Miracle-dz/UniFAR-FTUs huggingface dataset:
GeNGe: systematic generation of gene regulatory networks

Summary: The analysis of gene regulatory networks (GRNs) is a central goal of bioinformatics highly accelerated by the advent of new experimental techniques, such as RNA interference. A battery of reverse engineering methods has been developed in recent years to reconstruct the underlying GRNs from these and other experimental data. However, the performance of the individual methods is poorly understood and validation of algorithmic performances is still missing to a large extent. To enable such systematic validation, we have developed the web application GeNGe (GEne Network GEnerator), a controlled framework for the automatic generation of GRNs. The theoretical model for a GRN is a non-linear differential equation system. Networks can be user-defined or constructed in a modular way with the option to introduce global and local network perturbations. Resulting data can be used, e.g. as benchmark data for evaluating GRN reconstruction methods or for predicting effects of perturbations as theoretical counterparts of biological experiments. Availability: Available online at http://genge.molgen.mpg.de Contact: hache@molgen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
Investigative Research As a Knowledge-Generation Method: Discovering and Uncovering

The authors explicate investigative research as a formal research method for knowledge generation. The impetus comes from two recent developments that have reexamined the nature of knowledge generation: paradigmatic shift from methodological individualism to methodological relationalism, and the rise of indigenous psychology. We identify three germane intellectual attitudes: examining the evidence, vigilance against deceptive appearance, and recognition of ignorance. Investigative research has the advantage of bringing the investigator to observe closely and directly phenomena of interest, relying on disciplined, naturalistic, and in-depth observations over time in diverse contexts. It is particularly suitable for uncovering, understanding, and reporting social phenomena that may be hidden from or not easily accessible to observers. Investigative research can function as a guardian of social conscience through (a) maintaining vigilance against institutional corruptions or threats to civic virtues; and (b) reexaminations of published evidence that serve to tighten quality control and ethical integrity in scientific research.
Health‐related quality of life in pediatric liver transplant recipients compared with other chronic disease groups

Limbers CA, Neighbors K, Martz K, Bucuvalas JC, Webb T, Varni JW, Alonso EM, on behalf of the Studies of Pediatric Liver Transplantation (SPLIT) Functional Outcomes Group (FOG). Health‐related quality of life in pediatric liver transplant recipients compared with other chronic disease groups. Pediatr Transplantation 2011: 15: 245–253. © 2010 John Wiley & Sons A/S.
Evaluating Decision Makers: The Role of Choice Congruence and Outcome

Two studies were conducted in which decision makers were evaluated by subjects who had agreed or disagreed with the decision maker's choice. Subjects read one of two vignettes describing the alternatives available to the decision maker, indicated which alternative they personally favored, and then learned about the decision maker's choice and the outcome that occurred. Study 1 varied whether the outcomes of the decision maker's choice were positive or negative, and whether the subject's preferred option matched (congruent choice) or did not match (incongruent choice) that of the decision maker. Subjects rated the extent to which they thought the decision maker was worthy of praise (in the case of positive outcomes) or blame (in the case of negative outcomes), and the decision maker's likableness and competence. Results revealed a strong effect of congruence on attributions of praise and blame: More praise was ascribed to an agreeing decision maker and more blame to a disagreeing decision maker. The degree.
Automatic sound detection and recognition for noisy environment

This paper addresses the problem of automatic detection and recognition of impulsive sounds, such as glass breaks, human screams, gunshots, explosions or door slams. A complete detection and recognition system is described and evaluated on a sound database containing more than 800 signals distributed among six different classes. Emphasis is set on robust techniques, allowing the use of this system in a noisy environment. The detection algorithm, based on a median filter, features a highly robust performance even under important background noise conditions. In the recognition stage, two statistical classifiers are compared, using Gaussian Mixture Models (GMM) and Hidden Markov Models (HMM), respectively. It can be shown that a rather good recognition rate (98% at 70dB and above 80% for 0dB signal-to-noise ratios) can be reached, even under severe gaussian white noise degradations.
Joint Tabling of Logic Program Abductions and Updates

Abductive logic programs offer a formalism to declaratively represent and reason about problems in a variety of areas: diagnosis, decision making, hypothetical reasoning, etc. On the other hand, logic program updates allow us to express knowledge changes, be they internal (or self) and external (or world) changes. Abductive logic programs and logic program updates thus naturally coexist in problems that are susceptible to hypothetical reasoning about change. Taking this as a motivation, in this paper we integrate abductive logic programs and logic program updates by jointly exploiting tabling features of logic programming. The integration is based on and benefits from the two implementation techniques we separately devised previously, viz., tabled abduction and incremental tabling for query-driven propagation of logic program updates. A prototype of the integrated system is implemented in XSB Prolog.
Effects of Hydrogen Peroxide on Wound Healing in Mice in Relation to Oxidative Damage

It has been established that low concentrations of hydrogen peroxide (H(2)O(2)) are produced in wounds and is required for optimal healing. Yet at the same time, there is evidence that excessive oxidative damage is correlated with poor-healing wounds. In this paper, we seek to determine whether topical application of H(2)O(2) can modulate wound healing and if its effects are related to oxidative damage. Using a C57BL/6 mice excision wound model, H(2)O(2) was found to enhance angiogenesis and wound closure at 10 mM but retarded wound closure at 166 mM. The delay in closure was also associated with decreased connective tissue formation, increased MMP-8 and persistent neutrophil infiltration. Wounding was found to increase oxidative lipid damage, as measured by F(2)-isoprostanes, and nitrative protein damage, as measured by 3-nitrotyrosine. However H(2)O(2) treatment did not significantly increase oxidative and nitrative damage even at concentrations that delay wound healing. Hence the detrimental effects of H(2)O(2) may not involve oxidative damage to the target molecules studied.
Toward developing a simulated workplace laboratory for adults with high functioning autism spectrum disorders

Objective: Adults with high functioning autism spectrum disorders (HF-ASD) often experience difficulty in sustaining employment, yet little is known about workplace deficits in this population. This study aimed to assess the workplace performance of individuals with HF-ASDs in a previously validated laboratory workplace simulation environment. Method: Seven subjects of both sexes, ages 18 - 21 with a clinical diagnosis of ASD were brought in for a 10- hour workplace simulation, with a series of structured and unstructured tasks designed to elicit DSM-IV Attention Deficit and Hyperactivity Disorder (ADHD) symptoms and to provide objective measures of workplace performance. Results: HF-ASD participants performed significantly worse than Controls on several tasks throughout the day, particularly in the afternoon. Although HF-ASD subjects did not report elevated symptoms of ADHD, they completed significantly less of the unstructured tasks than Controls. Conclusion: These findings suggest that unstructured work activities and a lack of self-awareness are two primary areas of workplace deficits for individuals with HF-ASD.
Multifetal pregnancy reduction and selective termination

Multifetal pregnancy reduction has had a major impact upon perinatal morbidity and mortality following iatrogenic multiple pregnancies. There are still residual risks, however, that are higher for higher order multiples than for pregnancies that started out at lower numbers. There are many, but not complete, parallels between reductions for number per se, and selective termination because of diagnosed abnormalities.
Spaan Fellow Working Papers in Second or Foreign Language Assessment Volume 3 2005

This study investigated the usefulness of the cloze-elide objective language task (Manning, 1987) in a test of teacher English language proficiency in Quebec, Canada. While the task has demonstrated its usefulness recently in low-stakes language diagnostic testing in a New Zealand university context (Elder & von Randow, 2008), it is important to examine its usefulness in other contexts. In addition, evidence was collected regarding the construct being addressed by this particular task, something that has not yet been examined. A cloze-elide task was administered to 346 preservice teachers at a Montreal university, in addition to other direct and indirect tasks, as part of a high-stakes exam for teacher certification. It was decided that the cloze-elide task would be deemed useful if it distinguished between English and French native speakers (assuming that French native speakers would be more in need of language support). In addition, the task would be deemed useful if it had sufficient face validity to be accepted by the test takers. Results from regression analysis show that the cloze-elide did not effectively predict language group. In addition, results on the authentic teacher communication tasks of the exam also did not predict language group, suggesting that distinguishing between English and French native speakers may not be useful, or may not even be possible in all cases in the Quebec context. A survey with students after the exam provided insight into students’ suspicion of the task. In addition, students’ descriptions of their reading strategies during the cloze elide task provided insight into the construct represented by the task. For example, students demonstrated awareness of the need to balance topdown and bottom-up approaches to the text. This study underlines the importance of considering the local context in determining test task usefulness, as well considering the input from the test takers themselves in test task validation.
Contributos para a construção de um texto foneticamente equilibrado para o Português-Europeu

OBJECTIVO: o objectivo deste estudo consiste na criacao de um Texto Foneticamente Equilibrado para o Portugues-Europeu (PE) designado "O Sol". METODO: quatro sujeitos da regiao de Setubal, entre [21-49] anos (dois do sexo feminino e dois do masculino) leram em voz alta o texto "O Sol". As gravacoes realizadas com Olympus (VN- 240PC e VN- 2100PC com microfones integrados) serviram para a contabilizacao dos fonemas produzidos. Os procedimentos foram: 1) a comparacao entre as frequencias relativas dos fonemas do "O Sol" e as frequencias relativas descritas no PF_fone, atraves do coeficiente de correlacao de Pearson e do teste de Mann-Whitney; 2) a comparacao entre a transcricao larga e a estreita, verificando-se os fenomenos de coarticulacao; e 3) a analise dos formatos silabicos. RESULTADOS: a analise estatistica demonstrou que as frequencias relativas de ocorrencia dos fonemas do texto "O Sol" tem uma correlacao forte com as do PF_fone (r = 0,924). As medianas das frequencias relativas de ocorrencia dos fonemas do texto foram significativamente iguais das do PF_fone (p<.05). CONCLUSAO: o texto "O Sol" esta proximo de um texto foneticamente equilibrado ideal, uma vez que se verificaram os pressupostos pre-definidos. Fonologicamente, apresenta os formatos silabicos mais frequentes no PE, verificou-se ainda uma diminuicao na frequencia relativa de fonemas na transcricao estreita, devido a fenomenos de coarticulacao. Futuros trabalhos incidirao no aumento da amostra.
Investigating the Effect of Mindfulness Training on Heart Rate Variability in Mental Health Outpatients: A Pilot Study

Depression is associated with increased cardiac morbidity and mortality in people with and without cardiac risk factors, and this relationship is, in part, mediated by heart rate variability (HRV). Increased heart rate and reduced HRV are common in depressed patients, which may explain their higher cardiac risk. This pilot study investigated whether mindfulness-based cognitive therapy (MBCT) promoted objective changes in (1) HRV, and (2) depressive symptoms and quality of life, in mental health outpatients. Twenty-seven adults meeting criteria for DSM-IV Axis I disorders completed an 8-week MBCT program. Data were collected on three occasions, 8 weeks apart; twice before and once after MBCT. Participants completed the Short Form-36 and the Center for Epidemiological Studies Depression Scale (CES-D) at each test period. Heart rate and HRV were measured during electrocardiographic monitoring before and after a cognitive stressor. At baseline, 78% of participants met criteria for depression (CES-D ≥16). Multivariate analyses revealed a significant treatment effect for SF-36 physical summary score and depression (as a dichotomous variable), but not for HRV. This pilot study highlights the immediate psychological and health benefits of MBCT. Low power may have influenced the lack of a finding of an association between HRV and MBCT. However, the feasibility of the study design has been established, and supports the need for larger and longer-term studies of the potential physiological benefits of MBCT for cardiac health.
Analysis of the sound attack in context of computer evaluation of the singing voice quality

Sound attack is meant as the initiation of the tone. Good attack involves the simultaneous start of exhalation along with the emission of sound. This situation is known as a soft attack. Much more common is a hard type of attack, which is normally used while speaking. It involves tightening of the vocal cords before the expiration. Unfortunately, this state is tiring for the ligaments and can cause damage to the voice. The idea was to propose a method to analyse this problem, which in the future would become a part of set of methods for computer analysis of the singing voice. This article presents a method of the extraction of attack parameters. The estimation of these parameters is carried out with the recorded audio samples. In the study sound sample of 'a' registered several times for each pitch will be used.
The Rho-GEF Gef3 interacts with the septin complex and activates the GTPase Rho4 during fission yeast cytokinesis

Unlike the six other Rho GEFs in fission yeast, Gef3 colocalizes with and depends on septins to localize during late cytokinesis. Gef3 binds to GDP-Rho4 and accelerates its nucleotide exchange in vitro. Moreover, Gef3 modulates Rho4 activity in vivo and works in the same genetic pathways as Rho4 to regulate septation in fission yeast cytokinesis.
Deoxygenation of the Baltic Sea during the last century

Significance Oxygen-deficient waters are expanding globally in response to warming and coastal eutrophication. Coastal ecosystems provide valuable services to humans, but these services are severely reduced with decreasing oxygen conditions. In the Baltic Sea, oxygen-deficient waters have expanded from 5,000 to over 60,000 km2 with large decadal fluctuations over the last century, reducing the potential fish yield and favoring noxious algal blooms. This increase is due to the imbalance between oxygen supply from physical processes and oxygen demand from consumption of organic material, enhanced by nutrient inputs and temperature increases. Further nutrient reductions will be necessary to restore a healthier Baltic Sea and counteract effects from warming. Deoxygenation is a global problem in coastal and open regions of the ocean, and has led to expanding areas of oxygen minimum zones and coastal hypoxia. The recent expansion of hypoxia in coastal ecosystems has been primarily attributed to global warming and enhanced nutrient input from land and atmosphere. The largest anthropogenically induced hypoxic area in the world is the Baltic Sea, where the relative importance of physical forcing versus eutrophication is still debated. We have analyzed water column oxygen and salinity profiles to reconstruct oxygen and stratification conditions over the last 115 y and compare the influence of both climate and anthropogenic forcing on hypoxia. We report a 10-fold increase of hypoxia in the Baltic Sea and show that this is primarily linked to increased inputs of nutrients from land, although increased respiration from higher temperatures during the last two decades has contributed to worsening oxygen conditions. Although shifts in climate and physical circulation are important factors modulating the extent of hypoxia, further nutrient reductions in the Baltic Sea will be necessary to reduce the ecosystems impacts of deoxygenation.
Inversion of seismoacoustic data using genetic algorithms and a posteriori probability distributions

The goal of many underwater acoustic modeling problems is to find the physical parameters of the environment. With the increase in computer power and the development of advanced numerical models it is now feasible to carry out multiparameter inversion. The inversion is posed as an optimization problem, which is solved by a directed Monte Carlo search using genetic algorithms. The genetic algorithm presented in this paper is formulated by steady‐state reproduction without duplicates. For the selection of ‘‘parents’’ the object function is scaled according to a Boltzmann distribution with a ‘‘temperature’’ equal to the fitness of one of the members in the population. The inversion would be incomplete if not followed by an analysis of the uncertainties of the result. When using genetic algorithms the response from many environmental parameter sets has to be computed in order to estimate the solution. The many samples of the models are used to estimate the a posteriori probabilities of the model parameters. T.
Coupling an Advanced Land Surface–Hydrology Model with the Penn State–NCAR MM5 Modeling System. Part I: Model Implementation and Sensitivity

Abstract This paper addresses and documents a number of issues related to the implementation of an advanced land surface–hydrology model in the Penn State–NCAR fifth-generation Mesoscale Model (MM5). The concept adopted here is that the land surface model should be able to provide not only reasonable diurnal variations of surface heat fluxes as surface boundary conditions for coupled models, but also correct seasonal evolutions of soil moisture in the context of a long-term data assimilation system. In a similar way to that in which the modified Oregon State University land surface model (LSM) has been used in the NCEP global and regional forecast models, it is implemented in MM5 to facilitate the initialization of soil moisture. Also, 1-km resolution vegetation and soil texture maps are introduced in the coupled MM5–LSM system to help identify vegetation/water/soil characteristics at fine scales and capture the feedback of these land surface forcings. A monthly varying climatological 0.15° × 0.15° green .
Spatio-Temporal Modeling of BGP Routing Table Evolution

Modeling the routing table growth is vital to the BGP operation. The temporal evolution of the routing table size has been researched to anticipate the memory limitation of BGP routers. However, route aggregation and compression techniques make it difficult to expect the actual memory size from the routing table size. Therefore, further evolution models focusing on the spatial routing table structure are required to evaluate the tolerance of these techniques to future routing table growth. In this paper, we create an evolution model focusing on spatio-temporal route changes using ten-year BGP routing table datasets. We categorize route variations into three types; new, fragmented, and vanished and then create a model for each type. We also demonstrate the characteristics of the model parameters in these ten years.
The role of affordances for working memory for objects

Given the widespread evidence for the importance of the motor system in conceptual memory and language processing, we investigated if action affordances also play a role in visual working memory for objects. Familiar (Experiment 1) and novel (Experiment 2) objects were presented in an N-back working memory task. The potential role of affordances was investigated by presenting manipulable (e.g., fork) and nonmanipulable (e.g., chimney) objects. Results showed that a concurrent motor task did not interfere differently with memory for objects with and without affordances. We conclude that motor affordances play no role in visual working memory.
Transgender Transitions: Sex/Gender Binaries in the Digital Age

Contemporary representations of transgendered people often reinforce rigid gender binaries of masculinity and femininity, leading transgendered individuals to feel they must seek out hormones or surgery to “correctly align” their bodies with their gender. Cultural texts (e.g., films, television, Internet, digital texts) reinforce this “pre-op or post-op” ideology for trans identity. The pre-op or post-op MTF or FTM binary mandates an alignment with the heterosexual gender system (feminine female or masculine male). In this article, the author focuses on trans identities and how representations codify the need or desire for surgery and hormones and examines the paradoxical reification of gender and sexual stereotypes (particularly dichotomization) by electronic media for transgender consumers of these media at the same time that these same sources provide an abundance of information for those who would otherwise not be made aware of the resources available to them. The competition between marketing of products and services for transgender individuals and provision of otherwise nonprofitable information for the same individuals ranging from normalizing, informing of sources of help and health information is examined as well as the use of the Internet as a medium for transitioning individuals to share their experiences. This article argues that instead of a culture of hormones and surgery, teachers, medical professionals, and counselors should embrace and educate towards acceptance of trans identities and bodies that does not rely on the mandate of hormones or surgeries. Finally, the impact of the dissemination of information in the uncontrolled environment of the Internet illustrates the impact of culture on media and vice versa.