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https://www.readbyqxmd.com/read/29345009/choosing-non-redundant-representative-subsets-of-protein-sequence-data-sets-using-submodular-optimization
#1
Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble
Selecting a non-redundant representative subset of sequences is a common step in many bioinformatics workflows, such as the creation of non-redundant training sets for sequence and structural models or selection of "operational taxonomic units" from metagenomics data. Previous methods for this task, such as CD-HIT, PISCES and UCLUST, apply a heuristic threshold-based algorithm that has no theoretical guarantees. We propose a new approach based on submodular optimization. Submodular optimization, a discrete analogue to continuous convex optimization, has been used with great success for other representative set selection problems...
January 18, 2018: Proteins
https://www.readbyqxmd.com/read/29330460/enhanced-skeletal-muscle-ribosome-biogenesis-yet-attenuated-mtorc1-and-ribosome-biogenesis-related-signalling-following-short-term-concurrent-versus-single-mode-resistance-training
#2
Jackson J Fyfe, David J Bishop, Jonathan D Bartlett, Erik D Hanson, Mitchell J Anderson, Andrew P Garnham, Nigel K Stepto
Combining endurance training with resistance training (RT) may attenuate skeletal muscle hypertrophic adaptation versus RT alone; however, the underlying mechanisms are unclear. We investigated changes in markers of ribosome biogenesis, a process linked with skeletal muscle hypertrophy, following concurrent training versus RT alone. Twenty-three males underwent eight weeks of RT, either performed alone (RT group, n = 8), or combined with either high-intensity interval training (HIT+RT group, n = 8), or moderate-intensity continuous training (MICT+RT group, n = 7)...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29316715/twelve-weeks-of-medium-intensity-exercise-therapy-affects-the-lipoprotein-profile-of-multiple-sclerosis-patients
#3
Winde Jorissen, Tim Vanmierlo, Inez Wens, Veerle Somers, Bart Van Wijmeersch, Jeroen F Bogie, Alan T Remaley, Bert O Eijnde, Jerome J A Hendriks
Multiple sclerosis (MS) is an inflammatory auto-immune disease of the central nervous system (CNS). Serum glucose alterations and impaired glucose tolerance (IGT) are reported in MS patients, and are commonly associated with the development of cardio-metabolic co-morbidities. We previously found that a subgroup of MS patients shows alterations in their lipoprotein profile that are similar to a pre-cardiovascular risk profile. In addition, we showed that a high-intensity exercise training has a positive effect on IGT in MS patients...
January 8, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29302090/an-approach-for-some-in-advanced-pharmacy-informatics-education
#4
Allen Flynn, Brent I Fox, Kevin A Clauson, Terry L Seaton, Elizabeth Breeden
Computerization is transforming health care while the quantity and complexity of biomedical knowledge rapidly grows. Today, all clinicians use health information technology (HIT), but only some pharmacists need to be cross-trained in "all" that advanced informatics entails so they can devise new and better information systems to support the pharmacy practice of the future. We propose a dual approach to informatics education in pharmacy: incorporate fundamental informatics education into pharmacy curricula for all students; and train some students interested in becoming informatics experts to design, develop, implement, and evaluate novel HIT for pharmacy...
November 2017: American Journal of Pharmaceutical Education
https://www.readbyqxmd.com/read/29290650/structural-shift-of-gut-microbiota-during-chemo-preventive-effects-of-epigallocatechin-gallate-on-colorectal-carcinogenesis-in-mice
#5
Xin Wang, Tao Ye, Wen-Jie Chen, You Lv, Zong Hao, Jun Chen, Jia-Ying Zhao, Hui-Peng Wang, Yuan-Kun Cai
AIM: To investigate the effect of epigallocatechin gallate (EGCG) on structural changes of gut microbiota in colorectal carcinogenesis. METHODS: An azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colitis mouse model was established. Forty-two female FVB/N mice were randomly divided into the following three groups: group 1 (10 mice, negative control) was treated with vehicle, group 2 (16 mice, positive control) was treated with AOM plus vehicle, and group 3 (16 mice, EG) was treated with AOM plus EGCG...
December 14, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29285887/hit-dexter-a-machine-learning-model-for-the-prediction-of-frequent-hitters
#6
Conrad Stork, Johannes Wagner, Nils-Ole Friedrich, Christina de Bruyn Kops, Martin Šícho, Johannes Kirchmair
False-positive assay readouts caused by badly behaving compounds (frequent hitters, pan-assay interference compounds - PAINS, aggregators and others) continue to pose a major challenge to experimental screening. Few in silico methods exist that allow the prediction of such problematic compounds. We report on the development of Hit Dexter, two extremely randomized trees classifiers for the prediction of compounds likely to trigger positive assay readouts either by true promiscuity or by assay interference. The models were trained on a well-prepared dataset extracted from the PubChem Bioassay database, consisting of approximately 311k compounds tested for activity on at least 50 proteins...
December 29, 2017: ChemMedChem
https://www.readbyqxmd.com/read/29282565/hawkrank-a-new-scoring-function-for-protein-protein-docking-based-on-weighted-energy-terms
#7
Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu, Tingjun Hou
Deciphering the structural determinants of protein-protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for the structural modeling of PPIs, such as protein-protein docking, are quite needed to complement existing experimental techniques. The reliability of a protein-protein docking method is dependent on the ability of the scoring function to accurately distinguish the near-native binding structures from a huge number of decoys...
December 28, 2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29276494/no-sensory-compensation-for-olfactory-memory-differences-between-blind-and-sighted-people
#8
Agnieszka Sorokowska, Maciej Karwowski
Blindness can be a driving force behind a variety of changes in sensory systems. When vision is missing, other modalities and higher cognitive functions can become hyper-developed through a mechanism called sensory compensation. Overall, previous studies suggest that olfactory memory in blind people can be better than that of the sighted individuals. Better performance of blind individuals in other-sensory modalities was hypothesized to be a result of, among others, intense perceptual training. At the same time, if the superiority of blind people in olfactory abilities indeed results from training, their scores should not decrease with age to such an extent as among the sighted people...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/29262272/effects-of-carbohydrate-mouth-rinse-and-caffeine-on-high-intensity-interval-running-in-a-fed-state
#9
Simon Devenney, Shane Mangan, Marcus Shortall, Kieran Collins
The current study aims to identify if mouth rinsing with a 6% carbohydrate solution (CMR) and mouth rinsing and ingestion of caffeine (CMR+CAFF) can affect exercise performance during steady state (SS) running and high intensity intervals (HIT) in comparison to a 0% control solution (PLA), when in a fed state. Eight recreationally trained males completed three trials (CMR, CMR + CAFF, and PLA) of 45-min SS run and a HIT protocol (90% peak treadmill velocity) until fatigue in a double blinded, repeated measures study...
December 20, 2017: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
https://www.readbyqxmd.com/read/29226142/computational-exploration-for-lead-compounds-that-can-reverse-the-nuclear-morphology-in-progeria
#10
Shailima Rampogu, Ayoung Baek, Minky Son, Amir Zeb, Chanin Park, Raj Kumar, Gihwan Lee, Donghwan Kim, Yeonuk Choi, Yeongrae Cho, Yohan Park, Seok Ju Park, Keun Woo Lee
Progeria is a rare genetic disorder characterized by premature aging that eventually leads to death and is noticed globally. Despite alarming conditions, this disease lacks effective medications; however, the farnesyltransferase inhibitors (FTIs) are a hope in the dark. Therefore, the objective of the present article is to identify new compounds from the databases employing pharmacophore based virtual screening. Utilizing nine training set compounds along with lonafarnib, a common feature pharmacophore was constructed consisting of four features...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29225901/immediate-response-in-markers-of-inflammation-and-angiogenesis-during-exercise-a-randomised-cross-over-study-in-heart-transplant-recipients
#11
Marianne Yardley, Thor Ueland, Pål Aukrust, Annika Michelsen, Elisabeth Bjørkelund, Lars Gullestad, Kari Nytrøen
Background: The present study explored and compared the immediate responses in markers of inflammation and angiogenesis in maintenance heart transplant (HTx) recipients before, during and after sessions of high-intensity interval training (HIT) versus moderate-intensity continuous training (MICT). The study aimed to explain some of the trigger mechanisms behind HIT in HTx recipients. Methods: This cross-over study included 14 HTx patients (mean±SD age: 53±13 years; time since HTx, 3±2 years)...
2017: Open Heart
https://www.readbyqxmd.com/read/29214926/aerobic-training-performed-at-ventilatory-threshold-improves-liver-enzymes-and-lipid-profile-related-to-non-alcoholic-fatty-liver-disease-in-adolescents-with-obesity
#12
Camila Tc de Lira, Marcos Am Dos Santos, Priscyla P Gomes, Yara L Fidelix, Ana Co Dos Santos, Thiago Rs Tenório, Mara C Lofrano-Prado, Wagner L do Prado
BACKGROUND: Despite the positive effects of high-intensity training on weight management and health-related outcomes, it is postulated that high-intensity training may also induce oxidative stress, increasing hepatic damage. AIM: The aim of this study was to compare the effects of low versus high-intensity training on biomarkers related to non-alcoholic fatty liver disease (NAFLD) in adolescents with obesity. METHODS: For this study 107 adolescents (15 ± 1 years) with obesity (BMI = 34...
December 2017: Nutrition and Health
https://www.readbyqxmd.com/read/29207983/protocol-for-project-impact-improving-millions-hearts-for-provider-and-community-transformation-a-quasi-experimental-evaluation-of-an-integrated-electronic-health-record-and-community-health-worker-intervention-study-to-improve-hypertension-management-among
#13
Priscilla M Lopez, Jennifer Zanowiak, Keith Goldfeld, Katarzyna Wyka, Ahmad Masoud, Susan Beane, Rashi Kumar, Phoebe Laughlin, Chau Trinh-Shevrin, Lorna Thorpe, Nadia Islam
BACKGROUND: The Million Hearts® initiative aims to prevent heart disease and stroke in the United States by mobilizing public and private sectors around a core set of objectives, with particular attention on improving blood pressure control. South Asians in particular have disproportionately high rates of hypertension and face numerous cultural, linguistic, and social barriers to accessing healthcare. Interventions utilizing Health information technology (HIT) and community health worker (CHW)-led patient coaching have each been demonstrated to be effective at advancing Million Hearts® goals, yet few studies have investigated the potential impact of integrating these strategies into a clinical-community linkage initiative...
December 6, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/29206457/adverpred-web-service-for-prediction-of-adverse-effects-of-drugs
#14
Sergey M Ivanov, Alexey A Lagunin, Anastasia V Rudik, Dmitry A Filimonov, Vladimir V Poroikov
Application of structure-activity relationships (SARs) for the prediction of adverse effects of drugs (ADEs) has been reported in many published studies. Training sets for the creation of SAR models are usually based on drug label information which allows for the generation of data sets for many hundreds of drugs. Since many ADEs may not be related to drug consumption, one of the main problems in such studies is the quality of data on drug-ADE pairs obtained from labels. The information on ADEs may be included in three sections of the drug labels: "Boxed warning," "Warnings and Precautions," and "Adverse reactions...
December 22, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29201082/pharmacophore-based-virtual-screening-approach-to-identify-selective-pde4b-inhibitors
#15
Anand Gaurav, Vertika Gautam
Phosphodiesterase 4 (PDE4) has been established as a promising target in asthma and chronic obstructive pulmonary disease. PDE4B subtype selective inhibitors are known to reduce the dose limiting adverse effect associated with non-selective PDE4B inhibitors. This makes the development of PDE4B subtype selective inhibitors a desirable research goal. To achieve this goal, ligand based pharmacophore modeling approach is employed. Separate pharmacophore hypotheses for PDE4B and PDE4D inhibitors were generated using HypoGen algorithm and 106 PDE4 inhibitors from literature having thiopyrano [3,2-d] Pyrimidines, 2-arylpyrimidines, and triazines skeleton...
2017: Iranian Journal of Pharmaceutical Research: IJPR
https://www.readbyqxmd.com/read/29199783/physical-and-technical-demands-of-elite-beach-volleyball-according-to-playing-position-and-gender
#16
Simone Natali, Davide Ferioli, Antonio LA Torre, Matteo Bonato
BACKGROUND: Beach volleyball is a team sport played by two teams of two players on a sand court divided by a net. To date, research has mainly focused on male beach volleyball players. Therefore, the aim of this study was to assess work-rest ratio and physical actions between males and females according to their role. METHODS: Forty-two elite beach volley players (24 males and 18 females) were filmed during 12 beach volleyball matches of the Swatch Major Series 2016 of the beach volleyball World Tour in Poreč in (Croatia)...
December 1, 2017: Journal of Sports Medicine and Physical Fitness
https://www.readbyqxmd.com/read/29181781/recognition-of-transposed-melodies-effects-of-pitch-distance-and-harmonic-distance
#17
Abigail L Kleinsmith, W Trammell Neill
People easily recognize a familiar melody in a previously unheard key, but they also retain some key-specific information. Does the recognition of a transposed melody depend on either pitch distance or harmonic distance from the initially learned instances? Previous research has shown a stronger effect of pitch closeness than of harmonic similarity, but did not directly test for an additional effect of the latter variable. In the present experiment, we familiarized participants with a simple eight-note melody in two different keys (C and D) and then tested their ability to discriminate the target melody from foils in other keys...
November 27, 2017: Psychonomic Bulletin & Review
https://www.readbyqxmd.com/read/29173930/birth-outcomes-in-relation-to-intimate-partner-violence
#18
Ping-Hsin Chen, Sue Rovi, Marielos L Vega, Theodore Barrett, Ko-Yu Pan, Mark S Johnson
OBJECTIVES: Intimate partner violence (IPV)during pregnancy is a significant public health problem. Approximately 324,000 IPV victimizations occur during pregnancy each year. However, research on the impact of IPV on birth outcomes yields conflicting findings. This study examines the association of IPV with birth outcomes among pregnant women. STUDY DESIGN: We used a retrospective cohort study design to analyze data from chart reviews of a random sample of 1542 pregnant women...
January 2017: Journal of the National Medical Association
https://www.readbyqxmd.com/read/29161767/effects-of-different-endurance-exercise-modalities-on-migraine-days-and-cerebrovascular-health-in-episodic-migraineurs-a-randomized-controlled-trial
#19
Henner Hanssen, Alice Minghetti, Stefano Magon, Anja Rossmeissl, Maria Rasenack, Athina Papadopoulou, Christopher Klenk, Oliver Faude, Lukas Zahner, Till Sprenger, Lars Donath
BACKGROUND: Aerobic exercise training is a promising complementary treatment option in migraine and can reduce migraine days and improve retinal microvascular function. Our aim was to elucidate whether different aerobic exercise programs at high vs. moderate intensities distinctly affect migraine days as primary outcome and retinal vessel parameters as a secondary. METHODS: In this randomized controlled trial, migraine days were recorded by a validated migraine diary in 45 migraineurs of which 36 (female: 28; age: 36 (SD:10)/ BMI: 23...
November 21, 2017: Scandinavian Journal of Medicine & Science in Sports
https://www.readbyqxmd.com/read/29154212/consensus-scoring-model-for-the-molecular-docking-study-of-mtor-kinase-inhibitor
#20
Dong-Dong Li, Xiang-Feng Meng, Qiang Wang, Pan Yu, Lin-Guo Zhao, Zheng-Ping Zhang, Zhen-Zhong Wang, Wei Xiao
The discovery of mammalian target of rapamycin (mTOR) kinase inhibitors has always been a research hotspot of antitumor drugs. Consensus scoring used in the docking study of mTOR kinase inhibitors usually improves hit rate of virtual screening. Herein, we attempt to build a series of consensus scoring models based on a set of the common scoring functions. In this paper, twenty-five kinds of mTOR inhibitors (16 clinical candidate compounds and 9 promising preclinical compounds) are carefully collected, and selected for the molecular docking study used by the Glide docking programs within the standard precise (SP) mode...
November 6, 2017: Journal of Molecular Graphics & Modelling
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