gebhart/patrepeval huggingface dataset:
Multi‐factorial engineering of heterologous polyketide production in <i>Escherichia coli</i> reveals complex pathway interactions (2011)

Polyketides represent a significant fraction of all natural products. Many possess pharmacological activity which makes them attractive drug candidates. The production of the parent macrocyclic aglycones is catalyzed by multi-modular polyketide synthases utilizing short-chain acyl-CoA monomers. When producing polyketides through heterologous hosts, one must not only functionally express the synthase itself, but activate the machinery used to generate the required substrate acyl-CoA's. As a result, metabolic engineering of these pathways is necessary for high-level production of heterologous polyketides. In this study, we over-express three different pathways for provision of the two substrates (propionyl-CoA and (2S)-methylmalonyl-CoA) utilized for the biosynthesis of 6-deoxyerythronolide B (6-dEB; the macrolactone precursor of erythromycin): (1) a propionate → propionyl-CoA → (2S)-methylmalonyl-CoA pathway, (2) a methylmalonate → methylmalonyl-CoA → propionyl-CoA pathway, and (3) a succinate → succinyl-CoA → (2R)-methylmalonyl-CoA → (2S)-methylmalonyl-CoA → propionyl-CoA pathway. The current study revealed that propionate is a necessary component for greater than 5 mg L(-1) titers. Deletion of the propionyl-CoA:succinate CoA transferase (ygfH) or over-expression of the transcriptional activator of short chain fatty acid uptake improved titer to over 100 mg L(-1), while the combination of the two improved titer to over 130 mg L(-1). The addition of exogenous methylmalonate could also improve titer to over 100 mg L(-1). Expression of a Streptomyces coelicolor A3(2) methylmalonyl-CoA epimerase, in conjunction with over-expression of Escherichia coli's native methylmalonyl-CoA mutase, allowed for the incorporation of exogenously fed succinate into the 6-dEB core.
A Class Of Nonlinear Predictor Functions For The Speech Signal (1996)

The method of linear prediction has found considerable application in coding speech efficiently. The objective of the linear predictor is to remove all &quot;predictable&quot; redundancy from the source, and thus the residual may be efficiently coded. In the spectral domain, the linear prediction may be thought of as a whitening filter, with the residual having a noiselike characteristic. In practice, this all-pole model is not a perfect representation. As the linear all-pole model is only an approximation over a short interval to the true speech signal, it is reasonable to ask whether there are any nonlinear components which may be predicted and hence removed in the coding stage -- this would lead to a smaller average prediction residual. In this paper, we report some results using the Volterra series both as a direct-form preditor and as a predictor for the linear prediction (LP) residual. 1. INTRODUCTION A primary objective in low bitrate speech coding is to reduce the representation of the...
Synthesis of dynemicin A models (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of dynemicin A modelsK. C. Nicolaou, C. K. Hwang, A. L. Smith, and S. V. WendebornCite this: J. Am. Chem. Soc. 1990, 112, 20, 7416–7418Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ja00176a064https://doi.org/10.1021/ja00176a064research-articleACS PublicationsRequest reuse permissionsArticle Views814Altmetric-Citations87LEARN 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
<i>Arabidopsis</i> disrupted in <i>SQD2</i> encoding sulfolipid synthase is impaired in phosphate-limited growth (2002)

The sulfolipid sulfoquinovosyldiacylglycerol is one of the three nonphosphorous glycolipids that provide the bulk of the structural lipids in photosynthetic membranes of seed plants. Unlike the galactolipids, sulfolipid is anionic at physiological pH because of its 6-deoxy-6-sulfonate-glucose (sulfoquinovose) head group. The biosynthesis of this lipid proceeds in two steps: first, the assembly of UDP-sulfoquinovose from UDP-glucose and sulfite, and second, the transfer of the sulfoquinovose moiety from UDP-sulfoquinovose to diacylglycerol. The first reaction is catalyzed by the SQD1 protein in Arabidopsis. Here we describe the identification of the SQD2 gene of Arabidopsis. We propose that this gene encodes the sulfoquinovosyltransferase catalyzing the second step of sulfolipid biosynthesis. Expression of SQD1 and SQD2 in Escherichia coli reconstituted plant sulfolipid biosynthesis in this bacterium. Insertion of a transfer DNA into this gene in Arabidopsis led to complete lack of sulfolipid in the respective sqd2 mutant. This mutant showed reduced growth under phosphate-limited growth conditions. The results support the hypothesis that sulfolipid can function as a substitute of anionic phospholipids under phosphate-limited growth conditions. Along with phosphatidylglycerol, sulfolipid contributes to maintaining a negatively charged lipid-water interface, which presumably is required for proper function of photosynthetic membranes.
Ein PKI-basiertes Protokoll für sichere und praktikable Onlinewahlen (2010)

Wir stellen ein Protokoll für Onlinewahlen vor, welches auf dem Schema von Ohkubo et al. [13] basiert. Besonders an diesem Protokoll ist, dass der Auszähler nicht vertrauenswürdig sein muss. Der geheime Schlüssel des Auszählers wird am Ende der Wahl veröffentlicht und ermöglicht so die universelle Verifizierbarkeit der Stimmauszählung. Wir diskutieren die Sicherheit des Protokolls angesichts der allgemein anerkannten Sicherheitsanforderungen für elektronische Wahlschemata.
Resource Allocation Scheme Based on Spectrum Sensing for Device-to-Device Communications Underlaying Cellular Networks (2013)

셀룰러 네트워크에서 D2D 통신을 지원하기 위해서는 기존의 셀룰러 통신과 D2D 통신이 셀룰러 자원을 공유하므로 주파수 효율성과 간섭에 대한 고려가 반드시 필요하다. 따라서 D2D 통신을 위한 자원할당은 셀룰러 통신과의 간섭을 최소화하면서 동시에 주파수 재사용에 따른 스펙트럼 이용 효율을 최대화하는 것이 바람직하다. 본 논문에서는 D2D 단말과 기지국이 상호 협력적인 방법으로 D2D 자원을 할당하는 기법을 제안한다. D2D 단말은 스펙트럼 센싱을 통해 셀룰러 단말과 다른 D2D 단말로부터 오는 간섭을 인지하여 최적의 셀룰러 자원을 선택하여 기지국에 보고한다. 기지국은 해당 셀룰러 단말과 D2D 단말이 동일한 자원을 공유하도록 자원할당을 함으로써 간섭의 영향을 최소화한다. 3GPP LTE (Long Term Evolution)-Advanced 환경에서 모의실험을 통해 제안한 자원할당 기법의 성능을 검증한다. For D2D communications underlaying cellular networks, it is essential to consider the mutual interference between the existing cellular communications and D2D communications as well as the spectral efficiency, as they need to share the same frequency. Accordingly, a resource allocation scheme should be designed in such a way that minimizes the mutual interference and maximizes the spectrum utilization efficiency at the same time. In this paper, we propose a resource allocation scheme based on cooperation of the base station and D2D terminals. Specifically, a D2D terminal senses the cellular spectrum to recognize the interference condition, chooses the best cellular resource, and reports the information to the base station. The base station allocates D2D resource such that the corresponding D2D link and cellular link share the same resource. The performance of the proposed resource allocation scheme is ated through compu under 3GPP LTE-Advanced scenarios.
Highly Attenuated <i>Bordetella pertussis</i> Strain BPZE1 as a Potential Live Vehicle for Delivery of Heterologous Vaccine Candidates (2007)

Bordetella pertussis, the causative agent of whooping cough, is a promising and attractive candidate for vaccine delivery via the nasal route, provided that suitable attenuation of this pathogen has been obtained. Recently, the highly attenuated B. pertussis BPZE1 strain has been described as a potential live pertussis vaccine for humans. We investigated here the use of BPZE1 as a live vehicle for heterologous vaccine candidates. Previous studies have reported the filamentous hemagglutinin (FHA), a major B. pertussis adhesin, as a carrier to express foreign antigens in B. pertussis. In this study, we also examined the BrkA autotransporter as a surface display system. Three copies of the neutralizing peptide SP70 from enterovirus 71 (EV71) were fused to FHA or in the passenger domain of BrkA, and each chimera was expressed in BPZE1. The FHA-(SP70)3 and BrkA-(SP70)3 chimeras were successfully secreted and exposed at the bacterial surface, respectively. Nasal administration of the live recombinant strains triggered a strong and sustained systemic anti-SP70 antibody response in mice, although the titers and neutralizing activities against EV71 were significantly higher in the sera of mice immunized with the BrkA-(SP70)3-producing strain. These data indicate that the highly attenuated BPZE1 strain is a potential candidate for vaccine delivery via the nasal route with the BrkA autotransporter as an alternative to FHA for the presentation of the heterologous vaccine antigens.
Quantitative EEG for the detection of brain ischemia (2012)

Monitoring in most intensive care units (ICUs) is limited to continuous assessments of cardiopulmonary function, whereas brain monitoring has traditionally been limited to serial neurological examinations and infrequent imaging studies. Increasingly it is becoming clear that secondary neurological complications, such as seizures and brain ischemia, are also seen in the medical-surgical ICU population and are not limited to patients with primarily neurological injury. Electroencephalography (EEG) offers a continuous, real-time, non-invasive measure of brain function. Originally developed for the characterization of seizures and epilepsy, continuous EEG monitoring (cEEG) has been used for seizure detection in the ICU. Additionally, cEEG has been used as a method of identifying subclinical brain injury during neurosurgical procedures, such as carotid endarterectomy, and for ischemia detection, global function assessment, medication titration, and prognostication [1].
Variation in enzyme digestibility and gelatinization behavior of corn starch granule fractions (1982)

Dent, waxy, and Amylomaize V and VII starches that were fractionated according to granule size and found to vary in amylose content were hydrolysed by α-amylase. Rate of hydrolysis for dent and waxy maize starches was directly proportional to surface area of granules. The same effect was observed for most amylomaize fractions, but those low in amylose had relatively high hydrolysis rates. Gelatinization temp. and enthalpy of amylomaizes increased with decreasing granule size.
Refractory Diborides of Zirconium and Hafnium (2007)

This paper reviews the crystal chemistry, synthesis, densification, microstructure, mechanical properties, and oxidation behavior of zirconium diboride (ZrB 2 ) and hafnium diboride (HfB 2 ) ceramics. The refractory diborides exhibit partial or complete solid solution with other transition metal diborides, which allows compositional tailoring of properties such as thermal expansion coefficient and hardness. Carbothermal reduction is the typical synthesis route, but reactive processes, solution methods, and pre‐ceramic polymers can also be used. Typically, diborides are densified by hot pressing, but recently solid state and liquid phase sintering routes have been developed. Fine‐grained ZrB 2 and HfB 2 have strengths of a few hundred MPa, which can increase to over 1 GPa with the addition of SiC. Pure diborides exhibit parabolic oxidation kinetics at temperatures below 1100°C, but B 2 O 3 volatility leads to rapid, linear oxidation kinetics above that temperature. The addition of silica scale formers such as SiC or MoSi 2 improves the oxidation behavior above 1100°C. Based on their unique combination of properties, ZrB 2 and HfB 2 ceramics are candidates for use in the extreme environments associated with hypersonic flight, atmospheric re‐entry, and rocket propulsion.
Compressing Integers for Fast File Access (1999)

Journal Article Compressing Integers for Fast File Access Get access Hugh E. Williams, Hugh E. Williams Search for other works by this author on: Oxford Academic Google Scholar Justin Zobel Justin Zobel Search for other works by this author on: Oxford Academic Google Scholar The Computer Journal, Volume 42, Issue 3, 1999, Pages 193–201, https://doi.org/10.1093/comjnl/42.3.193 Published: 01 January 1999
In Vitro Comparison of Topical Microbicides for Prevention of Human Immunodeficiency Virus Type 1 Transmission (2004)

A standardized protocol was used to compare cellular toxicities and anti-human immunodeficiency virus type 1 (HIV-1) activities of candidate microbicides formulated for human use. The microbicides evaluated were cellulose acetate phthalate (CAP), Carraguard, K-Y plus nonoxynol-9 (KY-N9), PRO 2000 (0.5 and 4%), SPL7013 (5%), UC781 (0.1 and 1%), and Vena Gel, along with their accompanying placebos. Products were evaluated for toxicity on cervical and colorectal epithelial cell lines, peripheral blood mononuclear cells (PBMCs), and macrophages (MPhi) by using an ATP release assay, and they were tested for their effect on transepithelial resistance (TER) of polarized epithelial monolayers. Anti-HIV-1 activity was evaluated in assays for transfer of infectious HIV-1 from epithelial cells to activated PBMCs and for PBMC and MPhi infection. CAP, Carraguard, PRO 2000, SPL7013, and UC781 along with their placebos were 20- to 50-fold less toxic than KY-N9 and Vena Gel. None of the nontoxic product concentrations disrupted the TER. Transfer of HIV-1(Ba-L) from epithelial cells to PBMCs and PBMC and MPhi infection with laboratory-adapted HIV-1(Ba-L) and HIV-1(LAI) isolates were inhibited by all products except Carraguard, KY-N9, and Vena Gel. KY-N9, Vena Gel, and Carraguard were not effective in blocking PBMC infection with primary HIV-1(A), HIV-1(C), and HIV-1(CRF01-AE) isolates. The concordance of these toxicity results with those previously reported indicates that our protocol may be useful for predicting toxicity in vivo. Moreover, our systematic anti-HIV-1 testing provides a rational basis for making better informed decisions about which products to consider for clinical trials.
The MHC Class II Immunopeptidome of Lymph Nodes in Health and in Chemically Induced Colitis (2016)

We recently described a mass spectrometry-based methodology that enables the confident identification of hundreds of peptides bound to murine MHC class II (MHCII) molecules. In this article, we describe its application to the characterization of MHCII-bound peptides isolated from lymph nodes (LNs) of C57BL/6 mice. More than 1000 peptides could be identified in individual analyses, allowing a direct comparison of the MHCII peptidome in different types of normal LNs or in animals with colitis. The peptide length distribution and consensus sequences in axillary, brachial, inguinal, and mesenteric LNs were virtually identical, and a substantial portion of identified peptides corresponded to proteins found in all LNs. However, skin-specific proteins Sbsn and Dmkn and intestine-specific proteins Dmbt1, Krt19, and Maoa, among others, were exclusively identified in skin-draining and mesenteric LNs, respectively. Differences in peptide-presentation patterns were also observed when comparing healthy mice and mice with dextran sodium sulfate-induced colitis. Peptides derived from a subset of proteins (including IgE, Bank1, chondroitin sulfate synthase 2, Cmip, and Fth1) were exclusively identified in mice with colitis, revealing changes in the peptidome associated with the inflammatory process, as well as activation and clonal expansion of B cells.
New insights into deformation and fluid flow processes in the Nankai Trough accretionary prism: Results of Ocean Drilling Program Leg 190 (2001)

The Nankai Trough accretionary prism is considered an “end‐member” prism accreting a coarse terrigenous sediment section in a setting with structural simplicity, unparalleled resolution by seismic and other geophysical techniques, and large historic earthquakes. It therefore has been the focus of Ocean Drilling Program (ODP) drilling to address several unresolved questions concerning accretionary processes and prism evolution. At six sites cored along two transects across the Nankai Trough accretionary prism during ODP Leg 190, lithostratigraphy and sediment diagenesis vary markedly. For the first time, reference sites at the seaward ends of the two transects defined the stratigraphic framework of the accreting/subducting Shikoku Basin sedimentary section. A thick section of Miocene turbidites and smectite‐rich mudstone is present within the subducting section at the Ashizuri site. The turbidites and mudstones are absent in the correlative section at the Muroto site; variations in lithology, mineralogy, and hydrologic properties of the incoming sediments probably contribute to the difference in prism wedge taper between the two transects, while possibly controlling the seismic character of the active plate boundary. The décollement in both transects is localized within a common stratigraphic unit (∼5.9–7 Ma) within the lower Shikoku Basin facies. The décollement is also a major boundary for both physical and mechanical properties. A broad low‐chloride pore water anomaly in the lower Shikoku Basin unit, first identified at Site 808, progressively decreases in magnitude from prism to basin along the Muroto Transect. Physical properties relationships, evidence for mineralogic changes in the sediments, and pore fluid chemistry suggest that the chloride anomaly results primarily from in situ diagenetic reactions in the sediments, possibly augmented by flow of freshened fluid from depth. New constraints on stratigraphy and age of units along more landward parts of the Muroto Transect have dramatically changed our ideas about the tectonic evolution of the prism in this area. Growth of the seaward‐most part of the prism took place very rapidly, with 40 km of accretion within the past 2 Myr. This rate is at least 3 times greater than growth rates in a comparable prism.
Quantifying tumor-infiltrating immune cells from transcriptomics data (2018)

By exerting pro- and anti-tumorigenic actions, tumor-infiltrating immune cells can profoundly influence tumor progression, as well as the success of anti-cancer therapies. Therefore, the quantification of tumor-infiltrating immune cells holds the promise to unveil the multi-faceted role of the immune system in human cancers and its involvement in tumor escape mechanisms and response to therapy. Tumor-infiltrating immune cells can be quantified from RNA sequencing data of human tumors using bioinformatics approaches. In this review, we describe state-of-the-art computational methods for the quantification of immune cells from transcriptomics data and discuss the open challenges that must be addressed to accurately quantify immune infiltrates from RNA sequencing data of human bulk tumors.
Activity of anti‐<i>Porphyromonas gingivalis</i> egg yolk antibody against gingipains <i>in vitro</i> (2007)

Our findings suggest that IgY-GP may be an effective immunotherapeutic agent in the treatment of periodontitis.
Holographic radar imaging privacy techniques utilizing dual-frequency implementation (2008)

Over the last 15 years, the Pacific Northwest National Laboratory has performed significant research and development activities to enhance the state of the art of holographic radar imaging systems to be used at security checkpoints for screening people for concealed threats hidden under their garments. These enhancement activities included improvements to privacy techniques to remove human features and providing automatic detection of body-worn concealed threats. The enhanced privacy and detection methods used both physical and software imaging techniques. The physical imaging techniques included polarization-diversity illumination and reception, dual-frequency implementation, and high-frequency imaging at 60 GHz. Software imaging techniques to enhance the privacy of the person under surveillance included extracting concealed threat artifacts from the imagery to automatically detect the threat. This paper will focus on physical privacy techniques using dual-frequency implementation.
PET Radioimmunoscintigraphy of Renal Cell Cancer Using <sup>89</sup> Zr-Labeled cG250 Monoclonal Antibody in Nude Rats (2004)

The cG250 antibody can be stably labeled with the positron-emitter 89Zr, while preserving the immunoreactivity of the moAb. In this rat model, the in vivo biodistribution of 89Zr-Df-cG250 was identical to that of 111In-DTPA-cG250. Immuno-PET of RCC is feasible with 89Zr-cG250, and relatively small tumors could be visualized, even without a dedicated PET camera for small animals.
Polymerization of vinylidene fluoride-d<sub>2</sub>. Minimal regiosequence and branch defects and assignment of preferred chain-growth direction from the deuterium isotope effect (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymerization of vinylidene fluoride-d2. Minimal regiosequence and branch defects and assignment of preferred chain-growth direction from the deuterium isotope effectR. E. Cais and J. M. KometaniCite this: Macromolecules 1984, 17, 9, 1887–1889Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://pubs.acs.org/doi/10.1021/ma00139a049https://doi.org/10.1021/ma00139a049research-articleACS PublicationsRequest reuse permissionsArticle Views191Altmetric-Citations37LEARN 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-Alertsclose Get e-Alerts
Defining the genomic landscape of head and neck cancers through next‐generation sequencing (2014)

Next-generation sequencing (NGS) has revolutionized the field of genomics and improved our understanding of cancer biology. Advances have been achieved by sequencing tumor DNA and using matched normal DNA to filter out germ line variants to identify cancer-specific changes. The identification of high incidences of activating mutations in head and neck squamous cell carcinoma (HNSCC) amenable to drug targeting has been made, with clear distinctions between the mutational profile of HPV-positive and HPV-negative tumors. This wealth of new understanding undoubtedly ameliorates our understanding of HNSCC cancer biology and elucidates clear targets for drug targeting which will guide future personalized medicine.