bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution
Authors: Jones Christopher T , Youssef Noor , Susko Edward , Bielawski Joseph P 
Published: November 2019

AbstractA central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega &gt; 1$. As it is becoming increasingly clear that $\omega &gt; 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]
Effect of fluoroscopically guided corticosteroid injection versus oral nonsteroidal anti-inflammatory drugs for treatment of coccydynia: A randomized, controlled, single-blind study
Authors: Safari Mir Bahram , Tabrizi Ali , Hassani Ebrahim , Nabiyi Farnood , Mohammadi Sedra , Dindarian Sina 
Published: November 2019

Background:
Coccydynia is a major cause of coccyx pain that can result in chronic pain as well as reduced functional performance in patients. The aim of this study was to compare the efficacy of fluoroscopically guided corticosteroid injection with an oral nonsteroidal anti-inflammatory drug (NSAID) to relieve coccyx pain.

Methods:
In a clinical trial study, 28 patients with coccydynia who were randomly divided into two groups and matched based on sex, age, and body mass index. One group was treated with celecoxib 200 mg (every 12 hr) for 1 mo along with regular use of a tailbone pillow while sitting on hard surfaces. The second group received local periarticular injection of methylprednisolone acetate 40 mg along with lidocaine 1%, which was fluoroscopically guided. The patients were followed for 4 mo.

Results:
There was a significant difference in pain severity of the patients when compared with their condition at the beginning of the study in each group (P<0.001). The final pain severity of NSAID group and steroid group was 37.9±14.2 mm and 38.7±16.1 mm, respectively, which was not significantly different. Also the trend of pain severity was similar between the two groups.

Conclusions:
Corticosteroid injection for coccydynia treatment at least has the same advantages of oral NSAID medication. Regarding its single-dose administration and reasonable price, it can be considered as an alternative modality in treatment of this disease if the target patient is selected correctly.

Level of Evidence:
Level I.
Perineural Invasion as a Clue to Malignant Behavior in a Dermatofibroma
Authors: Santos-Briz Angel , García-Gavín Juan , Pastushenko Ievgenia , Sayagués José María , Rodríguez-Peralto José Luis , Requena Luis 
Published: November 2019

Abstract:
Dermatofibroma (DF) represents one of the most common mesenchymal proliferations of the skin. Their recurrence rate, even when incompletely excised, is very low, whereas the atypical, aneurysmal, and cellular variants have recurrence rates of up to 20% each. Extraordinary rare malignant lesions with metastases to lymph nodes and/or lung have been described. We report a 64-year-old woman with a long history (years) of a skin lesion on her right arm that became painful during the last months. Histologically, it consisted of a conventional cellular DF in which perineural invasion was present. Subsequently, the lesion showed a clinically aggressive course with recurrences, sarcomatous transformation, and pulmonary metastases. Given that no predictive morphological features have been identified to separate classical benign DF from rare metastasizing forms, perineural invasion in an otherwise conventional DF could be a histopathologic clue for an adverse prognosis and should provoke a closer clinical follow-up.
A Comparison of Fat Graft Processing Techniques: Outcomes in 1,158 Procedures in Prosthetic Breast Reconstructions
Authors: Chiu Wen-Kuan , Fracol Megan , Feld Lauren N. , Qiu Cecil S. , Kim John Y.S. 
Published: November 2019

Background:
As fat grafting in breast reconstruction evolves, questions of technique and outcomes persist. We compared 2 common fat processing techniques—decantation (DEC) versus closed wash and filtration (CWF)—with regard to outcomes and efficacy.

Methods:
Chart review of a single surgeon experience with breast fat grafting was performed. Data extracted included demographics, technique, complications, graft volume, and revision rates. Secondarily, the timeline of complication profiles was analyzed. Lastly, subgroup analysis of radiated versus nonradiated breast outcomes was performed.

Results:
One thousand one hundred fifty-eight fat grafting procedures were performed on 775 breasts (654 DEC, 504 CWF). Time-to-event analysis for all complications showed no difference between groups. Independent risk factors for fat necrosis included DEC technique, body mass index >30 kg/m2, and fat injection >75 mL. The majority of cases of fat necrosis, cyst/nodule formation, ultrasounds, and biopsies occurred more than 6 months after grafting. Average graft volume was lower in DEC compared with CWF breasts (50.6 versus 105.0 mL, P < 0.01), and more DEC breasts required repeat fat grafting procedures (39.9% versus 29.6%, P < 0.01). Radiated breasts received larger fat graft volume (89.9 versus 72.4 mL, P < 0.01) and required more fat graft procedures (average 1.62 versus 1.47, P < 0.01).

Conclusions:
This study represents the largest series of breast reconstruction fat grafting to date. DEC harvest technique may be a risk factor for fat necrosis, which results in less fat injection and greater need for repeat procedures. Similarly, radiated breasts require larger graft volume and more repeat procedures.
A novel surgical predictive model for Chinese Crohn's disease patients
Authors: Dong Yuan , Xu Li , Fan Yihong , Xiang Ping , Gao Xuning , Chen Yong , Zhang Wenyu , Ge Qiongxiang 
Published: November 2019

Abstract
Due to the complexity of Crohn's disease (CD), it is difficult to predict disease course with a single stratification factor or biomarker. A logistic regression (LR) model has been proposed by Guizzetti et al to stratify patients with CD-related surgical risk, which could help decision-making on disease treatment. However, there are no reports on relevant studies on Chinese population. The aim of the study is to present and validate a novel surgical predictive model to facilitate therapeutic decision-making for Chinese CD patients. Data was extracted from retrospective full-mode electronic medical records, which contained 239 CD patients and 1524 instances. Two sub-datasets were generated according to different attribute selection strategies, both of which were split into training and testing sets randomly. The imbalanced data in the training sets was addressed by synthetic minority over-sampling technique (SMOTE) algorithm before model development. Seven predictive models were employed using 5 popular machine learning algorithms: random forest (RF), LR, support vector machine (SVM), decision tree (DT) and artificial neural networks (ANN). The performance of each model was evaluated by accuracy, precision, F1-score, true negative (TN) rate, and the area under the receiver operating characteristic curve (AuROC). The result revealed that RF outperformed all other baseline models on both sub-datasets. The 10 leading risk factors for CD-related surgery returned from RF for attribute ranking were changes of radiology, presence of a fistula, presence of an abscess, no infliximab use, enteroscopy findings, C-reactive protein, abdominal pain, white blood cells, erythrocyte sedimentation rate and platelet count. The proposed machine learning model can accurately predict the risk of surgical intervention in Chinese CD patients, which could be used to tailor and modify the treatment strategies for CD patients in clinical practice.
The efficacy of dexketoprofen for migraine attack
Authors: Yang Baohua , Xu Zhili , Chen Linglong , Chen Xinguo , Xie Yuequn 
Published: November 2019

Abstract

Background:
The efficacy of dexketoprofen for migraine attack remains controversial. We conduct a systematic review and meta-analysis to explore the influence of dexketoprofen supplementation versus placebo on pain control in migraine attack patients.

Methods:
We search PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases through March 2019 for randomized controlled trials (RCTs) assessing the effect of dexketoprofen supplementation versus placebo on pain control for migraine attack patients. This meta-analysis is performed using the random-effect model.

Results:
Five RCTs involving 794 patients are included in the meta-analysis. Overall, compared with control group for migraine attack, dexketoprofen supplementation is associated with substantially increased pain free at 2 hours (RR = 1.90; 95% CI = 1.43–2.53; P < .0001), pain free at 48 hours (RR = 1.63; 95% CI = 1.07–2.49; P = .02), good or excellent treatment (RR = 1.48; 95% CI = 1.24–1.78; P < .0001) and pain relief at 2 hours (RR = 1.80; 95% CI = 1.17–2.77; P = .007), as well as reduced need for rescue drug (RR = 0.64; 95% CI = 0.43–0.94; P = .02), with no significant increase in adverse events (RR = 1.51; 95% CI = 0.87–2.62; P = .14).

Conclusion:
Dexketoprofen supplementation benefits to improve pain control at 48 hours and reduce the need for rescue drug in migraine attack patients.
Nursing care in anti-N-methyl-d-aspartate receptor encephalitis
Authors: Yang Li , Jiang Qian , Guan Hongzhi , Bo Haixin 
Published: November 2019

Abstract
Anti-N-methyl-d-aspartate receptor (anti-NMDAR) encephalitis is a paraneoplastic limbic encephalitis, recently identified.
To summarize our experience in the nursing care of patients with anti-NMDAR encephalitis managed with surgery and pharmacotherapy.
This study included 45 patients treated between July 2015 and November 2016. Laparoscopic oophorocystectomy was performed in 11 female patients with teratomas. Eleven patients required tracheal intubation or tracheotomy and ventilation.
The patients were hospitalized for an average of 25.2 days. The mental and neurological symptoms were significantly relieved 23.6 ± 4.8 days after surgery or immunotherapy. Near-normal function was restored in 11 patients, while 34 patients had varying degrees of dysfunction at discharge. After follow-up of 1 to 18 months, 24 patients were found to have permanent impairments.
Appropriate symptomatic nursing care is required to ensure the safety of patients with anti-NMDAR encephalitis.
Repair of a defect in the cervical trachea with thyroid-pericardium flap
Authors: Xie Hui , Zhang Yuqian , Yu Fenglei , Wang Xiang 
Published: November 2019

Abstract

Rationale:
Primary end-to-end anastomosis is common in adult trachea resection. Nevertheless, considering that the utilization of grafts is still essential for restoring defect in long-segment tracheal resection surgery, long-segment tracheal resection and reconstruction still remain challenging. Herein we present a novel case in which we resected a large tracheal mass and reconstructed the long-segment defect through using a thyroid-pericardium flap, which has not been reported yet.

Patient concerns:
A 35-year old male patient was admitted due to ‘Repeated dry cough for 2 years, shortness of breath after activities for 1 month’. Patient had no other obvious symptoms.

Diagnoses:
CT revealed that a large neoplasm was located in the cervical trachea and the pedicle was in the tracheal membrane, with total length of approximately 6 cm. Positron emission tomography computed tomography demonstrated an abnormally elevated levels of glucose metabolism in the upper part of the posterior tracheal wall. Therefore, this lesion was primarily considered as a malignancy.

Interventions:
The patient was performed by a primary resection of long-segment tracheal mass followed by thyroid-pericardium composite tissue flap for reconstruction.

Outcome:
The operation was successful, without hydrops or pneumatosis in the mediastinum. One week postoperatively, CT showed that there was no pneumomediastinum and mediastinal abscess. Three weeks postoperatively, fiber bronchoscope showed the flap with normal color and the unobstructed tracheal cavity. The patient healed without complication.

Lessons:
The thyroid-pericardium flap is a convenient, secure, and effective material for long-segment trachea mass resection and reconstruction.
Predictors affecting anterolateral thigh flap in reconstruction of upper extremity
Authors: Li Di , Long Feng , Lei Ming 
Published: November 2019

Abstract
Our study is aim to explore predictors for failure of anterolateral thigh (ALT) flap in the reconstruction of upper extremity.
We performed a retrospective study for 509 patients who underwent ALT flap in the reconstruction of upper extremity. Among them, 27 patients suffered from necrosis of ALT flap (necrosis group, NG) and 482 gained survival of this flap (survival group, SG). We collected possible factors including 3 aspects: demographic variables – age, sex, body mass index (BMI), history of hypertension, diabetes, heart disease, smoking and alcohol, trauma mechanism, and postmenopausal; surgical-related variables – surgical duration, blood loss, number of reconstructed veins, flap size, perforator type, diameter of perforator, and vein graft; blooding variables – hemoglobin, D-dimer, white blood cell, red blood cell, and platelet count (PLT). We compared the above data between NG and SG by univariate, multivariate, and Kaplan–Meier method coupled with a log-rank test linear regression analysis.
The survival incidence of ALT flap repairing upper extremity was 94.7% (482 of 509). The outcome of univariate analysis showed that age (53.5 ± 9.2), BMI (26.7 ± 4.5), larger flap size (24.3∗9.2), D-dimer (0.58 ± 0.10), and PLT (278.1 ± 34.4) in NG were significantly higher than these (44.2 ± 7.9, 22.3 ± 4.2, 19.1∗7.9, 0.48 ± 0.08, 236.6 ± 30.5) in SG. However, diameter of perforator (1.07 ± 0.02) in NG was markedly smaller than that (1.12 ± 0.02) in SG. Additionally, female patients, postmenopausal, patients with using venous stapler or 1 reconstructed vein had a higher failure rate. Multivariate and Kaplan–Meier method implied the same results.
In summary, many factors were related with failure of ALT in the reconstruction of upper extremity. Postmenopausal, D-dimer, and PLT were the first considered as risk factors for ALT flap repairing upper extremity.
Neuropathic painful complications due to endopelvic nerve lesions after robot-assisted laparoscopic prostatectomy
Authors: Cascella Marco , Quarto Giuseppe , Grimaldi Giovanni , Izzo Alessandro , Muscariello Raffaele , Castaldo Luigi , Di Caprio Barbara , Bimonte Sabrina , Del Prete Paola , Cuomo Arturo , Perdonà Sisto 
Published: November 2019

Abstract

Rationale:
Robot-assisted laparoscopic prostatectomy (RALP) is the most frequent strategy used for the surgical remedy of patients with localized prostate cancer. Although there is awareness about potential patient positioning nerve injuries, iatrogenic nerve lesions are less described in the literature. Here, we report 3 cases of patients who presented with neuropathic painful complications due to RALP-associated nerve lesions.

Patient concerns:
A 62-year-old patient (case 1), a 72-year-old male (case 2), and a 57-year-old patient (case 3) presented at the clinic with symptoms of neuropathic pain after RALP surgery.

Diagnosis:
Patients were diagnosed with a potential injury of different branches of the pudendal nerve (cases 1 and 2), and left obturator nerve (case 3).

Interventions:
Patients underwent multimodal pharmacologic treatment through pregabalin, weak opioids, strong opioid, paracetamol, and adjuvants. In cases 2 and 3, a multidisciplinary approach was needed. As the patients responded to conservative treatment, invasive approaches were not necessary.

Outcomes:
After treatment, the patients of case 1 showed pain relief after 4 days, paresthesia resolved in 15 days, whereas the anal crushing sensation lasted for approximately 1 month. In case 2, after 4 weeks of treatment, the patient experienced a considerable decrement in pain intensity with complete response after 4 months. In case 3, pain relief was achieved after 2 days, motor symptoms recovery after 2 weeks, and neuropathic features resolved completely after 5 weeks although the obturator sign resolved within 2 months.

Lessons:
The RALP-associated neurologic injuries may occur even when performed by highly experienced surgeons. A better understanding of the potential iatrogenic nerve lesions can surely allow an improvement in the surgical technique. A multidisciplinary approach and early multimodal pain strategy are mandatory for managing these complications.
Prognostic significance of KIF2A and KIF20A expression in human cancer
Authors: Li Xing , Shu Kunpeng , Wang Zhifeng , Ding Degang 
Published: November 2019

Abstract

Background:
The kinesin family (KIF) is reported to be aberrantly expressed and significantly correlated with survival outcomes in patients with various cancers. This meta-analysis was carried out to quantitatively evaluate the prognostic values of partial KIF members in cancer patients.

Methods:
Two well-known KIF members, KIF2A and KIF20A, were investigated to evaluate their potential values as novel prognostic biomarkers in human cancer. A comprehensive literature search was carried out of the PubMed, EMBASE, Cochrane Library, and Web of Science databases up to April 2019. Pooled hazard ratios (HRs) and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the association of KIF2A and KIF20A expression with overall survival (OS) and clinicopathological parameters.

Results:
Twenty-five studies involving 7262 patients were finally incorporated, including nine about KIF2A and sixteen about KIF20A. Our results indicated that patients with high expression of KIF2 and KIF20A tended to have shorter OS than those with low expression (HR = 2.23, 95% CI = 1.87–2.65, P < .001; HR = 1.77, 95% CI = 1.57–1.99, P < .001, respectively). Moreover, high expression of these 2 KIF members was significantly associated with advanced clinical stage (OR = 1.98, 95% CI: 1.57–2.50, P < .001; OR = 2.63, 95% CI: 2.03–3.41, P < .001, respectively), positive lymph node metastasis (OR = 2.32, 95% CI: 1.65–3.27, P < .001; OR = 2.13, 95% CI: 1.59–2.83, P < .001, respectively), and distant metastasis (OR = 2.20, 95% CI: 1.21–3.99, P = .010; OR = 5.25, 95% CI: 2.82–9.77, P < .001, respectively); only high KIF20A expression was related to poor differentiation grade (OR = 1.82, 95% CI: 1.09–3.07, P = .023).

Conclusions:
High expression of KIF2 and KIF20A in human cancer was significantly correlated with worse prognosis and unfavorable clinicopathological features, suggesting that these 2 KIF members can be used as prognostic biomarkers for different types of tumors. PROSPERO REGISTRATION NUMBER: CRD42019134928.
Pediatric CNS Tumor Patients Have Significantly Lower Requirement of Tissue Plasminogen Activator for Episodes of Central Venous Catheter Dysfunction Compared With Other Pediatric Oncology Patients: Results of a Population-based Cohort Study
Authors: Howie Chelsea , Crooks Bruce , Moorehead Paul , Kulkarni Ketan 
Published: November 2019

Purpose:
Central venous catheters (CVCs) are an important component of care delivery in pediatric oncology patients. However, CVC dysfunction is a common problem. Tissue plasminogen activator (tPA) is often administered to re-establish function, however, specific experience in pediatric patients with central nervous system (CNS) tumors is lacking. The goal of this study was to investigate the CVC experience and use of tPA for episodes of CVC dysfunction in pediatric patients with CNS tumors in comparison with other patients.

Methods:
Medical records of all pediatric oncology patients from the 4 Atlantic provinces in Canada (Nova Scotia, New Brunswick, Prince Edward Island, and Newfoundland and Labrador) were reviewed. Data collected included demographics, treatment, details of CVCs along with CVC dysfunction, and tPA use.

Results:
The cohort consisted of 1152 pediatric oncology patients, 222 (19.3%) of whom had CNS tumors. CVC dysfunction requiring tPA administration occurred in 12 (5.4%) of patients with CNS tumors compared with 182 (19.6%) of patients with non-CNS tumors (P=0.0001). Multivariate logistic regression analysis showed that administration of tPA for CVC dysfunction was 2.5 times more likely in patients with non-CNS tumors than those with CNS tumors (P=0.012; 95% confidence interval, 1.3-4.9).

Conclusions:
Our study showed that pediatric patients with CNS tumors require significantly less frequent administration of tPA for episodes of CVC dysfunction than patients with non-CNS tumors after adjusting for confounding factors. Hypotheses for this include: potential biologic differences of tumors, the role of the blood-brain barrier, or systematic differences in intensity of treatments.