Miracle-dz/UniFAR-FTUs huggingface dataset:
Ontogenic Expression Pattern and Genetic Polymorphisms of the Fatty Acid Transport Protein 4 (FATP4) Gene in Chinese Chicken Populations

In the current research, the polymorphism of FATP4 gene was analyzed in Erlang Mountainous chickens. A total of nine genetic variants were identified by FATP4 gene sequencing analysis across the chicken samples. Significant associations (p < 0.05) were observed for two SNPs (g.5608778C>T and g.5608814G>A in exon 6) with certain carcass traits (such as live weight, carcass weight, eviscerated weight) in S01 and S05 populations, respectively. Meanwhile, in S05 population, haplotype 3 (T-G) and haplotype 2 (C-A) were associated with higher and lower partial carcass traits such as live weight, carcass weight, eviscerated weight and semi-eviscerated weight, respectively. Moreover, we investigated the expression profile of this gene during ontogenesis in Mountainous black-boned chicken. Quantitative real-time PCR analysis showed that FATP4 mRNA had the highest expression level in small intestine tissue over all other tissues examined. The FATP4 mRNA levels presented remarkable developmental changes with age in the various tissues. These results suggested that the FATP4 gene might play an important role in controlling chicken carcass traits.
Learning Precise Timing with LSTM Recurrent Networks

The temporal distance between events conveys information essential for numerous sequential tasks such as motor control and rhythm detection. While Hidden Markov Models tend to ignore this information, recurrent neural networks (RNNs) can in principle learn to make use of it. We focus on Long Short-Term Memory (LSTM) because it has been shown to outperform other RNNs on tasks involving long time lags. We find that LSTM augmented by "peephole connections" from its internal cells to its multiplicative gates can learn the fine distinction between sequences of spikes spaced either 50 or 49 time steps apart without the help of any short training exemplars. Without external resets or teacher forcing, our LSTM variant also learns to generate stable streams of precisely timed spikes and other highly nonlinear periodic patterns. This makes LSTM a promising approach for tasks that require the accurate measurement or generation of time intervals.
Automated Migration of Hierarchical Data to Relational Tables using Programming-by-Example

While many applications export data in hierarchical formats like XML and JSON, it is often necessary to convert such hierarchical documents to a relational representation. This paper presents a novel programming-by-example approach, and its implementation in a tool called Mitra, for automatically migrating tree-structured documents to relational tables. We have evaluated the proposed technique using two sets of experiments. In the first experiment, we used Mitra to automate 98 data transformation tasks collected from StackOverflow. Our method can generate the desired program for 94% of these benchmarks with an average synthesis time of 3.8 seconds. In the second experiment, we used Mitra to generate programs that can convert real-world XML and JSON datasets to full-fledged relational databases. Our evaluation shows that Mitra can automate the desired transformation for all datasets.
Intrinsic platelet reactivity before P2Y12 blockade contributes to residual platelet reactivity despite high-level P2Y12 blockade by prasugrel or high-dose clopidogrel

Summary It was the objective of this study to determine whether the intrinsic platelet response to adenosine diphosphate (ADP) before thienopyridine exposure contributes to residual platelet reactivity to ADP despite high level P2Y12 blockade by prasugrel (60 mg loading dose [LD]), 10 mg daily maintenance dose [MD]) or high-dose clopidogrel (600 mg LD, 150 mg daily MD). High residual platelet function during clopidogrel therapy is associated with poor clinical outcomes. It remains unknown whether the relationship between platelet reactivity prior to treatment with clopidogrel (300 mg LD, 75 mg daily MD) and residual on-treatment platelet reactivity is maintained after more potent P2Y12 inhibition. PRINCIPLE-TIMI 44 was a randomised, double-blind, twophase crossover study of prasugrel compared with high-dose clopidogrel in 201 patients undergoing cardiac catheterisation for planned percutaneous coronary intervention. ADP-stimulated platelet-monocyte aggregates, platelet surface P-selectin and platelet aggregation were measured pre-treatment, during LD (6 h and 18–24 h) and MD (15 d). Correlations of pre-treatment to on-treatment values were determined by Spearman rank order. Prasugrel resulted in greater platelet inhibition than high-dose clopidogrel for each measure. However, for both drugs, pre-treatment reactivity to ADP predicted 6 h, 18–24 h and 15 day reactivity to ADP (correlations 0.24–0.62 for platelet-monocyte aggregates and P-selectin). In conclusion, a patient's intrinsic platelet response to ADP before exposure to thienopyridines contributes to residual platelet reactivity to ADP despite high level P2Y12 blockade with high-dose clopidogrel or even higher level P2Y12 blockade with prasugrel. Patients who are hyper-responsive to ADP pre-treatment are more likely to be hyper-responsive to ADP on-treatment, which may be relevant to therapeutic strategies.
Identification of a Small GTPase Inhibitor Using a High-Throughput Flow Cytometry Bead-Based Multiplex Assay

Small GTPases are key regulators of cellular activity and represent novel targets for the treatment of human diseases using small-molecule inhibitors. The authors describe a multiplex, flow cytometry bead-based assay for the identification and characterization of inhibitors or activators of small GTPases. Six different glutathione-S-transferase (GST)—tagged small GTPases were bound to glutathione beads, each labeled with a different red fluorescence intensity. Subsequently, beads bearing different GTPase were mixed and dispensed into 384-well plates with test compounds, and fluorescent—guanosine triphosphate (GTP) binding was used as the readout. This novel multiplex assay allowed the authors to screen a library of almost 200,000 compounds and identify more than 1200 positive compounds, which were further verified by dose-response analyses, using 6- to 8-plex assays. After the elimination of false-positive and false-negative compounds, several small-molecule families with opposing effects on GTP binding activity were identified. The authors detail the characterization of MLS000532223, a general inhibitor that prevents GTP binding to several GTPases in a dose-dependent manner and is active in biochemical and cell-based secondary assays. Live-cell imaging and confocal microscopy studies revealed the inhibitor-induced actin reorganization and cell morphology changes, characteristic of Rho GTPases inhibition. Thus, high-throughput screening via flow cytometry provides a strategy for identifying novel compounds that are active against small GTPases.
The effect of head-nod recognition in human-robot conversation

This paper reports on a study of human participants with a robot designed to participate in a collaborative conversation with a human. The purpose of the study was to investigate a particular kind of gestural feedback from human to the robot in these conversations: head nods. During these conversations, the robot recognized head nods from the human participant. The conversations between human and robot concern demonstrations of inventions created in a lab. We briefly discuss the robot hardware and architecture and then focus the paper on a study of the effects of understanding head nods in three different conditions. We conclude that conversation itself triggers head nods by people in human-robot conversations and that telling participants that the robot recognizes their nods as well as having the robot provide gestural feedback of its nod recognition is effective in producing more nods.
Identification, Molecular Cloning of IL-1β and Its Expression Profile during Nocardia seriolae Infection in Largemouth Bass, Micropterus salmoides

In the present study, IL-1β cDNA was identified and analyzed from largemouth bass (Micropterus salmoides). Full length IL-1β mRNA was obtained using Rapid Amplification of cDNA Ends (RACE), which contains 78 bp 3′-UTR, a 455 bp 5′-UTR, and an open reading frame (ORF) of 702 bp coding for 233 amino acid residues. The molecular weight and theoretical isoelectric point of largemouth bass IL-1β protein was predicted to be 26.7 kDa and 6.08 respectively. A largemouth bass IL-1β phylogenetic analysis showed a close relation to the IL-1βs of striped trumpeter (Latris lineata), Chinese perch (Siniperca chuatsi), and Japanese sea bass (Lateolabrax japonicus). Peptidoglycan upregulated IL-1β in the spleen and head kidney, while lipopolysaccharide upregulated detectable levels of IL-1β in the spleen only. Largemouth bass, challenged with Nocardia seriolae (1.0 × 106 cfu/mL), showed a significant increase in IL-1β at 3 and 5 days post infection (dpi) in the spleen, while in the head kidney significant expression was found at 2 and 3 dpi, peaking at 3 dpi. Furthermore, tumor necrosis factor α (TNF-α) showed significantly higher expression in the spleen at 3 and 5 dpi, and in the head kidney at 1 and 3 dpi, with expression decreasing at 5 dpi in both tissues.
Quality of Life in Patients with Thalassemia Major and Intermedia in Kerman-Iran (I.R.)

Thalassemia is the most common hemoglobin disorder in the world and thalassemia major and intermedia stand among the most severe forms. Due to recent improvements in treatment, patients with thalassemia have longer life expectancies; hence it is of utmost importance to pay careful attention to their quality of life together with life expectancy. This study was conducted to assess the quality of life in patients with thalassemia and also to compare it between thalassemia major and intermedia. In this cross-sectional study, patients who referred for blood transfusion or follow-up visits were evaluated for their quality of life (QOL). Short Form-36 questionnaire was applied to evaluate QOL. In this study, 308 patients with a mean age of 22.95±4.82 years were evaluated. The scores of QOL were regarded as moderate in eight domains under evaluation; the least score was given to General Health (53.05±16.96) whereas the highest score was given to Physical Functioning (67.95±22.68). The QOL in the patients with thalassemia major was better than those with thalassemia intermedia regarding Physical Functioning and Role Limitation Emotional domains. Compared to injecting chelators, patients who received oral chelators showed to have a better QOL considering Social Functioning and Mental Health domain. The patients under study didn’t have a satisfying QOL ; the QOL of patients with thalassemia major was better than that of patients with thalassemia intermedia in only 2 domains of sf-36(Physical Functioning & Role limitation-Emotional). It is then essential that experts pay proper attention to improve QOL among patients.
Evaluating Co‐primary Endpoints Collectively in Clinical Trials

Often a treatment is assessed by co‐primary endpoints so that a comprehensive picture of the treatment effect can be obtained. Co‐primary endpoints can be different medical assessments angled at different aspects of a disease, therefore, are used collectively to strengthen evidence for the treatment effect. It is common sense that if a treatment is ineffective, the chance to show that the treatment is effective in all co‐primary endpoints should be small. Therefore, it may not be necessary to require all the co‐primary endpoints to be statistically significant at the 1‐sided 0.025 level to control the error rate of wrongly approving an ineffective treatment. Rather it is reasonable to allow certain variation for the p ‐values within a range close to 0.025. In this paper, statistical methods are developed to derive decision rules to evaluate co‐primary endpoints collectively. The decision rules control the error rate of wrongly accepting an ineffective treatment at the level of 0.025 for a study and the error rate at a slightly higher level for a treatment that works for all the co‐primary endpoints except perhaps one. The decision rules also control the error rates for individual endpoints. Potential applications in clinical trials are presented (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Object detection with Gabor filters and cumulative histograms

Proposes an algorithm for segmentation and extracting an object region by using Gabor filters. Gabor filters are exploited to extract spatial frequency in some orientations, and not only the outputs of Gabor filters but also color information is used to construct the features at each image pixel. The criterion is devised so as to consider the similarity, the region size and the region shape factors in order to efficiently merge the features. In general, a complex object may be segmented into multiple regions. However for the purpose of detecting such a complex object, we represent the object region by the normalized cumulative histogram of features. From experimental results, it is found that the proposed algorithm is able to efficiently detect the object regions such as cars in images of usual traffic scenes.
Evolution of Genome Size and Complexity in Pinus

Background Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood. Methodology/Principal Findings Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA. Conclusions/Significance Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.
2,3,7,8-Tetrachlorodibenzo-p-dioxin poly(ADP-ribose) polymerase (TiPARP, ARTD14) is a mono-ADP-ribosyltransferase and repressor of aryl hydrocarbon receptor transactivation

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-inducible poly(ADP-ribose) polymerase (TiPARP/ARTD14) is a member of the PARP family and is regulated by the aryl hydrocarbon receptor (AHR); however, little is known about TiPARP function. In this study, we examined the catalytic function of TiPARP and determined its role in AHR transactivation. We observed that TiPARP exhibited auto-mono-ADP-ribosyltransferase activity and ribosylated core histones. RNAi-mediated knockdown of TiPARP in T-47D breast cancer and HuH-7 hepatoma cells increased TCDD-dependent cytochrome P450 1A1 (CYP1A1) and CYP1B1 messenger RNA (mRNA) expression levels and recruitment of AHR to both genes. Overexpression of TiPARP reduced AHR-dependent increases in CYP1A1-reporter gene activity, which was restored by overexpression of AHR, but not aryl hydrocarbon receptor nuclear translocator. Deletion and mutagenesis studies showed that TiPARP-mediated inhibition of AHR required the zinc-finger and catalytic domains. TiPARP and AHR co-localized in the nucleus, directly interacted and both were recruited to CYP1A1 in response to TCDD. Overexpression of Tiparp enhanced, whereas RNAi-mediated knockdown of TiPARP reduced TCDD-dependent AHR proteolytic degradation. TCDD-dependent induction of AHR target genes was enhanced in Tiparp−/− mouse embryonic fibroblasts compared with wildtype controls. Our findings show that TiPARP is a mono-ADP-ribosyltransferase and a transcriptional repressor of AHR, revealing a novel negative feedback loop in AHR signalling.
POSIX-Compliant Portable Code Synthesis for Embedded Systems

In a large class of embedded systems, dynamic multithreading using traditional OS techniques is infeasible due to memory and processing overheads or lack of operating systems (OS) availability for the target embedded processor. In this work, we propose a source-to-source translator that takes a POSIX compliant multithreaded C program as input and generates an equivalent, embedded processor independent, single threaded ANSI C program, to be compiled using the embedded processor-specific tool chain. The output of our tool is a highly tuned ANSI C program that embodies the applicationspecific embedded scheduler and dynamic multithreading infrastructure along with the user code. In this work, we outline the implementation details of our source-to-source translator and show the feasibility of the proposed technique by comparing execution efficiency to approaches based on Java-VM and traditional UNIX based POSIX implementations.
Ability of tetraploid rat blastocysts to support fetal development after complementation with embryonic stem cells

This study was undertaken to generate rat offspring via tetraploid blastocyst complementation with embryonic stem (ES) cells. Tetraploid blastocysts were prepared by electrofusion of blastomeres from two‐cell stage embryos, and subsequent in vivo culture for 4 days. Microinjection into the tetraploid blastocoel of an inner cell mass isolated by immunosurgery resulted in the generation of rat offspring, suggesting the successful contribution of tetraploid blastocysts to their placenta. Tetraploid blastocyst complementation was attempted with a total of 4 ES cell lines (2 lines of female karyotype and 2 lines of male karyotype). In the rESWIv‐3i‐5 (XX) cell line, normal‐sized fetuses with heartbeats were harvested on E11.5 (12.1%), E12.5 (9.5%), and E13.5 (9.1%), but no viable fetuses were detected on E14.5. Similarly, use of the rESWIv‐3i‐1 (XX) cell line resulted in no viable fetus production on E14.5. Using the rESBLK2i‐1 (XY) cell line, viable fetuses were harvested not only on E11.5–E13.5 (2.6–5.5%), but also on E14.5 (3.0%). The transfer of a total of 487 tetraploid blastocysts complemented with rESBLK2i‐1 cells resulted in 256 implantation sites (52.6%) on E21.5, but no viable offspring was detected. Use of the rESBLK2i‐1/huKO (XY) cell line also resulted in no viable offspring production on E21.5. Analyses of the methylation pattern in differentially methylated regions and transcript level of genes that are imprinted in mice (H19, Meg3, Igf2r, Peg5, and Peg10) in the E14.5 conceptuses indicated a marked difference between the ES cell‐derived and control normal fetuses, but not between the tetraploid and control diploid placenta. Mol. Reprod. Dev. 79:402–412, 2012. © 2012 Wiley Periodicals, Inc.
MODELLING AUXILIARY FEATURES in TANDEM SYSTEMS

Tandem systems transform the cepstral features into posterior probabilities of subword units using artificial neural networks (ANNs), which are processed to form input features for conventional speech recognition systems. They have been shown to perform better than conventional speech recognition systems using cepstral features. Recent studies have shown that modelling cepstral features with auxiliary sources of knowledge leads to improvement in the performance of speech recognition systems. In this paper, we study two approaches to incorporate auxiliary knowledge sources such as pitch frequency, short-term energy, etc. (referred to as auxiliary features), in a tandem-based automatic speech recognition system. In the first approach, we model the auxiliary features in the process of training an ANN, which is later used to extract tandem-features. In the second approach, we extract the tandem-features from an ANN trained with cepstral features only and then model them jointly with auxiliary features. Recognition studies conducted on a connected word recognition task under clean and noisy conditions show that the performance of the tandem system can be improved by incorporating auxiliary features.
Macroscopic Modelling and Simulation of Multi-lane Traffic

In this work a macroscopic lane-changing model is incorporated to a single-class second-order gas-kinetic (GKT) traffic flow model to simulate multi-lane traffic flow dynamics. The lane-changing terms, simulating lane-changes due to vehicle interactions as well as spontaneous ones, are introduced as source and sink terms into the traffic flow equations. The numerical integration is based on an accurate and robust high-resolution finite volume relaxation scheme, where the nonlinear system of the macroscopic partial differential equations are first recast to a diagonilizable semi-linear system. A fifth order in space WENO scheme is used for spatial discretization, while time integration is based on a high-order implicit-explicit Runge-Kutta method. Numerical simulations, considering a two-lane highway flow where a bottleneck is formed due to a lane closure, demonstrate the ability of the proposed methodology to efficiently simulate the corresponding traffic dynamics.
Spots, traps, and patches: asymptotic analysis of localized solutions to some linear and nonlinear diffusive systems

Localized spatial patterns commonly occur for various classes of linear and nonlinear diffusive processes. In particular, localized spot patterns, where the solution concentrates at discrete points in the domain, occur in the nonlinear reaction–diffusion (RD) modeling of diverse phenomena such as chemical patterns, biological morphogenesis, and the spatial distribution of urban crime. In a 2D spatial domain we survey some recent and new results for the existence, linear stability, and slow dynamics of localized spot patterns by using the Brusselator RD model as the prototypical example. In the context of linear diffusive systems with localized solution behavior, we will discuss some previous results for the determination of the mean first capture time for a Brownian particle in a 2D domain with localized traps, and the determination of the persistence threshold of a species in a 2D landscape with patchy food resources. Common features in the analysis of all of these spatially localized patterns are emphasized, including the key role of certain matrices involving various Green’s functions, and the derivation and study of new classes of interacting particle systems and discrete variational problems arising from various asymptotic reductions. The mathematical tools include matched asymptotic analysis based on strong localized perturbation theory, spectral analysis, the analysis of nonlocal eigenvalue problems, and bifurcation theory. Some specific open problems are highlighted and, more broadly, we will discuss a few new research frontiers for the analysis of localized patterns in multi-dimensional domains.