gebhart/patrepeval huggingface dataset:
PI3K Inhibition Impairs BRCA1/2 Expression and Sensitizes BRCA-Proficient Triple-Negative Breast Cancer to PARP Inhibition (2012)

Treatment options are limited for patients with TNBCs. PARP inhibitors have clinical activity restricted to a small subgroup of patients with BRCA mutations. Here, we show that PI3K blockade results in HR impairment and sensitization to PARP inhibition in TNBCs without BRCA mutations, providing a rationale to combine PI3K and PARP inhibitors in this indication. Our findings could greatly expand the number of patients with breast cancer that would benefit from therapy with PARP inhibitors. On the basis of our findings, a clinical trial with BKM120 and olaparib is being initiated in patients with TNBCs.
Observation of chemical-fusion reactions of fullerenes in the negative-ion channel (1994)

We observed the phenomenon of chemical fusion of fullerenes in a laser-desorption mass-spectrometric investigation of adduct compounds ${\mathit{R}}_{\mathit{n}}$${\mathrm{C}}_{60}$ (R=${\mathrm{C}}_{6}$${\mathrm{H}}_{5}$${\mathrm{CH}}_{2}$ or ${\mathrm{C}}_{9}$${\mathrm{H}}_{7}$) in the negative-ion channel. The radicals were believed to play a key role in the formation of stable higher-mass fullerenes and doubly charged negative ions of ${\mathrm{C}}_{60}$ in the gas phase, in our case. These results imply that the heat of fusion has to be released by evaporating small even-numbered fragments or by collison with the radicals ruptured from the ${\mathrm{C}}_{60}$ cage.
Cysteines in the transmembrane region of major histocompatibility complex antigens are fatty acylated via thioester bonds. (1984)

Exogenous radioactive palmitic acid is incorporated post-translationally into the HLA-B and -DR heavy chains, but not HLA-A heavy chains or -DR light chains of the human B lymphoblastoid cells JY and T51 . Protease digestions localize the label to the transmembrane region of the B7 heavy chain. Both B7 and DR heavy chains have a cysteine in the transmembrane hydrophobic region, while the A2 heavy chain and DR light chains have none. Palmitic acid is covalently linked to these transmembrane cysteines via a thioester bond since: 1) the label is not removed by organic extraction or boiling in sodium dodecyl sulfate and dithiothreitol, but is released at room temperature by methanolic KOH as methyl palmitate, and by hydroxylamine as palmitohydroxamate . 2) The pH sensitivity and kinetics of release by hydroxylamine and Tris are similar to those of palmitoyl-CoA (thioester linkage) and unlike those of methyl palmitate and palmitoyllysophosphatidylcholine ( hydroxyester linkages). 3) Neutral hydroxylamine treatment (but not neutral Tris treatment) generates sites that can be reduced and alkylated in the transmembrane region of B7 heavy chain and to a lesser extent in DR heavy chain. 4) Organic extraction of pronase digests of labeled B7 yields peptides containing palmitate and cysteine (but not serine or threonine) which co-migrate by thin layer chromatography. A population of beta 2-microglobulin molecules not associated with heavy chains is palmitylated , but not via a thioester linkage.
Proteins of the inner and outer centromere of mitotic chromosomes (1989)

We have used immunocytochemistry and molecular cloning methods to identify and characterize structural polypeptides of the centromere. These studies permit us to resolve two distinct regions: the inner and outer centromere, (i) Components of the outer centromere: autoantibodies from certain patients with rheumatic disease identify a family of three immunologically related polypeptides that we have designated CENP-A (17 kDa), CENP-B (80 kDa), and CENP-C (140 kDa). CENP-B has been cloned and sequenced. DNA sequence analysis indicates that this polypeptide possesses two large regions with extraordinary concentrations of acidic residues (region I: 61 residues with 79% glu + asp; region II: 31 residues with 87% glu + asp). Despite this concentration of negative charge, immunocytochemical experiments suggest that CENP-B may be a DNA binding protein. In these experiments, the levels of CENP-B are seen to vary reproducibly from chromosome to chromosome. The role of CENP-B in vivo is unknown. However, it is unlikely to bind directly to the spindle microtubules since it is found at an inactive centromere that apparently does not attach to the spindle. (ii) Components of the inner centromere: we have injected mice with the whole chromosome scaffold fraction to elicit production of monoclonal antibodies. One such antibody identifies two structurally related polypeptides (the INCENP antigens, 135 and 155 kDa) that are preferentially located between the sister chromatids at the centromere. The INCENP antigens undergo dramatic movements from the chromosomes to the central spindle during mitosis. They are ultimately sequestered in the midbody and discarded. Several lines of evidence suggest that the INCENP polypeptides may be involved in the regulation of sister chromatid separation at the metaphase–anaphase transition.Key words: mitosis, centromere, CENP antigens, INCENP antigens, kinetochore, disjunction.
Biochemistry, cell biology and molecular biology of lipids ofSaccharomyces cerevisiae (1998)

The yeast Saccharomyces cerevisiae is a powerful experimental system to study biochemical, cell biological and molecular biological aspects of lipid synthesis. Most but not all genes encoding enzymes involved in fatty acid, phospholipid, sterol or sphingolipid biosynthesis of this unicellular eukaryote have been cloned, and many gene products have been functionally characterized. Less information is available about genes and gene products governing the transport of lipids between organelles and within membranes, turnover and degradation of complex lipids, regulation of lipid biosynthesis, and linkage of lipid metabolism to other cellular processes. Here we summarize current knowledge about lipid biosynthetic pathways in S. cerevisiae and describe the characteristic features of the gene products involved. We focus on recent discoveries in these fields and address questions on the regulation of lipid synthesis, subcellular localization of lipid biosynthetic steps, cross-talk between organelles during lipid synthesis and subcellular distribution of lipids. Finally, we discuss distinct functions of certain key lipids and their possible roles in cellular processes.
Establishment, Differentiation, Electroporation, Viral Transduction, and Nuclear Transfer of Bovine and Porcine Mesenchymal Stem Cells (2005)

Mesenchymal stem cells (MSCs) reside in the bone marrow and have the potential for multilineage differentiation, into bone, cartilage, and fat, for example. In this study, bovine and porcine MSCs were isolated, cultured to determine their replication ability, and differentiated with osteogenic medium and 5-azacytine. Both bovine and porcine undifferentiated MSCs were electroporated and virally transduced to test the efficiency of genetic modification and the maintainance of differentiation ability thereafter. Nuclear transfer experiments were carried out with bovine and porcine MSCs, both at the undifferentiated state and following differentiation. Our results indicate that bovine and porcine MSCs have limited lifespans in vitro--approximately 50 population doublings. They can be efficiently differentiated and characterized along the osteogenic lineage by morphology, alkaline phosphatase, Von Kossa, oil red stainings, and RT-PCR. Electroporation and selection induce high levels of EGFP expression in porcine but not in bovine MSCs. Following genetic modification, MSCs retain their pluridifferentiation ability as parental cells. Cloned embryos derived from bovine and porcine undifferentiated MSCs and their derivatives along the osteogenic lineage give rise to consistently high preimplantation development comparable to adult fibroblasts.
Enzyme release by bovine neutrophils. (1995)

Release of enzymes from cytoplasmic granules has been postulated to have a major role in neutrophil-mediated tissue injury. Secretion or release of primary granules, specific granules, and cytosolic enzymes by bovine neutrophils was examined by quantifying the release of beta-glucuronidase, B12-binding protein, and lactate dehydrogenase, respectively, in response to predetermined amounts of phorbol myristate acetate, calcium ionophore, and opsonized zymosan. These responses were compared with the enzyme release induced by exposure to live or dead, unopsonized or opsonized Pasteurella haemolytica. The greatest release of beta-glucuronidase, B12-binding protein, and lactate dehydrogenase was observed in neutrophils exposed to live organisms partially because of neutrophil lysis. Bovine neutrophils respond markedly to particulate agonists, live or dead, pathogenic or nonpathogenic, by a selective release of specific granules, an effect enhanced by opsonization. Particulate agonists induce minimal primary granule release other than that induced by cell death. Because bovine neutrophils contain quantitatively high numbers of specific granules, the high rate of secretion/release in response to P haemolytica organisms could have a major role in the tissue responses that characterize the lesions of pneumonic pasteurellosis.
Bistability and pulsations in semiconductor lasers with inhomogeneous current injection (1982)

Bistability and pulsation at microwave frequencies are observed in CW GaAs semiconductor lasers with inhomogeneous current injection. Inhomogeneous current injection is achieved with a segmented contact structure. Crucial to the understanding of the characteristics of this device is the discovery of a negative differential electrical resistance across the contacts of the absorbing section. Depending on the electrical bias condition, this negative differential resistance leads to bistability or light-jumps and self pulsations. A simple model based on conventional rate equations with a linear gain dependence on carrier density explains the observed behavior and suggests a new mechanism in inhomogeneously pumped diode lasers for light-jumps and pulsations which does not depend on the condition for the usually proposed repetitively <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</tex> -switching. Investigation of the switching dynamics of this bistable optoelectronic device reveals a delay time which is critically dependent on the trigger pulse amplitude and typically on the order of a few nanoseconds with power-delay products of 100 pJ. The observed critical slowing down and its origin is discussed. We also report on the characteristic of this laser coupled to an external optical cavity and we demonstrate successfully that this bistable laser can be used as a self coupled stylus for optical disk readout with an excellent signal to noise ratio.
Single-Dose Pharmacokinetics and Pharmacodynamics of IPX203 in Patients With Advanced Parkinson Disease: A Comparison With Immediate-Release Carbidopa-Levodopa and With Extended-Release Carbidopa-Levodopa Capsules (2018)

Objective IPX203 is an investigational oral extended-release capsule formulation of carbidopa-levodopa (CD-LD). The aim of this study was to characterize the single-dose pharmacodynamics, pharmacokinetics, and safety of IPX203 in subjects with advanced Parkinson disease compared with immediate-release (IR) CD-LD and extended-release CD-LD (Rytary). Methods This was a randomized, open-label, rater-blinded, multicenter, single-dose crossover study. Blinded clinicians assessed subject's motor state and Movement Disorders Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) part III scores for up to 10 hours postdose. Duration of effect was determined using improvement thresholds in the MDS-UPDRS part III. Results Levodopa concentrations increased rapidly and similarly across all 3 treatments and were sustained for a longer duration after IPX203 dosing. All treatments exhibited a rapid onset of pharmacodynamic effect, whereas IPX203 had a significantly longer duration of effect based on MDS-UPDRS part III scores compared with IR CD-LD ( P &lt; 0.0001) and Rytary ( P ≤ 0.0290). IPX203 had a 2.7-hour advantage over IR CD-LD ( P &lt; 0.0001) and a 0.9-hour advantage over Rytary in “off” time ( P = 0.023) and in “good on” time (2.6 hours more than IR CD-LD, P &lt; 0.0001; 0.9 hours more than Rytary, P = 0.0259) as measured by the Investigator Assessment of Subject's Motor State. Subjects were 77% more likely to require rescue following IR CD-LD treatment compared with IPX203 (hazard ratio, 0.23; P &lt; 0.0001). More subjects reported treatment-emergent adverse effects during IR CD-LD (28.0%) and IPX203 (19.2%) than during Rytary (8.0%) treatment. Conclusions Compared with Rytary and IR CD-LD, IPX203 had a longer pharmacodynamic effect consistent with LD pharmacokinetics for the 3 treatments. The safety and tolerability of IPX203 were similar to those of IR CD-LD and Rytary.
Functional Role of Type I and Type II Interferons in Antiviral Defense (1994)

Mice lacking the known subunit of the type I interferon (IFN) receptor were completely unresponsive to type I IFNs, suggesting that this receptor chain is essential for type I IFN-mediated signal transduction. These mice showed no overt anomalies but were unable to cope with viral infections, despite otherwise normal immune responses. Comparison of mice lacking either type I or type II IFN receptors showed that, at least in response to some viruses, both IFN systems are essential for antiviral defense and are functionally nonredundant.
The human T-cell V gamma gene locus: cloning of new segments and study of V gamma rearrangements in neoplastic T and B cells (1988)

The authors have analyzed the involvement of V gamma and J gamma segments in TRG gamma rearrangement from a series of 40 acute lymphoblastic leukemia (ALL), including 25 T- and 15 B-lineage cases, in which TRG gamma are rearranged. Sixty-five rearranged alleles were studied. The authors first describe the cloning and sequencing of two variable segments, V gamma 11 and psi V gamma 12, which rearrange in T- and B-neoplastic cells. To date three subgroups of translatable V gamma segments have been described. The authors show that V gamma 11 is the unique member of a new fourth V gamma subgroup that also rearranges in normal polyclonal T cells and that psi V gamma 12 is located at 5- kilobase (kb) downstream to V gamma 11. As shown by DNA sequence analysis, V gamma 11 shares a 60% homology with V gamma 10 (third subgroup) and a 50% homology with V gamma 9 (second subgroup) but no appreciable homology with the V gamma segments from the first family. In contrast to psi V gamma 12, V gamma 11 is translatable. In this paper the authors have also attempted to determine which V gamma segments were rearranged in the ALL cases by hybridization with a J gamma probe and genomic probes specific of the four subgroups. In the 54 instances in which the rearrangement was consistent with J gamma 1 or J gamma 2 involvement, the authors have identified the corresponding V gamma segments and have not found any other rearrangements suggestive of the existence of further V regions. The V gamma segments, belonging to the first subgroup, were the most frequently used (41 alleles). V gamma 9, V gamma 10, V gamma 11, and psi V gamma 12 were found rearranged in cases 3, 4, 5, and 1, respectively. No cases using the pseudo psi V gamma 1, psi V gamma 5, and psi V gamma 6 segments were found. Pseudo V gamma segments were not found rearranged in T cells, while V gamma 2 and V gamma 4, segments are frequently used. In contrast to the V gamma I gene rearrangement, the involvement of the V gamma II, V gamma III, and V gamma IV subgroups was most frequently observed in T-ALL with stage II differentiation (CD7+, CD4+, and/or CD8+, CD3-), than in those with stage I (CD7+, CD4-, CD8-, CD3-), than in those with stage I (CD7+, CD4-, CD8-, CD3-) and stage III (CD7+, CD4+/-CD8+/-CD3+).(ABSTRACT TRUNCATED AT 400 WORDS)
Structure and Properties of Triolein-Based Polyurethane Networks (2002)

Polyurethane networks based on vegetable oils have very heterogeneous composition, and it is difficult to find a close correlation between their structure and properties. To establish benchmark structure-properties relationships, we have prepared model polyurethane networks based on triolein and 4,4'-diphenylmethane diisocyanate (MDI). Cross-linking in the middle of fatty acid chains leaves significant parts of the triglyceride as dangling chains. To examine their effect on properties, we have synthesized another polyurethane network using triolein without dangling chains (removed by metathesis). The structure of polyols was studied in detail since it affects the structure of polyurethane networks. The network structure was analyzed from swelling and mechanical measurements and by applying network and rubber elasticity theories. The cross-linking density in both networks was found to be close to theoretical. The triolein-based model network displayed modulus (around 6 MPa), tensile strength (8.7 MPa), and elongation at break (136%), characteristic of hard rubbers. Glass transition temperatures of the networks from triolein and its metathesis analogue were 25 and 31.5 degrees C, respectively.
The IFNAR1 subunit of the type I IFN receptor complex contains a functional nuclear localization sequence (2004)

A nuclear localization sequence (NLS) in the type II interferon (IFN) IFN gamma, which is responsible for the nuclear translocation of both the ligand and the alpha-subunit (IFNGR1) of the receptor complex, has previously been characterized and its role in signaling examined in detail. We have now identified an NLS in the type I IFN receptor (IFNAR) common subunit IFNAR1 from humans and show that the human IFNAR1 subunit can translocate to the nucleus following human IFN beta stimulation. An NLS in human IFNAR1 is located in the extracellular domain of IFNAR1 within the sequence (382)RKIIEKKT (numbered for the precursor form). Nuclear import by the NLS functions in a conventional fashion requiring cytosolic import factors, is energy-dependent and inhibited by the prototypical NLS of the SV40 large T-antigen. These studies provide a mechanism for nuclear import of IFNAR1, as well as for type I IFN ligands, and a starting point for studying an alternate role for IFNAR1 in nuclear signaling within the type I IFN system.
Swelling behavior of Na- and Ca-montmorillonite up to 150°C by in situ X-Ray diffraction experiments (2009)

Abstract The effects of temperature on the swelling properties of smectites are important for a variety of different geological conditions, but studies on this topic have been rather limited. The purpose of this study was to investigate the swelling behavior of Na- and Ca-montmorillonite at various temperatures greater than room temperature, up to 150°C, using in situ X-ray diffraction (XRD) analysis. A sample chamber was designed, the temperature and humidity of which were controlled precisely, for environmental in situ measurements. The XRD measurements were performed at small relative humidity (RH) intervals for precise observation of the swelling behavior. The swelling behavior of Na-montmorillonite showed distinct zero-, one-, and two-layer hydration states. The basal spacings of Na-montmorillonite changed continuously with RH for various temperatures in the transition region between the zero- and one-layer hydration states, and the swelling curves of the transition region moved to greater degrees of RH with increasing temperature. The basal spacings jumped from the one- to two-layer hydration states for all temperatures at almost the same RH. The basal spacings of Ca-montmorillonite changed continuously from the zero- to the two-layer hydration states at all temperatures. This behavior is remarkably different from that of Na-montmorillonite. At low-RH conditions, the d 001 value of Ca-montmorillonite decreased with increasing temperature. The swelling curves of Ca-montmorillonite did not show a plateau at any temperature for the one-layer hydration state. The swelling curves of Ca-montmorillonite moved to greater RH with temperature, similar to the transformation region between the zero- and one-layer hydration states in Na-montmorillonite. These differences between Na- and Ca-montmorillonite are related to the hydration powers of exchangeable cations.
Penetrating Ballistic-Like Brain Injury in the Rat: Differential Time Courses of Hemorrhage, Cell Death, Inflammation, and Remote Degeneration (2006)

Acute and delayed cerebral injury was assessed in a recently developed rat model of a penetrating ballistic-like brain injury (PBBI). A unilateral right frontal PBBI trajectory was used to induce survivable injuries to the frontal cortex and striatum. Three distinct phases of injury progression were observed. Phase I (primary injury, 0-6 h) began with immediate (<5 min) intracerebral hemorrhage (ICH) that reached maximal volumetric size at 6 h (27.0 +/- 2.9 mm(3)). During Phase II (secondary injury, 6-72 h), a core lesion of degenerate neurons surrounding the injury track expanded into peri-lesional areas to reach a maximal volume of 69.9 +/- 6.1 mm(3) at 24 h. The core lesion consisted of predominately necrotic cell death and included marked infiltration of both neutrophils (24 h) and macrophages (72 h). Phase III (delayed degeneration, 3-7 days) involved the degeneration of neurons and fiber tracts remote from the core lesion including the thalamus, internal capsule, external capsule, and cerebral peduncle. Overall, different time courses of hemorrhage, lesion evolution, and inflammation were consistent with complementary roles in injury development and repair, providing key information about these mediators of primary, secondary, and delayed brain injury development. The similarities/differences of PBBI to other focal brain injury models are discussed.
Synthesis and characterization of fluorescently labeled core cross‐linked star polymers (2008)

Abstract A series of fluorescently labeled core cross‐linked star (CCS) polymers were synthesized via the “arm‐first” approach, employing atom transfer radical polymerization (ATRP) to control the resulting architecture. The initiator p ‐toluenesulfonyl chloride (TsCl) was used to synthesize “living” poly(methyl methacrylate) (PMMA) macroinitiator, which was subsequently cross‐linked to generate the CCS polymers. Divinylbenzene (DVB) was used as the cross‐linker and 7‐[4‐(trifluoromethyl)coumarin] methacrylamide ( F 1 , λ ex = 343 nm) was added as a fluorescent labeling monomer. A range of PMMA/DVB/ F 1 based CCS polymers were synthesized with the core domain made selectively fluorescent by using varying amounts of monomer F 1 . The core functionalized stars were characterized using gel permeation chromatography (GPC) equipped with multi‐angle laser light scattering (MALLS), refractive index (RI), and UV–visible detectors. The fluorescence quantum yield (Φ F ) and the amount of fluorescent monomer incorporated into the core were quantified by UV–visible and fluorescence spectrophotometry. It was recognized that the overall molecular weights of the stars produced, along with their core molecular weight, decreased as the mol % of monomer F 1 was increased relative to cross‐linker. Visual confirmation of F 1 incorporation was obtained by fluorescence microscopy of thin polymer films cast on glass substrates. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2422–2432, 2008
Aza-dibenzocyclooctynes for fast and efficient enzyme PEGylation via copper-free (3+2) cycloaddition (2009)

A strained aza-dibenzocyclooctyne was prepared via a high-yielding synthetic route. Copper-free, strain-promoted click reaction with azides showed excellent kinetics, and a functionalised aza-cyclooctyne was applied in fast and efficient PEGylation of enzymes.