Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence of BRAF mutations in a Polish cohort of PTC patients - preliminary results.

INTRODUCTION Genetic alterations involving the mitogen-activated protein kinase (MAPK) pathway are frequently demonstrated in papillary thyroid cancer (PTC). BRAF(V600E), the most frequent mutation in adult patients, is present in approximately 50% of PTC. Most clinical studies have demonstrated an association of BRAF(V600E) mutation with aggressive clinicopathological characteristics and high tumour recurrence, although the results are controversial. In this study we present the preliminary results of BRAF mutation frequence in a group of 88 Polish patients with papillary thyroid cancer (PTC) and relate it to the outcome all DTC patients operated in 2004 and 2005. BRAF (V600E) mutation was diagnosed in 38 (43%) of cases. MATERIAL AND METHODS The presence of BRAF mutation was evaluated in 88 PTC tumours. DNA was isolated from tissue parafin blocks, and the mutation V600E was evaluated by sequence analysis with an AbiPrism 377 and 3130 xl genetic analyzer (Life Technologies). Statistical analysis was carried out with the use of SPSS 12 software. The chi² and Kaplan-Meyer survival analysis were performed. RESULTS From all analyzed clinico-pathological factors, only older age positively correlated with BRAF mutation frequency (p = 0.0017). Lymph node/distant metastases, multifocality, and extra-thyroid extension did not correlate with BRAF status. One cancer related death and two reccurences were observed in the BRAF+ group while one relapse was diagnosed in the BRAF- group. CONCLUSIONS Although many studies document BRAF mutation as a prognostic factor in PTC our results underline that it is too early to consider it as a routine clinical predictive factor.
Is It Really Clear?

• Summary: The methodological challenge of adapting research tools to the needs of the study population takes on paramount importance when participants have cultural, social, cognitive, or other needs rendering commonly used questionnaires problematic. This article describes research tools' exploratory adaptation to a sample of Israeli deaf adults, during a comparative study of 101 deaf adults aged 28 to 51 years and 57 hearing adults aged 24 to 52. Levinger (2003) conducted a large study on this sample, investigating the links between adults' personal, familial, and societal variables and their ability to separate from parents and establish spousal intimacy. • Findings: The present article is a sub-study focusing on the adaptation of the larger study's design of specific tools to examine the deaf population. It describes the tools' preparation, administration, and analysis, including examination of the various versions' compatibility and the versions' cultural and linguistic adaptation to the participants' needs. The study included five research tools containing 125 questions altogether. To minimize the biasing risks due to deaf adults' reading comprehension difficulties or misinterpretations of questions' intent, we prepared three versions for each of the tools except for the 30-item demographic questionnaire: a) the original written version in regular Hebrew, matched to participants for gender, b) a revised written version in easy language (adapted to the deaf population and gender-matched), and c) a videotaped sign language version. Taking part in preparing the various versions were deaf representatives of the deaf community and hearing translators into Israeli Sign Language. • Applications : This article discusses methodological repercussions of these adaptations; compares the choices made by participants regarding the various adaptations offered them; and highlights the importance of familiarity with participants' characteristics and unique needs.
FOCUS: a usable & effective approach to OLED display power management

In this paper, we present the design and implementation of Focus, a system for effectively and efficiently reducing power consumption of OLED displays on smartphones. These displays, while becoming exceedingly common still consume significant power. The key idea of Focus is that we use the notion of saliency to save display power by dimming portions of the applications that are less important to the user. We envision Focus being especially useful during low battery situations when usability is less important than power savings. We tested Focus using 15 applications running on a Samsung Galaxy S III and show that it saves, on average, between 23 to 34% of the OLED display power with little impact on task completion times. Finally, we present the results of a user study, involving 30 participants that shows that Focus, even with its dimming behaviour, is still quite usable.
Perceptions of Accredited Social Health Activists on Depression: A Qualitative Study from Karnataka, India

Background: Depression is a significant public health concern in India, associated with a large treatment gap. Assessing perceptions of Accredited Social Health Activists (ASHAs) on depression can be invaluable as they are selected to work at the interface between their own communities and the health-care delivery system. Aims and Objectives: This study aimed at utilizing a qualitative approach to examine the ASHAs' understanding of depression, their mental health-care practices specific to depression, and their capacity-building needs with regard to identification and helping persons with depression. Subjects and Methods: A cross-sectional qualitative study using two focus group discussions was conducted. The sample comprised 14 ASHAs in the age range of 25–45 years from Bengaluru urban district. The data were analyzed manually by the method of directed content analysis. Results: The ASHAs were found to have inadequate knowledge of the signs and symptoms of depression, its biopsychosocial nature, and its impact on functioning. Causation of depression was narrated in terms of psychosocial stressors. The majority expressed the need for primarily psychosocial interventions for depression. All participants reported their motivation to obtain training in identifying persons with depression and providing simple psychosocial intervention for them. Conclusion: This study indicates that ASHAs have poor knowledge of depression, which could be leading to its low recognition and treatment in the communities they work in. They are therefore likely to benefit from capacity building on depression which includes familiar nomenclature, biopsychosocial elucidation of the illness, life-span approach, understanding of its impact on various domains of functioning, and the treatments available.
A novel, coupling driven, low power bus coding technique for minimizing capacitive crosstalk in VLSI interconnects

In current VLSI technology, interconnects have become the predominant source of power dissipation. Particularly in DSM technology, the spacing between interconnects is very less leading to the dominance of coupling capacitance over self capacitance. In 0.13 mum technology, it has been found that 75% of the power consumption is due to the coupling capacitance whereas only 25% is due to self capacitance. Thus, earlier schemes which concentrated on minimizing the substrate capacitances are not valid in these buses. Considering these aspects, this paper proposes a novel encoding technique that reduces the switching activity due to capacitive coupling resulting in lower power overhead. The simulation results show that the power dissipation in a bus is reduced by about 23% with this encoding technique. The encoding and decoding circuits have been designed and the power consumed has been compared with those of other coding schemes
Catheter locks, heparin and biofilm: what is this the risk?

Interestingly, however, among the ‘low’ cardiovascular risk participants 7 had an elevated TnT and 35 had a normal TnT. Although the numbers of patients are small, these data suggest that an elevated TnT in ‘low’ cardiovascular risk renal transplant recipients identifies a group who are at increased risk of all-cause mortality. Undoubtedly, renal transplant recipients with high cardiovascular risk profiles should undergo aggressive riskfactor modification irrespective of their TnT level. However, the results of our study suggest that an elevated TnT level identifies a group of renal transplant recipients who are at increased risk of all-cause mortality and who may be overlooked if the risk assessment is based on the presence of traditional cardiovascular risk factors. TnT is a biochemical marker readily available in clinical practice that can enhance the current methods used to stratify risk in renal transplant recipients. An elevated TnT level can identify a subgroup of patients who may well benefit from more aggressive cardiovascular risk-factor modification.
POEM: Identifying Joint Additive Effects on Regulatory Circuits

Motivation: Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress toward a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such “modularization” approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects. Results: Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs. Availability: The software described in this article is available at csgi.tau. ac.il/POEM/.
Changes in Early L2 Cue-Weighting of Non-Native Speech: Evidence from Learners of Mandarin Chinese

This study examined how cue-weighting of a non-native speech cue changes during early adult second language (L2) acquisition. Ten native English speaking learners of Mandarin Chinese performed a speeded AX-discrimination task during months 1, 2, and 3 of a first-year Chinese course. Results were compared to ten native Mandarin speakers. Learners’ reaction time and d-prime results became more native-like after two months of classroom study but plateaued thereafter. Multidimensional scaling results showed a similar shift to more native-like cue-weighting as learners attended more to pitch direction and less to pitch height. Despite the improvements, learners’ month 3 configuration of cueweighting differed from that of native speakers; learners appeared to weight pitch end points rather than overall pitch directions. These results suggest that learners’ warping of the weights of dimensions underlying the perceptual space changes rapidly during early acquisition and can plateau like other measures of L2 acquisition. Previous perceptual learning studies may have only captured initial L2 perception gains, not the learning plateau that often follows. New methods of perceptual learning, especially for tonal languages, are needed to advance learners off the plateau.
Circadian and sleep-wake dependent impact on neurobehavioral function

Variations in waking neurobehavioral or cognitive functioning are closely linked to endogenous 24-h rhythm (circadian pacemaker) and time awake. We summarize studies in which the contribution of the circadian pacemaker and time awake on neurobehavioral function was investigated. Stable and high levels of attention and vigilance can only be maintained when the circadian timing system opposes the wake-dependent deterioration of alertness and performance. Planning performance in a maze tracing task was also affected by time awake, whereas circadian modulation was less pronounced. Additional to circadian phase position and the level of sleep pressure, rapid eye movement sleep may play a role in acquiring specific procedural skills in a sequence learning task. We conclude that circadian phase and time awake have a substantial impact on short and stimulating planning tasks, which are related to the prefrontal cortex, and on sequence learning that requires activation of striatal brain regions.
Information-Theoretic Inference of Gene Networks Using Backward Elimination

Unraveling transcriptional regulatory networks is essential for understanding and predicting cellular responses in different developmental and environmental contexts. Information-theoretic methods of network inference have been shown to produce high-quality reconstructions because of their ability to infer both linear and non-linear dependencies between regulators and targets. In this paper, we introduce MRNETB an improved version of the previous information-theoretic algorithm, MRNET, which has competitive performance with state-of-the-art algorithms. MRNET infers a network by using a forward selection strategy to identify a maximally-independent set of neighbors for every variable. However, a known limitation of algorithms based on forward selection is that the quality of the selected subset strongly depends on the first variable selected. In this paper, we present MRNETB, an improved version of MRNET that overcomes this limitation by using a backward selection strategy followed by a sequential replacement. Our new variable selection procedure can be implemented with the same computational cost as the forward selection strategy. MRNETB was benchmarked against MRNET and two other information-theoretic algorithms, CLR and ARACNE. Our benchmark comprised 15 datasets generated from two regulatory network simulators, 10 of which are from the DREAM4 challenge, which was recently used to compare over 30 network inference methods. To assess stability of our results, each method was implemented with two estimators of mutual information. Our results show that MRNETB has significantly better performance than MRNET, irrespective of the mutual information estimation method. MRNETB also performs comparably to CLR and significantly better than ARACNE indicating that our new variable selection strategy can successfully infer high-quality networks.
Genetic Relationship between Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus Strains from France and from International Sources: Delineation of Genomic Groups

ABSTRACT Cluster analysis of the SmaI patterns, generated by pulsed-field gel electrophoresis, of 44 methicillin-resistant (MRSA) and 118 methicillin-sensitive (MSSA) Staphylococcus aureus strains isolated in various French hospitals and 61 MRSA and 48 MSSA strains from 20 other countries revealed 20 genomic groups distributed into four distantly related phylogenic branches. Eighty-three of the 105 MRSA strains (79%) were clustered in the six genomic groups of phylogenic branch I; and 154 of the 166 MSSA strains (92.8%) were clustered in the 14 genomic groups of phylogenic branches II, III, and IV. Agreement between genomic group and two other markers, esterase type and phage group, was obtained, emphasizing the clonal structure of the population. The genomic groups were delineated by esterase type. The distribution of the strains within the genomic groups was independent of their geographical origin; French strains were clustered with strains from other countries. The three types of the staphylococcal cassette chromosome mec (SCCmec) complex were distributed according to genomic groups. Most of the time, type I and type II SCCmec complexes were found in the MRSA strains belonging to the same genomic groups. In contrast, the type III SCCmec complex was specific to the MRSA strains belonging to the three genomic groups characterized by a common esterase type.
The influence of controlled motivation alongside autonomous motivation: Maladaptive, buffering, or additive effects?

Contrary to self-determination theory (SDT) tenets, research indicates that controlled motivation towards sport may not be associated with maladaptive outcomes, if accompanied by high autonomous motivation. However, the measures of controlled motivation employed in many of these studies have been criticised for the lack of content validity (i.e. Sport Motivation Scale [SMS]). This study examined the influence two different measures (SMS and Behavioural Regulation in Sport Questionnaire [BRSQ]) have on empirical support for competing hypotheses concerning the influence of controlled motivation on athletes' sport experiences. A cross-sectional design was employed. Gaelic football players (N = 395, M = 13.36 years) answered questionnaires to assess motivation, flow, and burnout. Multivariate analysis of variances indicated that when the SMS was employed, controlled motivation appeared adaptive, or at least innocuous, when autonomous motivation was high. When the BRSQ was used, controlled motivation appeared maladaptive, or at best innocuous, when autonomous motivation was high. While these findings do not indicate that one measure produces controlled motivation scores that are more valid than the other, compared with the SMS-based results, the BRSQ-based findings are more in line with SDT tenets.
Catestatin Gly364Ser Variant Alters Systemic Blood Pressure and the Risk for Hypertension in Human Populations via Endothelial Nitric Oxide Pathway

Catestatin (CST), an endogenous antihypertensive/antiadrenergic peptide, is a novel regulator of cardiovascular physiology. Here, we report case–control studies in 2 geographically/ethnically distinct Indian populations (n≈4000) that showed association of the naturally-occurring human CST-Gly364Ser variant with increased risk for hypertension (age-adjusted odds ratios: 1.483; P=0.009 and 2.951; P=0.005). Consistently, 364Ser allele carriers displayed elevated systolic (up to ≈8 mm Hg; P=0.004) and diastolic (up to ≈6 mm Hg; P=0.001) blood pressure. The variant allele was also found to be in linkage disequilibrium with other functional single-nucleotide polymorphisms in the CHGA promoter and nearby coding region. Functional characterization of the Gly364Ser variant was performed using cellular/molecular biological experiments (viz peptide–receptor binding assays, nitric oxide [NO], phosphorylated extracellular regulated kinase, and phosphorylated endothelial NO synthase estimations) and computational approaches (molecular dynamics simulations for structural analysis of wild-type [CST-WT] and variant [CST-364Ser] peptides and docking of peptide/ligand with &bgr;-adrenergic receptors [ADRB1/2]). CST-WT and CST-364Ser peptides differed profoundly in their secondary structures and showed differential interactions with ADRB2; although CST-WT displaced the ligand bound to ADRB2, CST-364Ser failed to do the same. Furthermore, CST-WT significantly inhibited ADRB2-stimulated extracellular regulated kinase activation, suggesting an antagonistic role towards ADRB2 unlike CST-364Ser. Consequently, CST-WT was more potent in NO production in human umbilical vein endothelial cells as compared with CST-364Ser. This NO-producing ability of CST-WT was abrogated by ADRB2 antagonist ICI 118551. In conclusion, CST-364Ser allele enhanced the risk for hypertension in human populations, possibly via diminished endothelial NO production because of altered interactions of CST-364Ser peptide with ADRB2 as compared with CST-WT.
Fingerprint calibrated centroid and scalar product correlation RSSI positioning in large environments

The design and result of a fingerprint calibrated weighted centroid localization (FCWC) algorithm is outlined, discussed and evaluated against the UJIIndoorLoc data set. The algorithm is suitable for situations where positions of access points are not known but reference RSSI measurements can be taken in an indoor environment, as it is typically done for fingerprint algorithms. The algorithm comprises a calibration step which is based on the recorded RSSI fingerprints: By performing reverse localization, “Virtual positions” of the access points are calculated. The virtual positions do not necessarily need to closely match the real positions of the access points. The proposed FCWC algorithm uses weighted centroid, which is analogue to center of gravity. The weight function is based on the given RSSI value between the reference point and the WiFi access point, and is manually calibrated by adjusting 2 global parameters. After the virtual positions have been assigned, position estimates can be calculated using RSSI readings of a rover. This is again performed by applying weighted centroid, the position is obtained via the weighted vector sum of the virtual positions of the access points. For comparison, also a scalar product correlation fingerprinting (SPCF) algorithm has been implemented. In the paper, the background of the FCWC and SPCF algorithm, the weight function, and the obtained results are discussed.
Presidential Elections in Ireland: From Partisan Predictability to the End of Loyalty

This article assesses the seven presidential elections held in Ireland between 1945 and 2011 and argues that the best way of understanding these contests is to divide them into two separate categories: the four contests from 1945 to 1973 and the three contests from 1990 to 2011. The first category of presidential elections reflects the entirely stable and predictable pattern of party competition that represented politics in Ireland after Fianna Fáil first came to power in 1932. The second category reflects an entirely different type of politics in Ireland: one where presidential elections took place against a backdrop of a changing party system and an increasingly volatile electorate, where ties of party loyalty would loosen substantially over a 20-year period. The presidential contests of 1990, 1997 and 2011 all show evidence of increasing voter disconnect from the party system, and a shift away from the defining features of previous presidential elections. Predictable political stability has been replaced by a weakening of partisan voting as candidates come under more and more public scrutiny. By assessing the nomination processes, election campaigns and outcomes of Ireland's presidential elections, evidence is shown of striking change in the dynamic of the elections from 1990.
INVESTIGATIONS OF FOLIAGE EFFECT ON MODERN WIRELESS COMMUNICATION SYSTEMS: A REVIEW

In this paper, a large number of studies of the efiect of the foliage on single or lines of trees on modern wireless communication systems are reviewed. The paper is focused on the experimental works mainly done for commercial applications such as cellular communication and high speed point-to-point flxed link at the microwave and millimeter wave frequencies. For this review study, the development of the foliage loss prediction methods and the factors in∞uencing the tree-induced shadowing efiect are highlighted. In view of current research work in this area, some possible future works are proposed to improve the performance of modern wireless communication systems with the efiect of foliage.