Miracle-dz/UniFAR-FTUs huggingface dataset:
The Schizophrenia Risk Allele C of the TCF4 rs9960767 Polymorphism Disrupts Sensorimotor Gating in Schizophrenia Spectrum and Healthy Volunteers

In a large-scale meta-analysis, it has been recently shown that the transcription factor 4 (TCF4) gene is among the most prominent susceptibility genes for schizophrenia. Moreover, transgenic mice overexpressing TCF4 in the brain display a reduction of sensorimotor gating measured by prepulse inhibition (PPI) of the acoustic startle response (ASR). PPI is heritable and has been established as an important translational endophenotype of schizophrenia. We therefore investigated the impact of the schizophrenia susceptibility gene TCF4 (rs9960767) on sensorimotor gating of the ASR in healthy humans and in patients with a schizophrenia spectrum disorder. We assessed PPI, startle reactivity, and habituation of the ASR in two independent samples. The first sample consisted of 107 healthy volunteers from London, UK. The second sample was a schizophrenia spectrum group (n = 113) of 73 schizophrenia patients and 40 individuals at high risk for schizophrenia from Bonn, Germany (total sample n = 220). In both samples, PPI was strongly decreased in carriers of the schizophrenia risk allele C of the TCF4 gene (meta-analysis across both samples: p = 0.00002), whereas startle reactivity and habituation were unaffected by TCF4 genotype. Sensorimotor gating is modulated by TCF4 genotype, indicating an influential role of TCF4 gene variations in the development of early information-processing deficits in schizophrenia.
Arabidopsis DUO POLLEN3 Is a Key Regulator of Male Germline Development and Embryogenesis[C][W]

Male germline development in angiosperms produces the pair of sperm cells required for double fertilization. A key regulator of this process in Arabidopsis thaliana is the male germline-specific transcription factor DUO POLLEN1 (DUO1) that coordinates germ cell division and gamete specification. Here, we uncover the role of DUO3, a nuclear protein that has a distinct, but overlapping role with DUO1 in male germline development. DUO3 is a conserved protein in land plants and is related to GON-4, a cell lineage regulator of gonadogenesis in Caenorhabditis elegans. Mutant duo3-1 germ cells either fail to divide or show a delay in division, and we show that, unlike DUO1, DUO3 promotes entry into mitosis independent of the G2/M regulator CYCB1;1. We also show that DUO3 is required for the expression of a subset of germline genes under DUO1 control and that like DUO1, DUO3 is essential for sperm cell specification and fertilization. Furthermore, we demonstrate an essential sporophytic role for DUO3 in cell division and embryo patterning. Our findings demonstrate essential developmental roles for DUO3 in cell cycle progression and cell specification in both gametophytic and sporophytic tissues.
A Detailed Comparison of Probabilistic Approaches for Coping with Unfair Ratings in Trust and Reputation Systems

The unfair rating problem exists when a buying agent models the trustworthiness of selling agents by also relying on ratings of the sellers from other buyers. Different probabilistic approaches have been proposed to cope with this issue. In this paper, we first summarize these approaches and provide a detailed categorization of them. This includes our own "personalized" approach for addressing this problem. Based on the implication of such analysis, we then focus on experimental comparison of our approach with two key models in a framework that simulates a dynamic electronic marketplace environment. We specifically examine different scenarios, including ones where the majority of buyers are dishonest, buyers lack personal experience with sellers, sellers may vary their behavior, and buyers may provide a large number of ratings. Our study provides the basis for deciding which approach is most appropriate to employ, in which scenario.
Conserved Streptococcus pneumoniae Spirosomes Suggest a Single Type of Transformation Pilus in Competence

The success of S. pneumoniae as a major human pathogen is largely due to its remarkable genomic plasticity, allowing efficient escape from antimicrobials action and host immune response. Natural transformation, or the active uptake and chromosomal integration of exogenous DNA during the transitory differentiated state competence, is the main mechanism for horizontal gene transfer and genomic makeover in pneumococci. Although transforming DNA has been proposed to be captured by Type 4 pili (T4P) in Gram-negative bacteria, and a competence-inducible comG operon encoding proteins homologous to T4P-biogenesis components is present in transformable Gram-positive bacteria, a prevailing hypothesis has been that S. pneumoniae assembles only short pseudopili to destabilize the cell wall for DNA entry. We recently identified a micrometer-sized T4P-like pilus on competent pneumococci, which likely serves as initial DNA receptor. A subsequent study, however, visualized a different structure - short, ‘plaited’ polymers - released in the medium of competent S. pneumoniae. Biochemical observation of concurrent pilin secretion led the authors to propose that the ‘plaited’ structures correspond to transformation pili acting as peptidoglycan drills that leave DNA entry pores upon secretion. Here we show that the ‘plaited’ filaments are not related to natural transformation as they are released by non-competent pneumococci, as well as by cells with disrupted pilus biogenesis components. Combining electron microscopy visualization with structural, biochemical and proteomic analyses, we further identify the ‘plaited’ polymers as spirosomes: macromolecular assemblies of the fermentative acetaldehyde-alcohol dehydrogenase enzyme AdhE that is well conserved in a broad range of Gram-positive and Gram-negative bacteria.
Colorectal Cancer Screening—Who, How, and When?

Colorectal cancer (CRC) is the third most common cancer worldwide. It is amenable to screening as it occurs in premalignant, latent, early, and curable stages. PubMed, Cochrane Database of Systematic Reviews, and national and international CRC screening guidelines were searched for CRC screening methods, populations, and timing. CRC screening can use direct or indirect tests, delivered opportunistically or via organized programs. Most CRCs are diagnosed after 60 years of age; most screening programs apply to individuals 50–75 years of age. Screening may reduce disease-specific mortality by detecting CRC in earlier stages, and CRC incidence by detecting premalignant polyps, which can subsequently be removed. In randomized controlled trials (RCTs) guaiac fecal occult blood testing (gFOBt) was found to reduce CRC mortality by 13%–33%. Fecal immunochemical testing (FIT) has no RCT data comparing it to no screening, but is superior to gFOBt. Flexible sigmoidoscopy (FS) trials demonstrated an 18% reduction in CRC incidence and a 28% reduction in CRC mortality. Currently, RCT evidence for colonoscopy screening is scarce. Although not yet corroborated by RCTs, it is likely that colonoscopy is the best screening modality for an individual. From a population perspective, organized programs are superior to opportunistic screening. However, no nation can offer organized population-wide colonoscopy screening. Thus, organized programs using cheaper modalities, such as FS/FIT, can be tailored to budget and capacity.
Make Humans Randomize

This paper presents results from an experiment studying a two-person 4x4 pure coordination game. We seek to identify a labeling of actions that induces subjects to select all options with the same probability. Such a display of actions must be free from salient properties that might be used by participants to coordinate. Testing 23 different sets of labels, we identify two sets that produce a distribution of subjects’ choices which approximate the uniform distribution quite well. Our design can be used in studies intending to compare the behavior of subjects who play against a random mechanism with that of participants who play against human counterparts.
Variations in the bitterness perception-related genes TAS2R38 and CA6 modify the risk for colorectal cancer in Koreans

Bitterness perception is known to be an important factor in individuals’ dietary behaviors and is also associated with the sensing of nutritious/noxious molecules for subsequent metabolic responses in multiple organs. Therefore, the genetic variation in bitterness sensing may be associated with diet-related diseases, including colorectal cancer (CRC). We investigated the influence of variations in the bitterness-sensing genes taste receptor type 2 member 38 (TAS2R38) and carbonic anhydrase 6 (CA6) on the consumption of food, tobacco and alcohol and the risk of CRC in Koreans. The study population consisted of 681 cases and 1361 controls, and their intake of vegetables, fruits, fiber, fat-food and sweets was analyzed. The genotypes for TAS2R38 A49P, V262A and I296V and CA6 rs2274333 A/G were assessed using the MassArray technique. Our findings suggested that the TAS2R38 diplotype, CA6 rs2274333 and their combined genotype had a negligible influence on dietary and alcohol intake. The combined TAS2R38-CA6 AVI/AVI-AA genotype was associated with higher tobacco consumption than the other genotypes in CRC cases only. However, the genetic variations were a significant risk factor for CRC. The TAS2R38 AVI/AVI diplotype and CA6 G allele were associated with a reduced risk of CRC. Moreover, when the combined genotypes of the subjects were analyzed, possessing both the variant diplotype/variant allele (AVI/AVI+G*) was associated with a greater reduction in the risk of CRC (adjusted OR = 0.49; 95%CI: 0.34–0.74). In summary, variations in the bitterness perception genes TAS2R38 and CA6 did not influence the examined food intake in Koreans. However, those genetic variants were a decisive modifying factor of CRC susceptibility.
Analysis of thermoelastic and dissipative effects related to the fatigue of 2024 T3 aluminium alloy

In this paper the fatigue phenomena of 2024 T3 aluminium alloy were studied in terms of thermal and calorimetric effects during uniaxial cyclic loading. Thermoelastic coupling sources and dissipation were separately estimated by using infrared thermal data and a local simplified form of the heat equation. The simplifications are essentially based on the assumption that the uniaxial fatigue test remains homogeneous until a macroscopic fatigue crack occurs within the gauge section of the specimen. Heat sources were then compared to predictions derived from mechanical data by assuming a linear isotropic thermoelastic behaviour of the material and by neglecting the influence of thermomechanical couplings on the hysteresis area of fatigue cycles.
Predicted time dependence of the switching field for magnetic materials.

A scaling relationship between switching fields, of which remanent coercivity is a prominent example, and measurement time is derived. The energy barrier to thermal fluctuations is found to exhibit a (3/2-power dependence on the difference between the applied field and the nonthermally assisted switching field. This (3/2-power dependence contrasts with the 2-power dependence which has been widely assumed in the literature. Implications for magnetic viscosity and the orientational dependence of the time-dependent switching field in certain small, isolated particles are also discussed.
THE U -LAGRANGIAN OF A CONVEX FUNCTION

At a given point p , a convex function f is diﬀerentiable in a certain subspace U (the subspace along which ∂f ( p ) has 0-breadth). This property opens the way to deﬁning a suitably restricted second derivative of f at p . We do this via an intermediate function, convex on U . We call this function the U -Lagrangian; it coincides with the ordinary Lagrangian in composite cases: exact penalty, semideﬁnite programming. Also, we use this new theory to design a conceptual pattern for superlinearly convergent minimization algorithms. Finally, we establish a connection with the Moreau-Yosida regularization.
Evidence for the Retention of Two Evolutionary Distinct Plastids in Dinoflagellates with Diatom Endosymbionts

Dinoflagellates harboring diatom endosymbionts (termed “dinotoms”) have undergone a process often referred to as “tertiary endosymbiosis”—the uptake of algae containing secondary plastids and integration of those plastids into the new host. In contrast to other tertiary plastids, and most secondary plastids, the endosymbiont of dinotoms is distinctly less reduced, retaining a number of cellular features, such as their nucleus and mitochondria and others, in addition to their plastid. This has resulted in redundancy between host and endosymbiont, at least between some mitochondrial and cytosolic metabolism, where this has been investigated. The question of plastidial redundancy is particularly interesting as the fate of the host dinoflagellate plastid is unclear. The host cytosol possesses an eyespot that has been postulated to be a remnant of the ancestral peridinin plastid, but this has not been tested, nor has its possible retention of plastid functions. To investigate this possibility, we searched for plastid-associated pathways and functions in transcriptomic data sets from three dinotom species. We show that the dinoflagellate host has indeed retained genes for plastid-associated pathways and that these genes encode targeting peptides similar to those of other dinoflagellate plastid-targeted proteins. Moreover, we also identified one gene encoding an essential component of the dinoflagellate plastid protein import machinery, altogether suggesting the presence of a functioning plastid import system in the host, and by extension a relict plastid. The presence of the same plastid-associated pathways in the endosymbiont also extends the known functional redundancy in dinotoms, further confirming the unusual state of plastid integration in this group of dinoflagellates.
Functional organization of the fusiform gyrus revealed with connectivity profiles

Within the object recognition‐related ventral visual stream, the human fusiform gyrus (FG), which topographically connects the striate cortex to the inferior temporal lobe, plays a pivotal role in high‐level visual/cognitive functions. However, though there are many previous investigations of distinct functional modules within the FG, the functional organization of the whole FG in its full functional heterogeneity has not yet been established. In the current study, a replicable functional organization of the FG based on distinct anatomical connectivity patterns was identified. The FG was parcellated into medial (FGm), lateral (FGl), and anterior (FGa) regions using diffusion tensor imaging. We validated the reasonability of such an organizational scheme from the perspective of resting‐state whole brain functional connectivity patterns and the involvement of functional subnetworks. We found corroborating support for these three distinct modules, and suggest that the FGm serves as a transition region that combines multiple stimuli, the FGl is responsible for categorical recognition, and the FGa is involved in semantic understanding. These findings support two organizational functional transitions of the ventral temporal gyrus, a posterior/anterior direction of visual/semantic processing, and a media/lateral direction of high‐level visual processing. Our results may facilitate a more detailed study of the human FG in the future. Hum Brain Mapp 37:3003–3016, 2016. © 2016 Wiley Periodicals, Inc.
Some stability results for Picard iterative process in uniform space.

The following concepts shall be required in the sequel: Definition 1.1 [5, 27]. A uniform space (X,Φ) is a nonempty set X equipped with a nonempty family Φ of subsets of X ×X satisfying the following properties: (i) if U is in Φ, then U contains the diagonal {(x, x) |x ∈ X}; (ii) if U is in Φ and V is a subset of X ×X which contains U, then V is in Φ; (iii) if U and V are in Φ, then U ∩ V is in Φ; (iv) if U is in Φ, then there exists V in Φ, such that, whenever (x, y) and (y, z) are in V, then (x, z) is in U ; (v) if U is in Φ, then {(y, x) |(x, y) ∈ U} is also in Φ. Φ is called the uniform structure of X and its elements are called entourages or neighbourhoods or surroundings. The space (X,Φ) is called quasiuniform if property (v) is omitted. The notions of an A-distance and an E-distance were introduced by Aamri and El Moutawakil [1] to prove some common fixed point theorems for some new contractive or expansive maps in uniform space. In [1], the following contractive definition was employed: Let f, g : X → X be selfmappings of X. Then, we have
Identification of Epstein-Barr Virus (EBV) Nuclear Antigen 2 (EBNA2) Target Proteins by Proteome Analysis: Activation of EBNA2 in Conditionally Immortalized B Cells Reflects Early Events after Infection of Primary B Cells by EBV

ABSTRACT The Epstein-Barr virus (EBV) is a ubiquitous B-lymphotropic herpesvirus associated with several malignant tumors, e.g., Burkitt's lymphoma and Hodgkin's disease, and is able to efficiently immortalize primary B lymphocytes in vitro. The growth program of infected B cells is initiated and maintained by the viral transcription factor EBV nuclear antigen 2 (EBNA2), which regulates viral and cellular genes, including the proto-oncogene c-myc. In our study, patterns of protein expression in B cells with and without EBNA2 were analyzed by two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. For this purpose, we used a conditional immortalization system for EBV, a B cell line (EREB2-5) that expresses an estrogen receptor-EBNA2 fusion protein. In order to discriminate downstream targets of c-Myc from c-Myc-independent EBNA2 targets, we used an EREB2-5-derived cell line, P493-6, in which c-Myc is expressed under the control of a tetracycline-regulated promoter. Of 20 identified EBNA2 target proteins, 11 were c-Myc dependent and therefore most probably associated with proliferation, and one of these proteins was a posttranslationally modified protein, i.e., hypusinylated eIF5a. Finally, to estimate the relevance of EBNA2 targets during early EBV infection, we analyzed the proteomes of primary B cells before and after infection with EBV. The protein expression pattern induced upon EBV infection was similar to that following EBNA2 activation. These findings underscore the value of EREB2-5 cells as an appropriate model system for the analysis of early events in the process of EBV-mediated B-cell immortalization.
High‐order resting‐state functional connectivity network for MCI classification

Brain functional connectivity (FC) network, estimated with resting‐state functional magnetic resonance imaging (RS‐fMRI) technique, has emerged as a promising approach for accurate diagnosis of neurodegenerative diseases. However, the conventional FC network is essentially low‐order in the sense that only the correlations among brain regions (in terms of RS‐fMRI time series) are taken into account. The features derived from this type of brain network may fail to serve as an effective disease biomarker. To overcome this drawback, we propose extraction of novel high‐order FC correlations that characterize how the low‐order correlations between different pairs of brain regions interact with each other. Specifically, for each brain region, a sliding window approach is first performed over the entire RS‐fMRI time series to generate multiple short overlapping segments. For each segment, a low‐order FC network is constructed, measuring the short‐term correlation between brain regions. These low‐order networks (obtained from all segments) describe the dynamics of short‐term FC along the time, thus also forming the correlation time series for every pair of brain regions. To overcome the curse of dimensionality, we further group the correlation time series into a small number of different clusters according to their intrinsic common patterns. Then, the correlation between the respective mean correlation time series of different clusters is calculated to represent the high‐order correlation among different pairs of brain regions. Finally, we design a pattern classifier, by combining features of both low‐order and high‐order FC networks. Experimental results verify the effectiveness of the high‐order FC network on disease diagnosis. Hum Brain Mapp 37:3282–3296, 2016. © 2016 Wiley Periodicals, Inc.
A DELAY-DEPENDENT APPROACH TO DESIGN STATE ESTIMATOR FOR DISCRETE STOCHASTIC RECURRENT NEURAL NETWORK WITH INTER V AL TIME-V ARYING DELAYS

This paper deals with the problem of state estimation for discrete stochastic recurrent neural network with interval time-delays. The activation functions are assumed to be globally Lipschitz continuous. Attention is focused on the design of a state estimator which ensures the global stability of the estimation error dynamics. A delay-dependent condition with dependence on the upper and lower bounds of the delays is given in terms of a linear matrix inequality (LMI) to solve the neuron state estimation problem. When this LMI is feasible, the expression of a desired state estimator is also presented. In addition, slack matrices are introduced to reduce the conservatism of the condition. A numerical example is provided to demonstrate the applicability of the proposed approach.
A Fresh Look into the Handoff Mechanism of IEEE 802.11s under Mobility

Seamless mobility in legacy multi-hop IEEE 802.11 Wi-Fi network is difficult to accomplish due to the lack of handoff mechanism. IEEE 802.11s MAC layer protocol adds the feature of mobile mesh networking to standard Wi-Fi by providing layer-2 routing and handoff mechanisms. With ubiquitous connectivity and seamless handoff, many applications requiring continuous data streaming like video, VOIP, file downloading, etc. become possible in Wi-Fi networks that requires mobility support like highways, railways and underground transportation. In this paper we study the handoff mechanism of IEEE 802.11s protocol extensively in a real mobile testbed. Our testbed comprises three mesh nodes, one of which is installed on a vehicle for finding the impact of vehicle speed on 802.11s handoff mechanism. We found that the vehicle speed does not drastically affect the performance metrics during handoff as previously understood. Moreover the results show frequent handoffs during mobility. This is called the ping pong effect, which indicates the absence of hysteresis mechanism in 802.11s protocol. For improving the performance during handoffs we therefore suggest the use of hysteresis mechanism along with the airtime link metric being used in the default routing protocol of 802.11s.
Text normalization in code-mixed social media text

This paper addresses the problem of text normalization, an often overlooked problem in natural language processing, in code-mixed social media text. The objective of the work presented here is to correct English spelling errors in code-mixed social media text that contains English words as well as Romanized transliteration of words from another language, in this case Bangla. The targeted research problem also entails solving another problem, that of word-level language identification in code-mixed social media text. We employ a CRF based machine learning approach followed by post-processing heuristics for the word-level language identification task. For spelling correction, we used the noisy channel model of spelling correction. In addition, the spell checker model presented here tackles wordplay, contracted words and phonetic variations. Overall, the word-level language identification achieved 90.5% accuracy and the spell checker achieved 69.43% accuracy on the detected English words.