Miracle-dz/UniFAR-FTUs huggingface dataset:
Trends in HIV prevalence and sexual behaviour among young people aged 15–24 years in countries most affected by HIV

Objectives In 2001 the United Nations (UN) Declaration of Commitment was signed by 189 countries with a goal to reduce HIV prevalence among young people by 25% by 2010. Progress towards this target is assessed. In addition, changes in reported sexual behaviour among young people aged 15–24 years are investigated. Methods Thirty countries most affected by HIV were invited to participate in the study. Trends in HIV prevalence among young antenatal clinic (ANC) attendees were analysed using data from sites that were consistently included in surveillance between 2000 and 2008. Regression analysis was used to determine if the UN target had been reached. Trends in prevalence data from repeat national population-based surveys were also analysed. Trends in sexual behaviour were analysed using data from repeat standardised national population-based surveys between 1990 and 2008. Results Seven countries showed a statistically significant decline of 25% or more in HIV prevalence among young ANC attendees by 2008, in rural or urban areas or in both: Botswana, Côte d'Ivoire, Ethiopia, Kenya, Malawi, Namibia and Zimbabwe. Three further countries showed a significant decline in HIV prevalence among young women (Zambia) or men (South Africa, Tanzania) in national surveys. Seven other countries are on track, whereas four are unlikely to reach the goal by 2010. Nine countries did not have adequate data to assess prevalence trends. Indications suggestive of changes towards less risky sexual behaviour were observed in the majority of countries. In eight countries with significant declines in HIV prevalence, significant changes were also observed in sexual behaviour in either men or women for at least two of the three sexual behaviour indicators. Conclusions Declines in HIV prevalence among young people were documented in the majority of countries with adequate data and in most cases were accompanied by changes in sexual behaviour. Further data, research and more rigorous analysis at country level are needed to understand the associations between programmatic efforts, reported behavioural changes and changes in prevalence and incidence of HIV.
A clinical decision rule for triage of children under 5 years of age with hydrocarbon (kerosene) aspiration in developing countries

Background. Unintended hydrocarbon ingestion is a common reason for pediatric hospitalization in the developing world. Objective. To derive a clinical decision rule, to identify patients likely to require a higher level facility (resource-requiring cases), that can be used at primary health care facilities with limited diagnostic and therapeutic resources. Methods. A prospective study of children 2 to 59 months old presenting to a poison treatment facility within 2 hours of oral hydrocarbon exposure. History and objective signs were recorded at admission and at 6, 12, 24 and, if present, 48 hours. Inclusion in the resource-requiring outcome group required: oxygen saturation <94%; any CNS depression; any treatment with (salbutamol); any care in the ICU; or death. Results. 256 met the inclusion criteria and completed the study. Of these, 170 had a course requiring resources unavailable at most primary health care facilities, and 86 did not. The presence of wheezing, any alteration in consciousness (lethargy or any restlessness), or a rapid respiratory rate for age (RR ≥50/min if age < 12mo, ≥ 40/min if age ≥ 12 mo) at presentation identified 167 of 170 of these patients (sensitivity 0.98). Thirty-six of 86 patients classified as non-resource requiring were correctly identified (specificity 0.42). No combination of clinical symptoms provided better discrimination while preserving sensitivity. Conclusions. This study suggests a triage decision rule based on the presence of wheezing, altered consciousness, or a rapid respiratory rate within 2 hours of hydrocarbon exposure. Such a rule requires validation in other settings.
SEVEN Families of Adolescents and Adults With Intellectual and Developmental Disabilities

This chapter focuses on past and present themes in research on families of adolescents and adults with intellectual and developmental disabilities (IDD), as well as suggested future directions. We focused on three types of family relationships: relationships between the parent and the adolescent/adult with IDD (including parental well-being), parents’ marital relationships, and sibling relationships (including sibling well-being). A common past theme for each of these types of relationships was a focus on between-group differences, which encompassed comparisons between disability and typically developing samples, as well as comparisons between disability groups. Present research themes included investigation of risk and protective factors, a widening of the outcomes that are investigated, and recognition of the interactive influences of multiple relationships. A number of suggestions for future research are described, including the need for more diverse samples, importance of longitudinal research, incorporating the perspectives of all members of the family, and developing effective family supports
Leptin-Dependent and Leptin-Independent Paracrine Effects of Perivascular Adipose Tissue on Neointima Formation

Objective—Clinical and experimental evidence suggests that periadventitial adipose tissue may modulate vascular lesion formation. The aim of this study was to determine the role of perivascular leptin expression on neointima formation and to differentiate it from local inflammation and systemically elevated leptin levels. Approach and Results—Increased neointima formation after carotid artery injury was observed in hyperleptinemic, diet–induced obese wild-type mice, but not in leptin-deficient ob/ob mice. High-fat diet was associated with increased leptin expression in visceral adipose tissue (VAT) as well as in perivascular adipose tissue. Perivascular leptin overexpression achieved by adenoviral vectors enhanced intimal cell proliferation and neointima formation in wild-type mice, but not in leptin receptor–deficient mice. Perivascular transplantation of VAT from high-fat diet–induced obese wild-type mice around the carotid artery of immunodeficient mice also promoted neointima formation, without affecting body weight or systemic leptin levels, and this effect was absent, if VAT from ob/ob mice was used. On the contrary, perivascular transplantation of VAT from ob/ob mice fed high-fat diet, characterized by marked immune cell accumulation, promoted neointimal hyperplasia also in the absence of leptin. In vitro, recombinant leptin and VAT-conditioned medium increased human arterial smooth muscle cell proliferation in a (partly) leptin-dependent manner. Conclusions—Our findings suggest that locally elevated leptin levels may promote neointima formation, independent of obesity and systemic hyperleptinemia, but also underline the importance of perivascular inflammation in mediating the increased cardiovascular risk in obesity.
Therapeutic Abortion: A Follow-up Study

A psychiatric and psychological follow-up assessment of 21 patients accepted for abortion on psychiatric grounds, 21 patients denied abortion on psychiatric grounds and 11 patients accepted for abortion on medical grounds was carried out. A history of prior psychiatric illness appeared to be a pointer towards therapeutic termination of pregnancy when psychiatrically disturbed pregnant women were referred for assessment. Despite a high incidence of short-lived guilt reactions, this particular group of patients generally reported a beneficial effect on their lives 2 years later. Many, but not all, of the psychiatrically disturbed patients who were refused abortion became reconciled to the decision. The medical group who were aborted tended to view the operation as an unfortunate necessity. A decision for or against termination of pregnancy must take account of many factors—previous psychiatric history, present mental state, patient's attitude towards the pregnancy, marital adjustment, personality structure and medical condition
Introduction of oncogenes into mammary glands in vivo with an avian retroviral vector initiates and promotes carcinogenesis in mouse models

We have adapted the avian leukosis virus RCAS (replication-competent avian sarcoma-leukosis virus LTR splice acceptor)-mediated somatic gene transfer technique to introduce oncogenes into mammary cells in mice transgenic for the avian subgroup A receptor gene, tva, under control of the mouse mammary tumor virus (MMTV) promoter. Intraductal instillation of an RCAS vector carrying the polyoma middle T antigen (PyMT) gene (RCAS-PyMT) induced multiple, oligoclonal tumors within 3 weeks in infected mammary glands of MMTV-tva transgenic mice. The rapid appearance of these tumors from a relatively small pool of infected cells (estimated to be ≈2 × 103 cells per gland by infection with RCAS carrying a GFP gene; RCAS-GFP) was accompanied by a high fraction of cells positive for Ki67, Cyclin D1, and c-Myc, implying strong proliferation competence. Furthermore, the tumors displayed greater cellular heterogeneity than did tumors arising in MMTV-PyMT mice, suggesting that RCAS-PyMT transforms a relatively immature cell type. Infection of mice transgenic for both MMTV-Wnt-1 and MMTV-tva with RCAS virus carrying an activated Neu oncogene dramatically enhanced tumor formation over what is observed in uninfected bitransgenic animals. We conclude that infection of mammary glands with retrovirus vectors is an efficient means to screen candidate oncogenes for their capacity to initiate or promote mammary carcinogenesis in the mouse.
Ethylene signaling in Arabidopsis involves feedback regulation via the elaborate control of EBF2 expression by EIN3.

SUMMARY EIN3 is a key transcription factor in the signaling pathway of the plant hormone ethylene in Arabidopsis. Ethylene signaling suppresses the 26S proteasome-mediated proteolysis of EIN3, the accumulation of which induces ethylene-responsive gene expression. The proteolysis of EIN3 has been suggested to be mediated by the E3 ubiquitin ligase SCF(EBF1/2) that contains either of the two closely related F-box proteins, EBF1 or EBF2. Here, we demonstrate feedback regulation of ethylene signaling that results from the direct upregulation of the EBF2 gene by EIN3. Although EBF1 and EBF2 show comparable activities as repressors of EIN3-dependent transcription, our analysis of transgenic Arabidopsis plants has revealed that the EBF2 promoter, but not the EBF1 promoter, is activated by ethylene. Furthermore, the results of protoplast transient assays in vivo and electrophoretic mobility shift assays in vitro have revealed that EIN3 can bind and activate the EBF2 promoter, indicating that EIN3 modulates EBF2 gene expression in planta. An ebf2 mutant transformed with the EBF2 gene under the control of a mutant promoter in which the EIN3-binding site was disrupted still showed an ethylene hyper-responsive phenotype, indicating the physiological relevance of EIN3-mediated activation of the EBF2 gene in the downregulation of ethylene signaling. We show an additional finding that a sequence downstream of the EBF2 coding region is also involved in modulations of both the EBF2 expression level and sensitivity to ethylene. These results thus indicate that the fine-tuning of ethylene signaling involves the intricate regulation of EBF2 expression in Arabidopsis.
Bistability in myo-Inositol Utilization by Salmonella enterica Serovar Typhimurium

ABSTRACT The capability of Salmonella enterica serovar Typhimurium strain 14028 (S. Typhimurium 14028) to utilize myo-inositol (MI) is determined by the genomic island GEI4417/4436 carrying the iol genes that encode enzymes, transporters, and a repressor responsible for the MI catabolic pathway. In contrast to all bacteria investigated thus far, S. Typhimurium 14028 growing on MI as the sole carbon source is characterized by a remarkable long lag phase of 40 to 60 h. We report here that on solid medium with MI as the sole carbon source, this human pathogen exhibits a bistable phenotype characterized by a dissection into large colonies and a slow-growing bacterial background. This heterogeneity is reversible and therefore not caused by mutation, and it is not observed in the absence of the iol gene repressor IolR nor in the presence of at least 0.55% CO2. Bistability is correlated with the activity of the iolE promoter (PiolE), but not of PiolC or PiolD, as shown by promoter-gfp fusions. On the single-cell level, fluorescence microscopy and flow cytometry analysis revealed a gradual switch of PiolE from the “off” to the “on” status during the late lag phase and the transition to the log phase. Deletion of iolR or the addition of 0.1% NaHCO3 induced an early growth start of S. Typhimurium 14028 in minimal medium with MI. The addition of ethoxyzolamide, an inhibitor of carboanhydrases, elongated the lag phase in the presence of bicarbonate. The positive-feedback loop via repressor release and positive induction by bicarbonate-CO2 might allow S. Typhimurium 14028 to adapt to rapidly changing environments. The phenomenon described here is a novel example of bistability in substrate degradation, and, to our knowledge, is the first demonstration of gene regulation by bicarbonate-CO2 in Salmonella.
Metabolic Factors and Chronic Hepatitis C: A Complex Interplay

In the last years, several lines of evidence showed how metabolic factors may influence the natural history of patients with chronic hepatitis C. Chronic HCV infection is able to perturb the metabolic homeostasis of the host, in a context of complex interactions where pre-existent metabolic status and genetic background play an important role, allowing us to state that HCV infection is a systemic disease. In this review, we discuss the most recent lines of evidence on the main metabolic factors that are known to be associated with CHC, namely, insulin resistance/type 2 diabetes, steatosis, visceral obesity, atherosclerosis, vitamin D, menopause, fructose and coffee intake, lipoproteins, methylenetetrahydrofolate reductase status, and hyperuricaemia. In particular, we focus on the pathophysiological mechanisms underlying the correlation between HCV infection and metabolic disorders, the impact of metabolic factors on the progression of liver and non-liver-related diseases, and, on the contrary, the possible influence of chronic HCV infection on metabolic features. In this setting, the importance of a multifaceted evaluation of CHC patients and a prompt correction of modifiable metabolic risk factors should be emphasized.
Spectrum hierarchies and subdiagonal functions

The spectrum of a first-order sentence is the set of cardinalities of its finite models. Relatively little is known about the subclasses of spectra that are obtained by looking only at sentences with a specific signature. In this paper, we study natural subclasses of spectra and their closure properties under simple subdiagonal functions. We show that many natural closure properties turn out to be equivalent to the collapse of potential spectrum hierarchies. We prove all of our results using explicit transformations on first-order structures.
Uncoupling skeletal and connective tissue patterning: conditional deletion in cartilage progenitors reveals cell-autonomous requirements for Lmx1b in dorsal-ventral limb patterning

Integration of muscle, connective tissue and skeletal patterning during development is essential for proper functioning of the musculoskeletal system. How this integration is achieved is poorly understood. There is ample evidence suggesting that skeletal pattern is programmed autonomously, whereas muscle pattern is, for the most part, programmed non-cell-autonomously. Connective tissues depend upon both muscle and skeletal tissues for their proper survival and development. Here, we employed a novel approach to dissect the coordination of musculoskeletal patterning during mouse limb development. Using both conditional gain- and loss-of-function approaches, we selectively deleted or activated the LIM-homeodomain transcription factor Lmx1b in skeletal progenitors using a Sox9-Cre knock-in allele. As Lmx1b is both necessary and sufficient to specify dorsal pattern, this approach allowed us to investigate the effect of selectively deleting or activating Lmx1b in skeletal progenitors on muscle, connective and skeletal tissues during limb development. Our results indicate that whereas Lmx1b activity is required autonomously in skeletal progenitors to direct dorsal pattern, loss or gain of Lmx1b activity in skeletal progenitors has no effect on muscle or connective tissue patterning. Hence, we show for the first time that skeletal and connective tissue patterning can be uncoupled, indicating a degree of autonomy in the formation of the musculoskeletal system.
Robust prediction of consensus secondary structures using averaged base pairing probability matrices

MOTIVATION Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. RESULTS We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. AVAILABILITY The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna. org/papers/McCaskillMEA/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Cerebrovascular and cardiovascular measurements during neurally mediated syncope induced by head-up tilt.

BACKGROUND AND PURPOSE This study examines changes in systemic hemodynamics and in cerebral blood velocity that occur during neurally mediated syncope (NMS) to determine whether cerebral autoregulation is intact or impaired in patients with recurrent NMS. METHODS Beat-to-beat recordings of heart rate, blood pressure (volume clamp photoplethysmography), stroke volume (impedance cardiography), and right middle cerebral artery blood velocity (transcranial Doppler sonography) were performed at rest and during 80 degrees head-up tilt. Twelve patients with NMS and 10 healthy control subjects were studied. RESULTS Baseline values and the initial response to head-up tilt of control subjects and patients with NMS were similar. The mean latency to onset of syncope was 11.8 +/- 11.1 minutes. At syncope, heart rate, systolic and diastolic blood pressure, and diastolic cerebral blood velocity decreased significantly, whereas systolic cerebral blood velocity did not change. Calculated cerebrovascular resistance was significantly reduced from 1.85 +/- 0.60 to 1.32 +/- 0.27 mm Hg/cm per second, whereas the pulsatility index increased from 0.92 +/- 0.16 to 1.52 +/- 0.21. We never observed a change in cerebral blood velocity before the rapid decline in blood pressure, nor did we observe any significant change in respiratory pattern. CONCLUSIONS The decrease in cerebrovascular resistance during NMS indicates that the integrity of cerebrovascular autoregulation is maintained even when syncope is imminent. The selective loss of diastolic flow during syncope and the increase in pulsatility index are likely caused by collapse of downstream vessels as diastolic blood pressure decreases below the critical closing pressure of cerebral vessels.
Antimicrobial suture wound closure for cerebrospinal fluid shunt surgery: a prospective, double-blinded, randomized controlled trial.

OBJECT Implantation of cerebrospinal fluid (CSF) shunting devices is associated with a 5-15% risk of infection as cited in contemporary pediatric neurosurgical literature. Shunt infections typically require complete removal of the device and prolonged antibiotic treatment followed by shunt replacement. Moreover, shunt infections are commonly associated with prolonged hospital stays, potential comorbidity, and the increased risk of neurological compromise due to ventriculitis or surgical complications. The authors prospectively evaluated the incidence of CSF shunt infection following shunt procedures performed using either antimicrobial suture (AMS) or conventional suture. METHODS In a single-center, prospective, double-blinded, randomized controlled trial, the authors enrolled 61 patients, among whom 84 CSF shunt procedures were performed over 21 months. Randomization to the study (AMS) or control (placebo) group was stratified to minimize the effect of known shunt infection risk factors on the findings. Antibacterial shunt components were not used. The primary outcome measure was the incidence of shunt infection within 6 months of surgery. RESULTS The shunt infection rate in the study group was 2 (4.3%) of 46 procedures and 8 (21%) of 38 procedures in the control group (p = 0.038). There were no statistically significant differences in shunt infection risk factors between the groups (procedure type and time, age < 6 months, weight < 4 kg, recent history of shunt infection). No suture-related adverse events were reported in either group. CONCLUSIONS These results support the suggestion that the use of AMS for CSF shunt surgery wound closure is safe, effective, and may be associated with a reduced risk of postoperative shunt infection. A larger randomized controlled trial is needed to confirm this association.