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https://www.readbyqxmd.com/read/28098823/integrative-mirna-gene-expression-analysis-enables-refinement-of-associated-biology-and-prediction-of-response-to-cetuximab-in-head-and-neck-squamous-cell-cancer
#1
Loris De Cecco, Marco Giannoccaro, Edoardo Marchesi, Paolo Bossi, Federica Favales, Laura D Locati, Lisa Licitra, Silvana Pilotti, Silvana Canevari
This paper documents the process by which we, through gene and miRNA expression profiling of the same samples of head and neck squamous cell carcinomas (HNSCC) and an integrative miRNA-mRNA expression analysis, were able to identify candidate biomarkers of progression-free survival (PFS) in patients treated with cetuximab-based approaches. Through sparse partial least square-discriminant analysis (sPLS-DA) and supervised analysis, 36 miRNAs were identified in two components that clearly separated long- and short-PFS patients...
January 14, 2017: Genes
https://www.readbyqxmd.com/read/28098789/implications-of-changing-temperatures-on-the-growth-fecundity-and-survival-of-intermediate-host-snails-of-schistosomiasis-a-systematic-review
#2
REVIEW
Chester Kalinda, Moses Chimbari, Samson Mukaratirwa
Climate change has been predicted to increase the global mean temperature and to alter the ecological interactions among organisms. These changes may play critical roles in influencing the life history traits of the intermediate hosts (IHs). This review focused on studies and disease models that evaluate the potential effect of temperature rise on the ecology of IH snails and the development of parasites within them. The main focus was on IH snails of schistosome parasites that cause schistosomiasis in humans...
January 13, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28098590/analgesia-and-sedation-requirements-in-mechanically-ventilated-trauma-patients-with-acute-preinjury-use-of-cocaine-and-or-amphetamines
#3
Bridgette Kram, Shawn J Kram, Michelle L Sharpe, Michael L James, Maragatha Kuchibhatla, Mark L Shapiro
BACKGROUND: The purpose of this study was to determine whether mechanically ventilated trauma patients with a positive urine drug screen (UDS) for cocaine and/or amphetamines have different opioid analgesic and sedative requirements compared with similar patients with a negative drug screen for these stimulants. METHODS: This retrospective, single-center cohort study at a tertiary care, academic medical and level 1 trauma center in the United States included patients ≥16 years of age who were admitted to an adult intensive care unit with a diagnosis of trauma between 2009 and 2013 with a UDS documented within 24 hours of admission, and were mechanically ventilated for >24 hours...
January 16, 2017: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/28098436/bringing-3d-tumor-models-to-the-clinic-predictive-value-for-personalized-medicine
#4
REVIEW
Kathrin Halfter, Barbara Mayer
Current decision-guiding algorithms in cancer drug treatment are based on decades of research and numerous clinical trials. For the majority of patients, this data is successfully applied for a systemic disease management. For a number of patients however, treatment stratification according to clinically based risk criteria will not be sufficient. The most effective treatment options are ideally identified prior to the start of clinical drug therapy. This review will discuss the implementation of three-dimensional (3D) cell culture models as a preclinical testing paradigm for the efficacy of clinical cancer treatment...
January 18, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28098324/ionic-screening-and-dissociation-are-crucial-for-understanding-chemical-self-propulsion-in-polar-solvents
#5
Aidan T Brown, Wilson C K Poon, Christian Holm, Joost de Graaf
Polar solvents like water support the bulk dissociation of themselves and their solutes into ions, and the re-association of these ions into neutral molecules in a dynamic equilibrium, e.g., H2O2 ⇌ H(+) + HO2(-). Using continuum theory, we study the influence of these association-dissociation reactions on the self-propulsion of colloids driven by surface chemical reactions (chemical swimmers). We find that association-dissociation reactions should have a strong influence on swimmers' behaviour, and therefore should be included in future modelling...
January 18, 2017: Soft Matter
https://www.readbyqxmd.com/read/28098322/flory-theory-of-randomly-branched-polymers
#6
Ralf Everaers, Alexander Y Grosberg, Michael Rubinstein, Angelo Rosa
Randomly branched polymer chains (or trees) are a classical subject of polymer physics with connections to the theory of magnetic systems, percolation and critical phenomena. More recently, the model has been reconsidered for RNA, supercoiled DNA and the crumpling of topologically-constrained polymers. While solvable in the ideal case, little is known exactly about randomly branched polymers with volume interactions. Flory theory provides a simple, unifying description for a wide range of branched systems, including isolated trees in good and θ-solvent, and tree melts...
January 18, 2017: Soft Matter
https://www.readbyqxmd.com/read/28098310/a-computational-model-predicts-genetic-nodes-that-allow-switching-between-species-specific-responses-in-a-conserved-signaling-network
#7
Adriana T Dawes, David Wu, Karley K Mahalak, Edward M Zitnik, Natalia Kravtsova, Haiwei Su, Helen M Chamberlin
Cell signaling networks regulate a variety of developmental and physiological processes, and changes in their response to external stimuli are often implicated in disease initiation and progression. To elucidate how different responses can arise from conserved signaling networks, we have developed a mathematical model of the well-characterized Caenorhabditis vulval development network involving EGF, Wnt and Notch signaling that recapitulates biologically observed behaviors. We experimentally block a specific element of the EGF pathway (MEK), and find different behaviors in vulval development in two Caenorhabditis species, C...
January 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28098303/topologically-inferring-pathway-activity-for-precise-survival-outcome-prediction-breast-cancer-as-a-case
#8
Wei Liu, Wei Wang, Guohua Tian, Wenming Xie, Li Lei, Jiujin Liu, Wanxun Huang, Liyan Xu, Enmin Li
Accurately predicting the survival outcome of patients is of great importance in clinical cancer research. In the past decade, building survival prediction models based on gene expression data has received increasing interest. However, the existing methods are mainly based on individual gene signatures, which are known to have limited prediction accuracy on independent datasets and unclear biological relevance. Here, we propose a novel pathway-based survival prediction method called DRWPSurv in order to accurately predict survival outcome...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28098161/modelling-of-occupational-exposure-to-inhalable-nickel-compounds
#9
Benjamin Kendzia, Beate Pesch, Dorothea Koppisch, Rainer Van Gelder, Katrin Pitzke, Wolfgang Zschiesche, Thomas Behrens, Tobias Weiss, Jack Siemiatycki, Jerome Lavoué, Karl-Heinz Jöckel, Roger Stamm, Thomas Brüning
The aim of this study was to estimate average occupational exposure to inhalable nickel (Ni) using the German exposure database MEGA. This database contains 8052 personal measurements of Ni collected between 1990 and 2009 in adjunct with information on the measurement and workplace conditions. The median of all Ni concentrations was 9 μg/m(3) and the 95th percentile was 460 μg/m(3). We predicted geometric means (GMs) for welders and other occupations centered to 1999. Exposure to Ni in welders is strongly influenced by the welding process applied and the Ni content of the used welding materials...
January 18, 2017: Journal of Exposure Science & Environmental Epidemiology
https://www.readbyqxmd.com/read/28097672/collective-resistance-despite-complicity-high-identifiers-rise-above-the-legitimization-of-disadvantage-by-the-in-group
#10
Gloria Jiménez-Moya, Rosa Rodríguez-Bailón, Russell Spears, Soledad de Lemus
How do individuals deal with group disadvantage when their fellow in-group members conceive it as legitimate? Integrating research on the normative conflict model (Packer, 2008, Pers. Soc. Psychol. Rev., 12, 50) and collective action, we expect high identifiers to reject the in-group norm of legitimacy that justifies the inequality, and to assert that the group is actually able and willing to contest the disadvantage by collective means. In Study 1 and Study 2, we tested this hypothesis in different intergroup contexts...
January 17, 2017: British Journal of Social Psychology
https://www.readbyqxmd.com/read/28097603/comprehensive-preclinical-evaluation-of-a-multi-physics-model-of-liver-tumor-radiofrequency-ablation
#11
Chloé Audigier, Tommaso Mansi, Hervé Delingette, Saikiran Rapaka, Tiziano Passerini, Viorel Mihalef, Marie-Pierre Jolly, Raoul Pop, Michele Diana, Luc Soler, Ali Kamen, Dorin Comaniciu, Nicholas Ayache
PURPOSE: We aim at developing a framework for the validation of a subject-specific multi-physics model of liver tumor radiofrequency ablation (RFA). METHODS: The RFA computation becomes subject specific after several levels of personalization: geometrical and biophysical (hemodynamics, heat transfer and an extended cellular necrosis model). We present a comprehensive experimental setup combining multimodal, pre- and postoperative anatomical and functional images, as well as the interventional monitoring of intra-operative signals: the temperature and delivered power...
January 17, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28097441/elevated-preoperative-neutrophil-to-lymphocytes-ratio-predicts-poor-prognosis-after-esophagectomy-in-t1-esophageal-cancer
#12
Kenichi Nakamura, Naoya Yoshida, Yoshifumi Baba, Keisuke Kosumi, Tomoyuki Uchihara, Yuki Kiyozumi, Mayuko Ohuchi, Takatsugu Ishimoto, Masaaki Iwatsuki, Yasuo Sakamoto, Masayuki Watanabe, Hideo Baba
BACKGROUND: The neutrophil-to-lymphocyte ratio (NLR) has been reported to predict the prognosis of various malignant tumors, including esophageal cancer. However, no previous reports have supported the use of the preoperative NLR as an independent prognostic marker focused on superficial (T1) esophageal cancer. The aim of this study was to elucidate the prognostic impact of the preoperative NLR in T1 esophageal cancer. METHODS: This retrospective study recruited 245 consecutive patients with T1 esophageal cancer who underwent subtotal esophagectomy between 2005 and 2016...
January 17, 2017: International Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28097417/bistability-induced-by-generalist-natural-enemies-can-reverse-pest-invasions
#13
Sten Madec, Jérôme Casas, Guy Barles, Christelle Suppo
Analytical modeling of predator-prey systems has shown that specialist natural enemies can slow, stop and even reverse pest invasions, assuming that the prey population displays a strong Allee effect in its growth. We aimed to formalize the conditions in which spatial biological control can be achieved by generalists, through an analytical approach based on reaction-diffusion equations. Using comparison principles, we obtain sufficient conditions for control and for invasion, based on scalar bistable partial differential equations...
January 17, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28097232/vps34-regulates-myofibril-proteostasis-to-prevent-hypertrophic-cardiomyopathy
#14
Hirotaka Kimura, Satoshi Eguchi, Junko Sasaki, Keiji Kuba, Hiroki Nakanishi, Shunsuke Takasuga, Masakazu Yamazaki, Akiteru Goto, Hiroyuki Watanabe, Hiroshi Itoh, Yumiko Imai, Akira Suzuki, Noboru Mizushima, Takehiko Sasaki
Hypertrophic cardiomyopathy (HCM) is a common heart disease with a prevalence of 1 in 500 in the general population. Several mutations in genes encoding cardiac proteins have been found in HCM patients, but these changes do not predict occurrence or prognosis and the molecular mechanisms underlying HCM remain largely elusive. Here we show that cardiac expression of vacuolar protein sorting 34 (Vps34) is reduced in a subset of HCM patients. In a mouse model, muscle-specific loss of Vps34 led to HCM-like manifestations and sudden death...
January 12, 2017: JCI Insight
https://www.readbyqxmd.com/read/28097076/a-critical-issue-in-model-based-inference-for-studying-trait-based-community-assembly-and-a-solution
#15
Cajo J F Ter Braak, Pedro Peres-Neto, Stéphane Dray
Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is observed on species, the environment on sites and the mediating abundance on species-site combinations. A number of correlation-based methods, such as the community weighted trait means method (CWM), the fourth-corner correlation method and the multivariate method RLQ, have been proposed to estimate such trait-environment associations. In these methods, valid statistical testing proceeds by performing two separate resampling tests, one site-based and the other species-based and by assessing significance by the largest of the two p-values (the pmax test)...
2017: PeerJ
https://www.readbyqxmd.com/read/28097073/handling-stress-may-confound-murine-gut-microbiota-studies
#16
Cary R Allen-Blevins, Xiaomeng You, Katie Hinde, David A Sela
BACKGROUND: Accumulating evidence indicates interactions between human milk composition, particularly sugars (human milk oligosaccharides or HMO), the gut microbiota of human infants, and behavioral effects. Some HMO secreted in human milk are unable to be endogenously digested by the human infant but are able to be metabolized by certain species of gut microbiota, including Bifidobacterium longum subsp. infantis (B. infantis), a species sensitive to host stress (Bailey & Coe, 2004). Exposure to gut bacteria like B...
2017: PeerJ
https://www.readbyqxmd.com/read/28097060/why-choose-random-forest-to-predict-rare-species-distribution-with-few-samples-in-large-undersampled-areas-three-asian-crane-species-models-provide-supporting-evidence
#17
Chunrong Mi, Falk Huettmann, Yumin Guo, Xuesong Han, Lijia Wen
Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n = 33), White-naped Crane (Grus vipio, n = 40), and Black-necked Crane (Grus nigricollis, n = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models)...
2017: PeerJ
https://www.readbyqxmd.com/read/28097057/a-gene-expression-study-of-dorso-ventrally-restricted-pigment-pattern-in-adult-fins-of-neolamprologus-meeli-an-african-cichlid-species
#18
Ehsan Pashay Ahi, Kristina M Sefc
Fish color patterns are among the most diverse phenotypic traits found in the animal kingdom. Understanding the molecular and cellular mechanisms that control in chromatophore distribution and pigmentation underlying this diversity is a major goal in developmental and evolutionary biology, which has predominantly been pursued in the zebrafish model system. Here, we apply results from zebrafish work to study a naturally occurring color pattern phenotype in the fins of an African cichlid species from Lake Tanganyika...
2017: PeerJ
https://www.readbyqxmd.com/read/28097008/preclinical-findings-predicting-efficacy-and-side-effect-profile-of-ly2940094-an-antagonist-of-nociceptin-receptors
#19
Jeffrey M Witkin, Linda M Rorick-Kehn, Mark J Benvenga, Benjamin L Adams, Scott D Gleason, Karen M Knitowski, Xia Li, Steven Chaney, Julie F Falcone, Janice W Smith, Julie Foss, Kirsti Lloyd, John T Catlow, David L McKinzie, Kjell A Svensson, Vanessa N Barth, Miguel A Toledo, Nuria Diaz, Celia Lafuente, Alma Jiménez, Alfonso Benito, Conception Pedregal, Maria A Martínez-Grau, Anke Post, Michael A Ansonoff, John E Pintar, Michael A Statnick
Nociceptin/Orphanin FQ (N/OFQ) is a 17 amino acid peptide whose receptor is designated ORL1 or nociceptin receptor (NOP). We utilized a potent, selective, and orally bioavailable antagonist with documented engagement with NOP receptors in vivo to assess antidepressant- and anxiolytic-related pharmacological effects of NOP receptor blockade along with measures of cognitive and motor impingement. LY2940094 ([2-[4-[(2-chloro-4,4-difluoro-spiro[5H-thieno[2,3-c]pyran-7,4'-piperidine]-1'-yl)methyl]-3-methyl-pyrazol-1-yl]-3-pyridyl]methanol) displayed antidepressant-like behavioral effects in the forced-swim test in mice, an effect absent in NOP (-/-) mice...
December 2016: Pharmacology Research & Perspectives
https://www.readbyqxmd.com/read/28097003/application-of-a-systems-pharmacology-model-for-translational-prediction-of-herg-mediated-qtc-prolongation
#20
Verena Gotta, Zhiyi Yu, Frank Cools, Karel van Ammel, David J Gallacher, Sandra A G Visser, Frederick Sannajust, Pierre Morissette, Meindert Danhof, Piet H van der Graaf
Drug-induced QTc interval prolongation (Δ QTc) is a main surrogate for proarrhythmic risk assessment. A higher in vivo than in vitro potency for hERG-mediated QTc prolongation has been suggested. Also, in vivo between-species and patient populations' sensitivity to drug-induced QTc prolongation seems to differ. Here, a systems pharmacology model integrating preclinical in vitro (hERG binding) and in vivo (conscious dog Δ QTc) data of three hERG blockers (dofetilide, sotalol, moxifloxacin) was applied (1) to compare the operational efficacy of the three drugs in vivo and (2) to quantify dog-human differences in sensitivity to drug-induced QTc prolongation (for dofetilide only)...
December 2016: Pharmacology Research & Perspectives
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