MHCPred : a server for quantitative prediction of peptide-MHC binding

Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-base multivariate statistical approach to the quantitative prediction of peptide binding to major histocom-patibility complexes (MHC), the key checkpoint on the antigen presentation pathway within adaptive,cellular immunity. MHCPred implements robust statistical models for both Class I alleles (HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203,HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3301, HLA-A*6801, HLA-A*6802 and HLA-B*3501) and Class II alleles (HLA-DRB*0401, HLA-DRB*0401and HLA-DRB* 0701).

The effects of material variations in high value manufacturing industries

It has never been easy for manufacturing companies to understand their confidence level in terms of how accurate and to what degree of flexibility parts can be made. This brings uncertainty in finding the most suitable manufacturing method as well as in controlling their product and process verification systems. The aim of this research is to develop a system for capturing the company’s knowledge and expertise and then reflect it into an MRP (Manufacturing Resource Planning) system. A key activity here is measuring manufacturing and machining capabilities to a reasonable confidence level. For this purpose an in-line control measurement system is introduced to the company. Using SPC (Statistical Process Control) not only helps to predict the trend in manufacturing of parts but also minimises the human error in measurement. Gauge R&R (Repeatability and Reproducibility) study identifies problems in measurement systems. Measurement is like any other process in terms of variability. Reducing this variation via an automated machine probing system helps to avoid defects in future products.Developments in aerospace, nuclear, oil and gas industries demand materials with high performance and high temperature resistance under corrosive and oxidising environments. Superalloys were developed in the latter half of the 20th century as high strength materials for such purposes. For the same characteristics superalloys are considered as difficult-to-cut alloys when it comes to formation and machining. Furthermore due to the sensitivity of superalloy applications, in many cases they should be manufactured with tight tolerances. In addition superalloys, specifically Nickel based, have unique features such as low thermal conductivity due to having a high amount of Nickel in their material composition. This causes a high surface temperature on the work-piece at the machining stage which leads to deformation in the final product.Like every process, the material variations have a significant impact on machining quality. The main cause of variations can originate from chemical composition and mechanical hardness. The non-uniform distribution of metal elements is a major source of variation in metallurgical structures. Different heat treatment standards are designed for processing the material to the desired hardness levels based on application. In order to take corrective actions, a study on the material aspects of superalloys has been conducted. In this study samples from different batches of material have been analysed. This involved material preparation for microscopy analysis, and the effect of chemical compositions on hardness (before and after heat treatment). Some of the results are discussed and presented in this paper.

Macroeconomic characteristics and inventory investment: a multi-country study

The paper is a new element in a series of studies analyzing macroeconomic inventory behavior by use of multi-country data. In this paper, seven hypotheses are tested with positive result. These hypotheses include subjects like relations of inventories with growth and with some other macroeconomic indicators of the use of GDP and the long-term tendencies of global inventory formations. Multivariate statistical analysis is used for evaluation.

A kockázat mint látens fogalom (Risk - A latent concept)

A kockázat statisztikai értelemben közvetlenül nem mérhető, azaz látens fogalom éppen úgy, mint a gazdasági fejlettség, a szervezettség vagy az intelligencia. Mi bennünk a közös? A kockázat is komplex fogalom, több mérhető tényezőt foglal magában, és bár sok tényezőjét mérjük, fel sem tételezzük, hogy pontos eredményt kapunk. Ebben a megközelítésben az elemző kezdettől fogva tudja, hogy hiányos az ismerete. Ezt Bélyácz [2011[ nyomán úgy is megfogalmazhatjuk: „A statisztikusok tudják, hogy valamit éppen nem tudnak.” / === / From statistical point of view risk, like economic development is a latent concept. Typically there is no one number which can explicitly estimate or project risk. Variance is used as a proxy in finance to measure risk. Other professions are using other concepts for risk. Underwriting is the most important step in insurance business to analyse exposure. Actuaries evaluate average claim size and the probability of claim to calculate risk. Bayesian credibility can be used to calculate insurance premium combining frequencies and empirical knowledge, as a prior. Different types of risks can be classified into a risk matrix to separate insurable risk. Only this category can be analysed by multivariate statistical methods, which are based on statistical data. Sample size and frequency of events are relevant not only in insurance, but in pension and investment decisions as well.

Egyéni és kormányzati felelősség a vállalkozói kultúrában – Európában és Magyarországon = Individual and state responsibility in entrepreneurial culture – In Europe and Hungary

Tanulmányunkban a European Values Study adatai alapján megvizsgáljuk, miben tér el Európában a vállalkozók értékrendje más társadalmi csoportokétól, különös tekintettel az egyéni és a kormányzati felelősségvállalás megítélésére. Kísérletet teszünk a vállalkozói értékrend különböző szintjei – személyes, társadalmi és kormányzattal kapcsolatos értékrend – közötti összefüggések feltárására. Összehasonlítjuk, mennyire jellemzi a vállalkozói értékrend az egyes európai országok lakosságát, kiemelt figyelmet fordítva Magyarországra. Egy hazai vállalkozói adatbázis alapján megvizsgáljuk, hogy a magyar vállalkozók értékrendje eltér-e az európai átlagtól, továbbá milyen törésvonalak húzódnak a vállalkozói populáción belül az értékrend szempontjából. _____ Data from the European Values Study are used to examine what sets apart the normative views of entrepreneurs from those of other social groups in Europe about individual and state responsibility. Different levels of an individual’s value system are distinguished: personal, social and state-related values are differentiated. The interrelationships among these levels are explored. Using multivariate statistical analysis, we examine the prevalence of ‘entrepreneurial’ views in European countries, especially in Hungary. Relying on data from a survey of 300 Hungarian small entrepreneurs, we explore if their value system differs from the average value system of European entrepreneurs. Finally, we examine the factors social and economic factors that influence entrepreneurs’ views on personal and state responsibility.

Shifting N and P limitation along a north-south gradient of mangrove estuaries in South Florida

A multivariate statistical analysis was applied to a 10 year, multiparameter data set in an effort to describe the spatial dependence and inherent variation of water quality patterns in the mangrove estuaries of Ten Thousand Islands – Whitewater Bay area. Principal component analysis (PCA) of 16 water quality parameters collected monthly resulted in five groupings, which explained 72.5% of the variance of the original variables. The “Organic” component (PCI) was composed of alkaline phosphatase activity, total organic nitrogen, and total organic carbon; the “Dissolved Inorganic N” component (PCII) contained NO 3 − , NO 2 − , and NH 4 + ; the “Phytoplankton” component (PCIII) was made up of total phosphorus, chlorophyll a, and turbidity; dissolved oxygen and temperature were inversely related (PCIV); and salinity and soluble reactive phosphorus made up PCV. A cluster analysis of the mean and SD of PC scores resulted in the spatial aggregation of the 47 fixed stations into six classes having similar water quality, which we defined as: Mangrove Rivers, Whitewater Bay, Gulf Islands, Coot Bay, Blackwater River, and Inland Waterway. Marked differences in physical, chemical, and biological characteristics among classes were illustrated by this technique. Comparison of medians and variability of parameters among classes allowed large scale generalizations as to underlying differences in water quality in these regions. A strong south to north gradient in estuaries from high N - low P to low N - high P was ascribed to marked differences in landuse, freshwater input, geomorphology, and sedimentary geology along this tract. The ecological significance of this gradient discussed along with potential effects of future restoration plans.

``This is your brain on drugs'': The public policy of anti -drug programming. An exploratory analysis of media and other sources of drug information for adolescents

In the 1980s, government agencies sought to utilize research on drug use prevention to design media campaigns. Enlisting the assistance of the national media, several campaigns were designed and initiated to bring anti-drug use messages to adolescents in the form of public service advertising. This research explores the sources of information selected by adolescents in grades 7 through 12 and how the selection of media and other sources of information relate to drug use behavior and attitudes and perceptions related to risk/harm and disapproval of friends' drug-using activities.^ Data collected from 1989 to 1992 in the Miami Coalition School Survey provided a random selection of secondary school studies. The responses of these students were analyzed using multivariate statistical techniques.^ Although many of the students selected media as the source for most of their information on the effects of drugs on the people who use them, the selection of media was found to be positively related to alcohol use and negatively related to marijuana use. The selection of friends, brothers, or sisters was a statistically significant source for adolescents who smoke cigarettes, use alcohol or marijuana.^ The results indicate that the anti-drug use messages received by students may be canceled out by media messages perceived to advocate substance use and that a more persuasive source of information for adolescents may be friends and siblings. As federal reports suggest that the economic costs of drug abuse will reach an estimated $150 billion by 1997 if current trends continue, prevention policy that addresses the glamorization of substance use remains a national priority. Additionally, programs that advocate prevention within the peer cluster must be supported, as peers are an influential source for both inspiring and possibly preventing drug use behavior. ^

Indicador de vulnerabilidade agropecuária a extremos climáticos para o nordeste do Brasil

The effects of climate change on human societies have become the focus of many researchers for their research. Understanding weather patterns (circulation of the atmosphere, precipitation, temperature) is essences for predicting extreme weather, but analyze how these extreme events act in our society and look for ways to reduce the impact caused by these events is the great challenge. Using a concept very in the humanities and social sciences to understand these impacts and the adaptation of the society's vulnerability. The objective of this work is to develop and apply a methodology for evaluating fining scale and quantify the vulnerability of the Brazilian Northeast to climatic extremes, developing a methodology that combines aspects of vulnerability to drought, as well as socioeconomic and climatic indicators used to assess exposure, ability to adaptation and the sensitivity of geographical microregions of the region. The assessment of the susceptibility or degree of exposure to risk is the regional using the SPI (Standardized Precipitation Index) by the degree of magnitude dried (MD), the rate of precipitation such as PCD (Precipitation Concentration Degree) and PCP (Precipitation Period Concentration) helped characterize and regional climatology, these indices showed satisfactory results in the pilot study of Rio Grande do Norte to assess the degree of exposure to drought. Regarding sensitivity agricultural / livestock multivariate statistical technique to factor analysis showed acceptable results for the proposed model using data for the period 1990-1999 (P1). The application of the analysis of vulnerability considering the adaptive capacity, as the adaptive disability have almost similar results with much of the region's vulnerability to extreme south of Bahia state as a part of the semiarid region has a degree of vulnerability among moderate and mean

Variação entre os pronomes tu e você na função de sujeito na fala de Natal (RN): uma abordagem sociofuncionalista

In this dissertation, under the light of a sociofunctionalist approach (TAVARES, 2003; 2013; GORSKI; TAVARES, 2013), I analyze 378 data of pronouns tu and você extracted from 12 conversations belonging to Natal Conversational Data Base (CUNHA, 2010). I have the following objectives: (i) mapping linguistic and extralinguistic specialization trends of second person singular subject pronouns tu and você in the speech of Natal (RN); (ii) assessing the role of the principle of persistence (HOPPER, 1991) as a possible motivating factor of specialization trends of pronouns tu and você; (iii) identify in which of the six pronouns subsystems proposed by Scherre et al. (2009) is situated the speech community of Natal portrayed in this study. In order to achieve the proposed objectives, I submitted the data to multivariate statistical analysis, which have provided frequencies and relative weights.I obtained, as relevant factor groups, according to the statistical analysis, the nature of the relationship between the interlocutors (if the relationship is asymmetric, less intimate, and more formal, the use of você is favored; if the relationship is symmetrical, intimate and informal, the use of tu is favored); the degree of formality of the environment in which the conversation takes place (in more informal environments tu was favored; in more formal environments você were favored); and the type of discourse (reported / not reported) (tu was favored in not reported discourse and você was favored in reported discourse). Based on results regarding to these factors groups, I organized a panorama of specializations of pronouns tu and você, noting that tu seems specialized for more informal contexts of use than those for which você seems specialized. The motivation underlying these trends of specialization may be the principle of persistence, since along its historical development, você carries a trace of greater formality or, at least, less intimacy, when contrasted to tu. Finally, I concluded that, of the six pronoun subsystems proposed by Scherre et al. (2009), the speech community of Natal can be framed in the fifth, characterized by variable use of subject pronouns tu and você, with more frequent use of você than tu, and rare occurrence of agreement of tu with second-person singular verb.

Foraminíferos, ostracodes e microfauna associada da plataforma continental equatorial norte-rio-grandense, NE Brasil: área Porto do Mangue a Galinhos

This study was conducted in the adjacent Brazilian equatorial inner shelf to Rio Grande do Norte, between the region of Porto do Mangue and Galinhos. The main objective is the characterization of biogenic sediments, especially foraminifera and ostracod collected on the surface of the seafloor. The methodology involved standard procedures including literature, surveys, processing of samples in the laboratory and identification of foraminifera and ostracods by genera or species under stereo microscopy and scanning electron microscopy (SEM). Multivariate statistical analyzes and study of ecological indexes were also applied to the study of foraminifera. Three transects, from inner shelf to slope were sampled: profile 01 (east, near Galos), profile 02 (center, near the city of Macau) and profile 03 (west, near Ponta do Mel). Results indicated the predominance of benthic foraminifera and little plankton occurrence. Benthic foraminifera genera observed in abundance were Quinqueloculina, Textularia, Globigerina and Pyrgo, Quinqueloculina, Textularia, Pyrgo, Ammonia, Elphidium, Pseudononion, Peneroplis, Bolivina and Poroeponides, occurred more frequently. Less frequently been described Amphistegina, Archaias, Bigenerina, Cibicides, Cassidulina, Amphicorina, Cornuspira, Paterina, Hopkunsina, Oolina, Uvigerina, Fusenkoina, Nonionella, Amphisorus, Wiesrella, Reussella, Reophax, Nodosaria, Marginulina and Cyclogyra. Six genera of ostracods were also identified: Puriana variabilis / P. convoluted?, Loxoconcha sp, Bairdiidae, Xestoleberis sp, Hemicytheridae and Ruggiericythere sp. Groups of organisms found in the studied shelf presented chemical composition of Ca, C, O, Na, Cl, Al, Mg, and Si. The proportions of chemical elements may vary according to the type of biogenic sediment, with the highest values identified as Ca, C, Cl, Na and O. The absolute dating by carbon 14 method indicated sediments of different colors (light and dark), correspond to a single age from 3000 to 6000 years BP, related to the Quaternary. These data intend to complement information about biogenic sediments in the Brazilian continental shelf, especially in the Northeast, where there is a lack of such studies.

Foraminíferos, ostracodes e microfauna associada da plataforma continental equatorial norte-rio-grandense, NE Brasil: área Porto do Mangue a Galinhos

This study was conducted in the adjacent Brazilian equatorial inner shelf to Rio Grande do Norte, between the region of Porto do Mangue and Galinhos. The main objective is the characterization of biogenic sediments, especially foraminifera and ostracod collected on the surface of the seafloor. The methodology involved standard procedures including literature, surveys, processing of samples in the laboratory and identification of foraminifera and ostracods by genera or species under stereo microscopy and scanning electron microscopy (SEM). Multivariate statistical analyzes and study of ecological indexes were also applied to the study of foraminifera. Three transects, from inner shelf to slope were sampled: profile 01 (east, near Galos), profile 02 (center, near the city of Macau) and profile 03 (west, near Ponta do Mel). Results indicated the predominance of benthic foraminifera and little plankton occurrence. Benthic foraminifera genera observed in abundance were Quinqueloculina, Textularia, Globigerina and Pyrgo, Quinqueloculina, Textularia, Pyrgo, Ammonia, Elphidium, Pseudononion, Peneroplis, Bolivina and Poroeponides, occurred more frequently. Less frequently been described Amphistegina, Archaias, Bigenerina, Cibicides, Cassidulina, Amphicorina, Cornuspira, Paterina, Hopkunsina, Oolina, Uvigerina, Fusenkoina, Nonionella, Amphisorus, Wiesrella, Reussella, Reophax, Nodosaria, Marginulina and Cyclogyra. Six genera of ostracods were also identified: Puriana variabilis / P. convoluted?, Loxoconcha sp, Bairdiidae, Xestoleberis sp, Hemicytheridae and Ruggiericythere sp. Groups of organisms found in the studied shelf presented chemical composition of Ca, C, O, Na, Cl, Al, Mg, and Si. The proportions of chemical elements may vary according to the type of biogenic sediment, with the highest values identified as Ca, C, Cl, Na and O. The absolute dating by carbon 14 method indicated sediments of different colors (light and dark), correspond to a single age from 3000 to 6000 years BP, related to the Quaternary. These data intend to complement information about biogenic sediments in the Brazilian continental shelf, especially in the Northeast, where there is a lack of such studies.

Infecções por enterobacteriaceae resistente aos carbapenêmicos em hospital de ensino: epidemiologia e caracterização molecular

Introduction: The production of KPC (Klebsiella pneumoniae carbapenemase) has become an important mechanism of carbapenem-resistance among Enterobacteriaceae strains. In Brazil, KPC is already widespread and its incidence has increased significantly, reducing treatment options. The “perfect storm” combination of the absence of new drug developmentand the emergence of multidrug-resistant strains resulted in the need for the use of older drugs, with greater toxicity, such as polymyxins. Aims: To determine the occurrence of carbapenemase-producing strains in carbapenem-resistant Enterobacteriaceae isolated from patients with nosocomial infection/colonization during September/2014 to August/2015, to determine the risk factors associated with 30-day- mortality and the impact of inappropriate therapy. Materials and Methods: We performed a case control study to assess the risk factors (comorbidities, invasive procedures and inappropriate antimicrobial therapy) associated with 30-day-mortality, considering the first episode of infection in 111 patients. The resistance genes blaKPC, blaIMP, blaVIM and blaNDM-1 were detected by polymerase chain reaction technique. Molecular typing of the strains involved in the outbreak was performed by pulsed field gel electrophoresis technique. The polymyxin resistance was confirmed by the microdilution broth method. Results: 188 episodes of carbapenem-resistant Enterobacteriaceae infections/colonizations were detected; of these, 122 strains were recovered from the hospital laboratory. The presence of blaKPC gene were confirmed in the majority (74.59%) of these isolates. It was not found the presence of blaIMP , blaVIM and blaNDM-1 genes. K. pneumoniae was the most frequent microorganism (77,13%), primarily responsible for urinary tract infections (21,38%) and infections from patients of the Intensive Care Unit (ICU) (61,38%). Multivariate statistical analysis showed as predictors independently associated with mortality: dialysis and bloodstream infection. The Kaplan-Meier curve showed a lower probability of survival in the group of patients receiving antibiotic therapy inappropriately. Antimicrobial use in adult ICU varied during the study period, but positive correlation between increased incidence of strains and the consumption was not observed. In May and July 2015, the occurrence rates of carbapenem-resistant Enterobacteriaceae KPC-producing per 1000 patient-days were higher than the control limit established, confirming two outbreaks, the first caused by colistin-susceptible KPC-producing K. pneumoniae isolates, with a polyclonal profile and the second by a dominant clone of colistin-resistant (≥ 32 μg/mL) KPC-producing K. pneumoniae. The cross transmission between patients became clear by the temporal and spatial relationships observed in the second outbreak, since some patients occupied the same bed, showing problems in hand hygiene adherence among healthcare workers and inadequate terminal disinfection of environment. The outbreak was contained when the ICU was closed to new admissions. Conclusions: The study showed an endemicity of K. pneumoniae KPC-producing in adult ICU, progressing to an epidemic monoclonal expansion, resulted by a very high antibiotic consumption of carbapenems and polymyxins and facilitated by failures in control measures the unit.

Principal Component Analysis of Results Obtained from Finite-Difference Time-Domain Algorithms

Finite-Differences Time-Domain (FDTD) algorithms are well established tools of computational electromagnetism. Because of their practical implementation as computer codes, they are affected by many numerical artefact and noise. In order to obtain better results we propose using Principal Component Analysis (PCA) based on multivariate statistical techniques. The PCA has been successfully used for the analysis of noise and spatial temporal structure in a sequence of images. It allows a straightforward discrimination between the numerical noise and the actual electromagnetic variables, and the quantitative estimation of their respective contributions. Besides, The GDTD results can be filtered to clean the effect of the noise. In this contribution we will show how the method can be applied to several FDTD simulations: the propagation of a pulse in vacuum, the analysis of two-dimensional photonic crystals. In this last case, PCA has revealed hidden electromagnetic structures related to actual modes of the photonic crystal.

Modelação e análise de um sistema flexível de produção

A modelação dos sistemas industriais apresenta para as organizações uma vantagem estratégica no domínio do estudo dos seus processos produtivos. Através da modelação será possível aumentar o conhecimento sobre os sistemas podendo permitir, quando possível, melhorias na gestão e planeamento da produção. Este conhecimento poderá permitir também um aumento da eficiência dos processos produtivos, através da melhoria ou eliminação das principais perdas detetadas no processo. Este trabalho tem como principal objetivo o desenvolvimento e validação de uma ferramenta de modelação, previsão e análise para sistemas produtivos industriais, tendo em vista o aumento do conhecimento sobre estes. Para a execução e desenvolvimento deste trabalho, foram utilizadas e desenvolvidas várias ferramentas, conceitos, metodologias e fundamentos teóricos conhecidos da bibliografia, como OEE (Overall Equipment Effectiveness), RdP (Redes de Petri), Séries Temporais, Kmeans, ou SPC (Statistical Process Control). A ferramenta de modelação, previsão e análise desenvolvida e descrita neste trabalho, mostrou-se capaz de auxiliar na deteção e interpretação das causas que influenciam os resultados do sistema produtivo e originam perdas, demonstrando as vantagens esperadas. Estes resultados foram baseados em dados reais de um sistema produtivo.

Guideline-based decision support has a small, non-sustained effect on transthoracic echocardiography ordering frequency.

BACKGROUND: Guidance for appropriate utilisation of transthoracic echocardiograms (TTEs) can be incorporated into ordering prompts, potentially affecting the number of requests. METHODS: We incorporated data from the 2011 Appropriate Use Criteria for Echocardiography, the 2010 National Institute for Clinical Excellence Guideline on Chronic Heart Failure, and American College of Cardiology Choosing Wisely list on TTE use for dyspnoea, oedema and valvular disease into electronic ordering systems at Durham Veterans Affairs Medical Center. Our primary outcome was TTE orders per month. Secondary outcomes included rates of outpatient TTE ordering per 100 visits and frequency of brain natriuretic peptide (BNP) ordering prior to TTE. Outcomes were measured for 20 months before and 12 months after the intervention. RESULTS: The number of TTEs ordered did not decrease (338±32 TTEs/month prior vs 320±33 afterwards, p=0.12). Rates of outpatient TTE ordering decreased minimally post intervention (2.28 per 100 primary care/cardiology visits prior vs 1.99 afterwards, p<0.01). Effects on TTE ordering and ordering rate significantly interacted with time from intervention (p<0.02 for both), as the small initial effects waned after 6 months. The percentage of TTE orders with preceding BNP increased (36.5% prior vs 42.2% after for inpatients, p=0.01; 10.8% prior vs 14.5% after for outpatients, p<0.01). CONCLUSIONS: Ordering prompts for TTEs initially minimally reduced the number of TTEs ordered and increased BNP measurement at a single institution, but the effect on TTEs ordered was likely insignificant from a utilisation standpoint and decayed over time.