Miracle-dz/UniFAR-FTUs huggingface dataset:
Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs

Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.
Effects of Argumentation Based Inquiry Approach on Disadvantaged Students\' Science Achivement

Purpose of this study was to explore the effects of using the Argumentation Based Inquiry (ABI) approach (adopted from the Science Writing Heuristic - SWH approach) on students’ learning chemistry subjects in the primary school. Quasi-experimental, pre-posttest design was applied. The study involved two 8 th grade classes of one teacher from a primary school in a disadvantaged social economic area of Erzurum. While one of the randomly selected section, the treatment group, engaged in argumentation based inquiry activities by using the ABI approach and students wrote activity report for each activity individually, the other section, the control group, instructed with usual approach used by the instructor in the previous semesters. The study was implemented in the properties and structures of matter unit. As data collection tools, chemistry subject based tests (9 multiple choice questions and 4 open-ended questions) were developed and used as pre and post assessments. The pre-posttest was generated by using national and international question banks. Analysis of the tests indicated that groups were not statistically different at the pre-test but statistically different at the post-test. The treatment group outperformed the control group and students’ writing score correlated with post-test score. Also, there was a significant correlation between test scores and students’ reports generated during the activities.
Memory-Enhanced Neural Networks and NMF for Robust ASR

In this article we address the problem of distant speech recognition for reverberant noisy environments. Speech enhancement methods, e. g. , using non-negative matrix factorization (NMF), are succesful in improving the robustness of ASR systems. Furthermore, discriminative training and feature transformations are employed to increase the robustness of traditional systems using Gaussian mixture models (GMM). On the other hand, acoustic models based on deep neural networks (DNN) were recently shown to outperform GMMs. In this work, we combine a state-of-the art GMM system with a deep Long Short-Term Memory (LSTM) recurrent neural network in a double-stream architecture. Such networks use memory cells in the hidden units, enabling them to learn long-range temporal context, and thus increasing the robustness against noise and reverberation. The network is trained to predict frame-wise phoneme estimates, which are converted into observation likelihoods to be used as an acoustic model. It is of particular interest whether the LSTM system is capable of improving a robust state-of-the-art GMM system, which is confirmed in the experimental results. In addition, we investigate the efficiency of NMF for speech enhancement on the front-end side. Experiments are conducted on the medium-vocabulary task of the 2nd `CHiME' Speech Separation and Recognition Challenge, which includes reverberation and highly variable noise. Experimental results show that the average word error rate of the challenge baseline is reduced by 64% relative. The best challenge entry, a noise-robust state-of-the-art recognition system, is outperformed by 25% relative.
The UDP-Glucuronate Decarboxylase Gene Family in Populus: Structure, Expression, and Association Genetics

In woody crop plants, the oligosaccharide components of the cell wall are essential for important traits such as bioenergy content, growth, and structural wood properties. UDP-glucuronate decarboxylase (UXS) is a key enzyme in the synthesis of UDP-xylose for the formation of xylans during cell wall biosynthesis. Here, we isolated a multigene family of seven members (PtUXS1-7) encoding UXS from Populus tomentosa, the first investigation of UXSs in a tree species. Analysis of gene structure and phylogeny showed that the PtUXS family could be divided into three groups (PtUXS1/4, PtUXS2/5, and PtUXS3/6/7), consistent with the tissue-specific expression patterns of each PtUXS. We further evaluated the functional consequences of nucleotide polymorphisms in PtUXS1. In total, 243 single-nucleotide polymorphisms (SNPs) were identified, with a high frequency of SNPs (1/18 bp) and nucleotide diversity (πT = 0.01033, θw = 0.01280). Linkage disequilibrium (LD) analysis showed that LD did not extend over the entire gene (r 2<0.1, P<0.001, within 700 bp). SNP- and haplotype-based association analysis showed that nine SNPs (Q <0.10) and 12 haplotypes (P<0.05) were significantly associated with growth and wood property traits in the association population (426 individuals), with 2.70% to 12.37% of the phenotypic variation explained. Four significant single-marker associations (Q <0.10) were validated in a linkage mapping population of 1200 individuals. Also, RNA transcript accumulation varies among genotypic classes of SNP10 was further confirmed in the association population. This is the first comprehensive study of the UXS gene family in woody plants, and lays the foundation for genetic improvements of wood properties and growth in trees using genetic engineering or marker-assisted breeding.
Prognostic factors in patients with hepatitis B virus-related hepatocellular carcinoma undergoing nucleoside analog antiviral therapy

In the present era of entecavir (ETV) use for chronic hepatitis B (CHB), the prognostic factors in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) remain unclear. The aims of the present study were to investigate the prognostic factors in patients with HBV-related HCC treated with ETV who underwent curative therapy. A total of 74 HBV-related HCC patients treated with ETV who underwent curative therapy were analyzed. Predictive factors associated with overall survival (OS) and recurrence-free survival (RFS) were examined using univariate and multivariate analysis. Our study population included 49 males and 25 females with a median age of 62 years. The median observation period was 3.4 years (range, 0.2–11.5 years). The 1-, 3- and 5-year cumulative OS rates were 100, 89.8 and 89.8%, respectively. The corresponding RFS rates were 82.8, 52.1 and 25.6%, respectively. In this study, 73 patients (98.6%) achieved an HBV DNA level of <400 copies/ml during the follow-up period. No viral breakthrough hepatitis, as defined by 1 log increase from nadir, was observed during ETV therapy. According to multivariate analysis, only hepatitis B e antigen (HBeAg) positivity was significantly associated with OS [hazard ratio (HR), 0.058; 95% confidence interval (CI), 0.005–0.645; P=0.020)], whereas HCC stage (HR, 0.359; 95% CI, 0.150–0.859; P=0.021), HBeAg positivity (HR, 0.202; 95% CI, 0.088–0.463; P<0.001) and γ-glutamyl transpeptidase ≥50 IU/l (HR, 0.340; 95% CI, 0.152–0.760; P=0.009) were significant predictive factors linked to RFS. In conclusion, HBeAg positivity was significantly associated with OS and RFS in HBV-related HCC patients treated with ETV who underwent curative therapy. In such patients, close observation is required, even after curative therapy for HCC.
CRISPR guide RNA design for research applications

The rapid rise of CRISPR as a technology for genome engineering and related research applications has created a need for algorithms and associated online tools that facilitate design of on‐target and effective guide RNAs (gRNAs). Here, we review the state of the art in CRISPR gRNA design for research applications of the CRISPR‐Cas9 system, including knockout, activation, and inhibition. Notably, achieving good gRNA design is not solely dependent on innovations in CRISPR technology. Good design and design tools also rely on availability of high‐quality genome sequence and gene annotations, as well as on availability of accumulated data regarding off‐targets and effectiveness metrics.
MENGEMBANGKAN KEMAMPUAN KOMUNIKASI DAN DISPOSISI MATEMATIK SISWA SMP MELALUI DISCOVERY LEARNING

Penelitian ini ditujukan untuk menelaah peranan discovery learning terhadap kemampuan komunikasi dan disposisi matematik siswa SMP, serta asosiasi antara keduanya. Penelitian ini adalah bagian dari tesis magister dan bagian dari Penelitian Hibah Pascasarjana DIKTI pada tahun 2015. Studi ini adalah suatu quasi eksperimen dengan disain pretest-postes kelompok kontrol yang melibatkan 62 siswa kelas 8 dari satu SMP di Garut yang ditetapkan secara purposif. Instrumen penelitian ini adalah tes uraian kemampuan komunikasi matematik, dan skala disposisi matematik m, dan skala persepsi siswa terhadap pembelajarandan percaya diri siswa yang mendapat pembodel Likert. Penelitian menemukan bahwa kemampuan komunikasi matematik siswa yang mendapat discovery learning lebih baik daripada siswa yang mendapat pembelajaran konvensional. Namun, tidak terdapat perbedaan disposisi matematik siswa pada kedua pembelajaran tersebut. Selain itu ditemukan pula tidak terdapat asosiasi antara kemampuan komunikasi matematik dan disposisi matematik. Kata kunci: komunikasi matematik, disposisi matematik, discovery learning. ABSTRACT This study was intended to analyze the role of discovery learning (DL) in enhancing the students’ mathematical communication ability and disposition. This study was a part of a master’s thesis and a sub-study of a Postgraduate Research Grant provided by the Directorat General of Higher Education in 2015. This study adopted a pretest-postest quasi-experimental control group design involving 62 eighth-grade students of a yunior high school in Garut which were chosen puposively. The instruments of this study consisted of an essay test on mathematical communication ability, and a mathematical disposition (MD) scale. The study revealed that students getting treatment on discovery learning (DL) attained better grades on mathematical communication ability than students taught by conventional teaching, though the grades were at medium level. However, there was no difference in grades of mathematical dispositions among students in the two groups and the grades were fairly good. Also, there was a relation between mathematical communication skills and dispositions. Keyword: mathematical communication, mathematical disposition, discovery learning
Subsampling Methods for Persistent Homology

Persistent homology is a multiscale method for analyzing the shape of sets and functions from point cloud data arising from an unknown distribution supported on those sets. When the size of the sample is large, direct computation of the persistent homology is prohibitive due to the combinatorial nature of the existing algorithms. We propose to compute the persistent homology of several subsamples of the data and then combine the resulting estimates. We study the risk of two estimators and we prove that the subsampling approach carries stable topological information while achieving a great reduction in computational complexity.
Expression and Characterization of Serotype 2 Streptococcus suis Arginine Deiminase

Background: Arginine deiminase (ArcA) has been speculated to facilitate the intracellular survival of Streptococcus suis under acidic conditions. However, the physical and biological properties and function of SS2-ArcA have not yet been elucidated. Methods: Recombinant SS2-ArcA (rSS2-ArcA) was expressed and purified using Ni-NTA affinity chromatography. Under various pH and temperature conditions, the enzymatic properties of purified rSS2-ArcA and crude native SS2-ArcA were determined. Results: The SS2-arcA-deduced amino acid sequence contained a conserved catalytic triad (Cys399-His273-Glu218). The optimum temperature and pH of 47-kDa rSS2-ArcA and crude native SS2-ArcA were 42°C and pH 7.2. The rSS2-ArcA and crude native SS2-ArcA were stable for 3 h at 4 and 25°C, respectively. The pH stability and dependency tests suggested that rSS2-ArcA and crude native SS2-ArcA were functionally active in acidic conditions. The L-arginine substrate binding affinity (Km) values of rSS2-ArcA (specific activity 16.00 U/mg) and crude native SS2-ArcA (specific activity 0.23 U/mg) were 0.058 and 0.157 mM, respectively. rSS2-ArcA exhibited a weak binding affinity with the common ArcA inhibitors L-canavanine and L-NIO. Furthermore, the partial inactivation of SS2-ArcA significantly impaired the viability and growth of SS2 at pH 4.0, 6.0, and 7.5. Conclusions: This study profoundly demonstrated the involvement of ArcA enzymatic activity in S. suis survival under acidic conditions.
Protein Kinase Modulation of Dendritic K+ Channels in Hippocampus Involves a Mitogen-Activated Protein Kinase Pathway

We investigated mitogen-activated protein kinase (MAPK) modulation of dendritic, A-type K+ channels in CA1 pyramidal neurons in the hippocampus. Activation of cAMP-dependent protein kinase A (PKA) and protein kinase C (PKC) leads to an increase in the amplitude of backpropagating action potentials in distal dendrites through downregulation of transient K+ channels in CA1 pyramidal neurons in the hippocampus. We show here that both of these signaling pathways converge on extracellular-regulated kinases (ERK)-specific MAPK in mediating this reduction in dendritic K+ current, which is confirmed, in parallel, by biochemical assays using phosphospecific antibodies against the ppERK and pKv4.2. Furthermore, immunostaining indicates dendritic localization of ppERK and pKv4.2. Taken together, these results demonstrate that dendritic, A-type K+ channels are dually regulated by PKA and PKC through a common downstream pathway involving MAPK, and the modulation of these K+channels may be accounted for by the phosphorylation of Kv4.2 subunits.
Leaving a Legacy: Parental Migration and School Outcomes among Young Children in the Philippines

This article examines the link between parental migration and young children's education using data from the Philippine country study of the Child Health and Migrant Parents in South-East Asia (CHAMPSEA) Project. The key research question probed here is: what difference does parental migration make to the school outcomes of young children? Specifically, it looks at factors that explain children's school progression (school pacing) and academic performance (school achievement) using multiple regression analysis. These questions are explored using CHAMPSEA data gathered from a survey of children under 12 years of age and their households in Laguna and Batangas (n=487).
An X-ray survey in SA 57 with XMM-Newton

Context. The maximum number density of Active Galactic Nuclei (AGNs), as deduced from X-ray studies, occurs at z < 1, with lower luminosity objects peaking at smaller redshifts. Optical studies lead to a different evolutionary behaviour, with a number density peaking at z ≈ 2 independently of the intrinsic luminosity, but this result is limited to active nuclei brighter than the host galaxy. A selection based on optical variability can detect low luminosity AGNs (LLAGNs), where the host galaxy light prevents the identification by non-stellar colours. Aims. We want to collect X-ray data in a field where it exists an optically-selected sample of “variable galaxies”, i.e. variable objects with diffuse appearance, to investigate the X-ray and optical properties of the population of AGNs, particularly of low luminosity ones, where the host galaxy is visible. Methods. We observed a field of 0.2 deg 2 in the Selected Area 57, for 67 ks with XMM-Newton. We detected X-ray sources, and we correlated the list with a photographic survey of SA 57, complete to BJ ∼ 23 and with available spectroscopic data. Results. We obtained a catalogue of 140 X-ray sources to limiting fluxes 5 × 10 −16 ,2 × 10 −15 erg cm −2 s −1 in the 0.5–2 keV and 2–10 keV respectively, 98 of which are identified in the optical bands. The X-ray detection of part of the variability-selected candidates confirms their AGN nature. Diffuse variable objects populate the low luminosity side of the sample. Only 25/44 optically-selected QSOs are detected in X-rays. 15% of all QSOs in the field have X/O < 0.1.
Maturation of the adolescent brain

Adolescence is the developmental epoch during which children become adults – intellectually, physically, hormonally, and socially. Adolescence is a tumultuous time, full of changes and transformations. The pubertal transition to adulthood involves both gonadal and behavioral maturation. Magnetic resonance imaging studies have discovered that myelinogenesis, required for proper insulation and efficient neurocybernetics, continues from childhood and the brain’s region-specific neurocircuitry remains structurally and functionally vulnerable to impulsive sex, food, and sleep habits. The maturation of the adolescent brain is also influenced by heredity, environment, and sex hormones (estrogen, progesterone, and testosterone), which play a crucial role in myelination. Furthermore, glutamatergic neurotransmission predominates, whereas gamma-aminobutyric acid neurotransmission remains under construction, and this might be responsible for immature and impulsive behavior and neurobehavioral excitement during adolescent life. The adolescent population is highly vulnerable to driving under the influence of alcohol and social maladjustments due to an immature limbic system and prefrontal cortex. Synaptic plasticity and the release of neurotransmitters may also be influenced by environmental neurotoxins and drugs of abuse including cigarettes, caffeine, and alcohol during adolescence. Adolescents may become involved with offensive crimes, irresponsible behavior, unprotected sex, juvenile courts, or even prison. According to a report by the Centers for Disease Control and Prevention, the major cause of death among the teenage population is due to injury and violence related to sex and substance abuse. Prenatal neglect, cigarette smoking, and alcohol consumption may also significantly impact maturation of the adolescent brain. Pharmacological interventions to regulate adolescent behavior have been attempted with limited success. Since several factors, including age, sex, disease, nutritional status, and substance abuse have a significant impact on the maturation of the adolescent brain, we have highlighted the influence of these clinically significant and socially important aspects in this report.
Functional Development of Fronto-Striato-Parietal Networks Associated with Time Perception

Compared to our understanding of the functional maturation of executive functions, little is known about the neurofunctional development of perceptive functions. Time perception develops during late adolescence, underpinning many functions including motor and verbal processing, as well as late maturing higher order cognitive skills such as forward planning and future-related decision making. Nothing, however, is known about the neurofunctional changes associated with time perception from childhood to adulthood. Using functional magnetic resonance imaging we explored the effects of age on the brain activation and functional connectivity of 32 male participants from 10 to 53 years of age during a time discrimination task that required the discrimination of temporal intervals of seconds differing by several hundred milliseconds. Increasing development was associated with progressive activation increases within left lateralized dorsolateral and inferior fronto-parieto-striato-thalamic brain regions. Furthermore, despite comparable task performance, adults showed increased functional connectivity between inferior/dorsolateral interhemispheric fronto-frontal activation as well as between inferior fronto-parietal regions compared with adolescents. Activation in caudate, specifically, was associated with both increasing age and better temporal discrimination. Progressive decreases in activation with age were observed in ventromedial prefrontal cortex, limbic regions, and cerebellum. The findings demonstrate age-dependent developmentally dissociated neural networks for time discrimination. With increasing age there is progressive recruitment of later maturing left hemispheric and lateralized fronto-parieto-striato-thalamic networks, known to mediate time discrimination in adults, while earlier developing brain regions such as ventromedial prefrontal cortex, limbic and paralimbic areas, and cerebellum subserve fine-temporal processing functions in children and adolescents.
A Survey of State of the Art Biomedical Text Mining Techniques for Semantic Analysis

The abstract is to be in fully-justified italicized text, at the top of the left-hand column as it is here, below the author information. Use the word "Abstract" as the title, in 12-point Times, boldface type, centered relative to the column, initially capitalized. The abstract is to be in 10-point, single-spaced type, and up to 150 words in length. Leave two blank lines after the abstract, then begin the main text.