gebhart/patrepeval huggingface dataset:
Continued blood cell formation in spherical bodies in a long-term mouse spleen culture (1991)

During the primary culture of spleen fragments of newborn mice, a spherical body (d = circa 200 to 300 microns) as a three-dimensional cellular organization was formed. Continued production of blood cells from the spherical body was observed without changing its size for about 2 months of culture. Without growth factor, the spherical bodies produced mainly lymphocytes and macrophages. Addition of interleukin-3 enhanced their granulocyte formation, and this enhancement was observed even after a prolonged maintenance without growth factors. The spherical bodies were composed of a uniform mixture of endothelial cells and fibroblasts within the body, and cell-cell contacts between lymphocytes and fibroblasts were notable in the periphery. With prolonged culture, the spherical bodies showed a definite change in their structure by sorting two cell types and the blood cell production gradually decreased. These results suggested that a three-dimensional structure was required for the maintenance, growth, and differentiation of blood cell progenitors in the long-term spleen culture.
Performance Limits of Time Synchronization in Wireless Sensor Networks (2008)

We propose a new approach to evaluate the ultimate performance limit of time synchronization in wireless sensor networks based on the estimation theory. In particular the lower bound on the variance of the average synchronization error in a fully connected network is derived by taking into account the statistical characterization of the message delivering time.
Stability of Hydrogen/Hydrocarbon Blended Fuel Flames (2003)

Anexperimentalandnumericalinvestigationispresented todelineatetheeffectson thestability ofnaturalgasjet e ames when hydrogen is added. It is observed that the e ame liftoff height decreases nonlinearly with the addition of hydrogen in a natural gas e ame. Blowout velocity sharply increases with theincrease of hydrogen content in the mixture. It is evident that hydrogen fuel dominates the stability behavior of the mixed fuel. The turbulent mixing rate of nonreacting hydrogen/hydrocarbon hybrid fuel was computed numerically. The Favre averaged Navier ‐ Stokes equations were solved numerically, and the local concentrations of hydrogen and hydrocarbon fuels were calculated for different inlet mixture conditions. The signie cance of the local concentration on the e ame stability mechanism is presented. Nomenclature BH = function of mass diffusivity of atom H BO = function of mass diffusivity of atom O BOH = function of mass diffusivity of radical OH Cr = concentration of the reactant mixture DH = binary diffusion coefe cient of H atom DO = binary diffusion coefe cient of O atom DOH = binary diffusion coefe cient of OH radical dj = burner diameter H = characteristic e ame length, Eq. (4) h = e ame length k 0 = general rate of reaction for hydrocarbon fuel L H = normalized liftoff height RH = Reynolds number based on characteristics e ame length H Re j = jet exit Reynolds number r = multiplication factor .SL/max = maximum laminar e ame speed for pure fuel Ub = blowout velocity Un = normalized blowout velocity
Protein structure modeling in the proteomics era (2004)

Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects -- to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques.
NEW GLIOMA-ASSOCIATED AUTO-ANTIBODIES (2014)

BACKGROUND: Accumulating evidence has demonstrated that the immune system can recognize the antigenic changes in cancer cells, and further develop autoantibodies against these tumor-associated antigens (TAAs). Therefore, these cancer-associated autoantibodies might be used to identify the antigenic changes of cellular proteins involved in the transformation process. Antibodies to tumor antigens have advantages over other serum proteins as potential cancer biomarkers as they are highly specific and easily identified with high quality secondary reagents. Currently, there is a paucity of studies on autoantibodies against TAAs in gliomas. Here we examined the antibodies against TAAs in a Phase I clinical trial of patients with recurrent gliomas treated with the intratumoral injection of Delta-24-RGD oncolytic adenovirus (Fred Lang, Neurosurgery, MDACC, Director of the Trial). METHODS: Sera from 37 patients were analysed before the administration of Delta-24-RGD and then at several time points after the administration of the adenovirus. A solid phase-modified ELISA was used to assess antibodies against the following 31 antigens: BRAF, CABYR, CRISP3, CSAG2, DHFR, FHLT17, GAGE1, LDHC, MAGEA1, MAGEA3, MAGEA4, MAGEB6, MAPK1, MUC1, NLRP4, NYESO1, p53, PBK, PRAME, SOX2, SPANXA1,SSX2, TSGA10, TSSK6, TULP2, XAGE2, ZNF165. Expression of the proteins in tumors was confirmed using western blot and/or immunohistochemistry. Data were the result of at least two independent experiments. RESULTS: 1. The majority of the patients with recurrent gliomas harbor antibodies against TAAs. 2. The titer of antibodies against TAAs drastically decreased after total resection of the tumor. 3. After surgery the antibodies became again detectable predicting relapse. 4. 80% of patients' sera have antibodies against cancer testis antigens including NYESO1 and MAGE. 5. 60% of the patients showed antibodies against MAGEA1 o MAGEA3. 6. 40% of patients were positive for NYESO1 antibodies. 7. A small percentage of patients have antibodies against BRAF or SOX2. CONCLUSIONS: We report for the first time a systematic analysis of cancer-associated antibodies in patients with recurrent gliomas treated with oncolytic adenoviruses. As illustrated in this study, the serological screening of patients using solid phase ELISA for well characterized antigens offers new opportunities for analyzing the repertoire of the humoral immune response to human gliomas. Many of the listed antibodies were never analyzed before in gliomas. More intensive screening of patients after surgery may include frequent antibody screening (i.e. every 3–6 months) as an adjunct to serial MRIs. Of further clinical relevance several of the cancer/testis antigens identified are promising targets for cancer vaccines. SECONDARY CATEGORY: Tumor Biology.
Secreted aspartic proteinase (Sap) activity contributes to tissue damage in a model of human oral candidosis (1999)

Secreted aspartic proteinases (Saps) are important virulence factors during Candida albicans mucosal or disseminated infections. A differential expression of individual SAP genes has been shown previously in a model of oral candidosis based on reconstituted human epithelium (RHE), and in the oral cavity of patients. In this study, the ultrastructural localization of distinct groups of Sap isoenzymes expressed during RHE infection was shown by immunoelectron microscopy using specific polyclonal antibodies directed against the gene products of SAP1-3 and SAP4-6. Large amounts of Sap1-3 antigen were found within C. albicans yeast and hyphal cell walls, often predominantly in close contact with epithelial cells, whereas lower quantities of Sap4-6 were detected in hyphal cells. To elucidate the relevance of the expressed Saps during oral infections, we examined the effect of the aspartic proteinase inhibitor, pepstatin A, during infection of the RHE. The extent of lesions caused by the strain SC5314 was found to be strongly reduced by the inhibitor, indicating that proteinase activity contributes to tissue damage in this model. To clarify which of the SAP genes are important for tissue necrosis, the histology of RHE infection with Deltasap1, Deltasap2, Deltasap3, Deltasap4-6 and three Deltasap1/3 double mutants were examined. Although tissue damage was not blocked completely with these mutants, an attenuated phenotype was observed for each of the single sap null mutants, and was more strongly attenuated in the Deltasap1/3 double null mutants. In contrast, the lesions caused by the Deltasap4-6 triple mutant were at least as severe as those caused by SC5314. During infection with the mutants, we observed that the SAP gene expression pattern of the Deltasap1 and the Deltasap1/3 mutants was altered in comparison with the wild-type strain. Expression of SAP5 was observed only during infection with the Deltasap1/3 mutant, whereas upregulation of SAP2 and SAP8 transcripts was observed in the Deltasap1 and the Deltasap1/3 mutants. These results suggest that Sap1-3, but not Sap4-6, contribute to tissue damage in this model. Furthermore, C. albicans may compensate for the deletion of certain SAP genes by upregulation of alternative SAP genes.
A deductive database system PACADE for the three dimensional structure of protein (2002)

Describes a deductive database system PACADE (Protein Atomic Coordinate Analyzer with Deductive Engine) which facilitates a search of three dimensional data kept at the Brookhaven's Protein Data Bank. This system has the following features. Recursive relations can be handled. Long range connectivities between amino acids in proteins can be searched from short range connectivities. The system involves deduction from the approach of bottom up evaluation. Unlike Prolog, it always computes all answers without a description of the control by users and always terminates. This system makes use of query processing techniques proposed for computer science, hence queries are processed efficiently.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Figure 3 from Phenotypic Reversion of Invasive Neurofibromin-Deficient Schwannoma by FTS: Ras Inhibition Reduces BMP4/Erk/Smad Signaling (2023)

Supplementary Figure 3 from Phenotypic Reversion of Invasive Neurofibromin-Deficient Schwannoma by FTS: Ras Inhibition Reduces BMP4/Erk/Smad Signaling
Application of transient infrared spectroscopy to intramolecular energy transfer in [(phen)(CO)3ReI(NC)RuII(CN)(bpy)2]+ (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplication of transient infrared spectroscopy to intramolecular energy transfer in [(phen)(CO)3ReI(NC)RuII(CN)(bpy)2]+Jon R. Schoonover, Keith C. Gordon, Roberto Argazzi, William H. Woodruff, Carlo A. Bignozzi, R. Brian Dyer, Thomas J. Meyer, and Kristen A. PetersonCite this: J. Am. Chem. Soc. 1993, 115, 23, 10996–10997Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/ja00076a070https://doi.org/10.1021/ja00076a070research-articleACS PublicationsRequest reuse permissionsArticle Views239Altmetric-Citations59LEARN 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
Injections of the neuroprotective peptide NAP to newborn mice attenuate head-injury-related dysfunction in adults (2003)

The prophylactic neuroprotective effects of NAP, a femtomolar-acting neuroprotective peptide were tested in a mouse model of head trauma. NAP was injected for the first 3 weeks of life and head injury was initiated at 4 months. After trauma, mice were tested for their performance by evaluating damaged motor ability, balance and alertness. Comparison of the performance 1 h and 1 week after injury indicated that NAP treatment resulted in faster and enhanced recovery. In a 5-day Morris water maze test with mice suffering moderate to severe injuries, only the NAP-treated group learned to find the hidden platform in the maze. Furthermore, NAP treatment resulted in decreased mRNA expression of the inflammation marker, Mac-1. Thus, a potentially new prophylactic treatment against neurodegeneration is suggested.
Safety and immunogenicity of 3 doses of BNT162b2 and CoronaVac in children and adults with inborn errors of immunity (2022)

Our study (NCT04800133) aimed to determine the safety and immunogenicity in patients with IEIs receiving a 3-dose primary series of mRNA vaccine BNT162b2 (age 12+) or inactivated whole-virion vaccine CoronaVac (age 3+) in Hong Kong, including Omicron BA.1 neutralization, in a nonrandomized manner. Intradermal vaccination was also studied. Thirty-nine patients were vaccinated, including 16 with homologous intramuscular 0.3ml BNT162b2 and 17 with homologous intramuscular 0.5ml CoronaVac. Two patients received 3 doses of intradermal 0.5ml CoronaVac, and 4 patients received 2 doses of intramuscular BNT162b2 and the third dose with intradermal BNT162b2. No safety concerns were identified. Inadequate S-RBD IgG and surrogate virus neutralization responses were found after 2 doses in patients with humoral immunodeficiencies and especially so against BA.1. Dose 3 of either vaccine increased S-RBD IgG response. T cell responses against SARS-CoV-2 antigens were detected in vaccinated IEI patients by intracellular cytokine staining on flow cytometry. Intradermal third dose vaccine led to high antibody response in 4 patients. The primary vaccination series of BNT162b2 and CoronaVac in adults and children with IEIs should include 3 doses for optimal immunogenicity.
A Fully Flexible Handheld Wireless Estrogen Sensing Device (2022)

A ultra-lightweight, portable sensing system was developed as a means to detect the amounts of estradiol (E2) in a solution of 0.1 M phosphate buffer. This was done by screen printing a 3-electrode sensor made from a silver/ silver chloride counter electrode, silver reference electrode, and carbon/ ordered mesoporous carbon/ graphite working electrode. This sensor was connected to a custom developed data acquisition circuit, consisting of the LMP91000, a low-power analog front end (AFE) potentiostat paired with the ESP32 microprocessor from Espressif. This circuit was equipped with a USB connection for the purpose of data acquisition and programming, as well as a OLED digital display and a Bluetooth connectivity to display data wirelessly. This apparatus was found to detect estrogen successfully in the range of 5 nM through 5 uM with a slope error of 0.000946 and an R<sup>2</sup> value of 0.9901 utilizing cyclic voltammetry.
Byzantine Fault-Tolerant Deferred Update Replication (2011)

Replication is a well-established approach to increasing database availability. Many database replication protocols have been proposed for the crash-stop failure model, in which servers fail silently. Fewer database replication protocols have been proposed for the byzantine failure model, in which servers may fail arbitrarily. This paper considers deferred update replication, a popular database replication technique, under byzantine failures. The paper makes two main contributions. First, it shows that making deferred update replication tolerate byzantine failures is quite simple. Second, the paper presents a byzantine-tolerant mechanism to execute read-only transactions at a single server.
Global climate change impact on built heritage and cultural landscapes (2006)

Although climate change over the next hundred years is likely have a range of direct and indirect effects on the natural environment, almost no studies exist as yet on the impact on cultural heritage. The Noah's Ark Project focuses on the effects of climate change on Europe's built heritage and cultural landscapes over the next century. The current outputs allow the advancement of different scenarios, which highlight how some processes of building decay will be accelerated or intensified by climate change, while others will be delayed. The linking of global changes to the response of the archaeological and historic built heritage, in terms of materials and structures, remains a challenge.
Titanium diboride ceramic fiber composites for Hall-Heroult cells (2023)

An improved cathode structure for Hall-Heroult cells for the electrolytic production of aluminum metal. This cathode structure is a preform fiber base material that is infiltrated with electrically conductive titanium diboride using chemical vapor infiltration techniques. The structure exhibits good fracture toughness, and is sufficiently resistant to attack by molten aluminum. Typically, the base can be made from a mat of high purity silicon carbide fibers. Other ceramic or carbon fibers that do not degrade at temperatures below about 1000 deg. C can be used.
Tumor-Promoting Ly-6G+ SiglecFhigh Cells Are Mature and Long-Lived Neutrophils (2020)

Myeloid cells co-expressing the markers CD11b, Ly-6G, and SiglecF can be found in large numbers in murine lung adenocarcinomas and accelerate cancer growth by fostering tumor cell invasion, angiogenesis, and immunosuppression; however, some of these cells' fundamental features remain unexplored. Here, we show that tumor-infiltrating CD11b<sup>+</sup> Ly-6G<sup>+</sup> SiglecF<sup>high</sup> cells are bona fide mature neutrophils and therefore differ from other myeloid cells, including SiglecF<sup>high</sup> eosinophils, SiglecF<sup>high</sup> macrophages, and CD11b<sup>+</sup> Ly-6G<sup>+</sup> myeloid-derived suppressor cells. We further show that SiglecF<sup>high</sup> neutrophils gradually accumulate in growing tumors, where they can live for several days; this lifespan is in marked contrast to that of their SiglecF<sup>low</sup> counterparts and neutrophils in general, which live for several hours only. Together, these findings reveal distinct attributes for tumor-promoting SiglecF<sup>high</sup> neutrophils and help explain their deleterious accumulation in the tumor bed.
Binding specificities of wild-type and cloned Escherichia coli strains that recognize globo-A (1989)

In this study we compared the specificity for the globoseries of glycolipids of Escherichia coli expressing the O-negative, A-positive (ONAP) adhesin and clones transformed with the pap-like (prs or pap-2) gene cluster. Receptor-active glycolipids were identified by the ability of radiolabeled bacteria to bind to the glycolipids on thin-layer chromatogram plates. The ONAP adhesin and pap-like clones bound with high affinity to the globo-A and Forssman glycolipids. The ONAP strains did not recognize other glycolipids of the globoseries. In contrast, the pap-like clones also showed weak binding to globotriaosylceramide and reacted weakly with Gal alpha 1----4 Gal beta-latex beads. We suggest that the pap-like and ONAP adhesins recognize an epitope shared by the globo-A and Forssman structures, e.g., terminal GalNAc alpha 1----3 bound to Gal alpha 1----4Gal beta-containing glycolipids.
Interaction of Salmonella enterica serovar Typhi with cultured epithelial cells: roles of surface structures in adhesion and invasion (2008)

In this study we investigate the ability of Salmonella enterica serovar Typhi (S. Typhi) surface structures to influence invasion and adhesion in epithelial cell assay systems. In general, S. Typhi was found to be less adherent, invasive and cytotoxic than S. enterica serovar Typhimurium (S. Typhimurium). Culture conditions had little effect on adhesion of S. Typhi to cultured cells but had a marked influence on invasion. In contrast, bacterial growth conditions did not influence S. Typhi apical invasion of polarized cells. The levels of S. Typhi, but not S. Typhimurium, invasion were increased by application of bacteria to the basolateral surface of polarized cells. Expression of virulence (Vi) capsule by S. Typhi resulted in a modest reduction in adhesion, but profoundly reduced levels of invasion of non-polarized cells. However, Vi capsule expression had no affect on invasion of the apical or basolateral surfaces of polarized cells. Mutation of the staA, tcfA or pilS genes did not affect invasion or adhesion in either the presence or the absence of Vi capsule.
Effect of multi‐branched PDLA additives on the mechanical and thermomechanical properties of blends with PLLA (2015)

ABSTRACT Stereocomplex formation between poly( l ‐lactic acid) (PLLA) and poly( d ‐lactic acid) (PDLA) in the melt state was investigated and altered via the addition of multi‐branched poly( d ‐lactide) (PDLA) additives. Two different multi‐branched PDLA additives, a 3‐arm and 4‐arm star‐shaped polymeric structure, were synthesized as potential heat resistance modifiers and incorporated into PLLA at 5, 10, and 20 (w/w) through melt blending. Mechanical and thermomechanical properties of these blends were compared with linear poly( l ‐lactide) (PLLA) as well as with blends formed by the addition of two linear PDLA analogs that had similar molecular weights to their branched counterparts. Blends with linear PDLA additives exhibited two distinct melting peaks at 170–180°C and 200–250°C which implied that two distinct crystalline domains were present, that of the homopolymer and that of the stereocomplex, the more stable crystalline structure formed by the co‐crystallization of both d ‐ and l ‐lactide enantiomers. In contrast, blends of PLLA with multi‐branched PDLA formed a single broad melting peak indicative of mainly formation of the stereocomplex, behavior which was confirmed by X‐ray diffraction (XRD) analysis. The heat deflection temperature determined by thermal mechanical analysis was improved for all blends compared to neat PLLA, with increases of up to180°C for 20% addition of the 3‐arm PLLA additive. Rheological properties of the blends, as characterized by complex viscosity (η*), remained stable over a wide temperature range. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 132 , 42858.