gebhart/patrepeval huggingface dataset:
Cardiac Gene Expression (2007)

Cardiac Gene Expression: Methods and Protocols presents both cutting-edge and established methods for studying cardiac gene expression. The protocols provide a template for solid research, and cover the process through screening, analysis, characterization, and functional confirmation of novel genes or known genes with a new function. Section I, Cardiac Gene Expression Profiling: The Global Perspective, discusses several different approaches to examining, identifying, and analyzing changes in transcriptome gene expression. Section II, Cardiac Gene Regulation: Gene-Specific mRNA Measurement in the Myocardium, outlines more sensitive and gene-targeted expression methods. Section III, Cardiac Gene Regulation: Promoter Characterization in the Myocardium, provides protocols for the study of underlying gene regulation mechanisms by focusing on the interaction of transcription factors with their cognate cis binding elements. Section IV, In Silico Assessment of Regulatory cis-Elements and Gene Regulation, and Section V, Cardiac Single Network Polymorphisms, emphasize new analytical approaches for deciphering the functional elements buried in the 3 billion nucleotides of the human genome and other model genomes. The concluding section, Gene Overexpression and Targeting in the Myocardium, highlights methods that facilitate overexpression or cardiac-specific targeted gene deletion
Rate of Pathology From Atypical Glandular Cell Pap Tests Classified by the Bethesda 2001 Nomenclature (2006)

II-2.
A comparison of fractional-pel interpolation filters in HEVC and H.264/AVC (2012)

The fractional-pel interpolation filter adopted in H.264/AVC improves motion compensation greatly. Recently, a new DCT-based fractional-pel interpolation filter is adopted in the oncoming standard HEVC. We are interested in the differences between these two types of fractional-pel interpolation filters. In this paper we describe the derivations of fractional-pel interpolation filters in HEVC and H.264/AVC in detail, and compare them on properties of frequency responses. We find that the half-pel interpolation filters in HEVC and H.264/AVC are very similar, but the low-pass properties of quarter-pel interpolation filters in HEVC are much better than those in H.264/AVC. Experimental results validate this phenomenon, the fractional-pel interpolation in H.264/AVC tends to increase BD-rates by more than 10% compared with that in HEVC, and this performance loss mainly comes from quarter-pel interpolation filters. On the other hand, the complexity of fractional-pel interpolation filtering in HEVC is greatly increased than that in H.264/AVC.
Heparanase Levels Are Elevated in the Urine and Plasma of Type 2 Diabetes Patients and Associate with Blood Glucose Levels (2011)

Heparanase is an endoglycosidase that specifically cleaves heparan sulfate side chains of heparan sulfate proteoglycans. Utilizing an ELISA method capable of detection and quantification of heparanase, we examined heparanase levels in the plasma and urine of a cohort of 29 patients diagnosed with type 2 diabetes mellitus (T2DM), 14 T2DM patients who underwent kidney transplantation, and 47 healthy volunteers. We provide evidence that heparanase levels in the urine of T2DM patients are markedly elevated compared to healthy controls (1162 ± 181 vs. 156 ± 29.6 pg/ml for T2DM and healthy controls, respectively), increase that is statistically highly significant (P<0.0001). Notably, heparanase levels were appreciably decreased in the urine of T2DM patients who underwent kidney transplantation, albeit remained still higher than healthy individuals (P<0.0001). Increased heparanase levels were also found in the plasma of T2DM patients. Importantly, urine heparanase was associated with elevated blood glucose levels, implying that glucose mediates heparanase upregulation and secretion into the urine and blood. Utilizing an in vitro system, we show that insulin stimulates heparanase secretion by kidney 293 cells, and even higher secretion is observed when insulin is added to cells maintained under high glucose conditions. These results provide evidence for a significant involvement of heparanase in diabetic complications.
Characterization of the functionalization reaction product of poly(styryl)lithium with ethylene oxide (1988)

Abstract The functionalization reaction of poly(styryl)lithiums ( M n = 1.3–9.9 × 10 3 ) with ethylene oxide in benzene proceeds quantitatively ( &gt; 99%) to produce the corresponding hydroxyethylated polymer as determined by vapor phase osmometry, size exclusion chromatography, end‐group titration, thin layer chromatography, and 1 H‐ and 13 C‐NMR spectroscopy. 13 C‐NMR spectral analysis of the functionalized polystyrene with M n = 1.3 × 10 3 was consistent with addition of only one ethylene oxide unit to poly(styryl)lithium, i.e., no evidence for ethylene oxide oligomerization was observed.
Human Anti-CD40 Antagonist Antibody Triggers Significant Antitumor Activity against Human Multiple Myeloma (2005)

Monoclonal antibodies (mAb) directed against lineage-specific B-cell antigens have provided clinical benefit for patients with hematologic malignancies, but to date no antibody-mediated immunotherapy is available for multiple myeloma. In the present study, we assessed the efficacy of a fully human anti-CD40 mAb CHIR-12.12 against human multiple myeloma cells. CHIR-12.12, generated in XenoMouse mice, binds to CD138-expressing multiple myeloma lines and freshly purified CD138-expressing cells from >80% multiple myeloma patients, as assessed by flow cytometry. Importantly, CHIR-12.12 abrogates CD40L-induced growth and survival of CD40-expressing patient multiple myeloma cells in the presence or absence of bone marrow stromal cells (BMSC), without altering constitutive multiple myeloma cell proliferation. Immunoblotting analysis specifically showed that PI3-K/AKT, nuclear factor-kappaB (NF-kappaB), and extracellular signal-regulated kinase activation induced by CD40L (5 mug/mL) was inhibited by CHIR-12.12 (5 mug/mL). Because CD40 activation induces multiple myeloma cell adhesion to both fibronectin and BMSCs, we next determined whether CHIR-12.12 inhibits this process. CHIR-12.12 decreased CD40L-induced multiple myeloma cell adhesion to fibronectin and BMSCs, whereas control human IgG1 did not. Adhesion of multiple myeloma cells to BMSCs induces interleukin-6 (IL-6) and vascular endothelial growth factor (VEGF) secretion, and treatment of multiple myeloma cells with CD40L further enhanced adhesion-induced cytokine secretion; conversely, CHIR-12.12 blocks CD40L-enhanced IL-6 and VEGF secretion in cocultures of multiple myeloma cells with BMSCs. Finally, CHIR-12.12 triggered lysis of multiple myeloma cells via antibody-dependent cellular cytotoxicity (ADCC) but did not induce ADCC against CD40-negative multiple myeloma cells, confirming specificity against CD40-expressing multiple myeloma cells. These results provide the preclinical rationale for clinical trials of CHIR-12.12 to improve patient outcome in multiple myeloma.
Analysis of exosome release and its prognostic value in human colorectal cancer (2011)

A significant proportion of extracellular nucleic acids in plasma circulate highly protected in tumor-specific exosomes, but it is unclear how the release of exosomes is modulated in carcinogenesis. We quantified by cytometry exosomes in plasma of 91 colorectal cancer patients to evaluate their potential as a tumor indicator and their repercussions on diagnosis and prognosis. We examined the involvement of TSAP6, a TP53-regulated gene involved in the regulation of vesicular secretion, in levels of circulating exosomes in plasma of colorectal patients and in HCT116 TP53-(wild-type and null) human colorectal cancer cell lines. The fraction of exosomes in cancer patients was statistically higher than in healthy controls (mean rank ¼ 53.93 vs. 24.35). High levels of exosomes in plasma of patients correlated with high levels of carcino-embryonic antigen (P ¼ 0.029) and with poorly differentiated tumors (P ¼ 0.039) and tended to have shorter overall survival than patients with low levels (P ¼ 0.056). Release of exosomes did not correlate with TSAP6 expression; and regulation of TSAP6 by TP53 was not shown either in tumor samples or in HCT116 cell lines. Although it was not suggested that the TP53/TSAP6 pathway regulates the release of exosomes into the plasma of colorectal cancer patients, the level of circulating exosomes may be used as a tumor indicator, because it correlates with poor prognosis parameters and shorter survival.
Fidelity of DNA Synthesis (1982)

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
Apolipoprotein C3 SstI polymorphism and triglyceride levels in Asian Indians (2002)

Our study shows a significant association between rare S2 allele and HTG in Asian Indians.
Differential Expression of Cancer-Related Proteins in Paired Breast Milk Samples from Women with Breast Cancer (2012)

These proteins may play a role in assessing a woman's risk of pregnancy-associated breast cancer. Because of variable protein concentration among patients and the limited sample size, the results are considered preliminary.
Beta-lactam antibiotics as a possible novel therapy for managing epilepsy and autism, a case report and review of literature. (2015)

Autism is a disorder of unknown etiology. There are few FDA approved medications for treating autism. Co-occurring autism and epilepsy is common, and glutamate antagonists improve some symptoms of autism. Ceftriaxone, a beta-lactam antibiotic, increases the expression of the glutamate transporter 1 which decreases extracellular glutamate levels. It is hypothesized that modulating astrocyte glutamate transporter expression by ceftriaxone or cefixime might improve some symptoms of autism. This case report of a child with autism and epilepsy suggests a decrease in seizures after taking cefixime.
Suggestive evidence for linkage of schizophrenia to markers at chromosome 15q13–14 in Taiwanese families (2001)

In order to evaluate the linkage of schizophrenia to loci at chromosome 15q, we genotyped six microsatellite markers at chromosome 15q11-14 in 52 Taiwanese schizophrenic families. Two phenotype models (narrow: DSM-IV schizophrenia only; and broad: including schizophrenia, schizoaffective, and other nonaffective psychotic disorders) were used to define the disease phenotype. Maximum nonparametric linkage scores (NPL scores) of 3.33 (P = 0.0003) and 2.96 (P = 0.0008) were obtained at the marker D15S976 under broad and narrow models, respectively. Positive linkage results were also observed at the marker D15S1360, previously reported to have significant linkage to a neurophysiological deficit of schizophrenia, with NPL scores of 2.71 (P = 0.003) and 2.78 (P = 0.002) under broad and narrow models, respectively. The results provide suggestive linkage evidence of schizophrenia to loci at chromosome 15q13-14 in an ethnically distinct Taiwanese sample.
Exposure to Human Immunodeficiency Virus Type I-Specific T Helper Cell Responses before Detection of Infection by Polymerase Chain Reaction and Serum Antibodies (1991)

A healthy individual at risk for human immunodeficiency virus type 1 (HIV-1) infection was studied longitudinally for 19 months for evidence of exposure to and infection with HIV. Peripheral blood mononuclear cells (PBMC) were tested at 1, 5, 13, 16, and 19 months for T helper (Th) cell function by in vitro-generated proliferation and interleukin-2 production in response to four synthetic peptides corresponding to env of HIV. PBMC were also tested for proviral DNA using gag primers by the polymerase chain reaction (PCR) at 0, 5, 10, 13, 16, and 19 months. HIV serology by ELISA and p24 antigen and Western blot analyses were done on samples taken at 0, 1, 5, 10, 13, 16, and 19 months. The results indicated that both Th cell tests were positive during months 5-19. In contrast, the PCR and all serologic assays were negative except for month 19, when the assays became positive. These results, based on the longitudinal study of one individual, showed that the Th cell tests can reveal exposure to HIV-1 antigens several months before evidence of viral infection is detected, even by PCR.
Nanowire Composite Thermoelectric Devices (2002)

This paper discusses the design, fabrication and testing of a novel thermoelectric device comprised of arrays of silicon nanowires embedded in a polymer matrix. By exploiting the low thermal conductivity of the composite and presumably high power factor of the nanowires, a high figure of merit should result. Arrays were first synthesized using a vapor-liquid-solid (VLS) process leading to one-dimensional growth of single-crystalline nanowires. To provide both structural support and thermal isolation between nanowires, parylene, a low thermal conductivity and extremely conformal polymer, was embedded within the arrays. Mechanical polishing and oxygen plasma etching techniques were used to expose the nanowire tips and a metal contact was deposited on the top surface. Scanning electron microscopy pictures illustrate the results of the fabrication processes. Using the 3ω technique, the effective thermal conductivity of the nanowire matrix was measured.
The relationship between bovine major histocompatibility complex class II polymorphism and disease studied by use of bull breeding values (1990)

The predictive value of class II DQ and DYA polymorphisms of the bovine major histocompatibility (MHC) complex (BoLA) for the incidence of disease in dairy cattle was estimated in a sample of 196 progeny-tested AI bulls of the Swedish Red and White breed. The BoLA DQ and DYA types of the bulls were determined by analysing restriction fragment length polymorphisms (RFLPs). Breeding values of bulls for clinical mastitis, all diseases including clinical mastitis and diseases other than clinical mastitis were used as measures of disease resistance or susceptibility. The relationship between MHC polymorphism and bull breeding values for disease resistance was evaluated statistically by linear regression analysis. A significant association between the haplotype DQ1A and susceptibility to clinical mastitis was revealed. No other DQ haplotype nor the DYA locus has a significant effect on any of the disease traits studied.
Evaluation of carboplatin pharmacokinetics in the absence and presence of paclitaxel. (1996)

In a clinical trial of paclitaxel (Taxol) and carboplatin in combination, the severity of thrombocytopenia was less than would be expected with an equivalent dose of carboplatin alone. To determine whether a pharmacokinetic interaction was responsible for this observation, the effect of pretreatment with Taxol on the pharmacokinetics of carboplatin was examined in 11 patients. Each patient was randomized to one of two treatment groups that determined the order of drug treatments. The treatments were carboplatin as a 30-min infusion alone or immediately following 175 mg/m2 Taxol administered as a 3-h i.v. infusion. The treatments were separated by 1 week. The carboplatin dose was chosen to produce a target area under the concentration-time curve (AUC) of 3.75 mg-min/ml according to a previously published formula (A. H. Calvert et al., J. Clin Oncol., 7: 1748-1756, 1989). The mean administered dose of carboplatin was 338 mg. Serial blood samples were collected over 24 h and analyzed for total and free platinum, and, in some patients, Taxol. The pharmacokinetics of carboplatin (i.e., total clearance and volume of distribution at steady state), was not significantly affected by pretreatment with Taxol. Total clearances of carboplatin were 67.2 +/- 28.8 ml/min and 64.6 +/- 27.9 ml/min in the absence and presence of Taxol, respectively (P = 0.56). The AUC of free carboplatin (3.45 mg-min/ml) obtained in the absence of Taxol was not significantly different from that measured in the presence of Taxol (3.27 mg-min/ml). The AUC of carboplatin in both the absence and presence of Taxol agreed with the projected target AUC of 3.75 mg-min/ml. In conclusion, the application of an individualized dosing strategy is valid for the calculation of the carboplatin dose in this combination. The pharmacokinetics of carboplatin is not altered by pretreatment with Taxol at a standard dose, and a pharmacokinetic interaction is not responsible for the altered toxicity of the combination.
Digital-ticket-controlled digital ticket circulation (1999)

This paper presents a new digital-ticket circulating scheme and trust management scheme for a digital ticket. A digital ticket is a digital medium that guarantees certain rights of the owner and it includes software licenses, resource access tickets, event tickets, and plane tickets. The circulation of digital tickets comprises three types of principal transactions: issuance, transfer, and redemption. Depending on the application, various conditions must be satisfied to execute these transactions, e.g., only qualified shops can issue the tickets and only a certain agent can transfer the tickets. This paper introduces circulation control tickets, which are required to issue, transfer, redeem a ticket, and proposes specifying the required control ticket types in the ticket to be circulated itself using the Generalized Ticket Definition Language. The ticket circulating system issues, transfers, or redeems a ticket only if the control tickets are owned by the participants of the transacti...
Reversible RNA ModificationN1-Methyladenosine (m1A) in mRNA and tRNA (2018)

Abstract More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from N6-methyladenosine (m6A), N1-methyladenosine (m1A) has been found as a reversible modification in tRNA and mRNA. m1A occurs at positions 9, 14, and 58 of tRNA, with m1A58 being critical for tRNA stability. Other than the hundreds of m1A sites in mRNA and long non-coding RNA transcripts, transcriptome-wide mapping of m1A also identifies &amp;gt;20 m1A sites in mitochondrial genes. m1A in the coding region of mitochondrial transcripts can inhibit the translation of the corresponding proteins. In this review, we summarize the current understanding of m1A in mRNA and tRNA, covering high-throughput sequencing methods developed for m1A methylome, m1A-related enzymes (writers and erasers), as well as its functions in mRNA and tRNA.
Trehalose and anhydrobiosis in tardigrades – evidence for divergence in responses to dehydration (2007)

To withstand desiccation, many invertebrates such as rotifers, nematodes and tardigrades enter a state known as anhydrobiosis, which is thought to require accumulation of compatible osmolytes, such as the non-reducing disaccharide trehalose to protect against dehydration damage. The trehalose levels of eight tardigrade species comprising Heterotardigrada and Eutardigrada were observed in five different states of hydration and dehydration. Although many species accumulate trehalose during dehydration, the data revealed significant differences between the species. Although trehalose accumulation was found in species of the order Parachela (Eutardigrada), it was not possible to detect any trehalose in the species Milnesium tardigradum and no change in the trehalose level has been observed in any species of Heterotardigrada so far investigated. These results expand our current understanding of anhydrobiosis in tardigrades and, for the first time, demonstrate the accumulation of trehalose in developing tardigrade embryos, which have been shown to have a high level of desiccation tolerance.
Therapeutic potential of antisense oligonucleotides as modulators of alternative splicing (2020)

An estimated 60% of all human genes undergo alternative splicing, a highly regulated process that produces splice variants with different functions. Such variants have been linked to a variety of cancers, and genetic diseases such as thalassemia and cystic fibrosis. This Perspective describes a promising approach to RNA repair based on the use of antisense oligonucleotides to modulate alternative splicing and engender the production of therapeutic gene products.
Global Economic Burden of Norovirus Gastroenteritis (2016)

The total economic burden is greatest in young children but the highest cost per illness is among older age groups in some regions. These large costs overwhelmingly are from productivity losses resulting from acute illness. Low, middle, and high income countries all have a considerable economic burden, suggesting that norovirus gastroenteritis is a truly global economic problem. Our findings can help identify which age group(s) and/or geographic regions may benefit the most from interventions.
Influence of Si/Al Ratio of ZSM-5 Zeolite on the Properties of Lignin Pyrolysis Products (2013)

The pyrolysis of softwood (SW) kraft lignin in the presence of various H-ZSM-5 zeolites with different SiO2/Al2O3 mole ratios from 23/1–280/1 as additives were examined at 600 °C. Nuclear magnetic resonance (NMR), including quantitative 13C, 31P NMR, and heteronuclear single-quantum correlation (HSQC)-NMR, and gel permeation chromatography (GPC) were used to characterize various pyrolysis oils. On the basis of the results of the 13C and 31P NMR for pyrolysis oils, the use of H-ZSM-5 zeolites during the pyrolysis process caused the near complete decomposition of aliphatic hydroxyl and carboxyl groups. With the exception of carboxylic acid, the H-ZSM-5 zeolite with a relatively higher SiO2/Al2O3 mole ratio was more effective at the elimination of methoxyl groups, ether bonds, and aliphatic C–C bonds, and dehydration of aliphatic hydroxyl groups during pyrolysis. However, the H-ZSM-5 zeolite with a very large SiO2/Al2O3 mole ratio, such as 280, has only limited effects on the properties of upgraded pyrolysis oil. After the use of zeolite, the pyrolysis oils contain some polyaromatic hydrocarbons, the content of which decreased with an increasing SiO2/Al2O3 mole ratio of zeolite. GPC results show that the molecular weight decreased by 8–16% after the use of H-ZSM-5 zeolites.
Geochemical Exploration for Petroleum (1985)

Geochemical methods used in exploring for oil and natural gas are based on the premise that hydrocarbons migrate upward from subsurface petroleum accumulations and produce anomalous patterns near the surface. Geochemical exploration techniques are both direct or indirect. Direct techniques require analysis of microquantities of hydrocarbons that occur in the free state in the soil interstices or that are adsorbed on the fine-grained portions of the soil. Indirect geochemical methods are based on the detection, in near-surface soils or in vegetation, of inorganic alteration products that result from upward migration of hydrocarbons.