Athletic Identity of Students Actively Involved in Sports and Its Relationship with Induced Stress

Theexpression of the athletic identity in academic environments may become a stress-reducing and a stress-enhancing factor depending on the conditions of the environment when expressing one’s athletic identity (Chen et al., 2010).Methods. 214 students (105 females and 109 males) took part in the research. All of them were first year students of the first level of studies (i.e. BA studies) at Lithuanian Sports University. All the students were actively practicing sports. Their age ranged from 18 to 25 with the age average of 19.24 (0.76). Thestudymadeuseofquestionnaires: ReederStressAssessmentScale and Athletic Identity Questionnaire (AIQ).Conclusions. The stress levels experienced by students actively practicing sports and possessing a more prominent athletic identity yet not going for results in sports are lower than those experienced by students with a less prominent athletic identity

Robust Identification of Target Genes and Outliers in Triple-negative Breast Cancer Data

Correct classification of breast cancer sub-types is of high importance as it directly affects the therapeutic options. We focus on triple-negative breast cancer (TNBC) which has the worst prognosis among breast cancer types. Using cutting edge methods from the field of robust statistics, we analyze Breast Invasive Carcinoma (BRCA) transcriptomic data publicly available from The Cancer Genome Atlas (TCGA) data portal. Our analysis identifies statistical outliers that may correspond to misdiagnosed patients. Furthermore, it is illustrated that classical statistical methods may fail in the presence of these outliers, prompting the need for robust statistics. Using robust sparse logistic regression we obtain 36 relevant genes, of which ca. 60\% have been previously reported as biologically relevant to TNBC, reinforcing the validity of the method. The remaining 14 genes identified are new potential biomarkers for TNBC. Out of these, JAM3, SFT2D2 and PAPSS1 were previously associated to breast tumors or other types of cancer. The relevance of these genes is confirmed by the new DetectDeviatingCells (DDC) outlier detection technique. A comparison of gene networks on the selected genes showed significant differences between TNBC and non-TNBC data. The individual role of FOXA1 in TNBC and non-TNBC, and the strong FOXA1-AGR2 connection in TNBC stand out. Not only will our results contribute to the breast cancer/TNBC understanding and ultimately its management, they also show that robust regression and outlier detection constitute key strategies to cope with high-dimensional clinical data such as omics data

Universal sequence map (USM) of arbitrary discrete sequences

BACKGROUND: For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. RESULTS: We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM), is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR). The latter enables the representation of 4 unit type sequences (like DNA) as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. CONCLUSIONS: USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules

Computing distribution of scale independent motifs in biological sequences

The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of the fractal structure of that coordinate system. Consequently, the investigation of distribution of symbolic motifs at multiple scales is hampered by an inexact association between distance and sequence dissimilarity. A solution to this problem could unleash the use of iterative maps as phase-state representation of sequences where its statistical properties can be conveniently investigated. In this study a family of kernel density functions is described that accommodates the fractal nature of iterative function representations of symbolic sequences and, consequently, enables the exact investigation of sequence motifs of arbitrary lengths in that scale-independent representation. Furthermore, the proposed kernel density includes both Markovian succession and currently used alignment-free sequence dissimilarity metrics as special solutions. Therefore, the fractal kernel described is in fact a generalization that provides a common framework for a diverse suite of sequence analysis techniques

Twiner: correlation-based regularization for identifying common cancer gene signatures

© The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Background: Breast and prostate cancers are typical examples of hormone-dependent cancers, showing remarkable similarities at the hormone-related signaling pathways level, and exhibiting a high tropism to bone. While the identification of genes playing a specific role in each cancer type brings invaluable insights for gene therapy research by targeting disease-specific cell functions not accounted so far, identifying a common gene signature to breast and prostate cancers could unravel new targets to tackle shared hormone-dependent disease features, like bone relapse. This would potentially allow the development of new targeted therapies directed to genes regulating both cancer types, with a consequent positive impact in cancer management and health economics. Results: We address the challenge of extracting gene signatures from transcriptomic data of prostate adenocarcinoma (PRAD) and breast invasive carcinoma (BRCA) samples, particularly estrogen positive (ER+), and androgen positive (AR+) triple-negative breast cancer (TNBC), using sparse logistic regression. The introduction of gene network information based on the distances between BRCA and PRAD correlation matrices is investigated, through the proposed twin networks recovery (twiner) penalty, as a strategy to ensure similarly correlated gene features in two diseases to be less penalized during the feature selection procedure. Conclusions: Our analysis led to the identification of genes that show a similar correlation pattern in BRCA and PRAD transcriptomic data, and are selected as key players in the classification of breast and prostate samples into ER+ BRCA/AR+ TNBC/PRAD tumor and normal tissues, and also associated with survival time distributions. The results obtained are supported by the literature and are expected to unveil the similarities between the diseases, disclose common disease biomarkers, and help in the definition of new strategies for more effective therapies.This work was supported by national funds through Fundação para a Ciência e a Tecnologia (FCT) with references UID/EEA/50008/2019 (Instituto de Telecomunicações), UID/CEC/50021/2019 (INESC-ID), UID/EMS/50022/2019 (IDMEC, LAETA), PREDICT (PTDC/CCI-CIF/29877/2017), and PERSEIDS (PTDC/EMS-SIS/0642/2014).info:eu-repo/semantics/publishedVersio

Učinkovitost kratkog savjetovanja usmjerenog na rješavanje problema (SFBC) koje srednjoškolci imaju u nastavi tjelesne kulture

Some scholars (Barr-Anderson et al., 2008; Cairney et al., 2012) have suggested that deficiencies in physical education (PE) classes are an important cause of the age-related decline in physical activity. The school PE curricula are ineffective and should be improved (Cairney et al., 2012). The purpose of this study was to determine the effectiveness of solution-focused brief counselling (SFBC) as a method of dealing with the problems faced by senior students during physical education classes with a view to developing interventions to increase students’ physical activity. Solution-focused brief counselling (SFBC) was applied as a method of dealing with the problems faced by senior students during physical education classes with a view to developing interventions to increase students’ physical activity. Following SFBC, 66.3% of participants reported medium or major progress in dealing with a severe problem related to physical activity (F = 164.30, p = .001 compared to control group) and physical education teachers observed positive changes in the students’ behaviour during physical education classes (Communication problems: t=10.86, p < .001; Insufficient involvement in PE classes: t=8.43, p < .001). SFBC is suitable for counselling adolescents at school as it is a brief, well-structured and flexible approach that helps to improve the quality of physical education classes.Neki znanstvenici (Barr-Anderson i sur., 2008; Cairney i sur., 2012;) smatrali su da su nedostaci u nastavi tjelesne kulture (TK) važni razlozi smanjene fizičke aktivnost koja je dobno vezana. Kurikul iz TK je neučinkovit te ga je potrebno poboljšati (Cairney i sur., 2012). Svrha ovoga istraživanja bila je odrediti učinkovitost kratkog savjetovanja usmjerenoga na rješenje problema (SFBC) kao metode kojom se mogu riješiti problemi s kojima se suočavaju srednjoškolci za vrijeme nastave TK s ciljem razvoja intervencije koje bi povećale učeničku fizičku aktivnost. Kratko savjetovanje usmjereno na rješavanje problema (SFBC) primijenjeno je kao metoda koja se koristi sa srednjoškolcima kada se suoče s problemom u nastavi TK s ciljem razvijanja intervencije koje bi pomogle u povećanju fizičke aktivnosti učenika. Nakon SFBC-a, 66,3 % sudionika izvijestilo je o srednjem ili većem napredovanju u suočavanju s teškim problemima vezanima uz fizičku aktivnost (F = 164,30, p = ,001 u usporedbi s kontrolnom skupinom), a nastavnici TK opazili su pozitivne promjene kod ponašanja učenika za vrijeme nastave iz TK (t, p < ,001). SFBC je odgovarajuća metoda za savjetovanje adolescenata u školi s obzirom na to da je kratka, dobro strukturirana i fleksibilna metoda koja pomaže u poboljšanju kvalitete nastave TK

Optimization strategies for metabolic networks

<p>Abstract</p> <p>Background</p> <p>The increasing availability of models and data for metabolic networks poses new challenges in what concerns optimization for biological systems. Due to the high level of complexity and uncertainty associated to these networks the suggested models often lack detail and liability, required to determine the proper optimization strategies. A possible approach to overcome this limitation is the combination of both kinetic and stoichiometric models. In this paper three control optimization methods, with different levels of complexity and assuming various degrees of process information, are presented and their results compared using a prototype network.</p> <p>Results</p> <p>The results obtained show that Bi-Level optimization lead to a good approximation of the optimum attainable with the full information on the original network. Furthermore, using Pontryagin's Maximum Principle it is shown that the optimal control for the network in question, can only assume values on the extremes of the interval of its possible values.</p> <p>Conclusions</p> <p>It is shown that, for a class of networks in which the product that favors cell growth competes with the desired product yield, the optimal control that explores this trade-off assumes only extreme values. The proposed Bi-Level optimization led to a good approximation of the original network, allowing to overcome the limitation on the available information, often present in metabolic network models. Although the prototype network considered, it is stressed that the results obtained concern methods, and provide guidelines that are valid in a wider context.</p

Nekrotisierende Enterokolitis des Frühgeborenen und Cholestase

Diese retrospektive case-control Studie ist über einen sechsjährigen Zeitraum von 1994 bis 1999 ausgelegt mit der Zielsetzung, eine mögliche Korrelation zwischen dem Auftreten der nekrotisierenden Enterokolitis des Frühgeborenen und der Cholestase festzustellen. Es wurden in 552 neonatologischen Aufnahmen mit einem Geburtsgewicht &#8804;2500g und einer Gestationszeit &#8804;33 Wochen 51 Patienten mit nekrotisierender Enterokolitis (NEC) identifiziert (8,9% der Aufnahmen mit diesen Auswahlkriterien). Es handelte sich somit ausschließlich um Frühgeborene. Das mittlere Geburtsgewicht betrug 1023g und rangierte von 355g bis 2020g, wobei 90% der Patienten unter 1500g lagen, und die mittlere Gestationszeit betrug 28,2 Wochen (24 bis inklusive 33 Schwangerschaftwochen). Die Inzidenz der NEC war in männlichen Patienten höher als in weiblichen (männl. 29 Fälle, weibl. 22 Fälle). Von den 51 NEC-Fällen erkrankten 14 Patienten (27%) im Anschluss an die NEC an Cholestase, im Vergleich zur Kontrollgruppe (n=51, matched pairs-Prinzip), in der 3 Cholestasefälle auftraten (p=0,008). Die Cholestasegruppe wies Gestationszeiten zwischen 24 und 32 Wochen mit einer mittleren Gestationszeit von 28,3 Wochen auf, was demjenigen der NEC-Patienten ohne Cholestase (28,2 Wochen) und der Kontrollgruppe entspricht. 13 der 14 Cholestasefälle (93%) entwickelten sich erst nach Absetzen der totalen parenteralen Ernährung (TPE). Das Auftreten der NEC korrelierte invers mit dem Gestationsalter (r=-0,83) und mit dem Geburtsgewicht (r=-0,43), kürzere Gestationszeiten korrelierten mit höherem Manifestationsalter der NEC (r=-0,32), ebenso wie ein geringeres Geburtsgewicht (r=-8,4). Die NEC trat zwischen 1 und 122 Tagen postpartum auf (Mittelwert 27,9 Tage, Median 23 Tage). In dieser Studie wurde eine höhere NEC-Inzidenz in Mehrlingsgeburten festgestellt. 18,1% der insgesamt 83 aufgenommenen Mehrlinge, die unseren Suchkriterien entsprachen, erkrankten an NEC (im Gegensatz zu 7,3% der übrigen Patienten). Die epidemiologischen Daten ergaben eine NEC-Epidemie im Jahre 1998, da 21 Fälle (41,2% des Patientenkollektivs) in diesem Jahr auftraten. Die Keime, die in diesen Fällen identifiziert worden sind, ebenso wie deren Häufigkeitsverteilung in dieser Gruppe, entsprechen jedoch weitgehend denen des Gesamtkollektivs. Trotz der auffällig hohen Fallzahl konnte kein einzelner Erreger für die Epidemie verantwortlich gemacht werden. Unreifere Säuglinge entwickelten einen schwereren Krankheitsverlauf (r=-0,40), und in geringerem Maße auch Patienten mit niedrigerem Geburtsgewicht (r=-0,17). Die mikrobiologischen Daten ergaben eine Assoziation des Erregers Enterobacter cloacae mit einem schwereren und komplikationsreicheren Verlauf der NEC, zumal unter den betroffenen Patienten der Schweregrad höher war (p=0,001) und Darmperforationen (p=0,08) und letale Ausgänge der NEC (p=0,03) häufiger waren. Außerdem entwickelten diese Patienten häufiger eine Cholestase als die übrigen Patienten (p<0,05). Patienten mit Staphylococcus epidermidis zeigten ebenfalls schwerere Krankheitsbilder (Schweregrad 4,6 im Vergleich zu 3,8, p=0,27). Von den 51 NEC-Fällen erkrankten 14 Patienten (27%) im Anschluss an die NEC an Cholestase, im Vergleich zur Kontrollgruppe (n=51, matched pairs-Prinzip), in der 3 Cholestasefälle auftraten (p=0,008). Die Cholestasegruppe wies Gestationszeiten zwischen 24 und 32 Wochen mit einer mittleren Gestationszeit von 28,3 Wochen auf, was demjenigen der NEC-Patienten ohne Cholestase (28,2 Wochen) und der Kontrollgruppe entspricht. 13 der 14 Cholestasefälle (93%) entwickelten sich erst nach Absetzen der totalen parenteralen Ernährung (TPE). Diese Ergebnisse lassen auf einen pathophysiologischen Zusammenhang beider Krankheitsbilder schließen, wobei die Cholestase als Folge der NEC auftritt. Die Neugeborenencholestase unterliegt einer multifaktoriellen Pathogenese, die in der hier dargestellten Hypothese mit derjenigen der NEC verflochten ist und das Auftreten der Cholestase im Frühgeborenen als eine Folge der NEC, unabhängig von der TPE, erklären könnte. Die Ergebnisse dieser Studie unterstützen diese Hypothese gemeinsamer Schädigungsmomente (ischämisches Ereignis und darauffolgende Inflammation, Infektion) und Risikofaktoren (Prämaturität), die sowohl den Darm als auch die Leber betreffen. In beiden Organen trägt derselbe Risikofaktor, die Prämaturität, zur Ausbildung der Krankheitsbilder bei und fördert somit auch deren gemeinsames Auftreten in Frühgeborenen. Im Darm führt diese Unreife zu einer Imbalance zwischen den schädigenden und den protektiven Mechanismen der Mukosa, so dass die Keiminvasion und die Entstehung einer NEC erleichtert werden. In der Leber sind nach heutigen Erkenntnissen neben der noch schwachen Immunabwehr vor allem die reduzierte Aktivität der zellulären Transportmechanismen für die Pathogenese der Cholestase maßgeblich. Außerdem sind beide Organe ähnlichen Durchblutungsbedingungen ausgesetzt, d.h. Ereignisse, die zu einem reduzierten Blutfluss im Mesenterium führen und die die vom Truncus coeliacus abgehenden Gefäße mit einbeziehen, beeinflussen auch die Leber. Die Inflammation im Darm kann durch eine überschießende Zytokinproduktion, die für unreife Neugeborene charakteristisch ist, über den venösen Abfluss die Leber mit einbeziehen und dort zur Entstehung der Cholestase beitragen. Die bakterielle Komponente in der Pathogenese der NEC kann durch Endotoxine, die die Leber über die Pfortader erreichen, die Hepatozyten sowohl direkt als auch über die Induktion einer Entzündungsreaktion schädigen. Die bereits bekannte und hier nochmals bestätigte Assoziation des Erregers Enterobacter cloacae mit der neonatalen Cholestase und die Tatsache, dass es sich um ein endotoxinbildendes Bakterium handelt, bestärken zusammen mit diesen Ergebnissen die Vermutung, dass die NEC-assoziierte Cholestase des Frühgeborenen unter anderem auch auf einer infektiösen, vermutlich durch Endotoxine vermittelten Komponente, beruht.In this retrospective case-control study we analyzed archived data from patients admitted over a six-year time period from 1994 to 1999. The aim of this study was to confirm a possible correlation between the incidence of necrotizing enterocolitis and cholestasis in the premature newborn. In 552 neonatologic admissions with a birth weight &#8804;2500g and a gestation time &#8804;33 weeks 51 patients with necrotizing enterocolitis (NEC) were identified (8,9% of admissions with these selection criteria). The mean birth weight was 1023g and ranged from 355g to 2020g with 90% of patients having birth weights inferior to 1500g and the mean gestation time was 28,2 weeks (range: 24-33 weeks gestation). The incidence of NEC was higher in male than in female patients (males: 29, females: 22). 14 of 51 NEC cases (27%) developed cholestasis after NEC, as opposed to 3 patients in the control group (p=0,008; control group: n=51, matched pairs). The cholestasis group showed gestation periods ranging from 24 to 32 weeks with a mean gestation period of 28,3 weeks, which matched the NEC patients without cholestasis (28,2 weeks) and the control group (28,6 weeks). 13 of 14 cholestasis cases (93%) only appeared after discontinuation of total parenteral nutrition (TPE). The occurrence of NEC revealed an inverse correlation to both gestation time (r=-0,83) and birth weight (r=-0,43); shorter gestation periods and decreasing birth weight correlated with higher age at manifestation of NEC (r=-0,32 and r=-0,84 respectively). NEC emerged between 1 and 122 days post partum (mean 27,9 days, median 23 days). 18,1% of 83 admitted multiple birth-infants with the stipulated criteria for this study (birth weight and gestation time limitations) developed NEC, as opposed to 7,3% of the remaining patients, thus showing a higher incidence of NEC in these patients. Epidemiological data showed a NEC epidemic in 1998, when 21 cases of NEC (41,2% of all analyzed patients) occurred in this year. The identified pathogens in those patients did not significantly differ from the overall NEC group. In spite of the conspicuously high number of cases no single causative pathogen could be made responsible for the epidemic. Increasing immaturity in preterm newborns and to a lesser extent in infants with lower birth weight correlated with graver illness (r=-0,40 and r=-0,17 respectively). Analysis of microbiological data revealed an association of the bacterium Enterobacter cloacae with more severe progression of illness and an increasing rate of complications in NEC patients. These cases achieved higher ratings in Bell’s staging system (p=0,001) and had significant incidence of intestinal perforation (p=0,08) and lethal outcome (p=0,03). Furthermore, these patients also developed cholestasis more frequently (p<0,05). Patients with Staphylococcus epidermidis also showed more serious illness (severity score 4,6 as opposed to 3,8 of remaining patients, p=0,27). These results strongly indicate a pathophysiologic association of NEC and cholestasis, in which cholestasis arises as a consequence of NEC. Both recent and older publications concerning NEC and cholestasis repeatedly mention an associated occurrence of both afflictions, but it was always assumed that cholestasis presents due to TPE in the management of NEC. Cholestasis of the newborn underlies multifactorial pathogenesis which in our hypothesis is interwoven with the pathogenesis of NEC, and both factors could explain the occurrence of cholestasis in the premature newborn as a consequence of NEC regardless of TPE. The results of this study support our hypothesis of common damaging events (ischemic episode with consequent inflammation, infection) and risc factors (prematurity) affecting gut and liver. In both organs the risc factor prematurity contributes to the development of the two illnesses and thus also increases their simultaneous manifestation in premature newborns. In the gut this immaturity leads to an imbalance between protective mechanisms of the mucosa and damaging processes increasing the occurrence of NEC. The actual consensus concerning the pathogenesis of cholestasis is that a weak immune system and especially the reduced activity of hepatocellular transport mechanisms are causative of the affliction. Additionally both organs depend on the same blood supply conditions, i.e. events leading to a reduced blood flow in the mesenterium which include the arteries originating in the celiac trunk also affect the liver. Gut inflammation can contribute to the development of cholestasis because of the excessive cytokine production characteristic of premature newborns and its influence on the liver via the venous system of the intestine. The microbiological component in the pathogenesis of NEC, mainly the bacterial endotoxins reaching the liver through the portal vein, can cause hepatic injury either directly or by inducing inflammatory response. The known association of Enterobacter cloacae with neonatal cholestasis as confirmed in this study and its endotoxin-producing capability both support the assumption that NEC associated cholestasis of the premature newborn is partly based upon an endotoxin-mediated infectious component

CHANGE OF THE AMORPHOUS CARBON FILMS BY LASER NANOSECOND PULSE IRRADIATION

Diamond like carbon (DLC) thin films was deposited, using ion beam deposition (IBD). Samples were irradiated by the first (1064 nm), the second (532 nm), and the third (355 nm) laser harmonics, changing pulse number per spot, irradiation power intensity. After the laser irradiation films were analyzed by scanning electron microscopy (SEM), null-ellipsometry Gaertner L117 operating with He – Ne laser (λHe-Ne = 632.8 nm), Fourier transform infrared (FTIR), and Raman scattering (RS) spectroscopes, Vickers hardness method. After the annealing by first harmonic (70 MW/cm2) caused SiC and nc – Si formation in the substrate boundary, the slight increase of the sp2 C=C sites fraction. A weak influence was on the surface morphology and microhardness values. Using the second, and the third laser harmonics noticeably caused modification of the DLC samples: graphitization process and formation of the SiC and SiOH fractions

Fractal MapReduce decomposition of sequence alignment

This work was supported in part by the Center for Clinical and Translational Sciences of the University of Alabama at Birmingham under contract no. 5UL1 RR025777-03 from NIH National Center for Research Resources, by the National Cancer Institute grant 1U24CA143883-01, by the European Union FP7 PNEUMOPATH (HEALTH F3 2009 222983).Background: The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics algorithm development. In some cases an algorithm will find a natural distribution via use of map functions to process vectorized components, followed by a reduce of aggregate intermediate results. However, for some data analysis procedures such as sequence analysis, a more fundamental reformulation may be required. Results: In this report we describe a solution to sequence comparison that can be thoroughly decomposed into multiple rounds of map and reduce operations. The route taken makes use of iterated maps, a fractal analysis technique, that has been found to provide a "alignment-free" solution to sequence analysis and comparison. That is, a solution that does not require dynamic programming, relying on a numeric Chaos Game Representation (CGR) data structure. This claim is demonstrated in this report by calculating the length of the longest similar segment by inspecting only the USM coordinates of two analogous units: with no resort to dynamic programming. Conclusions: The procedure described is an attempt at extreme decomposition and parallelization of sequence alignment in anticipation of a volume of genomic sequence data that cannot be met by current algorithmic frameworks. The solution found is delivered with a browser-based application (webApp), highlighting the browser's emergence as an environment for high performance distributed computing. Availability: Public distribution of accompanying software library with open source and version control at http://usm.github.com. Also available as a webApp through Google Chrome's WebStore http://chrome.google.com/webstore: search with "usm".publishersversionpublishe