gebhart/patrepeval huggingface dataset:
Online Speech Dereverberation Using Kalman Filter and EM Algorithm (2014)

Speech signals recorded in a room are commonly degraded by reverberation. In most cases, both the speech signal and the acoustic system of the room are unknown and time-varying. In this paper, a scenario with a single desired sound source and slowly time-varying and spatially-white noise is considered, and a multi-microphone algorithm that simultaneously estimates the clean speech signal and the time-varying acoustic system is proposed. The recursive expectation-maximization scheme is employed to obtain both the clean speech signal and the acoustic system in an online manner. In the expectation step, the Kalman filter is applied to extract a new sample of the clean signal, and in the maximization step, the system estimate is updated according to the output of the Kalman filter. Experimental results show that the proposed method is able to significantly reduce reverberation and increase the speech quality. Moreover, the tracking ability of the algorithm was validated in practical scenarios using human speakers moving in a natural manner.
Humoral immune response against melanoma antigens induced by vaccination with cytokine gene‐modified autologous tumor cells (2003)

Although the existence of a humoral response against tumor-associated antigens is well appreciated, a systematic analysis of its possible induction by the tumor remains missing. We compared the specific IgG response of Stage IV melanoma patients during vaccination. Patients had been treated within 2 clinical trials with autologous tumor cells gene-modified for IL-7 or IL-12. A panel of 27 tumor-associated antigens (HD-MM-01 to HD-MM-27) was isolated by a SEREX screening of a testis cDNA library using a pool of 5 sera from patients after vaccination. All antigens were retested with individual sera of 12 patients both pre- and post-vaccination. A serological response was induced during vaccination against 18 antigens. Remarkably, induction was detected only in patients included in the screening pool. The low overlap between sero-reactivity of the 12 patients suggested a very individualized immunological reaction. Two of 5 sera included in the screening pool exhibited a high frequency of induced humoral responses. The same patients had been shown to have a high Karnovsky index and had generated lytic cytotoxic T cells against the tumor. Besides 2 known cancer-germline genes (SCP-1 and PLU-1), the other isolated antigens were expressed in a non-tumor-specific fashion as analyzed by virtual Northern blot or RT-PCR. The properties of homologues to several of the identified tumor-antigens, especially PLU-1, SCP-1, DNEL2, CLOCK, and PIASx-alpha, suggest further investigation of their possible function in malignant melanoma. We conclude that a strong humoral response against tumor-associated antigens is inducible by tumor cells and that this response is very individual.
Genetic Analysis of a Gene Cluster for Cyclohexanol Oxidation in Acinetobacter sp. Strain SE19 by In Vitro Transposition (2000)

Biological oxidation of cyclic alcohols normally results in formation of the corresponding dicarboxylic acids, which are further metabolized and enter the central carbon metabolism in the cell. We isolated an Acinetobacter sp. from an industrial wastewater bioreactor that utilized cyclohexanol as a sole carbon source. A cosmid library was constructed from Acinetobacter sp. strain SE19, and oxidation of cyclohexanol to adipic acid was demonstrated in recombinant Escherichia coli carrying a SE19 DNA segment. A region that was essential for cyclohexanol oxidation was localized to a 14-kb fragment on the cosmid DNA. Several putative open reading frames (ORFs) that were expected to encode enzymes catalyzing the conversion of cyclohexanol to adipic acid were identified. Whereas one ORF showed high homology to cyclohexanone monooxygenase from Acinetobacter sp. strain NCIB 9871, most of the ORFs showed only moderate homology to proteins in GenBank. In order to assign functions of the various ORFs, in vitro transposon mutagenesis was performed using the cosmid DNA as a target. A set of transposon mutants with a single insertion in each of the ORFs was screened for cyclohexanol oxidation in E. coli. Several of the transposon mutants accumulated a variety of cyclohexanol oxidation intermediates. The in vitro transposon mutagenesis technique was shown to be a powerful tool for rapidly assigning gene functions to all ORFs in the pathway.
Real-time isothermal RNA amplification of toxic marine microalgae using preserved reagents on an integrated microfluidic platform (2012)

Quantitation of specific RNA sequences is a useful technique in marine biology that can elucidate cell abundance, speciation and viability, especially for early detection of harmful algal blooms. We are thus developing an integrated microfluidic system for cell concentration and lysis, RNA extraction/purification and quantitative RNA detection for environmental applications. The portable system is based on a microfluidic cartridge, or "lab-card", using a low-cost injection moulded device, with a laminated lid. Here we present real-time isothermal RNA amplification using reagent master-mixes preserved on-chip in a gel at 4 °C for up to eight months. We demonstrate quantitation by reference to an internal control in a competitive assay with 500 cell equivalents of the toxic microalga Karenia brevis. Annealing of primers, amplification at 41 °C and real-time fluorescence detection of the internal control and target using sequence-specific molecular beacons were all performed on-chip.
Identification of nucleotides responsible for enhancer activity of sterol regulatory element in low density lipoprotein receptor gene. (1990)

Sterol-dependent regulation of the low density lipoprotein (LDL) receptor promoter has been localized previously to a 16-base pair sequence, designated repeat 2, in the 5'-flanking region of the gene. In the current study, we show that the central 10 nucleotides of repeat 2 are crucial for the sterol regulatory activity. This sequence includes an octamer, designated sterol regulatory element 1 (SRE-1), which was identified previously in the promoter of the gene for 3-hydroxy-3-methylglutaryl coenzyme A synthase, a sterol-regulated enzyme of cholesterol biosynthesis. We made a series of single-base substitutions within a 1471-base pair fragment of the intact LDL receptor promoter, introduced the mutant plasmids into hamster cells by transfection, and measured mRNA levels in the absence and presence of sterols. Substitutions within the 10-base pair sequence in repeat 2 largely prevented the induction of transcription which occurs in the absence of sterols. None of these point mutations affected transcription in the presence of sterols. Like an enhancer, the SRE-1 in repeat 2 functioned in an orientation-independent manner. We interpret these findings to indicate that the SRE-1 of the LDL receptor promoter is a conditional positive element that cooperates with other elements to enhance transcription in the absence of sterols and loses its function in the presence of sterols.
ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins (2001)

The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenous agents such as microbes, inflammatory and environmental stimuli. However, the full repertoire of ARE-containing mRNAs is unknown. Here, we explore the distribution of AREs in human mRNA sequences. Computational derivation of a 13-bp ARE pattern was performed using multiple expectation maximization for motif elicitations (MEME) and consensus analyses. This pattern was statistically validated for the specificity towards the 3'-untranslated region and not coding region. The computationally derived ARE pattern is the basis of a database which contains non-redundant full-length ARE-mRNAs. The ARE-mRNA database (ARED; http://rc.kfshrc.edu.sa/ared) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins that belong to different biological processes and are important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins.
Tracking Error and Pricing Efficiency of the Taiwan 50 ETFs (2009)

The article investigates the tracking performance and pricing efficiency of the Taiwan 50 tracking funds (TTT)- the first exchange-traded-fund in Taiwan. We decompose the discrepancy between the NAV return and return of the target index into four components. Results show that a large portion of tracking error can be attributable to the cumulative cash dividends. Other components of tracking error, including management fee, dividend reinvestment, and index replication error, contribute less to the TTT tracking error. It should be noted that the index replication error tends to enlarge as cash dividends are disseminated, indicating that a more sophisticated portfolio rebalancing is needed at time of TTT dividend payout.
Pricing efficiency of TTT is measured by the intraday deviation of market prices from the NAVs, taking the transaction costs and potential execution delay into account. Both ex-post and ex-ante analysis support the general pricing efficiency of the TTT market. Large price deviations, although rarely occurring, tend to persist for a longer time and provide higher arbitrage profits. Regression analysis further shows that the mispricing and arbitrage opportunities are positively related to market volatility and TTT volume: and negatively related to the degree of market maturity. Results suggest that the pricing efficiency of TTT is maintained by frequent and prompt arbitrage activities.
Key Words: ETFs, Tracking error, Pricing efficiency, Arbitrage, Taiwan
THE GREEN FLUORESCENT PROTEIN (1998)

In just three years, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a highly visible, efficiently emitting internal fluorophore is both intrinsically fascinating and tremendously valuable. High-resolution crystal structures of GFP offer unprecedented opportunities to understand and manipulate the relation between protein structure and spectroscopic function. GFP has become well established as a marker of gene expression and protein targeting in intact cells and organisms. Mutagenesis and engineering of GFP into chimeric proteins are opening new vistas in physiological indicators, biosensors, and photochemical memories.
Interactive broadcast terminal system using MPEG-2 and MPEG-4 (2002)

Interactive broadcast terminal system was designed for bidirectional interactive television service based on the MPEG-2/4 standards and ATSC broadcast specification. In order to implement user interactivity, MPEG-4 contents are carried by MPEG-2 PES or private section. Additional information combined as XML format is transmitted by DSM-CC data carousel while ATSC-PSIP is used to transfer the EPG information. IP is used to handle the bi-directional user interaction data through return channel.
Alphavirus Vectors for Gene Therapy Applications (2001)

High-titer alphavirus vectors have been generated for efficient gene delivery both in vitro and in vivo. Studies on CNS infection via intranasal and peripheral injections with virulent and avirulent replication-competent Semliki Forest virus (SFV) strains has demonstrated the potential of gene delivery. Replication-deficient alphavirus particles have shown high local transgene expression of a transient nature in rodent brain. Alphavirus vectors have been demonstrated to induce apoptosis in infected human tumor cell lines and SFV vectors expressing interleukin-12 resulted in tumor regression in a B16 murine melanoma model. Repeated SFV injections led to stronger anti-tumor effects without immunogenic response detected against SFV. It has also been shown that intra-tumoral SFV-injections into nude mice with implanted human lung carcinomas led to tumor regression. Likewise, injection of replicative SFV-LacZ RNA resulted in tumor response as well as prophylactic protection against tumor formation. Alphaviruses have also showed potential in vaccine production. Additionally, modifications in the envelope structure of Sindbis virus resulted in substantial change in host range and demonstrated the feasibility of targeting alphavirus vectors. Moreover, SFV has been used as an expression vector for the generation of high-titer retrovirus-like particles. Recent alphavirus vector development has introduced novel non-cytopathogenic vectors, tightly temperature-regulated vectors as well as replication-persistent forms that should prolong the duration of expression. Alphavirus vectors can therefore be considered as highly potential gene delivery vehicles for future gene therapy applications, especially where only short-term expression is required, or even preferred.
Listeriolysin and IrpA are major protein targets of the human humoral response against Listeria monocytogenes (1997)

We have examined the human humoral immune response directed against proteins of Listeria monocytogenes in both healthy individuals and listeriosis patients. Two major targets for an antibody response were found in individuals that did not suffer from listeriosis: listeriolysin (Hly) and the recently described internalin-related protein (IrpA). In contrast, the humoral response in listeriosis patients appears to be more heterogeneous and included Hly, IrpA, InlB, and ActA as major targets.
Enhancement of prostate cancer xenograft growth with whole-body radiation and vascular endothelial growth factor. (1997)

Prostate cancer research has been limited by the slow growth of human prostate tumors In athymic rodent models. This study sought to determine if low-dose radiation and vascular endothelial growth factor (VEGF) could enhance the development of PC-3 human prostate adenocarcinoma xenotransplanted into nude mice. Whole body radiation (2 Gy) was delivered only once, whereas VEGF (39 ng total/mouse) was injected subcutaneously over a 17-day period. The combination of the two agents, compared to nontreated controls, resulted in significantly higher tumor incidence (100% versus 50%) and more-rapid tumor progression (1288 mm3 versus 190 mm3 by day 60). Treatment-associated changes were observed in body weights and assays of blood and spleen cells. In addition, 3H-thymidine uptake by PC-3 cells cultured in the presence of VEGF and transforming growth factor-beta 1 was compared. These results show that low-dose, whole-body radiation and VEGF can be used in concert safely and effectively to facilitate growth of PC-3 prostate tumor and that the mechanisms of interaction may involve leukocyte modulation.
Multi-label learning by instance differentiation (2007)

Multi-label learning deals with ambiguous examples each may belong to several concept classes simultane-ously. In this learning framework, the inherent ambigu-ity of each example is explicitly expressed in the out-put space by being associated with multiple class la-bels. While on the other hand, its ambiguity is only implicitly encoded in the input space by being repre-sented by only a single instance. Based on this recog-nition, we hypothesize that if the inherent ambiguity can be explicitly expressed in the input space appropri-ately, the problem of multi-label learning can be solved more effectively. We justify this hypothesis by propos-ing a novel multi-label learning approach named INS-DIF. The core of INSDIF is instance differentiation that transforms an example into a bag of instances each of which reflects the example’s relationship with one of the possible classes. In this way, INSDIF directly ad-dresses the inherent ambiguity of each example in the input space. A two-level classification strategy is em-ployed to learn from the transformed examples. Appli-cations to automatic web page categorization, natural scene classification and gene functional analysis show that our approach outperforms several well-established multi-label learning algorithms.
Enhanced immuno-detection of shed extracellular domain of HER-2/neu (2009)

HER-2/neu oncogene is over-expressed and amplified in patients associated with metastatic breast cancer. An increased level (>15 ng/mL) in the shed extracellular domain (sECD-HER 2/neu) is indicative of the potential presence and as-sociated progression of this disease. A fluo-rescent ELISA incorporating the newly devel-oped ALYGNSA antibody-orientation system revealed a 10-fold increase in sensitivity (≤0.63 ng/mL) of sECD-HER 2/neu when compared to a control standard ELISA kit (≤7.5 ng/mL). This enhanced mode of detection has the potential to not only address breast and other cancers per se but also permit an in depth evaluation of “shed extracellular domains”, in general, and the role of these “proteolytic derived factors” in physiological signalling at normal levels.
A Comparison between Multi-Layer Perceptrons and Convolutional Neural Networks for Text Image Super-Resolution (2015)

International audience
A scaleable manufacturing process for pro‐EP‐B2, a cysteine protease from barley indicated for celiac sprue (2007)

Celiac Sprue is an inflammatory disease of the small intestine triggered by ingestion of dietary gluten, a family of glutamine and proline rich proteins found in common foodgrains such as wheat, rye, and barley. One potential therapy for this lifelong disease anticipates using an oral protease to detoxify gluten in vivo. Recent studies have shown that EP-B2 (endoprotease B, isoform 2) from barley is a promising example of such a glutenase, thus warranting its large-scale production for animal safety and human clinical studies. Here we describe a scaleable fermentation, refolding and purification process for the production of gram to kilogram quantities of pro-EP-B2 (zymogen form of EP-B2) in a lyophilized form. A fed-batch E. coli fermentation system was developed that yields 0.3-0.5 g purified recombinant protein per liter culture volume. Intracellular degradation of pro-EP-B2 during the fermentation was overcome by manipulating the fermentation temperature and duration of protein expression. A simple refolding protocol was developed using a fast dilution method to refold the enzyme at concentrations greater than 0.5 mg/mL. Kinetic analysis showed that pro-EP-B2 refolding is a first-order reaction with an estimated rate constant of 0.15 h(-1). A lyophilization procedure was developed that yielded protein with 85% recoverable activity after 7 weeks of storage at room temperature. The process was successfully scaled up to 100 L with comparable purity and recovery.
Polarized actin bundles formed by human fascin‐1: their sliding and disassembly on myosin II and myosin V in vitro (2003)

Fascin-1 is a putative bundling factor of actin filaments in the filopodia of neuronal growth cones. Here, we examined the structure of the actin bundle formed by human fascin-1 (actin/fascin bundle), and its mode of interaction with myosin in vitro. The distance between cross-linked filaments in the actin/bundle was 8-9 nm, and the bundle showed the transverse periodicity of 36 nm perpendicular to the bundle axis, which was confirmed by electron microscopy. Decoration of the actin/fascin bundle with heavy meromyosin revealed that the arrowheads of filaments in the bundle pointed in the same direction, indicating that the bundle has polarity. This result suggested that fascin-1 plays an essential role in polarity of actin bundles in filopodia. In the in vitro motility assay, actin/fascin bundles slid as fast as single actin filaments on myosin II and myosin V. When myosin was attached to the surface at high density, the actin/fascin bundle disassembled to single filaments at the pointed end of the bundle during sliding. These results suggest that myosins may drive filopodial actin bundles backward by interacting with actin filaments on the surface, and may induce disassembly of the bundle at the basal region of filopodia.
Bis(trimethylstannyl)benzopinacolate-mediated intermolecular free-radical carbon-carbon bond-forming reactions: a new one-carbon homologation (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBis(trimethylstannyl)benzopinacolate-mediated intermolecular free-radical carbon-carbon bond-forming reactions: a new one-carbon homologationDavid J. Hart and Franklin L. SeelyCite this: J. Am. Chem. Soc. 1988, 110, 5, 1631–1633Publication Date (Print):March 1, 1988Publication History Published online1 May 2002Published inissue 1 March 1988https://pubs.acs.org/doi/10.1021/ja00213a051https://doi.org/10.1021/ja00213a051research-articleACS PublicationsRequest reuse permissionsArticle Views829Altmetric-Citations101LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Outpatient Biopsies of the Palatine Tonsil: Access to Lymphoid Tissue for Assessment of Human Immunodeficiency Virus RNA Titers (1996)

Sufficient tonsillar tissue can be obtained in an outpatient clinic setting to quantitate lymphoid HIV titers by the new branched-DNA signal amplification method with relative ease and without complication. The biopsy method described here affords ready access to the lymphoreticular system, which may help to advance our understanding of the pathogenesis of myriad immune diseases without the need for excisional node biopsies.
Disruption of an intermonomer salt bridge in the p53 tetramerization domain results in an increased propensity to form amyloid fibrils (2005)

We describe in molecular detail how disruption of an intermonomer salt bridge (Arg337-Asp352) leads to partial destabilization of the p53 tetramerization domain and a dramatically increased propensity to form amyloid fibrils. At pH 4.0 and 37 degrees C, a p53 tetramerization domain mutant (p53tet-R337H), associated with adrenocortical carcinoma in children, readily formed amyloid fibrils, while the wild-type (p53tet-wt) did not. We characterized these proteins by equilibrium denaturation, 13C(alpha) secondary chemical shifts, (1H)-15N heteronuclear NOEs, and H/D exchange. Although p53tet-R337H was thermodynamically less stable, NMR data indicated that the two proteins had similar secondary structure and molecular dynamics. NMR derived pK(a) values indicated that at low pH the R337H mutation partially disrupted an intermonomer salt bridge. Backbone H/D exchange results showed that for at least a small population of p53tet-R337H molecules disruption of this salt bridge resulted in partial destabilization of the protein. It is proposed that this decrease in p53tet-R337H stability resulted in an increased propensity to form amyloid fibrils.