Miracle-dz/UniFAR-FTUs huggingface dataset:
A Functional Tyr1306Cys Variant in LARG Is Associated With Increased Insulin Action in Vivo

Diminished insulin sensitivity is a characteristic feature of type 2 diabetes. Inhibition of insulin action, resulting in reduced skeletal muscle glucose uptake, is mediated in part through stimulation of RhoA activity. One regulator of RhoA activity is leukemia-associated Rho guanine nucleotide exchange factor (LARG). The LARG gene maps to a region on chromosome 11q23-24 that shows genetic linkage to BMI and type 2 diabetes in Pima Indians. Because of its role in RhoA activation, the LARG gene was analyzed as a positional candidate gene for this linkage. Sequencing of the LARG gene and genotyping of variants identified several polymorphisms that were associated with in vivo rates of insulin-mediated glucose uptake, at both physiological and maximally stimulating insulin concentrations, among 322 nondiabetic Pima Indians who had undergone a hyperinsulinemic-euglycemic clamp. The strongest association with rate of glucose uptake was found with a Tyr1306Cys polymorphism (P < 0.0001, adjusted for age, sex, percent body fat, and nuclear family membership). In transient transfection studies in NIH3T3 cells, the LARG(Cys1306) protein had reduced activity compared with LARG(Tyr1306) protein (P < 0.05). We propose that the Tyr1306Cys substitution in LARG, through its differential activation of RhoA, increases insulin sensitivity in nondiabetic Pima Indians.
Functional variants in DCAF4 associated with lung cancer risk in European populations

Cullin-RING ubiquitin ligases (CRLs) responsible for substrate specificity of ubiquitination play a key role in cell-cycle control and DNA damage response. In this study, we assessed associations between 16 599 SNPs in 115 CRL genes and lung cancer risk by using summary data of six published genome-wide association studies (GWASs) of 12 160 cases and 16 838 cases of European ancestry. As a result, we identified three independent SNPs in DCAF4 (rs117781739, rs12587742 and rs2240980) associated with lung cancer risk (odds ratio = 0.91, 1.09 and 1.09, respectively; 95% confidence interval = 0.88-0.95, 1.05-1.14 and 1.05-1.13, respectively; and P = 3.99 × 10-6, 4.97 × 10-5 and 1.44 × 10-5, respectively) after multiple comparison correction by a false discovery rate <0.05. Since SNP rs12587742 is located within the promoter region and one CpG island of DCAF4, we further performed in silico functional analyses and found that the rs12587742 variant A allele was associated with an increased mRNA expression (P = 2.20 × 10-16, 1.79 × 10-13 and 0.001 in blood cells, normal lung tissues and tumor tissues of lung squamous carcinoma, respectively) and a decreased methylation status (P = 2.48 × 10-9 and 0.032 in adipose and lung tumor tissues, respectively). Moreover, evidence from differential expression analyses further supported an oncogenic effect of DCAF4 on lung cancer, with higher mRNA levels in both lung squamous carcinoma and adenocarcinoma (P = 4.48 × 10-11 and 1.22 × 10-9, respectively) than in adjacent normal tissues. Taken together, our results suggest that rs12587742 is associated with an increased lung cancer risk, possibly by up-regulating mRNA expression and decreasing methylation status of DCAF4.
Generative Training for 3D-Retrieval

A digital library for non-textual, multimedia documents can be defined by its functionality: markup, indexing, and retrieval. For textual documents, the techniques and algorithms to perform these tasks are well studied. For non-textual documents, these tasks are open research questions: How to markup a position on a digitized statue? What is the index of a building? How to search and query for a CAD model? If no additional, textual information is available, current approaches cluster, sort and classify non-textual documents using machine learning techniques, which have a cold start problem: they either need a manually labeled, sufficiently large training set or the (automatic) clustering / classification result may not respect semantic similarity. We solve this problem using procedural modeling techniques, which can generate arbitrary training sets without the need of any ârealâ data. The retrieval process itself can be performed with any method. In this article we describe the histogram of inverted distances in detail and compare it to salient local visual features method. Both techniques are evaluated using the Princeton Shape Benchmark (Shilane et al., 2004). Furthermore, we improve the retrieval results by diffusion processes.
ICLIC: Interactive categorization of large image collections

We present a new approach for the analysis of large image collections. We argue that categorization plays an important role in this process, not only to label images as end result, but also during exploration. Furthermore, to increase the effectiveness and efficiency of the categorization process we enable the use of all available metadata, treated as multivariate data. We identified images, attributes, and categories as important aspects and integrated these in a system called ICLIC. The system consists of four views that are connected by the selection of images, which is a central action in the approach. By using a minimalist interface with only standard metaphors, users are enabled to use the system in short time. The system enables complex queries in a natural way, and it can deal with collections containing more than 100,000 images and more than 1,000 metadata attributes. This was confirmed by two evaluation cycles with domain experts.
Co-ordination of early and late ripening events in apples is regulated through differential sensitivities to ethylene

In this study, it is shown that anti-sense suppression of Malus domestica 1-AMINO-CYCLOPROPANE-CARBOXYLASE OXIDASE (MdACO1) resulted in fruit with an ethylene production sufficiently low to be able to assess ripening in the absence of ethylene. Exposure of these fruit to different concentrations of exogenous ethylene showed that flesh softening, volatile biosynthesis, and starch degradation, had differing ethylene sensitivity and dependency. Early ripening events such as the conversion of starch to sugars showed a low dependency for ethylene, but a high sensitivity to low concentrations of ethylene (0.01 μl l−1). By contrast, later ripening events such as flesh softening and ester volatile production showed a high dependency for ethylene but were less sensitive to low concentrations (needing 0.1 μl l−1 for a response). A sustained exposure to ethylene was required to maintain ripening, indicating that the role of ethylene may go beyond that of ripening initiation. These results suggest a conceptual model for the control of individual ripening characters in apple, based on both ethylene dependency and sensitivity.
Sexual Encounters: Gay Male College Students' Use of the Internet and Social Media.

There have been many studies that focus on understanding various aspects of human sexuality and how it relates to college students. However, the current research focuses on heterosexual students, leaving a void in the research that focuses on gay male college students. Even more crucially, there is a void in research that focuses on the sexual risks gay male college students’ face and how their actions impact their well-being. The purpose of this phenomenological study was to explore gay male college students’ sexual behavior and its implications in higher education and gay male health practices. The Health Belief Model and Ecological Gay Identity Development model were used as guiding frameworks and foundations to explore the tricking encounters and culture experienced by gay male college students. The data from this study produced a total of four significant and frequently interwoven themes. The themes were as follows: tricking encounters and use of the Internet and social media, masculinity and body image issues, awareness of STD issues and personal safety, and adequacy of campus resources. In addition, conclusions, limitations, implications and recommendations for future research are presented in this study. This study contains adult content and graphic language.
Changes in left atrial volume in diabetes mellitus: more than diastolic dysfunction?

AIM To evaluate left atrial (LA) volume and function as assessed by strain and strain rate derived from 2D speckle tracking and their association with diastolic dysfunction (DD) in patients with diabetes mellitus (DM). METHODS AND RESULTS Seventy three patients with DM were compared with age- and gender-matched normal controls; 30 patients with DM alone were compared to those with hypertension (HT) alone. The maximum LA volume, traditional measures of atrial function, 2D strain and strain rate were analysed. The LA indexed volume (LAVI) was larger in DM group than that in normal controls (38.2 ± 9.9 vs. 20.5 ± 4.8 ml/m(2), P< 0.0001), as well as in DM alone compared with hypertensive patients (33.9 ± 10 vs. 25.7 ± 8 ml/m(2), P< 0.0001). Global strain was significantly reduced in the DM group compared with that in normal controls (22.5 ± 8.67 vs. 30.6 ± 8.27%; P< 0.0001) but was similar with HT. There was a weak correlation between LAVI and global strain with increasing grades of DD (r= 0.439, P< 0.0001 and r= - 0.316, P< 0.0001, respectively) in the diabetic group. However, there was no significant difference in LAVI between these groups. A logistic regression analysis for predictors of LAVI demonstrated that only diabetes was a determinant of LAVI. Patients with diabetes showed a significant reduction in global strain compared with normal controls but no difference with increasing grades of diastolic function. CONCLUSIONS LA enlargement in DM is independent of associated HT and diastolic function. LA enlargement is associated with LA dysfunction as evaluated by 2D strain. It is likely that a combination of DD and a diabetic atrial myopathy contribute to LA enlargement in patients with DM.
Plasticity and trade-offs in physiological traits of intertidal mussels subjected to freshwater-induced environmental variation

Environmental gradients play an important role in shaping geographic variability in coastal marine populations. Thus, the ability of organisms to cope with these changes will depend on their potential to acclimatize, or adapt, to these new environmental conditions. We investigated the spatial variability in biological responses shown by Perumytilus purpuratus mussels collected from 2 intertidal areas experiencing contrasting freshwater input influences (river-influenced vs. marine conditions). To highlight the role of plasticity and adaptive potential in biological responses, we performed a reciprocal-transplant experiment and measured relevant phenotypic traits including mortality, growth, calcification, metabolism, and chemical composition of the shell periostra cum. We determined that mussels exposed to river-influenced conditions had increased metabolic rates and reduced growth rates, as compared to mussels experiencing marine conditions (p < 0.05). While the energy investment strategies of the 2 local populations resulted in similar net calcification rates, these rates decreased significantly when mussels were transplanted to the river-influenced site. Stressful conditions at the river-influenced site were evidenced by decreased survivorship across treatments. Freshwater inputs modify the organic composition of the shell periostracum through a significant reduction in polysaccharides. Although our field experiment did not identify specific environmental factors underlying these contrasting phenotypic changes, the results imply that plasticity plays a strong role when P. purpuratus is exposed to some combination of natural (e.g. salinity) and anthropogenic influences (e.g. pollution), and that the lack of exposure to freshwater may promote less tolerant mussels with greater potential for local adaptation.
P2P storage systems: How much locality can they tolerate?

Large scale peer-to-peer systems are foreseen as a way to provide highly reliable data storage at low cost. To achieve high durability, such P2P systems encode the user data in a set of redundant fragments and distribute them among the peers. In this paper, we study the impact of different data placement strategies on the system performance when using erasure codes redundancy schemes. We compare three policies: two of them local, in which the data are stored in logical neighbors, and the other one global, in which the data are spread randomly in the whole system. We focus on the study of the probability to lose a data block and the bandwidth consumption to maintain enough redundancy. We use simulations to show that, without resource constraints, the average values are the same no matter which placement policy is used. However, the variations in the use of bandwidth are much more bursty under the local policies. When the bandwidth is limited, these bursty variations induce longer maintenance time and henceforth a higher risk of data loss. Finally, we propose a new external reconstruction strategy and a suitable degree of locality that could be introduced in order to combine the efficiency of the global policy with the practical advantages of a local placement.
Possibilities for preservation of coarse particles in pelleting process to improve feed quality characteristics

Poultry diets are mainly used in pelleted form because pellets have many advantages compared to mash feed. On the other hand, pelleting causes reduction of feed particle size. The aim of this research was to investigate the possibility of increasing the content of coarse particles in pellets, and, at the same time, to produce pellets with satisfactory quality. In this research, the three grinding treatments of corn were applied using hammer mill with three sieve openings diameter: 3 mm (HM-3), 6 mm (HM-6) and 9 mm (HM-9). These grinding treatments were combined in pelleting process with three gaps between rollers and the die of pellet press (roller-die gap, RDG) (0.30, 1.15 and 2.00 mm) and three moisture contents of the pelleted material (14.5, 16.0 and 17.5%). The increased coarseness of grinding by the hammer mill resulted in the increased amount of coarse particles in pellets, especially when the smallest RDG was applied (0.30 mm), but pellet quality was greatly reduced. Increasing of RDG improved the quality of pellets produced from coarsely ground corn, but reduced the content of coarse particles in pellets and increased specific energy consumption of the pellet press. Increasing the moisture content of material to be pelleted (MC) significantly reduced energy consumption of the pellet press, but there was no significant influence of MC on particle size after pelleting and on the pellet quality. The optimal values of the pelleting process parameters were determined using desirability function method. The results of optimization process showed that to achieve the highest possible quantity of coarse particles in the pellets, and to produce pellets of satisfactory quality, with the lowest possible energy consumption of the pellet press, the coarsest grinding on hammer mill (HM-9), the largest RDG (2 mm) and the highest MC (17.5%) should be applied.
Facilitating digital communication in seniors

The foundation of this research is a push to familiarize young-old (65-85) with technology that will facilitate social connections as they age. This research analysed the acceptation and use of the readily available mature tablet applications, Skype and DropBox as an aid to facilitate communication between seniors and their various support networks. The usability of existing apps took place in Australia and India and the findings compared. Participants who had high levels of skill were asked to be peer team leaders and given around 10 people to look after. The participants were then phoned and asked to complete a questionnaire on their attitudes and experiences using the software, while the team leaders were interviewed in person about their experiences. A large number of participants were already familiar with and using some kind of electronic communication software to talk with friends and family, while DropBox proved more difficult with participants finding understanding of its mechanisms and usefulness challenging. This research acts as a pilot for further research into assistive technologies both in Australia and India.
Robust Fuzzy Control of Nonlinear Fuzzy Impulsive Singular Perturbed Systems with Time-varying Delay

— The problem of robust fuzzy control for a class of nonlinear fuzzy impulsive singular perturbed systems with time-varying delay is investigated by employing Lyapunov functions. The nonlinear delay system is built based on the well-known T–S fuzzy model. The so-called parallel distributed compensation idea is employed to design the state feedback controller. Sufficient conditions for global exponential stability of the closed-loop system are derived in terms of linear matrix inequalities (LMIs), which can be easily solved by LMI technique. Some simulations illustrate the effectiveness of the proposed method.
Serious Gaming Analytics: What Students' Log Files Tell Us about Gaming and Learning

In this paper we explore existing log files of the VIBOA environmental policy game. Our aim is to identify relevant player behaviours and performance patterns. The VIBOA game is a 50 hours master level serious game that supports inquiry-based learning: students adopt the role of an environmental consultant in the (fictitious) consultancy agency VIBOA, and have to deal with complex, multi-faceted environmental problems in an academic and methodologically sound way. A sample of 118 master students played the game. We used learning analytics to extract relevant data from the logging and find meaningful patterns and relationships. We observed substantial behavioural variability across students. Correlation analysis suggest a behavioural trade that reflects the rate of “switching” between different game objects or activities. We were able to establish a model that uses switching indicators as predictors for the efficiency of learning. Also we found slight evidence that students who display increased switching behaviours need more time to complete the games. We conclude the paper by critically evaluating our findings, making explicit the limitations of our study and making suggestions for future research that links together learning analytics and serious gaming.
Growth mixture modeling with non‐normal distributions

A limiting feature of previous work on growth mixture modeling is the assumption of normally distributed variables within each latent class. With strongly non‐normal outcomes, this means that several latent classes are required to capture the observed variable distributions. Being able to relax the assumption of within‐class normality has the advantage that a non‐normal observed distribution does not necessitate using more than one class to fit the distribution. It is valuable to add parameters representing the skewness and the thickness of the tails. A new growth mixture model of this kind is proposed drawing on recent work in a series of papers using the skew‐t distribution. The new method is illustrated using the longitudinal development of body mass index in two data sets. The first data set is from the National Longitudinal Survey of Youth covering ages 12–23 years. Here, the development is related to an antecedent measuring socioeconomic background. The second data set is from the Framingham Heart Study covering ages 25–65 years. Here, the development is related to the concurrent event of treatment for hypertension using a joint growth mixture‐survival model. Copyright © 2014 John Wiley & Sons, Ltd.
The Unstructured N-terminal Region of Arabidopsis Group 4 Late Embryogenesis Abundant (LEA) Proteins Is Required for Folding and for Chaperone-like Activity under Water Deficit*

Late embryogenesis abundant (LEA) proteins are a conserved group of proteins widely distributed in the plant kingdom that participate in the tolerance to water deficit of different plant species. In silico analyses indicate that most LEA proteins are structurally disordered. The structural plasticity of these proteins opens the question of whether water deficit modulates their conformation and whether these possible changes are related to their function. In this work, we characterized the secondary structure of Arabidopsis group 4 LEA proteins. We found that they are disordered in aqueous solution, with high intrinsic potential to fold into α-helix. We demonstrate that complete dehydration is not required for these proteins to sample ordered structures because milder water deficit and macromolecular crowding induce high α-helix levels in vitro, suggesting that prevalent conditions under water deficit modulate their conformation. We also show that the N-terminal region, conserved across all group 4 LEA proteins, is necessary and sufficient for conformational transitions and that their protective function is confined to this region, suggesting that folding into α-helix is required for chaperone-like activity under water limitation. We propose that these proteins can exist as different conformers, favoring functional diversity, a moonlighting property arising from their structural dynamics.
Sorting Nexin 6 Enhances Lamin A Synthesis and Incorporation into the Nuclear Envelope

Nuclear lamins are important structural and functional proteins in mammalian cells, but little is known about the mechanisms and cofactors that regulate their traffic into the nucleus. Here, we demonstrate that trafficking of lamin A, but not lamin B1, and its assembly into the nuclear envelope are regulated by sorting nexin 6 (SNX6), a major component of the retromer that targets proteins and other molecules to specific subcellular locations. SNX6 interacts with lamin A in vitro and in vivo and links it to the outer surface of the endoplasmic reticulum in human and mouse cells. SNX6 transports its lamin A cargo to the nuclear envelope in a process that takes several hours. Lamin A protein levels in the nucleus augment or decrease, respectively, upon gain or loss of SNX6 function. We further show that SNX6-dependent lamin A nuclear import occurs across the nuclear pore complex via a RAN-GTP-dependent mechanism. These results identify SNX6 as a key regulator of lamin A synthesis and incorporation into the nuclear envelope.
Low energy hadron physics in holographic QCD

We present a holographic dual of four-dimensional, large N_c QCD with massless flavors. This model is constructed by placing N_f probe D8-branes into a D4 background, where supersymmetry is completely broken. The chiral symmetry breaking in QCD is manifested as a smooth interpolation of D8 - anti-D8 pairs in the supergravity background. The meson spectrum is examined by analyzing a five-dimensional Yang-Mills theory that originates from the non-Abelian DBI action of the probe D8-brane. It is found that our model yields massless pions, which are identified with Nambu-Goldstone bosons associated with the chiral symmetry breaking. We obtain the low-energy effective action of the pion field and show that it contains the usual kinetic term of the chiral Lagrangian and the Skyrme term. A brane configuration that defines a dynamical baryon is identified with the Skyrmion. We also derive the effective action including the lightest vector meson. Our model is closely related to that in the hidden local symmetry approach, and we obtain a Kawarabayashi-Suzuki-Riazuddin-Fayyazuddin-type relation among the couplings. Furthermore, we investigate the Chern-Simons term on the probe brane and show that it leads to the Wess-Zumino-Witten term. The mass of the \eta' meson is also considered, and we formulate a simple derivation of the \eta' mass term satisfying the Witten-Veneziano formula from supergravity.