Miracle-dz/UniFAR-FTUs huggingface dataset:
HY5, Circadian Clock-Associated 1, and a cis-Element, DET1 Dark Response Element, Mediate DET1 Regulation of Chlorophyll a/b-Binding Protein 2 Expression1

DET1 is a pleiotropic regulator of Arabidopsis development and controls the expression of many light-regulated genes. To gain a better understanding of the mechanism by which DET1 controls transcription from light-regulated promoters, we identified elements in the chlorophyll a/b-binding protein 2 (CAB2) promoter that are required for DET1-mediated expression. Using a series of reporter constructs in which the luciferase gene is controlled by CAB2 promoter fragments, we defined two DET1-responsive elements in the CAB2 promoter that are essential for proper CAB2 transcription. A 40-bp DET1 dark-response element (DtRE) is required for both dark and root-specific repression of CAB2, whereas the known CAB upstream factor-1 element is required for DET1 activation-associated effects in the light and repression in the roots. HY5, a factor that binds CAB upstream factor-1, is also required for DET1 effects in the light. DtRE binds two distinct activities in Arabidopsis seedling extracts: a novel activity with binding site CAAAACGC that we have named CAB2 DET1-associated factor 1 plus an activity that is likely to be the myb transcription factor Circadian Clock-Associated 1. Both activities are altered in dark-grown det1 extracts as compared with wild type, correlating a change in extractable DNA binding activity with a major change in CAB2 expression. We conclude that DET1 represses the CAB2 promoter in the dark by regulating the binding of two factors, CAB2 DET1-associated factor 1 and Circadian Clock-Associated 1, to the DtRE.
A Repetitive DNA Element Regulates Expression of the Helicobacter pylori Sialic Acid Binding Adhesin by a Rheostat-like Mechanism

During persistent infection, optimal expression of bacterial factors is required to match the ever-changing host environment. The gastric pathogen Helicobacter pylori has a large set of simple sequence repeats (SSR), which constitute contingency loci. Through a slipped strand mispairing mechanism, the SSRs generate heterogeneous populations that facilitate adaptation. Here, we present a model that explains, in molecular terms, how an intergenically located T-tract, via slipped strand mispairing, operates with a rheostat-like function, to fine-tune activity of the promoter that drives expression of the sialic acid binding adhesin, SabA. Using T-tract variants, in an isogenic strain background, we show that the length of the T-tract generates multiphasic output from the sabA promoter. Consequently, this alters the H. pylori binding to sialyl-Lewis x receptors on gastric mucosa. Fragment length analysis of post-infection isolated clones shows that the T-tract length is a highly variable feature in H. pylori. This mirrors the host-pathogen interplay, where the bacterium generates a set of clones from which the best-fit phenotypes are selected in the host. In silico and functional in vitro analyzes revealed that the length of the T-tract affects the local DNA structure and thereby binding of the RNA polymerase, through shifting of the axial alignment between the core promoter and UP-like elements. We identified additional genes in H. pylori, with T- or A-tracts positioned similar to that of sabA, and show that variations in the tract length likewise acted as rheostats to modulate cognate promoter output. Thus, we propose that this generally applicable mechanism, mediated by promoter-proximal SSRs, provides an alternative mechanism for transcriptional regulation in bacteria, such as H. pylori, which possesses a limited repertoire of classical trans-acting regulatory factors.
A Feature Encoding Based on Fuzzy Codebook for Large-Scale Image Recognition

Feature encoding is an important step in image representation pipeline. In recent works, a codebook approach is generally used for image representation, and image is represented by codebook based encoding of extracted local descriptors. The Fisher Vector (FV) encoding is known as a powerful technique, however the memory cost of the codebook is rapidly increased dependence on the dimensionality of local feature. This paper presents a feature encoding technique based on compact codebook by using fuzzy clustering. Our approach contains two ideas. The first idea is to modify the fuzzy clustering for suitable calculation of high-dimensional vectors such as a local feature. The second idea is to update the codebook to each image, and embed its difference to image feature by using KL divergence. Our approach recorded 1.04% higher rate than FV on Caltech-101 dataset. The advantage of our approach is that the model parameter of the codebook is small.
Characteristics of perisinusoidal collagenization in liver cirrhosis: computer-assisted quantitative analysis.

OBJECTIVE To determine the respective roles of septal fibrosis, necroinflammatory activity, iron deposition, steatosis, and patterns of nodular and septal remodeling in the collagenization of the perisinusoidal space in livers from patients undergoing transplantation for alcoholic or posthepatitis C cirrhosis and to ascertain whether perisinusoidal collagenization has clinical implications added to those of septal fibrosis. STUDY DESIGN Sixty-six hepatectomy specimens from patients undergoing liver transplantation for cirrhosis were analyzed. Thirty-two alcoholic and 34 posthepatitis C cirrhoses were included. Picro Sirius-stained slides were examined with polarized light and the amount of perisinusoidal collagenization measured by computerized image analysis. Size distributions of septa and nodules were assessed by mathematical morphology methods. RESULTS The septal and perisinusoidal fibrosis indices and Knodell and Pugh-Child scores showed significant differences between alcoholic and posthepatitis cirrhoses. Correlation between septal fibrosis and perisinusoidal collagenization was weak, though significant. Both variables correlated significantly with the clinical score. The correlation was negative between septal fibrosis or perisinusoidal collagenization and the Knodell score. CONCLUSION Perisinusoidal collagenization was not a feature of all cases of cirrhosis, although it was more prominent in alcoholics. For the whole series, it significantly correlated with the clinical score, which increased significantly when high perisinusoidal collagenization was added to high septal fibrosis. No absolute dependence was found between perisinusoidal collagenization and septal fibrosis; percentage of slender fibrous septa and amount of iron deposition were other factors entered in the regression equation.
Screening Tests for Cushing's Syndrome: Urinary Free Cortisol Role Measured by LC-MS/MS.

INTRODUCTION AND AIM As initial screening for Cushing's syndrome (CS), The Endocrine Society guidelines recommend one of the following: the 1-mg dexamethasone suppression test (DST) or late-night salivary cortisol (LNSC) or urinary free cortisol (UFC) measurement. We examined the diagnostic performance of the above-mentioned tests in a series of patients. MATERIALS AND METHODS We retrospectively analyzed 137 patients with clinical conditions suggestive of hypercortisolism: 38 with confirmed CS diagnosis and 99 without (termed non-CS). UFC was measured by liquid chromatography tandem-mass spectrometry, whereas LNSC by the radioimmunometric method and serum cortisol were measured by a chemiluminescence immunoassay. RESULTS Comparing CS vs non-CS, a cutoff of 138 nmol/L after 1-mg DST revealed the best specificity (SP; 97%), whereas the 50-nmol/L cutoff confirmed the best sensitivity (SE; 100%); the SE and SP for LNSC greater than 14.46 nmol/L were, respectively, 84% and 89%, whereas the SE and SP for UFC greater than 170 nmol per 24 hours, they were 97% and 91%. Overall, UFC revealed both a combined higher positive and a lower negative likelihood ratio among first-line tests (respectively 10.7 and 0.03). Computing a receiver-operating curve -contrast analysis to compare the power of each single test with that of the others, alone or combined (DST+LNSC, DST+UFC, and LNSC+UFC) or with that of all the tests together (DST+LNSC+UFC), the UFC assay was at least as good as all the other possible combinations. CONCLUSIONS Measuring UFC by liquid chromatography tandem-mass spectrometry achieves the best accuracy in diagnosing CS among patients presenting with suspected hypercortisolism.
Dietary Nucleotides Can Up-Regulate Antigen-Specific Th1 Immune Responses and Suppress Antigen-Specific IgE Responses in Mice

Background: It has been reported that dietary nucleotides enhance T helper cell activities. In this study, we have determined the effects of dietary nucleotides on antigen-specific Th1 and Th2 responses and IgE responses. Methods: Ovalbumin (OVA)-specific T cell receptor (TCR) transgenic (OVA-TCR Tg) mice, 3 weeks old, were fed a nucleotide-free diet (NT(–) diet) or the NT(–) diet supplemented with dietary nucleotides (NT(+) diet) for 4 weeks. Cytokine production by spleen cells and macrophages obtained from these mice was measured in vitro. BALB/c mice, 3 weeks old, immunized intraperitoneally with OVA adsorbed onto alum, were fed the NT(–) diet or the NT(+) diet for 4 weeks. Serum levels of antigen-specific antibodies in the BALB/c mice were determined by ELISA. Results: The level of production of antigen-specific interferon-γ by spleen cells was significantly higher in the OVA-TCR Tg mice fed the NT(+) diet than in the control mice. The levels of secretion of bioactive IL-12 by spleen cells and peritoneal macrophages were also significantly increased in the NT(+) diet group. The serum OVA-specific IgE level was significantly decreased in BALB/c mice fed the NT(+) diet compared with those fed the NT(–) diet. Conclusion: These results show that dietary nucleotides up-regulate the antigen-specific Th1 immune response through the enhancement of IL-12 production and suppress the antigen-specific IgE response.
Seroepidemiology of human bocavirus defined using recombinant virus-like particles.

BACKGROUND Human bocavirus (HBoV) is a newly identified human parvovirus for which seroepidemiology and antigenic properties remain undefined. METHODS The HBoV VP2 gene, expressed from a baculovirus vector, produced virus-like particles (VLPs), which were used to raise rabbit anti-HBoV antisera and to develop an enzyme-linked immunosorbent assay (ELISA). The VLP-based ELISA was used to screen for HBoV-specific immunoglobulin G antibodies in a convenience sample of 270 serum specimens, mostly from children, obtained at Yale-New Haven Hospital; 208 specimens were also screened for erythrovirus B19-specific antibodies by a B19 VLP-based ELISA. RESULTS Immunofluorescence and ELISA showed that human parvoviruses HBoV and B19 are antigenically distinct. By the HBoV VLP-based ELISA, 91.8% and 63.6% of serum specimens from infants in the first and second months of life, respectively, were found to be seropositive, as were 45.4% from 3-month-old infants and 25.0% from 4-month-old infants. The percentages of HBoV-seropositive children increased to 40.7%-60.0% for children 5-47 months of age and to >85% for individuals >or=48 months old. However, the overall percentage of B19-seropositive individuals was <40.5% for all age groups screened. CONCLUSIONS HBoV infection is common during childhood, but a minority of children and young adults screened have evidence of B19 infection.
Group sequential methods for cluster randomization trials with binary outcomes

Background Cluster randomization trials in which intact social units are randomly assigned to different intervention groups have become very popular in recent years, particularly for the evaluation of innovations in the delivery of health care. An extensive literature dealing with the associated methodological challenges has also appeared. Although the monitoring of such trials using formal stopping rules is clearly indicated when the outcomes are irreversible and individual-level data are available sequentially, simple and reliable statistical methods that may be used for this purpose are currently not available. Purpose To investigate the validity of standard group sequential methods when applied to cluster randomization trials having binary outcomes. Methods The large sample distributions for each of five test statistics computed from sequentially accumulated data are derived. A simulation study is performed to evaluate the finite sample properties of these statistics when applied to the interim analysis of cluster randomization trials. Data from the World Health Organization antenatal care trial [1] are used to illustrate the methods. Results Each of the joint distributions is shown to be characterized by a covariance structure that asymptotically satisfies an independent increments structure, a foundation that simplifies group sequential methods [2]. The simulation study reveals that four of the five test statistics evaluated provide satisfactory performance with as few as 10 clusters allocated to each of two interventions. Limitations The applicability of our results to effect estimation following a group sequential cluster randomization trial is not investigated, although a theoretical foundation which may be used for this purpose is presented. Conclusions Standard group sequential methods can be applied to cluster randomization trials when interim analyses are warranted.
American Sign Language and Early Literacy: Research as Praxis

This thesis presents an ethnographic action research study of Deaf and hearing parents and infants participating in a family American Sign Language (ASL) literacy program in Ontario. The thesis documents the context for parents and children’s learning of ASL in an environment where resources for supporting early ASL literacy have been scarce. At the time of the study, restrictions were placed on young Deaf and hard of hearing children’s learning of ASL, as the Ontario government’s Infant Hearing Program frequently did not provide ASL services to children who received cochlear implants or auditory-verbal therapy. This operational language policy of Ontario infant hearing screening and early intervention services was maintained despite evidence for the benefits that learning ASL confers on spoken and written language development in Deaf children. In this context, participation in a family ASL literacy program is a means for both supporting emerging ASL literacy in young children and resisting pathologizing Discourses (Gee, 2008) regarding signed language and Deaf identity. Through semi-structured interviews and observations of six individual families or parent-child dyads, the study documents participants’ encounters with gatekeepers who regulate Deaf children and their families’ access to ASL. At the same time, the setting of the ASL Parent-Child Mother Goose Program is presented as a Deaf cultural space and
Immunization with nonstructural proteins E1 and E2 of cottontail rabbit papillomavirus stimulates regression of virus-induced papillomas

Cottontail rabbit papillomavirus is the major animal model for cancer-associated papillomaviruses. Here we show that vaccination with the nonstructural proteins E1 and E2 induces the regression of virus-induced papillomas and that vaccination is equally effective when proteins are given with and without adjuvant. There was no correlation between antibody levels and regression, suggesting that tumor regression may be due to a cell-mediated response.
Efficacy of interpersonal therapy‐group format adapted to post‐traumatic stress disorder: an open‐label add‐on trial

Background: Post‐traumatic stress disorder (PTSD) is a highly prevalent condition, yet available treatments demonstrate only modest efficacy. Exposure therapies, considered by many to be the “gold‐standard” therapy for PTSD, are poorly tolerated by many patients and show high attrition. We evaluated interpersonal therapy, in a group format, adapted to PTSD (IPT‐G PTSD), as an adjunctive treatment for patients who failed to respond to conventional psychopharmacological treatment. Methods: Research participants included 40 patients who sought treatment through a program on violence in the department of psychiatry of Federal University of São Paulo (UNIFESP). They had received conventional psychopharmacological treatment for at least 12 weeks and failed to have an adequate clinical response. After signing an informed consent, approved earlier by the UNIFESP Ethics Review Board, they received a semi‐structured diagnostic interview (SCID‐I), administered by a trained mental health worker, to confirm the presence of a PTSD diagnosis according to DSM‐IV criteria. Other instruments were administered, and patients completed out self‐report instruments at baseline, and endpoint to evaluate clinical outcomes. Results: Thirty‐three patients completed the trial, but all had at least one second outcome evaluation. There were significant improvements on all measures, with large effect sizes. Conclusions: IPT‐G PTSD was effective not only in decreasing symptoms of PTSD, but also in decreasing symptoms of anxiety and depression. It led to significant improvements in social adjustment and quality of life. It was well tolerated and there were few dropouts. Our results are very preliminary; they need further confirmation through randomized controlled clinical trials. Depression and Anxiety, 2010. © 2009 Wiley‐Liss, Inc.
Heaviest Drinking Locations and the Most Drunk There Predict the Likelihood of Fighting and Being Assaulted

Preference for on-premise drinking affects likelihood of aggression, but how venue affects victimization by other drinkers is less studied. We investigated influence of heavy consumption in specific venues on fighting and assaults by other drinkers in the 2000 U.S. National Alcohol Survey, a representative telephone survey of adults (n = 7,612). In the prior year 4.5% current drinkers were assaulted by drinkers, while < 2% reported fighting while drinking. Logistic regression analyses showed that where one drank most, and usual and peak amounts drunk there, each influenced risks of fighting and (less) being assaulted. For drinking and fighting, heaviest context, usual amount, and difference between usual and peak were all highly significant, but adding age and impulsivity/sensation seeking eliminated effect of venue. Victimization risk curves for maximum were exponential: A peak of 10+ drinks showed odds ratios when at another's home, one's own home, and a bar of 4.5, 5.3 and 10.3, respectively (reference 1–2 home drinks); risk curves were steeper for fighting. Maximum amount consumed dominates the venue in which one drinks the most, once selectivity based on personal characteristics is attended to. We suggest interventions should emphasize ways of addressing overdrinking within a range of settings.
Safety and Efficacy of Autologous Intra-articular Platelet Lysates in Early and Intermediate Knee Osteoarthrosis in Humans: A Prospective Open-Label Study

Objective:To explore the safety and benefit from intra-articular autologous platelet lysate (PL) injection in early and intermediate knee osteoarthritis. Design:Open-label prospective study. Setting:Laboratory. Patients:Adult patients, aged 35 to 70 years, with a history of chronic pain or swelling on one or both knees and imaging findings (radiograph or magnetic resonance imaging) of degenerative changes in the joint of grade I or II on the Kellgren scale were included. Interventions:Autologous PL was given in the knee joint by percutaneous intra-articular route every 3 weeks for a total of 3 injections. Main Outcome Measures:Response was evaluated by nonnormalized Knee Osteoarthritis and Disability Outcome Score (KOOS). Results:There was a significant improvement in the 5 aspects evaluated at weeks 32 and 52 compared with baseline. Symptoms score significantly improved at weeks 32 and 52 from a mean of 11.1 at baseline to 9.0 (P < 0.0001) and 8.7 (P < 0.0001). Stiffness score significantly improved at weeks 32 and 52 from 2.2 at baseline to 1.7 (P < 0.022) and 1.6 (P < 0.016). Pain score improved at 32 weeks and at 52 weeks from a baseline of 14.2 to 9.8 (P < 0.0001) and 9.2 (P < 0.0001). Daily Living score improved from 25.0 to 18.7 at 32 weeks (P < 0.0001) and to 15.6 at 52 weeks (P < 0.0001). Sport score improved from 10.7 to 8.4 at 32 weeks (P < 0.0001) and to 8.1 at 52 weeks (P < 0.0001). Conclusions:Intra-articular PL significantly improved score of all aspects evaluated by KOOS. Platelet lysate seems to be a safe product. Clinical Relevance:To the best of our knowledge, this is the first clinical study addressing the use of autologous PL as a treatment measure for knee osteoarthrosis (KOA). There are no studies published regarding the treatment of KOA by intra-articular injections of PL. The previous studies were on the use of platelet-rich plasma (PRP) treatment for KOA. Platelet-rich plasma use has been in place for several years, however, a standardized protocol has not yet been established. Platelet lysate represents a safe, economical, easy to prepare, and easy to apply source of growth factors in the treatment of KOA. A head-to-head study is needed to compare PRP with PL in KOA.
Income-related Inequality of Health and Health Care Utilization

Using data of the China Health and Nutrition Surveys(CHNS),this paper tests for the extent of deviations from the principle of horizontal equity-i.e.those in equal need to be treated equally and computes the contribution of income in health inequality and utilization inequality of health care.The main conclusion is that there is pro-rich inequality in health and use of health care,income contribution to inequality of health care use accounts for 0.13—0.2. Insurance also enlarges the inequality of health care use.Inequality of health of rural is bigger than urban,both rural and urban health inequality is increasing.From 1991 to 2006,urban and rural changes in income account for 7.08% and 13.38% respectively of rising inequality.
Implementation Of E-Government In South Africa, Successes And Challenges. The Way Forward

The advances in technology hold great potential for helping the South African government respond to its challenges namely, better service delivery, better procurement, efficient working and better communication with citizens and businesses. The implementation of eGovernment initiatives is taking place on many fronts and in many ways in South Africa. Through the implementation of an egovernment initiatives, the South African government aims to provide higher quality & faster service to the public. This article provides a broad overview of eGovernment policy initiatives undertaken by the South African government. It highlights the successes and the challenges of egovernance. It also maps out a way forward. Keywords— eGovernment, Public Service, initiatives, challenges.