Miracle-dz/UniFAR-FTUs huggingface dataset:
Motor-induced Suppression of the Auditory Cortex

Sensory responses to stimuli that are triggered by a self-initiated motor act are suppressed when compared with the response to the same stimuli triggered externally, a phenomenon referred to as motor-induced suppression (MIS) of sensory cortical feedback. Studies in the somatosensory system suggest that such suppression might be sensitive to delays between the motor act and the stimulus onset, and a recent study in the auditory system suggests that such MIS develops rapidly. In three MEG experiments, we characterize the properties of MIS by examining the M100 response from the auditory cortex to a simple tone triggered by a button press. In Experiment 1, we found that MIS develops for zero delays but does not generalize to nonzero delays. In Experiment 2, we found that MIS developed for 100-msec delays within 300 trials and occurs in excess of auditory habituation. In Experiment 3, we found that unlike MIS for zero delays, MIS for nonzero delays does not exhibit sensitivity to sensory, delay, or motor-command changes. These results are discussed in relation to suppression to self-produced speech and a general model of sensory motor processing and control.
Graphemic, associative, and syntactic priming effects at a brief stimulus onset asynchrony in lexical decision and naming

The present set of experiments investigated graphemic, associative, and syntactic priming effects in both a lexical decision and a naming task. In all the experiments, a three-word maskng procedure (word-prime-target) with a 60-ms stimulus onset asynchrony between prime and target was used to limit strategic effects
Psychometric properties of the Five-Digit Test in patients with stroke

Abstract Purpose: To examine the ecological validity, predictive validity, and responsiveness of the Five Digit Test (FDT) in patients with stroke. Methods: We included inpatients with stroke (n = 144, 114 and 105 in the ecological validity, predictive validity, and responsiveness analysis, respectively) in the study. At admission, the FDT and Barthel Index (BI) were assessed; at discharge, the FDT, BI, Postural Assessment Scale for Stroke Patients (PASS), and Mobility Subscale of the Stroke Rehabilitation Assessment of Movement (MO-STREAM) were assessed. Results: In the ecological validity analysis, the scores of the selective and alternating attention indices of the FDT were moderately correlated with those of the BI at admission and discharge (Spearman ρ = –0.38 to –0.45). In the predictive validity analysis, the scores of the two attention indices of the FDT at admission were moderately correlated with the scores of the BI, PASS, and MO-STREAM at discharge (ρ = –0.33 to –0.45). In the responsiveness analysis, the two attention indices of the FDT between admission and discharge had large differences (success rate difference = 0.56–0.67, Wilcoxon Z = –5.90 to –6.60). Conclusion: Our results indicate that the selective and alternating attention indices of the FDT have acceptable ecological validity, predictive validity, and good responsiveness in patients with stroke. Implications for Rehabilitation The Five Digit Test (FDT), an efficient and culture-free assessment tool, has been used to assess selective attention and alternating attention The selective index and alternating attention index of the FDT showed acceptable ecological validity, predictive validity, and good responsiveness in patients with stroke.
Spatial Fading Correlation for Local Scattering: A Condition of Angular Distribution

Local scattering in the vicinity of the receiver or the transmitter leads to the formation of a large number of multipath components along different spatial angles. A condition of angular distribution, which is valid for only a uniform linear array, is proposed in this paper to justify whether the spatial fading correlation (SFC) remains simple as a Bessel function. If an angular distribution satisfies the condition, a class of angular distributions is revealed and results in simplifying the analysis of the SFC. To demonstrate its practical use, we apply the condition to several angular distributions that are considered in previous works. It is found that cosine and von Mises distributions follow the condition, whereas uniform, Gaussian, and Laplacian distributions do not satisfy the condition, and then, one needs to calculate the sinusoidal coefficients in the SFC computation.
AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals.

Introduction of transgene DNA may lead to specific degradation of RNAs that are homologous to the transgene transcribed sequence through phenomena named post-transcriptional gene silencing (PTGS) in plants, quelling in fungi, and RNA interference (RNAi) in animals. It was shown previously that PTGS, quelling, and RNAi require a set of related proteins (SGS2, QDE-1, and EGO-1, respectively). Here we report the isolation of Arabidopsis mutants impaired in PTGS which are affected at the Argonaute1 (AGO1) locus. AGO1 is similar to QDE-2 required for quelling and RDE-1 required for RNAi. Sequencing of ago1 mutants revealed one amino acid essential for PTGS that is also present in QDE-2 and RDE-1 in a highly conserved motif. Taken together, these results confirm the hypothesis that these processes derive from a common ancestral mechanism that controls expression of invading nucleic acid molecules at the post-transcriptional level. As opposed to rde-1 and qde-2 mutants, which are viable, ago1 mutants display several developmental abnormalities, including sterility. These results raise the possibility that PTGS, or at least some of its elements, could participate in the regulation of gene expression during development in plants.
The impact of serotonin receptor 1A and 2A gene polymorphisms and interactions on suicide attempt and suicide risk in depressed patients with insufficient response to treatment – a European multicentre study

So far, associations between serotonergic neurotransmission pathways and suicidality have been reported. The aim of our study was to investigate the role of genetic polymorphisms and gene–gene interactions of the 5-HTR1A and the 5-HTR2A gene on suicide risk and/or a personal history of suicide attempts. A total of 374 major depressive disorder patients, adequately treated with antidepressants for at least 4 weeks, were collected in the context of a European multicentre study on treatment-resistant depression. We assessed suicidality using the Mini International Neuropsychiatric Interview and the Hamilton Rating Scale for Depression (HAM-D). Treatment response was defined as HAM-D⩽17 and remission as HAM-D⩽7 after 4 weeks of adequate antidepressant treatment. The 5-HTR1A rs6295 (C-1019G) single nucleotide polymorphism (SNP) and the 5-HTR2A rs7997012, rs6313, rs643627 and rs17288723 SNPs were selected for genotyping. Using logistic regression analyses, no association (P<0.05) could be found between any SNP and neither suicide risk nor personal history of suicide attempts. Interactions between 5HTR1A rs6295 and 5HTR2A rs6313 in suicide risk, and 5HTR1A rs6295 and 5HTR2A rs643627 in a personal history of suicide attempts have been reported (P=0.027 and 0.036, respectively); however, the results did not survive multiple testing correction. In conclusion, our study shows no association between 5HTR1A or 5HTR2A gene polymorphisms and both current suicide risk and personal history of suicide attempts. In addition, epistatic effects of 5HTR1A and 5HTR2A genes on suicidal behaviour were not significant, although sample size limitations do not allow definitive conclusions.
Software for PID design: Benefits and pitfalls

The most common PID design methods in industry are based on formulas. This article will present some major advantages of instead using the power of computer based softwares for PID controller design. The Matlab based software used in this work was developed in 2007 and derives robust, IAE minimizing, PID controllers. The experiences of using this software are collected in this article and include control signal activity limitation due to measurement noise, controller design on an industrial Friction Stir Welding process and fast controller design for large batches of processes. It is shown that the properties of the software make it suitable for design of PID controllers and in PID research. There are, however, some possible design pitfalls that the user needs to be aware of. Some of these are presented as well.
Contemporary Reviews in Cardiovascular Medicine Exercise Rehabilitation in Peripheral Artery Disease Functional Impact and Mechanisms of Benefits

Exercise therapy combined with com-prehensive secondary prevention has the potential to benefitpatients with PAD by preserving or improving functionalcapacity and reducing cardiovascular events. Accordingly,this review will address the relation between exercise intol-erance and outcomes in patients with PAD; the effects ofexercise training in PAD and the many possible mechanismsof benefit; and the potential role of comprehensive secondaryprevention programs in these patients.
Overexpression of Monocyte Chemoattractant Protein 1 in the Brain Exacerbates Ischemic Brain Injury and is Associated with Recruitment of Inflammatory Cells

Brain cells produce cytokines and chemokines during the inflammatory process after stroke both in animal models and in patients. Monocyte chemoattractant protein 1 (MCP-1), one of the proinflammatory chemokines, can attract monocytes to the tissue where MCP-1 is overexpressed. However, the role of MCP-1 elevation in stroke has not been explored in detail. The authors hypothesized that elevated MCP-1 levels would lead to increased influx of monocytes and increased brain infarction size in stroke induced by middle cerebral artery occlusion with partial reperfusion. There were no differences in blood pressure, blood flow, or vascular architecture between wild-type mice and transgenic MBP-JE mice. Twenty-four to 48 hours after middle cerebral artery occlusion, brain infarction volumes after ischemia were significantly larger in MBP-JE mice than in wild-type controls and were accompanied by increased local transmigration and perivascular accumulation of macrophages and neutrophils. These results indicate that MCP-1 can contribute to inflammatory injury in stroke.
Predator–prey cycles in an aquatic microcosm: testing hypotheses of mechanism

Summary 1 Fussmann et al. (2000 ) presented a simple mechanistic model to explore predator–prey dynamics of a rotifer species feeding on green algae. Predictions were tested against experimental data from a chemostat system housing the planktonic rotifer Brachionus calyciflorus and the green alga Chlorella vulgaris . 2 The model accurately predicted qualitative behaviour of the system (extinction, equilibria and limit cycles), but poorly described features of population cycles such as the period and predator–prey phase relationship. These discrepancies indicate that the model lacked some biological mechanism(s) crucial to population cycles. 3 Here candidate hypotheses for the ‘missing biology’ are quantified as modifications to the existing model and are evaluated for consistency with the chemostat data. The hypotheses are: (1) viability of eggs produced by rotifers increases with food concentration, (2) nutritional value of algae increases with nitrogen availability, (3) algal physiological state varies with the accumulation of toxins in the chemostat and (4) algae evolve in response to predation. 4 Only Hypothesis 4 is compatible with empirical observations and thus may provide important insight into how prey evolution affects predator–prey dynamics.
Concluding Remarks

Significant efforts were made by EU and MS to tackle these challenges, which resulted in the creation of indicators and data bases, development of guidelines and other tools for the improvement of mental health interventions, and creation of networks supporting research, care and policy development. Yet, despite all these efforts, a lot remains to be done. A significant proportion of the general European population, including children and adolescents, has unmet need for mental health care. In promotion and prevention there is also a huge gap: the majority of the populations don’t benefit from the interventions that have proved to be effective in these domains.
SEMI-PLANAR PERFORMANCE ANALYSIS AND KISSING CIRCLE SENSITIVITY

This paper looks at the problem of searching the plane for an object with multiple agents, in co-ordinated search. Also the problem of how to deal with noise within the context of Fakete’s [3] Kissing Circles algorithm is addressed and a method of coping is conjectured. The relative performance of a family of redezvous search algorithms for mulit-agent search in the plane. Some very strict assumptions have been made to idealize the circumstance in order to simplify the analysis.
SUSTAINABLE URBAN PLANNING IN A CROSS-BORDER CONTEXT: A CASE STUDY

The trinational agglomeration of Basel is a very densely populated region attracting more and more inhabitants and employers. The use of space to provide housing and office space has become a sensitive matter in cross-border cooperation as the developments in one parts directly affects the other parts of the agglomeration. Currently, the Canton of Basel-Stadt (Switzerland) plans to delocalize its harbor and to use the harbor site for urban developments. The area borders the cities of Weil am Rhein (Germany) and Huningue (France). For this reason, the Building and Traffic Department of the Canton Basel-Stadt, the city of Weil am Rhein (Germany) and the city of Huningue (France) have defined a trinational perimeter with the aim to develop a trinational sustainable urban district: 3Land. The project partners have developed a common set of sustainability criteria to ensure sustainability of the urban developments within the 3Land-area. It appears, however, that the notion of sustainability is defined differently in the three countries and determined by different legislations and actors in urban planning. For instance, municipalities in France may apply a particular tool for pilot projects that allows them to apply specific criteria on a site that go beyond the existing legislation. In Switzerland, foundations play in important role in fostering sustainable urban development on private property. In Germany, municipalities need to consider specific social criteria if they want to apply to national funding programs. This paper will explore the method that has been implemented in order to ensure sustainability in a cross-border context and its limitations.
Modelling β − Trefoil Proteins Using an Object-Oriented Database

This article describes on-going work using an object-oriented database, P/FDM, to build 3D homology models of β-trefoil proteins such as Interleukin-1 (IL-1), by exploiting existing structural data from known structures of the same fold. The model-building procedure is based on the powerful querying capabilities of P/FDM that allows data access, navigation, and computation to be mixed freely and easily in order to formulate complex structural queries. The database can be queried using a Java-based graphical user interface. Using the P/FDM β−trefoil database, the above approach allows to “cut-and-paste” fragments from existing β−trefoil structures to build the model. The structural part of the database contains objects for the description of proteins, as well as β-trefoil structure-specific entities. Data are organised according to a global β-trefoil structural alignment based on superposition of the 18 core residues of the fold, identified from previous structural studies. The database is currently populated with 46 trefoil domains and further structures are being added in order to make available a richer collection of “spare parts” for modelling. Future enhancements such as improved side chain placement and fragment clustering are also described.
Integration of peroxisomes into an endomembrane system that governs cellular aging

The peroxisome is an organelle that has long been known for its essential roles in oxidation of fatty acids, maintenance of reactive oxygen species (ROS) homeostasis and anaplerotic replenishment of tricarboxylic acid (TCA) cycle intermediates destined for mitochondria. Growing evidence supports the view that these peroxisome-confined metabolic processes play an essential role in defining the replicative and chronological age of a eukaryotic cell. Much progress has recently been made in defining molecular mechanisms that link cellular aging to fatty acid oxidation, ROS turnover, and anaplerotic metabolism in peroxisomes. Emergent studies have revealed that these organelles not only house longevity-defining metabolic reactions but can also regulate cellular aging via their dynamic communication with other cellular compartments. Peroxisomes communicate with other organelles by establishing extensive physical contact with lipid bodies, maintaining an endoplasmic reticulum (ER) to peroxisome connectivity system, exchanging certain metabolites, and being involved in the bidirectional flow of some of their protein and lipid constituents. The scope of this review is to summarize the evidence that peroxisomes are dynamically integrated into an endomembrane system that governs cellular aging. We discuss recent progress in understanding how communications between peroxisomes and other cellular compartments within this system influence the development of a pro- or anti-aging cellular pattern. We also propose a model for the integration of peroxisomes into the endomembrane system governing cellular aging and critically evaluate several molecular mechanisms underlying such integration.
Identification and Survey of a Novel Avian Coronavirus in Ducks

The rapid discovery of novel viruses using next generation sequencing (NGS) technologies including DNA-Seq and RNA-Seq, has greatly expanded our understanding of viral diversity in recent years. The timely identification of novel viruses using NGS technologies is also important for us to control emerging infectious diseases caused by novel viruses. In this study, we identified a novel duck coronavirus (CoV), distinct with chicken infectious bronchitis virus (IBV), using RNA-Seq. The novel duck-specific CoV was a potential novel species within the genus Gammacoronavirus, as indicated by sequences of three regions in the viral 1b gene. We also performed a survey of CoVs in domestic fowls in China using reverse-transcription polymerase chain reaction (RT-PCR), targeting the viral nucleocapsid (N) gene. A total of 102 CoV positives were identified through the survey. Phylogenetic analysis of the viral N sequences suggested that CoVs in domestic fowls have diverged into several region-specific or host-specific clades or subclades in the world, and IBVs can infect ducks, geese and pigeons, although they mainly circulate in chickens. Moreover, this study provided novel data supporting the notion that some host-specific CoVs other than IBVs circulate in ducks, geese and pigeons, and indicated that the novel duck-specific CoV identified through RNA-Seq in this study is genetically closer to some CoVs circulating in wild water fowls. Taken together, this study shed new insight into the diversity, distribution, evolution and control of avian CoVs.
Tuberculosis Knowledge among University Students in Indonesia

The rising tuberculosis (TB) incidence has become one of the main health issues in the world. The objective of this study is to understand TB knowledge and what factors may predict students’ TB knowledge among University students in Indonesia. This study included a total of 200 students. Convenient sampling was used to recruit students for the study. Univariate analysis utilized, such as t-test and one-way ANOVA and Pearson correlations coefficient. Stepwise multiple regression analysis was used to understand which factors can predict the TB knowledge. Overall, the mean score for TB knowledge among the students was 9.49 out of 14. Most of the respondents were male, and included several ethnicities, such as Sunda and non-Sunda. The variables associated with TB knowledge were gender, education, major field of study, and heard of TB. Moreover, the study found that, as predictors, the variables that influenced knowledge about TB ranked according to relevance were: major field of study and educational background. Health promotion among students is very important to improve their knowledge related to TB disease. The findings could be used for designing the university strategic programs in measuring the knowledge of TB among their students. Students with accurate knowledge of TB can help reduce its prevalence in Indonesia.
NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees

Large scale gene duplication is a major force driving the evolution of genetic functional innovation. Whole genome duplications are widely believed to have played an important role in the evolution of the maize, yeast, and vertebrate genomes. The use of evolutionary trees to analyze the history of gene duplication and estimate duplication times provides a powerful tool for studying this process. Many studies in the molecular evolution literature have used this approach on small data sets, using analyses performed by hand. The rapid growth of genetic sequence data will soon allow similar studies on a genomic scale, but such studies will be limited unless the analysis can be automated. Even existing data sets admit alternative hypotheses that would be too tedious to consider without automation. In this paper, we describe a program called NOTUNG that facilitates large scale analysis, using both rooted and unrooted trees. When tested on trees analyzed in the literature, NOTUNG consistently yielded results that agree with the assessments in the original publications. Thus, NOTUNG provides a basic building block for inferring duplication dates from gene trees automatically and can also be used as an exploratory analysis tool for evaluating alternative hypotheses.
Trophic network structure emerges through antagonistic coevolution in temporally varying environments

Understanding the mechanisms underlying ecological specialization is central to our understanding of community ecology and evolution. Although theoretical work has investigated how variable environments may affect specialization in single species, little is known about how such variation impacts bipartite network structure in antagonistically coevolving systems. Here, we develop and analyse a general model of victim–enemy coevolution that explicitly includes resource and population dynamics. We investigate how temporal environmental heterogeneity affects the evolution of specialization and associated community structure. Environmental productivity influences victim investment in resistance, which will shape patterns of specialization through its regulating effect on enemy investment in infectivity. We also investigate the epidemiological consequences of environmental variability and show that enemy population density is maximized for intermediate lengths of productive seasons, which corresponds to situations where enemies can evolve higher infectivity than victims can evolve defence. We discuss our results in the light of empirical studies, and further highlight ways in which our model applies to a range of natural systems.