Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerating Needleman-Wunsch global alignment algorithm with GPUs

Over the recent decades, bioinformatics has acquired a major concern due to the rapid growth in biological data that includes protein structures and genome sequences. Many considerable efforts have been conducted by computer scientists, mathematicians and biologists to coup with complex biological problems such as sequence alignment problem, using several techniques to formulate/model the targeted biological problems as computational problems and design algorithms to solve them in an accurate and efficient manner. Needleman-Wunsch algorithm as well as other alignment algorithms have been the subject of many studies to improve their performance due to their importance and the large scale of the data they have to handle (e.g., aligning strings of hundreds of thousands of characters). Approaches included a mixture of different parallel implementations using specialized hardware such as Graphical Processing Units (GPUs) and a vectorized approach of reading and processing the input data. In this work, a parallel implementation of NW algorithm is presented using GPU due to its efficiency and high speed, to solve the slowness problem associated with this algorithm when processing large data sets, as well as to enhance the performance of the algorithm especially when processing vectors of adjacent cells parallel to the matrix miner diagonal. The experiments show that the proposed implementation improves the performance of the algorithm by 99%.
Interaction Between the Innate and Adaptive Immune Systems is Required to Survive Sepsis and Control Inflammation After Injury

Substantial clinical and laboratory research has revealed that major injury causes abnormalities in both the innate and adaptive immune systems. However, the relative importance of each of these systems in the immune dysfunction after injury is poorly understood and difficult to establish by clinical studies alone. Rag1 (−/−) C57BL/6 mice (Rag1), which lack an adoptive immune system, and immune-sufficient wild-type (WT) C57BL/6 mice underwent 25% total body surface area burn injury or sham injury under anesthesia and were subjected to cecal ligation and puncture (CLP) at day 10 postinjury, a time of high CLP mortality in this model. To test the effect of adaptive immune deficiency on inflammatory cytokine production after injury, adaptive cell-depleted splenocytes from sham and burn WT and Rag1 mice were stimulated with LPS, and TNF-&agr; and IL-6 production were assayed at days 1 and 7 postinjury. Intracellular expression of TNF&agr; and IL-6 by F4/80 macrophages was also assessed on day 7 by intracellular cytokine staining. Finally, Rag1 animals were reconstituted with WT splenocytes, and the effect of such reconstitution on CLP survival and cytokine production was determined. Survival of sham WT animals after CLP was significantly higher (P < 0.01) than survival of burn WT and Rag1 sham and burn animals, all of which had equivalently low survival. Reconstitution of Rag1 animals with WT splenocytes restored CLP survival to WT sham levels. Splenocytes from Rag1 burn mice showed significantly augmented cytokine production when compared with WT burn mice on day 7 (P < 0.05). Reconstitution of Rag1 mice with WT splenocytes at the time of injury returned cytokine production to WT levels. Intracellular cytokine expression in F4/80 macrophages was increased to a similar degree after burn, but not sham burn injury in Rag1, reconstituted Rag1 and WT animals. These studies demonstrate that the adaptive immune system is necessary for protection from polymicrobial sepsis and plays a significant role in regulating the inflammatory response to injury.
Ethnicity and degree attainment

In this paper, we investigate the low degree attainment of ethnic minority students in higher education in England. Using a partial proportional odds model and data from the Higher Education Statistics Agency for qualifiers who started their course of study in 2002/03, we find that even after controlling for the majority of factors which we would expect to have an impact on attainment, being from a minority ethnic community is still statistically significant in explaining final attainment, although the gap has been significantly reduced.
Social Processes and Pedagogy in Online Learning

Online learning environments offer efficient ways of interconnecting group members and satisfying their communicative needs. However, learning does not proceed through shared communication alone; all groups imply social processes and learning groups demand an additional pedagogical intention. Popular online learning systems satisfactorily enable the management of students and teaching staff but offer limited tools to support familiar educational techniques and even fewer to support the essential processes of group dynamics that accompany learning. This article draws from both the literature of learning and of interpersonal and social interaction to define those characteristics of an online group that support learning and proceeds to use these criteria as a tool to evaluate currently available systems.
A New Strategy to Find Targets for Anticancer Therapy: Chemokine CXCL14/BRAK Is a Multifunctional Tumor Suppressor for Head and Neck Squamous Cell Carcinoma

In order to find a suppressor(s) of tumor progression in vivo for head and neck squamous cell carcinoma (HNSCC), we searched for molecules downregulated in HNSCC cells when the cells were treated with epidermal growth factor (EGF), whose receptor is frequently overactivated in HNSCC. The expression of BRAK, which is also known as CXC chemokine ligand 14 (CXCL14), was downregulated significantly by the treatment of HNSCC cells with EGF as observed by cDNA microarray analysis followed by reverse-transcriptase polymerase chain reaction analysis and western blotting. The EGF effect on the expression of CXCL14/BRAK was attenuated by the copresence of inhibitors of the EGF receptor, MEK, and ERK. The rate of tumor formation in vivo of BRAK-expressing vector-transfected tumor cells in athymic nude mice or SCID mice was significantly lower than that of mock vector-transfected ones. In addition tumors formed in vivo by the BRAK-expressing cells were significantly smaller than those of the mock-transfected ones. These results indicate that CXCL14/BRAK is a chemokine having suppressive activity toward tumor progression of HNSCC in vivo. Our approach will be useful to find new target molecules to suppress progression of tumors of various origins in addition to HNSCC.
An Efficient Framework for Road Sign Detection and Recognition

Road sign detection and recognition is a significant and challenging issue not only for assisting drivers but also navigating mobile robots. In this paper, we propose a novel and fast approach for the automatic detection and recognition of road signs. First, we use Hue Saturation Intensity (HSI) color space to segment the road signs color. And then we locate the road signs based on the geometry symmetry, as almost all the shapes of road sign shapes are symmetrical such circle, rectangle, triangle and octagon. The proposed shape feature is further applied to classify the shape initially. Finally, the road signs are exactly recognized by support vector machine (SVM) classifiers. We test our proposed method on real road images and the experimental results show that it can detect and recognize road signs rapidly and accurately. Copyright © 2014 IFSA Publishing, S. L.
Oral Supplementation of Glutamine Attenuates the Progression of Nonalcoholic Steatohepatitis in C57BL/6J Mice.

Background: Universally accepted therapeutic strategies for the treatment of nonalcoholic steatohepatitis (NASH) are still lacking. Studies suggest a preventive effect of oral Gln supplementation on the development of NASH; however, whether Gln also has therapeutic potential for pre-existing NASH has not yet been clarified.Objective: The aim of the present study was to determine whether Gln prevents the progression of diet-induced NASH in mice.Methods: For 8 wk, female C57BL/6J mice (6-8 wk old) were pair-fed a liquid Western-style diet [WSD, 25% of energy from fat, 50% wt:wt fructose, 0.16% wt:wt cholesterol] or control diet (C diet) to induce liver damage. From week 8 to 13, they were pair-fed the C diet or WSD alone or supplemented with l-Gln to provide 2.1 g/kg body weight (C diet + Gln or WSD + Gln). Energy intake was adjusted to the group with the lowest energy intake. Indexes of liver damage and inflammation, intestinal barrier function, and toll-like receptor 4 (Tlr4) signaling in the liver were determined.Results: The liver histology scores significantly increased from 8 to 13 wk (+31%) in WSD-fed mice and were significantly higher than in controls (P ≤ 0.05 for both time comparisons), whereas scores did not differ between C diet-fed and WSD + Gln-fed mice after 13 wk of feeding. The occludin protein concentrations in the small intestinal tissue were similarly reduced in both WSD-fed groups when compared with controls [WSD compared with C diet (-53%) and C diet + Gln (-42%), P ≤ 0.05; WSD + Gln compared with C diet + Gln (-34%), P ≤ 0.05] after 13 wk, whereas the expression of myeloid differentiation primary response gene 88 mRNA and concentration of inducible nitric oxide synthase and 4-hydroxynonenal protein adducts were significantly higher only in livers of WSD-fed mice (P ≤ 0.05 for the WSD group compared with all other groups; WSD + Gln group compared with the C diet groups: NS). Conclusion: Taken together, our data suggest that oral Gln supplementation protects mice from the progression of pre-existing, WSD-induced NASH.
Analytic perturbation theory: A new approach to the analytic continuation of the strong coupling constant α S into the timelike region

The renormalization group applied to perturbation theory is ordinarily used to define the running coupling constant in the spacelike region. However, to describe processes with timelike momenta transfers, it is important to have a self-consistent determination of the running coupling constant in the timelike region. The technique called analytic perturbation theory (APT) allows a consistent determination of this running coupling constant. The results are found to disagree significantly with those obtained in the standard perturbative approach. Comparison between the standard approach and APT is carried out to two loops, and threshold matching in APT is applied in the timelike region. {copyright} {ital 1998} {ital The American Physical Society}
Association Between Serum Cortisol and Chronic Kidney Disease in Patients with Essential Hypertension

Background/Aims: Serum cortisol level is elevated in patients with essential hypertension. We aimed at investigating the association of serum cortisol levels with parameters of renal function in essential hypertension. Methods: One hundred and seventy-eight patients with essential hypertension participated in the study. Fasting serum samples were collected at 8:00 am. Renal function was measured as estimated glomerular filtration rate (eGFR) calculated by the Chronic Kidney Disease Epidemiology Collaboration creatinine- cystatin C equation (eGFRcr-cys). Correlation analysis and stepwise regression analysis were used to detect the relationship between cortisol and eGFRcr-cys. The distributions of serum cortisol were split by the tertiles and subjects were stratified into those with low, median and high levels accordingly. Results: Serum cortisol levels were significantly higher in subjects whose eGFRcr-cys<90 ml/min/1.73 m2 than subjects whose eGFRcr-cys>90 ml/min/1.73 m2 (394.0±93.4 vs. 343.2±98.4 nmol/L, P=0.001). Age, systolic blood pressure, and serum total cholesterol, uric acid, cortisol levels were significantly associated with eGFRcr-cys, serum levels of creatinine and cystatin C. After adjusting for clinical factors, serum cortisol level had a statistically significant negative association with the eGFRcr-cys (β=-0.19, P=0.027), and positive associations with cystatin C (β=0.31, P=0.001) and creatinine (β=0.14, P=0.044). With the increment of cortisol tertile, the eGFRcr-cys significantly decreased (93.18±14.36 vs. 84.61±14.67 vs. 81.29±12.36 ml/min/1.73 m2 for low, median and high tertile, respecively, P=0.001). Conclusion: Serum cortisol level was negatively correlated with eGFRcr-cys in subjects with essential hypertension. Further studies are needed to investigate whether cortisol plays a role in hypertensive nephropathy development.
Topic change detection based on prosodic cues in unimodal setting

Speech is considered as the most dominant way for people to interact with each other. But speech cannot be merely characterized as sequence of sound units. There are some non-verbal elements, such as prosodic cues, that lend naturalness to speech. Prosodic cues such as rhythm, stress and intonation are crucial to investigate because they play an important role in human-human as well as in human-machine communication. They help to compensate many hidden meanings omitted from spoken language. The goal of this study was to investigate the correlation between non-verbal acoustic cues and topic shift in unimodal setting and to show how prosodic information can be used as a signal to detect topic change within conversation.
Comparison of Epithelial Differentiation and Immune Regulatory Properties of Mesenchymal Stromal Cells Derived from Human Lung and Bone Marrow

Mesenchymal stromal cells (MSCs) reside in many organs including lung, as shown by their isolation from fetal lung tissues, bronchial stromal compartment, bronchial-alveolar lavage and transplanted lung tissues. It is still controversial whether lung MSCs can undergo mesenchymal-to-epithelial-transition (MET) and possess immune regulatory properties. To this aim, we isolated, expanded and characterized MSCs from normal adult human lung (lung-hMSCs) and compared with human bone marrow-derived MSCs (BM-hMSCs). Our results show that lung-MSCs reside at the perivascular level and do not significantly differ from BM-hMSCs in terms of immunophenotype, stemness gene profile, mesodermal differentiation potential and modulation of T, B and NK cells. However, lung-hMSCs express higher basal level of the stemness-related marker nestin and show, following in vitro treatment with retinoic acid, higher epithelial cell polarization, which is anyway partial when compared to a control epithelial bronchial cell line. Although these results question the real capability of acquiring epithelial functions by MSCs and the feasibility of MSC-based therapeutic approaches to regenerate damaged lung tissues, the characterization of this lung-hMSC population may be useful to study the involvement of stromal cell compartment in lung diseases in which MET plays a role, such as in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis.
Ankle dynamic in stroke patients: Agonist vs. antagonist muscle relations

Introduction: Atypical ankle patterns of muscle activity during gait are commonly reported in patients with stroke. These findings can be due to changes between tibialis anterior (TA) and soleus (SOL) coactivation mechanisms. Objective: To compare the electromyographic activity (EMGa) of SOL and TA muscles and antagonist coactivation (C) level in the contralateral (CONTRA) and ipsilateral (IPSI) limbs to the side of the stroke lesion during the stance phase of the gait cycle. Methods: Twelve subjects with a stroke episode participated in this study. The electromyographic signal of TA and SOL and ground reaction forces were acquired while subjects walked at their self-selected speed. Values of ground reaction forces were used to divide the stance phase of gait into initial contact, midstance, and terminal stance. In each sub-phase, the magnitude of TA and SOL was calculated as well as the level of the antagonist C. Results: Although no statistical differences were found, mean values of SOL EMGa were lower in the IPSI limb in all stance phases in relation to the CONTRA limb, and the opposite was observed in the TA EMGa. Moreover, higher mean levels of antagonist C were only found during the initial contact sub-phase in the CONTRA limb and in the other sub-phases in the IPSI limb. Besides, statistical differences were observed only during midstance. Conclusion: In stroke subjects, the antagonist C level during midstance of gait may reflect the dysfunction of the neuronal system over the IPSI limb.
Male Survivors of Childhood Sexual Abuse: A Qualitative Study and Issues for Clinical Consideration

ABSTRACT This qualitative study explored the effects of childhood sexual abuse with 10 adult male survivors. The men who participated in the research were largely motivated by their perception that North American society does not acknowledge the sexual abuse of boys. They described the abuse as having significantly affected their sexual identity, as well as their emotional and sexual relationships as adults. The implications of these issues for clinical intervention are described.
Distribution of teichoic acid in the cell wall of Bacillus subtilis

Hydrolysis of the cell wall of Bacillus subtilis 168 by autolysins or lysozyme resulted in the exposure of glucosylated teichoic acid molecules as evidenced by increased precipitation of [14C] concanavalin A. The number of concanavalin A-reactive sites increased significantly after only limited enzymatic digestion of the walls. Quantitative analyses of [14C] concanavalin A-treated wall or wall hydrolysate complexes indicate that approximately one-half of the teichoic acid molecules are surface-exposed, whereas the remainder are probably embedded within the peptidoglycan matrix. Treatment of the cell walls with sodium dodecyl sulfate or Triton X-100 did not result in new concanavalin A-reactive sites. Partial autolysis diminished the ability of the cell walls to adsorb bacteriophage phi25. Fluorescein-labeled concanavalin A bound intensely over the entire surface of growing B. subtilis 168 cells, suggesting that teichoic acid molecules are located on the total solvent-exposed surface area of the bacteria.
The behavioural biology of aggression

Preface 1. The history and aims of aggression research 2. A functional framework for the evolution of aggression 3. Protective aggression: a functional analysis 4. Mechanisms of protective aggression and their relation to function 5. Parental aggression: a functional analysis 6. Mechanisms of parental aggression and their relation to function 7. Competitive aggression: a functional analysis 8. Mechanisms of competitive aggression and their relation to function 9. fighting strategies: game theory models 10. Mechanisms of fighting strategies References Indices.
Relationships, talk about feelings, and the development of affect regulation in early childhood.

Interest in the development of affect regulation in early childhood has focused until recently chiefly on two issues: the development of “impulse control” in children and the clinical implications of individual differences in such emotional control. In charting the growth of children's control of their own anger, frustration, distress, or excitement, researchers have given most of their attention, justifiably, to developments in the second and third years of life. To parents, the development of their children's ability to argue rather than resort to physical violence, to wait rather than wail, to contain their impatience rather than explode in tantrums is clearly a major achievement during these years. Yet in this period children's emotional behavior and their powers of influencing their own and others' affective states expand far more broadly than a focus solely on the “damping down” of extremes of anger, distress, and excitement would imply. Children's displays of uninhibited anger or frustration do indeed change markedly, increasing sharply in the second year and decreasing in the third, as Frances Goodenough's classic study in the 1930s showed (Goodenough, 1931). But if we include in our notion of “affect regulation” children's interactions with others - that is, if we see affect regulation not simply as a private “homeostatic” mechanism but also as a feature of children's relationships with others - then this period of the second and third year must be highlighted even more as one of the major developmental changes in children's control and influence over their emotional states.
IMAGES OF TURKEY AND THEIR RELIGIOUS AND GENDER-SPECIFIC CONNOTATIONS

ABSTRACT This article is based on the results of a research project on current configurations of European identity and religiously interpreted cleavages in the EU. The article questions how the European secularised majority expresses its own religious roots and gender relations by means of a gender-specific discourse on the 'other' religion. In a qualitative and comparative research design, Austrian and French print media were selected for discourse analysis. The French and Austrian print media discourses analysed here, though, reveal that gender relations and religion are particularly significant. In line with the key methodological principles of the research tradition, the research process can be characterised as non-linear, grounded and reflexive. The study is based on an in-depth analysis of a relatively small number of texts. The individual case studies were drawn together and compared across countries. The aim of this article was to analyse the relations between the gender-specific construction of the “other” religion and constructions of the “European own”. In both French and Austrian cases, references to Islam as the 'other religion' are often used for reinforcing specific national understandings of secularity and laicism. Keywords: Gender, European Union, Religion, Print Media. TURKIYE'NIN IMAJI VE BUNUN DINI VE TOPLUMSAL CINSIYET ODAKLI CAĞRIŞIMLARI OZET Bu makale Avrupa kimliginin guncel yapilari ve AB'deki dini olarak yorumlanan celiskiler hakkinda yapilmis bir arastirma projesinin sonuclarini temel almaktadir. Makale, laik Avrupa cogunlugunun kendi dini koklerini ve toplumsal cinsiyet iliskilerini “oteki” din uzerine toplumsal cinsiyet odakli bir soylem araciligiyla nasil konumlandirdigini sorgulamaktadir. Niteleyici ve karsilastirmali bir arastirma tasarimi icerisinde soylem analizi icin Avusturya ve Fransa yazili basini secilmistir. Burada incelenen Avusturya ve Fransa yazili basininin soylemleri ise toplumsal cinsiyet iliskileri ile dinin ozellikle onemli oldugunu gostermistir. Arastirma geleneginin temel yontemsel esaslarina gore arastirma sureci dogrusal olmayan, sabit ve refleksif olarak nitelenebilir. Calisma nispeten az sayida metnin derinlemesine analizine dayanmaktadir. Tekil olay incelemeleri bir araya getirilmis ve ulkeler arasinda karsilastirilmistir. Bu makalenin amaci “oteki” dinin toplumsal cinsiyet odakli insasi ile Avrupa'nin “kendi din” insasi arasindaki iliskileri analiz etmektir. Fransiz ve Avusturya durumlarinin ikisinde de Islam'a “oteki din” olarak yapilan atiflar genellikle laikligin belirli milli anlayislarinin guclendirilmesi icin kullanilmaktadir. Anahtar Kelimler: Toplumsal Cinsiyet, Avrupa Birligi, Din, Yazili Basin.