Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable and robust community detection via Proximity-based Cut and Merge

Online Social Networks (OSNs) heavily rely on community detection algorithms to support many of their core services. Common functions such as friend recommendation, and timeline personalization all require the fast discovery of communities over some massive graph(s). For such applications, scalability, flexibility and speed are much more important than marginal improvement in the theoretical quality of the results. While the community detection problem has been studied intensively in the past, existing work tends to emphasize on theoretical optimality than the aforementioned practical needs. In this paper, we present a 2-stage framework called Proximity-Based Cut and Merge (PBCM), for scalable and robust community detection. In the first stage, edges between low proximity nodes are eliminated in one pass. In the second stage, high proximity nodes are merged iteratively to produce results conforming to the intuitive notion of community. We explore the design space via extensive numerical evaluation to instantiate an effective community detection algorithm under the framework, and compare the performance of PBCM-based designs against state-of-the-art baselines. Our results show that the proposed PBCM framework is effective, scalable and robust. We also demonstrate the flexibility of PBCM by extending it to handle both overlapping and non-overlapping communities.
Epigenetic silencing of checkpoint with fork-head associated and ring finger gene expression in esophageal cancer

Checkpoint with fork-head associated and ring finger (CHFR) is a mitotic checkpoint gene with tumor-suppressor functions. Previous studies have described the hypermethylation of the CpG island in the promoter region as a key mechanism involved in silencing tumor suppressor genes. The epigenetic alterations regulating CHFR expression and the clinical significance of CHFR downregulation remain unclear. A total of 40 patients with esophageal squamous cell carcinoma who underwent primary resection were enrolled in this study. CHFR mRNA expression was quantified, followed by an evaluation of the methylation status using methylation-specific polymerase chain reaction (MSP) techniques in 29 patients. The correlation between CHFR expression and MSP status was then analyzed. In addition, the significance of CHFR expression was determined, with respect to clinicopathological features and overall survival. Aberrant hypermethylation of the CHFR gene was observed in 13 of 29 primary esophageal cancers. The CHFR expression levels of the methylated status samples was significantly lower than that of the unmethylated status samples (P=0.014). CHFR expression levels did not exhibit clinical significance with respect to the patient characteristics or overall survival. Hypermethylation of the CHFR gene is a common event in the development of primary esophageal cancer. CpG island hypermethylation of the promoter region in the CHFR gene is a key mechanism involved in silencing the CHFR gene in patients with esophageal cancer.
Synthesis of linear antenna array using genetic algorithm with cost based roulette to maximize side lobe level reduction

This paper discusses the deployment of Genetic algorithm optimization method for synthesis of antenna array radiation pattern in adaptive beam forming. The synthesis problem discussed is to find the weights of the antenna array elements that are optimum to provide the radiation pattern with maximum reduction in the side lobe level. This technique proved its effectiveness in improving the performance of the antenna array.
An incremental and user feedback-based ontology matching approach

Ontologies are being used in order to define common vocabularies to describe the elements of schemas involved in a particular application. The problem of finding correspondences between ontologies concepts, called ontology matching, consists in the discovery of correspondences between terms of vocabularies (represented by ontologies) used by various applications. The majority of solutions proposed in the literature, despite being fully automatic, has heuristic nature and may produce non-satisfactory results. The problem intensifies when dealing with large data sources. The goal of this paper is to propose a method for generation and incremental refinement of correspondences between ontologies. The proposed approach uses filtering techniques, as well as user feedback to support the generation and refinement of such matches. For validation purposes, a tool was developed and some experiments were conducted.
Role for p300 in Stabilization of p53 in the Response to DNA Damage*

The nuclear p300/CBP proteins function as coactivators of gene transcription. Here, using cells deficient in p300 or CBP, we show that p300, and not CBP, is essential for ionizing radiation-induced accumulation of the p53 tumor suppressor and thereby p53-mediated growth arrest. The results demonstrate that deficiency of p300 results in increased degradation of p53. Our findings suggest that p300 contributes to the stabilization and transactivation function of p53 in the cellular response to DNA damage.
Does 3D 360 video enhance user's VR experience?: An Evaluation Study

Technology for virtual reality has evolved at a fast pace and so is its affordability. Equipment such as head-mounted displays are now available for the average consumer at reasonable prices and this potentiates the use of contents such as video 360 in a more natural way. The purpose of this study was to measure the sense of presence and cybersickness comparing subjects by gender while experiencing a virtual reality application composed by type of VIDEO (360 video and 3D 360 video) using an head-mounted display. A Portuguese version of the Igroup Presence Questionnaire (IPQ) was used together with the Simulator Sickness Questionnaire (SSQ). The results have revealed that there are no significant differences across 2D and 3D videos in the sense of presence or cybersickness.
Summarization of Yes/No Questions Using a Feature Function Model

Answer summarization is an important problem in the study of Question and Answering. In this paper, we deal with the general questions with “Yes/No” answers in English. We design 1) a model to score the relevance of the answers and the questions, and 2) a feature function combining the relevance and opinion scores to classify each answer to be “Yes”, “No” or “Neutral”. We combine the opinion features together with two weighting scores to solve this problem and conduct experiments on a real word dataset. Given an input question, the system firstly detects if it can be simply answered by “Yes/No” or not, and then outputs the resulting voting numbers of “Yes” answers and “No” answers to this question. We also first proposed the accuracy, precision, and recall to the “Yes/No” answer detection.
Exploring users' appropriation and post‐implementation managerial intervention in the context of industry IOIS

Although the literature has repeatedly shown that inter‐organizational information systems (IOIS) are prone to abandonment and low levels of adoption, a great deal of research examining such unsatisfactory outcomes has focused on phenomena occurring in the early stages of the implementation, thus, leaving the post‐implementation period under‐explored. This paper presents a conceptual lens through which we study two interrelated post‐implementation phenomena: managerial intervention and users' appropriation. Specifically, we develop a structurational model to examine IOIS management intervention to boost IOIS assimilation, the situated and emergent appropriations of the IOIS that followed and the ongoing adaptations by those intervening in these processes. Actors shape the context for others' actions by offering modalities of structuring – i.e. new meanings, new procedures, new software applications – which are then taken up in practice by adopters, giving rise to both intended and unintended outcomes. The paper contributes with a multi‐level process‐based study that (1) conceives IOIS assimilation as an episodic process in which there are dialectical tensions between users and IOIS management; and (2) identifies two forms of managerial intervention targeting diverse aspects of the institutional context that lead to assimilation.
Validation and Reliability of the Neuropathic Pain Scale (NPS) in Multiple Sclerosis

ObjectiveCentral neuropathic pain occurs in around 28% of patients with multiple sclerosis (MS). The Neuropathic Pain Scale (NPS) has received preliminary validation in peripheral neuropathic pain conditions. The aim of this study was to validate its use in MS central pain syndromes. MethodsWe administered the NPS to 141 patients with MS, together with the Short Form McGill Pain Questionnaire (SFMPQ), the Hospital Anxiety and Depression Scale (HADS), and Short Form 36 Health Survey (SF-36). ResultsCronbach's α was 0.78 (95% CI 0.69; 0.83), implying a high degree of internal consistency. Three factors, “Familiar,” “Superficial,” and “Alien Perception,” were extracted, accounting for 64% of the variance. The NPS 10-item total correlates with: the SFMPQ 15-item total score, ρ=0.63 (95% CI 0.49; 0.74), its Visual Analog Scale, ρ=0.49 (95% CI 0.33; 0.64), the transformed Pain domain of the SF-36 ρ=−0.49 (95% CI −0.63; −0.32), but not with its remaining seven health domains, or with either the HADS anxiety or the depression scores. Limits of agreement for short-term test or re-test reliability of the 100 point NPS total (median 2 days, range 1 to 7) were −12 to 14 and when administered to 78 patients who rated their neuropathic pain the “Same” [median interval 33 days (range 19 to 126), the long-term test or re-test correlation coefficient was 0.71 (95% CI 0.6; 0.79)]. DiscussionThe NPS appears a useful tool in the assessment of neuropathic pain in MS patients and possibly in measuring outcomes of therapeutic interventions.
Immunoassay Methods and their Applications in Pharmaceutical Analysis: Basic Methodology and Recent Advances

Immunoassays are bioanalytical methods in which the quantitation of the analyte depends on the reaction of an antigen (analyte) and an antibody. Immunoassays have been widely used in many important areas of pharmaceutical analysis such as diagnosis of diseases, therapeutic drug monitoring, clinical pharmacokinetic and bioequivalence studies in drug discovery and pharmaceutical industries. The importance and widespread of immunoassay methods in pharmaceutical analysis are attributed to their inherent specificity, high-throughput, and high sensitivity for the analysis of wide range of analytes in biological samples. Recently, marked improvements were achieved in the field of immunoassay development for the purposes of pharmaceutical analysis. These improvements involved the preparation of the unique immunoanalytical reagents, analysis of new categories of compounds, methodology, and instrumentation. The basic methodologies and recent advances in immunoassay methods applied in different fields of pharmaceutical analysis have been reviewed.
Energy-efficient in-memory database computing

The efficient and flexible management of large datasets is one of the core requirements of modern business applications. Having access to consistent and up-to-date information is the foundation for operational, tactical, and strategic decision making. Within the last few years, the database community sparked a large number of extremely innovative research projects to push the envelope in the context of modern database system architectures. In this paper, we outline requirements and influencing factors to identify some of the hot research topics in database management systems. We argue that—even after 30 years of active database research—the time is right to rethink some of the core architectural principles and come up with novel approaches to meet the requirements of the next decades in data management. The sheer number of diverse and novel (e.g., scientific) application areas, the existence of modern hardware capabilities, and the need of large data centers to become more energy-efficient will be the drivers for database research in the years to come.
Exposure to welding fumes is associated with hypomethylation of the F2RL3 gene: a cardiovascular disease marker

Background Welders are at risk for cardiovascular disease. Recent studies linked tobacco smoke exposure to hypomethylation of the F2RL3 (coagulation factor II (thrombin) receptor-like 3) gene, a marker for cardiovascular disease prognosis and mortality. However, whether welding fumes cause hypomethylation of F2RL3 remains unknown. Methods We investigated 101 welders (median span of working as a welder: 7 years) and 127 unexposed controls (non-welders with no obvious exposure to respirable dust at work), age range 23–60 years, all currently non-smoking, in Sweden. The participants were interviewed about their work history, lifestyle factors and diseases. Personal sampling of respirable dust was performed for the welders. DNA methylation of F2RL3 in blood was assessed by pyrosequencing of four CpG sites, CpG_2 (corresponds to cg03636183) to CpG_5, in F2RL3. Multivariable linear regression analysis was used to assess the association between exposure to welding fumes and F2RL3 methylation. Results Welders had 2.6% lower methylation of CpG_5 than controls (p<0.001). Higher concentrations of measured respirable dust among the welders were associated with hypomethylation of CpG_2, CpG_4 and CpG_5 (β=−0.49 to −1.4, p<0.012); p<0.029 adjusted for age, previous smoking, passive smoking, education, current residence and respirator use. Increasing the number of years working as a welder was associated with hypomethylation of CpG_4 (linear regression analysis, β=−0.11, p=0.039, adjusted for previous smoking). Previous tobacco smokers had 1.5–4.7% (p<0.014) lower methylation of 3 of the 4 CpG sites in F2RL3 (CpG_2, CpG_4 and CpG_5) compared to never-smokers. A non-significant lower risk of cardiovascular disease with more methylation was observed for all CpG sites. Conclusions Welding fumes exposure and previous smoking were associated with F2RL3 hypomethylation. This finding links low-to-moderate exposure to welding fumes to adverse effects on the cardiovascular system, and suggests a potential mechanistic pathway for this link, via epigenetic effects on F2RL3 expression.
Reconstituted nuclei depleted of a vertebrate GLFG nuclear pore protein, p97, import but are defective in nuclear growth and replication

Xenopus egg extracts provide a powerful system for in vitro reconstitution of nuclei and analysis of nuclear transport. Such cell- free extracts contain three major N-acetylglucosaminylated proteins: p200, p97, and p60. Both p200 and p60 have been found to be components of the nuclear pore. Here, the role of p97 has been investigated. Xenopus p97 was isolated and antisera were raised and affinity purified. Immunolocalization experiments indicate that p97 is present in a punctate pattern on the nuclear envelope and also in the nuclear interior. Peptide sequence analysis reveals that p97 contains a GLFG motif which defines a family of yeast nuclear pore proteins, as well as a peptide that is identical at 11/15 amino acids to a specific member of the GLFG family, NUP116. An additional peptide is highly homologous to a second sequence found in NUP116 and other members of the yeast GLFG family. A monoclonal antibody to the GLFG domain cross-reacts with a major Xenopus protein of 97 kD and polyclonal antiserum to p97 recognizes the yeast GLFG nucleoporin family. The p97 antiserum was used to immunodeplete Xenopus egg cytosol and p97-deficient nuclei were reconstituted. The p97-depleted nuclei remained largely competent for nuclear protein import. However, in contrast to control nuclei, nuclei deficient in p97 fail to grow in size over time and do not replicate their chromosomal DNA. ssDNA replication in such extracts remains unaffected. Addition of the N-acetylglucosaminylated nuclear proteins of Xenopus or rat reverses these replication and growth defects. The possible role(s) of p97 in these nuclear functions is discussed.
Common ADRB2 Haplotypes Derived from 26 Polymorphic Sites Direct β2-Adrenergic Receptor Expression and Regulation Phenotypes

Background The β2-adrenergic receptor (β2AR) is expressed on numerous cell-types including airway smooth muscle cells and cardiomyocytes. Drugs (agonists or antagonists) acting at these receptors for treatment of asthma, chronic obstructive pulmonary disease, and heart failure show substantial interindividual variability in response. The ADRB2 gene is polymorphic in noncoding and coding regions, but virtually all ADRB2 association studies have utilized the two common nonsynonymous coding SNPs, often reaching discrepant conclusions. Methodology/Principal Findings We constructed the 8 common ADRB2 haplotypes derived from 26 polymorphisms in the promoter, 5′UTR, coding, and 3′UTR of the intronless ADRB2 gene. These were cloned into an expression construct lacking a vector-based promoter, so that β2AR expression was driven by its promoter, and steady state expression could be modified by polymorphisms throughout ADRB2 within a haplotype. “Whole-gene” transfections were performed with COS-7 cells and revealed 4 haplotypes with increased cell surface β2AR protein expression compared to the others. Agonist-promoted downregulation of β2AR protein expression was also haplotype-dependent, and was found to be increased for 2 haplotypes. A phylogenetic tree of the haplotypes was derived and annotated by cellular phenotypes, revealing a pattern potentially driven by expression. Conclusions/Significance Thus for obstructive lung disease, the initial bronchodilator response from intermittent administration of β-agonist may be influenced by certain β2AR haplotypes (expression phenotypes), while other haplotypes may influence tachyphylaxis during the response to chronic therapy (downregulation phenotypes). An ideal clinical outcome of high expression and less downregulation was found for two haplotypes. Haplotypes may also affect heart failure antagonist therapy, where β2AR increase inotropy and are anti-apoptotic. The haplotype-specific expression and regulation phenotypes found in this transfection-based system suggest that the density of genetic information in the form of these haplotypes, or haplotype-clusters with similar phenotypes can potentially provide greater discrimination of phenotype in human disease and pharmacogenomic association studies.
Navigating a tool end in a specific direction: stick-tool use in kea (Nestor notabilis)

This study depicts how captive kea, New Zealand parrots, which are not known to use tools in the wild, employ a stick-tool to retrieve a food reward after receiving demonstration trials. Four out of six animals succeeded in doing so despite physical (beak curvature) and ecological (no stick-like materials used during nest construction) constraints when handling elongated objects. We further demonstrate that the same animals can thereafter direct the functional end of a stick-tool into a desired direction, aiming at a positive option while avoiding a negative one.
Extended histories: improving regularity and performance in correlation prefetchers

Data Prefetchers identify and make use of any regularity present in the history/training stream to predict future references and prefetch them into the cache. The training information used is typically the primary misses seen at a particular cache level, which is a filtered version of the accesses seen by the cache. In this work we demonstrate that extending the training information to include secondary misses and hits along with primary misses helps improve the performance of prefetchers. In addition to empirical evaluation, we use the information theoretic metric entropy, to quantify the regularity present in extended histories. Entropy measurements indicate that extended histories are more regular than the default primary miss only training stream. Entropy measurements also help corroborate our empirical findings. With extended histories, further benefits can be achieved by triggering prefetches during secondary misses also. In this paper we explore the design space of extended prefetch histories and alternative prefetch trigger points for delta correlation prefetchers. We observe that different prefetch schemes benefit to a different extent with extended histories and alternative trigger points. Also the best performing design point varies on a per-benchmark basis. To meet these requirements, we propose a simple adaptive scheme that identifies the best performing design point for a benchmark-prefetcher combination at runtime. In SPEC2000 benchmarks, using all the L2 accesses as history for prefetcher improves the performance in terms of both IPC and misses reduced over techniques that use only primary misses as history. The adaptive scheme improves the performance of CZone prefetcher over Baseline by 4.6% on an average. These performance gains are accompanied by a moderate reduction in the memory traffic requirements.
The modal distribution of protein isoelectric points reflects amino acid properties rather than sequence evolution

Two‐dimensional gel electrophoresis, a routine application in proteomics, separates proteins according to their molecular mass (Mr) and isoelectric point (pI). As the genomic sequences for more and more organisms are determined, the Mr and pI of all their proteins can be estimated computationally. The examination of several of these theoretical proteome plots has revealed a multimodal pI distribution, however, no conclusive explanation for this unusual distribution has so far been presented. We examined the pI distribution of 115 fully sequenced genomes and observed that the modal distribution does not reflect phylogeny or sequence evolution, but rather the chemical properties of amino acids. We provide a statistical explanation of why the observed distributions of pI values are multimodal.
A high performance algorithm using pre-processing for the sparse matrix-vector multiplication

The authors propose a feature-extraction-based algorithm (FEBA) for sparse matrix-vector multiplication. The key idea of FEBA is to exploit any regular structure present in the sparse matrix by extracting it and processing it separately. The order in which these structures are extracted is determined by the relative efficiency with which they can be processed. The authors have tested FEBA on IBM 3000 VF for matrices from the Harwell Boeing and OSL collection. The results obtained were on average five times faster than the ESSL routine which is based on the ITPACK storage structure. <<ETX>>