gebhart/patrepeval huggingface dataset:
Adenovirus Vector-Mediatedin VivoGene Transfer of OX40 Ligand to Tumor Cells Enhances Antitumor Immunity of Tumor-Bearing Hosts (2004)

OX40 ligand (OX40L), the ligand for OX40 on activated CD4+ T cells, has adjuvant properties for establishing effective T-cell immunity, a potent effector arm of the immune system against cancer. The hypothesis of this study is that in vivo genetic engineering of tumor cells to express OX40L will stimulate tumor-specific T cells by the OX40L-OX40 engagement, leading to an induction of systemic antitumor immunity. To investigate this hypothesis, s.c. established tumors of three different mouse cancer cells (B16 melanoma, H-2b; Lewis lung carcinoma, H-2b; and Colon-26 colon adenocarcinoma, H-2d) were treated with intratumoral injection of a recombinant adenovirus vector expressing mouse OX40L (AdOX40L). In all tumor models tested, treatment of tumor-bearing mice with AdOX40L induced a significant suppression of tumor growth along with survival advantages in the treated mice. The in vivo AdOX40L modification of tumors evoked tumor-specific cytotoxic T lymphocytes in the treated host correlated with in vivo priming of T helper 1 immune responses in a tumor-specific manner. Consistent with the finding, the antitumor effect provided by intratumoral injection of AdOX40L was completely abrogated in a CD4+ T cell-deficient or CD8+ T cell-deficient condition. In addition, ex vivo AdOX40L-transduced B16 cells also elicited B16-specific cytotoxic T lymphocyte responses, and significantly suppressed the B16 tumor growth in the immunization-challenge experiment. All of these results support the concept that genetic modification of tumor cells with a recombinant OX40L adenovirus vector may be of benefit in cancer immunotherapy protocols.
Comparison of Six Radiographic Projections to Assess Femoral Head/Neck Asphericity (2006)

Prognostic study, level II-1 (retrospective study).
Genome-Wide Analysis of Promoter Methylation Associated with Gene Expression Profile in Pancreatic Adenocarcinoma (2011)

We expected that the identification of aberrantly hypermethylated and silenced genes will have diagnostic, prognostic, and therapeutic applications.
pH as a Trigger of Peptide β-Sheet Self-Assembly and Reversible Switching between Nematic and Isotropic Phases (2003)

The hierarchical self-assembly of rationally designed synthetic peptides into beta-sheet tapes, ribbons, fibrils, and fibers opens up potentially useful routes to soft-solidlike materials such as hydrogels, organogels, or liquid crystals. Here, it is shown how incorporation of Glu (-CH(2)CH(2)COOH) or Orn (-CH(2)CH(2)CH(2)NH(2)) into the primary structure of an 11 amino acid peptide enables self-assembly to be rapidly (seconds) and reversibly controlled by simply changing pH. Solutions of monomeric peptide, typically at concentrations in excess of 0.003 v/v, can be switched within seconds to, for example, nematic gel states comprised of interconnected orientationally ordered arrays of fibrils or vice versa. This is to be compared with the lyophilized peptide dissolution route to nematic fluids and gels which is impracticably long, taking many hours or even days. An important design principle, that stabilization of fibrillar dispersions requires of the order of one unit of net positive or negative charge per peptide molecule, is first demonstrated and then used to design an 11 amino acid peptide P(11)-3 (CH(3)CO-Gln-Gln-Arg-Phe-Gln-Trp-Gln-Phe-Gln-Gln-Gln-NH(2)) whose self-assembly behavior is independent of pH (1 < pH < 10). pH control is then incorporated by appropriately positioning Glu or Orn side chains so that the peptide-peptide free energy of interaction in the tapelike substructure is strongly influenced by direct electrostatic forces between gamma-COO(-) in Glu(-) or delta-NH(3)(+) in Orn(+), respectively. This design principle is illustrated by the behavior of two peptides: P(11)-4 (CH(3)CO-Gln-Gln-Arg-Phe-Glu-Trp-Glu-Phe-Glu-Gln-Gln-NH(2)) which can be switched from its nematic to its isotropic fluid state by increasing pH and P(11)-5 (CH(3)CO-Gln-Gln-Orn-Phe-Orn-Trp-Orn-Phe-Gln-Gln-Gln-NH(2)) designed to exhibit the converse behavior. Acid-base titrations of fibrillar dispersions reveal deprotonation of the gamma-COOH of Glu or of the delta-NH(3)(+) of Orn(+) occurs over wide bands of up to 5 pH units, a feature of polyelectrolytes. The values of the energy parameters controlling self-assembly can therefore be smoothly and continuously varied by changing pH. This enables isotropic fluid-to-nematic transitions to be triggered by relatively small additions of acid or base, typically 1 part in 10(3) by volume of 1 M HCl or NaOH.
HER3 Overexpression and Survival in Solid Tumors: A Meta-analysis (2012)

Expression of HER3 is associated with worse survival in solid tumors. The influence of HER3 may be greater in those tumors where HER2 is commonly overexpressed.
Safety, pharmacokinetics (PK), and pharmacodynamics (PD) of WAY-195725 (2005)

Background WAY-195725 can selectively and reversibly inhibit cytosolic phospholipase A2α (cPLA2α) to block the biosynthesis of prostaglandins (PG), thromboxanes (TX), leukotrienes (LT), and platelet-activating factor by inhibiting the release of arachidonic acid. It has been proposed treatment for the management of rheumatoid arthritis, osteoarthritis, and dysmenorrhea. Objective To evaluate the safety, PK, and PD of WAY-195725 following oral single dose administration in healthy subjects. Methods Healthy subjects (N=90) were studied in a randomized, double-blind, placebo-controlled, positive (ibuprofen)-controlled, ascending single dose study. The safety, tolerability, PK, and PD of WAY-195725 (10–600 mg) were assessed. A23187 (Ca++ ionophore) was used to stimulate whole blood ex vivo to produce PGE2, LTB4, and TXB2. Results The oral absorption of WAY-19725 was slow (tmax: 2~3 h). WAY-195725 inhibited PGE2, TXB2 and LTB4 with mean IC50 (ng/mL) of 40.2, 40.8 and 199, respectively. Ibuprofen, a positive control, inhibited both PGE2 and TXB2, but not LTB4, which coincides to ibuprofen's pharmacological profile as a COX-1,2 inhibitor. WAY-195725 was well tolerated in all the dose cohorts. Conclusion Significant WAY-195725 concentration-dependent inhibition is apparent for all three biomarkers (PGE2, TXB2 and LTB4), which conforms to WAY-195725's pharmacological profile as a potent cPLA2α inhibitor. Clinical Pharmacology & Therapeutics (2005) 77, P51–P51; doi: 10.1016/j.clpt.2004.12.086
Effect of temperature on the saccharide composition obtained after ?-amylolysis of starch (1999)

The hydrolysis of starch to low-molecular-weight products (normally characterised by their dextrose equivalent (DE), which is directly related to the number-average molecular mass) was studied at different temperatures. Amylopectin potato starch, lacking amylose, was selected because of its low tendency towards retrogradation at lower temperatures. Bacillus licheniformis alpha-amylase was added to 10% [w/w] gelatinised starch solutions. The hydrolysis experiments were done at 50, 70, and 90 degrees C. Samples were taken at defined DE values and these were analysed with respect to their saccharide composition. At the same DE the oligosaccharide composition depended on the hydrolysis temperature. This implies that at the same net number of bonds hydrolysed by the enzyme, the saccharide composition was different. The hydrolysis temperature also influenced the initial overall molecular-weight distribution. Higher temperatures led to a more homogenous molecular weight distribution. Similar effects were observed for alpha-amylases from other microbial sources such as Bacillus amyloliquefaciens and Bacillus stearothermophilus. Varying the pH (5.1, 6.2, and 7.6) at 70 degrees C did not significantly influence the saccharide composition obtained during B. licheniformis alpha-amylase hydrolysis. The underlying mechanisms for B. licheniformis alpha-amylase were studied using pure linear oligosaccharides, ranging from maltotriose to maltoheptaose as substrates. Activation energies for the hydrolysis of individual oligosaccharides were calculated from Arrhenius plots at 60, 70, 80, and 90 degrees C. Oligosaccharides with a degree of polymerisation exceeding that of the substrate could be detected. The contribution of these oligosaccharides increased as the degree of polymerisation of the substrate decreased and the temperature of hydrolysis increased. The product specificity decreased with increasing temperature of hydrolysis, which led to a more equal distribution between the possible products formed. Calculations with the subsite map as determined for the closely related alpha-amylase from B. amyloliquefaciens reconfirmed this finding of a decreased substrate specificity with increased temperature of hydrolysis. Copyright 1999 John Wiley & Sons, Inc.
Prevalence of Ureaplasma urealyticum and Ureaplasma parvum in semen of infertile and healthy men (2009)

Ureaplasma urealyticum is a causative agent of non-gonococcal urethritis and is implicated in the pathogenesis of prostatitis, epididymitis and infertility. The organism is more common in partners of infertile than fertile marriages. U. urealyticum infections not only jeopardize fertility but also pose a risk for infertility treatment and resulting pregnancies. The aim of this study was to determine the prevalence of U. urealyticum and Ureaplasma parvum in semen of infertile and healthy men by polymerase chain reaction (PCR). Semen samples were obtained from infertile patients and healthy controls and were subjected to the routine andrological analysis and PCR. DNA was extracted by the Cadieux method, and analysed by PCR protocol with specific primers for urease and multiple-banded antigen genes. Ureaplasmas were detected significantly by PCR in 12 of 100 (12%) semen specimens from infertile patients and in three of 100 (3%) healthy men. The volume of semen fluid, concentration of sperm cells, and sperm cell with normal morphology were significantly decreased in infertile men. In the group of infertile patients with PCR positive for Ureaplasmas, the volume, count and morphology of semen samples were lower than in the infertile patients with PCR-negative results. U. urealyticum species in semen of infertile men was found to be high (9%) than in healthy controls (1%). Detection rate for U. parvum was 3% in the infertile group and 2% in healthy men. The results indicate that U. urealyticum species is more common in specimens of infertile men. The percentage of normal sperm cells, the volume of semen and the percentage of sperm cells with motility in the PCR positive for U. urealyticum species group were lower than in the PCR positive for U. parvum group.
Selective coloration of spiro pyridopyrans for guanosine derivatives (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective coloration of spiro pyridopyrans for guanosine derivativesMasahiko Inouye, Kwangshik Kim, and Teijiro KitaoCite this: J. Am. Chem. Soc. 1992, 114, 2, 778–780Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/ja00028a065https://doi.org/10.1021/ja00028a065research-articleACS PublicationsRequest reuse permissionsArticle Views1234Altmetric-Citations64LEARN 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
Association of Specific Symptoms and Metabolic Risks with Serum Testosterone in Older Men (2006)

There is no evidence that a uniform structure of testosterone concentrations and complaints exists within the cohort of elderly male patients. Rather, in aging male patients, psychosomatic complaints and metabolic risk relate to testosterone in a symptom-specific manner.
Primer Pheromones in Social Hymenoptera (2007)

Social insect are profoundly influenced by primer pheromones (PPhs), which are efficient means for maintaining social harmony in the colony. PPhs act by affecting the physiology of the recipients with a subsequent shift in their behavior, and many PPhs have a releaser effect (i.e., changing the probability of performing a certain behavior upon perception). In this review we try to clarify the interplay between such dual pheromonal effects. Only a few PPhs have been identified, and we provide evidence for their existence in multiple species of social Hymenoptera, which is the most extensively studied of the social insects. We focus on the regulation of reproduction, social policing, and task allocation. Considering PPhs in a broad sense, we also discuss fertility signals and the role of cuticular hydrocarbons as putative PPhs. Identification of the underlying chemistry of PPhs offers insights into insect physiology and the evolution of social behavior. PPhs of the honey bee are used to demonstrate the complexity of pheromonal communication in social insects.
Experimental studies on viscofluids for intraocular surgery (1998)

Viscofluids irrigated using a high-pressure system combined the advantages of continuous irrigation of fluids and the protective qualities of viscoelastics in this rabbit eye study.
An amplification and ligation-based method to scan for unknown mutations in DNA (2002)

A new approach is presented for the sensitive and selective scanning for unknown DNA mutations, based on ligation-mediated PCR and the use of the glycosylases TDG and MutY. These two highly selective enzymes together can detect about 70% of commonly observed polymorphisms and mutations in human tumors. DNA is cross-hybridized to form mismatches at the positions of point mutations, de-phosphorylated to eliminate any pre-existing phosphorylated DNA ends, and then exposed to enzymatic treatment to remove mismatched thymidine (TDG) or adenine (MutY). The resulting apurinic/apyrimidinic sites at the position of the mismatches are heat-converted to 5'-phosphate-containing strand breaks, the DNA is denatured, and an oligonucleotide is ligated at the position of the newly created 5'-phosphate-containing DNA ends. The ligated oligonucleotide then participates in a PCR reaction that amplifies exponentially only the mutation-containing fragments. Using this method, A-->G mutations in a p53 (TP53)-containing system, T-->G, G-->A, and C-->A, mutations in the Ku gene (XRCC5), and ATM, gene for a number of patient-derived genomic DNA samples have been successfully screened. This PCR-based assay is capable of detecting one mutated allele in 100 normal alleles and requires 5 to 100 ng of genomic DNA as starting material. The assay allows final visualization of the mutated fragments on a common ethidium gel or biotinylation and use in a capture format, potentially allowing the isolation of diverse mutated DNA fragments simultaneously. This versatile new approach should allow high throughput detection of DNA alterations and application in diverse areas of human mutation research.
SKALP/elafin is an inducible proteinase inhibitor in human epidermal keratinocytes (1994)

Skin-derived antileukoproteinase (SKALP), otherwise known as elafin, is a recently discovered epidermal proteinase inhibitor with specificity for polymorphonuclear leukocyte (PMN)-derived elastase and proteinase-3; in addition to the proteinase-inhibiting domain, SKALP contains several transglutaminase substrate motifs. SKALP is virtually absent in normal human epidermis but is found in a number of inflammatory skin diseases, including psoriasis. Here we report the induction and processing of SKALP in vivo and in vitro. SKALP expression in vivo could be demonstrated following injury in normal human epidermis, using histology, western blotting, northern blotting and a functional assay. In vitro, SKALP expression was studied in conventional submerged keratinocyte culture systems and in keratinocytes cultured in an air-liquid interface model. Induction of SKALP activity in epidermis could be measured as early as 16 hours after skin injury; immunohistological examination showed that SKALP expression was confined to the outer layers of the stratum spinosum and the stratum granulosum. Northern blot analysis revealed a 0.8 kb transcript, both in vivo (psoriatic skin, injured skin) and in vitro (cultured keratinocytes). Western blot analysis showed that the major SKALP form in vivo was a low molecular mass fragment, containing the antiproteinase domain. In all cultures that were positive for SKALP, larger (8-10 kDa) forms of SKALP, containing the N-terminal transglutaminase substrate motifs in addition to the antiproteinase domain, were found. SKALP expression in cultured cells was found to be dependent on the system used. In a submerged culture system, SKALP could be induced by fetal calf serum.(ABSTRACT TRUNCATED AT 250 WORDS)
Training Products of Experts by Minimizing Contrastive Divergence (2002)

It is possible to combine multiple latent-variable models of the same data by multiplying their probability distributions together and then renormalizing. This way of combining individual "expert" models makes it hard to generate samples from the combined model but easy to infer the values of the latent variables of each expert, because the combination rule ensures that the latent variables of different experts are conditionally independent when given the data. A product of experts (PoE) is therefore an interesting candidate for a perceptual system in which rapid inference is vital and generation is unnecessary. Training a PoE by maximizing the likelihood of the data is difficult because it is hard even to approximate the derivatives of the renormalization term in the combination rule. Fortunately, a PoE can be trained using a different objective function called "contrastive divergence" whose derivatives with regard to the parameters can be approximated accurately and efficiently. Examples are presented of contrastive divergence learning using several types of expert on several types of data.
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples (2010)

Reductions in the cost of sequencing have enabled whole-genome sequencing to identify sequence variants segregating in a population. An efficient approach is to sequence many samples at low coverage, then to combine data across samples to detect shared variants. Here, we present methods to discover and genotype single-nucleotide polymorphism (SNP) sites from low-coverage sequencing data, making use of shared haplotype (linkage disequilibrium) information. For each population, we first collect SNP candidates based on independent sequence calls per site. We then use MARGARITA with genotype or phased haplotype data from the same samples to collect 20 ancestral recombination graphs (ARGs). We refine the posterior probability of SNP candidates by considering possible mutations at internal branches of the 40 marginal ancestral trees inferred from the 20 ARGs at the left and right flanking genotype sites. Using a population genetic prior distribution on tree-branch length and Bayesian inference, we determine a posterior probability of the SNP being real and also the most probable phased genotype call for each individual. We present experiments on both simulation data and real data from the 1000 Genomes Project to prove the applicability of the methods. We also explore the relative tradeoff between sequencing depth and the number of sequenced samples.
Low Temperature Hybrid Bonding for Die to Wafer Stacking Applications (2021)

The direct bond interconnect (DBI®) technology is a platform technology that offers a hermetically sealed hybrid bond with solid metal-metal (Cu-Cu is the most common) interconnect at a relatively low thermal budget. The Xperi wafer to wafer hybrid bonding technology has been in high volume production since 2015. The Xperi die to wafer hybrid bonding technology, DBI® Ultra, is now ready for industry adoption and ramp to manufacturing. The bond takes place at room temperature in an ambient environment in a class 1000 cleanroom; therefore, offers bond throughput comparable to mass reflow flip chip assembly. A low temperature batch anneal after bonding results in a solid Cu-Cu connection surrounded by dielectric for improved thermal performance. The value of the hybrid bonded Cu-Cu technology may be realized at various interconnect pitches for different applications. For die to wafer and die to die application with through silicon vias (TSVs), significant performance and cost advantages can be achieved at sub-40um pitch through elimination of both the solder and underfill materials from the package. Additionally, the technology may be scaled to sub-micron interconnects to enable widespread disaggregation and chiplet architecture innovation. Xperi's development efforts target the sub-40um pitch die-to-wafer stacking, which can be enabled with the existing Si supply chain. Previously, we have reported assembly results with daisy chain die in single layer and in die-to-wafer stacking with or without TSVs. In this paper, we report on a 5-die stack hybrid bonded module with TSV and the latest fabrication, assembly process, electrical testing and reliability performance. The reliability tests include autoclave, high temperature storage and temperature cycling with pre-conditioning at MSL3 per JEDEC specification.
GM-CSF enhances 3F8 monoclonal antibody-dependent cellular cytotoxicity against human melanoma and neuroblastoma (1989)

3F8 is a murine monoclonal IgG3 antibody specific for the tumor-associated antigen ganglioside GD2. Previous in vitro studies suggest that tumor regressions observed in a phase I clinical trial of 3F8 may be attributable to complement activation by 3F8 and to 3F8-dependent cellular cytotoxicity (ADCC) with lymphocytes. We now describe 3F8-mediated ADCC of GD2-positive tumor targets (melanoma and neuroblastoma) with human granulocytes and report that recombinant human granulocyte-macrophage colony-stimulating factor (GM-CSF) enhanced this phenomenon. Cytotoxicity required binding of 3F8 to the low-affinity Fc receptor type III (CD16) on the granulocytes and was poor with tumor-binding monoclonal antibodies of other immunoglobulin (ie, non-IgG3) subclasses. GM-CSF (2 to 20 ng/mL) increased ADCC by 93% to 267% at limiting dilutions of 3F8 (1 microgram/mL). With most GD2-positive cell lines tested, this effect translated into a tenfold or greater augmentation in 3F8 efficiency at mediating ADCC. Comparable enhancement occurred whether GM-CSF was present in the ADCC assay or granulocytes were incubated with GM-CSF and washed before the assay. Nonoxidative mechanisms may be important for ADCC since 3F8 mediated ADCC with granulocytes from two children with chronic granulomatous disease; this cytotoxicity was also enhanced by GM-CSF. Since GM-CSF induces a neutrophilia in patients, our data suggest that this cytokine may have the potential of amplifying 3F8 antitumor activity in patients by increasing effector cell numbers and by priming granulocytes for greater cytotoxicity.