Miracle-dz/UniFAR-FTUs huggingface dataset:
Putative IL-10 Low Producer Genotypes Are Associated with a Favourable Etanercept Response in Patients with Rheumatoid Arthritis

Outcome predictors of biologic therapeutic drugs like TNF inhibitors are of interest since side effects like serious infections or malignancy cannot be completely ruled out. Response rates are heterogeneous. The present study addressed the question whether in patients with rheumatoid arthritis (RA) interleukin-10 (IL-10) promoter genotypes with potential relevance for IL-10 production capacity are associated with response to long-term treatment with etanercept. Caucasian RA patients that, according to the EULAR criteria, responded well (n = 25), moderately (n = 17) or not (n = 8) to etanercept therapy (median 36 months, range 4–52), and 160 matched controls were genotyped for the IL-10 promoter SNPs -2849 G>A (rs6703630), -1082 G>A (rs1800896), -819 C>T (rs1800871) and -592 C>A (rs1800872). Haplotypes were reconstructed via mathematic model and tested for associations with disease susceptibility and therapy response. We identified the four predominant haplotypes AGCC, GATA, GGCC, and GACC in almost equal distribution. Patients that responded well carried the putative IL-10 low producer allele -2849 A or the haplotypes AGCC and GATA (RR 2.1 and 4.0, respectively; 95% CI 1.1–4.0 and 1.1–14.8), whereas an unfavourable response was associated with carriage of the putative high producer haplotype GGCC (RR 1.9, 95% CI 1.1–3.3). No significant associations of alleles or haplotypes with disease susceptibility were observed. In RA, a low IL-10 production which is genetically determined rather by haplotypes than by SNPs may favour the response to etanercept treatment. Iatrogenic blockade of TNF may reveal proinflammatory effects of its endogeneous antagonist IL-10. Further studies are needed to correlate these genetic findings to direct cytokine measurements.
The clinical utility of nonword repetition for children living in the rural south of the US

Nonword repetition (NWR) tasks have been shown to minimize cultural biases in language assessment. In the current study, we further examined the clinical utility of NWR with 83 children who lived in the rural south of the US; 33 were African American and 50 were White, with 16 classified as specifically language impaired (SLI) 6‐year‐olds and 67 classified as either age‐matched or younger controls. Main effects were found for group, with the children in the SLI group earning lower NWR scores than the controls. A main effect for syllable length but not race was also documented. The group and syllable length effects could not be explained by differences in the children's articulation abilities or by potential differences in the children's use of vernacular dialect. Discriminant analysis indicated that NWR had a diagnostic accuracy rate of 81% for the 6‐year‐olds, but sensitivity was low (56%). When combined with scores from one other nonbiased assessment tool, however, the diagnostic accuracy of NWR increased to 90%, with rates of sensitivity and specificity above 80%.
A Dynamic View of Circular Colorings

The main contributions of this paper are three-fold. First, we use a dynamic approach based on Reiter's pioneering work on Karp-Miller computation graphs to give a new and short proof of Mohar's Minty-type Theorem. Second, we bridge circular colorings and discrete event dynamic systems to show that the Barbosa and Gafni's results on circular chromatic number can be generalized to edge-weighted symmetric directed graphs. Third, we use the above-mentioned dynamic view of circular colorings to construct new improved lower bounds on the circular chromatic number of a graph. We show as an example that the circular chromatic number of the line graph of the Petersen graph can be determined very easily by using these bounds.
Performance Bounds on Sparse Representations Using Redundant Frames

We consider approximations of signals by the elements of a frame in a complex vector space of dimension $N$ and formulate both the noiseless and the noisy sparse representation problems. The noiseless representation problem is to find sparse representations of a signal $\mathbf{r}$ given that such representations exist. In this case, we explicitly construct a frame, referred to as the Vandermonde frame, for which the noiseless sparse representation problem can be solved uniquely using $O(N^2)$ operations, as long as the number of non-zero coefficients in the sparse representation of $\mathbf{r}$ is $\epsilon N$ for some $0 \le \epsilon \le 0.5$, thus improving on a result of Candes and Tao \cite{Candes-Tao}. We also show that $\epsilon \le 0.5$ cannot be relaxed without violating uniqueness. The noisy sparse representation problem is to find sparse representations of a signal $\mathbf{r}$ satisfying a distortion criterion. In this case, we establish a lower bound on the trade-off between the sparsity of the representation, the underlying distortion and the redundancy of any given frame.
Tasks, Queries, and Rankers in Pre-Retrieval Performance Prediction

Query performance prediction estimates the effectiveness of a query in advance of human judgements. Accurate prediction could be used, for example, to trigger special processing, select query variants, or choose whether to search at all. Prediction evaluations have not distinguished effects due to query wording from effects due to the underlying information need, nor from effects due to performance of the retrieval system itself. Here we use five rankers, 100 tasks, and 28,869 queries to distinguish these three effects over six pre-retrieval predictors. We see that task effects dominate those due to query or ranker; that many "query performance predictors" are in fact predicting task difficulty; and that this makes it difficult to use these algorithms.
Visualisation and characterisation of oestrogen receptor α‐positive neurons expressing green fluorescent protein under the control of the oestrogen receptor α promoter

Oestrogen receptor (ER)α plays important roles in the development and function of various neuronal systems through activation by its ligands, oestrogens. To visualise ERα‐positive neurons, we generated transgenic (tg) mice expressing green fluorescent protein (GFP) under the control of the ERα promoter. In three independent tg lines, GFP‐positive neurons were observed in areas previously reported to express ERα mRNA, including the lateral septum, bed nucleus of the stria terminalis, medial preoptic nucleus (MPO), hypothalamus, and amygdala. In these areas, GFP signals mostly overlapped with ERα immunoreactivity. GFP fluorescence was seen in neurites and cell bodies of neurons. In addition, the network and detailed structure of neurites were visible in dissociated and slice cultures of hypothalamic neurons. We examined the effect of oestrogen deprivation by ovariectomy on the structure of the GFP‐positive neurons. The area of ERα‐positive cell bodies in the bed nucleus of the stria terminalis and MPO was measured by capturing the GFP signal and was found to be significantly smaller in ovariectomy mice than in control mice. When neurons in the MPO were infected with an adeno‐associated virus that expressed small hairpin RNA targeting the ERα gene, an apparent induction of GFP was observed in this area, suggesting a negative feedback mechanism in which ERα controls expression of the ERα gene itself. Thus, the ERα promoter–GFP tg mice will be useful to analyse the development and plastic changes of the structure of ERα‐expressing neurons and oestrogen and its receptor‐mediated neuronal responses.
Ultrafast transport dynamics of p-i-n photodetectors under high-power illumination

We studied ultrafast transport dynamics of highspeed p-i-n photodetectors under high illumination using an electrooptic sampling technique. Under high illumination, saturation nonlinearities were found to be dominated by a space-charge-screening effect. A transient forward external current was also observed, which was attributed to an underdamped plasma oscillation. The external bias required to compensate these nonlinear effects increased with increased illumination.
Addressing Adoption and Research Design Decisions Simultaneously

Methods to estimate the cost-effectiveness of technologies are well developed with increasing experience of their application to inform adoption decisions in a timely way. However, the experience of using similarly explicit methods to inform the associated research decisions is less well developed despite appropriate methods being available with an increasing number of applications in health. The authors demonstrate that evaluation of both adoption and research decisions is feasible within typical time and resource constraints relevant to policy decisions, even in situations in which data are sparse and formal elicitation is required. In addition to demonstrating the application of expected value of sample information (EVSI) in these circumstances, the authors examine and carefully distinguish the impact that the research decision is expected to have on patients while enrolled in the trial, those not enrolled, and once the trial reports. In doing so, the authors are able to account for the range of opportunity cost associated with research and evaluate a number of research designs including length of follow-up and sample size. The authors also explore the implications for research design of conducting research while the technology is approved for widespread use and whether approval should be withheld until research reports. In doing so, the authors highlight the impact of irrecoverable opportunity costs when the initial costs of a technology are compensated only by later gains in health outcome.
The nucleoporin Nup60p functions as a Gsp1p–GTP-sensitive tether for Nup2p at the nuclear pore complex

The nucleoporins Nup60p, Nup2p, and Nup1p form part of the nuclear basket structure of the Saccharomyces cerevisiae nuclear pore complex (NPC). Here, we show that these necleoporins can be isolated from yeast extracts by affinity chromatography on karyopherin Kap95p-coated beads. To characterize Nup60p further, Nup60p-coated beads were used to capture its interacting proteins from extracts. We find that Nup60p binds to Nup2p and serves as a docking site for Kap95p–Kap60p heterodimers and Kap123p. Nup60p also binds Gsp1p–GTP and its guanine nucleotide exchange factor Prp20p, and functions as a Gsp1p guanine nucleotide dissociation inhibitor by reducing the activity of Prp20p. Yeast lacking Nup60p exhibit minor defects in nuclear export of Kap60p, nuclear import of Kap95p–Kap60p-dependent cargoes, and diffusion of small proteins across the NPC. Yeast lacking Nup60p also fail to anchor Nup2p at the NPC, resulting in the mislocalization of Nup2p to the nucleoplasm and cytoplasm. Purified Nup60p and Nup2p bind each other directly, but the stability of the complex is compromised when Kap60p binds Nup2p. Gsp1p–GTP enhances by 10-fold the affinity between Nup60p and Nup2p, and restores binding of Nup2p–Kap60p complexes to Nup60p. The results suggest a dynamic interaction, controlled by the nucleoplasmic concentration of Gsp1p–GTP, between Nup60p and Nup2p at the NPC.
Structural basis of tropism of Escherichia coli to the bladder during urinary tract infection

The first step in the colonization of the human urinary tract by pathogenic Escherichia coli is the mannose‐sensitive binding of FimH, the adhesin present at the tip of type 1 pili, to the bladder epithelium. We elucidated crystallographically the interactions of FimH with D‐mannose. The unique site binding pocket occupied by D‐mannose was probed using site‐directed mutagenesis. All but one of the mutants examined had greatly diminished mannose‐binding activity and had also lost the ability to bind human bladder cells. The binding activity of the mono‐saccharide D‐mannose was delineated from this of mannotriose (Man(α1–3)[Man(α1–6)]Man) by gener‐ating mutants that abolished D‐mannose binding but retained mannotriose binding activity. Our structure/function analysis demonstrated that the binding of the monosaccharide α‐D‐mannose is the primary bladder cell receptor for uropathogenic E. coli and that this event requires a highly conserved FimH binding pocket. The residues in the FimH mannose‐binding pocket were sequenced and found to be invariant in over 200 uropathogenic strains of E. coli. Only enterohaemorrhagic E. coli (EHEC) possess a sequence variation within the mannose‐binding pocket of FimH, suggesting a naturally occurring mechanism of attenuation in EHEC bacteria that would prevent them from being targeted to the urinary tract.
Economic Coercion and Partner Violence Against Wives in Vietnam

Economic coercion refers to behaviors that control an intimate partner’s ability to acquire, use, and maintain economic resources. Little is known about economic coercion in Vietnam. Using survey responses from 533 married women ages 18 to 50 years, we estimated multinomial logistic regression models to compare the determinants of exposure to economic coercion only, co-occurring economic coercion, and any psychological, physical, or sexual intimate partner violence (IPV), and any IPV only, relative to no exposure. Women who, in their childhood, witnessed physical IPV against their mother had higher odds of exposure to co-occurring economic coercion and any IPV as an adult (adjusted Odds Ratio = 3.54, 95% confidence interval [CI] = [1.84, 6.83]) and any IPV only (adjust Odds Ratio = 1.75, 95% CI = [1.00, 3.06]), but not economic coercion only. Women who experienced violence as a child had higher odds of exposure to any IPV only (adjusted Odds Ratio = 1.63, 95% CI = [1.04, 2.56]) but not economic coercion only. Women with more schooling had higher odds of exposure to economic coercion only (adjusted Odds Ratio = 1.17, 95% CI = [1.03, 1.33]) but not other forms of violence. Overall, the estimates from the three models differed significantly. Thus, the determinants of economic coercion and common forms of IPV may differ. More research should focus on men’s perpetration of economic coercion.
Overcoming hierarchical difficulty by hill-climbing the building block structure

The Building Block Hypothesis suggests that Genetic Algorithms (GAs) are well-suited for hierarchical problems, where efficient solving requires proper problem decomposition and assembly of solution from sub-solution with strong non-linear interdependencies. The paper proposes a hill-climber operating over the building block (BB) space that can efficiently address hierarchical problems. The new Building Block Hill-Climber (BBHC) uses hill-climb search experience to learn the problem structure. The neighborhood structure is adapted whenever new knowledge about the underlaying BB structure is incorporated into the search. This allows the method to climb the hierarchical structure by revealing and solving consecutively the hierarchical levels. It is expected that for fully non-deceptive hierarchical BB structures the BBHC can solve hierarchical problems in linearithmic time. Empirical results confirm that the proposed method scales almost linearly with the problem size thus clearly outperforms population based recombinative methods.
Neuropathological Consequences of Gestational Exposure to Concentrated Ambient Fine and Ultrafine Particles in the Mouse

Increasing evidence indicates that the central nervous system (CNS) is a target of air pollution. We previously reported that postnatal exposure of mice to concentrated ambient ultrafine particles (UFP; ≤100 nm) via the University of Rochester HUCAPS system during a critical developmental window of CNS development, equivalent to human 3rd trimester, produced male-predominant neuropathological and behavioral characteristics common to multiple neurodevelopmental disorders, including autism spectrum disorder (ASD), in humans. The current study sought to determine whether vulnerability to fine (≤2.5 μm) and UFP air pollution exposure extends to embryonic periods of brain development in mice, equivalent to human 1st and 2nd trimesters. Pregnant mice were exposed 6 h/day from gestational days (GDs) 0.5-16.5 using the New York University VACES system to concentrated ambient fine/ultrafine particles at an average concentration of 92.69 μg/m3 over the course of the exposure period. At postnatal days (PNDs) 11-15, neuropathological consequences were characterized. Gestational air pollution exposures produced ventriculomegaly, increased corpus callosum (CC) area and reduced hippocampal area in both sexes. Both sexes demonstrated CC hypermyelination and increased microglial activation and reduced total CC microglia number. Analyses of iron deposition as a critical component of myelination revealed increased iron deposition in the CC of exposed female offspring, but not in males. These findings demonstrate that vulnerability of the brain to air pollution extends to gestation and produces features of several neurodevelopmental disorders in both sexes. Further, they highlight the importance of the commonalities of components of particulate matter exposures as a source of neurotoxicity and common CNS alterations.
Systemic intestinal metabolism of 1-naphthol. A study in the isolated vascularly perfused rat small intestine.

Using a vascularly and luminally perfused rat small intestine, we studied the systemic intestinal metabolism of the model substrate 1-naphthol (1-N) to 1-naphthol-beta-D-glucuronide (1-NG). An intestinal extraction ratio of 0.30 +/- 0.02 was found for 1-N. This implies that intestinal metabolism represents up to 14% of the total plasma clearance of 1-N in the rat in vivo. The formed 1-NG was preferentially released into the vascular perfusate, suggesting specialized transport carriers for 1-NG in brushborder and basolateral membrane. When the vascular flow rate was decreased from 10 to 0.5 ml/min, the clearance of 1-N appeared to be completely flow dependent. The apparent conflict between a low extraction ratio (0.30 +/- 0.02 at all flows investigated) and a flow rate-limited 1-N clearance can be explained by the presence of an intestinal vascular bed with a high extraction ratio. We suggest that 1-N is completely extracted from the mucosal blood flow. This view was confirmed by the results of experiments in which the capillary flow of the intestinal mucosa was decreased by infusion of noradrenaline. As a result a temporary decrease in the 1-N extraction ratio was observed. The contribution of the intestine to the total clearance can be masked by the hepatic clearance, because the blood supply to the intestine and liver is coupled in series. An equation was derived to describe the relative contribution of the intestine to the mesenteric clearance of the intestine-liver system. It appears that the effective contribution of the intestine to the mesenteric clearance is of little interest for high extraction drugs. (ABSTRACT TRUNCATED AT 250 WORDS)
Sequential Mining: Patterns and Algorithms Analysis

This paper presents and analysis the common existing sequential pattern mining algorithms. It presents a classifying study of sequential pattern-mining algorithms into five extensive classes. First, on the basis of Apriori-based algorithm, second on Breadth First Search-based strategy, third on Depth First Search strategy, fourth on sequential closed-pattern algorithm and five on the basis of incremental pattern mining algorithms. At the end, a comparative analysis is done on the basis of important key features supported by various algorithms. This study gives an enhancement in the understanding of the approaches of sequential pattern mining.
Structure of complex networks: Quantifying edge-to-edge relations by failure-induced flow redistribution

Abstract The analysis of complex networks has so far revolved mainly around the role of nodes and communities of nodes. However, the dynamics of interconnected systems is often focalized on edge processes, and a dual edge-centric perspective can often prove more natural. Here we present graph-theoretical measures to quantify edge-to-edge relations inspired by the notion of flow redistribution induced by edge failures. Our measures, which are related to the pseudo-inverse of the Laplacian of the network, are global and reveal the dynamical interplay between the edges of a network, including potentially non-local interactions. Our framework also allows us to define the embeddedness of an edge, a measure of how strongly an edge features in the weighted cuts of the network. We showcase the general applicability of our edge-centric framework through analyses of the Iberian power grid, traffic flow in road networks, and the C. elegans neuronal network.
Detecting Novel Features of an Environment Using Habituation

In this paper a novelty filter is introduced which allows a robot operating in an unstructured environment to produce a self-organised model of its surroundings and to detect deviations from the learned model. The environment is perceived using the robot’s 16 sonar sensors. The algorithm produces a novelty measure for each sensor scan relative to the model it has learned. This means that it highlights stimuli which have not been previously experienced. The novelty filter proposed uses a model of habituation. Habituation is a decrement in behavioural response when a stimulus is presented repeatedly. Robot experiments are presented which demonstrate the reliable operation of the filter in a number of environments.
Adaptative combination rule and proportional conflict redistribution rule for information fusion

This paper presents two new promising combina- tion rules for the fusion of uncertain and potentially highl y conflicting sources of evidences in the theory of belief func - tions established first in Dempster-Shafer Theory (DST) and then recently extended in Dezert-Smarandache Theory (DSmT). Our work is to provide here new issues to palliate the well-known limitations of Dempster's rule and to work beyond its limits of applicability. Since the famous Zadeh' s criticism of Dempster's rule in 1979, many researchers have proposed new interesting alternative rules of combination to palliate the weakness of Dempster's rule in order to provide acceptable results specially in highly conflicting situati ons. In this work, we present two new combination rules: the class of Adaptive Combination Rules (ACR) and a new effi- cient Proportional Conflict Redistribution (PCR) rule. Bot h rules allow to deal with highly conflicting sources for stati c and dynamic fusion applications. We present some inter- esting properties for ACR and PCR rules and discuss some simulation results obtained with both rules for Zadeh's pro b- lem and for a target identification problem.
Meteorological forcing of the Adriatic: present vs. projected climate conditions

Meteorological forcing of the Adriatic is examined under the present and predicted climate conditions. Fields from the time slice-experiment per- formed with ECHAM4 model (W. May and E. Roeckner: A time-slice experi- ment with the ECHAM4 AGCM at high resolution - the impact of horizontal resolution on annual mean climate change, Climate Dynamics, 17, 2001, 407-420) are closely analysed for the Adriatic region. Results obtained for the control period, when compared to a number of data, are found to repro- duce the main features of the present-day surface heat flux, water flux and wind field above the Adriatic. In the future, the Adriatic should experience a reduction of heat loss to the atmosphere as well as an enhanced evaporation accompanied with a reduced precipitation leading to an overall increase of fresh-water loss to the atmosphere. The changes in synoptic activity should lead to an abatement of bora winds and to a reduced frequency of sirocco events which, however, are expected to be much more persistent. Finally, changes in the dynamics of the Adriatic, induced by altered meteorological forcing, are briefly discussed.