gebhart/patrepeval huggingface dataset:
Molecular predictors of cognitive involvement in female carriers of fragile X syndrome (1994)

<h3>Objective.</h3> —Fragile X syndrome is caused by a mutation involving expansion of a CGG trinucleotide repeat segment in the fragile X mental retardation—1 (<i>FMR1</i>) gene on the long arm of the X chromosome. This study was undertaken to determine the relative impact of three molecular characteristics of the<i>FMR1</i>mutation— number of CGG repeats, methylation status, and X inactivation ratio—on the cognitive involvement of female carriers of fragile X syndrome. <h3>Design.</h3> —Retrospective study with new DNA analysis of known female carriers of fragile X syndrome. <h3>Setting.</h3> —Molecular studies were conducted in a university-based DNA diagnostic laboratory. Patients were originally ascertained through a regional fragile X clinic in a university-affiliated pediatric hospital. <h3>Patients.</h3> —Forty-eight female carriers of fragile X syndrome were studied, including 22 with a premutation (a small expansion to approximately 50 to 200 CGG repeats), 23 with a full mutation (a full expansion to &gt;200 CGG repeats), and three with both types of mutations (mosaics). <h3>Results.</h3> —Median IQ score was significantly lower for females with a full mutation than for females with a premutation. No significant relationship was found between IQ score and number of CGG repeats or percentage methylation of the mutant allele within each mutation category. In addition, no significant relationship was found between IQ score and the proportion of normal<i>FMR1</i>alleles on the active X chromosome in the carrier female group as a whole or in either mutation subgroup. Comparisons of leukocytes and saliva-borne epithelial cells in certain full-mutation carriers revealed striking differences in<i>FMR1</i>mutation sizes. <h3>Conclusions.</h3> —Mutation category remains the most important predictor of affectedness in female carriers of fragile X syndrome. Our data do not support use of the proportion of normal<i>FMR1</i>alleles on the active X chromosome as a predictor of cognitive involvement in female carriers with full mutations. Individual tissue-specific differences exist in the heterogeneous sizes of full mutations and in the presence of premutation/full-mutation mosaicism. (<i>JAMA</i>. 1994;271:507-514)
Comparison of MUC-1 mucin expression in epithelial and non-epithelial cancer cell lines and demonstration of a new short variant form (MUC-1/Z) (1997)

Mucins, including MUC-1, are generally considered to be products of epithelial tissues and of their tumors. To examine the possible expression of MUC-1 in other cell types, a panel of human epithelial and non-epithelial tumor cell lines was studied by reverse transcriptase polymerase chain reaction (RT-PCR), Northern blot analysis, immunocytology and radioimmunoprecipitation. Using the highly sensitive RT-PCR method, products corresponding to the non-repetitive 5' and 3' MUC-1 sequences were detected in all the cell lines examined. Amplified products lacking the tandem repeat region of MUC-1, including a new short form (designated MUC-1/Z) different from the previously reported MUC-1/Y protein, were also detected in most cell lines tested. Northern blot analysis, using a probe to the variable number tandem repeat (VNTR) region, confirmed the presence of MUC-1 mRNA in the astrocytoma, melanoma and neuroblastoma cell lines studied. MUC-1 protein was detected by immunocytology in these cell lines using monoclonal antibody (MAb) 139H2. Immunoprecipitation analysis with [3H]-glucosamine-labeled cell lysates and MAb 139H2 or an antibody to the cytoplasmic domain, CT-1, detected MUC-1 protein in 2 epithelial cell lines, an astrocytoma cell line (SK-MG-4) but not in the melanoma and neuroblastoma cell lines studied. Northern blot analysis using a probe to the 3' end of MUC-1 mRNA, confirmed the presence of MUC-1 mucin and also identified short products corresponding to the size of the short variant forms. Protein products corresponding to the MUC-1/Y and MUC-1/Z variant forms were not observed using either [3H]-glucosamine-labeled OVCAR-3 cells or [3H]-amino acid-labeled MCF-7 cells and either CT-1 antibody or MAb 232A1, detecting an epitope to the C-terminal region. Thus, depending on the sensitivity of the assay used, varying amounts of MUC-1 mRNA and protein could be detected in non-epithelial tumor cell lines. Although the amounts of MUC-1 in these cell lines are much lower than in carcinomas, it is possible that MUC-1 mucin serves a similar function in non-epithelial as in epithelial cells. The possible role of MUC-1/Y and MUC-1/Z variant forms in these cell lines is not understood.
Nucleoside analogs to manage sequence divergence in nucleic acid amplification and SNP detection (2018)

Described here are the synthesis, enzymology and some applications of a purine nucleoside analog (H) designed to have two tautomeric forms, one complementary to thymidine (T), the other complementary to cytidine (C). The performance of H is compared by various metrics to performances of other 'biversal' analogs that similarly rely on tautomerism to complement both pyrimidines. These include (i) the thermodynamic stability of duplexes that pair these biversals with various standard nucleotides, (ii) the ability of the biversals to support polymerase chain reaction (PCR), (iii) the ability of primers containing biversals to equally amplify targets having polymorphisms in the primer binding site, and (iv) the ability of ligation-based assays to exploit the biversals to detect medically relevant single nucleotide polymorphisms (SNPs) in sequences flanked by medically irrelevant polymorphisms. One advantage of H over the widely used inosine 'universal base' and 'mixed sequence' probes is seen in ligation-based assays to detect SNPs. The need to detect medically relevant SNPs within ambiguous sequences is especially important when probing RNA viruses, which rapidly mutate to create drug resistance, but also suffer neutral drift, the second obstructing simple methods to detect the first. Thus, H is being developed to detect variants of viruses that are rapidly mutating.
Investigation of Engine Oil Effect on Abnormal Combustion in Turbocharged Direct Injection - Spark Ignition Engines (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Abnormal combustion referred to as Low Speed Pre-Ignition (LSPI) may restrict low speed torque improvements in turbocharged Direct Injection (DI) - Spark Ignition (SI) Engines. Recent investigations have reported that the auto-ignition of an engine oil droplet from the piston crevice in the combustion chamber may cause unexpected and random LSPI. This study shows that engine oil formulations have significant effects on LSPI. We found that the spontaneous ignition temperature of engine oil, as determined using High-Pressure Differential Scanning Calorimetry (HP-DSC) correlates with LSPI frequency in a prototype turbocharged DI-SI engine. Based on these findings, we believe that the oxidation reaction of the oil is very important factor to the LSPI. Our test data, using a prototype engine, shows both preventative and contributory effects of base oil and metal-based engine oil additives.&lt;/div&gt;&lt;/div&gt;
The TRANSPORT INHIBITOR RESPONSE2 Gene Is Required for Auxin Synthesis and Diverse Aspects of Plant Development (2009)

The plant hormone auxin plays an essential role in plant development. However, only a few auxin biosynthetic genes have been isolated and characterized. Here, we show that the TRANSPORT INHIBITOR RESPONSE2 (TIR2) gene is required for many growth processes. Our studies indicate that the tir2 mutant is hypersensitive to 5-methyl-tryptophan, an inhibitor of tryptophan synthesis. Further, treatment with the proposed auxin biosynthetic intermediate indole-3-pyruvic acid (IPA) and indole-3-acetic acid rescues the tir2 short hypocotyl phenotype, suggesting that tir2 may be affected in the IPA auxin biosynthetic pathway. Molecular characterization revealed that TIR2 is identical to the TAA1 gene encoding a tryptophan aminotransferase. We show that TIR2 is regulated by temperature and is required for temperature-dependent hypocotyl elongation. Further, we find that expression of TIR2 is induced on the lower side of a gravitropically responding root. We propose that TIR2 contributes to a positive regulatory loop required for root gravitropism.
Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome (2010)

To study positioning of the polypeptide release factor eRF1 toward a stop signal in the ribosomal decoding site, we applied photoactivatable mRNA analogs, derivatives of oligoribonucleotides. The human eRF1 peptides cross-linked to these short mRNAs were identified. Cross-linkers on the guanines at the second, third, and fourth stop signal positions modified fragment 31-33, and to lesser extent amino acids within region 121-131 (the "YxCxxxF loop") in the N domain. Hence, both regions are involved in the recognition of the purines. A cross-linker at the first uridine of the stop codon modifies Val66 near the NIKS loop (positions 61-64), and this region is important for recognition of the first uridine of stop codons. Since the N domain distinct regions of eRF1 are involved in a stop-codon decoding, the eRF1 decoding site is discontinuous and is not of "protein anticodon" type. By molecular modeling, the eRF1 molecule can be fitted to the A site proximal to the P-site-bound tRNA and to a stop codon in mRNA via a large conformational change to one of its three domains. In the simulated eRF1 conformation, the YxCxxxF motif and positions 31-33 are very close to a stop codon, which becomes also proximal to several parts of the C domain. Thus, in the A-site-bound state, the eRF1 conformation significantly differs from those in crystals and solution. The model suggested for eRF1 conformation in the ribosomal A site and cross-linking data are compatible.
Reversible Microbial Colonization of Germ-Free Mice Reveals the Dynamics of IgA Immune Responses (2010)

The lower intestine of adult mammals is densely colonized with nonpathogenic (commensal) microbes. Gut bacteria induce protective immune responses, which ensure host-microbial mutualism. The continuous presence of commensal intestinal bacteria has made it difficult to study mucosal immune dynamics. Here, we report a reversible germ-free colonization system in mice that is independent of diet or antibiotic manipulation. A slow (more than 14 days) onset of a long-lived (half-life over 16 weeks), highly specific anticommensal immunoglobulin A (IgA) response in germ-free mice was observed. Ongoing commensal exposure in colonized mice rapidly abrogated this response. Sequential doses lacked a classical prime-boost effect seen in systemic vaccination, but specific IgA induction occurred as a stepwise response to current bacterial exposure, such that the antibody repertoire matched the existing commensal content.
Growth-Promoting Interaction of IGF-II with the Insulin Receptor during Mouse Embryonic Development (1997)

Genetic analyses of dwarfing phenotypes resulting from targeted mutagenesis of the genes encoding the insulin-like growth factors (IGF-I and IGF-II) and their cognate type 1 IGF receptor (IGF1R) have demonstrated that this signaling system is a major determinant of mouse embryonic growth. Of the two IGF ligands, IGF-I interacts exclusively with IGF1R, whereas IGF-II recognizes an additional receptor (XR), because the growth retardation of embryos lacking both IGR1R and IGF-II (30% of normal birthweight) is more severe than that manifested in either class of single Igf1r or Igf2 null mutants (45 and 60% of normal, respectively). To determine whether XR is the insulin receptor (IR), we examined embryos nullizygous for both Igf1r and Insr. While the growth of embryos lacking solely IR is affected very mildly and only at the end of gestation, concomitant absence of IGF1R results in a severe growth-deficiency phenotype (30% of normal size at birth) that is first detected at Embryonic Day 13.5 and is also characterized by transient edema, curly tail, generalized organ hypoplasia, including the muscles, developmental delays in ossification, and thin epidermis. The Igf1r/Insr double nullizygotes are phenotypically indistinguishable from double mutants lacking IGF1R and IGF-II and from other double and triple mutants in which all of the IGF ligand/receptor interactions have been eliminated. Therefore, these results provide genetic evidence that the growth-promoting function of IGF-II during mouse embryogenesis is mediated in part by signaling through the insulin receptor.
Deregulated cyclooxygenase-2 expression in oral premalignant tissues. (2002)

Establishment of an early and reliable biomarker for oral carcinogenesis whose expression can be monitored through noninvasive techniques will enable early diagnosis of cancer. Cyclooxygenases (COXs) have been implicated previously in several human malignancies, and the therapeutic benefit of specific COX-2 inhibitors has been elucidated. The expression of COX-2 and subsequent markers of malignant progression was studied in archival human specimens representing premalignant and malignant stages of oral cancer. We find that changes in COX-2 gene expression precede changes in expression of biomarkers related to apoptosis and angiogenesis in oral premalignant tissues as a veritable phenotype. We also report for the first time COX-2 mRNA variants in dysplastic samples and in a human papillomavirus-transformed cell line HOK-16B, indicating a possible stabilization of COX-2 message by human papillomavirus infection as an early event in oral cancer. Expression of other markers of tumor progression related to apoptosis and angiogenesis pathway genes shows relatively low level of changes in oral premalignant tissue. However, a determinant shift toward decrease in antitumor immunity was observed by cytokine gene expression profile changes.
Atomic Force Microscopy (1990)

In 1986 Gerd Binnig and Heinrich Rohrer shared the Nobel Prize in Physics for inventing the scanning tunneling microscope and discovering that it can image individual surface atoms with unprecedented resolution. The success of the scanning tunneling microscope has led to the invention of a host of other “scanning probe” microscopes, which rely on mechanically scanning a sharp tip over a sample surface. The atomic force microscope is one of the most successful of these new devices.
Evidence for the Existence of a Pseudoknot Structure at the 3‘ Terminus of the Flavivirus Genomic RNA (1996)

The 3'-terminal nucleotides of the flavivirus genomic RNA form conserved secondary structures that may function as cis-acting signals for RNA replication. Here we provide evidence for the existence of a conserved pseudoknot structure at the 3' terminus of the flavivirus genomic RNA. A truncated version of the West Nile virus (WNV) 3'-terminal RNA sequence was used as the model for these studies. Circular dichroism spectra indicated the presence of a highly structured RNA conformation with a significant amount of A-form helix. Ribonuclease probing not only confirmed the presence of the predicted secondary structure, which consists of a long stem-loop (SL1) and a shorter stem-loop (SL2), but also suggested that base pairing occurs between nucleotides in the loop of SL2 and those in an internal loop strand located on the 5' side of SL1. Analysis of three mutant RNAs further supported the existence of pseudoknot interactions. UV-melting analysis of the WNV 3' model RNA showed three transitions with significant hyperchromicity at approximately 46, 62, and 79 degrees C. UV-melting analysis with either SL1 or SL2 RNA alone suggested that the 62 and 79 degree C transitions represent the unfolding of SL2 and SL1, respectively. The 46 degree C transition is most likely due to the opening of the proposed tertiary structure. A similar melting curve was obtained for another flavivirus (dengue-3 virus) 3'-terminal RNA, providing further support for the conservation of the structure among flaviviruses. Molecular modeling of the RNA indicated that a pseudoknot structure is a stereochemically and energetically reasonable model for the 3' terminus of flavivirus genomic RNA.
Baculovirus expression vectors: a laboratory manual. (1992)

Acknowledgments How To Use This Manual PART I: AN OVERVIEW OF BACULOVIRUSES 1: Virus Structure and the Infection Process 2: Gene Organization, Regulation, and Function 3: Virus-Host Interactions 4: Summary of Baculovirus Features Relevant to Expression Factors PART II: CHOOSING A TRANSFER PLASMID AND PARENT VIRUS 5: Choice of Virus and Host Species 6: Choice of Transfer Plasmid 7: Available Transfer Plasmids 8: Choosing a Parent Virus for Use in Vector Construction 9: Optimizing Expression: Tailoring the Heterologous Gene to the Transfer Plasmid and the Baculovirus Expression System PART III: METHODS FOR VECTOR CONSTRUCTION AND GENE EXPRESSION 10: Safety Considerations 11: Insect Cell Culture 12: Virus Methods 13: Contransfection and Recombinant Virus Identification 14: Characterizing Recombinant Gene Expression 15: Post-Translational Modification PART IV: METHODS FOR SCALE-UP OF PROTEIN PRODUCTION AND USE OF INSECT LARVAE 16: David L. Clemm: Scale-Up of Protein Production in a Stirred Bioreactor 17: Cheryl Isaac Murphy: Scale-Up of Protein Production in an Airlift Fermenter 18: Insect Rearing and Infection Appendix 1: Nucleotide Sequence of AcMNPV Polyhedrin Region Appendix 2: Nucleotide Sequence of AcMNPV p10 Region Appendix 3: List of Genes Expressed in the Baculovirus Expression System Appendix 4: Suppliers Appendix 5: Stock Solutions Appendix 6: Excel Spreadsheet for TCID[5[0 Calculation References Index
The transcriptional activator NtrC controls the expression and activity of glutamine synthetase in Herbaspirillum seropedicae (2000)

The role of the Ntr system in Herbaspirillum seropedicae was determined via ntrB and ntrC mutants. Three phenotypes were identified in these mutants: Nif−, deficiency in growth using nitrate, and low glutamine synthetase (GS) activity. All phenotypes were restored by the plasmid pKRT1 containing the intact glnA, ntrB and ntrC genes of H. seropedicae. The promoter region of glnA was subcloned into a β-galactosidase fusion vector and the results suggested that NtrC positively regulates the glnA promoter in response to low nitrogen. The H. seropedicae ntrC and ntrB mutant strains showed a deficiency of adenylylation/deadenylylation of GS, indicating that NtrC and NtrB are involved in both transcription and activity control of GS in this organism.
Ultrahigh finesse fiber Fabry-Perot interferometers (1986)

Fiber Fabry-Perots have been built with a finesse of 500 and throughput of 30-40 percent. The devices are piezoelectrically scanned and operate at 1.52μm, and have free spectral ranges of 1000, 500, 333, and 250 MHz, with linewidth resolution as small as 0.5 MHz. The sources of loss which limit the attainable finesse have been identified and analyzed.
Structural genomics of human proteins – target selection and generation of a public catalogue of expression clones (2005)

Protein expression and sequence data of 1414 E. coli expression clones representing 537 different proteins are presented. 139 human proteins (18%) could be expressed and purified in soluble form and with the expected size. All E. coli expression clones are publicly available to facilitate further functional characterisation of this set of human proteins.
Dried blood spots (DBS): a valuable tool for HIV surveillance in developing/tropical countries (2002)

Dried blood spots (DBS) on filter paper have been used as a practical method of sample collection in sero-surveillance studies of numerous diseases. DBS may be particularly useful for HIV screening in remote areas, in which unrefrigerated transfer time to a laboratory may take a number of days. In this study, we evaluate the ability to detect human immunodeficiency virus (HIV) type-1 antibodies from DBS that have been subjected to a tropical climate in southern India for 6 days. DBS were prepared from blood samples of 59 known HIV-positive individuals and 30 known HIV-negative individuals. ELISA and Western blot results from DBS that were subjected to a mean temperature of 35.8 degrees C and humidity of 73% for 6 days had a sensitivity of 100% and 92%, respectively, and a specificity of 100% and 100%, respectively. Based on these findings, we conclude that DBS sampling could serve as a cost-effective and convenient tool for widespread HIV sero-surveillance in remote areas within tropical countries.
Cardiac Gene Therapy: Optimization of Gene Delivery Techniques In Vivo (2009)

Vector-mediated cardiac gene therapy holds tremendous promise as a translatable platform technology for treating many cardiovascular diseases. The ideal technique is one that is efficient and practical, allowing for global cardiac gene expression, while minimizing collateral expression in other organs. Here we survey the available in vivo vector-mediated cardiac gene delivery methods--including transcutaneous, intravascular, intramuscular, and cardiopulmonary bypass techniques--with consideration of the relative merits and deficiencies of each. Review of available techniques suggests that an optimal method for vector-mediated gene delivery to the large animal myocardium would ideally employ retrograde and/or anterograde transcoronary gene delivery,extended vector residence time in the coronary circulation, an increased myocardial transcapillary gradient using physical methods, increased endothelial permeability with pharmacological agents, minimal collateral gene expression by isolation of the cardiac circulation from the systemic, and have low immunogenicity.
Development of a Process to Prepare 2-Cyanopyrimidine on Commercial Scale (1996)

2-Chloropyrimidine is converted to 2-cyanopyrimidine under very mild conditions in nearly quantitative yield using 1,4-diazabicyclo[2.2.2]octane as catalyst. The development of the process for commercial batch production of 2-cyanopyrimidine regarding processing of the materials in technical equipment, process safety, conservation, economic raw material use and work load is described.
Cytokine cross‐talk between phagocytic cells and lymphocytes: Relevance for differentiation/activation of phagocytic cells and regulation of adaptive immunity (1993)

Cytokines represent one of the most important elements in the communication among different cell types. They play an increasingly better understood role in the communication among hematopoietic cells and in particular in the reciprocal regulation of effector cell types of innate or natural resistance (phagocytic cells and Natural Killer (NK) cells) and those of adaptive immunity (T and B lymphocytes). Lymphocytes produce several cytokines with either stimulatory (e.g., colony stimulatory factor) or suppressive (e.g., tumor necrosis factors and interferons) effects on proliferation of early hematopoietic cells. Many of these cytokines, alone or acting in synergistic combinations, also have a differentiation-inducing ability on immature myeloid cells and act as powerful potentiators of the cellular functions of terminally differentiated phagocytic cells. The communication between lymphocytes and phagocytic cells is not unidirectional, as phagocytic cells produce factors that regulate lymphocyte activation. In addition to their role as antigen presenting cells expressing costimulatory accessory molecules and secreting cytokines (e.g., IL-1, IL-6, TNF), phagocytic cells have been recently shown to produce Natural Killer cell Stimulatory Factor (NKSF/IL-12). IL-12 is a heterodimeric cytokine with important modulatory functions on cytotoxicity of NK and T cells, lymphocyte proliferation, lymphokine production, and development of T helper cell subsets. These communications between phagocytic cells and lymphocytes are further regulated by negative and positive feedback mechanisms that contribute to maintain the homeostasis of the system in physiologic conditions and to govern the changes in this equilibrium needed for the response to infectious or other foreign agents.