Miracle-dz/UniFAR-FTUs huggingface dataset:
Confounder‐adjusted estimates of the risk difference using propensity score‐based weighting

Confounder‐adjusted estimates of the risk difference are often difficult to obtain by direct regression adjustment. Estimates can be obtained from a propensity score‐based method using inverse probability‐of‐exposure weights to balance groups defined by exposure status with respect to confounders. Simulation was used to evaluate the performance of this method. The simulation model incorporated a binary confounder and a normally distributed confounder into logistic models of exposure status, and disease status conditional on exposure status. Data were generated for combinations of values of several design parameters, including the odds ratio relating each of the confounders to exposure status, the odds ratio relating each of the confounders to disease status and the total sample size. For most design parameter combinations (474 of 486), the absolute bias in the estimated risk difference was less than 1 percentage point, and it was never greater than 3 percentage points. The confidence interval generally had close to nominal 95 per cent coverage, but was prone to poor coverage levels (as low as 78.5 per cent) when both the confounder‐to‐exposure and confounder‐to‐outcome odds ratios were 5, consistent with strong confounding. The simulation results showed that the conditions that are favourable for good performance of the weighting method are: reasonable overlap in the propensity score distributions of the exposed and non‐exposed groups and a large sample size. Copyright © 2010 John Wiley & Sons, Ltd.
Study on the bone marrow mesenchymal stem cells induced drug resistance in the U937 cells and its mechanism.

BACKGROUND The hematopoietic microenvironment (HM) plays a critical role in malignant cell growth, patient survival, and response to chemotherapy in hematologic malignancies. However, mechanisms associated with this environmental influence remain unclear. In this study, we investigated the role of bone marrow derived mesenchymal stem cells (MSCs) in U937 cell line, to find out the relations between leukemia drug resistance and the MSCs. METHODS U937 cells were cultured in suspension or grew adherently with MSCs. The cell growth curve was drawn and the cell cycle was measured by flow cytometry. Apoptosis and sensitivity of U937 to daunoblastina (DNR) were quantified by DNA ladder detection and trypan blue exclusion assays, respectively. The gene expression profile chip technology was used to determine and analyze the changes in apoptosis-related gene expression after adherent culture and the expression of MDR1 mRNA was assessed by reverse transcriptional polymerase chain reaction (RT-PCR) at the same time. RESULTS In the adherent culture, the proliferation of the U937 cells was inhibited, the G0/G1 phase cells increased (F = 64.9726, P < 0.0001), G2/M phase cells were decreased (F = 98.1361, P < 0.0001) and the natural apoptosis rate was decreased (F = 24.0866, P < 0.0001) compared with those in the suspended culture. U937 cell viability was enhanced and cell apoptosis was blocked during DNR treatment in adherent culture with MSCs. Thirty-nine differently expressed genes were screened from the 487 apoptosis related genes in the adherent culture U937 cells. Among the 37 upregulated genes, Bcl-XL was upregulated most significantly. Two genes were downregulated. Adherent culture did not induce MDR1 mRNA expression in U937 cells. CONCLUSIONS MSCs play a role in modulating the proliferation of U937 cells and response of U937 cells to DNR, and Bcl-XL apoptosis-inhibiting gene may be most important in determining the sensitivity of leukemic cells to treatment, which is not related to MDR1.
Glutathione S‐transferase gene polymorphisms and risk and survival of pancreatic cancer

Pancreatic cancer is a multifactorial disease with metastasis‐prone and therapy‐resistant nature. The authors hypothesized that genetic variants of glutathione S‐transferase (GST) affect detoxification of carcinogens and anticancer agents in the human pancreas and, thus, the risk and survival of pancreatic cancer.
Cutting Edge: TRAIL Deficiency Accelerates Hematological Malignancies1

TNF apoptosis-inducing ligand is attracting considerable interest as a potential extrinsic tumor suppressor mechanism, although previous reports have conveyed somewhat contrasting views regarding the likely importance of this pathway. In this study, we provide the first evaluation of spontaneous tumor formation over the life span of TRAIL-deficient mice. Interestingly, >25% of these mice do develop lymphoid malignancies after 500 days of life. TRAIL suppressed the initiation and development of both tumors of lymphoid and stromal origin in the context of the loss of at least one p53 allele. Specific examination of the role of TRAIL in Her2/neu oncogene-driven mammary epithelial cancer revealed no critical role for TRAIL despite the inherent TRAIL sensitivity of such mammary carcinomas. Overall, the data indicate an important function of TRAIL in controlling carcinogenesis, but suggest that further examination of this pathway in epithelial malignancies is warranted.
Controls of dissolved organic matter quality: evidence from a large‐scale boreal lake survey

Inland waters transport large amounts of dissolved organic matter (DOM) from terrestrial environments to the oceans, but DOM also reacts en route, with substantial water column losses by mineralization and sedimentation. For DOM transformations along the aquatic continuum, lakes play an important role as they retain waters in the landscape allowing for more time to alter DOM. We know DOM losses are significant at the global scale, yet little is known about how the reactivity of DOM varies across landscapes and climates. DOM reactivity is inherently linked to its chemical composition. We used fluorescence spectroscopy to explore DOM quality from 560 lakes distributed across Sweden and encompassed a wide climatic gradient typical of the boreal ecozone. Six fluorescence components were identified using parallel factor analysis (PARAFAC). The intensity and relative abundance of these components were analyzed in relation to lake chemistry, catchment, and climate characteristics. Land cover, particularly the percentage of water in the catchment, was a primary factor explaining variability in PARAFAC components. Likewise, lake water retention time influenced DOM quality. These results suggest that processes occurring in upstream water bodies, in addition to the lake itself, have a dominant influence on DOM quality. PARAFAC components with longer emission wavelengths, or red‐shifted components, were most reactive. In contrast, protein‐like components were most persistent within lakes. Generalized characteristics of PARAFAC components based on emission wavelength could ease future interpretation of fluorescence spectra. An important secondary influence on DOM quality was mean annual temperature, which ranged between −6.2 and +7.5 °C. These results suggest that DOM reactivity depends more heavily on the duration of time taken to pass through the landscape, rather than temperature. Projected increases in runoff in the boreal region may force lake DOM toward a higher overall amount and proportion of humic‐like substances.
Sensitivity Analysis of the Human Visual System for Depth Cues in Stereoscopic 3-D Displays

Three-dimensional (3-D) displays provide a more realistic experience of entertainment by providing its viewers an added sensation of depth by artificially exploiting light rays to stimulate certain depth cues in the human visual system, especially binocular stereopsis. Due to its close relationship with human visual perception, mass market deployment of 3-D displays will be significantly dependant upon addressing the related perceptual factors such as visual comfort. In order to address the perceptual factors, it is very important to understand how humans experience depth on 3-D displays and how sensitive they are for different depth cues. In this paper, the sensitivity of humans for different depth cues is analyzed as applicable to 3-D viewing on stereoscopic displays. Mathematical models are derived to explain the just noticeable difference in depth (JNDD) for three different depth cues, namely binocular disparity, retinal blur, and relative size. Extensive subjective assessments are performed on a stereoscopic display with passive polarized glasses and on an auto-stereoscopic display to validate the mathematical models for JNDD. It is expected that the proposed models will have important use cases in 3-D display designing as well as 3-D content production.
Functional Regulation of MyD88-Activated Interferon Regulatory Factor 5 by K63-Linked Polyubiquitination

ABSTRACT Interferon regulatory factor 5 (IRF-5) plays an important role in the innate antiviral and inflammatory response. Specific IRF-5 haplotypes are associated with dysregulated expression of type I interferons and predisposition to autoimmune disorders. IRF-5 is activated by Toll-like receptor 7 (TLR7) and TLR9 via the MyD88 pathway, where it interacts with both MyD88 and the E3 ubiquitin ligase, TRAF6. To understand the role of these interactions in the regulation of IRF-5, we examined the role of ubiquitination and showed that IRF-5 is subjected to TRAF6-mediated K63-linked ubiquitination, which is important for IRF-5 nuclear translocation and target gene regulation. We show that while the murine IRF-5 and human IRF-5 variant 4 (HuIRF-5v4) and HuIRF-5v5 are ubiquitinated, an IRF-5 bone marrow variant mutant containing an internal deletion of 288 nucleotides is not ubiquitinated. Lysine residues at positions 410 and 411 in a putative TRAF6 consensus binding domain of IRF-5 are the targets of K63-linked ubiquitination. Mutagenesis of these two lysines abolished IRF-5 ubiquitination, nuclear translocation, and the IFNA promoter-inducing activity but not the IRF-5-TRAF6 interaction. Finally, we show that IRAK1 associates with IRF-5 and that this interaction precedes and is required for IRF-5 ubiquitination and activation. Thus, our findings offer a new mechanistic insight into IRF-5 gene induction program through hitherto unknown processes of IRF-5 ubiquitination.
The SYNTAX score is correlated with long-term outcomes of coronary artery bypass grafting for complex coronary artery lesions.

OBJECTIVES We analysed retrospectively the long-term outcomes of conventional coronary artery bypass grafting (CABG) as employed routinely for complex coronary lesions by observing patients with low (0-22), intermediate (23-32) and high (≥33) SYNTAX scores. The purpose of this study was to evaluate the correlation between the SYNTAX score and long-term major adverse cardiac and cerebrovascular events (MACCEs) including all-cause death, stroke, myocardial infarction (MI) and repeat revascularization after CABG. METHODS The study enrolled 396 consecutive patients with stable and untreated left main and/or three-vessel disease, who had been referred to our heart team from 2000 through 2009. They all routinely underwent conventional CABG. The three groups (low score; n = 159, intermediate score; n = 150, high score; n = 87) were compared, looking at the primary endpoint of MACCE and its components. We also analysed the effects of diverse variables on long-term MACCEs after the operation. RESULTS The cumulative 10-year MACCE rates in patients with low, intermediate and high SYNTAX score were 25.3, 35.8 and 48.1%, respectively. The Kaplan-Meier cumulative event curves showed a significantly higher MACCE rate after CABG in patients with a higher SYNTAX score than in those with a lower score (log-rank P = 0.0012). This was mainly because of a significantly increased rate of repeat revascularization in the higher SYNTAX score group (log-rank P = 0.0032). The cumulative rate of repeat revascularization at 10 years in patients having low, intermediate and high SYNTAX score were, respectively, 4.6, 15.7 and 16.8%. The cumulative rates of the combined outcomes of death/stroke/MI at 10 years did not show statistical differences between the three groups (22.3% with low, 25.0% with intermediate and 38.4% with high score, log-rank P = 0.063). In the multivariable analysis, the SYNTAX score [hazard ratio (HR) 1.03, P = 0.0043] and logistic EuroSCORE II (HR 1.34, P = 0.0012) were found to be significant predictors of long-term MACCEs. CONCLUSIONS The SYNTAX score is correlated with long-term outcomes, in terms of MACCEs, after conventional CABG for complex coronary lesions and is prognostic of long-term outcomes of CABG for patients with complex lesions.
Clostridium difficile infection in newly diagnosed pediatric patients with inflammatory bowel disease: Prevalence and risk factors

Background: Epidemiological and microbiological data suggest that Clostridium difficile infection (CDI) plays a substantial role in the clinical initiation of inflammatory bowel disease (IBD). The aim of the present study was to investigate the prevalence and risk factors of CDI in newly diagnosed pediatric patients with IBD. Methods: The current investigation was a retrospective study. All patients newly diagnosed with IBD in the pediatric gastroenterology clinic in Warsaw between 2007 and 2010 were included in the present study. The patients were diagnosed according to Porto criteria and microbiology evaluation screening tests for CDI were conducted. Risk factors including prior hospitalization, use of antibiotics within 2 months of CDI detection, colonic involvement, and the duration of symptoms were evaluated. CDI diagnosis was based on a positive stool enzyme immunoassay. Results: In the present study, 134 patients were evaluated (54 patients with Crohn's disease, and 80 with ulcerative colitis; 87% of the patients had colonic disease). The average age of the patients was 12.3 years, and the prevalence of CDI was 47% (95% confidence interval [CI], 38%–56%). Significant differences in the prevalence of CDI between patients with Crohn's disease and ulcerative colitis (P = 0.72; odds ratio [OR] = 1.187, 95% CI, 0.56–2.52) were not observed. The risk of CDI was associated with an increase in the age of the patient and the severity of the disease. Conclusions: The prevalence of CDI in newly diagnosed IBD patients was high and was independent of the type of disease. (Inflamm Bowel Dis 2011;)
Lock-up Expiry and Trading Volume Behaviour of Malaysian Initial Public Offering’s

The study aims to investigate the lock-up provisions of initial public offering’s (IPOs) and its effects on trading volume changes around the lock-up expiry date of Malaysian IPOs by using both the event study methodology and the comparison period returns approach (CPRA). Unlike the US and the UK, Malaysia’s lock-up length is fixed and the number of shares that should be under the lock-up is pre-determined by the security commission. The sample comprises 379 Malaysian IPOs, issued from January 2001 to December 2011. The results of the event study methodology and CPRA shows a positive abnormal trading volume at lock-up expiry date for IPO market, except for the ACE market, construction and technology sectors, which is negative and is not consistent with our hypothesis and there is no evidence in previous literatures regarding the significant negative trading volume before and after the lock-up. High trading volume at and around the lock-up expiration is compatible with shareholders’ selling due to diversification reasons and wealth recognition and which is also an indication of insider’s lack of confidence about a company’s future prospect. Significant negative trading volume can be interpreted in a way that insiders of those related boards and sectors do not sell their shares significantly but would rather watch what would happen to the market and are optimistic about Market’s future. Furthermore, when we do not adjust the trading volume for the market, the CPRA methodology does not show abnormal trading volume between event window and non-event windows.
Molecular dynamics simulation of the interfacial structure of [Cnmim][PF6] adsorbed on a graphite surface: effects of temperature and alkyl chain length

The structures and diffusion behaviors of a series of ionic liquids [Cnmim][PF6] (n = 1, 4, 8 and 12) on a graphite surface have been investigated by means of molecular dynamics simulation. It was found that three or four ordering layers of ionic liquids were formed near the graphite surface, and this layering structure was stable over the temperature range investigated. At the liquid/vacuum interface, the ionic liquid with a butyl chain had a monolayer ordering surface, while [C8mim][PF6] and [C12mim][PF6] exhibited a bilayer ordering with a polar domain sandwiched between two orientational nonpolar domains. More impressively, the simulated results showed that for the ionic liquids with alkyl chains longer than C4, the adjacent alkyl chains in the whole film tended to be parallel to each other, with the imidazolium rings packed closely together. This indicated that the ionic liquids have a better regulated short-range structure than was previously expected. It was also found that both in the bottom layer and in the bulk region, the diffusion of the alkyl chains was much faster than that of the polar groups. However, as the alkyl chain length increased, the charge delocalization in the cation and the enhanced van der Waals interaction between the nonpolar groups contributed by reducing this difference in the diffusivity of major groups.
Plethysmographic comparison of breathing pattern in heaves (recurrent airway obstruction) versus experimental bronchoconstriction or hyperpnea in horses.

BACKGROUND Horses with recurrent airway obstruction (heaves) are described as exhibiting "increased abdominal effort," but it is unknown whether this translates to an effective contribution to ventilation. HYPOTHESIS We hypothesized that heaves is characterized by asynchrony between rib cage and abdominal motions, and that the abdominal component is the major contributor to ventilation. ANIMALS The rib cage versus abdominal motion in naturally occurring heaves (n = 15) was compared to controls at rest (n = 7) and during hyperpnea because of lobeline treatment, and the effects of histamine-induced bronchoconstriction in controls (n = 10). METHODS Flow patterns, phase angle (theta) between the rib and abdominal compartments, abdominal (Vabd) contribution to tidal volume (VT), and lung mechanics were measured. RESULTS Findings unique to the heaves group included the loss of biphasic expiratory flow, severely increased theta with the abdomen consistently lagging behind the rib cage, and a reduced contribution of the abdomen to ventilation. A subgroup of heaves (n = 5) with abdominal paradox showed a significant (P < .05) reduction in tidal volume, and increased respiratory rate. Bronchodilation reduced theta in heaves (P = .06), but theta remained significantly higher after bronchodilation than found in controls. CONCLUSIONS AND CLINICAL IMPORTANCE We conclude that breathing pattern in horses with heaves is characterized by severe rib cage/abdominal asynchrony, with the rib cage motion in synchrony with flow, therefore dominating ventilation. In a subset of heaves, the abdominal compartment (diaphragm, abdominal muscles) was completely out of synchrony with flow ("abdominal paradox") despite the clinical appearance of "increased abdominal effort. "
Uncertainty quantification for radio interferometric imaging: I. proximal MCMC methods

Uncertainty quantification is a critical missing component in radio interferometric imaging that will only become increasingly important as the big-data era of radio interferometry emerges. Since radio interferometric imaging requires solving a high-dimensional, ill-posed inverse problem, uncertainty quantification is difficult but also critical to the accurate scientific interpretation of radio observations. Statistical sampling approaches to perform Bayesian inference, likeMarkov chainMonte Carlo (MCMC) sampling, can in principle recover the full posterior distribution of the image, from which uncertainties can then be quantified. However, traditional high-dimensional samplingmethods are generally limited to smooth (e.g. Gaussian) priors and cannot be used with sparsity-promoting priors. Sparse priors, motivated by the theory of compressive sensing, have been shown to be highly effective for radio interferometric imaging. In this article proximal MCMC methods are developed for radio interferometric imaging, leveraging proximal calculus to support non-differential priors, such as sparse priors, in a Bayesian framework. Furthermore, three strategies to quantify uncertainties using the recovered posterior distribution are developed: (i) local (pixel-wise) credible intervals to provide error bars for each individual pixel; (ii) highest posterior density credible regions; and (iii) hypothesis testing of image structure. These forms of uncertainty quantification provide rich information for analysing radio interferometric observations in a statistically robust manner.
Technological Progress and Change in Market Concentration in the U. S., 1963-77

What effect does R & D-induced technological progress have on market structure? Do the concentration ratios, the most-used indices of market structure, increase or decrease in an industry that is faced with a high level of technological opportunity and exploits it through a high rate of R & D? This paper focusses on a model by Nelson and Winter as a theoretical starting point to deal with this question. In the Nelson and Winter model, concentration increases as a result of dynamic competition in the technologically progressive industries. But their model does not allow entry, and the effect on concentration may be reversed if the possibility of entry is considered. Empirically, this paper shows that concentration ratios in the high-R&D industries have decreased in the United States during 1963-77.
The Prevalence of Overweight and Obesity Among Aging Female Inmates

The purpose of this study was to examine the prevalence of overweight and obesity in a sample of older female inmates (N = 458). Results indicate that 34% of older female inmates were overweight and 36% were obese; similar percentages were noted for the general population. Race and age were found to be significantly associated with the body mass index categories of healthy weight and obese. White inmates were significantly more likely to be of a healthy weight and significantly less likely to be obese than Black inmates. Age was positively associated with healthy weight and negatively associated with obesity. These two variables remained significant even after they were introduced into logistic regression models predicting healthy weight and obesity. Findings indicate the need for programming to improve the health of this population.