Miracle-dz/UniFAR-FTUs huggingface dataset:
Myocarditis: An Interleukin-1-Mediated Disease?

Myocarditis is defined by WHO as an inflammatory disease affecting the myocardium, diagnosed by endomyocardial biopsy (EMB) using established histological, immunological, and immunohistochemical criteria; it may be idiopathic, infectious, or autoimmune (1–4). A wide variety of histological myocarditis patterns have been described according to the diverse etiologies and to the stage of the disease at the time of EMB ascertainment. Viral infections represent the most common cause in Europe and North America (5). Different viral genomes can be detected in the myocardium of patients with myocarditis and dilated cardiomyopathy (DCM) using molecular techniques (6–14). When no infectious agents are identified on EMB and other known causes are excluded, autoimmune myocarditis (AMy) is the presumed etiology (15). These so-called “autoimmune myocarditis” or “virus-negative myocarditis” may occur as a distinct disease with exclusive cardiac involvement, or in the context of systemic autoimmune or inflammatory disorders with extracardiac involvement (5, 16–23). It is likely that several etiologic types of myocarditis confluence in a common immune-mediated pathogenic process leading to chronic inflammation and tissue damage. Irrespective of triggering agents, acute inflammation may progress to subacute and chronic stages and eventually result in tissue remodeling, fibrosis, contractile dysfunction, and finally DCM (4, 6, 8, 24–29). Besides contractile dysfunction, both early myocardial inflammation and late fibrotic changes play a critical role in the development of the arrhythmic burden, which makes myocarditis one of the leading causes of sudden death (19, 27–31). Clearly, treatment interventions effectively curbing the acute inflammatory process at an early stage can prevent late cardiac remodeling and improve patient’s outcome. Emerging evidence on the pathogenic mechanisms underlying cardiac inflammation is paving the way to novel, promising treatment strategies for myocarditis.
Diaphragm dome surface segmentation in CT data sets: a 3D active appearance model approach

Knowledge about the location of the diaphragm dome surface, which separates the lungs and the heart from the abdominal cavity, is of vital importance for applications like automated segmentation of adjacent organs (e.g., liver) or functional analysis of the respiratory cycle. We present a new 3D Active Appearance Model (AAM) approach to segmentation of the top layer of the diaphragm dome. The 3D AAM consists of three parts: a 2D closed curve (reference curve), an elevation image and texture layers. The first two parts combined represent 3D shape information and the third part image intensity of the diaphragm dome and the surrounding layers. Differences in height between dome voxels and a reference plane are stored in the elevation image. The reference curve is generated by a parallel projection of the diaphragm dome outline in the axial direction. Landmark point placement is only done on the (2D) reference curve, which can be seen as the bounding curve of the elevation image. Matching is based on a gradient-descent optimization process and uses image intensity appearance around the actual dome shape. Results achieved in 60 computer generated phantom data sets show a high degree of accuracy (positioning error -0.07+/-1.29 mm). Validation using real CT data sets yielded a positioning error of -0.16+/-2.95 mm. Additional training and testing on in-vivo CT image data is ongoing.
Stimulating Weight Stigma in Future Experimental Designs on Physical Activity - Development and Pilot Validation of a Video Instrument

Objective: There is a need for more experimental research on weight stigma and physical activity, specifically among men with obesity. Yet, validated procedures are required. The goal of this study was i) to develop a 10-min video instrument for the experimental induction of physical activity-related weight stigma (including a neutral control video), and ii) to collect information with regards to its content, face, construct, and criterion validity. Methods: To ensure content and face validity, two experts gave repeated feedback on the video development. In addition, two novices reviewed the video. Subsequently, we conducted a separate experiment: 60 adult men (18-52 years, 31 with overweight, 29 with normal weight) were randomly assigned to one of the two video conditions, stratified by BMI. Results: After the treatment, the stigma group showed higher scores of negative affect and attitudes against obesity (convergent validity). As expected, there were no differences in measures of depression and general stress (discriminant validity). The BMI of the participants in the stigma group correlated positively with some indicators of negative affect (criterion validity). Conclusion: Our study provides preliminary evidence for the validity of the video tool. Therefore, it can be used in future trials to investigate the effects of weight stigma on physical activity behavior.
Membrane Repair Mechanisms against Permeabilization by Pore-Forming Toxins

Permeabilization of the plasma membrane represents an important threat for any cell, since it compromises its viability by disrupting cell homeostasis. Numerous pathogenic bacteria produce pore-forming toxins that break plasma membrane integrity and cause cell death by colloid-osmotic lysis. Eukaryotic cells, in turn, have developed different ways to cope with the effects of such membrane piercing. Here, we provide a short overview of the general mechanisms currently proposed for plasma membrane repair, focusing more specifically on the cellular responses to membrane permeabilization by pore-forming toxins and presenting new data on the effects and cellular responses to the permeabilization by an RTX (repeats in toxin) toxin, the adenylate cyclase toxin-hemolysin secreted by the whooping cough bacterium Bordetella pertussis, which we have studied in the laboratory.
Strength Determinants of Jump Height in the Jump Throw Movement in Women Handball Players.

McGhie, D, Østerås, S, Ettema, G, Paulsen, G, and Sandbakk, Ø. Strength determinants of jump height in the jump throw movement in women handball players. J Strength Cond Res XX(X): 000-000, 2018-The purpose of the study was to improve the understanding of the strength demands of a handball-specific jump through examining the associations between jump height in a jump throw jump (JTJ) and measures of lower-body maximum strength and impulse in handball players. For comparison, whether the associations between jump height and strength differed between the JTJ and the customarily used countermovement jump (CMJ) was also examined. Twenty women handball players from a Norwegian top division club participated in the study. Jump height was measured in the JTJ and in unilateral and bilateral CMJ. Lower-body strength (maximum isometric force, one-repetition maximum [1RM], impulse at ∼60% and ∼35% 1RM) was measured in seated leg press. The associations between jump height and strength were assessed with correlation analyses and t-tests of dependent r's were performed to determine if correlations differed between jump tests. Only impulse at ∼35% 1RM correlated significantly with JTJ height (p < 0.05), whereas all strength measures correlated significantly with CMJ heights (p < 0.001). The associations between jump height and strength were significantly weaker in the JTJ than in both CMJ tests for all strength measures (p = 0.001-0.044) except one. Maximum strength and impulse at ∼60% 1RM did not seem to sufficiently capture the capabilities associated with JTJ height, highlighting the importance of employing tests targeting performance-relevant neuromuscular characteristics when assessing jump-related strength in handball players. Further, CMJ height seemed to represent a wider range of strength capabilities and care should be taken when using it as a proxy for handball-specific movements.
Genomic and environmental determinants and their interplay underlying phenotypic plasticity

Significance Integrated analysis of genotype by environment can reveal the pattern and mechanistic interplay underlying the observed phenotype dynamics. A critical question needs to be answered to enhance our ability to conduct genomic and environmental analysis of varied phenotypic plasticity observed in natural field conditions: How to uncover patterns at different levels to facilitate complex trait dissection and performance prediction. In this study, we first uncovered the pattern of genotype response to different environments. We then uncovered the pattern generated by the combination of environmental factors and the pattern of genetic effects at the individual gene level across environments. Finally, we demonstrated that trait dissection to individual genes and genome-wide performance prediction can be conducted through a joint genomic regression analysis framework. Observed phenotypic variation in living organisms is shaped by genomes, environment, and their interactions. Flowering time under natural conditions can showcase the diverse outcome of the gene–environment interplay. However, identifying hidden patterns and specific factors underlying phenotypic plasticity under natural field conditions remains challenging. With a genetic population showing dynamic changes in flowering time, here we show that the integrated analyses of genomic responses to diverse environments is powerful to reveal the underlying genetic architecture. Specifically, the effect continuum of individual genes (Ma1, Ma6, FT, and ELF3) was found to vary in size and in direction along an environmental gradient that was quantified by photothermal time, a combination of two environmental factors (photoperiod and temperature). Gene–gene interaction was also contributing to the observed phenotypic plasticity. With the identified environmental index to quantitatively connect environments, a systematic genome-wide performance prediction framework was established through either genotype-specific reaction-norm parameters or genome-wide marker-effect continua. These parallel genome-wide approaches were demonstrated for in-season and on-target performance prediction by simultaneously exploiting genomics, environment profiling, and performance information. Improved understanding of mechanisms for phenotypic plasticity enables a concerted exploration that turns challenge into opportunity.
Predictive value of liver and spleen stiffness in advanced alcoholic cirrhosis with refractory ascites

Abstract Background Recurrent ascitic decompensation is a frequent complication of advanced alcoholic liver disease. Ascites can be controlled by transjugular intrahepatic portosystemic shunt (TIPS) implantation, but specific pre-procedural outcome predictors are not well established. Liver and spleen stiffness measurement (LSM, SSM) correlate with outcome of compensated liver disease, but data for decompensated cirrhosis disease are scarce. Therefore, the predictive value of LSM and SSM was evaluated in patients with refractory ascites treated with TIPS insertion or receiving conservative therapy. Material and Methods Patients with alcoholic liver cirrhosis and recurrent or refractory ascites were stratified according to TIPS eligibility. LSM was prospectively assessed by transient elastography (TE, XL probe) and point shear wave elastography (pSWE). pSWE was also used for SSM. The primary study endpoint was transplant-free survival after 12 months. In addition, correlation of LSM and SSM with TIPS complications was analyzed. Results 43 patients (16 % female, age 55.5 [28.6 – 79.6] years) were recruited, n = 20 underwent TIPS and n = 23 were treated with repeated paracenteses only. 15 patients died and five underwent liver transplantation during follow-up. LSM and SSM at baseline did not predict the patients’ outcome in the TIPS cohort and in patients with conservative therapy. SSM was increased in two cases with spontaneous TIPS occlusion and declined after revision. Conclusion LSM and SSM cannot be recommended for risk stratification in cirrhotic patients with refractory ascites. SSM may be useful in monitoring TIPS function during follow-up.
Changes in the EV-A71 Genome through Recombination and Spontaneous Mutations: Impact on Virulence

Enterovirus 71 (EV-A71) is a major etiological agent of hand, foot and mouth disease (HFMD) that mainly affects young children less than five years old. The onset of severe HFMD is due to neurological complications bringing about acute flaccid paralysis and pulmonary oedema. In this review, we address how genetic events such as recombination and spontaneous mutations could change the genomic organization of EV-A71, leading to an impact on viral virulence. An understanding of the recombination mechanism of the poliovirus and non-polio enteroviruses will provide further evidence of the emergence of novel strains responsible for fatal HFMD outbreaks. We aim to see if the virulence of EV-A71 is contributed solely by the presence of fatal strains or is due to the co-operation of quasispecies within a viral population. The phenomenon of quasispecies within the poliovirus is discussed to reflect viral fitness, virulence and its implications for EV-A71. Ultimately, this review gives an insight into the evolution patterns of EV-A71 by looking into its recombination history and how spontaneous mutations would affect its virulence.
Sterol 27-Hydroxylase Polymorphism Significantly Associates With Shorter Telomere, Higher Cardiovascular and Type-2 Diabetes Risk in Obese Subjects

Background/objectives The pathologic relationship linking obesity and lipid dismetabolism with earlier onset of aging-related disorders, including cardiovascular disease (CVD) and type-2 diabetes (T2D), is not fully elucidate. Chronic inflammatory state, in obese individuals, may accelerate cellular aging. However, leukocyte telomere length (LTL), the cellular biological aging indicator, is elusively linked with obesity. Recent studies indicate that sterol 27-hydroxylase (CYP27A1) is an emerging antiatherogenic enzyme, that, by converting extrahepatic cholesterol to 27-hydroxycholesterol, facilitates cholesterol removal via high-density lipoprotein-cholesterol (HDL-C). We tested the hypothesis that obese subjects who carry at least three copies of CYP27A1 low-hydroxylation (LH) activity genome-wide-validated alleles (rs4674345A, rs1554622A, and rs4674338G) present premature aging, as reflected in shorter LTL and higher levels of CVD/T2D risk factors, including reduced HDL-C. Subjects/methods Obese subjects from SPHERE project {n = 1,457; overweight [body mass index (BMI) 25–30 kg/m2] 65.8% and severe-obese (BMI > 30 kg/m2) 34.2%} were characterized for the presence from 0 to 6 LH-CYP27A1 allele copy number. Univariate and multivariable sex–age–smoking-adjusted linear-regression models were performed to compare CVD/T2D risk factors and biological aging (LTL) in relation to the combined BMI-LH groups: overweight-LH: 0–2, overweight-LH: 3–6, severe-obese-LH: 0–2, and severe-obese-LH: 3–6. Results Higher LTL attrition was found in severe-obese than overweight individuals (p < 0.001). Multivariable model reveals that among severe-obese patients those with LH: 3–6 present higher LTL attrition than LH: 0–2 (p < 0.05). Univariate and multivariable models remarkably show that insulin resistance is higher both in overweight-LH: 3–6 vs overweight-LH: 0–2 (p < 0.001) and in severe-obese-LH: 3–6 vs severe-obese-LH: 0–2 (p < 0.0001), and HDL-C is lower in overweight-LH: 3–6 than overweight-LH: 0–2 (p < 0.05 and p < 001). Finally, most of the well-known (i.e., blood pressure, heart rate, waist to hip, triglycerides, and HDL-C) and novel CVD risk factors [i.e., inflammation markers (C-reactive protein, leukocytes, and chemoattractant protein-1), fibrinogen, and glucose homeostasis (i.e., insulin resistance, and glycated hemoglobin)] are substantially (p < 0.0001) altered in severe-obese-LH: 0–2 vs overweight-LH: 0–2, pointing to the fact that obesity leads to worsen the CVD/T2D risk factor profile. Conclusion Our study supports evidence that CYP27A1 genetic characterization identifies persons at higher risk to develop CVD and T2D, on which better converge preventive measures, and opens new perspectives on mechanisms that link obesity with aging-related disorders.
The closed form of Mad2 is bound to Mad1 and Cdc20 at unattached kinetochores

The spindle assembly checkpoint (SAC) ensures accurate chromosome segregation by delaying anaphase onset in response to unattached kinetochores. Anaphase is delayed by the generation of the mitotic checkpoint complex (MCC) composed of the checkpoint proteins Mad2 and BubR1/Bub3 bound to the protein Cdc20. Current models assume that MCC production is catalyzed at unattached kinetochores and that the Mad1/Mad2 complex is instrumental in the conversion of Mad2 from an open form (O-Mad2) to a closed form (C-Mad2) that can bind to Cdc20. Importantly the levels of Mad2 at kinetochores correlate with SAC activity but whether C-Mad2 at kinetochores exclusively represents its complex with Mad1 is not fully established. Here we use a recently established C-Mad2 specific monoclonal antibody to show that Cdc20 and C-Mad2 levels correlate at kinetochores and that depletion of Cdc20 reduces Mad2 but not Mad1 kinetochore levels. Importantly reintroducing wild type Cdc20 but not Cdc20 R132A, a mutant form that cannot bind Mad2, restores Mad2 levels. In agreement with this live cell imaging of fluorescent tagged Mad2 reveals that Cdc20 depletion strongly reduces Mad2 localization to kinetochores. These results support the presence of Mad2-Cdc20 complexes at kinetochores in agreement with current models of the SAC but also argue that Mad2 levels at kinetochores cannot be used as a direct readout of Mad1 levels.
Compressed image restoration based on edge enhancement field of experts

Images encoded at low bit rate may suffer from blocking artifacts, which dramatically degrade the visual quality. In this paper, we propose a postprocessing image restoration scheme for JPEG compressed images based on the maximum a posteriori criterion. A degradation model, represent by additive Gaussian noise model, is proposed to simulate JPEG compression process, while the original image is modeled as a high order Markov random field (MRF) based on the fields of experts framework. Meanwhile, an enhancement algorithm is proposed to restore the high frequency (HF) components. Experiment results have demonstrated that the proposed scheme can reproduce higher-quality images in terms of both objective and subjective quality.
Synthesis and Characterization of Carboxyethylated Lignosulfonate.

Lignosulfonate is a byproduct of the sulfite pulping process and has limited use in industry. The main objective of this study was to investigate the carboxyethylation of lignosulfonate to increase its charge density to broaden its applications. The carboxyethylation of lignosulfonate was optimized under the conditions of 30 wt % NaOH, 2.0 mol mol-1 2-chloropropinic acid/lignosulfonate, 90 °C, 0.5 h, and 0.03 mol 2-chloropropinic acid, which produced carboxyethylated lignosulfonate with a charge density and molecular weight of -3.51 meq g-1 and 46 493 g mol-1 , respectively. The mechanism of the carboxyethylation reaction using 2-chloropropinic acid by an SN 1 pathway in an alkaline solution was discussed. Methylation was also used to mask the phenolic hydroxide groups of lignosulfonate to investigate if carboxyethylation occurred on aliphatic hydroxide groups of lignosulfonate. The produced carboxyethylated lignosulfonate was characterized by using FTIR spectroscopy, NMR spectroscopy, gel permeation chromatography, and elemental and functional group analyses. Basic 1 H-1 H 2 D COSY NMR spectroscopy was used to record the coupled spins of the carboxyethyl group on carboxyethylated lignosulfonate. The information from 1 D 1 H NMR and 2 D NMR COSY spectroscopy provided evidence for the existence of a 1-carboxyethyl group on the carboxyethylated lignosulfonate structure.
Improving latent variable descriptiveness with AutoGen

Powerful generative models, particularly in Natural Language Modelling, are commonly trained by maximizing a variational lower bound on the data log likelihood. These models often suffer from poor use of their latent variable, with ad-hoc annealing factors used to encourage retention of information in the latent variable. We discuss an alternative and general approach to latent variable modelling, based on an objective that combines the data log likelihood as well as the likelihood of a perfect reconstruction through an autoencoder. Tying these together ensures by design that the latent variable captures information about the observations, whilst retaining the ability to generate well. Interestingly, though this approach is a priori unrelated to VAEs, the lower bound attained is identical to the standard VAE bound but with the addition of a simple pre-factor; thus, providing a formal interpretation of the commonly used, ad-hoc pre-factors in training VAEs.
Two-dimensional orthogonal DCT expansion in triangular and trapezoid regions

It is known that the 2-D DCT basis is complete and orthogonal in a rectangular region. In this paper, we introduce the way to generate the complete and orthogonal 2-D DCT basis in a trapezoid region or a triangular region without using the complicated Gram-Schmidt method. Moreover, since a polygon can be decomposed several triangular regions, the proposed method is also suitable for the polygonal region. Our algorithm can much generalize the JPEG algorithm. Instead of dividing an image into 8 by 8 blocks, we can divide an image into trapezoid or triangular regions and then transform and code each of them. In addition to the DCT basis, our method can also be used for generating the 2-D complete and orthogonal DFT basis, KLT basis, Legendre basis, Hadamard (Walsh) basis, and polynomial basis in the trapezoid and triangular regions.
Sensing of Substrate Vibrations in the Adult Cicada Okanagana rimosa (Hemiptera: Cicadidae)

Abstract Detection of substrate vibrations is an evolutionarily old sensory modality and is important for predator detection as well as for intraspecific communication. In insects, substrate vibrations are detected mainly by scolopidial (chordotonal) sense organs found at different sites in the legs. Among these sense organs, the tibial subgenual organ (SGO) is one of the most sensitive sensors. The neuroanatomy and physiology of vibratory sense organs of cicadas is not well known. Here, we investigated the leg nerve by neuronal tracing and summed nerve recordings. Tracing with Neurobiotin revealed that the cicada Okanagana rimosa (Say) (Hemiptera: Cicadidae) has a femoral chordotonal organ with about 20 sensory cells and a tibial SGO with two sensory cells. Recordings from the leg nerve show that the vibrational response is broadly tuned with a threshold of about 1 m/s2 and a minimum latency of about 6 ms. The vibratory sense of cicadas might be used in predator avoidance and intraspecific communication, although no tuning to the peak frequency of the calling song (9 kHz) could be found.
Towards an Information Theoretic Model for Online Message Authorship Identification

In this paper, we present an online text message author identification model based on information theory measures. We have identified nineteen specific writing features or identifiers from three text categories: characters, words, and sentences. These identifiers are employed to create unique user signatures. These signatures are used to recognize authors via relative entropy metrics. We have examined the proposed method on the Enron e-mail data set which contains a large number of emails from 150 people. Our results show that the proposed model can be used effectively for monitoring and identifying authorship of such documents as emails, chat conversations, web logs, forum posts, and more so for closed sets of users such as a research facility, an enterprise, or an organization.