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https://www.readbyqxmd.com/read/27922095/co-expression-network-analyses-identify-functional-modules-associated-with-development-and-stress-response-in-gossypium-arboreum
#1
Qi You, Liwei Zhang, Xin Yi, Kang Zhang, Dongxia Yao, Xueyan Zhang, Qianhua Wang, Xinhua Zhao, Yi Ling, Wenying Xu, Fuguang Li, Zhen Su
Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921275/preoperative-characteristics-of-the-p-r-o-s-t-a-t-e-scores-a-novel-predictive-tool-for-the-risk-of-positive-surgical-margin-after-radical-prostatectomy
#2
Ben Xu, Cheng Luo, Qian Zhang, Jie Jin
OBJECTIVES: To propose a novel scoring system to predict the risk of positive surgical margin (PSM) after radical prostatectomy (RP) in prostate cancer (PCa) patients. MATERIALS AND METHODS: Eight reproducible variables available from preoperative characteristics of PCa patients were measured: PSA level (P), ratio of positive biopsy needles (R), obesity (O), scores of Gleason (S), T stage by preoperative MRI scan (T), age (A), tumor volume (T) and experience of the surgeon (E)...
December 5, 2016: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/27921000/distress-in-infertile-males-in-manipal-india-a-clinic-based-study
#3
Ansha Patel, Podila Satya Venkata Narasimha Sharma, Pratapkumar Narayan, Binu Valsalakumari Sreekumaran Nair, Dinesh Narayanakurup, Praveena Joglekar Pai
BACKGROUND: Being infertile comes as an overwhelming realization for couples trying to conceive. In consideration of rising rates of infertility worldwide, clinicians in India have also begun exploring this field for new possibilities, development and research. The purpose of this study was to estimate the proportion and predictors of infertility specific stress in males diagnosed with primary infertility. METHODS: This cross-sectional research was conducted in an assisted reproduction center, Manipal, India, on 300 infertile married males...
October 2016: Journal of Reproduction & Infertility
https://www.readbyqxmd.com/read/27920788/vegetative-and-adaptive-traits-predict-different-outcomes-for-restoration-using-hybrids
#4
Philip A Crystal, Nathanael I Lichti, Keith E Woeste, Douglass F Jacobs
Hybridization has been implicated as a driver of speciation, extinction, and invasiveness, but can also provide resistant breeding stock following epidemics. However, evaluating the appropriateness of hybrids for use in restoration programs is difficult. Past the F1 generation, the proportion of a progenitor's genome can vary widely, as can the combinations of parental genomes. Detailed genetic analysis can reveal this information, but cannot expose phenotypic alterations due to heterosis, transgressive traits, or changes in metabolism or development...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27920726/hrvanalysis-a-free-software-for-analyzing-cardiac-autonomic-activity
#5
Vincent Pichot, Frédéric Roche, Sébastien Celle, Jean-Claude Barthélémy, Florian Chouchou
Since the pioneering studies of the 1960s, heart rate variability (HRV) has become an increasingly used non-invasive tool for examining cardiac autonomic functions and dysfunctions in various populations and conditions. Many calculation methods have been developed to address these issues, each with their strengths and weaknesses. Although, its interpretation may remain difficult, this technique provides, from a non-invasive approach, reliable physiological information that was previously inaccessible, in many fields including death and health prediction, training and overtraining, cardiac and respiratory rehabilitation, sleep-disordered breathing, large cohort follow-ups, children's autonomic status, anesthesia, or neurophysiological studies...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27920410/a-novel-splice-site-mutation-in-the-aspm-gene-underlies-autosomal-recessive-primary-microcephaly
#6
Jamil A Hashmi, Khalid M Al-Harbi, Khushnooda Ramzan, Alia M Albalawi, Amir Mehmood, Mohammed I Samman, Sulman Basit
BACKGROUND: Autosomal recessive primary microcephaly (MCPH) is a clinically and genetically heterogeneous disorder. Patients with MCPH exhibit reduced occipito-frontal head circumference and non-progressive intellectual disability. To date, 17 genes have been known as an underlying cause of MCPH in humans. ASPM (abnormal spindle-like, microcephaly associated) is the most commonly mutated MCPH gene. OBJECTIVE: Identify the genetic defect underlying MCPH in a Saudi family...
November 2016: Annals of Saudi Medicine
https://www.readbyqxmd.com/read/27920089/world-endometriosis-society-consensus-on-the-classification-of-endometriosis
#7
Neil P Johnson, Lone Hummelshoj, G David Adamson, Jörg Keckstein, Hugh S Taylor, Mauricio S Abrao, Deborah Bush, Ludwig Kiesel, Rulla Tamimi, Kathy L Sharpe-Timms, Luk Rombauts, Linda C Giudice
STUDY QUESTION: What is the global consensus on the classification of endometriosis that considers the views of women with endometriosis? SUMMARY ANSWER: We have produced an international consensus statement on the classification of endometriosis through systematic appraisal of evidence and a consensus process that included representatives of national and international, medical and non-medical societies, patient organizations, and companies with an interest in endometriosis...
December 5, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27919990/validation-and-enhancement-of-the-clinicopathological-melanoma-nomogram-via-incorporation-of-a-molecular-marker-in-the-primary-tumor
#8
Samer A Naffouje, Rand Naffouje, Jinsong Chen, George I Salti
BACKGROUND/AIM: To validate the melanoma nomogram and improve its function in prediction of nodal dissemination by incorporating a molecular marker in the model. Microphthalmia transcription factor (MITF) is an important regulator of melanocyte homeostasis and differentiation. We have shown that the grade of MITF expression in primary melanoma cells can serve as a predictor of nodal status. Many efforts to identify the nodal spread in cutaneous melanoma using non-invasive means have been recently undertaken...
December 2016: Anticancer Research
https://www.readbyqxmd.com/read/27919493/eleven-episodes-of-recurrent-optic-neuritis-of-the-same-eye-for-22-years-eventually-diagnosed-as-neuromyelitis-optica-spectrum-disorder
#9
Yih Chian Yew, Jyh Yung Hor, Thien Thien Lim, Ruban Kanesalingam, Yee Ming Ching, Masita Arip, P E Samuel Easaw, Gaik Bee Eow
It is difficult to predict whether a particular attack of neuromyelitis optica spectrum disorder (NMOSD) will affect the optic nerve [optic neuritis (ON): unilateral or bilateral], spinal cord (myelitis), brain or brainstem, or a combination of the above. We report an interesting case of recurrent ON of the same eye for a total of 11 episodes in a Chinese woman. Over a period of 22 years, the attacks only involved the left eye, and never the right eye and also no myelitis. For a prolonged duration, she was diagnosed as recurrent idiopathic ON...
November 2016: Multiple Sclerosis and related Disorders
https://www.readbyqxmd.com/read/27919446/immunohistochemistry-as-an-accurate-tool-for-evaluating-braf-v600e-mutation-in-130-samples-of-papillary-thyroid-cancer
#10
Zakaria Y Abd Elmageed, Andrew B Sholl, Koji Tsumagari, Zaid Al-Qurayshi, Fulvio Basolo, Krzysztof Moroz, A Hamid Boulares, Paul Friedlander, Paulo Miccoli, Emad Kandil
BACKGROUND: BRAF(V600E) mutation has been investigated by immunohistochemistry and has shown high sensitivity and specificity. We aim to investigate the accuracy of immunohistochemistry versus molecular testing of BRAF(V600E) in papillary thyroid cancer using a large number of polymerase chain reaction-positive BRAF(V600E) papillary thyroid cancer tissues. METHODS: We stained 130 formalin-fixed papillary thyroid cancer specimens using the VE1 antibody: 100 BRAF(V600E) positive and 30 BRAF(V600E) negative confirmed by PCR...
December 2, 2016: Surgery
https://www.readbyqxmd.com/read/27919280/patient-derived-xenografts-a-relevant-preclinical-model-for-drug-development
#11
REVIEW
Luca Pompili, Manuela Porru, Carla Caruso, Annamaria Biroccio, Carlo Leonetti
Identifying appropriate preclinical cancer models remains a major challenge in increasing the efficiency of drug development. A potential strategy to improve patient outcomes could be selecting the 'right' treatment in preclinical studies performed in patient-derived xenografts (PDXs) obtained by direct implants of surgically resected tumours in mice. These models maintain morphological similarities and recapitulate molecular profiling of the original tumours, thus representing a useful tool in evaluating anticancer drug response...
December 5, 2016: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/27919275/rayyan-a-web-and-mobile-app-for-systematic-reviews
#12
Mourad Ouzzani, Hossam Hammady, Zbys Fedorowicz, Ahmed Elmagarmid
BACKGROUND: Synthesis of multiple randomized controlled trials (RCTs) in a systematic review can summarize the effects of individual outcomes and provide numerical answers about the effectiveness of interventions. Filtering of searches is time consuming, and no single method fulfills the principal requirements of speed with accuracy. Automation of systematic reviews is driven by a necessity to expedite the availability of current best evidence for policy and clinical decision-making. We developed Rayyan ( http://rayyan...
December 5, 2016: Systematic Reviews
https://www.readbyqxmd.com/read/27919220/deepqa-improving-the-estimation-of-single-protein-model-quality-with-deep-belief-networks
#13
Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
BACKGROUND: Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem. RESULTS: We introduce a novel single-model quality assessment method DeepQA based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy, physio-chemical characteristics, and structural information...
December 5, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27918579/a-graph-centric-approach-for-metagenome-guided-peptide-and-protein-identification-in-metaproteomics
#14
Haixu Tang, Sujun Li, Yuzhen Ye
Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27918472/a-review-of-computational-methods-for-finding-non-coding-rna-genes
#15
REVIEW
Qaisar Abbas, Syed Mansoor Raza, Azizuddin Ahmed Biyabani, Muhammad Arfan Jaffar
Finding non-coding RNA (ncRNA) genes has emerged over the past few years as a cutting-edge trend in bioinformatics. There are numerous computational intelligence (CI) challenges in the annotation and interpretation of ncRNAs because it requires a domain-related expert knowledge in CI techniques. Moreover, there are many classes predicted yet not experimentally verified by researchers. Recently, researchers have applied many CI methods to predict the classes of ncRNAs. However, the diverse CI approaches lack a definitive classification framework to take advantage of past studies...
December 3, 2016: Genes
https://www.readbyqxmd.com/read/27918434/mass-transport-through-nanostructured-membranes-towards-a-predictive-tool
#16
Siavash Darvishmanesh, Bart Van der Bruggen
This study proposes a new mechanism to understand the transport of solvents through nanostructured membranes from a fundamental point of view. The findings are used to develop readily applicable mathematical models to predict solvent fluxes and solute rejections through solvent resistant membranes used for nanofiltration. The new model was developed based on a pore-flow type of transport. New parameters found to be of fundamental importance were introduced to the equation, i.e., the affinity of the solute and the solvent for the membrane expressed as the hydrogen-bonding contribution of the solubility parameter for the solute, solvent and membrane...
December 2, 2016: Membranes
https://www.readbyqxmd.com/read/27918291/approximate-analytical-solutions-to-the-double-stance-dynamics-of-the-lossy-spring-loaded-inverted-pendulum
#17
Mohammad Shahbazi, Uluç Saranlı, Robert Babuška, Gabriel A D Lopes
This paper introduces approximate time-domain solutions to the otherwise non-integrable double-stance dynamics of the 'bipedal' spring-loaded inverted pendulum (B-SLIP) in the presence of non-negligible damping. We first introduce an auxiliary system whose behavior under certain conditions is approximately equivalent to the B-SLIP in double-stance. Then, we derive approximate solutions to the dynamics of the new system following two different methods: (i) updated-momentum approach that can deal with both the lossy and lossless B-SLIP models, and (ii) perturbation-based approach following which we only derive a solution to the lossless case...
December 5, 2016: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/27918282/conditioned-object-preference-an-alternative-approach-to-measuring-reward-learning-in-rats
#18
Bruce C Kennedy, Maulika Kohli, Jamie J Maertens, Paulina S Marell, Jonathan C Gewirtz
Pavlovian conditioned approach behavior can be directed as much toward discrete cues as it is toward the environmental contexts in which those cues are encountered. The current experiments characterized a tendency of rats to approach object cues whose prior exposure had been paired with reward (conditioned object preference, COP). To demonstrate the phenomenon, rats were conditioned to associate cocaine or saline with two different objects. Rats acquired a preference, assessed using investigation times directed toward each object, for the cocaine-paired object following conditioning...
November 2016: Learning & Memory
https://www.readbyqxmd.com/read/27918183/finding-structure-in-data-using-multivariate-tree-boosting
#19
Patrick J Miller, Gitta H Lubke, Daniel B McArtor, C S Bergeman
Technology and collaboration enable dramatic increases in the size of psychological and psychiatric data collections, but finding structure in these large data sets with many collected variables is challenging. Decision tree ensembles such as random forests (Strobl, Malley, & Tutz, 2009) are a useful tool for finding structure, but are difficult to interpret with multiple outcome variables which are often of interest in psychology. To find and interpret structure in data sets with multiple outcomes and many predictors (possibly exceeding the sample size), we introduce a multivariate extension to a decision tree ensemble method called gradient boosted regression trees (Friedman, 2001)...
December 2016: Psychological Methods
https://www.readbyqxmd.com/read/27918182/theory-guided-exploration-with-structural-equation-model-forests
#20
Andreas M Brandmaier, John J Prindle, John J McArdle, Ulman Lindenberger
Structural equation model (SEM) trees, a combination of SEMs and decision trees, have been proposed as a data-analytic tool for theory-guided exploration of empirical data. With respect to a hypothesized model of multivariate outcomes, such trees recursively find subgroups with similar patterns of observed data. SEM trees allow for the automatic selection of variables that predict differences across individuals in specific theoretical models, for instance, differences in latent factor profiles or developmental trajectories...
December 2016: Psychological Methods
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