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https://www.readbyqxmd.com/read/27915479/trends-in-next-generation-sequencing-and-a-new-era-for-whole-genome-sequencing
#1
REVIEW
Sang Tae Park, Jayoung Kim
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27915304/invasive-aspergillosis-in-acute-myeloid-leukemia-are-we-making-progress-in-reducing-mortality
#2
Giulia Dragonetti, Marianna Criscuolo, Luana Fianchi, Livio Pagano
The incidence of invasive fungal disease (IFD) has varied during the last decades. However, over the years, we have observed a progressive reduction of mortality, mainly due to wider use of prophylactic antifungal therapy (i.e., new azoles, such as posaconazole), the development of new and more effective antifungal drugs (lipid compounds of amphotericin B, candins, and azoles of the previous generation) and improvement of diagnostic tools. Based on a number of international studies across three decades, the attributable mortality rate for IFD and invasive aspergillosis (IA) among patients with acute myeloid leukemia (AML) has progressively declined...
December 2, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/27915230/phi-base-a-new-interface-and-further-additions-for-the-multi-species-pathogen-host-interactions-database
#3
Martin Urban, Alayne Cuzick, Kim Rutherford, Alistair Irvine, Helder Pedro, Rashmi Pant, Vidyendra Sadanadan, Lokanath Khamari, Santoshkumar Billal, Sagar Mohanty, Kim E Hammond-Kosack
The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions...
December 3, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27915171/progress-in-the-development-of-%C3%AE-lactams-as-n-acylethanolamine-acid-amidase-naaa-inhibitors-synthesis-and-sar-study-of-new-potent-n-o-substituted-derivatives
#4
R Petracca, S Ponzano, S M Bertozzi, O Sasso, D Piomelli, T Bandiera, F Bertozzi
The anti-inflammatory effects resulting from raising the levels of palmitoylethanolamide (PEA), an endogenous bioactive lipid, led to envisage N-Acylethanolamine Acid Amidase (NAAA), the cysteine hydrolase mainly responsible for PEA degradation, as an attractive target for small molecule inhibitors. Previous work in our group identified serine-derived β-lactams as potent and systemically active inhibitors of NAAA activity. Aiming to expand the SAR study around this class of compounds, we investigated the effect of the substitution on the endocyclic nitrogen by designing and synthesizing a series of N-substituted β-lactams...
November 23, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27914894/scope-manual-curation-and-artifact-removal-in-the-structural-classification-of-proteins-extended-database
#5
John-Marc Chandonia, Naomi K Fox, Steven E Brenner
SCOPe (Structural Classification of Proteins - extended, http://scop.berkeley.edu) is a database of relationships between protein structures that extends the Structural Classification of Proteins (SCOP) database. SCOP is an expert-curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. SCOPe classifies the majority of protein structures released since SCOP development concluded in 2009, using a combination of manual curation and highly precise automated tools, aiming to have the same accuracy as fully hand-curated SCOP releases...
November 30, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27914728/-nanotechnology-a-new-paradigm-in-atherosclerosis-treatment
#6
Virna M Martín Giménez, María Belén Ruiz-Roso, Alejandra Beatriz Camargo, Diego Kassuha, Walter Manucha
Atherosclerosis, a known and prevalent disease, causes progressive deterioration of affected vessels, inducing a blood flow reduction with different complications, and its symptoms usually manifest in advanced stages of the disease. Therefore, the classic therapeutic alternatives are insufficient because the damages are many times irreversible. For this reason, there is a need to implement intelligent forms of drug administration and develop new therapeutic targets that reduce the progression of atherosclerotic lesion...
November 30, 2016: Clínica e Investigación en Arteriosclerosis
https://www.readbyqxmd.com/read/27914632/the-us-food-and-drug-administration-s-risk-evaluation-and-mitigation-strategy-rems-program-current-status-and-future-direction
#7
Jasmanda Wu, Juhaeri Juhaeri
The US Food and Drug Administration (FDA) Amendments Act of 2007 granted the FDA new authorities to enhance drug safety by requiring application holders to submit a proposed Risk Evaluation and Mitigation Strategy (REMS). A REMS is a required risk management plan that uses tools beyond the package insert. REMS elements may include a medication guide and patient package insert for patients and a communication plan focused on health care professionals. Elements to assure safe use (ETASUs) are put in place to mitigate a specific known serious risk when other less restrictive elements of a REMS are not sufficient to mitigate such risk...
November 30, 2016: Clinical Therapeutics
https://www.readbyqxmd.com/read/27914540/evaluation-of-antidesmone-alkaloid-as-a-photosynthesis-inhibitor
#8
Olívia Moreira Sampaio, Murilo Marinho de Castro Lima, Thiago André Moura Veiga, Beatriz King-Díaz, Maria Fátima das Graças Fernandes da Silva, Blas Lotina-Hennsen
Antidesmone, isolated from Waltheria brachypetala Turcz., owns special structural features as two α,β-unsaturated carbonyl groups and a side alkyl chain that can compete with the quinones involved in the pool of plastoquinones at photosystem II (PSII). In this work, we showed that the alkaloid is an inhibitor of Hill reaction and its target was located at the acceptor side of PSII. Studies of chlorophyll (Chl) a fluorescence showed a J-band that indicates direct action of antidesmone in accumulation of QA(-) (reduced plastoquinone A) due to the electron transport blocked at the QB (plastoquinone B) level similar to DCMU...
November 2016: Pesticide Biochemistry and Physiology
https://www.readbyqxmd.com/read/27914493/patient-factors-associated-with-quality-of-life-in-atrial-fibrillation
#9
Tiffany C Randolph, DaJuanicia N Simon, Laine Thomas, Larry A Allen, Gregg C Fonarow, Bernard J Gersh, Peter R Kowey, James A Reiffel, Gerald V Naccarelli, Paul S Chan, John A Spertus, Eric D Peterson, Jonathan P Piccini
BACKGROUND: As treatment options for atrial fibrillation (AF) increase, more attention is focused on patients' experiences and quality of life (QoL). However, little is known about the factors associated with these outcomes. METHODS: The Atrial Fibrillation Effect on QualiTy-of-life (AFEQT) is a disease-specific QoL tool for AF, with domain and summary scores ranging from 0 (the worst QoL) to 100. Using multivariable linear regression, we evaluated factors associated with baseline AFEQT Summary and Subscale Scores in ORBIT AF, a large, community-based AF registry...
December 2016: American Heart Journal
https://www.readbyqxmd.com/read/27914056/parallel-computational-protein-design
#10
Yichao Zhou, Bruce R Donald, Jianyang Zeng
Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914051/integration-of-molecular-dynamics-based-predictions-into-the-optimization-of-de-novo-protein-designs-limitations-and-benefits
#11
Henrique F Carvalho, Arménio J M Barbosa, Ana C A Roque, Olga Iranzo, Ricardo J F Branco
Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913889/ocular-pharmacology-of-tear-film-dry-eye-and-allergic-conjunctivitis
#12
Shilpa Gulati, Sandeep Jain
Dry Eye Disease (DED) is "a multifactorial disease of the tears and ocular surface that results in symptoms of discomfort, visual disturbance, and tear-film instability with potential damage to the ocular surface." DED comprises two etiologic categories: aqueous-deficient dry eye (ADDE) and evaporative dry eye (EDE). Diagnostic workup of DED should include clinical history, symptom questionnaire, fluorescein TBUT, ocular surface staining grading, Schirmer I/II, lid and meibomian pathology, meibomian expression, followed by other available tests...
December 3, 2016: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/27913843/molecular-evolution-in-historical-perspective
#13
Edna Suárez-Díaz
In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms...
December 2, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913818/-amyloid-positron-emission-tomography-with-18-%C3%A2-f-florbetaben-in-the-diagnostic-workup-of-dementia-patients
#14
S Schönecker, C Prix, T Raiser, N Ackl, E Wlasich, G Stenglein-Krapf, E Mille, M Brendel, O Sabri, M Patt, H Barthel, P Bartenstein, J Levin, A Rominger, A Danek
BACKGROUND: To this day the definite diagnosis of Alzheimer's disease still relies on post-mortem histopathological detection of neurofibrillary tangles and beta-amyloid deposits. Amyloid positron emission tomography (PET) is a new diagnostic tool that enables the in vivo quantification of pathological beta-amyloid deposits. The aim of the current study was to evaluate to what extent (18)F-florbetaben-PET (FBB-PET) influences the diagnosis of patients with dementia. MATERIAL AND METHODS: Imaging with FBB-PET was performed on 33 patients from our outpatient department for cognitive neurology...
December 2, 2016: Der Nervenarzt
https://www.readbyqxmd.com/read/27913721/application-based-hearing-screening-in-the-elderly-population
#15
Leonid Livshitz, Reem Ghanayim, Carmi Kraus, Raymond Farah, Ella Even-Tov, Yaniv Avraham, Adi Sharabi-Nov, Peter Gilbey
OBJECTIVES: The effects of age-related hearing loss are severe. Early detection is essential for maximum benefit. However, most hearing-impaired adults delay obtaining treatment. Diagnostic hearing testing at an appropriate facility is impractical, and new methods for screening audiometry aim to provide easy access for patients and reliable outcomes. The purpose of this study was to examine the accuracy of application-based hearing screening in an elderly population. METHODS: The uHear application was downloaded to an iPad...
January 2017: Annals of Otology, Rhinology, and Laryngology
https://www.readbyqxmd.com/read/27913617/evaluating-sequence-based-genomic-prediction-with-an-efficient-new-simulator
#16
Miguel Pérez-Enciso, Natalia Forneris, Gustavo de Los Campos, Andrés Legarra
The vast amount of sequence data to analyze complex traits is posing new challenges in terms of analysis and interpretation of the results. Although simulation is a fundamental tool to investigate the reliability of genomic analyses and to optimize experimental design, existing software cannot simulate complete genomes realistically. To remedy this, we have developed a new strategy (Sequence Based Virtual Breeding, SBVB) that consists of using real sequence data and simulating new offspring genomes and phenotypes in a very efficient and flexible manner...
December 2, 2016: Genetics
https://www.readbyqxmd.com/read/27913547/new-treatment-approaches-to-von-willebrand-disease
#17
Michelle Lavin, James S O'Donnell
von Willebrand disease (VWD) is the commonest inherited bleeding disorder and results from either a quantitative or qualitative deficiency in the plasma glycoprotein von Willebrand factor (VWF). Recent large cohort studies have significantly enhanced our understanding of the molecular mechanisms involved in the pathogenesis of VWD. In contrast, however, there have been relatively few advances in the therapeutic options available for the treatment of bleeding in patients with VWD. Established treatment options include tranexamic acid, 1-deamino-8-d-arginine vasopressin (DDAVP), and plasma-derived VWF concentrates...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913513/minimal-residual-disease-in-mantle-cell-lymphoma-insights-into-biology-and-impact-on-treatment
#18
Eva Hoster, Christiane Pott
Despite the recent substantial improvement of clinical outcome in mantle cell lymphoma (MCL), resistance to immunochemotherapy and common relapses are challenges for long-term tumor control. The assessment of minimal residual disease (MRD) by real-time quantitative polymerase chain reaction has emerged as a widely feasible and standardized tool for direct assessment of therapy-induced reduction of tumor burden and regrowth after cytotoxic treatment in MCL, with much improved sensitivity compared with conventional staging procedures...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913491/prognostic-factors-in-follicular-lymphoma-new-tools-to-personalize-risk
#19
Carla Casulo
Follicular lymphoma (FL) is the most common indolent lymphoma, and it has a long median overall survival (OS). However, the recent discovery of clinical and biological prognostic biomarkers in FL is shedding light on FL heterogeneity and the need for a precise and risk-stratified individual approach at diagnosis and relapse. Many FL patients who are asymptomatic with indolent disease can be vulnerable to the toxicity, emotional distress, and financial burden of overtreatment. Yet a subset of FL patients develop chemoresistance to standard chemoimmunotherapy, experience transformation to aggressive lymphoma and rapid progression, and represent the population most in need of novel therapies and curative approaches...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913474/prognostication-of-chronic-lymphocytic-leukemia-in-the-era-of-new-agents
#20
Barbara Eichhorst, Michael Hallek
The prognosis of chronic lymphocytic leukemia (CLL) is very heterogeneous. Therefore, a plethora of prognostic factors has been identified to allow a better prediction of the individual prognosis of a given patient. The clinical staging systems by Rai and Binet have been the backbone of clinical management for several decades. The advent of genetic and biochemical markers, as well as next-generation sequencing has provided several markers that can predict the prognosis of patients with CLL. Using this knowledge, several scores have been created to improve predicting overall survival and/or treatment-free survival...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
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