Miracle-dz/UniFAR-FTUs huggingface dataset:
Strains of the East Asian (W/Beijing) Lineage of Mycobacterium tuberculosis Are DosS/DosT-DosR Two-Component Regulatory System Natural Mutants

ABSTRACT As part of our ongoing efforts to uncover the phenotypic consequences of genetic variability among clinical Mycobacterium tuberculosis isolates, we previously reported that isolates of the “East Asian” or “W/Beijing” lineage constitutively overexpress the coordinately regulated transcriptional program known as the DosR regulon under standard in vitro conditions. This phenotype distinguishes the W/Beijing lineage from all other M. tuberculosis lineages, which normally induce expression of this regulon only once exposed to low oxygen or nitric oxide, both of which result in inhibition of bacterial respiration and replication. Transcription of the DosR regulon is controlled through a two-component regulatory system comprising the transcription factor DosR and two possible cognate histidine sensor kinases, DosS and DosT. Through sequence analysis of a carefully selected set of isolates representing each of the major M. tuberculosis lineages, we describe herein a naturally occurring frameshift mutation in the gene encoding the DosT sensor kinase for isolates of the most recently evolved W/Beijing sublineages. Intriguingly, the occurrence of the frameshift mutation correlates precisely with the appearance of the constitutive DosR regulon phenotype displayed by the same “modern” W/Beijing strains. However, complementation studies have revealed that the mutation in dosT alone is not directly responsible for the constitutive DosR regulon phenotype. Our data serve to highlight the evolutionary pressure that exists among distinct M. tuberculosis lineages to maintain tight control over DosR regulon expression.
Effects of formulation variables on the particle size and viability of L.casei-loaded in whey protein-Ca-alginate microparticles

The health benefits of the probiotics are becoming more recognized and utilized nowadays. Among lactic acid bacteria, Lactobacillus casei has been found to colonize human GIT and exert meany health benefits. The aim of this research was to evaluate the influence of the formulation variables of L. casei-loaded whey-protein-Ca-alginate microparticles on the particle size and the survival of the mentioned probiotic during the processing.Overall effects of the formulation variables pointed to the dominant influence of the concentration of whey protein on the particle size , followed by the concentration of alginate. Higher concentration of whey protein and alginate in the coating medium resulted in increased particle size. Also, the data pointed to the dominant influence of the concentration of alginate and Ca Cl2 on the viability prior to-, and this trend continues after lyophilization. Significant negative effect of the alginate-whey protein interactions on the viability after lyophilization was observed, suggesting competition of the polymers and the probiotic for the same bonding sites
Assembling recursively stored sparse matrices

Recently, we have introduced an approach to multicore computations on sparse matrices using recursive partitioning, called Recursive Sparse Blocks (RSB). In this document, we discuss issues involved in assembling matrices in the RSB format. Since the main expected application area is iterative methods, we compare the performance of matrix assembly to that of matrix-vector multiply (SpMV), outlining both scalability of the method and execution times ratio.
An epidemiological study of Plesiomonas shigelloides diarrhoea among Japanese travellers

Plesiomonas shigelloides is often regarded as a non-pathogenic bacterial species that is occasionally isolated from patients with diarrhoea. However, a review of travellers returning to Japan with diarrhoeal illness through Kansai Airport revealed that the incidence of P. shigelloides from microbiologically confirmed cases increased from 23·2% in 1987 to 77·8% in 1999. We carried out a descriptive epidemiological study to identify patterns associated with diarrhoea due to this organism. Selected P. shigelloides isolates from this patient group were compared by pulsed-field gel electrophoresis of SpeI total chromosomal DNA digests to determine their genetic heterogeneity. Over the study period (whole of 1996 and first 2 months of 1999), 1149 of 1659 (69·3%) patients with microbiologically confirmed gastroenteritis yielded P. shigelloides. Infection was characterized by watery diarrhoea five times per day that persisted for 3 days. No statistically significant association was found between factors such as age, gender, destination, length of trip, but multivariable logistic regression analysis revealed an association between additional symptoms (vomiting, fever, abdominal pain) age and gender. The molecular fingerprints of a selection of 39 isolates and 3 reference strains of P. shigelloides were highly variable and each had a unique profile. We conclude that although P. shigelloides infections are usually mild and self-limiting, this organism may contribute to a significant proportion of travellers' diarrhoea in the Orient. The species is characterized by great heterogeneity at the DNA level.
Parent weight change as a predictor of child weight change in family-based behavioral obesity treatment.

BACKGROUND Family-based behavioral weight control treatment involves the parent in the modification of child and parent eating and activity change. OBJECTIVE To assess if parent standardized body mass index (z-BMI) change predicts child z-BMI change. DESIGN Secondary data analysis based on parent and child z-BMI changes from 3 family-based, randomized, controlled weight control studies. Hierarchical regression models tested whether parent z-BMI change increased prediction of child z-BMI change through treatment and 24-month follow-up beyond other factors that influence child weight change, such as child age, sex, socioeconomic status, and baseline child and parent z-BMI. Differences in child z-BMI change as a function of quartiles of parental z-BMI change were tested using an analysis of covariance. SETTING Pediatric obesity research clinic. PARTICIPANTS Obese 8- to 12-year-old children and their parents from 142 families who participated in family-based weight control programs. MAIN OUTCOME MEASURES Child and parent z-BMI changes over time. RESULTS Parent z-BMI change significantly predicted child z-BMI change for the 0- to 6-month (P<.001) and 0- to 24-month (P <.009) time points. In hierarchical regression models, parent z-BMI change was a significant incremental predictor of child z-BMI change at 6 and 24 months, with the additional r(2) ranging from 11.6% at 6 months (P <.001) to 3.8% at 24 months (P =.02). Parents in the highest quartile of z-BMI change had children with significantly greater z-BMI change than that of children with parents in the other quartiles (P =.01). CONCLUSION Parent z-BMI change is an independent predictor of obese child z-BMI change in family-based behavioral treatment, and youth benefit the most from parents who lose the most weight in family-based behavioral treatments.
The Economic Impact of User-Generated and Firm-Published Online Content : Directions for Advancing the Frontiers in Electronic

An important use of the Internet today is in providing a platform for consumers to disseminate information about products they transact with as well as about themselves. Indeed, through the use of Web 2.0 tools like blogs and opinion forums, a large amount of content is being generated by users in the online world. Consequently, we have seen online markets develop into social shopping channels, and facilitate the creation of online communities and social networks. Firms are also using technology mediated spaces to reveal information about their buyers. The increasing avenues for online content creation have changed the fundamental nature of information in terms of volume, availability and importance. A lot of that publicly available content has concrete economic value that is often embedded in it. To date, businesses, government organizations and customers have not fully incorporated such information in their decision making and policy formulation processes, either because the value of the intellectual capital, or appropriate methods for measuring that value have not been identified. This book chapter is a call for research that aims to measure the economic value of various kinds of user-generated and firm-published content on the web. As an example, a vital piece of socio-cultural information that is increasingly being published on the web is the geographical location of market participants and members of virtual communities. The availability of users' location information, either disclosed by users themselves or published by firms, opens up a plethora of opportunities for research examining how geographical location shapes consumer search and purchase behavior on the Internet. As another example of increasingly ubiquitous user-generated social information, members who use electronic markets as a forum for social interaction, reveal a lot of personal information describing themselves. The availability of this self-descriptive information generated by users in an online community can enable researchers to examine how economic exchanges in the online world are being influenced by social exchanges between various entities. While the above instances are about the availability of users' personal information, there are more detailed forums that provide information about users' actual experiences with sellers or with products in rich textual format. For example, when buyers cannot deterministically assess the quality of a seller's fulfillment characteristics ex-ante in an electronic market, the textual feedback posted by buyers describing their transaction experience can influence other buyers' purchase decisions, and thus affect sellers' future performances. Similarly, based on the rich theoretical literature …
Virus specific cell‐mediated immunity may play a role in controlling reactivated human herpesvirus 6B in patients under measles induced immunosuppression

For a better understanding of the cellular immune responses to reactivated HHV 6B the lymphoproliferative response to human herpesvirus 6B (HHV 6B) antigen was measured in three consecutive specimens obtained biweekly from 22 young children and infants suffering from acute measles, and in 19 influenza patients and nine healthy control subjects. HHV 6B DNA in peripheral blood mononuclear cells (PBMCs) was detected in 18 of 22 subjects with measles, but not in the influenza patients or the healthy population. A novel reactivation profile of HHV 6B was found in patients with measles in the milder form of immunosuppression than in patients with organ transplantation. HHV 6B specific lymphoproliferation activities increased correspondingly with reactivation of HHV 6B assessed by detecting HHV 6B DNA in PBMCs in patients with measles, but no significant change in either the antibody response to HHV 6B or DNAemia occurred in serial specimens obtained either from patients with influenza or healthy subjects. This novel form of HHV 6B reactivation without antibody response was observed in patients with measles. The dynamic fluctuations in lymphoproliferative responses in measles may represent the balance between HHV 6B reactivation and its suppression by the host immune system. J. Med. Virol. 86:658–665, 2014. © 2014 Wiley Periodicals, Inc.
Complexity of Counting Subgraphs: Only the Boundedness of the Vertex-Cover Number Counts

For a class C of graphs, #Sub(C) is the counting problem that, given a graph H from C and an arbitrary graph G, asks for the number of subgraphs of G isomorphic to H. It is known that if C has bounded vertex-cover number (equivalently, the size of the maximum matching in C is bounded), then #Sub(C) is polynomial-time solvable. We complement this result with a corresponding lower bound: if C is any recursively enumerable class of graphs with unbounded vertexcover number, then #Sub(C) is #W[1]-hard parameterized by the size of H and hence not polynomial-time solvable and not even fixed-parameter tractable, unless FPT is equal to #W[1]. As a first step of the proof, we show that counting kmatchings in bipartite graphs is #W[1]-hard. Recently, Curticapean [ICALP 2013] proved the #W[1]-hardness of counting k-matchings in general graphs; our result strengthens this statement to bipartite graphs with a considerably simpler proof and even shows that, assuming the Exponential Time Hypothesis (ETH), there is no f(k)*n^o(k/log(k)) time algorithm for counting k-matchings in bipartite graphs for any computable function f. As a consequence, we obtain an independent and somewhat simpler proof of the classical result of Flum and Grohe [SICOMP 2004] stating that counting paths of length k is #W[1]-hard, as well as a similar almost-tight ETH-based lower bound on the exponent.
Extracorporeal Shock Wave Therapy: Current Evidence

Objectives: The aim of this article is to provide a concise review of the basic science of extracorporeal shock wave therapy (ESWT) and to perform a systematic review of the literature for the use of ESWT in the treatment of fractures and delayed unions/nonunions. Data Sources: Articles in the English or German language were identified for the systematic review by searching PubMed-MEDLINE from 1966 until 2008, Cochrane Database of Systematic Reviews, Cochrane Database of Abstracts of Reviews of Effects, Cochrane Central Register of Controlled Trials, and relevant meeting abstracts from 2007 to 2008. Moreover, the bibliographies of the identified articles were reviewed. Study Selection: We included clinical outcome studies of ESWT in the treatment of fractures and delayed unions/nonunions. Reports with less than 10 patients were excluded. Nonunions after corrective osteotomies or arthrodeses were excluded. Data Extraction: Sample size, level of evidence, definition of delayed union, definition of nonunion, time from injury to shock wave treatment, location of fracture, union rate, and complications were extracted from the identified articles. Data Synthesis: Data of 924 patients undergoing ESWT for delayed union/nonunion were extracted from 10 studies. All articles were graded as level 4 studies. The overall union rate was 76% (95% confidence interval 73%-79%). The union rate was significantly higher in hypertrophic nonunions than in atrophic nonunions. Conclusion: Data from level 4 studies suggest that shock wave therapy seems to stimulate the healing process in delayed unions/nonunions. However, further investigations are required.
Fibroblast Growth Factor-23 and Incident Atrial Fibrillation: The Multi-Ethnic Study of Atherosclerosis (MESA) and the Cardiovascular Health Study (CHS)

Background— Fibroblast growth factor-23 (FGF-23) is a hormone that promotes urinary phosphate excretion and regulates vitamin D metabolism. Circulating FGF-23 concentrations increase markedly in chronic kidney disease and are associated with increased risk of clinical cardiovascular events. FGF-23 may promote atrial fibrillation (AF) by inducing left ventricular hypertrophy and diastolic and left atrial dysfunction. Methods and Results— We tested the associations of circulating FGF-23 concentration with incident AF among 6398 participants in the Multi-Ethnic Study of Atherosclerosis (MESA) and 1350 participants in the Cardiovascular Health Study (CHS), all free of clinical cardiovascular disease at baseline. Over a median of 7.7 and 8.0 years of follow-up, we observed 291 and 229 incident AF events in MESA and CHS, respectively. In multivariable Cox proportional hazards models, each 2-fold-higher FGF-23 concentration was associated with a 41% higher risk of incident AF in MESA (hazard ratio, 1.41; 95% confidence interval, 1.13–1.76; P=0.003) and a 30% higher risk of incident AF in CHS (hazard ratio, 1.30; 95% confidence interval, 1.05–1.61; P=0.016) after adjustment for potential confounding characteristics, including kidney disease. Serum phosphate concentration was significantly associated with incident AF in MESA (hazard ratio, 1.15 per 0.5 mg/dL; 95% confidence interval, 1.02–1.31; P=0.023) but not CHS. In MESA, an association of low estimated glomerular filtration rate with incident AF was partially attenuated by adjustment for FGF-23. Conclusion— Higher circulating FGF-23 concentration is associated with incident AF and may, in part, explain the link between chronic kidney disease and AF.
A systematic review of potential long-term effects of sport-related concussion

Objective Systematic review of possible long-term effects of sports-related concussion in retired athletes. Data sources Ten electronic databases. Study selection Original research; incidence, risk factors or causation related to long-term mental health or neurological problems; individuals who have suffered a concussion; retired athletes as the subjects and possible long-term sequelae defined as >10 years after the injury. Data extraction Study population, exposure/outcome measures, clinical data, neurological examination findings, cognitive assessment, neuroimaging findings and neuropathology results. Risk of bias and level of evidence were evaluated by two authors. Results Following review of 3819 studies, 47 met inclusion criteria. Some former athletes have depression and cognitive deficits later in life, and there is an association between these deficits and multiple prior concussions. Former athletes are not at increased risk for death by suicide (two studies). Former high school American football players do not appear to be at increased risk for later life neurodegenerative diseases (two studies). Some retired professional American football players may be at increased risk for diminishment in cognitive functioning or mild cognitive impairment (several studies), and neurodegenerative diseases (one study). Neuroimaging studies show modest evidence of macrostructural, microstructural, functional and neurochemical changes in some athletes. Conclusion Multiple concussions appear to be a risk factor for cognitive impairment and mental health problems in some individuals. More research is needed to better understand the prevalence of chronic traumatic encephalopathy and other neurological conditions and diseases, and the extent to which they are related to concussions and/or repetitive neurotrauma sustained in sports.
Journal of Neuroengineering and Rehabilitation Open Access Motor Rehabilitation Using Virtual Reality

Virtual Reality (VR) provides a unique medium suited to the achievement of several requirements for effective rehabilitation intervention. Specifically, therapy can be provided within a functional, purposeful and motivating context. Many VR applications present opportunities for individuals to participate in experiences, which are engaging and rewarding. In addition to the value of the rehabilitation experience for the user, both therapists and users benefit from the ability to readily grade and document the therapeutic intervention using various systems. In VR, advanced technologies are used to produce simulated, interactive and multi-dimensional environments. Visual interfaces including desktop monitors and head-mounted displays (HMDs), haptic interfaces, and real-time motion tracking devices are used to create environments allowing users to interact with images and virtual objects in real-time through multiple sensory modalities. Opportunities for object manipulation and body movement through virtual space provide frameworks that, in varying degrees, are perceived as comparable to similar opportunities in the real world. This paper reviews current work on motor rehabilitation using virtual environments and virtual reality and where possible, compares outcomes with those achieved in real-world applications.
Wavelet analogue of the Ginzburg–Landau energy and its Γ-convergence

Fourier analysis provides many elegant approaches to differential operators and related tools in PDE-based image processing. Our work develops the idea of using a more localized basis than the Fourier one in the context of variational methods based on diffuse interfaces ([17], [5], [6]). Our philosophy involves looking for new types of pseudo-differential energy functionals, which inherit important properties of classical functionals, but leave out the computational drawbacks associated with the discrete differentiation. Wavelets appeared in the variational context in a number of works (e.g. [8] and [13]). We use a well-known characterization of function regularity in terms of the wavelet coefficients, we also take a widely used PDE-based functional to become a prototype of the new energy we design. However, our approach is conceptually different from the wavelet-PDE techniques that use wavelets to solve PDEs numerically [4], [11] as well as those involving differentiation in the wavelet domain [9]. The energy functional we study is entirely “derivative-free” as it is defined; nevertheless, it exhibits behavior analogous to the ones of energies used in material science and fluid dynamics. In classical fluid models, an interface between two fluids is treated as infinitely thin and sharp, and is endowed with properties such as surface tension. Diffuse-interface theories replace this sharp interface with continuous variations of an order parameter, such as density, in a way consistent with microscopic theories of the interface. In the inhomogeneous systems which involve domains of well-defined phases separated by a distinct interface, the diffuse-interface description assumes the smoothness of the transition between phases and approaches the sharp interface model asymptotically. At the same time, if used in signal processing applications, diffuse-interface models