Miracle-dz/UniFAR-FTUs huggingface dataset:
ENTEROAGGREGATIVE ESCHERICHIA COLI INFECTION IN A RABBIT MODEL

Summary Type strains of enteroaggregative Escherichia coli EAEC (17‐2, serotype O3:H2; JM 221, serotype O92:H33), isolates from an adult and a child with diarrhoea and an asymptomatic colonised child were used to orally infect adult rabbits. The experimental animals were followed up and sacrificed at defined time periods. Colonisation of both small and large intestine was seen with all strains and isolates used. Isolates from an adult patient with diarrhoea (MP 27) and from an asymptomatic colonised child from the community (KM 1337) were recovered from the small intestine during the first week of infection and subsequently from the large intestine. A total of seven rabbits was infected with MP 27; while colonising the gastrointestinal tract of all seven rabbits, this isolate caused diarrhoea in only one. On ultrastructural examination, the rabbits infected with 17‐2 showed invasion of lymphoid follicles. Bacteria were seen in intercellular spaces and within M cells, a finding that has not previously been described. It is clearly possible to produce gut colonisation by oral infection with EAEC in adult rabbits with normal flora.
Venous thromboembolism risk factors and practices of prophylaxis: ENDORSE study results in Portugal.

BACKGROUND Venous thromboembolism (VTE) risk assessment is a cornerstone for the achievement of best practices and outcomes. Epidemiologic data and practices related to venous thromboprophylaxis as considered by the global ENDORSE study, (Epidemiologic International Day for the Evaluation of Patients at Risk for Venous Thromboembolism in the Acute Hospital Care Setting), enrolled 68,183 patients from 32 countries, in which Portugal. Within ENDORSE, data from all participant countries analyzed to determine their risk of VTE and to evaluate the suitability of prophylaxis. METHODS European patients were enrolled from randomly selected hospitals in Portugal (European Hospital Register), according to ENDORSE study inclusion/exclusion criteria. The Seventh ACCP evidence-based consensus guidelines were employed to evaluate VTE risk and prophylaxis use. RESULTS From a total of 3,145 beds assessed, 2,183 were considered eligible and 1,632 met all criteria. Of these, 860 (52.7%; 95% CI 50.3-55.1) were at risk of VTE: 525 surgical patients (68.9%; 95% CI 65.5-72.1) and 335 medical patients (38.5%; 95% CI 35.3-41.2). The rate of prophylaxis according to ACCP guidelines in overall patients at risk was 58.5% (503 patients). The prophylaxis rate for VTE was 59% (310 patients) in surgical patients and 57.6% (n=193) in medical patients. 39.7% of surgical patients and 39.4 % of medical patients who did not meet the criteria for prophylaxis were also on prophylaxis with an anticoagulant, which was considered to be inappropriate. CONCLUSIONS More than a half of these hospitalized patients in Portugal were deemed at risk of VTE and less than two-thirds of them received appropriate prophylaxis. New strategies are required for implementation of venous thromboprophylaxis in Portuguese hospitals.
Towards an Approach for Aspect-Oriented Software Reengineering

This paper presents a reengineering approach to help in migrating pure object-oriented codes to a mixture of objects and aspects. The approach focuses on aspect-mining to identify potential crosscutting concerns to be modeled and implemented as aspects, and on refactoring techniques to reorganize the code according to aspectoriented paradigm by using code transformations it is possible to recover the aspect-oriented design using a transformational system. With the recovered design it is possible to add or modify the system requirements in a CASE tool, and to generate the codes in an executable language, in this case AspectJ.
Non-canonical functions of the tuberous sclerosis complex-Rheb signalling axis

The protein products of the tuberous sclerosis complex ( TSC ) genes, TSC1 and TSC2, form a complex, which inhibits the small G‐protein, Ras homolog enriched in brain (Rheb). The vast majority of research regarding these proteins has focused on mammalian Target of Rapamycin (mTOR), a target of Rheb. Here, we propose that there are clinically relevant functions and targets of TSC1, TSC2 and Rheb, which are independent of mTOR. We present evidence that such non‐canonical functions of the TSC‐Rheb signalling network exist, propose a standard of evidence for these non‐canonical functions, and discuss their potential clinical and therapeutic implications for patients with TSC and lymphangioleiomyomatosis (LAM).
A RAPID PERMETHYLATION OF GLYCOLIPID, AND POLYSACCHARIDE CATALYZED BY METHYLSULFINYL CARBANION IN DIMETHYL SULFOXIDE.

An effective, and rapid permethylation of complex carbohydrates noted in the head ing is to be reported in this letter. Methy lation of a complex carbohydrate is a difficult and painstaking task, but if successful, it offers good confir_nation of the chemical structure (e.g. 1-3). With more recognition of the significance of complex carbohydrates, roles played in determination of specificities of hormones, immunity, biological transport, and in various pathological phenomena, it has become more urgent to learn the chemical structure. For this purpose, permethylation on a micro scale applicable to the complex carbohydrates is desired. The alcoxide for mation, greatly catalyzed by methylsulfinyl carbanion (I) in dimethyl sulfoxide, followed by methylation with methyl iodide was found to be applicable, in some degree, for this purpose. Since Whistler and BeMiller des cribed an extraction of glycogen from tissue by dimethyl sulfoxide (4), 'non-aqueous' chemical reactions might be carried out in this extremely polar, but stable solvent. Not only glycogen but also 'Fr. 4-urinary glyco protein' (5, 6), ovomucoid, a certain sub fraction of the Wilson gastric mucin, and various glycolipids were found to the more or less soluble in this solvent. Therefore, it was undertaken to demonstrate the presence of various kinds of acyl residue in this solvent by ` hydroxylaminolysis' of the urinary glyco protein * While studying along this line, the author learned that Corey and his group developed a new reaction, using methyl sulfinyl carbanion, the conjugate base of dimethyl sulfoxide (7). The Witting type synthesis was achieved with great ease (8, 9) by a strong nucleophilic property of the carbanion on one hand, and on the other
Electrical Properties and Microstructures of Tb4O7-Doped Bi4Ti3O12 Ceramics

The electrical properties of Tb4O7-bismuth titanate (Bi3.3Tb0.6Ti3O12) prepared by a conventional ceramic technique have been investigated. At applied d.c. field below 200V/mm, the current-voltage curve of Tb-doped sample exhibits a simple ohmic behavior. The impedance spectrum of Tb-doped sample indicates that consist of semiconducting grain and moderately insulating grain boundary regions. XRD, SEM and EPMA analyses reveal crystalline phase characterized by a Bi-layered perovskite structure of Bi4Ti3O12 and the distribution of every element is uniform. Tb-doped sample exhibit randomly oriented and plate-like morphology.
Anorexia Nervosa: Outcome and Prognostic Factors after 20 Years

Forty-one patients with anorexia nervosa, admitted to the Maudsley Hospital between 1959 and 1966, were followed up after a mean of 20 years. An assessment of general outcome (based on the Morgan-Russell scales) yielded three outcome categories: ‘good’ (n = 12), ‘intermediate’ (n = 13) and ‘poor’ (n = 15). Six patients (15%) had died from causes related to anorexia nervosa; at least 15% had developed bulimia nervosa. There was a general consistency between the follow-up at 20 years and that previously conducted five years after admission, although with a few individual patients there were serious prognostic errors at the earlier follow-up. A poorer outcome was associated with a later age of onset, a history of neurotic and personality disturbances, disturbed relationships in the family and a longer duration of illness.
Systematic Review and Meta-Analysis of L1-VLP-Based Human Papillomavirus Vaccine Efficacy against Anogenital Pre-Cancer in Women with Evidence of Prior HPV Exposure

Background It is unclear whether L1-VLP-based human papillomavirus (HPV) vaccines are efficacious in reducing the likelihood of anogenital pre-cancer in women with evidence of prior vaccine-type HPV exposure. This study aims to determine whether the combined results of the vaccine trials published to date provide evidence of efficacy compared with control (hepatitis A vaccine/placebo). Methods A systematic review and meta-analysis was conducted. Randomized-controlled trials (RCTs) were identified from MEDLINE, Embase, Web of Science, PubMed, Cochrane Central Register of Controlled Trials and references of identified studies. The bivalent vaccine containing HPV-16 and 18 VLPs from GlaxoSmithKline Biologicals (Rixenstart, Belgium), the quadrivalent vaccine containing HPV-6, 11, 16, and 18 VLPs from Merck & Co., Inc., (Whitehouse Station, NJ USA), and the HPV-16 monovalent vaccine from Merck Research Laboratories (West Point, PA USA) were evaluated. Findings Three RCT reports and two post-trial cohort studies were eligible, comprising data from 13,482 women who were included in the vaccine studies but had evidence of HPV infection at study entry. Data on efficacy was synthesized using the Mantel-Haenszel weighted fixed-effect approach, or where there was heterogeneity between studies, the DerSimonian and Laird weighted random-effect approach. The mean odds ratio (OR) and 95% confidence interval (CI) for the association between Cervarix, Gardasil and HPV-16 monovalent vaccine and HPV-associated cervical intraepithelial neoplasia grade 3 or worse was 0·90 (95% CI: 0·56, 1·44). For the association between Gardasil and HPV-associated vulval/vaginal intraepithelial neoplasia grades 2–3, the overall OR and 95% CI was 2.25 (95% CI: 0·78, 6.50). Sample size and follow-up were limited. Conclusions There was no evidence that HPV vaccines are effective in preventing vaccine-type HPV associated pre-cancer in women with evidence of prior HPV exposure. Small effects of vaccination however cannot be excluded and a longer-term benefit in preventing re-infection remains possible.
A genetic case-control study confirms the implication of SMAD7 and TNF locus in the development of proliferative vitreoretinopathy.

PURPOSE Proliferative vitreoretinopathy (PVR) is still the major cause of failure of retinal detachment (RD) surgery and although the risk for developing this complication is associated with some clinical characteristics, the correlation is far from absolute, raising the possibility of genetic susceptibility. The objective of this study was to analyze the genetic contribution to PVR in patients undergoing RD surgery, the Retina 4 Project. METHODS A candidate gene association study was conducted in 2006 in a Spanish population of 450 patients suffering from primary rhegmatogenous RD. Replication was carried out in a larger population undergoing RD surgery at several European centers among 546 new patients. Single nucleotide polymorphism (SNP) of 30 genes known to be involved with inflammation were analyzed. For replication stage, those genes previously detected as significantly associated with PVR were genotyped. Distribution of allelic and haplotypic frequencies in case and control group were analyzed. Single and haplotypic analysis were assessed. The Rosenberg two-stage method was used to correct for single and multiple analyses. RESULTS After correction for multiple comparisons, four genes were significantly associated with PVR: SMAD7 (P = 0.004), PIK3CG (P = 0.009), TNF locus (P = 0.0005), and TNFR2 (P = 0.019) In the European sample, replication was observed in SMAD7 (P = 0.047) and the TNF locus (P = 0.044). CONCLUSIONS These results confirm the genetic contribution to PVR and the implication of SMAD7 and TNF locus in the development of PVR. This finding may have implications for understanding the mechanisms of PVR and could provide a potential new therapeutic target for PVR prophylaxis.
Hazard assessment for a pharmaceutical mixture detected in the upper Tennessee River using Daphnia magna

ABS TRACT: Widespread use of pharmaceuticals has resulted in mixture concentrations ranging from mg/L in effluent to µg/L concentrations in surface water. In a 2008 study, 13 pharmaceuticals, ranging in amounts from 0.0028 to 0.1757 µg/l, were identified in the Tennessee River, USA and its tributaries. In order to address the need for risk assessment of environmentally relevant pharmaceutical mixtures, Daphnia magna 21-d life cycle tests were performed on a mixture of 11 of the 13 pharmaceuticals as well as on the individual components of the mixture. Mixture exposures were based on the same initial ratios of individual compounds, up to 1000x the initial mixture concentrations . The endpoints of mortality, time to first brood, size, and fecundity were assessed. The LOEC of the 11- pharmaceutical mixture was determined to be 100x greater than the measured mixture concentration detected in the Tennessee River, with the NOEC being 75x that of the measured mixture. Single concentrations of pharmaceuticals within the mixture up to the 100x LOEC were not statistically different from control for any of the assessed endpoints. Thus, no single pharmaceutical was deemed predominately responsible for the mixture toxicity at the concentrations tested. While mixtures of pharmaceuticals are common in many systems, based on the findings of the present study, they may not pose a significant acute or chronic hazard to aquatic invertebrates at current concentrations.
Bacterial seed endophytes: genera, vertical transmission and interaction with plants

Summary Although the importance of plant-associated microorganisms for plant growth and health was getting more recognition recently, the role of seed-associated microorganisms, and especially seed endophytic bacteria, still is underestimated. Nevertheless, these associations could be beneficial for germination and seedling establishment as seed endophytic bacteria are already present in these very early plant growth stages. Moreover, bacteria with beneficial characteristics can be selected by the plants and could be transferred via the seed to benefit the next generation. In this paper, the current literature concerning bacterial endophytes that have been isolated from seeds of different plant species is reviewed. Their colonization routes, localization inside seeds and mode of transmission as well as their role and fate during germination and seedling development are discussed. At the end, some examples of bacterial seed endophytes with applications as a plant growth-promoting or biocontrol agent are given.
Sparsity-Aware Sensor Selection: Centralized and Distributed Algorithms

The selection of the minimum number of sensors within a network to satisfy a certain estimation performance metric is an interesting problem with a plethora of applications. We explore the sparsity embedded within the problem and propose a relaxed sparsity-aware sensor selection approach which is equivalent to the unrelaxed problem under certain conditions. We also present a reasonably low-complexity and elegant distributed version of the centralized problem with convergence guarantees such that each sensor can decide itself whether it should contribute to the estimation or not. Our simulation results corroborate our claims and illustrate a promising performance for the proposed centralized and distributed algorithms.
Converging to Efficiency: the Ramón y Cajal Program Experience

We analyze the evolution on the design of a policy measure promoted by the Spanish Government: the Ramon y Cajal Program. In the first calls of the Program, an eligibility requirement for a researcher was a preacceptance from at least one Spanish research institution. This requirement was removed in the fourth call. We model the recruiting process as a twosided matching model to find the reason for the new design. We model the situation as if research centers decided by majority to play either the old or the new mechanism. Our results prove that in a repeated game and assuming that research personnel is scarce, even endogamic centers will prefer the new mechanism after a finite number of calls. We also analyze application data for the first five calls, finding empirical support to our assumptions and theoretical findings.
CFPRS : Collaborative Filtering Privacy Recommender System for Online Social Networks

Social-networking sites (SNSs) are known to be among the most prevalent methods of online communication. Owing to their increasing popularity, online privacy has become a critical issue for these sites. The tools presently being utilized for privacy settings are too ambiguous for ordinary users to understand and the specified policies are too complicated. In this paper, a collaborative filtering privacy recommender system is proposed. The implementation of the system was initiated by examining the users’ attitudes toward privacy; whereby the most significant factors impacting users’ attitudes towards privacy were determined to be location, religion and gender. The next step involved the classification of the users into various groups on the basis of the above factors. The paper presents a method of integrating the identified factors into the collaborative filtering algorithm to improve the filtering process. The evaluation of results reflects the accuracy of recommendations and proves that the use of the clustering model assisted the CF recommender in its creation of appropriate recommendations for each user.
Tuberculosis, HIV, and poverty: temporal trends in Brazil, the Americas, and worldwide.

OBJECTIVE To analyze the temporal trends of the incidence and prevalence of tuberculosis, with and without HIV co-infection, as well as of the associated mortality, in Brazil, the Americas, and worldwide. METHODS We collected data related to tuberculosis, with and without HIV co-infection, between 1990 and 2010, in Brazil, the Americas, and worldwide. Temporal trends were estimated by linear regression. RESULTS We identified a trend toward a decrease in tuberculosis prevalence and mortality, and that trend was more pronounced in Brazil and the Americas than worldwide. There was also a trend toward an increase in the incidence of tuberculosis/HIV co-infection, as well as in the rates of detection of new cases of active and latent tuberculosis. The incidence of tuberculosis was found to trend downward in Brazil, whereas it trended upward worldwide. Tuberculosis incidence rates correlated positively with poverty rates and with HIV incidence rates. CONCLUSIONS Social inequality and the advent of AIDS are the major factors that aggravate the current situation of tuberculosis. In this context, methodical approaches to the assessment of surveillance activities are welcome, because they will identify situations in which the reported tuberculosis data do not reflect the true incidence of this disease.
Finite state lattice vector quantization for wavelet-based image coding

It is well known that there exists strong energy correlation between various subbands of a real-world image. A new powerful technique of Finite State Vector Quantization (FSVQ) has been introduced to fully exploit the self-similarity of the image in wavelet domain across different scales. Lattices in R/sup N/ have considerable structure, and hence, Lattice VQ offers the promise of design simplicity and reduced complexity encoding. The combination of FSVQ and LVQ gives rise to the so-called FSLVQ, which is proved to be successful in exploiting the energy correlation across scales and is simple enough in implementation.
Obesity and Diabetes in New York City, 2002 and 2004

Introduction Obesity and diabetes have increased rapidly nationwide, yet reliable information on these disease trends in local urban settings is unavailable. We undertook this study to characterize trends in obesity and diagnosed diabetes from 2002 to 2004 among white, black, and Hispanic adult residents of New York City. Methods We used data from the Community Health Survey, an annual random-digit–dial telephone survey of approximately 10,000 New York City adults aged 18 years or older, and from the Behavioral Risk Factor Surveillance System, a similar nationwide survey. Main outcome measures were body mass index (BMI), calculated from self-reported height and weight, and self-reported diabetes. Results In 2 years, the prevalence of obesity increased 17% in New York City, from 19.5% in 2002 to 22.8% in 2004 (P < .0001). The prevalence of diagnosed diabetes also increased 17%, from 8.1% in 2002 to 9.5% in 2004 (P < .01). Nationally, the prevalence of obesity increased by 6% during this same time period (P < .05), and diabetes prevalence did not increase significantly. The median BMI among white adults in New York City was 25.1 kg/m2, significantly lower than among Hispanics (26.4 kg/m2) and blacks (26.6 kg/m2, P < .05). The prevalence of diabetes increased across all BMI categories. Discussion The rapid increase in obesity and diabetes in New York City suggests the severity of these twin epidemics and the importance of collecting and analyzing local data for local programming and policy making.
Pyrosequencing the Bemisia tabaci Transcriptome Reveals a Highly Diverse Bacterial Community and a Robust System for Insecticide Resistance

Background Bemisia tabaci (Gennadius) is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci. Despite its prevalence, little is known about B. tabaci at the genome level. To fill this gap, an invasive B. tabaci B biotype was subjected to pyrosequencing-based transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes. Methodology and Principal Findings Using Roche 454 pyrosequencing, 857,205 reads containing approximately 340 megabases were obtained from the B. tabaci transcriptome. De novo assembly generated 178,669 unigenes including 30,980 from insects, 17,881 from bacteria, and 129,808 from the nohit. A total of 50,835 (28.45%) unigenes showed similarity to the non-redundant database in GenBank with a cut-off E-value of 10–5. Among them, 40,611 unigenes were assigned to one or more GO terms and 6,917 unigenes were assigned to 288 known pathways. De novo metatranscriptome analysis revealed highly diverse bacterial symbionts in B. tabaci, and demonstrated the host-symbiont cooperation in amino acid production. In-depth transcriptome analysis indentified putative molecular markers, and genes potentially involved in insecticide resistance and nutrient digestion. The utility of this transcriptome was validated by a thiamethoxam resistance study, in which annotated cytochrome P450 genes were significantly overexpressed in the resistant B. tabaci in comparison to its susceptible counterparts. Conclusions This transcriptome/metatranscriptome analysis sheds light on the molecular understanding of symbiosis and insecticide resistance in an agriculturally important phloem-feeding insect pest, and lays the foundation for future functional genomics research of the B. tabaci complex. Moreover, current pyrosequencing effort greatly enriched the existing whitefly EST database, and makes RNAseq a viable option for future genomic analysis.