gebhart/patrepeval huggingface dataset:
Analysis of t(15;17) chromosomal breakpoint sequences in therapy‐related versus de novo acute promyelocytic leukemia: Association of DNA breaks with specific DNA motifs at PML and RARA loci (2010)

We compared genomic breakpoints at the PML and RARA loci in 23 patients with therapy-related acute promyelocytic leukemia (t-APL) and 25 de novo APL cases.Eighteen of 23 t-APL cases received the topoisomerase II poison mitoxantrone for their primary disorder. DNA breaks were clustered in a previously reported 8 bp "hot spot" region of PML corresponding to a preferred site of mitoxantrone-induced DNA topoisomerase II-mediated cleavage in 39% of t-APL occurring in patients exposed to this agent and in none of the cases arising de novo (P = 0.007). As to RARA breakpoints, clustering in a 3' region of intron 2 (region B) was found in 65% of t-APL and 28% of de novo APL patients, respectively. Scan statistics revealed significant clustering of RARA breakpoints in region B in t-APL cases (P = 0.001) as compared to de novo APL (P = 1). Furthermore, approximately 300 bp downstream of RARA region B contained a sequence highly homologous to a topoisomerase II consensus sequence. Biased distribution of DNA breakpoints at both PML and RARA loci suggest the existence of different pathogenetic mechanisms in t-APL as compared with de novo APL.
P4–423: Small‐molecule lead identification for inhibition of tau oligomer formation (2013)

There is a need for alternative approaches for the development of disease-modifying therapeutics for Alzheimer's disease (AD) as all phase III drug development programs to-date based on the amyloid hypothesis have failed to meet their clinical endpoints. Research advances indicate that pre-tangle aggregates of tau cause transmission of pathology and symptoms related to memory formation validating tau oligomers as a target for drug discovery. A highly differentiated HTS assay (proximity-based) was developed to discover inhibitors of tau oligomer formation and transferred to MHTSC to screen a drug-like library of 100,000 compounds. Cytotoxicity studies were performed using SH-SY5Y neuroblastoma cells on a high throughput platform. Medicinal chemistry analysis was performed that enabled clustering of hits into chemical series that demonstrated a preliminary SAR. HTS hit triage was performed including confirmation of activity in primary assays with dose response, mass spec evaluation of structure and purity, elimination of reactive species, and removal of known/suspected promiscuous inhibitors or compounds that may contribute to tau aggregation at high concentrations. Lastly, lead series were prioritized based on an analysis of novelty, freedom-to-operate, and the potential for intellectual property on composition of matter. For neurocytotoxicity, 338 active hits and 3 toxic control compounds were evaluated. Cell growth was inhibited at less than 50 uM by fifty compounds and the controls. Only 14 compounds had IC50 values <10 uM. Medicinal chemistry analysis was performed on the 576 most active inhibitors from the HTS assay. Cytotoxic compounds were eliminated and initial SAR was developed with compounds clustered by structure type. The clustering revealed that there are 3 large series (>10 compounds), 6 medium series (4 - 5 compounds), 8 small sized series (2 - 3 compounds), and 22 singletons. The preliminary analysis of the structures clearly demonstrates that certain structural classes are active in this assay. It also indicates that hit optimization is possible since a range of potency is observed within structural classes. The HTS has achieved the important goal of finding viable compounds as starting points for medicinal chemical optimization to generate leads.
Multiple mechanisms for the phosphorylation of C-terminal regulatory sites in rabbit muscle glycogen synthase expressed in COS cells (1996)

Glycogen synthase can be inactivated by sequential phosphorylation at the C-terminal residues Ser652 (site 4), Ser648 (site 3c), Ser644 (site 3b) and Ser640 (site 3a) catalysed by glycogen synthase kinase-3. In vitro, glycogen synthase kinase-3 action requires that glycogen synthase has first been phosphorylated at Ser656 (site 5) by casein kinase II. Recently we demonstrated that inactivation is linked only to phosphorylation at site 3a and site 3b, and that, in COS cells, modification of these sites can occur by alternative mechanisms independent of any C-terminal phosphorylations [Skurat and Roach (1995) J. Biol. Chem. 270, 12491-12497]. To address these mechanisms multiple Ser-->Ala mutations were introduced in glycogen synthase such that only site 3a or site 3b remained intact. Additional mutation of Arg637-->Gln eliminated phosphorylation of site 3a, indicating that Arg637 may be important for recognition of site 3a by its corresponding protein kinase(s). Similarly, additional mutation of Pro645-->Ala eliminated phosphorylation of site 3b, indicating a possible involvement of 'proline-directed' protein kinase(s). Mutation of Arg637 alone did not activate glycogen synthase as expected from the loss of phosphorylation at site 3a. Rather, mutation of both Arg637 and the Ser-->Ala substitution at site 3b was required for substantial activation. The results suggest that sites 3a and 3b can be phosphorylated independently of one another by distinct protein kinases. However, phosphorylation of site 3b can potentiate phosphorylation of site 3a, by an enzyme such as glycogen synthase kinase-3.
Nanomechanics of Lipid Bilayers: Heads or Tails? (2010)

Understanding the effect of mechanical stress on membranes is of primary importance in biophysics. Here we use force spectroscopy AFM to quantitatively characterize the nanomechanical stability of supported lipid bilayers as a function of their chemical composition. The onset of plastic deformation reveals itself as a repetitive jump in the approaching force curve, which represents a molecular fingerprint for the bilayer mechanical stability. By systematically probing a set of chemically distinct supported lipid bilayers (SLBs), we first show that both the headgroup and tail have a decisive effect on their mechanical properties. While the mechanical stability of the probed SLBs linearly increases by 3.3 nN upon the introduction of each additional -CH(2)- in the chain, it exhibits a significant dependence on the phospholipid headgroup, ranging from 3 nN for DPPA to 66 nN for DPPG. Furthermore, we also quantify the reduction of the membrane mechanical stability as a function of the number of unsaturations and molecular branching in the chemical structure of the apolar tails. Finally, we demonstrate that, upon introduction of cholesterol and ergosterol, contrary to previous belief the mechanical stability of membranes not only increases linearly in the liquid phase (DLPC) but also for phospholipids present in the gel phase (DPPC). Our results are discussed in the framework of the continuum nucleation model. This work highlights the compelling effect of subtle variations in the chemical structure of phospholipid molecules on the membrane response when exposed to mechanical forces, a mechanism of common occurrence in nature.
Involvement of Phospholipase Cγ1 in Mouse Egg Activation Induced by a Truncated Form of the C-kit Tyrosine Kinase Present in Spermatozoa (1998)

Microinjection of a truncated form of the c-kit tyrosine kinase present in mouse spermatozoa (tr-kit) activates mouse eggs parthenogenetically, and tr-kit- induced egg activation is inhibited by preincubation with an inhibitor of phospholipase C (PLC) (Sette, C., A. Bevilacqua, A. Bianchini, F. Mangia, R. Geremia, and P. Rossi. 1997. Development [Camb.]. 124:2267-2274). Co-injection of glutathione-S-transferase (GST) fusion proteins containing the src-homology (SH) domains of the gamma1 isoform of PLC (PLCgamma1) competitively inhibits tr-kit- induced egg activation. A GST fusion protein containing the SH3 domain of PLCgamma1 inhibits egg activation as efficiently as the whole SH region, while a GST fusion protein containing the two SH2 domains is much less effective. A GST fusion protein containing the SH3 domain of the Grb2 adaptor protein does not inhibit tr-kit-induced egg activation, showing that the effect of the SH3 domain of PLCgamma1 is specific. Tr-kit-induced egg activation is also suppressed by co-injection of antibodies raised against the PLCgamma1 SH domains, but not against the PLCgamma1 COOH-terminal region. In transfected COS cells, coexpression of PLCgamma1 and tr-kit increases diacylglycerol and inositol phosphate production, and the phosphotyrosine content of PLCgamma1 with respect to cells expressing PLCgamma1 alone. These data indicate that tr-kit activates PLCgamma1, and that the SH3 domain of PLCgamma1 is essential for tr-kit-induced egg activation.
Aneuploidy Detection in Pigs Using Comparative Genomic Hybridization: From the Oocytes to Blastocysts (2012)

Data on the frequency of aneuploidy in farm animals are lacking and there is the need for a reliable technique which is capable of detecting all chromosomes simultaneously in a single cell. With the employment of comparative genomic hybridization coupled with the whole genome amplification technique, this study brings new information regarding the aneuploidy of individual chromosomes in pigs. Focus is directed on in vivo porcine blastocysts and late morulas, 4.7% of which were found to carry chromosomal abnormality. Further, ploidy abnormalities were examined using FISH in a sample of porcine embryos. True polyploidy was relatively rare (1.6%), whilst mixoploidy was presented in 46.8% of embryos, however it was restricted to only a small number of cells per embryo. The combined data indicates that aneuploidy is not a prevalent cause of embryo mortality in pigs.
A Comparative Study of Bioorthogonal Reactions with Azides (2006)

Detection of metabolites and post-translational modifications can be achieved using the azide as a bioorthogonal chemical reporter. Once introduced into target biomolecules, either metabolically or through chemical modification, the azide can be tagged with probes using one of three highly selective reactions: the Staudinger ligation, the Cu(I)-catalyzed azide-alkyne cycloaddition, or the strain-promoted [3 + 2] cycloaddition. Here, we compared these chemistries in the context of various biological applications, including labeling of biomolecules in complex lysates and on live cell surfaces. The Cu(I)-catalyzed reaction was found to be most efficient for detecting azides in protein samples but was not compatible with live cells due to the toxicity of the reagents. Both the Staudinger ligation and the strain-promoted [3 + 2] cycloaddition using optimized cyclooctynes were effective for tagging azides on live cells. The best reagent for this application was dependent upon the specific structure of the azide. These results provide a guide for biologists in choosing a suitable ligation chemistry.
Exergue (1984)

« Dans une discipline qui ne doit sa valeur scientifique qu’aux concepts théoriques que Freud a forgés dans le progrès de son expérience mais qui, d’être encore mal critiqués et de conserver pour autant l’ambiguïté de la langue vulgaire, profitent de ces résonances non sans encourir les malentendus, il nous semblerait prématuré de rompre la tradition de leur terminologie.Mais il nous semble que ces termes ne peuvent que s’éclaircir à ce qu’on établisse leur équivalence au langage actuel de l’...
Estrogen Receptor Status by Immunohistochemistry Is Superior to the Ligand-Binding Assay for Predicting Response to Adjuvant Endocrine Therapy in Breast Cancer (1999)

IHC is superior to the LBA for assessing ER status in primary breast cancer because it is easier, safer, and less expensive, and has an equivalent or better ability to predict response to adjuvant endocrine therapy.
Duration of effect of interferon aerosol prophylaxis of vesicular stomatitis virus infection in mice (1985)

Mice were exposed for 8 h to continuous small-particle aerosols containing natural mouse alpha interferon (estimated dosage 100 U per mouse) or one of two concentrations of hybrid recombinant alpha interferon A/D bgl (estimated dosages of 100 and 10,000 U per mouse, respectively). On days 1, 3, 5, 7, and 9 after exposure to these interferons, three mice from each group were inoculated intranasally with 100 PFU of vesicular stomatitis virus. Control mice were exposed to aerosols of saline or inoculated intraperitoneally with either natural mouse alpha interferon (350 U) or one of two doses of hybrid recombinant alpha interferon A/D bgl (350 or 35,000 U) and challenged similarly. Of mice injected intraperitoneally, only those given 35,000 U of hybrid recombinant alpha interferon A/D bgl 24 h before virus challenge were protected from pulmonary infection, compared with the saline-treated control mice. Of mice given 100 U of either interferon by small-particle aerosol, only those exposed 24 h before inoculation of vesicular stomatitis virus had reduced pulmonary titers of the virus. However, of mice given ca. 10,000 U of hybrid recombinant alpha interferon A/D bgl by small-particle aerosol, all groups except those exposed 9 days before virus inoculation had significantly reduced lung virus titers.
An inhibitor of HIV-1 protease modulates proteasome activity, antigen presentation, and T cell responses (1998)

Inhibitors of the protease of HIV-1 have been used successfully for the treatment of HIV-1-infected patients and AIDS disease. We tested whether these protease inhibitory drugs exerted effects in addition to their antiviral activity. Here, we show in mice infected with lymphocytic choriomeningitis virus and treated with the HIV-1 protease inhibitor ritonavir a marked inhibition of antiviral cytotoxic T lymphocyte (CTL) activity and impaired major histocompatibility complex class I-restricted epitope presentation in the absence of direct effects on lymphocytic choriomeningitis virus replication. A potential molecular target was found: ritonavir selectively inhibited the chymotrypsin-like activity of the 20S proteasome. In view of the possible role of T cell-mediated immunopathology in AIDS pathogenesis, the two mechanisms of action (i.e., reduction of HIV replication and impairment of CTL responses) may complement each other beneficially. Thus, the surprising ability of ritonavir to block the presentation of antigen to CTLs may possibly contribute to therapy of HIV infections but potentially also to the therapy of virally induced immunopathology, autoimmune diseases, and transplantation reactions.
Getting All Turned Around Over the Origins of Life on Earth (1995)

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Properties of membrane-associated sialyltransferase of Escherichia coli. (1975)

Membrane-associated sialyltransferase complexes in Escherichia coli K-235 can be dissociated by lipid deletion and reassembled by the addition of undecaprenyl phosphate, a unique membrane-bound lipid coenzyme. Following disruption of the cells by pressure disintegration and centrifugal fractionation, the sialyltransferase activity is assocatied with both a "particulate" and "soluble" complex. Kinetic studies as well as sugar nucleotide, metal ion, pH, ammonium sulfate, and thiol reagent requirements showed these two complexes contained functionally identical enzymatic activities. Isopycnic sucrose density gradient centrifugation studies carried out on unfractionated total membranes established that these sialytransferase activities were associated with membrane hybrids composed of different relative amounts of inner and outer membranes. Enzyme localization studies employing DPNH oxidase, a marker for the inner membrane, and relative phospholipid to protein composition determinations in the two complexes, provided added support for this conclusion. Sialyl polymer synthesis was not dependent on the incorporation of other monosaccharides and had no demonstrable metal ion requirement. Kinetic studies showed that the Km for cytidine 5-monophospho-N-acetylneuraminic acid in intact soluble and particulate enzyme preparations was 8.1 times 10-5M and 9.2 times 105M, respectively. Similarly, both enzyme complexes had nearly identical Vmax values. Following reassembly of delipidated enzyme preparations, however, there was a 10-fold increase in the Km value for the particulate enzyme and a 3-fold increase for the soluble enzyme. This increase was accompanied by an increase of approximately the same magnitude in the Vmax values. Since the lipid coenzyme was limiting in intact enzyme preparations, the increase in Vmax reflected an increase in the concentration of the active lipid in reconstituted complexes. Sialyl polymer synthesis in intact membrane preparations was stimulated by the exogenous addition of lipid. Insertion of the carrier lipid was dependent on temperature. At 37 degrees, a 120% increase in sialytransferase activity was observed while only a 35% increase was observed at 30 percent. At 20 degrees, no stimulation occurred. Fluidity of the lipid phase is apparently required for proper function of this membraneassociated enzyme complex. Thus, at 20 degrees, a temperature below the membrane lipid transition temperature, the lipids are relatively immobile.
Charge substitution shows that repulsive electrostatic interactions impede the oligomerization of Alzheimer amyloid peptides (2005)

The strong pH dependence of A beta oligomerization could arise from favorable intermolecular charge-charge interactions between His and carboxylate groups, or, alternatively, by mutual electrostatic repulsion of peptide molecules. To test between these two possibilities, the pH dependence of the oligomerization of A beta and three charge substitution variants with Asp, Glu and His substituted by Ala is measured. All four peptides oligomerize, as detected by thioflavin T fluorescence, turbidity, and amyloid fibril formation; therefore, specific charge-charge interactions are nonessential for oligomerization. The strong negative correlation between net charge and oligomerization indicates that electrostatic repulsion between A beta monomers impedes their association.
Synthesis of a Sialic Acid Containing Complex‐Type N‐Glycan on a Solid Support (2009)

A new solid-phase synthesis of N-linked glycans featuring 1) highly stereoselective beta-mannosylation and microfluidic alpha-sialylation and 2) efficient glycosylation of the N-phenyltrifluoroacetimidate units on JandaJel resin is reported. Reagent concentration effects by a fluorous solvent are effectively applied, and the use of these methods results in the first synthesis of a sialic acid containing complex-type N-glycan on a solid support.
Unifying model for molecular determinants of the preselection Vβ repertoire (2013)

The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We quantified Vβ use in the preselection Tcrb repertoire and report relative contributions of 13 distinct features that may shape their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and predicted quality of recombination signal sequences (RSSs). We show that, in contrast to functional Vβ gene segments, all pseudo-Vβ segments are sequestered in transcriptionally silent chromatin, which effectively suppresses wasteful recombination. Importantly, computational analyses provide a unifying model, revealing a minimum set of five parameters that are predictive of Vβ use, dominated by chromatin modifications associated with transcription, but largely independent of precise spatial proximity to DβJβ clusters. This learned model-building strategy may be useful in predicting the relative contributions of epigenetic, spatial, and RSS features in shaping preselection V repertoires at other antigen receptor loci. Ultimately, such models may also predict how designed or naturally occurring alterations of these loci perturb the preselection use of variable gene segments.
Towards a streaming SQL standard (2008)

This paper describes a unification of two different SQL extensions for streams and its associated semantics. We use the data models from Oracle and StreamBase as our examples. Oracle uses a time-based execution model while StreamBase uses a tuple-based execution model. Time-based execution provides a way to model simultaneity while tuple-based execution provides a way to react to primitive events as soon as they are seen by the system. The result is a new model that gives the user control over the granularity at which one can express simultaneity. Of course, it is possible to ignore simultaneity altogether. The proposed model captures ordering and simultaneity through partial orders on batches of tuples. The batching and the ordering are encapsulated in and can be modified by means of a powerful new operator that we call SPREAD. This paper describes the semantics of SPREAD and gives several examples of its use.
A vision of cell death: insights into immune privilege (1997)

Immune privilege is a term applied to several organs that have a unique relationship with the immune response. These sites prohibit the spread of inflammation since even minor episodes can threaten organ integrity and function. The most prominent examples of these are the eye, brain and reproductive organs where immune responses either do not proceed, or proceed in a manner different from other areas. Once thought to be a passive process relying on physical barriers, immune privilege can now be viewed as an active process that utilizes multiple mechanisms to maintain organ function. Recently there has been a renewed interest in immune privilege when it was shown that two privileged sites (the eye and testes) constitutively express FasL, which functions by killing lymphoid cells that invade these areas. Here we will examine the role of FasL in immune privilege and discuss how this molecule interacts with other elements of the inflammatory response to maintain organ integrity in the face of potentially damaging immune reactions.
Mapping regions of herpes simplex virus type 1 glycoprotein I required for formation of the viral Fc receptor for monomeric IgG (1997)

Glycoprotein E (gE) and glycoprotein I (gI) of herpes simplex virus type 1 (HSV-1) form a complex that binds the Fc domain of monomeric IgG. In this study, we used two approaches to map the regions of gI-1 required for formation of the HSV-1 Fc receptor for monomeric IgG. First, we constructed six plasmids encoding gD-1/gI-1 fusion proteins. Each fusion protein contains a large gI-1 peptide inserted into the ectodomain of gD-1. gD-1/gI-1 fusion proteins were coexpressed with gE-1 using a transfection-infection assay in which cells were transfected with individual fusion protein constructs and then infected with a gE+/gI- virus. Cells were then assayed for monomeric IgG binding using immunofluorescence microscopy. Transfection-infection with two of six fusion proteins conferred monomeric IgG binding activity to cells, whereas cells infected with gE+/gI- virus alone failed to bind IgG monomers. The smallest gI-1 peptide to confer monomeric IgG binding activity contained amino acids 43 to 192. To more precisely map the region of gI-1 required for monomeric IgG binding, we constructed a panel of 10 gI-1 linker insertion mutants. Transfection-infection studies identified two mutants containing linker insertions at gI-1 amino acids 128 and 145, which failed to bind monomeric IgG. The other eight mutants demonstrated wild-type IgG binding activity. Taken together, these results indicate that the region of gI-1 between amino acids 128 and 145 is required for formation of the HSV-1 Fc receptor for monomeric IgG.