bluuebunny/crossref_metadata_2025_split huggingface dataset:
Critical Evaluation of the Methodologic Quality of the Top 50 Cited Articles Relating to Knee Dislocation and Multiligamentous Knee Injury
Authors: Hankins David A. , Fletcher Ian E. , Prieto Fermin , Ockuly Andrew C. , Myers Orrin B. , Treme Gehron P. , Veitch Andrew J. , Wascher Daniel C. , Schenck Robert C. , Richter Dustin L. 
Published: November 2019

Background: Many studies have evaluated the management of knee dislocations (KDs) and multiligamentous knee injuries (MLKIs). However, no study to date has analyzed the quality of the most cited articles in this literature. Hypothesis: There is a positive correlation between the number of article citations in the KD and MLKI literature and their methodologic quality. Study Design: Systematic review. Methods: The Web of Science online database was searched to identify the top 50 cited articles in KD and MLKI care. Demographic data were recorded for each study. The Modified Coleman Methodology Score (MCMS) and the Methodological Index for Non-randomized Studies (MINORS) were used to analyze the methodological quality of each article. Spearman correlation coefficients ( r s) were then calculated. Results: The articles identified were published between 1958 and 2015 in a wide variety of peer-reviewed journals (n = 16). The majority of study level of evidence (LOE) was of low quality (level 5, 16%; level 4, 54%; level 3, 16%; level 2, 14%). There were no studies of level 1 evidence. The mean MCMS and MINORS scores were 29.0 (SD, 19.1; range, 3-72) and 6.1 (SD, 3.7; range, 0-14), respectively. No significant correlation was identified between the number of citations and the publication year, LOE, MCMS, or MINORS ( r s = 0.123 [ P = .396]; r s = 0.125 [ P = .389]; r s = 0.182 [ P = .204]; and r s = 0.175 [ P = .224], respectively). Positive correlations were observed between improved MCMS and MINORS scores and more recent year of publication ( r s = 0.43 [ P = .002]; r s = 0.32 [ P = .022]) as well as improved study LOE ( r s = 0.65 [ P < .001]; r s = 0.67 [ P < .001]). Conclusion: The top 50 cited articles on KD and MLKI care consisted of low LOE and methodological quality, with no existing level 1 articles. There was no significant correlation between the number of citations and publication year, LOE, or study methodological quality. Positive correlations were observed between later publication date and improved methodological quality.
Medial Femoral Condyle Free Flap Reconstruction of Complex Foot and Ankle Pathology
Authors: Stranix John T. , Piper Merisa L. , Azoury Said C. , Kozak Geoffrey , Ben-Amotz Oded , Wapner Keith L. , Levin L. Scott 
Published: November 2019

Background: Complex hindfoot pathology may benefit from vascularized bone flap reconstruction rather than traditional bone grafting techniques. Medial femoral condyle (MFC) flaps provide vascularized periosteum, skin, and corticocancellous bone. Methods: A retrospective, single-institution cohort study of consecutive MFC flaps performed for complicated hindfoot reconstruction between 2013 and 2019 was reviewed. Radiologic follow-up assessed osseous union and clinical outcomes were evaluated with the American Orthopaedic Foot & Ankle Society (AOFAS) hindfoot score. Thirty MFC flaps were performed in 28 patients for complex hindfoot pathology. Twenty-seven flaps had adequate clinical and radiographic follow-up (mean 15.8 months). Results: The majority presented with avascular necrosis (83%) and failed prior operations (67%, mean 3.1). Most hindfoot procedures involved arthrodesis (n = 24, 80%); tibiotalocalcaneal (n = 11) and talonavicular (n = 7) most frequently. Mean osseous flap volume was 10.3 cm3 (range 1.7-18.4 cm3); one flap required takeback for venous congestion but no total flap losses occurred. Primary osseous union was initially achieved in 20 patients (74%, mean 217 days). Six flaps developed interface nonunion; 5 underwent revision arthrodesis and ultimately achieved union in 24/27 flaps (89%, mean 271 days). Risk factors for nonunion were body mass index (BMI) >30 ( P = .017) and prior arthrodesis ( P = .042). Mean AOFAS hindfoot scores increased significantly from 52.3 preoperatively to 70.7 postoperatively ( P < .001). Subscore analysis demonstrated significant improvement in postoperative pain scores from 14.2 to 27.3 out of 40 ( P < .001). Conclusion: The MFC free flap provided vascularized bone for complicated foot and ankle reconstruction with relatively low donor site morbidity, promising osseous union results, and improved functional outcomes. Level of Evidence: Level IV, retrospective case series.
Anatomy of the Distal End of Flexor Digitorum Longus Tendon and Percutaneous Release Technique: A Cadaveric Study
Authors: Wei Baofu , Yao Ruoyu , Amendola Annunziato 
Published: November 2019

Background: The transfer of flexor-to-extensor is widely used to correct lesser toe deformity and joint instability. The flexor digitorum longus tendon (FDLT) is percutaneously transected at the distal end and then routed dorsally to the proximal phalanx. The transected tendon must have enough mobility and length for the transfer. The purpose of this study was to dissect the distal end of FDLT and identify the optimal technique to percutaneously release FDLT. Methods: Eight fresh adult forefoot specimens were dissected to describe the relationship between the tendon and the neurovascular bundle and measure the width and length of the distal end of FDLT. Another 7 specimens were used to create the percutaneous release model and test the strength required to pull out FDLT proximally. The tendons were randomly released at the base of the distal phalanx (BDP), the space of the distal interphalangeal joint (SDIP), and the neck of the middle phalanx (NMP). Results: At the distal interphalangeal (DIP) joint, the neurovascular bundle begins to migrate toward the center of the toe and branches off toward the center of the toe belly. The distal end of FDLT can be divided into 3 parts: the distal phalanx part (DPP), the capsule part (CP), and the middle phalanx part (MPP). There was a significant difference in width and length among the 3 parts. The strength required to pull out FDLT proximally was about 168, 96, and 20 N, respectively, for BDP, SDIP, and NMP. Conclusion: The distal end of FDLT can be anatomically described at 3 locations: DPP, CP, and MPP. The tight vinculum brevis and the distal capsule are strong enough to resist proximal retraction. Percutaneous release at NMP can be performed safely and effectively. Clinical Relevance: Percutaneous release at NMP can be performed safely and effectively during flexor-to-extensor transfer.
Comparison of Time and Cost Savings Using Different Cost Methodologies for Patient-Specific Instrumentation vs Standard Referencing in Total Ankle Arthroplasty
Authors: Savage-Elliott Ian , Wu Victor J. , Wu Isabella , Heffernan John Timothy , Rodriguez Ramon 
Published: November 2019

Background: Patient-specific 3-D printing cutting blocks (PSI) have been used instead of traditional intramedullary cutting guides. We hypothesized that PSI would lead to significantly decreased operating room (OR) time and significant cost savings to our institution with noninferior radiographic outcomes and no difference in expected vs actual implant size when compared with standard referencing (SR). Methods: Patients who had undergone total ankle replacements at our institution from 2013 through 2016 were included in the study. Associations between demographic variables and postoperative alignment in the SR vs PSI group were calculated using the Wilcoxon rank-sum test and the intraclass correlation coefficient. The cost of the operation was calculated using both an institutionally based fixed cost of OR time and using Time Driven Activity Based Cost (TDABC) accounting. A total of 43 patients were included in the study, 13 in the SR group and 30 in the PSI group. Results: Operative time (168 vs 137 minutes) and tourniquet time (123 vs 113 minutes) were significantly lower in the PSI vs the SR group. PSI predictions were accurate 100% of the time for tibial components and 83% of the time for talar components. Average costs of TAA using PSI were significantly reduced by $7597.00 when using traditional OR accounting, whereas PSI was $836.00 more expensive on average using TDABC accounting. Conclusion: Further research is needed to determine the cost-effectiveness of PSI vs SR in TAA; however, it does appear to save time intraoperatively. The long-term effect on clinical outcomes requires further study. Level of Evidence: Level III, case-control study.
iTRAQ-based quantitative proteomic analysis provides insight for molecular mechanism of neuroticism
Authors: Tian Lei , You Hong-Zhao , Wu Hao , Wei Yu , Zheng Min , He Lei , Liu Jin-Ying , Guo Shu-Zhen , Zhao Yan , Zhou Ren-Lai , Hu Xingang 
Published: November 2019

Abstract

Background
Neuroticism is a core personality trait and a major risk factor for several mental and physical diseases, particularly in females, who score higher on neuroticism than men, on average. However, a better understanding of the expression profiles of proteins in the circulating blood of different neurotic female populations may help elucidate the intrinsic mechanism of neurotic personality and aid prevention strategies on mental and physical diseases associated with neuroticism.

Methods
In our study, female subjects were screened for inclusion by the Eysenck Personality Questionnaire (EPQ), Beck Depression Inventory (BDI), Beck Anxiety Inventory (BAI) scales and routine physical examination. Subjects who passed the examination and volunteered to participate were grouped by neuroticism using EPQ scores (0 and 1 = low neuroticism group; > 5 = high neuroticism group). Proteins in serum samples of the two neuroticism groups were identified using isobaric tags for relative and absolute quantification (iTRAQ) technology.

Results
A total of 410 proteins exhibited significant differences between high and low neuroticism, 236 proteins were significantly upregulated and 174 proteins were significantly downregulated. Combine the results of GO and KEGG enrichment analysis of differences proteins between high and low neuroticism with the PPI network, it could be observed that the Alpha-synuclein (SNCA), ATP7A protein (ATP7A), Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (GNG2), cyclin-dependent kinase 6 (CDK6), myeloperoxidase (MPO), azurocidin (AZU1), Histone H2B type 1-H (HIST1H2BH), Integrin alpha-M (ITGAM) and Matrix metalloproteinase-9 (MMP9) might participate in the intrinsic mechanism of neuroticism by regulating response to catecholamine stimulus, catecholamine metabolic process, limbic system development and transcriptional misregulation in cancer pathway.

Conclusions
Our study revealed the characteristics of the neurotic personality proteome, which might be intrinsic mechanism of the neurotic population.
Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle
Authors: Jivanji Swati , Worth Gemma , Lopdell Thomas J. , Yeates Anna , Couldrey Christine , Reynolds Edwardo , Tiplady Kathryn , McNaughton Lorna , Johnson Thomas J. J. , Davis Stephen R. , Harris Bevin , Spelman Richard , Snell Russell G. , Garrick Dorian , Littlejohn Mathew D. 
Published: November 2019

AbstractBackgroundWhite spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein–Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein–Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date.ResultsUsing imputed whole-genome sequence data, we conducted a genome-wide association analysis in 2973 mixed-breed cows and bulls. Highly significant quantitative trait loci (QTL) were found on chromosomes 6 and 22, highlighting the well-established coat color genesKITandMITFas likely responsible for these effects. These results are in broad agreement with previous studies, although we also report a third significant QTL on chromosome 2 that appears to be novel. This signal maps immediately adjacent to thePAX3gene, which encodes a known transcription factor that controlsMITFexpression and is the causal locus for white spotting in horses. More detailed examination of these loci revealed a candidate causal mutation inPAX3(p.Thr424Met), and another candidate mutation (rs209784468) within a conserved element in intron 2 ofMITFtranscripts expressed in the skin. These analyses also revealed a mechanistic ambiguity at the chromosome 6 locus, where highly dispersed association signals suggested multiple or multiallelic QTL involvingKITand/or other genes in this region.ConclusionsOur findings extend those of previous studies that reportedKITas a likely causal gene for white spotting, and report novel associations between candidate causal mutations in both theMITFandPAX3genes. The sizes of the effects of these QTL are substantial, and could be used to select animals with darker, or conversely whiter, coats depending on the desired characteristics.
MiPepid: MicroPeptide identification tool using machine learning
Authors: Zhu Mengmeng , Gribskov Michael 
Published: November 2019

Abstract

Background
Micropeptides are small proteins with length < = 100 amino acids. Short open reading frames that could produces micropeptides were traditionally ignored due to technical difficulties, as few small peptides had been experimentally confirmed. In the past decade, a growing number of micropeptides have been shown to play significant roles in vital biological activities. Despite the increased amount of data, we still lack bioinformatics tools for specifically identifying micropeptides from DNA sequences. Indeed, most existing tools for classifying coding and noncoding ORFs were built on datasets in which “normal-sized” proteins were considered to be positives and short ORFs were generally considered to be noncoding. Since the functional and biophysical constraints on small peptides are likely to be different from those on “normal” proteins, methods for predicting short translated ORFs must be trained independently from those for longer proteins.

Results
In this study, we have developed MiPepid, a machine-learning tool specifically for the identification of micropeptides. We trained MiPepid using carefully cleaned data from existing databases and used logistic regression with 4-mer features. With only the sequence information of an ORF, MiPepid is able to predict whether it encodes a micropeptide with 96% accuracy on a blind dataset of high-confidence micropeptides, and to correctly classify newly discovered micropeptides not included in either the training or the blind test data. Compared with state-of-the-art coding potential prediction methods, MiPepid performs exceptionally well, as other methods incorrectly classify most bona fide micropeptides as noncoding. MiPepid is alignment-free and runs sufficiently fast for genome-scale analyses. It is easy to use and is available at https://github.com/MindAI/MiPepid.

Conclusions
MiPepid was developed to specifically predict micropeptides, a category of proteins with increasing significance, from DNA sequences. It shows evident advantages over existing coding potential prediction methods on micropeptide identification. It is ready to use and runs fast.
Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae
Authors: Solano-De la Cruz Marco Tulio , Adame-García Jacel , Gregorio-Jorge Josefat , Jiménez-Jacinto Verónica , Vega-Alvarado Leticia , Iglesias-Andreu Lourdes Georgina , Escobar-Hernández Esteban Elías , Luna-Rodríguez Mauricio 
Published: November 2019

AbstractBackgroundUpon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case ofVanilla planifoliaJacks., a worldwide economically important crop, it is susceptible toFusarium oxysporumf. sp.vanillae(Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection withFov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection.ResultsAnalysis of global gene expression profiles upon infection byFovindicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi.ConclusionsThe screening of transcriptional changes ofV. planifoliaJacks upon infection byFov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection byFov. Altogether, the results presented here highlight potential molecular players that might be further studied to improveFov-induced resistance in vanilla plants.
Bacteriological profile, risk factors and antimicrobial susceptibility patterns of symptomatic urinary tract infection among students of Mekelle University, northern Ethiopia
Authors: Gebremariam Guesh , Legese Haftom , Woldu Yemane , Araya Tadele , Hagos Kiflom , GebreyesusWasihun Araya 
Published: November 2019

Abstract

Background
Bacterial infection of the urinary tract is among the common reasons for seeking medical attention in the community. Rapidly increasing antibiotic resistance of uropathogens is resulting in limited treatment options. Therefore, knowledge of the current uropathogens and their antibiotic susceptibility is important for better treatment of urinary tract infection.

Methods
A cross-sectional study design was conducted from February to September thirty, 2017 among students who came to Mekelle University student’s clinics with symptomatic urinary tract infection during the study period.. Mid-stream urine specimens were collected from 341individuals with suspected urinary tract infection for bacteriological identification and antimicrobial susceptibility testing. Data on socio-demographic, clinical and risk factors were also collected using a structured questionnaire.

Results
Among the 341 study participants, 72(21.1%) showed significant bacteriuria. Escherichia coli (48.6%), Coagulase-negative staphylococci (23%), Staphylococcus aureus (13.5%), and Klebsiella spp. (8.1%) were common bacterial isolates. Resistance to ampicillin (81–100%), amoxicillin/clavulanic acid (77–93.6%), co- trimoxazole (55 72.3%), nalidixic acid (57.4%) and tetracycline (46–55.5%) was seen by most isolates. Multidrug resistance was observed in 73% of the bacterial isolates, and 25.5% of the Gram-negative isolates were extended-spectrum beta-lactamase producers. Being female, a history of urinary tract infection, a history of catheterization and frequent sexual activity were found to be statistically associated with urinary tract infection.

Conclusion
Urinary tract infection is a problem among university students with a prevalence of 21.1%. All isolates have developed resistance to most of the commonly used antibiotics. Therefore, health education on the transmission and causes of urinary tract infection are recommended for the students.
Triple negative breast cancer and platinum-based systemic treatment: a meta-analysis and systematic review
Authors: Pandy Jessa Gilda P. , Balolong-Garcia Joanmarie C. , Cruz-Ordinario Mel Valerie B. , Que Frances Victoria F. 
Published: November 2019

AbstractBackgroundTriple negative breast cancer (TNBC) represents 15–20% of breast cancers. Due to its heterogeneity and high rates of relapse, there is a need to optimize treatment efficacy. Platinum chemotherapy is still controversial and currently not recommended as first-line treatment for TNBC. Recent studies have shown promising activity of this regimen. This study was done to evaluate the effect of platinum chemotherapy on pathologic complete response (pCR) after neoadjuvant treatment for early TNBC and progression-free survival (PFS) in metastatic TNBC.MethodsA systematic search of Pubmed, Embase, Cochrane, Clinical trials databases and hand search were done to identify randomized controlled trials (RCTs) investigating the use of platinum-based chemotherapy in adults with TNBC. Studies were appraised using the Cochrane Collaboration tool. Using the random effects model, pooled Odds ratios (ORs) with 95% confidence intervals (CI) for pCR, and Hazard Ratios (HRs) with 95%CI for PFS were analyzed.ResultsEleven RCTs were included (N = 2946). Platinum-based chemotherapy showed pCR benefit of 40%vs27% (OR1.75,95% CI 1.46–2.62,p < 0.0001) in the neo-adjuvant setting. Subgroup analysis showed increased pCR rates (44.6%vs27.8%) with platinum plus taxane regimen (p < 0.0001). In metastatic TNBC, three RCTs were analyzed (N = 531), platinum treatment did not show PFS advantage (HR1.16,95%CI 0.90–1.49,p = 0.24).ConclusionPlatinum chemotherapy is associated with increased pCR rates in TNBC, hence it is a viable option for patients in the neoadjuvant setting. Subgroup analysis showed that the combination of platinum and taxanes (Carboplatin/Paclitaxel) improved pCR. However, no PFS advantage was seen in metastatic TNBC. Given the current conflicting data in metastatic TNBC, further exploration with additional powered studies is needed.