bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Impact of Atherosclerotic Cardiovascular Risk on Graft Failure in Deceased-Donor Renal Transplantation
Authors: Hsu Grace , Sparkes Tracy M. , Reed Brent N. , Gale Stormi E. , Crossley Brian E. , Ravichandran Bharath R. 
Published: June 2021

Introduction: Pretransplant cardiovascular risk may be amplified after renal transplant, but little is known about its impact on graft outcomes. Research question: The purpose of this study was to determine if pretransplant cardiovascular risk was associated with graft outcomes. Design: This retrospective study included deceased-donor renal transplant recipients from 2010-2015. Atherosclerotic cardiovascular disease risk for patients without prior disease was calculated and patients were categorized into high (score >20%), intermediate (7.5-20%), and low risk (<7.5%). Patients with and without prior cardiovascular disease were also compared. The main endpoint was graft failure at 3-years post-transplant. Other outcomes included major adverse cardiovascular events, biopsy-proven rejection, and mortality. Results: In patients without prior atherosclerotic cardiovascular disease (N = 115), graft failure rates (4.5% vs 11.3% vs 12.5%; ( P = 0.64) and major adverse cardiovascular events (9.1% vs 13.2% vs 5.0%; P = 0.52) were similar in the high, intermediate, and low risk groups. In those with prior disease (N = 220), rates of primary nonfunction (6.8% vs 1.7%; P = 0.04), major adverse cardiovascular events (7.3% vs 2.6%; P = 0.01), and heart failure (10.9% vs 3.5%; P = 0.02) were higher than those without cardiovascular; rates of major adverse cardiovascular events and heart failure were insignificant after adjusting for age, gender, and race. Other outcomes were not different. Outcomes did not differ based on pretransplant cardiovascular risk. Discussion: Pretransplant atherosclerotic cardiovascular disease was associated with increased early graft failure but similar outcomes at 3-years, suggesting cardiac risk alone should not exclude transplantation.
Minimally Invasive Plication of the Diaphragm: A Single-Center Prospective Study
Authors: Nardini Marco , Jayakumar Shruti , Migliore Marcello , Nosotti Mario , Paul Ian , Dunning Joel 
Published: June 2021

Objective Plication of the diaphragm is a life-changing procedure for patients affected by diaphragm paralysis. Traditionally, this procedure is performed through a thoracotomy. Access to the diaphragm via this incision is poor and the indications for surgery are limited to patients who can actually sustain such an invasive approach and associated morbidities. A minimally invasive approach was developed to improve the surgical management of diaphragm paralysis. Methods Patients underwent minimally invasive diaphragm plication either by video-assisted or robotic surgery through a 3-port technique with CO2 insufflation. Patients were followed at the routine 6-week clinic and also by telephone consultation 6 to 12 months postoperatively. Data were collected on postoperative complications, postoperative pain or numbness, symptomatic improvement, and change to quality of life following surgery. Results Forty-eight patients underwent 49 minimally invasive diaphragm plication. Median postoperative length of hospital stay was 4 days (range: 2 to 34 days) and there were no cases of mortality. Mean reduction in Medical Research Council dyspnea score per patient was 2.2 points (mode: 3 points). Twenty-eight patients (77.8%) reported a significant symptomatic improvement enabling improvements in quality of life, and 97.2% ( n = 35) were satisfied with the surgical outcome. Conclusions Minimally invasive diaphragm plication is a safe procedure associated with prompt postoperative recovery. It is effective at reducing debilitating dyspnea and improving quality of life.
Parachute-Induced Pectoralis Major Tears in Military Servicemembers: What Is the Functional Recovery?
Authors: Shaw K. Aaron , Brown Scott , Moreland Colleen M. , Antosh Ivan J. , Parada Stephen A. 
Published: June 2021

Background: Although the most common injury mechanism for pectoralis major (PM) tears is an eccentric loading mechanism typically caused by bench pressing, within the military, there is a unique injury mechanism associated with airborne operations. The results of operative repair for these parachute-induced PM tears have not been previously reported. Purpose/Hypothesis: To assess the functional outcomes in military servicemembers undergoing operative repair of parachute-induced PM tears. We hypothesized that functional recovery would be impaired with delayed surgical intervention. Study Design: Cohort study; Level of evidence, 3. Methods: Included were active duty military servicemembers who underwent operative repair for PM tears caused by a parachute-induced mechanism. Charts were reviewed to identify characteristic, injury, and surgical variables. Patients completed the functional outcome assessment with the Disabilities of the Arm, Shoulder and Hand (DASH) and the American Shoulder and Elbow Surgeons (ASES) questionnaires. Outcomes were compared between patients treated within 6 weeks of injury and those treated beyond 6 weeks. Results: Of the 68 identified PM tears, 25 were the result of parachute-induced mechanisms. A total of 13 patients consented and completed the functional outcome assessment. The mean patient age was 30.6 ± 6.4 years, and the mean follow-up period was 5.46 ± 1.26 years. Ten patients underwent repair within 6 weeks of injury, and the remaining 3 patients underwent repair at a mean of 338 days after injury (95% CI, -42.8 to 718.8 days), a significant difference between groups ( P = .006). All 13 patients were able to return to military duties at a mean of 6 months from injury. Patients treated within 6 weeks of injury had significantly higher functional outcomes (DASH score, 6.17 vs 26.67; P = .018; ASES score, 85.97 vs 49.5; P = .008), with greater strength performance compared with preinjury (bench press, 90.58% vs 38.95%; P = .0057; push-ups, 81.9% vs 23.8%; P = .023) compared with patients treated beyond 6 weeks of injury. Conclusion: Operative repair of parachute-induced PM tears within 6 weeks of injury provided a superior functional and strength recovery when compared with delayed surgical repair. Acute repair should be recommended for military servicemembers who experience this unique injury mechanism.
Telemedicine Training in the COVID Era: Revamping a Routine OSCE to Prepare Medicine Residents for Virtual Care
Authors: Boardman Davis , Wilhite Jeffrey A , Adams Jennifer , Sartori Daniel , Greene Richard , Hanley Kathleen , Zabar Sondra 
Published: June 2021

Background: During the rapid onset of the pandemic, clinicians transitioned from traditional outpatient practice to virtual modalities for providing routine care to patient panels. Like training programs nationwide, telemedicine training and assessment had not been systematically incorporated into our residency. In response, a scheduled Internal Medicine (IM) Objective Structured Clinical Examination (OSCE) was adapted to a remote modality to become virtual care-focused learning experience for trainees and to provide valuable feedback to educators. Methods: Standardized Patients (SPs) rated residents on their communication (including information gathering, relationship development and patient education), patient activation and satisfaction, and telemedicine skills. Analyses included a comparison of domain scores for residents who participated in both the 2020 remote and 2019 in-person OSCEs, and a review of written resident comments about the virtual OSCE. Results: During 2020’s video visit OSCE (VOSCE), residents (n = 23) excelled at nonverbal communication but struggled with virtual physical exams and information gathering. In debrief, residents expressed substantial interest in more opportunity to practice virtual visit skills going forward. In comparing scores of the virtual care (2020) OSCE with the in-person (2019) version, the small subset of residents who participated in both assessments (n = 9) performed similarly on communication skills, patient satisfaction and activation. Patient education scores were significantly lower during the virtual care OSCE ( P = .008). Conclusion: Our reformulated OSCE accomplished 3 goals including; (1) physically distancing residents from SPs per COVID regulations, (2) providing residents with the opportunity to practice critical virtual visit skills, and (3) alerting our educators to curricular improvement areas. Our methods are useful for other institutions and have applications to the larger medical education community.
Infrastructural and Knowledge Barriers to Accessing Acute Stroke Care at a Regional Tertiary Facility in Kenya
Authors: Mithi Caroline , Shah Jasmit , Mativo Peter , Sokhi Dilraj Singh 
Published: June 2021

The delivery of definitive acute stroke care in Africaremains low due to prehospital barriers, and these are known to be country-specific. There have been no studies on elucidating these barriers in Kenya. Objectives: We sought to identify the nature of barriers to acute stroke care for patients presenting to our hospital in Nairobi, Kenya. Materials and Methods: We conducted a prospective cross-sectional study atour tertiary regional referral center from August 2018 to March 2019 for patients presenting with an acutestroke. We consented participants (patients or their registered next-of-kin) to fill out a questionnaire on their journey from stroke-onset to the ward bed, and about their knowledge about stroke. Results: We recruited 103 participants. Only 25.2% arrived to hospital within 3.5 h (early arrival) of stroke onset. The significant factors causing delay were:distance from hospital, traffic, visiting another hospital first, and lack of transport vehicle. Factors significantly associated ( P<.05) with early arrival were: older age, non-African ethnic origin, bystander present at stroke onset, living near (<15km) the hospital, and knowledge of stroke. Almost 80% believed stress was a major risk factor and that dizziness was a cardinal symptom. Only 50% knew of the availability of thrombolysis/thrombectomy and their roles in stroke treatment, and only 37.9% knew the correct time limits for these. Conclusions: We identified a number of prehospital barriers to reaching hospital on time for definitive stroke treatment, which have implications on the structure of emergency services for stroke in our city. Our study also revealed interesting observations on the public’s understanding about stroke, calling for a tailored public awareness campaign to improve stroke knowledge.
High expression of LAMA3/AC245041.2 gene pair associated with KRAS mutation and poor survival in pancreatic adenocarcinoma: a comprehensive TCGA analysis
Authors: Tian Chengming , Li Xiyao , Ge Chunlin 
Published: June 2021

Abstract
Background
Pancreatic adenocarcinoma (PAAD) is one of the most challenging cancers with high morbidity and mortality. KRAS mutations could occur as an early event in PAAD. The present study aimed to identify the differentially expressed lncRNAs (DE-lncRNAs) and differentially expressed mRNAs (DE-mRNAs) in KRAS-mutant PAAD to explore the pathogenesis and the underlying molecular mechanism of PAAD development.

Methods
Clinical data of TCGA–PAAD patients were downloaded from the TCGA database and subjected to survival analysis along with the KRAS mutation information data. Weighted gene correlation network analysis (WGCNA) and univariate Cox regression analysis were conducted to construct prognostic risk models to identify the hub DE-mRNAs and DE-lncRNAs associated with PAAD prognosis. GO and KEGG enrichment analyses of the identified hub DE-mRNAs were performed. Multivariate cox regression analysis was performed to analyze the overall prognosis of age, gender, pathologic_T, and KRAS mutations, following which the differences in the clinical characteristics of risk score1 and risk score2 were analyzed. Finally, the mRNAs–lncRNA–TFs regulatory network was constructed.

Results
Functional enrichment analysis was performed after screening 1671 DE-mRNAs and 324 DE-lncRNAs. It was observed that the associated pathways were enriched mainly in the modulation of chemical synaptic transmission, synaptic membrane, ion-gated channel activity, ligand−receptor interactions that stimulate neural tissue, among others. The univariate Cox regression analysis screened 117 mRNAs and 36 lncRNAs, and the risk ratio models of the mRNAs and lncRNAs were constructed. LAMA3 (mRNA) and AC245041.2 (lncRNA) exhibited a strong expression correlation in the respective two risk models. The genes in the samples with a high expression of these two genes were enriched in several pathways associated with transcription factors (TFs), among which the TFs ATF5, CSHL1, NR1I2, SIPA1, HOXC13, HSF2, and HOXA10 were shared by the two groups. The core enrichment genes in the common TF pathways were collated, and the mRNAs–lncRNAs–TFs regulatory network was constructed.

Conclusion
In the present study, novel prognostic mRNAs and lncRNAs were identified, and their respective prognostic models and nomograms were constructed to guide clinical practice. An mRNAs–lncRNAs–TFs regulatory network was also constructed, which could assist further research in the future.
Simulation study and comparative evaluation of viral contiguous sequence identification tools
Authors: Glickman Cody , Hendrix Jo , Strong Michael 
Published: June 2021

Abstract
Background
Viruses, including bacteriophages, are important components of environmental and human associated microbial communities. Viruses can act as extracellular reservoirs of bacterial genes, can mediate microbiome dynamics, and can influence the virulence of clinical pathogens. Various targeted metagenomic analysis techniques detect viral sequences, but these methods often exclude large and genome integrated viruses. In this study, we evaluate and compare the ability of nine state-of-the-art bioinformatic tools, including Vibrant, VirSorter, VirSorter2, VirFinder, DeepVirFinder, MetaPhinder, Kraken 2, Phybrid, and a BLAST search using identified proteins from the Earth Virome Pipeline to identify viral contiguous sequences (contigs) across simulated metagenomes with different read distributions, taxonomic compositions, and complexities.

Results
Of the tools tested in this study, VirSorter achieved the best F1 score while Vibrant had the highest average F1 score at predicting integrated prophages. Though less balanced in its precision and recall, Kraken2 had the highest average precision by a substantial margin. We introduced the machine learning tool, Phybrid, which demonstrated an improvement in average F1 score over tools such as MetaPhinder. The tool utilizes machine learning with both gene content and nucleotide features. The addition of nucleotide features improves the precision and recall compared to the gene content features alone.Viral identification by all tools was not impacted by underlying read distribution but did improve with contig length. Tool performance was inversely related to taxonomic complexity and varied by the phage host. For instance, Rhizobium and Enterococcus phages were identified consistently by the tools; whereas, Neisseria prophage sequences were commonly missed in this study.

Conclusion
This study benchmarked the performance of nine state-of-the-art bioinformatic tools to identify viral contigs across different simulation conditions. This study explored the ability of the tools to identify integrated prophage elements traditionally excluded from targeted sequencing approaches. Our comprehensive analysis of viral identification tools to assess their performance in a variety of situations provides valuable insights to viral researchers looking to mine viral elements from publicly available metagenomic data.
Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa
Authors: Kaech Heidi , Dennis Alice B. , Vorburger Christoph 
Published: June 2021

Abstract
Background
Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly.

Results
We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402.

Conclusions
Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host’s obligatory endosymbiont B. aphidicola.
Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development
Authors: Zhang Hengyou , Hu Zhenbin , Yang Yuming , Liu Xiaoqian , Lv Haiyan , Song Bao-Hua , An Yong-qiang Charles , Li Zhimin , Zhang Dan 
Published: June 2021

Abstract
Background
Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement.

Results
In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40 days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules.

Conclusions
Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.
Microscopy and chemical analyses reveal flavone-based woolly fibres extrude from micron-sized holes in glandular trichomes of Dionysia tapetodes
Authors: Bourdon Matthieu , Gaynord Josephine , Müller Karin H. , Evans Gareth , Wallis Simon , Aston Paul , Spring David R. , Wightman Raymond 
Published: June 2021

Abstract
Background
Dionysia tapetodes, a small cushion-forming mountainous evergreen in the Primulaceae, possesses a vast surface-covering of long silky fibres forming the characteristic “woolly” farina. This contrasts with some related Primula which instead form a fine powder. Farina is formed by specialized cellular factories, a type of glandular trichome, but the precise composition of the fibres and how it exits the cell is poorly understood. Here, using a combination of cell biology (electron and light microscopy) and analytical chemical techniques, we present the principal chemical components of the wool and its mechanism of exit from the glandular trichome.

Results
We show the woolly farina consists of micron-diameter fibres formed from a mixture of flavone and substituted flavone derivatives. This contrasts with the powdery farina, consisting almost entirely of flavone. The woolly farina in D. tapetodes is extruded through specific sites at the surface of the trichome’s glandular head cell, characterised by a small complete gap in the plasma membrane, cell wall and cuticle and forming a tight seal between the fibre and hole. The data is consistent with formation and thread elongation occurring from within the cell.

Conclusions
Our results suggest the composition of the D. tapetodes farina dictates its formation as wool rather than powder, consistent with a model of thread integrity relying on intermolecular H-bonding. Glandular trichomes produce multiple wool fibres by concentrating and maintaining their extrusion at specific sites at the cell cortex of the head cell. As the wool is extensive across the plant, there may be associated selection pressures attributed to living at high altitudes.
Minimising radiation exposure in catheter ablation of ventricular arrhythmias
Authors: Jan Matevž , Žižek David , Prolič Kalinšek Tine , Kuhelj Dimitrij , Trunk Primož , Kolar Tadeja , Kšela Juš , Rauber Martin , Yazici Mehmet 
Published: June 2021

Abstract
Background
Conventional fluoroscopy guided catheter ablation (CA) is an established treatment option for ventricular arrhythmias (VAs). However, with the complex nature of most procedures, patients and staff bare an increased radiation exposure. Near-zero or zero-fluoroscopy CA is an alternative method which could substantially reduce or even eliminate the radiation dose. Our aim was to analyse procedural outcomes with fluoroscopy minimising approach for treatment of VAs in patients with structurally normal hearts (SNH) and structural heart disease (SHD).

Methods
Fifty-two (age 53.4 ± 17.8 years, 38 male, 14 female) consecutive patients who underwent CA of VAs in our institution between May 2018 and December 2019 were included. Procedures were performed primarily with the aid of the three-dimensional electro-anatomical mapping system and intra-cardiac echocardiography. Fluoroscopy was considered only in left ventricular (LV) summit mapping for coronary angiography and when epicardial approach was planned. Acute and long-term procedural outcomes were analysed.

Results
Sixty CA procedures were performed. Twenty-five patients had SHD-related VAs (Group 1) and 27 patients had SNH (Group 2). While Group 1 had significantly higher total procedural time (256.9 ± 71.7 vs 123.6 ± 42.2 min; p < 0.001) compared to Group 2, overall procedural success rate [77.4% (24/31) vs 89.7% (26/29); p = 0.20)] and recurrence rate after the first procedure [8/25, (32%) vs 8/27, (29.6%); p = 0.85] were similar in both groups. Fluoroscopy was used in 3 procedures in Group 1 where epicardial approach was needed and in 4 procedures in Group 2 where LV summit VAs were ablated. Overall procedure-related major complication rate was 5%.

Conclusions
Fluoroscopy minimising approach for CA of VAs is feasible and safe in patients with SHD and SNH. Fluoroscopy could not be completely abolished in VAs with epicardial and LV summit substrate location.