , Wei Xianming , Voss-Fels Kai P. , Hayes Ben J. 
Published: October 2021

Abstract
Background
High-density SNP arrays are now available for a wide range of crop species. Despite the development of many tools for generating genetic maps, the genome position of many SNPs from these arrays is unknown. Here we propose a linkage disequilibrium (LD)-based algorithm to allocate unassigned SNPs to chromosome regions from sparse genetic maps. This algorithm was tested on sugarcane, wheat, and barley data sets. We calculated the algorithm’s efficiency by masking SNPs with known locations, then assigning their position to the map with the algorithm, and finally comparing the assigned and true positions.

Results
In the 20-fold cross-validation, the mean proportion of masked mapped SNPs that were placed by the algorithm to a chromosome was 89.53, 94.25, and 97.23% for sugarcane, wheat, and barley, respectively. Of the markers that were placed in the genome, 98.73, 96.45 and 98.53% of the SNPs were positioned on the correct chromosome. The mean correlations between known and new estimated SNP positions were 0.97, 0.98, and 0.97 for sugarcane, wheat, and barley. The LD-based algorithm was used to assign 5920 out of 21,251 unpositioned markers to the current Q208 sugarcane genetic map, representing the highest density genetic map for this species to date.

Conclusions
Our LD-based approach can be used to accurately assign unpositioned SNPs to existing genetic maps, improving genome-wide association studies and genomic prediction in crop species with fragmented and incomplete genome assemblies. This approach will facilitate genomic-assisted breeding for many orphan crops that lack genetic and genomic resources.
Removal of EpCAM-positive tumor cells from blood collected during major oncological surgery using the Catuvab device- a pilot study
Authors: Winter Andreas , Zacharowski Kai , Meybohm Patrick , Schnitzbauer Andreas , Ruf Peter , Kellermann Claudia , Lindhofer Horst 
Published: October 2021

AbstractBackgroundIntraoperative blood salvage (IBS) is regarded as an alternative to allogeneic blood transfusion excluding the risks associated with allogeneic blood. Currently, IBS is generally avoided in tumor surgeries due to concern for potential metastasis caused by residual tumor cells in the erythrocyte concentrate.MethodsThe feasibility, efficacy and safety aspects of the new developedCatuvabprocedure using the bispecific trifunctional antibody Catumaxomab was investigated in an ex-vivo pilot study in order to remove residual EpCAM positive tumor cells from the autologous erythrocyte concentrates (EC) from various cancer patients, generated by a IBS device.ResultsTumor cells in intraoperative blood were detected in 10 of 16 patient samples in the range of 69–2.6 × 105but no residual malignant cells in the final erythrocyte concentrates afterCatuvabprocedure. IL-6 and IL-8 as pro-inflammatory cytokines released during surgery, were lowered in mean 28-fold and 52-fold during theCatuvabprocedure, respectively, whereas Catumaxomab antibody was detected in 8 of 16 of the final EC products at a considerable decreased and uncritical residual amount (37 ng in mean).ConclusionThe preliminary study results indicate efficacy and feasibility of the new medical deviceCatuvaballowing potentially the reinfusion of autologous erythrocyte concentrates (EC) produced by IBS device during oncological high blood loss surgery. An open-label, multicenter clinical study on the removal of EpCAM-positive tumor cells from blood collected during tumor surgery using theCatuvabdevice is initiated to validate these encouraging results.
The 10-year incidence of hypertension across blood pressure categories in a population-based cohort in southwestern Sweden
Authors: Lindblad Ulf , Lundholm Klara , Eckner Jenny , Li Ying , Råstam Lennart , Hellgren I. Margareta , Daka Bledar 
Published: October 2021

Abstract
Background
To explore the determinants of incident hypertension, and especially the impact of baseline blood pressure categories, in a representative Swedish population.

Methods
A 10-year longitudinal study of residents aged 30–74. Blood pressures were measured and categorized according to ESH guidelines with optimal blood pressure < 120/80 mmHg, normal 120–129/80–84 mmHg, and high normal 130–139/85–89 mmHg. Incident hypertension was defined as ongoing treatment or three consecutive blood pressure readings ≥ 140/ ≥ 90 mmHg (one or both) at follow-up, while those with ≥ 140 and/or ≥ 90 mmHg at only one or two visits were labelled as unstable. After excluding subjects with hypertension, ongoing blood pressure lowering medication or a previous CVD event at baseline, 1099 remained for further analyses.

Results
Sixteen (2.6%) subjects with optimal baseline blood pressure had hypertension at follow up. Corresponding numbers for subjects with normal, high normal and unstable blood pressure were 55 (19.4%), 50 (39.1%) and 46 (74.2%), respectively. Compared with subjects in optimal group those in normal, high normal and unstable blood pressure categories had significantly higher risk to develop manifest hypertension with odds ratios OR and (95% CI) of 7.04 (3.89–12.7), 17.1 (8.88–33.0) and 84.2 (37.4–190), respectively, with adjustment for age, BMI and family history for hypertension. The progression to hypertension was also independently predicted by BMI (p < 0.001), however, not by age.

Conclusions
Subjects with high normal or unstable blood pressure should be identified in clinical practice, evaluated for global hypertension risk and offered personalized advice on lifestyle modification for early prevention of manifest hypertension and cardiovascular disease.
Factors associated with quality of care in inflammatory bowel diseases: a view from patient’s side using the IQCARO quality of care decalogue
Authors: Casellas F. , Calvet Xavier , Carpio D. , Vera I. , Saldaña R. , Mínguez M. , Marín L. , Juliá B. ,   GETECCU, GETEII and ACCU
Published: October 2021

Abstract
Background
Quality of care (QoC) is a highly important topic in inflammatory bowel disease (IBD). We recently elaborated a decalogue of QoC indicators (IQCARO-QoC) developed by IBD patients. The aim of the present study was to assess the factors associated with patients’ evaluation of QoC in Spain using the IQCARO-QoC Decalogue recently developed by IBD patients.

Methods
A survey including patients’ socio-demographic and clinical characteristics, and the IQCARO-QoC Decalogue, was completed by IBD patients. We described patients’ assessment of QoC across Spanish patients. A univariable and multivariable analysis was performed to explore the associations between patients’ characteristics and QoC.

Results
Questionnaires from 788 participant patients were analysed. Participants’ mean age was 43.4 years, 63% were females and 58% had Crohn’s disease. The mean QoC score was 8.1 (± 2.4 SD) points out of a maximum of 10. Items with the lowest score were related to the provision of information and the implication of the medical team throughout the entire patient care. Factors associated with better QoC scores included: being employed better disease control, fewer numbers of unscheduled visits, and being followed by a gastroenterologist specialized in IBD.

Conclusions
Spanish patients’ reported QoC seems to be globally good although there is room for improvement, especially in providing adequate information to patients. Care provided by specialized IBD gastroenterologists seems to be related with higher QoC scores.
A case report of delayed lower intestinal bleeding after organophosphate poisoning
Authors: Hung Wei , Tsai Tsung-Heng , Chen Jian-Han 
Published: October 2021

Abstract
Background
Organophosphate poisoning is a serious issue and it results in significant casualties in developing countries. Since agriculture remains an important and necessary sector of human society and organophosphate are commonly used in agriculture, it is difficult to prevent organophosphate poisoning. Gastrointestinal bleeding is not a common but life threatening symptom of organophosphate poisoning. We report a rare case of gastrointestine bleeding due to organophosphate poisoning.

Case presentation
A 78-year-old woman presented to our hospital approximately 12 h after ingesting a mouthful of organophosphate and benzodiazepines in a suicide attempt. Six weeks after successful medical treatment for respiratory failure, she developed recurring melena. Colonoscopy and esophagogastroduodenoscopy findings were negative for ulcers or bleeding. Enteroscopy revealed severe circumferential ulcers with luminal narrowing 10 cm proximal to the ileocecal valve. The patient underwent a 100-cm ileum resection after failed medical treatment and recovered uneventfully. The resected terminal ileum demonstrated severe inflammation and a sharp transitional zone between the healthy and injured mucosa approximately 50 cm proximal to the ileocecal valve. Pathological examination revealed an injured mucosa with inflammatory cell infiltration and structural damage. This case highlights a rare event of OP poisoning with late-onset lower gastrointestinal bleeding, which prolonged the patient’s recovery course and parenteral alimentation period.

Conclusion
We report a rare case of a patient with organophosphate poisoning, with late-onset lower GI tract bleeding, which raised clinical awareness regarding the organophosphate poisoning that induce intestinal symptoms.
The length of susceptibility vessel sign predicts early neurological deterioration in minor acute ischemic stroke with large vessel occlusion
Authors: He Lanying , Wang Jian , Wang Feng , Zhang Lili , Zhang Lijuan , Zhao Wang , Weng Xiechuan , Xu Fan 
Published: October 2021

Abstract
Background
Patients with acute large vessel occlusion (LVO) presenting with minor stroke are at risk of early neurological deterioration (END). The present study aimed to evaluate the frequency and potential predictors of END in patients with medical management and LVO presenting with minor stroke. The relationship between SVS length and END was also investigated.

Methods
This was a prospective multicenter study. Consecutive patients were collected with anterior circulation. LVO presented with minor stroke [National Institutes of Health Stroke Scale (NIHSS) ≤ 4] within 24 h following onset. END was defined as a deterioration of NIHSS ≥4 within 24 h, without parenchymal hemorrhage. The length of the susceptibility vessel sign (SVS) was measured using the T2* gradient echo imaging.

Results
A total of 134 consecutive patients with anterior circulation LVO presenting with minor stroke were included. A total of 27 (20.15%) patients experienced END following admission. Patients with END exhibited longer SVS and higher baseline glucose levels compared with subjects lacking END (P < 0.05). ROC curve analysis indicated that the optimal cutoff point SVS length for END was SVS ≥ 9.45 mm. Multivariable analysis indicated that longer SVS [adjusted odds ratio (aOR), 2.03; 95% confidence interval (CI), 1.45–2.84; P < 0.001] and higher baseline glucose (aOR,1.02; 95% CI, 1.01–1.03; P = 0.009) levels were associated with increased risk of END. When SVS ≥ 9.45 mm was used in the multivariate logistic regression, SVS ≥ 9.45 mm (aOR, 5.41; 95%CI, 1.00–29.27; P = 0.001) and higher baseline glucose [aOR1.01; 95%CI, 1.00–1.03; P = 0.021] were associated with increased risk of END.

Conclusions
END was frequent in the minor stroke patients with large vessel occlusion, whereas longer SVS and higher baseline glucose were associated with increased risk of END. SVS ≥ 9.45 mm was a powerful independent predictor of END.
Universal versus selective screening for gestational diabetes mellitus among antenatal clinic attendees in Abakaliki: using the one-step 75 gram oral glucose tolerance test
Authors: Nwali Silas Alegu , Onoh Robinson Chukwudi , Dimejesi Ikechukwu Bo , Obi Vitus Okwuchukwu , Jombo Sunday Emmanuel , Edenya Oghenevwogaga Obukohwo 
Published: October 2021

AbstractAimTo compare universal screening with selective risk factor based screening for GDM, using the one-step 75 g oral glucose tolerance test (OGTT).Materials and methodA cross-sectional, comparison between universal and selective risk factor based screening for GDM, among 400 antenatal care clients at Alex-Ekwueme Federal University Teaching Hospital Abakaliki (AE-FUTHA). All the participants had 75 g OGTT at 24–28 weeks of gestation and risk factor screening for GDM. All 400 participants formed the universal group while participants with one or more of the considered risk factors formed the selective risk factor group.Data were analyzed using IBM SPSS version 20. Statistical comparison was done using t- test for continuous variables. Logistics regression was used to determine the level of associations of the independent predictors for hyperglycemia. Level of significance was set atP < 0.05.ResultsThe point prevalence of GDM using universal and selective screening were 11.51 and 7.93% respectively, giving a selective screening miss rate of 31.11%. The sensitivity, specificity, positive predictive value and negative predictive value were 73.58, 48.82, 19.12 and 92.51% respectively for the selective risk factor based screening compared to universal screening.On multivariate analysis; age ≥ 35 years, weight ≥ 90 kg, history of previous GDM and hypertension were significantly related to the development of hyperglycemia.ConclusionSelective risk factor based screening missed 31.11% of patients with GDM when compare to Universal screening with one step 75 g OGTT. Universal screening for GDM using the one step 75 g OGTT is recommended for pregnant women and more studies are needed to compare pregnancy outcomes for pregnant women diagnosed with GDM with and without risk factors.
Ferroptosis regulators, especially SQLE, play an important role in prognosis, progression and immune environment of breast cancer
Authors: Tang Wenqing , Xu Fangshi , Zhao Meng , Zhang Shuqun 
Published: October 2021

Abstract
Background
Ferroptosis, a new form of programmed cell death, has great potential for cancer treatment. However, the roles of ferroptosis-related (FR) genes in breast cancer (BC) remain elusive.

Materials and methods
Using TCGA database, a novel FR risk signature was constructed through the Lasso regression analysis. Meanwhile, its prognostic value was assessed by a series of survival analyses. Besides, a nomogram was constructed to predict the overall survival rate (OSR) of individual at 1,3,5 year. Four validation cohorts (n = 2248), including METABRIC, GSE58812, GSE20685 and ICGC-KR datasets, were employed to test the prognostic value of FR risk signature. The effects of FR risk signature on BC immune microenvironment were explored by CIBERSORT algorithm and ssGSEA method. The histological expressions of FR risk genes were presented by HPA database. The biofunctions of SQLE were determined by qPCR, MTT, wound-healing and Transwell assays.

Results
We constructed a novel FR risk signature consisting of eight genes. High FR risk led a poor prognosis and was identified as an independent prognostic factor. Besides, A higher proportion of patients with luminal A type was observed in low-risk group (53%), while a higher proportion of patients with basal type in high-risk group (24%). FR risk score could discriminate the prognostic difference of most clinical subgroups, except for M1 stage, HER2 and basal types. Moreover, its prognostic value was successfully validated in other four cohorts. Through immune analyses, we found that the reduced infiltration levels of CD8+ and NK cells, whereas the enhanced activity of antigen presentation process appeared in high FR risk. Then, FR risk score was found to weakly correlate with the expressions of six immune checkpoints. Through the experiments in vitro, we confirmed that overexpression of SQLE could promote, whereas blocking SQLE could inhibit the proliferative, migrative and invasive abilities of BC cells.

Conclusions
FR risk signature was conducive to BC prognostic assessment. High FR risk level was closely associated with BC immunosuppression, but may not predict ICIs efficacy. Moreover, SQLE was identified as a crucial cancer-promoting gene in BC. Our findings provide new insights into prognostic assessment and molecular mechanism of BC.