Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytokines in tear fluid of patients with ocular graft-versus-host disease after allogeneic stem cell transplantation

Purpose To investigate the profile of cytokines in tear fluid of patients after allogeneic stem cell transplantation (allo-SCT) and determine their relation to the presence and manifestations of ocular graft-versus-host disease (GvHD). Methods In this cross sectional study tear fluid was collected in 34 consecutive adult patients that previously underwent allo-SCT (16 with ocular GvHD and 18 without) and 16 age- and gender-matched healthy controls using the Schirmer test under local anesthesia. Tear fluid was analyzed by multiplex immunoassay for the presence of interleukin (IL)-2, IL-4, IL-6, IL-10, IL-17, tumor necrosis factor (TNF)-α and interferon (IFN)-γ. Levels of measured cytokines were correlated with the findings in slit lamp examination and the Ocular Surface Disease Index (OSDI). Results The levels of IL-6 and IFN-γ in tear fluid in ocular GvHD patients were significantly elevated in comparison to patients without ocular GvHD and healthy controls (p<0.005 for each) The levels of IFN-γ correlated with the Schirmer score (r=-0.48, p<0.0001) and tear break up time (TBUT; r=-0.38, p=0.03). Tear IL-6 levels correlated with complaints of dry eyes (r=0.39, p=0.02), tear production (r=-0.59, p<0.0001), fluorescent staining of the cornea (r=0.42, p=0.01), and with the OSDI score (r=0.40, p=0.005). Conclusions IL-6 and IFN-γ were elevated in tear fluid of patients with ocular GvHD and correlated with different symptoms of dry eye disease, suggesting that IFN-γ is elevated during the early stages and IL-6 is involved in later stages of ocular GVHD and exhibits moreover an association with its severity.
Do Minimum Wages Really Reduce Teen Employment? Accounting for Heterogeneity and Selectivity in State Panel Data

Traditional estimates of minimum wage effects include controls for state unemployment rates and state and year fixed-effects. Using CPS data on teens for the period 1990 – 2009, we show that such estimates fail to account for heterogeneous employment patterns that are correlated with selectivity among states with minimum wages. As a result, the estimates are often biased and vary with the source of identifying variation. Including controls for long-term growth differences among states and for heterogeneous economic shocks renders the employment and hours elasticities indistinguishable from zero and rules out any but small disemployment effects. Dynamic evidence further shows the nature of bias in traditional estimates, and it also rules out more negative long run effects. We do not find evidence of heterogeneous employment effects in different parts of the business cycle. We also consider predictable versus unpredictable changes in the minimum wage by looking at indexation of the minimum wage in some states.
A non-randomised trial of an art therapy intervention for patients with haematological malignancies to support post-traumatic growth

The aim of this study was to determine the effect of art therapy on post-traumatic growth in patients with haematological malignancies in a non-randomised trial (n = 36, intervention group; n = 129, control group). Art therapy was administered over a period of 22 weeks in small groups. Post-traumatic growth was measured with the Stress-Related Growth Scale. After controlling for the effect of potential confounders, no difference in post-traumatic growth was observed between the intervention and control groups after 22 weeks. There was no evidence for an effect of weekly group sessions with art therapy on post-traumatic growth in patients with haematological malignancies.
Ferroelectric and Electrical Properties of Potassium Nitrate Thin Composite Layers

The ferroelectric and electrical properties of potassium nitrate (KNO3): polyvinylidene fluoride (PVDF) composite layers prepared by melt press method have been studied. The stability of ferroelectric phase (phase –III) of potassium nitrate (KNO3) in the composite layers at room temperature have been analyzed. The temperature dependence of ferroelectric hysteresis loop (P-E) characteristics have been investigated in the composite layers. The electrical conductivity (σ) and dielectric behaviour of composite layers have been characterized. The conductivity and dielectric variation with temperature during heating and cooling modes has been found to provide the knowledge of phase transition in the composite. The capacitance –-voltage (C-V) and conductance - voltage (G-V) characteristics clearly show the ferroelectric butterfly loop, which is attributed to the features of ferroelectricity in the composite layers at room temperature. The coexistence of ferroelectric phase (phase III) with paraelectric phase (phase II) has also been observed at room temperature in the composite layers during dielectric and conductivity measurements.
Low HIV testing uptake following diagnosis of a sexually transmitted infection in Spain: implications for the implementation of efficient strategies to reduce the undiagnosed HIV epidemic

ABSTRACT Sexually transmitted infections (STIs) are recognized as one of the conditions in which HIV testing is most clearly indicated. We analyse whether people diagnosed with an STI are being tested for HIV according to the experience of participants in an outreach rapid testing programme in Spain. Between 2008 and 2010, 6293 individuals underwent rapid testing and completed a self-administered questionnaire. We calculated the percentage of individuals that were diagnosed with an STI in the last 5 years and identified the setting where the last episode occurred. We then determined the percentage not receiving an HIV test after the last STI diagnosis and estimated the associated factors. Overall, 17.3% (N = 959) of participants reported an STI diagnosis in the last 5 years, of which 81.5% occurred in general medical settings. Sixty-one percent reported not undergoing HIV testing after their last STI diagnosis, 2.2% of whom reported they had refused the test. Not receiving an HIV test after the last STI diagnosis was independently associated with not being a man who has sex with men (MSM), having had fewer sexual partners, being diagnosed in general medical settings and having received a diagnosis other than syphilis. An unacceptably large percentage of people diagnosed with STI are not being tested for HIV because healthcare providers frequently fail to offer the test. Offering routine HIV testing at general medical settings, regardless of the type of STI diagnosed and population group, should be a high priority and is probably a more efficient strategy than universal screening in general healthcare settings.
Detecting similar software applications

Although popular text search engines allow users to retrieve similar web pages, source code search engines do not have this feature. Detecting similar applications is a notoriously difficult problem, since it implies that similar highlevel requirements and their low-level implementations can be detected and matched automatically for different applications. We created a novel approach for automatically detecting Closely reLated ApplicatioNs (CLAN) that helps users detect similar applications for a given Java application. Our main contributions are an extension to a framework of relevance and a novel algorithm that computes a similarity index between Java applications using the notion of semantic layers that correspond to packages and class hierarchies. We have built CLAN and we conducted an experiment with 33 participants to evaluate CLAN and compare it with the closest competitive approach, MUDABlue. The results show with strong statistical significance that CLAN automatically detects similar applications from a large repository of 8,310 Java applications with a higher precision than MUDABlue.
Genomic Analysis and Surveillance of the Coronavirus Dominant in Ducks in China

The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in chickens and ducks using a conserved RT-PCR assay. The viral genome harbors a tandem repeat which is rare in vertebrate RNA viruses. The repeat is homologous to some proteins of various cellular organisms, but its origin remains unknown. Many substitutions, insertions, deletions, and some frameshifts and recombination events have occurred in the genome of the DdCoV, as compared with the coronavirus dominant in chickens (CdCoV). The distances between DdCoV and CdCoV are large enough to separate them into different species within the genus Gammacoronavirus. Our surveillance demonstrated that DdCoVs and CdCoVs belong to different lineages and occupy different ecological niches, further supporting that they should be classified into different species. Our surveillance also demonstrated that DdCoVs and CdCoVs are prevalent in live poultry markets in some regions of China. In conclusion, this study shed novel insight into the genetic diversity, evolution, distribution, and taxonomy of the coronaviruses circulating in chickens and ducks.
Performance evaluation of prioritized handoff schemes in mobile cellular networks

This paper deals with the performance analysis of two prioritized handoff schemes for mobile cellular networks in which handoff attempts finding all channels busy are queued for a maximum time. Fixed channel assignment is assumed. In the first prioritized handoff scheme considered, handoff attempts are queued according to the first-in-first-out (FIFO) policy. Conversely, the second scheme resorts to an ideal nonpreemptive priority queueing policy to enhance system performance. Differently from previous works, in this paper the performance analysis is carried out on the basis of a model which takes into account the event that a call may terminate when the mobile user is waiting for a handoff. Comparisons with simulation results and analytical predictions derived by means of alternative approaches highlight a better estimation accuracy for the proposed method. Moreover, it is also demonstrated here that the FIFO policy allows performance very close to that of the ideal prioritized handoff scheme and, hence, that it is a solution suitable for applications in mobile cellular networks where a high service quality is required.
JC Virus Minor Capsid Proteins Vp2 and Vp3 Are Essential for Virus Propagation

ABSTRACT Virus-encoded capsid proteins play a major role in the life cycles of all viruses. The JC virus capsid is composed of 72 pentamers of the major capsid protein Vp1, with one of the minor coat proteins Vp2 or Vp3 in the center of each pentamer. Vp3 is identical to two-thirds of Vp2, and these proteins share a DNA binding domain, a nuclear localization signal, and a Vp1-interacting domain. We demonstrate here that both the minor proteins and the myristylation site on Vp2 are essential for the viral life cycle, including the proper packaging of its genome.
IL-33 ameliorates Alzheimer’s disease-like pathology and cognitive decline

Significance Dysfunction of the innate immune system is involved in the pathogenesis of Alzheimer’s disease (AD); however, the pathophysiological mechanisms underlying these dysfunctions are unclear. Here we report that stimulation of IL-33/ST2 signaling rescues memory deficits and reduces the accumulation of β-amyloid in APP/PS1 mice that exhibit select pathologies associated with AD. Although impaired IL-33/ST2 signaling is associated with early progression of AD, IL-33 injection rescues contextual memory deficits and reduces the accumulation of β-amyloid in APP/PS1 mice. IL-33 skews the microglia toward an alternative activation state with enhanced Aβ phagocytic capacity and elevated antiinflammatory gene expression, which results in a decreased proinflammatory response in the brain. Thus, this study suggests that IL-33 can be developed as a new therapeutic intervention for AD. Alzheimer’s disease (AD) is a devastating condition with no known effective treatment. AD is characterized by memory loss as well as impaired locomotor ability, reasoning, and judgment. Emerging evidence suggests that the innate immune response plays a major role in the pathogenesis of AD. In AD, the accumulation of β-amyloid (Aβ) in the brain perturbs physiological functions of the brain, including synaptic and neuronal dysfunction, microglial activation, and neuronal loss. Serum levels of soluble ST2 (sST2), a decoy receptor for interleukin (IL)-33, increase in patients with mild cognitive impairment, suggesting that impaired IL-33/ST2 signaling may contribute to the pathogenesis of AD. Therefore, we investigated the potential therapeutic role of IL-33 in AD, using transgenic mouse models. Here we report that IL-33 administration reverses synaptic plasticity impairment and memory deficits in APP/PS1 mice. IL-33 administration reduces soluble Aβ levels and amyloid plaque deposition by promoting the recruitment and Aβ phagocytic activity of microglia; this is mediated by ST2/p38 signaling activation. Furthermore, IL-33 injection modulates the innate immune response by polarizing microglia/macrophages toward an antiinflammatory phenotype and reducing the expression of proinflammatory genes, including IL-1β, IL-6, and NLRP3, in the cortices of APP/PS1 mice. Collectively, our results demonstrate a potential therapeutic role for IL-33 in AD.
Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation

DNA looping is important for gene repression and activation in Escherichia coli and is necessary for some kinds of gene regulation and recombination in eukaryotes. We are interested in sequence-nonspecific architectural DNA-binding proteins that alter the apparent flexibility of DNA by producing transient bends or kinks in DNA. The bacterial heat unstable (HU) and eukaryotic high-mobility group B (HMGB) proteins fall into this category. We have exploited a sensitive genetic assay of DNA looping in living E. coli cells to explore the extent to which HMGB proteins and derivatives can complement a DNA looping defect in E. coli lacking HU protein. Here, we show that derivatives of the yeast HMGB protein Nhp6A rescue DNA looping in E. coli lacking HU, in some cases facilitating looping to a greater extent than is observed in E. coli expressing normal levels of HU protein. Nhp6A-induced changes in the DNA length-dependence of repression efficiency suggest that Nhp6A alters DNA twist in vivo. In contrast, human HMGB2-box A derivatives did not rescue looping.
Glypican4 promotes cardiac specification and differentiation by attenuating canonical Wnt and Bmp signaling

Glypicans are heparan sulphate proteoglycans (HSPGs) attached to the cell membrane by a glycosylphosphatidylinositol (GPI) anchor, and interact with various extracellular growth factors and receptors. The Drosophila division abnormal delayed (dally) was the first glypican loss-of-function mutant described that displays disrupted cell divisions in the eye and morphological defects in the wing. In human, as in most vertebrates, six glypican-encoding genes have been identified (GPC1-6), and mutations in several glypican genes cause multiple malformations including congenital heart defects. To understand better the role of glypicans during heart development, we studied the zebrafish knypek mutant, which is deficient for Gpc4. Our results demonstrate that knypek/gpc4 mutant embryos display severe cardiac defects, most apparent by a strong reduction in cardiomyocyte numbers. Cell-tracing experiments, using photoconvertable fluorescent proteins and genetic labeling, demonstrate that Gpc4 ‘Knypek’ is required for specification of cardiac progenitor cells and their differentiation into cardiomyocytes. Mechanistically, we show that Bmp signaling is enhanced in the anterior lateral plate mesoderm of knypek/gpc4 mutants and that genetic inhibition of Bmp signaling rescues the cardiomyocyte differentiation defect observed in knypek/gpc4 embryos. In addition, canonical Wnt signaling is upregulated in knypek/gpc4 embryos, and inhibiting canonical Wnt signaling in knypek/gpc4 embryos by overexpression of the Wnt inhibitor Dkk1 restores normal cardiomyocyte numbers. Therefore, we conclude that Gpc4 is required to attenuate both canonical Wnt and Bmp signaling in the anterior lateral plate mesoderm to allow cardiac progenitor cells to specify and differentiate into cardiomyocytes. This provides a possible explanation for how congenital heart defects arise in glypican-deficient patients. SUMMARY: The study of zebrafish embryos deficient for Gpc4 reveals that it is essential for efficient cardiomyocyte differentiation, providing insights into how mutations in glypicans can cause congenital heart defects.
Cell-specific differences in activation of NF-kappa B regulatory elements of human immunodeficiency virus and beta interferon promoters by tumor necrosis factor

Three aspects of the involvement of tumor necrosis factor in human immunodeficiency virus (HIV) pathogenesis were examined. Tumor necrosis factor alpha (TNF-alpha) mRNA production was analyzed by polymerase chain reaction amplification in monocytic U937 cells and in a chronically HIV infected U937 cell line (U9-IIIB). TNF-alpha RNA was undetectable in U937 cells, whereas a low constitutive level was detected in U9-IIIB cells. Paramyxovirus infection induced a 5- to 10-fold increase in the steady-state level of TNF-alpha RNA in U9-IIIB cells compared with U937 cells, suggesting that HIV-infected monocytic cells produced higher levels of TNF-alpha than did normal cells after a secondary virus infection. The effects of TNF-alpha on gene expression were examined by transient expression assays using reporter chloramphenicol acetyltransferase plasmids linked to regulatory elements from the HIV long terminal repeat (LTR) and the beta interferon promoter. In U937 and Jurkat T lymphoid cells, the inducibility of the different hybrid promoters by TNF-alpha or phorbol ester varied in a cell type- and promoter context-specific manner; the levels of gene activity of NF-kappa B-containing plasmids correlated directly with induction of NF-kappa B DNA-binding activity. Although the intact beta interferon promoter was only weakly stimulated by phorbol ester or TNF-alpha, multimers of the PRDII NF-kappa B-binding domain were inducible by both agents. TNF-alpha was able to increase expression of the HIV LTR in T cells, but in monocytic cells, TNF-alpha did not induce the HIV LTR above a constitutive level of activity. This level of NF-kappa B-independent activity appears to be sufficient for virus multiplication, since TNF-alpha treatment had no effect on the kinetics of de novo HIV type 1 (HIV-1) infection and viral RNA production in U937 cells. However, in Jurkat cells, TNF-alpha dramatically enhanced the spread of HIV-1 through the cell population and increased viral RNA synthesis, indicating that in T cells HIV-1 multiplication was stimulated by TNF-alpha treatment.
In Vitro Antimicrobial and Anti-Tumor Activities of Intracellular and Extracellular extracts of Aspergillus niger and Aspergillus flavus var. columinaris

Fungi are known to produce a vast array of secondary metabolites that are gaining importance for their biotechnological applications. In the present study, the crude methanolic extracts of Aspergillus niger and Aspergillus flavus var. columinaris were tested by the disc diffusion method and minimal inhibitory concentration (MIC) determination for detection of antimicrobial activity against ten species of microorganisms: Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC 31488, Pseudomonas aeruginosa ATTC 27853, Shigella dysenteriae ATCC 13313, Proteus vulgaris ATCC 6380, Salmonella typhimurium (LIO, locally isolated organism), Bacillus cereus ATCC 11778, Enterococcus faecalis (LIO), Staphylococcus aureus ATCC 25923 and Candida albicans ATCC 10231 and by the sulforhodamine B (SRB) assay method to test their in vitro anti-tumor activity. The extracellular extracts of both fungi showed their activity against Gram-negative bacteria only. The antibacterial activity of extracellular extract of Aspergillus flavus var. columinaris was higher than that of extracellular extract of Aspergillus niger. Candida albicans was sensitive to the intracellular extract of Aspergillus flavus var. columinaris. The extracellular extracts of both isolated fungi were having more cytotoxic effect than their intracellular extracts. IC50 (concentration of extract required to reduce cell survival by 50%) of extracellular extract of Aspergillus niger was the most reducible one (0.905 μg/ml) followed by the extracellular extract of Aspergillus flavus var. columinaris (1.48 μg/ml). The IC50 of the intracellular extracts was approximately similar among two isolates (3.50 μg/ml for Aspergillus niger and 3.03 μg/ml for Aspergillus flavus var. columinaris). In conclusion, the extracellular extract of Aspergillus flavus var. columinaris possesses antibacterial activity against Gram-negative bacteria. While the extracellular extracts of Aspergillus niger and Aspergillus flavus var. columinaris have in vitro anti-tumor activity, which support their use in medicines. It is hoped that this study would lead to the establishment of some extracts that could be used to formulate new and more potent antimicrobial and anticancer drugs.
Associations between Polymorphisms in Glucuronidation and Sulfation Enzymes and Mammographic Breast Density in Premenopausal Women in the United States

Objective: Sex hormones are metabolized to less active compounds via (a) glucuronidation catalyzed by UDP-glucuronosyltransferases (UGT) and (b) sulfation catalyzed by sulfotransferases (SULT). Functional UGT and SULT polymorphisms can affect clearance of sex hormones, thereby influencing exposure in hormone-sensitive tissues, such as the breast. We assessed relationships between functional polymorphisms in the UGT and SULT genes and breast density in premenopausal women. Methods: One hundred seventy-five women ages 40 to 45 years, who had a screening mammogram taken within the previous year, provided a genomic DNA sample. Mammograms were digitized to obtain breast density measures. Using generalized linear regression, we assessed associations between percent breast density and polymorphisms in the UGT1A and UGT2B families, SULT1A1, and SULT1E1. Results: Women with the SULT1A1(H213/H213) genotype had 16% lower percent breast density compared with women with the SULT1A1(R213/R213) genotype after controlling for ethnicity (P = 0.001). Breast density was 5% lower among women carrying at least one copy of the UGT1A1(TA7)-UGT1A3(R11)-UGT1A3(A47) haplotype compared with the UGT1A1(TA6)-UGT1A3(W11R)-UGT1A3(V47A) haplotype (P = 0.07). No associations were observed between polymorphisms in the UGT2B family or SULT1E1 and breast density. Conclusion: Polymorphisms in SULT1A1 and the UGT1A locus may influence percent breast density in premenopausal women. Cancer Epidemiol Biomarkers Prev; 19(2); 537–46