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https://www.readbyqxmd.com/read/29218871/extracting-a-biologically-relevant-latent-space-from-cancer-transcriptomes-with-variational-autoencoders
#1
Gregory P Way, Casey S Greene
The Cancer Genome Atlas (TCGA) has profiled over 10,000 tumors across 33 different cancer-types for many genomic features, including gene expression levels. Gene expression measurements capture substantial information about the state of each tumor. Certain classes of deep neural network models are capable of learning a meaningful latent space. Such a latent space could be used to explore and generate hypothetical gene expression profiles under various types of molecular and genetic perturbation. For example, one might wish to use such a model to predict a tumor's response to specific therapies or to characterize complex gene expression activations existing in differential proportions in different tumors...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29217767/hypothetical-route-of-the-introduction-of-schmallenberg-virus-into-ireland-using-two-complementary-analyses
#2
Guy McGrath, Simon J More, Ronan O'Neill
Ireland lost its official freedom from Schmallenberg virus (SBV) in October 2012. The route of introduction is uncertain, with long-distance displacement of infected Culicoides, biting midges, by suitable wind flows considered to be the most likely source. The authors investigated the potential introduction of SBV into Ireland through a Culicoides incursion event in the summer of 2012. They conducted SBV serology on archived bovine sera to identify the prospective dispersal window, then used atmospheric dispersion modelling during periods around this window to identify environmental conditions the authors considered suitable for atmospheric dispersal of Culicoides from potential infected source locations across Southern England...
December 7, 2017: Veterinary Record
https://www.readbyqxmd.com/read/29217523/detecting-recent-positive-selection-with-a-single-locus-test-bi-partitioning-the-coalescent-tree
#3
Zongfeng Yang, Junrui Li, Thomas Wiehe, Haipeng Li
Many population genomic studies have been conducted in the past to search for traces of recent events of positive selection. These traces, however, can be obscured by temporal variation of population size or other demographic factors. To reduce the confounding impact of demography, the coalescent tree topology has been used as an additional source of information for detecting recent positive selection in a population or a species. Based on the branching pattern at the root, we partition the hypothetical coalescent tree, inferred from a sequence sample, into two subtrees...
December 7, 2017: Genetics
https://www.readbyqxmd.com/read/29216532/spontaneous-regression-of-pancreatic-cancer-a-case-report-and-literature-review
#4
Ken Min Chin, Chung Yip Chan, Ser Yee Lee
INTRODUCTION: Spontaneous regression of cancer is defined as the partial or complete disappearance of malignant disease without treatment, or in the presence of therapy that is deemed inadequate to exert an influence on malignant disease, as composed by Tilden Everson and Warren Cole in the 1960s. It has been a topic of major interest in the field of medical and surgical oncology. It is poorly understood and scantily documented. Factors associated and postulated pathogeneses are at best, hypothetical...
December 2, 2017: International Journal of Surgery Case Reports
https://www.readbyqxmd.com/read/29215368/numeracy-and-interpretation-of-prognostic-estimates-in-intracerebral-hemorrhage-among-surrogate-decision-makers-in-the-neurologic-icu
#5
Nikita Leiter, Melissa Motta, Robert M Reed, Temitope Adeyeye, Debra L Wiegand, Nirav G Shah, Avelino C Verceles, Giora Netzer
OBJECTIVE: Clinicians caring for patients with intracerebral hemorrhage must often discuss prognosis and goals of care with their patients' surrogate decision makers, and may make numeric estimates of likelihood of survival and functional independence, informed by validated prediction models. Surrogates' prognostic estimates are often discordant with physicians', suggesting that physicians' numeric statements may not be accurately interpreted. We sought to assess the relationship between numeracy and interpretation of prognostic estimates in intracerebral hemorrhage among surrogate decision makers...
December 5, 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/29214470/clinical-and-anti-aging-effect-of-mud-bathing-therapy-for-patients-with-fibromyalgia
#6
Toyoki Maeda, Yoshihiro Kudo, Takahiko Horiuchi, Naoki Makino
Spa bathing is known as a medical treatment for certain diseases causing chronic pains. Spa water contains mineral components which lower the specific heat of the water, resulting in a higher efficiency to warm body-core temperature. This phenomenon yields pain-relieving effect for rheumatoid arthritis, low back pain, sciatic neuralgia, fibromyalgia, etc. Here we introduce medical and biological effects of mud-spa-bathing therapy for fibromyalgia other than pain relief, the changes of blood examination data, and the telomere length of circulating leukocytes...
December 6, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29214231/ab-initio-chemical-safety-assessment-a-workflow-based-on-exposure-considerations-and-non-animal-methods
#7
Elisabet Berggren, Andrew White, Gladys Ouedraogo, Alicia Paini, Andrea-Nicole Richarz, Frederic Y Bois, Thomas Exner, Sofia Leite, Leo A van Grunsven, Andrew Worth, Catherine Mahony
We describe and illustrate a workflow for chemical safety assessment that completely avoids animal testing. The workflow, which was developed within the SEURAT-1 initiative, is designed to be applicable to cosmetic ingredients as well as to other types of chemicals, e.g. active ingredients in plant protection products, biocides or pharmaceuticals. The aim of this work was to develop a workflow to assess chemical safety without relying on any animal testing, but instead constructing a hypothesis based on existing data, in silico modelling, biokinetic considerations and then by targeted non-animal testing...
November 2017: Computational Toxicology
https://www.readbyqxmd.com/read/29212725/the-functional-syndrome-linking-individual-trait-variability-to-ecosystem-functioning
#8
Allan Raffard, Antoine Lecerf, Julien Cote, Mathieu Buoro, Remy Lassus, Julien Cucherousset
Phenotypic variability is increasingly assessed through functional response and effect traits, which provide a mechanistic framework for investigating how an organism responds to varying ecological factors and how these responses affect ecosystem functioning. Covariation between response and effect traits has been poorly examined at the intraspecific level, thus hampering progress in understanding how phenotypic variability alters the role of organisms in ecosystems. Using a multi-trait approach and a nine-month longitudinal monitoring of individual red-swamp crayfish (Procambarus clarkii), we demonstrated that most of the measured response and effect traits were partially stable during the ontogeny of individuals...
December 6, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29212526/structural-and-functional-annotation-of-hypothetical-proteins-of-human-adenovirus-prioritizing-the-novel-drug-targets
#9
Muhammad Naveed, Sana Tehreem, Muhammad Usman, Zoma Chaudhry, Ghulam Abbas
OBJECTIVE: Human adenoviruses are small double stranded DNA viruses that provoke vast array of human diseases. Next generation sequencing techniques increase genomic data of HAdV rapidly, which increase their serotypes. The complete genome sequence of human adenovirus shows that it contains large amount of proteins with unknown cellular or biochemical function, known as hypothetical proteins. Hence, it is indispensable to functionally and structurally annotate these proteins to get better understanding of the novel drug targets...
December 6, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29212490/attitudes-towards-assisted-suicide-and-euthanasia-among-care-dependent-older-adults-50-in-austria-the-role-of-socio-demographics-religiosity-physical-illness-psychological-distress-and-social-isolation
#10
Erwin Stolz, Hannes Mayerl, Peter Gasser-Steiner, Wolfgang Freidl
BACKGROUND: Care-dependency constitutes an important issue with regard to the approval of end-of-life decisions, yet attitudes towards assisted suicide and euthanasia are understudied among care-dependent older adults. We assessed attitudes towards assisted suicide and euthanasia and tested empirical correlates, including socio-demographics, religiosity, physical illness, psychological distress and social isolation. METHODS: A nationwide cross-sectional survey among older care allowance recipients (50+) in private households in Austria was conducted in 2016...
December 7, 2017: BMC Medical Ethics
https://www.readbyqxmd.com/read/29210943/survey-of-the-american-neurotology-society-on-cochlear-implantation-part-2-surgical-and-device-related-practice-patterns
#11
Matthew L Carlson, Brendan P O'Connell, Christine M Lohse, Colin L Driscoll, Alex D Sweeney
OBJECTIVE: To examine surgical and device-related cochlear implant practice patterns across centers in the United States. METHODS: Cross-sectional survey of the American Neurotology Society (ANS). RESULTS: A total of 81 surveys were returned from ANS members who report regular involvement in cochlear implant care. Overall there was a broad distribution in age and clinical experience, with most respondents reporting Accreditation Council for Graduate Medical Education (ACGME) accreditation in neurotology and employment at an academic center...
November 28, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/29210031/adjuvant-statin-therapy-for-esophageal-adenocarcinoma-a-cost-utility-analysis
#12
Rebekah Fong Soe Khioe, Chris Skedgel, Andrew Hart, Michael Philip Nelson Lewis, Leo Alexandre
BACKGROUND: Emerging preclinical evidence indicates statins, medications commonly used in the prevention of cardiovascular disease (CVD), inhibit proliferation, promote apoptosis and limit invasiveness of esophageal adenocarcinoma (EAC). Population-based observational data demonstrate statin treatment after diagnosis of EAC is associated with significant reductions in all-cause and cancer-specific mortality. A feasibility study of adjuvant statin therapy following potentially curative resection for EAC has been completed, with planned progression to a full phase III, randomized controlled trial...
December 5, 2017: PharmacoEconomics
https://www.readbyqxmd.com/read/29209844/a-new-method-for-quantifying-the-phylogenetic-redundancy-of-biological-communities
#13
Carlo Ricotta, Giovanni Bacaro, Marco Caccianiga, Bruno E L Cerabolini, Sandrine Pavoine
The increasing use of phylogenetic methods in community ecology recognizes that accumulated evolutionary differences among species mirror, to some extent, ecological processes. The scope of this work is thus to propose a new method for the measurement of community-level phylogenetic redundancy, which takes into account the branching pattern of the underlying phylogeny. Like for functional redundancy, a measure of phylogenetic redundancy can be described as a normalized measure in the range (0-1) that relates the observed community-level phylogenetic diversity to the value of a hypothetical assemblage with the same abundance distribution of the focal community in which all species had independent evolution...
December 5, 2017: Oecologia
https://www.readbyqxmd.com/read/29209261/do-true-and-false-intentions-differ-in-level-of-abstraction-a-test-of-construal-level-theory-in-deception-contexts
#14
Sofia Calderon, Erik Mac Giolla, Pär Anders Granhag, Karl Ask
The aim was to examine how people mentally represent alleged future actions-their true and false intentions. In two experiments, participants were asked to either tell the truth (i.e., express true intentions) or lie (i.e., express false intentions) about performing future tasks. Drawing on Construal Level Theory, which proposes that psychologically distant events are more abstractly construed than proximal ones, it was predicted that liars would have more abstract mental representations of the future tasks than truth tellers, due to differences in hypotheticality (i...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/29206942/understanding-decision-making-in-cardiac-imaging-determinants-of-appropriate-use
#15
Ricardo Fonseca, Kim Jose, Thomas H Marwick
Aims: Appropriate Use Criteria (AUC) for echocardiography were developed in 2007 to facilitate decision-making, reduce variability in test utilization, and encourage rational use of imaging. However, there is little evidence that the AUC have favourably influenced ordering behaviour. This study explores the factors that contribute to clinicians requesting echocardiograms with a focus on appropriate use. Methods and results: Semi-structured face-to-face interviews with cardiologists and non-cardiologists who had requested echocardiograms were conducted at an Australian tertiary hospital...
November 30, 2017: European Heart Journal Cardiovascular Imaging
https://www.readbyqxmd.com/read/29205551/regulatory-genes-coordinating-antibiotic-induced-changes-in-promoter-activity-and-early-transcriptional-termination-of-the-mycobacterial-intrinsic-resistance-gene-whib7
#16
Ján Burian, Charles J Thompson
Diseases caused by various Mycobacterium sp., especially Mycobacterium tuberculosis, are a major burden on global health care. Due to high intrinsic antibiotic resistance, treatment options are severely limited. In mycobacteria, WhiB7 coordinates intrinsic resistance to a broad range of antibiotics. While WhiB7 has been established as an auto-regulatory transcriptional activator, the signals and genes needed to induce its expression are poorly understood. Using Mycobacterium smegmatis as a model, we coupled transposon mutagenesis and next generation sequencing with WhiB7-specific antibiotic selection to identify genes that contribute to WhiB7 regulation and function...
December 4, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29205366/diagnostic-staging-laparoscopy-in-gastric-cancer-treatment-a-cost-effectiveness-analysis
#17
Kevin Li, John G D Cannon, Sam Y Jiang, Tanmaya D Sambare, Douglas K Owens, Eran Bendavid, George A Poultsides
BACKGROUND AND OBJECTIVES: Accurate preoperative staging helps avert morbidity, mortality, and cost associated with non-therapeutic laparotomy in gastric cancer (GC) patients. Diagnostic staging laparoscopy (DSL) can detect metastases with high sensitivity, but its cost-effectiveness has not been previously studied. We developed a decision analysis model to assess the cost-effectiveness of preoperative DSL in GC workup. METHODS: Analysis was based on a hypothetical cohort of GC patients in the U...
December 4, 2017: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29205123/neuronal-traffic-signals-in-tardive-dyskinesia-not-enough-stop-in-the-motor-striatum
#18
Stephen M Stahl
Tardive dyskinesia is a disturbance in the balance between dopamine receptor stimulation and dopamine receptor blockade in the motor striatum, with hypothetically too much stimulation of supersensitive D2 receptors, resulting in "don't stop" signaling to motor output.
December 2017: CNS Spectrums
https://www.readbyqxmd.com/read/29205078/an-oral-pharyngeal-scope-for-objective-oropharyngeal-examination-a-new-device-for-oropharyngeal-study
#19
Koichi Tsunoda, Rika Kobayashi, Akiko Kada, Akiko M Saito, Fumiyuki Goto, Yoichiro Sugiyama, Yasuo Hisa, Kenji Kondo, Atsunobu Tsunoda, Keizo Horibe, Hayato Misawa, Toru Sasaki, Takanozawa Minako, Hiroshi Nishino
OBJECTIVE: There has been little progress in examination of the oropharynx with a light source such as electric light, a penlight, or a forehead mirror over the past 100 years. It is therefore necessary to develop methods to display and record oropharyngeal observations. METHOD: Since the aim of this study was to assess the safeness to use from the perspective of physicians, medical staffs, patients, and patients' families and usefulness of pharyngeal scope, the number of devices was limited, the number of patients was not set based on hypothetical statistical tests...
December 5, 2017: Acta Oto-laryngologica
https://www.readbyqxmd.com/read/29205074/overweight-and-obesity-risk-factors-in-children-aged-3-7-years-a-prospective-study-in-the-city-of-krak%C3%A3-w
#20
Małgorzata Kowal, Stanisław Matusik, Maciej Wojciech Pilecki, Łukasz Kryst, Jan Sobiecki, Agnieszka Woronkowicz
BACKGROUND: Early identified factors determining overweight and obesity in childhood may be important for preventive purposes. AIM: To evaluate the influence of the commonly accepted and hypothetical risk factors for overweight/obesity and their mutual relations, using the method of classification trees. SUBJECTS AND METHODS: The data were collected during anthropometric surveys carried out in 2010 in Kraków, Poland. The study involved 1042 pre-school children aged 3-7 years...
December 2017: Annals of Human Biology
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