gebhart/patrepeval huggingface dataset:
Target Sites of Herbicide Action (2020)

Biochemistry and Genetic Control of the Photosys-tem-II Herbicide Target Site. Inhibition of Carotenoid Biosynthesis by Herbicides. Herbicide-Induced Radical Damage and Antioxida-tive Systems. Fatty Acid Biosynthesis - A Target Site of Herbicide Action. Herbicide Interference with Cell Division in Plants. Herbi-cides as Inhibitors of Amino Acid Biosynthesis. Gibberellins: Metabolic Pathways and Inhibitors of Biosynthesis. Producing Her-bicide-Resistant Plants by Gene Transfer Technology. Modern As-pects of Enzyme Inhibition with Particular Emphasis on Reaction-In-termediate Analogs and Other Potent, Reversible Inhibitors. New Plant-Specific Targets for Future Herbicides. Index.
Crosstalk between the Estrogen Receptor and the HER Tyrosine Kinase Receptor Family: Molecular Mechanism and Clinical Implications for Endocrine Therapy Resistance (2008)

Breast cancer evolution and tumor progression are governed by the complex interactions between steroid receptor [estrogen receptor (ER) and progesterone receptor] and growth factor receptor signaling. In recent years, the field of cancer therapy has witnessed the emergence of multiple strategies targeting these specific cancer pathways and key molecules (ER and growth factor receptors) to arrest tumor growth and achieve tumor eradication; treatment success, however, has varied and both de novo (up front) and acquired resistance have proven a challenge. Recent studies of ER biology have revealed new insights into ER action in breast cancer and have highlighted the role of an intimate crosstalk between the ER and HER family signaling pathways as a fundamental contributor to the development of resistance to endocrine therapies against the ER pathway. The aim of this review article is to summarize the current knowledge on mechanisms of resistance of breast cancer cells to endocrine therapies due to the crosstalk between the ER and the HER growth factor receptor signaling pathways and to explore new available therapeutic strategies that could prolong duration of response and circumvent endocrine resistant tumor growth.
Membrane topology of the Drosophila OR83b odorant receptor (2007)

By analogy to mammals, odorant receptors (ORs) in insects, such as Drosophila melanogaster, have long been thought to belong to the G-protein coupled receptor (GPCR) superfamily. However, recent work has cast doubt on this assumption and has tentatively suggested an inverted topology compared to the canonical N(out) - C(in) 7 transmembrane (TM) GPCR topology, at least for some Drosophila ORs. Here, we report a detailed topology mapping of the Drosophila OR83b receptor using engineered glycosylation sites as topology markers. Our results are inconsistent with a classical GPCR topology and show that OR83b has an intracellular N-terminus, an extracellular C-terminus, and 7TM helices.
Controlled doping of phthalocyanine layers by cosublimation with acceptor molecules: A systematic Seebeck and conductivity study (1998)

We investigate the doping of vanadyl–phthalocyanine by a fluorinated form of tetracyano-quinodimethane as an example of controlled doping of thin organic dye films by cosublimation of matrix and dopant. The electrical parameters of the films derived from conductivity and Seebeck measurements show that the results largely follow standard models used to describe the doping of crystalline semiconductors; e.g., a smooth shift of the Fermi level towards the valence states with increasing doping is observed. Other effects, like the superlinear increase of conductivity with the molar doping ratio, need the inclusion of additional effects like percolation.
Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Clinical Practice Guideline Update (2013)

The Update Committee recommends that HER2 status (HER2 negative or positive) be determined in all patients with invasive (early stage or recurrence) breast cancer on the basis of one or more HER2 test results (negative, equivocal, or positive). Testing criteria define HER2-positive status when (on observing within an area of tumor that amounts to >10% of contiguous and homogeneous tumor cells) there is evidence of protein overexpression (IHC) or gene amplification (HER2 copy number or HER2/CEP17 ratio by ISH based on counting at least 20 cells within the area). If results are equivocal (revised criteria), reflex testing should be performed using an alternative assay (IHC or ISH). Repeat testing should be considered if results seem discordant with other histopathologic findings. Laboratories should demonstrate high concordance with a validated HER2 test on a sufficiently large and representative set of specimens. Testing must be performed in a laboratory accredited by CAP or another accrediting entity. The Update Committee urges providers and health systems to cooperate to ensure the highest quality testing.
Fatty Acid Specificity in Lipase-Catalyzed Synthesis of Glucoside Esters (1992)

The fatty acid specificity of the B-lipase derived from Candida antarctica was investigated in the synthesis of esters of ethyl D-glucopyranoside. The specificity was almost identical with respect to straight-chain fatty acids with 10 to 18 carbon atoms. However, lower fatty acids such as hexanoic and octanoic acid and the unsaturated 9-cis-octadecenoic acid were found to be poor substrates of the enzyme. As a consequence of this selectivity, these fatty acids were accumulated in the unconverted fraction when ethyl D-glucopyranoside was esterified with an excess of a mixture of fatty acids. This accumulation can reduce the overall effectiveness of the process as the activity of the lipase was found to be reduced when exposed to high concentrations of short-chain fatty acids. Finally, using a simplified experimental set-up, the specificity of the C. antarctica B-lipase was compared to the specificity of lipases derived from C. rugosa, Mucor miehei, Humicola, and Pseudomonas. Apart from the C. rugosa lipase, which exhibited a very poor performance, all the enzymes showed a very similar specificity with respect to fatty acids longer than octanoic acid while only the C. antarctica B-lipase showed activity towards sort-chain fatty acids.
Monoclonal IgM antibody protection in mice against infection with an encapsulated strain of Staphylococcus epidermidis (1991)

Passive protective activities of three different classes of monoclonal antibodies in mice against challenge with strain ATCC 31432 (capsular type I) of Staphylococcus epidermidis were examined. Monoclonal IgM antibody passively protected mice against challenge with the homologous strain, whereas monoclonal IgG1 and IgG2b antibodies did not. The protective activity of IgM was absorbed by the cell surface antigen extracted from the homologous strain but not by the antigen from heterologous strains. Rapid reduction of viable cells took place in the peritoneal cavity of mice immunized with monoclonal IgM as early as 6 h after the challenge with the homologous strain. An enzyme-linked immunosorbent inhibition assay showed there was remarkable inhibition with the homologous cell surface antigen but not with heterologous preparations from other strains. Results suggest that in the mouse the major passive protection against the S. epidermidis strain is provided by the IgM antibody to the cell surface antigen.
Xenobiotic Effects on Intestinal Stem Cell Proliferation in Adult Honey Bee (Apis mellifera L) Workers (2014)

The causes of the current global decline in honey bee health are unknown. One major group of hypotheses invokes the pesticides and other xenobiotics to which this important pollinator species is often exposed. Most studies have focused on mortality or behavioral deficiencies in exposed honey bees while neglecting other biological functions and target organs. The midgut epithelium of honey bees presents an important interface between the insect and its environment. It is maintained by proliferation of intestinal stem cells throughout the adult life of honey bees. We used caged honey bees to test multiple xenobiotics for effects on the replicative activity of the intestinal stem cells under laboratory conditions. Most of the tested compounds did not alter the replicative activity of intestinal stem cells. However, colchicine, methoxyfenozide, tetracycline, and a combination of coumaphos and tau-fluvalinate significantly affected proliferation rate. All substances except methoxyfenozide decreased proliferation rate. Thus, the results indicate that some xenobiotics frequently used in apiculture and known to accumulate in honey bee hives may have hitherto unknown physiological effects. The nutritional status and the susceptibility to pathogens of honey bees could be compromised by the impacts of xenobiotics on the maintenance of the midgut epithelium. This study contributes to a growing body of evidence that more comprehensive testing of xenobiotics may be required before novel or existing compounds can be considered safe for honey bees and other non-target species.
Scientific and Political Impediments to Successful Islet Transplantation (1997)

Islet transplantation is a treatment for diabetes that has the potential to normalize glucose levels and prevent the development of complications. In spite of the simplicity of the concept and the urgent need to provide such a treatment to patients, there has been a frustrating lack of progress. This perspective delves into the scientific and political impediments to success. The scientific barriers are the need to find a satisfactory source of insulin-producing tissue and the requirement to prevent this tissue from being destroyed by immune rejection and autoimmunity. The problems and potential of allografts, xenografts, and the development of cell lines are discussed. Multiple approaches to the prevention of immune destruction are considered, including immunobarrier devices, immunosuppression, development of tolerance, and genetic manipulation. The political barriers discussed include the problems of high expectations, the controversy surrounding targeted research, the balance between basic and applied research, the roles of industry and academia, the concerns about xenotransplantation, and the difficulties in developing a planned approach to the problem.
An Increased Percentage of Long Amyloid β Protein Secreted by Familial Amyloid β Protein Precursor (βApp 717 ) Mutants (1994)

Normal processing of the amyloid beta protein precursor (beta APP) results in secretion of a soluble 4-kilodalton protein essentially identical to the amyloid beta protein (A beta) that forms insoluble fibrillar deposits in Alzheimer's disease. Human neuroblastoma (M17) cells transfected with constructs expressing wild-type beta APP or the beta APP717 mutants linked to familial Alzheimer's disease were compared by (i) isolation of metabolically labeled 4-kilodalton A beta from conditioned medium, digestion with cyanogen bromide, and analysis of the carboxyl-terminal peptides released, or (ii) analysis of the A beta in conditioned medium with sandwich enzyme-linked immunosorbent assays that discriminate A beta 1-40 from the longer A beta 1-42. Both methods demonstrated that the 4-kilodalton A beta released from wild-type beta APP is primarily but not exclusively A beta 1-40. The beta APP717 mutations, which are located three residues carboxyl to A beta 43, consistently caused a 1.5- to 1.9-fold increase in the percentage of longer A beta generated. Long A beta (for example, A beta 1-42) forms insoluble amyloid fibrils more rapidly than A beta 1-40. Thus, the beta APP717 mutants may cause Alzheimer's disease because they secrete increased amounts of long A beta, thereby fostering amyloid deposition.
Casein kinase II phosphorylates p34cdc2 kinase in G1 phase of the HeLa cell division cycle. (1992)

The activity of p34cdc2 kinase is regulated in the phases of vertebrate cell cycle by mechanisms of phosphorylation and dephosphorylation. In this paper, we demonstrate that casein kinase II (CKII) phosphorylates p34cdc2 in vivo and in vitro at Ser39 during the G1 phase of HeLa cell division cycle. Human p34cdc2 shows a typical phosphorylation sequence motif site for CKII at Ser39 (ES39EEE). In our experiments, either p34cdc2 expressed and purified from bacteria or p34cdc2 immunoprecipitated from HeLa cells enriched in G1 by elutriation were substrates for in vitro phosphorylation by CKII. Phosphoamino acid analysis, N-chlorosuccinimide mapping, and two-dimensional tryptic mapping of p34cdc2 phosphorylated in vitro were performed to determine the phosphorylation site. A synthetic peptide spanning residues 33-50 of human p34cdc2, including the CKII site, was used to map the site. In addition, phosphorylation at Ser39 also occurs in vivo, since p34cdc2 is phosphorylated during G1 on serine, and its two-dimensional tryptic map shows two phosphopeptides that comigrate exactly with the synthetic peptides used as standard.
Wound Healing: An Overview (2006)

Understanding wound healing today involves much more than simply stating that there are three phases: inflammation, proliferation, and maturation. Wound healing is a complex series of reactions and interactions among cells and "mediators." Each year, new mediators are discovered and our understanding of inflammatory mediators and cellular interactions grows. This article will attempt to provide a concise overview on wound healing and wound management.
A mutational analysis of the insulin gene transcription control region: expression in beta cells is dependent on two related sequences within the enhancer. (1987)

Cell-specific expression of the insulin gene is controlled by cis-acting DNA sequences located within approximately equal to 350 base pairs of the 5' flanking DNA immediately upstream from the transcription start site. Using synthetic oligonucleotides, we have constructed a systematic series of block replacement mutants spanning this region. No single sequence appears to be absolutely required for expression. However, three of the mutants exhibit 5-10 times less activity and several others show 2-3 times less. Simultaneous mutation of two of the most mutationally sensitive regions leads to virtual abolition of activity. These two elements are structurally related and presumably represent key components of the machinery determining the cell-specific expression of the insulin gene.
[Decrease of basal levels of gastrin following H. pylori eradication]. (1995)

H. pylori eradication in patients with duodenal ulcer was associated with a significant decrease in basal levels of serum gastrin. Although the verification of such a decrease doesn't have an optimal relationship between sensitivity and specificity, it could be an aid as a useful non-invasive method to monitor the efficiency of therapy, both in H. pylori eradication and in the resolution of the associated gastritis. This procedure is also associated with early results and a low cost.
The complete sequence of the 1,683-kb pSymB megaplasmid from the N 2 -fixing endosymbiont Sinorhizobium meliloti (2001)

Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N(2)-fixing bacterium Sinorhizobium meliloti revealed that the replicon has a high gene density with a total of 1,570 protein-coding regions, with few insertion elements and regions duplicated elsewhere in the genome. The only copies of an essential arg-tRNA gene and the minCDE genes are located on pSymB. Almost 20% of the pSymB sequence carries genes encoding solute uptake systems, most of which were of the ATP-binding cassette family. Many previously unsuspected genes involved in polysaccharide biosynthesis were identified and these, together with the two known distinct exopolysaccharide synthesis gene clusters, show that 14% of the pSymB sequence is dedicated to polysaccharide synthesis. Other recognizable gene clusters include many involved in catabolic activities such as protocatechuate utilization and phosphonate degradation. The functions of these genes are consistent with the notion that pSymB plays a major role in the saprophytic competence of the bacteria in the soil environment.
Spectroscopic study of the surface of zeolite Y. II. Infrared spectra of structural hydroxyl groups and adsorbed water on alkali, alkaline earth, and rare earth ion-exchanged zeolites (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpectroscopic study of the surface of zeolite Y. II. Infrared spectra of structural hydroxyl groups and adsorbed water on alkali, alkaline earth, and rare earth ion-exchanged zeolitesJohn William WardCite this: J. Phys. Chem. 1968, 72, 12, 4211–4223Publication Date (Print):November 1, 1968Publication History Published online1 May 2002Published inissue 1 November 1968https://pubs.acs.org/doi/10.1021/j100858a046https://doi.org/10.1021/j100858a046research-articleACS PublicationsRequest reuse permissionsArticle Views1265Altmetric-Citations144LEARN 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 Get e-Alerts
The prognostic influence of tumour-infiltrating lymphocytes in cancer: a systematic review with meta-analysis (2011)

Any future studies should be carefully designed, to prevent overestimating the effect of TILs on prognosis. In this context, ratios between TIL subsets may be more informative.
An Industrially Viable Catalyst System for Palladium‐Catalyzed Telomerizations of 1,3‐Butadiene with Alcohols (2004)

Abstract The telomerization reaction of 1,3‐butadiene with alcohols to give alkyl octadienyl ethers in the presence of palladium–carbene catalysts has been studied in detail. Unprecedented catalyst efficiency with turnover numbers (TON) up to 1 500 000 and turnover frequencies (TOF) up to 100 000 h −1 have been obtained after optimization for the reaction of methanol in the presence of an excess of in situ generated carbene ligands. High yields (75–97 %) and catalyst productivities (TON 15 000–100 000) are observed for other aliphatic alcohols and phenols. For comparison five carbene–palladium(0) complexes have been synthesized and characterized by X‐ray crystallography. Both electronic and steric effects on the stability and reactivity of the catalysts have been discussed on the basis of density functional theory calculations.
Enzyme Pattern and Aerobic Growth of Saccharomyces cerevisiae Under Various Degrees of Glucose Limitation (1968)

The enzyme pattern of Saccharomyces cerevisiae was followed during batch growth and in continuous culture in a synthetic medium limited for glucose under aerobic conditions. Seven enzymes were measured: succinate-cytochrome c oxidoreductase, malate dehydrogenase, nicotinamide adenine dinucleotide-linked glutamate dehydrogenase, malate synthase, isocitrate lyase, aldolase, and nicotinamide adenine dinucleotide phosphate (NADP(+))-linked glutamate dehydrogenase. During fermentation of glucose and high growth rate (mu) during the first log phase in batch experiments, the first five enzymes (group I) were repressed, and aldolase and NADP(+)-linked glutamate dehydrogenase (group II) were derepressed. During growth on the accumulated ethyl alcohol and lower mu, the group I enzymes were preferentially formed and the other two were repressed. A sequence of derepression of the group I enzymes was found during the shift from glucose to ethyl alcohol metabolism, which can be correlated with a strong increase in the percentage of single (nonbudding) cells in the population. A correlation between the state of cells in the budding cycle and enzyme repression and derepression is suggested. In continuous culture, the enzyme pattern was shown to be related to the growth rate. The group I enzymes were repressed at high growth rates, while the group II enzymes were derepressed. Each enzyme exhibits a different dependence. The enzyme pattern is shown to depend on the rate of substrate consumption as well as on the type of metabolism and to be correlated with the budding cycle. The enzyme pattern is considered to be controlled by changes of intracellular catabolic or metabolic conditions inherent in the division cycle.
Genetic algorithms for a robust 3-D MR-CT registration (2000)

The aim of this paper is to present an original usage of genetic algorithms as a robust search space sampler in application to 3-D medical image elastic registration. An overview of the standard steps of a registration algorithm is given. We focus on the genetic algorithms use and particularly on the problem of extraction of the optimal solution among the final genetic population. We provide an original encoding scheme relying on a structural approach of point matching and then point out the need for a local optimization process. We then illustrate the algorithm with a concrete registration example and assert the results with a direct multivolume rendering tool. Finally, the algorithm is applied on the vanderbilt medical image database to assert the robustness and in order to compare it with other techniques.
Proteins present in bovine papillomavirus particles (1987)

Analysis by two-dimensional gel electrophoresis and silver staining of heavy full, light full, and empty bovine papillomavirus particles has shown that the major capsid protein L1 is highly modified. Besides exhibiting at least 13 isoelectric point variants of approximately the same molecular mass (54 kilodaltons), it is suggested that an additional heavier protein chain (69 kilodaltons) is also derived from L1 by glycosylation. These modifications may stabilize the particle structure. Treatment with neuraminidase reduces the number of modification products detectable, with a concomitant increase in the more basic forms of L1. Although it was not possible to detect histones in any of the preparations, proteins of similar molecular mass were detected. Therefore, it is suggested that the basic tails of L1 bind to the DNA in a manner similar to that of histone. Calculation of the theoretical mobilities of the papillomavirus proteins shows good agreement with the actual position of L1 and its isoelectric point variants and suggests that two of the proteins with molecular masses similar to those of the histones may actually be coded by the bovine papillomavirus E7 and E5 open reading frames.
Fractional Vortices as Evidence of Time-Reversal Symmetry Breaking in High-Temperature Superconductors (1995)

We argue that recent experiments by Kirtley et al. may show evidence of time-reversal symmetry breaking in ${\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}{O}_{7}$ at crystal grain boundaries. We illustrate this through a Ginzburg-Landau model calculation. Further experimental tests are proposed.
Finding Meaning in the Resistance of Preschool Children: Critical Theory Takes an Interpretive Look (2017)

Offers an analysis to resistant behavior of preschool children that goes beyond lack of socialization. This interpretation focuses upon the social and cultural meanings of individual and group behaviors. The article is concerned with the acts of the children that run contrary to, or simply outside of, the sanctioned school activities. This is an important vantage from which to analyze preschool resistance because some important behaviors can be identified at the point when they are first likely to occur; when young children, as members of a peer group, first meet figures of authority.