Miracle-dz/UniFAR-FTUs huggingface dataset:
Insights into the Role of Bcl6 in Follicular Th Cells Using a New Conditional Mutant Mouse Model

The transcriptional repressor Bcl6 controls development of the follicular Th cell (TFH) lineage, but the precise mechanisms by which Bcl6 regulates this process are unclear. A model has been proposed whereby Bcl6 represses the differentiation of T cells into alternative effector lineages, thus favoring TFH cell differentiation. Analysis of T cell differentiation using Bcl6-deficient mice has been complicated by the strong proinflammatory phenotype of Bcl6-deficient myeloid cells. In this study, we report data from a novel mouse model where Bcl6 is conditionally deleted in T cells (Bcl6fl/flCreCD4 mice). After immunization, programmed death -1 (PD-1)high TFH cells in Bcl6fl/flCreCD4 mice are decreased >90% compared with control mice, and Ag-specific IgG is sharply reduced. Residual PD-1highCXCR5+ TFH cells in Bcl6fl/flCreCD4 mice show a significantly higher rate of apoptosis than do PD-1highCXCR5+ TFH cells in control mice. Immunization of Bcl6fl/flCreCD4 mice did not reveal enhanced differentiation into Th1, Th2, or Th17 lineages, although IL-10 expression by CD4 T cells was markedly elevated. Thus, T cell–extrinsic factors appear to promote the increased Th1, Th2, and Th17 responses in germline Bcl6-deficient mice. Furthermore, IL-10 may be a key target gene for Bcl6 in CD4 T cells, which enables Bcl6 to promote the TFH cell phenotype. Finally, our data reveal a novel mechanism for the role of Bcl6 in promoting TFH cell survival.
Frequency of exercise-induced ST-T-segment deviations and cardiac arrhythmias in recreational endurance athletes during a marathon race: results of the prospective observational Berlin Beat of Running study

Objectives While regular physical exercise has many health benefits, strenuous physical exercise may have a negative impact on cardiac function. The ‘Berlin Beat of Running’ study focused on feasibility and diagnostic value of continuous ECG monitoring in recreational endurance athletes during a marathon race. We hypothesised that cardiac arrhythmias and especially atrial fibrillation are frequently found in a cohort of recreational endurance athletes. The main secondary hypothesis was that pathological laboratory findings in these athletes are (in part) associated with cardiac arrhythmias. Design Prospective observational cohort study including healthy volunteers. Setting and participants One hundred and nine experienced marathon runners wore a portable ECG recorder during a marathon race in Berlin, Germany. Athletes underwent blood tests 2–3 days prior, directly after and 1–2 days after the race. Results Overall, 108 athletes (median 48 years (IQR 45–53), 24% women) completed the marathon in 249±43 min. Blinded ECG analysis revealed abnormal findings during the marathon in 18 (16.8%) athletes. Ten (9.3%) athletes had at least one episode of non-sustained ventricular tachycardia, one of whom had atrial fibrillation; eight (7.5%) individuals showed transient ST-T-segment deviations. Abnormal ECG findings were associated with advanced age (OR 1.11 per year, 95% CI 1.01 to 1.23), while sex and cardiovascular risk profile had no impact. Directly after the race, high-sensitive troponin T was elevated in 18 (16.7%) athletes and associated with ST-T-segment deviation (OR 9.9, 95% CI 1.9 to 51.5), while age, sex and cardiovascular risk profile had no impact. Conclusions ECG monitoring during a marathon is feasible. Abnormal ECG findings were present in every sixth athlete. Exercise-induced transient ST-T-segment deviations were associated with elevated high-sensitive troponin T (hsTnT) values. Trial registration ClinicalTrials.gov NCT01428778; Results.
Breath Volatile Organic Compound Profiling of Colorectal Cancer Using Selected Ion Flow-tube Mass Spectrometry

Objective:Identify changes in volatile organic compounds (VOCs) concentration within exhaled breath observed with colorectal cancer (CRCa) relative to control groups.Validate the presence of discriminative VOCs in a prospective cohort.Identify VOC changes related to CRCa recurrence following surgical resection. Background: Breath VOCs have the potential to noninvasively diagnose cancer. Methods: Exhaled breath samples were collected using 2-L double-layered Nalophan bags, and were analyzed using selected-ion-flow-tube mass-spectrometry. Gold-standard test for comparison was endoscopy for luminal inspection and computed tomography (CT) to confirm cancer recurrence. Three studies were conducted:Profiling study: 150 patients; 50 CRCa and 100 controls;Independent diagnostic validation: 79 patients; 25 CRCa and 54 controls;Independent clinical validation with tumor recurrence: 40 patients; 19 postoperative (no recurrence), and 21 CRCa recurrences. Results:In multivariate analysis, propanal was significantly elevated in the cancer cohort compared with control patients. Using a threshold of 28 ppbv, this gave a sensitivity of 96% and specificity of 76% for CRCa diagnosis.In a prospective cohort, using a propanal threshold of 28 ppbv, this gave a sensitivity of 83.3% and specificity of 84.7%. Following surgery, propanal reduced to levels expected in control patients, and with recurrence, levels increased significantly. Using a threshold of 28 ppbv, the sensitivity for identification of CRCa recurrence was 71.4% and specificity was 90.9%. Conclusion: This study suggests the association of a single breath biomarker with the primary presence and recurrence of CRCa. Further multicenter validation studies are required to validate these findings.
Civil Society

Civil society is the interface between the public and the private: the rules and dispositions that define the relationships between the state and other social institutions, shaping both the state and these private entities. The first part of this chapter considers the apparent tension between the public and the private. The chapter then argues that, in contrast, the state should see the private realm as a necessary and beneficial counterpart to the public. This section invokes the idea of ‘invisible hand’ systems. It is an argument from the invisible hand that allows us to reconcile the restricted concern that is characteristic of the economic and social realms with the broader concern of the state, showing these to be complementary rather than set in tension. The chapter concludes by examining the constitutional structures needed to facilitate success in the private realm.
A Closer Look at Revealed Comparative Advantage: Gross-versus Value Added Trade Flows

With the availability of international value added trade data it has become evident that gross export data and value added data do not provide the same information. Although gross exports crosses national borders and is the target of trade policy, value added data tell us what fragment in the production chain is internationally competitive in a particular country. With respect to comparative advantage the differences between the two types of data are often illustrated by means of examples using a single sector. In the Ricardian theory of comparative advantage, however, the position of a commodity versus all other commodities in a country determines whether or not a sector has a comparative (dis)-advantage. This implies that distributions of comparative advantage of all sectors should be compared and not just individual sectors. In this paper we determine the distributions of Revealed Comparative Advantage (RCA) in terms of gross exports and value added for 40 countries. A Systematic comparison of these distributions shows that the distributions of RCA calculated with gross exports and value added data are indeed significantly different from each other. After establishing these significant differences we use the Great Recession as an example to determine which RCA measure has the largest information content regarding the real economy. We find that RCA calculated with value added data is the most telling.
Does a Good Workforce Influence Restaurant Performance or Does Good Restaurant Performance Influence the Workforce?

Workforce focus is one of the Baldrige Award's criteria, and it consists of two factors: workforce environment and workforce engagement. This study develops unit-level measures of workforce environment and workforce engagement and tests whether they affect two important outcomes, namely, intent to quit and unit sales per customer. Using a time-lagged research design, the results show that workforce environment and workforce engagement lead to unit results.
High-risk features of lupus nephritis: importance of race and clinical and histological factors in 166 patients.

BACKGROUND The pleomorphic nature of lupus nephritis has confounded efforts to refine estimates of prognosis. Consideration of interactions among prognostic factors may help to identify high-risk patients. METHODS By univariate and multivariate survival analysis, race and attributes of severe active lupus nephritis were evaluated as potentially important prognostic factors in 166 patients upon entry into prospective therapeutic trials of lupus kidney disease. RESULTS Black patients were significantly more likely than others to develop renal insufficiency. Cellular crescents emerged as the most predictive active pathological feature and interstitial fibrosis was the strongest chronic histological prognostic factor. Combinations of these morphological attributes identified particularly high-risk individuals. Patients with 50% or more cellular crescents and those with less extensive cellular crescents plus moderate to severe interstitial fibrosis were at markedly increased risk for doubling serum creatinine compared to those who lacked these histologic features (P < 0.0001). Azotaemia, anaemia, hypocomplementaemia, hypertension, tubular atrophy and glomerular sclerosis were also associated with an increased probability of renal function deterioration. Serum creatinine, haematocrit, race, and kidney pathology data emerged as independent predictors of renal insufficiency. Black patients in this study were more likely than the others to have high-risk histological features, including extensive cellular crescents (> or = 50%) and moderate to severe interstitial fibrosis, prior to randomization. CONCLUSIONS Combinations of high-risk demographic, clinical and histological attributes identify patients at increased risk for progressive renal function deterioration. Several factors, including the severity of kidney biopsy findings, probably contribute to the poor prognosis of Black patients in this study population.
Phylogenic Diversity and Taxonomic Problems of the Dictyosphaerium Morphotype within the Parachlorella Clade (Chlorellaceae, Trebouxiophyceae)

The Parachlorella clade was put forward as a group within the family Chlorellaceae in 2004. Recent molecular analyses have revealed that Dictyosphaerium morphotype algae form several independent lineages within the Parachlorella clade, and new genera and species have been established. In this study, we focus on the diversity of Dictyosphaerium morphotype algae within the Parachlorella clade, based on 42 strains from China. We used combined analyses of morphology and molecular data based on SSU and internal transcribed spacer region (ITS) rDNA sequences to characterize these algae. In addition, the secondary structure of ITS2 was compared to delineate new lineages. Our results revealed high phylogenic diversity of Dictyosphaerium morphotype algae, and we describe five distinct lineages. We examined the morphological features of these five lineages, and morphological differences are difficult to find compared with other Dictyosphaerium morphotype algae. The five distinct lineages were not described as new genera currently. We lastly discuss the taxonomic problems regarding the Dictyosphaerium morphotype within the Parachlorella clade, and possible solutions are considered.
The Building Block versus Stumbling Block Debate of Regionalism: From the Perspective of Service Trade Liberalization in Asia

When debating the pros and cons of economic regionalism, have we focused more on trade in goods at the expense of services? This article argues that regionalism is certainly a building block not a stumbling block to a multilateral trading system, using the service liberalization scheme of the Association of Southeast Asian Nations (ASEAN) as a case study. At the same time, it is critical to set out a proper institutional arrangement to ensure that regional service liberalization initiatives reinforce the global service regime. This article proposes an amendment of the current Article V of the General Agreements on Trade in Services (GATS) to define the appropriate relationship between multilateralism and regionalism in the context of services.
Asymmetric long-run effects in the oil industry

This paper analyzes long term dependence between the market value of oil firms and oil prices. Applying nonlinear cointegration, the results show that in the long-run oil price hikes and falls show different adjustments to the equilibrium. Using a momentum threshold autoregressive model (MTAR), we find that for oil producing firms, the adjustment is faster for oil price falls than for oil price hikes, but we do not find a difference on the speed of adjustment for oil integrated firms. Moreover, testing for asymmetric cointegration, we also find that oil price falls impact substantially the value of oil producers and integrated firms, but the same is not found for oil price hikes. Overall, the evidence suggests that firm value stays above equilibrium relationship when there are oil price hikes.
Motion correction of PET brain images through deconvolution: I. Theoretical development and analysis in software simulations

Image quality is significantly degraded even by small amounts of patient motion in very high-resolution PET scanners. Existing correction methods that use known patient motion obtained from tracking devices either require multi-frame acquisitions, detailed knowledge of the scanner, or specialized reconstruction algorithms. A deconvolution algorithm has been developed that alleviates these drawbacks by using the reconstructed image to estimate the original non-blurred image using maximum likelihood estimation maximization (MLEM) techniques. A high-resolution digital phantom was created by shape-based interpolation of the digital Hoffman brain phantom. Three different sets of 20 movements were applied to the phantom. For each frame of the motion, sinograms with attenuation and three levels of noise were simulated and then reconstructed using filtered backprojection. The average of the 20 frames was considered the motion blurred image, which was restored with the deconvolution algorithm. After correction, contrast increased from a mean of 2.0, 1.8 and 1.4 in the motion blurred images, for the three increasing amounts of movement, to a mean of 2.5, 2.4 and 2.2. Mean error was reduced by an average of 55% with motion correction. In conclusion, deconvolution can be used for correction of motion blur when subject motion is known.
Temperature-dependent small RNA expression in Drosophila melanogaster

ABSTRACT Temperature has a major impact on gene expression in ectotherms. But until recently, it was not clear in which way, if any, small non-coding RNAs such as miRNAs or piRNAs contribute to thermosensitive gene regulation. We have recently shown that temperature-responsive miRNAs in Drosophila drive adaptation to different ambient temperatures on the transcriptome level. Moreover, we demonstrated that higher temperatures lead to a more efficient piRNA-dependent transposon silencing, possibly due to heat-induced unfolding of RNA secondary structures. In this commentary, we will dwell upon particular interesting aspects connected to our findings, hoping that our point of view may encourage other scientists to address some of the questions raised here. We will particularly focus on aspects related to climate-dependent transposon propagation in evolution and putative transgenerational epigenetic effects of altered small RNA transcriptomes. We further briefly indicate how temperature-responsive miRNAs may confound the interpretation of data obtained from experiments comprising heat-shock treatment which is a widely used technique not only in Drosophila genetics.
Unsupervised Clustering of Quantitative Image Phenotypes Reveals Breast Cancer Subtypes with Distinct Prognoses and Molecular Pathways

Purpose: To identify novel breast cancer subtypes by extracting quantitative imaging phenotypes of the tumor and surrounding parenchyma and to elucidate the underlying biologic underpinnings and evaluate the prognostic capacity for predicting recurrence-free survival (RFS). Experimental Design: We retrospectively analyzed dynamic contrast–enhanced MRI data of patients from a single-center discovery cohort (n = 60) and an independent multicenter validation cohort (n = 96). Quantitative image features were extracted to characterize tumor morphology, intratumor heterogeneity of contrast agent wash-in/wash-out patterns, and tumor-surrounding parenchyma enhancement. On the basis of these image features, we used unsupervised consensus clustering to identify robust imaging subtypes and evaluated their clinical and biologic relevance. We built a gene expression–based classifier of imaging subtypes and tested their prognostic significance in five additional cohorts with publically available gene expression data but without imaging data (n = 1,160). Results: Three distinct imaging subtypes, that is, homogeneous intratumoral enhancing, minimal parenchymal enhancing, and prominent parenchymal enhancing, were identified and validated. In the discovery cohort, imaging subtypes stratified patients with significantly different 5-year RFS rates of 79.6%, 65.2%, 52.5% (log-rank P = 0.025) and remained as an independent predictor after adjusting for clinicopathologic factors (HR, 2.79; P = 0.016). The prognostic value of imaging subtypes was further validated in five independent gene expression cohorts, with average 5-year RFS rates of 88.1%, 74.0%, 59.5% (log-rank P from <0.0001 to 0.008). Each imaging subtype was associated with specific dysregulated molecular pathways that can be therapeutically targeted. Conclusions: Imaging subtypes provide complimentary value to established histopathologic or molecular subtypes and may help stratify patients with breast cancer. Clin Cancer Res; 23(13); 3334–42. ©2017 AACR.
Law enforcement by courts: Political economy and impact on firms.

The subject of this thesis is judicial enforcement of contracts and property rights and its economic implications. The first chapter introduces the topic, discusses the issues involved in empirical research on law enforcement, and surveys the literature. The second chapter develops an analytical method for empirical identification of relative policy preferences and competence of judges. The third chapter studies the impact of judicial selection on law enforcement. The fourth chapter analyses the effect of predictability of law enforcement on firms' finances. In chapter two, I develop a model of judicial decision making in a two tier court system. It shows that relative preferences of the two courts can be identified by comparing appellate court reversal rates for different types of lower court decisions. I use this result to analyze the data on Russia's commercial courts which I collected for this purpose. The findings show that regional courts favour small firms relatively more than courts of appeal. In chapter three, I compare selection of judges by the legislator with that by the executive branch. First, I analyze the differences in the incentives of the two offices theoretically. Second, I empirically exploit a natural experiment in judicial appointment procedures in Russian courts. I find that judges selected by the legislature favour small firms more than judges appointed by the executive. In the fourth chapter, I show both empirically and analytically that greater predictability in law enforcement encourages credit to firms. The data from Russia indicates that more predictable courts stimulate lending by raising the number of firms that have access to bank financing. In contrast, trade credit is only weakly affected by court performance.
A stereo vision-based augmented reality system with a wide range of registration

Proposes a vision-based augmented reality system with a wide range of registration. To realize an augmented reality system, it is required to geometrically register real and virtual worlds. In the case of a vision-based augmented reality with marker tracking, its measurement range is usually limited because markers placed in the real world should be captured by cameras. The proposed method realizes a stereo vision-based augmented reality system with a wide range of registration by automatically detecting and tracking new, markers that come into sight. The feasibility of the system has been successfully demonstrated through experiments.
Multi-Finger Interaction and Synergies in Finger Flexion and Extension Force Production

The aim of this study was to discover finger interaction indices during single-finger ramp tasks and multi-finger coordination during a steady state force production in two directions, flexion, and extension. Furthermore, the indices of anticipatory adjustment of elemental variables (i.e., finger forces) prior to a quick pulse force production were quantified. It is currently unknown whether the organization and anticipatory modulation of stability properties are affected by force directions and strengths of in multi-finger actions. We expected to observe a smaller finger independency and larger indices of multi-finger coordination during extension than during flexion due to both neural and peripheral differences between the finger flexion and extension actions. We also examined the indices of the anticipatory adjustment between different force direction conditions. The anticipatory adjustment could be a neural process, which may be affected by the properties of the muscles and by the direction of the motions. The maximal voluntary contraction (MVC) force was larger for flexion than for extension, which confirmed the fact that the strength of finger flexor muscles (e.g., flexor digitorum profundus) was larger than that of finger extensor (e.g., extensor digitorum). The analysis within the uncontrolled manifold (UCM) hypothesis was used to quantify the motor synergy of elemental variables by decomposing two sources of variances across repetitive trials, which identifies the variances in the uncontrolled manifold (VUCM) and that are orthogonal to the UCM (VORT). The presence of motor synergy and its strength were quantified by the relative amount of VUCM and VORT. The strength of motor synergies at the steady state was larger in the extension condition, which suggests that the stability property (i.e., multi-finger synergies) may be a direction specific quantity. However, the results for the existence of anticipatory adjustment; however, no difference between the directional conditions suggests that feed-forward synergy adjustment (changes in the stability property) may be at least independent of the magnitude of the task-specific apparent performance variables and its direction (e.g., flexion and extension forces).