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https://www.readbyqxmd.com/read/28232198/a-modification-of-the-phylip-program-a-solution-for-the-redundant-cluster-problem-and-an-implementation-of-an-automatic-bootstrapping-on-trees-inferred-from-original-data
#1
Makoto K Shimada, Tsunetoshi Nishida
Felsenstein's PHYLIP package of molecular phylogeny tools has been used globally since 1980. The programs are receiving renewed attention because of their character-based user interface, which has the advantage of being scriptable for use with large-scale data studies based on super-computers or massively parallel computing clusters. However, occasionally we found, the PHYLIP Consense program output text file displays two or more divided bootstrap values for the same cluster in its result table, and when this happens the output Newick tree file incorrectly assigns only the last value to that cluster that disturbs correct estimation of a consensus tree...
April 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27775267/-neonatal-surgical-site-infection-multicentric-survey-on-prophylactic-measures
#2
M Fernández Ibieta, O Girón Vallejo, I Martínez Castaño, P Reyes Ríos, K Cabrejos Perotti, J Rojas Ticona, J M Sánchez Morote, G Zambudio Carmona, M J Guirao Piñera, M J Aranda García, A Trujillo Ascanio, J I Ruiz Jiménez, R Ruiz-Pruneda, N Méndez-Aguirre
OBJECTIVES: Surgical site infection (SSI) has a considerable impact on neonatal morbidity. There are known risk factors such type of surgery (clean/contaminated), prematurity, surgical length, hypoalbuminemia, previous infection, prolonged mechanical ventilation, and so on. Many perioperative factors have not been studied, opposite to adults. We have developed a survey on intraoperative attitudes and measures, as surgical wound management in Neonates among pediatric surgeons, to seek for a wider consense...
January 13, 2015: Cirugía Pediátrica: Organo Oficial de la Sociedad Española de Cirugía Pediátrica
https://www.readbyqxmd.com/read/24433507/novel-treatment-of-acute-promyelocytic-leukemia-as%C3%A2-o%C3%A2-retinoic-acid-and-retinoid-pharmacology
#3
REVIEW
George Zhu, Sarah E Mische, Beatrice Seigneres
Acute promyelocytic leukemia(APL), a specific characteristic of t(15;17) chromosome translocation, represents 5% to 15% of cases of acute nonlymphocytic leukemia. An alternative approach is to consider retinoic acid(all-trans RA, ATRA or 13-cis RA or 9-cis RA) plus chemotherapy or RA plus As₂O₃ regimens as now novel therapy. Molecular gene analyses are conclusive in vivo evidence that oncogenic PML/RARa plays a crucial role in APL leukemogenesis. As a novel approach to APL treatment, one possible the action of RA, A consense sequence (5'-TCAGGTCATGACCTGA-3') has been postulated for the thyroid hormone (TRE) and retinoic acid responsive element (RARE) containing half palindromes, which located in the promoter region of target genes...
2013: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/23597749/cytochrome-b-as-a-useful-tool-for-the-identification-of-blowflies-of-forensic-interest-diptera-calliphoridae
#4
Maite GilArriortua, Marta I Salona Bordas, Laura M Cainé, Fátima Pinheiro, Marian M de Pancorbo
In Forensic Entomology the fast and accurate identification of insects collected at the scene of events is essential if errors are to be avoided in estimating infestation times of interest and determining the post-mortem interval (PMI). Traditional identification based on morphological characteristics can be complicated due to physical similarities between different species, especially at immature stages. Genetic analysis provides a fast and reliable identification method. In this paper, molecular analysis is focused on a fragment of 307bp of the mitochondrial DNA region that codes for cytochrome b (cyt b)...
May 10, 2013: Forensic Science International
https://www.readbyqxmd.com/read/19179643/the-functional-importance-of-telomere-clustering-global-changes-in-gene-expression-result-from-sir-factor-dispersion
#5
Angela Taddei, Griet Van Houwe, Shigeki Nagai, Ionas Erb, Erik van Nimwegen, Susan M Gasser
Budding yeast telomeres and cryptic mating-type loci are enriched at the nuclear envelope, forming foci that sequester silent information regulators (SIR factors), much as heterochromatic chromocenters in higher eukaryotes sequester HP1. Here we examine the impact of such subcompartments for regulating transcription genome-wide. We show that the efficiency of subtelomeric reporter gene repression depends not only on the strength of SIR factor recruitment by cis-acting elements, but also on the accumulation of SIRs in such perinuclear foci...
April 2009: Genome Research
https://www.readbyqxmd.com/read/18523191/a-seven-gene-multilocus-genus-wide-approach-to-the-phylogeny-of-mycobacteria-using-supertrees
#6
Sophie Mignard, Jean-Pierre Flandrois
This is the first study that estimates mycobacterial phylogeny using the maximum-likelihood method (PhyML-aLRT) on a seven-gene concatenate (hsp65, rpoB, 16S rRNA, smpB, sodA, tmRNA and tuf) and the super distance matrix (SDM) supertree method. Two sets of sequences were studied: a complete seven gene sequence set (set R, type strains of 87 species) and an incomplete set (set W, 132 species) with some missing data. Congruencies were computed by using the consense program (phylip package). The evolution rate of each gene was determined, as was the evolution rate of each strain for a given gene...
June 2008: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/17992123/evidence-and-interdisciplinary-consense-based-german-guidelines-diagnosis-and-surveillance-of-melanoma
#7
Claus Garbe, Axel Hauschild, Matthias Volkenandt, Dirk Schadendorf, Wilhelm Stolz, Uwe Reinhold, Rolf-Dieter Kortmann, Christoph Kettelhack, Bernhard Frerich, Ulrich Keilholz, Reinhard Dummer, Günther Sebastian, Wolfgang Tilgen, Gerold Schuler, Andreas Mackensen, Roland Kaufmann
Melanoma is a malignant tumor that arises from melanocytic cells and primarily involves the skin. The most important exogenous etiological factor is exposure to ultraviolet irradiation. Diagnosis of melanoma is based primarily on its clinical features, and the A-B-C-D rule is useful in identifying pigmented lesions, which are suspicious for melanoma (Asymmetry, Border irregular, Color inhomogeneous and Diameter more than 5 mm). Dermoscopy is very helpful in clarifying the differential diagnosis of pigmented lesions...
December 2007: Melanoma Research
https://www.readbyqxmd.com/read/17411399/consensus-framework-for-exploring-microarray-data-using-multiple-clustering-methods
#8
Ted Laderas, Shannon McWeeney
The large variety of clustering algorithms and their variants can be daunting to researchers wishing to explore patterns within their microarray datasets. Furthermore, each clustering method has distinct biases in finding patterns within the data, and clusterings may not be reproducible across different algorithms. A consensus approach utilizing multiple algorithms can show where the various methods agree and expose robust patterns within the data. In this paper, we present a software package - Consense, written for R/Bioconductor - that utilizes such an approach to explore microarray datasets...
2007: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/17329016/testosterone-and-erectile-function-from-basic-research-to-a-new-clinical-paradigm-for-managing-men-with-androgen-insufficiency-and-erectile-dysfunction
#9
REVIEW
Abdulmaged M Traish, Irwin Goldstein, Noel N Kim
OBJECTIVES: Androgens are essential for the development and growth of the penis, and they regulate erectile physiology by multiple mechanisms. Our goal is to provide a concise overview of the basic research and how this knowledge can be translated into a new clinical paradigm for patient management. In addition, this new paradigm may serve as a basis for stimulating constructive debate regarding the use of testosterone in men, and to promote new, innovative basic and clinical research to further understand the underlying mechanisms of androgen action in restoring erectile physiology...
July 2007: European Urology
https://www.readbyqxmd.com/read/16786642/-effects-of-alcoholic-beverages-on-the-fatty-acid-spectrum-of-the-expired-air-condensate-lipids-in-patients-with-tuberculosis-of-the-respiratory-organs
#10
O B Pikas
Results are highlighted of the study into the pulmonary surfactant in healthy subjects. as well as in those afflicted with pulmonary tuberculosis who abused alcoholic drinks, with the aid of the chromotography techniques. It has been ascertained that activity of the pulmonary surfactant is dependent upon the clinical form of tuberculosis, its extension and presence of alcoholism. The lipid polyunsaturated fatty acids, with the linoleic (C18:2) and arachidonic (C20:4) acids being the most sensitive ones to the process of lipid peroxidation (LPO), and the study into the spectrum of lipid fatty acids in the expired air consensate suggest intencity of LPO in the pulmonary surfactant and permit carrying out its correction in a timely fashion during the process of treatment...
October 2000: Likars'ka Sprava
https://www.readbyqxmd.com/read/16422990/the-penile-implant-for-erectile-dysfunction
#11
REVIEW
John J Mulcahy, Edouardo Austoni, James H Barada, Hyung Ki Choi, W J Hellstrom, Wayne J G Hellstrom, Sudhakar Krishnamurti, Ignacio Moncada, Dirk Schultheiss, Dirk Shultheiss, Michael Sohn, Hunter Wessells
INTRODUCTION: Penile prostheses, introduced as the first effective organic treatment for erectile dysfunction over three decades ago, have an important role in the treatment of erectile dysfunction when other nonprosthetic treatment options have proven unsatisfactory. Although they are the least chosen and most invasive treatment option, they have the highest satisfaction rate of all available ED options and provide a predictable and reliable result. AIM: To provide recommendations/guidelines concerning state-of-the-art knowledge for utilization of the penile prosthesis in the management of men with erectile dysfunction...
July 2004: Journal of Sexual Medicine
https://www.readbyqxmd.com/read/16422983/clinical-evaluation-and-management-strategy-for-sexual-dysfunction-in-men-and-women
#12
Dimitrios Hatzichristou, Raymond C Rosen, Gregory Broderick, Anita Clayton, Beatrice Cuzin, Leonard Derogatis, Mark Litwin, Eric Meuleman, Michael O'Leary, Frances Quirk, Richard Sadovsky, Allen Seftel
INTRODUCTION: The optimal approach for identification and evaluation of the sexual problems in men and women in primary care or general medicine practice has not been consensed. AIM: To provide recommendations/guidelines concerning state-of-the-art knowledge for clinical evaluation and management strategies in the evaluation and treatment of sexual dysfunction in men and women, emphasizing evidence-based medicine and a patient-centered framework. METHODS: An International Consultation in collaboration with the major urology and sexual medicine associations assembled over 200 multidisciplinary experts from 60 countries into 17 committees...
July 2004: Journal of Sexual Medicine
https://www.readbyqxmd.com/read/16077869/-asperger-syndrome-diagnosis-criteria-and-clinical-picture
#13
Ernesto Wahlberg
Asperger syndrome (A.S) is not a very well-known disorder due to its recent incorporation to the international nosography of mental disorders during the early 90s. The intention of this article is to describe the clinical picture with its symptomatic diversity. It will show how the diagnostic criteria were developed since the presentation by Asperger in 1944, to the classification consensed nowadays. It also presents the situations in which this diagnosis is most frequent to facilitate its detection and to permit a more extensive assessment leading to a more accurate treatment...
July 2005: Vertex: Revista Argentina de Psiquiatriá
https://www.readbyqxmd.com/read/15680582/vertebrate-2xrbd-hnrnp-proteins-a-comparative-analysis-of-genome-mrna-and-protein-sequences
#14
COMPARATIVE STUDY
Akintunde A Akindahunsi, Antonella Bandiera, Giorgio Manzini
hnRNP proteins are involved in many cell functions, primarily in pre-mRNA processing. We report here a comparative analysis of the genes of the 2xRBD members of the hnRNP family and of their expression products. Starting from the seven well characterized hnRNP members of human and murine origin (A0, A1, A2/B1, A3, AB, D and DL) and the three MuSashI-like proteins with related RBD tandems (MSI1, MSI2 and DAZAP1), we identified through BLAST search 12 homologous genes in the genome of Danio rerio and 10 in the genome of Takifugu rubripes, which can be divided into three subgroups, each with its highly conserved exon/intron structure, matching perfectly the exon/intron structures found in human and mouse genes...
February 2005: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/15625823/-somatic-mutations-of-pig-a-gene-in-chinese-patients-with-paroxysmal-nocturnal-hemoglobinuria
#15
T Du, C Xu, Z Zhang
OBJECTIVE: To explore the somatic mutations of PIG-A gene in Chinese patients with paroxysmal nocturnal hemoglobinuria (PNH) and to compare these mutations with those in non-Chinese PNH patients. METHODS: Seven overlapping regions of PIG-A cDNA from granulocytes of 4 PNH patients were amplified by RT-PCR. The mutant segments were identified by HA/SSCP and then cloned and sequenced. RESULTS: In 4 Chinese PNH patients five small PIG-A mutations were found, including four single base substitutions (resulting in 1 consense mutations and 3 missense mutations) and one single base deletion causing a frameshift)...
October 1997: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/15361809/effective-dosing-and-dose-equivalency-of-second-generation-antipsychotic-medications
#16
REVIEW
Peter F Buckley
Dosing patterns with second-generation antipsychotic medications (SGAs) are dynamic, with some SGAs surpassing current recommendations while others are declining in dose since their initial regulatory guidelines. Pertinent recent studies and available pharmacoepidemiologic reports, information, and expert consenses are reviewed herein to illuminate current thinking on the topic of dosing with SGAs. There is a need for fixed-dose studies of each SGA. Additionally, dosing should be a primary consideration when designing and subsequently interpreting comparative studies between SGAs...
September 2004: CNS Spectrums
https://www.readbyqxmd.com/read/14740309/-treatment-of-anaphylactic-reactions-a-review-of-guidelines-and-recommendations
#17
REVIEW
A Ranft, E F Kochs
In the present review, guidelines and recommendations for the treatment of anaphylactic reactions are presented and evaluated. Herefore, publications of German and non-German societies and expert groups have been selected and, in addition to that, we have chosen a number of articles that were cited frequently and, as far as we are concerned, have a relevant meaning for this theme. None of the traditionally applied remedies - epinephrine and intravascular volume, histamine receptor blockade, inhaled betamimetics and steroids - have been proven efficacious by means of evidence-based medicine...
January 2004: Anästhesiologie, Intensivmedizin, Notfallmedizin, Schmerztherapie: AINS
https://www.readbyqxmd.com/read/12140577/-upper-gastrointestinal-bleeding-related-to-dieulafoy-lesion
#18
Carlos Contardo
Dieulafoy lesion is an unsual source of upper astrointestinal bleeding with a frequency ranging from 0.3 to 6.7% of the reported literature, although at present it is more frequently diagnosed. It usually begins abruptly with massive bleeding and hemodynamic involvement. The higher prevalence is found in older people and because this group of patients is generally affected by other diseases, Dieulafoy lesion may be life threatening. A thick arterial blood vessel flows through the mucosa and submucosa and in more than 75% of cases the lesion is mostly found within 6 cm of the cardia...
October 2000: Revista de Gastroenterología del Perú: órgano Oficial de la Sociedad de Gastroenterología del Perú
https://www.readbyqxmd.com/read/11965722/-grading-intraductal-breast-carcinoma
#19
S Popovska, I Iordanov, T Betova, G Baĭchev, T Deliĭski
Mammographic screening has led to increased detection of intraductal carcinoma of the breast (IdC). IdC is y heterogeneous disorder with different clinical outcomes. The study was designed to confirm consensibility of the three-tiered classification, accepted by Thomas Jefferson University Consensus Conference since 1997. The study population comprised 30 patients with IdC including patients with T1 mic and T1a. Sixty percent of IdC were classified as II-nd grade, 27% were III-rd grade and 13% as I-st grade...
1999: Akusherstvo i Ginekologii︠a︡
https://www.readbyqxmd.com/read/11697149/-complications-of-acute-ent-infections
#20
W Müller
Acute infections in the head and neck belong to the most frequent human diseases and account for a high percentage of prescriptions for oral antibiotics. Because most infections only need symptomatic treatment and with the doubtful benefit of antibiotic treatment in some studies there is consense that routinely prescribed antibiotics for infections of the upper airway should be abandoned. Uncritical use of antibiotics is a likely cause for an increasing rate of drug resistant bacteria and many antibiotics have side effects...
October 18, 2001: Praxis
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