Miracle-dz/UniFAR-FTUs huggingface dataset:
Harnessing Multiple Source Test Cases in Metamorphic Testing: A Case Study in Bioinformatics

Metamorphic testing (MT) has been applied to software verification, validation and quality assessment. In mostprevious studies, research has focused on deriving metamorphic relations (MRs) such that the input of one or more follow-up testcases is generated from one source test case. We note that some programs under test (PUT) naturally take multiple inputs andprocess them simultaneously to generate multiple outputs. This type of programs are common in the field of big data analysisand bioinformatics. This means, in the source execution of the program, we can obtain multiple outputs from multiple sourcetest cases. Here we consider a type of MR in which multiple follow-up test cases are generated from multiple source testcases simultaneously. We hypothesise that harnessing the outputs from multiple source test cases enables us to obtain additionalinformation about the PUT, and therefore allows us to construct more effective MRs. In this paper, we designed a new MR to testa popular RNA sequence alignment program. Since the MR was designed based on a desirable property of the PUT (which usesa complex heuristic algorithm) rather than a necessary property, violation of this MR indicates the program outputs deviate fromuser expectation, hence this MR can be used for assessing the quality of the outputs. Furthermore, we note that outputs ofthe follow-up test cases allow us to putatively assign alignment information to some sequences that were not aligned in the sourcetest cases, hence potentially identifying and correcting these 'false negative' outputs. We believe this case study provides importantinsight into designing MRs based on multiple source test cases, and how testing results can be used to improve the performanceof some heuristic-based programs.
Review of Context Aware Access Control Approaches on Web Data

st century is the age of netizens. Internet has become a source of knowledge and platform for social media. Social networking sites have gained huge momentum among all age groups and the popularity has attracted users to devote hours on social networking and contributing to a huge repository of information at every minute. Privacy of this information becomes a critical function of the database. Since personal information of the user is subject to cyber crimes therefore, database level privacy is a fundamental requirement to protect the data. The rapid growth of web on the basis of applications and information system have farther expanded the risk exposure of databases and therefore, nowadays data protection is more important than previous. It is more significant to safeguard data not only from external intruders but also internal intruders. In this paper the various access control scheme and its models to attain the confidentiality, integrity and possibility of objectives of database security in the organization are discussed.
Featured CME Topic: Spirituality Religious Involvement and Adult Mortality in the United States: Review and Perspective

Results: Taken together, the existing research indicates that religious involvement is related to US adult mortality risks. The evidence is strongest for public religious attendance and across specific religious denominations. The evidence is weakest for private religious activity. The mechanisms by which religious involvement appear to influence mortality include aspects of social integration, social regulation, and psychological resources.
The High Prevalence and Diversity of Chlamydiales DNA within Ixodes ricinus Ticks Suggest a Role for Ticks as Reservoirs and Vectors of Chlamydia-Related Bacteria

ABSTRACT The Chlamydiales order is composed of nine families of strictly intracellular bacteria. Among them, Chlamydia trachomatis, C. pneumoniae, and C. psittaci are established human pathogens, whereas Waddlia chondrophila and Parachlamydia acanthamoebae have emerged as new pathogens in humans. However, despite their medical importance, their biodiversity and ecology remain to be studied. Even if arthropods and, particularly, ticks are well known to be vectors of numerous infectious agents such as viruses and bacteria, virtually nothing is known about ticks and chlamydia. This study investigated the prevalence of Chlamydiae in ticks. Specifically, 62,889 Ixodes ricinus ticks, consolidated into 8,534 pools, were sampled in 172 collection sites throughout Switzerland and were investigated using pan-Chlamydiales quantitative PCR (qPCR) for the presence of Chlamydiales DNA. Among the pools, 543 (6.4%) gave positive results and the estimated prevalence in individual ticks was 0.89%. Among those pools with positive results, we obtained 16S rRNA sequences for 359 samples, allowing classification of Chlamydiales DNA at the family level. A high level of biodiversity was observed, since six of the nine families belonging to the Chlamydiales order were detected. Those most common were Parachlamydiaceae (33.1%) and Rhabdochlamydiaceae (29.2%). “Unclassified Chlamydiales” (31.8%) were also often detected. Thanks to the huge amount of Chlamydiales DNA recovered from ticks, this report opens up new perspectives on further work focusing on whole-genome sequencing to increase our knowledge about Chlamydiales biodiversity. This report of an epidemiological study also demonstrates the presence of Chlamydia-related bacteria within Ixodes ricinus ticks and suggests a role for ticks in the transmission of and as a reservoir for these emerging pathogenic Chlamydia-related bacteria.
Sentiment classification of online political discussions: a comparison of a word-based and dependency-based method

Online political discussions have received a lot of attention over the past years. In this paper we compare two sentiment lexicon approaches to classify the sentiment of sentences from political discussions. The first approach is based on applying the number of words between the target and the sentiment words to weight the sentence sentiment score. The second approach is based on using the shortest paths between target and sentiment words in a dependency graph and linguistically motivated syntactic patterns expressed as dependency paths. The methods are tested on a corpus of sentences from online Norwegian political discussions. The results show that the method based on dependency graphs performs significantly better than the word-based approach.
Family Physician Involvement in Cancer Care Follow-up: The Experience of a Cohort of Patients With Lung Cancer

PURPOSE There has been little research describing the involvement of family physicians in the follow-up of patients with cancer, especially during the primary treatment phase. We undertook a prospective longitudinal study of patients with lung cancer to assess their family physician’s involvement in their follow-up at the different phases of cancer. METHODS In 5 hospitals in the province of Quebec, Canada, patients with a recent diagnosis of lung cancer were surveyed every 3 to 6 months, whether they had metastasis or not, for a maximum of 18 months, to assess aspects of their family physician’s involvement in cancer care. RESULTS Of the 395 participating patients, 92% had a regular family physician but only 60% had been referred to a specialist by him/her or a colleague for the diagnosis of their lung cancer. A majority of patients identified the oncology team or oncologists as mainly responsible for their cancer care throughout their cancer journey, except at the advanced phase, where a majority attributed this role to their family physician. At baseline, only 16% of patients perceived a shared care pattern between their family physician and oncologists, but this proportion increased with cancer progression. Most patients would have liked their family physician to be more involved in all aspects of cancer care. CONCLUSIONS Although patients perceive that the oncology team is the main party responsible for the follow-up of their lung cancer, they also wish their family physicians to be involved. Better communication and collaboration between family physicians and the oncology team are needed to facilitate shared care in cancer follow-up.
Enhancing Metagenomics Investigations of Microbial Interactions with Biofilm Technology

Investigations of microbial ecology and diversity have been greatly enhanced by the application of culture-independent techniques. One such approach, metagenomics, involves sample collections from soil, water, and other environments. Extracted nucleic acids from bulk environmental samples are sequenced and analyzed, which allows microbial interactions to be inferred on the basis of bioinformatics calculations. In most environments, microbial interactions occur predominately in surface-adherent, biofilm communities. In this review, we address metagenomics sampling and biofilm biology, and propose an experimental strategy whereby the resolving power of metagenomics can be enhanced by incorporating a biofilm-enrichment step during sample acquisition.
Estrogen increases synaptic connectivity between single presynaptic inputs and multiple postsynaptic CA1 pyramidal cells: A serial electron-microscopic study

Dendritic spines are sites of the vast majority of excitatory synaptic input to hippocampal CA1 pyramidal cells. Estrogen has been shown to increase the density of dendritic spines on CA1 pyramidal cell dendrites in adult female rats. In parallel with increased spine density, estrogen has been shown also to increase the number of spine synapses formed with multiple synapse boutons (MSBs). These findings suggest that estrogen-induced dendritic spines form synaptic contacts with preexisting presynaptic boutons, transforming some previously single synapse boutons (SSBs) into MSBs. The goal of the current study was to determine whether estrogen-induced MSBs form multiple synapses with the same or different postsynaptic cells. To quantify same-cell vs. different-cell MSBs, we filled individual CA1 pyramidal cells with biocytin and serially reconstructed dendrites and dendritic spines of the labeled cells, as well as presynaptic boutons in synaptic contact with labeled and unlabeled (i.e., different-cell) spines. We found that the overwhelming majority of MSBs in estrogen-treated animals form synapses with more than one postsynaptic cell. Thus, in addition to increasing the density of excitatory synaptic input to individual CA1 pyramidal cells, estrogen also increases the divergence of input from individual presynaptic boutons to multiple postsynaptic CA1 pyramidal cells. These findings suggest the formation of new synaptic connections between previously unconnected hippocampal neurons.
Linearity analysis on a series-split capacitor array for high-speed SAR ADCs

A novel capacitor array structure for successive approximation register (SAR) ADC is proposed. This circuit efficiently utilizes charge recycling to achieve high-speed of operation and it can be applied to high-speed and low-to-medium-resolution SAR ADC. The static linearity performance, namely the INL and DNL, of the proposed structure is theoretically analyzed and behavioral simulations are performed to demonstrate its effectiveness. Simulation results show that to achieve the same conversion performance the proposed capacitor array structure can reduce the average power consumed from the reference ladder by 90%, as compared to the binary-weighted splitting capacitor array structure.
EFFECTS OF DIFFERENT LEVELS OF INBREEDING ON PROGENY FITNESS IN PLANTAGO CORONOPUS

Inbreeding depression (δ) is a major selective force favoring outcrossing in flowering plants. Many phenotypic and genetic models of the evolution of selfing conclude that complete outcrossing should evolve whenever inbreeding depression is greater than one‐half, otherwise selfing should evolve. Recent theoretical work, however, has challenged this view and emphasized (1) the importance of variation in inbreeding depression among individuals within a population; and (2) the nature of gene action between deleterious mutations at different loci (epistasis) as important determinants for the evolution of plant mating systems. The focus of this study was to examine the maintenance of inbreeding depression and the relationship between inbreeding level and inbreeding depression at both the population and the individual level in one population of the partially self‐fertilizing plant Plantago coronopus (L.). Maternal plants, randomly selected from an area of about 50 m2 in a natural population, were used to establish lines with expected inbreeding coefficients (f) of 0, 0.25, 0.50, 0.75, and 0.875. Inbreeding depression was estimated both in the greenhouse and at the site of origin of the maternal plants by comparing growth, survival, flowering, and seed production of the progeny with different inbreeding coefficients. No significant inbreeding depression for these fitness traits was detected in the greenhouse after 16 weeks. This was in strong contrast to the field, where the traits all displayed significant inbreeding depression and declined with increased inbreeding. The results were consistent with the view that mutation to mildly deleterious alleles is the primary cause of inbreeding depression. At the family level, significantly different maternal line responses (maternal parent × inbreeding level interaction) provide a mechanism for the invasion of a selfing variant into the population through any maternal line exhibiting purging of its genetic load. At the population level, evidence for synergistic epistasis was detected for the probability of flowering, but not for total seed production. At the family level, however, a significant interaction between inbreeding level and maternal families for both traits was observed, indicating that epistasis could play a role in the expression of inbreeding depression among maternal lines.
Identification and Characterization of a Chitin-binding Protein Purified from Coelomic Fluid of the Lugworm Arenicola marina Defining a Novel Protein Sequence Family*

Background: The immune system of the lugworm depends solely on innate pattern recognition molecules. Results: AML-1 was isolated from the coelomic fluid, cloned and characterized as a pattern recognition receptor that binds chitin. Conclusion: AML-1 is the first polychaete lectin cloned and characterized. Significance: AML-1 represents a novel protein sequence family that may give rise to a new protein structure. We have isolated a novel type of lectin named Arenicola marina lectin-1 (AML-1) from the lugworm A. marina. The lectin was purified from the coelomic fluid by affinity chromatography on a GlcNAc-derivatized column and eluted with GlcNAc. On SDS-PAGE, AML-1 showed an apparent molecular mass of 27 and 31 kDa in the reduced state. The N-terminal amino acid sequences were identical in these two bands. In the unreduced state, a complex band pattern was observed with bands from 35 kDa to more than 200 kDa. Two different full-length clones encoding polypeptides of 241 and 243 amino acids, respectively, were isolated from a coelomocyte cDNA library. The two clones, designated AML-1a and AML-1b, were 92% identical at the protein level and represent a novel type of protein sequence family. Purified AML-1 induced agglutination of rabbit erythrocytes, which could be inhibited by N-acetylated saccharides. Recombinant AML-1b showed the same band pattern as the native protein, whereas recombinant AML-1a in the reduced state lacked a 27 kDa band. AML-1b bound GlcNAc-derivatized columns and chitin, whereas AML-1a did not bind to these matrices. Immunohistochemical analysis revealed that AML-1 is expressed by coelomocytes in the nephridium and in round cells in the epidermis and in eggs. Moreover, AML-1 expression was up-regulated in response to a parasitic infection. We conclude that AML-1 purified from coelomic fluid is encoded by AML-1b and represents a novel type of protein family that binds acetylated components.
The Role of IL-17 and TH17 Cells in the Bone Catabolic Activity of PTH

Osteoimmunology is field of research dedicated to the study of the interactions between the immune system and bone. Among the cells of the immune system that regulate the skeleton in health and disease are T lymphocytes, T cells secrete inflammatory/osteoclastogenic cytokines such as RANKL, TNF, and IL-17, as well as factors that stimulate bone formation, including Wnt ligands. In addition, T cells regulate the differentiation and life span of stromal cells via CD40L and other costimulatory molecules expressed on their surface. Consensus exists that parathyroid hormone (PTH) induces bone loss by increasing the production of RANKL by osteocytes and osteoblast. However, new evidence suggests that PTH expands Th17 cells and increases IL-17 levels in mice and humans. Studies in the mouse of further shown that Th17 cell produced IL-17 acts as an “upstream cytokine” that increases the sensitivity of osteoblasts and osteocytes to PTH. As a result, PTH stimulates osteocytic and osteoblastic release of RANKL. Therefore, PTH cause bone loss only in the presence of IL-17 signaling. This article reviews the evidence that the effects of PTH are mediated not only by osteoblasts and osteocytes, but also T cells and IL-17.
Low cost inkjet printing for the fast prototyping of surface EMG detection systems

In the last years, printing techniques have been developed for the realization of electronic circuits using functional inks. In this field inkjet printing technology has a number of attractive features and received a lot of interest with the development of specifically designed functional inks, including conductive inks based on silver nanoparticles or organic polymers. Some works in literature investigated the use of inkjet printing technique for the development of electrophysiological sensors. The aim of this work was to explore the potentialities of low cost inkjet printing for the prototyping of high-density electrode arrays for the detection of surface electromyographic signal (sEMG). A low cost inkjet system for the printing of conductive tracks based on standard office printer has been setup and tested for the prototyping of sEMG detection systems. The setup allowed the printing of high density bidimensional electrode arrays. The sEMG detection systems have been tested on the abductor pollicis muscle and biceps brachii muscle during isometric and dynamic contractions. The detected signals show a good quality and a stable contact without movement artifacts. The proposed system offers the possibility to design and print electrode arrays with different electrode patterns in a few minutes. This characteristic allows developing sEMG detection systems that can be adapted to the anatomy of the muscles under investigation in a short time. Keywords— Surface EMG, Inkjet, electrodes
Fibrosis regression induced by intravenous gammaglobulin treatment

Objectives: To review case histories of patients in whom fibrosis played a significant role in the pathogenesis of their disease, and to determine whether intravenous gammaglobulin (IVIg) contributed to the regression of their fibrotic condition. Methods: Eight patients with excess fibrotic reaction in the course of diverse diseases were analysed; a tendency that reverted with different IVIg treatment options. Myelofibrosis was predominant in three patients (a patient with a myeloproliferative syndrome, one with systemic lupus erythematosus, and one with Sjögren’s syndrome). Three patients had scleroderma as their main feature, one patient had hepatitis C cirrhosis, and one had idiopathic thrombocytopenic purpura. Results: Fibrotic excess was reduced in all the patients by IVIg treatment. In five patients the disease as a whole benefited from the infusion of immunoglobulins. Conclusion: IVIg may enhance resorption of fibrosis and promote healing in patients with fibrotic associated disorders.
Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

Dynamic Imprinting Gene imprinting—the silencing of either a maternally derived or paternally derived gene allele—is controlled in large part by DNA methylation. In plants, imprinting occurs in the endosperm, which nourishes the embryonic plant. Gehring et al. (p. 1447) and Hsieh et al. (p. 1451) analyzed the dynamics of DNA methylation in the endosperm and embryo of Arabidopsis and found extensive demethylation in the endosperm, suggesting that many imprinted genes are likely to exist. Gehring et al. characterized five imprinted genes in detail. Four of the 10 known imprinted genes are related homeodomain transcription factors. Furthermore, 5′ sequences demethylated in several of the genes were found to be derived from transposable elements, which supports the idea that imprinting arose as a by-product of silencing invading DNA. Gene function in Arabidopsis endosperm depends on whether a gene is maternally or paternally inherited. DNA methylation is an epigenetic mark associated with transposable element silencing and gene imprinting in flowering plants and mammals. In plants, imprinting occurs in the endosperm, which nourishes the embryo during seed development. We have profiled Arabidopsis DNA methylation genome-wide in the embryo and endosperm and found that large-scale methylation changes accompany endosperm development and endosperm-specific gene expression. Transposable element fragments are extensively demethylated in the endosperm. We discovered new imprinted genes by the identification of candidates associated with regions of reduced endosperm methylation and preferential expression in endosperm relative to other parts of the plant. These data suggest that imprinting in plants evolved from targeted methylation of transposable element insertions near genic regulatory elements followed by positive selection when the resulting expression change was advantageous.
C-Kit Binding Properties of Hesperidin (a Major Component of KMP6) as a Potential Anti-Allergic Agent

Accumulation of mast cells can be causally related to several allergic inflammations. Stem cell factor (SCF) as a mast cell chemotaxin induces mast cell migration. To clarify a new effect of Pyeongwee-San extract (KMP6, a drug for indigestion) for the treatment of allergy, we investigated the effects of KMP6 on SCF-induced migration of rat peritoneal mast cells (RPMCs). A molecular docking simulation showed that hesperidin, a major component of KMP6, controls the SCF and c-kit binding by interaction with the active site of the c-kit. KMP6 and hesperidin significantly inhibited SCF-induced migration of RPMCs (P<0.05). The ability of the SCF to enhance morphological alteration and F-actin formation was also abolished by treatment with KMP6 or hesperidin. KMP6 and hesperidin inhibited SCF-induced p38 MAPK activation. In addition, SCF-induced inflammatory cytokine production was significantly inhibited by treatment with KMP6 or hesperidin (P<0.05). Our results show for the first time that KMP6 potently regulates SCF-induced migration, p38 MAPK activation and inflammatory cytokines production through hindrance of SCF and c-kit binding in RPMCs. Such modulation may have functional consequences during KMP6 treatment, especially mast cell-mediated allergic inflammation disorders.
Socio-technical Dynamics: Cooperation of Emergent and Established Organisations in Crises and Disasters

Increasing ubiquitousness of information and communication technology exerts influence on crisis and disaster management. New media enable citizens to rapidly self-organise in emergent groups. Theoretical framing of their interactions with established organisations is lacking. To address this, we conduct a thematic analysis on qualitative data from the European migration crisis of 2015. We draw on context-rich material from both emergent groups and established organisation. To represent our findings, we introduce the notion of socio-technical dynamics. We derive implications for computer supported cooperative work in crises and disasters. These insights contribute to the efficient involvement of emergent groups in established systems.