Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Regulatory Networks Lessons from Yeast to Humans

With the advent of high throughput techniques, data in molecular biology are accumulating at a staggering rate. Assays such as DNA and tissue microarrays illuminate the molecular mechanisms underlying cellular functions from multiple perspectives. This flood of data bears much promise for novel insights about the workings of living cells and organisms (1). Despite early enthusiasm and extensive investment, we are still far from achieving this vision. Although the utility of microarrays for diagnosis and molecular characterization of disease has been extensively demonstrated (2–4), and studies are providing increasingly rich detailed signatures of biological and clinical phenotypes, a substantial gap remains between these phenomenological observations and a mechanistic understanding of cellular systems. Here we focus on attempts to uncover the workings of regulatory (transcriptional) networks from transcription profiles. This requires a shift from describing patterns in the data (e.g., clustering and signatures of differentially expressed genes) toward finding biologically relevant models that explain the observed changes in transcription, thus entailing a methodologic shift in experimental design, analysis methods, and evaluation approaches. As always, a major hurdle is extracting a true biological signal from noisy measurements. As in many previous cases, such developments are easier to carry out in the context of a unicellular model organism. Indeed, much progress has been made in recent years in elucidating the regulatory networks of bakers’ yeast, Saccharomyces cerevisiae, using expression profiles, genomic sequences, chromatin immunoprecipitation data, and protein–protein interactions, all collected on a genome-wide scale. These data have been analyzed by a dazzling array of computational methods, with some surprising success stories, as we will show below. Can these studies scale to mammalian systems? Clearly, mammalian systems are more challenging in several aspects. These include both the increased complexity of the regulatory mechanisms involved and the experimental limitations on manipulating these systems. Nevertheless, as we argue below, by carefully combining experimental design and computational tools we are now poised to directly tackle the challenge of inferring regulatory networks in such settings.
Kurzpsychoedukation bei bipolaren Patienten

Zusammenfassung Neben der medikamentösen Behandlung stellt auch die Psychotherapie einen wichtigen Baustein in der Versorgung bipolarer Patienten dar. Dabei kommt der Psychoedukation eine zentrale Bedeutung bei. Insbesondere deshalb, da die unterschiedlichen Komponenten dieser Intervention wie die Erarbeitung von Krankheitsmodellen, die Darstellung von möglichen Verläufen oder das Erkennen von Frühwarnzeichen wichtige Punkte für den weiteren Krankheitsverlauf sind. Die bereits existierenden Psychoedukationsprogramme sind außerhalb universitärer Strukturen im klinischen Alltag, vor allem im ambulanten Setting, aufgrund ihrer großen Anzahl an Modulen oft schwierig umzusetzen. Die Kurzpsychoedukation für bipolare Patienten (PEB) nach Erfurth, Dobmeier und Zechendorf (3) versucht, diese vorhandene Lücke in der Psychoedukationsversorgung zu schließen. Es hat sich gezeigt, dass sich PEB in der klinischen Praxis gut umsetzen lässt.
Simulation-based Assessment of Performance-Workload Tradeoffs for System Design Evaluation

Ideally, when selecting a system design or re-design, the selected option should balance workload and performance. However, previous research suggests that the relationship between workload and performance is nonlinear, thus achieving one, does not imply achieving the other. To ensure that a system will meet performance and workload goals, system designers should investigate the expected workload and performance tradeoffs of the potential system designs. This study uses discrete event simulation to demonstrate how to perform workload-performance tradeoffs when designing or re-designing a system, using a baseline system and three alternative designs. By examining the relationship between workload and performance, the study demonstrates how to identify the impacts that design alternatives can have on workload and performance. The study finds that four types of decision circumstances can occur: 1) a single preferred alternative is identified, 2) multiple preferred alternatives are identified, 3) no preferred alternative is identified, and 4) alternatives achieve conflicting goals. Each of these circumstances has unique implications for the design selection decision.
Incidence and age-specific presentation of restrictive eating disorders in children: a Canadian Paediatric Surveillance Program study.

OBJECTIVES To document and describe the incidence and age-specific presentation of early-onset restrictive eating disorders in children across Canada. DESIGN Surveillance study. Cases were ascertained through the Canadian Paediatric Surveillance Program by surveying approximately 2453 Canadian pediatricians (a 95% participation rate) monthly during a 2-year period. SETTING Canadian pediatric practices. PARTICIPANTS Pediatricians and pediatric subspecialists. MAIN OUTCOME MEASURES A description of clinical presentations and characteristics of eating disorders in this population and the incidence of restrictive eating disorders in children. RESULTS The incidence of early-onset restrictive eating disorders in children aged 5 to 12 years seen by pediatricians was 2.6 cases per 100 000 person-years. The ratio of girls to boys was 6:1, and 47.1% of girls and 54.5% of boys showed signs of growth delay. Forty-six percent of children were below the 10th percentile for body mass index, 34.2% were initially seen with unstable vital signs, and 47.2% required hospital admission. Only 62.1% of children met criteria for anorexia nervosa. Although children with anorexia nervosa were more likely to be medically compromised, some children who did not meet criteria for anorexia nervosa were equally medically unstable. CONCLUSIONS Young children are seen with clinically significant restrictive eating disorders, with the incidence exceeding that of type 2 diabetes mellitus. These eating disturbances can result in serious medical consequences, ranging from growth delay to unstable vital signs, which can occur in the absence of weight loss or other restrictive eating disorder symptoms.
Tulip: lightweight entity recognition and disambiguation using wikipedia-based topic centroids

This article presents Tulip, an ERD system submitted to the ERD 2014: Entity Recognition and Disambiguation Challenge. The objective of the proposed system is to spot mentions of entities in a document and link the mentions to corresponding Freebase articles. To achieve it, Tulip prunes the set of entity candidates focusing on a core subset of related entities capturing the context of the document. The relationship strength is measured as a similarity to a topic centroid generated from entity features. Each entity is represented by an accurate and compact feature vector extracted from a category graph built based on information from 120 language versions of Wikipedia. Given the core set of accepted entities Tulip uses the Wikipedia-based feature vectors to extract more related entities from the document text. Tulip received the first prize in the long document track with F1 score of 0.74, which confirms the effectiveness of our system. At the same, the system was faster than all other submissions with latency under 0.29 seconds.
Improving Technical Writing through Professional Expression Exercises in a Computer Science Graduate Program

Building quality programs based on workforce skills, such as technical writing, is considered an effective means for recruitment and retention in higher education, especially in the areas of science, technology, engineering and math. In computer science, technical writing can be especially challenging due to the complexity of technical documents. This work incorporated the use of professional expression activities in the computer science graduate curriculum at Nova Southeastern University. Additionally, the results support continual building of the quality of the Master of Science in Computer Science and technical writing in the discipline.
Supporting customers' decision making with Rated Tags

In this paper, we present an empirical study that conducts the impact of Rated Tags on customers' decision making process in online stores. A Rated Tag is a combination of a user-generated tag and a 5-star rating scale. The Rated Tags system aims to support consumers' decisions and therefore falls into the category of interactive decision aids. The questions answered in this paper are whether Rated Tags can increase the decision making quality and decrease the decision effort of consumers. For this purpose, we have extracted 100 real customer reviews from amazon.de, which were assigned Rated Tags. The customer reviews and Rated Tags were used as a basis for the decision making process of our participants. The results of the study are promising. Participants of the Rated Tags group had an increased decision quality and a decreased decision making effort compared to the participants of the control group.
Recent updated aspects of colicins of Enterobacteriaceae

The colicins are protein compounds produced by, and active against, Escherichia coli and others members of Enterobacteriaceae family. At least 34 different colicins have been described and found to share an interesting number of features. In the present review we focus on the major characteristics of colicins of gram-negative bacteria and explore their production and practical applications.The colicins are protein compounds produced by, and active against, Escherichia coli and others members of Enterobacteriaceae family. At least 34 different colicins have been described and found to share an interesting number of features. In the present review we focus on the major characteristics of colicins of gram-negative bacteria and explore their production and practical applications.
Neuromyths in Education: Prevalence among Spanish Teachers and an Exploration of Cross-Cultural Variation

Enthusiasm for research on the brain and its application in education is growing among teachers. However, a lack of sufficient knowledge, poor communication between educators and scientists, and the effective marketing of dubious educational products has led to the proliferation of numerous ‘neuromyths. ’ As a first step toward designing effective interventions to correct these misconceptions, previous studies have explored the prevalence of neuromyths in different countries. In the present study we extend this applied research by gathering data from a new sample of Spanish teachers and by meta-analyzing all the evidence available so far. Our results show that some of the most popular neuromyths identified in previous studies are also endorsed by Spanish teachers. The meta-analytic synthesis of these data and previous research confirms that the popularity of some neuromyths is remarkably consistent across countries, although we also note peculiarities and exceptions with important implications for the development of effective interventions. In light of the increasing popularity of pseudoscientific practices in schools worldwide, we suggest a set of interventions to address misconceptions about the brain and education.
Autoconcepto adolescente y clase social

L a imagen que cada uno tiene de sí mismo, a diferencia de otros constructos psicológicos, es en gran manera operativo. Procede de la acción, condicionándola y significándola. Por eso las diferencias entre los términos autoimagen, autoconcepto, autopercepción frente al de autoestima e incluso al de autoeficacia, son más bien conceptuales. En su expresión y en su influencia en la conducta fácilmente aparece un matiz evaluativo, de positividad o negatividad, de la propia imagen y de la ejecución (Coopersmith, S., 1967). Bandura, A. (1986) señala tres fuentes posibles y combinables en la formación del autoconcepto:
Up-Regulation of the Nedd2 Gene Encoding an ICE/Ced-3-Like Cysteine Protease in the Gerbil Brain after Transient Global Ischemia

We assessed the expression of several genes encoding pro-apoptotic cysteine proteases similar to interleukin-1β converting enzyme (ICE) and nematode Ced-3 in association with delayed neuronal death (DND) after transient forebrain ischemia in Mongolian gerbil. The levels of the two species of Nedd2 mRNA concomitantly increased about twofold in the whole forebrain at 3–6 h after 10-min ischemia and declined to the basal level by 24 h. In situ hybridization revealed that the Nedd2 gene was up-regulated in some neuronal populations in CA1 and CA3 regions of the hippocampus. In contrast, expression of ICE, CPP32/Yama/Apopain, and TX/ICErelII did not change within 48 h. These observations raise the possibility that up-regulation of Nedd2 in the vulnerable neurons may contribute to the proteolytic processes preceding the manifestation of apoptosis and/or necrosis after ischemic insult.
Developmental Regulation of a Local Positive Autocontrol of Supraoptic Neurons

Mature oxytocin (OT) and vasopressin (AVP) magnocellular neurons of the hypothalamic supraoptic nuclei (SON) autocontrol their electrical activity via somatodendritic release of their respective peptides. Because OT and AVP are synthesized early in development and could play an important role in the maturation of these neurons, we checked whether the peptides are released within the SON and act on their secreting neurons during 3 weeks of postnatal development. We used patch-clamp recordings from SON neurons in rat hypothalamic horizontal slices to show that the spontaneous electrical activity of immature SON neurons is blocked by OT or AVP receptor antagonists, demonstrating a basal somatodendritic release of the peptides. Application of OT or AVP depolarizes SON neurons and stimulates activity typical of the corresponding mature neurons. This effect is directly on SON neurons because it is recorded in dissociated neurons. Radioimmunoassays from isolated SON were used to show that each peptide facilitates its own release at a somatodendritic level, exhibiting a self-sustaining positive feedback loop. This autocontrol is not uniform during development because the proportion of neurons depolarized by the peptides, the amplitude of the depolarization, and the propensity of the peptides to facilitate their own release are maximal during the second postnatal week and decrease thereafter. These data are consistent with a role of autocontrol in the maturation of SON neurons because it is maximal during the delimited period of postnatal development that corresponds to the period of major synapse formation.
Augmented set of features for confidence estimation in spoken term detection

Discriminative confidence estimation along with confidence normalisation have been shown to construct robust decision maker modules in spoken term detection (STD) systems. Discriminative confidence estimation, making use of termdependent features, has been shown to improve the widely used lattice-based confidence estimation in STD. In this work, we augment the set of these term-dependent features and show a significant improvement in the STD performance both in terms of ATWV and DET curves in experiments conducted on a Spanish geographical corpus. This work also proposes a multiple linear regression analysis to carry out the feature selection. Next, the most informative features derived from it are used within the discriminative confidence on the STD system.
Mapping Dictionaries: A Spreading Activation Approach

In this paper we apply a spreading activation algorithm to the problem of mapping senses between machine readable dictionaries, which is required in order to combined information extracted from them. The algorithm is run over networks automatically constructed from dictionary definition texts. On a sample corpus of sense definitions, our strategy correctly identifies the corresponding homograph in a second dictionary in 97% of the cases, and the correct sense within that homograph in 90% of the cases. This result is a substantial improvement over previously proposed strategies, such as Lesk's method. It also demonstrates that spreading activation strategies, which have rarely been used in computational lexicography, are one means to exploit the full potential of relations implicitly encoded in machine-readable dictionaries. The authors would like to thank Lisa Lassek for her contribution to the work of this project.
Semi-automated adaptation of service interactions

In today's Web, many functionality-wise similar Web services are offered through heterogeneous interfaces (operation definitions) and business protocols (ordering constraints defined on legal operation invocation sequences). The typical approach to enable interoperation in such a heterogeneous setting is through developing adapters. There have been approaches for classifying possible mismatches between service interfaces and business protocols to facilitate adapter development. However, the hard job is that of identifying, given two service specifications, the actual mismatches between their interfaces and business protocols. In this paper we present novel techniques and a tool that provides semi-automated support for identifying and resolution of mismatches between service interfaces and protocols, and for generating adapter specification. We make the following main contributions: (i) we identify mismatches between service interfaces, which leads to finding mismatches of type of signature, merge/split, and extra/missing messages; (ii) we identify all ordering mismatches between service protocols and generate a tree, called mismatch tree, for mismatches that require developers' input for their resolution. In addition, we provide semi-automated support in analyzing the mismatch tree to help in resolving such mismatches. We have implemented the approach in a tool inside IBM WID (WebSphere Integration Developer). Our experiments with some real-world case studies show the viability of the proposed approach. The methods and tool are significant in that they considerably simplify the problem of adapting services so that interoperation is possible.
The influence of environment, behavior, and attention deficits on cognitive development in school-aged children

• A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers.
Detecting Protein Candidate Fragments Using a Structural Alphabet Profile Comparison Approach

Predicting accurate fragments from sequence has recently become a critical step for protein structure modeling, as protein fragment assembly techniques are presently among the most efficient approaches for de novo prediction. A key step in these approaches is, given the sequence of a protein to model, the identification of relevant fragments - candidate fragments - from a collection of the available 3D structures. These fragments can then be assembled to produce a model of the complete structure of the protein of interest. The search for candidate fragments is classically achieved by considering local sequence similarity using profile comparison, or threading approaches. In the present study, we introduce a new profile comparison approach that, instead of using amino acid profiles, is based on the use of predicted structural alphabet profiles, where structural alphabet profiles contain information related to the 3D local shapes associated with the sequences. We show that structural alphabet profile-profile comparison can be used efficiently to retrieve accurate structural fragments, and we introduce a fully new protocol for the detection of candidate fragments. It identifies fragments specific of each position of the sequence and of size varying between 6 and 27 amino-acids. We find it outperforms present state of the art approaches in terms (i) of the accuracy of the fragments identified, (ii) the rate of true positives identified, while having a high coverage score. We illustrate the relevance of the approach on complete target sets of the two previous Critical Assessment of Techniques for Protein Structure Prediction (CASP) rounds 9 and 10. A web server for the approach is freely available at http://bioserv.rpbs. univ-paris-diderot.fr/SAFrag.
Viabilité biologique et économique pour la gestion durable de pêcheries mixtes

L’objectif general de la these est de modeliser les principaux processus biologiques et economiques regissant des pecheries multi-especes et multi-flottilles afin de proposer des strategies viables pour la gestion durable de ces pecheries mixtes, dans un contexte stochastique et multiobjectif. Plus specifiquement, cette these utilise des analyses de co-viabilite stochastique pour etudier les arbitrages entre des objectifs contradictoires de gestion (conservation, et viabilite economique et sociale) des pecheries mixtes. Deux pecheries mixtes sont analysees dans cette these : la pecherie francaise mixte demersale du golfe de Gascogne et la pecherie crevettiere australienne du Nord (NPF). Ces deux pecheries sont multi-especes, et utilisent des strategies multiples de peche, induisant des impacts directs et indirects sur les ecosystemes. Cette these propose une application de la co-viabilite stochastique a ces deux cas, en prenant en compte leur histoire, leur contexte socio-politique et les differences dans les strategies et objectifs de gestion. Les resultats suggerent que le status quo peut etre considere comme une strategie biologiquement durable mais socio economiquement a risque dans les deux pecheries (ainsi qu’a risque ecologique dans le cas de la pecherie australienne). Les simulations realisees pour le golfe de Gascogne permettent de comparer les arbitrages associes a differentes reductions de capacites par flottille et de montrer qu’il existe des solutions de gestion permettant la co-viabilite du systeme (viabilite biologique des differentes especes considerees et viabilite socio-economique des flottilles) contrairement a des strategies de gestion mono-specifiques ou basees sur la maximisation de la rente. Dans la pecherie crevettiere australienne, l’analyse montre que les strategies de diversification permettent de limiter le risque economique contrairement aux strategies plus specialisees.
Methods and tools for exploring novice compilation behaviour

Our research explores what we call compilation behaviour: the programming behaviour a student engages in while repeatedly editing and compiling their programs. This edit-compile cycle often represents students' attempts to make their programs syntactically, as opposed to semantically, correct. Over the course of two years, we have observed first-year university students learning to program in Java, collecting and studying thousands of snapshots of their programs from one compilation to the next. At the University of Kent, students are introduced to programming in an objects-first style using BlueJ, an environment intended for use by novice programmers.