gebhart/patrepeval huggingface dataset:
Laboratory diagnosis of invasive candidiasis (1990)

Severe infections due to Candida species have become more frequent during the past two decades because of the increasing numbers of immunosuppressed patients being treated in our hospitals. Distinguishing colonization from invasive disease requires knowledge of the pathogenetic mechanisms leading to invasion. To assist the clinician in therapeutic decisions, clinical microbiologists should identify to species Candida organisms isolated from immunosuppressed patients. Quantitative or semiquantitative cultures of urine, burn tissues, intravascular catheter tips, and bronchoalveolar lavage specimens may provide useful information. Immunofluorescent staining of certain specimens can enhance diagnostic yield. The lysis-centrifugation blood culture technique offers some advantages over traditional broth techniques in detecting Candida fungemia. Antibody testing is of limited diagnostic value in highly immunosuppressed patients. Developing simple and reliable tests for detecting antigens or metabolites of Candida spp. in the sera of infected patients has proven difficult. Methods for typing Candida albicans are evolving. Typing should prove useful for studying the epidemiology of candidiasis in hospitalized patients.
Increase of the Catalytic Activity of Phospholipase C-γ1 by Tyrosine Phosphorylation (1990)

Phospholipase C-gamma 1 (PLC-gamma 1), an isozyme of the phosphoinositide-specific phospholipase C family, which occupies a central role in hormonal signal transduction pathways, is an excellent substrate for the epidermal growth factor (EGF) receptor tyrosine kinase. Epidermal growth factor elicits tyrosine phosphorylation of PLC-gamma 1 and phosphatidylinositol 4,5-bisphosphate hydrolysis in various cell lines. The ability of tyrosine phosphorylation to activate the catalytic activity of PLC-gamma 1 was tested. Tyrosine phosphorylation in intact cells or in vitro increased the catalytic activity of PLC-gamma 1. Also, treatment of EGF-activated PLC-gamma 1 with a tyrosine-specific phosphatase substantially decreased the catalytic activity of PLC-gamma 1. These results suggest that the EGF-stimulated formation of inositol 1,4,5-trisphosphate and diacylglycerol in intact cells results, at least in part, from catalytic activation of PLC-gamma 1 through tyrosine phosphorylation.
Whole genome amplification of single cells: mathematical analysis of PEP and tagged PCR (1995)

We construct a mathematical model for two whole genome amplification strategies, primer extension preamplification (PEP) and tagged polymerase chain reaction (tagged PCR). An explicit formula for the expected target yield of PEP is obtained. The distribution of the target yield and the coverage properties of these two strategies are studied by simulations. From our studies we find that polymerase with high processivity may increase the efficiency of PEP and tagged PCR.
Comprehensive Survey of Combinatorial Library Synthesis:  1998 (1999)

ADVERTISEMENT RETURN TO ISSUEReviewNEXTComprehensive Survey of Combinatorial Library Synthesis: 1998Roland E. Dolle and Kingsley H. NelsonView Author Information Department of Chemistry, Pharmacopeia, Inc., CN 5350, Princeton, New Jersey 08543-5350 Cite this: J. Comb. Chem. 1999, 1, 4, 235–282Publication Date (Web):July 13, 1999Publication History Received29 April 1999Published online13 July 1999Published inissue 1 July 1999https://pubs.acs.org/doi/10.1021/cc9900192https://doi.org/10.1021/cc9900192review-articleACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views1356Altmetric-Citations252LEARN 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 options SUBJECTS:Agonists,Inhibitors,Monomers,Peptides and proteins,Receptors Get e-Alerts
Three Interferometric Methods for Measuring the Thickness of Layers of the Tear Film (1999)

The thickness of different layers of the tear film has been measured by three types of interference method, namely, wavelength-dependent fringes (WDFs), thickness-dependent fringes (TDFs), and angle-dependent fringes (ADFs). This review begins with a discussion of characteristics which are common to all these methods--high-, intermediate-, and low-index layers, phase, optical path difference, and contrast. For each of the three methods, we present a figure showing constructive and destructive interference, derive equations for calculating tear layer thickness, describe a typical optical system, and show representative results. The particular advantages and limitations of each method are discussed. Given the clinical importance of the tear film in dry eye syndrome and contact lens wear, it is unfortunate that there are considerable discrepancies among the results of interferometric and other methods for measuring tear film thickness; further development of these noninvasive, interferometric methods should help to provide a clearer picture of the thickness of different layers of the tear film, in normal and dry eyes, and in contact lens wear.
Symbolic array dataflow analysis for array privatization and program parallelization (1995)

Array dataflow information plays an important role for successful automatic parallelization of Fortran programs. This paper proposes a powerful symbolic array dataflow analysis to support array privatization and loop parallelization for programs with arbitrary control flow graphs and acyclic call graphs. Our scheme summarizes array access information using guarded array regions and propagates such regions over a Hierarchical Supergraph (HSG). The use of guards allows us to use the information in IF conditions to sharpen the array dataflow analysis and thereby to handle difficult cases which elude other existing techniques. The guarded array regions retain the simplicity of set operations for regular array regions in common cases, and they enhance regular array regions in complicated cases by using guards to handle complex symbolic expressions and array shapes. Scalar values that appear in array subscripts and loop limits are substituted on the fly during the array information propagation, which disambiguates the symbolic values precisely for set operations. We present efficient algorithms that implement our scheme. Initial experiments of applying our analysis to Perfect Benchmarks show promising results of improved array privatization.
Isolation of a cytotoxin from L-form Salmonella typhimurium (1993)

A cytotoxin protein was isolated from the sodium dodecyl sulphate (SDS)-solubilized extract of the stable L forms of Salmonella typhimurium by ion-retardation chromatography, ion-exchange chromatography, isoelectric focusing and gel filtration. The purified toxin, with a molecular mass of 32 kDa and with isoelectric point of 6.4, was thermolabile and trypsin-sensitive. Against mouse macrophages, its cytolytic effect was detectable in vitro at concentrations higher than 0.7 μg/ml, with a complete lysis obtained at 5 μg/ml. In contrast, it stimulated C3H/HeJ macrophages in the dose range of 0.1–0.5 μg/ml to allow the cell to respond to endotoxin, resulting in the significant production of tumor necrosis factor α. By Northern blot analysis, this effect was detectable at a dose as low as 0.01 μg/ml. These findings suggest that the transformation of bacillary S. typhimurium into L forms in vivo may induce alterations in host resistance against murine typhoid.
Pilot trial of autologous dendritic cells loaded with tumor lysate(s) from allogeneic tumor cell lines in patients with metastatic medullary thyroid carcinoma (2009)

Immunotherapy with autologous dendritic cells (DCs) loaded with tumor lysate(s) from allogeneic tumor cell lines is a novel strategy to induce immune responses in cancer patients. We report on a pilot trial of autologous DCs pulsed with tumor cell lysate derived from allogeneic medullary thyroid carcinoma (MTC) cell lines in patients with metastatic MTC. The purpose of this study was to assess the safety, resulting immune responses and clinical activity of the DCs. DCs were injected into a groin lymph node at 3-week intervals. Monitoring included serial calcitonin tumor marker measurements, radiological imaging and immunological in vitro tests (T-cell Interferon-γ detection assay, T-cell cytotoxicity assay). Ten patients (median age 47 years, range 29-77) were enrolled. DC vaccinations were well-tolerated and safe. After a median follow-up of 11 months, (range 7-26), 3 (30%) of 10 patients had stable disease, while 7 (70%) of the patients progressed during treatment. In 2 patients with stable disease, calcitonin decreased below treatment levels, paralleled by a T-cell-mediated immune response. Notably, treatment with DCs pulsed with a combination of different tumor cell lysates was followed by a calcitonin decrease in 4 patients who had previously experienced a calcitonin increase during monotherapy with DCs pulsed with a single lysate. Allogeneic tumor cell lysate-based DC immunotherapy is well-tolerated and safe. Combined treatment with different tumor cell lysate-pulsed DCs increases the likelihood of a calcitonin tumor marker response and should therefore be preferred over monotherapy with DCs pulsed with a single lysate.
Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes (2010)

From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosome. Only a very limited number of such genes are known, and the definition and terminologies used for them are highly variable in the public databases. In this work, we have computationally identified and manually curated 751 conjoined genes (CGs) in the human genome that are supported by at least one mRNA or EST sequence available in the NCBI database. 353 representative CGs, of which 291 (82%) could be confirmed, were subjected to experimental validation using RT-PCR and sequencing methods. We speculate that these genes are arising out of novel functional requirements and are not merely artifacts of transcription, since more than 70% of them are conserved in other vertebrate genomes. The unique splicing patterns exhibited by CGs reveal their possible roles in protein evolution or gene regulation. Novel CGs, for which no transcript is available, could be identified in 80% of randomly selected potential CG forming regions, indicating that their formation is a routine process. Formation of CGs is not only limited to human, as we have also identified 270 CGs in mouse and 227 in drosophila using our approach. Additionally, we propose a novel mechanism for the formation of CGs. Finally, we developed a database, ConjoinG, which contains detailed information about all the CGs (800 in total) identified in the human genome. In summary, our findings reveal new insights about the functionality of CGs in terms of another possible mechanism for gene regulation and genomic evolution and the mechanism leading to their formation.
The antibiotics micrococcin and thiostrepton interact directly with 23S rRNA nucleotides 1067A and 1095A (1994)

The antibiotics thiostrepton and micrococcin bind to the GTPase region in domain II of 23S rRNA, and inhibit ribosomal A-site associated reactions. When bound to the ribosome, these antibiotics alter the accessibility of nucleotides 1067A and 1095A towards chemical reagents. Plasmid-coded Escherichia coli 23S rRNAs with single mutations at positions 1067 or 1095 were expressed in vivo. Mutant ribosomes are functional in protein synthesis, although those with transversion mutations function less effectively. Antibiotics were bound under conditions where wild-type and mutant ribosomes compete in the same reaction for drug molecules; binding was analysed by allele-specific footprinting. Transversion mutations at 1067 reduce thiostrepton binding more than 1000-fold. The 1067G substitution gives a more modest decrease in thiostrepton binding. The changes at 1095 slightly, but significantly, lower the affinity of ribosomes for thiostrepton, again with the G mutation having the smallest effect. Micrococcin binding to ribosomes is reduced to a far greater extent than thiostrepton by all the 1067 and 1095 mutations. Extrapolating these results to growing cells, mutation of nucleotide 1067A confers resistance towards micrococcin and thiostrepton, while substitutions at 1095A confer micrococcin resistance, and increase tolerance towards thiostrepton. These data support an rRNA tertiary structure model in which 1067A and 1095A lie in close proximity, and are key components in the drug binding site. None of the mutations alters either the higher order rRNA structure or the binding of r-proteins. We therefore conclude that thiostrepton and micrococcin interact directly with 1067A and 1095A.
Combination adjuvants: the next generation of adjuvants? (2010)

Adjuvants are critical components of many vaccines. The majority of existing vaccines contain a single adjuvant. Owing to their inherent limitations, no single adjuvant is capable of inducing all the protective immune responses required in the many different vaccines. Consequently, investigators are exploring the potential of using formulations with multiple adjuvants in a vaccine. An emerging paradigm is that careful selection of adjuvant combinations can result in complementary and even synergistic enhancement of immune responses to vaccines. This approach is promising and presents tremendous opportunities for vaccinologists to tailor immune responses to specific vaccines. In this article, adjuvant combinations at different stages of development will be reviewed.
Efficient hepatitis C virus cell culture system: What a difference the host cell makes (2005)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Serodiagnosis of Histoplasmosis and Blastomycosis (1987)

"Serodiagnosis of Histoplasmosis and Blastomycosis." American Review of Respiratory Disease, 136(2), pp. 254–255
Partial Amino Acid Sequence of a Novel 40-kDa Human Aortic Protein, with Vitronectin-like, Fibrinogen-like, and Calcium Binding Domains: Aortic Aneurysm-Associated Protein-40 (AAAP-40) [Human MAGP-3, Proposed] (1996)

A microfibrillar protein (40 kDa) purified from the adventitia of the human abdominal aorta is immunoreactive with IgG harvested from the wall of abdominal aortic aneurysms. We have partially sequenced this protein and found that it has fibrinogen alpha-, beta-, and gamma-like domains, a vitronectin-like domain, and a possible site for binding calcium. Because of homologies with other microfibril-associated glycoproteins and because it is the third member of the family to be characterized in man, we suggest the name MAGP-3.
Modified Dipicolinic Acid Ligands for Sensitization of Europium(III) Luminescence (2006)

The effect of substitution at the 4 and 3,5 positions in the pyridine ring of europium(III) pyridine-2,6-dicarboxylate complexes has been investigated with particular emphasis on sensitization of the Eu3+ ion. Sensitization of the Eu3+ 615-nm emission was achieved through excitation of the ligands in which the 4 substituent was -H, -OH, and -Cl and the 3,5 position was -H. In these cases, the ligand-to-Eu3+ ratio was confirmed as being 3:1. The sensitization was found to increase following substitution of the 4 position in the order Cl > H > OH. This is attributed to energy transfer occurring from the ligands into different Eu3+ intra-atomic energy levels, with spin selection rules governing the efficiency of this process. The Eu3+ luminescence lifetime was measured and found to vary from 1.16 to 2.90 ms depending on the excitation energy, ligand, and solvent. For the case of the 3,5-dibromo-4-hydroxy derivative, no sensitization was observed and a ligand-to-Eu3+ ratio of 1:1 was found. The solubility of these complexes in water and their long emission lifetime make them attractive for use as probes in biological systems.
Sequence variants of the gene encoding chemoattractant receptor expressed on Th2 cells (CRTH2) are associated with asthma and differentially influence mRNA stability (2004)

The gene, CRTH2, encoding a receptor for prostaglandin D(2) (PGD(2)), is located within the peak linkage region for asthma on chromosome (Chr.) 11q reported in African American families. Family-based analysis of asthma and two common SNPs [G1544C and G1651A (rs545659)] in the 3'-untranslated region of CRTH2 showed significant evidence of linkage in the presence of disequilibrium for the 1651G allele (P = 0.003) of SNP rs545659. Haplotype analysis yielded additional evidence of linkage disequilibrium for the 1544G-1651G haplotype (P < 0.001). Population-based case-control analyses were conducted in two independent populations, and demonstrated significant association of the 1544G-1651G haplotype with asthma in an African American population (P = 0.004), and in a population of Chinese children (P < 0.001). Moreover, in the Chinese children the frequency of the 1651G allele in near-fatal asthmatics was significantly higher than mild-to-moderate asthmatics (P = 0.001) and normal controls (P < 0.001). The 1651G allele of SNP re545659 was also associated with a higher degree of bronchial hyperresponsiveness (P < 0.027). Transcriptional pulsing experiments showed that the 1544G-1651G haplotype confers a significantly higher level of reporter mRNA stability, when compared with a non-transmitted haplotype (1544C-1651A), suggesting that the CRTH2 gene on Chr. 11q is a strong candidate gene for asthma.
60.3: AMOLED Displays using Transfer‐Printed Integrated Circuits (2010)

Abstract Active‐matrix OLED (AMOLED) displays can be controlled by transfer‐printed microscale silicon integrated circuits (ICs) in place of conventional thin‐film transistors (TFTs). Such OLED displays are robust and exhibit excellent performance. The OLED pixels exhibit excellent uniformity, angular independence, color gamut, brightness, environmental robustness, and can be operated at very high frame rates.
Functionalized Cyclopropenes As Bioorthogonal Chemical Reporters (2012)

Chemical reporters are unique functional groups that can be used to label biomolecules in living systems. Only a handful of broadly applicable reporters have been identified to date, owing to the rigorous demands placed on these functional groups in biological settings. We describe here a new chemical reporter-cyclopropene-that can be used to target biomolecules in vitro and in live cells. A variety of substituted cyclopropene scaffolds were synthesized and found to be stable in aqueous solution and in the presence of biological nucleophiles. Furthermore, some of the cyclopropene units were metabolically introduced into cell surface glycans and subsequently detected with covalent probes. The small size and selective reactivity of cyclopropenes will facilitate efforts to tag diverse collections of biomolecules in vivo.
Interpreting estimates of treatment effects: implications for managed care. (2008)

How should health care professionals choose among the many therapies claimed to be efficacious for treating specific disorders? The practice of evidence-based medicine provides an answer. Advocates of this approach urge health care professionals to base treatment choices on the best evidence from systematic research on both the efficacy and adverse effects of various therapeutic alternatives. Ideally, health care professionals would compare different treatments by referring to randomized, double-blind, head-to-head trials that compared the treatment options. Although individual medications are typically well researched when these placebo-controlled studies are performed, studies that directly compare treatments are rare. In the absence of direct head-to-head trials, other evidence comes from indirect comparisons of two or more therapies by examining individual studies involving each treatment.

This article provides an introductory review of methods of such indirect comparisons of therapies across studies, provides examples of how these methods can be used to make treatment decisions, and presents a general overview of relevant issues and statistics for readers interested in understanding these methods more thoroughly.
Extension of mismatched 3' termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase. (1989)

The unusually high error rate of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) suggests that polymerization errors by this enzyme contribute to the genetic variability of the AIDS virus. We have analyzed the mechanism for HIV-1 RT infidelity by studying two distinct steps that might lead to base substitution mutations: nucleotide misinsertions and elongation from 3'-terminal DNA mispairs. Our results indicate that the capacity of HIV-1 RT to polymerize nucleotides onto mispaired termini is a major factor in the production of mutations by this enzyme. When a noncomplementary dAMP was inserted opposite a template adenine by HIV-1 RT, the nascent 3'-terminal A.A mispair was readily extended by subsequent incorporation of the next complementary nucleotide. The frequencies of nucleotide addition onto 3'-terminal A-A, A-C, and A-G mispairs were determined by quantitating the amount of extended primers with a gel electrophoresis assay and by measuring mutagenesis after hybridization of mismatched primers opposite an amber mutation in bacteriophage phi X174 DNA. The mispair extension frequencies are approximately 50-fold higher by HIV-1 RT than by the mammalian replicative enzyme DNA polymerase alpha.
2-Chloro-1,3-dimethylimidazolinium Chloride. 1. A Powerful Dehydrating Equivalent to DCC (1999)

2-Chloro-1,3-dimethylimidazolinium chloride (DMC) (3) can act as a powerful dehydrating agent, replacing DCC (1) under nearly neutral conditions. Its application to acylation and dehydration is described.
Alkoxyboration: Ring-Closing Addition of B–O σ Bonds across Alkynes (2014)

For nearly 70 years, the addition of boron-X σ bonds to carbon-carbon multiple bonds has been employed in the preparation of organoboron reagents. However, the significantly higher strength of boron-oxygen bonds has thus far precluded their activation for addition, preventing a direct route to access a potentially valuable class of oxygen-containing organoboron reagents for divergent synthesis. We herein report the realization of an alkoxyboration reaction, the addition of boron-oxygen σ bonds to alkynes. Functionalized O-heterocyclic boronic acid derivatives are produced using this transformation, which is mild and exhibits broad functional group compatibility. Our results demonstrate activation of this boron-O σ bond using a gold catalysis strategy that is fundamentally different from that used previously for other boron addition reactions.