Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytokine-like 1 (CYTL1) Regulates the Chondrogenesis of Mesenchymal Cells*

To identify novel molecules regulating chondrogenesis and cartilage development, we screened a cartilage-specific expressed sequence tag data base. Cytokine-like 1 (Cytl1), a possible cytokine candidate with unknown function that was originally identified in bone marrow-derived CD34-positive cells, was selected for functional characterization. In view of the initial observation that Cytl1 is predominantly expressed in chondrocytes and cartilage, we investigated its possible role in chondrogenesis and hypertrophic maturation of chondrocytes. Cytl1 expression was very low in mesenchymal cells, dramatically increased during chondrogenesis, and decreased during hypertrophic maturation, both in vivo and in vitro. The role of Cytl1 in chondrogenesis and hypertrophic maturation was examined by treating chondrifying mesenchymal cells with exogenous Cytl1 or ectopic expression of Cytl1. Notably, exogenous Cytl1 caused chondrogenic differentiation of mouse limb bud mesenchymal cells during micromass culture. Lentivirus-mediated overexpression of Cytl1 additionally induced chondrogenic differentiation of mesenchymal cells. However, Cytl1 did not affect the hypertrophic maturation of chondrocytes. Cytl1 exerted its chondrogenic effect via stimulation of Sox9 transcriptional activity. In addition, Cytl1 caused expression of insulin-like growth factor 1, which has a capacity to induce chondrogenesis. Thus, our results collectively suggest that chondrocyte-specific Cytl1 regulates chondrogenesis as a novel autocrine factor, but not hypertrophic maturation of chondrocytes during cartilage development.
Private Cleanliness, Public Mess: Purity, Pollution and Space in Kottar, South India

Vasil, Raj and H.K. Yoon 1996. New Zealallders of Asillli Origill. Institute of Policy Studies: Victoria University of Wellington. Ward, C. and E. -y' Lin 2005. 'Immigration, Acculturation and National Identity', in: New Zealal1d Idelltities. Departures and Destillatiolls. H. ]. Liu, T. McCreanor, T. McIntosh and T. Teaiwa (eds), pp. 155-73. Wellington: Victoria Uni"ersity Press. Webster, A. 2001. Spiral of Values. Hawera: Alpha Publications. CHAPTER 3
Effects of dispersed point substitutions in Repeat 1 of human interphotoreceptor retinoid binding protein (IRBP).

PURPOSE The purpose of this study was to measure the effects of mutations on the retinol binding capability of human Repeat 1 of interphotoreceptor retinoid-binding protein (IRBP). First, we predicted important functional amino acids by several computer programs. We also noted the lack of shared functions between Tail-specific protease (Tsp) and IRBP, which bear sequence similarity, and this aided in predicting functional residues. We analyzed the effects of point substitutions on the retinol and fatty acid binding properties of Repeat 1 of human IRBP at 25 and 50 degrees C. METHODS To find residues critical to retinol binding that might affect function, a series of thirteen mutations were created by site-specific mutagenesis between positions 140 and 280 in Repeat 1 of human IRBP. These mutants were expressed, purified, and tested for binding properties. The conformations of the proteins were examined by circular dichroism (CD) scans. RESULTS Seven of the mutations exhibited reduced binding capacity, and five were not expressed at high enough levels to assess binding activity. Four of the mutants were purified, and their CD scans were very similar to those of Repeat 1. Only one of the mutations did not affect binding, folding, or expression when compare to wild type Repeat 1. CONCLUSIONS Several IRBP mutants containing point mutations retained native structure but lost retinol binding function. The data suggest that retinol binding is affected by many different amino acid substitutions in or near a binding pocket. That even a single point substitution can profoundly affect binding without affecting overall conformation suggests that much of Domain B (from amino acid positions 80 to 300) is involved with ligand binding. This excludes three previously proposed IRBP-retinol binding mechanisms: (1) retinol binds to a small portion of the protein repeat, (2) retinol can bind to any hydrophobic patch in the protein, and (3) native conformation is not required for retinol binding to the repeat.
Mechanism of Progressive Heart Failure and Significance of Pulmonary Hypertension in Obstructive Hypertrophic Cardiomyopathy

Background— There are limited data on the prevalence, pathophysiology, and management implications of pulmonary hypertension in patients with obstructive hypertrophic cardiomyopathy and advanced heart failure. Methods and Results— To assess the clinical significance of measured cardiopulmonary hemodynamics in hypertrophic cardiomyopathy patients with heart failure, we retrospectively assessed right heart catheterization data in 162 consecutive patients with outflow tract gradients (median [interquartile range], 90 mm Hg [70–110 mm Hg]), 59±11 years old, and 49% men, predominately New York Heart Association class III/IV status. Pulmonary hypertension (mean pulmonary artery pressure, ≥25 mm Hg) was present in 82 patients (51%), including 29 (18%) regarded as moderate-severe (mean pulmonary artery pressure, ≥35 mm Hg) and 28 (34%) also had increased pulmonary vascular resistance >3.0 WU. The pulmonary artery wedge pressure was ⩽15 mm Hg in 54%, indicating that left atrial hypertension was absent in a majority of patients. Notably, 9 patients (11%) met hemodynamic criteria for precapillary pulmonary hypertension (mean pulmonary artery pressure, ≥25 mm Hg; pulmonary vascular resistance, >3.0 WU; pulmonary artery wedge pressure, ⩽15 mm Hg). Over a median follow-up of 327 days (90–743 days) after surgical myectomy (or alcohol septal ablation), 92% and 95% of patients with or without preoperative pulmonary hypertension, respectively, were asymptomatic or mildly symptomatic. One postoperative death occurred in a 59-year-old woman with acute respiratory failure and mean pulmonary artery pressure of 65 mm Hg. Conclusions— Pulmonary hypertension was common in obstructive hypertrophic cardiomyopathy patients with advanced heart failure. Although possibly a contributor to preoperative heart failure, pulmonary hypertension did not significantly influence clinical and surgical outcome. Notably, a novel patient subgroup was identified with resting invasive hemodynamics consistent with pulmonary vascular disease.
Statistical Study of Imported APIs by PE Type Malware

In this paper we introduce a statistical study which enable us to know which are Windows APIs that are most imported by malware codes. To do that, we have used a given number of infected Portable Executable (PE) files and another number of none infected ones. We used statistical Khi2 test to set if an API is likely used by malware or not. We guess that a given work is necessary and important for behavior-based malware detection, especially which use API importations to analyze PE codes. For experimentation purpose, we have used a large set of PE files extracted from known databases to perform our analysis and establish our conclusions.
Geocoding Addresses from a Large Population-based Study: Lessons Learned

Background Geographic information systems (GIS) and spatial statistics are useful for exploring the relation between geographic location and health. The ultimate usefulness of GIS depends on both completeness and accuracy of geocoding (the process of assigning study participants’ residences latitude/longitude coordinates that closely approximate their true locations, also known as address matching). The goal of this project was to develop an iterative geocoding process that would achieve a high match rate in a large population-based health study. Methods Data were from a study conducted in Wisconsin using mailing addresses of participants who were interviewed by telephone from 1988 to 1995. We standardized the addresses according to US Postal Service guidelines, used desktop GIS geocoding software and two versions of the Topologically Integrated Geographic Encoding and Referencing street maps, accessed Internet mapping engines for problematic addresses, and recontacted a small number of study participants’ households. We also tabulated the project’s cost, time commitment, software requirements, and brief notes for each step and their alternatives. Results Of the 14,804 participants, 97% were ultimately assigned latitude/longitude coordinates corresponding to their respective residences. The remaining 3% were geocoded to their zip code centroid. Conclusion The multiple methods described in this work provide practical information for investigators who are considering the use of GIS in their population health research.
A Distributed, Complete Method for Multi-Agent Constraint Optimization

We present in this paper a new complete method for distributed constraint optimization. This is a utility-propagation method, inspired by the sum-product algorithm. The original algorithm requires fixed message sizes, linear memory, and is time-linear in the size of the problem. However, it is correct only for tree-shaped constraint networks. In this paper, we show how to extend the algorithm to arbitrary topologies using cycle cutsets, while preserving the linear message size and memory requirements. We present some preliminary experimental results on randomly generated problems. The algorithm is formulated for optimization problems, but can be easily applied to satisfaction problems as well.
The diagnostic accuracy of multi-frequency bioelectrical impedance analysis in diagnosing dehydration after stroke

Background Non-invasive methods for detecting water-loss dehydration following acute stroke would be clinically useful. We evaluated the diagnostic accuracy of multi-frequency bioelectrical impedance analysis (MF-BIA) against reference standards serum osmolality and osmolarity. Material/Methods Patients admitted to an acute stroke unit were recruited. Blood samples for electrolytes and osmolality were taken within 20 minutes of MF-BIA. Total body water (TBW%), intracellular (ICW%) and extracellular water (ECW%), as percentages of total body weight, were calculated by MF-BIA equipment and from impedance measures using published equations for older people. These were compared to hydration status (based on serum osmolality and calculated osmolarity). The most promising Receiver Operating Characteristics curves were plotted. Results 27 stroke patients were recruited (mean age 71.3, SD10.7). Only a TBW% cut-off at 46% was consistent with current dehydration (serum osmolality >300 mOsm/kg) and TBW% at 47% impending dehydration (calculated osmolarity ≥295–300 mOsm/L) with sensitivity and specificity both >60%. Even here diagnostic accuracy of MF-BIA was poor, a third of those with dehydration were wrongly classified as hydrated and a third classified as dehydrated were well hydrated. Secondary analyses assessing diagnostic accuracy of TBW% for men and women separately, and using TBW as a percentage of lean body mass showed some promise, but did not provide diagnostically accurate measures across the population. Conclusions MF-BIA appears ineffective at diagnosing water-loss dehydration after stroke and cannot be recommended as a test for dehydration, but separating assessment by sex, and using TBW as a percentage of lean body weight may warrant further investigation.
Facilitating Middle Level Pre-Service Teachers' Literacy Integration in Early Field Experiences.

This study explored how pre-service teachers integrated literacy in middle level social studies. This study was conducted in the context of the Common Core State Standards (CCSS) and their focus on disciplinary literacy, the Council for the Accreditation of Educator Preparation (CAEP) Standards and their focus on rich clinical experiences, and concepts of interdisciplinary and integrated curriculum central to middle level philosophy (NMSA, 2010). Three pre-service teachers in their first extended field practicum took part in this collective case study (Yin, 2009). We identified two key findings. First, these pre-service teachers primarily integrated literacy in ways that were brief, teacher-directed, and sometimes optional for students. Second, and more promising, the pre-service teachers integrated more complex disciplinary literacy tasks when they made connections among literacy strategies, the content, and their students’ needs. These more complex literacy tasks often were developed through collaborative, structured conversations between each pre-service teacher and the university supervisor.
Intraoperative Fluorescence Imaging for Personalized Brain Tumor Resection: Current State and Future Directions

Introduction Fluorescence-guided surgery is one of the rapidly emerging methods of surgical “theranostics. ” In this review, we summarize current fluorescence techniques used in neurosurgical practice for brain tumor patients as well as future applications of recent laboratory and translational studies. Methods Review of the literature. Results A wide spectrum of fluorophores that have been tested for brain surgery is reviewed. Beginning with a fluorescein sodium application in 1948 by Moore, fluorescence-guided brain tumor surgery is either routinely applied in some centers or is under active study in clinical trials. Besides the trinity of commonly used drugs (fluorescein sodium, 5-aminolevulinic acid, and indocyanine green), less studied fluorescent stains, such as tetracyclines, cancer-selective alkylphosphocholine analogs, cresyl violet, acridine orange, and acriflavine, can be used for rapid tumor detection and pathological tissue examination. Other emerging agents, such as activity-based probes and targeted molecular probes that can provide biomolecular specificity for surgical visualization and treatment, are reviewed. Furthermore, we review available engineering and optical solutions for fluorescent surgical visualization. Instruments for fluorescent-guided surgery are divided into wide-field imaging systems and hand-held probes. Recent advancements in quantitative fluorescence-guided surgery are discussed. Conclusion We are standing on the threshold of the era of marker-assisted tumor management. Innovations in the fields of surgical optics, computer image analysis, and molecular bioengineering are advancing fluorescence-guided tumor resection paradigms, leading to cell-level approaches to visualization and resection of brain tumors.
Two-dimensional unconfined seepage flow toward a highway cut slope

The unconfined gravity-flow system near a free-outflow boundary such as a highway cut slope was investigated by using a higher-order numerical model. Unlike the Dupuit–Forchheimer equation, which is applicable mainly to a hydraulic flow problem, the proposed model accounts for the effects of the vertical component of the flow for a full treatment of the problem of plane phreatic flow. The model equations were numerically solved by means of a finite-difference scheme. Their accuracy was then verified using the solutions of the full two-dimensional potential-flow method and rigorous mathematical approaches, revealing that for a face slope flatter than 70º, the differences between the solutions of the model and the earlier approaches for the relative seepage-face height were nearly negligible. The comparison results also demonstrated the substantial effects of the slope of the downstream face on this height and the seepage discharge. Furthermore, the accuracies of the model predictions for the phreatic-surface profile and the distributions of the piezometric head at different vertical sections are much better than the earlier method, which approximates the trapezoidal-shaped aquifer by its equivalent rectangular one. Such a satisfactory performance may be attributed to the model’s higher-order correction factor for the effects of the phreatic-surface curvature and steep slope.
Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl

Nuclear disasters at Chernobyl and Fukushima provide examples of effects of acute ionizing radiation on mutations that can affect the fitness and distribution of species. Here, we investigated the prevalence of Microbotryum lychnidis‐dioicae, a pollinator‐transmitted fungal pathogen of plants causing anther‐smut disease in Chernobyl, its viability, fertility and karyotype variation, and the accumulation of nonsynonymous mutations in its genome. We collected diseased flowers of Silene latifolia from locations ranging by more than two orders of magnitude in background radiation, from 0.05 to 21.03 μGy/h. Disease prevalence decreased significantly with increasing radiation level, possibly due to lower pollinator abundance and altered pollinator behaviour. Viability and fertility, measured as the budding rate of haploid sporidia following meiosis from the diploid teliospores, did not vary with increasing radiation levels and neither did karyotype overall structure and level of chromosomal size heterozygosity. We sequenced the genomes of twelve samples from Chernobyl and of four samples collected from uncontaminated areas and analysed alignments of 6068 predicted genes, corresponding to 1.04 × 107 base pairs. We found no dose‐dependent differences in substitution rates (neither dN, dS, nor dN/dS). Thus, we found no significant evidence of increased deleterious mutation rates at higher levels of background radiation in this plant pathogen. We even found lower levels of nonsynonymous substitution rates in contaminated areas compared to control regions, suggesting that purifying selection was stronger in contaminated than uncontaminated areas. We briefly discuss the possibilities for a mechanistic basis of radio resistance in this nonmelanized fungus.
Photonic detection and characterization of DNA using sapphire microspheres

Abstract. A microcavity-based deoxyribonucleic acid (DNA) optical biosensor is demonstrated for the first time using synthetic sapphire for the optical cavity. Transmitted and elastic scattering intensity at 1510 nm are analyzed from a sapphire microsphere (radius 500 μm, refractive index 1.77) on an optical fiber half coupler. The 0.43 nm angular mode spacing of the resonances correlates well with the optical size of the sapphire sphere. Probe DNA consisting of a 36-mer fragment was covalently immobilized on a sapphire microsphere and hybridized with a 29-mer target DNA. Whispering gallery modes (WGMs) were monitored before the sapphire was functionalized with DNA and after it was functionalized with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). The shift in WGMs from the surface modification with DNA was measured and correlated well with the estimated thickness of the add-on DNA layer. It is shown that ssDNA is more uniformly oriented on the sapphire surface than dsDNA. In addition, it is shown that functionalization of the sapphire spherical surface with DNA does not affect the quality factor (Q≈104) of the sapphire microspheres. The use of sapphire is especially interesting because this material is chemically resilient, biocompatible, and widely used for medical implants.
The influence of category representations on exemplar generation

The present study examined the influence of category representations on exemplar generation, which has been neglected in previous category research. An experiment on college students manipulated the category representation of insects in three conditions (prototypes, exemplars, and the hybrid of prototypes and exemplars). Participants were asked to generate as many exemplars as possible. The results demonstrate that category representations affect and constrain exemplar generation. The new findings are as follows. In the prototype and hybrid conditions with the prototype representation, people tend to generate more valid exemplars by using the prototype mutation mechanism, and exemplar generation conforms to the family resemblance structure. Exemplar generation in the hybrid condition is additionally constrained by known exemplars. In the exemplar condition, people tend to generate fewer valid exemplars by using miscellaneous strategies, and their exemplar generation may not conform to the family resemblance structure.
Homology of the 74-kD cytoplasmic dynein subunit with a flagellar dynein polypeptide suggests an intracellular targeting function

In previous work we found cytoplasmic dynein to be a complex of two catalytic heavy chains and at least seven co-purifying polypeptides of unknown function. The most prominent of these is a 74-kD electrophoretic species which can be resolved as two to three bands by SDS-PAGE. We have now selected a series of overlapping rat brain cDNAs encoding the 74-kD species. The deduced sequence of a full-length cDNA predicts a 72,753 D polypeptide which includes the amino acid sequences of nine peptides determined by NH2-terminal microsequencing. PCR performed on first strand rat brain cDNA together with the sequence of a partially matching tryptic peptide indicated the existence of at least three isoforms of the 74-kD cytoplasmic dynein subunit. Comparison with known sequences revealed that the carboxyl-terminal half of the polypeptide is 26.4% identical and 47.7% similar to the product of the Chlamydomonas ODA6 gene, a 70-kD intermediate chain of flagellar outer arm dynein. Immunoblot analysis with a monoclonal antibody to the 74-kD species indicated a widespread tissue distribution, as expected for a cytoplasmic dynein subunit. Nonetheless, the antibody recognized a 67-kD species in ram sperm flagella and pig tracheal cilia, supporting the existence of distinct but related cytoplasmic and axonemal polypeptides in mammals. In view of evidence for a role for the ODA6 gene product in anchoring flagellar dynein to the A subfiber microtubule in the axoneme, we predict an analogous role for the 74-kD polypeptide, perhaps in mediating the interaction of cytoplasmic dynein with membranous organelles and kinetochores.
A method for extracting the leaf litter distribution area in forest using chip feature

ABSTRACT The leaf litter layer is an important surface coverage in the forest ecosystem, which imposes an important influence on soil and water conservation and affects the soil physical and chemical characteristics as well as the ecological environment. It is also a significant factor in estimating vegetation coverage. Currently, most remote-sensing methods to obtain leaf litter target are based on the analysis of the spectral features. However, the leaf litter and the soil background are easily confused. The traditional image processing method based on the pixel spectral information alone fails to make full use of the texture and shape information of the target and diminishes the extraction effect. With the research object focused on the continuous distribution area of leaf litter, whose features are intra-class complicated and inter-class boundary blurred, this article proposes a method to extract the leaf litter distribution area in forest by using the Convolutional Neural Network (CNN) to automatically retrieve the image block (which is also called image chip) features. The ResNet50, VGG16, and VGG19 models based on CNN are, respectively, used to extract and to learn the features of the image chips so that they can automatically obtain the deeper, more abstractive and representative features. The accuracy of this method in leaf litter target extraction has reached 95.1% which demonstrated that this new method has higher classification accuracy and better generalization ability than the traditional method of manually selecting image features. Moreover, the use of pretraining models can solve the problem in deep learning with small sample size. Through the study of scale effects, we also found the appropriate segmentation scale for the chips.