Miracle-dz/UniFAR-FTUs huggingface dataset:
"self"-conscious objects in Object-Z

Within the field of object oriented type theory, much attention has been devoted to the notion of self and Self-types. In contrast, relatively little attention has been paid to this topic in studies on object oriented specification language semantics. In the context of language semantics, the notion of self poses two problems. Firstly, it involves an awareness by an object of its own identity, and hence a capacity for self referential method invocations. Secondly, the usual reference model for object identity maps object identities to object values. This means that an object's identity is not normally considered to be a part of its value. And so a value for self is not normally in scope. The way that a semantics resolves the scope problem can affect one's ability to use the semantics to reason about an object independently of its environment. The paper motivates the inclusion of a concept of self in object oriented formal specification languages, and shows how this concept can be accommodated within the semantics of Object-Z. We show that a useful consequence of making objects 'self'-aware is that messages between objects can be 'tagged' with the identity of the sender object; this facilitates the task of reasoning about object interaction.
Incorporation of flow and QoS control in multicast routing architectures

Many multicast routing protocols consider only the unicast shortest paths between every pair of source and destination in a group (often based on the number of hops) to setup a multicast tree, such as DVMRP and CBT. Furthermore, they do not offer the ability to consider the resource savings possible in the presence of multiple data flows sharing common paths in a tree, such as CBT and PIM. These aspects hamper resource-efficient routing. In this light, our paper describes flow-based resource allocation control in multicast tree setups. Our proposed model has two aspects: (i) exploring alternate paths to connect a joining user to a tree, should the unicast shortest path not have sufficient bandwidth to sustain the new data flow; and (ii) downstream resource allocation to merge a new data flow with the on-going flows in a tree. (i). Requires 'multi-path connectivity' information at routers in the network, while (ii) requires flow aggregation information to be exchanged between on-tree routers. The model is evaluated by simulation studies. The proposed model can be useful in integrated service networks that contain both low and high bandwidth links, such as future Internet.
Optimal static strain sensor placement for truss bridges

A method to identify optimal strain sensor placement for examining structural static responses is presented. The method is based on the use of numerical optimization. Based on an assumed set of applied static forces, the optimal sensor placement can be obtained, and the measured strains can be used to provide the information needed to describe the structural stiffness. For example, the cross-sectional area can be determined by minimizing the difference between the analytical and measured strains. This approach is used to identify the optimized sensor placement. The objective of this study is to identify the minimum number of static strain sensors and the optimal sensor layout needed to evaluate a bridge’s structural condition. This study includes an automatic model parameter identification method, optimal static strain sensor placement, damage detection, and application to an actual bridge.
Greek drug price cuts will have knock on effects across Europe, industry warns

The European drug industry has warned that the Greek government’s decision to reduce what it is prepared to pay for certain medicines by up to 27% will have a detrimental impact not only in Greece but elsewhere in Europe. The warning by the European Federation of Pharmaceutical Industries and Associations (EFPIA), which represents the research based drug industry in Europe, follows the decision by two Danish companies to withdraw some of their products from the Greek market. The federation notes that the reduction in prices “will inevitably raise the likelihood of increased parallel exports of medicinal products from Greece, diverting supplies needed …
Global Control of GacA in Secondary Metabolism, Primary Metabolism, Secretion Systems, and Motility in the Rhizobacterium Pseudomonas aeruginosa M18

ABSTRACT The rhizobacterium Pseudomonas aeruginosa M18 can produce a broad spectrum of secondary metabolites, including the antibiotics pyoluteorin (Plt) and phenazine-1-carboxylic acid (PCA), hydrogen cyanide, and the siderophores pyoverdine and pyochelin. The antibiotic biosynthesis of M18 is coordinately controlled by multiple distinct regulatory pathways, of which the GacS/GacA system activates Plt biosynthesis but strongly downregulates PCA biosynthesis. Here, we investigated the global influence of a gacA mutation on the M18 transcriptome and related metabolic and physiological processes. Transcriptome profiling revealed that the transcript levels of 839 genes, which account for approximately 15% of the annotated genes in the M18 genome, were significantly influenced by the gacA mutation during the early stationary growth phase of M18. Most secondary metabolic gene clusters, such as pvd, pch, plt, amb, and hcn, were activated by GacA. The GacA regulon also included genes encoding extracellular enzymes and cytochrome oxidases. Interestingly, the primary metabolism involved in the assimilation and metabolism of phosphorus, sulfur, and nitrogen sources was also notably regulated by GacA. Another important category of the GacA regulon was secretion systems, including H1, H2, and H3 (type VI secretion systems [T6SSs]), Hxc (T2SS), and Has and Apr (T1SSs), and CupE and Tad pili. More remarkably, GacA inhibited swimming, swarming, and twitching motilities. Taken together, the Gac-initiated global regulation, which was mostly mediated through multiple regulatory systems or factors, was mainly involved in secondary and primary metabolism, secretion systems, motility, etc., contributing to ecological or nutritional competence, ion homeostasis, and biocontrol in M18.
Efeitos do exercício na redução do risco de quedas em mulheres idosas com osteoporose

OBJECTIVE: This study aims to evaluate the effect of progressive muscular strength and proprioception training program on the balance and decrease in the risk of falls in women with osteoporosis. METHOD: 82 sedentary women aged 60-75 years with osteoporosis were selected and randomized in two groups: the intervention group comprised 41 patients submitted to an 18-week progressive muscular strength and proprioception training of quadriceps associated to drug therapy for osteoporosis; and control group, formed by 41 patients submitted to drug therapy only. The balance and fall risk were evaluated using the Balance Berg Scale (BBS) and calculating the Fall Index (FI). The number of fall was assessed six months before the research and the following six months. RESULTS: 69 patients completed the research. The program improved the functional balance (p<0.001) shown by BBS, decreased the risk of falls evidenced by the general score of FI (p<0.004) and also a decrease in the total number of falls. The experimental group showed significant lower number of falls when compared to the control group (p<0.001). CONCLUSION: The association of progressive strength of quadriceps and proprioceptive training is effective to prevent falls and reduce risk factors. The quantitative model to predict risk of falls might be useful to identify the risk of falls in the elderly. Trial registration: 082213-ANZCTR.
Distributed simultaneous localization and mapping for mobile robot networks via hybrid dynamic belief propagation

This article proposes a hybrid dynamic belief propagation for simultaneous localization and mapping in the mobile robot network. The positions of landmarks and the poses of moving robots at each time slot are estimated simultaneously in an online and distributed manner, by fusing the odometry data of each robot and the measurements of robot–robot or robot–landmark relative distance and angle. The joint belief state of all robots and landmarks is encoded by a factor graph and the marginal posterior probability distribution of each variable is inferred by belief propagation. We show how to calculate, broadcast, and update messages between neighboring nodes in the factor graph. Specifically, we combine parametric and nonparametric techniques to tackle the problem arisen from non-Gaussian distributions and nonlinear models. Simulation and experimental results on publicly available dataset show the validity of our algorithm.
Identification of YsaP, the Pilotin of the Yersinia enterocolitica Ysa Type III Secretion System

ABSTRACT Secretins are multimeric outer membrane pore-forming proteins found in complex export systems in Gram-negative bacteria. All type III secretion systems (T3SSs) have a secretin, and one of these is the YsaC secretin of the chromosomally encoded Ysa T3SS of Yersinia enterocolitica. In some cases, pilotin proteins, which are outer membrane lipoproteins, are required for their cognate secretins to multimerize and/or localize to the outer membrane. However, if secretin multimers mislocalize to the inner membrane, this can trigger the protective phage shock protein (Psp) stress response. During a screen for mutations that suppress YsaC toxicity to a psp null strain, we isolated several independent mutations predicted to increase expression of the YE3559 gene within the Ysa pathogenicity island. YE3559, which we have named ysaP, is predicted to encode a small outer membrane lipoprotein, and this location was confirmed by membrane fractionation. Elevated ysaP expression increased the steady-state level of YsaC but made it less toxic to a psp null strain, and it also decreased YsaC-dependent induction of psp gene expression. Subsequent experiments showed that YsaP was not required for YsaC multimerization but was required for the multimers to localize to the outer membrane. Consistent with this, a ysaP null mutation compromised protein export by the Ysa T3SS. All these observations suggest that YsaP is the pilotin for the YsaC secretin. This is only the second pilotin to be characterized for Yersinia and one of only a small number of pilotins described for all bacteria. IMPORTANCE Secretins are essential for the virulence of many bacterial pathogens and also play roles in surface attachment, motility, and competence. This has generated considerable interest in understanding how secretins function. However, their fundamental differences from typical outer membrane proteins have raised various questions about secretins, including how they are assembled into outer membrane multimers. Pilotin proteins facilitate the assembly of some secretins, but only a small number of pilotins have been identified, slowing efforts to understand common and distinct features of secretin assembly. This study provides an important advance by identifying a novel member of the pilotin family and also demonstrating a method of pilotin discovery that could be broadly applied.
Role of Macrolides as Immunomodular Agents

In addition to being effective antimicrobial agents, macrolides have been associated with interesting nonantibacterial antiinflammatory properties. It appears that they may exert nontraditional antimicrobial effects against difficult organisms such as Pseudomonas aeruginosa by interfering with bacterial virulence factors (eg, alginate production, quorum-sensing mechanisms, biofilm formation). It has been suggested they have the potential for being used in the treatment of chronic airway inflammatory conditions. Growing evidence indicates that macrolides may exert disease-modifying effects in conditions such as asthma, cystic fibrosis, bronchiectasis, and in posttransplant bronchiolitis. They inhibit synthesis and/or secretion of proinflammatory cytokines, inhibit phagocytosis, decrease eosinophilic inflammation, increase mucociliary transport, reduce goblet cell secretion, decrease bronchoconstriction, and inhibit cholinergic responses of airway smooth muscle. Among the many factors involved in the inflammatory cascade, macrolides appear to interfere particularly with neutrophil recruitment and activation. Undoubtedly, the role of macrolides in the treatment of the inflammatory component of chronic disorders needs to be more firmly established.
Multiplicity of 3-Ketosteroid-9α-Hydroxylase Enzymes in Rhodococcus rhodochrous DSM43269 for Specific Degradation of Different Classes of Steroids

ABSTRACT The well-known large catabolic potential of rhodococci is greatly facilitated by an impressive gene multiplicity. This study reports on the multiplicity of kshA, encoding the oxygenase component of 3-ketosteroid 9α-hydroxylase, a key enzyme in steroid catabolism. Five kshA homologues (kshA1 to kshA5) were previously identified in Rhodococcus rhodochrous DSM43269. These KshADSM43269 homologues are distributed over several phylogenetic groups. The involvement of these KshA homologues in the catabolism of different classes of steroids, i.e., sterols, pregnanes, androstenes, and bile acids, was investigated. Enzyme activity assays showed that all KSH enzymes with KshADSM43269 homologues are C-9 α-hydroxylases acting on a wide range of 3-ketosteroids, but not on 3-hydroxysteroids. KshA5 appeared to be the most versatile enzyme, with the broadest substrate range but without a clear substrate preference. In contrast, KshA1 was found to be dedicated to cholic acid catabolism. Transcriptional analysis and functional complementation studies revealed that kshA5 supported growth on any of the different classes of steroids tested, consistent with its broad expression induction pattern. The presence of multiple kshA genes in the R. rhodochrous DSM43269 genome, each displaying unique steroid induction patterns and substrate ranges, appears to facilitate a dynamic and fine-tuned steroid catabolism, with C-9 α-hydroxylation occurring at different levels during microbial steroid degradation.
Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution

ABSTRACT Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution of S. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal S. enterica strains to 11 previously sequenced S. enterica genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known S. enterica sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches between S. enterica clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks.
Anaerobic Mycobacterium tuberculosis Cell Death Stems from Intracellular Acidification Mitigated by the DosR Regulon

ABSTRACT Mycobacterium tuberculosis is a strict aerobe capable of prolonged survival in the absence of oxygen. We investigated the ability of anaerobic M. tuberculosis to counter challenges to internal pH homeostasis in the absence of aerobic respiration, the primary mechanism of proton efflux for aerobic bacilli. Anaerobic M. tuberculosis populations were markedly impaired for survival under a mildly acidic pH relative to standard culture conditions. An acidic environmental pH greatly increased the susceptibilities of anaerobic bacilli to the collapse of the proton motive force by protonophores, to antimicrobial compounds that target entry into the electron transport system, and to small organic acids with uncoupling activity. However, anaerobic bacilli exhibited high tolerance against these challenges at a near-neutral pH. At a slightly alkaline pH, which was near the optimum intracellular pH, the addition of protonophores even improved the long-term survival of bacilli. Although anaerobic M. tuberculosis bacilli under acidic conditions maintained 40% lower ATP levels than those of bacilli under standard culture conditions, ATP loss alone could not explain the drop in viability. Protonophores decreased ATP levels by more than 90% regardless of the extracellular pH but were bactericidal only under acidic conditions, indicating that anaerobic bacilli could survive an extreme ATP loss provided that the external pH was within viable intracellular parameters. Acidic conditions drastically decreased the anaerobic survival of a DosR mutant, while an alkaline environment improved the survival of the DosR mutant. Together, these findings indicate that intracellular acidification is a primary challenge for the survival of anaerobic M. tuberculosis and that the DosR regulon plays a critical role in sustaining internal pH homeostasis. IMPORTANCE During infection, M. tuberculosis bacilli are prevalent in environments largely devoid of oxygen, yet the factors that influence the survival of these severely growth-limited and metabolically limited bacilli remain poorly understood. We determined how anaerobic bacilli respond to fluctuations in environmental pH and observed that these bacilli were highly susceptible to stresses that promoted internal acidic stress, whereas conditions that promoted an alkaline internal pH promoted long-term survival even during severe ATP depletion. The DosR regulon, a major regulator of general hypoxic stress, played an important role in maintaining internal pH homeostasis under anaerobic conditions. Together, these findings indicate that in the absence of aerobic respiration, protection from internal acidification is crucial for long-term M. tuberculosis survival.
Flavobacterium johnsoniae GldK, GldL, GldM, and SprA Are Required for Secretion of the Cell Surface Gliding Motility Adhesins SprB and RemA

ABSTRACT Flavobacterium johnsoniae cells move rapidly over surfaces by gliding motility. Gliding results from the movement of adhesins such as SprB and RemA along the cell surface. These adhesins are delivered to the cell surface by a Bacteroidetes-specific secretion system referred to as the type IX secretion system (T9SS). GldN, SprE, SprF, and SprT are involved in secretion by this system. Here we demonstrate that GldK, GldL, GldM, and SprA are each also involved in secretion. Nonpolar deletions of gldK, gldL, or gldM resulted in the absence of gliding motility and in T9SS defects. The mutant cells produced SprB and RemA proteins but failed to secrete them to the cell surface. The mutants were resistant to phages that use SprB or RemA as a receptor, and they failed to attach to glass, presumably because of the absence of cell surface adhesins. Deletion of sprA resulted in similar but slightly less dramatic phenotypes. sprA mutant cells failed to secrete SprB and RemA, but cells remained susceptible to some phages and retained some limited ability to glide. The phenotype of the sprA mutant was similar to those previously described for sprE and sprT mutants. SprA, SprE, and SprT are needed for secretion of SprB and RemA but may not be needed for secretion of other proteins targeted to the T9SS. Genetic and molecular experiments demonstrate that gldK, gldL, gldM, and gldN form an operon and suggest that the proteins encoded by these genes may interact to form part of the F. johnsoniae T9SS.
Correspondence Matching with Modal Clusters

The modal correspondence method of Shapiro and Brady aims to match point-sets by comparing the eigenvectors of a pairwise point proximity matrix. Although elegant by means of its matrix representation, the method is notoriously susceptible to differences in the relational structure of the point-sets under consideration. In this paper, we demonstrate how the method can be rendered robust to structural differences by adopting a hierarchical approach. To do this, we place the modal matching problem in a probabilistic setting in which the correspondences between pairwise clusters can be used to constrain the individual point correspondences. We demonstrate the utility of the method on a number of synthetic and real-world point-pattern matching problems.
Early Consumption of Peanuts in Infancy Is Associated With a Low Prevalence of Peanut Allergy

Du Toit G, Katz Y, Sasieni P, et al. J Allergy Clin Immunol . 2008;122(5):984–991 PURPOSE OF THE STUDY. To determine the prevalence of peanut allergy (PA) among Israeli and United Kingdom Jewish children and to evaluate the relationship of PA to peanut consumption by infants and mothers. STUDY POPULATION. The study included Jewish children between the ages of 4 and 19 years who attended targeted primary and high schools. Eligible Jewish schools in greater London, United Kingdom, and Israeli schools in the Mehoz Merkaz region of Tel Aviv were selected because they were thought to represent comparable residential environments. The mothers of Jewish infants 4 to 24 months of age in general practitioner clinics in the United Kingdom and Tipat Halav clinics in Israel were also surveyed about the timing of ingestion of peanut. METHODS. Two validated questionnaires were used. The Food Allergy Questionnaire was completed by high school pupils …
REGENERATION OF THE PANCREAS FROM THE PANCREATIC DUCT

In my use of the word regeneration, I shall mean the growth of new pancreas tissue from the pancreas duct remnants. These experiments were suggested by the regeneration of pancreas tissue from the pancreatic duct stump in totally depancreatized dogs kept alive with insulin. Suffice it to say here that more than 0.5 gm. of normal pancreas tissue regenerated in the course of eight months, at the end of which time the animal was killed. The finding seemed of sufficient importance to test ( a ) the capacity of the duct to regenerate new pancreas tissue in situ and ( b ) when transferred to other parts of the body. The method used was as follows: Pups about 8 weeks of age were selected, the assumption being that young duct tissue possessed a greater capacity for regeneration of pancreas tissue. All the pancreas in each dog was removed except a portion of the tail.