gebhart/patrepeval huggingface dataset:
Thermodynamics of porphyrin sublimation (2000)

The saturated vapor pressures of tetraphenylporphyrin H 2 TPP , its four-coordinated metallo-complexes MTPP ( M ≡ Ni , Cu , Zn , Pd , Ag , Cd ) and some phenyl-substituted derivatives H 2 T ( R ) PP ( R ≡ 2-, 3-, 4- CH 3 ; 2-, 4- F ; 2-, 3-, 4- Cl ; 3-, 4- Br ; 3,5- C ( CH 3 ) 3 ) have been measured using the inert gas flow method. The values of sublimation enthalpy Δ sub H m and entropy Δ sub S m are calculated. On the basis of the kinetic vapor pressure dependence, the start temperatures of thermal destruction of the investigated porphyrins are determined. The temperatures of melting of the tetraphenylporphyrin metallo-complexes measured by the DSC method are in linear correlation with the Δ sub H m values. The correlation between the thermodynamic functions of porphyrin sublimation (Δ sub H m , Δ sub S m , Δ sub G m ) and the literature data on the crystal structure of the compounds is considered. The Δ sub H m values obtained by some authors by different methods are compared with the results of our investigations. Possible reasons for discrepancies in the results are discussed.
FlumeJava (2010)

MapReduce and similar systems significantly ease the task of writing data-parallel code. However, many real-world computations require a pipeline of MapReduces, and programming and managing such pipelines can be difficult. We present FlumeJava, a Java library that makes it easy to develop, test, and run efficient data-parallel pipelines. At the core of the FlumeJava library are a couple of classes that represent immutable parallel collections, each supporting a modest number of operations for processing them in parallel. Parallel collections and their operations present a simple, high-level, uniform abstraction over different data representations and execution strategies. To enable parallel operations to run efficiently, FlumeJava defers their evaluation, instead internally constructing an execution plan dataflow graph. When the final results of the parallel operations are eventually needed, FlumeJava first optimizes the execution plan, and then executes the optimized operations on appropriate underlying primitives (e.g., MapReduces). The combination of high-level abstractions for parallel data and computation, deferred evaluation and optimization, and efficient parallel primitives yields an easy-to-use system that approaches the efficiency of hand-optimized pipelines. FlumeJava is in active use by hundreds of pipeline developers within Google.
Antibody-Dependent Killing of Erythrocyte and Tumor Targets by Macrophage-Related Cell Lines: Enhancement by PPD and LPS (1977)

Five murine macrophage or monocyte-related tumor cell lines in culture were compared for antibody-dependent lysis (ADL) of a tumor target (T lymphoma EL4) and lysis and phagocytosis of sheep erythrocytes (RBC). Some lines were effective only with RBC targets, while others were capable of lysing these and tumor targets. Both murine alloantisera to H-2 and Thy 1.2 antigens on the target cells and rabbit anti-mouse spleen and anti-mouse thymus sera directed target lysis, while normal mouse or rabbit sera were inactive. Preincubation of macrophage line RAW264 with lipopolysaccharide (LPS) or purified protein derivative from Mycobacteria (PPD) for 2 days resulted in an average of 76% or 86% increase, respectively, in ADL of RBC, although there was no stimulation in RBC phagocytosis or in nonspecific or antibody-dependent lysis of tumor targets. These results indicate that macrophage cell types are capable of antibody-dependent tumor lysis, that macrophages are probably heterogeneous in effector cell activities, and that they can be stimulated to increased ADL in the complete absence of other cell types.
Functional Consequences of α-Synuclein Tyrosine Nitration (2004)

Previous studies have shown the presence of nitrated alpha-synuclein (alpha-syn) in human Lewy bodies and other alpha-syn inclusions. Herein, the effects of tyrosine nitration on alpha-syn fibril formation, lipid binding, chaperone-like function, and proteolytic degradation were systematically examined by employing chromatographically isolated nitrated monomeric, dimeric, and oligomeric alpha-syn. Nitrated alpha-syn monomers and dimers but not oligomers accelerated the rate of fibril formation of unmodified alpha-syn when present at low concentrations. Immunoelectron microscopy revealed that nitrated monomers and dimers are incorporated into the fibrils. However, the purified nitrated alpha-syn monomer by itself was unable to form fibrils. Nitration of the tyrosine residue at position 39 was largely responsible for decreased binding of nitrated monomeric alpha-syn to synthetic vesicles, which correlated with an impairment of the nitrated protein to adopt alpha-helical conformation in the presence of liposomes. The chaperone-like activity of alpha-syn was not inhibited by nitration or oxidation. Furthermore, the 20 S proteasome and calpain I degraded nitrated monomeric alpha-syn, although at a slower rate compared with control alpha-syn. Collectively, these data suggest that post-translational modification of alpha-syn by nitration can promote the formation of intracytoplasmic inclusions that constitute the hallmark of Parkinson disease and other synucleinopathies.
Comparison of a Novel Method vs the Friedewald Equation for Estimating Low-Density Lipoprotein Cholesterol Levels From the Standard Lipid Profile (2013)

clinicaltrials.gov Identifier: NCT01698489.
Multi-function interface unit for applied potential tomography (1988)

In applied potential tomography, the negative effects of measurement precision due to multiplexer feedthrough and crosstalk and of connection stray capacitances have been highlighted. Envisaging a fully parallel configuration, a circuit is suggested that, when coupled with each electrode, can function as a current source with feedback, as a short circuit to ground or as a voltage buffer, following the positions of a set of local switches. A local regulation system helps to reduce crosstalk and improves the precision when the unit functions as a current source. A local buffer and switching system and a stray capacitance compensation circuit help to reduce stray capacitances and their effects on measurement accuracy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Chip in a lab: Microfluidics for next generation life science research (2013)

Microfluidic circuits are characterized by fluidic channels and chambers with a linear dimension on the order of tens to hundreds of micrometers. Components of this size enable lab-on-a-chip technology that has much promise, for example, in the development of point-of-care diagnostics. Micro-scale fluidic circuits also yield practical, physical, and technological advantages for studying biological systems, enhancing the ability of researchers to make more precise quantitative measurements. Microfluidic technology has thus become a powerful tool in the life science research laboratory over the past decade. Here we focus on chip-in-a-lab applications of microfluidics and survey some examples of how small fluidic components have provided researchers with new tools for life science research.
Components of the Salmonella Flagellar Export Apparatus and Classification of Export Substrates (1999)

Until now, identification of components of the flagellar protein export apparatus has been indirect. We have now identified these components directly by establishing whether mutants defective in putative export components could translocate export substrates across the cytoplasmic membrane into the periplasmic space. Hook-type proteins could be exported to the periplasm of rod mutants, indicating that rod protein export does not have to precede hook-type protein export and therefore that both types of proteins belong to a single export class, the rod/hook-type class, which is distinct from the filament-type class. Hook-capping protein (FlgD) and hook protein (FlgE) required FlhA, FlhB, FliH, FliI, FliO, FliP, FliQ, and FliR for their export to the periplasm. In the case of flagellin as an export substrate, because of the phenomenon of hook-to-filament switching of export specificity, it was necessary to use temperature-sensitive mutants and establish whether flagellin could be exported to the cell exterior following a shift from the permissive to the restrictive temperature. Again, FlhA, FlhB, FliH, FliI, and FliO were required for its export. No suitable temperature-sensitive fliQ or fliR mutants were available. FliP appeared not to be required for flagellin export, but we suspect that the temperature-sensitive FliP protein continued to function at the restrictive temperature if incorporated at the permissive temperature. Thus, we conclude that these eight proteins are general components of the flagellar export pathway. FliJ was necessary for export of hook-type proteins (FlgD and FlgE); we were unable to test whether FliJ is needed for export of filament-type proteins. We suspect that FliJ may be a cytoplasmic chaperone for the hook-type proteins and possibly also for FliE and the rod proteins. FlgJ was not required for the export of the hook-type proteins; again, because of lack of a suitable temperature-sensitive mutant, we were unable to test whether it was required for export of filament-type proteins. Finally, it was established that there is an interaction between the processes of outer ring assembly and of penetration of the outer membrane by the rod and nascent hook, the latter process being of course necessary for passage of export substrates into the external medium. During the brief transition stage from completion of rod assembly and initiation of hook assembly, the L ring and perhaps the capping protein FlgD can be regarded as bona fide export components, with the L ring being in a formal sense the equivalent of the outer membrane secretin structure of type III virulence factor export systems.
Clostripain: production and use for peptide synthesis. (1991)

The arginine-specific protease Clostripain could efficiently be produced following improved fermentation and isolation procedures. Preparative scale kinetically controlled peptide synthesis of -Arg-Pro- and Arg-Xaa- containing peptides could successfully be performed in high yields with free and immobilized enzyme preparations.
Aspects of Progression in Breast Carcinoma : from ductal carcinoma in situ to invasive cancer (2012)

In the past decades our knowledge concerning breast cancer progression from ductal carcinoma in situ (DCIS) to invasive cancer has grown rapidly. However, molecular factors driving the progression are still largely unknown. In the first study, we investigated tumor evolution in breast cancer by analyzing TP53 mutation status in tumors from various stages of the disease. Presence of the same TP53 mutations in both DCIS and invasive components from the same tumor indicates same cellular origin. The role of mutant TP53 in the progression of breast cancer is less clear and may vary between subtypes. In the second study, we studied the prognosis of basal-like DCIS in a large population-based cohort. Basal-like DCIS was associated with about doubled but not statistically significant risk for local recurrence compared with the other molecular subtypes. Molecular subtype was a better prognostic parameter than histopathological grade. In the third study, we studied markers in primary DCIS in relation to type of recurrence. Interestingly, recurrences after an ER-/HER2+, ER negative or EGFR positive primary DCIS were more often of the in situ type. The molecular subtype ER+/HER2+, FOXA1 positivity and FOXC1 positivity were risk factors for any recurrence. In the fourth study, we proposed a histological classification system for a new entity: neoductgenesis. We also evaluated histologic criteria for neoductgenesis. According to our criteria, good agreements among pathologists were achieved. Neoductgenesis was related to more aggressive tumor biology and to mammographic features. The result indicates potential benefits for women earlier considered having pure DCIS but later diagnosed as breast carcinoma with neoductgenesis, suggesting a need to develop appropriate treatment regiments. Our findings have to be repeated and the relation to prognosis warrants further studies.
Evaluation of Features for Author Name Disambiguation Using Linear Support Vector Machines (2012)

Author name disambiguation allows to distinguish between two or more authors sharing the same name. In a previous paper, we have proposed a name disambiguation framework in which for each author name in each article we build a context consisting of classification codes, bibliographic references, co-authors, etc. Then, by pair wise comparison of contexts, we have been grouping contributions likely referring to the same people. In this paper we examine which elements of the context are most effective in author name disambiguation. We employ linear Support Vector Machines (SVM) to find the most influential features.
Human mini-chromosomes in mouse embryonal stem cells (1997)

We have introduced human mini-chromosomes of 4 Mb and approximately 15 Mb in size into mouse embryonal stem cells. Although these human mini-chromosomes are stable in hamster and chicken cells, they re-arrange or segregate aberrantly in the embryonal stem cells and are rapidly lost in the absence of selection. However, one of the mini-chromosomes re-arranged, acquired mouse centromeric sequences and was then stably maintained for at least 60 population doublings in culture. This mini-chromosome, which is 4 Mb in size, is a candidate for a mouse germ line chromosome vector.
Endoplasmic Reticulum Stress and Diabetes Mellitus. (2003)

Pancreatic beta-cells are strongly engaged in protein secretion and have highly developed endoplasmic reticulum (ER). Proper folding of polypeptide into a three-dimensional structure is essential for cellular function and protein malfolding can threaten cell survival. Various conditions can perturb the protein folding in the ER, which is collectively called ER stress. In order to adapt ER stress conditions, the cells respond in three distinct ways such as transcriptional induction of ER chaperones, translational attenuation, and ER-associated degradation (ERAD). However, when ER functions are severely impaired, the cell is eliminated by apoptosis via transcriptional induction of CHOP/GADD153, the activation of cJUN NH2-terminal kinase, and/or the activation of caspase-12. Recent studies have revealed that beta-cell is one of the most susceptible cells for ER stress, and ER stress-mediated apoptosis in beta-cells can be a cause of diabetes. A comprehensive understanding of the impact of the ER stress pathway in beta-cells and how it relates to the development of diabetes may contribute to provide new targets for the prevention and treatment of this disease.
Recurrent varicella-zoster virus infections in apparently immunocompetent children (1991)

Fourteen generally healthy children (5 females, 9 males, ages 18 months to 13 years) who have developed 2 to 5 attacks of chickenpox are described. Herpes zoster also occurred in 2 of 14 children. No case of chickenpox was severe or associated with complications. General studies of immunoglobulins, specific antibodies to immunization agents, complement and lymphocyte subpopulation number and function indicated that 1 of 14 had low serum IgA and 3 of 14 lacked antibody to 1 (n = 2) or 2 (n = 1) immunization agents. Varicella-zoster virus (VZV)-specific immune studies showed that the children developed VZV-antibody titers by enzyme-linked immunosorbent assay of 1:640 to 1:10 240. By immunoblot assay all appeared to develop a normal spectrum of antibodies to individual VZV proteins. All but one developed VZV cellular immune responses with stimulation indices ranging from 3.6 to 174. Sequential follow-up of 8 patients revealed 1 who became seronegative and 2 who lost VZV cell-mediated immune responses. Chickenpox may recur more frequently than is generally recognized. General and VZV-specific immune investigations are unlikely to indicate a reason.
Signal Transduction in Electrically Stimulated Bone Cells (2001)

The initial events in signal transduction were found to be different when capacitive coupling was compared with inductive coupling and with combined electromagnetic fields; the initial event with capacitive coupling is Ca(2+) ion translocation through cell-membrane voltage-gated calcium channels, whereas the initial event with inductive coupling and with combined electromagnetic fields is the release of Ca(2+) from intracellular stores. The final pathway, however, is the same for all three signals-that is, there is an increase in cytosolic Ca(2+) and an increase in activated cytoskeletal calmodulin.
Substance P (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubstance PBengt E. B. Sandberg and Leslie L. IversenCite this: J. Med. Chem. 1982, 25, 9, 1009–1015Publication Date (Print):September 1, 1982Publication History Published online1 May 2002Published inissue 1 September 1982https://pubs.acs.org/doi/10.1021/jm00351a001https://doi.org/10.1021/jm00351a001research-articleACS PublicationsRequest reuse permissionsArticle Views268Altmetric-Citations94LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Function of Semliki Forest virus E3 peptide in virus assembly: replacement of E3 with an artificial signal peptide abolishes spike heterodimerization and surface expression of E1 (1990)

The Semliki Forest virus spike glycoproteins E1 and p62 form a heterodimeric complex in the endoplasmic reticulum (ER) and are transported as such to the cell surface. In the mature virus particle, the heterodimeric association of E1 and E2 (the cleavage product of p62) is maintained, but as a more labile and acid-sensitive oligomer than the E1-p62 complex. The E3 peptide forms the N-terminal part of the p62 precursor and carries the signal for the translocation of p62 into the lumen of the ER. The question of whether E3 is also important in the formation and stabilization of the E1-p62 heterodimer has been addressed here with the aid of an E3 deletion mutant cDNA. In this construct, the entire E3 was replaced with a cleavable, artificial signal sequence which preserved the membrane topology of an authentic E2. The E3 deletion, when expressed via a recombinant vaccinia virus, abolished heterodimerization of the spike proteins. It also resulted in the complete retention of E1 in the ER and almost total inhibition of E2 transport to the plasma membrane. The oligomerization and transport defect of E1 expressed from the E3 deletion mutant could be complemented with a wild-type p62 provided from a separate coding unit in double infections. These results point to a central role of E3 in complex formation and transport of the viral structural components to the site of budding. In conjunction with earlier work (M. Lobigs and H. Garoff, J. Virol. 64:1233-1240, 1990; J. Wahlberg, W. A. M. Boere, and H. Garoff, J. Virol. 63:4991-4997, 1989), the data support a model of spike protein oligomerization control of Semliki Forest virus assembly and disassembly which may be mediated by the presence of E3 in the uncleaved p62 precursor and release of E3 after cleavage.
Genetic polymorphisms of the beta 2-adrenergic receptor in nocturnal and nonnocturnal asthma. Evidence that Gly16 correlates with the nocturnal phenotype. (1995)

Nocturnal asthma represents a unique subset of patients with asthma who experience worsening symptoms and airflow obstruction at night. The basis for this phenotype of asthma is not known, but beta 2-adrenergic receptors (beta 2AR) are known to downregulate overnight in nocturnal asthmatics but not normal subjects or nonnocturnal asthmatics. We have recently delineated three polymorphic loci within the coding block of the beta 2AR which alter amino acids at positions 16, 27, and 164 and impart specific biochemical and pharmacologic phenotypes to the receptor. In site-directed mutagenesis/recombinant expression studies we have found that glycine at position 16 (Gly16) imparts an accelerated agonist-promoted downregulation of beta 2AR as compared to arginine at this position (Arg16). We hypothesized that Gly16 might be overrepresented in nocturnal asthmatics and thus determined the beta 2AR genotypes of two well-defined asthmatic cohorts: 23 nocturnal asthmatics with 34 +/- 2% nocturnal depression of peak expiratory flow rates, and 22 nonnocturnal asthmatics with virtually no such depression (2.3 +/- 0.8%). The frequency of the Gly16 allele was 80.4% in the nocturnal group as compared to 52.2% in the nonnocturnal group, while the Arg16 allele was present in 19.6 and 47.8%, respectively. This overrepresentation of the Gly16 allele in nocturnal asthma was significant at P = 0.007 with an odds ratio of having nocturnal asthma and the Gly16 polymorphism being 3.8. Comparisons of the two cohorts as to homozygosity for Gly16, homozygosity for Arg16, or heterozygosity were also consistent with segregation of Gly16 with nocturnal asthma. There was no difference in the frequency of polymorphisms at loci 27 (Gln27 or Glu27) and 164 (Thr164 or Ile164) between the two groups. Thus the Gly16 polymorphism of the beta 2AR, which imparts an enhanced downregulation of receptor number, is overrepresented in nocturnal asthma and appears to be an important genetic factor in the expression of this asthmatic phenotype.
Cleavage-Sites in Protein Targeting Signals (1991)

Proteins in both prokaryotic and eukaryotic cells have to find their way among a plethora of subcellular compartments. The targeting information in most cases resides in distinct stretches of amino acids or targeting peptides (TPs). The sequence characteristics of a number of different TPs have been defined by comparative sequence analysis and experimental studies. TPs targeting proteins for secretion, for import into mitochondria, and for import into chloroplasts will be reviewed, with particular emphasis on the patterns of amino acids that define their cleavage sites.
Automatic scan prescription for brain MRI (2001)

Diagnostic brain MRI scans are usually performed by trained medical technologists who manually prescribe the position and orientation of a scanning volume. In this study, a fully automatic computer algorithm is described which compensates for variable patient positioning and acquires brain MRI scans in a predefined reference orientation. The method involves acquiring a rapid water-only pilot scan, segmenting the brain surface, and matching it to a reference surface. The inverse matching transformation is then used to adapt a geometric description of the desired scanning volume, defined relative to the reference surface, to the current patient. Both pilot scan and processing are performed within 30 sec. The method was tested in 25 subjects, and consistently recovered orientation differences between the reference and each subject to within ±5°. Compared to manual prescription, automatic scan prescription promises many potential benefits, including reduced scan times, reproducible scan orientations along anatomically preferable orientations, and better reproducibility for longitudinal studies. Magn Reson Med 45:486–494, 2001. © 2001 Wiley-Liss, Inc.