Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorescence in situ hybridisation analysis of formalin-fixed paraffin-embedded tissue sections in the diagnostic work-up of non-Burkitt high grade B-cell non-Hodgkin's lymphoma: a single centre's experience

Aims In recent years the genetic aberrations associated with diffuse large B-cell lymphoma and the new subtype described in the 2008 revision of the WHO classification, ‘B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma’ have been increasingly well defined. Recurrent genetic abnormalities include rearrangements involving MYC (8q24), BCL2 (18q21) and BCL6 (3q27); as the prognostic and therapeutic implications associated with these abnormalities are clarified their accurate identification at diagnosis is becoming increasingly critical. We describe our experience of using a panel of fluorescence in situ hybridisation (FISH) probes on formalin-fixed paraffin-embedded tissue sections in the diagnostic work-up of 162 patients with non-Burkitt high grade B-cell non-Hodgkin's lymphomas (HG-BNHL). Methods BCL6, IGH-BCL2 and MYC status were determined prospectively in sequential patients presenting with HG-BNHL, with respect to the presence of rearrangements and copy number changes. Small numbers of samples were analysed retrospectively or were studied at relapse in previously untested patients. Results FISH analysis was successful in 160/162 (99%) cases, with abnormalities detected in 118/160 (74%). Conclusions FISH analysis of formalin-fixed paraffin-embedded tissue sections is a highly reproducible technique with an excellent success rate for the detection of genetic abnormalities which will play an increasingly important role in improving risk stratification of patients with HG-BNHL.
Promotions, Multiskilling and Incentives for Skills

We study incentives for skill acquisition when skills cannot be contracted on. Our framework has two features. First, workers can acquire both rm specic and general skills at a cost, and second, job assignments signal skill acquisition to a less informed labor market. Our key insight is that each skill performs a dierent function. The rm specic
Mobility of people with lower limb amputations: scales and questionnaires: a review

Objective and design: A systematic literature review to compare mobility scales used for lower limb amputees. A literature search was carried out by computerized search of biomedical literature including Medline and Embase. The studies included were published between 1978 and 1998 and including the following keywords: amputation, artificial limbs, prosthesis, lower limb, activities of daily living, mobility. Results: Thirty-five studies were identified; 19 had a measurement of separate levels of mobility comparable to each other. Sixteen studies used ordinal and ratio scales without separate levels of mobility. The widest range of measurement found was the scale from ‘walking with prosthesis without a walking aid’ to ‘totally confined to bed’. The Stanmore Harold Wood mobility scale was published most frequently. None of the 35 studies presented give a continuous measurement of mobility. Conclusion: A multitude of measurement scales and questionnaires are available for differ in methods and measuring range. Measuring mobility by a scale has been shown to have limitations. Several authors did extensive research but they all measure only a number of aspects of mobility. Consensus about the measurement of mobility of lower limb amputees is not available in the recent literature.
Endothelial Progenitor Cells in the Pathogenesis of Idiopathic Pulmonary Fibrosis: An Evolving Concept

Background Idiopathic pulmonary fibrosis (IPF) has been associated with abnormal vascular remodeling. Bone marrow derived endothelial progenitor cells (EPCs) are considered to possess lung tissue repair and vascular remodeling properties. Objectives The study aimed to assess early EPCs levels and EPCs endogenous vascular endothelial growth factor (VEGF) expression in IPF. In order to examine alterations in the mobilization of EPCs from the bone marrow we measured plasma VEGF. Main Results Twenty-three patients with IPF and fifteen healthy subjects were included. The number of early EPCs colonies was markedly reduced in IPF patients vs controls (6.00±6.49 vs 49.68±16.73, respectively, p<0.001). EPCs were further decreased in patients presenting systolic pulmonary arterial pressure (sPAP)≥35 mmHg. The number of colonies per well correlated negatively with P(A-a)O2 (r = −0.750, p<0.001). Additionally, VEGF mRNA levels were significantly increased in IPF patients. There were no differences observed in VEGF plasma levels in IPF patients when compared to controls. Conclusions The current data suggest that inadequate levels of early EPCs may potentially contribute to suppressed repair and recovery of the damaged pulmonary endothelium and thereby may drive the sequence of events in profibrogenic direction. Increased VEGFmRNA levels in the clinical context of IPF may represent a compensatory mechanism to overcome reduced EPCs levels.
Ubiquitination of the PI3-kinase VPS-34 promotes VPS-34 stability and phagosome maturation

Apoptotic cells generated by programmed cell death are engulfed by phagocytes and enclosed within membrane-bound phagosomes. Maturation of apoptotic cell–containing phagosomes leads to formation of phagolysosomes where cell corpses are degraded. The class III phosphatidylinositol 3-kinase (PI3-kinase) VPS-34 coordinates with PIKI-1, a class II PI3-kinase, to produce PtdIns3P on phagosomes, thus promoting phagosome closure and maturation. Here, we identified UBC-13, an E2 ubiquitin–conjugating enzyme that functions in the same pathway with VPS-34 but in parallel to PIKI-1 to regulate PtdIns3P generation on phagosomes. Loss of ubc-13 affects early steps of phagosome maturation, causing accumulation of cell corpses. We found that UBC-13 functions with UEV-1, a noncatalytic E2 variant, and CHN-1, a U-box–containing E3 ubiquitin ligase, to catalyze K63-linked poly-ubiquitination on VPS-34 both in vitro and in Caenorhabditis elegans. Loss of ubc-13, uev-1, or chn-1 disrupts ubiquitin modification of VPS-34 and causes significantly reduced VPS-34 protein levels. Our data suggest that K63-linked ubiquitin modification serves as a general mechanism to modulate VPS-34 stability in multiple processes.
Morning stiffness response with delayed-release prednisone after ineffective course of immediate-release prednisone

Objective: To assess morning stiffness in rheumatoid arthritis (RA) patients switched from immediate-release (IR) to delayed-release (DR) prednisone. Method: Circadian Administration of Prednisone in Rheumatoid Arthritis-1 (CAPRA-1) is a 12-week, randomized, multicentre, active-controlled study of morning stiffness that consisted of a double-blind phase and a 9-month open-label extension. Patients receiving IR prednisone with no significant improvement after the double-blind study were switched to DR prednisone. Morning stiffness duration and median absolute and relative changes in pain and global assessment were evaluated (3, 6, and 9 months). Results: In patients switched from IR to DR prednisone (n = 110), statistically significant reductions in morning stiffness occurred over 3 months and were sustained for 9 months. Absolute reduction of morning stiffness was ~50 min with > 40% relative reduction at each visit. Interleukin (IL)-6 levels were reduced by the same amount. Statistically significant and clinically meaningful mean reductions in morning stiffness were maintained at > 67 min at each visit along with significant improvements in pain and patient global assessment. There was no evidence of tachyphylaxis seen over the 9-month study. Conclusions: Patients receiving disease-modifying anti-rheumatic drugs (DMARDs) and IR prednisone who had not had significant reductions in morning stiffness demonstrated statistically significant and clinically meaningful improvements when switched to DR prednisone.
A random matrix model of communication via antenna arrays

A random matrix model is introduced that probabilistically describes the spatial and temporal multi–path propagation between a transmitting and receivi ng antenna array with a limited number of scatterers for mobile radio and indoor environments. The model characterizes the channel by its richness delay profilewhich gives the number of scattering objects as a function of the path delay. Each delay is assigned the eigenvalue distribution o f a random matrix that depends on the number of scatterers, receive antennas, and transmit anten nas. The model allows to calculate signal–to–interference–and noise ratios and channel capacities for large antenna arrays analytically and quantifies up to wh at extent rich scattering improves performance. Index terms — antenna arrays, random matrices, Stieltjes transform, in ter–symbol interference, information rates, channel models, multiuser communicati on, fading channels This work was presented in part at 38th Ann. Allerton Conf. on Commun. , Contr. & Comp., Oct. 2000 and the IEEE International Conference on Communications (ICC), Helsin ki, Finland, June 2001. yVienna Research Center for Telecommunications (FTW), mueller@ftw.at.
Politeness Strategies Used in Text Messaging

One aspect of short message service (SMS) communication through a cell phone is use of politeness strategies. As it is extensively argued that females are more polite language users, the present study sought to describe the strategies used by these two groups and to find out whether there is any significant difference between male and female English as a foreign language (EFL) learners in the use of positive and negative politeness strategies in sending SMS to their professors, considering that there is an asymmetric power relation and social distance between them. To this end, a corpus of 300 L1 (Persian) and L2 (English) request messages was compiled. Results of qualitative and quantitative data analysis showed no significant difference between the two groups. Results of the study have implication in politeness research.
Robust Gaussian Process Regression with a Student-t Likelihood

This paper considers the robust and efficient implementation of Gaussian process regression with a Student-t observation model, which has a non-log-concave likelihood. The challenge with the Student-t model is the analytically intractable inference which is why several approximative methods have been proposed. Expectation propagation (EP) has been found to be a very accurate method in many empirical studies but the convergence of EP is known to be problematic with models containing non-log-concave site functions. In this paper we illustrate the situations where standard EP fails to converge and review different modifications and alternative algorithms for improving the convergence. We demonstrate that convergence problems may occur during the type-II maximum a posteriori (MAP) estimation of the hyperparameters and show that standard EP may not converge in the MAP values with some difficult data sets. We present a robust implementation which relies primarily on parallel EP updates and uses a moment-matching-based double-loop algorithm with adaptively selected step size in difficult cases. The predictive performance of EP is compared with Laplace, variational Bayes, and Markov chain Monte Carlo approximations.
Cancer risks from exposure to vehicular air pollution: a household level analysis of intra-ethnic heterogeneity in Miami, Florida

ABSTRACT Quantitative environmental justice (EJ) research has relied on aggregated data from census units to determine disproportionate hazard exposure. Additionally, variables typically used to analyze ethnic inequities in exposure (e.g., percent Hispanic) are too broad and assume a degree of homogeneity that may not exist, given the diversity of ethnic minority populations. We address these limitations through a study that utilizes primary household level survey data and cancer risk estimates from the National-Scale Air Toxics Assessment (NATA) to analyze intra-ethnic inequities in exposure to vehicular air pollutants in the Miami metropolitan area, Florida. Our analysis disaggregates the Hispanic category based on five characteristics (language proficiency, U.S. citizenship, nativity, unemployment status, and national origin) and finds that risk burdens are significantly higher for Hispanic respondents who are foreign-born, unemployed, and of Cuban origin. Findings highlight the advantages of downscaling EJ analyses to the household level and considering intra-ethnic heterogeneity in EJ research and policy.
MERCURY EXPOSURE IN UTERO AND DURING INFANCY

Mercury in blood samples was speciated from mothers and their infants up to 2 mo after delivery. There were significant correlations between umbilical cord blood and maternal blood for methylmercury (MeHg) and inorganic mercury (I-Hg) levels. The MeHg levels in cord blood were significantly higher than in maternal blood, while I-Hg levels were about the same. The maternal MeHg and I-Hg levels remained stable during the sampling period, whereas the MeHg concentration in infant blood decreased more than 45% between the 72-h and 2 mo sampling times. The I-Hg levels in infant blood were low at birth, and remained low during the sampling period. The results of the present study do not support I-Hg absorption through milk as a significant source of exposure. However, the number of observations is small, and a larger study is warranted in order to verify the data.
Orchestrated Regulation of Nogo Receptors, Lotus, AMPA Receptors and BDNF in an ECT Model Suggests Opening and Closure of a Window of Synaptic Plasticity

Electroconvulsive therapy (ECT) is an efficient and relatively fast acting treatment for depression. However, one severe side effect of the treatment is retrograde amnesia, which in certain cases can be long-term. The mechanisms behind the antidepressant effect and the amnesia are not well understood. We hypothesized that ECT causes transient downregulation of key molecules needed to stabilize synaptic structure and to prevent Ca2+ influx, and a simultaneous increase in neurotrophic factors, thus providing a short time window of increased structural synaptic plasticity. Here we followed regulation of NgR1, NgR3, LOTUS, BDNF, and AMPA subunits GluR1 and GluR2 flip and flop mRNA levels in hippocampus at 2, 4, 12, 24, and 72 hours after a single episode of induced electroconvulsive seizures (ECS) in rats. NgR1 and LOTUS mRNA levels were transiently downregulated in the dentate gyrus 2, 4, 12 and 4, 12, 24 h after ECS treatment, respectively. GluR2 flip, flop and GluR1 flop were downregulated at 4 h. GluR2 flip remained downregulated at 12 h. In contrast, BDNF, NgR3 and GluR1 flip mRNA levels were upregulated. Thus, ECS treatment induces a transient regulation of factors important for neuronal plasticity. Our data provide correlations between ECS treatment and molecular events compatible with the hypothesis that both effects and side effects of ECT may be caused by structural synaptic rearrangements.
Fast and Robust Pyramid-based Image Processing

Multi-scale manipulations are central to image editing but they are also prone to halos. Achieving artifact-free results requires sophisticated edge-aware techniques and careful parameter tuning. These shortcomings were recently addressed by the local Laplacian filters, which can achieve a broad range of effects using standard Laplacian pyramids. However, these filters are slow to evaluate and their relationship to other approaches is unclear. In this paper, we show that they are closely related to anisotropic diffusion and to bilateral filtering. Our study also leads to a variant of the bilateral filter that produces cleaner edges while retaining its speed. Building upon this result, we describe an acceleration scheme for local Laplacian filters that yields speed-ups on the order of 50×. Finally, we demonstrate how to use local Laplacian filters to alter the distribution of gradients in an image. We illustrate this property with a robust algorithm for photographic style transfer.
CANONICAL CONTACT STRUCTURES ON FIBRED SINGULARITY LINKS

We identify the canonical contact structure on any singula rity link which fibers over the circle by drawing a Legendrian handlebody dia gram of one of its Stein fillings. We also prove that the Euler class of such a contact s ructure vanishes although the Stein filling we construct has non-vanishing first Chern clas s.
Custom Load Shedding for Non-Cooperative Network Monitoring Applications

Network monitoring applications are prone to continuous overload situations due to the extreme and highly variable data rates of network traffic, traffic anomalies and network attacks. These overload situations can have a severe and unpredictable impact on the accuracy of monitoring applications, right when they are most valuable to network operators. Load shedding via traffic sampling has recently been proposed as an effective alternative to overprovisioning for efficiently handling overload situations in network monitoring. However, not all monitoring applications are robust against sampling and often other techniques can be devised to shed load more effectively. In order to provide a generic solution for arbitrary applications, we propose a load shedding scheme that, besides supporting standard sampling techniques, allows network monitoring applications to define custom load shedding methods. The main novelty of our approach is that the monitoring system can delegate the task of shedding excess load to applications in a safe manner and still achieve robustness in the presence of non-cooperative and selfish users. We use real-world packet traces and deploy a real implementation of our load shedding scheme in a large university network in order to show the robustness of our monitoring system against deliberate traffic anomalies and queries that fail to shed load correctly. Our results also show that the monitoring system is able to preserve a high degree of accuracy and fairness during extreme overload conditions.
What Rationality Assumption? or, How ‘Positive Political Theory’ Rests on a Mistake

In this article I address the reception of game-theoretic methods in political science. In particular I challenge the notion that such methods afford a plausible basis for what is commonly called ‘positive political theory’ (PPT). The standard rationale for PPT suggests that the point of formal models is, starting from ‘the’ rationality assumption, to derive predictions that can then be tested empirically. I argue that this standard rationale is hopelessly confused. The confusion stems from the assumption that game-theoretic models are empirically testable in some direct sense. This view is far from unanimously accepted among game theorists outside political science. I argue instead that game-theoretic models are best understood as tools for exploring the operation and limits of one set of basic causal mechanisms. I show how this works in practice and on that basis reassert the value of formal models in political science.
and Hypertension Quantitative Analysis of Lung Perfusion in Patients with Primary Pulmonary

The aim of this study was to evaluate quantitatively the heterogeneity of lung perfusion scans in patients with primary pulmonary hypertension (PPH) and to compare it with the severity of disease. Methods: Lung perfusion scans were obtained on 22 patients with PPH and 12 age-matched control subjects. The perfused area rates (PARs) were calculated by dividing the lung area in each 10% threshold width from 10% to 100% of maximal counts by total lung area. The total absolute difference in the PAR between each patient and the mean control value was assumed as the perfusion index of the lung (P index). The P index was compared with hemodynamic parameters and the right ventricular ejection fraction (RVEF), including 7 patients who received long-term vasodilator therapy. Results: The P index correlated significantly with mean pulmonary arterial pressure (P 0.001) and RVEF (P 0.05). In patients with vasodilator therapy, the P index was improved significantly after therapy (P 0.05) and was associated with a reduction in pulmonary arterial pressure. Conclusion: Quantitative assessment of lung perfusion irregularity might provide useful information about the severity of disease and the effect of therapy in addition to the routine visual representation.
Singaporean Caregivers’ Experiences of Placing a Relative into Long Term Care

ABSTRACT Objective: Caregivers experience many difficulties and challenges with the process of providing care particularly at times of transition, such as when the care recipient moves into a nursing home. This qualitative study aims to understand caregiver experiences of this important process. Methods: Twelve interviews were conducted with caregivers with an older relative in a nursing home in Singapore. The resulting data was analysed through thematic analysis. Results: Five themes were identified: Filial and cultural expectations shape caregivers’ experience of pre-placement decisions and post-placement; View of the placement decision; Continued impact of caring; Engagement with the institution and Maintaining the relationship. Conclusions: Caregivers were found to place significant emphasis on cultural values, specifically on filial piety. This impacted their caregiving role prior to placement, when making the decision to place their relative into a nursing home and in their continued involvement after placement. Despite the changing role, the placement experience was fraught with persisting difficulties involving maintaining the relationship with the resident and developing a new relationship with the nursing home.
CCL19 as a Chemokine Risk Factor for Posttreatment Lyme Disease Syndrome: a Prospective Clinical Cohort Study

ABSTRACT Approximately 10% to 20% of patients optimally treated for early Lyme disease develop persistent symptoms of unknown pathophysiology termed posttreatment Lyme disease syndrome (PTLDS). The objective of this study was to investigate associations between PTLDS and immune mediator levels during acute illness and at several time points following treatment. Seventy-six participants with physician-documented erythema migrans and 26 healthy controls with no history of Lyme disease were enrolled. Sixty-four cytokines, chemokines, and inflammatory markers were measured at each visit for a total of 6 visits over 1 year. An operationalized definition of PTLDS incorporating symptoms and functional impact was applied at 6 months and 1 year following treatment completion, and clinical outcome groups were defined as the return-to-health, symptoms-only, and PTLDS groups. Significance analysis of microarrays identified 7 of the 64 immune mediators to be differentially regulated by group. Generalized logit regressions controlling for potential confounders identified posttreatment levels of the T-cell chemokine CCL19 to be independently associated with clinical outcome group. Receiver operating characteristic analysis identified a CCL19 cutoff of >111.67 pg/ml at 1 month following treatment completion to be 82% sensitive and 83% specific for later PTLDS. We speculate that persistently elevated CCL19 levels among participants with PTLDS may reflect ongoing, immune-driven reactions at sites distal to secondary lymphoid tissue. Our findings suggest the relevance of CCL19 both during acute infection and as an immunologic risk factor for PTLDS during the posttreatment phase. Identification of a potential biomarker predictor for PTLDS provides the opportunity to better understand its pathophysiology and to develop early interventions in the context of appropriate and specific clinical information.