Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-endoscopic diagnosis of atrophic gastritis with a blood test. Correlation between gastric histology and serum levels of gastrin-17 and pepsinogen I: a multicentre study

Background and aims Serum levels of gastrin-17 (S-G-17) and pepsinogen I (S-PGI) are biomarkers of gastric antral and corpus mucosa, respectively. In a prospective multicentre investigation, we determined whether these tests, together with the assay of Helicobacter pylori antibodies, are a non-endoscopic tool for the diagnosis of atrophic gastritis. Materials and methods The series comprised 404 consecutive adult outpatients undergoing diagnostic upper-gastrointestinal endoscopy for various dyspeptic symptoms in five outpatient clinics. Gastric biopsies from the antrum and corpus (at least two biopsies from both sites) were available from all patients, and they were evaluated according to the guidelines of the updated Sydney system. S-PGI and S-G-17 were assayed with ELISA methods using monoclonal antibodies to pepsinogen I and amidated gastrin-17. In addition to the fasting level (S-G-17fast), a postprandial S-G-17 (S-G-17prand) level was measured 20 min after ingestion of a protein-rich drink. H. pylori antibodies were determined using a polyclonal EIA method. Results S-G-17prand (and S-G-17fast) and S-PGI levels decreased with increasing grade of atrophy of the antrum or corpus, respectively. S-G-17prand levels were significantly lower in patients with advanced (moderate or severe) atrophic antral H. pylori gastritis than in those with non-atrophic H. pylori gastritis. All patients with a resected antrum demonstrated S-G-17prand levels that were almost undetectable. Of the nine patients with an H. pylori-positive moderate or severe atrophic antral gastritis, six had S-G-17prand levels below 5 pmol/l. Similarly, S-PGI levels were significantly lower in patients with advanced corpus atrophy than in those without. Of the 45 patients with moderate or severe corpus atrophy in endoscopic biopsies, 35 patients had S-PGI levels < 25 μg/l. By using the cut-off levels for S-G-17prand and S-PGI with the best discrimination, the sensitivity and specificity of the blood test panel in delineation of patients with advanced atrophic gastritis (either in the antrum or the corpus, or both) were 83% and 95%, respectively. The predictive values of the positive and negative test results were 75% and 97%, respectively. In the diagnosis of atrophic gastritis, the application of S-G-17fast showed a slightly lower sensitivity and specificity than the application of S-G-17prand as a biomarker for antral atrophy. Conclusions The diagnosis of atrophic gastritis obtained with the blood test panel of S-G-17, S-PGI and H. pylori antibodies is in good agreement with the endoscopic and biopsy findings. The panel is a tool for non-endoscopic diagnosis and screening of atrophic gastritis.
The vector innovations structural time series framework

The vector innovations structural time series framework is proposed as a way of modelling a set of related time series. As with all multivariate approaches, the aim is to exploit potential interseries dependencies to improve the fit and forecasts. The model is based around an unobserved vector of components representing features such as the level and slope of each time series. Equations that describe the evolution of these components through time are used to represent the inter-temporal dependencies. The approach is illustrated on a bivariate dataset comprising Australian exchange rates of the UK pound and US dollar. The forecasting accuracy of the new modelling framework is compared to other common uni- and multivariate approaches in an experiment using time series from a large macroeconomic database.
Vitamin D Insufficiency in Arabs and South Asians Positively Associates with Polymorphisms in GC and CYP2R1 Genes

Background A number of genetic studies have reported an association between vitamin D related genes such as group-specific component gene (GC), Cytochrome P450, family 2, subfamily R, polypeptide 1 (CYP2R1) and 7-dehydrocholesterol reductase/nicotinamide-adenine dinucleotide synthetase 1 (DHCR7/NADSYN1) and serum levels of the active form of Vitamin D, 25 (OH) D among African Americans, Caucasians, and Chinese. Little is known about how genetic variations associate with, or contribute to, 25(OH)D levels in Arabs populations. Methods Allele frequencies of 18 SNPs derived from CYP2R1, GC, and DHCR7/NADSYN1 genes in 1549 individuals (Arabs, South Asians, and Southeast Asians living in Kuwait) were determined using real time genotyping assays. Serum levels of 25(OH)D were measured using chemiluminescence immunoassay. Results GC gene polymorphisms (rs17467825, rs3755967, rs2282679, rs7041 and rs2298850) were found to be associated with 25(OH)D serum levels in Arabs and South Asians. Two of the CYP2R1 SNPs (rs10500804 and rs12794714) and one of GC SNPs (rs1155563) were found to be significantly associated with 25(OH)D serum levels only in people of Arab origin. Across all three ethnicities none of the SNPs of DHCR7/NADSYN1 were associated with serum 25(OH)D levels and none of the 18 SNPs were significantly associated with serum 25(OH)D levels in people from South East Asia. Conclusion Our data show for the first time significant association between the GC (rs2282679 and rs7041), CYP2R1 (rs10741657) SNPs and 25(OH)D levels. This supports their roles in vitamin D Insufficiency in Arab and South Asian populations respectively. Interestingly, two of the CYP2R1 SNPs (rs10500804 and rs12794714) and one GC SNP (rs1155563) were found to correlate with vitamin D in Arab population exclusively signifying their importance in this population.
WHAT INFLUENCES TEACHERS TO USE ICT IN ROAD SAFETY EDUCATION

The aim of this study was to investigate the factors that influence teachers’ intention to use the educational software of road safety education “The Chariot of the Sun” in their teaching. This software was aimed at a target group of 8-13 year-olds and was intended to provide teachers and students with information, interaction and activities to stimulate learning about road safety. The objectives of the study were to: 1) investigate the influence of attitude toward the behaviour, subjective norm and perceived behavioural control on teachers’ intention; and 2) compare the predictive validity of the Theory of Reasoned Action (TRA) (Ajzen and Fishbein, 1980) and the Theory of Planned Behaviour (TPB) (Ajzen, 1991) in predicting teachers’ intention. A total of 228 teachers of primary schools in Greece were surveyed about their intention to use “The Chariot of the Sun” in their teaching. The results showed that teachers’ intention was influenced by the perceived behavioural control (beta=.508), attitude toward the behaviour (beta=.230) and subjective norm (beta=.145). In, addition, the results showed that the TRA and TPB in general did provide a framework for the prediction of intention. However, the TPB did account for more variance in teachers’ intention than the TRA. Results of the study are discussed in terms of increasing the intention of teachers to use ICT in their teaching.
Diagnostic value of cytokeratin 7 and parvalbumin in differentiating chromophobe renal cell carcinoma from renal oncocytoma.

OBJECTIVE To investigate the diagnostic value of cytokeratin 7 (CK7) and parvalbumin at mRNA and protein levels. STUDY DESIGN CK7 and parvalbumin mRNA expression levels in 23 oncocytomas and 32 chromophobe renal cell carcinomas (RCCs) were examined using gene expression microarrays. Immunohistochemistry was performed using monoclonal antibodies specific for CK7 or parvalbumin in 41 chromophobe RCCs and 55 oncocytomas. RESULTS CK7 mRNA was overexpressed in 18 of 32 chromophobe RCCs but only 3 of 23 oncocytomas. Parvalbumin mRNA was overexpressed in 15 of 32 chromophobe RCCs and only 4 of 23 oncocytomas. In contrast, CK7 mRNA underexpression was noted in 13 of 23 oncocytomas and only 6 of 32 chromophobe RCCs, while parvalbumin underexpression was seen in 14 of 23 oncocytomas but only 6 of 32 chromophobe RCCs. By immunohistochemistry, 27 of 41 (66%) chromophobe RCCs expressed CK7 diffusely compared to only 3 of 55 (5%) oncocytomas. Diffuse parvalbumin expression was seen in all 41 of 41 (100%) chromophobe RCCs and only in 26 of 55 (47%) oncocytomas. CONCLUSION Both mRNA and protein expression levels of CK7 appear significantly higher in chromophobe RCC compared to oncocytoma (p < 0.001). Parvalbumin expression is less specific but often displays a patchy pattern in oncocytomas. Our study provides further evidence that CK7 and parvalbumin immunostains may be useful in differentiating oncocytoma from chromophobe RCC in problematic cases. Negative or patchy staining (< 50% cells) for CK7 and/or parvalbumin strongly favors the diagnosis of oncocytoma.
Longitudinal Study of Intestinal Entamoeba histolytica Infections in Asymptomatic Adult Carriers

ABSTRACT To gain insight into the dynamics of intestinal Entamoeba histolytica infection, a longitudinal study was performed over an observation period of 15 months with a group of 383 randomly selected adult individuals (mean age, 38.5 years) living in an area of amebiasis endemicity in central Vietnam. Ameba infection was diagnosed by using species-specific PCR and DNA extracted directly from fecal samples. The results indicated an E. histolytica prevalence of 11.2% and an annual new infection rate of 4.1% in the study population. Follow-up of the 43 individuals who were E. histolytica positive at enrollment suggested a regular exponential decline in infection of about 3% per month and a mean half-life of infection of more than 15 months. However, the reinfection rate for this group of participants was 2.7 times higher than that predicted for the study population as a whole. Both the reappearance of the parasite after successful treatment of E. histolytica infection and changes in “genetic fingerprints” of parasites during the course of infection revealed an annual new infection rate of about 11.5%. Thus, the mean half-life of E. histolytica infection was calculated to be 12.9 months (95% confidence interval, 10.2 to 15.6 months). Notably, none of the participants developed symptoms compatible with invasive intestinal amebiasis, and only one of the subjects developed an amebic liver abscess during the observation period.
Determinants of Scanpath Regularity in Reading

Scanpaths have played an important role in classic research on reading behavior. Nevertheless, they have largely been neglected in later research perhaps due to a lack of suitable analytical tools. Recently, von der Malsburg and Vasishth (2011) proposed a new measure for quantifying differences between scanpaths and demonstrated that this measure can recover effects that were missed with the traditional eyetracking measures. However, the sentences used in that study were difficult to process and scanpath effects accordingly strong. The purpose of the present study was to test the validity, sensitivity, and scope of applicability of the scanpath measure, using simple sentences that are typically read from left to right. We derived predictions for the regularity of scanpaths from the literature on oculomotor control, sentence processing, and cognitive aging and tested these predictions using the scanpath measure and a large database of eye movements. All predictions were confirmed: Sentences with short words and syntactically more difficult sentences elicited more irregular scanpaths. Also, older readers produced more irregular scanpaths than younger readers. In addition, we found an effect that was not reported earlier: Syntax had a smaller influence on the eye movements of older readers than on those of young readers. We discuss this interaction of syntactic parsing cost with age in terms of shifts in processing strategies and a decline of executive control as readers age. Overall, our results demonstrate the validity and sensitivity of the scanpath measure and thus establish it as a productive and versatile tool for reading research.
Mycobacterium africanum—Review of an Important Cause of Human Tuberculosis in West Africa

Mycobacterium africanum consists of two phylogenetically distinct lineages within the Mycobacterium tuberculosis complex, known as M. africanum West African 1 and M. africanum West African 2. These lineages are restricted to West Africa, where they cause up to half of human pulmonary tuberculosis. In this review we discuss the definition of M. africanum, describe the prevalence and restricted geographical distribution of M. africanum West African 1 and 2, review the occurrence of M. africanum in animals, and summarize the phenotypic differences described thus far between M. africanum and M. tuberculosis sensu stricto.
On two-dimensional indexability and optimal range search indexing

In this paper we settle several longstanding open problems in theory of indexability and external orthogonal range searching. In the rst part of the paper, we apply the theory of indexability to the problem of two-dimensional range searching. We show that the special case of 3-sided querying can be solved with constant redundancy and access overhead. From this, we derive indexing schemes for general 4-sided range queries that exhibit an optimal tradeo between redundancy and access overhead. In the second part of the paper, we develop dynamic external memory data structures for the two query types. Our structure for 3-sided queries occupies O(N=B) disk blocks, and it supports insertions and deletions in O(log B N) I/Os and queries in O(log B N + T=B) I/Os, where B is the disk block size, N is the number of points, and T is the query output size. These bounds are optimal. Our structure for general (4-sided) range searching occupies O (N=B)(log(N=B))= log log B N disk blocks and answers queries in O(log B N + T=B) I/Os, which are optimal. It also supports updates in O (log B N)(log(N=B))= log log B N I/Os. Center for Geometric Computing, Department of Computer Science, Duke University, Box 90129, Durham, NC 27708{0129. Supported in part by the U.S. Army Research O ce through MURI grant DAAH04{96{1{0013 and by the National Science Foundation through ESS grant EIA{9870734. Part of this work was done while visiting BRICS, Department of Computer Science, University of Aarhus, Denmark. Email: large@cs.duke. edu. yDepartment of Computer Sciences, University of Texas at Austin, Austin, TX 78712-1188. Email vsam@cs.utexas. edu zCenter for Geometric Computing, Department of Computer Science, Duke University, Box 90129, Durham, NC 27708{0129. Supported in part by the U.S. Army Research O ce through MURI grant DAAH04{96{1{0013 and by the National Science Foundation through grants CCR{9522047 and EIA{9870734. Part of this work was done while visiting BRICS, Department of Computer Science, University of Aarhus, Denmark and I.N. R.I. A. , Sophia Antipolis, France. Email: jsv@cs.duke. edu.
Dynamic Topic Adaptation for Phrase-based MT

Translating text from diverse sources poses a challenge to current machine translation systems which are rarely adapted to structure beyond corpus level. We explore topic adaptation on a diverse data set and present a new bilingual variant of Latent Dirichlet Allocation to compute topic-adapted, probabilistic phrase translation features. We dynamically infer document-specific translation probabilities for test sets of unknown origin, thereby capturing the effects of document context on phrase translations. We show gains of up to 1.26 BLEU over the baseline and 1.04 over a domain adaptation benchmark. We further provide an analysis of the domain-specific data and show additive gains of our model in combination with other types of topic-adapted features.
[Lead and cadmium concentration in human semen].

OBJECTIVES The aim of our study was to specify influence of lead and cadmium on semen parameters. MATERIAL AND METHODS Concentrations of both elements were determined in semen samples by atomic absorption spectrophotometry of 57 men with teratozoospermic, astenozoospermic and oligozoospermic (studied group) and 39 normozoospermic group (control group). Semen morphology was conducted in accordance with WHO regulations. RESULTS AND CONCLUSIONS We did not find any difference in concentration of these elements in both groups. We found a positive correlation between lead and cadmium in seminal plasma.
Mathematical Modeling of Li-Ion Battery Using Genetic Algorithm Approach for V2G Applications

This paper presents an electric circuit-based battery and a capacity fade model suitable for electric vehicles (EVs) in vehicle-to-grid applications. The circuit parameters of the battery model (BM) are extracted using genetic algorithm-based optimization method. A control algorithm has been developed for the battery, which calculates the processed energy, charge or discharge rate, and state of charge limits of the battery in order to satisfy the future requirements of EVs. A complete capacity fade analysis has been carried out to quantify the capacity loss with respect to processed energy and cycling. The BM is tested by simulation and its characteristics such as charge and discharge voltage, available and stored energy, battery power, and its capacity loss are extracted. The propriety of the proposed model is validated by superimposing the results with four typical manufacturers' data. The battery profiles of different manufacturers' like EIG, Sony, Panasonic, and Sanyo have been taken and their characteristics are compared with proposed models. The obtained battery characteristics are in close agreement with the measured (manufacturers' catalogue) characteristics.
TAXES AND GROWTH: TESTING THE NEOCLASSICAL AND ENDOGENOUS GROWTH MODELS

"Changes in the tax rate alter real growth permanently in an endogenous growth model, but only temporarily in a neoclassical model, where the only permanent effect is a decrease in the steady-state level of output per capita. Using data from the 1960'1992 period for a panel of 11 Organization of Economic Cooperation and Development economies, this paper's empirical results support the following conclusions. First, consistent with the tax smoothing hypothesis, tax rates have exhibited significant persistent changes while output growth rates have not. Second, a higher tax rate permanently reduces the level of output but has no permanent effects on the output growth rate. These findings are inconsistent with endogenous growth mechanisms and suggest that the relationship between output and the tax rate is best described by the neoclassical growth model. (JEL" E62, 041) Copyright 1999 Western Economic Association International.
Straight from the source: Accounting for scientific success

How do highly cited scientists account for their success? A number of approaches have been used to explain scientific success, but none incorporates scientists’ own understandings, which are critical to a complete, process-oriented explanation. We remedy this oversight by incorporating scientists’ own descriptions of the value of their work, as reflected in essays written by authors of highly cited articles (‘Citation Classics’). As cultural objects, these essays reveal not only factors perceived to be associated with success but also reflect narrative conventions, and thereby elucidate the culture surrounding success. We enlist Charles Ragin’s Qualitative Comparative Analysis to analyze how factors mentioned in these accounts work in conjunction. Our results show that three ingredients – relationships, usefulness to others, and overcoming challenges – are found in a large majority of scientific success stories.
Noncirrhotic hepatocellular carcinoma: etiology and occult hepatitis B virus infection in a hepatitis B virus-endemic area

Background: Although hepatocellular carcinoma (HCC) usually develops in cirrhotic livers, a minority of cases occur in noncirrhotic livers (NCLs). We investigated etiology, clinicopathological features, and occult hepatitis B virus (HBV) infection (OBI) in patients with NCL HCC in an HBV-endemic area. Methods: A total of 710 patients who underwent resection or transplantation for HCC at the National Cancer Center (NCC), Korea, were enrolled. HCC and fibrosis stage were diagnosed pathologically. Results: A total of 178 patients (25%) did not have cirrhosis (NCL group). The main cause of HCC was HBV infection (77.2%), followed by cryptogenic disease (11.0%). The prevalence of NCL was 19.2%, 32.5%, 50.0%, and 48.7% among patients with HBV, hepatitis C virus (HCV), alcoholic, and cryptogenic disease, respectively (p < 0.05); corresponding nonfibrosis rates were 8.1%, 0%, 19.0%, and 24.3%, respectively. The NCL group was significantly older, with a larger tumor size, smaller tumor number, lower tumor stage, and more frequent non-HBV etiology. Among non-HBV HCC cases, 130 (80.2%) had antibodies against HBV core (HBc) and 55 (38.5%) had OBI. OBI-positive rates of 0%, 31.8%, and 52.6% were detected among HCV, alcoholic, and cryptogenic HCC cases, respectively. OBI did not correlate with advanced fibrosis. The NCL and liver cirrhosis (LC) groups did not differ in median overall survival. Conclusion: Regardless of etiology, a significant number of HCC patients, including half of nonviral cases, did not have LC. Half of cryptogenic HCC cases had OBI. This study promotes an understanding of fibrosis and OBI among patients with HCC in an HBV-endemic area.
Can Fixation on Main Images Predict Visual Appeal of Homepages?

Research suggests that a main image on a homepage creates a distinct visual hierarchy that maybe inherently appealing to people. This in turn suggests that main images may play an important role in shaping user aesthetic reactions to a homepage. Research also shows that images of people are effective in drawing attention and that these images are pleasing to users. Grounded in these two lines of research, we show that fixation on main images has significant positive relation to visual appeal ratings of 24 homepages. We also show that when images of people are included in the main image, they attract more attention. Our results also show that users give higher visual appeal ratings to homepages that include images of people in their main image. These results and their implication for theory and practice are discussed.
Statistical Applications in Genetics and Molecular Biology Super Learner

When trying to learn a model for the prediction of an outcome given a set of covariates, a statistician has many estimation procedures in their toolbox. A few examples of these candidate learners are: least squares, least angle regression, random forests, and spline regression. Previous articles (van der Laan and Dudoit (2003); van der Laan et al. (2006); Sinisi et al. (2007)) theoretically validated the use of cross validation to select an optimal learner among many candidate learners. Motivated by this use of cross validation, we propose a new prediction method for creating a weighted combination of many candidate learners to build the super learner. This article proposes a fast algorithm for constructing a super learner in prediction which uses V-fold cross-validation to select weights to combine an initial set of candidate learners. In addition, this paper contains a practical demonstration of the adaptivity of this so called super learner to various true data generating distributions. This approach for construction of a super learner generalizes to any parameter which can be defined as a minimizer of a loss function.