Miracle-dz/UniFAR-FTUs huggingface dataset:
Impaired intermediate formation in mouse embryos expressing reduced levels of Tbx6

Intermediate mesoderm (IM) is the strip of tissue lying between the paraxial mesoderm (PAM) and the lateral plate mesoderm that gives rise to the kidneys and gonads. Chick fate mapping studies suggest that IM is specified shortly after cells leave the primitive streak and that these cells do not require external signals to express IM‐specific genes. Surgical manipulations of the chick embryo, however, revealed that PAM‐specific signals are required for IM differentiation into pronephros—the first kidney. Here, we use a genetic approach in mice to examine the dependency of IM on proper PAM formation. In Tbx6 null mutant embryos, which form 7–9 improperly patterned anterior somites, IM formation is severely compromised, while in Tbx6 hypomorphic embryos, where somites form but are improperly patterned along the axis, the impact to IM formation is lessened. These results suggest that IM and its derivatives, the kidneys and the gonads, are directly or indirectly dependent on proper PAM formation. This has implications for humans harboring Tbx6 mutations which are known to have somite‐derived defects including congenital scoliosis.
New Insight into Sperm Capacitation: A Novel Mechanism of 17β-Estradiol Signalling

17β-estradiol (estradiol) is a natural estrogen regulating reproduction including sperm and egg development, sperm maturation—called capacitation—and sperm–egg communication. High doses can increase germ cell apoptosis and decrease sperm count. Our aim was to answer the biological relevance of estradiol in sperm capacitation and its effect on motility and acrosome reaction to quantify its interaction with estrogen receptors and propose a model of estradiol action during capacitation using kinetic analysis. Estradiol increased protein tyrosine phosphorylation, elevated rate of spontaneous acrosome reaction, and altered motility parameters measured Hamilton-Thorne Computer Assisted Semen Analyzer (CASA) in capacitating sperm. To monitor time and concentration dependent binding dynamics of extracellular estradiol, high-performance liquid chromatography with tandem mass spectrometry was used to measure sperm response and data was subjected to kinetic analysis. The kinetic model of estradiol action during sperm maturation shows that estradiol adsorption onto a plasma membrane surface is controlled by Langmuir isotherm. After, when estradiol passes into the cytoplasm, it forms an unstable adduct with cytoplasmic receptors, which display a signalling autocatalytic pattern. This autocatalytic reaction suggests crosstalk between receptor and non-receptor pathways utilized by sperm prior to fertilization.
Early Intervention is Important to Prevent Sensitization to New Allergens

We review current management for allergic rhinitis and possible new treatments for this condition. Management of allergic rhinitis includes promotion of protective factors, avoidance of allergens, and possibly immunotherapy. In recent years, the incidence of allergic rhinitis has increased in many countries. Early intervention at different stages is an important part of management. Allergic disease in infants has been described as the allergic march, commencing with atopic dermatitis accompanied by infantile asthma and progressing to perennial allergic rhinitis induced by house dust mite allergy. In order to prevent polysensitization, allergen-specific immunotherapy should probably be initiated at an earlier age, especially in children with rhinitis who show monosensitization to house dust mite antigens.
Alv: a Console-based Viewer for Molecular Sequence Alignments

The multiple sequence alignment (MSA) is a common entity in comparative analysis of sequences representing molecules such as DNA, RNA, and proteins. An MSA lines up the sequence building blocks (letters representing nucleotides for DNA/RNA and amino acids for proteins) to form the basis for a hypothesis of how the molecules have evolved, and is computed using, for example, software like Clustal Omega (Sievers & Higgins, 2014), MAFFT (Katoh & Standley, 2013), MUSCLE (Edgar, 2004), MACSE (Ranwez, Harispe, Delsuc, & Douzery, 2011), and hmmalign (Eddy, 2015). MSAs have many applications, from advanced analyses such as inferring evolutionary trees (phylogenies) or identifying function in subsequences, to basic use like visual inspection of data. We have written a tool named alv to support quick and basic viewing of MSAs (Arvestad, 2018).
Dynamical stochastic resonance for non-uniform illumination image enhancement

Images taken under poor illumination conditions have low contrast and dark tones. General dark image enhancement algorithms cannot effectively enhance these images without introducing over-enhancement, detail loss, and noise amplification. In this study, a simple and fast enhancement technique of non-uniform illumination images is proposed based on dynamical stochastic resonance (DSR). The low-contrast images are enhanced through the nonlinear iteration by solving monostable Langevin equation. Iteration parameters are dynamically adjusted according to the intensity distribution of the original images, which ensure the balance of visibility and naturalness in the entire areas. A threshold is defined to automatically confirm the optimal outputs. The enhanced image is obtained by fusing the DSR result, original component, and illumination compensation component. The computational time, no-reference perceptual quality assessment, and lightness order error are measured to evaluate the performance of experimental results. The subjective and objective comparison with state-of-the-art methods shows that our method performs well to enhance the non-uniform illumination images with a low-computational complexity.
Gravity: Estimation Methods for Gravity Models in R

Gravity models are used to explain bilateral flows related to the sizes of bilateral partners, a measure of distance between them and other influences on interaction costs. The underlying idea is rather simple. The greater the masses of two bodies and the smaller the distance between them, the stronger their attraction. For a state-of-the-art exposition about cross-sectional data see Wölwer, Breßlein, & Burgard (2018).
New Impressions in Interaction Design: A Task Taxonomy for Elastic Displays

Abstract Novel shape-changing interfaces promise to provide a rich haptic experience for human-computer interaction. As a specific instance of shape-changing interfaces, Elastic Displays provide large interaction surfaces that can be temporally deformed using force-touch. The unique property of these displays is that they automatically return to their initial flat state. Recently, several review and position papers have stimulated a discussion towards consolidating the knowledge about shape-changing interfaces. The knowledge about Elastic Displays is similarly scattered across multiple publications from recent years. This paper contributes a task taxonomy based on productive uses of Elastic Displays found in literature, on the web, and in our interaction lab. This taxonomy emphasizes tasks, but also encompasses general aspects regarding content types, visualization technology, and interaction styles. All aspects of the taxonomy are illustrated using case studies from literature.
Achieving Strong Security and Member Registration for Lattice-based Group Signature Scheme with Verifier-local Revocation

A fully dynamic group signature scheme with member registration and member revocation with strong security is desirable when using group signatures in real life. Langlois, Ling, Nguyen, and Wang (PKC 2014) presented the first lattice-based group signature scheme with member revocation. Even though their scheme employs the most flexible revocation approach called Verifier-local revocation, their scheme relied on a weaker security notion and did not provide a member registration mechanism. In this paper, we obtain a fully dynamic group signature scheme by proposing a group joining protocol to their scheme. Moreover we discuss the difficulties of achieving both fully-dynamicity and strong security at the same time and provide a scheme with solutions for those difficulties.
Visible light accelerates the ultraviolet A‐induced degradation of eumelanin and pheomelanin

Exposure to excess ultraviolet (UV) A radiation induces the degradation/modification of both eumelanin and pheomelanin that may be deleterious to pigmented tissues. Although the spectral distribution of solar energy comprises nearly half of visible light (VL), few studies have been conducted to examine the role of VL in the photodegradation of both types of melanin, either VL alone or in combination with UVA. In this study, we examined the effects of physiological doses of VL (150 to 300 J cm−2) alone or in combination with a physiological dose of UVA (20 J cm−2) in normal human epidermal melanocytes. The degradation/modification of melanin structures was evaluated by our chemical degradation—high performance liquid chromatography methods. The results show that VL accelerates UVA‐induced changes in the structural features of both eumelanin and pheomelanin, although VL or UVA alone induced only minor changes in melanin structure. The differential spectral method provides support for the additive effects of VL.
Embedded Computation versus Embodied Interaction: Connected Objects for Connected Thinking

Abstract What will future creativity-based work in collaboration with ubiquitous, AI-driven systems be like? In this paper, we argue that following a ‘tangible interaction’ approach can be beneficial in this context. We describe six connected objects that illustrate how the quality of future creative work could be designed. The objects aim to shape embedded computation in ways that support embodied interaction. They include a place for sacrificing one’s phone, an olfactory calendar, a reader/writer for cloud data in everyday objects, a concrete-based data logger, a slot machine for recombining old ideas into new ones, and a dimmer for artificial intelligence. We summarize the results of a critical reflection of the prototypes in an argument for designing interactions that foster collaborative creative processes between embodied humans in a world of embedded computation.
Healthy Food Options at Dollar Discount Stores Are Equivalent in Quality and Lower in Price Compared to Grocery Stores: An Examination in Las Vegas, NV

Food deserts indicate limited access to and affordability of healthy foods. One potential mediator is the availability of healthy food in non-traditional outlets such as dollar-discount stores, stores selling produce at the fixed $1 price. The purpose of this study was to compare availability, quality, price differences in ‘healthier’ versus ‘regular’ food choices, price per each food item, and summary score in dollar-discount stores to grocery stores in Las Vegas using the NEMS-S; a protocol consisting of three subscores—availability, quality, price of healthier versus regular food, and a summary score. A 25% sample of grocery stores (n = 40) and all dollar-discount stores (n = 14) were evaluated. t-tests showed that dollar-discount stores were less likely to price healthy options lower than their unhealthy alternatives (mean (M) = 1.0 vs. M = 2.5; p < 0.001) and had reduced availability (M = 20.50 vs. M = 23.80; p < 0.001) compared to grocery stores. The quality of produce did not differ (M = 5.93 vs. M = 6.00; p = 0.34). Price comparisons revealed that 84.2% of produce and 89.5% of other food items were significantly less expensive at the dollar-discount stores, with only two items being more expensive. While dollar-discount stores did have lower availability, they provided quality fresh and healthy foods which were usually less expensive. Findings indicate that dollar discount stores may be an existing community asset, and considering them as such may aid in efforts to strengthen the overall food system. Practitioners should consider dollar discount stores when assessing the community food environment and designing and implementing outreach programs, as they may bridge some disparities in access.
Mapping theme trends and knowledge structure on adipose-derived stem cells: a bibliometric analysis from 2003 to 2017.

AIM To investigate the theme trends and knowledge structure of adipose-derived stem cells (ADSCs) related literatures by using bibliometric analysis. MATERIALS & METHODS Co-word analysis, strategic diagram and social network analysis were employed. RESULTS In line with strategic diagrams, ADSC differentiation and transplantation as main undeveloped themes in 2003-2007 were partially replaced by regeneration medicine and ADSCs for myocardial infarction in 2008 to 2012, and then partially replaced by miRNAs in ADSC genetics and nerve regeneration in 2013 to 2017. Based on social network analysis, regenerative medicine/methods, myocardial infarction/therapy, as well as miRNAs/genetics, and nerve regeneration/physiology were considered the emerging hot spots in 2008 to 2012 and 2013 to 2017. CONCLUSION The undeveloped themes and emerging hot spots could be considered as new research topics.
Pressure management as an occupational stress risk factor in irritable bowel syndrome

Abstract Irritable Bowel Syndrome (IBS) is the most prevalent functional gastrointestinal disorder. Psychosocial stress is one of the pathogenic factors involved in the pathogenesis of IBS. The Pressure Management Indicator (PMI) is a validated questionnaire to analyze all aspects of occupational stress—a model involving sources of pressure, the mechanisms of coping, the personality, and the resulting effects of the interaction between these 3 elements. The purpose of this study was to analyze the association between socio-professional stress effects in IBS, and the relationship of IL-6 levels and salivary cortisol with occupational stress. We conducted a prospective cross-sectional study on 76 patients (39 patients with IBS, diagnosed according to the Rome III criteria and 37 healthy controls) who were investigated using a validated self-administered questionnaire: PMI. The biologic markers of chronic stress were analyzed using salivary cortisol and the immune response with serum interleukin 6 (IL-6). The IBS patients corresponded to the following subtypes: diarrhea-predominant: 22, constipation-predominant: 14 and mixed: 3. All the socio-professional pressure effects variables and scales were statistically significant, in an inversely proportional relation with IBS. Lower scores (poor effects) were found in IBS subjects. The adjusted odds ratios of having IBS versus healthy subjects for the socio-professional pressure effects scales were: 0.81 (95% confidence interval (CI) 0.72–0.88), for satisfaction, 0.85 (95% CI 0.78–0.91) for organization, 0.85 (95% CI 0.79–0.91) for mental wellbeing and 0.8 (95% CI 0.71–0.87) for physical wellbeing (P <.001). Also, the serum IL-6 levels were significantly higher in IBS than in controls (p < 0.001). There was no statistical difference between the salivary levels of cortisol between IBS patients and controls (P = .898). The level of occupational stress was higher in IBS patients compared to healthy subjects (socio-professional stress effects were lower in IBS patients) and correlated with IL-6 levels. Salivary cortisol was not associated with occupational pressure management.
Impact of an energy- and nutrient-reduced diet containing 10% lignocellulose on animal performance, body composition and egg quality of dual purpose laying hens

ABSTRACT In response to ethical concerns regarding the killing of day-old male chicks of layer breeds, the use of dual purpose chickens is increasingly discussed in public while data on nutritional requirements of dual purpose laying hens are not available. The present study examined the impact of an energy- and nutrient-reduced diet containing lignocellulose on performance, body composition and egg quality of dual purpose hens. Female Lohmann Dual chicks were allocated to 12 pens and fed two different diets for 52 weeks: a control (CON) and a treatment diet (LC), based on CON but diluted with 10% lignocellulose. During the trial, animal performance, whole-body composition and egg quality parameters of hens were consistently ascertained. The results showed that LC-fed hens had lower body weights compared to those receiving CON (p < 0.05). During the laying period, feed intake was increased in LC-fed hens (p < 0.001). LC-fed hens showed a higher egg production and egg mass resulting in an improved feed efficiency (p < 0.05) and laid smaller eggs compared to CON-fed hens (p < 0.001). At 52 weeks of age, bodies of LC-fed hens had higher protein and lower fat contents than those fed with CON diet (p ≤ 0.001). Mean body weight was positively correlated to the body fat content (p = 0.004) and body fat content was negatively correlated to the egg production (p = 0.043). Analyses of the egg quality showed that yolk mass at all sampling points and albumen mass at 27 and 42 weeks were lower in hens fed with diet LC compared to those fed with diet CON (p< 0.05). In conclusion, the feeding of energy- and nutrient-reduced diets containing 10% lignocellulose reduced the body fat content and simultaneously improved the laying performance in dual purpose hens.
Device-Type Influence in Crowd-based Natural Language Translation Tasks (short paper)

The effect of users’ interaction devices and their platform (mobile vs. desktop) should be taken into account when evaluating the performance of translation tasks in crowdsourcing contexts. We investigate the influence of the device type and platform in a crowd-based translation workflow. We implement a crowd translation workflow and use it for translating a subset of the IWSLT parallel corpus from English to Arabic. In addition, we consider machine translations from a state-ofthe-art machine translation system which can be used as translation candidates in a human computation workflow. The results of our experiment suggest that users with a mobile device judge translations systematically lower than users with a desktop device, when assessing the quality of machine translations. The perceived quality of shorter sentences is generally higher than the perceived quality of longer sentences.
CaptureBias Supporting Media Scholars with Ambiguity-Aware Bias Representation for News Videos

In this project we explore the presence of ambiguity in textual and visual media and its inﬂuence on accurately understanding and capturing bias in news. We study this topic in the context of supporting media scholars and social scientists in their media analysis. Our focus lies on racial and gender bias as well as framing and the comparison of their manifestation across modalities, cultures and languages. In this paper we lay out a human in the loop approach to investigate the role of ambiguity in detection and interpretation of bias
Applications of Machine Learning in Dota 2: Literature Review and Practical Knowledge Sharing

We present the review of recent applications of Machine Learning in Dota 2. It includes prediction of the winning team from the drafting stage of the game, calculating optimal jungling paths, predict the result of teamﬁghts, recommendataion engine for the draft, and detection of in-game roles with emphasis on win prediction from team composition data. Besides that we discuss our own experience with making Dota 2 Machine Learning hachathon and Kaggle competitions
Prognostic impact of the Controlling Nutritional Status score following curative nephrectomy for patients with renal cell carcinoma

Abstract We aimed to evaluate the prognostic significance of the preoperative Controlling Nutritional Status (CONUT) score in patients with renal cell carcinoma (RCC), and then compared its accuracy of the prognostic nutritional index (PNI), neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio (PLR) as predictors of survival. We included 635 patients who underwent nephrectomy for RCC from January 2004 to July 2014. The X-tile program was used to determine the optimal cut-off values for CONUT score, PNI, NLR, and PLR. The median follow-up duration after surgery was 48.40 (29.30–80.10) months. The optimal cutoff values were 2 for CONUT score, 48 for PNI, 3.5 for NLR and 204.7 for PLR by X-tile program with cancer-specific survival (CSS) as end-point. Higher CONUT score, NLR and PLR, and lower PNI were statistically associated with worse OS and CSS in the univariate analysis. Multivariate analysis showed that higher CONUT score was an independent predictor for OS (HR = 3.012; 95% CI, 1.525–5.948; P = .001) and CSS (HR = 3.001; 95% CI, 1.290–6.984; P = .011), and CONUT score was superior to PNI, NLR, and PLR according to the HR. Therefore, preoperative CONUT score can be a strong independent predictor in RCC patients after nephrectomy.
A novel robust multivariate regression approach to optimize multiple surfaces

Response surface methodology involves relationships between different variables, specifically experimental inputs as controllable factors, and a response or responses by incorporating uncontrollable factors named nuisance. In order to optimize these response surfaces, we should have accurate response models. A common approach to estimate a response surface is the ordinary least squares (OLS) method. Since OLS is very sensitive to outliers, some robust approaches have been discussed in the literature. Most problems face with more than one response which are mostly correlated, that are called multi-response problem. This paper presents a new approach which takes the benefits of robust multivariate regression to cope with the mentioned difficulties. After estimating accurate response surfaces, optimization phase should be applied in order to have proper combination of variables and optimum solutions. Global criterion method of multi-objective optimization has also been used to reach a compromise solution which improves all response variables simultaneously. Finally, the proposed approach is described analytically by a numerical example.
The Oxidized Protein Repair Enzymes Methionine Sulfoxide Reductases and Their Roles in Protecting against Oxidative Stress, in Ageing and in Regulating Protein Function

Cysteine and methionine residues are the amino acids most sensitive to oxidation by reactive oxygen species. However, in contrast to other amino acids, certain cysteine and methionine oxidation products can be reduced within proteins by dedicated enzymatic repair systems. Oxidation of cysteine first results in either the formation of a disulfide bridge or a sulfenic acid. Sulfenic acid can be converted to disulfide or sulfenamide or further oxidized to sulfinic acid. Disulfide can be easily reversed by different enzymatic systems such as the thioredoxin/thioredoxin reductase and the glutaredoxin/glutathione/glutathione reductase systems. Methionine side chains can also be oxidized by reactive oxygen species. Methionine oxidation, by the addition of an extra oxygen atom, leads to the generation of methionine sulfoxide. Enzymatically catalyzed reduction of methionine sulfoxide is achieved by either methionine sulfoxide reductase A or methionine sulfoxide reductase B, also referred as to the methionine sulfoxide reductases system. This oxidized protein repair system is further described in this review article in terms of its discovery and biologically relevant characteristics, and its important physiological roles in protecting against oxidative stress, in ageing and in regulating protein function.