Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone H3K27ac separates active from poised enhancers and predicts developmental state

Developmental programs are controlled by transcription factors and chromatin regulators, which maintain specific gene expression programs through epigenetic modification of the genome. These regulatory events at enhancers contribute to the specific gene expression programs that determine cell state and the potential for differentiation into new cell types. Although enhancer elements are known to be associated with certain histone modifications and transcription factors, the relationship of these modifications to gene expression and developmental state has not been clearly defined. Here we interrogate the epigenetic landscape of enhancer elements in embryonic stem cells and several adult tissues in the mouse. We find that histone H3K27ac distinguishes active enhancers from inactive/poised enhancer elements containing H3K4me1 alone. This indicates that the amount of actively used enhancers is lower than previously anticipated. Furthermore, poised enhancer networks provide clues to unrealized developmental programs. Finally, we show that enhancers are reset during nuclear reprogramming.
Adaptive partitioning of urban facades

Automatically discovering high-level facade structures in unorganized 3D point clouds of urban scenes is crucial for applications like digitalization of real cities. However, this problem is challenging due to poor-quality input data, contaminated with severe missing areas, noise and outliers. This work introduces the concept of adaptive partitioning to automatically derive a flexible and hierarchical representation of 3D urban facades. Our key observation is that urban facades are largely governed by concatenated and/or interlaced grids. Hence, unlike previous automatic facade analysis works which are typically restricted to globally rectilinear grids, we propose to automatically partition the facade in an adaptive manner, in which the splitting direction, the number and location of splitting planes are all adaptively determined. Such an adaptive partition operation is performed recursively to generate a hierarchical representation of the facade. We show that the concept of adaptive partitioning is also applicable to flexible and robust analysis of image facades. We evaluate our method on a dozen of LiDAR scans of various complexity and styles, and the image facades from the eTRIMS database and the Ecole Centrale Paris database. A series of applications that benefit from our approach are also demonstrated.
Effects of iodinated contrast and field strength on gadolinium enhancement: Implications for direct MR arthrography

To optimize direct magnetic resonance (MR) arthrography by determining the effect of dilution of gadolinium in iodinated contrast, saline, or albumin on T1‐weighted, T2‐weighted, and gradient‐recalled echo (GRE) images, and the effect of scanner field strength.
Understanding event attendance through analysis of human crowd behavior in social networks

Understanding human crowd mobility has found important applications in several commercial domains such as marketing, recommendation systems and resource planning. In this paper we investigate users' social activities and interactions developed in "human-centered participatory sensing" groups and perform an analysis to understand human crowd behavior. We exploit two popular real and heterogeneous datasets for our analysis: an event based social network (Meetup) dataset and a checkin-based geosocial network (Foursquare) dataset, to understand user attendance in social community events and provide insights into the factors that influence users to attend events.
Allelic Richness following Population Founding Events – A Stochastic Modeling Framework Incorporating Gene Flow and Genetic Drift

Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution.
1 Covariate Shift by Kernel Mean Matching

Given sets of observations of training and test data, we consider the problem of re-weighting the training data such that its distribution more closely matches that of the test data. We achieve this goal by matching covariate distributions between training and test sets in a high dimensional feature space (specifically, a reproducing kernel Hilbert space). This approach does not require distribution estimation. Instead, the sample weights are obtained by a simple quadratic programming procedure. We provide a uniform convergence bound on the distance between the reweighted training feature mean and the test feature mean, a transductive bound on the expected loss of an algorithm trained on the reweighted data, and a connection to single class SVMs. While our method is designed to deal with the case of simple covariate shift (in the sense of Chapter ? ), we have also found benefits for sample selection bias on the labels. Our correction procedure yields its greatest and most consistent advantages when the learning algorithm returns a classifier/regressor that is “simpler” than the data might suggest.
Complex interactions of transcription factors in mediating cytokine biology in T cells

T‐helper (Th) cells play critical roles within the mammalian immune system, and the differentiation of naive CD4+ T cells into distinct T‐helper subsets is critical for normal immunoregulation and host defense. These carefully regulated differentiation processes are controlled by networks of cytokines, transcription factors, and epigenetic modifications, resulting in the generation of multiple CD4+ T‐cell subsets, including Th1, Th2, Th9, Th17, Treg, and Tfh cells. In this review, we discuss the roles of transcription factors in determining the specific type of differentiation and in particular the role of interleukin‐2 (IL‐2) in promoting or inhibiting Th differentiation. In addition to discussing master regulators and subset‐specific transcription factors for distinct T‐helper cell populations, we focus on signal transducer and activator of transcription (STAT) proteins and on the cooperative action of interferon regulatory factor 4 (IRF4) with activator protein 1 (AP‐1) family proteins and STAT3 in the assembly of complexes that broadly influence T‐cell differentiation.
Problems and Results on Finite and Infinite Graphs

I . Let oc be an ordinal number which has no immediate predecessor . G(cx) denotes a graph whose vertices have order type or . Hajnal, Milner and I conjectured [4] that every G(cx) either contains an infinite path or an independent set of type cc . We proved our conjecture for c c< w, m +2 and our method breaks down completely for or m i n+2 . Hajnal, Milner and I proved that every G(oc) either contains a c4 or an independent set of type cc . In fact we proved that G(oc) either contains a K(n ;K 0 ) (i .e . a bipartite graph of n white and N O black vertices) or an independent set of type cx . Our proof was never published since Laver [5] proved our conjecture : Let be an order type without fixed points . Then G(J) either contains C 4 or an independent set of type t .
Mechanisms of Iron Entrainment into Slag due to Rising Gas Bubbles

Iron droplets can be entrained into the slag phase when gas bubbles pass through the molten iron/slag interface. The physical phenomena occurring during passage of single bubbles through the interface were investigated by using in-situ X-ray transmission techniques and optical microscopy of the cooled specimens afterwards. Based on the X-ray observations, two mechanisms of entrainment of iron droplets into slag were proposed: large droplets are entrained by jet formation, fine droplets by the rupture of the metal film covering the gas bubble releasing from the iron/slag interface, respectively. The results provide novel erudition of the interaction between the ascending gas bubbles and the slag/iron systems.
In Color Perception, Size Matters

In designing colors for digital visualization systems. one of the most critical factors is the interaction between size and color appearance. Whereas artists and visual designers understand this, recommendations for using color in visualization rarely address the issue, or even recognize it. The goal is to keep the user focused on the data, with color simply one of many tools used toward problem solving and discovery.
How Does the Market Value Toxic Assets?

Abstract How does the market value “toxic” structured-credit securities? We study the valuation of what is possibly the most toxic of all toxic assets: the equity tranche of a collateralized debt obligation (CDO). In theory, CDO equity should be similar in nature to bank stock since both represent residual claims on a portfolio of loans. We find CDO equity returns are much more related to stock returns than to fixed-income returns. CDO equity returns track the returns of financial stocks much more closely than any other industry. Nearly two-thirds of the variation in CDO returns can be explained by fundamentals.
Antidepressant-induced rapid cycling: another perspective.

BACKGROUND Depressive symptoms are the main cause of morbidity in bipolar patients, but concern about antidepressant-induced rapid cycling has limited antidepressant use in such patients. This paper evaluates the validity and the prevalence of antidepressant-induced rapid cycling. METHODS The literature regarding antidepressant induced rapid cycling is reviewed, focusing on two issues: 1) does antidepressant-induced rapid cycling occur only in patients who become manic or hypomanic on antidepressants; 2) can the apparent shortening of cycle length on antidepressants be attributable simply to the fact that antidepressants alleviate depression and can precipitate mania or hypomania. RESULTS The suggestion that antidepressants can induce rapid cycling is derived primarily from patients who become manic or hypomanic on antidepressants. The fact that antidepressants alleviate depression and precipitate mania can explain most of the available data, without invoking the poorly defined concept of antidepressant-induced rapid cycling. CONCLUSIONS Bipolar patients who are stable on mood stabilizers, who don't become manic or hypomanic on anti-depressants, can be safely treated with antidepressants without excessive concern about inducing rapid cycling.
Interstitial pneumonitis in patients infected with the human immunodeficiency virus.

BACKGROUND--A study was performed to identify the clinical, radiographic, and histopathological features of interstitial pneumonitis in patients infected with the human immunodeficiency virus. METHODS--A retrospective review was made of the case notes, chest radiographs, and histopathological results of seven HIV-1 antibody positive patients with symptomatic diffuse pulmonary disease and a pathological diagnosis of non-specific interstitial pneumonitis. RESULTS--All patients had dyspnoea, with or without cough, and chest radiographs showing diffuse infiltrates. The arterial oxygen tension ranged widely from 5.9 to 13.1 kPa. The initial clinical diagnosis was Pneumocystis carinii pneumonia in most cases. The pathological diagnosis was made by transbronchial biopsy in one case and by open lung biopsy in six cases. The interstitial pneumonitis consisted of a patchy lymphocytic infiltrate composed of B cells in focal aggregates and T cells in a more diffuse distribution. The T cell population was a mixture of CD4+ and CD8+ cells. The histological findings contrast with the more extensive infiltrate of predominantly CD8+ lymphocytes seen in HIV-associated lymphocytic interstitial pneumonitis which occurs mainly in children. The condition ran a subacute course. Three patients spontaneously improved and three improved with steroid therapy. Long term survival was less than three years, the prognosis being determined by other infective or neoplastic complications. CONCLUSIONS--Non-specific interstitial pneumonitis usually presents with an illness resembling Pneumocystis carinii pneumonia but occurs when the CD4 and total lymphocyte counts are still preserved. The pneumonitis resolves spontaneously or responds to steroids, and does not itself lead directly to the patient's death. It does, however, appear to mark a downturn in the course of HIV infection.
2. Introduction

Type III secretion system expression in oxygen-limited Pseudomonas aeruginosa cultures is stimulated by isocitrate lyase activity. Open Biol 3: 120131. Subject Area: microbiology/biochemistry/molecular biology Type III secretion system expression in oxygen-limited Pseudomonas aeruginosa cultures is stimulated by isocitrate lyase activity 1. Summary Pseudomonas aeruginosa is an opportunistic human pathogen and a common cause of chronic infections in individuals with cystic fibrosis (CF). Oxygen limitation was recently reported to regulate the expression of a major virulence determinant in P. aeruginosa, the type III secretion system (T3SS). Here, we show that expression of the T3SS in oxygen-limited growth conditions is strongly dependent on the glyoxylate shunt enzyme, isocitrate lyase (ICL; encoded by aceA), which was previously shown to be highly expressed in CF isolates. ICL-dependent regulation of the T3SS did not alter the expression level of the master transcriptional regulator, ExsA, but did affect expression of the T3 structural proteins, effectors and regulators (ExsC, ExsD and ExsE). An aceA mutant displayed enhanced bio-film formation during anaerobic growth, which suggested that AceA-dependent modulation of type III secretion might impinge upon the RetS/LadS signalling pathways. Indeed, our data suggest that RetS is able to mediate some of its effects through AceA, as expression of aceA in trans partially restored T3SS expression in a retS mutant. Our findings indicate that AceA is a key player in the metabolic regulation of T3SS expression during oxygen-limited growth of P. aeruginosa. To the best of our knowledge, this is the first demonstration that the T3SS can be regulated by factors that do not affect ExsA expression levels. Pseudomonas aeruginosa is an opportunistic human pathogen and a major cause of chronic infections in individuals with cystic fibrosis (CF). P. aeruginosa expresses a highly regulated protein secretion machinery called the type III secretion system (T3SS), which translocates a specific subset of exotoxin effector proteins (ExoS or ExoU, ExoT and ExoY) directly into the host cell cytosol where they mediate their pathogenic effects [1–5]. The T3SS regulon consists of approximately 40 coordinately regulated genes which are arranged into five operons, encoding the needle complex, translocation apparatus and regulator proteins; the effectors and chaperones are encoded elsewhere on the genome [6]. Transcription of the regulon is directly coupled to secretion through a cascade of interactions involving ExsC, ExsD and ExsE, which ultimately impinge upon the master transcriptional activator of T3SS gene expression,
Computational modelling of rubber-like materials under monotonic and cyclic loading

The simulation of rubber-like material behaviour by means of the finite element method has been described in this study. Proper material models for the numerical description of static hyper-elasticity, the ideal Mullins effect and the Mullins effect with permanent deformation were proposed, respectively. The second focus of this study was the verification of numerical constitutive models by means of experimental evidence. It was concluded that Gao's model with only two parameters describes the mechanical behaviour of rubber-like material adequately. The model parameters estimated from simple tension are valid for other loading conditions (compression and shear) if the specimens are made of the same material. This property is crucial for the general use of Gao's elastic model. The present work demonstrated that both the continuum damage mechanics model and the pseudo-elastic model combined with Gao's elastic model are capable of simulating the Mullins effect in their own characteristic way. The pseudo-elastic model significantly simplifies the identification of model parameters. Finally, combination of the pseudo-elastic concept and Gao's model was used to construct a specific model for the description of Mullins effect with permanent deformation. The evolution of stress softening, the permanent deformation and all turning points in the numerical simulations were reproduced well compared to experimental data.
Measurement method of light transmittance of layered metal-dielectric metamaterial

We propose a measurement method of light transmittance of metamaterials by directly contacting the metamaterial on a Si photodiode. Our measurement method enables direct detection of not only the propagation wave component but also the evanescent wave component through the metamaterial. In this paper, we fabricated a layered metal-dielectric metamaterial composed of Ag/Al2O3 layers on the Si photodiode. The transmittance property of evanescent wave was measured. This result indicates that our measurement system detects evanescent wave transferred through the fabricated metamaterial.
Association between markers of glucose metabolism and risk of colorectal adenoma.

BACKGROUND & AIMS Diabetes is a risk factor for colorectal cancer. We studied the association between markers of glucose metabolism and metabolic syndrome and the presence of colorectal adenomas in a large number of asymptomatic men and women attending a health screening program in South Korea. We also investigated whether these associations depend on adenoma location. METHODS In a cross-sectional study, we measured fasting levels of glucose, insulin, hemoglobin A1c, and C-peptide and calculated homeostatic model assessment (HOMA) values (used to quantify insulin resistance) for 19,361 asymptomatic South Korean subjects who underwent colonoscopy examinations from January 2006 to June 2009. Participants completed a standardized self-administered health questionnaire and a validated semiquantitative food frequency questionnaire. Blood samples were collected on the day of the colonoscopy; fasting blood samples were also collected. Robust Poisson regression was used to model the associations of glucose markers with the prevalence of any adenoma. RESULTS Using detailed multivariable-adjusted dose-response models, the prevalence ratios (aPR, 95% confidence interval [CI]) for any adenoma, comparing the 90th with the 10th percentile, were 1.08 (1.00-1.16; P = .04) for fasting glucose, 1.07 (0.99-1.15; P = .10) for insulin, 1.09 (1.02-1.18, P = .02) for HOMA, 1.09 (1.01-1.17; P = .02) for hemoglobin A1c, and 1.14 (1.05-1.24; P = .002) for C-peptide. The corresponding ratios for nonadvanced adenomas were 1.11 (0.99-1.25; P = .08), 1.10 (0.98-1.24; P = .12), 1.15 (1.02-1.29; P = .02), 1.14 (1.01-1.28; P = .03), and 1.20 (1.05-1.37; P = .007), respectively. The corresponding ratios for advanced adenomas were 1.32 (0.94-1.84; P = .11), 1.23 (0.87-1.75; P = .24), 1.30 (0.92-1.85; P = .14), 1.13 (0.79-1.61; P = .50), and 1.67 (1.15-2.42; P = .007), respectively. Metabolic syndrome was associated with the prevalence of any adenoma (aPR, 1.18; 95% CI, 1.13-1.24; P < .001), nonadvanced adenoma (aPR, 1.30; 95% CI, 1.20-1.40; P < .001), and advanced adenoma (aPR, 1.42; 95% CI, 1.14-1.78; P = .002). Associations were similar for adenomas located in the distal versus proximal colon. CONCLUSIONS Increasing levels of glucose, HOMA values, levels of hemoglobin A1c and C-peptide, and metabolic syndrome are significantly associated with the prevalence of adenomas. Adenomas should be added to the list of consequences of altered glucose metabolism.
Review article: diagnosis and investigation of gastro‐oesophageal reflux disease in Japanese patients

Gastro‐oesophageal reflux disease (GERD) encompasses a wide range of disorders defined by either reflux‐related symptoms or by complications of gastro‐oesophageal reflux. The most characteristic GERD symptoms are heartburn and acid regurgitation. Patients with these symptoms are in most cases easily identifiable and diagnosis is made on the basis of symptoms alone. For patients with a decreased frequency of heartburn, diagnosis is more difficult, and endoscopy is the single best test for diagnosis of GERD. A major difference between the West and Asia is the frequency of endoscopic investigation. In Japan, the earlier high prevalence of stomach cancers resulted in the increased use of endoscopy as an investigational tool for dyspeptic symptoms and today endoscopy continues to be widely available as a diagnostic tool. However, the overall sensitivity of endoscopy for the diagnosis of GERD is less than 50% since not all patients will have oesophagitis at the time of endoscopy. Ambulatory pH monitoring is therefore a frequently used diagnostic tool as it allows correlation between reflux events and symptoms, and is especially useful in patients with atypical or extraoesophageal symptoms. Oesophageal manometry is also an excellent test to evaluate oesophageal function and to measure sphincter pressure and while it may not provide an unequivocal diagnosis of GERD it is a useful tool with which to evaluate oesophageal function.
Accuracy of Colposcopically Directed Biopsy: Results from an Online Quality Assurance Programme for Colposcopy in a Population-Based Cervical Screening Setting in Italy

Purpose. To report the accuracy of colposcopically directed biopsy in an internet-based colposcopy quality assurance programme in northern Italy. Methods. A web application was made accessible on the website of the regional Administration. Fifty-nine colposcopists out of the registered 65 logged in, viewed a posted set of 50 digital colpophotographs, classified them for colposcopic impression and need for biopsy, and indicated the most appropriate site for biopsy with a left-button mouse click on the image. Results. Total biopsy failure rate, comprising both nonbiopsy and incorrect selection of biopsy site, was 0.20 in CIN1, 0.11 in CIN2, 0.09 in CIN3, and 0.02 in carcinoma. Errors in the selection of biopsy site were stable between 0.08 and 0.09 in the three grades of CIN while decreasing to 0.01 in carcinoma. In multivariate analysis, the risk of incorrect selection of biopsy site was 1.97 for CIN2, 2.52 for CIN3, and 0.29 for carcinoma versus CIN1. Conclusions. Although total biopsy failure rate decreased regularly with increasing severity of histological diagnosis, the rate of incorrect selection of biopsy site was stable up to CIN3. In multivariate analysis, CIN2 and CIN3 had an independently increased risk of incorrect selection of biopsy site.