24 research outputs found
Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark
No full textBACKGROUND: Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS: For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS: 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION: The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility
Preferenčné vyhľadávanie založené na viacrozmernom B-strome
No full textTitle: Preference Top-k Search Based on Multidimensional B-Tree Author: RNDr. Matúš Ondreička Department: Department of Software Engineering Faculty of Mathematics and Physics Charles University in Prague Supervisor: Prof. RNDr. Jaroslav Pokorný, CSc. Author's e-mail address: [email protected] Supervisor's e-mail address: [email protected] Abstract: In this thesis, we focus on the top-k search according to user pref- erences by using B+ -trees and the multidimensional B-tree (MDB-tree). We use model of user preferences based on fuzzy functions, which enable us to search according to a non-monotone ranking function. We propose model of sorted list based on the B+ -tree, which enables Fagin's algorithms to search for the top-k objects according to a non-monotone ranking function. We apply this model in the Internet environment with data on different remote servers. Furthermore, we designed novel dynamic tree-based data structures, namely, MDB-tree composed of B+ -trees, MDB-tree with lists, MDB-tree with groups of B+ -trees and multiple-ordered MDB-tree. Concurrently, we have developed novel top-k algorithms, namely, the MD algorithm, the MXT algorithm and their variants which are able search for the top-k objects ac- cording to a non-monotone ranking function. These top-k algorithms are efficient...Názov: Prefernčné top-k vyhľadávanie založené na viacrozmernom B-strome Autor: RNDr. Matúš Ondreička Katedra: Katedra softwarového inženýrství Matematicko-fyzikální fakulta Univerzita Karlova v Praze Školiteľ: Prof. RNDr. Jaroslav Pokorný, CSc. Email autora: [email protected] Email školiteľa: [email protected] Abstrakt: V tejto práci sa zameriavame na top-k vyhľadávanie podľa použí- vateľských preferencií s použitím B+ -stromov a viacrozmerného B-stromu (MDB-strom). Používame model používateľských preferencií založený na fuzzy funkciách, ktorý nám umožňuje vyhľadávať podľa nemonotónnej ohod- nocovacej funkcie. Navrhujeme model zotriedeného zoznamu založený na B+ -strome, ktorý umožní faginovym algoritmom vyhľadávať k najlepších ob- jektov podľa nemonotónnej ohodnocovanej funkcie. Tento model používame v prostredí internetu s dátami na rôznych vzdialených serveroch. Okrem toho sme navrhli nové dynamické stromové štruktúry, konkrétne MDB-strom zložený z B+ -stromov, MDB-strom so zoznamami, MDB-strom so skupinami B+ -stromov a viacnásobne zoradený MDB-strom. Súčasne sme vyvinuli nové top-k algoritmy, konkrétne MD algoritmus, MXT algoritmus a ich varianty, ktoré dokážu vyhľadávať k najlepších objektov podľa nemonotónnej ohodno- covacej funkcie. Tieto top-k algoritmy sú efektívne, pretože dokážu...Katedra softwarového inženýrstvíDepartment of Software EngineeringFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult
A Search For Radioactivity In Natural Vanadium.
No full textPhDNuclear physicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/181262/2/0007739.pd
Correlation of expression of CD31 and smooth muscle actin SMA with morphological characteristics of rectal adenocarcinoma
No full textUVOD: Adenokarcinom rektuma je jedno od najčešćih malignih oboljenja ljudi, sa čestim razvojem metastaza u limfnim čvorovima i jetri. Obzirom da stadijum bolesti najviše utiče na terapijski pristup i ishod bolesti, neophodna su istraživanja u cilju boljeg razumevanja sklonosti tumora ka invaziji i metastazama. Tumorska invazija obuhvata kompleksnu reakciju tumorskih ćelija i strome tumora, pri čemu se smatra da je za stvaranje dezmoplastične strome najpre odgovorna aktivacija miofibroblasta, dok je angiogeneza esencijalna za metastatski potencijal tumora. Različite i malobrojne studije koje su koristile „image“ analizu su često dale kontradiktorne rezultate u vezi međusobnog uticaja tumorskih ćelija i okolnih parametara strome i skolonosti tumora ka invaziji i metastazama. Ovakvi rezultati su naveli autora da koristeći „image“ analizu pokuša da što preciznije izmeri vrednosti sastavnih delova strome i utvrdi njihovu povezanost sa morfološkim karakteristikama tumora.
CILj: Histohemijsko i imunohistohemijsko proučavanje strome adenokaricnoma rektuma, odnosno određivanje vrednosti miofibroblasta, dezmoplazije, kao i gustine, obima i vrednosti endotelijalne površine („endothelial area“, EA) vaskularnih prostora koristeći „image“ analizu.INTRODUCTION: Adenocarcinoma of the rectum is one of the most common malignant diseases in humans, with frequent development of metastases in the lymph nodes and liver. Since the stage of the disease is the most important parametar affecting the therapeutic approach and outcome of the disease, it is necessary to do research in order to better understand the tendency toward tumor invasion and metastasis. Tumor invasion involves a complex reaction of the tumor cells and the tumor stroma, wherein it is considered that the activation of myofibroblasts is primarily responsible for the formation of desmoplastic stroma, whereas angiogenesis is essential for the metastatic potential of the tumor. A few different studies that have used the "image" analysis gave contradictory results regarding the mutual influence of tumor cells and surrounding stromal parameters and the tendency for tumor invasion and metastasis. These results prompted the author to use "image" analysis, with attempt to accurately measure the value of the constituent parts of the stroma and establish their relationship with morphological characteristics of the tumor.
AIM: Histochemical and immunohistochemical study of stromal component of rectal adenocarcinoma and to determine the value of myofibroblasts, desmoplasia and density, perimeter and assessment of endothelial surface ("endothelial area", EA) of vascular spaces using the "image" analysis
Correlation of expression of CD31 and smooth muscle actin SMA with morphological characteristics of rectal adenocarcinoma
No full textUVOD: Adenokarcinom rektuma je jedno od najčešćih malignih oboljenja ljudi, sa čestim razvojem metastaza u limfnim čvorovima i jetri. Obzirom da stadijum bolesti najviše utiče na terapijski pristup i ishod bolesti, neophodna su istraživanja u cilju boljeg razumevanja sklonosti tumora ka invaziji i metastazama. Tumorska invazija obuhvata kompleksnu reakciju tumorskih ćelija i strome tumora, pri čemu se smatra da je za stvaranje dezmoplastične strome najpre odgovorna aktivacija miofibroblasta, dok je angiogeneza esencijalna za metastatski potencijal tumora. Različite i malobrojne studije koje su koristile „image“ analizu su često dale kontradiktorne rezultate u vezi međusobnog uticaja tumorskih ćelija i okolnih parametara strome i skolonosti tumora ka invaziji i metastazama. Ovakvi rezultati su naveli autora da koristeći „image“ analizu pokuša da što preciznije izmeri vrednosti sastavnih delova strome i utvrdi njihovu povezanost sa morfološkim karakteristikama tumora.
CILj: Histohemijsko i imunohistohemijsko proučavanje strome adenokaricnoma rektuma, odnosno određivanje vrednosti miofibroblasta, dezmoplazije, kao i gustine, obima i vrednosti endotelijalne površine („endothelial area“, EA) vaskularnih prostora koristeći „image“ analizu.INTRODUCTION: Adenocarcinoma of the rectum is one of the most common malignant diseases in humans, with frequent development of metastases in the lymph nodes and liver. Since the stage of the disease is the most important parametar affecting the therapeutic approach and outcome of the disease, it is necessary to do research in order to better understand the tendency toward tumor invasion and metastasis. Tumor invasion involves a complex reaction of the tumor cells and the tumor stroma, wherein it is considered that the activation of myofibroblasts is primarily responsible for the formation of desmoplastic stroma, whereas angiogenesis is essential for the metastatic potential of the tumor. A few different studies that have used the "image" analysis gave contradictory results regarding the mutual influence of tumor cells and surrounding stromal parameters and the tendency for tumor invasion and metastasis. These results prompted the author to use "image" analysis, with attempt to accurately measure the value of the constituent parts of the stroma and establish their relationship with morphological characteristics of the tumor.
AIM: Histochemical and immunohistochemical study of stromal component of rectal adenocarcinoma and to determine the value of myofibroblasts, desmoplasia and density, perimeter and assessment of endothelial surface ("endothelial area", EA) of vascular spaces using the "image" analysis
RC SMOOTHING OF SPECTRA
No full textAuthor Institution: Department of Physics, Michigan State University East LansingBy convoluting an exponential function with calculated spectra consisting of single and multiple sets of lines of various widths and line shapes, we have determined the effects that time constant (RC) has on recorded spectra. For equivalent experiments, in which the scanning rates d/dt are equal, we have concluded that the optimum value of RC is essentially independent of whether the spectrum is to be digitized or not, and independent of the sampling rate if digitization is used. A trade-off among the desirable and undesirable effects of RC leads us to recommend a value of RC about one-tenth of the full width at half height of the sharpest individual lines in the observed spectrum. This research was supported by a grant from the National Science Foundation
Barraca valenciana – chata znad Zatoki Walenckiej
No full textRural houses of the Barraca Valenciana type stand out from the Spanish folk architecture
with their spectacular yet relatively simple form. Their architectural expression is made up
of clay, whitewashed walls and steep, thatched roofs. The entrance placed in the gable
wall is often preceded by a pergola. The author discuss it in the context of the architecture
of societies that use the languages belonging to the Occitano-Romance group and in
a broader European perspective.Wiejskie domy mieszkalne typu barraca valenciana wyróżniają się spośród hiszpańskiej
architektury ludowej spektakularną, choć stosunkowo prostą formą. Na ich wyraz architektoniczny
składają się gliniane, bielone ściany i strome dachy pokryte strzechą. Wejście
umieszczone w ścianie szczytowej, często poprzedza pergola. Autor omawiają je w kontekście
architektury społeczeństw, które posługują się językami należącymi grupy oksytanoromańskiej
oraz w szerszej perspektywie europejskiej
