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Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed...
October 21, 2016: Briefings in Bioinformatics
Jun Li, Jie Ao, Kai Li, Jie Zhang, Yanyan Li, Le Zhang, Yuyan Wei, Di Gong, Junping Gao, Weiwei Tan, Lugang Huang, Lunxu Liu, Ping Lin, Yuquan Wei
Multidrug resistance (MDR) is one of the most important contributors to the high mortality of cancer and remains a major concern. We previously found that zinc finger protein 32 (ZNF32), an important transcription factor associated with cancer in Homo sapiens, protects tumor cells against cell death induced by oxidative stress and other stimuli. We thus hypothesized that ZNF32 might enable the tolerance of cancer cells to anti-tumor drugs because higher ZNF32 expression has been found in cancer tissues and in drug-resistant lung adenocarcinoma (AC) cells...
October 20, 2016: Cell Death & Disease
S Sun, Y Wang, H Chen, L Fang, Y Cui, X Han, D Wu, H Li, M Ye, X Zhao, J Liu
BACKGROUND: Sip1/Tuftelin Interacting Protein (STIP) is highly conserved from Caenorhabditis elegans to Homo sapiens and has essential biological functions. However, its function in leukemia remains unknown. METHODS: Clinic Samples and cell model were used in this article to investigate the expression of STIP in lymphoblastic leukemia. The functional research of STIP was performed in ARH-77 by siRNA transfection, Immunofluorescence, cell count, cell cycle analysis, quantitative real-time RT-PCR, Sub-cellular Fractionation assays, Immunoprecipitation and Western blotting...
October 18, 2016: Current Molecular Medicine
Yuko M Komesu, Rebecca G Rogers, Robert E Sapien, Ronald M Schrader, Timothy Simmerman-Sierra, Andrew R Mayer, Loren H Ketai
INTRODUCTION AND HYPOTHESIS: We describe the rationale and methodology for a study comparing mind-body treatment and pharmacotherapy in women with urgency urinary incontinence (UUI). To explore brain associations in UUI, a subset of patients will also undergo functional magnetic resonance imaging (fMRI). We hypothesize that hypnotherapy, a mind-body intervention, will be at least as effective as pharmacotherapy in treating UUI. We also hypothesize that fMRI findings will change following treatment, with changes potentially differing between groups...
October 17, 2016: International Urogynecology Journal
Cheng He, Gregory Scalia, Darren L Walters, Andrew Clarke
We describe a successful transcatheter, transapical mitral valve implant within a failed mitral bioprosthesis (valve-in-valve) in a symptomatic 86-year-old patient with prohibitive surgical risks, using the new Sapien 3 balloon-expandable valve. Post-deployment echocardiographic profile of the valve-in-valve was satisfactory and the patient was discharged from hospital uneventfully. This is the first reported case of the Sapien 3 valve used in the mitral valve-in-valve setting.
June 21, 2016: Heart, Lung & Circulation
Lauren Alpert Sugden, Sohini Ramachandran
Human population genomic studies have repeatedly observed a decrease in heterozygosity and an increase in linkage disequilibrium with geographic distance from Africa. While multiple demographic models can generate these patterns, many studies invoke the serial founder effect model, in which populations expand from a single origin and each new population's founders represent a subset of genetic variation in the previous population. The model assumes no admixture with archaic hominins, however, recent studies have identified loci in Homo sapiens bearing signatures of archaic introgression...
October 12, 2016: Current Opinion in Genetics & Development
Christina Backes, Tim Kehl, Daniel Stöckel, Tobias Fehlmann, Lara Schneider, Eckart Meese, Hans-Peter Lenhof, Andreas Keller
In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways...
October 13, 2016: Nucleic Acids Research
Maria Elena Miletto Petrazzini, Christian Agrillo, Véronique Izard, Angelo Bisazza
Numerous studies have shown that many animal species can be trained to discriminate between stimuli differing in numerosity. However, in the absence of generalization tests with untrained numerosities, what decision criterion was used by subjects remains unclear: the subjects may succeed by selecting a specific number of items (a criterion over absolute numerosities), or by applying a more general relative numerosity rule, for example, selecting the larger/smaller quantity of items. The latter case may require more powerful representations, supporting judgments of order ("more/less") beyond simple "same/different" judgments, but a relative numerosity rule may also be more adaptive...
October 13, 2016: Journal of Comparative Psychology
Brian Hare
The challenge of studying human cognitive evolution is identifying unique features of our intelligence while explaining the processes by which they arose. Comparisons with nonhuman apes point to our early-emerging cooperative-communicative abilities as crucial to the evolution of all forms of human cultural cognition, including language. The human selfdomestication hypothesis proposes that these early-emerging social skills evolved when natural selection favored increased in-group prosociality over aggression in late human evolution...
October 12, 2016: Annual Review of Psychology
Nicole Barbaro, Todd K Shackelford
Male-perpetrated female-directed violence (FDV) may be associated with greater sexual access to a female. Accordingly, FDV is expected to be associated with greater copulation frequency. Research on nonhuman primates affirms this hypothesis, but no previous research has investigated this relationship in humans (Homo sapiens). The current research tests the hypothesis that FDV is associated with in-pair copulation frequency and, thus, may function as a form of sexual coercion. It was predicted that men who perpetrate FDV will secure more in-pair copulations than men who do not perpetrate violence (Prediction 1a), and that average monthly rates of FDV would positively correlate with in-pair copulation frequency (Prediction 1b)...
August 15, 2016: Journal of Comparative Psychology
Roland Hilling-Smith, James Cockburn, Maureen Dooley, Jessica Parker, Andrea Newton, Andrew Hill, Uday Trivedi, Adam de Belder, David Hildick-Smith
: Transcatheter aortic valve implantation (TAVI) and balloon aortic valvuloplasty (BAV) are now well established percutaneous procedures. These procedures almost always require bursts of rapid ventricular pacing to temporarily reduce cardiac output to facilitate the procedure, usually done via a temporary pacing wire inserted into the right ventricle. We describe a case series of 132 cases of TAVI and 76 BAV done using ventricular pacing via the left ventricular lead by simply connecting one electrode to the patient's skin and one electrode through the left ventricular (LV) wire...
October 11, 2016: Catheterization and Cardiovascular Interventions
Paul Grouchy, Gabriele M T D'Eleuterio, Morten H Christiansen, Hod Lipson
The emergence of symbolic communication is often cited as a critical step in the evolution of Homo sapiens, language, and human-level cognition. It is a widely held assumption that humans are the only species that possess natural symbolic communication schemes, although a variety of other species can be taught to use symbols. The origin of symbolic communication remains a controversial open problem, obfuscated by the lack of a fossil record. Here we demonstrate an unbroken evolutionary pathway from a population of initially noncommunicating robots to the spontaneous emergence of symbolic communication...
October 10, 2016: Scientific Reports
Ezhilarasi Krishnamoorthy, Sameer Hassan, Luke Elizabeth Hanna, Indira Padmalayam, Rama Rajaram, Vijay Viswanathan
Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role...
October 4, 2016: Journal of Theoretical Biology
Zofia M Sikorska-Piwowska, Antoni L Dawidowicz
The authors examined a large random sample of skulls from two species of macaques: rhesus monkeys and cynomolgus monkeys. The skulls were measured, divided into age and sex groups and thoroughly analysed using statistical methods. The analysis shows that skulls of young rhesuses are considerably more domed, i.e. have better-developed neurocrania, than their adult counterparts. Male and female skulls, on the other hand, were found to be very similar, which means that sexual dimorphism of the rhesus macaque was suppressed...
October 7, 2016: Folia Morphologica (Warsz)
Baifan Wang, Xin Wen, Zhen Xi
Protoporphyrinogen IX oxidase (PPO, EC catalyzes the oxidation of protoporphyrinogen IX (protogen IX) to protoporphyrin IX (proto IX) in the haem/chlorophyll biosynthetic pathway. Although extensive studies of PPO have already afforded many insights into its biological function and its significance to agriculture and medicine, details of the enzymatic mechanism as well as the nature of the specific amino acids involved in substrate binding still remain largely unknown due to the lack of structural information about protogen IX binding to PPO...
October 2016: Molecular Informatics
Humberto Contreras-Cornejo, Germán Saucedo-Correa, Javier Oviedo-Boyso, Juan José Valdez-Alarcón, Víctor Manuel Baizabal-Aguirre, Marcos Cajero-Juárez, Alejandro Bravo-Patiño
The Notch signaling pathway is a reiteratively used cell to cell communication pathway that triggers pleiotropic effects. The correct regulation of the pathway permits the efficient regulation of genes involved in cell fate decision throughout development. This activity relies notably on the CSL proteins, (an acronym for CBF-1/RBPJ-κ in Homo sapiens/Mus musculus respectively, Suppressor of Hairless in Drosophila melanogaster, Lag-1 in Caenorhabditis elegans) which is the unique transcription factor and DNA binding protein involved in this pathway...
2016: Cell Division
Jian Zhao, Xiaofeng Song, Kai Wang
RNA-Seq based transcriptome assembly has been widely used to identify novel lncRNAs. However, the best-performing transcript reconstruction methods merely identified 21% of full-length protein-coding transcripts from H. sapiens. Those partial-length protein-coding transcripts are more likely to be classified as lncRNAs due to their incomplete CDS, leading to higher false positive rate for lncRNA identification. Furthermore, potential sequencing or assembly error that gain or abolish stop codons also complicates ORF-based prediction of lncRNAs...
October 6, 2016: Scientific Reports
L Fu, Y L Hou, X Ding, Y J Du, H Q Zhu, N Zhang, W R Hou
The complementary DNA (cDNA) of the giant panda (Ailuropoda melanoleuca) ferritin light polypeptide (FTL) gene was successfully cloned using reverse transcription-polymerase chain reaction technology. We constructed a recombinant expression vector containing FTL cDNA and overexpressed it in Escherichia coli using pET28a plasmids. The expressed protein was then purified by nickel chelate affinity chromatography. The cloned cDNA fragment was 580 bp long and contained an open reading frame of 525 bp. The deduced protein sequence was composed of 175 amino acids and had an estimated molecular weight of 19...
August 30, 2016: Genetics and Molecular Research: GMR
Yigal Abramowitz, Hasan Jilaihawi, Tarun Chakravarty, Yoshio Maeno, Hiroyuki Kawamori, Yoshio Kazuno, Geeteshwar Mangat, Tanya Rami, Zev Allison, David Anderson, Larry Chan, Wen Cheng, Raj R Makkar
OBJECTIVES: Aortic valve preparation with balloon aortic valvuloplasty (BAV) has been previously considered mandatory during transcatheter aortic valve implantation (TAVI) procedures. BAV-inherent risks including stroke, conduction abnormalities, and reduced device profile size established the rationale for safe valve deployment without the need for aggressive valve preparation. We investigate the feasibility and safety of performing Sapien 3 (S3; Edwards Lifesciences) balloon-expandable TAVI with moderate or without predilation (PD)...
October 2016: Journal of Invasive Cardiology
Shaimaa Sait, Timothy Fawcett, George Blanck
Mutant peptides resulting from cancer drivers or passenger mutations are expected to have the potential to serve as a basis for cancer vaccines. However, a number of parameters regulate vaccine-associated immunogenicity, including the suitability of a peptide for binding to an antigen-presenting molecule or antibody. In order to obtain a basic indication of the prospect of human cancer epitope identification via current database development strategies, an overlap of the mutant Homo sapiens epitopes listed on the Immune Epitope Database (IEDB) and the mutant peptides indicated by The Cancer Genome Atlas (TCGA) somatic mutation database was obtained...
October 2016: Oncology Letters
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