Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual-tropic HIV type 1 isolates vary dramatically in their utilization of CCR5 and CXCR4 coreceptors

Objective(s):Dual HIV-1 utilizes cellular CCR5 and CXCR4 coreceptors to enter host cells. Recent studies indicate that the ability of these viruses to use both coreceptors varies significantly in cell lines expressing CXCR4 or CCR5; however, it is not clear whether differences in coreceptor mediated infection in vitro reflect infection of primary cells in vivo. Methods:We evaluated coreceptor usage of dual envelope clones from patient viruses using a single-cycle pseudovirus assay conducted in cell lines and a replication-competent assay performed using peripheral blood mononuclear cells. Dual envelope clones were selected and classified into three groups, R5>X4, R5≈X4, and X4>R5, based on their ability to mediate entry by using CXCR4 and CCR5 in a pseudovirus assay. Results:We observed a high degree of concordance between measurements of coreceptor-mediated entry in pseudovirus and peripheral blood mononuclear cell assays. R5>X4 viruses were efficiently inhibited by a CCR5 antagonist, but not a CXCR4 antagonist, whereas X4>R5 viruses were efficiently inhibited by a CXCR4 antagonist, but not a CCR5 antagonist. R5≈X4 viruses were not inhibited, or only partially inhibited, by either a CCR5 or a CXCR4 antagonist alone. Conclusions:These observations indicate that measurements of coreceptor use determined using pseudoviruses and coreceptor-expressing cell lines are generally concordant with the results obtained using replication-competent assays and peripheral blood mononuclear cell. This suggests that a considerable fraction of dual viruses preferentially infect either CCR5 or CXCR4 target cells in vivo. The clinical implications of preferential coreceptor utilization by dual viruses, that is, HIV-1 pathogenesis and response to coreceptor antagonists, require additional studies.
Export and Innovation Activities in the German Service Sector: Empirical Evidence at the Firm Level

In this paper we analyse the relationship between export and innovation activities of German service sector companies using data from the 1997 wave of the Mannheim Innovation Panel in the Service Sector. There is a lot of support for the Schumpeterian hypothesis of export activities being mainly driven by innovation activities. Factor endowment theories are only partially supported. While human capital significantly improves export performance, labour costs hamper it only in selected branches. Moreover, allowing for simultaneity we find that export activities do not enforce innovation activities.
The Psychophysics of Retrospective and Prospective Timing

In two experiments, different groups of subjects heard four musical selections and then estimated the duration of each selection. Some groups made retrospective time estimates while others made prospective estimates. In both experiments, analyses of the psychophysical relation between perceived and actual duration showed that the slopes of straight-line fits were flatter and accounted for a smaller proportion of the variance under retrospective as compared with prospective conditions. In addition, in experiment 1, retrospective subjects were less accurate in rank ordering the selections from longest to shortest. There was also a serial-order effect, with selections estimated longer when they occurred early in the sequence. In experiment 2 the slopes decreased as the selections in a series became longer. Both retrospective and prospective estimates also exhibited a context effect, in that estimates of a given selection were influenced by the relative durations of the other three selections in the series. The results on inaccurate retrospective judgments raise questions about prior research on stimulus factors and retrospective timing. However, similarities under retrospective and prospective conditions suggest that timing under these conditions, although different in some respects, reflects a similar process.
QFT based robust controller design for fourth-order boost dc-dc switching power converter

In this paper, a systematic procedure is proposed for robust digital controller design for higher order switching power converters using Quantitative Feedback Theory. A robust voltage mode controller is then directly designed in discrete-time domain for a fourth-order boost dc-dc switching power converter operating in continuous conduction mode. A simplified flowchart that describes the detailed design procedure is developed and based on that controller is designed to ensure stability, robustness, command tracking and disturbance rejection features that are desirable from power supplies. The performance of the designed controller is analyzed through computer simulations and then verified experimentally on a 28 V, 30 W laboratory prototype converter. Simulation and experimental results are in correlation and show that the controller is able to stabilize the system for the predefined range of perturbations in load and source voltage while satisfying all the constraints placed during controller design.
Risk factors and outcome in ambulatory assault victims presenting to the acute emergency department setting: Implications for secondary prevention studies in PTSD

Prevention of post‐traumatic stress disorder (PTSD) in trauma victims is an important public health goal. Planning for the studies required to validate prevention strategies requires identification of subjects at high risk and recruitment of unbiased samples that represent the larger high‐risk population (difficult because of the avoidance of many trauma victims). This study recruited high‐risk victims of interpersonal violence (sexual or physical assault) presenting to an urban emergency department for prospective 1‐ and 3‐month follow‐up. Of 546 victims who were approached about participating, only 56 agreed to be contacted and only 46 participated in either the 1‐ or 3‐month interviews. Of the 46, 43 had been previously victimized with a mean of over six traumas in the group; 21% had prior PTSD, 85% had prior psychiatric illness, and 37% had prior substance abuse. Sixty‐seven percent had positive urine for alcohol or drugs on presentation. Fifty‐six percent developed PTSD at 1 or 3 months with the rate declining between 1 and 3 months. There was high use of medical and psychiatric services. These findings document both the difficulty of recruiting large samples of high‐risk assault victims to participate in research, and the high rate of prior traumatization, PTSD, substance use, and psychiatric morbidity in these subjects which, if still active at the time of victimization, may complicate efforts to document preventive treatment effects. Depression and Anxiety 19:77–84, 2004. © 2004 Wiley‐Liss, Inc.
Nef Can Enhance the Infectivity of Receptor-Pseudotyped Human Immunodeficiency Virus Type 1 Particles

ABSTRACT Nef is an accessory protein of human immunodeficiency virus type 1 (HIV-1) that enhances the infectivity of progeny virions when expressed in virus-producing cells. The requirement for Nef for optimal infectivity is, at least in part, determined by the envelope (Env) glycoprotein, because it can be eliminated by pseudotyping HIV-1 particles with pH-dependent Env proteins. To investigate the role of Env in the function of Nef, we have examined the effect of Nef on the infectivity of Env-deficient HIV-1 particles pseudotyped with viral receptors for cells expressing cognate Env proteins. We found that Nef significantly enhances the infectivity of CD4-chemokine receptor pseudotypes for cells expressing HIV-1 Env. Nef also increased the infectivity of HIV-1 particles pseudotyped with Tva, the receptor for subgroup A Rous sarcoma virus (RSV-A), even though Nef had no effect if the pH-dependent Env protein of RSV-A was used for pseudotyping. However, Nef does not always enhance viral infectivity if the normal orientation of the Env-receptor interaction is reversed, because the entry of Env-deficient HIV-1 into cells expressing the vesicular stomatitis virus G protein was unaffected by Nef. Together, our results demonstrate that the presence of a viral Env protein during virus production is not required for the ability of Nef to increase viral infectivity. Furthermore, since the infectivity of Tva pseudotypes was blocked by inhibitors of endosomal acidification, we conclude that low-pH-dependent entry does not always bypass the requirement for Nef.
Antiphospholipid syndrome in Latin American patients: clinical and immunologic characteristics and comparison with European patients

The objective of this study was to analyse the prevalence and characteristics of the main clinical and immunological manifestations at the onset and during the evolution of the disease in a cohort of patients from Latin America (mainly of mestizo origin) and to compare the Latin American with the European patients. Clinical and serological characteristics of 100 APS patients from Mexico and Ecuador were collected in a protocol form that was identical to that used to study the `Euro-Phospholipid' cohort. The cohort consisted of 93 female patients (93.0%) and seven (7.0%) male patients. There were 91 mestizos (91.0%), seven whites (7.0%) and two Amerindians (2.0%). The most common manifestations were livedo reticularis (40.0%), migraine (35.0%), inferior extremity deep vein thrombosis (32.0%), thrombocytopenia (28.0%) and hemolytic anemia (20.0%). Several clinical manifestations were more prevalent in Latin American than in European patients and they included mainly neurological (migraine, transient global amnesia, acute ischemic encephalopathy, amaurosis fugax) and cutaneous (livedo reticularis, skin ulcerations, superficial cutaneous necrosis, multiple subungual splinter hemorrhages) manifestations as well as hemolytic anemia. The APS has a wide variety of clinical and immunological manifestations at the onset and during the evolution of the disease and the ethnic origin in addition to environmental and socioeconomic factors can modify the disease expression. Lupus (2007) 16, 366—373.
Evaluation of Fluorescence-Based Amplified Fragment Length Polymorphism Analysis for Molecular Typing in Hospital Epidemiology: Comparison with Pulsed-Field Gel Electrophoresis for Typing Strains of Vancomycin-Resistant Enterococcus faecium

ABSTRACT Fluorescence-based amplified fragment length polymorphism (fbAFLP) is a novel assay based on the fluorescent analysis of an amplified subset of restriction fragments. The fbAFLP assay involves the selective PCR amplification of restriction fragments from a total digest of genomic DNA. The ligation of adapters with primer-specific sites coupled with primers containing selective nucleotides allowed the full potential of PCR to be realized while maintaining the advantages of restriction endonuclease analysis. Fluorescence-based fragment analysis with polyacrylamide gel electrophoresis provides the accurate band sizing required for homology assessment. The large number of phylogenetically informative characters obtained by fbAFLP is well suited for cluster analysis and database development. The method demonstrated excellent reproducibility and ease of performance and interpretation. We typed 30 epidemiologically well-characterized isolates of vancomycin-resistant enterococci from an outbreak in a university hospital by fbAFLP. Clustering of fbAFLP data matched epidemiological, microbiological, and pulsed-field gel electrophoresis data. This study demonstrates the unprecedented utility of fbAFLP for epidemiological investigation. Future developments in standardization and automation will set fbAFLP as the “gold standard” for molecular typing in epidemiology.
PREVALENCE OF CONGENITALLY MISSING MAXILLARY LATERAL INCISOR AND PEG LATERALS IN A LOCAL ORTHODONTIC POPULATION

Objective: The study was conducted to investigate the prevalence of maxillary lateral incisor agenesis and variation in its size in an orthodontic population and to relate its frequency with different skeletal malocclusions and gender. Material and Methods: Sample consisted of 361 patients, of which 193 were female and 168 were male with the age range12-35 years. Panoramic radiographs were used to diagnose the agenesis of maxillary lateral incisor (LI) and dental casts for presence of peg laterals, <ANB was measured from lateral cephalograms. Results: Thirty four (9.42%) patients were found to have agenesis of maxillary lateral incisor, of which 44.12% were female and 55.88% were male. Patient having peg laterals were 5.26%. Among the different skeletal classifications, patients with skeletal class I malocclusion had bilaterally missing LI (52.94%), patients with class II malocclusion had equal frequency of bilateral and left unilateral missing LI (38.46%) and skeletal class III patients had a greater frequency of right unilateral missing LI (75.00%). The highest incidence was of presence of bilateral peg laterals (52.63%) in both female and male patients (50.00% and 54.55% respectively). Conclusions: Bilateral agenesis of LI with skeletal class I malocclusion is more common and occurs predominantly among male population.
The incidence of cleft lip, cleft palate, hydrocephalus and spina bifida at Queen Elizabeth Central Hospital, Blantyre, Malawi.

OBJECTIVES To determine the incidence of cleft lip, cleft palate, spina bifida and hydrocephalus; and to compare these with those of Asian and European subjects. DESIGN A retrospective study. SETTING The Queen Elizabeth Central Hospital (QECH) in Blantyre, Malawi. SUBJECTS Delivery and nursery records compiled between January 1998 and December 1999 were studied. MAIN OUTCOME MEASURES To measure the incidence of cleft lip, cleft palate, spina bifida and hydrocephalus. RESULTS Of the total 25562 births, 39 (0.2%) had defects; eight boys and 31 girls. Clefts (all types) comprised the largest group, 43.6%, with an incidence of 0.67/1 000; spina bifida, 30.8% with an incidence of 0.47/1000; hydrocephalus, 15.4%, and an incidence of 0.23/1000; and spina bifida with hydrocephalus, 10.3%, with 0.16/1000 incidence. The respective mean (SD) birth weights for clefts (all types), spina bifida, hydrocephalus and spina bifida with hydrocephalus were 2806.47 (569.07) g, 2650.00 (360.55) g 2610.00 (720.97) g and 3362.50 (696.87) g respectively. CONCLUSION Our findings show a higher incidence of spina bifida in Malawians than in Caucasians and Orientals, but the incidence was lower than Omani subjects. The incidence of clefts and hydrocephalus in black Malawians, however, was lower than previously reported in other population groups, and hydrocephalus probably showed the lowest incidence among blacks in the continent. Furthermore, congenital malformations affected more girls than boys 4:1, but the infants had normal birth weight.
Vitamin D status in patients with bullous pemphigoid

in patients with advanced soft tissue sarcoma: analysis of publications from the last 10 years. Ann Oncol 2011; 22:1266–72. 6 Cascio MJ, O’Donnell RJ, Horvai AE. Epithelioid sarcoma expresses epidermal growth factor receptor but gene amplification and kinase domain mutations are rare. Mod Pathol 2010; 23:574–80. 7 Crawford Y, Ferrara N. VEGF inhibition: insights from preclinical and clinical studies. Cell Tissue Res 2009; 335:261–9. 8 George S, Merriam P, Maki RG et al. Multicenter phase II trial of sunitinib in the treatment of nongastrointestinal stromal tumor sarcomas. J Clin Oncol 2009; 27:3154–60. 9 Tariq Mahmood S, Agresta S, Vigil CE et al. Phase II study of sunitinib malate, a multitargeted tyrosine kinase inhibitor in patients with relapsed or refractory soft tissue sarcomas. Focus on three prevalent histologies: leiomyosarcoma, liposarcoma and malignant fibrous histiocytoma. Int J Cancer 2011; 129:1963–9. 10 Sleijfer S, Ray-Coquard I, Papai Z et al. Pazopanib, a multikinase angiogenesis inhibitor, in patients with relapsed or refractory advanced soft tissue sarcoma: a phase II study from the European organisation for research and treatment of cancer–soft tissue and bone sarcoma group (EORTC study 62043). J Clin Oncol 2009; 27:3126–32. 11 Judson I. Targeted therapies in soft tissue sarcomas. Ann Oncol 2010; 21 (Suppl. 7):vii277–80.
On formalizing fairness in prediction with machine learning

Machine learning algorithms for prediction are increasingly being used in critical decisions affecting human lives. Various fairness formalizations, with no firm consensus yet, are employed to prevent such algorithms from systematically discriminating against people based on certain attributes protected by law. The aim of this article is to survey how fairness is formalized in the machine learning literature for the task of prediction and present these formalizations with their corresponding notions of distributive justice from the social sciences literature. We provide theoretical as well as empirical critiques of these notions from the social sciences literature and explain how these critiques limit the suitability of the corresponding fairness formalizations to certain domains. We also suggest two notions of distributive justice which address some of these critiques and discuss avenues for prospective fairness formalizations.
The clonal nature of pityriasis lichenoides.

BACKGROUND Pityriasis lichenoides et varioliformis acuta (PLEVA) and pityriasis lichenoides chronica (PLC) are benign lymphocytic infiltrates of the skin that classically present as either a recurrent papulonecrotic eruption (PLEVA) or a persistent, scaling, papular eruption (PLC). Observations of both types of lesions present on individual patients have led to speculation that both entities are related. Previous studies evaluating the DNA of biopsy specimens from patients with PLEVA and PLC revealed clonal T-cell receptor beta gene rearrangements. OBJECTIVE To analyze and compare the T-cell populations between lesions of PLEVA and PLC. DESIGN Retrospective and prospective analysis of patient tissue samples, classified by histologic analysis. Extracted DNA from 13 skin biopsy specimens with the diagnosis of PLC and 14 skin biopsy specimens with the diagnosis of PLEVA was analyzed by polymerase chain reaction/denaturing gradient gel electrophoresis (PCR/DGGE). SETTING Molecular diagnostic laboratory at an academic medical center. PATIENTS Twenty-seven tissue samples were obtained from patients with a histologic diagnosis of PLEVA or PLC. These samples were analyzed by PCR/DGGE. MAIN OUTCOME MEASURE The presence or absence of T-cell receptor gene rearrangements on PCR/DGGE analysis corresponding to a clonal population of T cells. RESULTS Of 14 PLEVA specimens, 8 (57%) demonstrated monoclonal T-cell receptor gene rearrangements; 1 (8%) of 13 PLC specimens showed a gene rearrangement (P =.008, Fisher exact test). CONCLUSIONS Our results demonstrate the polyclonal nature of the lymphocytic infiltrate found in almost all of the PLC specimens, which contrasts with the monoclonal nature found in most of the PLEVA specimens. These differences may represent different stages of the clinical evolution of a single entity that results from varying host immune responses to pathogenic factors. Specifically, we propose that PLEVA is a benign clonal T-cell disorder in which the clone arises from a subset of T cells in lesions of PLC. The host immune response to this clone determines the clinical and histologic findings in PLEVA.
The triadic intersubjective matrix in supervision: The use of disclosure to work through painful affects

The use of the psychoanalyst's subjective reactions as a tool to better understand his/her patient has been a central feature of clinical thinking in recent decades. While there has been much discussion and debate about the analyst's use of countertransference in individual psychoanalysis, including possible disclosure of his/her feelings to the patient, the literature on supervision has been slower to consider such matters. The attention to parallel processes in supervision has been helpful in appreciating the impact of affects arising in either the analyst/patient or the supervisor/analyst dyads upon the analytic treatment and its supervision. This contribution addresses the ways in which overlapping aspects of the personalities of the supervisor, analyst and patient may intersect and create resistances in the treatment. That three‐way intersection, described here as the triadic intersubjective matrix, is considered inevitable in all supervised treatments. A clinical example from the termination phase of a supervised analysis of an adolescent is offered to illustrate these points. Finally, the question of self‐disclosure as an aspect of the supervisory alliance is also discussed.
Homocysteine, MTHFR C677 T, Vitamin B12, and Folate Levels in Thai Children With Ischemic Stroke: A Case-control Study

Hyperhomocysteinemia has been identified as a risk factor for venous and arterial thrombosis especially in adult populations. Twenty-eight patients with an initial diagnosis of ischemic stroke and 100 controls, aged ≤18 years, were enrolled in this study. The mean plasma total homocysteine (tHcy) levels in patients and controls were significantly different with values of 8.7±3.6 and 7.5±2.4 μmol/L, respectively (P=0.01). The plasma tHcy at the 95th percentile was 11.5 μmol/L and patients whose plasma tHcy was above the 95th percentile had an odds ratio of 8.2 (95% confidence interval 1.4-47.2, P=0.02) for developing ischemic stroke. The genetic and acquired factors that could have affected plasma tHcy levels were studied and no differences were found between patients and controls. Factors that were investigated were vitamin B12, red blood cell folate, and serum folate levels as well as methylenetetrahydrofolate reductase C677T polymorphism. It is of note, however, that subjects whose plasma tHcy was above the 95th percentile had significantly lower serum folate levels (P=0.02).
Overcoming the (Apparent) Problem of Inconsistency in Origin-Destination Matrix Estimations

Recently a number of models for the estimation of origin-destination trip matrices from traffic counts have been presented. One class of models assumes knowledge of the proportional usage of each link by the interzonal traffic. These models result in an underspecified, and often inconsistent, system of linear equations. Several authors have addressed the problem of inconsistency by, in different ways, changing the traffic count data so as to achieve consistency. We argue that, modeling-wise, this is not a sound approach because inconsistent data is a natural part of any origin-destination matrix estimation problem. By using a stochastic programming approach the inconsistent input data becomes a natural part of the estimation process. This is done by viewing the traffic counts as realizations of some unknown underlying distribution of traffic flows.