gebhart/patrepeval huggingface dataset:
Reduced expression levels of let-7c in human breast cancer patients (2015)

Circulating microRNAs (miRNAs) are important in the diagnosis of a number of diseases, since serum or plasma miRNAs are more stable compared with miRNA isolated from blood samples. The aim of the present study was to investigate the association between the expression levels of serum let-7c miRNA and the clinical diagnosis of breast cancer (BC). The circulating let-7c levels of 90 BC patients and 64 healthy controls were determined by performing a reverse transcription-quantitative polymerase chain reaction assay. The results demonstrated that let-7c expression was downregulated in the BC tissues compared with the paracarcinoma control tissues. In addition, the let-7c expression in the serum of BC patients was significantly lower compared with the healthy controls (P<0.01). Using a cutoff value of 0.374×10<sup>3</sup> copies/ml, the serum expression levels of let-7c exhibited 87.5% sensitivity and 78.9% specificity for distinguishing BC patients from healthy controls (area under the receiver operating characteristic curve, 0.848; 95% confidence interval, 0.785-0.911). Furthermore, the results demonstrated that the serum expression levels of let-7c were significantly higher in premenopausal compared with postmenopausal patients (P<0.05), supporting the hypothesis that postmenopausal status may affect the serum expression levels of let-7c. However, no statistically significant differences were detected in the serum levels of let-7c between ER (or PR)-positive and -negative patients. Therefore, the current study hypothesized that serum let-7c may be used as a novel and valuable biomarker for the diagnosis of BC.
Evaluation of Endogenous Plasma Peptide Extraction Methods for Mass Spectrometric Biomarker Discovery (2006)

Peptides have a role in the inflammatory response, tumor biology, and endocrine processes, presenting them as appealing biomarker candidates. However, peptide extraction efficacy for clinical profiling remains a pivotal technological challenge, as maximum coverage of the plasma peptidome is limited by a range of factors including the inherent complexity of human plasma and the lower concentration of peptides compared to abundant proteins. The aim of this study was to evaluate commonly employed peptide extraction methodologies in terms of total number of peptides detected and the mass range of peptides observed by MALDI. Despite showing coelution of proteins, solid-phase extraction (SPE) methods exhibited superior plasma peptide recovery than ultrafiltration, acetonitrile (ACN) precipitation, or size-exclusion chromatography methods under conditions employed in the study. Not surprisingly, in line with studies challenging the veracity of many peptide biomarker studies, the majority of identified peptides eluted from SPE methods corresponded to proteolytic truncations of the most abundant plasma proteins. The prefractionation of plasma with acetonitrile precipitation prior to SPE provided distinct ion signal profiles and is worthy of further study. In conclusion, this study favors the use of SPE in peptide extraction protocols for increased biomarker coverage and diversity from the plasma peptidome.
Phenyliodonium Zwitterion as an Efficient Electrophile in the Palladium-Catalyzed Suzuki-Type Reaction:  A Novel Method for the Synthesis of 3-Aryl-4-hydroxycoumarins (2002)

[reaction: see text] A palladium-catalyzed coupling reaction of phenyliodonium zwitterions with aryl boronic acids has been developed. The unique characteristics of the mild reaction conditions and convenient synthetic accessibility of phenyliodonium zwitterions make this method a valuable tool for generating diversified 3-aryl-4-hydroxycoumarins.
Synthesis of both enantiomers of .gamma.-substituted .alpha.,.beta.-unsaturated .gamma.-lactones (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of both enantiomers of .gamma.-substituted .alpha.,.beta.-unsaturated .gamma.-lactonesR. Bloch and L. GilbertCite this: J. Org. Chem. 1987, 52, 20, 4603–4605Publication Date (Print):October 1, 1987Publication History Published online1 May 2002Published inissue 1 October 1987https://pubs.acs.org/doi/10.1021/jo00229a031https://doi.org/10.1021/jo00229a031research-articleACS PublicationsRequest reuse permissionsArticle Views493Altmetric-Citations89LEARN 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
Genomic Analysis by Deep Sequencing of the Probiotic Lactobacillus brevis KB290 Harboring Nine Plasmids Reveals Genomic Stability (2013)

We determined the complete genome sequence of Lactobacillus brevis KB290, a probiotic lactic acid bacterium isolated from a traditional Japanese fermented vegetable. The genome contained a 2,395,134-bp chromosome that housed 2,391 protein-coding genes and nine plasmids that together accounted for 191 protein-coding genes. KB290 contained no virulence factor genes, and several genes related to presumptive cell wall-associated polysaccharide biosynthesis and the stress response were present in L. brevis KB290 but not in the closely related L. brevis ATCC 367. Plasmid-curing experiments revealed that the presence of plasmid pKB290-1 was essential for the strain's gastrointestinal tract tolerance and tendency to aggregate. Using next-generation deep sequencing of current and 18-year-old stock strains to detect low frequency variants, we evaluated genome stability. Deep sequencing of four periodic KB290 culture stocks with more than 1,000-fold coverage revealed 3 mutation sites and 37 minority variation sites, indicating long-term stability and providing a useful method for assessing the stability of industrial bacteria at the nucleotide level.
High-pressure Raman and infrared study ofHfW2O8 (2001)

The high-pressure Raman and infrared spectra of hafnium tungstate $({\mathrm{HfW}}_{2}{\mathrm{O}}_{8})$ are measured up to 24 GPa at room temperature. The changes under pressure of the stretching and bending modes of the ${\mathrm{WO}}_{4}$ tetrahedra, as well as lattice modes have been studied. An estimate of the thermal-expansion coefficient has been made based upon the mode Gr\"uneisen parameters and found to be in reasonable agreement with the measured value. The high-pressure spectra indicate that the \ensuremath{\alpha}-\ensuremath{\gamma} phase transition occurs at 0.6--0.9 GPa, in agreement with previous work. Around 2 GPa, ${\mathrm{HfW}}_{2}{\mathrm{O}}_{8}$ undergoes an irreversible transition from the \ensuremath{\gamma} phase to an amorphous structure.
A Quantitative Assay for Tyrosine Sulfation and Tyrosine Phosphorylation in Peptides (1990)

A method was developed to measure sulfation and phosphorylation of tyrosine in proteins after alkaline hydrolysis, ion-exchange chromatography, reaction with [3H]dinitrofluorobenzene and subsequent thin-layer chromatography. The method allows the detection of 10-20 pmol of modified tyrosine and was applied to determine the content of tyrosine-phosphate and -sulfate in fibrinogens, thyroglobulin, alpha-casein, cytochrome c and glyceraldehyde dehydrogenase.
Isolated limb perfusion in the sarcoma-bearing rat: a novel preclinical gene delivery system. (1997)

Reliable site-specific delivery of genetic constructs remains a challenging component of gene-based therapy of solid tumors. Isolated limb perfusion (ILP) continues to be evaluated for treatment of locally advanced soft tissue sarcomas because this approach uniquely directs therapeutic agents into the tumor-bearing extremity without significant systemic leak. In light of these considerations, we tested the hypothesis that ILP could be used to deliver genes carried in viral vectors to the sarcoma-bearing rat extremity, resulting in demonstrable gene transfer into the tumor. ILP was performed in rats by cannulating the femoral artery and vein, isolating the hind limb from systemic circulation by tourniquet, and cycling perfusate for 15 min at a rate of 2.4 ml/min. Leakage into the systemic circulation was 7.5% of the total perfusate concentrated in the isolated limb, as determined by perfusion with technetium 99m-tagged RBCs. We used the ILP technique to perfuse rat hind limbs bearing syngeneic fibrosarcoma tumor nodules with the replication-defective adenovirus Ad5LacZ, which expresses the bacterial beta-galactosidase. 5-Bromo-4-chloro-3-indolyl-beta-D-galactoside staining of the perfused limb tissues confirmed gene transfer to the tumor and peritumoral tissue, demonstrating that the tumor was part of the perfusion circuit and that gene therapy delivered via this method was feasible. These results suggest that adaptation of this preclinical gene delivery model to administer genetic constructs aimed at controlling tumor growth may prove beneficial to patients with extremity sarcomas.
Interleukin-2 enhancement of monoclonal antibody-mediated cellular cytotoxicity against human melanoma. (1987)

Disialoganglioside GD2 is present on human neuroblastoma and melanoma cells. 3F8 is a murine IgG3 monoclonal antibody specific for GD2, which has shown antitumor effects in patients in preliminary clinical studies. Since antibody mediated cellular cytotoxicity (ADCC) was one of the likely mechanisms producing these observed tumor regressions, the current study was carried out to investigate the activation of ADCC by interleukin-2 (IL-2). ADCC (against human neuroblastoma and melanoma cell lines in vitro) mediated by normal human peripheral blood lymphocytes was increased 100 to 330% after preincubation with IL-2. At limiting concentrations of 3F8 antibody (10 to 100 times less than the amount required by unactivated peripheral blood lymphocytes), activated peripheral blood lymphocytes still mediated efficient ADCC. Activation of ADCC was detected earlier than lymphokine activated killer cell (LAK) activity, required less IL-2 for optimum induction (50 versus 1000 units/ml), and was of equal or greater absolute magnitude (+10 to +200%) against the cell lines tested. ADCC and LAK were independent and additive when measured against the same cell line. The precursor cells for both LAK and activated ADCC bore IgG Fc receptors, but by day 4 of culture with IL-2 much of the LAK activity resided in the Fc negative, Leu11 negative population, and did not mediate ADCC. IL-2 activated ADCC may be of value alone or in conjunction with LAK cells in the therapy of tumors which bind the antibody 3F8.
Comparison of Rabbit Monoclonal and Mouse Monoclonal Antibodies in Immunohistochemistry in Canine Tissues (2005)

Rabbit monoclonal (RM) antibodies appear to have higher affinity for antigens than mouse monoclonal (MM) antibodies. However, RM antibodies have not been used in veterinary diagnostic immunohistochemistry. The authors compared reactivities of RM and MM antibodies on formalin-fixed, paraffin-embedded canine tissues, targeting 11 different antigens: CD3, CD79a, calcitonin, calretinin, chromogranin A, COX-2, estrogen receptor, Ki67, progesterone receptor, synaptophysin, and vimentin. Paraffin-embedded tissue sections were processed by 1 of 2 antigen-retrieval methods: 1) proteinase K digestion or 2) steam heat in citrate buffer. An additional set of slides did not receive antigen retrieval. Immunostaining was performed using an automated stainer, and scores were assigned to the different dilutions and antigen-retrieval methods on the basis of staining intensity and number of positive cells. Steam heat was usually the best antigen-retrieval method. The optimal dilution for each antibody was that which resulted in the highest specific staining and the lowest nonspecific (background) staining. The RM or MM antibodies yielded a specific reaction for all antigens examined except calretinin. The RM and MM antibodies yielded a specific reaction for 4 antigens only: COX-2, Ki67, synaptophysin, and vimentin. Three antigens (CD3, chromogranin A, and progesterone receptor) were detected only with RM antibodies, whereas the other 3 (CD79a, calcitonin, estrogen receptor) were detected only with MM antibodies. The results of this study differed from those reported for human tissues by the manufacturers of the antibodies. These results emphasize that, regardless of manufacturers' recommendations, each antibody must be individually standardized and validated before routine use in canine tissues.
Antioxidant Capacity and Polyphenols Components of Teas: Implications for Altering In Vivo Antioxidant Status (1999)

The Oxygen Radical Absorbance Capacity (ORAC) assay was used to determine the total antioxidant capacity of tea. Green and black teas (n = 18) had a mean antioxidant capacity of 761.1 ± 85.3 μmol Trolox Equivalents (TE) per g dry matter. However, their antioxidant capacity varied from 235 μmol to over 1526 μmol Trolox equivalents (TE)/g dry matter, and total phenolics ranged from 32 to 147 mg/g in different commercial teas. One tea phenolics extract had an antioxidant capacity of 4796 μmol TE/g dry matter and 625 mg total phenolics/g. On a dry matter basis, an antioxidant capacity of 761 μmol TE/g is considerably higher than any of the other fruits and vegetables measured in our laboratory. However, since dry tea is not consumed directly, brewing conditions may influence the final antioxidant capacity in the tea as consumed. We tested both green and black teas by placing one tea bag (1.95 g) in 150 ml (5 oz.) of boiling water. In the first brewed cup, approximately 84% of the total antioxidant activity was solubilized within the first 5 min of brewing. An additional 13% of the antioxidant activity was extracted into the second glass of 150 ml with an additional 5 min of brewing. At the dilutions obtained after the first brewing, the tea as consumed would contain approximately 8.31 μmol TE per ml. This total antioxidant capacity compares to other drinks from fruits and vegetables that had antioxidant capacity values ranging from 1.6 to 15 μmol TE/ml. At these antioxidant levels, consumption of 150 ml of tea could make a significant contribution to the total daily antioxidant capacity intake. (-)-Epicatechin and (+)-catechin, two components from tea, had an antioxidant capacity of 2.36 and 2.49 μmol/μmol or 8.13 and 8.58 μmol/mg, respectively. In 16 tea samples we observed a mean of 10.0 ± 0.6 μmol TE/mg total phenolics. Tea can be an important source of what has been referred to as “non-nutrient” antioxidant phytochemicals. However, with the variation that exists in antioxidant capacity with various tea preparations, measures of antioxidant capacity intake are critical to the study of intake and health outcomes and/or biomarkers of health outcomes.
ADENYLATE CYCLASE-COUPLED BETA-ADRENERGIC RECEPTORS: Structure and Mechanisms of Activation and Desensitization (1983)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Donor-specific transplantation tolerance: The paradoxical behavior of CD4+CD25+T cells (2004)

To investigate the antigen specificity of regulatory T cells capable of preventing transplant rejection, we have developed two different strategies to achieve tolerance to fully mismatched skin grafts in euthymic mice. A combination of nondepleting Abs targeting CD4, CD8, and CD154 (CD40 ligand) induces dominant transplantation tolerance to fully mismatched skin allografts. Such tolerance is antigen-specific, mediated by regulatory T cells, and can be extended through linked suppression to naïve lymphocytes. The same protocol, when combined with allogeneic bone marrow, enables the development of mixed hematopoietic chimerism and deletional tolerance. Although we cannot exclude that some regulatory T cells may persist in chimeric mice, these cells are insufficient to mediate linked suppression. CD4(+)CD25(+) T cells, whether taken from naïve mice or from mice tolerized through either treatment protocol, were always able to prevent rejection of skin grafts by naïve CD4(+) T cells, and did so with no demonstrable specificity for the tolerizing donor antigens. Such data question whether CD4(+)CD25(+) regulatory T cells alone can account for the antigen specificity of dominant transplantation tolerance.
Sulfur-tagged metal–organic frameworks and their post-synthetic oxidation (2009)

A series of sulfur-tagged zinc MOFs containing functionalised 4,4'-biphenyldicarboxylate ligands has been prepared: oxidative post-synthetic modification with dimethyldioxirane has converted the sulfide tags into sulfones, leaving the MOF networks intact.
Mapping the site of block by tetrodotoxin and saxitoxin of sodium channel II (1991)

The SS2 and adjacent regions of the 4 internal repeats of sodium channel II were subjected to single mutations involving, mainly, charged amino acid residues. These sodium channel mutants, expressed in Xenopus oocytes by microinjection of cDNA-derived mRNAs, were tested for sensitivity to tetrodotoxin and saxitoxin and for single-channel conductance. The results obtained show that mutations involving 2 clusters of predominantly negatively charged residues, located at equivalent positions in the SS2 segment of the 4 repeats, strongly reduce toxin sensitivity, whereas mutations of adjacent residues exert much smaller or no effects. This suggests that the 2 clusters of residues, probably forming ring structures, take part in the extracellular mouth and/or the pore wall of the sodium channel. This view is further supported by our finding that all mutations reducing net negative charge in these amino acid clusters cause a marked decrease in single-channel conductance.
<title>Pattern matching techniques for correcting low-confidence OCR words in a known context</title> (2000)

A commercial OCR system is a key component of a system developed at the National Library of Medicine for the automated extraction of bibliographic fields from biomedical journals. This 5-engine OCR system, while exhibiting high performance overall, does not reliably convert very small characters, especially those that are in italics. As a result, the 'affiliations' field that typically contains such characters in most journals, is not captured accurately, and requires a disproportionately high manual input. To correct this problem, dictionaries have been created from words occurring in this field (e.g., university, department, street addresses, names of cities, etc.) from 230,000 articles already processed. The OCR output corresponding to the affiliation field is then matched against these dictionary entries by approximate string-matching techniques, and the ranked matches are presented to operators for verification. This paper outlines the techniques employed and the results of a comparative evaluation.
Targeting the Eukaryotic Translation Initiation Factor 4E for Cancer Therapy (2008)

The eukaryotic translation initiation factor 4E (eIF4E) is frequently overexpressed in human cancers in relation to disease progression and drives cellular transformation, tumorigenesis, and metastatic progression in experimental models. Enhanced eIF4E function results from eIF4E overexpression and/or activation of the ras and phosphatidylinositol 3-kinase/AKT pathways and selectively increases the translation of key mRNAs involved in tumor growth, angiogenesis, and cell survival. Consequently, by simultaneously and selectively reducing the expression of numerous potent growth and survival factors critical for malignancy, targeting eIF4E for inhibition may provide an attractive therapy for many different tumor types. Recent work has now shown the plausibility of therapeutically targeting eIF4E and has resulted in the advance of the first eIF4E-specific therapy to clinical trials. These studies illustrate the increased susceptibility of tumor tissues to eIF4E inhibition and support the notion that the enhanced eIF4E function common to many tumor types may represent an Achilles' heel for cancer.
High-Power Continuous-Wave Directly-Diode-Pumped Fiber Raman Lasers (2015)

We describe novel fiber Raman lasers pumped directly by spectrally combined high power multimode laser diodes at ~975 nm and emitting at ~1019 nm. With a commercial multimode graded-index fiber, we reached 20 W of laser output power with a record slope efficiency of 80%. With an in-house double-clad fiber, the beam quality improved to M2 = 1.9, albeit with lower output power and slope efficiency due to higher fiber loss. We believe this is the first publication of a fiber Raman laser cladding-pumped directly by diodes.
53.4: Ultra‐Thin Flexible OLED Device (2007)

Abstract A new method of making ultra‐thin flexible organic light emitting diodes (OLEDs) using standard OLED fabrication facilities is reported. Through use of the Electronics on Plastic by Laser Release (EPLaR) technology, we have developed and demonstrated 18‐μm thick single‐pixel OLEDs. In this paper, besides describing the fabrication method, the electrical and optical performance of the flexible OLEDs is reported.
Solid-phase block copolymer synthesis by the iniferter technique (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolid-phase block copolymer synthesis by the iniferter techniqueTakayuki Otsu, Tetsuo Ogawa, and Tsuyoshi YamamotoCite this: Macromolecules 1986, 19, 7, 2087–2089Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/ma00161a056https://doi.org/10.1021/ma00161a056research-articleACS PublicationsRequest reuse permissionsArticle Views291Altmetric-Citations44LEARN 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