Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of neural coding through quantization with an information-based distortion measure

We discuss an analytical approach through which the neural symbols and corresponding stimulus space of a neuron or neural ensemble can be discovered simultaneously and quantitatively, making few assumptions about the nature of the code or relevant features. The basis for this approach is to conceptualize a neural coding scheme as a collection of stimulus-response classes akin to a dictionary or 'codebook', with each class corresponding to a spike pattern 'codeword' and its corresponding stimulus feature in the codebook. The neural codebook is derived by quantizing the neural responses into a small reproduction set, and optimizing the quantization to minimize an information-based distortion function. We apply this approach to the analysis of coding in sensory interneurons of a simple invertebrate sensory system. For a simple sensory characteristic (tuning curve), we demonstrate a case for which the classical definition of tuning does not describe adequately the performance of the cell studied. Considering a more involved sensory operation (sensory discrimination), we also show that, for some cells in this system, a significant amount of information is encoded in patterns of spikes that would not be discovered through analyses based on linear stimulus-response measures.
Non-typhoidal Salmonella bacteremia in adults.

BACKGROUND AND PURPOSE Very few studies have examined prognostic factors in adult patients with non-typhoidal Salmonella (NTS) bacteremia. The purpose of this study was to identify the prognostic factors of these patients. METHODS A total of 79 episodes of NTS bacteremia were identified in 73 patients between January 2001 and December 2003. Susceptibilities to various antimicrobials were determined using disk-diffusion tests and National Committee for Clinical Laboratory Standards criteria. Multiple logistic regression was used to evaluate the relationship between patients' characteristics and covariates of mortality. RESULTS There were only 5 episodes (6%) of gastroenteritis, two of which were due to Salmonella septicemia contracted abroad. Potentially predisposing factors were identifiable in 51 episodes (65%). Infections in 24 patients (30%) were due to serogroup B Salmonella and in 22 patients (28%), to serogroup C Salmonella. A logistic regression analysis selected two variables as independently influencing prognosis: coma (p=0.006) and septic shock (p=0.002). CONCLUSIONS Thus, most adult patients with NTS bacteremia do not develop gastroenteritis. Patients in shock or coma have poor prognosis, and susceptibility to third-generation cephalosporins, cefepime, and carbapenem is high.
A Construction of Almost Steiner Systems

Let n, k, and t be integers satisfying n>k>t≥2 . A Steiner system with parameters t, k, and n is a k‐uniform hypergraph on n vertices in which every set of t distinct vertices is contained in exactly one edge. An outstanding problem in Design Theory is to determine whether a nontrivial Steiner system exists for t≥6 . In this note we prove that for every k>t≥2 and sufficiently large n, there exists an almost Steiner system with parameters t, k, and n; that is, there exists a k‐uniform hypergraph on n vertices such that every set of t distinct vertices is covered by either one or two edges.
p63 Expression Defines a Lethal Subset of Muscle-Invasive Bladder Cancers

Background p63 is a member of the p53 family that has been implicated in maintenance of epithelial stem cell compartments. Previous studies demonstrated that p63 is downregulated in muscle-invasive bladder cancers, but the relationship between p63 expression and survival is not clear. Methodology/Principal Findings We used real-time PCR to characterize p63 expression and several genes implicated in epithelial-to-mesenchymal transition (EMT) in human bladder cancer cell lines (n = 15) and primary tumors (n = 101). We correlated tumor marker expression with stage, disease-specific (DSS), and overall survival (OS). Expression of E-cadherin and p63 correlated directly with one another and inversely with expression of the mesenchymal markers Zeb-1, Zeb-2, and vimentin. Non-muscle-invasive (Ta and T1) bladder cancers uniformly expressed high levels of E-cadherin and p63 and low levels of the mesenchymal markers. Interestingly, a subset of muscle-invasive (T2–T4) tumors maintained high levels of E-cadherin and p63 expression. As expected, there was a strongly significant correlation between EMT marker expression and muscle invasion (p<0.0001). However, OS was shorter in patients with muscle-invasive tumors that retained p63 (p = 0.007). Conclusions/Significance Our data confirm that molecular markers of EMT are elevated in muscle-invasive bladder cancers, but interestingly, retention of the “epithelial” marker p63 in muscle-invasive tumors is associated with a worse outcome.
Signature analysis for analog and mixed-signal circuit test response compaction

While the design of signature analyzers for digital circuits has been well researched in the past, signature analyzers for analog signals are relatively unknown. The primary difficulty in analyzing signatures for analog signals is that the latter are imprecise in nature. Therefore, deterministic signature analysis schemes, such as those based on finite-field arithmetic using linear feedback shift registers, are unsuitable for analog circuits. In this paper, a novel signature analysis scheme for analog and mixed signal circuits is proposed. The signatures possess the interesting property that if the input analog signal is imprecise within certain bounds (an inherent property of analog signals), then the generated signature is also imprecise within certain bounds. A failure is indicated by the generated signature being different from the expected signature by a margin greater than a predetermined threshold; the larger the effects of the failure, the larger the difference between the generated signature and the expected signature. The probabilities of aliasing and false rejection are also derived. Results for an example filter circuit are presented.
Effectiveness of an ergonomic intervention on the productivity of workers with upper-extremity disorders--a randomized controlled trial.

OBJECTIVES The aim of this study was to investigate the effectiveness of an ergonomic intervention on productivity loss at work caused by upper-extremity disorders (UED). METHODS Workers with medically verified UED were invited to participate. The intervention consisted of a physician contacting the worker's supervisor and an occupational physiotherapist conducting an ergonomic assessment at the worksite. Before and after the intervention, the employees self-assessed UED-related productivity loss (ie, decreased quality and quantity of the daily work output). We tested for differences between groups at 8 and sub-sequently 12 weeks. We also applied generalized estimating equation (GEE) to analyze repeated measures data. RESULTS Altogether 177 employees were randomized. The overall participation rate was 88%. At baseline, 54% of the intervention group and 58% of the control group reported productivity loss. The magnitude of productivity loss was 17% and 20%, respectively. At 8 weeks, both the proportion and magnitude of productivity loss were lower in the intervention than the control group, but the differences were statistically significant only at 12 weeks (proportion 25% versus 51%, magnitude 7% versus 18%, P=0.001 for both). Using GEE analyses, we also found the differences to be statistically significant (proportion 38% versus 52%, magnitude 12% versus 18%). The intervention only benefitted employees with 0-20% loss of productivity at baseline, not those with a higher initial productivity loss. CONCLUSIONS Early ergonomic intervention, in addition to adequate medical care, is effective in preventing and restoring self-reported productivity loss associated with UED.
Experimental Investigation of the Laminar Flow Along a Straight 135° Corner

The results of measurements in laminar flow along a straight 135° corner are presented. Near to the inlet edge plane the flow has an appearance resembling that reported by Zamir and Young for a 90° corner in which the isovels in transverse planes are concave outwards near the bisecting line of the corner, but unlike the 90° corner flow this characteristic diminishes with distance downstream in the case examined here. The analytical solution by Carrier is found to be a good representation of the flow in the 135° corner.
The influence of head and neck position on oropharyngeal leak pressure and cuff position with the flexible and the standard laryngeal mask airway.

UNLABELLED We conducted a randomized, cross-over study of 20 paralyzed anesthetized adult patients to test the hypothesis that oropharyngeal leak pressure and cuff position (assessed fiberoptically) vary with head and neck position for the flexible (FLMA) and standard laryngeal mask airway (LMA). Both devices were inserted into each patient in random order. Oropharyngeal leak pressure and fiberoptic position (including degree of rotation) were documented in four head and neck positions (neutral first, then flexion, then extension and rotation in random order) for each device. The size 5 was used for all patients, and the intracuff pressure was set at 60 cm H2O in the neutral position. All airway devices were inserted at the first attempt. Oropharyngeal leak pressure was similar for the FLMA and LMA in the neutral (22 vs 21 cm H2O), flexed (26 vs 26 cm H2O), and extended positions (19 vs 18 cm H2O) but was slightly higher for the LMA when the head was rotated (19 vs 22 cm H2O; P = 0.04). Compared with the neutral position, oropharyngeal leak pressure for the LMA was higher with flexion (26 vs 21 cm H2O; P = 0.0004) and lower with extension (18 vs 21 cm H2O; P = 0.03) but similar with rotation. Compared with the neutral position, oropharyngeal leak pressure for the FLMA was higher with flexion (26 vs 22 cm H2O; P = 0.0001) and lower with extension (19 vs 22 cm H2O; P = 0.03) and rotation (19 vs 22 cm H2O; P = 0.03). The difference in oropharyngeal leak pressure between flexion and extension was 7 and 8 cm H2O for the FLMA and LMA, respectively. Fiberoptic position was similar between devices and was unchanged by head and neck position. Rotation was not detected fiberoptically. We conclude that there are small changes in oropharyngeal leak pressure but no changes in cuff position in different head and neck positions for the FLMA and LMA. Oropharyngeal leak pressure may be improved by head and neck flexion and by avoiding extension. IMPLICATIONS There are small changes in oropharyngeal leak pressure but no changes in cuff position in different head and neck positions for the flexible and standard laryngeal mask airways. Oropharyngeal leak pressure may be improved by head and neck flexion and by avoiding extension.
Flt1 acts as a negative regulator of tip cell formation and branching morphogenesis in the zebrafish embryo

Endothelial tip cells guide angiogenic sprouts by exploring the local environment for guidance cues such as vascular endothelial growth factor (VegfA). Here we present Flt1 (Vegf receptor 1) loss- and gain-of-function data in zebrafish showing that Flt1 regulates tip cell formation and arterial branching morphogenesis. Zebrafish embryos expressed soluble Flt1 (sFlt1) and membrane-bound Flt1 (mFlt1). In Tg(flt1BAC:yfp) × Tg(kdrl:ras-cherry)s916 embryos, flt1:yfp was expressed in tip, stalk and base cells of segmental artery sprouts and overlapped with kdrl:cherry expression in these domains. flt1 morphants showed increased tip cell numbers, enhanced angiogenic behavior and hyperbranching of segmental artery sprouts. The additional arterial branches developed into functional vessels carrying blood flow. In support of a functional role for the extracellular VEGF-binding domain of Flt1, overexpression of sflt1 or mflt1 rescued aberrant branching in flt1 morphants, and overexpression of sflt1 or mflt1 in controls resulted in short arterial sprouts with reduced numbers of filopodia. flt1 morphants showed reduced expression of Notch receptors and of the Notch downstream target efnb2a, and ectopic expression of flt4 in arteries, consistent with loss of Notch signaling. Conditional overexpression of the notch1a intracellular cleaved domain in flt1 morphants restored segmental artery patterning. The developing nervous system of the trunk contributed to the distribution of Flt1, and the loss of flt1 affected neurons. Thus, Flt1 acts in a Notch-dependent manner as a negative regulator of tip cell differentiation and branching. Flt1 distribution may be fine-tuned, involving interactions with the developing nervous system.
Dietary risk factors for the development of insulin resistance in adolescent girls: a 3-year prospective study

Abstract Objective Identifying risk factors for insulin resistance in adolescence could provide valuable information for early prevention. The study sought to identify risk factors for changes in insulin resistance and fasting blood glucose levels. Design Prospective cohort of girls participating in the National Heart, Lung, and Blood Institute Growth and Health Study. Setting USA. Subjects Adolescent girls (n 774) assessed at the ages of 16–17 and 18–19 years. Over a 3-year period, measurements of fasting blood glucose and insulin and serum cotinine were taken, and dietary intake (3 d food diary), smoking status and physical activity levels were self-reported. Results Improvements in homeostasis model assessment of insulin resistance (HOMA-IR) were associated with increases in the percentage of energy intake from polyunsaturated fats (β = −3·33, 95 % CI −6·28, −0·39, P = 0·03) and grams of soluble fibre (β = −5·20, 95 % CI −9·81, −0·59, P = 0·03) between the ages of 16–17 and 18–19 years; with similar findings for insulin. Transitioning into obesity was associated with an increase in insulin (β = 6·34, 95 % CI 2·78, 9·91, P < 0·001) and HOMA-IR (β = 28·77, 95 % CI 8·13, 49·40, P = 0·006). Serum cotinine concentrations at 16–17 years, indicating exposure to tobacco, were associated with large increases (β = 15·43, 95 % CI 6·09, 24·77, P < 0·001) in fasting blood glucose concentrations. Conclusions Increases in the percentage of energy from polyunsaturated fat and fibre, and avoidance of excess weight gain and tobacco exposure, could substantially reduce the risk of insulin resistance in late adolescence.
Original MEMS-Based Single Pole Double Throw Topology for Millimeter Wave Space Communications

This paper presents the design, fabrication and characterization of a MEMS-Based Single Pole Double Throw (SPDT) circuit for millimeterwave applications. High performances are achieved thanks to an original circuit design based on MEMS synthesized quarter wave line combined with surface and bulk micromachinings of silicon. 0.6 dB insertion loss of the SPDT circuit was measured with an isolation of 21dB at 30GHz.
UvA-DARE Reward and punishment sensitivity in children with ADHD: validating the Sensitivity to Punishment and Sensitivity to Reward Questionnaire for Children (SPSR-C)

This study validates the Sensitivity to Punishment and Sensitivity to Reward Questionnaire for children (SPSRQ-C), using a Dutch sample of 1234 children between 6 – 13 years old. Factor analysis determined that a 4-factor and a 5-factor solution were best fitting, explaining 41% and 50% of the variance respectively. The 4-factor model was highly similar to the original SPSRQ factors found in adults (Punishment Sensitivity, Reward Responsivity, Impulsivity/ Fun-Seeking, and Drive). The 5-factor model was similar to the 4-factor model, with the exception of a subdivision of the Punishment Sensitivity factor into a factor with ‘ social-fear ’ items and a factor with ‘ anxiety ’ items. To determine external validity, scores of three groups of children with attention deficit hyperactivity disorder (ADHD) were compared on the EFA models: ADHD-only ( n =34), ADHD and autism spectrum disorder (ADHD+ASD; n =22), ADHD and oppositional defiant disorder (ADHD+ODD; n =22). All ADHD groups scored higher than typical controls on Reward Responsivity and on the ‘ anxiety ’ factor ( n =75). The ADHD-only and ADHD+ODD group scored higher than other groups on Impulsivity/Fun-Seeking and Drive, while the ADHD+ASD group scored higher on Punishment Sensitivity. The findings emphasize the value of the SPSRQ-C to quickly and reliably assess a child ’ s sensitivity to reinforcement, with the aim to provide individually-tailored behavioral interventions that utilize reward and reprimands.
Flatness of Semilinear Parabolic PDEs—A Generalized Cauchy–Kowalevski Approach

A generalized Cauchy-Kowalevski approach is proposed for flatness-based trajectory planning for boundary controlled semilinear systems of partial differential equations (PDEs) in a one-dimensional spatial domain. For this, the ansatz presented in “Trajectory planning for boundary controlled parabolic PDEs with varying parameters on higher-dimensional spatial domains” (T. Meurer and A. Kugi, IEEE Trans. Autom. Control, vol. 54, no, 8, pp. 1854-1868, Aug. 2009) using formal integration is generalized towards a unified design framework, which covers linear and semilinear PDEs including rather broad classes of nonlinearities arising in applications. In addition, an efficient semi-numerical solution of the implicit state and input parametrizations is developed and evaluated in different scenarios. Simulation results for various types of nonlinearities and a tubular reactor model described by a system of semilinear reaction-diffusion-convection equations illustrate the applicability of the proposed method.
Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis.

Many physiological and biochemical processes in plants exhibit endogenous rhythms with a period of about 24 h. Endogenous oscillators called circadian clocks regulate these rhythms. The circadian clocks are synchronized to the periodic environmental changes (e.g. day/night cycles) by specific stimuli; among these, the most important is the light. Photoreceptors, phytochromes, and cryptochromes are involved in setting the clock by transducing the light signal to the central oscillator. In this work, we analyzed the spatial, temporal, and long-term light-regulated expression patterns of the Arabidopsis phytochrome (PHYA to PHYE) and cryptochrome (CRY1 and CRY2) promoters fused to the luciferase (LUC(+)) reporter gene. The results revealed new details of the tissue-specific expression and light regulation of the PHYC and CRY1 and 2 promoters. More importantly, the data obtained demonstrate that the activities of the promoter::LUC(+) constructs, with the exception of PHYC::LUC(+), display circadian oscillations under constant conditions. In addition, it is shown by measuring the mRNA abundance of PHY and CRY genes under constant light conditions that the circadian control is also maintained at the level of mRNA accumulation. These observations indicate that the plant circadian clock controls the expression of these photoreceptors, revealing the formation of a new regulatory loop that could modulate gating and resetting of the circadian clock.
Expansion and tissue infiltration of an allospecific CD4+CD25+CD45RO+IL-7Rαhigh cell population in solid organ transplant recipients

It has been recently shown (Seddiki, N., B. Santner-Nanan, J. Martinson, J. Zaunders, S. Sasson, A. Landay, M. Solomon, W. Selby, S.I. Alexander, R. Nanan, et al. 2006. J. Exp. Med. 203:1693–1700.) that the expression of interleukin (IL) 7 receptor (R) α discriminates between two distinct CD4 T cell populations, both characterized by the expression of CD25, i.e. CD4 regulatory T (T reg) cells and activated CD4 T cells. T reg cells express low levels of IL-7Rα, whereas activated CD4 T cells are characterized by the expression of IL-7Rαhigh. We have investigated the distribution of these two CD4 T cell populations in 36 subjects after liver and kidney transplantation and in 45 healthy subjects. According to a previous study (Demirkiran, A., A. Kok, J. Kwekkeboom, H.J. Metselaar, H.W. Tilanus, and L.J. van der Laan. 2005. Transplant. Proc. 37:1194–1196.), we observed that the T reg CD25+CD45RO+IL-7Rαlow cell population was reduced in transplant recipients (P < 0.00001). Interestingly, the CD4+CD25+CD45RO+IL-7Rαhigh cell population was significantly increased in stable transplant recipients compared with healthy subjects (P < 0.00001), and the expansion of this cell population was even greater in patients with documented humoral chronic rejection compared with stable transplant recipients (P < 0.0001). The expanded CD4+CD25+CD45RO+IL-7Rαhigh cell population contained allospecific CD4 T cells and secreted effector cytokines such as tumor necrosis factor α and interferon γ, thus potentially contributing to the mechanisms of chronic rejection. More importantly, CD4+IL-7Rα+and CD25+IL-7Rα+ cells were part of the T cell population infiltrating the allograft of patients with a documented diagnosis of chronic humoral rejection. These results indicate that the CD4+CD25+IL-7Rα+ cell population may represent a valuable, sensitive, and specific marker to monitor allospecific CD4 T cell responses both in blood and in tissues after organ transplantation.
PNPLA3 variants specifically confer increased risk for histologic nonalcoholic fatty liver disease but not metabolic disease

Single nucleotide polymorphisms (SNPs) near 7 loci have been associated with liver function tests or with liver steatosis by magnetic resonance spectroscopy. In this study we aim to test whether these SNPs influence the risk of histologically‐confirmed nonalcoholic fatty liver disease (NAFLD). We tested the association of histologic NAFLD with SNPs at 7 loci in 592 cases of European ancestry from the Nonalcoholic Steatohepatitis Clinical Research Network and 1405 ancestry‐matched controls. The G allele of rs738409 in PNPLA3 was associated with increased odds of histologic NAFLD (odds ratio [OR] = 3.26, 95% confidence intervals [CI] = 2.11‐7.21; P = 3.6 × 10−43). In a case only analysis of G allele of rs738409 in PNPLA3 was associated with a decreased risk of zone 3 centered steatosis (OR = 0.46, 95% CI = 0.36‐0.58; P = 5.15 × 10−11). We did not observe any association of this variant with body mass index, triglyceride levels, high‐ and low‐density lipoprotein levels, or diabetes (P > 0.05). None of the variants at the other 6 loci were associated with NAFLD. Conclusion: Genetic variation at PNPLA3 confers a markedly increased risk of increasingly severe histological features of NAFLD, without a strong effect on metabolic syndrome component traits. (HEPATOLOGY 2010)