Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Decision Problems with Cooperative and Strategic Agents and Asymmetric Information.

Dynamic decision problems with cooperative and strategic agents and asymmetric information by Deepanshu Vasal Chair: Achilleas Anastasopoulos There exist many real world situations involving multiple decision makers with asymmetric information, such as communication systems, social networks, economic markets and many others. Through this dissertation, we attempt to enhance the conceptual understanding of such systems and provide analytical tools to characterize the optimum or equilibrium behavior. Specifically, we study four discrete time, decentralized decision problems in stochastic dynamical systems with cooperative and strategic agents. The first problem we consider is a relay channel where nodes’ queue lengths, modeled as conditionally independent Markov chains, are nodes’ private information, whereas nodes’ actions are publicly observed. This results in non-classical information pattern. Energy-delay tradeoff is studied for this channel through stochastic control techniques for cooperative agents. Extending this model for strategic users, in the second problem we study a general model with N strategic players having conditionally independent, Markovian types and publicly observed actions. This results in a dynamic game with asymmetric information. We present a forward/backward sequential decomposition algorithm to find a class of perfect Bayesian equilibria of the game. Using this methodology, in the third problem, we study a general two player dynamic LQG
Detection of clonal T-cell receptor gamma gene rearrangements with the use of the polymerase chain reaction in cutaneous lesions of mycosis fungoides and Sézary syndrome.

BACKGROUND AND DESIGN We used the amplification of junctional V (variable)-J joining sequences of the rearranged T-cell receptor gamma (TCR gamma) genes by polymerase chain reaction for rapid and sensitive detection of a clonal T-cell population in a total of 51 skin specimens obtained from 45 patients with mycosis fungoides, five patients with Sézary syndrome, and 29 patients with chronic inflammatory dermatoses. RESULTS A clonal TCR gamma gene rearrangement was present in all tumors (3/3, 100%) and in most infiltrated plaques (16/22, 73%) and erythrodermas (10/12, 83%). In the patch stage, a clonal subset was found in more than half of the cases (8/14, 57%), whereas no clonality was observed in the controls. We also amplified the V-J sequences of the Igh locus coding for the heavy chain of immunoglobulins, without evidence of clonal rearrangement. These data were compared with those from in situ immunophenotypic analysis. Moreover, by using the same assay with successive dilutions of standard clonal T-cell DNA, a semiquantitative study of the T-cell clone was carried out in some cases. The highest ratios of clonal DNA were observed in advanced stages. CONCLUSIONS These data validate polymerase chain reaction V gamma-J gamma as a rapid, sensitive tool that can be used in the routine analysis of clonality in cutaneous lesions of mycosis fungoides and in the early diagnosis of mycosis fungoides and Sézary syndrome. Semiquantitative studies suggest that the malignant T-cell clone follows a selective process during the course of the progressive form of mycosis fungoides.
A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase.

Hepatitis C virus (HCV) nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase (RdRp) has acquired a unique beta-hairpin in the thumb subdomain which protrudes toward the active site. We report here that this beta-hairpin plays an important role in positioning the 3' terminus of the viral RNA genome for correct initiation of replication. The presence of this beta-hairpin interferes with polymerase binding to preannealed double-stranded RNA (dsRNA) molecules and allows only the single-stranded 3' terminus of an RNA template to bind productively to the active site. We propose that this beta-hairpin may serve as a "gate" which prevents the 3' terminus of the template RNA from slipping through the active site and ensures initiation of replication from the terminus of the genome. This hypothesis is supported by the ability of a beta-hairpin deletion mutant that utilizes dsRNA substrates and initiates RNA synthesis internally. The proposed terminal initiation mechanism may represent a novel replication strategy adopted by HCV and related viruses.
rpoB-Based Identification of Nonpigmented and Late-Pigmenting Rapidly Growing Mycobacteria

ABSTRACT Nonpigmented and late-pigmenting rapidly growing mycobacteria (RGM) are increasingly isolated in clinical microbiology laboratories. Their accurate identification remains problematic because classification is labor intensive work and because new taxa are not often incorporated into classification databases. Also, 16S rRNA gene sequence analysis underestimates RGM diversity and does not distinguish between all taxa. We determined the complete nucleotide sequence of the rpoB gene, which encodes the bacterial β subunit of the RNA polymerase, for 20 RGM type strains. After using in-house software which analyzes and graphically represents variability stretches of 60 bp along the nucleotide sequence, our analysis focused on a 723-bp variable region exhibiting 83.9 to 97% interspecies similarity and 0 to 1.7% intraspecific divergence. Primer pair Myco-F-Myco-R was designed as a tool for both PCR amplification and sequencing of this region for molecular identification of RGM. This tool was used for identification of 63 RGM clinical isolates previously identified at the species level on the basis of phenotypic characteristics and by 16S rRNA gene sequence analysis. Of 63 clinical isolates, 59 (94%) exhibited <2% partial rpoB gene sequence divergence from 1 of 20 species under study and were regarded as correctly identified at the species level. Mycobacterium abscessus and Mycobacterium mucogenicum isolates were clearly distinguished from Mycobacterium chelonae; Mycobacterium mageritense isolates were clearly distinguished from “Mycobacterium houstonense. ” Four isolates were not identified at the species level because they exhibited >3% partial rpoB gene sequence divergence from the corresponding type strain; they belonged to three taxa related to M. mucogenicum, Mycobacterium smegmatis, and Mycobacterium porcinum. For M. abscessus and M. mucogenicum, this partial sequence yielded a high genetic heterogeneity within the clinical isolates. We conclude that molecular identification by analysis of the 723-bp rpoB sequence is a rapid and accurate tool for identification of RGM.
Diabetes and decline in heart disease mortality in US adults.

CONTEXT Mortality from coronary heart disease has declined substantially in the United States during the past 30 years. However, it is unknown whether patients with diabetes have also experienced a decline in heart disease mortality. OBJECTIVE To compare adults with diabetes with those without diabetes for time trends in mortality from all causes, heart disease, and ischemic heart disease. DESIGN, SETTING, AND PARTICIPANTS Representative cohorts of subjects with and without diabetes were derived from the First National Health and Nutrition Examination Survey (NHANES I) conducted between 1971 and 1975 (n = 9639) and the NHANES I Epidemiologic Follow-up Survey conducted between 1982 and 1984 (n = 8463). The cohorts were followed up prospectively for mortality for an average of 8 to 9 years. MAIN OUTCOME MEASURE Changes in mortality rates per 1000 person-years for all causes, heart disease, and ischemic heart disease for the 1982-1984 cohort compared with the 1971-1975 cohort. RESULTS For the 2 periods, nondiabetic men experienced a 36.4% decline in age-adjusted heart disease mortality compared with a 13.1% decline for diabetic men. Age-adjusted heart disease mortality declined 27% in nondiabetic women but increased 23% in diabetic women. These patterns were also found for all-cause mortality and ischemic heart disease mortality. CONCLUSIONS The decline in heart disease mortality in the general US population has been attributed to reduction in cardiovascular risk factors and improvement in treatment of heart disease. The smaller declines in mortality for diabetic subjects in the present study indicate that these changes may have been less effective for people with diabetes, particularly women.
Oxidative Stress and Increased Type-IV Collagenase Levels in Bronchoalveolar Lavage Fluid from Newborn Babies

Oxidative stress may increase lung permeability by up-regulation of matrix-metalloproteinase-9 (MMP-9), a type-IV collagenase that can disrupt alveolar basement membranes. We have compared a marker of oxidative stress (protein carbonyl residues) with levels of MMP-9 and its inhibitor, tissue inhibitor of metalloproteinase-1 (TIMP-1), in bronchoalveolar lavage samples from newborn babies. Bronchoalveolar lavage samples (n = 87, two from each time point) were taken in the first 6 postnatal days from 41 ventilated babies: 18 of <29 wk gestation, 10 of 29–36 wk, 9 term with persistent fetal circulation, and 4 term without lung disease. Respiratory disease severity at the time of bronchoalveolar lavage was assessed using the arterial–alveolar oxygen tension ratio. One sample from each time point was used for the measurement of MMP-9 by zymography and TIMP-1 by ELISA. The second sample was used to measure carbonyl group concentrations, also using an ELISA. Correlations were calculated between protein carbonyls, arterial–alveolar oxygen tension ratio, and MMP-9 and TIMP-1 concentrations. Significant correlations were found between carbonyl concentrations and arterial–alveolar oxygen tension ratio (r = −0.325, p = 0.0031, n = 81), MMP-9 (r = 0.331, p < 0.0029, n = 79), and TIMP-1 (r = 0.436, p < 0.0001, n = 87). Worsening respiratory disease in newborn babies is associated with increased carbonyl concentrations in neonatal bronchoalveolar lavage fluid, and these correlated with MMP-9 and TIMP-1 levels. Increased oxidative stress may damage the lung by increasing type-IV collagenase activity, causing disruption of the extracellular matrix.
A novel typology of media clusters

ABSTRACT Is the clustering of audio-visual companies in London’s Soho really the same as the clustering of Berlin’s new media industry? The media cluster approach has gained a lot of attention not only in academia, but also in political discourse. But, as appealing as the media cluster concept is, one of the most fundamental issues is the comparability of the phenomenon. This article tackles this issue and an analysis of 43 case studies has been conducted. The case studies have been grouped to find a new typology for media clusters. The research revealed six different types: The Creative Region, the Giant Anchor, the Specialized Area, the Attracting Enabler, the Real Estate and the Pooling Initiative. The typologies showed that they distinguish especially in their geographical scale and specialization in media activities, while at the same time cluster types can be found in the same area. They are driven by four rationales: agglomeration, urbanization, localization economies and artificial formation.
Cocoa extracts reduce oligomerization of amyloid-β: implications for cognitive improvement in Alzheimer's disease.

BACKGROUND Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder, characterized by pathological aggregates of amyloid peptide-β (Aβ) and tau protein. Currently available therapies mediate AD symptoms without modifying disease progression. Polyphenol-rich diets are reported to reduce the risk for AD. OBJECTIVE In the present study, we investigated the AD disease-modifying effects of cocoa, a rich source of flavanols, which are a class of polyphenols. We hypothesized that cocoa extracts interfere with amyloid-β oligomerization to prevent synaptic deficits. METHODS We tested the effects of three different cocoa extracts, viz. Natural, Dutched, and Lavado extracts, on Aβ42 and Aβ40 oligomerization, using photo-induced cross-linking of unmodified proteins technique. To assess the effects of cocoa extracts on synaptic function, we measured long term potentiation in mouse brain hippocampal slices exposed to oligomeric Aβ. RESULTS Our results indicate that cocoa extracts are effective in preventing the oligomerization of Aβ, with Lavado extract being most effective. Lavado extract, but not Dutched extract, was effective in restoring the long term potentiation response reduced by oligomeric Aβ. CONCLUSION Our findings indicate that cocoa extracts have multiple disease-modifying properties in AD and present a promising route of therapeutic and/or preventative initiatives.
Influence of type of exchange fluid on survival in therapeutic apheresis for thrombotic thrombocytopenic purpura

Thrombotic thrombocytopenic purpura (TTP) is a potentially lethal disease that may respond favorably to plasma infusion or therapeutic plasma exchange (TPE) with frozen plasma (FP) as the exchange fluid. Frozen plasma from which the cryo‐precipitated fraction has been removed (cryopoor plasma, CP) has reportedly been useful in refractory cases in which a response to FP is not being observed. We report a retrospective analysis of all cases of TTP treated by TPE with either FP (1985–1989) or CP (1989–1993) as exchange fluid at a large tertiary care hospital between the years 1985 and 1993. A severity score index was compiled for each patient using the platelet count, mental status, hematocrit, and renal function at the time of diagnosis. Nineteen patients were treated with FP (group I) and 18 patients with CP (group 2). Groups did not differ in age, gender, race, hematologic parameters, or severity scores. Patients treated with CP, however, had more plasma exchanges (14 ± 10 vs. 12 ± 8, respectively) and more fluid exchanged than these treated with FP (50 L ± 36 vs. 37 L ± 40, respectively). Survival was 72% in the CP group and 47% in the FP group.
Euglycemic hyperinsulinemia augments amino acid uptake by human leg tissues during hyperaminoacidemia.

The effect of insulin on leg and whole body protein turnover was determined by leg exchange and plasma kinetics of [15N]phenylalanine and [1-13C]leucine during amino acid (AA) sufficiency. Eight healthy subjects were studied during AA infusion alone and during infusion of glucose and insulin (0.29 nmol.m-2.min-1) with additional AA. Insulin strongly stimulated the positive leg AA balance seen with AA (AA alone, 2.6 +/- 6.1 vs. insulin + AA, 33.1 +/- 5.8 nmol phenylalanine . 100 g leg-1.min-1; P less than 0.001). Phenylalanine uptake by leg tissues rose during insulin plus AA (47.3 +/- 11.5 vs. 73.1 +/- 7.3 nmol. 100 g-1.min-1; P = 0.022) but with only a slight reduction in leg phenylalanine release (44.7 +/- 8.1 vs. 40.0 +/- 7.9 nmol.100 g-1.min-1). Leg nonoxidative leucine plus alpha-ketoisocaproate (KIC) uptake was increased slightly with insulin (129 +/- 26 vs. 146 +/- 21 nmol.100 g-1. min-1), but leg leucine oxidation increased fourfold (P = 0.012). Leg leucine plus KIC release was reduced by insulin (120 +/- 17 vs. 84 +/- 10 nmol.100 g-1.min-1; P = 0.005); endogenous leucine appearance of leucine and phenylalanine decreased with insulin (leucine, 1.97 +/- 0.08 vs. 1.65 +/- 0.10; phenylalanine, 0.76 +/- 0.03 vs. 0.54 +/- 0.08 mumols.kg-1.min-1; P less than 0.02). The results suggest that insulin, given with sufficient amino acids, may stimulate leg and whole body protein balance by mechanisms including stimulation of protein synthesis and inhibition of protein breakdown.
Sickle Cell Vaso-occlusive Crisis Is Associated with Abnormalities in the Ratio of Vasoconstrictor to Vasodilator Prostanoids

ABSTRACT: Plasma levels of 6-keto-prostaglandin F1α (6kPGF1α) and thromboxane (Tx) B2 have been assessed in sickle cell disease (SCD) with discrepant results. Inasmuch as direct measurement of plasma prostanoids is fraught with the problem of interfering substances, we assessed plasma 6kPGF1α and TxB2 levels in patients with SCD by RIA after extraction of eicosanoids and separation by HPLC. We demonstrate that the 6kPGF1α and TxB2 levels in children with SCD in steady state as well as in vaso-occlusive crisis (VOC) are significantly lower when compared with those from age-matched controls. The VOC plasma 6kPGF1α and TxB2 levels were, however, significantly elevated when compared with those from children in steady state. Changes similar to those noted with unpaired plasma samples were also observed when paired steady state and VOC plasmas from the same patients were assessed. The ratio of TxB2 to 6kPGF1α, was, however, significantly elevated in patients with SCD in crisis when compared with eicosanoid ratios obtained during steady state. In an attempt to understand whether the abnormality in 6kPGF1α was due to an impairment in endothelial cell prostacyclin-regenerating ability, we compared the ability of plasma from controls and children with SCD to activate arachidonic acid (AA) release and prostacyclin production by [14C]AA-prelabeled bovine aortic endothelial cells. Our results suggest that the decreased 6kPGF1α levels in plasma from children with SCD was not due to an effect on substrate AA release but rather a modulatory effect of sickle plasma components on endothelial cell cyclooxygenase activity. Although a decreased production of prostacyclin has previously been suggested to play a role in the initiation and/or propagation of vaso-occlusion in SCD, our study demonstrates a relative increase during VOC of 6kPGF1α levels over those observed in steady state. However, the rise in 6kPGF1α is accompanied by an increase in levels of TxB2 such that the ratio of TxB2 to 6kPGF1α is significantly increased during VOC. The imbalance in the production of vasoactive eicosanoids, TxA2 and prostacyclin, could potentially play a role in the potentiation of VOC in patients with SCD.
Sonographic measurement of the umbilical cord area and the diameters of its vessels during pregnancy

The objective was to determine the cross-sectional area of the umbilical cord, its diameter and the diameter of its vessels to establish a reference curve for these parameters during pregnancy, through a prospective cross-sectional study, including 2,310 low-risk pregnancies between 12 and 40 weeks’ gestation. Means and standard deviations (SDs), plus the 10th, 50th and 90th percentiles for each measurement were calculated using polynomial regression analysis. Mann–Whitney, Kruskal–Wallis and Wilcoxon tests were used for statistical analysis. These parameters increased significantly with gestational age. The area of the cord also varied significantly with parity. Their new reference curves for low risk pregnancies were calculated using polynomial regression, and an almost linear increase in values was found up to 32 weeks of pregnancy, tending to stabilise from then onwards. The regression equation of the umbilical cord area according to gestational age (GA) was: –1.417 + 0.3026*GA–0.008*GA2 + 0.000007*GA3 and the degree of adjustment (R2) was 0.89.
Allergic eye disease – a clinical challenge

Currently, six basic allergic eye diseases are recognized. In seasonal (SAC) and perennial allergic conjunctivitis (PAC), the allergic response is mediated predominantly by mast cells, whereas the more severe conditions, vernal (VKC) and atopic keratoconjunctivitis (AKC) and giant papillary conjunctivitis (GPC), are associated with a preponderance of T cells. Acute allergic conjunctivitis (AAC) occurs when a large quantity of allergen inoculates the eye and is usually self‐limiting. SAC, the most common ocular allergy, is the ocular component of hayfever. PAC in the UK is most commonly caused by the house‐dust mite (HDM); diagnosis is confirmed by skin‐prick tests, eosinophils in the conjunctival smear, and raised tear or serum total IgE. SAC and PAC can usually be managed with chromone eyedrops and antihistamines. VKC usually presents in children under 10 years of age and mainly affects boys. Sufferers frequently have a personal or family history of atopy. Corneal involvement can occur in VKC, making it potentially sight‐threatening. AKC occurs in atopic adults, and like VKC it affects the cornea. VKC and AKC require steroid treatment under specialist supervision; minimization of the steroid dose can often be achieved with use of a chromone. GPC occurs due to repeated contact of the conjunctival surface with a foreign surface, such as contact lenses. Attention to lens hygiene or switching to different lenses and treatment with a chromone are frequently effective. In all allergic eye diseases contact with the precipitating allergen should be avoided as far as possible.
Prostate cancer in Germany among migrants from the Former Soviet Union

Background : In Germany, prostate cancer is the leading cause of cancer and the third leading cause of death from cancer in males. We investigate prostate cancer in Gernmany among migrants from the Former Soviet Union (FSU) and compare them to indigenous German population with regard to prostate cancer incidence, mortality and longitudinal effects. Methods : Data were obtained from two migrant cohorts residing in the federal states of North Rhine Westphalia (n=34,393) and Saarland (n=18,619). Vital status was ascertained through local population registries. Causes of death were obtained from the federal statistical office or from local health authorities. Cancer incidence of the Saarland cohort was derived from the Saarland Cancer Registry using record linkage. Results : From 1990 to 2005 we observed 3360 deaths of which 28 were due to prostate cancer. In the Saarland cohort 35 men were diagnosed with prostate cancer during the respective period. Migrants had lower prostate cancer incidence (SIR 0.74 (95% CI: 0.52–1.03)) and mortality (SMR 0.57 (95% CI: 0.38–0.83)) compared to the German population. Multivariate analysis showed a strong age effect on incidence meaning young migrants (below age 60) were diagnosed significantly more often with prostate cancer compared to Germans of the same age. However, mortality did not show any effects. Discussion : Lower prostate cancer mortality and incidence among migrants may reflect an ongoing situation in the FSU. Additionally, longitudinal analysis did not reveal convergence of migrant prostate cancer to German rates as expected from lifestyle driven cancer sites. Therefore, our results support the hypothesis of a genetic effect on prostate cancer risk.
Evaluation of scatter effects on image quality for breast tomosynthesis

Digital breast tomosynthesis uses a limited number of low-dose x-ray projections to produce a three-dimensional (3D) tomographic reconstruction of the breast. The purpose of this investigation was to characterize and evaluate the effect of scatter radiation on image quality for breast tomosynthesis. Generated by a Monte Carlo simulation method, scatter point spread functions (PSF) were convolved over the field of view (FOV) to estimate the distribution of scatter for each angle of tomosynthesis projection. The results demonstrated that in the absence of scatter reduction techniques, the scatter-to-primary ratio (SPR) levels for the average breast are quite high (~0.4 at the centre of mass), and increased with increased breast thickness and with larger FOV. Associated with such levels of x-ray scatter are cupping artifacts, as well as reduced accuracy in reconstruction values. The effect of x-ray scatter on the contrast, noise, and signal-difference-to-noise ratio (SDNR) in tomosynthesis reconstruction was measured as a function of tumour size. For example, the contrast in the reconstructed central slice of a tumour-like mass (14 mm in diameter) was degraded by 30% while the inaccuracy of the voxel value was 28%, and the reduction of SDNR was 60%. We have quantified the degree to which scatter degrades the image quality over a wide range of parameters, including x-ray beam energy, breast thickness, breast diameter, and breast composition. However, even without a scatter rejection device, the contrast and SDNR in the reconstructed tomosynthesis slice is higher than that of conventional mammographic projection images acquired with a grid at an equivalent total exposure.