bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Surgical Timing on Clinical Outcomes in Anatomic Double-Bundle Anterior Cruciate Ligament Reconstruction Using Hamstring Tendon Autografts
Authors: Baba Rikiya , Kondo Eiji , Iwasaki Koji , Joutoku Zenta , Onodera Jun , Onodera Tomohiro , Yagi Tomonori , Iwasaki Norimasa , Yasuda Kazunori 
Published: November 2019

Background: To date, no studies have analyzed the influence on clinical outcomes of the interval between an anterior cruciate ligament (ACL) injury and double-bundle (DB) reconstruction with hamstring tendon autografts. Hypotheses: (1) Performing ACL reconstruction sooner after an injury will reduce postoperative anterior and rotatory knee instability, (2) postoperative range of knee motion or functional results will not be affected by different intervals between injury and surgery, and (3) preoperative isokinetic peak torque of the quadriceps and hamstring muscles will be lower in patients undergoing surgery earlier, while postoperative muscle strength will not be affected by surgery timing. Study Design: Cohort study; Level of evidence, 3. Methods: This study was conducted on a total of 171 patients who had undergone anatomic DB ACL reconstruction with hamstring tendon autografts. The patients were divided into 3 groups based on the time to surgery: (1) ≤1 month after the injury (group E; n = 25), (2) between 1 and 3 months after the injury (group M; n = 72), and (3) >3 months after the injury (group D; n = 74). Patients were assessed for a minimum of 2 years after surgery. Results: Concerning postoperative anterior laxity, 1-way analysis of variance demonstrated a significant difference ( P = .0274) among the 3 groups. Anterior laxity was significantly less in group E than in group D ( P = .0206). Spearman rank correlation analysis showed a significant correlation (ρ = 0.200; P = .0327) between anterior knee laxity and time to surgery. Also, a significant correlation ( P = .0461) was found between the degree of the pivot-shift phenomenon and time to surgery. There were no significant differences in loss of knee extension or flexion among the 3 groups, nor were there any differences in the Lysholm knee score or International Knee Documentation Committee grade. Postoperatively, there were no significant differences in peak torque of the quadriceps or hamstring muscles among the 3 groups. Conclusion: Early DB reconstruction led to significantly less anterior laxity compared with delayed reconstruction. There were no significant differences in postoperative range of knee motion or functional results among the 3 time intervals between injury and surgery in this study.
Students’ Perspectives of a Community-Based Medical Education Programme in a Rural District Hospital
Authors: Adefuye Anthonio , Benedict Matthew , Bezuidenhout Johan , Busari Jamiu O 
Published: November 2019

Background: The adoption of community-based medical education (CoBME) into the undergraduate medical curriculum is in line with the SPICE model for medical curriculum proposed by Harden and colleagues. Students are the consumers of medical education and are, thus, the ideal evaluators of the efficacy of their own course and learning environment. To evaluate the quality of the CoBME programme in Botshabelo District Hospital (BDH), this study investigated student’s perceptions of their experience during their CoBME training at BDH. In addition, suggestions on how to enrich students’ experience during the CoBME posting were obtained from the participants. Methods: This research was designed as a qualitative (ethnographic) study that used a structured questionnaire, to obtain written statements from 120 fourth-year undergraduate medical students describing their experience during their CoBME training at BDH. The structured questionnaire in the form of an evaluation form was self-administered, consisted of only open-ended questions grouped into 4 main sections and was distributed manually (hard copy) to the participants. Results: Of the 120 questionnaires distributed, 84 were returned, giving a response rate of 70.0%. When asked to indicate what they liked or disliked about their CoBME training, ‘Good educators/staff’ and the ‘Poor attitude of some doctors’ were the themes that scored highly (25.1% and 19.4%) in the ‘likes’ and ‘dislikes’ category, respectively. Some of the major challenges faced during the CoBME training at BDH included: exposure to new learning environment (14.2%), clinical practice context (12.6%), and language barrier (7.2%). Participants stated that they gained knowledge of how to perform certain clinical procedures and acquired core clinical skills in the areas of formulating management and managing some medical emergencies during their training at BDH. Increasing the duration of training (25.6% coverage) was suggested as a major way to enrich students’ experience during the training at BDH. Conclusion: Findings by this study reveal that CoBME is a valuable pedagogical tool to enhance learning in undergraduate medical education and that more work is required to improve the quality of CoBME training in BDH. We believe that the findings by this study will inform future planning of CoBME training programmes in BDH.
A Metabolic Study of a Patient with Idiopathic Cyclical Thrombocytopenic Purpura
Authors: SKOOG WILLIAM A. , LAWRENCE JOHN S. , ADAMS WILLIAM S. 
Published: November 2019

Abstract
A woman with a history of thrombocytopenic purpura occurring approximately every twenty-eight days was studied extensively on the Metabolic Research Ward. The patient had been treated previously with splenectomy and hystero-oophorectomy without improvement. The cyclical nature of her thrombocytopenia was documented by repeated hematologic observations. Endocrinologic studies demonstrated no evidence of ovarian activity or cyclical variations in adrenal activity. Urinary gonadotropins (FSH) fell coincident with the fall in platelets and suggest that cyclical pituitary function might be related in some way. The exact etiologic mechanisms, however, were not disclosed by this study.
EBUS-TBNA in the rapid microbiological diagnosis of drug-resistant mediastinal tuberculous lymphadenopathy
Authors: Chhajed Prashant N. , Vaidya Preyas J. , Mandovra Neha P. , Chavhan Vinod B. , Lele Tejashree T. , Nair Rekha , Leuppi Jörg D. , Saha Avinandan 
Published: November 2019

This study aimed to examine the use of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) in the rapid diagnosis of mediastinal tuberculous lymphadenitis and drug-resistant mediastinal tuberculous lymphadenitis.A diagnosis of TB was confirmed by a positive Xpert MTB/RIF test orMycobacterium tuberculosisculture. Rifampicin-resistant TB (RR-TB) or multidrug-resistant TB (MDR-TB) was diagnosed upon the detection of rifampicin resistance by Xpert MTB/RIF or resistance to rifampicin and isoniazid by phenotypic drug susceptibility testing (DST).Xpert MTB/RIF was positive in 43 of 56 patients (77%) and TB culture was positive in 31 of 56 patients (55%). Of these 56 patients, 25 (45%) were Xpert MTB/RIF positive and TB culture negative, 13 (23%) were Xpert MTB/RIF negative and TB culture positive, and 18 (32%) were Xpert MTB/RIF positive and TB culture positive. 11 patients (20%) had drug-resistant TB: seven with RR/MDR-TB, one with pre-extensively drug-resistant (XDR) TB, two with XDR-TB and one with isoniazid mono-resistance.An Xpert MTB/RIF assay carried out on EBUS-TBNA specimens provides rapid diagnosis of TB. Xpert MTB/RIF testing appears to have additional and more rapid sensitivity compared with culture alone. Culture-based DST provides an additional exclusive yield and the full resistance profile in addition to or instead of rifampicin resistance.
Plasma receptor tyrosine kinase RET in pulmonary arterial hypertension diagnosis and differentiation
Authors: Säleby Joanna , Bouzina Habib , Ahmed Salaheldin , Lundgren Jakob , Rådegran Göran 
Published: November 2019

BackgroundPulmonary arterial hypertension (PAH) is a serious disease exhibiting unspecific symptoms, as a result of which diagnosis is often delayed and prognosis is poor. The underlying pathophysiology includes vasoconstriction and remodelling of small pulmonary arteries. As receptor tyrosine kinases (RTKs) and their ligands have been shown to promote PAH remodelling, our aim was to evaluate if their plasma levels may be utilised to differentiate between various causes of pulmonary hypertension.Methods28 biomarkers involved in RTK signalling were measured using proximity extension assays in venous plasma from patients with PAH (n=48), chronic thromboembolic pulmonary hypertension (CTEPH) (n=20), pulmonary hypertension due to diastolic (n=33) or systolic (n=36) heart failure and heart failure patients without pulmonary hypertension (n=15), as well as healthy controls (n=20).ResultsPlasma proto-oncogene tyrosine-protein kinase receptor Ret (RET) was decreased (p<0.04) in PAH compared with all disease groups and controls. RET generated a sensitivity of 64.6% and a specificity of 81.6% for detecting PAH from other disease groups. PAH and the other pulmonary hypertension groups showed elevated plasma tyrosine-protein kinase MER (p<0.01), vascular endothelial growth factor (VEGF)-A (p<0.02), VEGF-D (p<0.01), placental growth factor (p<0.01), amphiregulin (p<0.02), hepatocyte growth factor (p<0.01) and transforming growth factor-α (p<0.05) and decreased VEGF receptor-2 (p<0.04) and epidermal growth factor receptor (p<0.01) levels compared with controls.ConclusionPlasma RET differentiates patients with PAH from those with CTEPH, systolic or diastolic heart failure with or without pulmonary hypertension as well as healthy controls. Future studies would be of value to determine the clinical usefulness of RET as a biomarker and its link to PAH pathophysiology.
omicplotR: visualizing omic datasets as compositions
Authors: Giguere Daniel J. , Macklaim Jean M. , Lieng Brandon Y. , Gloor Gregory B. 
Published: November 2019

Abstract
Background
Differential abundance analysis is widely used with high-throughput sequencing data to compare gene abundance or expression between groups of samples. Many software packages exist for this purpose, but each uses a unique set of statistical assumptions to solve problems on a case-by-case basis. These software packages are typically difficult to use for researchers without command-line skills, and software that does offer a graphical user interface do not use a compositionally valid method.

Results
omicplotR facilitates visual exploration of omic datasets for researchers with and without prior scripting knowledge. Reproducible visualizations include principal component analysis, hierarchical clustering, MA plots and effect plots. We demonstrate the functionality of omicplotR using a publicly available metatranscriptome dataset.

Conclusions
omicplotR provides a graphical user interface to explore sequence count data using generalizable compositional methods, facilitating visualization for investigators without command-line experience.
Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks
Authors: Mohsen Attayeb , Park Jonguk , Chen Yi-An , Kawashima Hitoshi , Mizuguchi Kenji 
Published: November 2019

AbstractBackgroundTo increase the accuracy of microbiome data analysis, solving the technical limitations of the existing sequencing machines is required. Quality trimming is suggested to reduce the effect of the progressive decrease in sequencing quality with the increased length of the sequenced library. In this study, we examined the effect of the trimming thresholds (0–20 for QIIME1 and 0–30 for QIIME2) on the number of reads that remained after the quality control and chimera removal (the good reads). We also examined the distance of the analysis results to the gold standard using simulated samples.ResultsQuality trimming increased the number of good reads and abundance measurement accuracy in Illumina paired-end reads of the V3-V4 hypervariable region.ConclusionsOur results suggest that the pre-analysis trimming step should be included before the application of QIIME1 or QIIME2.
Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum
Authors: Yang Qi , Liu Shibiao , Han Xiaoning , Ma Jingyi , Deng Wenhong , Wang Xiaodong , Guo Huihong , Xia Xinli 
Published: November 2019

Abstract
Background
Gynostemma pentaphyllum is an important perennial medicinal herb belonging to the family Cucurbitaceae. Aerial stem-to-rhizome transition before entering the winter is an adaptive regenerative strategy in G. pentaphyllum that enables it to survive during winter. However, the molecular regulation of aerial stem-to-rhizome transition is unknown in plants. Here, integrated transcriptome and miRNA analysis was conducted to investigate the regulatory network of stem-to-rhizome transition.

Results
Nine transcriptome libraries prepared from stem/rhizome samples collected at three stages of developmental stem-to-rhizome transition were sequenced and a total of 5428 differentially expressed genes (DEGs) were identified. DEGs associated with gravitropism, cell wall biosynthesis, photoperiod, hormone signaling, and carbohydrate metabolism were found to regulate stem-to-rhizome transition. Nine small RNA libraries were parallelly sequenced, and seven significantly differentially expressed miRNAs (DEMs) were identified, including four known and three novel miRNAs. The seven DEMs targeted 123 mRNAs, and six pairs of miRNA-target showed significantly opposite expression trends. The GpmiR166b-GpECH2 module involved in stem-to-rhizome transition probably promotes cell expansion by IBA-to-IAA conversion, and the GpmiR166e-GpSGT-like module probably protects IAA from degradation, thereby promoting rhizome formation. GpmiR156a was found to be involved in stem-to-rhizome transition by inhibiting the expression of GpSPL13A/GpSPL6, which are believed to negatively regulate vegetative phase transition. GpmiR156a and a novel miRNA Co.47071 co-repressed the expression of growth inhibitor GpRAV-like during stem-to-rhizome transition. These miRNAs and their targets were first reported to be involved in the formation of rhizomes. In this study, the expression patterns of DEGs, DEMs and their targets were further validated by quantitative real-time PCR, supporting the reliability of sequencing data.

Conclusions
Our study revealed a comprehensive molecular network regulating the transition of aerial stem to rhizome in G. pentaphyllum. These results broaden our understanding of developmental phase transitions in plants.
Identification of Bna.IAA7.C05 as allelic gene for dwarf mutant generated from tissue culture in oilseed rape
Authors: Cheng Hongtao , Jin Fenwei , Zaman Qamar U. , Ding Bingli , Hao Mengyu , Wang Yi , Huang Yi , Wells Rachel , Dong Yun , Hu Qiong 
Published: November 2019

AbstractBackgroundPlant height is one of the most important agronomic traits in many crops due to its influence on lodging resistance and yield performance. Although progress has been made in the use of dwarfing genes in crop improvement, identification of new dwarf germplasm is still of significant interest for breeding varieties with increased yield.ResultsHere we describe a dominant, dwarf mutant G7 ofBrassica napuswith down-curved leaves derived from tissue culture. To explore the genetic variation responsible for the dwarf phenotype, the mutant was crossed to a conventional line to develop a segregating F2population. Bulks were formed from plants with either dwarf or conventional plant height and subjected to high throughput sequencing analysis via mutation mapping (MutMap). The dwarf mutation was mapped to a 0.6 Mb interval ofB. napuschromosome C05. Candidate gene analysis revealed that one SNP causing an amino acid change in the domain II ofBna.IAA7.C05may contribute to the dwarf phenotype. This is consistent with the phenotype of a gain-of-functionindole-3-acetic acid(iaa) mutant inBna.IAA7.C05reported recently. GO and KEGG analysis of RNA-seq data revealed the down-regulation of auxin related genes, including many otherIAAandsmall up regulated response(SAUR) genes, in the dwarf mutant.ConclusionOur studies characterize a new allele ofBna.IAA7.C05responsible for the dwarf mutant generated from tissue culture. This may provide a valuable genetic resource for breeding for lodging resistance and compact plant stature inB. napus.
Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars
Authors: Moura Marianna O. , Fausto Anna Karoline S. , Fanelli Amanda , Guedes Fernanda A. de F. , Silva Tatiane da F. , Romanel Elisson , Vaslin Maite F. S. 
Published: November 2019

Abstract
Background
Dicer-like proteins (DCLs) are essential players in RNA-silencing mechanisms, acting in gene regulation via miRNAs and in antiviral protection in plants and have also been associated to other biotic and abiotic stresses. To the best of our knowledge, despite being identified in some crops, cotton DCLs haven’t been characterized until now. In this work, we characterized the DCLs of three cotton species and analyzed their expression profiles during biotic stress.

Results
As main results, 11 DCLs in the allotetraploid cotton Gossypium hirsutum, 7 and 6 in the diploid G. arboreum and G. raimondii, were identified, respectively. Among some DCLs duplications observed in these genomes, the presence of an extra DCL3 in the three cotton species were detected, which haven’t been found in others eudicots. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant defense against virus, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (FM966) and another resistant (DO) to polerovirus CLRDV infection, were analyzed. Both cvs. Responded differently to virus infection. At the inoculation site, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. A time course of DCL expression in aerial parts far from inoculation site along infection showed that DCL2b and DCL4 were repressed 24 h after infection in the susceptible cotton. As CLRDV is aphid-transmitted, herbivore attack was also checked. Opposite expression pattern of DCL2a and b and DCL4 was observed for R and S cottons, showing that aphid feeding alone may induce DCL modulation.

Conclusions
Almost all the DCLs of the allotetraploide G. hirsutum cotton were found in their relative diploids. Duplications of DCL2 and DCL3 were found in the three species. All four classes of DCL responded to aphid attack and virus infection in G. hirsutum. DCLs initial responses against the virus itself and/or herbivore attack may be contributing towards virus resistance.
Value of dual Doppler echocardiography for prediction of atrial fibrillation recurrence after radiofrequency catheter ablation
Authors: Chen Fengjiao , Sun Qinliang , Li Hairu , Qu Shaohui , Yu Weidong , Jiang Shuangquan , Tian Jiawei 
Published: November 2019

Abstract
Background
Increasing evidence has been presented which suggests that left ventricular (LV) diastolic dysfunction may play an important role in the development of atrial fibrillation (AF). However, the potential for LV diastolic dysfunction to serve as a predictor of AF recurrence after radiofrequency catheter ablation remains unresolved.

Methods
Dual Doppler and M-PW mode echocardiography were performed in 67 patients with AF before ablation and 47 patients with sinus rhythm. The parameters measured within identical cardiac cycles included, the time interval between the onset of early transmitral flow peak velocity (E) and that of early diastolic mitral annular velocity (e’) (TE-e’), the ratio of E to color M-mode Doppler flow propagation velocity (Vp)(E/Vp), the Tei index, the ratio of E and mitral annular septal (S) peak velocity in early diastolic E/e’(S) and the ratio of E and mitral annular lateral (L) peak velocity E/e’(L). A follow-up examination was performed 1 year after ablation and patients were divided into two groups based on the presence or absence of AF recurrence. Risk estimations for AF recurrence were performed using univariate and multivariate logistic regression.

Results
TE-e’, E/Vp, the Tei index, E/e’(S) and E/e’(L) were all increased in AF patients as compared with the control group (p <  0.05). At the one-year follow-up examination, a recurrence of AF was observed in 21/67 (31.34%) patients. TE-e’ and the Tei index within the recurrence group were significantly increased as compared to the group without recurrence (p <  0.001). Results from multivariate analysis revealed that TE-e’ can provide an independent predictor for AF recurrence (p = 0.001).

Conclusions
Dual Doppler echocardiography can provide an effective and accurate technique for evaluating LV diastolic function within AF patients. The TE-e’ obtained within identical cardiac cycles can serve as an independent predictor for the recurrence of AF as determined at 1 year after ablation.
The feasibility of web surveys for obtaining patient-reported outcomes from cancer survivors: a randomized experiment comparing survey modes and brochure enclosures
Authors: Millar Morgan M. , Elena Joanne W. , Gallicchio Lisa , Edwards Sandra L. , Carter Marjorie E. , Herget Kimberly A. , Sweeney Carol 
Published: November 2019

AbstractBackgroundCentral cancer registries are often used to survey population-based samples of cancer survivors. These surveys are typically administered via paper or telephone. In most populations, web surveys obtain much lower response rates than paper surveys. This study assessed the feasibility of web surveys for collecting patient-reported outcomes via a central cancer registry.MethodsPotential participants were sampled from Utah Cancer Registry records. Sample members were randomly assigned to receive a web or paper survey, and then randomized to either receive or not receive an informative brochure describing the cancer registry. We calculated adjusted risk ratios with 95% confidence intervals to compare response likelihood and the demographic profile of respondents across study arms.ResultsThe web survey response rate (43.2%) was lower than the paper survey (50.4%), but this difference was not statistically significant (adjusted risk ratio = 0.88, 95% confidence interval = 0.72, 1.07). The brochure also did not significantly influence the proportion responding (adjusted risk ratio = 1.03, 95% confidence interval = 0.85, 1.25). There were few differences in the demographic profiles of respondents across the survey modes. Older age increased likelihood of response to a paper questionnaire but not a web questionnaire.ConclusionsWeb surveys of cancer survivors are feasible without significantly influencing response rates, but providing a paper response option may be advisable particularly when surveying older individuals. Further examination of the varying effects of brochure enclosures across different survey modes is warranted.