Miracle-dz/UniFAR-FTUs huggingface dataset:
Behavioural concern modelling for software change tasks

Many modification tasks on an existing software system result in changes to code that crosscuts the system's structure. Making these changes is difficult because a developer must understand large parts of the system, and must reason about how the modification will interact with the existing behaviour. Typically, developers make these kinds of changes using an ad-hoc approach with tools that help in gaining some understanding of the existing system, but that do not provide any specific support for reasoning about, implementing, or analyzing just that part of the system related to the modification. We present the behavioural concern modelling (BCM) approach and tool that provide direct support for a systematic approach to modification tasks. This approach enables a developer to create a partial, abstract, grounded behavioural model of a concern(s). By grounded, we mean that the relationship between the model and the code is explicit: A developer describes which code contributes to which parts of the model. The examples we describe use a finite state machine as a model. We show how the approach can help a developer capture a concern, reason about design options, and implement modifications.
A Neostriatal Habit Learning System in Humans

Amnesic patients and nondemented patients with Parkinson's disease were given a probabilistic classification task in which they learned which of two outcomes would occur on each trial, given the particular combination of cues that appeared. Amnesic patients exhibited normal learning of the task but had severely impaired declarative memory for the training episode. In contrast, patients with Parkinson's disease failed to learn the probabilistic classification task, despite having intact memory for the training episode. This double dissociation shows that the limbic-diencephalic regions damaged in amnesia and the neostriatum damaged in Parkinson's disease support separate and parallel learning systems. In humans, the neostriatum (caudate nucleus and putamen) is essential for the gradual, incremental learning of associations that is characteristic of habit learning. The neostriatum is important not just for motor behavior and motor learning but also for acquiring nonmotor dispositions and tendencies that depend on new associations.
Long‐term exposure to histamine induces the expression of an embryonic‐like motor pattern in an adult nervous system

Neuromodulatory inputs play important roles in shaping the outputs of neural networks. While the actions of neuromodulatory substances over the short term (seconds, minutes) have been examined in detail, far less is known about the possible longer‐term (hours) effects of these substances. To investigate this issue, we used the stomatogastric nervous system (STNS) of the lobster to examine the short‐ and long‐term effects of histamine on rhythmic network activity. The application of histamine to the entire STNS had strong inhibitory effects on all three of the STNS networks, observable within minutes. In contrast, longer‐term (> 1 h) application of histamine induced the expression of a single, unified rhythm involving neurons from all three networks. Selective application of histamine to different regions of the STNS demonstrated that a unified rhythm arises following the long‐term application of histamine to the commissural ganglia (CoGs; modulatory centres), but not the stomatogastric ganglion (site of neural networks). Strikingly, the single rhythm observed following the long‐term application of histamine to the CoGs exhibits many similarities with the single rhythm expressed by the embryonic STNS. Together, these results demonstrate that histamine has markedly different short‐ and long‐term effects on network activity; short‐term effects arising through direct actions on the networks and long‐term effects mediated by actions on modulatory neurons. Furthermore, they indicate that histamine is able to induce the expression of an embryonic‐like rhythm in an adult system, suggesting that long‐term actions of histamine may play key roles in the development of the STNS networks.
Validity in Image‐based Research: an elaborated illustration of the issues

This article is concerned with the trustworthiness of products of research which are derived from image-based data. Fundamentally it asks whether validity represents an appropriate measure of the quality of research which uses such data. Two examples of image-based research are taken from recent work undertaken by the authors. A comparison of these examples provides a well-grounded illustration of the issues confronted by the researchers in their attempt to consider the validity of their findings. The resulting discussion develops the argument that the concept of validity is particularly problematic in its application to image-based research. We present a tentative strategy for ensuring trustworthiness that is based on five key criteria: completeness, adequacy of interpretation, transparency, self-reflection and the aggregation of conflicting interpretations.
Crypto-Book: Bootstrapping Privacy Preserving Online Identities from Social Networks

Social networking sites supporting federated identities offer a convenient and increasingly popular mechanism for cross-site authentication. Unfortunately, they also exacerbate many privacy and tracking risks. We propose Crypto-Book, an anonymizing layer enabling cross-site authentication while reducing these risks. Crypto-Book relies on a set of independently managed servers that collectively assign each social network identity a public/private keypair. Only an identity's owner learns all the private key shares, and can therefore construct the private key, while all participants can obtain any user's public key, even if the corresponding private key has yet to be retrieved. Having obtained an appropriate key set, a user can then leverage anonymous authentication techniques such as linkable ring signatures to log into third-party web sites while preserving privacy. We have implemented a prototype of Crypto-Book and demonstrate its use with three applications: a Wiki system, an anonymous group communication system, and a whistleblower submission system. Our results show that for anonymity sets of size 100, Crypto-Book login takes 0.56s for signature generation by the client, 0.38s for signature verification on the server, and requires 5.6KB of communication bandwidth.
Guided Imagery and Relaxation for Women with Early Stage Breast Cancer

Abstract Fifty-two women with Stage I and Stage II breast cancer agreed to participate in a study to determine the effectiveness of two interventions, guided imagery and relaxation, to enhance psychological well-being. Participants were randomly assigned to either a guided imagery or relaxation group. Forty women completed the study. A student's t-test was used to analyze the quantitative results. Depression, anxiety and fatigue were significantly improved for the guided imagery group. There were no changes reported by the relaxation group. Women in both groups reportedly enjoyed the experience, found it helpful, and would recommend it to others. The majority of the women in both groups perceived that the treatment helped them to relax.
Decreased WWOX expression promotes angiogenesis in osteosarcoma

WWOX (WW domain-containing oxidoreductase) is known to be an important tumor suppressor in cancer. In this study, we used samples from 201 osteosarcoma patients to investigate the effects of WWOX on angiogenesis and invasion. WWOX levels were negatively correlated with RUNX2 and VEGF levels, but were not correlated with OPN levels. Among the clinicopathological characteristics examined, WWOX was associated only with response to neoadjuvant chemotherapy, and its expression in osteosarcoma tissues was a predictor of disease-free survival. WWOX promoted apoptosis and inhibited invasion and expression of bcl-2, OPN, RUNX2, and VEGF in osteosarcoma cells in vitro. In MG-63 cells, bcl-2 increased VEGF expression, while RUNX2 increased VEGF and OPN expression. Administration of DNA methylation inhibitors increased WWOX expression in MG-63 cells and methylation of WWOX gene promoter CpG island in the osteosarcoma of patients was associated with suppression of WWOX expression. Overexpression of WWOX in osteosarcoma cells inhibited tube formation in co-cultured HUVEC cells, and high WWOX expression was associated with decreased microvessel density (MVD). These results suggest that reduced WWOX expression in osteosarcoma inhibits apoptosis, promotes invasion and increases MVD.
Genomic drift and copy number variation of chemosensory receptor genes in humans and mice

Recent studies about the structural variation of genomic sequences have shown that there is a large amount of copy number variations (CNVs) of genes within species. Analyzing Redon et al.’s (2006) crude data on copy number variable regions (CNVRs), we previously showed that CNVs are particularly high for chemosensory receptor genes in human populations. In this paper, we reanalyzed the CNVs of these genes using more refined data by Perry et al. (2008). The results showed that the extent of CNVs is somewhat lower in this dataset than in the previous one, but that the extent is still substantial for olfactory receptor (OR), vomeronasal receptor (VR), and taste receptor (TR) genes. We also studied the CNVs for chemosensory receptor genes in mice, using CNVR data obtained from inbred strains. It was found that the extent of CNVs is quite substantial but is lower than that for human populations. However, because the mouse data came from inbred strains and might be biased, this conclusion should be regarded as tentative. Despite this reservation, the distribution of gene copy number for the OR gene family was approximately normal in both humans and mice, suggesting that genomic drift caused by random duplication and deletion of genes plays important roles in determining the evolutionary change of chemosensation.
Structure and motion from scene registration

We propose a method for estimating the 3D structure and the dense 3D motion (scene flow) of a dynamic nonrigid 3D scene, using a camera array. The core idea is to use a dense multi-camera array to construct a novel, dense 3D volumetric representation of the 3D space where each voxel holds an estimated intensity value and a confidence measure of this value. The problem of 3D structure and 3D motion estimation of a scene is thus reduced to a nonrigid registration of two volumes - hence the term ”Scene Registration”. Registering two dense 3D scalar volumes does not require recovering the 3D structure of the scene as a preprocessing step, nor does it require explicit reasoning about occlusions. From this nonrigid registration we accurately extract the 3D scene flow and the 3D structure of the scene, and successfully recover the sharp discontinuities in both time and space. We demonstrate the advantages of our method on a number of challenging synthetic and real data sets.
Recurrent Exposure to Subclinical Lipopolysaccharide Increases Mortality and Induces Cardiac Fibrosis in Mice

Background Circulating subclinical lipopolysaccharide (LPS) occurs in health and disease. Ingesting high fatty meals increases LPS that cause metabolic endotoxemia. Subclinical LPS in periodontal disease may impair endothelial function. The heart may be targeted as cardiac cells express TLR4, the LPS receptor. It was hypothesized that recurrent exposure to subclinical LPS increases mortality and causes cardiac fibrosis. Methods C57Bl/6 mice were injected with intraperitoneal saline (control), low dose LPS (0.1 or 1 mg/kg), or moderate dose LPS (10 or 20 mg/kg), once a week for 3 months. Left ventricular (LV) function (echocardiography), hemodynamics (tail cuff pressure) and electrocardiograms (telemetry) were measured. Cardiac fibrosis was assessed by picrosirius red staining and LV expression of fibrosis related genes (QRT-PCR). Adult cardiac fibroblasts were isolated and exposed to LPS. Results LPS injections transiently increased heart rate and blood pressure (<6 hours) and mildly decreased LV function with full recovery by 24 hours. Mice tolerated weekly LPS for 2–3 months with no change in activity, appearance, appetite, weight, blood pressure, LV function, oximetry, or blood chemistries. Mortality increased after 60–90 days with moderate, but not low dose LPS. Arrhythmias occurred a few hours before death. LV collagen fraction area increased dose-dependently from 3.0±0.5% (SEM) in the saline control group, to 5.6±0.5% with low dose LPS and 9.7±0.9% with moderate dose LPS (P<0.05 moderate vs low dose LPS, and each LPS dose vs control). LPS increased LV expression of collagen Iα1, collagen IIIα1, MMP2, MMP9, TIMP1, periostin and IL-6 (P<0.05 moderate vs low dose LPS and vs control). LPS increased α-SMA immunostaining of myofibroblasts. LPS dose-dependently increased IL-6 in isolated adult cardiac fibroblasts. Conclusions Recurrent exposure to subclinical LPS increases mortality and induces cardiac fibrosis.
The concept of process management

Presents a conceptual framework for process management of groups involved in action learning and action research. Discusses propositional, practical and experiential learning; and the concept of meta‐learning (learning to learn) in relation to the “learning organisation”. Presents a model of process management that concerns people and process, with implications for research in industry, government and higher education.
Consumers' preference shifts under the deletion of common features with varying attractiveness: An examination of competing explanations

When necessary, marketers might delete common features of a promotional package that have also been deleted by competitors. This research examined two hypotheses of how the deletion of common features of varying attractiveness affects consumers’ prior preferences. When participants were informed that a common feature of their available choices was unavailable, their preference decreased relatively for one alternative compared with another alternative. This effect was not contingent on the deleted feature’s attractiveness. The findings reveal that the deletion of common features tends to motivate consumers to disregard the overall utility of the prior preferred option rather than to activate confirmatory reasoning for consolidating a previous choice. Thus, by deleting common features of a promotional package, marketers risk altering consumers’ prior preferences and may lose their advantage over competitors. © 2008 Wiley Periodicals, Inc. Marketing in the service industry has become quite competitive, and almost every company offers promotional packages with flexible strategies to satisfy the dynamic needs of consumers. Promotions often change
Optimal multiband spectrum sensing in cognitive radio

In order to maximize the throughput in cognitive radio when primary communication system is an OFDM system, the optimal spectrum sensing is addressed. Firstly the single user sensing is discussed, and it is proved that the optimal sensing time that maximizes the throughput exists. In addition, the cooperative sensing using k-out-of-N fusion rule is considered. By analyzing the mathematical model of the throughput, a joint searching method is proposed to obtain the optimal sensing time and fusion rules which can maximize the throughput. In the simulation results, the correctness of theoretical analysis is verified.
Evaluating the Performance of DEEC Variants

Wireless Sensor Networks (WSNs) have many sensor nodes having restricted battery power, which transmit sensed data to the Base Station that needs high energy consumption. Numerous routing protocols have been proposed in this regard getting energy efficiency in heterogeneous situations. Though, each protocol is inappropriate for heterogeneous WSNs. Efficiency of WSNs declines as varying the heterogeneity of sensor nodes. This paper has evaluated the performance of various Distributed EnergyEfficient Clustering based protocols like DEEC, DDEEC, EDEEC, HDEEC, EDDEEC and TDEEC under numerous scenarios; comprising various level of heterogeneity. MATLAB tool is used for experimental purpose. The comparison has shown that the EDDEEC has very effective results over other DEEC variants due to its special feature of T-absolute i.e. it treats all heterogeneous sensor nodes with same election probability when each node has lesser energy than T-absolute.
Mitochondrial Disease in Autism Spectrum Disorder Patients: A Cohort Analysis

Background Previous reports indicate an association between autism spectrum disorders (ASD) and disorders of mitochondrial oxidative phosphorylation. One study suggested that children with both diagnoses are clinically indistinguishable from children with idiopathic autism. There are, however, no detailed analyses of the clinical and laboratory findings in a large cohort of these children. Therefore, we undertook a comprehensive review of patients with ASD and a mitochondrial disorder. Methodology/Principal Findings We reviewed medical records of 25 patients with a primary diagnosis of ASD by DSM-IV-TR criteria, later determined to have enzyme- or mutation-defined mitochondrial electron transport chain (ETC) dysfunction. Twenty-four of 25 patients had one or more major clinical abnormalities uncommon in idiopathic autism. Twenty-one patients had histories of significant non-neurological medical problems. Nineteen patients exhibited constitutional symptoms, especially excessive fatigability. Fifteen patients had abnormal neurological findings. Unusual developmental phenotypes included marked delay in early gross motor milestones (32%) and unusual patterns of regression (40%). Levels of blood lactate, plasma alanine, and serum ALT and/or AST were increased at least once in 76%, 36%, and 52% of patients, respectively. The most common ETC disorders were deficiencies of complex I (64%) and complex III (20%). Two patients had rare mtDNA mutations of likely pathogenicity. Conclusions/Significance Although all patients' initial diagnosis was idiopathic autism, careful clinical and biochemical assessment identified clinical findings that differentiated them from children with idiopathic autism. These and prior data suggest a disturbance of mitochondrial energy production as an underlying pathophysiological mechanism in a subset of individuals with autism.
Stigma and Genetic Risk: Perceptions of Stigma among Those at Risk for Huntington Disease (HD)

Advances in molecular genetics raise concerns about the potential for stigmatization of people at risk for genetic disorders. However, minimal research explores stigma from the perspective of people who live with genetic risk. Drawing upon 24 semi-structured interviews with at-risk people and their family members, this study explored perceptions of stigma in the context of Huntington disease (HD), a fatal genetic illness. Qualitative data analysis revealed four perceptions of stigma: 1) sympathy, not stigma, 2) genetic discrimination, 3) enacted stigma, and 4) dismissing stigma – ignorant others. While social others were often sympathetic towards at risk people and their affected relatives, instances of stigma were recounted in employment, insurance, clinical and social contexts. Visible HD symptomatology was a significant factor in stigma perception, and caregivers of people with HD were most likely to recount experiences with stigma. Findings suggest that both pre-test genetic counseling sessions and follow-up contact with clients include a discussion of stigma. Additionally, caregivers of people with HD might be a unique research or clinical group in the context of stigma and genetic risk.
Chill-inducing music enhances altruism in humans

Music is a universal feature of human cultures, and it has both fascinated and troubled many researchers. In this paper we show through the dictator game (DG) that an individual’s listening to preferred “chill-inducing” music may promote altruistic behavior that extends beyond the bounds of kin selection or reciprocal altruism. Participants were 22 undergraduate and postgraduate students who were divided into two groups, the in-group and the out-group, and they acted as dictators. The dictators listened to their own preferred “chill-inducing” music, to music they disliked, or to silence, and then played the DG. In this hypothetical experiment, the dictators were given real money (which they did not keep) and were asked to distribute it to the recipients, who were presented as stylized images of men and women displayed on a computer screen. The dictators played the DG both before and after listening to the music. Both male and female dictators gave more money after listening to their preferred music and less after listening to the music they disliked, whereas silence had no effect on the allocated amounts. The group to which the recipient belonged did not influence these trends. The results suggest that listening to preferred “chill-inducing” music promotes altruistic behavior.
Inactivation of Tbx1 in the pharyngeal endoderm results in 22q11DS malformations

The 22q11 deletion (22q11DS; velo-cardio-facial syndrome/DiGeorge syndrome) is characterized by defects in the derivatives of the pharyngeal apparatus. Mouse genetic studies have identified Tbx1, a member of the T-box family of transcription factors, as being responsible for the physical malformations of the syndrome. Mice heterozygous for a null mutation in Tbx1 have mild anomalies, whereas homozygous Tbx1 mutants die at birth with severe defects in the derivatives of the pharyngeal apparatus, including cleft palate, thymus gland aplasia and cardiac outflow tract malformations. Tbx1 is expressed in the splanchnic mesenchyme, the pharyngeal endoderm (PE) and in the core mesoderm of the pharyngeal apparatus. Tissue interactions between the epithelia and mesenchyme of the arches are required for development of the pharyngeal apparatus; the precise role of Tbx1 in each tissue is not known. To assess the role of Tbx1 in the PE, a conditional allele of Tbx1 was generated using the Cre/loxP system. Foxg1-Cre was used to drive PE-specific ablation of Tbx1. Conditional null mutants survived embryogenesis, but died in the neonatal period with malformations identical to the defects observed in Tbx1 homozygous null mutants. The abnormalities appear to be secondary to failed outgrowth of the pharyngeal pouches. These results show that Tbx1 in the PE is required for the patterning and development of the pharyngeal apparatus, thereby disrupting the formation of its derivative structures.