Miracle-dz/UniFAR-FTUs huggingface dataset:
The Genome of Ganderma lucidum Provide Insights into Triterpense Biosynthesis and Wood Degradation

Background Ganoderma lucidum (Reishi or Ling Zhi) is one of the most famous Traditional Chinese Medicines and has been widely used in the treatment of various human diseases in Asia countries. It is also a fungus with strong wood degradation ability with potential in bioenergy production. However, genes, pathways and mechanisms of these functions are still unknown. Methodology/Principal Findings The genome of G. lucidum was sequenced and assembled into a 39.9 megabases (Mb) draft genome, which encoded 12,080 protein-coding genes and ∼83% of them were similar to public sequences. We performed comprehensive annotation for G. lucidum genes and made comparisons with genes in other fungi genomes. Genes in the biosynthesis of the main G. lucidum active ingredients, ganoderic acids (GAs), were characterized. Among the GAs synthases, we identified a fusion gene, the N and C terminal of which are homologous to two different enzymes. Moreover, the fusion gene was only found in basidiomycetes. As a white rot fungus with wood degradation ability, abundant carbohydrate-active enzymes and ligninolytic enzymes were identified in the G. lucidum genome and were compared with other fungi. Conclusions/Significance The genome sequence and well annotation of G. lucidum will provide new insights in function analyses including its medicinal mechanism. The characterization of genes in the triterpene biosynthesis and wood degradation will facilitate bio-engineering research in the production of its active ingredients and bioenergy.
Neuroevolution for General Video Game Playing

General Video Game Playing (GVGP) allows for the fair evaluation of algorithms and agents as it minimizes the ability of an agent to exploit apriori knowledge in the form of game specific heuristics. In this paper we compare four possible combinations of evolutionary learning using Separable Natural Evolution Strategies as our evolutionary algorithm of choice; linear function approximation with Softmax search and e-greedy policies and neural networks with the same policies. The algorithms explored in this research play each of the games during a sequence of 1000 matches, where the score obtained is used as a measurement of performance. We show that learning is achieved in 8 out of the 10 games employed in this research, without introducing any domain specific knowledge, leading the algorithms to maximize the average score as the number of games played increases.
The influence of procedure justice on work engagement: The mediating role of organizational commitment

Based on the 350 samples from two companies of China Airline, the present study investigated the mediating effect of organizational commitment in the influence of procedure justice on work engagement. Study results indicated that the influence of procedural justice on work engagement is significant. Further study results showed that the affective commitment and normative commitment fully mediated the relationship of procedure justice and work engagement.
Differentially constrained mobile robot motion planning in state lattices

We present an approach to the problem of differentially constrained mobile robot motion planning in arbitrary cost fields. The approach is based on deterministic search in a specially discretized state space. We compute a set of elementary motions that connects each discrete state value to a set of its reachable neighbors via feasible motions. Thus, this set of motions induces a connected search graph. The motions are carefully designed to terminate at discrete states, whose dimensions include relevant state variables (e.g., position, heading, curvature, and velocity). The discrete states, and thus the motions, repeat at regular intervals, forming a lattice. We ensure that all paths in the graph encode feasible motions via the imposition of continuity constraints on state variables at graph vertices and compliance of the graph edges with a differential equation comprising the vehicle model. The resulting state lattice permits fast full configuration space cost evaluation and collision detection. Experimental results with research prototype rovers demonstrate that the planner allows us to exploit the entire envelope of vehicle maneuverability in rough terrain, while featuring real‐time performance. © 2009 Wiley Periodicals, Inc.
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

Motivation: De novo assemblies of genomes remain one of the most challenging applications in next-generation sequencing. Usually, their results are incomplete and fragmented into hundreds of contigs. Repeats in genomes and sequencing errors are the main reasons for these complications. With the rapidly growing number of sequenced genomes, it is now feasible to improve assemblies by guiding them with genomes from related species. Results: Here we introduce AlignGraph, an algorithm for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference genomes. It aligns paired-end (PE) reads and preassembled contigs or scaffolds to a close reference. From the obtained alignments, it builds a novel data structure, called the PE multipositional de Bruijn graph. The incorporated positional information from the alignments and PE reads allows us to extend the initial assemblies, while avoiding incorrect extensions and early terminations. In our performance tests, AlignGraph was able to substantially improve the contigs and scaffolds from several assemblers. For instance, 28.7–62.3% of the contigs of Arabidopsis thaliana and human could be extended, resulting in improvements of common assembly metrics, such as an increase of the N50 of the extendable contigs by 89.9–94.5% and 80.3–165.8%, respectively. In another test, AlignGraph was able to improve the assembly of a published genome (Arabidopsis strain Landsberg) by increasing the N50 of its extendable scaffolds by 86.6%. These results demonstrate AlignGraph’s efficiency in improving genome assemblies by taking advantage of closely related references. Availability and implementation: The AlignGraph software can be downloaded for free from this site: https://github.com/baoe/AlignGraph. Contact: thomas.girke@ucr.edu
Multimodal Corpus of Speech Production: Work in Progress

The paper introduces work-in-progress on multimodal articulatory data collection involving multiple instrumental techniques such as electrolaryngography (EGG), electropalatography (EPG) and electromagnetic articulography (EMA). The data is recorded from two native Estonian speakers (one male and one female), the target amount of the corpus is approximately one hour of speech from both subjects. In the paper the instrumental systems exploited for data collection and recording set-ups are introduced, examples of multimodal data analysis are given and the possible use of the corpus is discussed.
NEURAL MECHANISMS OF SHORT-TERM VISUAL PLASTICITY AND CORTICAL DISINHIBITION

iii ACKNOWLEDGEMENTS I wish to thank my advisor, Paul Corballis, for his guidance, patience, and friendship all these years. Without his mentorship I could never have made it this far. I would also like to thank my dissertation committee members Parks have always been a major source of inspiration and support. I cannot thank them enough. Most of all, I must express an incredible degree gratitude to my wife, Nadya, has been extremely patient and supportive over the years and particularly so these past few stressful months! iv
Global HPCC Benchmarks in Chapel : STREAM Triad , Random Access , and FFT ( Revision 1 . 4 — June 2007 Release )

Chapel is a new parallel programming language being developed by Cray Inc. as part of its participation in DARPA’s High Productivity Computing Systems program. In this article, we describe Chapel implementations of the global HPC Challenge (HPCC) benchmarks for the STREAM Triad, Random Access, and FFT computations. The Chapel implementations use 5–13× fewer lines of code than the reference implementations supplied by the HPCC team. All codes in this article compile and run with the current version of the Chapel compiler. We provide an introduction to Chapel, highlight key features used in our HPCC implementations, and discuss our plans and challenges for obtaining performance for these codes as our compiler development progresses. The full codes are listed in appendices to this article.
Analytic Black Hole Perturbation Approach to Gravitational Radiation

We review the analytic methods used to perform the post-Newtonian expansion of gravitational waves induced by a particle orbiting a massive, compact body, based on black hole perturbation theory. There exist two different methods of performing the post-Newtonian expansion. Both are based on the Teukolsky equation. In one method, the Teukolsky equation is transformed into a Regge-Wheeler type equation that reduces to the standard Klein Gordon equation in the flat-space limit, while in the other method (which was introduced by Mano, Suzuki, and Takasugi relatively recently, the Teukolsky equation is used directly in its original form. The former’s advantage is that it is intuitively easy to understand how various curved space effects come into play. However, it becomes increasingly complicated when one goes to higher and higher post-Newtonian orders. In contrast, the latter’s advantage is that a systematic calculation to higher post-Newtonian orders can be implemented relatively easily, but otherwise, it is so mathematical that it is hard to understand the interplay of higher order terms. In this paper, we review both methods so that their pros and cons may be seen clearly. We also review some results of calculations of gravitational radiation emitted by a particle orbiting a black hole.
Researched on a Novel PV Power Inverter Applied in Micro-Grid

A novel PV power inverter applied in micro-grid is developed in this paper. It runs not only in connected-grid but also in disconnected-grid and keeps voltage stable rapidly in transient process. When the inverter is connected with the grid, the inverter produces power as a current-source with voltage-current close loop control strategy. Once the islanding event takes place, it runs as a voltage-source, adopting voltage virtual value outer-loop and voltage instantaneous value inner-loop control strategy and fuzzy self-adjusting for PI parameters. Finally the experimental results demonstrate the effectiveness with PV experimental platform.
Sentence types in Kenyan sign language: a structuralist approach

This study is an attempt to identify and describe the various sentence types of the Kenya Sign Language (KSL) using structuralist approach. After giving some background information on the language and the elements of sign language, (SL) structure in chapter one and two, we identify the sentence types in KSL. We then proceed to analyse the syntactic structure of each type. The types identified and analysed are Declaratives, Asserted Declaratives statements, interrogatives sentences: Yes/No questions, wh-questions, conditional statements, Topicalization, Imperative sentences and Rhetorical sentences. We also show that the declarative sentence, is the most basic type. We proceed to discuss how the non-manual grammatical markers (NGMs) play an important syntactical role in determining the modality of manualy formed construction of different sentence types. We have observed that the word-sign order remains the same as the declaratives but the NGMs vary. the NGMs identified and used in this study are 'q' 'neg', 'nod' 'wh-q', It', 'cond', 'Imp', and 'rhet-q'. On the whole our work shows that the aforementioned NGMs form an important part of descriptive tools for the analysis of KSL sentences.
Determinants of exports and investment of manufacturing firms in Tanzania

Since the mid-1980s Tanzania has implemented a number of trade and fiscal policy reforms that were partly intended to encourage increased export activity by manufacturing firms. Macroeconomic data suggest that there has been little response. To understand this lack of response we need to increase our understanding of the features of manufacturing exporters in Tanzania. This paper is a first attempt, by presenting the findings from a survey of 83 firms. Large firms are more likely to export than other firms, and more large firms sustain their investments than smaller firms. We also find, independent of this relationship to size, that firms that sustain investment are more likely to export than those which do not sustain investment. One distinction between our findings and other studies is that parastatals, including firms with some government ownership, tend to be larger and are more likely to export and sustain investments than non-parastatals. Subscription by shareholders and personal savings are the two main sources of start-up capital, while company earnings are how most investments are financed. The findings are consistent with the view limited access to bank financing has been a major constraint to manufacturing, especially exporting. Outline
Detecting and Recovering the Tampered Image in Network

The main objective of this project is to figure out the tampered area of the received image and recovering the hidden information in the tampered zones. To detect a image, RS Channel Coding algorithm is used to check bits and for recovery reference bits are used. The proposed scheme significantly outperforms recent techniques in terms of picture essence for both watermarked and recovered image. The watermark image quality is achieved through spending less bit-budget on watermark, while image recovery quality is considerably improved based on the performance of designed sce and channel codes.
Understanding the Role of Likeability in the Peer Assessments of University Students’ Oral Presentation Skills: A Latent Variable Approach

ABSTRACT The purpose of the present study was twofold: (a) it examined the relationship between peer-rated likeability and peer-rated oral presentation skills of 96 student presenters enrolled in a science communication course, and (b) it investigated the relationship between student raters’ severity in rating presenters’ likeability and their severity in evaluating presenters’ skills. Students delivered an academic presentation and then changed roles to rate their peers’ performance and likeability, using an 18-item oral presentation scale and a 10-item likeability questionnaire, respectively. Many-facet Rasch measurement was used to validate the data, and structural equation modeling (SEM) was used to examine the research questions. At an aggregate level, likeability explained 19.5% of the variance of the oral presentation ratings and 8.4% of rater severity. At an item-level, multiple cause-effect relationships were detected, with the likeability items explaining 6–30% of the variance in the oral presentation items. Implications of the study are discussed.
Pattern-Coupled Sparse Bayesian Learning for Inverse Synthetic Aperture Radar Imaging

We propose a pattern-coupled sparse Bayesian learning method for inverse synthetic aperture radar (ISAR) imaging by exploiting a block-sparse structure inherent in ISAR target images. A two-dimensional pattern-coupled hierarchical Gaussian prior is proposed to model the pattern dependencies among neighboring scatterers on the target scene. An expectation-maximization (EM) algorithm is developed to infer the maximum a posterior (MAP) estimate of the hyperparameters, along with the posterior distribution of the sparse signal. Numerical results are provided to illustrate the effectiveness of the proposed algorithm.
Different Involvement of Promoter Methylation in the Expression of Organic Cation/Carnitine Transporter 2 (OCTN2) in Cancer Cell Lines

Organic cation/carnitine transporter 2 (OCTN2) is responsible for the cellular uptake of the antineoplastic agent, oxaliplatin. Epigenetic modification is a possible mechanism of altered drug-transporter expression in cancers, leading to altered efficacy of chemotherapeutic drugs. However, the mechanisms governing OCTN2 regulation are not completely understood. In this study, the low levels of OCTN2 in HepG2 and LS174T cells were elevated by the demethylating reagent, decitabine (DCA). To further reveal the epigenetic mechanism of down-regulation of OCTN2, we found that Region-1 within the OCTN2 promoter (spanning −354 to +85) was a determinant of OCTN2 expression in a luciferase reporter assay. Moreover, methylation-specific PCR (MSP) and bisulfite genomic sequencing showed that the degree of individual methylated CpG sites within this region was inversely correlated with the levels of OCTN2 in different cancer cells. Application of DCA to HepG2 and LS174T cells reversed the hypermethylation status of the OCTN2 promoter and increased OCTN2 expression, enhancing cellular uptake of oxaliplatin. Thus, we identified that promoter methylation is responsible for epigenetic down-regulation of OCTN2 in HepG2 and LS174T cells. Given the essential role of OCTN2 in cancer cell uptake of chemotherapeutics, and thus treatment efficacy, pretreatment with a demethylating reagent is a possible strategy for optimizing pharmacotherapies against cancers.
Uromodulin, an emerging novel pathway for blood pressure regulation and hypertension.

Tamm–Horsfall protein was discovered in 1950 by Igor Tamm and Frank Horsfall,1 using a salt precipitation procedure to isolate a potent inhibitor of viral hemagglutination from urine. Muchmore and Decker,2 in 1985, isolated a glycoprotein (calling it uromodulin) with in vitro immunosuppressive properties from urine of pregnant women. In 1987, Pennica et al3 confirmed by cDNA analysis that uromodulin and Tamm–Horsfall protein were identical proteins. Since the initial discovery and without any clear understanding of the function of uromodulin, it was only in 2002 when Hart et al4 identified causative uromodulin mutations in a subset of families having familial juvenile hyperuricemic nephropathy and medullary cystic kidney disease type 2 that interest in uromodulin biology and function was revived. Interest in uromodulin was further revitalized by genome-wide association studies (GWASs) in 2009/2010 showing an association between common single-nucleotide polymorphisms in the upstream region of the UMOD gene with renal function and hypertension.5–8 In 2013, 2 independent groups undertaking post-GWAS functional dissection of the UMOD loci provided molecular insights into a new pathway for hypertension and sodium homeostasis involving uromodulin and opening an exciting line of investigation that could enhance our understanding of renal tubule physiology, sodium homeostasis, blood pressure (BP) regulation, and potentially lead to novel therapies for hypertension.9,10 Uromodulin is a protein exclusively expressed by epithelial cells of the thick ascending limb of Henle’s loop (TAL; Figure 1). The 640 amino-acid precursor is cotranslationally translocated into the endoplasmic reticulum (ER), extensively glycosylated, glypiated, and glycosylphosphatidylinositol anchored to the apical tubular cell membrane. From here it is released by a specific, but as yet unidentified, serine protease(s). The released protein is excreted in the urine at a rate of 20 to 100 mg/d and represents the most abundant urinary protein in …
Mutant p53 facilitates somatic cell reprogramming and augments the malignant potential of reprogrammed cells

p53 deficiency enhances the efficiency of somatic cell reprogramming to a pluripotent state. As p53 is usually mutated in human tumors and many mutated forms of p53 gain novel activities, we studied the influence of mutant p53 (mut-p53) on somatic cell reprogramming. Our data indicate a novel gain of function (GOF) property for mut-p53, which markedly enhanced the efficiency of the reprogramming process compared with p53 deficiency. Importantly, this novel activity of mut-p53 induced alterations in the characteristics of the reprogrammed cells. Although p53 knockout (KO) cells reprogrammed with only Oct4 and Sox2 maintained their pluripotent capacity in vivo, reprogrammed cells expressing mutant p53 lost this capability and gave rise to malignant tumors. This novel GOF of mut-p53 is not attributed to its effect on proliferation, as both p53 KO and mut-p53 cells displayed similar proliferation rates. In addition, we demonstrate an oncogenic activity of Klf4, as its overexpression in either p53 KO or mut-p53 cells induced aggressive tumors. Overall, our data show that reprogrammed cells with the capacity to differentiate into the three germ layers in vitro can form malignant tumors, suggesting that in genetically unstable cells, such as those in which p53 is mutated, reprogramming may result in the generation of cells with malignant tumor-forming potential.
Lossy links, low power, high throughput

As sensor networks move towards general-purpose low-power wireless networks, there is a need to support both traditional low-data rate traffic and high-throughput transfer. To attain high throughput, existing protocols monopolize the network resources and keep the radio on for all nodes involved in the transfer, leading to poor energy efficiency. This becomes progressively problematic in networks with packet loss, which inevitably occur in any real-world deployment. We present burst forwarding, a generic packet forwarding technique that combines low power consumption with high throughput for multi-purpose wireless networks. Burst forwarding uses radio duty cycling to maintain a low power consumption, recovers efficiently from interference, and inherently supports both single streams and cross-traffic. We experimentally evaluate our mechanism under heavy interference and compare it to PIP, a state-of-the-art sensornet bulk transfer protocol. Burst forwarding gracefully adapts radio duty cycle both to the level of interference and to traffic load, keeping a low and nearly constant energy cost per byte when carrying TCP traffic.
On zero-point energy, stability and Hagedorn behavior of type-IIB strings on pp-waves

Type-IIB strings on many pp-wave backgrounds, supported either by 5-form or 3-form fluxes, have negative light-cone zero-point energy. This raises the question of their stability and poses possible problems in the definition of their thermodynamic properties. After having pointed out the correct way of calculating the zero-point energy, an issue not fully discussed in literature, we show that these type-IIB strings are classically stable and have well defined thermal properties, exhibiting a Hagedorn behavior.
Perverse Complementarity: Political Connections and the Use of Courts among Private Firms in China

Using survey data of over 3,900 private firms in China, we examine whether—and how—political connections promote or undermine the use of formal legal institutions. We find that politically connected firms are more inclined than nonconnected firms to use courts over informal avenues of dispute resolution. Furthermore, by comparing the effects of political connections on dispute-resolution patterns across regional institutional environments, we find that “know-who” (political influence over adjudication) dominates “know-how” (knowledge of navigating courts) in linking political connections to the use of courts. Contrary to canonical theories that predict the declining significance of connections following the expansion of courts, our study suggests that informal networks and formal laws are more likely to share a relationship of perverse complementarity in transitional and authoritarian contexts. Political connections are positively linked to the use of legal procedures, and the primary mechanism behind the.