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Jacob Huth, Timothée Masquelier, Angelo Arleo
We developed Convis , a Python simulation toolbox for large scale neural populations which offers arbitrary receptive fields by 3D convolutions executed on a graphics card. The resulting software proves to be flexible and easily extensible in Python, while building on the PyTorch library (The Pytorch Project, 2017), which was previously used successfully in deep learning applications, for just-in-time optimization and compilation of the model onto CPU or GPU architectures. An alternative implementation based on Theano (Theano Development Team, 2016) is also available, although not fully supported...
2018: Frontiers in Neuroinformatics
Amy O'Donnell, Latifa Abidi, Jamie Brown, Nadine Karlsson, Per Nilsen, Kerstin Roback, Janna Skagerström, Kristin Thomas
BACKGROUND: Despite robust evidence for their effectiveness, it has proven difficult to translate alcohol prevention activities into routine health care practice. Previous research has identified numerous provider-level barriers affecting implementation, but these have been less extensively investigated in the wider population. We sought to: (1) investigate patients' beliefs and attitudes to being asked about alcohol consumption in health care; and (2) identify the characteristics of those who are supportive of addressing alcohol consumption in health care...
March 21, 2018: BMC Public Health
Bo Ram Seol, Ho Kyung Choung, Seong Joon Kim
PURPOSE: To analyze stereopsis change before and after inferior oblique weakening surgery. METHODS: We retrospectively reviewed the medical records of 31 patients who had undergone inferior oblique weakening surgery. The factors analyzed included sex, age at surgery, preoperative and postoperative visual acuity (VA), time from first detection to surgery, degree of inferior oblique overaction (IOOA), primary/secondary IOOA, exotropia/hypertropia, bilaterality, and type of surgery...
March 19, 2018: Korean Journal of Ophthalmology: KJO
Rajiv Gandhi Govindaraj, Misagh Naderi, Manali Singha, Jeffrey Lemoine, Michal Brylinski
Rare, or orphan, diseases are conditions afflicting a small subset of people in a population. Although these disorders collectively pose significant health care problems, drug companies require government incentives to develop drugs for rare diseases due to extremely limited individual markets. Computer-aided drug repositioning, i.e., finding new indications for existing drugs, is a cheaper and faster alternative to traditional drug discovery offering a promising venue for orphan drug research. Structure-based matching of drug-binding pockets is among the most promising computational techniques to inform drug repositioning...
2018: NPJ Systems Biology and Applications
Stephen J Fletcher, Mikael Boden, Neena Mitter, Bernard J Carroll
Summary: Small RNAs play key roles in gene regulation, defense against viral pathogens and maintenance of genome stability, though many aspects of their biogenesis and function remain to be elucidated. SCRAM (Small Complementary RNA Mapper) is a novel, simple-to-use short read aligner and visualization suite that enhances exploration of small RNA datasets. Availability: The SCRAM pipeline is implemented in Go and Python, and is freely available under MIT license...
March 15, 2018: Bioinformatics
Igor Mandric, Sergey Knyazev, Alex Zelikovsky
Summary: Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome, and long repeats. An accurate assessment of scaffolding tools should take into account multiple locations of the same contig on the reference scaffolding rather than matching a repeat to a single best location...
March 14, 2018: Bioinformatics
Hajime Ohno, Hirokazu Sato, Yasuhiro Fukushima
To achieve the goals of Paris Agreement, global society is directing much effort in substantially reducing greenhouse gas (GHG) emissions. In addition to energy-related efforts, prevention of carbon release into the atmosphere with carbon capture and storage (CCS) and/or utilization of biomass resources is considered indispensable to achieving the global objective. In this study, considering carbon-containing goods as carbon reservoirs in our society similar to forests and reservoirs enabling CCS, the flow of materially utilized carbon was quantified by input-output-based material flow analysis (IO-MFA)...
March 16, 2018: Environmental Science & Technology
Li-Na Zhang, Yongping Song, Delong Liu
The prognosis of adults with relapsed/refractory (R/R) acute lymphoblastic leukemia (ALL) remains dismal even at this day and age. With salvage chemotherapy, only 29% (range 18 to 44%) of the patients with R/R ALL can be induced into complete remission (CR), with a median overall survival (OS) of 4 months (range 2-6 months). Blinatumomab and inotuzumab ozogamycin (IO) are immunotherapeutic agents that increased CR to 80% and extended survival to 7.7 months in this high-risk population of patients. In the last few years, chimeric antigen receptor (CAR)--engineered T cells have led to major progress in cancer immunotherapy...
March 15, 2018: Journal of Hematology & Oncology
Manuel Corpas, Nadezda V Kovalevskaya, Amanda McMurray, Fiona G G Nielsen
It is generally acknowledged that, for reproducibility and progress of human genomic research, data sharing is critical. For every sharing transaction, a successful data exchange is produced between a data consumer and a data provider. Providers of human genomic data (e.g., publicly or privately funded repositories and data archives) fulfil their social contract with data donors when their shareable data conforms to FAIR (findable, accessible, interoperable, reusable) principles. Based on our experiences via Repositive (https://repositive...
March 2018: PLoS Computational Biology
John Repass, Elizabeth Iorns, Alexandria Denis, Stephen R Williams, Nicole Perfito, Timothy M Errington
As part of the <ext-link ext-link-type="uri" xlink:href="">Reproducibility Project: Cancer Biology</ext-link>, we published a Registered Report (Repass et al., 2016), that described how we intended to replicate an experiment from the paper ' Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma' (Castellarin et al., 2012). Here we report the results. When measuring Fusobacterium nucleatum DNA by qPCR in colorectal carcinoma (CRC), adjacent normal tissue, and separate matched control tissue, we did not detect a signal for F...
March 13, 2018: ELife
Rajiv Gandhi Govindaraj, Michal Brylinski
BACKGROUND: Detecting similar ligand-binding sites in globally unrelated proteins has a wide range of applications in modern drug discovery, including drug repurposing, the prediction of side effects, and drug-target interactions. Although a number of techniques to compare binding pockets have been developed, this problem still poses significant challenges. RESULTS: We evaluate the performance of three algorithms to calculate similarities between ligand-binding sites, APoc, SiteEngine, and G-LoSA...
March 9, 2018: BMC Bioinformatics
Denitza Dimitrova Voutchkova, Birgitte Hansen, Vibeke Ernstsen, Søren Munch Kristiansen
Nationwide sampling campaign of treated drinking water of groundwater origin was designed and implemented in Denmark in 2013. The main purpose of the sampling was to obtain data on the spatial variation of iodine concentration and speciation in treated drinking water, which was supplied to the majority of the Danish population. This data was to be used in future exposure and epidemiologic studies. The water supply sector (83 companies, owning 144 waterworks throughout Denmark) was involved actively in the planning and implementation process, which reduced significantly the cost and duration of data collection...
March 7, 2018: International Journal of Environmental Research and Public Health
Xiaoke Li, Shuo Qi, Yuntao Jiao, Jing Gao, Hongbo Du
RATIONALE: Primary central nervous system lymphoma (PCNSL) with initial manifestations of constipation and intestinal obstruction (IO) is rare. PATIENT CONCERNS: A 50-year-old Chinese male patient was admitted to the gastroenterology department due to constipation and abdominal distention for 8 days. He had experienced intermittent back pain for 3 years prior to admission. Based on abdominal radiography, he was initially diagnosed with IO and treated with meal restriction and enemas...
March 2018: Medicine (Baltimore)
Sara Khor, Danielle Lavallee, Amy M Cizik, Carlo Bellabarba, Jens R Chapman, Christopher R Howe, Dawei Lu, A Alex Mohit, Rod J Oskouian, Jeffrey R Roh, Neal Shonnard, Armagan Dagal, David R Flum
Importance: Functional impairment and pain are common indications for the initiation of lumbar spine surgery, but information about expected improvement in these patient-reported outcome (PRO) domains is not readily available to most patients and clinicians considering this type of surgery. Objective: To assess population-level PRO response after lumbar spine surgery, and develop/validate a prediction tool for PRO improvement. Design, Setting, and Participants: This statewide multicenter cohort was based at 15 Washington state hospitals representing approximately 75% of the state's spine fusion procedures...
March 7, 2018: JAMA Surgery
Stephen R Thompson, Isabel S Y Lee, Susan Carroll, Sarah Bishop, Philip Douglas, Francis Lam, Chris Brown, Janet Williams, David Goldstein
BACKGROUND: Loco-regional failure is the predominant cause of death in anal squamous cell carcinoma. We assessed patterns of loco-regional recurrence to determine the impact of radiotherapy (RT) volumes on patient outcome. METHODS: Retrospective clinical study, including patients treated curatively with RT or chemo-radiotherapy between 1994 and 2007. RT fields/volumes were reviewed and compared with patterns of failure. Patients were classified as having whole pelvic radiotherapy (WPRT) if RT extended to L5/S1 or lower pelvic radiotherapy (LPRT) if it extended to the lower sacroiliac joints or below...
March 7, 2018: ANZ Journal of Surgery
Susan R Bryan, David P Crabb
Purpose: We demonstrate a new approach for assessing and visualizing visual field (VF) progression in clinics. Methods: Two summary measures for VF progression, Rate of Progression (RP) and Loss of Sight Years (LSY), are combined with a novel visualization (Hedgehog Plots). RP is calculated per eye using linear regression of mean deviation (MD) against time of follow-up. LSY is a novel parameter, linked to actuarial data, which estimates the number of years that a patient will have advanced bilateral VF loss in their predicted remaining lifetime...
February 2018: Translational Vision Science & Technology
Hongyang Zhang, Xiaojuan Shi, Long Wang, Xiaojie Li, Chao Zheng, Bo Gao, Xiaolong Xu, Xisheng Lin, Jinpeng Wang, Yangjing Lin, Jun Shi, Qiang Huang, Zhuojing Luo, Liu Yang
A fracture is the most dangerous complication of osteoporosis in patients because the associated disability and mortality rates are high. Osteoporosis impairs fracture healing and prognosis, but how intramembranous ossification (IO) or endochondral ossification (EO) during fracture healing are affected and whether these two kinds of ossification are different between glucocorticoid-induced osteoporosis (GIOP) and estrogen deficiency-induced osteoporosis (EDOP) are poorly understood. In this study, we established two bone repair models that exhibited repair via IO or EO and compared the pathological progress of each under GIOP and EDOP...
March 1, 2018: Scientific Reports
Steven G Schauer, Michael D April, Guyon J Hill, Jason F Naylor, Matthew A Borgman, Robert A De Lorenzo
BACKGROUND: United States (US) and coalition military medical units deployed to combat zones frequently encounter pediatric trauma patients. Pediatric patients may present unique challenges due to their anatomical and physiological characteristics and most military prehospital providers lack pediatric-specific training. A minimal amount of data exists to illuminate the prehospital care of pediatric patients in this environment. We describe the prehospital care of pediatric trauma patients in Iraq and Afghanistan...
March 1, 2018: Prehospital Emergency Care
Sara Carvalho, Ralph T H Leijenaar, Esther G C Troost, Janna E van Timmeren, Cary Oberije, Wouter van Elmpt, Lioe-Fee de Geus-Oei, Johan Bussink, Philippe Lambin
BACKGROUND: Lymph node stage prior to treatment is strongly related to disease progression and poor prognosis in non-small cell lung cancer (NSCLC). However, few studies have investigated metabolic imaging features derived from pre-radiotherapy 18F-fluorodeoxyglucose (FDG) positron-emission tomography (PET) of metastatic hilar/mediastinal lymph nodes (LNs). We hypothesized that these would provide complementary prognostic information to FDG-PET descriptors to only the primary tumor (tumor)...
2018: PloS One
Joe Wandy, Mu Niu, Diana Giurghita, Rónán Daly, Simon Rogers, Dirk Husmeier
Motivation: Mathematical modelling based on ordinary differential equations (ODEs) is widely used to describe the dynamics of biological systems, particularly in systems and pathway biology. Often the kinetic parameters of these ODE systems are unknown and have to be inferred from the data. Approximate parameter inference methods based on gradient matching (which do not require performing computationally expensive numerical integration of the ODEs) have been getting popular in recent years, but many implementations are difficult to run without expert knowledge...
February 27, 2018: Bioinformatics
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