Miracle-dz/UniFAR-FTUs huggingface dataset:
Retroviral Cyclin Enhances Cyclin-Dependent Kinase-8 Activity

ABSTRACT Alterations in the functional levels of cyclin-dependent kinase-8 (CDK8) or its partner, cyclin C, have been clearly associated with cancers, including colon cancer, melanoma, and osteosarcoma. Walleye dermal sarcoma virus encodes a retroviral cyclin (RV-cyclin) that localizes to interchromatin granule clusters and binds CDK8. It also binds to the Aα subunit (PR65) of protein phosphatase 2A (PP2A). Binding to the Aα subunit excludes the regulatory B subunit, but not the catalytic C subunit, in a manner similar to that of T antigens of the small DNA tumor viruses. The expression of the RV-cyclin enhances the activity of immune affinity-purified CDK8 in vitro for RNA polymerase II carboxy-terminal domain (CTD) and histone H3 substrates. PP2A also enhances CDK8 kinase activity in vitro for the CTD but not for histone H3. The PP2A enhancement of CDK8 is independent of RV-cyclin expression and likely plays a role in the normal regulation of CDK8. The manipulation of endogenous PP2A activity by inhibition, amendment, or depletion confirmed its role in CDK8 activation by triggering CDK8 autophosphorylation. Although RV-cyclin and PP2A both enhance CDK8 activity, their actions are uncoupled and additive in kinase reactions. PP2A may be recruited to CDK8 in the Mediator complex by a specific PP2A B subunit or additionally by the RV-cyclin in infected cells, but the RV-cyclin appears to activate CDK8 directly and in a manner independent of its physical association with PP2A.
Long‐term outcomes of health‐related quality of life following diverse thrombotic microangiopathy syndromes

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Psychosocial Oncology Supports for Men

Although men’s cancer experiences have received limited attention within the field of psychosocial oncology, increasing attention is being devoted to the development and evaluation of men-centered programs. This scoping review describes this emergent body of literature, detailing the focus, participation, and impact of interventions designed to help men with cancer build illness-specific knowledge, adapt to illness, manage side effects, distress, and uncertainty, sustain relationships, and more. Striving to build on existing knowledge, research gaps and opportunities are discussed, including a need for stronger methodologies, more tailored and targeted supports, attention to the experiences of men with nonprostate cancers, and the explicit integration of gender analyses in the research process.
Relationship of serum antimüllerian hormone concentration to age at menopause.

BACKGROUND Serum antimüllerian hormone (AMH) levels are highly correlated with antral follicle counts, while being menstrual cycle independent and easily measurable. However, AMH, unlike antral follicle counts, has not been tested as yet as a predictor of reproductive status. By relating AMH levels to the age distribution of reproductive events like onset of menopause, we tested this hypothesis. METHODS AMH levels were measured in 144 fertile normal volunteers and used to determine an estimate of mean AMH as a function of age. Data on the onset of menopause were obtained from the population-based Prospect-European Prospective Investigation into Cancer and Nutrition [Prospect-EPIC] cohort. Estimation of an AMH threshold to predict menopause was done by maximum likelihood using the observed (Prospect-EPIC) distribution of age at menopause and the predictive distribution from this AMH threshold. Predictions of age at menopause follow from an individual woman's AMH relative to percentiles of the distribution of AMH for a given age, and the corresponding percentiles of the predictive distribution of age at menopause. RESULTS There was good conformity between the observed distribution of age at menopause and that predicted from declining AMH levels. CONCLUSIONS The similarity between observed and predictive distributions of age at menopause supports the hypothesis that AMH levels are related to onset of menopause. Results of this study suggest that AMH is able to specify a woman's reproductive age more realistically than chronological age alone.
Phylogenetic and recombination analysis of genomic sequences of IHHNV

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is one of the most recurrent viral pathogens infecting penaeid shrimps. Although previous reports showed that genomic recombination happened among different IHHNV strains, no study has been carried out to systematically elucidate such recombination. In this study, we performed the phylogenetic and recombination analysis of IHHNV the available complete genomes sequences in GenBank. We have found two intra‐group recombination between lineages III and II of infectious group, one inter‐lineage recombination between lineage II of infectious group and non‐infectious group among IHHNV strains.
50 Years of CORDIC: Algorithms, Architectures, and Applications

Year 2009 marks the completion of 50 years of the invention of CORDIC (coordinate rotation digital computer) by Jack E. Volder. The beauty of CORDIC lies in the fact that by simple shift-add operations, it can perform several computing tasks such as the calculation of trigonometric, hyperbolic and logarithmic functions, real and complex multiplications, division, square-root, solution of linear systems, eigenvalue estimation, singular value decomposition, QR factorization and many others. As a consequence, CORDIC has been utilized for applications in diverse areas such as signal and image processing, communication systems, robotics and 3-D graphics apart from general scientific and technical computation. In this article, we present a brief overview of the key developments in the CORDIC algorithms and architectures along with their potential and upcoming applications.
Object Recognition Under Difficult Conditions Based on Superpixel

In computer vision the task of object recognition is to recognize a certain object in an provided image. For this task a description about the object of interest is learned from images. This process often involves the use of local features like SIFT [1] which can be extracted reliably from images, even if the resolution or the lighting conditions change. The drawback of such local features are that they may lose discriminative power to distinguish between similar objects or the object from the background. We proposed a system that utilizes superpixel [2]. The system is not only working on local features rather it packs the features belonging to one such superpixel and reject the whole area, if it is ambiguous. A superpixel is ambiguous if the system can not name an object with a high confidence to which object this superpixel could belong. By doing so we have achieved an improvement of over 10% on a difficult dataset.
Reversible and persistent decreases in cocaine self-administration after cholinesterase inhibition: different effects of donepezil and rivastigmine

We recently observed that pretreatment with the cholinesterase inhibitor, tacrine can produce long-lasting reductions in cocaine-reinforced behavior, described as persistent attenuation. In addition to inhibiting both acetylcholinesterase (AChE) and butyrylcholinesterase, tacrine can potentiate actions of dopamine. This study was carried out to evaluate the effects of donepezil (which selectively inhibits AChE) and rivastigmine (which inhibits both AChE and butyrylcholinesterase) on cocaine self-administration. High self-administration rats self-administered different doses of cocaine under a fixed ratio-5 schedule. Over a 4-day period, vehicle, donepezil, or rivastigmine was infused as animals were maintained in home cages (21 h per day), with signs of cholinergic stimulation (fasciculation, vacuous jaw movements, yawning, and diarrhea) scored by a blinded observer. Both compounds dose-dependently decreased cocaine self-administration, but differed in the potency and temporal pattern of their effects. Self-administration of low-dose cocaine was decreased to a greater degree by rivastigmine than donepezil (50% effective doses of 2.33 and 6.21 mg/kg/day, respectively), but this early effect did not continue beyond sessions immediately after treatment with rivastigmine. Group means for cocaine self-administration were decreased at some time points occurring between 1 and 3 days after the treatment with 10 mg/kg/day of donepezil (late effects), with decreases of more than 80% observed in some individual rats that persisted for 1 week or longer. Early, but not late, effects were correlated with signs of cholinergic stimulation. In summary, pretreatment with donepezil, but not rivastigmine produced persistent reductions in cocaine-reinforced behavior, which were not associated with signs of cholinergic stimulation.
Indexing methods for efficient parsing

This paper presents recent developments of an indexing technique aimed at improving parsing times. Although several methods exist today that serve this purpose, most of them rely on statistical data collected during lengthy training phases. Our goal is to obtain a reliable method that exhibits an optimal efficiency/cost ratio, without lengthy training processes. We focus here on static analysis of the grammar, a method that has unworthily received less attention in the last few years in computational linguistics. The paper is organized as follows: first, the parsing and indexing problem are introduced, followed by a description of the general indexing strategy for chart parsing; second, a detailed overview and performance analysis of the indexing technique used for typed-feature structure grammars is presented; finally, conclusions and future work are outlined.
The activity of paraoxonase type 1 (PON‐1) in boar seminal plasma and its relationship with sperm quality, functionality, and in vivo fertility

Paraoxonase 1 (PON‐1) is a hydrolytic enzyme present in body fluids, capable of protecting cells against oxidative stress. The hypothesis was hereby to test that PON‐1, present in seminal plasma (SP), acts protecting boar spermatozoa when showing a reasonable high activity in the ejaculate. SP‐PON‐1 activity differed (p < 0.001) among boars (from 0.10 to 0.29 IU/mL). Intra‐boar variability was also observed (p < 0.05), but only in two of the 15 boars. SP‐PON‐1 activity differed among ejaculate portions, showing the spermatozoa‐peak portion of spermatozoa‐rich ejaculate fraction the highest levels (0.35 ± 0.03 IU/mL, ranging from 0.12 to 0.69) and the post‐sperm ejaculate fraction the lowest levels (0.12 ± 0.01 IU/mL, ranging from 0.03 to 0.21). SP‐PON‐1 activity was positively correlated with the percentage of spermatozoa with rapid and progressive movement (p < 0.01) and negatively correlated with the generation of intracellular reactive oxygen species (p < 0.01) in semen samples after 72 h of liquid storage. SP‐PON‐1 activity was highest (p < 0.01) in boars with highest farrowing rates. In conclusion, SP‐PON‐1 activity differed among boars and ejaculate fractions/portions. SP‐PON‐1 activity was positively correlated with sperm quality and functionality of liquid‐stored semen samples and it evidenced a positive association with in vivo fertility.
Global Methylation Patterns in Idiopathic Pulmonary Fibrosis

Background Idiopathic Pulmonary Fibrosis (IPF) is characterized by profound changes in the lung phenotype including excessive extracellular matrix deposition, myofibroblast foci, alveolar epithelial cell hyperplasia and extensive remodeling. The role of epigenetic changes in determining the lung phenotype in IPF is unknown. In this study we determine whether IPF lungs exhibit an altered global methylation profile. Methodology/Principal Findings Immunoprecipitated methylated DNA from 12 IPF lungs, 10 lung adenocarcinomas and 10 normal histology lungs was hybridized to Agilent human CpG Islands Microarrays and data analysis was performed using BRB-Array Tools and DAVID Bioinformatics Resources software packages. Array results were validated using the EpiTYPER MassARRAY platform for 3 CpG islands. 625 CpG islands were differentially methylated between IPF and control lungs with an estimated False Discovery Rate less than 5%. The genes associated with the differentially methylated CpG islands are involved in regulation of apoptosis, morphogenesis and cellular biosynthetic processes. The expression of three genes (STK17B, STK3 and HIST1H2AH) with hypomethylated promoters was increased in IPF lungs. Comparison of IPF methylation patterns to lung cancer or control samples, revealed that IPF lungs display an intermediate methylation profile, partly similar to lung cancer and partly similar to control with 402 differentially methylated CpG islands overlapping between IPF and cancer. Despite their similarity to cancer, IPF lungs did not exhibit hypomethylation of long interspersed nuclear element 1 (LINE-1) retrotransposon while lung cancer samples did, suggesting that the global hypomethylation observed in cancer was not typical of IPF. Conclusions/Significance Our results provide evidence that epigenetic changes in IPF are widespread and potentially important. The partial similarity to cancer may signify similar pathogenetic mechanisms while the differences constitute IPF or cancer specific changes. Elucidating the role of these specific changes will potentially allow better understanding of the pathogenesis of IPF.
Use of cone-beam computed tomography for evaluation of surgical specimen of medication-related osteonecrosis of the jaw

Cone-beam computed tomography (CBCT) provides accurate anatomical details in three-dimensional and multiplanar reformation images for diagnosis and treatment planning. We examined one surgical specimen of medication-related osteonecrosis of the jaw (MRONJ) by CBCT. CBCT images of the surgical specimen of MRONJ showed osteolytic changes in the jaws, sclerotic lesion, and sequestrum separation. Furthermore, high-resolution mode (tube voltage, 90.0 kV; tube current, 4.00 mA; rotation time,16.8 s; field of view, 56 mm × 56 mm; thickness, 0.099 mm) was sharper than standard mode (tube voltage, 90.0 kV; tube current, 4.00 mA; rotation time, 16.8 s; field of view, 81 mm × 81 mm; thickness, 0.144 mm) and high-density mode (tube voltage, 90.0 kV; tube current, 4.00 mA; rotation time, 33.5 s; field of view, 81 mm × 81 mm; thickness, 0.144 mm). We showed that CBCT, especially the high-resolution mode, is useful for the evaluation of surgical specimen of the jaw, such as MRONJ. This report can be used for reference in future studies and in clinical settings.
A WAVELET-BASED GCC PREFILTERING ALGORITHM FOR SPEECH DOA ESTIMATION

—The phase transform preﬁlter based generalized cross-correlation is adopted widely in the estimation of the time-differences-of-arrival, since it performs very well under reverberant environment with low noise condition. However, it is not robust to high noise environments. In this paper, we propose to preﬁlter the signals in the wavelet domain with the aim of estimating the direction-of-arrival of speech source in the presence of low SNR. Simulation results show that our proposed algorithm can give rise to good direction-of-arrival performance compared with other well-known methods.
Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation[C][W][OA]

During the early stages of seed development, Arabidopsis (Arabidopsis thaliana) endosperm is syncytial and proliferates rapidly through repeated rounds of mitosis without cytokinesis. This stage of endosperm development is important in determining final seed size and is a model for studying aspects of cellular and molecular biology, such as the cell cycle and genomic imprinting. However, the small size of the Arabidopsis seed makes high-throughput molecular analysis of the early endosperm technically difficult. Laser capture microdissection enabled high-resolution transcript analysis of the syncytial stage of Arabidopsis endosperm development at 4 d after pollination. Analysis of Gene Ontology representation revealed a developmental program dominated by the expression of genes associated with cell cycle, DNA processing, chromatin assembly, protein synthesis, cytoskeleton- and microtubule-related processes, and cell/organelle biogenesis and organization. Analysis of core cell cycle genes implicates particular gene family members as playing important roles in controlling syncytial cell division. Hormone marker analysis indicates predominance for cytokinin signaling during early endosperm development. Comparisons with publicly available microarray data revealed that approximately 800 putative early seed-specific genes were preferentially expressed in the endosperm. Early seed expression was confirmed for 71 genes using quantitative reverse transcription-polymerase chain reaction, with 27 transcription factors being confirmed as early seed specific. Promoter-reporter lines confirmed endosperm-preferred expression at 4 d after pollination for five transcription factors, which validates the approach and suggests important roles for these genes during early endosperm development. In summary, the data generated provide a useful resource providing novel insight into early seed development and identify new target genes for further characterization.
MicroRNAs as Biomarkers in Cancer

MicroRNAs (miRNAs) are small non-coding RNA molecules, which in recent years have emerged to have enormous potential as biomarkers. Recently, there have been significant developments in understanding miRNA biogenesis, their regulatory mechanisms and role in disease process, and their potential as effective therapies. The identification of miRNAs as biomarkers provides possibilities for development of less or non-invasive and more specific methods for monitoring tumor growth and progression. This review summarizes the recent developments in methods to detect and quantitate miRNAs in body fluids and their applications as biomarkers in cancers. The prospect of miRNAs as potential diagnostic and prognostic biomarkers with clinical applications is significant as more evidence points to their central role in cancer pathobiology.
Downregulation of survivin and aurora A by histone deacetylase and RAS inhibitors: A new drug combination for cancer therapy

Histone deacetylase (HDAC) inhibitors, such as valproic acid (VPA), constitute a novel class of anticancer agents that cause an increase in acetylated histones and thus restore the expression of dormant tumor‐suppressor and other genes related to cell differentiation, cell‐cycle arrest or apoptosis of tumor cells. The Ras inhibitor farnesylthiosalicylic acid (FTS, salirasib) attenuates cancer cell proliferation in vitro and in vivo and, under certain circumstances, induces cell death. FTS by itself does not induce differentiation or complete growth arrest. The abovementioned activity of VPA as a differentiation agent suggested that it might be worth investigating its possible therapeutic potential in synergistic combination with FTS. Here, we examined whether the combined application of VPA and FTS could synergistically inhibit the proliferation of cancer cells that express oncogenic K‐Ras (A549 nonsmall‐cell lung carcinoma cells), DLD1 (colon carcinoma cells) or chronically active wild‐type K‐Ras and constitutively active B‐Raf (ARO, thyroid carcinoma cells). The results showed that combined treatment with VPA and FTS synergistically reduces proliferation in all of these cancer cell lines by downregulating Ras and blocking the expression of Survivin and Aurora A. These alterations, which were most pronounced following the combined treatment, led to a mitotic crisis, as reflected by mislocalization of the chromosomal passenger complex. Our findings thus demonstrate that combination therapy with VPA and FTS might offer a promising therapeutic approach to the treatment of epithelial tumors.
Treegion scheduling for wide issue processors

Instruction scheduling is one of the most important phases of compilation for high-performance processors. A compiler typically divides a program into multiple regions of code and then schedules each region. Many past efforts have focused on linear regions such as traces and superblocks. The linearity of these regions can limit speculation, leading to under-utilization of processor resources, especially on wide-issue machines. A type of non-linear region called a treegion is presented in this paper. The formation and scheduling of treegions takes into account multiple execution paths, and the larger scope of treegions allows more speculation, leading to higher utilization and better performance. Multiple scheduling heuristics for treegions are compared against scheduling for several types of linear regions. Empirical results illustrate that instruction scheduling using treegions treegion scheduling-holds promise. Treegion scheduling using the global weight heuristic outperforms the next highest performing region-superblocks by up to 20%.
The Application of Learning Theories into Abdullah: An Intelligent Arabic Conversational Agent Tutor

This paper outlines the research and development of a Conversational Intelligent tutoring System (CITS) named Abdullah focusing on the novel application of learning theories. Abdullah CITS is a software program intended to converse with students aged 10 to 12 years old about the essential topics in Islam in natural language. The CITS aims to mimic human Arabic tutor by engaging the students in dialogue using Modern Arabic language (MAL), and classical Arabic language (CAL), utilizing supportive evidence from the Quran and Hadith. Abdullah CITS is able to capture the userâs level of knowledge and adapt the tutoring session and tutoring style to suit that particular learnerâs level of knowledge. This is achieved through the inclusion of several learning theories implemented in Abdullahâs architecture, which are applied to make the tutoring suited to an individual learner. There are no known specific learning theories for CITS therefore the novelty of the approach is in the combination of well-known learning theories typically employed in a classroom environment. The system was evaluated through end user testing with the target age group in schools in Jordan and the UK. The initial evaluation has produced some positive results, indicating that Abdullah is gauging the individual learnerâs knowledge level and adapting the tutoring session to ensure learning gain is achieved.