Miracle-dz/UniFAR-FTUs huggingface dataset:
Distributed under Creative Commons Cc-by 4.0 Population Structure of Neisseria Gonorrhoeae Based on Whole Genome Data and Its Relationship with Antibiotic Resistance

Neisseria gonorrhoeae is the causative agent of gonorrhea, a sexually transmitted infection (STI) of major importance. As a result of antibiotic resistance, there are now limited options for treating patients. We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. The population structure and evolutionary forces within the pathogen population were analyzed. Our results indicated a cosmopolitan gonoccocal population mainly made up of five subgroups. The estimated ratio of recombination to mutation (r/m = 2.2) from our data set indicates an appreciable level of recombination occurring in the population. Strains with resistance phenotypes to more recent antibiotics (azithromycin and cefixime) were mostly found in two of the five population subgroups. How to cite this article Ezewudo et al. (2015), Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance.
Utility of urinary biomarkers in oral cancer.

OBJECTIVE Oral cancer is the leading malignancy in India, with tobacco playing a major role in the etiology. The aim of the present study was to quantify nitrate+nitrite (NO2+NO3) in tobacco products as well as to study tobacco exposure related biomarkers in controls, patients with oral precancers (OPC) and oral cancer patients. MATERIALS & METHODS Healthy individuals (n=90) were grouped into without habit of tobacco (NHT, n=30) and healthy individuals with habit of tobacco (WHT, n=60). Oral cancer patients with a tobacco habit were classified into abstinence (n=62) and non-abstinence (n=64) groups according to status at the study time. Urinary nicotine and cotinine levels were analyzed by modified high-pressure liquid chromatography (HPLC) using a UV detector. Levels of NO2+NO3 in tobacco and urine, and urinary thioether levels were estimated by spectrophotometry. RESULTS NO2+NO3 levels in different types of tobacco product ranged between 0.13 to 3.39 mg/g. The Odds Ratio (OR) analysis indicated positive associations of both smoking and chewing habits of tobacco with high risk of development of oral cancer. Urinary nicotine, cotinine and NO2+NO3 levels were significantly elevated in WHT, patients with OPC and oral cancer patients as compared with the NHT group. This was also the case for urinary thioether levels. Levels of urinary nicotine and cotinine were also higher in the non-abstinence group with oral cancers. CONCLUSION The results confirmed that tobacco chewing and smoking habits are prominent risk factors for development of oral cancer in the western part of India (Gujarat). Urinary nicotine, cotinine, NO2+NO3 and thioether levels can be helpful for screening programs for oral cancer.
Clustering near-duplicate images in large collections

Near-duplicate images introduce problems of redundancy and copyright infringement in large image collections. The problem is acute on the web, where appropriation of images without acknowledgment of source is prevalent. In this paper, we present an effective clustering approach for near-duplicate images, using a combination of techniques from invariant image local descriptors and an adaptation of near-duplicate text-document clustering techniques; we extend our earlier approach of near-duplicate image pairwise identification for this clustering approach. We demonstrate that our clustering approach is highly effective for collections of up to a few hundred thousand images. We also show --- via experimentation with real examples --- that ourapproach presents a viable solution for clustering near-duplicate images on the Web.
Family analysis of Werner's syndrome: A survey of 42 Japanese families with a review of the literature

Forty‐two Japanese families, including 80 individuals with Werner's syndrome were studied, confirming that this syndrome is inherited as an autosomal recessive trait. The incidence of malignancy was relatively high in these families and individuals with Werner's syndrome, although the incidence was not so high as was reported previously. HLA typing revealed no significant linkage with Werner's syndrome. The frequency of Werner's syndrome in Japan was estimated using two methods which indicated approximately 300 cases among 100 million people.
Angiographic and Clinical Impact of Successful Manual Thrombus Aspiration in Diabetic Patients Undergoing Primary PCI

Background. Diabetes mellitus is associated with worse angiographic and clinical outcomes after percutaneous coronary intervention (PCI). Aim. To investigate the impact of manual thrombus aspiration on in-stent restenosis (ISR) and clinical outcome in patients treated by bare-metal stent (BMS) implantation for ST-segment elevation myocardial infarction (STEMI). Methods. 100 diabetic patients were prospectively enrolled. They were randomly assigned to undergo either standard primary PCI (group A, 50 patients) or PCI with thrombus aspiration using Export catheter (group B, 50 patients). The primary endpoint was the rate of eight-month ISR. The secondary endpoint included follow-up for major adverse cardiac events (MACE). Results. Mean age of the study cohort was 59.86 ± 8.3 years, with 64 (64%) being males. Baseline characteristics did not differ between both groups. Eight-month angiogram showed that group B patients had significantly less late lumen loss (0.17 ± 0.35 versus 0.60 ± 0.42 mm, P < 0.001), with lower incidence of ISR (4% versus 16.6%, P < 0.001). There was a trend towards lower rate of MACE in the same group of patients. Conclusion. In diabetic patients undergoing primary PCI, manual thrombus aspiration (compared with standard PCI) was associated with better ISR rate after BMS implantation.
Protease-Activated Receptors: New Concepts in Regulation of G Protein-Coupled Receptor Signaling and Trafficking

Most G protein-coupled receptors (GPCRs) are reversibly activated upon ligand binding. However, activation of protease-activated G protein-coupled receptors (PARs) occurs through an irreversible proteolytic event that results in the generation of a tethered ligand that cannot diffuse away. This unusual mode of PAR activation raises important questions regarding the mechanisms responsible for termination of receptor signaling. There are currently four members of the PAR family. Thrombin activates PAR1, PAR3, and PAR4, whereas multiple trypsin-like serine proteases activate PAR2. The regulation of signaling by PAR1 has been extensively studied, whereas considerably less is known about the other PARs. It has been demonstrated that rapid termination of PAR1 signaling is critical in determining the magnitude and kinetics of the cellular protease response. Therefore, elucidating the molecular mechanisms involved in the regulation of PAR signaling is essential to fully understand protease-mediated responses. Recent findings indicate that novel mechanisms contribute to PAR1 desensitization, internalization, and down-regulation. This review focuses on the intracellular mechanisms that regulate PAR signaling and the recent progress in developing inhibitors of PAR signaling.
Progressive resistance strength training for improving physical function in older adults.

BACKGROUND Muscle weakness in old age is associated with physical function decline. Progressive resistance strength training (PRT) exercises are designed to increase strength. OBJECTIVES To assess the effects of PRT on older people and identify adverse events. SEARCH STRATEGY We searched the Cochrane Bone, Joint and Muscle Trauma Group Specialized Register (to March 2007), the Cochrane Central Register of Controlled Trials (The Cochrane Library 2007, Issue 2), MEDLINE (1966 to May 01, 2008), EMBASE (1980 to February 06 2007), CINAHL (1982 to July 01 2007) and two other electronic databases. We also searched reference lists of articles, reviewed conference abstracts and contacted authors. SELECTION CRITERIA Randomised controlled trials reporting physical outcomes of PRT for older people were included. DATA COLLECTION AND ANALYSIS Two review authors independently selected trials, assessed trial quality and extracted data. Data were pooled where appropriate. MAIN RESULTS One hundred and twenty one trials with 6700 participants were included. In most trials, PRT was performed two to three times per week and at a high intensity. PRT resulted in a small but significant improvement in physical ability (33 trials, 2172 participants; SMD 0.14, 95% CI 0.05 to 0.22). Functional limitation measures also showed improvements: e.g. there was a modest improvement in gait speed (24 trials, 1179 participants, MD 0.08 m/s, 95% CI 0.04 to 0.12); and a moderate to large effect for getting out of a chair (11 trials, 384 participants, SMD -0.94, 95% CI -1.49 to -0.38). PRT had a large positive effect on muscle strength (73 trials, 3059 participants, SMD 0.84, 95% CI 0.67 to 1.00). Participants with osteoarthritis reported a reduction in pain following PRT(6 trials, 503 participants, SMD -0.30, 95% CI -0.48 to -0.13). There was no evidence from 10 other trials (587 participants) that PRT had an effect on bodily pain. Adverse events were poorly recorded but adverse events related to musculoskeletal complaints, such as joint pain and muscle soreness, were reported in many of the studies that prospectively defined and monitored these events. Serious adverse events were rare, and no serious events were reported to be directly related to the exercise programme. AUTHORS' CONCLUSIONS This review provides evidence that PRT is an effective intervention for improving physical functioning in older people, including improving strength and the performance of some simple and complex activities. However, some caution is needed with transferring these exercises for use with clinical populations because adverse events are not adequately reported.
Effects of an energy-restricted diet rich in plant-derived α-linolenic acid on systemic inflammation and endothelial function in overweight-to-obese patients with metabolic syndrome traits

Plant-derived α-linolenic acid (ALA) may reduce the risk of CVD, possibly by decreasing systemic inflammation and improving endothelial function. In the present study, the effects of a hypoenergetic diet rich in ALA (3·4 g/d) on the biomarkers of systemic inflammation and vascular function were investigated in eighty-one overweight-to-obese patients with metabolic syndrome traits in comparison with a hypoenergetic diet low in ALA (0·9 g/d, control). After a 6-month dietary intervention, there were significant decreases in the serum concentrations of C-reactive protein (CRP), TNF-α, IL-6, soluble intercellular adhesion molecule-1 (sICAM-1), soluble endothelial selectin (sE-selectin) and asymmetric dimethylarginine in both dietary groups. However, no inter-group differences were observed for all these changes. The serum concentration of YKL-40 (human cartilage glycoprotein 39 or chitinase-3-like protein 1) decreased after the ALA diet when compared with the control diet (P< 0·05 for time × treatment interaction). Plasma concentrations of fibrinogen did not significantly change in the two dietary groups. The decreases in the serum concentrations of sICAM-1, sE-selectin, CRP and YKL-40 were significantly correlated with the decreases in body fat mass. In conclusion, the present study indicates that in overweight-to-obese patients with metabolic syndrome traits, both vascular function and inflammation are improved during body-weight loss. The high ALA intake led to a more pronounced reduction in the serum concentration of YKL-40 compared with the intake of the low-ALA control diet, indicating the existence of independent favourable physiological effects of ALA during weight loss.
Exploiting transplastomically modified Rubisco to rapidly measure natural diversity in its carbon isotope discrimination using tuneable diode laser spectroscopy

Carbon isotope discrimination (Δ) during C3 photosynthesis is dominated by the fractionation occurring during CO2-fixation by the enzyme Rubisco. While knowing the fractionation by enzymes is pivotal to fully understanding plant carbon metabolism, little is known about variation in the discrimination factor of Rubisco (b) as it is difficult to measure using existing in vitro methodologies. Tuneable diode laser absorption spectroscopy has improved the ability to make rapid measurements of Δ concurrently with photosynthetic gas exchange. This study used this technique to estimate b in vivo in five tobacco (Nicotiana tabacum L. cv Petit Havana [N,N]) genotypes expressing alternative Rubisco isoforms. For transplastomic tobacco producing Rhodospirillum rubrum Rubisco b was 23.8±0.7‰, while Rubisco containing the large subunit Leu-335-Val mutation had a b-value of 13.9±0.7‰. These values were significantly less than that for Rubisco from wild-type tobacco (b=29‰), a C3 species. Transplastomic tobacco producing chimeric Rubisco comprising tobacco Rubisco small subunits and the catalytic large subunits from either the C4 species Flaveria bidentis or the C3-C4 species Flaveria floridana had b-values of 27.8±0.8 and 28.6±0.6‰, respectively. These values were not significantly different from tobacco Rubisco.
Does breast density measured through population-based screening independently increase breast cancer risk in Asian females?

Purpose The purpose of this study was to investigate the effects of breast density on breast cancer risk among women screened via a nationwide mammographic screening program. Patients and methods We conducted a nested case–control study for a randomly selected population of 1,561 breast cancer patients and 6,002 matched controls from the National Cancer Screening Program. Breast density was measured and recorded by two independent radiologists using the Breast Imaging Reporting and Data System (BI-RADS). Associations between BI-RADS density and breast cancer risk were evaluated according to screening results, time elapsed since receiving non-recall results, age, and menopausal status after adjusting for possible covariates. Results Breast cancer risk for women with extremely dense breasts was five times higher (adjusted odds ratio [aOR] =5.0; 95% confidence interval [CI]) =3.7–6.7) than that for women with an almost entirely fatty breast, although the risk differed between recalled women (aOR =3.3, 95% CI =2.3–3.6) and women with non-recalled results (aOR =12.1, 95% CI =6.3–23.3, P-heterogeneity =0.001). aORs for BI-RADS categories of breast density were similar when subjects who developed cancer after showing non-recall findings during initial screening were grouped according to time until cancer diagnosis thereafter (<1 and ≥1 year). The prevalence of dense breasts was higher in younger women, and the association between a denser breast and breast cancer was stronger in younger women (heterogeneously dense breast: aOR =7.0, 95% CI =2.4–20.3, women in their 40s) than older women (aOR =2.5, 95% CI =1.1–6.0, women in their 70s or more). In addition, while the positive association remained, irrespective of menopausal status, the effect of a dense breast on breast cancer risk was stronger in premenopausal women. Conclusion This study confirmed an increased risk of breast cancer with greater breast density in Korean women which was consistent regardless of BI-RADS assessment category, time interval after initially non-recall results, and menopausal status.
Current‐aligned dewatering sheets and ‘enhanced’ primary current lineation in turbidite sandstones of the Marnoso‐arenacea Formation

Turbidite sandstones of the Miocene Marnoso‐arenacea Formation (northern Apennines, Italy) display centimetre to decimetre long, straight to gently curved, 0·5 to 2·0 cm regularly spaced lineations on depositional (stratification) planes. Sometimes these lineations are the planform expression of sheet structures seen as millimetre to centimetre long vertical ‘pillars’ in profile. Both occur in the middle and upper parts of medium‐grained and fine‐grained sandstone beds composed of crude to well‐defined stratified facies (including corrugated, hummocky‐like, convolute, dish‐structured and dune stratification) and are aligned sub‐parallel to palaeoflow direction as determined from sole marks often in the same beds. Outcrops lack a tectonic‐related fabric and therefore these structures may be confidently interpreted to be sedimentary in origin. Lineations resemble primary current lineations formed by the action of turbulence during bedload transport under upper stage plane bed conditions. However, they typically display a larger spacing and micro‐topography compared to classic primary current lineations and are not associated with planar‐parallel, finely laminated sandstones. This type of ‘enhanced lineation’ is interpreted to develop by the same process as primary current lineations, but under relatively high near‐bed sediment concentrations and suspended load fallout rates, as supported by laboratory experiments and host facies characteristics. Sheets are interpreted to be dewatering structures and their alignment to palaeoflow (only noted in several other outcrops previously) inferred to be a function of vertical water‐escape following the primary depositional grain fabric. For the Marnoso‐arenacea beds, sheet orientation may be linked genetically to the enhanced primary current lineation structures. Current‐aligned lineation and sheet structures can be used as palaeoflow indicators, although the directional significance of sheets needs to be independently confirmed. These indicators also aid the interpretation of dewatered sandstones, suggesting sedimentation under a traction‐dominated depositional flow – with a discrete interface between the aggrading deposit and the flow – as opposed to under higher concentration grain or hindered‐settling dominated regimes.
Stable and heritable gene silencing in the malaria vector Anopheles stephensi.

Heritable RNA interference (RNAi), triggered from stably expressed transgenes with an inverted repeat (IR) configuration, is an important tool for reverse genetic studies. Here we report on the development of stable RNAi in Anopheles stephensi mosquitoes, the major vector of human malaria in Asia. Trans genic mosquitoes stably expressing a RNAi transgene, designed to produce intron-spliced double-stranded RNA (dsRNA) targeting the green fluorescent protein EGFP gene, were crossed to an EGFP-expressing target line. EGFP expression was dramatically reduced at both the protein and RNA levels. The levels of gene silencing depended upon the RNAi gene copy number and its site of integration. These results demonstrate that specific RNAi-mediated knockdown of gene function can be achieved with high efficiency in Anopheles . This will be invaluable to systematically unravel the function of Anopheles genes determining the vectorial capacity of the malaria parasite.
Density Evolution for GF(q) LDPC Codes Via Simplified Message-passing Sets

A message-passing decoder for GF(q) low-density parity-check codes is defined, which uses discrete messages from a subset of all possible binary vectors of length q. The proposed algorithm is a generalization to GF(q) of Richardson and Urbanke's decoding "Algorithm E" for binary codes. Density evolution requires a mapping between the probability distribution spaces for the channel, variable and check messages, and under the proposed algorithm, exact density evolution is possible. Symmetries in the message densities permit reduction in the size of the probability distribution space. Noise thresholds are obtained for LDPC codes on discrete memoryless channels, and as with Algorithm E, are remarkably close to noise thresholds under more complex belief propagation decoding.
Estimation of the effect of nonisotropically distributed energy on the apparent arrival time in correlations

Correlations of random seismic noise are now widely used to retrieve the Green’s function between two points. Whereas this technique provides useful results in tomography and monitoring studies, it is mainly limited by an uneven distribution of noise sources. In that case, theoretical requirements are not completely fulfilled and we may wonder how reliable the reconstructed signals are, in particular for the purpose of estimating traveltime from correlations. This study finds a way to quantify effects of a nonisotropic noise field by estimating the arrival-time error resulting from a particular nonisotropic distribution of recorded wave intensity. Our study is based on a theoretical prediction of this bias and we successfully test the theory by comparing the theoretical expectation to real measurements from seismic-prospecting data. In particular, we distinguish between the effects of source distribution and the effects of medium heterogeneity between the sources and the region of receivers. We find relat.
Setting conservation management thresholds using a novel participatory modeling approach

We devised a participatory modeling approach for setting management thresholds that show when management intervention is required to address undesirable ecosystem changes. This approach was designed to be used when management thresholds: must be set for environmental indicators in the face of multiple competing objectives; need to incorporate scientific understanding and value judgments; and will be set by participants with limited modeling experience. We applied our approach to a case study where management thresholds were set for a mat‐forming brown alga, Hormosira banksii, in a protected area management context. Participants, including management staff and scientists, were involved in a workshop to test the approach, and set management thresholds to address the threat of trampling by visitors to an intertidal rocky reef. The approach involved trading off the environmental objective, to maintain the condition of intertidal reef communities, with social and economic objectives to ensure management intervention was cost‐effective. Ecological scenarios, developed using scenario planning, were a key feature that provided the foundation for where to set management thresholds. The scenarios developed represented declines in percent cover of H. banksii that may occur under increased threatening processes. Participants defined 4 discrete management alternatives to address the threat of trampling and estimated the effect of these alternatives on the objectives under each ecological scenario. A weighted additive model was used to aggregate participants’ consequence estimates. Model outputs (decision scores) clearly expressed uncertainty, which can be considered by decision makers and used to inform where to set management thresholds. This approach encourages a proactive form of conservation, where management thresholds and associated actions are defined a priori for ecological indicators, rather than reacting to unexpected ecosystem changes in the future.
The Holmes Group Report: Its Latent Political Agenda

As president of the Association of Independent Liberal Arts Colleges for Teacher Education, Alan Tom examines the Holmes Group proposal to eliminate the undergraduate teacher education major and sees more concern with the structure than the substance of reform and finds a deep commitment to a linear form of professional study. This, he contends, was the unconscious assertion by research-oriented universities of their own political interests.