Miracle-dz/UniFAR-FTUs huggingface dataset:
Regional wage determinants in Poland: the empirical verification of the NEG approach

The paper aims at explaining the regional wage determinants in Poland using the New Economic Geography approach. We test the hypothesis that regional wages are positively related to the regional economic potential, controlling for individual worker, firm, industry and regional characteristics. We demonstrate that the regional economic potential strongly influences the regional level of wages. Moreover, we find that individual characteristics also play an important role in wage determination in Poland.
Nonparametric Kernel Regression with Multiple Predictors and Multiple Shape Constraints

Nonparametric smoothing under shape constraints has recently received much well-deserved attention. Powerful methods have been proposed for imposing a single shape constraint such as monotonicity and concavity on univariate functions. In this paper, we extend the monotone kernel regression method in Hall and Huang (2001) to the multivariate and multi-constraint setting. We impose equality and/or inequality constraints on a nonparametric kernel regression model and its derivatives. A bootstrap procedure is also proposed for testing the validity of the constraints. Consistency of our constrained kernel estimator is provided through an asymptotic analysis of its relationship with the unconstrained estimator. Theoretical underpinnings for the bootstrap procedure are also provided. Illustrative Monte Carlo results are presented and an application is considered.
SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

MOTIVATION Accurately predicting protein secondary structure and relative solvent accessibility is important for the study of protein evolution, structure and function and as a component of protein 3D structure prediction pipelines. Most predictors use a combination of machine learning and profiles, and thus must be retrained and assessed periodically as the number of available protein sequences and structures continues to grow. RESULTS We present newly trained modular versions of the SSpro and ACCpro predictors of secondary structure and relative solvent accessibility together with their multi-class variants SSpro8 and ACCpro20. We introduce a sharp distinction between the use of sequence similarity alone, typically in the form of sequence profiles at the input level, and the additional use of sequence-based structural similarity, which uses similarity to sequences in the Protein Data Bank to infer annotations at the output level, and study their relative contributions to modern predictors. Using sequence similarity alone, SSpro's accuracy is between 79 and 80% (79% for ACCpro) and no other predictor seems to exceed 82%. However, when sequence-based structural similarity is added, the accuracy of SSpro rises to 92.9% (90% for ACCpro). Thus, by combining both approaches, these problems appear now to be essentially solved, as an accuracy of 100% cannot be expected for several well-known reasons. These results point also to several open technical challenges, including (i) achieving on the order of ≥ 80% accuracy, without using any similarity with known proteins and (ii) achieving on the order of ≥ 85% accuracy, using sequence similarity alone. AVAILABILITY AND IMPLEMENTATION SSpro, SSpro8, ACCpro and ACCpro20 programs, data and web servers are available through the SCRATCH suite of protein structure predictors at http://scratch.proteomics. ics.uci. edu.
A Fast Method for Extracting all Minimal Siphons from Maximal Unmarked Siphons of a Petri Net

In this paper, a fast method named algorithm 2is proposed to extract all minimal siphons from maximalunmarked siphons obtained by the MIP-based deadlockdetection method. Redundant computation is the majordisadvantage of an existing method named algorithm 1 andit greatly decreases the computational efficiency of minimalsiphons. In order to resolve this problem, the proposedmethod improves from three aspects. Firstly, no sink placesand transitions exist in the subnet of the tree. Secondly,no equal non-null node exists in the tree. Thirdly, if theremoval of one place from a subnet node leads to theremoval of all places in this node, the same place of its sonnode is unnecessary to compute repeatedly. The applicationsof algorithm 2 are illustrated with FMS examples in thefollowing sections and comparison of algorithm 1 withalgorithm 2 is also presented. At the end, the result fromexperiment shows that the proposed method has higherefficiency.
Alternative Zippering as an On-Off Switch for SNARE-Mediated Fusion

Membrane fusion between vesicles and target membranes involves the zippering of a four-helix bundle generated by constituent helices derived from target– and vesicle–soluble N-ethylmaleimide–sensitive factor attachment protein receptors (SNAREs). In neurons, the protein complexin clamps otherwise spontaneous fusion by SNARE proteins, allowing neurotransmitters and other mediators to be secreted when and where they are needed as this clamp is released. The membrane-proximal accessory helix of complexin is necessary for clamping, but its mechanism of action is unknown. Here, we present experiments using a reconstituted fusion system that suggest a simple model in which the complexin accessory helix forms an alternative four-helix bundle with the target-SNARE near the membrane, preventing the vesicle-SNARE from completing its zippering.
Accuracy of the Adaptive GRP Scheme and the Simulation of 2-D Riemann Problems for Compressible Euler Equations

The adaptive generalized Riemann problem (GRP) scheme for 2-D compressible fluid flows has been proposed in [J. Comput. Phys., 229 (2010), 1448-1466] and it displays the capability in overcoming difficulties such as the start-up error for a single shock, and the numerical instability of the almost stationary shock. In this paper, we will provide the accuracy study and particularly show the performance in simulating 2-D complex wave configurations formulated with the 2-D Riemann problems for compressible Euler equations. For this purpose, we will first review the GRP scheme briefly when combined with the adaptive moving mesh technique and consider the accuracy of the adaptive GRP scheme via the comparison with the explicit formulae of analytic solutions of planar rarefaction waves, planar shock waves, the collapse problem of a wedge-shaped dam and the spiral formation problem. Then we simulate the full set of wave configurations in the 2-D four-wave Riemann problems for compressible Euler equations [SIAM J. Math. Anal. , 21 (1990), 593-630], including the interactions of strong shocks (shock reflections), vortex-vortex and shock-vortex etc. This study combines the theoretical results with the numerical simulations, and thus demonstrates what Ami Harten observed “ for computational scientists there are two kinds of truth: the truth that you prove, and the truth you see when you compute ” [J. Sci. Comput. , 31 (2007), 185-193].
Mitotic Spindle Poles are Organized by Structural and Motor Proteins in Addition to Centrosomes

The focusing of microtubules into mitotic spindle poles in vertebrate somatic cells has been assumed to be the consequence of their nucleation from centrosomes. Contrary to this simple view, in this article we show that an antibody recognizing the light intermediate chain of cytoplasmic dynein (70.1) disrupts both the focused organization of microtubule minus ends and the localization of the nuclear mitotic apparatus protein at spindle poles when injected into cultured cells during metaphase, despite the presence of centrosomes. Examination of the effects of this dynein-specific antibody both in vitro using a cell-free system for mitotic aster assembly and in vivo after injection into cultured cells reveals that in addition to its direct effect on cytoplasmic dynein this antibody reduces the efficiency with which dynactin associates with microtubules, indicating that the antibody perturbs the cooperative binding of dynein and dynactin to microtubules during spindle/aster assembly. These results indicate that microtubule minus ends are focused into spindle poles in vertebrate somatic cells through a mechanism that involves contributions from both centrosomes and structural and microtubule motor proteins. Furthermore, these findings, together with the recent observation that cytoplasmic dynein is required for the formation and maintenance of acentrosomal spindle poles in extracts prepared from Xenopus eggs (Heald, R., R. Tournebize, T. Blank, R. Sandaltzopoulos, P. Becker, A. Hyman, and E. Karsenti. 1996. Nature (Lond.). 382: 420–425) demonstrate that there is a common mechanism for focusing free microtubule minus ends in both centrosomal and acentrosomal spindles. We discuss these observations in the context of a search-capture-focus model for spindle assembly.
Clinical factors and treatment outcomes associated with failure in the detection of urate crystal in patients with acute gouty arthritis

Background/Aims To investigate the rate of detection of monosodium urate (MSU) crystals in the synovial fluid (SF) of patients with acute gouty arthritis and factors associated with false-negative results. Methods A total of 179 patients with acute gouty arthritis who had undergone SF crystal examination were identified from the data warehouse of two university hospitals. Clinical and laboratory data were obtained from the medical records. Results The overall rate of detection of MSU crystals was 78.8%. In univariate analyses, the only significant differences between the variables of crystal-negative and crystal-positive patients were a lower C-reactive protein level (p = 0.040) and fewer patients undergoing emergent surgery in the crystal-positive group (p = 4.5 × 10-6). In logistic regression analyses, MSU crystal-negative results were significantly associated with the interval from arthritis onset to crystal examination (p = 0.042), and this was the most significant risk factor for arthroscopic surgery (p = 2.1 × 10-4). Seventeen patients who underwent arthroscopic surgery had a significantly longer hospital stay (p = 0.007) and a significant delay in gout treatment (p = 8.74 × 10-5). The distribution of crystal-negative patients differed significantly between the SF samples that were evaluated by both the laboratory medicine and the rheumatology departments (p = 1.2 × 10-14), and the κ value was 0.108. Conclusions Although several clinical features were associated with detection failure, SF MSU crystal identification was critically dependent on the observer. Considering the impact on the treatment outcomes, implementation of a quality control program is essential.
Towards a framework and a benchmark for testing tools for multi‐threaded programs

Multi‐threaded code is becoming very common, both on the server side, and very recently for personal computers as well. Consequently, looking for intermittent bugs is a problem that is receiving more and more attention. As there is no silver bullet, research focuses on a variety of partial solutions. We outline a road map for combining the research within the different disciplines of testing multi‐threaded programs and for evaluating the quality of this research. We have three main goals. First, to create a benchmark that can be used to evaluate different solutions. Second, to create a framework with open application programming interfaces that enables the combination of techniques in the multi‐threading domain. Third, to create a focus for the research in this area around which a community of people who try to solve similar problems with different techniques can congregate. We have started creating such a benchmark and describe the lessons learned in the process. The framework will enable technology developers, for example, developers of race detection algorithms, to concentrate on their components and use other ready made components (e.g. an instrumentor) to create a testing solution. Copyright © 2006 John Wiley & Sons, Ltd.
Associations between Urinary Phthalates and Metabolic Syndrome in NHANES 2005-2010

Title of Thesis: ASSOCIATIONS BETWEEN URINARY PHTHALATES AND METABOLIC SYNDROME IN NHANES 2005-2010. Mefruz S. Haque, Masters of Public Health, 2015 Directed By: Professor Cher M. Dallal, Department of Epidemiology and Biostatistics Phthalates, commonly used to make plastics more durable, are a group of endocrine disrupting chemicals (EDC), with potential for adverse metabolic consequences. Associations between exposure to 13 phthalate metabolites and the prevalence of metabolic syndrome (MetS) were examined among 5,409 U.S adults ≥ 18 years of age, who participated in the National Health and Nutrition Examination Survey from 2005-2010. MetS was assessed using clinical and questionnaire data. Odds Ratio (OR) and 95% Confidence Intervals (CI) adjusting for age, creatinine and key confounders, were estimated with multivariable logistic regression. Positive associations were observed between individual phthalate metabolites and MetS: (MCOP OR=1.31, 95% CI=1.40, 1.64, p-trend<.01; MCPP OR=1.39, 95% CI=1.09, 1.77, p-trend=0.01). In gender stratified analyses, findings with MCOPP and MCPP were restricted to women only. Phthalate metabolites may increase the prevalence of MetS; however, further studies are needed to better understand the role of EDCs in the development of MetS. ASSOCIATIONS BETWEEN URINARY PHTHALATES AND METABOLIC SYNDROME IN NHANES 2005-2010
Automated detection of Southeast Asian Ovalocytosis (SAO) obtained from thin blood smear microphotographs

Southeast Asian Ovalocytosis (SAO) is an erythrocyte disorder, which is characterized by oval-shaped cells with one or two transverse ridges or a longitudinal slit on blood smears. To check the SAO using thin blood smear requires expert manpower and is time consuming. This research was aimed to automatically detect the SAO from thin blood smear images. Digital images were acquired using a digital camera connected to a light microscope. Images underwent gray-scale conversion to decrease representation of images. Otsu? s Method was implemented to separate blood components and the background. All clumps present in the image were then processed to be separated using recursive bottleneck detection algorithm. The major and minor axes of each extracted erythrocyte were then obtained for the calculation of ratio. The ratio determined whether the erythrocyte is normal or oval, and a count was kept between them. The percentage of oval erythrocyte over total erythrocyte was used as the determination of SAO positive or negative. The major and minor axes of the erythrocytes were successfully detected with error rate lower than 1%. Thin blood smear sample, prepared and provided by Eijkman Institute for Molecular Biology Indonesia, were used to build and test of the proposed algorithm.
Modeling Sub-90nm On-Chip Variation Using Monte Carlo Method for DFM

For sub-90nm technology nodes and below, random fluctuations of within-die physical process properties are also known as random on-chip variation (OCV). It impacts on the VLSI/SoC design yields significantly. This paper presents a recent silicon test chip experiment result which uses a set of innovative nanometer test structures and Monte-Carlo-based three-dimensional electromagnetic RC simulations to achieve silicon-correlated corner modeling of OCV that can be applied to the upcoming statistics-based timing analysis (SSTA) for design for manufacturability (DFM). Modeling and correlating OCV based on the randomly varying physical process parameters is therefore achieved for the realistic corner modeling of advanced copper and low-K.
A Content Assist based Approach for Providing Rationale of Method Change for Object Oriented Programming

Software engineering requires modification of code during development and maintenance phase. During modification, a difficult task is to understand rationale of changed code. Present Integrated Development Environments (IDEs) attempt to help this by providing features integrated with different types of repositories. However, these features still consume developer's time as he has to switch from editor to another window for this purpose. Moreover, these features focus on elements available in present version of code, thus increasing the difficulty of finding rationale of an element removed or modified earlier. Leveraging different sources for providing information through code completion menus has been shown to be valuable, even when compared to standalone counterparts offering similar functionalities in literature. Literature also shows that it is one of the most used features for consuming information within IDE. Based on that, we prepare an Eclipse plug-in and a framework that allows providing reason of code change, at method granularity, across versions through a new code completion menu in IDE. These allow a software engineer to gain insight about rationale of removed or modified methods which are otherwise not available in present version of code. Professional software engineers participated in our empirical evaluation process and we observed that more than 80% participants considered this to be a useful approach for saving time and effort to understand rationale of method change. Later, based on their feedback, the plug-in and framework is modified to incorporate chronological factors. We perform quasi experimental evaluation with professional software engineers. It is found that time required to find rationale of method change is reduced to at least half compared to usual amount of time required for all the software engineers who participated in the quantitative evaluation. Index Terms—Software engineering, Mining software repositories, experimental software engineering.
RBCS1A and RBCS3B, two major members within the Arabidopsis RBCS multigene family, function to yield sufficient Rubisco content for leaf photosynthetic capacity

Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit (RBCS) is encoded by a nuclear RBCS multigene family in many plant species. The contribution of the RBCS multigenes to accumulation of Rubisco holoenzyme and photosynthetic characteristics remains unclear. T-DNA insertion mutants of RBCS1A (rbcs1a-1) and RBCS3B (rbcs3b-1) were isolated among the four Arabidopsis RBCS genes, and a double mutant (rbcs1a3b-1) was generated. RBCS1A mRNA was not detected in rbcs1a-1 and rbcs1a3b-1, while the RBCS3B mRNA level was suppressed to ∼20% of the wild-type level in rbcs3b-1 and rbcs1a3b-1 leaves. As a result, total RBCS mRNA levels declined to 52, 79, and 23% of the wild-type level in rbcs1a-1, rbcs3b-1, and rbcs1a3b-1, respectively. Rubisco contents showed declines similar to total RBCS mRNA levels, and the ratio of Rubisco-nitrogen to total nitrogen was 62, 78, and 40% of the wild-type level in rbcs1a-1, rbcs3b-1, and rbcs1a3b-1, respectively. The effects of RBCS1A and RBCS3B mutations in rbcs1a3b-1 were clearly additive. The rates of CO2 assimilation at ambient CO2 of 40 Pa were reduced with decreased Rubisco contents in the respective mutant leaves. Although the RBCS composition in the Rubisco holoenzyme changed, the CO2 assimilation rates per unit of Rubisco content were the same irrespective of the genotype. These results clearly indicate that RBCS1A and RBCS3B contribute to accumulation of Rubisco in Arabidopsis leaves and that these genes work additively to yield sufficient Rubisco for photosynthetic capacity. It is also suggested that the RBCS composition in the Rubisco holoenzyme does not affect photosynthesis under the present ambient [CO2] conditions.
Kinetics of C5a release in cardiac lymph of dogs experiencing coronary artery ischemia-reperfusion injury.

Previous studies of myocardial ischemia suggest that complement activation may play a central role in the inflammatory response during reperfusion. Our previous work has demonstrated neutrophil chemotactic activity to be present in reperfusion canine cardiac lymph after myocardial ischemia and infarction. To evaluate the contribution of the complement-dependent anaphylatoxin C5a to this neutrophil chemotactic activity, rabbit antiserum to canine C5a was prepared. At dilutions > 1:500 but < 1:2,000, the antiserum abolished the ability of zymosan-activated dog serum to induce a ruffled, bipolar morphology in isolated neutrophils used as a bioassay of chemotactic stimulation. This antiserum did not affect similar morphological changes in neutrophils exposed to platelet activating factor (10(-7)-10(-6) M) or recombinant human interleukin-8 (10(-9)-10(-8) M); thus, we deemed it functionally specific for canine C5a. In a pattern similar to what we previously reported, cardiac lymph collected before a 1-hour ligation of the left circumflex coronary artery had little ability to alter the morphology of canine neutrophils (shape change index, 11.3 +/- 4.6, mean +/- SEM; n = 7), but by 1 hour of reperfusion, lymph activated neutrophils significantly in five of seven dogs (mean shape change index, 72.6 +/- 17.7; p < 0.01). At 2 hours of reperfusion, neutrophil activation by lymph occurred in six of seven dogs (mean shape change index, 103.1 +/- 22.2). At 3 hours of reperfusion, cardiac lymph of only three of six dogs caused neutrophil activation, and at 4 hours of reperfusion, this activity was evident in lymph from only two of five dogs. (ABSTRACT TRUNCATED AT 250 WORDS)
An Analysis of the “ Elite ” Users on Yelp

Yelp.com is a popular website and mobile app that allows users to both read and post reviews and ratings of restaurants and business. It has a substantial userbase as well, with over 130 million visitors per month. Most customers of the site are casual users, occasionally searching the site to find a good restaurant in their area or expressing their opinions of a place they recently visited. However, there is a very particular set of users of the service which Yelp like to call their “Elite” users. According to Yelp, their Elite users are supposed to be a small group of in-the-know users who have a large impact on their local community. For example, Yelp claims that these users reveal the hot spots for fellow locals, serve as city ambassadors, and have sway in the community. [1] The purpose of our project is to investigate properties of Yelp’s Elite users. For this paper, we will focus on several of Yelp’s primary claims about their Elite users. First, Yelp states that its Elite users have high connectivity, which means that they are connected with many other users and interact often with members of their Yelp community. Second, Yelp claims that its Elite users make up the “true heart of the Yelp community. ” Third, Yelp claims that its users have high contribution, which means that the user has made a large impact on the site with meaningful and high-quality reviews. [1] The first goal of our project is to analyze whether the above claims about Yelp’s Elite users are valid. For this, we will specify several characteristics which we expect Elite users to have based on these claims. We will then perform analyses on Yelp’s dataset in order to determine whether these properties are truly represented among the Elite users. The secondary goal of our project is to find which properties are most indicative of Elite status on Yelp. The analyses for the first goal can be used for this purpose as well. This kind of information may be useful for those who are interested in becoming Elite members on Yelp. In order to become a member of the “Elite squad,” a user must go through an application process. Despite the suggestions presented above, Yelp doesn’t provide any specific criteria on exactly what characteristics a user must have to become Elite. The mystery behind the selection process for Elite users is well-documented. [2]