Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerated stochastic simulation of the stiff enzyme-substrate reaction.

The enzyme-catalyzed conversion of a substrate into a product is a common reaction motif in cellular chemical systems. In the three reactions that comprise this process, the intermediate enzyme-substrate complex is usually much more likely to decay into its original constituents than to produce a product molecule. This condition makes the reaction set mathematically "stiff. " We show here how the simulation of this stiff reaction set can be dramatically speeded up relative to the standard stochastic simulation algorithm (SSA) by using a recently introduced procedure called the slow-scale SSA. The speedup occurs because the slow-scale SSA explicitly simulates only the relatively rare conversion reactions, skipping over occurrences of the other two less interesting but much more frequent reactions. We describe, explain, and illustrate this simulation procedure for the isolated enzyme-substrate reaction set, and then we show how the procedure extends to the more typical case in which the enzyme-substrate reactions occur together with other reactions and species. Finally, we explain the connection between this slow-scale SSA approach and the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] formula, which has long been used in deterministic chemical kinetics to describe the enzyme-substrate reaction.
Lack of Association Between Dexamethasone and Long-Term Survival After Non-Small Cell Lung Cancer Surgery.

OBJECTIVE To evaluate the association between the use of intraoperative dexamethasone with an increase in recurrence-free survival (RFS) and overall survival (OS) after non-small cell lung cancer (NSCLC) surgery. DESIGN This was a propensity score-matched (PSM) retrospective study. SETTING Single academic center. PARTICIPANTS The study comprised patients with stage I through IIIa NSCLC. Patients were excluded if they were younger than 18 years, had missing data, and died within 30 days after surgery. MEASUREMENTS AND MAIN RESULTS Primary outcomes of the study were RFS and OS. The data were PSM. RFS and OS were evaluated using univariate and multivariate Cox proportional hazards models after PSM to assess the association between intraoperative dexamethasone use and the primary outcomes. A p value of<0.05 was considered statistically significant. After PSM, 436 patients were included in each treatment group. Adjusting for significant covariates, the multivariate analysis demonstrated no association between the use of dexamethasone and RFS (hazard ratio [95% confidence interval]: 0.98 [0.78-1.24]; p = 0.915). The multivariate analysis also demonstrated no association between the administration of dexamethasone and OS (hazard ratio [95% confidence interval]: 1.08 [0.81-1.44]; p = 0.58). CONCLUSIONS This study demonstrated that intraoperative dexamethasone administration to NSCLC patients was not associated with a significant impact on RFS and OS. The results were similar to a previous study on ovarian cancer patients. A randomized controlled study should be conducted to confirm the results of this study.
Predictive value of serum calprotectin (S100A8/A9) for clinical response after starting or tapering anti-TNF treatment in patients with rheumatoid arthritis

Objectives Calprotectin (S100A8/A9) has been correlated with disease activity in rheumatoid arthritis (RA). The aim of this study was to investigate the predictive value of serum calprotectin for clinical response after starting and tapering anti-tumour necrosis factor treatment in RA. Methods Serum samples and clinical outcomes were derived from two longitudinal RA studies. At baseline (starting or tapering of adalimumab or etanercept), calprotectin levels were determined by ELISA. In the Biologic Individual Optimised Treatment Outcome Prediction (BIO-TOP) study, treatment effect was assessed after 6 months using the European League Against Rheumatism (EULAR) response criteria. In the Dose Reduction Strategies of Subcutaneous TNF Inhibitors (DRESS) study, patients were classified at 18 months as being successfully dose reduced, discontinued or not able to reduce the dose. Area under the receiver operating characteristic curves (AUC) were generated to evaluate the predictive value of calprotectin and logistic prediction models were created to assess its added value. Results In the BIO-TOP study, calprotectin levels were higher in responders (n=50: 985 ng/mL (p25–p75: 558–1417)) compared with non-responders (n=75: 645 ng/mL (p25–p75: 415–973), p=0.04). AUC for predicting EULAR good response was 0.61 (95% CI 0.50 to 0.71). The prediction model with calprotectin (AUC 0.77, 95% CI 0.68 to 0.85) performed similarly to the baseline model (AUC 0.74, 95% CI 0.65 to 0.82, p=0.29). In the DRESS study, calprotectin levels were similar between the three groups (n=47; n=19; n=36) and calprotectin was not predictive for clinical response after tapering. Conclusions Serum calprotectin has some predictive value for clinical response after starting anti-TNF treatment, although it has no added value to other clinical factors. In patients with low disease activity, serum calprotectin is not predictive for clinical response after tapering anti-TNF treatment. Trial registration number NTR4647 (BIO-TOP study) and NTR3216 (DRESS study); Pre-results.
Comparative Evaluation of Physiochemical Properties of a Solid Fuel Derived from Adansonia digitata Trunk using Torrefaction

The effect of temperature on the physiochemical characteristics of a solid fuel or biocoal derived from the dried trunk of Adansonia digitata (Baobab) was studied using torrefaction processes. The chemical composition of the solid fuel or char obtained by wet (HTC) and dry torrefaction processes were determined by elemental and thermogravimetric (TGA) analyses. The Brunauer-Emmett-Teller (BET) surface area analyzer measured the porous texture and surface area of the prepared samples. The changes in the surface morphology and crystallinity of the prepared samples were evaluated by field-emission scanning electron microscopy (FE-SEM) and X-ray diffraction (XRD). The torrefaction process successfully improved the energy content from 16.8 MJ/kg to 22.0 MJ/kg, which was evidently higher than the starting precursors. The maximum energy yield obtained was 90.0% using dry torrefaction at 250 °C. The energy densification ratio was also higher for the char produced by the dry torrefaction process. However, the char produced by the HTC process at 250 °C showed the highest surface area. The pore diameter was higher for HTC-char produced at the same temperature. Overall the results revealed that the torrefaction of lignocellulosic biomass is beneficial for upgrading the fuel quality and energy densification of char residues.
Where the Truth Lies: Explaining the Credibility of Emerging Claims on the Web and Social Media

The web is a huge source of valuable information. However, in recent times, there is an increasing trend towards false claims in social media, other web-sources, and even in news. Thus, factchecking websites have become increasingly popular to identify such misinformation based on manual analysis. Recent research proposed methods to assess the credibility of claims automatically. However, there are major limitations: most works assume claims to be in a structured form, and a few deal with textual claims but require that sources of evidence or counter-evidence are easily retrieved from the web. None of these works can cope with newly emerging claims, and no prior method can give user-interpretable explanations for its verdict on the claim's credibility. This paper overcomes these limitations by automatically assessing the credibility of emerging claims, with sparse presence in web-sources, and generating suitable explanations from judiciously selected sources. To this end, we retrieve diverse articles about the claim, and model the mutual interaction between: the stance (i.e., support or refute) of the sources, the language style of the articles, the reliability of the sources, and the claim's temporal footprint on the web. Extensive experiments demonstrate the viability of our method and its superiority over prior works. We show that our methods work well for early detection of emerging claims, as well as for claims with limited presence on the web and social media.
When some is not every: Dissociating scalar implicature generation and mismatch

Making inferences beyond the literal meaning of sentences occurs with certain scalar expressions via scalar implicatures. For example, adults usually interpret some as some but not all. On the basis of behavioral research, it has been suggested that processing implicatures is cognitively costly. However, many studies have used cases where sentences with some did not match the context in which they were presented. Our study aimed to examine whether the processing cost is linked to implicature generation, to the mismatch between the implicature and the context, or to both processes. To do so, we explored the neural patterns of implicature generation and implicature mismatch using fMRI. Thirteen participants performed a sentence‐picture matching task (where pictures determined the context) with mismatched implicatures, successful implicatures or no implicature conditions. Several brain regions were identified when comparing cases of implicature mismatch and cases without implicatures. One of these regions, left‐IFG, was jointly activated for mismatched and successful implicatures, as observed in a conjunction analysis. By contrast, left‐MFG and medial‐frontal‐gyrus, were identified when comparing cases of implicature mismatch with cases of successful implicatures. Thus, the left IFG can be interpreted as being linked to implicature generation, whereas the other two areas seem to participate in the processing of the mismatch between the implicature and its context. Our results indicate that scalar implicatures induce processing cost in different ways. This should be considered in future research. Hum Brain Mapp 35:1503–1514, 2014. © 2013 Wiley Periodicals, Inc.
Evaluating pre-pregnancy dietary diversity vs. dietary quality scores as predictors of gestational diabetes and hypertensive disorders of pregnancy

Background Dietary diversity scores (DDS) are considered as metrics for monitoring the implementation of the UN’s Sustainable Development Goals, but they need to be rigorously evaluated. Objective To examine two DDS, the Food Groups Index (FGI), and the Minimum Dietary Diversity-Women (MDD-W), alongside two dietary quality scores, the Alternate Healthy Eating Index (AHEI-2010) and the Prime Diet Quality Score (PDQS), with risks of gestational diabetes mellitus (GDM) and hypertensive disorders of pregnancy (HDPs). Design The analysis included 21,312 (GDM) and 19,917 (HDPs) singleton births reported in the Nurses’ Health Study II cohort (1991–2001), among women without major chronic disease or GDM/HDPs. Scores were derived using prepregnancy diet collected by a comprehensive food frequency questionnaire. Multivariable models were utilized to calculate relative risks (RR) and confidence intervals (95%CIs). Results Incident GDM (n = 916) and HDPs (n = 1,421) were reported. The MDD-W and FGI were not associated with risk of GDM or HDPs, but the AHEI-2010 and PDQS were associated with a lower risk of GDM and marginally lower risk of HDP. The RR’s of GDM comparing the highest vs. lowest quintiles were 1.00 (95%CI: 0.79, 1.27; p-trend = 0.82) for MDD-W, 0.96 (95%CI: 0.76, 1.22; p-trend = 0.88) for FGI, 0.63 (95%CI: 0.50, 0.81; p-trend <0.0001) for the AHEI-2010 and 0.68 (95%CI: 0.54, 0.86; p-trend = 0.003) for the PDQS. Similarly, the RR’s of HDPs were 0.92 (95%CI: 0.75, 1.12, p-trend = 0.94) for MDD-W, 0.97 (95%CI: 0.79, 1.17; p-trend = 0.83) for FGI, 0.84 (95%CI: 0.70, 1.02; p-trend = 0.07) for AHEI-2010 and 0.89 (95%CI: 0.74, 1.09; p-trend = 0.07) for PDQS. Conclusions MDD-W and FGI did not predict the risk of GDM and HDPs. These DDS should not be widely used as metrics for achieving dietary goals in their present form. The Prime Diet Quality Score warrants further testing as a promising measure of a sustainable and healthy diet on a global scale.
Efficacy of emamectin benzoate, pyridalyl and methoxyfenozide on pomegranate butterfly, Virachola livia (Klug) (Lepidoptera: Lycanidae) in cultivated and reclaimed lands

The pomegranate butterfly, Virachola livia (Klug) (Lepidoptera: Lycanidae), is one of the most important pests in Egypt. Under pomegranate field conditions, the study was conducted from 2012 to 2013 to compare the efficacy of methoxyfenozide, pyridalyl and emamectin benzoate against pomegranate butterfly in cultivated and reclaimed lands at Assiut Governorate, Egypt. These insecticides demonstrated a significant low infestation of the pomegranate butterfly during 2012 and 2013 seasons compared to control field. Emamectin benzoate and pyridalyl were found to be highly effective for controlling V. livia with an average infestation of 0.33- 4.33% and 1.00- 6.67% compared to methoxyfenozide (0.33- 17.67%) in both cultivated and reclaimed lands, respectively. Data indicated that, the infestation was higher in the cultivated land than reclaimed land during 2012 and 2013 seasons. The change in temperature and relative humidity may affect the susceptibility of pomegranate fruits to the infestation by V. livia. In addition, results showed that all pomegranate trees under treated field had a significant increase in the average weight fruits by about 70-90% compared to control field. Methoxyfenozide, pyridalyl and emamectin benzoate can be considered as promising candidates to control the pomegranate butterfly, V. livia infestation in both cultivated and reclaimed lands.
The Influence of Remelting on the Quality of Prosthetic Cobalt Alloys

A commercial cobalt alloy applied in dental prosthetics was investigated. The scope of the work included the microstructure analysis, performance examination (tensile strength, microhardness, corrosion resistance), and dilatometric examination. The investigated alloy after a single remelting was characterised by higher tensile strength and hardness. There were not found the definite results with regard to the corrosion resistance of the examined materials. No significant change occurred in the coefficient of thermal expansion.
The Rise of the Sharing Economy: Estimating the Impact of Airbnb on the Hotel Industry

Peer-to-peer markets, collectively known as the sharing economy, have emerged as alternative suppliers of goods and services traditionally provided by long-established industries. The authors explore the economic impact of the sharing economy on incumbent firms by studying the case of Airbnb, a prominent platform for short-term accommodations. They analyze Airbnb's entry into the state of Texas and quantify its impact on the Texas hotel industry over the subsequent decade. In Austin, where Airbnb supply is highest, the causal impact on hotel revenue is in the 8%–10% range; moreover, the impact is nonuniform, with lower-priced hotels and hotels that do not cater to business travelers being the most affected. The impact manifests itself primarily through less aggressive hotel room pricing, benefiting all consumers, not just participants in the sharing economy. The price response is especially pronounced during periods of peak demand, such as during the South by Southwest festival, and is due to a differentiating feature of peer-to-peer platforms—enabling instantaneous supply to scale to meet demand.
Investigating the Multidimensionality of Need Fulfillment: A Bifactor Exploratory Structural Equation Modeling Representation

This article assesses the multidimensionality of the Basic Psychological Need Satisfaction and Frustration Scale (BPNSFS) using bifactor exploratory structural equation modeling (bifactor ESEM). The first study relies on a sample of community adults (N = 2,301), and revealed the superiority of a bifactor ESEM representation, supporting the 6-factor structure of BPNSFS ratings, and the presence of a single continuum of need fulfillment relative to 2 distinct dimensions reflecting need satisfaction and frustration. These results were replicated in a second representative sample of the Hungarian adult population (N = 504), as well as across gender, and found no evidence of differential item functioning as a function of age. Relative to males, females presented higher levels of relatedness satisfaction and lower levels of competence satisfaction. Finally, autonomy frustration decreased with age, whereas competence satisfaction and frustration presented opposite curvilinear tendencies, showing that the fulfillment of this need increased sharply for younger participants, a tendency that became less pronounced with age.
The VIMOS Ultra Deep Survey: Lyα emission and stellar populations of star-forming galaxies at 2 < z < 2.5

The aim of this paper is to investigate spectral and photometric properties of 854 faint (i(AB) less than or similar to 25 mag) star-forming galaxies (SFGs) at 2 \textless z \textless 2.5 using the VIMOS Ultra-Deep Survey (VUDS) spectroscopic data and deep multi-wavelength photometric data in three extensively studied extragalactic fields (ECDFS, VVDS, COSMOS). These SFGs were targeted for spectroscopy as a result of their photometric redshifts. The VUDS spectra are used to measure the UV spectral slopes (beta) as well as Ly alpha equivalent widths (EW). On average, the spectroscopically measured beta (-1.36 +/- 0.02), is comparable to the photometrically measured beta (-1.32 +/- 0.02), and has smaller measurement uncertainties. The positive correlation of beta with the spectral energy distribution (SED)-based measurement of dust extinction E-s(B-V) emphasizes the importance of beta as an alternative dust indicator at high redshifts. To make a proper comparison, we divide these SFGs into three subgroups based on their rest-frame Ly alpha EW: SFGs with no Ly alpha emission (SFGN; EW \textless= 0 angstrom), SFGs with Ly alpha emission (SFG(L); EW \textgreater 0 angstrom), and Ly alpha emitters (LAEs; EW \textgreater= 20 angstrom). The fraction of LAEs at these redshifts is beta 10%, which is consistent with previous observations. We compared best-fit SED-estimated stellar parameters of the SFG(N), SFG(L) and LAE samples. For the luminosities probed here (similar to L*), we find that galaxies with and without Ly alpha in emission have small but significant differences in their SED-based properties. We find that LAEs have less dust, and lower star-formation rates (SFR) compared to non-LAEs. We also find that LAEs are less massive compared to non-LAEs, though the difference is smaller and less significant compared to the SFR and E-s(B-V). When we divide the LAEs according to their Spitzer/IRAC 3.6 mu m fluxes, we find that the fraction of IRAC-detected (m(3.6) less than or similar to 25 mag) LAEs is much higher than the fraction of IRAC-detected narrow band (NB)-selected LAEs at z similar or equal to 2-3. This could imply that UV-selected LAEs host a more evolved stellar population, which represents a later stage of galaxy evolution, compared to NB-selected LAEs.
Anti-CD20 monoclonal antibody combined with adenovirus vector-mediated IL-10 regulates spleen CD4+/CD8+ T cells and T-bet/GATA-3 expression in NOD mice

Type 1 diabetes (T1D) is an autoimmune disease characterized by a selective destruction of insulin-secreting β-cells. Both T cells and B cells serve a crucial role in pathogenesis and development of T1D. CD20 is a specific membrane antigen of B lymphocytes, while interleukin (IL)-10 is an important cytokine secreted by T helper 2 cells and has a short half-life in vivo. The combined effect of anti-CD20 and IL-10 on immune function of mice with T1D remains unknown. In the present study, 30 non-obese diabetic (NOD) mice were treated with anti-CD20 and adenoviral vector-mediated interleukin-10 (Ad-mIL-10) therapy. Alterations in CD4+, CD8+, CD4+CD25+Foxp3+ T cells, T-box expressed in T-cells (T-bet), GATA-binding protein-3 (GATA-3) interferon-γ (IFN-γ) and IL-4 were detected by flow cytometry, reverse transcription-quantitative polymerase chain reaction in NOD mice spleen tissue. The present results suggested that anti-CD20 and IL-10 treatment in NOD mice can modulate the immune functions by upregulating GATA-3 and IL-4 expression as well as downregulating T-bet and IFN-γ expression, which are involved in the pathogenesis of T1D. The current findings may provide a potential method for T1D treatment and a novel preventive therapy for T1D. Combination of anti-CD20 and Ad-mIL-10 treatment had not only immune regulatory effects but also protective effects on islet β-cells in NOD mice with T1DM at the early stages, by regulating T-bet/GATA-3 expression and Th1/Th2 cell differentiation, which has the potential for diabetes prevention and therapy.
Edge Detection with Embedded Confidence

Computing the weighted average of the pixel values in a window is a basic module in many computer vision operators. The process is reformulated in a linear vector space and the role of the different subspaces is emphasized. Within this framework wellknown artifacts of the gradient-based edge detectors, such as large spurious responses can be explained quantitatively. It is also shown that template matching with a template derived from the input data is meaningful since it provides an independent measure of confidence in the presence of the employed edge model. The widely used three-step edge detection procedure - gradient estimation, non-maxima suppression, hysteresis thresholding - is generalized to include the information provided by the confidence measure. The additional amount of computation is minimal and experiments with several standard test images show the ability of the new procedure to detect weak edges.
Grapevine petioles are more sensitive to drought induced embolism than stems: evidence from in vivo MRI and microcomputed tomography observations of hydraulic vulnerability segmentation.

The 'hydraulic vulnerability segmentation' hypothesis predicts that expendable distal organs are more susceptible to water stress-induced embolism than the main stem of the plant. In the current work, we present the first in vivo visualization of this phenomenon. In two separate experiments, using magnetic resonance imaging or synchrotron-based microcomputed tomography, grapevines (Vitis vinifera) were dehydrated while simultaneously scanning the main stems and petioles for the occurrence of emboli at different xylem pressures (Ψx ). Magnetic resonance imaging revealed that 50% of the conductive xylem area of the petioles was embolized at a Ψx of -1.54 MPa, whereas the stems did not reach similar losses until -1.9 MPa. Microcomputed tomography confirmed these findings, showing that approximately half the vessels in the petioles were embolized at a Ψx of -1.6 MPa, whereas only few were embolized in the stems. Petioles were shown to be more resistant to water stress-induced embolism than previously measured with invasive hydraulic methods. The results provide the first direct evidence for the hydraulic vulnerability segmentation hypothesis and highlight its importance in grapevine responses to severe water stress. Additionally, these data suggest that air entry through the petiole into the stem is unlikely in grapevines during drought.