Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of infective endocarditis in patients with Staphylococcus aureus bacteraemia: the value of screening with echocardiography.

AIMS Staphylococcus aureus infective endocarditis (IE) is a critical medical condition associated with a high morbidity and mortality. In the present study, we prospectively evaluated the importance of screening with echocardiography in an unselected S. aureus bacteraemia (SAB) population. METHODS AND RESULTS From 1 January 2009 to 31 August 2010, a total of 244 patients with SAB at six Danish hospitals underwent screening echocardiography. The inclusion rate was 73% of all eligible patients (n= 336), and 53 of the 244 included patients (22%; 95% CI: 17-27%) were diagnosed with definite IE. In patients with native heart valves the prevalence was 19% (95% CI: 14-25%) compared with 38% (95% CI: 20-55%) in patients with prosthetic heart valves and/or cardiac rhythm management devices (P= 0.02). No difference was found between Main Regional Hospitals and Tertiary Cardiac Hospitals, 20 vs. 23%, respectively (NS). The prevalence of IE in high-risk patients with one or more predisposing condition or clinical evidence of IE were significantly higher compared with low-risk patients with no additional risk factors (38 vs. 5%; P < 0.001). IE was associated with a higher 6 months mortality, 14(26%) vs. 28(15%) in SAB patients without IE, respectively (P < 0.05). CONCLUSION SAB patients carry a high risk for development of IE, which is associated with a worse prognosis compared with uncomplicated SAB. The presenting symptoms and clinical findings associated with IE are often non-specific and echocardiography should always be considered as part of the initial evaluation of SAB patients.
Fungal peritonitis in children receiving peritoneal dialysis: a report of the NAPRTCS.

BACKGROUND The rarity of fungal peritonitis (FP) in children receiving chronic peritoneal dialysis (PD) has limited the amount of information available regarding the risk factors and management associated with this infection. METHODS We reviewed all cases of FP occurring in patients entered into the dialysis registry of the NAPRTCS between January 1992 and May 1996 in an attempt to identify risk factors for infection, treatment strategies, and patient outcome data. A total of 1592 patients who were less than 21 years of age were enrolled in the dialysis registry and received maintenance PD during the period of observation. RESULTS Of the total 1729 episodes of peritonitis in these patients occurring over 1732 patient-years of follow-up, FP accounted for 51 (2.9%) of the episodes. The patients on PD who developed FP were similar to those who did not develop FP with regard to race, gender, dialysis modality, and dialysis access characteristics. The overall peritonitis rate in patients who developed FP was 2.2 episodes per patient-year compared with 0.96 episodes per patient-year in the patients who did not develop this infection (P < 0.0001). In 25 (49%) cases, the FP was the patient's initial episode of peritonitis. Whereas recent antibiotic usage was present in 23 (56%) of 41 patients with FP, there was no statistically significant relationship (P = 0.26) noted between the presence of a gastrostomy and the development of FP. Candida species caused 33 of 42 (78.6%) FP episodes. Therapy consisted of PD catheter removal and Amphotericin B in the majority of patients. Six months after diagnosis, 27 patients remained on PD, twelve patients were receiving hemodialysis, and only three patients had died, in each case for reasons unrelated to their FP episode. CONCLUSION FP is an infrequent cause of peritonitis in children receiving chronic PD. The presence of a gastrostomy does not appear to predispose patients to the development of this infection, and successful therapy most often consists of a combination of antifungal medication and dialysis catheter removal. The outcome of FP in children appears to be more favorable than in the adult dialysis population.
Genomic insights on the structure , function and disease associations of lncRNAs 127

Most of the mammalian genome including a large fraction of the non-protein coding transcripts has been shown to be transcribed. Studies related to these non-coding RNA molecules have predominantly focused on smaller molecules like microRNAs. In contrast, long non-coding RNAs (lncRNAs) have long been considered to be transcriptional noise. Accumulating evidence suggests that lncRNAs are involved in key cellular and developmental processes. Several critical questions regarding functions and properties of lncRNAs and their circular forms remain to be answered. Increasing evidence from high-throughput sequencing screens also suggests the involvement of lncRNAs in diseases such as cancer, although the underlying mechanisms still need to be elucidated. Here, we discuss the current state of research in the field of lncRNAs, questions that need to be addressed in light of recent genome-wide studies documenting the landscape of lncRNAs, their functional roles and involvement in diseases. We posit that with the availability of high-throughput data sets it is not only possible to improve methods for predicting lncRNAs but will also facilitate our ability to elucidate their functions and phenotypes by using integrative approaches.
Bluetooth piconets coexistence: analytical investigation on the optimal operating conditions

The increasing demand for low cost and efficient short range radio communication tools led to the development of the Bluetooth technology, which is aimed at replacing the wires used to connect electronic devices. It is foreseen that, in the next future, Bluetooth based services will be provided in highly populated environments, such as airports and convention centers. The expected explosive penetration in the mass market of BT equipped devices operating in an uncoordinated way makes the issue of mutual interference a key aspect to be investigated in order to assess the real performance of this emerging technology. In this paper herein, we address the coexistence issue by analytically deriving a lower bound on the aggregated throughput offered by BT based WPANs (wireless personal are networks) deployed in the same region and by evaluating the optimum operating conditions.
Modulated repetition time look‐locker (MORTLL): A method for rapid high resolution three‐dimensional T1 mapping

To demonstrate a modification of the Look‐Locker (LL) technique that enables rapid high resolution T1 mapping over the physiologic range of intracranial T1 values, ranging from white matter to cerebrospinal fluid (CSF). This is achieved by use of a three‐dimensional (3D) balanced steady‐state free precession (b‐SSFP) acquisition (for high signal‐to‐noise and resolution) along with variable repetition time to allow effective full recovery of longitudinal magnetization.
A Normative Data Set for the Clinical Assessment of Achromatic and Chromatic Contrast Sensitivity Using a qCSF Approach.

Purpose The measurement of achromatic sensitivity has been an important tool for monitoring subtle changes in vision as the result of disease or response to therapy. In this study, we aimed to provide a normative data set for achromatic and chromatic contrast sensitivity functions within a common cone contrast space using an abbreviated measurement approach suitable for clinical practice. In addition, we aimed to provide comparisons of achromatic and chromatic binocular summation across spatial frequency. Methods We estimated monocular cone contrast sensitivity functions (CCSFs) using a quick Contrast Sensitivity Function (qCSF) approach for achromatic as well as isoluminant, L/M cone opponent, and S cone opponent stimuli in a healthy population of 51 subjects. We determined the binocular CCSFs for achromatic and chromatic vision to evaluate the degree of binocular summation across spatial frequency for these three different mechanisms in a subset of 20 subjects. Results Each data set shows consistent contrast sensitivity across the population. They highlight the extremely high cone contrast sensitivity of L/M cone opponency compared with the S-cone and achromatic responses. We also find that the two chromatic sensitivities are correlated across the healthy population. In addition, binocular summation for all mechanisms depends strongly on stimulus spatial frequency. Conclusions This study, using an approach well suited to the clinic, is the first to provide a comparative normative data set for the chromatic and achromatic contrast sensitivity functions, yielding quantitative comparisons of achromatic, L/M cone opponent, and S cone opponent chromatic sensitivities as a function of spatial frequency.
Assessing the STIRR model of best practices for blood-borne infections of clients with severe mental illness.

OBJECTIVES People with co-occurring severe mental illness and a substance use disorder are at markedly elevated risk of infection from HIV, hepatitis B virus (HBV), and hepatitis C virus (HCV), but they generally do not receive basic recommended screening or preventive and treatment services. Barriers to services include lack of programs offered by mental health providers and client refusal of available services. Clients from racial-ethnic minority groups are even less likely to accept recommended services. The intervention tested was designed to facilitate integrated infectious disease programming in mental health settings and to increase acceptance of such services among clients. METHODS A randomized controlled trial (N=236) compared enhanced treatment as usual (control) with a brief intervention to deliver best-practice services for blood-borne diseases in an urban sample of clients with co-occurring disorders who were largely from racial-ethnic minority groups. The "STIRR" intervention included Screening for HIV and HCV risk factors, Testing for HIV and hepatitis, Immunization against hepatitis A and B, Risk reduction counseling, and medical treatment Referral and support at the site of mental health care. RESULTS Clients randomly assigned to the STIRR intervention had high levels (over 80%) of participation and acceptance of core services. They were more likely to be tested for HBV and HCV, to be immunized against hepatitis A virus and HBV, and to increase their knowledge about hepatitis and reduce their substance abuse. However, they showed no reduction in risk behavior, were no more likely to be referred to care, and showed no increase in HIV knowledge. Intervention costs were $541 per client (including $234 for blood tests). CONCLUSIONS STIRR appears to be efficacious in providing a basic, best-practice package of interventions for clients with co-occurring disorders.
Linking Visual Attention and Number Processing in the Brain: The Role of the Temporo-parietal Junction in Small and Large Symbolic and Nonsymbolic Number Comparison

There exists a long-standing debate regarding whether small and large numerosities engage different networks of processing. The ability to rapidly enumerate small (14) numerosities is referred to as subitizing and is thought to be qualitatively different from large numerosity processing. Functional neuro-imaging studies have attempted to dissociate neural correlates of small and large number processing by contrasting subitizing with counting of numerosities just outside the subitizing range. In the present study, we used functional magnetic resonance imaging (fMRI) to contrast the processing of numerosities in the subitizing range with numerosities requiring estimation. Participants compared sequentially presented slides of either dots or Arabic numerals for their relative magnitude. We show that comparison of nonsymbolic numerosities in the subitizing range led to activation of the right temporo-parietal junction, while at the same time this region was found to be suppressed during large numerosity processing. Furthermore, relative suppression of this region was strongly associated with faster response times. In previous studies, this region has been implicated in stimulus-driven attention.We therefore contend that activation of the temporo-parietal junction during small number processing and the suppression thereof during large numerosity comparisons reflects differential reliance on stimulus-driven versus goal-directed attentional networks in the brain.
CD133 expression and α-fetoprotein levels define novel prognostic subtypes of HBV-associated hepatocellular carcinoma: A long-term follow-up analysis

Hepatocellular carcinoma (HCC) is a highly heterogeneous type of tumor, which may be caused by the stem/progenitor cell features of particular HCC cells. Recent studies have subclassified HCC into different prognostic subtypes according to just one stemness-associated marker. However, one stemness-associated marker is not sufficient to clearly define cancer stem cells, or to decipher the heterogeneous nature of HCC. For a more precise subtype classification for prognostic application, a combination of multiple stemness-associated markers is required. Cluster of differentiation 133 (CD133) and α-fetoprotein (AFP) are common stemness-associated markers for HCC that have not yet been employed for HCC subtype classification. In the present study, CD133 expression was assessed by immunohistochemistry in 127 hepatitis B virus-associated HCC tumor specimens. Based on CD133 immunostaining and serum AFP levels, the HCC cases were subclassified into four subtypes, which demonstrated different clinicopathological features and varying prognoses. Among the four subtypes, the number of tumor lesions, histological grade and vascular invasion were significantly different (P=0.002, P=0.018 and P=0.022, respectively). CD133+AFP+ HCC was associated with a relatively poor prognosis, CD133−AFP− HCC was associated with a relatively good prognosis, while CD133+AFP− HCC and CD133−AFP+ HCC were associated with an intermediate prognosis. These prognostic values were confirmed by borderline or statistical significance (between all groups, overall survival, P=0.061; recurrence-free survival, P=0.015). These results define a novel and simple system, based on CD133 and AFP, for classifying HCC into four distinct prognostic subtypes. This classification system may aid the assessment of patients with HCC for personalized therapy.
The reminiscence circumplex and autobiographical memory functions.

This study investigated the potential of a circumplex model to represent the functions of both reminiscence and autobiographical memory. Participants from four pre-existing data bases (i.e., Culley, LaVoie, & Gfeller, 2001; Webster, 1997, 2002; Webster & McCall, 1999) were combined, resulting in a total of 985 participants ranging in age from 17 to 96 (M age = 36.63 years). A total of 392 men (39.8%) and 591 women (60.1%), with two persons not reporting their gender, completed the Reminiscence Functions Scale (RFS) as part of the original four studies. The eight RFS factors were submitted to second-order factor analysis resulting in two orthogonal dimensions (self versus social and reactive/loss-oriented versus proactive/growth-oriented) accounting for 79.57% of the variance. Further, multidimensional scaling indicated that the original eight factors could be arranged in a circular fashion such that more closely related (i.e., more highly correlated) factors were placed closer together while factors less highly related were placed further apart. Advantages of a circumplex perspective for future theory and model development are illustrated.
Developmental Control of Stress Stimulons inStreptomyces coelicolor Revealed by Statistical Analyses of Global Gene Expression Patterns

ABSTRACT Stress-induced regulatory networks coordinated with a procaryotic developmental program were revealed by two-dimensional gel analyses of global gene expression. Four developmental stages were identified by their distinctive protein synthesis patterns using principal component analysis. Statistical analyses focused on five stress stimulons (induced by heat, cold, salt, ethanol, or antibiotic shock) and their synthesis during development. Unlike other bacteria, for which various stresses induce expression of similar sets of protein spots, inStreptomyces coelicolor heat, salt, and ethanol stimulons were composed of independent sets of proteins. This suggested independent control by different physiological stress signals and their corresponding regulatory systems. These stress proteins were also under developmental control. Cluster analysis of stress protein synthesis profiles identified 10 different developmental patterns or “synexpression groups. ” Proteins induced by cold, heat, or salt shock were enriched in three developmental synexpression groups. In addition, certain proteins belonging to the heat and salt shock stimulons were coregulated during development. Thus, stress regulatory systems controlling these stimulons were implicated as integral parts of the developmental program. This correlation suggested that thermal shock and salt shock stress response regulatory systems either allow the cell to adapt to stresses associated with development or directly control the developmental program.
Removal of AMPA Receptors (AMPARs) from Synapses Is Preceded by Transient Endocytosis of Extrasynaptic AMPARs

AMPA receptors (AMPARs) are dynamically regulated at synapses, but the time course and location of their exocytosis and endocytosis are not known. Therefore, we have used ecliptic pHluorin-tagged glutamate receptor 2 to visualize changes in AMPAR surface expression in real time. We show that synaptic and extrasynaptic AMPARs respond very differently to NMDA receptor activation; there is a rapid internalization of extrasynaptic AMPARs that precedes the delayed removal of synaptic AMPARs.
A comparison of measured HONO uptake and release with calculated source strengths in a heterogeneous forest environment

Abstract. Vertical mixing ratio profiles of nitrous acid (HONO) were measured in a clearing and on the forest floor in a rural forest environment. For the forest floor, HONO was found to predominantly deposit, whereas for the clearing, net deposition dominated only during nighttime and net emissions were observed during daytime. For selected days, net fluxes of HONO were calculated from the measured profiles using the aerodynamic gradient method. The emission fluxes were in the range of 0.02 to 0.07 nmol m−2 s−1 and thus were in the lower range of previous observations. These fluxes were compared to the strengths of postulated HONO sources. Laboratory measurements of different soil samples from both sites revealed an upper limit for soil biogenic HONO emission fluxes of 0.025 nmol m−2 s−1. HONO formation by light-induced NO2 conversion was calculated to be below 0.03 nmol m−2 s−1 for the investigated days, which is comparable to the potential soil fluxes. Due to light saturation at low irradiance, this reaction pathway was largely found to be independent of light intensity, i.e. it was only dependent on ambient NO2. We used three different approaches based on measured leaf nitrate loadings for calculating HONO formation from HNO3 photolysis. While the first two approaches based on empirical HONO formation rates yielded values in the same order of magnitude as the estimated fluxes, the third approach based on available kinetic data of the postulated pathway failed to produce noticeable amounts of HONO. Estimates based on reported cross sections of adsorbed HNO3 indicate that the lifetime of adsorbed HNO3 was only about 15 min, which would imply a substantial renoxification. Although the photolysis of HNO3 was significantly enhanced at the surface, the subsequent light-induced conversion of the photolysis product NO2 did not produce considerable amounts of HONO. Consequently, this reaction might occur via an alternative mechanism. By explicitly calculating HONO formation based on available kinetic data and simple parameterizations, we showed that (a) for low NOx the light-induced conversion of NO2 on humic acids is already light saturated by the early morning, (b) HONO formation from photolysis of adsorbed HNO3 appears to proceed via an alternative mechanism and (c) estimates of HONO emissions from soil are very sensitive to mass transfer and acidic soils do not necessarily favour HONO emissions.
HLA Class I-Restricted T-Cell Responses May Contribute to the Control of Human Immunodeficiency Virus Infection, but Such Responses Are Not Always Necessary for Long-Term Virus Control

ABSTRACT A rare subset of human immunodeficiency virus (HIV)-infected individuals maintains undetectable HIV RNA levels without therapy (“elite controllers”). To clarify the role of T-cell responses in mediating virus control, we compared HLA class I polymorphisms and HIV-specific T-cell responses among a large cohort of elite controllers (HIV-RNA < 75 copies/ml), “viremic” controllers (low-level viremia without therapy), “noncontrollers” (high-level viremia), and “antiretroviral therapy suppressed” individuals (undetectable HIV-RNA levels on antiretroviral therapy). The proportion of CD4+ and CD8+ T cells that produce gamma interferon (IFN-γ) and interleukin-2 (IL-2) in response to Gag and Pol peptides was highest in the elite and viremic controllers (P < 0.0001). Forty percent of the elite controllers were HLA-B*57 compared to twenty-three percent of viremic controllers and nine percent of noncontrollers (P < 0.001). Other HLA class I alleles more common in elite controllers included HLA-B*13, HLA-B*58, and HLA-B*81 (P < 0.05 for each). Within elite and viremic controller groups, those with protective class I alleles had higher frequencies of Gag-specific CD8+ T cells than those without these alleles (P = 0.01). Noncontrollers, with or without protective alleles, had low-level CD8+ responses. Thus, certain HLA class I alleles are enriched in HIV controllers and are associated with strong Gag-specific CD8+IFN-γ+IL-2+ T cells. However, the absence of evidence of T cell-mediated control in many controllers suggests the presence of alternative mechanisms for viral control in these individuals. Defining mechanisms for virus control in “non-T-cell controllers” might lead to insights into preventing HIV transmission or preventing virus replication.