Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration Profiling of Gene Function With Dense Maps of Transposon Integration

Understanding how complex networks of genes integrate to produce dividing cells is an important goal that is limited by the difficulty in defining the function of individual genes. Current resources for the systematic identification of gene function such as siRNA libraries and collections of deletion strains are costly and organism specific. We describe here integration profiling, a novel approach to identify the function of eukaryotic genes based upon dense maps of transposon integration. As a proof of concept, we used the transposon Hermes to generate a library of 360,513 insertions in the genome of Schizosaccharomyces pombe. On average, we obtained one insertion for every 29 bp of the genome. Hermes integrated more often into nucleosome free sites and 33% of the insertions occurred in ORFs. We found that ORFs with low integration densities successfully identified the genes that are essential for cell division. Importantly, the nonessential ORFs with intermediate levels of insertion correlated with the nonessential genes that have functions required for colonies to reach full size. This finding indicates that integration profiles can measure the contribution of nonessential genes to cell division. While integration profiling succeeded in identifying genes necessary for propagation, it also has the potential to identify genes important for many other functions such as DNA repair, stress response, and meiosis.
Effect of Barium Chloride Filler on the Adhesion Properties of Epoxidized Natural Rubber (ENR 25)-Based Adhesives

The adhesion properties of epoxidized natural rubber (ENR 25)-based adhesive were studied using barium chloride, coumarone-indene resin and toluene as the filler, tackifier and solvent respectively. Viscosity was determined by a Brookfield Viscometer whereas tack, shear and peel strength was measured by a Llyod Adhesion Tester. Results show that viscosity of adhesive increases gradually with increasing barium chloride loading. Loop tack, shear and peel strength indicates a maximum value at 10 parts per hundred parts of rubber (phr) of barium chloride, an observation that is attributed to the maximum wettability and compatibility of adhesive on the substrate.
A Survey of Crowdsourcing Systems

Crowd sourcing is evolving as a distributed problem-solving and business production model in recent years. In crowd sourcing paradigm, tasks are distributed to networked people to complete such that a company's production cost can be greatly reduced. In 2003, Luis von Ahn and his colleagues pioneered the concept of "human computation", which utilizes human abilities to perform computation tasks that are difficult for computers to process. Later, the term "crowdsourcing" was coined by Jeff Howe in 2006. Since then, a lot of work in crowd sourcing has focused on different aspects of crowd sourcing, such as computational techniques and performance analysis. In this paper, we give a survey on the literature on crowd sourcing which are categorized according to their applications, algorithms, performances and datasets. This paper provides a structured view of the research on crowd sourcing to date.
Overinterpretation is common in pathological diagnosis of appendix cancer during patient referral for oncologic care

Context Low-grade appendiceal mucinous neoplasm (LAMN) and appendiceal adenocarcinoma are known to cause the majority of pseudomyxoma peritonei (PMP, i.e. mucinous ascites); however, recognition and proper classification of these neoplasms can be difficult despite established diagnostic criteria. Objective To determine the pathological diagnostic concordance for appendix neoplasia and related lesions during patient referral to an academic medical center specialized in treating patients with PMP. Design The anatomic pathology laboratory information system was searched to identify cases over a two-year period containing appendix specimens with mucinous neoplasia evaluated by an outside pathology group and by in-house slide review at a single large academic medical center during patient referral. Results 161 cases containing appendix specimens were identified over this period. Forty-six of 161 cases (28.6%) contained appendiceal primary neoplasia or lesions. Of these, the originating pathologist diagnosed 23 cases (50%) as adenocarcinoma and 23 cases (50%) as LAMN; however, the reference pathologist diagnosed 29 cases (63.0%) as LAMN, 13 cases (28.3%) as adenocarcinoma, and 4 cases (8.7%) as ruptured simple mucocele. Importantly, for cases in which the originating pathologist rendered a diagnosis of adenocarcinoma, the reference pathologist rendered a diagnosis of adenocarcinoma (56.5%, 13 of 23), LAMN (39.1%, 9 of 23), or simple mucocele (4.3%, 1 of 23). The overall diagnostic concordance rate for these major classifications was 71.7% (33 of 46) with an unweighted observed kappa value of 0.48 (95% CI, 0.27–0.69), consistent with moderate interobserver agreement. All of the observed discordance (28.3%) for major classifications could be attributed to over-interpretation. In addition, the majority of LAMN cases (65.5%) had potential diagnostic deficiencies including over-interpretation as adenocarcinoma and lacking or discordant risk stratification (i.e. documentation of extra-appendiceal neoplastic epithelium). Conclusions Appendiceal mucinous lesions remain a difficult area for appropriate pathological classification with substantial discordance due to over-interpretation in this study. The findings highlight the critical need for recognition and application of diagnostic criteria regarding these tumors. Recently published consensus guidelines and a checklist provided herein may help facilitate improvement of diagnostic concordance and thereby reduce over-interpretation and potential overtreatment. Further studies are needed to determine the extent of this phenomenon and its potential clinical impact.
Quality of Life Among Veterans With Chronic Spinal Cord Injury and Related Variables

Background: In recent decades, the incidence of spinal cord injuries has increased. In a systemic review on epidemiology of traumatic spinal cord injury in developing countries reported 25.5/million cases per year. Objectives: To assess the quality of life (QOL) of the veterans among Iran-Iraq war with chronic spinal cord injuries (SCI) and to evaluate long-term impressions of SCI on their quality of life. Patients and Methods: Fifty-two veterans, all male, with chronic spinal cord injury from Iran-Iraq war (1980-1988) were interviewed and examined. The mean age of veterans at the time of interview was 49.3 years (38 to 80 years). Veterans were assessed by using a 36-item short-form (SF-36), hospital anxiety and depression scale (HADS) and the Barthel index. The presence or absence of pressure sores and spasticity were documented as well. Results: The mean age of veterans at the time of study was 49.3 years. Pearson's correlation test showed that depression and anxiety have a reverse association with mental component summary (MCS) scale and physical component summary (PCS) scale scores, respectively. Regression analysis showed a negative effect of depression and pressure sore on PCS. Moreover, no association was found between the duration of injury and age with quality of life. Conclusions: Lower QOL was found among veterans with chronic SCI. More researches on health-related quality of life (HRQOL) are needed to give us a better understanding of changes in life of patients with SCI and the ways to improve them.
An angular momentum approach to quadratic Fourier transform, Hadamard matrices, Gauss sums, mutually unbiased bases, the unitary group and the Pauli group

The construction of unitary operator bases in a finite-dimensional Hilbert space is reviewed through a nonstandard approach combining angular momentum theory and representation theory of SU(2). A single formula for the bases is obtained from a polar decomposition of SU(2) and is analyzed in terms of cyclic groups, quadratic Fourier transforms, Hadamard matrices and generalized Gauss sums. Weyl pairs, generalized Pauli operators and their application to the unitary group and the Pauli group naturally arise in this approach.
Beyond Cell Death – Antiapoptotic Bcl-2 Proteins Regulate Migration and Invasion of Colorectal Cancer Cells In Vitro

Migration and invasion of malignant cells are prerequisites for cancer progression and metastasis. The Bcl-2 family of proteins consists of about 25 members and has been extensively studied in the context of apoptosis. Despite the fact that small molecules targeting Bcl-2 proteins have already entered clinical trials, very few studies investigated a role of antiapoptotic Bcl-2 proteins beside cell death in the context of metastasis. The aim of this study was to dissect a potential role of the antiapoptotic Bcl-2 proteins Mcl-1, Bcl-2 and Bcl-xL on migration and invasion of colorectal cancer cells independent of their cell death control function. We used migration and invasion assays as well as three dimensional cell cultures to analyze colorectal cancer cell lines (HT29 and SW480) after siRNA mediated knockdown or overexpression of Mcl-1, Bcl-2 or Bcl-xL. We observed neither spontaneous cell death induction nor impaired proliferation of cells lacking Mcl-1, Bcl-2 or Bcl-xL. In contrast, knockdown of Mcl-1 led to increased proliferation. Strikingly, we demonstrate a profound impairment of both, migration and invasion, of colorectal cancer cells after Mcl-1, Bcl-2 or Bcl-xL knockdown. This phenotype was completely revised in cells overexpressing Mcl-1, Bcl-2 or Bcl-xL. The most pronounced effect among the investigated proteins was observed for Bcl-2. The data presented indicate a pivotal role of Mcl-1, Bcl-2 and Bcl-xL for migration and invasion of colorectal cancer cells independent of their known antiapoptotic effects. Thus, our study illustrates novel antitumoral mechanisms of Bcl-2 protein targeting.
Empirical Spectral Processes and Their Applications to Stationary Point Processes

We consider empirical spectral processes indexed by classes of functions for the case of stationary point processes Conditions for the measurability and equicontinuity of these processes and a weak convergence result are estab lished The results can be applied to the spectral analysis of point processes In particular we discuss the application to parametric and nonparametric spectral density estimation
A microarray analysis of early activated pathways in concanavalin A-induced hepatitis

ObjectiveTo explore the mechanisms of fulminant hepatitis (FH) in the early stages, and to determine the critical pathways in its initiation and progression.MethodsTwelve BALB/c mice were divided into four groups: one group left as negative control and sacrificed immediately after injection of phosphate-buffered saline (PBS), and another three groups with concanavalin A (Con A) administration sacrificed at 1, 3, and 6 h after injection. Affymetrix GeneChip® Mouse 430 2.0 Array was employed to evaluate the expression profile of each of the 12 samples. Further analysis was done on the microarray data to extract the genes that were differentially expressed. Enrichment analysis was carried out to determine relevant pathways within which regulated genes were significantly enriched.ResultsA total of 393, 8354 and 11344 differentially expressed genes were found, respectively, at three time points. During 0–1 h and 1–3 h, most of the pathways enriched with regulated genes were related to immune response and inflammation, among which Toll-like receptor (TLR) signaling and mitogen-activated protein kinase (MAPK) signaling appeared during both phases, while cytokine-cytokine receptor interaction, apoptosis, T cell receptor signaling, and natural killer (NK) cell-mediated cytotoxicity pathways emerged during the second phase. Pathways found to be significant during 3–6 h were mostly related to metabolic processes.ConclusionThe TLR signaling pathway dominates the early responses of Con A-induced FH in mice. It stimulates the production of type I cytokines, therefore recruiting and activating T/NK cells. Activated T/NK cells exert their cytotoxicity on hepatocytes through inducing death receptor-intermediated apoptosis, resulting in liver injury.
Management of patients with recently implanted coronary stents on dual antiplatelet therapy who need to undergo major surgery

Summary. About 5% of patients undergoing coronary stenting need to undergo surgery within the next year. The risk of perioperative cardiac ischemic events, particularly stent thrombosis (ST), is high in these patients, because surgery has a prothrombotic effect and antiplatelet therapy is often withdrawn in order to avoid bleeding. The clinical and angiographic predictors of ST are well known, and the proximity to an acute coronary syndrome adds to the risk. The current guidelines recommend delaying non‐urgent surgery for at least 6 weeks after the placement of a bare metal stent and for 6–12 months after the placement of a drug‐eluting stent, when the risk of ST is reduced. However, in the absence of formal evidence, these recommendations provide little support with regard to managing urgent operations. When surgery cannot be postponed, stratifying the risk of surgical bleeding and cardiac ischemic events is crucial in order to manage perioperative antiplatelet therapy in individual cases. Dual antiplatelet therapy should not be withdrawn for minor surgery or most gastrointestinal endoscopic procedures. Aspirin can be safely continued perioperatively in the case of most major surgery, and provides coronary protection. In the case of interventions at high risk for both bleeding and ischemic events, when clopidogrel withdrawal is required in order to reduce perioperative bleeding, perioperative treatment with the short‐acting intravenous glycoprotein IIb–IIIa inhibitor tirofiban is safe in terms of bleeding, and provides strong antithrombotic protection. Such surgical interventions should be performed at hospitals capable of performing an immediate percutaneous coronary intervention at any time in the case of acute myocardial ischemia.
Schema Extraction for Tabular Data on the Web

Tabular data is an abundant source of information on the Web, but remains mostly isolated from the latter's interconnections since tables lack links and computer-accessible descriptions of their structure. In other words, the schemas of these tables -- attribute names, values, data types, etc. -- are not explicitly stored as table metadata. Consequently, the structure that these tables contain is not accessible to the crawlers that power search engines and thus not accessible to user search queries. We address this lack of structure with a new method for leveraging the principles of table construction in order to extract table schemas. Discovering the schema by which a table is constructed is achieved by harnessing the similarities and differences of nearby table rows through the use of a novel set of features and a feature processing scheme. The schemas of these data tables are determined using a classification technique based on conditional random fields in combination with a novel feature encoding method called logarithmic binning, which is specifically designed for the data table extraction task. Our method provides considerable improvement over the well-known WebTables schema extraction method. In contrast with previous work that focuses on extracting individual relations, our method excels at correctly interpreting full tables, thereby being capable of handling general tables such as those found in spreadsheets, instead of being restricted to HTML tables as is the case with the WebTables method. We also extract additional schema characteristics, such as row groupings, which are important for supporting information retrieval tasks on tabular data.
An Estimation of X-Radiation output using mathematic model

Problem statement: Diagnosis x-ray radiation safety is key in medical examination. The quantity of patient radiation doses is beneficial for radiation protection of the patient. It was proposed that the equation for estimating the output (milliReongent, mR) from x-ray machines. Approach: A was 0.5, 0.8 and 1.0 for single phase, three phases and high frequency x-ray machines, respectively. To compare calculated output (mR) used this equation and measured output (mR) used ionizing chamber dosimeter. Results: The difference between the calculated and measured radiation dose was quite small. Conclusion: This equation could use to estimate output and it altered the reliable and inexpensive techniques for patient dose measurement in routine diagnostic x-ray examinations.
Evaluation of Clinical Meaning of Histological Subtypes of Intraductal Papillary Mucinous Neoplasm of the Pancreas

Objectives Prognostic value of histological subtypes of pancreatic intraductal papillary mucinous neoplasm (IPMN) has been reported to have conflicting results. The authors investigated the clinicopathological characteristics and prognostic significance of the histological subtypes of IPMNs with various degrees of dysplasia. Methods Two hundred thirteen patients with surgically treated pancreatic IPMN at a single tertiary care referral center were included. Pathological slides were thoroughly reviewed by a specialized pathologist. Results Of the 213 patients, 38 low-grade, 97 intermediate-grade, and 18 high-grade dysplasia and 59 IPMNs with an associated invasive carcinoma (invasive IPMN) were identified. Histological subtypes consisted of 135 gastric (63.4%), 38 intestinal (17.8%), 38 pancreatobiliary (17.8%), and 2 oncocytic types (0.9%). Histological subtypes were associated with radiological type (P < 0.001), degree of dysplasia (P < 0.001), and T stage (P < 0.001). The proportions of invasive IPMN were 14.1%, 42.1%, 57.9%, and 100% of gastric, intestinal, pancreatobiliary, and oncocytic types, respectively. Disease-specific survival was not affected by histological subtype in overall patients (P = 0.881). For invasive IPMNs, histological subtypes had a marginal significance on survival (P = 0.050), which lost statistical significance after multivariate analysis (P = 0.341). Conclusions Although histological subtypes are associated with the degree of dysplasia, histological subtypes have limited prognostic value for pancreatic IPMNs.
of Groningen Model selection in continuous test norming with

To compute norms from reference group test scores, continuous norming is preferred over traditional norming. A suitable continuous norming approach for continuous data is the use of the Box–Cox Power Exponential model, which is found in the generalized additive models for location, scale, and shape. Applying the Box–Cox Power Exponential model for test norming requires model selection, but it is unknown how well this can be done with an automatic selection procedure. In a simulation study, we compared the performance of two stepwise model selection procedures combined with four modelfit criteria (Akaike information criterion, Bayesian information criterion, generalized Akaike information criterion (3), cross-validation), varying data complexity, sampling design, and sample size in a fully crossed design. The new procedure combined with one of the generalized Akaike information criterion was the most efficient model selection procedure (i.e., required the smallest sample size). The advocated model selection procedure is illustrated with norming data of an intelligence test.
Specific C-Receptors for Itch in Human Skin

In microneurography experiments 56 unmyelinated nerve fibers were studied in the cutaneous branch of the peroneal nerve of healthy volunteers. Units were identified with the “marking” technique as mechanically and heat-responsive (CMH; n = 30), heat-responsive (CH; n = 13), or unresponsive to mechanical and heat stimulation (CMiHi;n = 13). None of the units showed spontaneous activity. These units were tested for responsiveness to iontophoresis of histamine (1 mA, 20 sec) from a small probe (diameter, 6 mm), which induced itch sensations lasting several minutes. Twenty-three units were unresponsive to histamine, and 25 units responded weakly with a few spike discharges after iontophoresis. Eight units, however, responded with sustained discharges to histamine, and their discharge patterns were matching the time course of the itch sensations. All C-units in this group were mechanically insensitive, and five of them were heat-responsive. They had very low conduction velocities of only 0.5 m/sec, on average, which is significantly lower than conduction velocities of the “polymodal” CMH units. This slow conduction velocities attributable to small axon diameters may be one reason why these units have not been encountered in previous studies. Histamine-sensitive C-units had very large innervation territories extending up to a diameter of 85 mm on the lower leg. We conclude that these C-fibers represent a new class of afferent nerve fibers with particularly thin axons but excessive terminal branching. This type of C-fiber probably represents the afferent units long searched for mediating itch sensations.
Bridging the Gap between Business Strategy and Software Development

In software-intensive organizations, an organizational management system will not guarantee organizational success unless the business strategy can be translated into a set of operational software goals. The Goal Question Metric (GQM) approach has proven itself useful in a variety of industrial settings to support quantitative software project management. However, it does not address linking software measurement goals to higher-level goals of the organization in which the software is being developed. This linkage is important, as it helps to justify software measurement efforts and allows measurement data to contribute to higher-level decisions. In this paper, we propose a GQM + Strategies ® measurement approach that builds on the GQM approach to plan and implement software measurement. GQM + Strategies ® provides mechanisms for explicitly linking software measurement goals to higher-level goals for the software organization, and further to goals and strategies at the level of the entire business. An example application of the proposed method is illustrated in the context of an example measurement initiative.
Analysis of Prostate Cancer Susceptibility Variants in South African Men: Replicating Associations on Chromosomes 8q24 and 10q11

Genome-wide association studies (GWAS) have implicated single nucleotide polymorphisms (SNPs) on chromosomes 2p15, 6q25, 7p15.2, 7q21, 8q24, 10q11, 10q26, 11q13, 17q12, 17q24, 19q13, and Xp11, with prostate cancer (PCa) susceptibility and/or tumour aggressiveness, in populations of African, European, and Asian ancestry. The objective of this study was to confirm these associations in South African Mixed Ancestry and White men. We evaluated 17 prioritised GWAS SNPs in South African cases (331 Mixed Ancestry and 155 White) and controls (178 Mixed Ancestry and 145 White). The replicated SNP associations for the different South African ethnic groups were rs7008482 (8q24) (p = 2.45 × 10−5), rs6983267 (8q24) (p = 4.48 × 10−7), and rs10993994 (10q11) (p = 1.40 × 10−3) in Mixed Ancestry men and rs10993994 (p = 1.56 × 10−9) in White men. No significant associations were observed for the analyses stratified by disease aggressiveness in the individual and the combined population group analysis. The present study demonstrates that a number of known PCa susceptibility variants may contribute to disease susceptibility in South African men. Larger genetic investigations extended to other South African population groups are warranted to confirm the role of these and other SNPs in disease susceptibility.