Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Pathogenic Viruses in Sewage Provided Early Warnings of Hepatitis A Virus and Norovirus Outbreaks

ABSTRACT Most persons infected with enterically transmitted viruses shed large amounts of virus in feces for days or weeks, both before and after onset of symptoms. Therefore, viruses causing gastroenteritis may be detected in wastewater, even if only a few persons are infected. In this study, the presence of eight pathogenic viruses (norovirus, astrovirus, rotavirus, adenovirus, Aichi virus, parechovirus, hepatitis A virus [HAV], and hepatitis E virus) was investigated in sewage to explore whether their identification could be used as an early warning of outbreaks. Samples of the untreated sewage were collected in proportion to flow at Ryaverket, Gothenburg, Sweden. Daily samples collected during every second week between January and May 2013 were pooled and analyzed for detection of viruses by concentration through adsorption to milk proteins and PCR. The largest amount of noroviruses was detected in sewage 2 to 3 weeks before most patients were diagnosed with this infection in Gothenburg. The other viruses were detected at lower levels. HAV was detected between weeks 5 and 13, and partial sequencing of the structural VP1protein identified three different strains. Two strains were involved in an ongoing outbreak in Scandinavia and were also identified in samples from patients with acute hepatitis A in Gothenburg during spring of 2013. The third strain was unique and was not detected in any patient sample. The method used may thus be a tool to detect incipient outbreaks of these viruses and provide early warning before the causative pathogens have been recognized in health care.
Identification of Freshwater Phycodnaviridae and Their Potential Phytoplankton Hosts, Using DNA pol Sequence Fragments and a Genetic-Distance Analysis

ABSTRACT Viruses that infect phytoplankton are an important component of aquatic ecosystems, yet in lakes they remain largely unstudied. In order to investigate viruses (Phycodnaviridae) infecting eukaryotic phytoplankton in lakes and to estimate the number of potential host species, samples were collected from four lakes at the Experimental Lakes Area in Ontario, Canada, during the ice-free period (mid-May to mid-October) of 2004. From each lake, Phycodnaviridae DNA polymerase (pol) gene fragments were amplified using algal-virus-specific primers and separated by denaturing gradient gel electrophoresis; 20 bands were extracted from the gels and sequenced. Phylogenetic analysis indicated that freshwater environmental phycodnavirus sequences belong to distinct phylogenetic groups. An analysis of the genetic distances “within” and “between” monophyletic groups of phycodnavirus isolates indicated that DNA pol sequences that differed by more than 7% at the inferred amino acid level were from viruses that infect different host species. Application of this threshold to phylogenies of environmental sequences indicated that the DNA pol sequences from these lakes came from viruses that infect at least nine different phytoplankton species. A multivariate statistical analysis suggested that potential freshwater hosts included Mallomonas sp. , Monoraphidium sp. , and Cyclotella sp. This approach should help to unravel the relationships between viruses in the environment and the phytoplankton hosts they infect.
Spontaneous Expression Recognition Using Universal Attribute Model

Spontaneous expression recognition refers to recognizing non-posed human expressions. In literature, most of the existing approaches for expression recognition mainly rely on manual annotations by experts, which is both time-consuming and difficult to obtain. Hence, we propose an unsupervised framework for spontaneous expression recognition that preserves discriminative information for the videos of each expression without using annotations. Initially, a large Gaussian mixture model called universal attribute model (UAM) is trained to learn the attributes of various expressions implicitly. Attributes are the movements of various facial muscles that are combined to form a particular facial expression. Then, a concatenated mean vector called the super expression-vector (SEV) is formed by using a maximum a posteriori adaptation of the UAM means for each expression clip. This SEV contains attributes from all the expressions resulting in a high dimensional representation. To retain only the attributes of that particular expression clip, the SEV is decomposed using factor analysis to produce a low-dimensional expression-vector. This procedure does not require any class labels and produces expression-vectors that are distinct for each expression irrespective of high inter-actor variability present in spontaneous expressions. On spontaneous expression datasets like BP4D and AFEW, we demonstrate that expression-vector achieves better performance than the state-of-the-art techniques. Furthermore, we also show that UAM trained on a constrained data set can be effectively used to recognize expressions in unconstrained expression videos.
Is Hysterectomy a Risk Factor for Vaginal Cancer

Several recent case series have called attention to a possible association between previous hysterectomy and the subsequent development of vaginal cancer. To study this relationship, we compared 49 patients with vaginal cancer with 49 controls matched for age, race, and prior cervical dysplasia or neoplasia. Patients and controls were alike in terms of exposure to estrogens. Twenty-four patients (49%) had had prior hysterectomies, of which 13 (27%) were for benign disease. Similarly, 24 controls had a history of a hysterectomy. The matched-pairs odds ratio relating prior hysterectomy to vaginal cancer was 1.00 based on these data, with a 95% confidence interval of 0.47 to 2.12. In the subsample of women without a history of cervical disease, a similar odds ratio appeared. Although the study sample size did not permit exclusion of a twofold increase in risk, the statistical power to detect an actual odds ratio of 2.5 is 76%. At this level of statistical power, our data suggest that hysterectomy has a low probability of being a risk factor for vaginal cancer when age and cervical disease are controlled for. In the absence of such a relationship, screening for vaginal cancer does not appear to be necessary for women who have had a hysterectomy for benign disease. ( JAMA 1986;256:601-603)
Use of attributed grammars in speech signal processing

This paper describes a theoretical model for syntactic signal processing, and the algorithmic implementation of the model for pitch and formant tracking applications. Classical and adaptive estimation models operate on the data with a specified window function, and no use is made of structural relationships beyond adjacent frames of data. This new model consists of a grammar which accepts new data based on the statistics of the data attributes, as well as structual constraints of the grammar. High probability sentences are constructed through a nondeterministic parsing of the data. In this manner it is possible to use all of the context surrounding a particular set of windowed data to improve the estimate and segmentation is simultaneously achieved. The model is extendable to higher level constructs.
GimpGirl grows up: Women with disabilities rethinking, redefining, and reclaiming community

In this article, we undertake a reflective narrative inquiry into the GimpGirl Community (GGC), an online group of women with disabilities. We explore 12 years of GGC activity through community archives and auto-biographic narratives of GGC organizers, to understand how these women actively created a safe and open space for like-minded individuals, how community members used diverse online technologies for community building and social interaction, and how these online tools allow some members to experiment with their notions of self and identity outside dominant discourses. Our analysis of the lived experiences of GGC members reveals how they challenge the boundary between ‘abled’ and ‘disabled,’ and enact agency beyond their marginalization as women and as individuals with disabilities.
Isolation of Bifidobacteria from Breast Milk and Assessment of the Bifidobacterial Population by PCR-Denaturing Gradient Gel Electrophoresis and Quantitative Real-Time PCR

ABSTRACT The objective of this work was to elucidate if breast milk contains bifidobacteria and whether they can be transmitted to the infant gut through breastfeeding. Twenty-three women and their respective infants provided samples of breast milk and feces, respectively, at days 4 to 7 after birth. Gram-positive and catalase-negative isolates from specific media with typical bifidobacterial shapes were identified to the genus level by F6PPK (fructose-6-phosphate phosphoketolase) assays and to the species level by 16S rRNA gene sequencing. Bifidobacterial communities in breast milk were assessed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and their levels were estimated by quantitative real-time PCR (qRTi-PCR). Bifidobacteria were present in 8 milk samples and 21 fecal samples. Bifidobacterium breve, B. adolescentis, and B. bifidum were isolated from milk samples, while infant feces also contained B. longum and B. pseudocatenulatum. PCR-DGGE revealed the presence of one to four dominant bifidobacterial bands in 22 milk samples. Sequences with similarities above 98% were identified as Bifidobacterium breve, B. adolescentis, B. longum, B. bifidum, and B. dentium. Bifidobacterial DNA was detected by qRTi-PCR in the same 22 milk samples at a range between 40 and 10,000 16S rRNA gene copies per ml. In conclusion, human milk seems to be a source of living bifidobacteria for the infant gut.
Evaluating the Complex: Alternative Models and Measures for Evaluating Collaboration among Substance use Services with Mental Health, Primary Care and other Services and Sectors

Many planners and administrators now look to “collaboration” or “integration” as a solution, or at least a partial solution, to challenges related to access and delivery of substance use and mental health services and health services in general. Among the major constraints in identifying best practices in this area and recommending optimal evaluation strategies are the plethora of terms and concepts used in the literature to describe collaboration or integration as well as the many alternative approaches and outcome expectations. It is helpful, therefore, to follow concrete steps to plan the evaluation, including the engagement of multiple stakeholders in the planning process and subsequent execution of the evaluation. The concrete evaluation strategies employed can follow a traditional, often linear model, of impact and are often categorized under the common typologies of process, outcome or economic evaluations. Each approach examines different domains of interest and can be at the individual/service level or at the level of the overall treatment system. Other less traditional evaluation models and methods based on systems theory, complex adaptive systems and developmental evaluation have much to offer the evaluation of interventions aimed at improving the collaboration and integration of substance use services with other health and social services and sectors. Realist evaluation is a particularly helpful approach that integrates many of the traditional approaches with these other models and methods.
Cardiac impairment in rabbits fed a high-fat diet is counteracted by dehydroepiandrosterone

2 The role of oxidative stress in the activating of downstream signalling leading to structural and 3 functional changes in the left ventricle of rabbits fed a high-fat diet for 12 wks and the effect of 4 dietary dehydroepiandrosterone supplementation, were analyzed. The animals showed 5 hyperglycemia, insulin-resistance, dyslipidemia and early features of cardiomyopathy, i.e. altered 6 myosin heavy-chain isoforrns, tissue degeneration and reduced contractility of the papillary muscle. 7 Dietary supplementation with dehydroepiandrosterone (0.02%,wt/wt) in these animals reduced 8 oxidative stress evaluated as levels of reactive oxygen species and hydroxynonenal levels, without 9 affecting high plasma glucose level or insulin resistance. Dehydroepiandrosterone supplementation lO also counteracted both the activation of redox-sensitive transcription factor and of nuclear Il trascription factor-kB, and the expression of tumor necrosis factor-alpha and of C-reactive protein-12 mRNA. Improvement of the oxidative balance counteracted the shift to myosin heavy chain
Adrenocortical carcinoma: clinical, morphologic, and molecular characterization.

PURPOSE To define multimolecular phenotypes of adrenocortical carcinoma (ACC) and to correlate outcome with morphologic and molecular parameters. PATIENTS AND METHODS Clinical data were analyzed for 124 patients, histopathologic slides for 67 primary tumors, and tissue specimens for 74 patients (38 primary and 36 metastatic tumors) with ACC and for 38 normal adrenal tissue samples. Molecular expression profiles were investigated by immunohistochemistry. The prognostic significance of 12 gross and histologic parameters in 67 primary ACCs was evaluated. Morphologic and protein expression patterns were correlated with disease-specific survival (DSS). Univariate influence of prognostic factors on DSS was analyzed by log-rank test and multivariate analysis by Cox regression. RESULTS The median follow-up period was 4.7 years. Significant predictors of DSS included distant metastasis at time of initial presentation; venous, capsular, and adjacent organ invasion; tumor necrosis, mitotic rate, atypical mitosis, and mdm-2 overexpression. Five-year DSS by number (one to six) of adverse histologic parameters was as follows: one to two, 84%; three to four, 37%; more than four, 9% (P =.005). The phenotype Ki-67(-)p53(-)mdm-2(+)cyclinD1(-)Bcl-2(-)p21(-)p27(+) was observed in 83% of normal and 3% of malignant adrenal tissue (P =.01). Molecular phenotypic expression was more heterogeneous in malignant than in normal (10 v five phenotypes) adrenal tissue. CONCLUSION Meticulous morphologic evaluation, mitotic count, and tumor stage are essential in determining prognosis for patients with ACC. Multimolecular phenotyping demonstrates that the molecular complexity and heterogeneity of these neoplasms are such that targeted therapy needs to be patient specific.
Specific DNA Binding of a Potential Transcriptional Regulator, Inosine 5′-Monophosphate Dehydrogenase-Related Protein VII, to the Promoter Region of a Methyl Coenzyme M Reductase I-Encoding Operon Retrieved from Methanothermobacter thermautotrophicus Strain ΔH

ABSTRACT Two methyl coenzyme M reductases (MCRs) encoded by the mcr and mrt operons of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus ΔH are expressed in response to H2 availability. In the present study, cis elements and trans-acting factors responsible for the gene expression of MCRs were investigated by using electrophoretic mobility shift assay (EMSA) and affinity particle purification. A survey of their operator regions by EMSA with protein extracts from mrt-expressing cultures restricted them to 46- and 41-bp-long mcr and mrt upstream regions, respectively. Affinity particle purification of DNA-binding proteins conjugated with putative operator regions resulted in the retrieval of a protein attributed to IMP dehydrogenase-related protein VII (IMPDH VII). IMPDH VII is predicted to have a winged helix-turn-helix DNA-binding motif and two cystathionine β-synthase domains, and it has been suspected to be an energy-sensing module. EMSA with oligonucleotide probes with unusual sequences showed that the binding site of IMPDH VII mostly overlaps the factor B-responsible element-TATA box of the mcr operon. The results presented here suggest that IMPDH VII encoded by MTH126 is a plausible candidate for the transcriptional regulator of the mcr operon in this methanogen.
PIRIFORMIS SYNDROME: A CLINICAL REVIEW.

Piriformis Syndrome is a cause for Low back pain which is most of the times misdiagnosed as it may mimic with various other conditions. Abnormal condition of the Piriformis muscle such as hypertrophy, inflammation, or anatomic variations may lead to this condition. Reported incidence rates for Piriformis Syndrome among patients with low back pain vary widely, from 5% to 36%. Etiology of Piriformis Syndrome is also variable. It can be primary due to anatomical problems or secondary due to various other causes like trauma, local ischemia, limb-length discrepancy etc. Diagnosis of Piriformis Syndrome is complex. History with various clinical tests along with MRI, EMG (Electromyography) and Diagnostic blocks may help to diagnose this condition. Here is a review of Piriformis syndrome for better understanding of the problem so that the diagnosis and management are appropriate.
Iodide Accumulation by Aerobic Bacteria Isolated from Subsurface Sediments of a 129I-Contaminated Aquifer at the Savannah River Site, South Carolina

ABSTRACT 129I is of major concern because of its mobility in the environment, excessive inventory, toxicity (it accumulates in the thyroid), and long half-life (∼16 million years). The aim of this study was to determine if bacteria from a 129I-contaminated oxic aquifer at the F area of the U.S. Department of Energy's Savannah River Site, SC, could accumulate iodide at environmentally relevant concentrations (0.1 μM I−). Iodide accumulation capability was found in 3 out of 136 aerobic bacterial strains isolated from the F area that were closely related to Streptomyces/Kitasatospora spp. , Bacillus mycoides, and Ralstonia/Cupriavidus spp. Two previously described iodide-accumulating marine strains, a Flexibacter aggregans strain and an Arenibacter troitsensis strain, accumulated 2 to 50% total iodide (0.1 μM), whereas the F-area strains accumulated just 0.2 to 2.0%. Iodide accumulation by FA-30 was stimulated by the addition of H2O2, was not inhibited by chloride ions (27 mM), did not exhibit substrate saturation kinetics with regard to I− concentration (up to 10 μM I−), and increased at pH values of <6. Overall, the data indicate that I− accumulation likely results from electrophilic substitution of cellular organic molecules. This study demonstrates that readily culturable, aerobic bacteria of the F-area aquifer do not accumulate significant amounts of iodide; however, this mechanism may contribute to the long-term fate and transport of 129I and to the biogeochemical cycling of iodine over geologic time.
High-efficiency frequency doubling of ultra-intense Nd:glass laser pulses

Efficient second harmonic conversion (70 - 80%) using Type II and Type I crystals is demonstrated with 400-fs, 1.053-micrometers laser pulses at intensities up to several hundreds of GW/cm2. The experimental results generally agree with the predictions of the code MIXER. For the Type II predelay scheme, evidence is obtained of pulse shortening down to approximately 100 fs.
Diverse Broad-Host-Range Plasmids from Freshwater Carry Few Accessory Genes

ABSTRACT Broad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. To do this, triparental matings were used such that the only required phenotype was the plasmid's ability to mobilize a nonconjugative plasmid. Based on complete genome sequences of 10 plasmids, only 5 carried identifiable accessory gene regions, and none carried antibiotic resistance genes. The plasmids belong to four known incompatibility groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of the plasmids were shown to have a broad host range, being able to transfer into alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic resistance genes, we resampled one of the sites and compared the proportion of captured plasmids that conferred antibiotic resistance to their hosts with the proportion of such plasmids captured from the effluent of a local wastewater treatment plant. Few of the captured plasmids from either site encoded antibiotic resistance. A high diversity of plasmids that encode no or unknown accessory functions is thus readily found in freshwater habitats. The question remains how the plasmids persist in these microbial communities.
Role of Campylobacter jejuni Respiratory Oxidases and Reductases in Host Colonization

ABSTRACT Campylobacter jejuni is the leading cause of human food-borne bacterial gastroenteritis. The C. jejuni genome sequence predicts a branched electron transport chain capable of utilizing multiple electron acceptors. Mutants were constructed by disrupting the coding regions of the respiratory enzymes nitrate reductase (napA::Cm), nitrite reductase (nrfA::Cm), dimethyl sulfoxide, and trimethylamine N-oxide reductase (termed Cj0264::Cm) and the two terminal oxidases, a cyanide-insensitive oxidase (cydA::Cm) and cbb3-type oxidase (ccoN::Cm). Each strain was characterized for the loss of the associated enzymatic function in vitro. The strains were then inoculated into 1-week-old chicks, and the cecal contents were assayed for the presence of C. jejuni 2 weeks postinoculation. cydA::Cm and Cj0264c::Cm strains colonized as well as the wild type; napA::Cm and nrfA::Cm strains colonized at levels significantly lower than the wild type. The ccoN::Cm strain was unable to colonize the chicken; no colonies were recovered at the end of the experiment. While there appears to be a role for anaerobic respiration in host colonization, oxygen is the most important respiratory acceptor for C. jejuni in the chicken cecum.
Growth of Enterococci in Unaltered, Unseeded Beach Sands Subjected to Tidal Wetting

ABSTRACT Enterococci are indicator bacteria used to assess the risk of acquiring enteric disease from swimming in marine waters. Previous work identified beach sands as reservoirs of enterococci which can be transported from the sand to the sea, where they may instigate beach advisories. The present study establishes that naturally occurring enterococci can replicate in beach sands under environmentally relevant conditions. In unseeded, nonsterile microcosm experiments, it was shown that intermittent wetting of sands by seawater, like that which would occur at the high tide line, stimulates the transient replication of enterococci at rates of 0.20 to 0.63 per day (equivalent to doubling times of 1.1 to 3.5 days). Replication was not observed in control microcosms that were not subjected to wetting. Enterococci were enumerated using both culture-dependent (membrane filtration and mEI media) and culture-independent (quantitative PCR [QPCR], 23S rRNA gene based) techniques, which allowed tracking of both culturable and total enterococcus populations. Inhibition of QPCR and DNA extraction efficiencies were accounted for in the interpretation of the QPCR results. The results provide evidence that enterococci may not be an appropriate indicator of enteric disease risk at recreational beaches subject to nonpoint sources of pollution.