bluuebunny/crossref_metadata_2025_split huggingface dataset:
D-dimer kit with a High FDP/D-Dimer Ratio is Useful for Diagnosing Thrombotic Diseases
Authors: Ikeda Nozomi , Wada Hideo , Ichikawa Yuhuko , Ezaki Minoru , Tanaka Motoko , Hiromori Shinya , Shiraki Katsuya , Moritani Isao , Yamamoto Akitaka , Shimpo Hideto , Shimaoka Motomu 
Published: January 2022

Introduction Although D-dimer is a useful biomarker of thrombosis, there are many D-dimer kits, with high and low fibrinogen and fibrin degradation products (FDP)/ D-dimer ratios. Methods Plasma D-dimer levels were measured using three different kits in critically ill patients to examine the usefulness of such measurements for detecting the thrombotic diseases and determining the correlation with the FDP and FDP/D-dimer ratio. Results Although three D-dimer kits showed marked utility for diagnosing disseminated intravascular coagulation (DIC) and peripheral arterial and venous thromboembolism (PAVTE), the D-dimer levels determined using the three kits varied among diseases. Indeed, one D-dimer kit showed a high FDP/D-dimer ratio, and another kit showed a low FDP/D-dimer ratio. D-dimer kit with low FDP/D-dimer ratio tended to have high cut-off values and low specificity for diagnosing DIC and PAVTE. In D-dimer kit with high FDP/D-dimer ratio, FDP/D-dimer ratios in patients with thrombosis was significantly higher than that in patients without thrombosis. Conclusion All three D-dimer kits show utility for detecting thrombotic diseases. However, the D-dimer levels determined using the kits varied due to differences in the FDP/D-dimer ratio. In combination with the FDP level, a D-dimer kit with a high FDP/D-dimer ratio may be useful.
Body mass index as a predictor of MS activity and progression among participants in BENEFIT
Authors: Manuel Escobar Juan , Cortese Marianna , Edan Gilles , Freedman Mark S , Hartung Hans-Peter , Montalbán Xavier , Sandbrink Rupert , Radü E-W , Barkhof Frederik , Wicklein Eva-Maria , Kappos Ludwig , Ascherio Alberto , Munger Kassandra L 
Published: January 2022

Background: There is a lack of studies on the association between obesity and conversion from a clinically isolated syndrome (CIS) to multiple sclerosis (MS). Objective: The aim of this study was to determine whether obesity predicts disease activity and prognosis in patients with CIS. Methods: Body mass index (BMI) at baseline was available for 464 patients with CIS in BENEFIT. Obesity was defined as BMI ⩾ 30 kg/m2 and normal weight as 18.5 ⩽ BMI < 25. Patients were followed up for 5 years clinically and by magnetic resonance imaging. Hazard of conversion to clinically definite (CDMS) or to 2001 McDonald criteria (MDMS) MS, annual rate of relapse, sustained progression on Expanded Disability Status Scale (EDSS), change in brain and lesion volume, and development of new brain lesions were evaluated. Results: Obese individuals were 39% more likely to convert to MDMS (95% CI: 1.02–1.91, p = 0.04) and had a 59% (95% CI: 1.01–2.31, p = 0.03) higher rate of relapse than individuals with normal weight. No associations were observed between obesity and conversion to CDMS, sustained progression on EDSS or magnetic resonance imaging (MRI) outcomes, except for a larger reduction of brain volume in obese smokers as compared to normal weight smokers (−0.82%; 95% CI: −1.51 to −0.12, p = 0.02). Conclusion: Obesity was associated with faster conversion to MS (MDMS) and a higher relapse rate.
Endovenous Iliocaval Revascularization for Transplant Kidney Salvage
Authors: Ruyssinck Laure , Lootens Liesbeth , Desender Liesbeth , Moreels Nathalie , Randon Caren 
Published: January 2022

Purpose: We report the case of a venous iliocaval recanalization to preserve a transplant kidney. Case Report: A young patient with a nephrotic syndrome caused by focal segmental glomerulosclerosis (FSGS) underwent a robot-assisted living-donor kidney transplant. The postoperative course was uneventful; serum creatinine at discharge was 1.51 mg/dL (normal range = 0.72–1.17 mg/dL). In the course of the following months, the patient was readmitted repeatedly due to acute kidney failure not related to rejection, recurrent FSGS, or anastomotic stenosis. All episodes started after prolonged standing and renal function improved after bed rest. Several hospital admissions and investigations later, phlebography revealed an occlusion of the inferior vena cava (IVC) and both common iliac veins with large collateral vessels through the azygos system. An endovenous recanalization of the iliocaval tract was performed, with subsequent normalization of transplant kidney function. Conclusion: Vascular complications after renal transplantation are an important cause of graft loss. We present an endovenous treatment option for a chronic occlusion of the IVC and common iliac vein with intermittent venous congestion as a cause of transplant failure.
Six-Strand Flexor Pollicis Longus Tendon Repairs With and Without Circumferential Sutures: A Multicenter Study
Authors: Lautenbach Géraldine , Guidi Marco , Tobler-Ammann Bernadette , Beckmann-Fries Vera , Oberfeld Elisabeth , Schrepfer Lorena , Hediger Sebastian , Kaempfen Alexandre , Vögelin Esther , Calcagni Maurizio 
Published: January 2022

Background: The purpose of this study is to assess outcomes in flexor pollicis longus tendon repairs with 6-strand core sutures with and without circumferential sutures. Methods: A 6-strand core suture technique with and without circumferential sutures was used. Thirty-three patients were summarized in the C group (circumferential group) and 16 patients in the NC group (non-circumferential group). After the surgery, the wrist was stabilized with a dorsal blocking splint and a controlled early active motion protocol was applied. At weeks 6, 13, and 26 data on demographics, type of injury, surgery, postoperative rehabilitation, complications such as re-rupture and the following outcome measurements were collected: range of motion and its recovery according to the Tang criteria, Kapandji score, thumb and hand strengths, Disabilities of the Arm, Shoulder and Hand score, and satisfaction. Results: There were no significant differences in range of motion and strength between the 2 treatment groups. In both groups, the outcome measurements increased over time and they expressed similar satisfaction with the surgical treatment. In 4 patients of the C group tendon repair ruptured and in 1 patient of the NC group. Conclusions: Six-strand repair technique is an effective procedure to assure early active motion after flexor pollicis longus tendon injuries and good results can also be achieved by omitting the circumferential suture.
Clinical Outcomes of Severely Angulated Fifth Metacarpal Neck Fractures Treated Nonsurgically
Authors: France Thomas J. , Leversedge Fraser J. , Lauder Alexander 
Published: January 2022

Background: Reasonable functional outcomes for nonoperative management of isolated, closed fifth metacarpal neck fractures with up to 70° angulation have been reported; however, reported outcomes for fractures with greater than 70° angulation are limited. This study describes clinical outcomes of nonsurgically treated fifth metacarpal neck fractures with angulation of greater than 70°. Methods: A retrospective review of patients treated between May 1, 2016, and May 1, 2020, included: (1) patients aged 18 years and above with an isolated, closed, fifth metacarpal neck fracture; (2) nonsurgical treatment; (3) healed fractures with angulation greater than 70° measured on oblique radiographs; and (4) minimum 6-month follow-up after injury. Photographic hand motion and patient-rated outcomes (Functional Hand Scale, Quick Disabilities of the Arm, Shoulder, and Hand [QuickDASH], 12-item Short-Form Health Survey [SF-12]) were collected and reported. Results: A total of 364 fractures were identified; 11% (40/364) demonstrated angulation of greater than 70° (range: 71°-82°); and 15 patients (inclusion rate: 38%, 15/40) with mean fracture angulation of 73° (range: 71°-77°) participated in the study. Mean follow-up was 32 months (range: 8-120 months), the dominant hand was injured in 87% (13/15) of patients, and 47% (7/15) of patients worked in manual labor. All patients scored the highest rating of “very good” (range: 26-30 of 30 points) on the functional hand scale. A QuickDASH score of zero (no morbidity) was reported in 80% (12/15) of patients. About 87% (13/15) of patients had average or above-average scores on the SF-12 (mean = 109, range: 84-115). Conclusions: Patients with healed, isolated, closed fifth metacarpal neck malunions with severe angulation greater than 70° demonstrated acceptable functional outcomes based on patient-rated outcomes scoring.
The representation of Indigenous peoples in chronic disease clinical trials in Australia, Canada, New Zealand, and the United States
Authors: Umaefulam Valerie , Kleissen Tessa , Barnabe Cheryl 
Published: January 2022

Background Indigenous peoples are overrepresented with chronic health conditions and experience suboptimal outcomes compared with non-Indigenous peoples. Genetic variations influence therapeutic responses, thus there are potential risks and harm when extrapolating evidence from the general population to Indigenous peoples. Indigenous population–specific clinical studies, and inclusion of Indigenous peoples in general population clinical trials, are perceived to be rare. Our study (1) identified and characterized Indigenous population–specific chronic disease trials and (2) identified the representation of Indigenous peoples in general population chronic disease trials conducted in Australia, Canada, New Zealand, and the United States. Methods For Objective 1, publicly available clinical trial registries were searched from May 2010 to May 2020 using Indigenous population–specific terms and included for data extraction if in pre-specified chronic disease. For identified trials, we extracted Indigenous population group identity and characteristics, type of intervention, and funding type. For Objective 2, a random selection of 10% of registered clinical trials was performed and the proportion of Indigenous population participants enrolled extracted. Results In total, 170 Indigenous population–specific chronic disease trials were identified. The clinical trials were predominantly behavioral interventions (n = 95). Among general population studies, 830 studies were randomly selected. When race was reported in studies (n = 526), Indigenous individuals were enrolled in 172 studies and constituted 5.6% of the total population enrolled in those studies. Conclusion Clinical trials addressing chronic disease conditions in Indigenous populations are limited. It is crucial to ensure adequate representation of Indigenous peoples in clinical trials to ensure trial data are applicable to their clinical care.
Attention to bone health in follow-up of gynaecological cancers in tertiary care
Authors: O’Gorman Catherine A , Minnock Sorcha , Mulhall Joseph , Gleeson Noreen 
Published: January 2022

Objective: Women with gynaecological cancers are at an increased risk of cancer treatment–induced bone loss, which impacts on their quality of life and overall survival. Clinical cancer follow-up reviews focus on cancer status and fail to attend to important health and quality-of-life issues. We questioned whether there was a care-gap between tertiary clinicians and primary care physicians in the management of bone health in this cohort. Significant care-gaps in relation to bone health have been demonstrated in other oncologic settings. The objective of this study was to determine the level of attention to bone health in the care of women living with and beyond gynaecological cancer at a tertiary referral centre for gynaecological oncology. Methods: Retrospective, observational cohort study of attention to bone health in the management and follow-up of gynaecological cancers. Results: This study shows that there has been suboptimal attention from the carers at a cancer centre to bone health during the oncological follow up of women undergoing treatment for gynaecological cancer. In those at particular risk of cancer treatment–induced bone loss (iatrogenic menopause and/or external beam pelvic radiotherapy), 52% of women had no reference to bone health in their notes, and 57% had no assessment of bone mineral density. Conclusion: Tertiary cancer carers may underestimate the importance of bone health or believe that it falls outside the remit of their gynaecologic oncology service. Further research is needed to explore whether these findings are indicative of a true care gap and to gain insight into possible corrective measures.
Differences in Shoulder Internal Rotation Strength Between Baseball Players With Ulnar Collateral Ligament Reconstruction and Healthy Controls
Authors: Kennedy Sean M. , Sheedy Philip , Klein Brooks , Gist Mason F. , Hannon Joseph P. , Conway John E. , Creed Kalyssa , Garrison J. Craig 
Published: January 2022

Background: Studies have indicated decreased shoulder internal rotation (IR) and external rotation (ER) strength in the throwing limb of baseball players after ulnar collateral ligament injury. There is limited evidence on the recovery of shoulder rotation strength after primary ulnar collateral ligament reconstruction (UCLR). Hypothesis: At the time of return to throwing, baseball players who underwent UCLR would demonstrate decreased IR and ER shoulder strength in the throwing arm as compared with healthy baseball players. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Male competitive high school and collegiate baseball athletes participated in this study. Athletes who underwent UCLR were compared with healthy controls who were matched by age, height, weight, and position. Bilateral isometric shoulder ER and IR strength was measured using a handheld dynamometer for all participants at the time of initial evaluation (UCLR group) and throughout the course of a season (healthy group). Independent t tests were run to calculate mean differences in ER and IR shoulder strength between the groups, with significance set at P < .05. Results: A total of 86 baseball athletes participated in this study (43 UCLR group, 43 healthy group). At the time of return to throwing (mean ± SD, 194 ± 30 days postoperatively), the 2 groups demonstrated no significant differences in nonthrowing arm ER or IR strength ( P = .143 and .994, respectively). No significant difference was found between groups for throwing arm ER strength ( P = .921); however, the UCLR group demonstrated significantly less throwing arm IR strength than the healthy group (144.2 ± 27.8 vs 157.6 ± 27.1 N; P = .023). Conclusion: The results of this study demonstrate that throwing arm rotator cuff strength may not fully recover before the initiation of a return-to-throwing program after UCLR. These data provide a potential framework for clinicians to assist in the management and exercise prescription of the baseball athlete after UCLR and before medical release and the initiation of a return-to-throwing program.
Managing Type 2 Diabetes: Beliefs and Daily Practices in First Generation Asian Indians in the United States
Authors: Deol Rupinder M , Thompson Lisa M , Chun Kevin M , Chesla Catherine 
Published: January 2022

Introduction Diabetes management and control remain poor in Asian Indians (AI) and is influenced by personal beliefs and cultural practices. Since AIs have a high prevalence of diabetes and are more likely develop complications earlier than any other ethnic group, understanding their beliefs and practices of diabetes management is essential. The purpose of this study was to examine and understand beliefs and practices about diabetes self-management in first-generation AI Hindus and Sikhs. Method Interpretative phenomenology was used to interview 12 first generation AI participants with type 2 diabetes to elicit beliefs and daily self-management practices of diabetes. Interpretative and thematic analysis were completed. Results Diabetes self-management was a balancing act influenced by Ayurvedic principles, allopathy and dietary practices; gender roles, insufficient knowledge and culturally inappropriate diabetes education. Discussion Culturally appropriate strategies that incorporate Ayurvedic principles, dietary practices, gender roles should be developed to improve diabetes management.
Practical Risk Scoring System for Predicting Severity of COVID-19 Disease
Authors: Petersen Jeffrey , Jhala Darshana 
Published: January 2022

Objectives: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19 disease, has become an international pandemic with numerous casualties. It had been noted that the severity of the COVID-19 disease course depends on several clinical, laboratory, and radiological factors. This has led to risk scoring systems in various populations such as in China, but similar risk scoring systems based on the American veteran population are sparse, particularly with the vulnerable Veteran population. As a simple risk scoring system would be very useful, we propose a simple Jhala Risk Scoring System (JRSS) to assess the severity of disease risk. Methods: A retrospective review of all SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) tests collected and performed at the regional Veterans Administration Medical Center (VAMC) serving the Philadelphia and surrounding areas from March 17th, 2020 to May 20th, 2020. Data was collected and analyzed in the same year. These tests were reviewed within the computerized medical record system for demographic, medical history, laboratory test history, and clinical course. Information from the medical records were then scored based on the criteria of the Jhala Risk Scoring System (JRSS). Results: The JRSS, based on age, ethnicity, presence of any lung disease, presence of cardiovascular disease, smoking history, and diabetes history with laboratory parameters correlated and predicted (with statistical significance) which patients would be hospitalized. Conclusion: The JRSS may play a role in informing which COVID-19 positive patients in the emergency room/urgent care for risk stratification.
Predicting the targets of IRF8 and NFATc1 during osteoclast differentiation using the machine learning method framework cTAP
Authors: Wang Honglin , Joshi Pujan , Hong Seung-Hyun , Maye Peter F. , Rowe David W. , Shin Dong-Guk 
Published: January 2022

Abstract
Background
Interferon regulatory factor-8 (IRF8) and nuclear factor-activated T cells c1 (NFATc1) are two transcription factors that have an important role in osteoclast differentiation. Thanks to ChIP-seq technology, scientists can now estimate potential genome-wide target genes of IRF8 and NFATc1. However, finding target genes that are consistently up-regulated or down-regulated across different studies is hard because it requires analysis of a large number of high-throughput expression studies from a comparable context.

Method
We have developed a machine learning based method, called, Cohort-based TF target prediction system (cTAP) to overcome this problem. This method assumes that the pathway involving the transcription factors of interest is featured with multiple “functional groups” of marker genes pertaining to the concerned biological process. It uses two notions, Gene-Present Sufficiently (GP) and Gene-Absent Insufficiently (GA), in addition to log2 fold changes of differentially expressed genes for the prediction. Target prediction is made by applying multiple machine-learning models, which learn the patterns of GP and GA from log2 fold changes and four types of Z scores from the normalized cohort’s gene expression data. The learned patterns are then associated with the putative transcription factor targets to identify genes that consistently exhibit Up/Down gene regulation patterns within the cohort. We applied this method to 11 publicly available GEO data sets related to osteoclastgenesis.

Result
Our experiment identified a small number of Up/Down IRF8 and NFATc1 target genes as relevant to osteoclast differentiation. The machine learning models using GP and GA produced NFATc1 and IRF8 target genes different than simply using a log2 fold change alone. Our literature survey revealed that all predicted target genes have known roles in bone remodeling, specifically related to the immune system and osteoclast formation and functions, suggesting confidence and validity in our method.

Conclusion
cTAP was motivated by recognizing that biologists tend to use Z score values present in data sets for the analysis. However, using cTAP effectively presupposes assembling a sizable cohort of gene expression data sets within a comparable context. As public gene expression data repositories grow, the need to use cohort-based analysis method like cTAP will become increasingly important.
Comparative genome analysis of plant ascomycete fungal pathogens with different lifestyles reveals distinctive virulence strategies
Authors: Wang Yansu , Wu Jie , Yan Jiacheng , Guo Ming , Xu Lei , Hou Liping , Zou Quan 
Published: January 2022

Abstract
Background
Pathogens have evolved diverse lifestyles and adopted pivotal new roles in both natural ecosystems and human environments. However, the molecular mechanisms underlying their adaptation to new lifestyles are obscure. Comparative genomics was adopted to determine distinct strategies of plant ascomycete fungal pathogens with different lifestyles and to elucidate their distinctive virulence strategies.

Results
We found that plant ascomycete biotrophs exhibited lower gene gain and loss events and loss of CAZyme-encoding genes involved in plant cell wall degradation and biosynthesis gene clusters for the production of secondary metabolites in the genome. Comparison with the candidate effectome detected distinctive variations between plant biotrophic pathogens and other groups (including human, necrotrophic and hemibiotrophic pathogens). The results revealed the biotroph-specific and lifestyle-conserved candidate effector families. These data have been configured in web-based genome browser applications for public display (http://lab.malab.cn/soft/PFPG). This resource allows researchers to profile the genome, proteome, secretome and effectome of plant fungal pathogens.

Conclusions
Our findings demonstrated different genome evolution strategies of plant fungal pathogens with different lifestyles and explored their lifestyle-conserved and specific candidate effectors. It will provide a new basis for discovering the novel effectors and their pathogenic mechanisms.
N7-methylguanosine modification of lncRNAs in a rat model of hypoxic pulmonary hypertension: a comprehensive analysis
Authors: Wang Huan , Chen Ren Biao , Zhang Si Ni , Zhang Rui Feng 
Published: January 2022

Abstract
Background
Long non-coding RNAs (lncRNAs) play a critical role in the pathogenesis of hypoxic pulmonary hypertension (HPH). The role of N7-methylguanosine (m7G) modification in lncRNAs has received increased attentions in recent years. However, the m7G-methylation of lncRNA in HPH has yet to be determined. We have therefore performed a transcriptome-wide analysis of m7G lncRNAs in HPH.

Results
Differentially-expressed m7Gs were detected in HPH, and m7G lncRNAs were significantly upregulated compared with non-m7G lncRNAs in HPH. Importantly, this was the first time that the upregulated m7G lncXR_591973 and m7G lncXR_592398 were identified in HPH.

Conclusion
This study provides the first m7G transcriptome-wide analysis of HPH. Importantly, two HPH-associated m7G lncRNAs were identified, although their clinical significance requires further validation.