Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins

Variation in DNA methylation is being increasingly associated with health and disease outcomes. Although DNA methylation is hypothesized to be a mechanism by which both genetic and non-genetic factors can influence the regulation of gene expression, little is known about the extent to which DNA methylation at specific sites is influenced by heritable as well as environmental factors. We quantified DNA methylation in whole blood at age 18 in a birth cohort of 1,464 individuals comprising 426 monozygotic (MZ) and 306 same-sex dizygotic (DZ) twin pairs. Site-specific levels of DNA methylation were more strongly correlated across the genome between MZ than DZ twins. Structural equation models revealed that although the average contribution of additive genetic influences on DNA methylation across the genome was relatively low, it was notably elevated at the highly variable sites characterized by intermediate levels of DNAm that are most relevant for epigenetic epidemiology. Sites at which variable DNA methylation was most influenced by genetic factors were significantly enriched for DNA methylation quantitative trait loci (mQTL) effects, and overlapped with sites where inter-individual variation correlates across tissues. Finally, we show that DNA methylation at sites robustly associated with environmental exposures such as tobacco smoking and obesity is also influenced by additive genetic effects, highlighting the need to control for genetic background in analyses of exposure-associated DNA methylation differences. Estimates of the contribution of genetic and environmental influences to DNA methylation at all sites profiled in this study are available as a resource for the research community (http://www.epigenomicslab.com/online-data-resources).
[MINI-PERCUTANEOUS NEPHROLITHOTRIPSY – OUR FIRST EXPERIENCE].

Urolithiasis is a significant problem in the developed countries due to the increased number of patients with stones. Just a few decades ago open surgery was the only surgical treatment which is today, in most cases, replaced with minimally-invasive methods. One of these new methods is mini-percutaneous nephrolihotripsy. We present four patients in whom mini-percutaneous nephrolithotripsy was performed. In all patients the stone was located in the renal pelvis. In three patients the stone was in the native kidney and in one in the transplanted kidney. In all patients laser lithotripsy was successfully performed. On the control x-ray the residual fragments were not found in any patients. Mini-percutaneous nephrolithotripsy is a minimally-invasive method which is successfull in the treatment of nephfrolithiasis in native and transplanted kidneys.
"Remote" myokine protects from pulmonary ischemia/reperfusion injury by a surprising "proximal" control mechanism.

The concept of remote ischemic preconditioning (RIPC) was first conceived more than quarter of a century ago in the context of myocardial ischemia/reperfusion (I/R) injury. It was originally based on the principle of “intra”-myocardial protection, i.e., to reduce myocardial I/R damage by subjecting the heart to cycles of “sub-lethal” myocardial I/R prior to prolonged coronary artery occlusion, which however was clinically restricted to elective cardiac surgery settings (1).
An informed transition? International medical graduates settling in the united states and canada

International medical graduates (IMGs) are medical professionals who have immigrated to the United States (US) or Canada (Ca) in hopes of integrating into the labor market. IMGs can be a very helpful resource supplying a diverse background and expertise to the medical system in the host country [Chen et al., ]. However, immigration and integration into a new country can be difficult processes due to differences in cultural norms, information sources, and information dissemination. In this study, we investigate the nature of information in the lived experiences of IMGs as they make a new life for themselves and their families in either the US or Canada. By so doing, we contribute to the limited body of research on this population by providing an informational perspective. Semi‐structured interviews were conducted with 20 IMGs residing in the US or Canada. Our findings indicate that IMGs spend an inordinate amount of time searching for occupational and employment‐related information, which includes information about retraining and residency programs, along with varied strategies to make sense of the new information landscapes. IMGs use various strategies to identify signposts and become conversant in the new landscape. Despite the limited sample, it becomes clear that one's ability to become literate in these new information environments leads to more positive outcomes (i.e., integrating the labor market, overall well‐being, belonging).
A Bayesian latent variable approach to aggregation of partial and top‐ranked lists in genomic studies

In genomic research, it is becoming increasingly popular to perform meta‐analysis, the practice of combining results from multiple studies that target a common essential biological problem. Rank aggregation, a robust meta‐analytic approach, consolidates such studies at the rank level. There exists extensive research on this topic, and various methods have been developed in the past. However, these methods have two major limitations when they are applied in the genomic context. First, they are mainly designed to work with full lists, whereas partial and/or top‐ranked lists prevail in genomic studies. Second, the component studies are often clustered, and the existing methods fail to utilize such information. To address the above concerns, a Bayesian latent variable approach, called BiG, is proposed to formally deal with partial and top‐ranked lists and incorporate the effect of clustering. Various reasonable prior specifications for variance parameters in hierarchical models are carefully studied and compared. Simulation results demonstrate the superior performance of BiG compared with other popular rank aggregation methods under various practical settings. A non–small‐cell lung cancer data example is analyzed for illustration.
Estimating the protein burden limit of yeast cells by measuring the expression limits of glycolytic proteins

The ultimate overexpression of a protein could cause growth defects, which are known as the protein burden. However, the expression limit at which the protein-burden effect is triggered is still unclear. To estimate this limit, we systematically measured the overexpression limits of glycolytic proteins in Saccharomyces cerevisiae. The limits of some glycolytic proteins were up to 15% of the total cellular protein. These limits were independent of the proteins’ catalytic activities, a finding that was supported by an in silico analysis. Some proteins had low expression limits that were explained by their localization and metabolic perturbations. The codon usage should be highly optimized to trigger the protein-burden effect, even under strong transcriptional induction. The S–S-bond-connected aggregation mediated by the cysteine residues of a protein might affect its expression limit. Theoretically, only non-harmful proteins could be expressed up to the protein-burden limit. Therefore, we established a framework to distinguish proteins that are harmful and non-harmful upon overexpression.
Heat shock protein 47 as indispensible participant in liver fibrosis: Possible protective effect of lactoferrin

Lactoferrin (LF) was previously suggested to have a protective effect against liver fibrosis by preventing hepatic stellate cells (HSCs) activation. The effect of LF on heat shock protein 47 (HSP47) has not yet been studied so this study was designed to investigate LF effect on HSP47 as a potential target for management of liver fibrosis and comparing it with silymarin (SM) in a thioacetamide (TAA)‐induced liver fibrosis model. Rats were divided into four groups; normal control, TAA (TAA‐treated), LF (LF + TAA‐treated), and SM (SM + TAA‐treated). After 6 weeks, both LF and SM improved the grade of cirrhosis, reduced collagen fibers deposition, inactivated HSCs, significantly decreased elevated liver enzymes, HSP47, hydroxyproline content, transforming growth factor‐beta 1, matrix metalloproteinase‐2, 8‐hydroxydeoxyguanosine, malondialdehyde, nitric oxide levels and the percentage of alpha smooth muscle actin positive HSCs compared with TAA group. Moreover, LF significantly increased the total antioxidant capacity compared with TAA group. It could be concluded that LF is a promising antifibrotic drug and could be considered as one of the HSP47 inhibitors but SM is still more potent. © 2018 IUBMB Life, 70(8):795–805, 2018
The peristomial plates of ophiuroids (Echinodermata: Ophiuroidea) highlight an incongruence between morphology and proposed phylogenies

The peristomial plates are skeletal components of the interbrachial frame (or mouth frame), which is located below the true mouth of ophiuroids. Whilst the peristomial plates were extensively described and used as diagnostic characters by some early workers, for the past 100 years they have been largely neglected as a taxonomic resource. In this investigation the peristomial plates of 48 species representing 21 families were examined directly, and information on a further 61 species, including representatives of another eight families, was obtained from the published literature. Observations were made with regard to fragmentation state, relative size and orientation of the peristomial plates. Although fragmentation state showed little consistency at any taxonomic level, relative size and orientation segregated a group of families comprising species with relatively small, inclined peristomial plates, viz. Ophiotrichidae, Ophiopholidae, Ophiactidae, Amphiuridae and Ophiocomidae, together with a single hemieuryalid species–Ophioplocus januarii. The distribution of peristomial plate traits was strongly correlated with that of several other character states pertaining to the interbrachial frame. This supported the proposition that two major types of interbrachial frame are present in ophiuroids (designated ‘A’ and ‘B’). Current phylogenies inferred from both morphological and molecular data imply that type B is derived and has evolved independently at least twice in the orders Amphilepidida and Ophiacanthida. This represents a remarkable example of evolutionary convergence. An analysis of the distribution of all interbrachial frame character states suggested that within the Amphilepidida paedomorphosis was probably responsible for the complete reversion of the interbrachial frame to the ancestral type A condition in two families (Ophiothamnidae and Amphilepididae) of suborder Gnathophiurina and possibly responsible for varying degrees of trait reversal in the four families of suborder Ophionereidina. Such paedomorphic events may have been associated with a secondary return to the deep-sea from shallow-sea environments.
Colored Stochastic Shadow Mapping for Direct Volume Rendering

Creating direct volume renderings with shadows can lead to a better perception of the rendered images. Deep shadow maps is an effective and efﬁcient approach to compute shadows at interactive rates. We propose an alternative approach based on colored stochastic shadow maps (CSSM), which can produce higher-quality colored shadows while using less texture memory. CSSM is based on a stochastic generation of the shadow map, which is queried multiple times for denoising during rendering
Combining active learning suggestions

We study the problem of combining active learning suggestions to identify informative training examples by empirically comparing methods on benchmark datasets. Many active learning heuristics for classification problems have been proposed to help us pick which instance to annotate next. But what is the optimal heuristic for a particular source of data? Motivated by the success of methods that combine predictors, we combine active learners with bandit algorithms and rank aggregation methods. We demonstrate that a combination of active learners outperforms passive learning in large benchmark datasets and removes the need to pick a particular active learner a priori. We discuss challenges to finding good rewards for bandit approaches and show that rank aggregation performs well.
Cassification of Movement Quality in A Weight-shifting Exercise

In exercise games, it is often possible to gain re-wards, i.e. points, by only partly completing an intended movement, which can undermine the effect of using such games for exercise. To ensure usability and reliability of exergames, correct movements must be accurately identiﬁed. Aim of the current study was to evaluate performance of machine learning models in classifying weight-shifting movements as correct or incorrect. Eleven healthy elderly (6 F) performed a stepping exercise in a correct (with weight shift) and an incorrect (without weight shift) version. A 3D Motion Capture (3DMoCap) system calculated joint center positions (JCPs); 2270 repetitions (1133 correct) were recorded. Random Forest (RF), k-Nearest Neighbor (k-NN) and Support Vector Machine (SVM) classiﬁcation models were built. Evaluation: 10fold leave-one-group-out cross validation (CV), repeated for all persons. Results showed high accuracy and recall in all classiﬁers. Average accuracy and recall was RF = 0.989, k-NN = 0.949, SVM = 0.958. Highest was RF on all JCPs, and SVM on shoulder JCPs (both 0.996). Lowest was k-NN on ankle JCPs (0.879). This study shows that all three models can distinguish correct and incorrect repetitions with high accuracy and recall, also by using selected JCPs. RF consistently outper-formed the other models.
A Hybrid Dynamic-Regenerative Damping Scheme for Energy Regeneration in Variable Impedance Actuators

Increasing research efforts have been made to improve the energy efficiency of variable impedance actuators (VIAs) through reduction of energy consumption. However, the harvesting of dissipated energy in such systems remains under-explored. This study proposes a novel variable damping module design enabling energy regeneration in VIAs by exploiting the regenerative braking effect of DC motors. The proposed damping module uses four switches to combine regenerative and dynamic braking, in a hybrid approach that enables energy regeneration without reduction in the range of damping achievable. Numerical simulations and a physical experiment are presented in which the proposed module shows an optimal trade-off between task-performance and energy efficiency.
Visualizing Large Time-series Data on Very Small Screens

In this paper, we present a space-efﬁcient visualization and an interaction technique for exploring time-series data on very small screens. The visualization is based on a simultaneous display of contextual visualization in the display border and focused interfaces in the center region of displays. The interaction technique utilizes ﬁsheye distortion to facilitate data selection and navigation interactions in the contextual visualization. The proposed techniques could beneﬁt a wide range of analysis applications on wearable devices. Two applications are highlighted to demonstrate the usefulness of the techniques.
Borderline tuberculoid leprosy mimicking sarcoidosis

Introduction: Leprosy is a chronic infectious granulomas disease caused by Mycobacterium leprae that can manifest as a wide variety of immunological and clinical features. Case summary: Here, we describe the case of a woman with clinical characteristics of borderline tuberculoid (BT) leprosy that manifested as 3 asymmetric skin lesions involving her hip and lower limbs. This unusual presentation was initially misdiagnosed as sarcoidosis because noncaseating granulomas are a histopathological feature of both diseases. Differentiation and the diagnosis of BT leprosy was achieved using real-time polymerase chain reaction (PCR) to amplify an M leprae specific DNA sequence and to detect serum antibodies specific to M leprae antigens. Accordingly, a 6-month course of multidrug therapy led to a marked improvement in the skin lesions. Conclusion: The use of auxiliary tests including real-time PCR to amplify an M leprae-specific DNA sequence, enzyme-linked immunosorbent assay, and dipstick detection of serum antibodies specific to M leprae antigens are good methods to obtain a correct diagnosis of BT leprosy.
Music subject classification based on lyrics and user interpretations

That music seekers consider song subject metadata to be helpful in their searching/browsing experience has been noted in prior published research. In an effort to develop a subject‐based tagging system, we explored the creation of automatically generated song subject classifications. Our classifications were derived from two different sources of song‐related text: 1) lyrics; and 2) user interpretations of lyrics collected from songmeanings.com. While both sources contain subject‐related information, we found that user‐generated interpretations always outperformed lyrics in terms of classification accuracy. This suggests that user interpretations are more useful in the subject classification task than lyrics because the semantically ambiguous poetic nature of lyrics tends to confuse classifiers. An examination of top‐ranked terms and confusion matrices supported our contention that users' interpretations work better for detecting the meaning of songs than what is conveyed through lyrics.
Low Ply Drawings of Trees and 2-Trees

Ply number is a recently developed graph drawing metric inspired by studying road networks. Informally, for each vertex v, which is associated with a point in the plane, a disk is drawn centered on v with a radius that is alpha times the length of the longest edge incident to v, for some constant alpha in (0, 0.5]. The ply number is the maximum number of disks that overlap at a single point. We show that any tree with maximum degree Delta has a 1-ply drawing when alpha = O(1 / Delta). We also show that when alpha = 1/2, trees can be drawn with logarithmic ply number, with an area that is polynomial for bounded-degree trees. Lastly, we show that this logarithmic upper bound does not apply to 2-trees, by giving a lower bound of Omega(sqrt(n / log n)) ply for any value of alpha.
Risk of Cervical Intraepithelial Neoplasia 2 or Worse by Cytology, Human Papillomavirus 16/18, and Colposcopy Impression: A Systematic Review and Meta-analysis.

OBJECTIVE To calculate pooled risk estimates for combinations of cytology result, human papillomavirus (HPV) 16/18 genotype and colposcopy impression to provide a basis for risk-stratified colposcopy and biopsy practice. DATA SOURCE A PubMed search was conducted on June 1, 2016, and a ClinicalTrials.gov search was conducted on June 9, 2018, using key words such as "uterine cervical neoplasms," "cervical cancer," "mass screening," "early detection of cancer," and "colposcopy. " METHODS OF STUDY SELECTION Eligible studies must have included colposcopic impression and either cytology results or HPV 16/18 partial genotype results as well as a histologic biopsy diagnosis from adult women. Manuscripts were reviewed for the following: cytology, HPV status, and colposcopy impression as well as age, number of women, and number of cervical intraepithelial neoplasia (CIN) 2, CIN 3, and cancer cases. Strata were defined by the various combinations of cytology, genotype, and colposcopic impression. TABULATION, INTEGRATION, AND RESULTS Of 340 abstracts identified, nine were eligible for inclusion. Data were also obtained from three unpublished studies, two of which have since been published. We calculated the risk of CIN 2 or worse and CIN 3 or worse based on cytology, colposcopy, and HPV 16/18 test results. We found similar risk patterns across studies in the lowest risk groups such that risk estimates were similar despite different referral populations and study designs. Women with a normal colposcopy impression (no acetowhitening), less than high-grade squamous intraepithelial lesion cytology, and HPV 16/18-negative were at low risk of prevalent precancer. Women with at least two of the following: high-grade squamous intraepithelial lesion cytology, HPV16- or HPV18-positive, and high-grade colposcopic impression were at highest risk of prevalent precancer. CONCLUSION Our results support a risk-based approach to colposcopy and biopsy with modifications of practice at the lowest and highest risk levels.
VisGuides: A Forum for Discussing Visualization Guidelines

This paper presents VisGuides, a discussion platform to facilitate the collection, evaluation, critique, revision, and dissemination of visualization guidelines. As visualization becomes a more widespread discipline with much more attention by designers and the general public, we need to ensure mechanisms for communicating, transferring, and accessing visualization knowledge. A visualization guideline can be anything ranging from good practices, empirical studies, and survey reports with the goal to inform visualization design and understanding. Thus, our forum aims (i) to collect visualization guidelines, (ii) to discuss guidelines and collect respective empirical references, and in the long run, (iii) to establish formal knowledge about guidelines by analyzing the forum content and the consensus of discussions. This paper describes the VisGuides forum and outlines our preliminary research towards shedding more light on visualization guidelines. VisGuides is accessible online at visguides.org.
Quantitative Analysis of the Global Proteome in Peripheral Blood Mononuclear Cells from Patients with New‐Onset Psoriasis

Psoriasis is a common chronic autoimmune skin disease involving the activation of T cells. To explore the proteomic signature of peripheral blood mononuclear cells, a quantitative analysis of their global proteome was conducted in samples from Chinese patients with new‐onset psoriasis (n = 31) and healthy controls (n = 32) using an integrated quantitative approach with tandem mass tag labeling and LC–MS/MS. Protein annotation, unsupervised hierarchical clustering, functional classification, functional enrichment and cluster, and protein–protein interaction analyses were performed. A total of 5178 proteins were identified, of which 4404 proteins were quantified. The fold‐change cutoff was set at 1.2 (patients vs controls); 335 proteins were upregulated, and 107 proteins were downregulated. The bioinformatics analysis indicated that the differentially expressed proteins were involved in processes related to the activation of immune cells including the nuclear factor kappa‐light‐chain‐enhancer of activated B cells (NF‐κB) pathway, cellular energy metabolism, and proliferation. Three upregulated proteins and two phosphorylated proteins in the NF‐κB pathway were verified or identified by Western blotting. These results confirm that the NF‐κB pathway is critical to psoriasis. In addition, many differentially expressed proteins identified in this study have never before been associated with psoriasis, and further studies on these proteins are necessary.