bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy and safety of apatinib in treatment of osteosarcoma after failed standard multimodal therapy
Authors: Tian Zhichao , Gu Zhiyuan , Wang Xin , Liu Zhiyong , Yao Weitao , Wang Jiaqiang , Zhang Peng , Cai Qiqing , Ge Hong 
Published: May 2019

Abstract
Recently, apatinib has been shown to be effective in treating sarcoma. This study aimed to assess the safety and efficacy of apatinib in the treatment of patients with osteosarcoma after failed of standard multimodal therapy and to compare the therapeutic effects of apatinib on osteosarcoma between high-dose group and low-dose group.
A total of 27 patients with osteosarcoma who received apatinib between January 2016 and August 2017 were retrospectively reviewed. Among the 27 patients, the objective response rate (ORR) and the disease control rate (DCR) were 25.93% and 66.67%, respectively. The median of progression-free survival (m-PFS) was 3.5 months (95% confidence interval [CI], 2.5–4.8 months), and the median of overall survival (m-OS) was 9.5 months (95% CI, 7.8–10.5 months). There was no statistically significant difference in ORR (36.36% vs 18.75%), DCR (63.64% vs 68.75%), m-PFS (4.3 months [95% CI, 1.8–7 months) vs 3.35 months (95% CI, 1.8–4 months]), and m-OS (9.5 months [95% CI, 7.8–10.5 months] vs 9.4 months [95% CI, 7.8–10.8 months]) (P > .05) between the high-dose group (the average dose was 659 mg/qd) and the low-dose group (the average dose was 516 mg/qd). Most of the adverse events (AEs) were in grade 1 or grade 2. The main AEs in grade 3 were hypertension, rash, weight loss, hand-foot syndrome, and diarrhea.
Apatinib is safe and effective in the treatment of advanced osteosarcoma. We recommend that the initial dose of apatinib should be 500 mg/qd in the treatment of osteosarcoma.
Failure of 3 different methods and biopsy sites to diagnose a patient with invasive colorectal cancer
Authors: Kim Daniel Dongiu , Litow Kyle Joseph , Lumbra Thomas James , Masri Mohammad Milhim 
Published: May 2019

Abstract

Rationale:
Colorectal cancer is one of the most commonly diagnosed cancers worldwide, and the majority arise from neoplastic adenomatous polyps. Bladder involvement in colorectal cancer is uncommon and found in approximately 3% of the cases, most commonly in sigmoid and rectal tumors and the diagnosis is classically based on biopsies of affected tissues.

Patient concerns:
A 68-year-old male with no significant past medical history underwent diagnostic colonoscopy for abdominal distension and constipation with positive fecal occult blood test ordered by the primary care physician.

Diagnosis:
Colonoscopy showed a sigmoid mass with biopsy finding of tubulovillous adenoma. Laparoscopy was performed for sigmoid colonic resection, but as the mass was large, a diverting loop colostomy and multiple biopsies were performed revealing tubulovillous adenoma again. Postoperative workup revealed right hydronephrosis, and cystoscopy was performed confirming bladder wall invasion with biopsies showing benign bladder wall tissue with no evidence of dysplasia or malignancy. Furthermore, computed tomography (CT)-guided core-needle biopsies of the colonic mass were performed but revealed adenomatous colonic mucosa without evidence of carcinoma.

Intervention:
Definitive surgical en bloc excision of the tumor and anterior bladder wall was performed with urology team until grossly free margins were attained. Final pathology revealed well-differentiated mucinous adenocarcinoma arising from a preexisting tubulovillous adenoma with direct invasion of the bladder wall.

Outcomes:
The patient's postoperative recovery was uneventful, and he was discharged 2 weeks postoperatively with planned adjuvant chemotherapy.

Lessons:
This case represents a classical presentation of invasive colorectal cancer. Perioperative workup, however, was confounded by failure of open, cystoscopic, and CT-guided biopsies to establish a tissue diagnosis for directed therapy. Upon literature review, evidence exists to support our approach to this unique dilemma.
Proximal versus total gastrectomy for proximal early gastric cancer
Authors: Xu Yixin , Tan Yulin , Wang Yibo , Xi Cheng , Ye Nianyuan , Xu Xuezhong 
Published: May 2019

Abstract

Background:
Recently, the incidence of proximal early gastric cancer (EGC) has been rising rapidly. Prevalent surgical methods are proximal gastrectomy (PG) and total gastrectomy (TG); however, which method is superior remains controversial. We conducted a systematic review and meta-analysis of original articles to compare the short- and long-term clinical outcomes of PG with TG for proximal EGC.

Methods:
Databases, including PubMed, Embase, Web of Science, and Cochrane Library were searched up to October 2018. The Newcastle-Ottawa scale was utilized to conduct quality assessments, and publication bias was evaluated using Egger test. STATA version 14.0 was used to perform the meta-analysis.

Results:
A total of 2036 patients with proximal EGC in 18 studies were included in the meta-analysis. The results showed that PG was potentially superior to TG regarding operation time, intraoperative blood loss volume, and long-term nutritional status. Overall survival between the PG and TG groups was not significantly different. PG was associated with a high incidence of 2 kinds of postoperative complications: anastomotic stenosis and reflux esophagitis. However, the incidence of these complications associated with esophagojejunostomy with double-tract reconstruction (DTR) was comparable with that of TG.

Conclusions:
PG has several advantages over TG for the treatment of proximal EGC, including surgical outcomes and long-term nutritional status. However, anastomotic stenosis and reflux esophagitis frequently occurred in patients undergoing PG. Esophagojejunostomy with DTR could offer a solution to reducing the incidence of these complications.
Intravenous iron versus oral iron or observation for gastrointestinal malignancies: a systematic review
Authors: Tang Grace H. , Dhir Vinita , Scheer Adena S. , Tricco Andrea C. , Sholzberg Michelle , Brezden-Masley Christine 
Published: May 2019

Background
Anemia is a common condition in patients with gastrointestinal cancer. Current evidence for the use of intravenous compared with oral iron in this clinical setting is inconclusive. A systematic review was performed to assess evidence on the efficacy of intravenous iron versus oral/observation in gastrointestinal cancer patients in the preoperative and postoperative setting.

Materials and methods
We searched Medline and Embase from inception until December 2017 with no language restrictions. Outcomes included hemoglobin response, red blood cell transfusion, and adverse events. Screening, data abstraction, and risk of bias appraisal were performed by two independent reviewers. The risk of bias was assessed using the Cochrane tools for randomized and nonrandomized studies.

Results
A total of 10 studies (three randomized-controlled trials and seven nonrandomized studies) were included. Of the six preoperative studies, five reported that hemoglobin was significantly higher in the intravenous group compared with oral iron/observation. Among the four postoperative studies, three studies suggested that hemoglobin was significantly higher in the intravenous group compared with oral iron/observation. The overall risk of bias for all randomized-controlled trials was low. Quality assessments for nonrandomized studies found the risk of bias to be moderate for four studies and critical for three studies.

Conclusion
Despite the limitations of the current body of evidence, there is a likely benefit to the use of intravenous iron in this patient population. Further confirmatory research is needed to draw empirical conclusions.
Association of Maternal First-Trimester Ondansetron Use With Cardiac Malformations and Oral Clefts in Offspring
Authors: Huybrechts Krista F. , Hernández-Díaz Sonia , Straub Loreen , Gray Kathryn J. , Zhu Yanmin , Patorno Elisabetta , Desai Rishi J. , Mogun Helen , Bateman Brian T. 
Published: May 2019

(Abstracted from JAMA 2018;320(23):2429–2437)
Nausea and vomiting is common in pregnancy and is reported to occur in up to 80% of women. About one-third of women with nausea and vomiting during pregnancy have symptoms that are clinically significant, and a small percentage develop hyperemesis gravidarum, which is the most common indication for hospital admission during the first part of pregnancy.
Association of Brain-Derived Neurotrophic Factor With Cognitive Function: An Investigation of Sex Differences in Patients With Type 2 Diabetes
Authors: Zhen Yan-Feng , Liu Xing-Yu , Li Yu-Kai , Fang Hui , Cassidy Ryan M. , Zhang Xiang Yang 
Published: May 2019

ABSTRACT

Objective
Although a reduction in brain-derived neurotrophic factor (BDNF) has been implicated as a cause of cognitive impairment in type 2 diabetes mellitus (T2DM), the role of sex in moderating this effect has not been explored.

Methods
We compared the difference in serum BDNF and performance on the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) between 96 men and 134 women with T2DM. We compared this with the difference in serum BDNF and performance in the control group (104 men, 144 women).

Results
Patients with T2DM performed worse on most RBANS indices (η2 = 0.372, all p < .05); within T2DM patients, men performed worse than women on the delayed memory score (74.1 (12.1) versus 79.9 (11.5), p = .002) and on the total score (71.4 (11.5) versus 76.5 (10.8), p = .025). Serum BDNF was lower in patients with T2DM versus controls (7.5 (2.7) ng/ml versus 11.5 (2.7) ng/ml, p < .001), and in men compared with women (6.9 (2.4) versus 7.9 (2.8), p = .024). Serum BDNF levels positively correlated with delayed memory score in patients with T2DM (β = 0.19, p = .007). However, this association was only observed in women, not in men (p
interaction = 0.04). Among healthy controls, no sex differences were noted in either RBANS or BDNF levels (η2 = 0.04, Cohen's d < 0.163, all p > .05).

Conclusions
Our results show sex differences in poorer cognitive performance, lower BDNF concentration, and their relationship in T2DM patients, suggesting that female sex may be a protective factor for cognitive decline in T2DM patients. However, the findings should be regarded as preliminary because of the cross-sectional design and chronicity of the diabetes.
Associations Between Objective Sleep and Ambulatory Blood Pressure in a Community Sample
Authors: Doyle Caroline Y. , Ruiz John M. , Taylor Daniel J. , Smyth Joshua W. , Flores Melissa , Dietch Jessica R. , Ahn Chul , Allison Matthew , Smith Timothy W. , Uchino Bert N. 
Published: May 2019

ABSTRACTObjectiveEpidemiologic data increasingly support sleep as a determinant of cardiovascular disease risk. Fewer studies have investigated the mechanisms underlying this relationship using objective sleep assessment approaches. Therefore, the aim of this study was to examine associations between daily blood pressure (BP) and both objectively assessed sleep duration and efficiency.MethodsA diverse community sample of 300 men and women aged 21 to 70 years, enrolled in the North Texas Heart Study, participated in the study. Actigraphy-assessed sleep was monitored for two consecutive nights with ambulatory BP sampled randomly within 45-minute blocks on the first and second day as well as the second night.ResultsOverall, sleep duration results paralleled those of sleep efficiency. Individuals with lower sleep efficiency had higher daytime systolic (B= −0.35, SE = 0.11,p= .0018,R2= 0.26) but not diastolic BP (B= −0.043, SE = 0.068,p= .52,R2= 0.17) and higher nighttime BP (systolic:B= −0.37, SE = 0.10,p< .001,R2= .15; diastolic:B= −0.20, SE = 0.059,p< .001,R2= .14). Moreover, lower sleep efficiency on one night was associated with higher systolic (B= −0.51, SE = 0.11,p< .001,R2= 0.23) and diastolic BP (B= −0.17, SE = 0.065,p= .012,R2= .16) the following day. When "asleep" BP was taken into account instead of nighttime BP, the associations between sleep and BP disappeared. When both sleep duration and efficiency were assessed together, sleep efficiency was associated with daytime systolic BP, whereas sleep duration was associated with nighttime BP.ConclusionsLower sleep duration and efficiency are associated with higher daytime systolic BP and higher nighttime BP when assessed separately. When assessed together, sleep duration and efficiency diverge in their associations with BP at different times of day. These results warrant further investigation of these possible pathways to disease.
Computed Tomography Angiography and Magnetic Resonance Angiography of Congenital Anomalies of Pulmonary Veins
Authors: Abdel Razek Ahmed Abdel Khalek , Al-Marsafawy Hala , Elmansy Maha , El-Latif Mahmoud Abd , Sobh Donia 
Published: May 2019

Abstract
We aimed to review computed tomography and magnetic resonance angiography of congenital anomalies of pulmonary veins. Total anomalous pulmonary venous return shows all pulmonary veins drain abnormally in another site rather than left atrium. Imaging can detect anomalous veins either supracardiac, infracardiac, or mixed. Partial anomalous pulmonary venous return shows some pulmonary vein have abnormal drainage that well delineated with computed tomography angiography. Scimitar syndrome is a type of partial anomalous pulmonary venous return where the pulmonary veins of the right lung drain infracardiac and is associated with right lung hypoplasia and dextrocardia. Pseudoscimitar show anomalous vein that takes a tortuous course and drains into the left atrium producing a false-positive scimitar sign. Cor triatriatum shows septum divide left atrium with proximal chamber receives blood flow from the pulmonary veins. Levoatriocardinal vein is an anomalous connection between the left atrium and anomalous vein from systemic venous system that is embryo logically derived from the cardinal veins. Computed tomography angiography can detect pulmonary vein stenosis, atresia, hypoplasia, and varix. Imaging is important for intimal diagnosis and detects the anomalous vessels and its connection, presence of stenosis, and associated other congenital cardiac anomalies. Also, it is a great role in assessment of patients after surgery.
Long-Term Characterization of Cranial Defects After Surgical Correction for Single-Suture Craniosynostosis
Authors: Skolnick Gary B. , Murthy Sindhoora , Patel Kamlesh B. , Huang Zhiyang , Naidoo Sybill D. , Ju Tao , Smyth Matthew D. , Woo Albert S. 
Published: May 2019

Introduction
Craniosynostosis is typically corrected surgically within the first year of life through cranial vault reconstruction. These procedures often leave open calvarial defects at the time of surgery, which are anticipated to close over time in a large proportion of cases. However, residual calvarial defects may result as long-term sequelae from cranial vault remodeling. When larger defects are present, they may necessitate further reconstruction for closure.
Better understanding of the calvarial osseous healing process may help to identify which defects will resolve or shrink to acceptable size and which will require further surgery. Our study aims to assess the long-term changes in defect size after cranial vault reconstruction for craniosynostosis.

Methods
One-year postoperative and long-term computed tomography scans were retrieved from the craniofacial anomalies archive. Analysis used custom software. All defects above the size of 1 cm2 were analyzed and tracked for calvarial location, surface area, and circularity. Monte Carlo simulation was performed to model the effect of initial defect size on the rate of defect closure.

Results
We analyzed a total of 74 defects. The mean ± SD initial defect surface area was 3.27 ± 3.40 cm2. The mean ± SD final defect surface area was 1.71 ± 2.54 cm2. The mean ± SD percent decrease was 55.06% ± 28.99%. There was a significant difference in the percentage decrease of defects in the parietal and frontoparietal locations: 68.4% and 43.7%, respectively (P = 0.001). Monte Carlo simulation results suggest that less than 10% of defects above the size of 9 cm2 will close to the size of 2.5 cm2 or less.

Conclusions
We describe and make available a novel validated method of measuring cranial defects. We find that the large majority of initial defects greater than 9 cm2 remain at least 1 in2 in size (2.5 cm2) 1 year postoperatively. In addition, there appear to be regional differences in closure rates across the cranium, with frontoparietal defects closing more slowly than those in the parietal region. This information will aid surgeons in the decision-making process regarding cranioplasty after craniosynostosis correction.
Pressure Injury Prevention: Outcomes and Challenges to Use of Resident Monitoring Technology in a Nursing Home
Authors: Yap Tracey L. , Kennerly Susan M. , Ly Kao 
Published: May 2019

PURPOSE:
We examined the usability, user perceptions, and nursing occupational subculture associated with introduction of a patient monitoring system to facilitate nursing staff implementation of standard care for pressure ulcer/injury prevention in the nursing home setting.

DESIGN:
Mixed methods, pre-/posttest design.

SUBJECTS AND SETTING:
Resident (n = 44) and staff (n = 38) participants were recruited from a 120-bed nursing home in the Southeast United States.

METHODS:
Digital data on frequency and position of residents were transmitted wirelessly from sensors worn on each resident's anterior chest to estimate nursing staff compliance with repositioning standard of care before and after visual monitors were activated to cue staff. The validated Nursing Culture Assessment Tool was used to determine changes in nursing culture. Benefits and challenges of implementation were assessed by 2 focus groups composed of 8 and 5 female members of the nursing staff (RN, LPN, CNA), respectively, and led by the three authors. Descriptive statistics were used for all quantitative variables, and inferential statistics were applied to categorical variables (χ2 test or Fisher exact test) and continuous variables (analyses of variance or equivalent nonparametric tests), respectively, where a 2-sided P value of <.05 was considered statistically significant.

RESULTS:
System use significantly (P = .0003) improved compliance with every 2-hour repositioning standards. The nursing culture normative ranking percentage increased from 30.9% to 58.2%; this difference was not statistically significant. Focus groups expressed satisfaction with the monitoring system and recommended improvements to support adaptation and use of technology.

CONCLUSIONS:
Study findings support the usability of the patient monitoring system to facilitate repositioning. Implementation of multiple strategies for training, supplies, and communication may enhance uptake and effectiveness.
Impact of Pressure Injuries on Patient Outcomes in a Korean Hospital
Authors: Han Yina , Jin Yinji , Jin Taixian , Lee Sun-Mi , Lee Ju-Young 
Published: May 2019

PURPOSE:The purpose of this study was to compare the effect of pressure injuries on mortality, hospital length of stay, healthcare costs, and readmission rates in hospitalized patients.DESIGN:A case-control study.SUBJECTS AND SETTING:The sample comprised 5000 patients admitted to a tertiary hospital located in Seoul Korea; 1000 patients with pressure injuries (cases) were compared to 4000 patients who acted as controls.METHODS:We retrospectively extracted clinical data from electronic health records. Study outcomes were mortality, hospital length of stay, healthcare costs, and readmission rates. The impact of pressure injuries on death and readmission was analyzed via multiple logistic regression, hospital deaths within 30 days were analyzed using the survival analysis and Cox proportional hazards regression, and impact on the length of hospitalization and medical costs were analyzed through a multiple linear regression.RESULTS:Developing a pressure injury was significantly associated with an increased risk of in-hospital mortality (odds ratio [OR], 3.94; 95% confidence interval [CI], 2.91-5.33), 30-days in-hospital mortality (OR, 2.18; 95% CI, 1.59-3.00), and healthcare cost (β = 11,937,333;P< .001). Pressure injuries were significantly associated with an extended length of hospitalization (β = 20.84;P< .001) and length of intensive care unit (ICU) stay (β = 8.16;P< .001). Having a pressure injury was significantly associated with an increased risk of not being discharged home (OR, 5.55; 95% CI, 4.35-7.08), along with increased risks of readmission (OR, 1.30; 95% CI, 1.05-1.62) and emergency department visits after discharge (OR, 1.70; 95% CI, 1.29-2.23).CONCLUSIONS:Development of pressure injuries influenced mortality, healthcare costs, ICU and hospital length of stay, and healthcare utilization following discharge (ie, readmission or emergency department visits). Hospital-level efforts and interdisciplinary approaches should be prioritized to develop interventions and protocols for pressure injury prevention.
Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production
Authors: Lennen Rebecca M. , Jensen Kristian , Mohammed Elsayed T. , Malla Sailesh , Börner Rosa A. , Chekina Ksenia , Özdemir Emre , Bonde Ida , Koza Anna , Maury Jérôme , Pedersen Lasse E. , Schöning Lars Y. , Sonnenschein Nikolaus , Palsson Bernhard O. , Sommer Morten O.A. , Feist Adam M. , Nielsen Alex T. , Herrgård Markus J. 
Published: May 2019

AbstractTolerance to high product concentrations is a major barrier to achieving economically viable processes for bio-based chemical production. Chemical tolerance mechanisms are often unknown, thus their rational design is not achievable. To reveal unknown tolerance mechanisms we used an automated platform to evolveEscherichia colito grow in previously toxic concentrations of 11 chemicals that have applications as polymer precursors, chemical intermediates, or biofuels. Re-sequencing of isolates from 88 independently evolved populations, reconstruction of mutations, and cross-compound tolerance profiling was employed to uncover general and specific tolerance mechanisms. We found that: 1) the broad tolerance of strains towards chemicals varied significantly depending on the chemical stress condition under which the strain was evolved; 2) the strains that acquired high levels of NaCl tolerance also became broadly tolerant to most chemicals; 3) genetic tolerance mechanisms included alterations in regulatory, cell wall, transcriptional and translational functions, as well as more chemical-specific mechanisms related to transport and metabolism; 4) using pre-tolerized starting strains can significantly enhance subsequent production of chemicals when a production pathway is inserted; and 5) only a subset of the evolved isolates showed improved production indicating that this approach is especially useful when a large number of independently evolved isolates are screened for production. We provide a comprehensive genotype-phenotype map based on identified mutations and growth phenotypes for 224 chemical tolerant strains.
Logomaker: Beautiful sequence logos in python
Authors: Tareen Ammar , Kinney Justin B. 
Published: May 2019

AbstractSequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA, and protein sequences, yet it is currently difficult to generate such logos within the Python programming environment. Here we introduce Logomaker, a Python API for creating publication-quality sequence logos. Logomaker can produce both standard and highly customized logos from any matrix-like array of numbers. Logos are rendered as vector graphics that are easy to stylize using standard matplotlib functions. Methods for creating logos from multiple-sequence alignments are also included.Availability and ImplementationLogomaker can be installed using the pip package manager and is compatible with both Python 2.7 and Python 3.6. Source code is available athttp://github.com/jbkinney/logomaker.Supplemental InformationDocumentation is provided athttp://logomaker.readthedocs.io.Contactjkinney@cshl.edu.