gebhart/patrepeval huggingface dataset:
Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis:  The Human Proteome (2004)

Large-scale protein identifications from highly complex protein mixtures have recently been achieved using multidimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) and subsequent database searching with algorithms such as SEQUEST. Here, we describe a probability-based evaluation of false positive rates associated with peptide identifications from three different human proteome samples. Peptides from human plasma, human mammary epithelial cell (HMEC) lysate, and human hepatocyte (Huh)-7.5 cell lysate were separated by strong cation exchange (SCX) chromatography coupled offline with reversed-phase capillary LC-MS/MS analyses. The MS/MS spectra were first analyzed by SEQUEST, searching independently against both normal and sequence-reversed human protein databases, and the false positive rates of peptide identifications for the three proteome samples were then analyzed and compared. The observed false positive rates of peptide identifications for human plasma were significantly higher than those for the human cell lines when identical filtering criteria were used, suggesting that the false positive rates are significantly dependent on sample characteristics, particularly the number of proteins found within the detectable dynamic range. Two new sets of filtering criteria are proposed for human plasma and human cell lines, respectively, to provide an overall confidence of >95% for peptide identifications. The new criteria were compared, using a normalized elution time (NET) criterion (Petritis et al. Anal. Chem. 2003, 75, 1039-1048), with previously published criteria (Washburn et al. Nat. Biotechnol. 2001, 19, 242-247). The results demonstrate that the present criteria provide significantly higher levels of confidence for peptide identifications from mammalian proteomes without greatly decreasing the number of identifications.
Protoplast transformation of group N streptococci with cryptic plasmids (1985)

By using an extension to group N streptococci of a contransformation procedure we have introduced 4 different-sized cryptic plasmids for Streptococcus lactis into the plasmid-free S. lactis IL1403. A mixture of 4 cryptic plasmids with an indicator plasmid (pHV1301) conferring erythromycin resistance was used for IL1403 protoplast transformation. Under such conditions, 41.5% of the erythromycin-resistant transformants were contransformed with one of the cryptic plasmids in addition to pHV1301. Indicator plasmid pHV1301 was later spontaneously segregated from doubly transformed cells. This protocol should be very useful for constructing lactic streptococcal strains bearing any phenotypically cryptic plasmid.
Discovery of Novel Orally Bioavailable Oxaborole 6-Carboxamides That Demonstrate Cure in a Murine Model of Late-Stage Central Nervous System African Trypanosomiasis (2010)

We report the discovery of novel boron-containing molecules, exemplified by N-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-6-yl)-2-trifluoromethylbenzamide (AN3520) and 4-fluoro-N-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-6-yl)-2-trifluoromethylbenzamide (SCYX-6759), as potent compounds against Trypanosoma brucei in vitro, including the two subspecies responsible for human disease T. b. rhodesiense and T. b. gambiense. These oxaborole carboxamides cured stage 1 (hemolymphatic) trypanosomiasis infection in mice when administered orally at 2.5 to 10 mg/kg of body weight for 4 consecutive days. In stage 2 disease (central nervous system [CNS] involvement), mice infected with T. b. brucei were cured when AN3520 or SCYX-6759 were administered intraperitoneally or orally (50 mg/kg) twice daily for 7 days. Oxaborole-treated animals did not exhibit gross signs of compound-related acute or subchronic toxicity. Metabolism and pharmacokinetic studies in several species, including nonhuman primates, demonstrate that both SCYX-6759 and AN3520 are low-clearance compounds. Both compounds were well absorbed following oral dosing in multiple species and also demonstrated the ability to cross the blood-brain barrier with no evidence of interaction with the P-glycoprotein transporter. Overall, SCYX-6759 demonstrated superior pharmacokinetics, and this was reflected in better efficacy against stage 2 disease in the mouse model. On the whole, oxaboroles demonstrate potent activity against all T. brucei subspecies, excellent physicochemical profiles, in vitro metabolic stability, a low potential for CYP450 inhibition, a lack of active efflux by the P-glycoprotein transporter, and high permeability. These properties strongly suggest that these novel chemical entities are suitable leads for the development of new and effective orally administered treatments for human African trypanosomiasis.
Comparison of Extensive Protein Fractionation and Repetitive LC-MS/MS Analyses on Depth of Analysis for Complex Proteomes (2009)

In-depth, reproducible coverage of complex proteomes is challenging because the complexity of tryptic digests subjected to LC-MS/MS analysis frequently exceeds mass spectrometer analytical capacity, which results in undersampling of data. In this study, we used cancer cell lysates to systematically compare the commonly used GeLC-MS/MS (1-D protein + 1-D peptide separation) method using four repetitive injections (2-D/repetitive) with a 3-D method that included solution isoelectric focusing and involved an equal number of LC-MS/MS runs. The 3-D method detected substantially more unique peptides and proteins, including higher numbers of unique peptides from low-abundance proteins, demonstrating that additional fractionation at the protein level is more effective than repetitive analyses at overcoming LC-MS/MS undersampling. Importantly, more than 90% of the 2-D/repetitive protein identifications were found in the 3-D method data in a direct protein level comparison, and the reproducibility between data sets increased to greater than 96% when factors such as database redundancy and use of rigid scoring thresholds were considered. Hence, high reproducibility of complex proteomes, such as human cancer cell lysates, readily can be achieved when using multidimensional separation methods with good depth of analysis.
Chemical ligation of oligonucleotides in the presence and absence of a template (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical ligation of oligonucleotides in the presence and absence of a templateSergei M. Gryaznov and Robert L. LetsingerCite this: J. Am. Chem. Soc. 1993, 115, 9, 3808–3809Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/ja00062a070https://doi.org/10.1021/ja00062a070research-articleACS PublicationsRequest reuse permissionsArticle Views546Altmetric-Citations58LEARN 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
Assembly of the exogenous extracellular matrix during basement membrane formation by alveolar epithelial cells in vitro (2000)

We found that immortalized alveolar type II epithelial cells (SV40-T2 cells) that were cultured on dense fibrillar collagen supplemented with Matrigel gel formed a thin and continuous lamina densa beneath them. Immunohistochemical analysis of laminin-1, type IV collagen, entactin (nidogen) and perlecan in the culture indicated that all these components were integrated into a sheet structure of basement membrane beneath the cells. Analysis of the temporal and spatial distribution of the basement membrane macromolecules revealed that the initial deposits of laminin-1 and entactin were significantly greater in area in the presence of Matrigel. These globular deposits and the coarse mesh of basement membrane macromolecules developed into a flat membranous basement membrane. In the absence of Matrigel, the SV40-T2 cells failed to form a continuous lamina densa, and the deposits stayed in the coarse mesh. The major biotinylated Matrigel components that were integrated into the basement membrane were laminin-1 and entactin. Furthermore, SV40-T2 cells supplemented with exogenous laminin-1 alone as well as laminin-1 contaminated with entactin formed a continuous lamina densa. These results indicate that the laminin-1 and entactin supplied from the Matrigel were incorporated into a basement membrane beneath the SV40-T2 cells, and contributed to the formation of basement membrane. Therefore, we concluded that the alveolar epithelial cells synthesize laminin-1, entactin, type IV collagen, and perlecan, but that they also needed to assemble exogenous laminin-1 into the basement membrane to complete its formation in vitro.
Rapid Genotyping of Swine Influenza Viruses (2011)

International audience
Rho GTPases and the Actin Cytoskeleton (1998)

The actin cytoskeleton mediates a variety of essential biological functions in all eukaryotic cells. In addition to providing a structural framework around which cell shape and polarity are defined, its dynamic properties provide the driving force for cells to move and to divide. Understanding the biochemical mechanisms that control the organization of actin is thus a major goal of contemporary cell biology, with implications for health and disease. Members of the Rho family of small guanosine triphosphatases have emerged as key regulators of the actin cytoskeleton, and furthermore, through their interaction with multiple target proteins, they ensure coordinated control of other cellular activities such as gene transcription and adhesion.
Continued Utilization of CCR5 Coreceptor by a Newly Derived T-Cell Line-Adapted Isolate of Human Immunodeficiency Virus Type 1 (1998)

The differential use of CC chemokine receptor 5 (CCR5) and CXC chemokine receptor 4 (CXCR4) may be intimately involved in the transmission and progression of human immunodeficiency virus infection. Changes in coreceptor utilization have also been noted upon adaptation of primary isolates (PI) to growth in established T-cell lines. All of the T-cell line-adapted (TCLA) viruses studied to date utilize CXCR4 but not CCR5. This observation had been suggested as an explanation for the sensitivity of TCLA, but not PI, viruses to neutralization by recombinant gp120 antisera and V3-directed monoclonal antibodies, but recent studies have shown coreceptor utilization to be independent of neutralization sensitivity. Here we describe a newly isolated TCLA virus that is sensitive to neutralization but continues to utilize both CXCR4 and CCR5 for infection. This finding further divorces coreceptor specificity from neutralization sensitivity and from certain changes in cell tropism. That the TCLA virus can continue to utilize CCR5 despite the changes that occur upon adaptation and in the apparent absence of CCR5 expression in the FDA/H9 T-cell line suggests that the interaction between envelope protein and coreceptor may be mediated by multiple weak interactions along a diffuse surface.
Photostimulated luminescence and thermally stimulated luminescence of some new X-ray storage phosphors (1991)

The photostimulated luminescence (PSL) and thermally stimulated luminescence (TSL) properties of two new X-ray storage phosphors, Ba2B5O9Br-Eu2+ and Ba5GeO4Br6-Eu2+, are reported and discussed. The PSL measurements show that bromine vacancies act as electron traps and that Eu2+ is involved in the hole trapping. A direct recombination mechanism, suggested by PSL results, is confirmed by TSL measurements. Analysis of the glow curves shows first-order kinetics in combination with low-frequency factors which is characteristic for centre-to-centre recombination.
INVARIANT DESCRIPTOR LEARNING USING A SIAMESE CONVOLUTIONAL NEURAL NETWORK (2016)

Abstract. In this paper we describe learning of a descriptor based on the Siamese Convolutional Neural Network (CNN) architecture and evaluate our results on a standard patch comparison dataset. The descriptor learning architecture is composed of an input module, a Siamese CNN descriptor module and a cost computation module that is based on the L2 Norm. The cost function we use pulls the descriptors of matching patches close to each other in feature space while pushing the descriptors for non-matching pairs away from each other. Compared to related work, we optimize the training parameters by combining a moving average strategy for gradients and Nesterov's Accelerated Gradient. Experiments show that our learned descriptor reaches a good performance and achieves state-of-art results in terms of the false positive rate at a 95 % recall rate on standard benchmark datasets.
The Colorado Thyroid Disease Prevalence Study (2000)

The prevalence of abnormal biochemical thyroid function reported here is substantial and confirms previous reports in smaller populations. Among patients taking thyroid medication, only 60% were within the normal range of TSH. Modest elevations of TSH corresponded to changes in lipid levels that may affect cardiovascular health. Individual symptoms were not very sensitive, but patients who report multiple thyroid symptoms warrant serum thyroid testing. These results confirm that thyroid dysfunction is common, may often go undetected, and may be associated with adverse health outcomes that can be avoided by serum TSH measurement.
Statins in the Treatment of Hepatitis C (2012)

Abstract This article does not have abstract.
Real-Time DSP Implementation of a Subband Beamforming Algorithm for Dual Microphone Speech Enhancement (2007)

A real-time digital signal processor (DSP) based implementation of a subband beamforming algorithm and its evaluation for dual microphone speech enhancement is presented. The algorithm, a calibrated constrained beamformer, is described theoretically and a real-time structure is proposed, including an efficient approach for multichannel data transformation. Measurements show that the battery driven DSP implementation supports 20 h operation-time, with an improved signal-to-noise ratio (SNR) of up to 14 dB in high-noise factory environment. Further, less than half the provided computational performance of the DSP is used by the proposed method, hence, processing of additional tasks may be included.
Recent Advances in p53 Research and Cancer Treatment (2011)

TP53, encoding p53, is one of the most famous tumor suppressor genes. The majority of human cancers demonstrate the inactivation of the p53 pathway. Mutant p53 not only, no longer, functions as a tumor suppressor but can also exert tumor-promoting effects. The basic function of p53 is to respond to cellular stress. We herein review the recent advances in p53 research and focus on apoptosis, cell cycle arrest, and senescence in response to stress. We also review the clinical applications of p53-based therapy for human cancer.
Synthesis of Lactones and Lactams (1993) (1993)

The Synthesis of Lactones and Lactams Appendix to The Synthesis of Lactones and Lactams' Indexes.
Session Initiation Protocol (SIP)-Specific Event Notification (2002)

This document describes an extension to the Session Initiation Protocol (SIP). The purpose of this extension is to provide an extensible framework by which SIP nodes can request notification from remote nodes indicating that certain events have occurred.
IL-12 in conjunction with dendritic cells enhances antiviral CD8+ CTL responses in vitro. (1996)

CD8+ cytolytic T lymphocytes (CTLs) are important mediators for resistance to infections and malignant diseases. IL-12 enhances proliferative and cytolytic responses by killer cells, but its function in the generation of human antiviral CD8+ T cell responses has not been defined. We therefore evaluated the role of IL-12 in the generation of CTLs to influenza-infected dendritic cells. IL-12 was not detectable in supernatants of infected-dendritic cells, or during CTL generation. Furthermore, anti-IL-12 antibody did not block CTL generation. However, exogenous IL-12 (30-300 pg/ml) enhanced CD8+ T cell proliferative and cytolytic responses. The effect was greatest in individuals with weak reactivity to influenza virus or at antigen-presenting cell (APC):T cell ratios of 1:100 or less. IL-12 augmented interferon-gamma production during CTL generation. The CTL enhancing effects of the cytokine, however, could not be blocked by neutralizing anti-interferon-gamma antibody. Together with IL-12, antigen-pulsed dendritic cells may be a useful approach for boosting CTL responses against infectious agents and malignancies.
A handle bar metaphor for virtual object manipulation with mid-air interaction (2012)

Commercial 3D scene acquisition systems such as the Microsoft Kinect sensor can reduce the cost barrier of realizing mid-air interaction. However, since it can only sense hand position but not hand orientation robustly, current mid-air interaction methods for 3D virtual object manipulation often require contextual and mode switching to perform translation, rotation, and scaling, thus preventing natural continuous gestural interactions. A novel handle bar metaphor is proposed as an effective visual control metaphor between the user's hand gestures and the corresponding virtual object manipulation operations. It mimics a familiar situation of handling objects that are skewered with a bimanual handle bar. The use of relative 3D motion of the two hands to design the mid-air interaction allows us to provide precise controllability despite the Kinect sensor's low image resolution. A comprehensive repertoire of 3D manipulation operations is proposed to manipulate single objects, perform fast constrained rotation, and pack/align multiple objects along a line. Three user studies were devised to demonstrate the efficacy and intuitiveness of the proposed interaction techniques on different virtual manipulation scenarios.
Bone Marrow Is a Reservoir of Repopulating Mesangial Cells during Glomerular Remodeling (2001)

The renal glomerulus, whose cellular components are developmentally derived from the mesenchyme, plays a pivotal role in filtratating plasma. Irretrievable changes of glomerular components are responsible for the initiation and progression of impaired renal function. Recently, it has been shown that functional stem cells exist in the bone marrow of adult bodies and that they can reconstitute damaged tissues of the mesenchymal origin. To examine whether the bone marrow provides stem cells to damaged glomeruli, transgenic rats carrying enhanced green fluorescence protein (EGFP rat) were established in a systemic and constitutive manner. After transplanting the bone marrow of EGFP rats into wild-type rats, the progeny of the transplanted marrow cells were tracked with a tag of EGFP. Recruitment of bone marrow-derived cells into glomeruli was dramatically facilitated in response to mesangiolysis evoked in anti-Thy1 antibody-mediated glomerulonephritis. In the restored glomeruli, 11% to 12% of glomerular cells were derived from the transplanted bone marrow. The number of bone marrow-derived CD45(+) cells transiently increased during the disease process, and CD45-negative cells constantly accounted for more than half of the bone marrow-derived population in glomeruli. Bone marrow-derived Thy1(+) cells kept increasing in number until the remodeling ceased and finally made up 7% to 8% of glomerular cells. Laser scanning microscopy displayed that the bone marrow-derived Thy1(+) cells provide structural support for glomerular capillaries, which indicates that they are mesangial cells. Although CD45(-)Thy1(-) bone marrow-derived cells exist during the remodeling of glomeruli, none of them expressed endothelial markers such as Factor VIII and RECA1 as long as they were tested. The results indicate that the bone marrow can give rise to mesangial cells in vivo.
Iron regulates ferritin mRNA translation through a segment of its 5' untranslated region. (1987)

In previous studies, we showed that acute administration of iron to intact rats or to rat hepatoma cells in culture induces synthesis of the iron-storage protein ferritin by activating translation of inactive cytoplasmic ferritin mRNAs for both the heavy (H) and the light (L) subunits. In the course of activation, these ferritin mRNAs are recruited onto polysomes. To elucidate the structural features of these mRNAs involved in the translational response to iron, a chimera was constructed from the 5' and 3' untranslated regions (UTRs) of ferritin L subunit mRNA fused to the reading frame of the mRNA of bacterial chloramphenicol acetyltransferase (CAT). This chimera and deletion constructs derived from it were introduced into a rat hepatoma cell line by retrovirus-mediated gene transfer. The complete chimera showed increased CAT activity in response to iron enrichment of the medium, whereas deletion of the first 67 nucleotides of the 5' UTR, which contain a highly conserved sequence, caused loss of regulation by iron. Whereas cis-acting sequences located in the 5' flanking regions of many genes have been repeatedly implicated in modulating their transcriptional expression, we report here a specific regulatory translational sequence found within the 5' UTR of a eukaryotic mRNA.
NK1.1+ thymocytes. Adult murine CD4-, CD8- thymocytes contain an NK1.1+, CD3+, CD5hi, CD44hi, TCR-V beta 8+ subset. (1990)

CD4-, CD8- thymocytes were purified from thymi obtained from normal C57BL/6 mice. By flow cytometry analysis, 5 to 10% of these double negative (DN) thymocytes were found to express NK1.1 on their surface. The NK1.1+ DN thymocytes were demonstrated, by two-color fluorescence, to be CD3lo, CD5hi, CD44hi, J11d-, B220-, MEL 14-, IL2R- with 60% expressing TCR-V beta 8 as determined by the mAb F23.1. In contrast, splenic and peripheral blood NK cells were NK1.1+, CD3-, CD5-, TCR-V beta 8- with 40 to 60% being MEL 14+. Unlike peripheral NK cells, fresh DN thymocytes enriched for NK1.1+ cells were unable to kill YAC-1, the classical murine NK cell target. However, these cells were able to mediate anti-CD3 redirected lysis even when they were assayed immediately after purification, i.e., with no culture or stimulation. These data demonstrate that adult murine thymocytes contain NK1.1+ cells which are distinct, both by function and phenotype, from peripheral NK cells. These data also raise the issue of a possible NK/T bipotential progenitor cell.
Green Cosmetic Surfactant from Rice: Characterization and Application (2015)

During recent years, microwave irradiation has been extensively used for performing green organic synthesis. The aim of this study was to synthesize, through a microwave-assisted irradiation process, a natural surfactant with O/W emulsifying properties. Our attention was focused on polyglycerol esters of fatty acids that are biocompatible and biodegradable non-ionic surfactants widely used in food and cosmetic products. The emulsifier was obtained using vegetable raw material from renewable sources: polyglycerol derived from vegetable glycerol and rice bran oil fatty acids. The natural emulsifier obtained was then characterized and evaluated for its emulsifying properties using different doses, oil phases, rheological additives, waxes, etc. The potential application in solar products, in comparison with other natural emulsifiers, was also evaluated.