Miracle-dz/UniFAR-FTUs huggingface dataset:
Burst of Young Retrogenes and Independent Retrogene Formation in Mammals

Retroposition and retrogenes gain increasing attention as recent studies show that they play an important role in human new gene formation. Here we examined the patterns of retrogene distribution in 8 mammalian genomes using 4 non-mammalian genomes as a contrast. There has been a burst of young retrogenes not only in primate lineages as suggested in a recent study, but also in other mammalian lineages. In mammals, most of the retrofamilies (the gene families that have retrogenes) are shared between species. In these shared retrofamilies, 14%–18% of functional retrogenes may have originated independently in multiple mammalian species. Notably, in the independently originated retrogenes, there is an enrichment of ribosome related gene function. In sharp contrast, none of these patterns hold in non-mammals. Our results suggest that the recruitment of the specific L1 retrotransposons in mammals might have been an important evolutionary event for the split of mammals and non-mammals and retroposition continues to be an important active process in shaping the dynamics of mammalian genomes, as compared to being rather inert in non-mammals.
A Graph-Embedding Approach to Hierarchical Visual Word Mergence

Appropriately merging visual words are an effective dimension reduction method for the bag-of-visual-words model in image classification. The approach of hierarchically merging visual words has been extensively employed, because it gives a fully determined merging hierarchy. Existing supervised hierarchical merging methods take different approaches and realize the merging process with various formulations. In this paper, we propose a unified hierarchical merging approach built upon the graph-embedding framework. Our approach is able to merge visual words for any scenario, where a preferred structure and an undesired structure are defined, and, therefore, can effectively attend to all kinds of requirements for the word-merging process. In terms of computational efficiency, we show that our algorithm can seamlessly integrate a fast search strategy developed in our previous work and, thus, well maintain the state-of-the-art merging speed. To the best of our survey, the proposed approach is the first one that addresses the hierarchical visual word mergence in such a flexible and unified manner. As demonstrated, it can maintain excellent image classification performance even after a significant dimension reduction, and outperform all the existing comparable visual word-merging methods. In a broad sense, our work provides an open platform for applying, evaluating, and developing new criteria for hierarchical word-merging tasks.
Viral Kinetics in Patients with Chronic Hepatitis C Treated with the Serine Protease Inhibitor Biln 2061

We analysed viral kinetics from a 2-day treatment with BILN 2061, a serine protease inhibitor of hepatitis C virus, in patients chronically infected with genotype 1 hepatitis C virus. The efficiency (ε), describing inhibition of viral production, was above 99.45% in all patients with minor or moderate fibrosis receiving doses of 200 mg and 500 mg twice daily and larger than in previous studies for interferon-based treatments. However, ε was slightly smaller in patients with cirrhosis given 200 mg and markedly smaller in patients given 25 mg. Estimates of viral clearance and infected-cell loss support conclusions on these rates and on treatment mechanisms from previous studies on interferon-α-based treatments.
SUBCUTANEOUS COURSE OF SAPHENOUS NERVE IN MIDTHIGH REGION

Address for Correspondence: Dr. Ranjana Verma, Assistant Professor, Department of Anatomy, Maulana Azad Medical College, New Delhi, India. E-Mail: abharanjana@yahoo.com Access this Article online Quick Response code Web site: *1 Assistant Professor, 2 & 3 Professor. Department of Anatomy, Maulana Azad Medical College, New Delhi, India. Saphenous nerve is a pure sensory nerve which may get compromised as a result of complication of a surgical procedure or entrapment leading to pain and numbness in the medial side of thigh, knee and leg. Secondly, adductor canal block is given very frequently now days to anaesthetize the saphenous nerve for providing analgesia after knee surgeries. During routine cadaveric dissection of the front of thigh, we observed an interesting finding that the saphenous nerve did not follow the usual course in the adductor canal. The saphenous nerve pierced the sartorius in the middle of adductor canal and became subcutaneous. This variant course of the saphenous nerve through the sartorius can be the site of entrapment or it may be the cause of failure of adductor canal block. Although saphenous nerve is a purely sensory nerve, in this condition there is possibility of having motor fibres also which may supply Sartorius while passing through it.
Sisterhood and tonal scaling

This paper discusses central aspects of the effects of hierarchical structure on tonal scaling in intonation. The core results of a number of phonetic studies on this topic, by Ladd, by van den Berg, Gussenhoven and Rietveld, as well as experimental results of our own, are reviewed. We review the suggestions of this earlier work and argue for an addition to the theory. The principle The deeper the steeper' says that downstep among sister nodes is relatively larger if these sister-nodes are relatively more deeply embedded in the prosodic representation.
The Clinical Significance of FilmArray Respiratory Panel in Diagnosing Community-Acquired Pneumonia

Aim FilmArray Respiratory Panel (FilmArray RP) test is an emerging diagnostic method in fast detecting multiple respiratory pathogens; the methodology and clinical significance of FilmArray RP in community-acquired pneumonia (CAP) diagnosis were evaluated in this study. Methods Specimens from 74 patients with CAP were analyzed and compared using FilmArray RP, traditional multiple PCR assay, bacterial (or fungal) culture, and serological detection. Results FilmArray RP and multiplex PCR showed 100% coincidence rate in detecting coronaviruses 229E, OC43, HKU1, and NL63, human metapneumovirus, influenza A and B, and parainfluenza viruses (PIV1, PIV2, and PIV4). There were 15 viral specimens tested as disagreement positive results. FilmArray RP had higher detection rate in detecting dual viral and Mycoplasma pneumoniae infection. The positive bacteria (or fungi) were found in 25 specimens. Conclusions This study demonstrated the capability of FilmArray RP for simultaneous detection of broad-spectrum respiratory pathogens and potential use in facilitating better patient care.
Dividends and Taxes

How do dividend taxes affect firm behavior and what are their distributional and efficiency effects? To answer these questions, the first problem is coming up with an explanation for why firms pay dividends, in spite of their tax penalty. This paper surveys three different models for why firms pay dividends, and then uses each model to examine the behavioral and efficiency effects of dividend taxes. The three models examined are: the %u201Cnew view,%u201D an agency cost explanation, and a signaling model. While all three models forecast dividends, their forecasts regarding other firm behavior, and their forecasts for the efficiency and distributional effects of a dividend tax, often differ. Given the evidence to date, we find the agency model is the one most consistent with the data.
Improving B-cell epitope prediction and its application to global antibody-antigen docking

Motivation: Antibodies are currently the most important class of biopharmaceuticals. Development of such antibody-based drugs depends on costly and time-consuming screening campaigns. Computational techniques such as antibody–antigen docking hold the potential to facilitate the screening process by rapidly providing a list of initial poses that approximate the native complex. Results: We have developed a new method to identify the epitope region on the antigen, given the structures of the antibody and the antigen—EpiPred. The method combines conformational matching of the antibody–antigen structures and a specific antibody–antigen score. We have tested the method on both a large non-redundant set of antibody–antigen complexes and on homology models of the antibodies and/or the unbound antigen structure. On a non-redundant test set, our epitope prediction method achieves 44% recall at 14% precision against 23% recall at 14% precision for a background random distribution. We use our epitope predictions to rescore the global docking results of two rigid-body docking algorithms: ZDOCK and ClusPro. In both cases including our epitope, prediction increases the number of near-native poses found among the top decoys. Availability and implementation: Our software is available from http://www.stats.ox.ac.uk/research/proteins/resources. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Characterization and Comparison of Fast Pyrolysis Bio-oils from Pinewood, Rapeseed Cake, and Wheat Straw Using 13C NMR and Comprehensive GC × GC

Fast pyrolysis bio-oils are feasible energy carriers and a potential source of chemicals. Detailed characterization of bio-oils is essential to further develop its potential use. In this study, quantitative 13C nuclear magnetic resonance (13C NMR) combined with comprehensive two-dimensional gas chromatography (GC × GC) was used to characterize fast pyrolysis bio-oils originated from pinewood, wheat straw, and rapeseed cake. The combination of both techniques provided new information on the chemical composition of bio-oils for further upgrading. 13C NMR analysis indicated that pinewood-based bio-oil contained mostly methoxy/hydroxyl (≈30%) and carbohydrate (≈27%) carbons; wheat straw bio-oil showed to have high amount of alkyl (≈35%) and aromatic (≈30%) carbons, while rapeseed cake-based bio-oil had great portions of alkyl carbons (≈82%). More than 200 compounds were identified and quantified using GC × GC coupled to a flame ionization detector (FID) and a time of flight mass spectrometer (TOF-MS). Nonaromatics were the most abundant and comprised about 50% of the total mass of compounds identified and quantified via GC × GC. In addition, this analytical approach allowed the quantification of high value-added phenolic compounds, as well as of low molecular weight carboxylic acids and aldehydes, which exacerbate the unstable and corrosive character of the bio-oil.
Antimicrobial sesquiterpene lactones from Artemisia sieberi

Abstract Two new sesquiterpene lactones 3R, 8R-dihydroxygermacr-4(15),9(10)-dien-6S,7S,11RH,12,6-olide (1) and 1R, 8S-dihydroxy-11R,13-dihydrobalchanin(2), together with two known compounds 11-epiartapshin (3) and 3′-hydroxygenkwanin (4), were isolated from Artemisia sieberi. Their structures were elucidated by 1D, 2D NMR, MS, and X-ray diffraction. Compound 4 inhibited Gram-positive bacteria Bacillus subtilis and Staphylococcus aureus with Minimal inhibitory concentration values of 50 and 25 μg/disk, respectively. All the isolated compounds exhibited moderate antifungal activities.
Robust Optimal Power Management System for a Hybrid AC/DC Micro-Grid

Hybrid ac/dc micro-grid is a new concept decoupling dc sources with dc loads and ac sources with ac loads, while power is exchanged between both sides using a bidirectional converter/inverter. This necessitates a supervisory control system to split power between its different resources, which has sparked attention on the development of power management systems (PMSs). In this paper, a robust optimal PMS (ROPMS) is developed for a hybrid ac/dc micro-grid, where the power flow in the micro-grid is supervised based on solving an optimization problem. Satisfying demanded power with maximum utilization of renewable resources, minimum usage of fuel-based generator, extending batteries lifetime, and limited utilization of the main power converter between the ac and dc micro-grids are important factors that are considered in this approach. Uncertainties in the resources output power and generation forecast errors, along with static and dynamic constraints of the resources, are taken into account. Furthermore, since uncertainties in the resources output power may result in fluctuations in the dc bus voltage, a two-level controller is used to regulate charge/discharge power of the battery banks. Effectiveness of the proposed supervisory system is evaluated through extensive simulation runs based on dynamical models of the power resources.
Keyboard acoustic emanations revisited

We examine the problem of keyboard acoustic emanations. We present a novel attack taking as input a 10-minute sound recording of a user typing English text using a keyboard, and then recovering up to 96% of typed characters. There is no need for a labeled training recording. Moreover the recognizer bootstrapped this way can even recognize random text such as passwords: In our experiments, 90% of 5-character random passwords using only letters can be generated in fewer than 20 attempts by an adversary; 80% of 10-character passwords can be generated in fewer than 75 attempts. Our attack uses the statistical constraints of the underlying content, English language, to reconstruct text from sound recordings without any labeled training data. The attack uses a combination of standard machine learning and speech recognition techniques, including cepstrum features, Hidden Markov Models, linear classification, and feedback-based incremental learning.
Dietary intake, overweight status, and perceptions of food insecurity among homeless Minnesotan youth

Youth, 9–18 years (n = 202), living in homeless shelters in Minneapolis, Minnesota, were assessed for height, weight, dietary intake, and perceptions of food insecurity. Perceptions of food security were measured by asking youth to respond to the statements (1) “There are times when we do not have enough food in the house,” (2) “I go to bed hungry at night,” (3) “I do not get enough to eat at home,” and (4) “Have you ever had to miss a meal (or not been able to eat) because there was no food at home? ” Additionally, questions evaluated coping mechanisms used by children to ward off hunger. Fifty‐five percent of the children reported not enough food in the house and 25% reported going to bed hungry. Youth had inadequate intakes of vitamin D, calcium, and potassium and the majority consumed less than the estimated average requirements (EAR) for vitamins A, C, and E, phosphorus, folate, and zinc. Fruits, vegetables, and dairy were also consumed below recommended levels. Forty‐five percent of boys and 50% of girls were at risk‐for‐overweight or were overweight. Overeating, eating anything, eating disliked foods, and eating at the homes of family and friends were identified as strategies to cope with food insecurity. Overeating when food is available may explain why we see a hunger‐obesity paradigm to the magnitude that we do among the poorest Americans. These strategies protect children from the immediate negative associations of poverty and hunger, but they may contribute to long‐term weight problems currently found in the US. Am. J. Hum. Biol., 2008. © 2008 Wiley‐Liss, Inc.
Citrate transport and metabolism in mammalian cells

Citrate, an organic trivalent anion, is a major substrate for generation of energy in most cells. It is produced in mitochondria and used either in the Krebs' cycle or released into cytoplasm through a specific mitochondrial carriers. Citrate can also be taken up from blood through different plasma membrane transporters. In the cytoplasm, citrate can be used ultimately for fatty acid synthesis, which is increased in cancer cells. Here, we review the ways in which citrate can be transported and discuss the changes in transport and metabolism that occur in cancer cells. The primary focus is on the prostate gland, which is known to produce and release large amounts of citrate during its normal secretory function. The significant changes that occur in citrate‐related metabolism and transport in prostate cancer are the second focus. This review strives to relate these mechanisms to molecular biology on the one hand and to clinical applications on the other.
The advantage of laser‐capture microdissection over whole tissue analysis in proteomic profiling studies

Laser‐capture microdissection (LCM) offers a reliable cell population enrichment tool and has been successfully coupled to MS analysis. Despite this, most proteomic studies employ whole tissue lysate (WTL) analysis in the discovery of disease biomarkers and in profiling analyses. Furthermore, the influence of tissue heterogeneity in WTL analysis, nor its impact in biomarker discovery studies have been completely elucidated. In order to address this, we compared previously obtained high resolution MS data from a cohort of 38 breast cancer tissues, of which both LCM enriched tumor epithelial cells and WTL samples were analyzed. Label‐free quantification (LFQ) analysis through MaxQuant software showed a significantly higher number of identified and quantified proteins in LCM enriched samples (3404) compared to WTLs (2837). Furthermore, WTL samples displayed a higher amount of missing data compared to LCM both at peptide and protein levels (p‐value < 0.001). 2D analysis on co‐expressed proteins revealed discrepant expression of immune system and lipid metabolisms related proteins between LCM and WTL samples. We hereby show that LCM better dissected the biology of breast tumor epithelial cells, possibly due to lower interference from surrounding tissues and highly abundant proteins. All data have been deposited in the ProteomeXchange with the dataset identifier PXD002381 (http://proteomecentral.proteomexchange.org/dataset/PXD002381).
Correct Capsid Assembly Mediated by a Conserved YXXLGL Motif in Prototype Foamy Virus Gag Is Essential for Infectivity and Reverse Transcription of the Viral Genome

ABSTRACT Unlike other retrovirus Gag proteins, the prototype foamy virus (PFV) p71gag protein is not processed into mature matrix (MA), capsid (CA), and nucleocapsid (NC) subunits. Little information about sequence motifs involved in FV capsid assembly and release is available. The recent analysis of candidate L-domain motifs in PFV Gag identified an evolutionarily conserved YXXL sequence motif with a potential function in capsid assembly. Here we provide support for the hypothesis that this motif does not function like a conventional L domain, by demonstrating that, unlike the PFV Gag PSAP L-domain motif, it cannot be functionally replaced by heterologous L-domain sequences. Furthermore, mutation of individual amino acids Y464, I466, L467, and L469, but not E465, to alanine led to reduced particle release and production of noninfectious, aberrant capsid structures, although relative structural protein incorporation and processing were not affected. In contrast, mutation of G468 to alanine resulted in an intermediate, temperature-sensitive phenotype characterized by reduced particle release and reduced infectivity. Despite similar relative RNA genome incorporation for all mutants, analysis and quantification of particle-associated viral nucleic acids demonstrated defects in genomic reverse transcription for all the noninfectious mutants, a process that, unlike that of orthoretroviruses, in the case of FVs takes place in the virus-producing cell. In correlation with the reduced infectivity, the G468A mutant displayed an intermediate level of genomic reverse transcription. Taken together, these results demonstrate that the conserved YXXLGL motif in PFV Gag is involved in correct capsid assembly, which in turn is essential for reverse transcription of the FV genome.
Therapeutic Discovery Identi fi cation of Docetaxel Resistance Genes in Castration-Resistant Prostate Cancer

Docetaxel-based chemotherapy is the standard first-line therapy in metastatic castration-resistant prostate cancer (CRPC). However,most patients eventuallydevelop resistance to this treatment. In this study,weaimed to identify keymolecular genes and networks associatedwith docetaxel resistance in twomodels of docetaxelresistant CRPC cell lines and to test for themost differentially expressed genes in tumor samples from patients with CRPC. DU-145 and PC-3 cells were converted to docetaxel-resistant cells, DU-145R and PC-3R, respectively. Whole-genome arrays were used to compare global gene expression between these four cell lines. Results showeddifferential expression of 243 genes (P< 0.05, Bonferroni-adjustedPvalues and log ratio > 1.2) that were common to DU-145R and PC-3R cells. These genes were involved in cell processes like growth, development, death, proliferation, movement, and gene expression. Genes and networks commonly deregulated in both DU-145R and PC-3R cells were studied by Ingenuity Pathways Analysis. Exposing parental cells to TGFB1 increased their survival in the presence of docetaxel, suggesting a role of the TGF-b superfamily in conferring drug resistance. Changes in expression of 18 selected geneswere validated by real-time quantitative reverse transcriptasePCR in all four cell lines and tested in a set of 11FFPEandfiveoptimal cutting temperature tumor samples. Analysis in patients showed a noteworthy downexpression ofCDH1 and IFIH1, among others, in docetaxel-resistant tumors. This exploratory analysis provides information about potential gene and network involvement in docetaxel resistance in CRPC. Further clinical validation of these results is needed to develop targeted therapies in patients with CRPC that can circumvent such resistance to treatment. Mol Cancer Ther; 1–11. 2011 AACR.
Text to phoneme alignment and mapping for speech technology: A neural networks approach

A common problem in speech technology is the alignment of representations of text and phonemes, and the learning of a mapping between them that generalizes well to unseen inputs. The state-of-the-art technology appears to be symbolic rule-based systems, which is surprising given the number of neural network systems for text to phoneme mapping that have been developed over the years. This paper explores why that may be the case, and demonstrates that it is possible for neural networks to simultaneously perform text to phoneme alignment and mapping with performance levels at least comparable to the best existing systems.
Positions and sizes of X-ray solar flare sources

Aims: The positions and source sizes of X-ray sources taking into account Compton backscattering (albedo) are investigated. Methods: Using a Monte Carlo simulation of X-ray photon transport including photo-electric absorption and Compton scattering, we calculate the apparent source sizes and positions of X-ray sources at the solar disk for various source sizes, spectral indices and directivities of the primary source. Results: We show that the albedo effect can alter the true source positions and substantially increase the measured source sizes. The source positions are shifted by up to ~0.5” radially towards the disk centre and 5 arcsec source sizes can be two times larger even for an isotropic source (minimum albedo effect) at 1 Mm above the photosphere. The X-ray sources therefore should have minimum observed sizes, and thus their FWHM source size (2.35 times second-moment) will be as large as ~7” in the 20-50 keV range for a disk-centered point source at a height of 1 Mm (~1.4”) above the photosphere. The source size and position change is greater for flatter primary X-ray spectra, a stronger downward anisotropy, for sources closer to the solar disk centre, and between the energies of 30 and 50 keV. Conclusions: Albedo should be taken into account when X-ray footpoint positions, footpoint motions or source sizes from e.g. RHESSI or Yohkoh data are interpreted, and we suggest that footpoint sources should be larger in X-rays than in either optical or EUV ranges.