Miracle-dz/UniFAR-FTUs huggingface dataset:
Full-Exon Pyrosequencing Screening of BRCA Germline Mutations in Mexican Women with Inherited Breast and Ovarian Cancer

Hereditary breast cancer comprises 10% of all breast cancers. The most prevalent genes causing this pathology are BRCA1 and BRCA2 (breast cancer early onset 1 and 2), which also predispose to other cancers. Despite the outstanding relevance of genetic screening of BRCA deleterious variants in patients with a history of familial cancer, this practice is not common in Latin American public institutions. In this work we assessed mutations in the entire exonic and splice-site regions of BRCA in 39 patients with breast and ovarian cancer and with familial history of breast cancer or with clinical features suggestive for BRCA mutations by massive parallel pyrosequencing. First we evaluated the method with controls and found 41–485 reads per sequence in BRCA pathogenic mutations. Negative controls did not show deleterious variants, confirming the suitability of the approach. In patients diagnosed with cancer we found 4 novel deleterious mutations (c.2805_2808delAGAT and c.3124_3133delAGCAATATTA in BRCA1; c.2639_2640delTG and c.5114_5117delTAAA in BRCA2). The prevalence of BRCA mutations in these patients was 10.2%. Moreover, we discovered 16 variants with unknown clinical significance (11 in exons and 5 in introns); 4 were predicted as possibly pathogenic by in silico analyses, and 3 have not been described previously. This study illustrates how massive pyrosequencing technology can be applied to screen for BRCA mutations in the whole exonic and splice regions in patients with suspected BRCA-related cancers. This is the first effort to analyse the mutational status of BRCA genes on a Mexican-mestizo population by means of pyrosequencing.
Church schools, educational markets and the rural idyll

Abstract Researchers have begun to explore the role that faith schools play in contemporary educational markets but the emphasis to date has been on urban rather than rural contexts. This article approaches the issue of marketisation through a qualitative case-study comparison of two Anglican primary schools in contrasting rural localities in England and Wales. Engaging with a range of stakeholders, including parents and pupils, the article explores reasons why the schools were valued, drawing on wider constructions of childhood, religion and rurality. The consequences of the schools’ popularity on factors such as traffic, parking, school ethos and local community ties are also considered. The findings of the study problematise some of the prevalent assumptions about marketisation, including the role of social class and geography in these processes. As such, the article makes an important contribution to the sociological literature on faith schools, rural schools and educational markets.
Real-Time Imaging of the Intracellular Glutathione Redox Potential in the Malaria Parasite Plasmodium falciparum

In the malaria parasite Plasmodium falciparum, the cellular redox potential influences signaling events, antioxidant defense, and mechanisms of drug action and resistance. Until now, the real-time determination of the redox potential in malaria parasites has been limited because conventional approaches disrupt sub-cellular integrity. Using a glutathione biosensor comprising human glutaredoxin-1 linked to a redox-sensitive green fluorescent protein (hGrx1-roGFP2), we systematically characterized basal values and drug-induced changes in the cytosolic glutathione-dependent redox potential (E GSH) of drug-sensitive (3D7) and resistant (Dd2) P. falciparum parasites. Via confocal microscopy, we demonstrated that hGrx1-roGFP2 rapidly detects E GSH changes induced by oxidative and nitrosative stress. The cytosolic basal E GSH of 3D7 and Dd2 were estimated to be −314.2±3.1 mV and −313.9±3.4 mV, respectively, which is indicative of a highly reducing compartment. We furthermore monitored short-, medium-, and long-term changes in E GSH after incubation with various redox-active compounds and antimalarial drugs. Interestingly, the redox cyclers methylene blue and pyocyanin rapidly changed the fluorescence ratio of hGrx1-roGFP2 in the cytosol of P. falciparum, which can, however, partially be explained by a direct interaction with the probe. In contrast, quinoline and artemisinin-based antimalarial drugs showed strong effects on the parasites' E GSH after longer incubation times (24 h). As tested for various conditions, these effects were accompanied by a drop in total glutathione concentrations determined in parallel with alternative methods. Notably, the effects were generally more pronounced in the chloroquine-sensitive 3D7 strain than in the resistant Dd2 strain. Based on these results hGrx1-roGFP2 can be recommended as a reliable and specific biosensor for real-time spatiotemporal monitoring of the intracellular E GSH in P. falciparum. Applying this technique in further studies will enhance our understanding of redox regulation and mechanisms of drug action and resistance in Plasmodium and might also stimulate redox research in other pathogens.
Extra: A Culturally Enriched Malay Text to Speech System.

This paper concerns the incorporation of naturalness into Malay Text-to-Speech (TTS) systems through the addition of a culturally-localized affective component. Previous studies on emotion theories were examined to draw up assumptions about emotions. These studies also include the findings from observations by anthropologists and researchers on culturalspecific emotions, particularly, the Malay culture. These findings were used to elicit the requirements for modeling affect in the TTS that conforms to the people of the Malay culture in Malaysia. The goal is to introduce a novel method for generating Malay expressive speech by embedding a localized ‘emotion layer’ called eXpressive Text Reader Automation Layer, abbreviated as eXTRA. In a pilot project, the prototype is used with Fasih, the first Malay Text-to-Speech system developed by MIMOS Berhad, which can read unrestricted Malay text in four emotions: anger, sadness, happiness and fear. In this paper however, concentration is given to the first two emotions. eXTRA is evaluated through open perception tests by both native and non-native listeners. The results show more than sixty percent of recognition rate, which confirmed the satisfactory performance of the approaches.
Emotional Intelligence, Emotions and Decision Making

This study is focused on the analysis of a series of elements which might favor people’s capacities to set objectives in areas in which they are personally invested in making right decisions. The capacity to set objectives is one of the main variables to assess management skills found in the academic literature. Our empirical findings reveal that even though the level of emotional intelligence and the frame of mind of participants have an important effect on this capacity, the activation of the neuronal circuits strongly linked to creativity and insightful problem solving, by means of some simple exercises based on recent discoveries in the neuroscience field, results in significant improvements in individuals’ capacity to generate appropriate objectives.
Yeast Ty1 Retrotransposition Is Stimulated by a Synergistic Interaction between Mutations in Chromatin Assembly Factor I and Histone Regulatory Proteins

ABSTRACT A screen for host mutations which increase the rate of transposition of Ty1 and Ty2 into a chromosomal target was used to identify factors influencing retroelement transposition. The fortuitous presence of a mutation in the CAC3 gene in the strain in which this screen was undertaken enabled us to discover that double mutaions of cac3 andhir3, but neither of the two single mutations, caused a dramatic increase in the rate of retrotransposition. We further showed that this effect was not due to an increase in the overall level of Ty1 mRNA. Two subtle cac3 phenotypes, slight methyl methanesulfonate (MMS) sensitivity and reduction of telomeric silencing, were significantly enhanced in the cac3 hir3 double mutant. In addition, the growth rate of the double mutant was reduced. HIR3 belongs to a class ofHIR genes that regulate the transcription of histones, while Cac3p, together with Cac1p and Cac2p, forms chromatin assembly factor I. Other combinations of mutations in cac andhir genes (cac3 hir1, cac3 hir2, and cac2 hir3) also increase Ty transposition and MMS sensitivity and reduce the growth rate. A model explaining the synergistic interaction between cac and hirmutations in terms of alterations in chromatin structure is proposed.
LOFAR detections of low-frequency radio recombination lines towards Cassiopeia A

Cassiopeia A was observed using the low-band antennas of the LOw Frequency ARray (LOFAR) with high spectral resolution. This allowed a search for radio recombination lines (RRLs) along the line-of-sight to this source. Five carbon α RRLs were detected in absorption between 40 and 50 MHz with a signal-to-noise ratio of >5 from two independent LOFAR data sets. The derived line velocities (vLSR ~ − 50 km s-1) and integrated optical depths (~13 s-1) of the RRLs in our spectra, extracted over the whole supernova remnant, are consistent within each LOFAR data set and with those previously reported. For the first time, we are able to extract spectra against the brightest hotspot of the remnant at frequencies below 330 MHz. These spectra show significantly higher (15–80 percent) integrated optical depths, indicating that there is small-scale angular structure of the order of ~1 pc in the absorbing gas distribution over the face of the remnant. We also place an upper limit of 3 × 10-4 on the peak optical depths of hydrogen and helium RRLs. These results demonstrate that LOFAR has the desired spectral stability and sensitivity to study faint recombination lines in the decameter band.
Interplanetary Lyman α line profiles: variations with solar activity cycle

Aims. Interplanetary Lyman α line profiles are derived from the SWAN H cell data measurements. The measurements cover a 6-year period from solar minimum (1996) to after the solar maximum of 2001. This allows us to study the variations of the line profiles with solar activity. Methods. These line profiles were used to derive line shifts and line widths in the interplanetary medium for various angles of the LOS with the interstellar flow direction. The SWAN data results were then compared to an interplanetary background upwind spectrum obtained by STIS/HST in March 2001. Results. We find that the LOS upwind velocity associated with the mean line shift of the IP Lyman α line varies from 25.7 km s −1 to 21.4 km s −1 from solar minimum to solar maximum. Most of this change is linked with variations in the radiation pressure. LOS kinetic temperatures derived from IP line widths do not vary monotonically with the upwind angle of the LOS. This is not compatible with calculations of IP line profiles based on hot model distributions of interplanetary hydrogen. We also find that the line profiles get narrower during solar maximum. Conclusions. The results obtained on the line widths (LOS temperature) show that the IP line is composed of two components scattered by two hydrogen populations with different bulk velocities and temperature. This is a clear signature of the heliospheric interface on the line profiles seen at 1 AU from the sun.
Natural Lie Algebra bundles on rank two s-K\

We prove that one can obtain natural bundles of Lie algebras on rank two s-K\"ahler manifolds, whose fibres are isomorphic to so(s+1,s+1), su(s+1,s+1) and sl(2s + 2,\R). In the most rigid case (which includes complex tori and abelian varieties) these bundles have natural flat connections, whose flat global sections act naturally on cohomology. We also present several natural examples of manifolds which can be equipped with an s-K\"ahler structure with various levels of rigidity: complex tori and abelian varieties, cotangent bundles of smooth manifolds and moduli of pointed elliptic curves.
Inhibition of hepatic ACAT decreases ApoB secretion in miniature pigs fed a cholesterol-free diet.

To test the hypothesis that hepatic cholesteryl ester is involved in the regulation of apolipoprotein (apo) B secretion into plasma, apoB kinetic studies were performed in six control miniature pigs and in six pigs after a 21-day administration of the acyl coenzyme A:cholesterol acyltransferase (ACAT) inhibitor DuP 128 (2.2 mg.kg-1.d-1 i.v.). Pigs were fed low-fat, cholesterol-free diets. Total plasma cholesterol, triglyceride, very-low-density lipoprotein (VLDL) triglyceride, and low-density lipoprotein (LDL) cholesterol decreased 18%, 29%, 40%, and 26% respectively (P < .03). 131I-VLDL and 125I-LDL were injected simultaneously into each animal, and apoB kinetics were analyzed by using multi-compartmental analysis (SAAM30). VLDL apoB pool size decreased significantly by 60% (0.32 versus 0.84 mg/kg), which was due to a 65% reduction in the VLDL apoB production or secretion rate (1.03 versus 2.94 mg.kg-1.h-1). The fractional catabolic rate was unchanged. LDL apoB pool size decreased nonsignificantly by 18% (5.61 versus 6.90 mg/kg) due entirely to a 24% decrease in production rate (0.26 versus 0.34 mg.kg-1.h-1). At necropsy, hepatic microsomal ACAT activity decreased by 68% (0.28 versus 0.88 nmol.min-1.mg-1; P < .0002). Although an increase in hepatic free cholesterol leading to a decreased LDL receptor expression might be expected, this did not occur. The concentration of hepatic cholesterol and the LDL apoB fractional catabolic rate were unaffected by DuP 128. In addition, the concentration of hepatic triglyceride and the activity of diacylglycerol acyltransferase were not altered by DuP 128, indicating a lack of effect of DuP 128 on hepatic triglyceride metabolism. We conclude that inhibition of hepatic cholesteryl ester synthesis in vivo decreases apoB secretion into plasma.
Service Component Architecture Extension for Sensor Networks

The role of small electronic devices has been growing over the past years. Many types of devices which allow for interaction with the environment can now be found in the market and there is large set of solutions for integration of mobile devices with enterprise systems. However, most such solutions focus only on providing base services for other SOA system elements. The paper presents an extension of the SCA programming model to include intelligent sensors and a concept of uniform programming model shared between sensor networks and standard computers. The architecture of such an extension is proposed and an initial prototype implementation is presented. The solution utilizes a proxy pattern, validated by a simple case study using Sun SPOTs and Sentilla. The advantages and limitations of the proposed extension are also discussed.
UvA-DARE (Digital Academic Repository) Learning from errors: Using vector-based compositional semantics for parse reranking

In this paper, we address the problem of how to use semantics to improve syntactic parsing, by using a hybrid reranking method: a k-best list generated by a symbolic parser is reranked based on parse-correctness scores given by a compositional, connectionist classiﬁer. This classi-ﬁer uses a recursive neural network to construct vector representations for phrases in a candidate parse tree in order to classify it as syntactically correct or not. Tested on the WSJ23, our method achieved a statistically signiﬁcant improvement of 0.20% on F-score (2% error reduction) and 0.95% on exact match, compared with the state-of-the-art Berkeley parser. This result shows that vector-based compositional semantics can be usefully applied in syntactic parsing, and demonstrates the beneﬁts of combining the symbolic and connectionist approaches.
A novel solution for achieving anonymity in wireless ad hoc networks

A mobile ad hoc network consists of mobile nodes that can move freely in an open environment. Communicating nodes in a wireless and mobile ad hoc network usually seek the help of other intermediate nodes to establish communication channels. In such an open environment, malicious intermediate nodes can be a threat to the security and/or anonymity of the exchanged data between the mobile nodes. While data encryption can protect the content exchanged between nodes, routing information may reveal valuable information about end users and their relationships. The main purposes of this paper are to study the possibility of achieving anonymity in ad hoc networks, and propose an anonymous routing protocol, similar to onion routing concept used in wired networks. Our protocol includes a mechanism to establish a trust among mobile nodes while avoiding untrustworthy nodes during the route discovery process. The major objective of our protocol is to allow only trustworthy intermediate nodes to participate in the routing protocol without jeopardizing the anonymity of the communicating nodes. We present our scheme, and report on its performance using an extensive set of simulation set of experiments using ns-2 simulator. Our results indicate clearly that anonymity can be achieved in mobile ad hoc networks, and the additional overhead of our scheme to DSR is reasonably low when compared to a non-secure DSR ad hoc routing protocol.
Feature selection for improved bandwidth extension of speech signals

The aim of artificial bandwidth extension (BWE) is to convert speech signals with "standard telephone" quality (frequencies up to 3.4 kHz) into 7 kHz wideband speech. The principal key to high quality BWE is the estimation of the spectral envelope of the wideband speech. In general, this estimation of the wideband spectral envelope is based on a number of features that are extracted from the narrowband input speech signal. We investigate potential features and evaluate their suitability for the BWE application. The quality of each feature is quantified in terms of the statistical measures of mutual information and separability. It turns out that the best BWE results are obtained by using a large feature "super-vector" (/spl rarr/ high mutual information) which is subsequently reduced in dimension by a linear discriminant analysis (/spl rarr/ large separability). This solution also helps to reduce the computational complexity of the estimation of the wideband spectral envelope.
Konstruksi Realitas Seratus Hari Pertama Pemerintahan Jokowi-Jusuf Kalla di Media Online: Analisis Wacana Kritis Model Norman Fairclough

Tugas utama media massa adalah mengonstruksi realitas. Konstruksi realitas di media massa direpresentasikan melalui penggunaan kosakata dan gramatikal. Tujuan penelitian ini adalah menganalisis wujud konstruksi realitas seratus hari pertama pemerintahan Jokowi-JK yang tercermin secara terkstual di media online Detik.com, Kompas.com, dan Republika Online. Metode pengumpulan data dalam penelitian yaitu metode simak dan metode pustaka. Adapun metode analisis data yang digunakan mengacu pada kerangka analisis wacana kritis Norman Fairclough yang mencakup deskriptif, interpretatif, dan eksplanatif. Hasil penelitian menunjukkan bahwa teks-teks berita seratus hari pertama pemerintahan Jokowi-JK menampilkan Jokowi sebagai presiden yang ingkar janji, presiden yang dikendalikan oleh partai politik pendukung, dan presiden yang berani dan tegas. Secara tekstual ketiga media online tersebut merepresentasikan kepemimpinan Jokowi dengan menggunakan kosakata dan gramatikal yang berbeda antara satu dengan yang lainnya. Perbedaaan penggunaan kosakata dan gramatikal berimpilikasi pada pada perbedaan orientasi penggunaan bahasa oleh media online Detik.com, Kompas.com, dan Republika Online. Wujud konstruski realitas seratus hari pertama pemerintahan Jokowi-JK dapat diamati melalui teks-teks berita yang dimuat oleh media online Detik.com, Kompas.com, dan Republika Online. Melalui teks-teks berita tersebut, Jokowi ditampilkan sebagai presiden yang ingkar janji, presiden yang dikendalikan oleh partai politik, dan presiden yang berani dan tegas. Namun, Peran bahasa di media online Detik.com cenderung mengubur dan mengaburkan realitas. Berbeda dengan Kompas.com yang menggunakan bahasa untuk mengkritisi tetapi sekaligus juga membela Presiden Jokowi. Peran bahasa di Republika Online juga berbeda dengan kedua media online sebelumnya. Republika Online menggunakan bahasa untuk mengkritisi dan memperjelas realitas, sekaligus juga untuk menunjukkan sikap oposisionalnya terhadap pemerintahan Jokowi-JK.The main task of mass media is to construct reality. Reality construction in mass media is presented through the use of vocabularies and grammar. The aim of this study is to analyze the pattern of reality construction of the first 100 days of Jokowi-JK administration textually reported in some online media (Detik.com, Kompas.com, and Republika.com). The method of data collection is observation and literature review whereas the data method analysis used refers to Norman Fairclough critical discourse analysis covering description, interpretation, and explanation. The study found that textual news of the first 100 days of Jokowi-JK government shows that Jokowi is a liar president and is fully controlled by his supporting political party, but he is strict and a risk taker.
Destination unknown? Study choices and graduate destinations of Hungarian youth in Slovakia

Focusing on Hungarian minority youth in a rural Slovakian setting, the paper explores the higher education aspirations and choices of young people amidst significant economic, political and educational reforms. Relying on mixed methods and a longitudinal design the research follows a cohort of high school students from their last year of secondary school through university up to their graduate destinations several years onwards. The collected data reveal three main study-work trajectories reflecting different trade-offs in terms of HE studies, graduate careers and ethnic identity maintenance all affecting the individuals’ life-chances as well as the future of the Hungarian community in Slovakia.
Socio-Cultural Values of Early Childhood Parenting (Ethnographic Research on Bugis Makassar South Sulawesi)

This research aimed was to determine the socio-cultural values of early childhood parenting in families Bugis Makassar. The study was conducted in the form of ethnographic studies by focusing on the care of children in a family environment. Data collected through participant observation, interviews focused, and documentation of ethnographic records. The data were then analyzed using a model of the domain analysis and time series. The results showed that the family Bugis Makassar South Sulawesi still adhere to a number of socio-cultural values of care as the values considered important to be preserved and handed down in early childhood parenting.
Effective Attack Models for Shilling Item-Based Collaborative Filtering Systems

Significant vulnerabilities have recently been identified in collaborative filtering recommender systems. These vulnerabilities mostly emanate from the open nature of such systems and their reliance on user-specified judgments for building profiles. Attackers who cannot be readily distinguished from ordinary users may introduce biased data in an attempt to force the system to “adapt” in a manner advantageous to them. A handful of simple attack models have, so far, been identified, and there appear to be significant differences in the susceptibility of different recommendation techniques to these attacks. In particular, item-based collaborative filtering has been found to offer some security advantages over user-based collaborative filtering. Our research in secure personalization is examining a range of more complex attack models and recommendation techniques, paying particular attention to the costs and benefits of mounting an attack. In this paper, we take a closer look at item-based collaborative filtering. In particular, we propose a new attack model that focuses on a subset of users with similar tastes and show that such an attack can be highly successful against an item-based algorithm.