Miracle-dz/UniFAR-FTUs huggingface dataset:
Innate immunity proteins in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis

ABSTRACT Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) may be caused by epithelial cell injury. Epithelial cells respond to injury by secreting innate immunity proteins. To investigate whether altered levels of innate immunity proteins are observed in COPD and IPF, the authors assessed secretory leukocyte protease inhibitor (SLPI), elafin, CC16, and β-defensin-2 levels by enzyme-linked immunosorbent assay (ELISA) in sputum supernatants from COPD patients (n = 19), smokers without COPD (n = 21), and never-smokers (n = 10) and in BALF supernatants from patients with IPF (n = 11) and subjects without IPF (n = 11). CC16 levels were decreased, whereas SLPI and elafin levels were increased in COPD patients (0.8 [0–4.2] μg/mL, 2.5 [0.3–10.5] μg/mL, 213 [152–318] pg/mL, respectively) compared to smokers without COPD (1.8 [0.1–21.2] μg/mL, 0.8 [0.2–2.6] μg/mL, 172 [71–473] pg/mL, respectively) and never-smokers (0.5 [0–4.8] μg/mL, 0.1 [0.05–0.6] μg/mL, 188 [129–218] pg/mL, respectively) (CC16: P = .001; SLPI: P <.001; elafin: P = .041). β-Defensin-2 was detected in smokers without COPD (98 [10–729] pg/mL) and never-smokers (74 [35–410] pg/mL), but not in COPD. SLPI and elafin levels did not differ between IPF patients and controls, but CC16 levels were increased in IPF (0.5 [0–2.3] versus 0.2 [0–0.3] μg/mL; P = .019). β-Defensin-2 was not detected in BALF. In conclusion, in COPD, secretion of CC16 and β-defensin-2 might be suppressed, whereas SLPI and elafin secretion is up-regulated. In IPF, only CC16 secretion is up-regulated.
Regulation of estrogen receptor messenger ribonucleic acid and protein levels in human breast cancer cell lines by sex steroid hormones, their antagonists, and growth factors.

Since sex steroid hormones and growth factors are known to modulate the proliferation of breast tumors, we have studied the effects of estrogen and progestin, their antagonists, and growth factors on the regulation of estrogen receptor (ER) mRNA and protein levels in T47D breast cancer cells, which contain low levels of ER, and in two sublines of MCF-7 cells which contain high ER levels. The mRNA levels were measured by Northern blot analysis using lambda OR8, a cDNA probe for ER, and protein levels were measured by hormone binding or Western blot analysis. Treatment of T47D cells with estradiol (E2) caused a 2.5-fold increase in ER mRNA (6.6 kilobases) levels after 48 h. The progestin R5020 evoked a marked decrease in ER mRNA and protein levels to 20% of control values, while the antiprogestin RU38,486 caused no change in ER. In MCF-7 cells, the effect of E2 on ER levels was dependent on the prior growth history of the cells. In cells grown in low estrogen [5% charcoal-dextran-treated calf serum with phenol red for 8 yr (MCF-7-K2)], which are still E2 responsive, treatment with E2, the antiestrogen LY117018, or both produced little change in ER mRNA or protein; in contrast, ER mRNA and protein were reduced by E2 to 40% and 50% of control levels, respectively, in MCF-7 cells (denoted MCF-7-K1) which had been maintained routinely in medium containing 5% calf serum. This decrease in ER mRNA was dose dependent; 10(-11) E2 reduced levels to 60%, and 10(-10) M E2 evoked the maximal drop to 40% of the control level in 2 days. LY117018 alone did not alter ER mRNA levels in these cells, but it completely prevented the down-regulation of ER by E2. Administration of progestin, but not antiprogestin, along with E2 partially prevented the decrease in ER evoked by E2. Addition of epidermal growth factor or insulin-like growth factor-I to MCF-7-K1 cells, which increased cell proliferation, had no detectable effect on ER levels. Treatment with transforming growth factor-beta, which decreased cell proliferation, reduced ER by about 20%. (ABSTRACT TRUNCATED AT 400 WORDS)
Early warnings of hazardous thunderstorms over Lake Victoria

Weather extremes have harmful impacts on communities around Lake Victoria in East Africa. Every year, intense nighttime thunderstorms cause numerous boating accidents on the lake, resulting in thousands of deaths among fishermen. Operational storm warning systems are therefore crucial. Here we complement ongoing early warning efforts based on numerical weather prediction, by presenting a new satellite data-driven storm prediction system, the prototype Lake Victoria Intense storm Early Warning System (VIEWS). VIEWS derives predictability from the correlation between afternoon land storm activity and nighttime storm intensity on Lake Victoria, and relies on logistic regression techniques to forecast extreme thunderstorms from satellite observations. Evaluation of the statistical model reveals that predictive power is high and independent of the type of input dataset. We then optimise the configuration and show that false alarms also contain valuable information. Our results suggest that regression-based models that are motivated through process understanding have the potential to reduce the vulnerability of local fishing communities around Lake Victoria. The experimental prediction system is publicly available under the MIT licence at http://github.com/wthiery/VIEWS.
Integration of hepatitis B virus: analysis of unoccupied sites

Hepatitis B virus (HBV) sequences integrated in the PLC/PRF/5 cell line (Alexander cells), which was derived from a human primary liver carcinoma, were previously extensively studied. Here we describe the analysis of the unoccupied sites of two linearly integrated forms of HBV DNA, AL-14 and AL-26, that were characterized previously. No major cellular DNA rearrangements were seen at the integration sites except for small deletions of host sequences: 2 kilobases of DNA in AL-14 and 17 base pairs (bp) in AL-26. The unoccupied site of AL-26 was found to be missing 182 bp, which previously mapped next to the right end of the integration sites of several independent clones. These were believed to be of cellular origin, but we show here that these 182 bp are in fact from unusual HBV sequences. Surprisingly, a region of this newly detected HBV DNA sequence is more homologous to that of woodchuck HBV DNA. Our analysis shows that the normal counterparts of both AL-14 and AL-26 contain minisatellite-like repetitive sequences. Based on the data presented here and our previous finding of HBV DNA integration at satellite sequences, we propose that genomic simple repetitive sequences are hot spots for HBV DNA integration.
Comparison of SOI Versus Bulk FinFET Technologies for 6T-SRAM Voltage Scaling at the 7-/8-nm Node

The electrostatic benefit of using a silicon-on-insulator (SOI) wafer substrate versus a bulk-silicon wafer substrate with optimized supersteep retrograde (SSR) doping for a low-power 7-/8-nm FinFET technology is investigated via 3-D device simulations and a fitted compact model to estimate the manufacturing yield of six-transistor SRAM cells. SOI FinFET technology is projected to provide only slight improvement in performance and minimum cell operating voltage as compared with SSR FinFET technology.
Characterizing the Uncertainty of the Fundamental Matrix

This paper deals with the analysis of the uncertainty of the fundamental matrix. The basic idea is to compute the fundamental matrix and its uncertainty at the same time. We give two different methods. The first one is a statistical approach. As in all statistical methods the precision of the results depends on the number of analyzed samples. This means that we can always improve our results if we increase the number of samples but this process is very time consuming. Alternatively, we propose a much simpler method which gives analytical results which are close to the results of the statistical method. Experiments with synthetic and real data have been conducted to validate the proposed methods. At the end of the paper, we provide three applications of the estimated uncertainty of the fundamental matrix: definition of the epipolar band for stereo matching, projective reconstruction, and self-calibration.
Hypercoagulabilty, venous thromboembolism, and death in patients with cancer

Summary Venous thromboembolism (VTE) is a frequent complication of malignancy. The aim of this study was to investigate whether multi-state modelling may be a useful quantitative approach to dissect the complex epidemiological relationship between hypercoagulability, VTE, and death in cancer patients. We implemented a three-state/three-transition unidirectional illness-death model of cancer-associated VTE in data of 1,685 cancer patients included in a prospective cohort study, the Vienna Cancer and Thrombosis Study (CATS). During the two-year follow-up period, 145 (8.6%) patients developed VTE, 79 (54.5%) died after developing VTE, and 647 (38.4%) died without developing VTE, respectively. VTE events during follow-up were associated with a three-fold increase in the risk of death (Transition Hazard ratio (HR)=2.98, 95% confidence interval [CI]: 2.36-3.77, p< 0.001). This observation was independent of cancer stage. VTE events that occurred later during follow-up exerted a stronger impact on the risk of death than VTE events that occurred at earlier time points (HR for VTE occurrence one year after baseline vs at baseline=2.30, 95% CI: 1.28-4.15, p=0.005). Elevated baseline D-dimer levels emerged as a VTE-independent risk factor for mortality (HR=1.07, 95% CI: 1.05-1.08, p< 0.001), and also predicted mortality risk in patients who developed VTE. A higher Khorana Score predicted both the risk for VTE and death, but did not predict mortality after cancer-associated VTE. In conclusion, multi-state modeling represents a very potent approach to time-to-VTE cohort data in the cancer population, and should be used for both observational and interventional studies on cancer-associated VTE.
IFRS Adoption in Emerging Markets: The Case of Jordan

The aim of this study is to research the adoption of International Financial Reporting Standards (IFRS) in Jordan, which was one of the first Middle Eastern emerging economies to adopt IFRS. The paper investigates the related factors that pressure and prevent such adoption over time, and illustrates the developmental aspects of such adoption. An interpretive methodology is employed, and perceptions of the study's participants are analysed regarding the adoption of IFRS in Jordan, which is an area that is under researched. Semiâ€ structured interviews were undertaken to collect Jordanian expertsâ€™ perceptions. Based on the empirical data analysis and prior theoretical and empirical literature, an adoption model was developed, which can serve future studies as well. The model illustrates the paradox of accounting changes in emerging economies, in which the actual conditions that pressure IFRS adoption are also the conditions that prevent full adoption. The model also provides an explanation of the implementation process of IFRS in emerging economies at both country and corporation levels. It combines practical features and related theories in an integrative model seeking to explain the phenomenon of IFRS as a new accounting regulation change.
A 12-bit charge-redistribution SAR ADC for silicon drift detector readout ASICs

This paper presents a first prototype of a 12-bit analog-to-digital converter (ADC) suitable for X and γ-ray multichannel readout front-ends for SDD signals processing. The task of the converter is the digitization of output multiplexed data at a sampling frequency up to 5 MS/s and about 11-bit accuracy. The chosen architecture is the fully-differential bridge-capacitor charge-redistribution (CR) successive-approximation-register (SAR) with monotonic switching algorithm. The chip is fabricated in a standard CMOS 0.35 μm 3.3 V technology and the ADC area occupancy is 0.42 mm2. The measured input-output characteristic shows monotonicity over the whole dynamic range while static parameters are -0.17/1.22 LSB and -2.2/2.2 LSB respectively for differential (DNL) and integral nonlinearity (INL). Dynamic performance consist in 68 dB SFDR, 66.5 dB SiNAD and an effective number of bits (ENOB) equal to 10.75 at 4 MS/s. An in-depth analysis of the circuit topology together with simulated and experimental results are here presented.
Factors that Influence Women Entrepreneurial Success in Malaysia : A Conceptual Framework Shamsul

A number of factors have been suggested to explain how the success among women entrepreneurs can be improved. To date, some factors have been considered to influence the success of women entrepreneurs such as human capital, networking, financial aids, and opportunity. Despite these studies, entrepreneurial characteristics have been suggested to be studied in order to determine the success among women entrepreneurs. Based on previous literature, there are four characteristics which frequently cited to influence the success among women entrepreneurs which are need for achievement, risk taking, self-confidence and creative and innovative. While for the success of women entrepreneurs, it will be measured by non-financial aspects because women will become less successful if compared in terms of financial aspects since they usually owned small and slower growing business. The contribution of the study are also discussed.
Overcoming the absence of socioeconomic data in medical records: validation and application of a census-based methodology.

BACKGROUND Most US medical records lack socioeconomic data, hindering studies of social gradients in health and ascertainment of whether study samples are representative of the general population. This study assessed the validity of a census-based approach in addressing these problems. METHODS Socioeconomic data from 1980 census tracts and block groups were matched to the 1985 membership records of a large prepaid health plan (n = 1.9 million), with the link provided by each individual's residential address. Among a subset of 14,420 Black and White members, comparisons were made of the association of individual, census tract, and census block-group socioeconomic measures with hypertension, height, smoking, and reproductive history. RESULTS Census-level and individual-level socioeconomic measures were similarly associated with the selected health outcomes. Census data permitted assessing response bias due to missing individual-level socioeconomic data and also contextual effects involving the interaction of individual- and neighborhood-level socioeconomic traits. On the basis of block-group characteristics, health plan members generally were representative of the total population; persons in impoverished neighborhoods, however, were underrepresented. CONCLUSIONS This census-based methodology offers a valid and useful approach to overcoming the absence of socioeconomic data in most US medical records.
Online discriminative tracker with selective feature update

Visual tracking has been a challenge in the computer vision field for a long time now because of the many uncertainties present. Ideally, a tracker should be able to withstand certain problems in tracking with minimal computation time. Some of the difficult situations are background clutter, partial occlusions and illumination changes to name a few. In this paper, a discriminative tracker using SURF descriptors is improved by using a Particle Filter framework for translation prediction and a novel selective feature update for the classifiers. This implementation is to address the issue of fast motion and drift during the online-learning process.
The developmental neurotoxicity of polybrominated diphenyl ethers: Effect of DE‐71 on dopamine in zebrafish larvae

The potential neurotoxicity of polybrominated diphenyl ethers (PBDEs) is still a great concern. In the present study, the authors investigated whether exposure to PBDEs could affect the neurotransmitter system and cause developmental neurotoxicity in zebrafish. Zebrafish embryos (2 h postfertilization) were exposed to different concentrations of the PBDE mixture DE‐71 (0–100 μg/L). The larvae were harvested at 120 h postfertilization, and the impact on dopaminergic signaling was investigated. The results revealed significant reductions in content of whole‐body dopamine and its metabolite, dihydroxyphenylacetic acid, in DE‐71–exposed larvae. The transcription of genes involved in the development of dopaminergic neurons (e.g., manf, bdnf, and nr4a2b) was significantly downregulated upon exposure to DE‐71. Also, DE‐71 resulted in a significant decrease of tyrosine hydroxylase and dopamine transporter protein levels in dopaminergic neurons. The expression level of tyrosine hydroxylase in forebrain neurons was assessed by whole‐mount immunofluorescence, and the results further demonstrated that the tyrosine hydroxylase protein expression level was reduced in dopaminergic neurons. In addition to these molecular changes, the authors observed reduced locomotor activity in DE‐71–exposed larvae. Taken together, the results of the present study demonstrate that acute exposure to PBDEs can affect dopaminergic signaling by disrupting the synthesis and transportation of dopamine in zebrafish, thereby disrupting normal neurodevelopment. In accord with its experimental findings, the present study extends knowledge of the mechanisms governing PBDE‐induced developmental neurotoxicity. Environ Toxicol Chem 2015;34:1119–1126. © 2015 SETAC
Comparison of genetic variation in growth performance on normal and novel host plants in a local population of a herbivorous ladybird beetle, Epilachna vigintioctomaculata

Local populations of herbivore species that display variation in host plant use are subject to natural selection for improved ability to use their own host species. Since natural selection changes the frequency of alleles that control host use, genetic variation in growth performance on host plants may change with each generation of selection. Therefore, within-population variations in the ability to use different hosts may reflect past selective forces. The present study reports the genetic variation in growth performance in a population of the herbivorous ladybird beetle, Epilachna vigintioctomaculata Motschulsky (Coccinellidae, Epilachninae) on both the normal host and a novel host. The present study found higher heritabilities for growth performance on the novel host than the normal host. The difference in heritabilities was caused by smaller among-family variance components on the normal host compared to those on the novel host. The results are compatible with the view that natural selection, which improved the ability of the population to use a particular host plant, has reduced genetic variation within that population in the ability to use that host plant. The pattern of reduced genetic variation in a population reared on the normal host observed in the present study is compared with that in another population, which showed local adaptation in the use of its own host plant. The effect of natural selection on differing host plant use on within-population genetic variation is discussed.
Consensus of second-order multi-agent systems under time-varying communication networks

The connectivity of information exchange network plays a key role in consensus-seeking for multi-agent systems. However, the absence of connectivity often occurs in practical application circumstances. In this paper, consensus problem of a class of second-order multi-agent systems under time-varying communication networks is considered, where the different connectivity conditions are discussed in detail. Sufficient and/or necessary conditions, based on the concept Integral Connectivity, are proposed to guarantee consensus. The simulation is also given to demonstrate the results.
Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil.

Stable isotope probing (SIP) is a novel technique to characterize structure and in situ function of active microbial populations, which is based on the incorporation of 13C-labelled substrates into nucleic acids. Here, we have traced methylotrophic members of a rice field soil microbial community, which became active upon continuous addition of 13C-methanol (< 22 mM) as studied in microcosms. By combining rRNA- and DNA-based SIP, as well as domain-specific real-time PCR detection of templates in fractions of centrifugation gradients, we were able to detect 13C-labelled bacterial rRNA after 6 days of incubation. Fingerprinting and comparative sequence analysis of 'heavy' bacterial rRNA showed that mostly members of the Methylobacteriaceae and a novel clade within the Methylophilaceae formed part of the indigenous methylotrophic community. Over time, however, the Methylophilaceae were enriched. Unexpectedly, nucleic acids of eukaryotic origin were detected, mostly in intermediately 13C-labelled gradient fractions. These eukaryotes were identified as fungi mostly related to Fusarium and Aspergillus spp. , and also Cercozoa, known as predatory soil flagellates. The detection of fungi and protozoa in 13C-enriched nucleic acid fractions suggests a possible involvement in either direct assimilation of label by the fungi, or a food web, i.e. that primary 13C-methanol consuming methylotrophs were decomposed by fungi and grazed by protozoa.
High-Resolution Genomic Analysis of Cribriform Neuroepithelial Tumors of the Central Nervous System

Abstract Cribriform neuroepithelial tumors (CRINET) are one of several recently characterized entities in the broad spectrum of solid tumors with SMARCB1-INI1 loss. This neoplasm seems to be exceedingly rare and displays unique neuropathologic and clinical features. To date, only a few cases of CRINET have been characterized from a molecular point of view. In this study, we investigated the molecular features of 3 cases of CRINET using multiplex ligation-dependent probe amplification and molecular inversion profiling approaches. Along with mutations and deletions of SMARCB1-INI1, molecular inversion profiling analysis revealed a stable genomic profile without significant large chromosomal changes. Focal alterations (gains) were observed in individual cases at chromosomes 4q12 (PDGFRA), 12q15 (MDM2), 7p15.1 (NPY), and 18q11.2 (CDH2). Genomic Identification of Significant Targets in Cancer analysis highlighted focal alterations, including gains at chromosomes 16q23.2 (MAF), 17q23 (AXIN2), and 8p12 (ADAM3A). No cases showed BRAFV600E or CTNNB1 mutations. These data indicate that CRINET present stable genetic features and lack alterations commonly identified in other pediatric brain tumors. Further studies are required to determine whether specific alterations and specific signaling pathways, in addition to SMARCB1-INI1, may be implicated in the biology of this rare tumor and whether there are additional molecular similarities between CRINET and atypical teratoid/rhabdoid tumors.
Ship wakes 3D simulation based on OSG

In 3D real-time simulation system of ocean scene, ship wakes' effect is important. Based on the dispersive nature of deepwater surface wave, particle system's movement models of bow wake were built. Stern wake's shape-like particle system model was built according to its field angle's distance-width formula. Then the two models were realized through OSG particle system on VS2010 platform. The application results show that this two methods have better 3D display effect and rendering efficiency.