Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of the narcosis target lipid model for petroleum products: Gasoline as a case study

The narcosis target lipid model (NTLM) was used to predict the toxicity of water‐accommodated fractions (WAFs) of six gasoline blending streams to algae (Pseudokirchnereilla subcapitata, formerly Selenastrum capricornutum), juvenile rainbow trout (Oncorhynchus mykiss), and water flea (Daphnia magna). Gasolines are comprised of hydrocarbons that on dissolution into the aqueous phase are expected to act via narcosis. Aquatic toxicity data were obtained using a lethal‐loading test in which WAFs were prepared using different gasoline loadings. The compositions of the gasolines were determined by analysis of C3 to C13 hydrocarbons grouped in classes of n‐alkanes, iso‐alkanes, aromatics, cyclic alkanes, and olefins. A model was developed to compute the concentrations of hydrocarbon blocks in WAFs based on gasoline composition and loading. The model accounts for the volume change of the gasoline, which varies depending on loading and volatilization loss. The predicted aqueous composition of WAFs compared favorably to measurements, and the predicted aqueous concentrations of WAFs were used in the NTLM to predict the aquatic toxicity of the gasolines. For each gasoline loading and species, total toxic units (TUs) were computed with an assumption of additivity. The acute toxicity of gasolines was predicted to within a factor of two for algae and daphnids. Predicted TUs overestimated toxicity to trout because of experimental factors that were not considered in the model. This analysis demonstrates the importance of aliphatic hydrocarbon loss to headspace during WAF preparation and the contribution of both aromatic and aliphatic hydrocarbons test to the toxicity of gasolines in closed systems and loss of aliphatics to headspace during WAF preparation. Model calculations indicate that satisfactory toxicity predictions can be achieved by describing gasoline composition using a limited number of aromatic and aliphatic hydrocarbon blocks with different octanol‐water partition coefficients.
A meta‐analytic framework for detection of genetic interactions

With varying, but substantial, proportions of heritability remaining unexplained by summaries of single‐SNP genetic variation, there is a demand for methods that extract maximal information from genetic association studies. One source of variation that is difficult to assess is genetic interactions. A major challenge for naive detection methods is the large number of possible combinations, with a requisite need to correct for multiple testing. Assumptions of large marginal effects, to reduce the search space, may be restrictive and miss higher order interactions with modest marginal effects. In this paper, we propose a new procedure for detecting gene‐by‐gene interactions through heterogeneity in estimated low‐order (e.g., marginal) effect sizes by leveraging population structure, or ancestral differences, among studies in which the same phenotypes were measured. We implement this approach in a meta‐analytic framework, which offers numerous advantages, such as robustness and computational efficiency, and is necessary when data‐sharing limitations restrict joint analysis. We effectively apply a dimension reduction procedure that scales to allow searches for higher order interactions. For comparison to our method, which we term phylogenY‐aware Effect‐size Tests for Interactions (YETI), we adapt an existing method that assumes interacting loci will exhibit strong marginal effects to our meta‐analytic framework. As expected, YETI excels when multiple studies are from highly differentiated populations and maintains its superiority in these conditions even when marginal effects are small. When these conditions are less extreme, the advantage of our method wanes. We assess the Type‐I error and power characteristics of complementary approaches to evaluate their strengths and limitations.
Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation

Inhibitors of histone deacetylases (HDACIs) have emerged as a new class of drugs for the treatment of human cancers and other diseases because of their effects on cell growth, differentiation, and apoptosis. In this study we have developed several quantitative structure-activity relationship (QSAR) models for 59 chemically diverse histone deacetylase class 1 (HDAC1) inhibitors. The variable selection k nearest neighbor (kNN) and support vector machines (SVM) QSAR modeling approaches using both MolconnZ and MOE chemical descriptors generated from two-dimensional rendering of compounds as chemical graphs have been employed. We have relied on a rigorous model development workflow including the division of the data set into training, test, and external sets and extensive internal and external validation. Highly predictive QSAR models were generated with leave-one-out cross-validated (LOO-CV) q2 and external R2 values as high as 0.80 and 0.87, respectively, using the kNN/MolconnZ approach and 0.93 and 0.87, respectively, using the SVM/MolconnZ approach. All validated QSAR models were employed concurrently for virtual screening (VS) of an in-house compound collection including 9.5 million molecules compiled from the ZINC7.0 database, the World Drug Index (WDI) database, the ASINEX Synergy libraries, and other commercial databases. VS resulted in 45 structurally unique consensus hits that were considered novel putative HDAC1 inhibitors. These computational hits had several novel structural features that were not present in the original data set. Four computational hits with novel scaffolds were tested experimentally, and three of them were confirmed active against HDAC1, with IC50 values for the most active compound of 1.00 microM. The fourth compound was later identified to be a selective inhibitor of HDAC6, a Class II HDAC. Moreover, two of the confirmed hits are marketed drugs, which could potentially facilitate their further development as anticancer agents. This study illustrates the power of the combined QSAR-VS method as a general approach for the effective identification of structurally novel bioactive compounds.
Holiday Effect in Stock Exchange of Thailand from January 1992 - August 2013

This study examines the holiday effect in the Stock Exchange of Thailand (SET) which includes both long and short holidays on different market timing. Moreover, we also observe the pattern of trading behavior of different types of investors by focusing on average net trading volume per day. An experiment is conducted using the daily SET index data from January 1, 1992 to August 31, 2013. There are totally 5,026 normal trading days with 283 pre-holidays. Both event study and regression-based approach are employed. The research found that the pre-holiday effect exists on SET and they are observable larger during the long holiday than the short holiday. We also found that during the pre-holiday, proprietary and foreign investors are the main sellers of the stock.
E‐cadherin promoter polymorphism (C‐160A) and risk of recurrence in patients with superficial bladder cancer

Tumor recurrence is a hallmark of superficial bladder cancer. Currently, a molecular marker for bladder cancer recurrence is lacking. E‐cadherin plays an important role in epithelial development and in the establishment and maintenance of cell–cell adhesion and tissue architecture. The purpose of this study is to investigate the association of an E‐cadherin promoter polymorphism (CDH1c‐160a) with the risk of bladder cancer recurrence. This study included 302 patients with superficial bladder cancer. Genomic DNA was extracted from peripheral blood lymphocytes and genotyping was performed using Taqman assay. Clinical data were collected by medical chart review. Cox proportional hazard model was used to estimate the hazard ratios (HRs) associated with genotypes while adjusting for age, gender, smoking status, tumor stage and grade where appropriate. During a median follow‐up of 27.65 months, 151 patients experienced disease recurrence. Subsequent analyses were restricted to Caucasians only due to the small sample size of other ethnic groups (13 in recurrence group and 15 in non‐recurrence group). Among the 274 Caucasian patients, 138 developed recurrence during the same length of follow‐up time. In Caucasian patients, having at least one variant A allele conferred a 32% reduction in recurrence risk (adjusted HR: 0.68; 95% CI: 0.48–0.96). The median recurrence‐free survival for patients carrying at least one variant A allele was significantly longer than that for patients with a homozygous CC genotype (40.4 vs 12.5 months, p = 0.04). Our findings suggest that the E‐cadherin promoter polymorphism may be a valuable molecular marker for bladder cancer recurrence.
Presence of Multiple Sites Containing Polar Material in Spherical Escherichia coli Cells That Lack MreB

ABSTRACT In rod-shaped bacteria, certain proteins are specifically localized to the cell poles. The nature of the positional information that leads to the proper localization of these proteins is unclear. In a screen for factors required for the localization of the Shigella sp. actin assembly protein IcsA to the bacterial pole, a mutant carrying a transposon insertion in mreB displayed altered targeting of IcsA. The phenotype of cells containing a transposon insertion in mreB was indistinguishable from that of cells containing a nonpolar mutation in mreB or that of wild-type cells treated with the MreB inhibitor A22. In cells lacking MreB, a green fluorescent protein (GFP) fusion to a cytoplasmic derivative of IcsA localized to multiple sites. Secreted full-length native IcsA was present in multiple faint patches on the surfaces of these cells in a pattern similar to that seen for the cytoplasmic IcsA-GFP fusion. EpsM, the polar Vibrio cholerae inner membrane protein, also localized to multiple sites in mreB cells and colocalized with IcsA, indicating that localization to multiple sites is not unique to IcsA. Our results are consistent with the requirement, either direct or indirect, for MreB in the restriction of certain polar material to defined sites within the cell and, in the absence of MreB, with the formation of ectopic sites containing polar material.
Stroke audit.

Medical audit is vital to ensure continuous quality assurance and quality improvements. We did a retrospective study to ascertain the adequacy of clinical documentation and the factors hindering early discharge after an acute stroke in a restructured hospital. The medical records of all patients with acute stroke who died or were discharged from a restructured hospital in Singapore in January and February 1999 were reviewed retrospectively. Demographic data and the presence or absence of clinical documentation were noted. Factors hindering the discharge of patients at Day 5, Day 10 of stroke and at final discharge were noted and classified into: stroke-related, complications of stroke, medical-related and social factors. There were 101 patients in the study cohort, 55 males (54.5%) and 46 females (45.5%). The mean age was 67.9 years (SD 12.3). Documentation in Barthel scores (0%), presence of depression (0%), mental scores (1.0%), visual problems (10.0%), bladder continence (39.6%), admission functional status (37.6%) and dysphagia (52.5%) were deficient. The mean length of stay (LOS) was 13.0 (SD 14.2) days. The main factor hindering discharge at Day 5 (90.4%), Day 10 (95.2%) and at final discharge (82.1%) was stroke-related problems. Poor function (60.3%) and dysphagia (15.8%) were the 2 most common stroke-related problems hindering final discharge. Complications of stroke, medical-related problems and social reasons hindered final discharge in 10.8%, 17.8% and 2.9% of patients respectively. This audit revealed inadequacy in clinical documentation in patients with acute stroke. The main hindrance to final discharge of patients was stroke-related problems. The 2 most important stroke-related problems were poor function and dysphagia.
Short-Term Forecasting Economic Activity in Germany: A Supply and Demand Side System of Bridge Equations

We present a comprehensive disaggregate approach for short-term forecasting economic activity in Germany by explicitly taking into account the supply or production side and the demand side of GDP. The GDP figures calculated by the two sides usually yield different results and the official GDP release is somewhere in between. We make use of this statistical procedure by separately modeling the two sides of GDP in a system of bridge equations at the most disaggregate level available and combining the resulting two aggregate GDP forecasts. Comparing several specification schemes in an out-of-sample forecast evaluation setup, we are able to find informative forecasts for most of the underlying GDP components. We then show first, that both approaches already yield informative aggregate forecasts for forecast horizons of up to 28 weeks and second, that combining the production side and the demand side projections substantially improves the forecast performance, in particular for the shorter forecast horizons.
Genome-wide scan for linkage to schizophrenia in a Spanish-origin cohort from Costa Rica.

Genetic isolates have been useful cohorts in which to search for genes underlying disorders of unknown pathology. One such cohort is thought to exist in the Central Valley of Costa Rica surrounding the city of San Jose. Previous investigators identified a rare dominant gene for hereditary deafness in this population, and a suggestive linkage of severe bipolar psychosis has been reported in another study. Ninety-nine families with at least one pair of siblings affected with schizophrenia or a schizophrenia-spectrum diagnosis had clinical evaluations and DNA collected for genotyping. The Marshfield Medical Research Foundation (NHLBI) Mammalian Genotyping Service performed all genotyping using 404 short-tandem repeat polymorphic markers (STRPs) spaced on average 10 cM apart. Data were analyzed using the nonparametric program, GeneHunterPlus. The population structure was investigated using the STRUCT program. No region was found with genome-wide significance for linkage. Using a phenotype of schizophrenia plus schizoaffective disorder, the highest maximum likelihood score (MLS) observed was 1.78 (P < 0.004) at 176.6 cM from pter on chromosome 5q, an area previously implicated by some other groups. In addition, five regions on chromosomes 1p, 2p, 2q, 14p, and 8p had MLSs above 1.0. All other regions produced scores below 1.0. Population genetic analysis reveals no evidence for population substructure, for admixture with other populations, such as Amerindians, or for inbreeding in the parental generation. The latter casts some doubt on this population being an isolate, although there was evidence of inbreeding among the offspring.
Structure of Human Spindlin1

Spindlin1, a meiotic spindle-binding protein that is highly expressed in ovarian cancer cells, was first identified as a gene involved in gametogenesis. It appeared to be a target for cell cycle-dependent phosphorylation and was demonstrated to disturb the cell cycle. Here we report the crystal structure of human spindlin1 to 2.2Å of resolution, representing the first three-dimensional structure from the spin/ssty (Y-linked spermiogenesis-specific transcript) gene family. The refined structure, containing three repeats of five/four anti-parallel β-strands, exhibits a novel arrangement of tandem Tudor-like domains. Two phosphate ions, chelated by Thr-95 and other residues, appear to stabilize the long loop between domains I and II, which might mediate the cell cycle regulation activity of spindlin1. Flow cytometry experiments indicate that cells expressing spindlin1 display a different cell cycle distribution in mitosis, whereas those expressing a T95A mutant, which had a great decrease in phosphorous content, have little effect on the cell cycle. We further identified associations of spindlin1 with nucleic acid to provide a biochemical basis for its cell cycle regulation and other functions.
Sensory grammars for sensor networks

One of the major goals of Ambient Intelligence and Smart Environments is to interpret human activity sensed by a variety of sensors. In order to develop useful technologies and a subsequent industry around smart environments, we need to proceed in a principled manner. This paper suggests that human activity can be expressed in a language. This is a special language with its own phonemes, its own morphemes (words) and its own syntax and it can be learned using machine learning techniques applied to gargantuan amounts of data collected by sensor networks. Developing such languages will create bridges between Ambient Intelligence and other disciplines. It will also provide a hierarchical structure that can lead to a successful industry.
Optical Coherence Tomography for Brain Imaging and Developmental Biology

Optical coherence tomography (OCT) is a promising research tool for brain imaging and developmental biology. Serving as a three-dimensional optical biopsy technique, OCT provides volumetric reconstruction of brain tissues and embryonic structures with micrometer resolution and video rate imaging speed. Functional OCT enables label-free monitoring of hemodynamic and metabolic changes in the brain in vitro and in vivo in animal models. Due to its noninvasiveness nature, OCT enables longitudinal imaging of developing specimens in vivo without potential damage from surgical operation, tissue fixation and processing, and staining with exogenous contrast agents. In this paper, various OCT applications in brain imaging and developmental biology are reviewed, with a particular focus on imaging heart development. In addition, we report findings on the effects of a circadian gene (Clock) and high-fat diet on heart development in Drosophila melanogaster. These findings contribute to our understanding of the fundamental mechanisms connecting circadian genes and obesity to heart development and cardiac diseases.
Debridement arthroplasty for osteoarthrosis of the elbow: 50 patients followed mean 5 years

The characteristics and surgical outcome of debridement arthroplasty were investigated in athletes and manual laborers with osteoarthrosis of the elbow. There were 26 elbows in athletes, and 24 elbows in laborers. The mean age was 32 years in athletes and 50 years in laborers. The osteoarthrosis was mainly mild in athletes, but moderate or severe in laborers. Debridement arthroplasty, consisting of resection, osteophytes and removal of loose bodies, was performed in all cases. The medial approach was most frequently employed. Surgery relieved pain and improved range of motion at an average follow-up of 59.5 months. Evaluation of the long-term outcomes at more than 5 years showed recurrence of mild osteoarthrosis with minimal symptoms. Debridement arthroplasty is an effective treatment in athletes and manual laborers with osteoarthrosis of the elbow.
An enhanced technique for generating hybrid coverage test cases using activity diagrams

The complexity of software projects is increasing rapidly and in turn both cost and time of the testing process have become a major proportion of the software development process. Thus, it has become a strong motivation to investigate model based testing methods to decrease the overall cost, effort and time of the testing process by automating the generation of the test cases as well as their execution. This paper proposes an enhanced approach for automatically generating test cases from activity diagrams. Category partition method is applied to generate the final set of reduced test cases. The proposed model validates the generated test paths during the generation process to ensure that they meet a hybrid coverage criterion. The proposed model is automated and applied to around forty different case studies in different domains. Experimental evaluation is demonstrated to prove that the proposed model saves time and cost, thus increases the performance of the testing process.
Phoenix Populism

This paper is the first exploratory analysis of the ideological features of extra-parliamentary radical-right populist parties in Romania, which, despite lacking parliamentary power, confirm the latent fertility of Romanian politics for populism. Using qualitative content analysis of programs and statutes, we identify a decreased relevance of ethnicity-based mobilization and an increased emphasis on cultural, religious, and/or gender-based criteria. All of the analyzed parties converge on the need for increased discipline and major anti-corruption measures, a smooth continuity with previous forms of populism. The extra-parliamentary group of Romanian radical populists resembles a phoenix, regularly rising from its ashes, although only partially renewed.
Regulation of lens cell growth and polarity by an embryo-specific growth factor and by inhibitors of lens cell proliferation and differentiation.

We used a double-label method, which monitors the rate at which cells enter S-phase of the cell cycle, to identify factors that control the growth of chicken embryo lens epithelial cells in vivo. With this assay, we identified a mitogen for lens epithelial cells in the anterior segment of the embryonic eye. When the anterior chamber was opened briefly, by tearing the cornea or displacing the lens, the growth-promoting activity was lost. None of the purified growth factors tested replaced this growth activity, including EGF, bFGF, PDGF, IGF-1, IGF-2, TGF beta and mixtures of these factors. However, chicken embryo serum or plasma did cause chicken embryo lens epithelial cells to progress through the cell cycle. The activity in serum was destroyed by heat and protease treatment. It was most active in serum from 10-day embryos, decreased with subsequent development and was undetectable from 2 days after hatching through adulthood. When embryo serum or plasma was mixed with vitreous humor or IGF-1, agents that induce lens fiber cell formation, cell elongation was prevented. In contrast to the mitogenic activity in serum, this inhibitor of differentiation was insensitive to trypsin treatment. We also identified an activity in vitreous humor that inhibited the growth-promoting agent in embryo serum. Plasma proteins readily enter the anterior chamber of the eye of chicken embryos. (ABSTRACT TRUNCATED AT 250 WORDS)