gebhart/patrepeval huggingface dataset:
An archaeal SET domain protein exhibits distinct lysine methyltransferase activity towards DNA‐associated protein MC1‐α (2005)

The evolutionarily conserved SET domain proteins in eukaryotes have been shown to function as site-specific histone lysine methyltransferases, and play an important role in regulating chromatin-mediated gene transcriptional activation and silencing. Structure-based sequence analysis has revealed that SET domains are also encoded by viruses and bacteria, as well as Archaea. However, their cellular functions remain elusive. In this study, we have characterized a SET domain protein from Methanosarcina mazei strain Gö1 that we refer to as Gö1-SET. We show that Gö1-SET exists as a homodimer in solution, and functions as a lysine methyltransferase with high substrate specificity that is dependent on the amino acid sequence flanking the lysine methylation site. Particularly, Gö1-SET exhibits selective methyltransferase activity towards one of the major archaeal DNA interacting protein MC1-alpha at lysine 37. Our findings suggest that SET domain proteins such as Gö1-SET may restructure archaeal chromatin that is composed of MC1-DNA complexes, and that modulation of chromatin structure by lysine methylation may have arisen before the divergence of the archaeal and eukaryotic lineages.
Characteristics of genomic alterations of lung adenocarcinoma in young never‐smokers (2018)

Non-small-cell lung cancer (NSCLC) has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. While never-smoker patients with NSCLC have been well studied through next generation sequencing, we have yet to recognize the potentially unique molecular features of young never-smoker patients with NSCLC. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients, who were diagnosed with lung adenocarcinoma (LUAD) at 45 years or younger. Besides the well-known gene mutations (e.g., TP53 and EGFR), our study identified several potential lung cancer-associated gene mutations that were rarely reported (e.g., HOXA4 and MST1). The lung cancer-related copy number variations (e.g., EGFR and CDKN2A) were enriched in our cohort (41.7%, 15/36) and the lung cancer-related structural variations (e.g., EML4-ALK and KIF5B-RET) were commonly observed (22.2%, 8/36). Notably, new fusion partners of ALK (SMG6-ALK) and RET (JMJD1C-RET) were found. Furthermore, we observed a high prevalence (63.9%, 23/36) of potentially targetable genomic alterations in our cohort. Finally, we identified germline mutations in BPIFB1 (rs6141383, p.V284M), CHD4 (rs74790047, p.D140E), PARP1 (rs3219145, p.K940R), NUDT1 (rs4866, p.V83M), RAD52 (rs4987207, p.S346*), and MFI2 (rs17129219, p.A559T) were significantly enriched in the young never-smoker patients with LUAD when compared with the in-house noncancer database (p < 0.05). Our study provides a detailed mutational portrait of LUAD occurring in young never-smokers and gives insights into the molecular pathogenesis of this distinct subgroup of NSCLC.
Molecular basis for a geographic variation of varicella-zoster virus recognized by a peptide antibody (1995)

A live attenuated varicella vaccine, derived from a Japanese isolate, is currently being widely used to modulate disease caused by varicella-zoster virus. Differentiation of the vaccine from wild-type isolates has been and will continue to be critical in the assessment of the vaccine in the United States. This has largely relied upon identification of characteristic DNA polymorphisms in the vaccine strain in the United States. This has largely relied upon identification of characteristic DNA polymorphisms in the vaccine strain. In this report, we describe the identification of a new sequence polymorphism, located in the N-terminal coding sequence of open reading frame (ORF) 10. This variation results in the synthesis of an ORF 10 protein that is differentially recognized by antibodies to an ORF 10 synthetic peptide. The variation appears to be completely restricted to Japanese strains, including that used for the live attenuated varicella vaccine. As such, this polymorphism and the antibodies that differentially recognize it could prove highly useful in the assessment of the Japanese vaccine in the United States.
The second time around (2008)

A look at the new &amp;quot;double jeopardy &amp;quot; laws in Queensland So what is ’double jeopardy’ anyway? Most students taking a Legal Studies course will sooner or later come across the concept of ’double jeopardy’, an old p(mciple of English common law wttich emigrated to Australia along with the First Fleet, and ultimately became embedded in the criminal laws of all Australian states and territories. It means simply that no person may be placed on trial more than once in respect of any criminal act on their part, whether they are convicted or acquitted at the end of the first trial. This does not prevent any appeal being raised against the outcome of the first trial, because this is regarded as b~mg part of the first trial process. But once the appeal process has
Conceptualization and Rationale for Consensus Definitions of Terms in Major Depressive Disorder (1991)

In 1988, the MacArthur Foundation Research Network on the Psychobiology of Depression convened a task force to examine the ways in which change points in the course of depressive illness had been described and the extent to which inconsistency in these descriptions might be impeding research on this disorder. We found considerable inconsistency across and even within research reports and concluded that research on depressive illness would be well served by greater consistency in the definition change points in the course of illness. We propose an internally consistent, empirically defined conceptual scheme for the terms remission, recovery, relapse, and recurrence. In addition, we propose tentative operational criteria for each term. Finally, we discuss ways to assess the usefulness of such operational criteria through reanalysis of existing data and the design and conduct of new experiments.
Suppression of Ongoing Adjuvant-Induced Arthritis by Neutralizing the Function of the p28 Subunit of IL-27 (2004)

IL-27 is a recently defined family member of the long-chain four-helix bundle cytokines, which consists of EBI3, an IL-12p40-related protein, and p28, an IL-12p35-related polypeptide. The role of IL-27 in the regulation of inflammatory autoimmune diseases has never been studied. The current study uses the DNA vaccination technology, and highly specific Abs to the p28 subunit of IL-27 that were generated by this technology, to delineate its role in the regulation of adjuvant-induced arthritis in Lewis rats. Neutralizing the in vivo function of IL-27 by targeted DNA vaccines and by Abs against IL-27 p28 that were produced in protected donors could rapidly suppress an ongoing disease. Disease suppression was associated with a reduced ex vivo production of inflammatory cytokines. We then used these Abs to investigate the mechanistic basis of disease suppression, showing that IL-27 is not only involved in directing the polarization of naive T cells, but also affects the proliferative response and cytokine production of Ag-specific effector/memory Th1 cells. This may explain, in part, its important role in the regulation of inflammatory autoimmune diseases, and also suggest novel ways of therapy.
Nanomolar concentration of NSC606985, a camptothecin analog, induces leukemic-cell apoptosis through protein kinase Cδ–dependent mechanisms (2005)

As a promising new class of anticancer drugs, camptothecins have advanced to the forefront of several areas of therapeutic and developmental chemotherapy. In the present study, we report that NSC606985, a rarely studied camptothecin analog, induces apoptosis in acute myeloid leukemia (AML) cells NB4 and U937 and inhibits the proliferation without cell death in breakpoint cluster region-Abelson murine leukemia (bcr-abl) kinase-carrying leukemic K562 cells. For apoptosis induction or growth arrest, nanomolar concentrations of NSC606985 are sufficient. At such low concentrations, this agent also significantly inhibits the clonogenic activity of hematopoietic progenitors from patients with AML. For apoptosis induction, NSC606985 rapidly induces the proteolytic activation of protein kinase Cdelta (PKCdelta) with loss of mitochondrial transmembrane potential (DeltaPsim) and caspase-3 activation. Cotreatment with rottlerin, a PKCdelta-specific inhibitor, completely blocks NSC606985-induced mitochondrial DeltaPsim loss and caspase-3 activation, while the inhibition of caspase-3 by z-DEVD-fluoromethyl ketone (Z-DEVD-fmk) only partially attenuates PKCdelta activation and apoptosis. These data indicate that NSC606985-induced PKCdelta activation is an early event upstream to mitochondrial DeltaPsim loss and caspase-3 activation, while activated caspase-3 has an amplifying effect on PKCdelta proteolysis. In addition, NSC606985-induced apoptosis by PKCdelta also involves caspase-3-independent mechanisms. Taken together, our results suggest that NSC606985 is a potential agent for the treatment of AML.
Mouse CD38 is down-regulated on germinal center B cells and mature plasma cells (1997)

Germinal center formation is the result of antigenic stimulation of B cells in a T cell-rich area. B cells cycle through the germinal centers, and a small percentage survive to become plasma cells or memory B cells. The transformation from a mature B cell into a germinal center B cell and finally into a terminally differentiated B cell is not well understood. Human CD38 is highly expressed on both germinal center B cells and plasma cells, and is useful in delineating these B cell subsets and in understanding the signaling events involved in the development of these B cells. To determine whether CD38 expression on activated germinal center B cells and postgerminal center B cells influences germinal center differentiation, we studied the expression of CD38 in the mouse. CD38 is expressed on follicular B cells in the Peyer's patches but is down-regulated on germinal center B cells located within the Peyer's patches. CD38dim/-B220+ germinal center B cells are also found in the spleens of immunized but not control mice, suggesting that Ag-stimulated germinal center formation is involved in the production of CD38dim/-B220+ B cells. Furthermore, mature plasma cells isolated from in vitro LPS cultures do not express CD38, but do contain high levels of cytoplasmic Ig. These results are in contrast to studies in humans in which CD38 is not found on follicular B cells but is highly expressed on germinal center B cells and plasma cells.
J‐binding protein increases the level and retention of the unusual base J in trypanosome DNA (2002)

The nuclear DNA of Trypanosoma brucei and other kinetoplastid flagellates contains the unusual base beta-d-glucosyl-hydroxymethyluracil, called J, replacing part of the thymine in repetitive sequences. We have described a 100 kDa protein that specifically binds to J in duplex DNA. We have now disrupted the genes for this J-binding protein (JBP) in T. brucei. The disruption does not affect growth, gene expression or the stability of some repetitive DNA sequences. Unexpectedly, however, the JBP KO trypanosomes contain only about 5% of the wild-type level of J in their DNA. Excess J, randomly introduced into T. brucei DNA by growing the cells in the presence of the J precursor 5-hydroxymethyldeoxyuridine, is lost by simple dilution as the KO trypanosomes multiply, showing that JBP does not protect J against removal. In contrast, cells containing JBP lose excess J only sluggishly. We conclude that JBP is able to activate the thymine modification enzymes to introduce additional J in regions of DNA already containing a basal level of J. We propose that JBP is a novel DNA modification maintenance protein.
Mutations in elongation factor EF-1 alpha affect the frequency of frameshifting and amino acid misincorporation in Saccharomyces cerevisiae. (1988)

A mutational analysis of the eukaryotic elongation factor EF-1 alpha indicates that this protein functions to limit the frequency of errors during genetic code translation. We found that both amino acid misincorporation and reading frame errors are controlled by EF-1 alpha. In order to examine the function of this protein, the TEF2 gene, which encodes EF-1 alpha in Saccharomyces cerevisiae, was mutagenized in vitro with hydroxylamine. Sixteen independent TEF2 alleles were isolated by their ability to suppress frameshift mutations. DNA sequence analysis identified eight different sites in the EF-1 alpha protein that elevate the frequency of mistranslation when mutated. These sites are located in two different regions of the protein. Amino acid substitutions located in or near the GTP-binding and hydrolysis domain of the protein cause suppression of frameshift and nonsense mutations. These mutations may effect mistranslation by altering the binding or hydrolysis of GTP. Amino acid substitutions located adjacent to a putative aminoacyl-tRNA binding region also suppress frameshift and nonsense mutations. These mutations may alter the binding of aminoacyl-tRNA by EF-1 alpha. The identification of frameshift and nonsense suppressor mutations in EF-1 alpha indicates a role for this protein in limiting amino acid misincorporation and reading frame errors. We suggest that these types of errors are controlled by a common mechanism or closely related mechanisms.
Influence of Diets Containing Eicosapentaenoic or Docosahexaenoic Acid on Growth and Metastasis of Breast Cancer Cells in Nude Mice (1995)

Future dietary intervention trials designed to reduce the risk of recurrence in the postsurgical breast cancer patient should include the evaluation of eicosapentaenoic acid and docosahexaenoic acid supplementation.
Retention of bacteria on a substratum surface with micro-patterned hydrophobicity (2000)

Bacteria adhere to almost any surface, despite continuing arguments about the importance of physico-chemical properties of substratum surfaces, such as hydrophobicity and charge in biofilm formation. Nevertheless, in vivo biofilm formation on teeth and also on voice prostheses in laryngectomized patients is less on hydrophobic than on hydrophilic surfaces. With the aid of micro-patterned surfaces consisting of 10-microm wide hydrophobic lines separated by 20-microm wide hydrophilic spacings, we demonstrate here, for the first time in one and the same experiment, that bacteria do not have a strong preference for adhesion to hydrophobic or hydrophilic surfaces. Upon challenging the adhering bacteria, after deposition in a parallel plate flow chamber, with a high detachment force, however, bacteria were easily wiped-off hydrophobic lines, most notably when these lines were oriented parallel to the direction of flow. Adhering bacteria detached slightly less from the hydrophilic spacings in between, but preferentially accumulated adhering on the hydrophilic regions close to the interface between the hydrophilic spacings and hydrophobic lines. It is concluded that substratum hydrophobicity is a major determinant of bacterial retention while it hardly influences bacterial adhesion.
Combinatorial and Evolution-Based Methods in the Creation of Enantioselective Catalysts (2001)

Combinatorial methods in the development of enantioselective homogeneous catalysts constitute a new branch of catalysis research. The goal is to prepare libraries of potential asymmetric catalysts, rather than choosing the traditional one-catalyst-at-a-time approach. Several conceptional advancements have been reported in the parallel preparation of chiral ligands. Currently the most meaningful systems constitute modularly constructed ligands on solid supports, which allow high degrees of structural diversity and thus the maximum probability of finding enantioselective catalysts or even new types of ligands for asymmetric catalysis. Search strategies have been developed which amongst other things, lead to catalysts not likely to have been discovered by traditional methods. Genuine application of such strategies involve thousands of catalysts and require high-throughput screening systems capable of assaying enantioselectivity. The first high-throughput ee-screening systems were in fact developed for use in the directed evolution of enantioselective enzymes, a process based on "evolution in the test tube" in which the appropriate methods of random mutagenesis, gene expression, and ee assays are combined. Since no screening system is likely to be universal, different approaches are necessary. Thus far these include assays based on UV/Vis, fluorescence, circular dichroism, mass spectrometry, and even modified gas chromatography as well as special forms of capillary electrophoresis. One of the most efficient systems involves the concept of the mass-spectrometric detection of deuterium-labeled pseudo-enantiomers and pseudo-prochiral compounds with which about 1000 exact ee determinations can be achieved per day, although the assay is restricted to kinetic resolution and/or reactions of prochiral compounds bearing enantiotopic groups. Super-high-throughput screening for enantioselectivity is possible in many cases by making use of chirally modified capillary array electrophoresis in a parallel step. Accordingly, 7000 to 30 000 ee determinations can be carried out per day. These and other analytical developments are expected to stimulate further research in the combinatorial search for asymmetric homogeneous catalysts and in the directed evolution of enantioselective enzymes for use in organic chemistry.
Selective IRAK4 Inhibition Attenuates Disease in Murine Lupus Models and Demonstrates Steroid Sparing Activity (2016)

The serine/threonine kinase IL-1R-associated kinase (IRAK)4 is a critical regulator of innate immunity. We have identified BMS-986126, a potent, highly selective inhibitor of IRAK4 kinase activity that demonstrates equipotent activity against multiple MyD88-dependent responses both in vitro and in vivo. BMS-986126 failed to inhibit assays downstream of MyD88-independent receptors, including the TNF receptor and TLR3. Very little activity was seen downstream of TLR4, which can also activate an MyD88-independent pathway. In mice, the compound inhibited cytokine production induced by injection of several different TLR agonists, including those for TLR2, TLR7, and TLR9. The compound also significantly suppressed skin inflammation induced by topical administration of the TLR7 agonist imiquimod. BMS-986126 demonstrated robust activity in the MRL/lpr and NZB/NZW models of lupus, inhibiting multiple pathogenic responses. In the MRL/lpr model, robust activity was observed with the combination of suboptimal doses of BMS-986126 and prednisolone, suggesting the potential for steroid sparing activity. BMS-986126 also demonstrated synergy with prednisolone in assays of TLR7- and TLR9-induced IFN target gene expression using human PBMCs. Lastly, BMS-986126 inhibited TLR7- and TLR9-dependent responses using cells derived from lupus patients, suggesting that inhibition of IRAK4 has the potential for therapeutic benefit in treating lupus.
Detection with multi-exit asymmetric boosting (2008)

We introduce a generalized representation for a boosted classifier with multiple exit nodes, and propose a method to training which combines the idea of propagating scores across boosted classifiers [14, 17] and the use of asymmetric goals [13]. A means for determining the ideal constant asymmetric goal is provided, which is theoretically justified under a conservative bound on the ROC operating point target and empirically near-optimal under the exact bound. Moreover, our method automatically minimizes the number of weak classifiers, avoiding the need to retrain a boosted classifier multiple times for empirical best performance as in conventional methods. Experimental results shows significant reduction in training time and number of weak classifiers, as well as better accuracy, compared to conventional cascades and multi-exit boosted classifiers.
Rheological properties of syndiotacticity‐rich ultrahigh molecular weight poly(vinyl alcohol) dilute solution (2001)

Abstract Viscoelastic behavior of the dilute solution of ultrahigh molecular weight syndiotactic poly(vinyl alcohol) (UHMW s‐PVA)/dimethyl sulfoxide (DMSO)/water was investigated through rheological response. Below a critical temperature, the dynamic storage modulus ( G ′) of the solution became greater than the dynamic loss modulus ( G ″) and the viscoelastic exponent for G ′ became smaller than that for G ″ before macroscopic gelation, which indicates the evolution of viscoelastic solid properties at the sol state. Also, the loss tangent (tan δ) of the solution below the critical temperature increased with increasing frequency. Consequently, the dilute solution of UHMW s‐PVA/DMSO/water showed the rheological behaviors as can be observed in general chemical or physical gel systems below the critical temperature. These results suggest that solid‐like heterogeneity prevailed in the solution before macroscopic gelation with decreasing temperature. Such heterogeneity was considered as phase‐separated domains attributed to spinodal decomposition. © 2001 John Wiley &amp; Sons, Inc. J Appl Polym Sci 82: 569–576, 2001
Carbonylative Polymerization of Propylene Oxide: A Multicatalytic Approach to the Synthesis of Poly(3-Hydroxybutyrate) (2010)

We report a highly efficient method for the synthesis of poly(3-hydroxybutyrate) by the carbonylative polymerization of propylene oxide. The use of compatible epoxide carbonylation and lactone polymerization catalysts allows for a one-pot reaction that eliminates the need to isolate and purify the toxic beta-butyrolactone intermediate.
Expression cloning of a cDNA encoding a novel murine B cell activation marker. Homology to human CD38. (1993)

A rat mAb (NIM-R5) has recently been prepared against a novel murine B cell activation marker. We report here isolation of a cDNA (1-19) encoding the B cell-derived protein recognized by NIM-R5 antibody. This cDNA contains an open reading frame that encodes a polypeptide of 304 amino acids with a predicted molecular weight of 34,500. The existence of a 22-amino acid hydrophobic region located 23 amino acids from the amino terminal of the deduced protein, together with four potential N-linked glycosylation sites, characterize the deduced protein encoded by I-19 cDNA as a typical type II transmembrane glycoprotein. Although I-19 cDNA appears to encode a novel murine protein, its nucleotide sequence and deduced amino acid sequence show approximately 70% homology to the previously reported sequence of human CD38, suggesting that I-19 cDNA encodes either the mouse homologue of CD38 or a closely related protein. Northern blot analysis of the expression of this cDNA product in a variety of cell types, together with immunoprecipitation of the recombinant protein expressed in BaF3 cells, indicated that I-19 cDNA encodes not only the epitope recognized by NIM-R5 but also a protein that is indistinguishable biochemically and in terms of distribution from the murine B cell activation marker recognized by NIM-R5 antibody. Chromosomal mapping studies have localized this locus to the proximal region of mouse chromosome 5. We anticipate that the availability of probes for the murine B cell activation marker recognized by NIM-R5, and the recombinant protein itself, will greatly aid efforts to define the role of this molecule in murine B cell development.
UROPLAKIN II AS A PROMISING MARKER FOR MOLECULAR DIAGNOSIS OF NODAL METASTASES FROM BLADDER CANCER: COMPARISON WITH CYTOKERATIN 20 (2005)

These results indicate that UP II might be a more useful marker than CK 20 for detecting micrometastases of bladder cancer in the pelvic lymph nodes, although a greater number of patients and longer followup are needed to come to a definitive conclusion.