Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards Unambiguous Edge Bundling: Investigating Confluent Drawings for Network Visualization

In this paper, we investigate Confluent Drawings (CD), a technique for bundling edges in node-link diagrams based on network connectivity. Edge-bundling techniques are designed to reduce edge clutter in node-link diagrams by coalescing lines into common paths or bundles. Unfortunately, traditional bundling techniques introduce ambiguity since edges are only bundled by spatial proximity, rather than network connectivity; following an edge from its source to its target can lead to the perception of incorrect connectivity if edges are not clearly separated within the bundles. Contrary, CDs bundle edges based on common sources or targets. Thus, a smooth path along a confluent bundle indicates precise connectivity. While CDs have been described in theory, practical investigation and application to real-world networks (i.e., networks beyond those with certain planarity restrictions) is currently lacking. Here, we provide the first algorithm for constructing CDs from arbitrary directed and undirected networks and present a simple layout method, embedded in a sand box environment providing techniques for interactive exploration. We then investigate patterns and artifacts in CDs, which we compare to other common edge-bundling techniques. Finally, we present the first user study that compares edge-compression techniques, including CD, power graphs, metro-style, and common edge bundling. We found that users without particular expertise in visualization or network analysis are able to read small CDs without difficulty. Compared to existing bundling techniques, CDs are more likely to allow people to correctly perceive connectivity.
A common variation in the promoter region of interleukin-6 gene shows association with exercise performance.

UNLABELLED Skeletal muscle-derived interleukin-6 (IL-6) is a pleiotropic cytokine which regulates body metabolism during strenuous physical exercise. OBJECTIVE The effect of a potentially functional single nucleotide polymorphism (SNP) -174G/C of the IL6 gene (rs1800795) promoter was examined on maximal oxygen uptake (VO2max), body mass index (BMI) and plasma IL-6 levels in response to physical training. Fifty four male military conscripts were studied for 8 weeks during their basic training. At weeks 1, 5 and 8, VO2max and anthropometrics were measured, and blood samples collected before and after acute aerobic exercise. Acute exercise increased plasma IL-6 in subjects with genotype CG. Moreover, during the 8-week training period, a tendency for increased plasma IL-6 was observed in subjects with this genotype. VO2max values increased in all genotype groups, but subjects with genotype CG made the greatest gains in VO2max. Training significantly decreased BMI only in subjects with genotype CG. Our findings suggest that the allele C may have an effect on plasma IL-6 response to acute exercise in healthy male subjects. Exercise training has a favourable effect on VO2max and BMI, with the most prominent effects in subjects with genotype CG. Thus we conclude that this SNP may account for individual response to exercise training. Key pointsAllele C of the IL6 promoter SNP -174G/C may have an effect on plasma IL-6 response to acute exercise.All subjects responded to physical exercise, but the improvement in VO2max and decrease in BMI after training are more pronounced in the individuals with genotype CG, hence the IL6 promoter SNP -174G/C may have an influence on training responses.The small number of subjects investigated in the present study warrants further research to confirm these findings in large cohorts.
Hardware-software cosynthesis for digital systems

As system design grows increasingly complex, the use of predesigned components, such as general-purpose microprocessors can simplify synthesized hardware. While the problems in designing systems that contain processors and application-specific integrated circuit chips are not new, computer-aided synthesis of such heterogeneous or mixed systems poses unique problems. The authors demonstrate the feasibility of synthesizing heterogeneous systems by using timing constraints to delegate tasks between hardware and software so that performance requirements can be met. System functionality is captured using the HardwareC hardware description language. The synthesis of an Ethernet-based network coprocessor is discussed as an example. <<ETX>>
On dimensions in emotion psychology

Is the study of the dimensional space that is meant to represent human emotions helpful in understanding the mechanisms underlying emotional processes? Emotional experience is frequently described along a certain number of dimensions, often including valence and arousal. This paper argues that dimensional models may obfuscate the mechanisms underlying the genesis of emotions. A parallel is drawn to dimensions of gustatory experience. Data are presented on the dimensional representation of taste, and compared with information about peripheral processing of basic tastes. While the obvious discrepancies might inspire more fascinating search for the next stage of gustatory processing, too little is known on basic emotional processing, in order to profit from a similar comparison.
Regulation of N-type voltage-gated calcium channels (Cav2.2) and transmitter release by collapsin response mediator protein-2 (CRMP-2) in sensory neurons

Collapsin response mediator proteins (CRMPs) mediate signal transduction of neurite outgrowth and axonal guidance during neuronal development. Voltage-gated Ca2+ channels and interacting proteins are essential in neuronal signaling and synaptic transmission during this period. We recently identified the presynaptic N-type voltage-gated Ca2+ channel (Cav2.2) as a CRMP-2-interacting partner. Here, we investigated the effects of a functional association of CRMP-2 with Cav2.2 in sensory neurons. Cav2.2 colocalized with CRMP-2 at immature synapses and growth cones, in mature synapses and in cell bodies of dorsal root ganglion (DRG) neurons. Co-immunoprecipitation experiments showed that CRMP-2 associates with Cav2.2 from DRG lysates. Overexpression of CRMP-2 fused to enhanced green fluorescent protein (EGFP) in DRG neurons, via nucleofection, resulted in a significant increase in Cav2.2 current density compared with cells expressing EGFP. CRMP-2 manipulation changed the surface levels of Cav2.2. Because CRMP-2 is localized to synaptophysin-positive puncta in dense DRG cultures, we tested whether this CRMP-2-mediated alteration of Ca2+ currents culminated in changes in synaptic transmission. Following a brief high-K+-induced stimulation, these puncta became loaded with FM4-64 dye. In EGFP and neurons expressing CRMP-2–EGFP, similar densities of FM-loaded puncta were observed. Finally, CRMP-2 overexpression in DRG increased release of the immunoreactive neurotransmitter calcitonin gene-related peptide (iCGRP) by ∼70%, whereas siRNA targeting CRMP-2 significantly reduced release of iCGRP by ∼54% compared with control cultures. These findings support a novel role for CRMP-2 in the regulation of N-type Ca2+ channels and in transmitter release.
A Semantic Kernel to Classify Texts with Very Few Training Examples

Web-mediated access to distributed information is a complex problem. Before any learning can start, Web objects (e.g. texts) have to be detected and flltered accurately. In this perspective, text categorization is a useful device to fllter out irrelevant evidence before other learning processes take place on huge sources of candidate information. The drawback is the need of a large number of training documents. One way to reduce such number relates to the use of more efiective document similarities based on prior knowledge. Unfortunately, previous work has shown that such information (e.g. WordNet) causes the decrease of retrieval accuracy. In this paper we propose kernel functions to add prior knowledge to learning algorithms for document classiflcation. Such kernels use a term similarity measure based on the WordNet hierarchy. The kernel trick is used to implement such space in a balanced and statistically coherent way. Cross-validation results show the beneflt of the approach for the Support Vector Machines when few training examples are available.
Multiple source shortest paths in a genus g graph

We give an <i>O</i>(<i>g</i><sup>2</sup><i>n</i>log <i>n</i>) algorithm to represent the shortest path tree from all the vertices on a single specified face <i>f</i> in a genus <i>g</i> graph. From this representation, any query distance from a vertex in <i>f</i> can be obtained in <i>O</i>(log <i>n</i>) time. The algorithm uses a kinetic data structure, where the source of the tree iteratively moves across edges in <i>f</i>. In addition, we give applications using these shortest path trees in order to compute the shortest non-contractible cycle and the shortest non-separating cycle embedded on an orientable 2-manifold in <i>O</i>(<i>g</i><sup>3</sup><i>n</i>log <i>n</i>) time.
Sporadic Campylobacter Infection in Infants: A Population-Based Surveillance Case-Control Study

Background: Campylobacter is an important cause of foodborne illness in infants (younger than 1 year of age), but little is known about the sources of infection in this age group. Methods: Eight sites in the Foodborne Diseases Active Surveillance Network (FoodNet) participated in a 24-month population-based case-control study conducted in 2002–2004. Cases were infants with laboratory-confirmed Campylobacter infection ascertained through active laboratory surveillance, and controls were infants in the community. Results: We enrolled 123 cases and 928 controls. Infants 0–6 months of age with Campylobacter infection were less likely to be breast-fed than controls [odds ratio (OR); 0.2; 95% confidence interval (CI), 0.1–0.6]. Risk factors for infants 0–6 months of age included drinking well water (OR 4.4; CI, 1.4–14) and riding in a shopping cart next to meat or poultry (OR 4.0; CI, 1.2–13.0). Risk factors for infants 7–11 months of age included visiting or living on a farm (OR 6.2; CI, 2.2–17), having a pet with diarrhea in the home (OR 7.6; CI, 2.1–28) and eating fruits and vegetables prepared in the home (OR 2.5, CI 1.2–4.9). Campylobacter infection was associated with travel outside the United States at all ages (OR 19.3; CI, 4.5–82.1). Conclusions: Several unique protective and risk factors were identified among infants, and these risk factors vary by age, suggesting that prevention measures be targeted accordingly. Breast-feeding was protective for the youngest infants and should continue to be encouraged.
Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens

Adaptation of pest species to laboratory conditions and selection for resistance to toxins in the laboratory are expected to cause inbreeding and genetic bottlenecks that reduce genetic variation. Heliothis virescens, a major cotton pest, has been colonized in the laboratory many times, and a few laboratory colonies have been selected for Bt resistance. We developed 350 bp Double-Digest Restriction-site Associated DNA-sequencing (ddRAD-seq) molecular markers to examine and compare changes in genetic variation associated with laboratory adaptation, artificial selection, and inbreeding in this non-model insect species. We found that allelic and nucleotide diversity declined dramatically in laboratory-reared H. virescens as compared with field-collected populations. The declines were primarily due to the loss of low frequency alleles present in field-collected H. virescens. A further, albeit modest decline in genetic diversity was observed in a Bt-selected population. The greatest decline was seen in H. virescens that were sib-mated for 10 generations, where more than 80% of loci were fixed for a single allele. To determine which regions of the genome were resistant to fixation in our sib-mated line, we generated a dense intraspecific linkage map containing 3 PCR-based, and 659 ddRAD-seq markers. Markers that retained polymorphism were observed in small clusters spread over multiple linkage groups, but this clustering was not statistically significant. Here, we confirmed and extended the general expectations for reduced genetic diversity in laboratory colonies, provided tools for further genomic analyses, and produced highly homozygous genomic DNA for future whole genome sequencing of H. virescens.
The University of Birmingham ( Live System ) Discrete Alterations of Brain Network Structural Covariance in Individuals at Ultra-High Risk for Psychosis

Background. Investigation of aberrant large-scale brain networks offers novel insight into the role these networks play in diverse psychiatric disorders, such as schizophrenia. While there are studies reporting altered functional brain connectivity in participants at ultra-high risk (UHR) for psychosis, it is unclear whether these alterations extend to structural brain networks. Methods. Whole-brain structural covariance patterns of 133 participants at UHR for psychosis (51 of whom subsequently developed psychosis) and 65 healthy controls (HC) were studied. Following data pre-processing (using VBM8), the mean signal in seed regions relating to specific networks (visual, auditory, motor, speech, semantic, executive, salience and default-mode) were extracted and voxel-wise analyses of covariance were conducted to compare the association between whole brain signal and each seed region for UHR and HC individuals. UHR participants who transitioned were compared to those who did not. Results. Significantly reduced structural covariance was observed in the UHR sample compared to HC for the default-mode network, and increased covariance for the motor and executive control networks. When those who transitioned to psychosis were compared with those who did not, aberrant structural covariance was observed in the salience, executive-control, auditory and motor networks.
Detecting Asthma Exacerbations in a Pediatric Emergency Department Using a Bayesian Network

OBJECTIVE To develop and evaluate a Bayesian network to identify patients eligible for an asthma-care guideline using only data available electronically at the time of patient triage. POPULATION Consecutive patients 2-18 years old who presented to a pediatric emergency department during a 2-month period. METHODS A network was developed and evaluated using clinical data from patient visits. An independent reference standard for asthma guideline eligibility was established and verified for each patient through chart review. Outcome measures were area under the receiver operating characteristic curve, sensitivity, specificity, predictive values, and likelihood ratios. RESULTS We enrolled 3,023 patient visits, including 385 who were eligible for guideline-based care. Area under the receiver operating curve for the network was 0.959 (95% CI = 0.933 - 0.977). At a fixed 90% sensitivity, specificity was 88.3%, positive predictive value was 44.7% and negative predictive value was 98.8%. The positive likelihood ratio was 7.69 and the negative likelihood ratio was 0.11. CONCLUSION The Bayesian network was able to detect patients eligible for an asthma guideline with high accuracy suggesting that this technique could be used to automatically initiate guideline use for eligible patients.
Feasibility of structural network clustering for group-based privacy control in social networks

Users of social networking sites often want to manage the sharing of information and content with different groups of people based on their differing relationships. However, grouping contacts places a significant configuration burden on the user. Automated approaches to grouping may have the potential to reduce this burden, however, their use remains largely untested. We investigate people's rationales when grouping their contacts for the purpose of controlling their privacy, finding six criteria that they commonly considered. We assess an automated approach to grouping, based on a network clustering algorithm, whose performance may be analogous to the human's use of some of these criteria. We find that the similarity between the groups created by people and those created by the algorithm is correlated with the modularity of their network. We also demonstrate that the particular clustering algorithm, SCAN, which detects hubs and outliers within a network can be beneficial for identifying contacts who are hard to group or for whom privacy preferences are inconsistent with the rest of their group.
Space, place and atmosphere. Emotion and peripherical perception in architectural experience

Architectural experiences are essentially multi-sensory and simultaneous, and a complex entity is usually grasped as an atmosphere, ambience or feeling. In fact, the judgement concerning the character of a space or place calls for categories of sensing that extend beyond the five Aristotelian senses, such as the embodied existential sense, and , as a result, the entity is perceived in a diffuse, peripheral and unconscious manner. Paradoxically, we grasp an atmosphere before we have consciously identified its constituent factors and ingredients. «We perceive atmospheres through our emotional sensibility – a form of perception that works incredibly quickly, and which we humans evidently need to help us survive», Peter Zumthor suggests. We are mentally and emotionally affected by works of art before we understand them, or we may not understand them intellectually at all. Sensitive artists and architects intuit experiential and emotive qualities of spaces, places and images. This capacity calls for a specific kind of imagination, an emphatic imagination . Atmospheres are percieved peripherally through diffuse vision interacting with other sense modalities, and they are experienced emotionally rather than intellectually. The studies on the differentiation of the two brain hemispheres suggest that atmospheres are perceived through the right hemisphere. Somewhat surprisingly, atmospheres are more conscious objectives in literature, cinema, theater, painting and music than in architecture, which has been traditionally approached formally and perceived primarily through focused vision. Yet, when we see a thing in focus, we are outsiders to it, whereas the experience of being in a space calls for peripheral and unfocused perception. One of the reasons for the experiential poverty of contemporary settings could be in the poverty of their peripheral stimuli.
Contravision: exploring users' reactions to futuristic technology

How can we best explore the range of users' reactions when developing future technologies that may be controversial, such as personal healthcare systems? Our approach -- ContraVision -- uses futuristic videos, or other narrative forms, that convey either negative or positive aspects of the proposed technology for the same scenarios. We conducted a user study to investigate what range of responses the different versions elicited. Our findings show that the use of two systematically comparable representations of the same technology can elicit a wider spectrum of reactions than a single representation can. We discuss why this is so and the value of obtaining breadth in user feedback for potentially controversial technologies.
ReviewBiomarkers in Breath Condensate: A promising New Non-invasive Technique in Free Radical Research

Oxidative stress is associated with a range of inflammatory lung diseases including asthma, adult respiratory distress syndrome, idiopathic pulmonary fibrosis, pneumonia, lung transplantation, chronic obstructive pulmonary disease, cystic fibrosis, bronchiectasis and lung cancer. Increased concentrations of reactive oxygen species (ROS) in the airways of such patients are reflected by elevated concentrations of oxidative stress markers in the breath, airways, lung tissue and blood. Traditionally, the measurement of these biomarkers has involved invasive procedures to procure the samples, or examine the compartments. As a consequence, there is a need for less invasive approaches to measure oxidative stress. Analysis of breath hydrocarbons has partly fulfilled this need, however only gas phase volatile constituents can be assessed by this approach. The collection of exhaled breath condensate (EBC) is a simple, non-invasive approach, which comprehensively samples the lower respiratory tract. It is currently used as a research and diagnostic tool in the free radical field, yielding information on redox disturbance and the degree and type of inflammation in the lung. With further technical developments, such an approach may ultimately have a role in the clinic, in helping to diagnose specific lung diseases. EBC can be exploited to assess a spectrum of potential biomarkers, thus generating a “finger print” characteristic of the disease. By assessing the nature of oxidative stress in this manner, the most appropriate therapy can be selected and the response to treatment monitored.
Chameleon: a software infrastructure for adaptive fault tolerance

This paper presents Chameleon, an adaptive software infrastructure for concurrently supporting different reliability levels in the same networked environment. Traditionally, fault tolerance has been provided through dedicated hardware, dedicated software, or a combination of both. Hardware solutions from manufacturers like Tandem have provided dedicated fault-tolerant machines with extensive hardware redundancy. Unfortunately, such solutions offer static levels of fault tolerance that remain fixed throughout the lifetime of the system. Software solutions, employed in distributed environments, involve replication of services in software to provide the requisite reliability level. However, to benefit from such solutions, applications need to be written with an intent to run in such an environment. Therefore, the benefits of such middleware go unnoticed to off-the-shelf applications. In contemporary networked computing systems, a broad range of commercial and scientific applications, with potentially varying reliability requirements, need to coexist. It is neither cost effective nor feasible to provide dedicated platforms for hardware-based fault tolerance for each application, or to rewrite each application to leverage off the specialized software middleware. We propose Chameleon as an infrastructure to provide adaptive levels of dependability to off-the-shelf applications with off-the-shelf unreliable hardware.
Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors

Beyond its role in genomic organization and compaction, the nucleosome is believed to participate in the regulation of gene transcription. Here, we report a computational method to evaluate the nucleosome sensitivity for a transcription factor over a given stretch of the genome. Sensitive factors are predicted to be those with binding sites preferentially contained within nucleosome boundaries and lacking 10 bp periodicity. Based on these criteria, the Acute Myeloid Leukemia-1a (AML-1a) transcription factor, a regulator of immune gene expression, was identified as potentially sensitive to nucleosomal regulation within the mouse Ly49 gene family. This result was confirmed in RMA, a cell line with natural expression of Ly49, using MNase-Seq to generate a nucleosome map of chromosome 6, where the Ly49 gene family is located. Analysis of this map revealed a specific depletion of nucleosomes at AML-1a binding sites in the expressed Ly49A when compared to the other, silent Ly49 genes. Our data suggest that nucleosome-based regulation contributes to the expression of Ly49 genes, and we propose that this method of predicting nucleosome sensitivity could aid in dissecting the regulatory role of nucleosomes in general.