bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
Authors: Amini Parisa , Nassiri Sina , Ettlin Julia , Malbon Alexandra , Markkanen Enni 
Published: July 2019

ABSTRACT
Spontaneous canine simple mammary carcinomas (mCA) are often viewed as models of human mCA. Cancer-associated stroma (CAS) is central for initiation and progression of human cancer, and is likely to play a key role in canine tumours as well. However, canine CAS lacks characterisation and it remains unclear how canine and human CAS compare. Formalin-fixed paraffin embedded (FFPE) tissue constitutes a valuable resource of patient material, but chemical crosslinking has largely precluded its analysis by next-generation RNA sequencing (RNAseq). We have recently established a protocol to isolate CAS and normal stroma from archival FFPE tumours using laser-capture microdissection followed by RNAseq. Using this approach, we have analysed stroma from 15 canine mCA. Our data reveal strong reprogramming of canine CAS. We demonstrate a high-grade molecular homology between canine and human CAS, and show that enrichment of upregulated canine CAS genes strongly correlates with the enrichment of an independently derived human stromal signature in the TCGA breast tumour dataset. Relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Finally, we establish the prognostic potential of the canine CAS signature in human samples, emphasising the relevance of studying canine CAS as a model of the human disease. In conclusion, we provide a proof-of-principle to analyse specific subsections of FFPE tissue by RNAseq, and compare stromal gene expression between human and canine mCA to reveal molecular drivers in CAS supporting tumour growth and malignancy.
Mechanics of nuclear membranes
Authors: Agrawal Ashutosh , Lele Tanmay P. 
Published: July 2019

ABSTRACT
Cellular nuclei are bound by two uniformly separated lipid membranes that are fused with each other at numerous donut-shaped pores. These membranes are structurally supported by an array of distinct proteins with distinct mechanical functions. As a result, the nuclear envelope possesses unique mechanical properties, which enables it to resist cytoskeletal forces. Here, we review studies that are beginning to provide quantitative insights into nuclear membrane mechanics. We discuss how the mechanical properties of the fused nuclear membranes mediate their response to mechanical forces exerted on the nucleus and how structural reinforcement by different nuclear proteins protects the nuclear membranes against rupture. We also highlight some open questions in nuclear envelope mechanics, and discuss their relevance in the context of health and disease.
Resistance Exercise–induced Changes in Muscle Phenotype Are Load Dependent
Authors: LIM CHANGHYUN , KIM HYO JEONG , MORTON ROBERT W. , HARRIS ROGER , PHILLIPS STUART M. , JEONG TAE SEOK , KIM CHANG KEUN 
Published: July 2019

ABSTRACT

Introduction
Lower-load (LL), higher-repetition resistance exercise training (RET) can increase muscle mass in a similar degree as higher-load (HL), lower-repetition RET. However, little is known about how LL and HL RET modulate other aspects of the RET phenotype such as satellite cells, myonuclei, and mitochondrial proteins. We aimed to investigate changes in muscle mass, muscle strength, satellite cell activity, myonuclear addition, and mitochondrial protein content after prolonged RET with LL and HL RET.

Methods
We recruited 21 young men and randomly assigned them to perform 10 wk RET (leg press, leg extension, and leg curl) three times per week with the following conditions: 80FAIL (80% one-repetition maximum [1RM] performed to volitional fatigue), 30WM (30%1RM with volume matched to 80FAIL), and 30FAIL (30%1RM to volitional fatigue). Skeletal muscle biopsies were taken from the vastus lateralis pre- and post-RET intervention.

Results
After 10 wk of RET, only 30FAIL and 80FAIL showed an increase in peak torque and type I fiber cross-sectional area (P < 0.05). Moreover, only 30FAIL resulted in a significant decrease in the myonuclear domain of type II muscle fibers and an increase in mitochondrial proteins related to autophagy, fission, and fusion (all P < 0.05).

Conclusion
We discovered that LL RET was effective at increasing the content of several mitochondrial proteins. Similar to previous research, we found that changes in muscle mass and strength were independent of load when repetitions were performed to volitional fatigue.
Updating the evidence on the effectiveness of the alcohol reduction app, Drink Less: using Bayes factors to analyse trial datasets supplemented with extended recruitment
Authors: Garnett Claire , Michie Susan , West Robert , Brown Jamie 
Published: July 2019

Background: A factorial experiment evaluating the Drink Less app found no clear evidence for main effects of enhanced versus minimal versions of five components but some evidence for an interaction effect. Bayes factors (BFs) showed the data to be insensitive. This study examined the use of BFs to update the evidence with further recruitment. Methods: A between-subject factorial experiment evaluated the main and two-way interaction effects of enhanced versus minimal version of five components of Drink Less. Participants were excessive drinkers, aged 18+, and living in the UK. After the required sample size was reached (n=672), additional data were collected for five months. Outcome measures were change in past week alcohol consumption and Alcohol Use Disorders Identification Test (AUDIT) score at one-month follow-up, amongst responders only (those who completed the questionnaire). BFs (with a half-normal distribution) were calculated (BF<0.33 indicate evidence for null hypothesis; 0.33<BF<3 indicate data are insensitive). Results: Of the sample of 2586, 342 (13.2%) responded to follow-up. Data were mainly insensitive but tended to support there being no large main effects of the enhanced version of individual components on consumption (0.22<BF<0.83) or AUDIT score (0.14<BF<0.98). Data no longer supported there being two-way interaction effects (0.31<BF<1.99). In an additional exploratory analysis, participants receiving four of the components averaged a numerically greater reduction in consumption than those not receiving any (21.6 versus 12.1 units), but the data were insensitive (BF=1.42). Conclusions: Data from extended recruitment in a factorial experiment evaluating components of Drink Less remained insensitive but tended towards individual and pairs of components not having a large effect. In an exploratory analysis, there was weak, anecdotal evidence for a synergistic effect of four components. In the event of uncertain results, calculating BFs can be used to update the strength of evidence of a dataset supplemented with extended recruitment.
The Zambian Preterm Birth Prevention Study (ZAPPS): Cohort characteristics at enrollment
Authors: Castillo Marcela C. , Fuseini Nurain M. , Rittenhouse Katelyn , Price Joan T. , Freeman Bethany L. , Mwape Humphrey , Winston Jennifer , Sindano Ntazana , Baruch-Gravett Courtney , Chi Benjamin H. , Kasaro Margaret P. , Litch James A. , Stringer Jeffrey S. A. , Vwalika Bellington 
Published: July 2019

Background: Sub-Saharan Africa bears a disproportionate burden of preterm birth and other adverse outcomes. A better understanding of the demographic, clinical, and biologic underpinnings of these adverse outcomes is urgently needed to plan interventions and inform new discovery. Methods: The Zambian Preterm Birth Prevention Study (ZAPPS) is a prospective observational cohort established at the Women and Newborn Hospital (WNH) in Lusaka, Zambia. We recruit pregnant women from district health centers and the WNH and offer ultrasound examination to determine eligibility. Participants receive routine obstetrical care, lab testing, midtrimester cervical length measurement, and serial fetal growth monitoring. At delivery, we assess gestational age, birthweight, vital status, and sex and assign a delivery phenotype. We collect blood, urine, and vaginal swab specimens at scheduled visits and store them in an on-site biorepository. In September 2017, enrollment of the ZAPPS Phase 1—the subject of this report—was completed. Phase 2, which is limited to HIV-uninfected women, reopened in January 2018. Results: Between August 2015 and September 2017, we screened 1784 women, of whom 1450 (81.2%) met inclusion criteria and were enrolled. The median age at enrollment was 27 years (IQR 23–32) and median gestational age was 16 weeks (IQR 13–18). Among women with a previous pregnancy (n=1042), 19% (n=194) reported a prior miscarriage. Among parous women (n=992), 41% (n=411) reported a prior preterm birth and 14% (n=126) reported a prior stillbirth. The HIV seroprevalence was 24%. Discussion: We have established a large cohort of pregnant women and newborns at the WNH to characterize the determinants of adverse birth outcomes in Lusaka, Zambia. Our overarching goal is to elucidate biological mechanisms in an effort to identify new strategies for early detection and prevention of adverse outcomes. We hope that findings from this cohort will help guide future studies, clinical care, and policy.
Systemic neoadjuvant chemotherapy in modern pancreatic cancer treatment: a systematic review and meta-analysis
Authors: Rangarajan K , Pucher PH , Armstrong T , Bateman A , Hamady ZZR 
Published: July 2019

Background Pancreatic ductal adenocarcinoma remains a disease with a poor prognosis despite advances in surgery and systemic therapies. Neoadjuvant therapy strategies are a promising alternative to adjuvant chemotherapy. However, their role remains controversial. This meta-analysis aims to clarify the benefits of neoadjuvant therapy in resectable pancreatic ductal adenocarcinoma. Methods Eligible studies were identified from MEDLINE, Embase, Web of Science and the Cochrane Library. Studies comparing neoadjuvant therapy with a surgery first approach (with or without adjuvant therapy) in resectable pancreatic ductal adenocarcinoma were included. The primary outcome assessed was overall survival. A random-effects meta-analysis was performed, together with pooling of unadjusted Kaplan–Meier curve data. Results A total of 533 studies were identified that analysed the effect of neoadjuvant therapy in pancreatic ductal adenocarcinoma. Twenty-seven studies were included in the final data synthesis. Meta-analysis suggested beneficial effects of neoadjuvant therapy with prolonged survival compared with a surgery-first approach, (hazard ratio 0.72, 95% confidence interval 0.69–0.76). In addition, R0 resection rates were significantly higher in patients receiving neoadjuvant therapy (relative risk 0.51, 95% confidence interval 0.47–0.55). Individual patient data analysis suggested that overall survival was better for patients receiving neoadjuvant therapy (P = 0.008). Conclusions Current evidence suggests that neoadjuvant chemotherapy has a beneficial effect on overall survival in resectable pancreatic ductal adenocarcinoma in comparison with upfront surgery and adjuvant therapy. Further trials are needed to address the need for practice change.
Novel Methylated DNA Markers Discriminate Advanced Neoplasia in Pancreatic Cysts: Marker Discovery, Tissue Validation, and Cyst Fluid Testing
Authors: Majumder Shounak , Taylor William R. , Yab Tracy C. , Berger Calise K. , Dukek Brian A. , Cao Xiaoming , Foote Patrick H. , Wu Chung Wah , Mahoney Douglas W. , Aslanian Harry R. , Fernández-Del Castillo Carlos , Doyle Leona A. , Farrell James J. , Fisher William E. , Lee Linda S. , Lee Yvonne N. , Park Walter , Rodrigues Clifton , Gould Rothberg Bonnie Elyssa , Salem Ronald R. , Simeone Diane M. , Urs Sumithra , Van Buren George , Smyrk Thomas C. , Allawi Hatim T. , Lidgard Graham P. , Raimondo Massimo , Chari Suresh T. , Kendrick Michael L. , Kisiel John B. , Topazian Mark D. , Ahlquist David A. 
Published: July 2019

OBJECTIVES:
Pancreatic cystic lesions (PCLs) may be precancerous. Those likely to harbor high-grade dysplasia (HGD) or pancreatic cancer (PC) are targets for surgical resection. Current algorithms to predict advanced neoplasia (HGD/PC) in PCLs lack diagnostic accuracy. In pancreatic tissue and cyst fluid (CF) from PCLs, we sought to identify and validate novel methylated DNA markers (MDMs) that discriminate HGD/PC from low-grade dysplasia (LGD) or no dysplasia (ND).

METHODS:
From an unbiased whole-methylome discovery approach using predefined selection criteria followed by multistep validation on case (HGD or PC) and control (ND or LGD) tissues, we identified discriminant MDMs. Top candidate MDMs were then assayed by quantitative methylation-specific polymerase chain reaction on archival CF from surgically resected PCLs.

RESULTS:
Of 25 discriminant MDMs identified in tissue, 13 were selected for validation in 134 CF samples (21 cases [8 HGD, 13 PC], 113 controls [45 ND, 68 LGD]). A tree-based algorithm using 2 CF-MDMs (TBX15, BMP3) achieved sensitivity and specificity above 90%. Discrimination was significantly better by this CF-MDM panel than by mutant KRAS or carcinoembryonic antigen, with areas under the receiver operating characteristic curve of 0.93 (95% confidence interval: 0.86–0.99), 0.71 (0.57–0.85), and 0.72 (0.60–0.84), respectively. Cutoffs for the MDM panel applied to an independent CF validation set (31 cases, 56 controls) yielded similarly high discrimination, areas under the receiver operating characteristic curve = 0.86 (95% confidence interval: 0.77–0.94, P = 0.2).

DISCUSSION:
Novel MDMs discovered and validated in tissue accurately identify PCLs harboring HGD/PC. A panel of 2 MDMs assayed in CF yielded results with potential to enhance current risk prediction algorithms. Prospective studies are indicated to optimize and further evaluate CF-MDMs for clinical use.
A Novel Method of Esophageal Remodeling: Thinking Outside the Box
Authors: Kochhar Rakesh , Ashat Munish , Reddy Yalaka Rami , Gulati Ajay , Lileswar Kaman , Sinha Saroj Kant 
Published: July 2019

ABSTRACT
Caustic esophageal strictures are complex strictures with high rates of recurrence and complications. Management of these strictures requires a multipronged approach including endoscopic dilation and complex surgeries. Even with these modalities, treatment of each patient has to be individualized because it requires high clinical discretion. We present a 38-year-old female woman who had required esophagostomy and total gastrectomy in the acute phase after caustic ingestion. The definitive surgical procedure was deferred because of cicatrization of the proximal esophageal remnant. We remodeled scarred esophagus using a novel technique, which facilitated definitive surgery.
More Than a Rash: Recurrent Hepatocellular Carcinoma After Liver Transplantation
Authors: Moraveji Sharareh , Pedersen Mark R. , Chandramouli Shruti , Kerr Thomas A. , Grant Lafaine M. 
Published: July 2019

ABSTRACT
Recurrent hepatocellular carcinoma (HCC) after liver transplant is uncommon in patients who have favorable pretransplant characteristics. We present a 56-year-old man with a history of liver transplant 8 weeks prior for hepatitis C cirrhosis and HCC who presented for shortness of breath. He was found to have a microangiopathic hemolytic anemia and an erythematous, nodular skin rash on his left lower abdomen. Biopsy of the skin rash would demonstrate metastatic HCC, determined to be the cause of hemolysis as well. Recurrent malignancy should be considered in patients with a history of HCC who present with new, unexplained skin nodules.
The Light at the End of the Tunnel
Authors: Mando Rufaat , Ceballos Darrel , Kumar Manoj , Abdul-Rahim Osama , Mizrahi Meir 
Published: July 2019

ABSTRACT
Approximately 5%–10% of common bile duct (CBD) stones cannot be removed by conventional methods because of altered anatomy. Percutaneous transhepatic cholangioscopic lithotomy has been cited as a viable alternative. A 69-year-old woman with a history of Roux-en-Y was found to have a lesion obstructing the CBD. A cholangioscope was advanced through a percutaneous transhepatic sheath and demonstrated an obstructing stone in the CBD that was removed with lithotripsy. The rate of successful stone removal with percutaneous transhepatic cholangioscopic lithotomy is 90%, with complication rates similar to endoscopic retrograde cholangiopancreatography and is an option in patients with altered surgical anatomy.
Successful Recanalization of a Long-Segment Complete Esophageal Stricture Using Endoscopic and Fluoroscopic Techniques
Authors: Lam Steven , Deivert Duane E. , Obuch Joshua C. 
Published: July 2019

ABSTRACT
Complete esophageal strictures are rare complications in patients who have received head and neck radiation therapy. Although mild strictures are generally amenable to dilation or stenting, management of these debilitating strictures is not well established. Treatment of long-segment obstructions is particularly complicated because documented techniques generally apply for strictures up to 3 cm in length. This report describes a successful recanalization of a long-segment complete esophageal stricture using combined antegrade-retrograde endoscopic therapy with adjunctive fluoroscopic techniques.
Mobile Barcode Based Examination Attendance System
Authors: Ullah Khan Rehman , Chua Yee Wee Vivian , Wong Sze Lui Valentina , Inam UlHaq Much. , Khan Yahya , Hardyman Barawi Mohd 
Published: July 2019

Smartphone usage has revolutionized the world to many settings including that of the education system with numerous potential and realized benefits. While the functions of smartphones, such as text messaging, multimedia, and Internet connectivity, may seem purely recreational, they can be used within the academic institution to manage students attendance to speed up the process of taking attendance by academic instructors, hence reduces time, human errors and redundant works as compared to the manual attendance system. In this paper, we introduced an automatic examination attendance system on smartphones based on the Barcode to automatically capture student examination attendance. Although many existing systems (Sudha et al. 2015) have been proposed using smartphones for automatic student attendance, there is little study known about a system that is specifically designed for capturing student examination attendance. The main difference among our system and existing systems is that existing systems are using extra hardware device Barcode reader while our system is using smartphone, which highly reduce the cost. Our experiment shows that our proposed student examination attendance system is better for capturing the student attendance information during the examination as compared to the general student attendance systems.
Biomedical Arrhythmia Heart Diseases Classification Based on Artificial Neural Network and Machine Learning Approach
Authors: Subbiah Stalin , Subramanian Suresh 
Published: July 2019

In present day, several types of developments are carried toward the medical application. There has been increased improvement in the processing of ECG signals. The accurate detection of ECG signals with the help of detection of P, Q, R and S waveform. However these waveforms are suffered from some disturbances like noise. Initially denoising the ECG signal using filters and detect the PQRS waveforms. Four filters are carried out to remove the ECG noises that are Median, Gaussian, FIR and Butterworth filter. ECG signal is analyzed or classify using Extreme Learning Machine (ELM) and it compared with Support Vector Machine (SVM) and Back Propagation Neural Network (BPNN). The paper classifies the ECG signal into two classes, Normal and Abnormal. ECG waveform is detected and analyzed using the 48 records of the MIT-BIH arrhythmia database. Denoising results are evaluated using MSE, RMSE, PSNR, NAE and NCC. The classifier performance is measured in terms of Sensitivity (Se), Positive Predictivity (PP) and Specificity (SP).
Improved Ant Colony on Feature Selection and Weighted Ensemble to Neural Network Based Multimodal Disease Risk Prediction (WENN-MDRP) Classifier for Disease Prediction Over Big Data
Authors: Nkundimana Joel Gakwaya , Manju Priya S 
Published: July 2019

As the big data is growing in biomedical and healthcare communities, so are precise analyses of medical data aids, premature disease identification, patient care as well as community services. On the other hand, the accuracy of the analysis decreases, if the medical data quality is imperfect. As a result, the choice of features from the dataset turns out to be an extremely significant task. Feature selection has exposed its efficiency in numerous applications by means of constructing modest and more comprehensive models, enlightening learning performance and preparing clean and clear data. The proposed method analyzes the difficulties of feature selection for big data analytics. Improved Ant Colony Optimization based Feature Selection (IACO) algorithm is presented for resolving this issue. The reconstruction of missing data before the incomplete data available was performed with help of latent factor mode. Therefore, it was not easy to choose the best features from the structured and unstructured data. the unheard technique which is called Weighted Ensemble Based Neural Network for multimodal disease risk prediction(WENN-MDRP) algorithm is implemented in order to provide the best features selection among structured as well as unstructured data. The research method provides improved prediction accuracy when matched with conventional techniques. In the MATLAB environment, the presented classifiers are implemented. The outcomes are computed in regard to recall, precision, accuracy, f-measure and error rate.
A Low Cost Thermal Imaging System for Medical Diagnostic Applications
Authors: Jayalatsumi U , Feza Naaz A , Sravani3 Kodavaluru , Anusha A , Vasavi Alla 
Published: July 2019

This paper presents a low cost thermal imaging system for medical diagnostic applications. Available systems are expensive and are mostly meant for industrial applications. In this paper the existing system which is a basic system consisting of thermopile based sensor which produces thermal array is replaced with a “Thermal Imaging Camera” for medical diagnosis applications. The thermal camera scans the entire body of the individual to diagnose the diseases ie, infrared radiations from the human body part and then converts them to electronic signal. If there is any lump or any other unusual change inside the body, then the body temperature at that particular part will alone be high or low which indicates the “Hypo” or “Hyper” condition of the disease. Scene captured by the thermal camera is represented as a matrix. Each element of matrix represents a temperature value. Temperature values are divided into different ranges and each range is represented by an RGB value by the Raspberry Pi. Based on this thermal camera image we can detect the exact location in individual body part and further for that part alone we can take test and detect what kind of disease the individual is suffering. This system can be used in wide applications in the field of medicine such as detection of breast cancer, fever screening, thyroid disease detection, early detection of risk for diabetic peripheral neuropathy, Reynaud’s phenomenon, orthopedics etc.