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https://www.readbyqxmd.com/read/29351315/large-scale-mapping-of-bioactive-peptides-in-structural-and-sequence-space
#1
Agustina E Nardo, M Cristina Añón, Gustavo Parisi
Health-enhancing potential bioactive peptide (BP) has driven an interest in food proteins as well as in the development of predictive methods. Research in this area has been especially active to use them as components in functional foods. Apparently, BPs do not have a given biological function in the containing proteins and they do not evolve under independent evolutionary constraints. In this work we performed a large-scale mapping of BPs in sequence and structural space. Using well curated BP deposited in BIOPEP database, we searched for exact matches in non-redundant sequences databases...
2018: PloS One
https://www.readbyqxmd.com/read/29351231/molecular-network-based-identification-of-competing-endogenous-rnas-in-thyroid-carcinoma
#2
Minjia Lu, Xingyu Xu, Baohang Xi, Qi Dai, Chenli Li, Li Su, Xiaonan Zhou, Min Tang, Yuhua Yao, Jialiang Yang
RNAs may act as competing endogenous RNAs (ceRNAs), a critical mechanism in determining gene expression regulations in many cancers. However, the roles of ceRNAs in thyroid carcinoma remains elusive. In this study, we have developed a novel pipeline called Molecular Network-based Identification of ceRNA (MNIceRNA) to identify ceRNAs in thyroid carcinoma. MNIceRNA first constructs micro RNA (miRNA)-messenger RNA (mRNA)long non-coding RNA (lncRNA) networks from miRcode database and weighted correlation network analysis (WGCNA), based on which to identify key drivers of differentially expressed RNAs between normal and tumor samples...
January 19, 2018: Genes
https://www.readbyqxmd.com/read/29350320/ethical-implications-in-vaccine-pharmacotherapy-for-treatment-and-prevention-of-drug-of-abuse-dependence
#3
Anna Carfora, Paola Cassandro, Alessandro Feola, Francesco La Sala, Raffaella Petrella, Renata Borriello
Different immunotherapeutic approaches are in the pipeline for the treatment of drug dependence. "Drug vaccines" aim to induce the immune system to produce antibodies that bind to drugs and prevent them from inducing rewarding effects in the brain. Drugs of abuse currently being tested using these new approaches are opioids, nicotine, cocaine, and methamphetamine. In human clinical trials, "cocaine and nicotine vaccines" have been shown to induce sufficient antibody levels while producing few side effects. Studies in humans, determining how these vaccines interact in combination with their target drug, are underway...
January 19, 2018: Journal of Bioethical Inquiry
https://www.readbyqxmd.com/read/29350129/new-medications-for-treatment-resistant-depression-a-brief-review-of-recent-developments
#4
Michael E Thase
There is a great unmet need for new medications with novel mechanisms of action that can effectively treat patients who do not benefit from standard antidepressant therapies. After a period in which it seemed as if the pharmaceutical pipeline for new antidepressants was going dry, the past decade has witnessed renewed interest, beginning with discovery of the antidepressant effects of ketamine. This article briefly highlights more recent research on ketamine and other investigational antidepressants.
December 2017: CNS Spectrums
https://www.readbyqxmd.com/read/29349498/plasma-metabolites-associated-with-type-2-diabetes-in-a-swedish-population-a-case-control-study-nested-in-a-prospective-cohort
#5
Lin Shi, Carl Brunius, Marko Lehtonen, Seppo Auriola, Ingvar A Bergdahl, Olov Rolandsson, Kati Hanhineva, Rikard Landberg
AIMS/HYPOTHESIS: The aims of the present work were to identify plasma metabolites that predict future type 2 diabetes, to investigate the changes in identified metabolites among individuals who later did or did not develop type 2 diabetes over time, and to assess the extent to which inclusion of predictive metabolites could improve risk prediction. METHODS: We established a nested case-control study within the Swedish prospective population-based Västerbotten Intervention Programme cohort...
January 18, 2018: Diabetologia
https://www.readbyqxmd.com/read/29348708/hybphylomaker-target-enrichment-data-analysis-from-raw-reads-to-species-trees
#6
Tomáš Fér, Roswitha E Schmickl
Summary: Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29347966/reprdb-and-pandb-minimalist-databases-with-maximal-microbial-representation
#7
Wei Zhou, Nicole Gay, Julia Oh
BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes...
January 18, 2018: Microbiome
https://www.readbyqxmd.com/read/29346583/datamed-an-open-source-discovery-index-for-finding-biomedical-datasets
#8
Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-Eui Kim, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Claudiu Farcas, Todd Johnson, Ron Margolis, George Alter, Susanna-Assunta Sansone, Ian M Fore, Lucila Ohno-Machado, Jeffrey S Grethe, Hua Xu
Objective: Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain. Materials and Methods: DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium...
January 13, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29346292/isoform-sequencing-and-state-of-art-applications-for-unravelling-complexity-of-plant-transcriptomes
#9
REVIEW
Dong An, Hieu X Cao, Changsheng Li, Klaus Humbeck, Wenqin Wang
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications...
January 18, 2018: Genes
https://www.readbyqxmd.com/read/29346071/identification-of-potential-inhibitors-against-nuclear-dam1-complex-subunit-ask1-of-candida-albicans-using-virtual-screening-and-md-simulations
#10
Himanshu Tripathi, Feroz Khan
Identification of hit compounds against specific target form the starting point for a drug discovery program. A consistent decline of new chemical entities (NCEs) in recent years prompted a challenge to explore newer approaches to discover potential hit compounds that in turn can be converted into leads, and ultimately drug with desired therapeutic efficacy. The vast amount of omics and activity data available in public databases offers an opportunity to identify novel targets and their potential inhibitors...
January 1, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29345486/facilitating-pipeline-progress-from-doctoral-degree-to-first-job
#11
Nadine J Kaslow, Debra A Bangasser, Catherine L Grus, Stephen R McCutcheon, Garth A Fowler
The sequence of professional development within psychology from doctoral education to first job represents a period of remarkable professional and personal growth for each trainee. However, this sequence also contains a variety of barriers that hinder progress through the pipeline. The myriad individual-, program-, and system-level barriers encountered by trainees in health service/other applied service psychology and in research basic/applied psychology are identified. To actively and systematically facilitate improved passage through major transition points, individual trainee and trainer, program- and system-level action steps are recommended...
January 2018: American Psychologist
https://www.readbyqxmd.com/read/29345117/candida-auris-a-systematic-review-and-meta-analysis-of-current-updates-on-an-emerging-multidrug-resistant-pathogen
#12
John Osei Sekyere
From 2009, Candida auris has emerged as a multidrug-resistant ascomycete yeast pathogen with the capacity for easy transmission between patients and hospitals, as well as persistence on environmental surfaces. Its association with high mortalities, breakthrough and persistent candidaemia, inconsistencies in susceptibility testing results, misidentification by available commercial identification systems and treatment failure, complicates its management and detection. Within the last nine years, C. auris has been increasingly reported from far-Eastern Asia, the Middle East, Africa, Europe, South and North America with substantial fatalities and misidentification...
January 18, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29345069/automation-aided-optimization-of-cloning-expression-and-purification-of-enzymes-of-the-bacterial-sialic-acid-catabolic-and-sialylation-pathways-enzymes-for-structural-studies
#13
Sneha Bairy, Lakshmi Narayanan Gopalan, Thanuja Gangi Setty, Sathya Srinivasachari, Lavanyaa Manjunath, Jay Prakash Kumar, Sai R Guntupalli, Sucharita Bose, Vinod Nayak, Swagatha Ghosh, Nitish Sathyanarayanan, Rhawnie Caing-Carlsson, Weixiao Yuan Wahlgren, Rosmarie Friemann, S Ramaswamy, Muniasamy Neerathilingam
The process of obtaining a well-expressing, soluble and correctly folded constructs can be made easier and quicker by automating the optimization of cloning, expression and purification. While there are many semiautomated pipelines available for cloning, expression and purification, there is hardly any pipeline that involves complete automation. Here, we achieve complete automation of all the steps involved in cloning and in vivo expression screening. This is demonstrated using 18 genes involved in sialic acid catabolism and the surface sialylation pathway...
January 17, 2018: Microbial Biotechnology
https://www.readbyqxmd.com/read/29344898/methods-for-high-throughput-drug-combination-screening-and-synergy-scoring
#14
Liye He, Evgeny Kulesskiy, Jani Saarela, Laura Turunen, Krister Wennerberg, Tero Aittokallio, Jing Tang
Gene products or pathways that are aberrantly activated in cancer but not in normal tissue hold great promises for being effective and safe anticancer therapeutic targets. Many targeted drugs have entered clinical trials but so far showed limited efficacy mostly due to variability in treatment responses and often rapidly emerging resistance. Toward more effective treatment options, we will need multi-targeted drugs or drug combinations, which selectively inhibit the viability and growth of cancer cells and block distinct escape mechanisms for the cells to become resistant...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344884/analyzing-dna-methylation-patterns-during-tumor-evolution
#15
Heng Pan, Olivier Elemento
Epigenetic modifications play a key role in cellular development and tumorigenesis. Recent large-scale genomic studies have shown that mutations in players of the epigenetic machinery and concomitant perturbation of epigenomic patterning are frequent events in tumors. Among epigenetic marks, DNA methylation is one of the best studied. Hyper- and hypo-methylation events of specific regulatory elements (such as promoters and enhancers) are sometimes thought to be correlated with expression of nearby genes. High-throughput bisulfite converted sequencing is currently the technology of choice for studying DNA methylation in base-pair resolution and on whole-genome scale...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344882/detection-of-combinatorial-mutational-patterns-in-human-cancer-genomes-by-exclusivity-analysis
#16
Hua Tan, Xiaobo Zhou
Cancer genes may tend to mutate in a co-mutational or mutually exclusive manner in a tumor sample of a specific cancer, which constitute two known combinatorial mutational patterns for a given gene set. Previous studies have established that genes functioning in different signaling pathways can mutate in the same sample, i.e., a tumor from one patient, while genes operating in the same pathway are rarely mutated in the same cancer genome. Therefore, reliable identification of combinatorial mutational patterns of candidate cancer genes has important ramifications in inferring signaling network modules in a particular cancer type...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344781/automated-3d-soma-segmentation-with-morphological-surface-evolution-for-neuron-reconstruction
#17
Donghao Zhang, Siqi Liu, Yang Song, Dagan Feng, Hanchuan Peng, Weidong Cai
The automatic neuron reconstruction is important since it accelerates the collection of 3D neuron models for the neuronal morphological studies. The majority of the previous neuron reconstruction methods only focused on tracing neuron fibres without considering the somatic surface. Thus, topological errors often present around the soma area in the results obtained by these tracing methods. Segmentation of the soma structures can be embedded in the existing neuron tracing methods to reduce such topological errors...
January 18, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29343741/species-distribution-modelling-contrasting-presence-only-models-with-plot-abundance-data
#18
Vitor H F Gomes, Stéphanie D IJff, Niels Raes, Iêda Leão Amaral, Rafael P Salomão, Luiz de Souza Coelho, Francisca Dionízia de Almeida Matos, Carolina V Castilho, Diogenes de Andrade Lima Filho, Dairon Cárdenas López, Juan Ernesto Guevara, William E Magnusson, Oliver L Phillips, Florian Wittmann, Marcelo de Jesus Veiga Carim, Maria Pires Martins, Mariana Victória Irume, Daniel Sabatier, Jean-François Molino, Olaf S Bánki, José Renan da Silva Guimarães, Nigel C A Pitman, Maria Teresa Fernandez Piedade, Abel Monteagudo Mendoza, Bruno Garcia Luize, Eduardo Martins Venticinque, Evlyn Márcia Moraes de Leão Novo, Percy Núñez Vargas, Thiago Sanna Freire Silva, Angelo Gilberto Manzatto, John Terborgh, Neidiane Farias Costa Reis, Juan Carlos Montero, Katia Regina Casula, Beatriz S Marimon, Ben-Hur Marimon, Euridice N Honorio Coronado, Ted R Feldpausch, Alvaro Duque, Charles Eugene Zartman, Nicolás Castaño Arboleda, Timothy J Killeen, Bonifacio Mostacedo, Rodolfo Vasquez, Jochen Schöngart, Rafael L Assis, Marcelo Brilhante Medeiros, Marcelo Fragomeni Simon, Ana Andrade, William F Laurance, José Luís Camargo, Layon O Demarchi, Susan G W Laurance, Emanuelle de Sousa Farias, Henrique Eduardo Mendonça Nascimento, Juan David Cardenas Revilla, Adriano Quaresma, Flavia R C Costa, Ima Célia Guimarães Vieira, Bruno Barçante Ladvocat Cintra, Hernán Castellanos, Roel Brienen, Pablo R Stevenson, Yuri Feitosa, Joost F Duivenvoorden, Gerardo A Aymard C, Hugo F Mogollón, Natalia Targhetta, James A Comiskey, Alberto Vicentini, Aline Lopes, Gabriel Damasco, Nállarett Dávila, Roosevelt García-Villacorta, Carolina Levis, Juliana Schietti, Priscila Souza, Thaise Emilio, Alfonso Alonso, David Neill, Francisco Dallmeier, Leandro Valle Ferreira, Alejandro Araujo-Murakami, Daniel Praia, Dário Dantas do Amaral, Fernanda Antunes Carvalho, Fernanda Coelho de Souza, Kenneth Feeley, Luzmila Arroyo, Marcelo Petratti Pansonato, Rogerio Gribel, Boris Villa, Juan Carlos Licona, Paul V A Fine, Carlos Cerón, Chris Baraloto, Eliana M Jimenez, Juliana Stropp, Julien Engel, Marcos Silveira, Maria Cristina Peñuela Mora, Pascal Petronelli, Paul Maas, Raquel Thomas-Caesar, Terry W Henkel, Doug Daly, Marcos Ríos Paredes, Tim R Baker, Alfredo Fuentes, Carlos A Peres, Jerome Chave, Jose Luis Marcelo Pena, Kyle G Dexter, Miles R Silman, Peter Møller Jørgensen, Toby Pennington, Anthony Di Fiore, Fernando Cornejo Valverde, Juan Fernando Phillips, Gonzalo Rivas-Torres, Patricio von Hildebrand, Tinde R van Andel, Ademir R Ruschel, Adriana Prieto, Agustín Rudas, Bruce Hoffman, César I A Vela, Edelcilio Marques Barbosa, Egleé L Zent, George Pepe Gallardo Gonzales, Hilda Paulette Dávila Doza, Ires Paula de Andrade Miranda, Jean-Louis Guillaumet, Linder Felipe Mozombite Pinto, Luiz Carlos de Matos Bonates, Natalino Silva, Ricardo Zárate Gómez, Stanford Zent, Therany Gonzales, Vincent A Vos, Yadvinder Malhi, Alexandre A Oliveira, Angela Cano, Bianca Weiss Albuquerque, Corine Vriesendorp, Diego Felipe Correa, Emilio Vilanova Torre, Geertje van der Heijden, Hirma Ramirez-Angulo, José Ferreira Ramos, Kenneth R Young, Maira Rocha, Marcelo Trindade Nascimento, Maria Natalia Umaña Medina, Milton Tirado, Ophelia Wang, Rodrigo Sierra, Armando Torres-Lezama, Casimiro Mendoza, Cid Ferreira, Cláudia Baider, Daniel Villarroel, Henrik Balslev, Italo Mesones, Ligia Estela Urrego Giraldo, Luisa Fernanda Casas, Manuel Augusto Ahuite Reategui, Reynaldo Linares-Palomino, Roderick Zagt, Sasha Cárdenas, William Farfan-Rios, Adeilza Felipe Sampaio, Daniela Pauletto, Elvis H Valderrama Sandoval, Freddy Ramirez Arevalo, Isau Huamantupa-Chuquimaco, Karina Garcia-Cabrera, Lionel Hernandez, Luis Valenzuela Gamarra, Miguel N Alexiades, Susamar Pansini, Walter Palacios Cuenca, William Milliken, Joana Ricardo, Gabriela Lopez-Gonzalez, Edwin Pos, Hans Ter Steege
Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343580/advancing-our-understanding-of-protective-maternal-immunity-as-a-guide-for-development-of-vaccines-to-reduce-congenital-cytomegalovirus-infections
#19
Sallie R Permar, Mark R Schleiss, Stanley A Plotkin
Human cytomegalovirus (HCMV) is the most common congenitally transmitted pathogen worldwide, impacting an estimated 1 million newborns annually. Congenital HCMV (cCMV) infection is a major global contributor to long-term neurologic deficits, including deafness, microcephaly, neurodevelopmental delay, as well as fetal loss and occasional infant mortality. Accordingly, a maternal vaccine to prevent cCMV continues to be a top public health priority. Nevertheless, we remain without a licensed vaccine. Maternal immunity provides partial protection, as the risk of vertical HCMV transmission from chronically infected mothers is reduced compared to settings in which the mother is newly infected during pregnancy...
January 17, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29343101/macon-a-web-tool-for-computing-dna-methylation-data-obtained-by-the-illumina-infinium-human-dna-methylation-beadarray
#20
Naoko Iida, Yoshihiro Okuda, Osamu Ogasawara, Satoshi Yamashita, Hideyuki Takeshima, Toshikazu Ushijima
AIM: Bioinformatics analysis for Illumina Infinium Human DNA methylation BeadArray is essential, but still remains difficult task for many experimental researchers. We here aimed to develop a browser-accessible bioinformatics tool for analyzing the BeadArray data. MATERIALS & METHODS: The tool was established as an analytical pipeline using R, Perl and Python programming languages. RESULTS: We introduced a method that groups neighboring probes into a genomic block, which facilitated efficient identification of densely methylated/unmethylated regions...
January 18, 2018: Epigenomics
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