gebhart/patrepeval huggingface dataset:
Candidate Serum Biomarkers for Prostate Adenocarcinoma Identified by mRNA Differences in Prostate Tissue and Verified with Protein Measurements in Tissue and Blood (2012)

Abstract BACKGROUND Improved tests are needed for detection and management of prostate cancer. We hypothesized that differential gene expression in prostate tissue could help identify candidate blood biomarkers for prostate cancer and that blood from men with advanced prostate disease could be used to verify the biomarkers presence in circulation. METHODS We identified candidate markers using mRNA expression patterns from laser-capture microdissected prostate tissue and confirmed tissue expression using immunohistochemistry (IHC) for the subset of candidates having commercial antisera. We analyzed tissue extracts with tandem mass spectrometry (MS/MS) and measured blood concentrations using immunoassays and MS/MS of trypsin-digested, immunoextracted peptides. RESULTS We selected 35 novel candidate prostate adenocarcinoma biomarkers. For all 13 markers having commercial antisera for IHC, tissue expression was confirmed; 6 showed statistical discrimination between nondiseased and malignant tissue, and only 5 were detected in tissue extracts by MS/MS. Sixteen of the 35 candidate markers were successfully assayed in blood. Four of 8 biomarkers measured by ELISA and 3 of 10 measured by targeted MS showed statistically significant increases in blood concentrations of advanced prostate cancer cases, compared with controls. CONCLUSIONS Seven novel biomarkers identified by gene expression profiles in prostate tissue were shown to have statistically significant increased concentrations in blood from men with advanced prostate adenocarcinoma compared with controls: apolipoprotein C1, asporin, cartilage oligomeric matrix protein, chemokine (C-X-C motif) ligand 11 (CXCL11), CXCL9, coagulation factor V, and proprotein convertase subtilisin/kexin 6.
DNA Microarrays in Clinical Oncology (2002)

Aberrant gene expression is critical for tumor initiation and progression. However, we lack a comprehensive understanding of all genes that are aberrantly expressed in human cancer. Recently, DNA microarrays have been used to obtain global views of human cancer gene expression and to identify genetic markers that might be important for diagnosis and therapy. We review clinical applications of these novel tools, discuss some important recent studies, identify promising avenues of research in this emerging field of study, and discuss the likely impact that expression profiling will have on clinical oncology.
Interpreting the clinical significance of the differential inhibition of cyclooxygenase-1 and cyclooxygenase-2 (1999)

The International Consensus Meeting on the Mode of Action of COX-2 Inhibition (ICMMAC) brought together 17 international experts in arthritis, gastroenterology and pharmacology on 5 6 December 1997. The meeting was convened to provide a definition of COX-2 specificity and to consider the clinical relevance of COX-2-specific agents. These compounds are a new class of drugs that specifically inhibit the enzyme COX-2 while having no effect on COX-1 across the whole therapeutic dose range. The objectives of the meeting were to review the currently available data regarding the roles and biology of COX-1 and COX-2, and to foster a consensus definition on COX-2 specificity. At the present time, no guidelines exist for the in vitro and in vivo assessment of COX specificity, and it was felt that consensus discussion might clarify some of these issues. The meeting also reviewed recent clinical data on COX-2-specific inhibitors. The following article reflects discussion at this meeting and provides a consensus definition of COX-2-specific inhibitors.
Pre-clinical and clinical diagnosis of scrapie by detection of PrP protein in tissues of sheep (1991)

The usefulness of detecting the scrapie-associated fibrillar protein (PrP) in the lymphoreticular organs of sheep as a diagnostic tool was investigated. The PrP was detected by means of a rabbit-anti-sheep PrP polyclonal antibody by Western blot analysis. PrP was detected in samples from the central nervous system (CNS) of five of six sheep showing clinical signs of natural scrapie infection, in spleen samples from four of the six sheep and in lymph node samples taken from three of the sheep. PrP was detected in the spleen and lymph node samples, but not in the CNS samples from one of the six sheep that was clinically and histopathologically abnormal. This animal appeared to be in the early clinical stage of the disease. A total of 47 clinically normal sheep were examined for the presence of PrP. It was detected in spleen samples from three of the 47 sheep and in lymph node samples from three of the 39 sheep tested. Similarly, PrP was detected in a sample of lymph node obtained surgically from one of three experimentally infected sheep 14 months after inoculation. The PrP-positive sheep and one of the remaining PrP-negative sheep showed clinical signs of scrapie six and five months later respectively. One sheep euthanased 18 months after experimental infection was positive for PrP in the CNS, spleen and lymph node, but five other sheep which were killed or died two, eight, 16, 18 and 21 months after infection were negative or doubtful for the detection of PrP.
Nonresonant Control of Multimode Molecular Wave Packets at Room Temperature (2002)

We demonstrate the creation and measurement of shaped multimode vibrational wave packets with overtone and combination mode excitation in CCl4. Excitation of wave packets through nonresonant impulsive stimulated Raman scattering allows for coherent control of molecular vibrations without passing through an electronic resonance. This technique is therefore very general and can be implemented in a large class of molecular gases and liquids at STP, which were previously inaccessible because their resonances are in the VUV.
Genetics of lipoprotein disorders. (1993)

Lipoproteins are circulating complexes of lipids and proteins, the transport and metabolism of which are directly controlled by apolipoproteins A-I, A-II, A-IV, B, C-I, C-II, C-III, D, E, and (a); lipoprotein-processing proteins lipoprotein lipase, hepatic lipase, lecithin-cholesterol acyltransferase, and cholesteryl ester-transfer protein; and lipoprotein receptors, low density lipoprotein (LDL) receptor, chylomicron remnant receptor, and scavenger receptors. Studies have shown a close association between lipoprotein abnormalities and coronary artery disease susceptibility. Four types of abnormalities are frequently seen: increased LDL cholesterol levels; decreased high density lipoprotein cholesterol levels, usually accompanied by increased triglyceride or very low density lipoprotein levels; increased concentrations of chylomicron remnants and intermediate density lipoproteins; and increased concentrations of an abnormal lipoprotein, lipoprotein (a). One or more of these abnormalities is present in 50-80% of myocardial infarction survivors. The exact pathogenic process whereby each of these abnormalities causes coronary artery disease is a subject of active investigation but beyond the scope of this brief presentation. However, the genetic contribution to each of these abnormal lipoprotein phenotypes is coming into focus and is discussed.
School Counselors' Perceptions about lnterventions for At-Risk Students Including Grade Retention: Implications for School Leaders (2014)

The term at-risk is used by educators and policymakers to describe a wide variety of students who struggle in schools (Kronholz, 2011). Factors associated with labeling students at-risk include minority status, poverty, language difficulties, low school attendance, and poor family support (Re~ Akpo-Sanni, Losike-Sedimo, 2012; Stockard, 2010). For many at-risk students, reading at a proficient level is a primary concern for school leaders and teachers (Allington, 2011; McAlenney & Coyne, 2011), especially with increased accountability including school sanctions for not closing reading achievement gaps (Chappell, Nunnery, Pribesh, & Hager, 2011). Although a plethora of interventions have been proposed to assist at-risk students, requiring students to repeat a grade continues to be used as a threat for students who are not proficient, despite evidence that suggests grade retention is detrimental to students on various outcomes (Battistin & Schizzerotto, 2012; Webley, 2012).
Generation of Megawatt Optical Solitons in Hollow-Core Photonic Band-Gap Fibers (2003)

The measured dispersion of a low-loss, hollow-core photonic band-gap fiber is anomalous throughout most of the transmission band, and its variation with wavelength is large compared with that of a conventional step-index fiber. For an air-filled fiber, femtosecond self-frequency--shifted fundamental solitons with peak powers greater than 2megawatts can be supported. For Xe-filled fibers, nonfrequency-shifted temporal solitons with peak powers greater than 5.5 megawatts can be generated, representing an increase in the power that can be propagated in an optical fiber of two orders of magnitude. The results demonstrate a unique capability to deliver high-power pulses in a single spatial mode over distances exceeding 200 meters.
Current strategies for the treatment of Alzheimer’s disease and other tauopathies (2006)

The pathological hallmarks of Alzheimer's disease (AD) include abnormal intra- and extraneuronal tau and amyloid accumulation, respectively, accompanied by gliosis, oxidative stress and neuron loss. The discovery of mutations within the tau gene itself that cause clinical dementia (i.e., fronto-temporal dementia with Parkinsonism linked to chromosome 17 [FTDP17]) demonstrated that disruption of normal tau function independent of amyloidogenesis was sufficient to cause neuronal loss and clinical dementia. These studies demonstrate the need for therapeutics that either decrease the total pool of tau or selectively reduce aberrant forms of tau (i.e., hyperphosphorylated, misfolded etc.). To this point, therapeutic development for tauopathies, including AD, have primarily focused on either the phosphorylation of tau, as it is a downstream target for many kinases and signalling cascades, or inhibition of tau aggregation. Recent developments, however, suggest that pharmacological targeting of other mechanisms may hold therapeutic promise for the treatment of tauopathies.
Soluble PD-1 aggravates progression of collagen-induced arthritis through Th1 and Th17 pathways (2015)

sPD-1 regulates peripheral T-cell responses in both human and murine RA. Thus, sPD-1 may represent an additional biomarker or target in immunomodulatory therapy for RA.
Sequence organization and cytological localization of the minor satellite of mouse (1988)

A complete 120 bp genomic consensus sequence for the mouse minor satellite has been determined from enriched L929 centromeric sequences. The extensive sequence homology existing between the major and minor satellite suggests an evolutionary relationship. Some sequences flanking the minor satellite has also been identified and they provide insight into centromeric DNA organization. Isotopic in situ hybridization analysis of the minor satellite to mouse L929 and Mus musculus metaphase spreads showed that this repetitive DNA class is localized specifically to centromeres of all chromosomes of the karyotype. With the use of high resolution non-isotopic fluorescence in situ hybridization the minor satellite is further localized to the outer surface of the centromere in a discrete region at or immediately adjacent to the kinetochore. Our cytological data suggests that the minor satellite might play a role in the organization of the kinetochore region rather than, as previously suggested, sites for general anchoring of the genome to the nuclear matrix.
Vesicular Stomatitis Virus: Mode of Transcription (1977)

Recent studies on the mechanism by which the virion-associated RNA polymerase of vesicular stomatitis virus transcribes RNA have revealed several new biological features of general interest. The mode of synthesis of the 5'-terminal cap structure of the mRNAs, the sequential transcription of the genes and the presence of a transcribed "leader" RNA segment are properties which are either not shown by other viruses, or have not yet been described. These features are probably inter-related with the primary transcription process, which itself may be a useful model for future studies on mRNA biosynthesis in eukaryotic systems.
Neoagarobiose as a Novel Moisturizer with Whitening Effect (1997)

Neoagarobiose, a disaccharide, showed a higher hygroscopic ability than glycerol or hyaluronic acid, typical moisturizing reagents. Beside, neoagarobiose whitened B16 murine melanoma cells, and showed low cytotoxicity. Therefore neoagarobiose was a rare reagent showing both moisturizing and whitening effects.
Mono-olefin chelate complexes of iron(0) and ruthenium(0) with an olefinic tertiary phosphine (1971)

Reaction of 2-vinylphenyl(diphenyl)phosphine, o-CH2: CH·C6H4·PPh2(sp), with M3(CO)12(M = Fe or Ru) gives monomeric complexes M(CO)3(sp) and M(CO)2(sp)2; the former are chelate mono-olefin complexes containing bidentate (sp), while Fe(CO)2(sp)2 is shown by our X-ray structural analysis to contain a bidentate (sp) ligand, and a monodentate P-bonded (sp) moiety, in a configuration approximating to a trigonal bipyramid.
Site and Mechanism of Antisense Inhibition by C-5 Propyne Oligonucleotides (1995)

Antisense gene inhibition occurs when an oligonucleotide (ON) has sufficient binding affinity such that it hybridizes its reverse complementary target RNA and prevents translation either by causing inactivation of the RNA (possibly by RNase H) or by interfering with a cellular process such as stalling a ribosome. The mechanisms underlying these processes were explored. Cellular antisense inhibition was evaluated in a microinjection assay using ON modifications which precluded or allowed in vitro RNase H cleavage of ON/RNA hybrids. RNase H-independent inhibition of protein synthesis could be achieved by targeting either the 5'-untranslated region or the 5'-splice junction of SV40 large T antigen using 2'-O-allyl phosphodiester ONs which contained C-5 propynylpyrimidines (C-5 propyne). Inhibition at both sites was 20-fold less active than inhibition using RNase H-competent C-5 propyne 2'-deoxy phosphorothioate ONs. In vitro analysis of association and dissociation of the two classes of ONs with complementary RNA showed that the C-5 propyne 2'-O-allyl phosphodiester ON bound to RNA as well as the C-5 propyne 2'-deoxy phosphorothioate ON. In vitro translation assays suggested that the two classes of ONs should yield equivalent antisense effects in the absence of RNase H. Next, ON/T antigen RNA hybrids were injected into the nuclei and cytoplasm of cells. Injection of C-5 propyne 2'-O-allyl phosphodiester ON/RNA hybrids resulted in expression of T antigen, implying that the ONs dissociated from the RNA in cells which likely accounted for their low potency. In contrast, when C-5 propyne 2'-deoxy phosphorothioate ON/T antigen RNA complexes were injected into the nucleus, the duplexes were stable enough to completely block T antigen translation, presumably by RNA inactivation. Thus, a dramatic finding is that C-5 propyne 2'-deoxy phosphorothioate ONs, once hybridized to RNA, are completely effective at preventing mRNA translation. The implication is that further increases in complex stability coupled with effective RNase H cleavage will not result in enhanced potency. We predict that the development of more effective ONs will only come from modifications which increase the rate of ON/RNA complex formation within the nucleus.
Species-specific antigens in salivary glands of phlebotomine sandflies (2001)

Saliva inoculated by sandfly females during feeding stimulated production of high levels of anti-saliva antibodies. To determine whether 3 species of the genus Phlebotomus have species-specific salivary antigens we performed dot-blots and immunoblots using sera from mice, hamsters and rabbits repeatedly bitten by sandflies. Important differences were found in the antigen components of the salivary gland lysates (SGL) of Phlebotomus papatasi, P. perniciosus and P. halepensis. In total 4-9 species-specific antigens were detected in each species by immunoblotting. Cross-reactivity was not detected between P. papatasi and the other species tested; in the SGL of P. papatasi sera from animals bitten by this species recognized 5-7 major antigens while sera from animals bitten by other species did not react. A weak cross-reaction was observed between P. perniciosus and P. halepensis; in SGL from P. perliciosus, the sera from rabbits and hamsters bitten by this species recognized about 8 intense bands while sera from animals bitten by P. halepensis reacted weakly with up to 4 saliva polypeptides.
Interleukin 10 Treatment of Psoriasis (1999)

Our data suggest that IL-10 therapy for psoriasis is safe and possibly clinically effective. Consequently, its value in psoriasis and similar immune diseases should be further determined. Dose-finding, placebo-controlled, double-blind trials are necessary now.
New Malaria Plan Called Ambitious By Some, Unrealistic by Others (2008)

It was standing room only last week at U.N. headquarters in New York City when a star-studded cast, including philanthropist Bill Gates, U2 rocker Bono, and British Prime Minister Gordon Brown, kicked off the latest in a string of grand plans to conquer malaria, the mosquito-transmitted scourge that kills some 1 million people a year, mostly African children.
Acetate Inhibition of Methanogenic, Syntrophic Benzoate Degradation (1988)

Acetate inhibited benzoate degradation by a syntrophic coculture of an anaerobic benzoate degrader (strain BZ-2) and Methanospirillum strain PM-1; the apparent K(i) for acetate was approximately 40 mM. The addition of acetate resulted in a decrease in the hydrogen concentration in the coculture, indicating that phenomena related to interspecies hydrogen transfer affected this value and that the effect of acetate on the benzoate-degrading partner was probably greater than the apparent K(i) for the coculture suggests.
Discrimination against purine–pyrimidine mispairs in the polymerase active site of DNA polymerase I: A structural explanation (2002)

We previously identified five derivatives of Klenow fragment DNA polymerase that have lower fidelity because of amino acid substitutions in the polymerase active site. One of these has alanine substituted for the invariant Glu-710, whose side chain interacts with the deoxyribose of the incoming dNTP. Here we show that the E710A enzyme has reduced fidelity for five of the 12 possible mismatches. All but one of these involve misinsertion of pyrimidines, including two transition mismatches A-dCTP and G-dTTP. In contrast, E710A polymerase error rates for the reciprocal C-dATP and T-dGTP transition mismatches were similar to those of the wild-type enzyme. The kinetics of formation of correct base pairs and transition mismatches by the wild-type and E710A polymerases, combined with information on the structure of the DNA polymerase active site and the asymmetry of wobble base pairs, provides a plausible explanation for the differential effects of the E710A mutation on fidelity. The data suggest that the Glu-710 side chain plays a pivotal role in excluding wobble base pairs between template pyrimidines and purine triphosphates by steric clash. Moreover, this same side chain enhances the stability of incoming correct dNTPs, such that loss of this interaction on removal of the side chain leads to lower selectivity against mismatches involving incoming pyrimidines.
Construction of a new interface for comprehensive supercritical fluid chromatography×reversed phase liquid chromatography (SFC×RPLC) (2008)

The design of a new interface to hyphen high efficiency supercritical fluid chromatography (SFC) and fast RPLC in a comprehensive configuration is described. SFC x RPLC is a viable alternative to normal phase (NP) LC x RPLC and is characterized by high orthogonality. Compared to NPLC x RPLC an additional advantage is the expansion of supercritical carbon dioxide (CO(2)) when exposed to atmospheric pressure leading to fractions consisting of solvents that are miscible with the second dimension RPLC mobile phase. The interface consists of a two-position/ten-port switching valve equipped with two packed octadecyl silica (C(18)) loops for effective trapping and focusing of the analytes after elution from the SFC dimension. The addition of a water make-up flow to the SFC effluent prior to entering the loops is of fundamental importance to efficiently focus the solutes on the C(18) material and to reduce interferences of expanded CO(2) gas on the second dimension separation. The features of the system are illustrated with the analysis of a lemon oil sample.
Parainfluenza Viruses (2003)

Human parainfluenza viruses (HPIV) were first discovered in the late 1950s. Over the last decade, considerable knowledge about their molecular structure and function has been accumulated. This has led to significant changes in both the nomenclature and taxonomic relationships of these viruses. HPIV is genetically and antigenically divided into types 1 to 4. Further major subtypes of HPIV-4 (A and B) and subgroups/genotypes of HPIV-1 and HPIV-3 have been described. HPIV-1 to HPIV-3 are major causes of lower respiratory infections in infants, young children, the immunocompromised, the chronically ill, and the elderly. Each subtype can cause somewhat unique clinical diseases in different hosts. HPIV are enveloped and of medium size (150 to 250 nm), and their RNA genome is in the negative sense. These viruses belong to the Paramyxoviridae family, one of the largest and most rapidly growing groups of viruses causing significant human and veterinary disease. HPIV are closely related to recently discovered megamyxoviruses (Hendra and Nipah viruses) and metapneumovirus.
Newly Identified Biomarkers for Detecting Circulating Tumor Cells in Lung Adenocarcinoma (2014)

Circulating tumor cells (CTCs) have been implicated in cancer prognosis and follow up. Detection of CTCs was considered significant in cancer evaluation. However, due to the heterogeneity and rareness of CTCs, detecting them with a single maker is usually challenged with low specificity and sensitivity. Previous studies concerning CTCs detection in lung cancer mainly focused on non-small cell lung carcinoma. Currently, there is no report yet describing the CTC detection with multiple markers in lung adenocarcinoma. In this study, by employing quantitative real-time PCR, we identified four candidate genes (mRNA) that were significantly elevated in peripheral blood mononuclear cells and biopsy tissue samples from patients with lung adenocarcinoma: cytokeratin 7 (CK7), Ca(2+)-activated chloride channel-2 (CLCA2), hyaluronan-mediated motility receptor (HMMR), and human telomerase catalytic subunit (hTERT). Then, the four markers were used for CTC detection; namely, positive detection was defined if at least one of the four markers was elevated. The positive CTC detection rate was 74.0% in patients with lung adenocarcinoma while 2.2% for healthy controls, 6.3% for benign lung disease, and 48.0% for non-adenocarcinoma non-small cell lung carcinoma. Furthermore, in a three-year follow-up study, patients with an increase in the detection markers of CTCs (CK7, CLCA2, HMMR or hTERT) on day 90 after first detection had shorter survival time compared to those with a decrease. These results demonstrate that the combination of the four markers with specificity and sensitivity is of great value in lung adenocarcinoma prognosis and follow up.