Miracle-dz/UniFAR-FTUs huggingface dataset:
Formal Analysis of the Alternating Bit Protocol by Temporal Petri Nets

Temporal Petri nets are Petri nets in which certain restrictions on the firings of transitions are represented by formulas containing temporal operators. The use of temporal Petri nets for formal specification and verification of the alternating bit protocol is discussed. The temporal Petri net which models the protocol is analyzed formally using the existing theory of omega -regular expressions and Buchi-automata. >
On the Computational Complexity of Best L1-approximation

It is well known that for a given continuous function f : [0, 1] → R and a number n there exists a unique polynomial pn ∈ Pn (polynomials of degree ≤ n) which best L1-approximates f . We establish the first upper bound on the complexity of the sequence (pn)n∈N, assuming f is polynomial-time computable. Our complexity analysis makes essential use of the modulus of uniqueness for L1-approximation presented in [13]. Mathematics Subject Classification: 41A52, 41A10, 68Q17, 03F10.
Tragic Beauties: Heroin Images and Heroin Users

We present selected findings from “An Ethnography of Young Heroin Users” concerning media and youth-subculture influences on the initiation and continuation of heroin use among young adults ages 18–25. One hundred and two male and female participants were administered depth interviews and structured questionnaires pertaining to heroin initiation and continuation practices. A number of participants mentioned media depictions of heroin and membership in specific youth cultures in relation to their own heroin use. This complex relationship between heroin use, media, and subcultures is discussed. A common theme emerged from the depth interviews of fatalistic life outlooks, which were often linked with negative childhood experiences as well as with heroin use. Some of these young addicts romanticized heroin use and the tragedy of overdose. These findings are discussed with reference to further research and possible interventions.
More on Penrose limits and non-local theories

We obtain the Penrose limit of six dimensional Non-Commutative Open String (NCOS6) theory and show that in the neighborhood of a particular null geodesic it leads to an exactly solvable string theory (unlike their counterparts in four or in other dimensions). We describe the phase structure of this theory and discuss the Penrose limit in different phases including Open D-string (OD1) theory. We compute the string spectrum and discuss their relations with the states of various theories at different phases. We also consider the case of general null geodesic for which the Penrose limit leads to string theory in the time dependent pp-wave background and comment on the renormalization group flow in the dual theory.
The International Journal of Biostatistics Biclustering of Gene Expression Data by an Extension of Mixtures of Factor Analyzers

A challenge in microarray data analysis concerns discovering local structures composed by sets of genes that show homogeneous expression patterns across subsets of conditions. We present an extension of the mixture of factor analyzers model (MFA) allowing for simultaneous clustering of genes and conditions. The proposed model is rather flexible since it models the density of highdimensional data assuming a mixture of Gaussian distributions with a particular omponentspecific covariance structure. Specifically, a binary and row stochastic matrix representing tissue membership is used to cluster tissues (experimental conditions), whereas the traditional mixture approach is used to define the gene clustering. An alternating expectation conditional maximization (AECM) algorithm is proposed for parameter estimation; experiments on simulated and real data show the efficiency of our method as a general approach to biclustering. The Matlab code of the algorithm is available upon request from authors.
A Metric for Automatic Word-Length Determination of Hardware Datapaths

A metric for the automatic determination of word lengths required for implementing DSP algorithms is proposed. The metric is capable of handling several error models computed between the fixed-point and the floating-point simulation results to model the impact of finite word lengths on the overall accuracy. It grades all the word-length combinations and guides a procedure towards the optimal solution. This metric was implemented in an automatic word-length determination tool to guide its search for better hardware implementations. It enables the creation of a framework for architecture and platform exploration
Genes Expressed in Pseudomonas putidaduring Colonization of a Plant-Pathogenic Fungus

ABSTRACT In vivo expression technology (IVET) was employed to study colonization of Phytophthora parasitica by a biological control bacterium, Pseudomonas putida 06909, based on a new selection marker. The pyrB gene, which encodes aspartate transcarbamoylase, an enzyme used for pyrimidine biosynthesis, was cloned from P. putida 06909. A pyrB-disrupted mutant did not grow in pyrimidine-deficient media unless it was complemented with pyrBC′ behind an active promoter. Thirty clones obtained from P. putida 06909 that were expressed on fungal hyphae but not on culture media were isolated by IVET based on the promoterless transcriptional fusion between pyrBC′ andlacZ. Nineteen of these clones were induced during late-stage bacterial growth in vitro, while 11 of the clones were expressed only when they were inoculated onto fungal hyphae. Restriction analysis of these 11 clones revealed that there were five unique clones. Sequence analyses of three of the five unique clones showed that the 3′ ends of the clones fused to pyrB were similar to genes encoding diacylglycerol kinase (DAGK), bacterial ABC transporters, and outer membrane porins. The sequences of the two other clones were not similar to the sequences of any of the genes in the database used. A LuxR family response regulator was found upstream of DAGK, and a LysR family response regulator was found upstream of the ABC transporter. The location of the inducible promoter of two clones suggested that DAGK and the ABC transporter are induced and may play a role in colonization of the fungus P. parasitica byP. putida 06909.
ARL4A acts with GCC185 to modulate Golgi complex organization

ADP-ribosylation factor-like protein 4A (ARL4A) is a developmentally regulated member of the ARF/ARL GTPase family. The primary structure of ARL4A is very similar to that of other ARF/ARL molecules, but its function remains unclear. The trans-Golgi network golgin GCC185 is required for maintenance of Golgi structure and distinct endosome-to-Golgi transport. We show here that GCC185 acts as a new effector for ARL4 to modulate Golgi organization. ARL4A directly interacts with GCC185 in a GTP-dependent manner. Sub-coiled-coil regions of the CC2 domain of GCC185 are required for the interaction between GCC185 and ARL4A. Depletion of ARL4A reproduces the GCC185-depleted phenotype, causing fragmentation of the Golgi compartment and defects in endosome-to-Golgi transport. GCC185 and ARL4A localize to the Golgi independently of each other. Deletion of the ARL4A-interacting region of GCC185 results in inability to maintain Golgi structure. Depletion of ARL4A impairs the interaction between GCC185 and cytoplasmic linker-associated proteins 1 and 2 (CLASP1 and CLASP2, hereafter CLASPs) in vivo, and abolishes the GCC185-mediated Golgi recruitment of these CLASPs, which is crucial for the maintenance of Golgi structure. In summary, we suggest that ARL4A alters the integrity of the Golgi structure by facilitating the interaction of GCC185 with CLASPs.
An Adaptive Sampling Approach to 3D Reconstruction of Weld Joint

We present an adaptive sampling approach to 3D reconstruction of the welding joint using the point cloud that is generated by a laser sensor. We start with a randomized strategy to approximate the surface of the volume of interest through selection of a number of pivotal candidates. Furthermore, we introduce three proposal distributions over the neighborhood of each of these pivots to adaptively sample from their neighbors to refine the original randomized approximation to incrementally reconstruct this welding space. We prevent our algorithm from being trapped in a neighborhood via permanently labeling the visited samples. In addition, we accumulate the accepted candidates along with their selected neighbors in a queue structure to allow every selected sample to contribute to the evolution of the reconstructed welding space as the algorithm progresses. We analyze the performance of our adaptive sampling algorithm in contrast to the random sampling, with and without replacement, to show a significant improvement in total number of samples that are drawn to identify the region of interest, thereby expanding upon neighboring samples to extract the entire region in a fewer iterations and a shorter computation time.
Hepatitis C Virus Stimulates the Expression of Cyclooxygenase-2 via Oxidative Stress: Role of Prostaglandin E2 in RNA Replication

ABSTRACT Hepatitis C virus (HCV) infection is a major cause of chronic liver disease, which can lead to the development of liver cirrhosis and hepatocellular carcinoma. Recently, the activation of cyclooxygenase-2 (Cox-2) has been implicated in the HCV-associated hepatocellular carcinoma. In this study, we focus on the signaling pathway leading to Cox-2 activation induced by HCV gene expression. Here, we demonstrate that the HCV-induced reactive oxygen species and subsequent activation of NF-κB mediate the activation of Cox-2. The HCV-induced Cox-2 was sensitive to antioxidant (pyrrolidine dithiocarbamate), Ca2+ chelator (BAPTA-AM), and calpain inhibitor (N-acetyl-Leu-Leu-Met-H). The levels of prostaglandin E2 (PGE2), the product of Cox-2 activity, are increased in HCV-expressing cells. Furthermore, HCV-expressing cells treated with the inhibitors of Cox-2 (celecoxib and NS-398) showed significant reduction in PGE2 levels. We also observed the enhanced phosphorylation of Akt and its downstream substrates glycogen synthase kinase-3β and proapoptotic Bad in the HCV replicon-expressing cells. These phosphorylation events were sensitive to inhibitors of Cox-2 (celecoxib and NS-398) and phosphatidylinositol 3-kinase (LY294002). Our results also suggest a potential role of Cox-2 and PGE2 in HCV RNA replication. These studies provide insight into the mechanisms by which HCV induces intracellular events relevant to liver pathogenesis associated with viral infection.
Evaluation of image quality metrics for sharpness enhancement

Image quality assessment has become a meaningful research field due to the explosive growth of image processing technologies in imaging industries. It is becoming more usual to quantify the quality of an image using image quality metrics, rather than carrying out time-consuming psychometric experiments. However, there is little research on the performance of image quality metrics on quality enhanced images. In this paper, we focus on images that have been enhanced by sharpening. A psychometric experiment was designed with observers giving scores to different images enhanced by sharpening on a display in a controlled dark environment. The results showed that full reference image quality metrics performed well when sharpening did not improve the visual image quality, while in images where sharpening increased the visual quality the performance was lower. No reference image quality metrics show better predictions than full reference image quality metrics in most cases.
Emergence of W135 meningococcal meningitis in Ghana

Neisseria meningitidis serogroup W135, well known for a long time as a cause of isolated cases of meningococcal meningitis, has recently increasingly been associated with disease outbreaks of considerable magnitude. Burkina Faso was hit by W135 epidemics in the dry seasons of 2002–2004, but only four W135 meningitis cases were recorded between February 2003 and March 2004 in adjoining Ghana. This reconfirms previous findings that bottlenecks exist in the spreading of new epidemic N. meningitidis clones within the meningitis belt of sub‐Saharan Africa. Of the four Ghanaian W135 meningitis patients one died and three survived, of whom one had profound neurosensory hearing loss and speech impairment. All four disease isolates were sensitive to penicillin G, chloramphenicol, ciprofloxacin and cefotaxime and had the multi‐locus sequence type (ST) 11, which is the major ST of the ET‐37 clonal complex. Pulsed‐field gel electrophoresis (PFGE) profiles of the Ghanaian disease isolates and recent epidemic isolates from Burkina Faso were largely identical. We conducted meningococcal colonization surveys in the home communities of three of the patients and in the Kassena Nankana District located at the border to Burkina Faso. W135 carriage rates ranged between 0% and 17.5%. When three consecutive surveys were conducted in the patient community with the highest carrier rate, persistence of W135 colonization over a period of 1 year was observed. Differences in PFGE profiles of carrier isolates taken at different times in the same patient community were indicative of rapid microevolution of the W135 bacteria, emphasizing the need for innovative fine typing methods to reveal the relationship between W135 isolates.
The Bayesian Rationale for Energy Functionals 1

One of the primary goals of low-level vision is to segment the domain D of an image I into the parts D i on which distinct surface patches, belonging to distinct objects in the scene, are visible. Although this sometimes requires high level knowledge about the shape and surface appearance of various classes of objects, there are many low-level clues about the appearance of the individual surface patches and the boundaries between them. For example, the surface patches usually have characteristic albedo patterns, textures, on them, and these textures often change sharply as you cross a boundary between two patches. Therefore , one approach to the segmentation problem has been to try to merge all the low-level clues for splitting and merging diierent parts of the domain D and come up with probability measures p(fD i g) of how likely a given segmentation fD i g is on the basis of all available low-level information, and what is the most likely segmentation. Alternately, one sets E(fD i g) = ? log(p(fD i g)), which one calls thèenergy' of the segmentation, and seeks the segmentation with the minimum energy. In general, these models have two parts: a prior model of possible scene segmen-tations, possibly including variables to describe other scene structures that are relevant (e.g. depth relationships), and a data model of what images are consistent with this prior model of the scene. If we write w for the variables used to describe the scene, e.g. the subsets D i or the set of all their boundary points ? , then the prior model is some probability space ((w ; p), where w is the set of all possible values of w. The model is speciied by giving the probability distribution p(w) on all these values. The data model is a larger probability space ((w;d ; p), where w;d is the set of all possible values of w and of all possible observed images I. This model is completed by giving the conditional probabilities p(Ijw) of any image I given the scene variables w, resulting in the joint probability distribution: p(I; w) = p(Ijw) p(w) The discussion above assumes implicitly that the spaces w and w;d are nite, although huge (e.g. the set of byte valued images I on a grid of size 256x256 has
Par-1 regulates bicoid mRNA localisation by phosphorylating Exuperantia

The Ser/Thr kinase Par-1 is required for cell polarisation in diverse organisms such as yeast, worms, flies and mammals. During Drosophila oogenesis, Par-1 is required for several polarisation events, including localisation of the anterior determinant bicoid. To elucidate the molecular pathways triggered by Par-1, we have performed a genome-wide, high-throughput screen for Par-1 targets. Among the targets identified in this screen was Exuperantia (Exu), a mediator of bicoid mRNA localisation. We show that Exu is a phosphoprotein whose phosphorylation is dependent on Par-1 in vitro and in vivo. We identify two motifs in Exu that are phosphorylated by Par-1, and show that their mutation abolishes bicoid mRNA localisation during mid-oogenesis. Interestingly, exu mutants in which Exu phosphorylation is specifically affected can to some extent recover from these bicoid mRNA localisation defects during late oogenesis. These results demonstrate that Par-1 establishes polarity in the oocyte by activating a mediator of bicoid mRNA localisation. Furthermore, our analysis reveals two phases of Exu-dependent bicoid mRNA localisation: an early phase that is strictly dependent on Exu phosphorylation and a late phase that is less phosphorylation dependent.
Carbon Dioxide–Rich Water Bathing Enhances Collateral Blood Flow in Ischemic Hindlimb via Mobilization of Endothelial Progenitor Cells and Activation of NO-cGMP System

Background—Carbon dioxide–rich water bathing has the effect of vasodilatation, whereas it remains undetermined whether this therapy exerts an angiogenic action associated with new vessel formation. Methods and Results—Unilateral hindlimb ischemia was induced by resecting the femoral arteries of C57BL/J mice. Lower limbs were immersed in CO2-enriched water (CO2 concentration, 1000 to 1200 mg/L) or freshwater (control) at 37°C for 10 minutes once a day. Laser Doppler imaging revealed increased blood perfusion in ischemic limbs of CO2 bathing (38% increase at day 28, P<0.001), whereas NG-nitro-l-arginine methyl ester treatment abolished this effect. Angiography or immunohistochemistry revealed that collateral vessel formation and capillary densities were increased (4.1-fold and 3.7-fold, P<0.001, respectively). Plasma vascular endothelial growth factor (VEGF) levels were elevated at day 14 (18%, P<0.05). VEGF mRNA levels, phosphorylation of NO synthase, and cGMP accumulation in the CO2-bathed hindlimb muscles were increased (2.7-fold, 2.4-fold, and 3.4-fold, respectively) but not in forelimb muscles. The number of circulating Lin−/Flk-1+/CD34− endothelial-lineage progenitor cells was markedly increased by CO2 bathing (24-fold at day 14, P<0.001). The Lin−/Flk-1+/CD34− cells express other endothelial antigens (endoglin and VE-cadherin) and incorporated acetylated LDL. Conclusions—Our present study demonstrates that CO2 bathing of ischemic hindlimb causes the induction of local VEGF synthesis, resulting in an NO-dependent neocapillary formation associated with mobilization of endothelial progenitor cells.
Risk factors for eating disturbances in young people with type 1 diabetes and chronic asthma : the role of parenting style and self-esteem

Background Research indicates that eating disturbances are twice as prevalent among adolescents with type 1 diabetes compared to their healthy peers; comparisons with other chronic illness groups are inconclusive. Adolescent self-esteem and parenting factors have been found to be associated with eating disturbances in type 1 diabetes. However, to date the literature is methodologically limited by a lack of comparison group, and has failed to consider the role of parent care and overprotection. Aims This study aimed to explore the relationship between adolescent-perceived parent care and overprotection, self-esteem and eating disturbances in a group of adolescents with type 1 diabetes compared to a group with asthma. Method Participants were 16 – 18 year old males and females with a diagnosis of type 1 diabetes (n = 65) or asthma (n = 37) recruited through NHS clinics. The Eating Disorder Examination-Questionnaire was used along with the Parental Bonding Instrument, as a measure of parent overprotection and care, and the Rosenberg Self-Esteem Scale. A cross-sectional, self-report questionnaire design was utilised. Results Unexpectedly, the asthma group reported significantly higher levels of eating psychopathology than the type 1 diabetes group. Significant negative associations were found between parent care and eating disturbances in both illness groups. Additionally, significant positive associations were found between parent overprotection and eating disturbances in the type 1 diabetes group, but not the asthma group. As predicted, self-esteem was strongly negatively correlated with eating disturbances in both groups. Conclusion Overall, the results suggest that adolescents with both asthma and type 1 diabetes may be vulnerable to higher levels of eating psychopathology, which in turn is associated with poorer self-esteem and less adaptive parenting. The findings are considered in relation to illness-related weight gain and the broader impact of chronic illness. The theoretical and clinical implications are discussed.
Different Calculations of Ankle-Brachial Index and Their Impact on Cardiovascular Risk Prediction

Background— An ankle-brachial index (ABI; ratio of ankle and brachial systolic blood pressure) <0.9 indicates peripheral arterial disease (PAD) and is a strong predictor of cardiovascular events. The aim of the present study was to address the prognostic value of different methods of ABI calculation. Methods and Results— In 831 patients admitted with chest pain for diagnostic heart catheterization, blood pressure of both anterior and posterior tibial arteries was measured. ABI was calculated for each leg with the higher of the 2 ankle pressures (current definition of the American Heart Association) or with the lower of the 2 ankle pressures (modified definition) in relation to the higher of the left or right brachial systolic blood pressure. For each patient, the lower ABI from both legs was used for further evaluation. Fifteen patients (1.8%) with ABI >1.5 were excluded. We compared patients with ABI <0.9 according to the current definition (with PAD, n=204 [25.0%]), those with ABI ≥0.9 according to the modified definition (without PAD, n=524 [64.2%]), and those with ABI <0.9 according to the modified definition and ≥0.9 according to the current definition (suspected PAD, n=88 [10.8%]). Follow-up data (median 6.6 years) were available for 812 patients (99.5%); 157 patients (19.3%) experienced cardiovascular events (cardiovascular death, myocardial infarction, or stroke). Patients without PAD had the lowest cardiovascular event rate, whereas event rates were comparable for patients with PAD and those with suspected PAD (14.8% versus 28.4% versus 25.0%, respectively). In a fully adjusted Cox regression analysis that included patients without PAD as the reference group, the hazard ratio (95% CI) was 1.56 (0.97 to 2.53) for patients with suspected PAD and 1.67 (1.16 to 2.40) for patients with PAD. Conclusions— When the higher ankle pressure is used for ABI calculation, a group of patients at high risk for cardiovascular events is overlooked. With a simple modification of ABI (use of the lower instead of the higher ankle pressure), more patients at risk could be identified.
Sensitivity of Mice to Endotoxin after Vaccination with BCG (Bacillus Calmette-Guérin)∗

Summary 1. It is shown that a single intravenous injection of BCG in mice induces a state of hyperreactivity to bacterial endotoxin. The LD50 for E. coli lipopolysaccharide is decreased from 357 μg in controls to 6 or 7 μg in BCG vaccinated animals. This change appears around the 5th day after vaccination. 2. Trehalose dimycolate, a component derived from virulent tubercle bacilli induces a similar state of hyperreactivity to endotoxin upon single or repeated injections.