Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulatory Activity of Autocrine IL-10 on Dendritic Cell Functions1

IL-10 is a critical cytokine that blocks the maturation of dendritic cells (DCs), but the relevance of autocrine IL-10 on DC functions has not been investigated. In this study, we found that immature monocyte-derived DCs released low but sizeable amounts of IL-10. After stimulation with bacteria, LPS, lipoteichoic acid, or soluble CD40 ligand, DCs secreted high levels of IL-10. Addition of an anti-IL-10-neutralizing Ab to immature DCs as well as to soluble CD40 ligand- or LPS-maturing DCs led to enhanced expression of surface CD83, CD80, CD86, and MHC molecules and markedly augmented release of TNF-α and IL-12, but diminished IL-10 mRNA expression. Moreover, DCs treated with anti-IL-10 Ab showed an increased capacity to activate allogeneic T cells and primed naive T cells to a more prominent Th1 polarization. DC maturation and IL-10 neutralization were associated with enhanced accumulation of the IL-10 receptor binding chain (IL-10R1) mRNA and intracellular IL-10R1 protein. In contrast, surface IL-10R1 and IL-10 binding activity diminished in mature DCs. These results indicate that autocrine IL-10 prevents spontaneous maturation of DCs in vitro, limits LPS- and CD40-mediated maturation, and increases IL-10 production by DCs. Moreover, IL-10R expression appears to be regulated by both transcriptional and posttranscriptional mechanisms. Endogenous IL-10 and IL-10R can be relevant targets for the manipulation of DC functions.
Variation of the time to aortic enhancement of fixed-duration versus fixed-rate injection protocols.

OBJECTIVE The objective of the study was to clarify whether a fixed-duration injection protocol is useful in determining the optimal scan delay time without the need for a bolus-tracking technique. MATERIALS AND METHODS Three hundred eighteen patients underwent a helical CT examination using a bolus-tracking technique. All the examinations were performed after administering a nonionic contrast medium (300 or 370 mg I/mL; 2 mL/kg of body weight for patients weighing < or = 75 kg, 150 mL for those weighing > 75 kg). The patients were assigned to one of three groups according to the injection protocol. The injection rate was alternated to 3 or 4 mL/sec in group 1. The injection duration was 38 or 47 sec in groups 2 and 3, respectively. The aortic arrival time and the 100-H threshold time in each patient were measured. The mean values and the variations in the aortic arrival time and 100-H threshold time according to the injection protocols and the contrast media were compared. RESULTS The mean variations (+/- SD) of aortic arrival times and 100-H thresholds in group 2 (aortic arrival time = 16.1 +/- 2.7 sec, 100-H threshold time = 19.6 +/- 2.9 sec) were smaller than in groups 1 (16.3 +/- 3.0 sec and 19.9 +/- 3.7 sec, respectively) and 3 (16.8 +/- 3.5 sec and 20.4 +/- 4.1 sec, respectively). However, the range of aortic arrival times and 100-H threshold times was more than 10 sec for all groups. The mean aortic arrival time and 100-H threshold time for all patients were 16.5 and 20.0 sec, respectively, and did not vary significantly with the injection protocol and concentration of contrast medium. CONCLUSION The individual variations of the aortic arrival and 100-H threshold times can be reduced using a fixed-duration injection technique, but there are still substantial variations. Therefore, a bolus-tracking technique is recommended for optimal timing of arterial phase scanning.
Three-Dimensional, Flexible Nanoscale Field-Effect Transistors as Localized Bioprobes

Nanoprobes of Cell Potential Direct electrical measurements of cell potentials usually face design compromises. Microelectrodes probe within the cytosol of cells but have a minimum size (hundreds of nanometers in width) for obtaining useful signals. Nanoscale field effect transistors (FETs) can have an active probe size of only tens of nanometers but generally allow only the outer cell potential to be measured. Tian et al. (p. 830) fabricated nanowires in which kinks could be introduced to create a sharp probe tip pointing away from the fabrication substrate. Coating the tip with a phospholipid bilayer allowed the probe to be inserted through the membranes of beating cardiac cells, where it could be used to follow temporal changes in cell potential. Kinked nanowire transistors can measure intracellular electric potentials. Nanoelectronic devices offer substantial potential for interrogating biological systems, although nearly all work has focused on planar device designs. We have overcome this limitation through synthetic integration of a nanoscale field-effect transistor (nanoFET) device at the tip of an acute-angle kinked silicon nanowire, where nanoscale connections are made by the arms of the kinked nanostructure, and remote multilayer interconnects allow three-dimensional (3D) probe presentation. The acute-angle probe geometry was designed and synthesized by controlling cis versus trans crystal conformations between adjacent kinks, and the nanoFET was localized through modulation doping. 3D nanoFET probes exhibited conductance and sensitivity in aqueous solution, independent of large mechanical deflections, and demonstrated high pH sensitivity. Additionally, 3D nanoprobes modified with phospholipid bilayers can enter single cells to allow robust recording of intracellular potentials.
Assessing and correcting for regression toward the mean in deviance-induced social conformity

Our understanding of the mechanisms underlying social conformity has recently advanced due to the employment of neuroscience methodology and novel experimental approaches. Most prominently, several studies have demonstrated the role of neural reinforcement-learning processes in conformal adjustments using a specifically designed and frequently replicated paradigm. Only very recently, the validity of the critical behavioral effect in this very paradigm was seriously questioned, as it invites the unwanted contribution of regression toward the mean. Using a straightforward control-group design, we corroborate this recent finding and demonstrate the involvement of statistical distortions. Additionally, however, we provide conclusive evidence that the paradigm nevertheless captures behavioral effects that can only be attributed to social influence. Finally, we present a mathematical approach that allows to isolate and quantify the paradigm’s true conformity effect both at the group level and for each individual participant. These data as well as relevant theoretical considerations suggest that the groundbreaking findings regarding the brain mechanisms of social conformity that were obtained with this recently criticized paradigm were indeed valid. Moreover, we support earlier suggestions that distorted behavioral effects can be rectified by means of appropriate correction procedures.
Parallel Approximation of Non-interactive Zero-sum Quantum Games

This paper studies a simple class of zero-sum games played by two competing quantum players: each player sends a mixed quantum state to a referee, who performs a joint measurement on the two states to determine the players' payoffs. We prove that an equilibrium point of any such game can be approximated by means of an efficient parallel algorithm, which implies that one-turn quantum refereed games, wherein the referee is specified by a quantum circuit, can be simulated in polynomial space.
Exploring Wound-Healing Genomic Machinery with a Network-Based Approach

The molecular mechanisms underlying tissue regeneration and wound healing are still poorly understood despite their importance. In this paper we develop a bioinformatics approach, combining biology and network theory to drive experiments for better understanding the genetic underpinnings of wound healing mechanisms and for selecting potential drug targets. We start by selecting literature-relevant genes in murine wound healing, and inferring from them a Protein-Protein Interaction (PPI) network. Then, we analyze the network to rank wound healing-related genes according to their topological properties. Lastly, we perform a procedure for in-silico simulation of a treatment action in a biological pathway. The findings obtained by applying the developed pipeline, including gene expression analysis, confirms how a network-based bioinformatics method is able to prioritize candidate genes for in vitro analysis, thus speeding up the understanding of molecular mechanisms and supporting the discovery of potential drug targets.
ORIGINAL ARTICLE: The association between serum thyrotropin (TSH) levels and bone mineral density in healthy euthyroid men

Objective Although osteoporosis is increasingly shown to occur in a considerable proportion of men, data on risk factors for male osteoporosis are limited. In this study, we investigated the association between serum thyrotropin (TSH) concentration and bone mineral density (BMD) in healthy euthyroid men.
Use of alternative remedies by psychiatric patients: illustrative vignettes and a discussion of the issues.

This clinical conference, in the form of several vignettes, focuses on the increasing importance for clinicians to actively attend to their patients’ uses of herbal “alternative” or “complementary” therapies. First, the prevalence of alternative therapy use is remarkably high. According to data from a national follow-up survey (1), in 1997 the probability of visiting an alternative practitioner was 46.3%, up from the initial 1990 survey figure of 33.8%, and the total number of visits to alternative therapy practitioners increased from 427 million in 1990 to 629 million in 1997, representing primarily an increase in the numbers of individuals visiting alternative practitioners, not an increase in the number of visits per person. In 1997 the amount of out-of-pocket money spent for alternative medicine professional services and herbal products was conservatively estimated to be $27 billion, comparable with the projected 1997 out-of-pocket expenditures for all U.S. physician services; this represents an increase in expenditures of 45.2% between 1990 and 1997. Second, of particular concern to psychiatrists and other mental health professionals, fatigue, headaches, insomnia, depression, and anxiety are among the most common reasons cited for seeking treatment from alternative practitioners (1, 2). These patients often seek treatment from psychiatrists while still taking, and often still believing in, their alternative remedies. Finally, we are witnessing an explosive marketing push for the development of new “nutraceuticals” or “pharmafoods,” i.e., purportedly therapeutic foodstuffs, and the emergence and rapid growth of an industry of food-like herbs marketed as alternative therapies that do not require approval by the U.S. Food and Drug Administration (FDA) (3, 4). This rapidly evolving trend is most clearly seen in herb-laced beverages ranging from brand-named teas to upscale soft drinks, all increasingly available at the local supermarket, as well as at specialty health food emporiums, and we can expect major increases in the rates at which patients seeking psychiatric care will have already been taking herbal alternative remedies that may or may not be active and that may or may not have positive or deleterious interactions with conventional treatments. All of this suggests that clinicians need to routinely and nonjudgmentally ask patients about their use of herbal alternative and complementary treatments, know enough about the more common ones to assess patients for deleterious effects or interactions, and know where to find legitimate information about other treatments. This clinical conference will first present cases demonstrating use of two of the more commonly used herbal alternative medicine compounds, present a third case dealing with staffpatient interactions concerning the use of herbal remedies, and end with a discussion of perspectives and attitudes that contemporary clinicians may find useful concerning their patients’ use of herbal alternative treatments.
Incidence and predictors of death, retention, and switch to second-line regimens in antiretroviral- treated patients in sub-Saharan African Sites with comprehensive monitoring availability.

BACKGROUND Antiretroviral treatment programs in sub-Saharan Africa have high rates of early mortality and loss to follow-up. Switching to second-line regimens is often delayed because of limited access to laboratory monitoring. METHODS Retrospective analysis was performed of a cohort of adults who initiated a standard first-line antiretroviral treatment at 5 public sector sites in 3 African countries. Monitoring included routine CD4 cell counts, human immunodeficiency virus RNA measures, and records of whether appointments were kept. Incidence and predictors of death, loss to follow-up, and switch to second-line regimens were analyzed by time-to-event approaches. RESULTS A total of 3749 patients were analyzed; at baseline, 37.1% were classified as having World Health Organization disease stage 3 or 4, and the median CD4 cell count was 192 cells/mL. First-line regimens were nevirapine based in 96.5% of patients; 17.7% of patients attended <95% of their drug pickup appointments. During 4545 person-years of follow-up, mortality was 8.6 deaths per 100 person-years and was predicted by lower baseline CD4 cell count, lower hemoglobin level, and lower body mass index (calculated as weight in kilograms divided by the square of height in meters); more-advanced clinical stage of infection; male sex; and more missed drug pickup appointments. Dropouts (which accrued at a rate of 2.1 dropouts per 100 person-years) were predicted by a lower body mass index, more missed visits and missed drug pickup appointments, and later calendar year. Incidence of switches to second-line regimens was 4.9 per 100 person-years; increased hazards were observed with lower CD4 cell count and earlier calendar year at baseline. In patients who switched, virological failure was predicted by combined clinical and CD4 criteria with 74% sensitivity and 30% specificity. CONCLUSIONS In an antiretroviral treatment program employing comprehensive monitoring, the probability of switching to second-line therapy was limited. Regular pickup of medication was a predictor of survival and was also strongly predictive of patient retention.
Triangle Listing Algorithms: Back from the Diversion

We show that most algorithms from the literature on listing the triangles of a graph have a common abstraction. Our unifying framework highlights that these seemingly different algorithms are in fact instantiations of a single generic procedure, and even suggests some additional variants. More importantly, it yields parsimonious implementations that are in general more efficient than those described in the original works. In addition, we show that the running time of nearly every triangle listing variant is in O(a(G)m), where a(G) is the arboricity of the graph and m the number of edges. So far this bound has been proven only for Chiba and Nishizeki's (SIAM J. Computing, 1985) triangle listing algorithm. Finally, algorithmic experimentation reveals that an improved implementation of this algorithm outperforms all subsequently proposed algorithms.
Development of sexually dimorphic vasotocinergic system in the bed nucleus of stria terminalis in chickens

The bed nucleus of stria terminalis (BnST) of the domestic fowl contains two groups of parvicellular vasotocinergic neurons that are sexually dimorphic. In adult cockerels, arginine vasotocin (AVT) synthesis is well expressed in the dorsolateral and ventromedial portions of the BnST, whereas in corresponding brain areas of hens, AVT synthesis is completely lacking. In the present study, in situ hybridization and immunocytochemical methods were used to compare the ontogeny of sexually dimorphic AVT gene expression in the BnST of male and female chickens from day 12 of embryonic development (E12) until the onset of sexual maturation. By E12, both parvicellular groups of AVT‐immunoreactive (AVT‐ir) perikarya in the developing BnST can be distinguished in some males, whereas in females their presence is questionable. A quantitative analysis, beginning at E14, showed that the parvicellular dorsolateral portion of the BnST of male embryos had more AVT perikarya compared with females. In contrast, no evident sex difference in distribution pattern and number of AVT mRNA containing neurons in this BnST portion was observable by in situ hybridization at E15. At E18, as well as on the first and second days posthatch (D1 and D2), no differences in the number of AVT synthesizing cells and intensity of immunoreactive staining in male versus female chickens were found. Between D2 and D7, the number of AVT‐ir cells in the BnST declined rapidly in both sexes until it disappeared completely in females before D35. In males, another increase in sexually dimorphic AVT‐ir cells and innervation of the lateral septum was associated with the onset of puberty and fully matched a pattern observed in adult fowls. These results demonstrate that the sexually dimorphic part of the AVT system undergoes sexual differentiation during early stages of ontogeny. J. Comp. Neurol. 408:46–60, 1999. © 1999 Wiley‐Liss, Inc.
Intrapleural fibrinolytic agents for empyema and complicated parapneumonic effusions: a meta-analysis.

BACKGROUND Randomized controlled trials have shown conflicting findings about the role of intrapleural fibrinolytic therapy for the treatment of empyema and complicated parapneumonic effusions in adult patients. OBJECTIVES To assess the clinical efficacy and summarize the current evidence of intrapleural fibrinolytic use in patients with empyema and complicated parapneumonic effusions in adult patients. METHODS We performed a meta-analysis of all properly randomized trials comparing intrapleural fibrinolytic agents with placebo in adult patients with empyema and complicated parapneumonic effusions. Outcome of primary interest was the reduction of death and surgical intervention. RESULTS We included five trials totaling 575 patients. The number of enrolled patients for each trial was small, except for the recent trial by Multicenter Intrapleural Sepsis Trial (MIST1) group. Compared with placebo, intrapleural fibrinolytic therapy was associated with a nonsignificant reduction in death and need for surgery (27.6% of the treatment group vs 32.8% of the control group; random-effects pooled risk ratio, 0.55; 95% confidence interval, 0.28 to 1.07; heterogeneity, p = 0.023). A separate analysis for outcomes on either death or need for surgery also showed nonsignificant results. CONCLUSION Our meta-analysis does not support the routine use of fibrinolytic therapy for all patients who require chest tube drainage for empyema or complicated parapneumonic effusions. However, there was significant heterogeneity of the treatment effects among the trials. Selected patients might benefit from the treatment.
Differential Inclusions , Control and Optimization 22 ( 2002 ) 79 – 95 NEW VERSIONS ON NIKAIDÔ ’ S COINCIDENCE THEOREM

In 1959, Nikaidô established a remarkable coincidence theorem in a compact Hausdorff topological space, to generalize and to give a unified treatment to the results of Gale regarding the existence of economic equilibrium and the theorems in game problems. The main purpose of the present paper is to deduce several generalized key results based on this very powerful result, together with some KKM property. Indeed, we shall simplify and reformulate a few coincidence theorems on acyclic multifunctions, as well as some Górniewicz-type fixed point theorems. Beyond the realm of monotonicity nor metrizability, the results derived here generalize and unify various earlier ones from the classic optimization theory. In the sequel, we shall deduce two versions of Nikaidô’s coincidence theorem about Vietoris maps from different approaches.
Comparison of Tissue Heat Balance- and Thermal Dissipation-Derived Sap Flow Measurements in Ring-Porous Oaks and a Pine

Sap flow measurements have become integral in many physiological and ecological investigations. A number of methods are used to estimate sap flow rates in trees, but probably the most popular is the thermal dissipation (TD) method because of its affordability, relatively low power consumption, and ease of use. However, there have been questions about the use of this method in ring-porous species and whether individual species and site calibrations are needed. We made concurrent measurements of sap flow rates using TD sensors and the tissue heat balance (THB) method in two oak species (Quercus prinus Willd. and Quercus velutina Lam.) and one pine (Pinus echinata Mill.). We also made concurrent measurements of sap flow rates using both 1 and 2-cm long TD sensors in both oak species. We found that both the TD and THB systems tended to match well in the pine individual, but sap flow rates were underestimated by 2-cm long TD sensors in five individuals of the two ring-porous oak species. Underestimations of 20–35% occurred in Q. prinus even when a “Clearwater” correction was applied to account for the shallowness of the sapwood depth relative to the sensor length and flow rates were underestimated by up to 50% in Q. velutina. Two centimeter long TD sensors also underestimated flow rates compared with 1-cm long sensors in Q. prinus, but only at large flow rates. When 2-cm long sensor data in Q. prinus were scaled using the regression with 1-cm long data, daily flow rates matched well with the rates measured by the THB system. Daily plot level transpiration estimated using TD sap flow rates and scaled 1 cm sensor data averaged about 15% lower than those estimated by the THB method. Therefore, these results suggest that 1-cm long sensors are appropriate in species with shallow sapwood, however more corrections may be necessary in ring-porous species.
Matching Based Kernels for Labeled Graphs

For various classification problems it is most natural to represent training examples as labeled graphs. As a result several kernel functions over these complex structures have been proposed in the literature so far. Most of them exploit the Cross Product Kernel between two sets resulting from the decompositions of corresponding graphs into subgraphs of a specific type. The similarities between the substructures are often computed using the 0 − 1 Kronecker Delta Kernel. This approach has two main limitations: (i) in general most of the subgraphs will be poorly correlated with the actual target variable, adversely affecting the generalization of a classifier and (ii) as no graded similarities on subparts are computed, the expressivity of the resulting kernels is reduced. To tackle the above problems we propose here a class of graph kernels based on set distance measures whose computation is based on specific pairs of points from the corresponding graph decompositions. The actual matching of elements from the two sets depends on a graded similarity (standard Euclidean metric in our case) between the elements of the two sets. To make our similarity measure positive semidefinite we exploit the notion of the proximity space induced by a given set distance measure. To practically demonstrate the effectiveness of our approach we report promising experimental results for the task of activity prediction of drug molecules.