gebhart/patrepeval huggingface dataset:
Early versus late fusion in semantic video analysis (2005)

Semantic analysis of multimodal video aims to index segments of interest at a conceptual level. In reaching this goal, it requires an analysis of several information streams. At some point in the analysis these streams need to be fused. In this paper, we consider two classes of fusion schemes, namely early fusion and late fusion. The former fuses modalities in feature space, the latter fuses modalities in semantic space. We show by experiment on 184 hours of broadcast video data and for 20 semantic concepts, that late fusion tends to give slightly better performance for most concepts. However, for those concepts where early fusion performs better the difference is more significant.
[Buffering effect of physical activity on hippocampus stress injury]. (2010)

目的 探讨体力运动对应激性海马损伤的减缓作用.方法 12只大鼠随机分为对照组、运动组,腹腔注射糖皮质激素-皮质酮(corticosterone,CORT,5 mg/只),观察海马DG群峰电位(population spike,PS)随时间的变化.结果注射CORT 85 min后,对照组大鼠PS明显降低,运动组PS维持正常,与同时间点对照组比较,差异有统计学意义(P＜0.05);结论 运动可减弱应激激素对海马机能的影响,并可减弱应激对海马的损伤。
Influenza Virus Resistance to Antiviral Agents: A Plea for Rational Use (2009)

Although influenza vaccine can prevent influenza virus infection, the only therapeutic options to treat influenza virus infection are antiviral agents. At the current time, nearly all influenza A/H3N2 viruses and a percentage of influenza A/H1N1 viruses are adamantane resistant, which leaves only neuraminidase inhibitors available for treatment of infection with these viruses. In December 2008, the Centers for Disease Control and Prevention released new data demonstrating that a high percentage of circulating influenza A/H1N1 viruses are now resistant to oseltamivir. In addition, oseltamivir-resistant influenza B and A/H5N1 viruses have been identified. Thus, use of monotherapy for influenza virus infection is irrational and may contribute to mutational pressure for further selection of antiviral-resistant strains. History has demonstrated that monotherapy for influenza virus infection leads to resistance, resulting in the use of a new monotherapy agent followed by resistance to that new agent and thus resulting in a background of viruses resistant to both drugs. We argue that combination antiviral therapy, new guidelines for indications for treatment, point-of-care diagnostic testing, and a universal influenza vaccination recommendation are critical to protecting the population against influenza virus and to preserving the benefits of antiviral agents.
Proteomic study via a non-gel based approach of meningococcal outer membrane vesicle vaccine obtained from strain CU385: A road map for discovering new antigens (2009)

This work presents the results from a study of the protein composition of outer membrane vesicles from VA-MENGOC-BC (Finlay Institute, Cuba), an available vaccine against serogroup B Neisseria meningitidis. Proteins were identified by means of SCAPE, a 2DE-free method for proteome studies. More than one hundred proteins were detected by tandem liquid chromatographymass spectrometry analysis of fractions enriched in peptides devoid of histidine or arginine residues, providing a detailed description of the vaccine. A bioinformatic analysis of the identified components resulted in the identification of 31 outer membrane proteins and three conserved hypothetical proteins, allowing the cloning, expression, purification and immunological study of two of them (NMB0088 and NMB1796) as new antigens.
<title>Shift-invariant optical neural network with holographic bipolar synapses</title> (1993)

An optoelectronic neocognitron neural network has been built at JPL and demonstrated for various automatic target recognition applications. A new technique of constructing and storing a large holographic synapses array at the Fourier plane has enabled the shift-invariant target recognition and tracking. In this paper, a recent development of an innovative bipolar holographic synapses synthesis technique is reported. Experimental demonstration of increased discrimination capability using this bipolar synapses is also provided.
Single‐stranded small interfering RNA are more immunostimulatory than their double‐stranded counterparts: A central role for 2′‐hydroxyl uridines in immune responses (2006)

It has recently become apparent that certain small interfering RNA (siRNA) sequences stimulate the innate immunity through endosomal Toll-like receptors (TLR), particularly TLR7 and TLR8. However, it remains unclear whether siRNA duplexes act as specific ligands for these receptors. To address this question and to overcome the problem of immune activation by siRNA, several RNA sequences were chemically synthesized and their effects were investigated. Results indicate that human peripheral blood mononuclear cells (PBMC) recognize and respond to a large number of sense or antisense single-stranded (ss) siRNA. In most cases immunostimulatory RNA motifs are more effectively recognized by innate immunity in the context of ss siRNA as compared to siRNA duplexes. Novel immunostimulatory RNA motifs were identified and their replacement with adenosines abrogated immune activation. Most notably, replacement of the 2'-hydroxyl uridines with either 2'-fluoro, 2'-deoxy or 2'-O-methyl uridines abrogated immune activation. Thus, immune recognition of RNA by TLR can be evaded by 2'-ribose modifications of only uridines. Collectively, the data should facilitate the development of siRNA therapeutics and expand the understanding of how RNA is sensed by innate immunity.
Synthesis, Characterization and Optical Constants of Silicon Oxycarbide (2017)

High refractive index glasses are preferred in integrated photonics applications to realize higher integration scale of passive devices. With a refractive index that can be tuned between SiO2 (1.45) and a-SiC (3.2), silicon oxycarbide SiOC offers this flexibility. In the present work, silicon oxycarbide thin films from 0.1 – 2.0 μm thickness are synthesized by reactive radio frequency magnetron sputtering a silicon carbide SiC target in a controlled argon and oxygen environment. The refractive index n and material extinction coefficient k of the silicon oxycarbide films are acquired with variable angle spectroscopic ellipsometry over the UV-Vis-NIR wavelength range. Keeping argon and oxygen gases in the constant ratio, the refractive index n is found in the range from 1.41 to 1.93 at 600 nm which is almost linearly dependent on RF power of sputtering. The material extinction coefficient k has been estimated to be less than 10-4 for the deposited silicon oxycarbide films in the visible and near-infrared wavelength regions. Morphological and structural characterizations with SEM and XRD confirms the amorphous phase of the SiOC films.
High Throughput Single Nucleotide Polymorphism Genotyping Technology (2000)

Single nucleotide polymorphisms (SNP) are the most abundant of all DNA polymorphisms. The rapid progress of genome projects presents a unique opportunity to genetic researchers if reliable high throughput methods can be developed for SNP typing. In this review we will discuss the broad variety of SNP typing formats and discuss their relative merits for direct and indirect association studies. We will also mention some of the possible technical advances which may impact SNP typing in the next few years.
Impact of post-translational modifications of proteins on the inflammatory process (2007)

PTM (post-translational modification) is the chemical modification of a protein after its translation. The well-studied PTM is phosphorylation, but, recently, PTMs have been re-focused by extensive studies on histone modifications and the discovery of the ubiquitin system. Histone acetylation is the well-established epigenetic regulator for gene expression. Recent studies show that different patterns of PTMs and cross-talk of individual modifications (acetylation, methylation, phosphorylation) are keys of gene regulation (known as the 'histone code'). As well as histone, non-histone proteins are also targets of acetylation. For instance, NF-kappaB (nuclear factor kappaB), a transcriptional factor, is regulated dynamically by acetylation/deacetylation. Acetylation of NF-kappaB [RelA (p65)] at Lys(310) enhances its transcriptional activity, which is inhibited by SIRT1 deacetylase, type III HDAC (histone deacetylase). We also found that acetylated NF-kappaB preferentially bound to the IL-8 (interleukin 8) gene promoter, but not to GM-CSF (granulocyte/macrophage colony-stimulating factor), suggesting NF-kappaB acetylation is involved in selective gene induction as well as an increased level of transcription. A receptor of glucocorticoid, a potent anti-inflammatory agent, is also a target of acetylation. The glucocorticoid receptor is highly acetylated after ligand binding but its deacetylation is necessary for gene repression through binding to NF-kappaB. As well as acetylation, other PTMs, such as nitration, carbonylation and ubiquitination on transcriptional/nuclear factors, are taking part in the inflammatory process. Cross-talk of individual modifications on proteins deserves further evaluation in the future (as 'protein code').
Hybrid Biomaterials for Tissue Engineering: A Preparative Method for PLA or PLGA-Collagen Hybrid Sponges (2000)

A novel hybrid biomaterial for tissue engineeringhas been developed by forming collagen microsponges in the pores of poly(alpha ester) sponge. Poly(alpha ester) sponge provides the skeleton with a high degree of mechanical strength, while the collagen provides cell compatibility. The Figure shows mouse fibroblast cells and bovine articular chondrocytes adhered to a PLGA–collagen hybrid sponge.
Involvement of Smad Signaling in Sphingosine 1-Phosphate-mediated Biological Responses of Keratinocytes (2004)

The lysophospholipid sphingosine 1-phosphate and the cytokine-transforming growth factor beta are both released from degranulating platelets at wound sites, suggesting a broad spectrum of effects involved in wound healing. Interestingly, both of these molecules have been previously shown to induce chemotaxis but to strongly inhibit the growth of keratinocytes, while stimulating the proliferation of fibroblasts. In contrast to sphingosine 1-phosphate, the signaling cascade of the growth factor has been extensively examined. Specifically, Smad3 has been shown to be an essential mediator of transforming growth factor beta-dependent chemotaxis of keratinocytes and mediates, in part, its growth-inhibitory effect. Here we show that sphingosine 1-phosphate, independently of transforming growth factor beta secretion, induces a rapid phosphorylation of Smad3 on its C-terminal serine motif and induces its partnering with Smad4 and the translocation of the complex into the nucleus. Moreover, sphingosine 1-phosphate fails to induce chemotaxis or inhibit the growth of Smad3-deficient keratinocytes, suggesting that Smad3 plays an unexpected functional role as a new target in sphingosine 1-phosphate signaling. Both sphingosine 1-phosphate receptors and the transforming growth factor beta-type I receptor serine/threonine kinase are essential for activation of Smad3 by this lysophospholipid and the dependent biological responses, indicating a novel cross-talk between serine/threonine kinase receptors and G-protein coupled receptors.
Pseudomonas aeruginosa and other predictors of mortality and morbidity in young children with cystic fibrosis (2002)

We conducted a registry-based study to determine prognostic indicators of 8-year mortality and morbidity in young children with cystic fibrosis (CF). Patients ages 1-5 years from the 1990 U.S. Cystic Fibrosis Foundation (CFF) National Patient Registry served as the study cohort (N = 3,323). Registry data provided information on baseline characteristics in 1990, 8-year mortality, and clinical outcomes in 1998.P. aeruginosa respiratory infection was found to be a major predictor of morbidity and mortality. The 8-year risk of death was 2.6 times higher in patients who had respiratory cultures positive for P. aeruginosa in 1990 (95% confidence interval 1.6, 4.1) than in children without P. aeruginosa in their respiratory cultures. Culture-positive patients in 1990 also had a significantly lower percent predicted forced expiratory volume in 1 sec (FEV(1)) and weight percentile at follow-up, and they had an increased risk of continued P. aeruginosa respiratory infection and hospitalization for acute respiratory exacerbation in 1998. Among the other predictors of increased morbidity and mortality were lower baseline weight percentiles and number of CF-related hospitalizations during the baseline year.These findings confirm reports from previous smaller studies of outcomes among young children with CF, and highlight the potential to decrease the morbidity and mortality of young patients with CF through early intervention.
Tissue distribution of breast cancer-associated antigens defined by monoclonal antibodies. (1985)

Balb/c mice were immunized with membrane preparations of primary and metastatic breast carcinomas or with live breast cancer cell lines. Sixty-two fusions were performed between immune splenocytes and SP2/0 mouse myeloma cells, and 107 hybridomas were cloned that produced antibody reactive with breast cancer membrane extract, cell lines, and frozen sections, but not with normal tissue membrane extracts or a human fibroblast line. Ninety-four monoclonal antibodies were purified and tested for binding to 16 normal tissue frozen sections and five blood cell types. Thirty-five of the 94 antibodies were also tested on breast cancer sections from 21 patients, 14 breast cancer cell lines, and 11 nonbreast tumor sections. Two of 94 antibodies showed no reactivity to any of the 21 normal tissues or 11 nonbreast neoplasms studied. These two antibodies, 451B7 and 452F2, bound 60% of the breast cancer cell lines and 25% of the breast cancer tissue sections. Eight additional antibodies bound three or fewer of 21 normal tissues. These antibodies bound 25-85% of breast cancer sections, 0-75% of breast cancer cell lines, and many of the nonbreast cancers. A comparison of normal tissues and nonbreast tumors bound by the breast cancer-reactive antibodies indicated that most of the cross-reacting normal tissue structures were epithelial in origin, and that the most cross-reactive nonbreast cancers were those of secondary sex organs (uterus, prostate, ovary).
Synthesis and Antitumor Activity of a Novel Series of 6-Substituted Pyrrolo[2,3-d]pyrimidine Thienoyl Antifolate Inhibitors of Purine Biosynthesis with Selectivity for High Affinity Folate Receptors and the Proton-Coupled Folate Transporter over the Reduced Folate Carrier for Cellular Entry (2010)

2-Amino-4-oxo-6-substituted pyrrolo[2,3-d]pyrimidines with a thienoyl side chain and four to six carbon bridge lengths (compounds 1-3) were synthesized as substrates for folate receptors (FRs) and the proton-coupled folate transporter (PCFT). Conversion of acetylene carboxylic acids to alpha-bromomethylketones and condensation with 2,4-diamino-6-hydroxypyrimidine afforded the 6-substituted pyrrolo[2,3-d]pyrimidines. Sonogashira coupling with (S)-2-[(5-bromo-thiophene-2-carbonyl)-amino]-pentanedioic acid diethyl ester, followed by hydrogenation and saponification, afforded 1-3. Compounds 1 and 2 potently inhibited KB and IGROV1 human tumor cells that express FR alpha, reduced folate carrier (RFC), and PCFT. The analogs were selective for FR and PCFT over RFC. Glycinamide ribonucleotide formyltransferase was the principal cellular target. In SCID mice with KB tumors, 1 was highly active against both early (3.5 log kill, 1/5 cures) and advanced (3.7 log kill, 4/5 complete remissions) stage tumors. Our results demonstrate potent in vitro and in vivo antitumor activity for 1 due to selective transport by FRs and PCFT over RFC.
Production and Characterization of Monoclonal Antibodies to Human Sclerostin (2009)

We developed and characterized monoclonal antibodies directed against the amino-terminal and carboxy-terminal regions of human and mouse sclerostin (scl). Amino-terminal and carboxy-terminal scl peptides with limited homology to scl domain-containing protein-1 were synthesized using f-moc chemistry. The peptides were conjugated to keyhole limpet hemocyanin and the conjugates were used for immunization of mice. Monoclonal antibodies were obtained and characterized using bacterially expressed and insect cell-expressed recombinant scl. The amino-terminal (IgG 2aK) and carboxy-terminal (IgG 2bK) antibodies bound bioactive sclerostin that was expressed in an insect-cell expression system with dissociation constants in the nanomolar range. The antibodies are potentially useful agents that can be used for modulating sclerostin bioactivity.
Identification of Mouse MD-2 Residues Important for Forming the Cell Surface TLR4-MD-2 Complex Recognized by Anti-TLR4-MD-2 Antibodies, and for Conferring LPS and Taxol Responsiveness on Mouse TLR4 by Alanine-Scanning Mutagenesis (2003)

The expression of MD-2, which associates with Toll-like receptor (TLR) 4 on the cell surface, confers LPS and LPS-mimetic Taxol responsiveness on TLR4. Alanine-scanning mutagenesis was performed to identify the mouse MD-2 residues important for conferring LPS and Taxol responsiveness on mouse TLR4, and for forming the cell surface TLR4-MD-2 complex recognized by anti-TLR4-MD-2 Ab MTS510. Single alanine mutations were introduced into mouse MD-2 (residues 17-160), and the mutants were expressed in a human cell line expressing mouse TLR4. Mouse MD-2 mutants, in which a single alanine mutation was introduced at Cys37, Leu71, Leu78, Cys95, Tyr102, Cys105, Glu111, Val113, Ile117, Pro118, Phe119, Glu136, Ile138, Leu146, Cys148, or Thr152, showed dramatically reduced ability to form the cell surface mouse TLR4-mouse MD-2 complex recognized by MTS510, and the mutants also showed reduced ability to confer LPS and Taxol responsiveness. In contrast, mouse MD-2 mutants, in which a single alanine mutation was introduced at Tyr34, Tyr36, Gly59, Val82, Ile85, Phe126, Pro127, Gly129, Ile153, Ile154, and His155 showed normal ability to form the cell surface mouse TLR4-mouse MD-2 complex recognized by MTS510, but their ability to confer LPS and Taxol responsiveness was apparently reduced. These results suggest that the ability of MD-2 to form the cell surface mouse TLR4-mouse MD-2 complex recognized by MTS510 is essential for conferring LPS and Taxol responsiveness on TLR4, but not sufficient. In addition, the required residues at codon numbers 34, 85, 101, 122, and 153 for the ability of mouse MD-2 to confer LPS responsiveness are partly different from those for Taxol responsiveness.
Induction of cytotoxic T lymphocytes and antitumor immunity with DNA vaccines expressing single T cell epitopes (1996)

Delivery of genetic expression constructs into living animals can effectively induce both humoral and cellular immunity to the expressed proteins. Here we test the effectiveness of genetic immunization with a minigene coding for single epitopes derived from mutant p53 or from HIV gp120. We show that when these constructs are delivered by particle bombardment-mediated DNA transfer into the skin of mice, it results in efficient induction of tumor protective CTL. The immunogenicity of the epitope derived from mutant p53 is significantly enhanced if the epitope sequence is fused in frame with the adenovirus E3 leader sequence to target the epitope to the endoplasmic reticulum, thus acting like a "genetic adjuvant." We conclude that genetic T cell epitope immunization is an alternative to peptide-based techniques for eliciting an effective immune response targeted against a single defined epitope. in some cases, the fusion of the gene product of the DNA vaccine vector with an endoplasmic reticulum targeting sequence may enhance immune induction.
Antibody structure determination using a combination of homology modeling, energy‐based refinement, and loop prediction (2014)

ABSTRACT We present the blinded prediction results in the Second Antibody Modeling Assessment (AMA‐II) using a fully automatic antibody structure prediction method implemented in the programs BioLuminate and Prime. We have developed a novel knowledge based approach to model the CDR loops, using a combination of sequence similarity, geometry matching, and the clustering of database structures. The homology models are further optimized with a physics‐based energy function (VSGB2.0), which improves the model quality significantly. H3 loop modeling remains the most challenging task. Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models. For the 10 human and mouse derived antibodies in this assessment, the average RMSDs for the homology model Fv and framework regions are 1.19 Å and 0.74 Å, respectively. The average RMSDs for five non‐H3 CDR loops range from 0.61 Å to 1.05 Å, and the H3 loop average RMSD is 2.91 Å using our knowledge‐based loop prediction approach. The ab initio H3 loop predictions yield an average RMSD of 1.28 Å when performed in the context of the crystal structure and 2.67 Å in the context of the homology modeled structure. Notably, our method for predicting the H3 loop in the crystal structure environment ranked first among the seven participating groups in AMA‐II, and our method made the best prediction among all participants for seven of the ten targets. Proteins 2014; 82:1646–1655. © 2014 Wiley Periodicals, Inc.
CO2‐dependent metabolic modulation in red blood cells stored under anaerobic conditions (2015)

Maintenance of ATP in the AN[CO2 ] arm demonstrates that ATP production is not solely a function of the pH effect on glycolysis. CO2 in anaerobic storage prevented the maintenance of DPG, and DPG production appears to be pH dependent. CO2 as well as O2 depletion provides metabolic advantage for stored RBCs.
IBD serological panels: Facts and perspectives (2007)

Beyond a defective innate immune response in inflammatory bowel disease (IBD), an increased immunological response toward microbial and self antigens has been intrinsically linked to the pathogenesis of such common immunopathologies of the gut. Mounting evidence indicates that increased seroreactivity toward certain antigens are a predictive and quantitative heritable trait, including the anti-Saccharomyces cerevisiae antibody (ASCA). Consistently, Candida albicans and Crohn's disease-associated NOD2 mutations have been recently identified as immunogen and genetic determinants for ASCA, respectively. In clinical practice, current panels of serological markers are not recommended for diagnosis, stratifying, and monitoring IBD. Therefore, prospective studies and highly sensitive serological panels of markers are eagerly awaited before guiding clinical decisions. Better understanding of the serological response in IBD might also provide new insights into their epidemiology and pathophysiology.
Influence of ovarian stimulation with HP-hMG or recombinant FSH on embryo quality parameters in patients undergoing IVF (2007)

Composition of gonadotrophin preparations used during ovarian stimulation has an impact on some embryo quality parameters. The capacity to implant of the top-quality embryos derived from stimulation with HP-hMG appears to be improved, although the mechanism needs to be elucidated.