gebhart/patrepeval huggingface dataset:
Structure−Activity Relationships of OligoguanidinesInfluence of Counterion, Diamine, and Average Molecular Weight on Biocidal Activities (2003)

A series of different oligomeric guanidines was prepared by polycondensation of guanidinium salts and four different diamines under varying conditions. The antimicrobial activities were evaluated against two to four microorganisms. MALDI-TOF-MS was used to analyze the different oligomers. It was found that in each case three major product type series are dominating. These series are linear and terminated with one guanidine and one amino group (type A), two amino groups (type B), or two guanidine groups (type C), respectively. By using 1,2-bis(2-aminoethoxy)ethane as the amino component, a considerable amount of two additional product series, consisting of cyclic structures, was detected (type D and E). It turned out that an average molecular mass of about 800 Da is necessary for an efficient antimicrobial activity. Lower Mw's result in a rapid decrease of activity. By using guanidinium carbonate as the starting material, oligomers with low biocidal activity were obtained, which was caused by incorporation of urea groups during the polycondensation. The diamine determines the distance between two guanidinium groups. It was shown that both 1,2-bis(2-aminoethoxy)ethane and hexamethylenediamine give oligomers with high biocidal activity. By increasing the chain length of the diamine, the biocidal activity drops again.
An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae. (1994)

L1 elements constitute a highly repetitive human DNA family (50,000 to 100,000 copies) lacking long terminal repeats and ending in a poly(A) tail. Some L1 elements are capable of retrotransposition in the human genome (Kazazian, H. H., Jr., C. Wong, H. Youssoufian, A. F. Scott, D. G. Phillips, and S.E. Antonarakis, Nature (London) 332:164-166, 1988). Although most are 5' truncated, a consensus sequence of complete L1 elements is 6 kb long and contains two open reading frames (ORFs) (Scott, A. F., B. J. Schmeckpeper, M. Abdelrazik, C. T. Comey, B. O'Hara, J. P. Rossiter, T. Cooley, P. Health, K. D. Smith, and L. Margolet, Genomics 1:113-125, 1987). The protein encoded by ORF2 has reverse transcriptase (RT) activity in vitro (Mathias, S. L., A. F. Scott, H. H. Kazazian, Jr., J. D. Boeke, and A. Gabriel, Science 254:1808-1810, 1991). Because L1 elements are so numerous, efficient methods for identifying active copies are required. We have developed a simple in vivo assay for the activity of L1 RT based on the system developed by Derr et al. (Derr, L. K., J. N. Strathern, and D. J. Garfinkel, Cell 67:355-364, 1991) for yeast HIS3 pseudogene formation. L1 ORF2 displays an in vivo RT activity similar to that of yeast Ty1 RT in this system and generates pseudogenes with unusual structures. Like the HIS3 pseudogenes whose formation depends on Ty1 RT, the HIS3 pseudogenes generated by L1 RT are joined to Ty1 sequences and often are part of complex arrays of Ty1 elements, multiple HIS3 pseudogenes, and hybrid Ty1/L1 elements. These pseudogenes differ from those previously described in that there are base pairs of unknown origin inserted at several of the junctions. In two of three HIS3 pseudogenes studied, the L1 RT appears to have jumped from the 5' end of a Ty1/L1 transcript to the poly(A) tract of the HIS3 RNA.
[Effect of sinorphan, an endopeptidase inhibitor on severe congestive cardiac insufficiency]. (1991)

Sinorphan is a powerful inhibitor of enkephalinases or endopeptidases 24-11, enzymes implicated in the degradation of the atrial natriuretic factor (ANF). In healthy volunteers, it increases plasma concentrations of endogenic ANF and increases diuresis and natriuresis. In order to study the tolerance and biological effects of pharmacological increase of plasma concentrations of endogenic ANF in severe congestive cardiac failure, 12 patients (in functional Classes III or IV of the NYHA classification) were given a single oral dose of 10, 20 or 40 mg of Sinorphan. Sinorphan was clinically well tolerated. The diastolic blood pressure decreased slightly (- 10 +/- 9 mmHg) but significantly (p less than 0.05). Systolic blood pressure and heart rate were unchanged. Despite spontaneously high plasma ANF concentrations (on average 15 times higher than normal subjects), Sinorphan induced an additional increase of 80 to 100% of plasma ANF concentration compared to the initial values (p less than 0.01) with no dose-dependent response for the dosages used. The inhibition of plasma endopeptidase activity attained 47% at the 30th minute. Urinary cyclic GMP excretion increased by 30% at the second hour (p less than 0.05). In addition, a statistically non significant tendency to increase diuresis and natriuresis was observed. These results show that Sinorphan increases plasma ANF concentrations by inhibition of its degradation in severe congestive cardiac failure and that this increase seems to be associated with potentially beneficial biological changes. The concept of endopeptidase inhibition should constitute a new therapeutic approach in cardiac failure, a situation in which the ANF seems to exert a favourable effect.(ABSTRACT TRUNCATED AT 250 WORDS)
Abstract 4816: Development of an integrated analysis platform of circulating melanoma cells for PD-L1 expression as a predictive biomarker (2014)

Abstract Novel therapies that target the PD-1/PD-L1 axis have shown great potential to improve survival for patients with advanced melanoma. However, there are limited predictive biomarkers to identify patients who may respond to this class of agents. Previous studies suggest that a subset of responders to PD-1/PD-L1 targeting therapies have expression of PD-L1 in tumor biopsies. The development of these predictive biomarkers is complicated by intratumoral heterogeneity across primary and metastatic lesions for PD-L1 expression. Circulating tumor cells (CTCs) are one potential source of tumor samples for serial analysis. An integrated CTC capture and analysis technology known as the VERSA (Versatile Exclusion-based Rare Sample Analysis) platform permits evaluation of CTCs at the protein, DNA and mRNA level for biomarkers of both therapeutic response and resistance. Using this platform, we have developed a method to isolate circulating tumor cells from patients with advanced melanoma. Using a cocktail of capture monoclonal antibodies including targets of CD146, GD2 and NG2, we have recovered cells across multiple cell lines with high efficiency. Using single antibody capture of SK-Mel-28 cells, capture was 52%, 54%, and 45% with CD146, GD2 and NG2 targets respectively. However, when using a cocktail of capture antibodies containing CD146, GD2 and NG2, capture increased to 92%. Similar results were obtained with other melanoma cell lines including, 624 and M21 cell lines. Cells were also stained for PD-L1 as a potential predictive biomarker of response to PD-L1 and PD-1 targeting immunotherapies. We are now collecting patient samples with this capture platform to identify CTCs expressing PD-L1 as a potential predictive biomarker to PD-1/PD-L1 targeting therapies. Citation Format: Benjamin K. Gibbs, Lindsay N. Strotman, Stephanie M. Thiede, Jamie M. Sperger, Benjamin P. Casavant, Scott M. Berry, David J. Beebe, Joshua M. Lang. Development of an integrated analysis platform of circulating melanoma cells for PD-L1 expression as a predictive biomarker. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4816. doi:10.1158/1538-7445.AM2014-4816
Investing at the Edge (1998)

Investing at the edge refers to investing in assets away from the center of the investment universe. In the center, passive investors should invest in a market capitalization index, such as the S&P 500 Index, to minimize residual risk.At the edge, active investors should not necessarily keep residual risk small. Therefore, they should consider edge investments, such as global small stocks, global real estate, venture capital, commodity futures, and certain derivatives.
Inducer-Specific Regulators of Tumor Necrosis Factor Alpha Production. (1996)

Novel potent regulators of tumor necrosis factor alpha (TNF-alpha) production by a human promyelocytic leukemia cell line, HL-60, were prepared. All the compounds showed inducer-specific and bidirectional regulation of TNF-alpha production, i.e., they enhanced 12-O-tetradecanoylphorbol-13-acetate-induced TNF-alpha production, while they inhibited okadaic acid-induced one.
Monoclonal antibodies to receptors for insulin and somatomedin-C. (1983)

Three monoclonal antibodies, designated alpha IR-1, alpha IR-2, and alpha IR-3, were prepared by fusing FO myeloma cells with spleen cells from a mouse immunized with a partially purified preparation of insulin receptors from human placenta. These antibodies were characterized by their ability to immunoprecipitate solubilized receptors labeled with 125I-insulin or 125I-somatomedin-C in the presence or absence of various concentrations of unlabeled insulin or somatomedin-C. alpha IR-1 preferentially immunoprecipitates insulin receptors and also less effectively immunoprecipitates somatomedin-C receptors, while alpha IR-2 and alph IR-3 preferentially immunoprecipitate somatomedin-C receptors, but may also weakly immunoprecipitate insulin receptors. These three monoclonal antibodies, as well as A410, a rabbit polyclonal antibody, were used to immunoprecipitate insulin and somatomedin-C receptors from solubilized human lymphoid (IM-9) cells and human placenta membranes that had been 125I-labeled with lactoperoxidase. Analysis of the immunoprecipitates by sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicates that both receptors are composed of alpha and beta subunits. The beta subunit of the insulin receptor (immunoprecipitated by alpha IR-1 and A410) has a slightly more rapid mobility than the corresponding subunit of the somatomedin-C receptor (immunoprecipitated by alpha IR-2 and alpha IR-3). Interestingly, the alpha subunit of the placenta somatomedin-C receptor has a slightly faster mobility than its counterpart from IM-9 cells. Immunoprecipitation of receptor that had been reduced and denatured to generate isolated subunits indicates that alpha IR-2 and alpha IR-3 interact with the alpha subunit of the somatomedin-C receptor while A410 interacts with both subunits of the insulin receptor. alpha IR-1 failed to react with reduced and denatured receptors.
Tissue distribution of the human GLUT3 glucose transporter. (1993)

The tissue distribution of the GLUT3 glucose transporter protein was examined in human tissues using a rabbit antiserum directed against the C-terminal peptide sequence of human GLUT3. This anti-serum was shown to recognize the human GLUT3 protein in Chinese hamster ovary cells transfected with GLUT3 cDNA and to immunoprecipitate an authentic glucose transport protein in brain and testis membranes, as assessed by glucose-inhibitable photolabeling with [3H] cytochalasin-B. The GLUT3 protein, migrating with an apparent mol wt of approximately 48 kilodaltons, was strongly expressed in brain and testis membranes as well as in spermatozoa. It was not detectable in membranes from erythrocytes, adipocytes, heart, skeletal muscle, liver, kidney, spleen, thyroid, and prostate. Very low levels may be present in placenta. In brain, GLUT3 protein was strongly expressed in grey matter regions and was only weakly expressed in white matter, suggesting that it may be important in providing glucose to regions of high metabolic activity, i.e. to areas associated with synaptic transmission. None was found in peripheral (femoral) nerve. It appeared to be stable for up to 47 h in autopsy brain tissue kept at 4 C. The tissue distribution of human GLUT3 protein thus appears to be highly restricted (brain and testis/spermatozoa), in contrast with a previous report. Its function may be to provide a high affinity glucose transport system in cells that are highly dependent on glucose as a fuel source.
Development of Infrared Lip Movement Sensor for Spoken Word Recognition (2007)

Lip movement of speaker is very informative for many application of speech signal processing such as multi-modal speech recognition and password authentication without speech signal. However, in collecting multi-modal speech information, we need a video camera, large amount of memory, video interface, and high speed processor to extract lip movement in real time. Such a system tends to be expensive and large. This is one reasons of preventing the use of multi-modal speech processing. In this study, we have developed a simple infrared lip movement sensor mounted on a headset, and made it possible to acquire lip movement by PDA, mobile phone, and notebook PC. The sensor consists of an infrared LED and an infrared photo transistor, and measures the lip movement by the reflected light from the mouth region. From experiment, we achieved 66% successfully word recognition rate only by lip movement features. This experimental result shows that our developed sensor can be utilized as a tool for multi-modal speech processing by combining a microphone mounted on the headset.
Expression of MAGE‐A12 in Oral Squamous Cell Carcinoma (2007)

Melanoma associated-A antigens (MAGE-A) are silent in normal tissues except testis. However, they are activated ina variety of different tumors. Thus, their expression is highly specific to cancer cells. Reverse transcription-nested polymerase chain reaction (RT-nPCR) is a highly sensitive technique that has been used successfully for the detection of MAGE genes in tissue samples. The aim of the study is to analyze the expression rate of MAGE-A12 in oral squamous cell carcinoma (OSCC) using a high sensitive RT-nPCR. Total of 57 tissue samples obtained from patients with OSCC and 20 normal oral mucosal (NOM) probes of otherwise healthy volunteers were included to this study. No expression of MAGE-A12 was observed in the non-neoplasticNOM tissues. MAGE-A12 was expressed in 49.1% of the investigated tumor samples. The correlation between malignant lesion and MAGE-A12 detection was significant (p<0.001). It is concluded that results of this study may indicate MAGE-A12 asa useful additional diagnostic marker especially for the early detection of OSCC distinguishing neoplastic transformation and detection of occult and/or rare disseminated cancer cells. In addition, MAGE-A12 expression in OSCC may also determine anew immunotherapeutic target and might be warranted to develop vaccine for OSCC
Cytotoxic CD4+ and CD8+ T lymphocytes, generated by mutant p21-ras (12VAL) peptide vaccination of a patient, recognize 12VAL-dependent nested epitopes present within the vaccine peptide and kill autologous tumour cells carrying this mutation (1997)

Mutant p21-ras proteins contain sequences that distinguish them from normal ras, and represent unique epitopes for T-cell recognition of antigen-bearing tumour cells. Here, we examined the capacity of CD4+ and CD8+ T cells, generated simultaneously by mutant-ras-peptide vaccination of a pancreatic-adenocarcinoma patient, to recognize and lyse autologous tumour cells harbouring corresponding activated K-ras epitopes. The patient was vaccinated with a purified 17mer ras peptide (KLVVVGAVGVGKSALTI), containing the Gly12 --> Val substitution. Responding T cells were cloned following peptide stimulation, and CD4+ and CD8+ peptide-specific cytotoxic T lymphocytes(CTL) were obtained. Transient pancreatic-adenocarcinoma cell lines(CPE) were established in cell culture from malignant ascites of the patient, and were shown to harbour the same K-ras mutation as found in the primary tumour. These cells were efficiently killed by the T-cell clones and CD8+-mediated cytotoxicity was HLA-class-I-restricted, as demonstrated by inhibition of lysis by anti-class-I monoclonal antibodies. By employing as targets different class-I-matched tumour cell lines expressing a 12Val mutation, we were able to demonstrate HLA-B35 as the restriction molecule, and further use of peptide-sensitized EBV-B cells as target cells identified VVVGAVGVG as the nonamer peptide responsible for CD8+-T-cell recognition. These data demonstrate that peptide vaccination with a single mutant p21-ras-derived peptide induces CD4+ and CD8+ CTL specific for nested epitopes, including the Gly --> Val substitution at codon 12, and that both these T-cell sub-sets specifically recognize tumour cells harbouring the corresponding K-ras mutation.
Minimum weight modified signed-digit representations and fast exponentiation (1989)

A method for speeding up integer exponentiation by using a modified signed-digit (MSD) representation of the exponent is described. The method works best when the weight of the representation is minimised. An algorithm for finding a minimum weight MSD representation is presented.
DNA vaccine–derived human IgG produced in transchromosomal bovines protect in lethal models of hantavirus pulmonary syndrome (2014)

Polyclonal immunoglobulin-based medical products have been used successfully to treat diseases caused by viruses for more than a century. We demonstrate the use of DNA vaccine technology and transchromosomal bovines (TcBs) to produce fully human polyclonal immunoglobulins (IgG) with potent antiviral neutralizing activity. Specifically, two hantavirus DNA vaccines [Andes virus (ANDV) DNA vaccine and Sin Nombre virus (SNV) DNA vaccine] were used to produce a candidate immunoglobulin product for the prevention and treatment of hantavirus pulmonary syndrome (HPS). A needle-free jet injection device was used to vaccinate TcB, and high-titer neutralizing antibodies (titers >1000) against both viruses were produced within 1 month. Plasma collected at day 10 after the fourth vaccination was used to produce purified α-HPS TcB human IgG. Treatment with 20,000 neutralizing antibody units (NAU)/kg starting 5 days after challenge with ANDV protected seven of eight animals, whereas zero of eight animals treated with the same dose of normal TcB human IgG survived. Likewise, treatment with 20,000 NAU/kg starting 5 days after challenge with SNV protected immunocompromised hamsters from lethal HPS, protecting five of eight animals. Our findings that the α-HPS TcB human IgG is capable of protecting in animal models of lethal HPS when administered after exposure provides proof of concept that this approach can be used to develop candidate next-generation polyclonal immunoglobulin-based medical products without the need for human donors, despeciation protocols, or inactivated/attenuated vaccine antigen.
High-amylose wheat generated by RNA interference improves indices of large-bowel health in rats (2006)

Foods high in resistant starch have the potential to improve human health and lower the risk of serious noninfectious diseases. RNA interference was used to down-regulate the two different isoforms of starch-branching enzyme (SBE) II (SBEIIa and SBEIIb) in wheat endosperm to raise its amylose content. Suppression of SBEIIb expression alone had no effect on amylose content; however, suppression of both SBEIIa and SBEIIb expression resulted in starch containing >70% amylose. When the >70% amylose wheat grain was fed to rats in a diet as a wholemeal, several indices of large-bowel function, including short-chain fatty acids, were improved relative to standard wholemeal wheat. These results indicate that this high-amylose wheat has a significant potential to improve human health through its resistant starch content.
High preoperative plasma tissue inhibitor of metalloproteinase-1 levels are associated with short survival of patients with colorectal cancer. (2000)

The objective of the present study was to measure preoperative plasma tissue inhibitor of metalloproteinase (TIMP)-1 levels in colorectal cancer patients and relate these values to clinical and biochemical patient characteristics. TIMP-1 levels were determined by ELISA in EDTA plasma samples collected preoperatively from 588 colorectal cancer patients. Plasma TIMP-1 levels were distributed with a median value of 141.1 microg/liter (range, 53.7-788.7 microg/liter). Whereas no significant differences were found in the median plasma TIMP-1 levels among patients with Dukes' stage A, B, and C disease, patients with Dukes' stage D disease had significantly higher plasma TIMP-1 levels (P < 0.0001); however, high plasma TIMP-1 levels were not restricted to advanced disease. A relatively weak correlation between plasma TIMP-1 level and age was found (r = 0.35; P < 0.0001). There was no significant difference in TIMP-1 levels between males and females (P = 0.97). Univariate analysis demonstrated an increasing risk of mortality with increasing TIMP-1 levels [scored as the log(e)(TIMP-1); hazard ratio = 3.3; 95% confidence interval, 2.6-4.2; P < 0.0001]. Including covariates (Dukes' stage, primary tumor location, gender, age, plasminogen activator inhibitor type 1, and soluble urokinase plasminogen activator receptor) in a multivariate analysis, TIMP-1 was retained in the final model (hazard ratio = 2.5; 95% confidence interval, 1.7-3.7; P < 0.0001). This study showed a highly significant association between preoperative plasma TIMP-1 levels and survival in colorectal cancer patients, with higher plasma TIMP-1 levels being associated with poor outcome. Independent of clinical parameters including Dukes' stage, plasma TIMP-1 levels were found to strongly predict prognosis of colorectal cancer patients. Additional studies are needed to validate the clinical usefulness of plasma TIMP-1 measurements.
Sequence Variants in Cell Cycle Control Pathway, X-ray Exposure, and Lung Cancer Risk: A Multicenter Case-Control Study in Central Europe (2006)

Exposure to ionizing radiation (IR) results in various types of DNA damage and is a suspected cause of lung cancer. An essential cellular machinery against DNA damage is cell cycle control, which is regulated by several genes, including TP53, CCND1, and CDKN2A. Therefore, we hypothesized that the genetic variants in these three genes influence the predisposition of lung cancer (i.e., CCND1 G870A, CDKN2A Ala(148)Thr, TP53 Arg(72)Pro, and 16-bp repeat in intron 3) and that the effect of X-ray on lung cancer risk can be modified by the presence of these genetic variations. The study was conducted in 15 centers in 6 countries of Central Europe between 1998 and 2002. A total of 2,238 cases and 2,289 controls were recruited and provided DNA samples. Cases with positive family history were analyzed separately. The joint effect of X-ray and previous risk genotypes was assessed, and modification by sequence variants on X-ray dose-response relationship with lung cancer risk was evaluated. We found an overall effect of TP53 intron 3 16-bp repeats [odds ratio (OR), 1.99; 95% confidence interval (95% CI), 1.27-3.13], which was stronger among cases with family history of lung cancer (OR, 2.98; 95% CI, 1.29-6.87). In addition, our results suggested an interaction that was greater than multiplicativity between TP53 intron 3 16-bp repeats and multiple X-ray exposures (interaction OR, 5.69; 95% CI, 1.33-24.3). We did not observe a main effect of CCND1 G870A polymorphism; however, the dose-response relationship between lung cancer risk and X-ray exposures was modified by CCND1 genotype with no risk from X-ray exposures among subjects who carried G/G genotype, intermediate risk [trend OR for X-ray, 1.16; 95% CI, 1.05-1.27) among subjects with G/A genotype, and highest risk [trend OR for X-ray, 1.29; 95% CI, 1.12-1.49) among subjects with A/A genotype. Sequence variants in cell cycle control pathway may increase the risk of lung cancer and modify the risk conferred by multiple X-ray exposures. However, a definite conclusion can only be drawn on replication by different studies among individuals who are highly exposed to IR.