gebhart/patrepeval huggingface dataset:
Procoagulant platelets: are they necrotic? (2010)

Apoptosis and necrosis represent distinct cell death processes that regulate mammalian development, physiology and disease. Apoptosis characteristically leads to the silent destruction and removal of cells in the absence of an inflammatory response. In contrast, necrotic cell death can induce physiologic inflammatory responses linked to tissue defense and repair. Although anucleate, platelets undergo programmed cell death, with apoptosis playing an important role in clearing effete platelets from the circulation. While it has long been recognized that procoagulant platelets exhibit characteristic features of dying cells, recent studies have demonstrated that platelet procoagulant function can occur independent of apoptosis. A growing body of evidence suggest that the biochemical, morphologic and functional changes underlying agonist-induced platelet procoagulant function are broadly consistent with cell necrosis, raising the possibility that distinct death pathways regulate platelet function and survival. In this article, we will discuss the mechanisms underlying apoptotic and necrotic cell death pathways and examine the evidence linking these pathways to the platelet procoagulant response. We will also discuss the potential contribution of these pathways to the platelet storage lesion and propose a simplified nomenclature to describe procoagulant platelets.
HIPPI-6400 -- Designing for speed (1998)

The emerging High Performance Parallel Interface 6400 Mbit/s interface (HIPPI-6400), is targeted as a local area network (LAN), or system area network (SAN), supporting data rates of 6400 Mbit/s (800 Mbyte/s). This is eight times the speed of Gigabit Ethernet. The features used, and the design choices made, for the data link and physical layers of HIPPI-6400, to achieve this unprecedented speed are the subject of this paper. HIPPI-6400 borrowed freely from other successful technologies such as ATM, Ethernet and the original HIPPI -- taking the best features of each and melding them with some new features. HIPPI-6400 is a cost effective reliable interconnect for distances up to 1 km; it intermixes large and small messages efficiently.
Sphingosine Phosphate Lyase Expression Is Essential for Normal Development in Caenorhabditis elegans (2003)

Sphingolipids are ubiquitous membrane constituents whose metabolites function as signaling molecules in eukaryotic cells. Sphingosine 1-phosphate, a key sphingolipid second messenger, regulates proliferation, motility, invasiveness, and programmed cell death. These effects of sphingosine 1-phosphate and similar phosphorylated sphingoid bases have been observed in organisms as diverse as yeast and humans. Intracellular levels of sphingosine 1-phosphate are tightly regulated by the actions of sphingosine kinase, which is responsible for its synthesis and sphingosine-1-phosphate phosphatase and sphingosine phosphate lyase, the two enzymes responsible for its catabolism. In this study, we describe the cloning of the Caenorhabditis elegans sphingosine phosphate lyase gene along with its functional expression in Saccharomyces cerevisiae. Promoter analysis indicates tissue-specific and developmental regulation of sphingosine phosphate lyase gene expression. Inhibition of C. elegans sphingosine phosphate lyase expression by RNA interference causes accumulation of phosphorylated and unphosphorylated long-chain bases and leads to poor feeding, delayed growth, reproductive abnormalities, and intestinal damage similar to the effects seen with exposure to Bacillus thuringiensis toxin. Our results show that sphingosine phosphate lyase is an essential gene in C. elegans and suggest that the sphingolipid degradative pathway plays a conserved role in regulating animal development.
Sensitivity of an Epstein-Barr Virus-Positive Tumor Line, Daudi, to Alpha Interferon Correlates with Expression of a GC-Rich Viral Transcript (1999)

The exquisite sensitivity of the Burkitt's lymphoma (BL)-derived cell line Daudi to type I interferons has not previously been explained. Here we show that expression of an Epstein-Barr virus (EBV) transcript, designated D-HIT (Y. Gao et al., J. Virol. 71:84-94, 1997), correlates with the sensitivity of different Daudi cell isolates (or that of other EBV-carrying cells, where known) to alpha interferon (IFN-alpha). D-HIT, transcribed from a GC-rich repetitive region (IR4) of the viral genome, is highly structured, responding to RNase digestion in a manner akin to double-stranded RNA. Comparing EBV-carrying BL cell lines with differing responses to IFN-alpha, we found the protein levels of the dsRNA-activated kinase, PKR, to be similar, whereas the levels of the autophosphorylated active form of PKR varied in a manner that correlated with endogenous levels of D-HIT expression. In a classical in vitro kinase assay, addition of either poly(I)-poly(C) or an in vitro-transcribed D-HIT homolog stimulated the autophosphorylation activity of PKR from IFN-alpha-treated cells in both EBV-positive and EBV-negative B lymphocytes. By transfection experiments, these RNAs were shown to reduce cell proliferation and to sensitize otherwise relatively insensitive Raji cells to IFN-alpha. The data lead to a model wherein the D-HIT viral RNA also serves as a possible transcriptional activator of IFN-alpha or cellular genes regulated by this cytokine.
The role of Math1 in inner ear development: Uncoupling the establishment of the sensory primordium from hair cell fate determination (2002)

During embryonic development of the inner ear, the sensory primordium that gives rise to the organ of Corti from within the cochlear epithelium is patterned into a stereotyped array of inner and outer sensory hair cells separated from each other by non-sensory supporting cells. Math1, a close homolog of the Drosophila proneural gene atonal, has been found to be both necessary and sufficient for the production of hair cells in the mouse inner ear. Our results indicate that Math1 is not required to establish the postmitotic sensory primordium from which the cells of the organ of Corti arise, but instead is limited to a role in the selection and/or differentiation of sensory hair cells from within the established primordium. This is based on the observation that Math1 is only expressed after the appearance of a zone of non-proliferating cells that delineates the sensory primordium within the cochlear anlage. The expression of Math1 is limited to a subpopulation of cells within the sensory primordium that appear to differentiate exclusively into hair cells as the sensory epithelium matures and elongates through a process that probably involves radial intercalation of cells. Furthermore, mutation of Math1 does not affect the establishment of this postmitotic sensory primordium, even though the subsequent generation of hair cells is blocked in these mutants. Finally, in Math1 mutant embryos, a subpopulation of the cells within the sensory epithelium undergo apoptosis in a temporal gradient similar to the basal-to-apical gradient of hair cell differentiation that occurs in the cochlea of wild-type animals.
Injectivity Loss in Polymer Floods: Causes, Preventions and Mitigations (2015)

Abstract Polymer flooding is an attractive option in hydrocarbon maturation plans. Several successful polymer floods and pilots have been implemented. One of the risks in polymer flooding is loss of injectivity. The consequences of loss of injectivity can be large. In conditions where matrix injection is required, reduction of injection rate may result in a much slower propagating polymer front and consequently later arrival of the anticipated oil bank eroding on the economic value of the EOR process. In extreme cases it can even lead to loss of the injector. Under fracturing conditions the loss of injectivity may be less noticeable, but it can lead to out of zone fracturing or fractures that grow too much in size and cause shortcuts to the producers or affect future infill well drilling. Reduction of injectivity is a generic concern in conventional waterfloods and can play an even larger factor when adding polymer to the waterflood. The increased viscosity of the injected polymer solution is the most obvious reason for an anticipated decrease in injectivity, but also other mechanisms can have an impact. These mechanisms include excessive polymer adsorption and associated permeability reduction, filtration of impurities in the polymer solution, fluid incompatibilities or reduced water quality. In this paper we will discuss the various causes for loss of injectivity and propose a structured approach for the associated prevention and mitigation options. Prevention includes (1) selection of the most appropriate polymer type; (2) best practices for preparation of the polymer solution; (3) safeguarding the water quality; and (4) enabling options for mitigation in case excessive injectivity loss is observed. The remediation step includes (1) the identification of the root-cause of an apparent injectivity problem; (2) the design of an appropriate clean-up treatment; (3) monitoring of the operation; and (4) implement measures to avoid repetition of the problem. We will include an overview of the preventive and mitigation options for the different causes of injectivity decline in polymer floods.
Regioselective Suzuki-Miyaura Cross-Coupling Reactions of 2,6-Dichloroquinoxaline (2012)

A variety of mono- and diarylated quinoxaline derivatives were prepared by site-selective Suzuki–Miyaura cross-coupling­ reactions of 2,6-dichloroquinoxaline. The selectivity is controlled by electronic parameters.
Adjuvants containing natural and synthetic Toll-like receptor 4 ligands (2013)

The last decade has seen an increased focus on the development of adjuvants for vaccines, and several novel adjuvants are now in licensed products or in late-stage clinical development. These advancements have been aided by the discovery of receptors and signaling pathways of the innate immune system and an increased understanding of how these innate responses influence the adaptive immune response. Successful vaccine development relies on knowledge of which adjuvants to use and the proper formulation of adjuvants and antigens to achieve safe, stable and immunogenic vaccines. In this review, the authors focus on the current use of natural and synthetic lipopolysaccharide analogues that retain their adjuvant properties with reduced toxicity compared with the parent compound for use in emerging vaccines. The authors review how these compounds initiate signal transduction through Toll-like receptor 4, insights from structure-function studies and how formulation parameters can influence their effectiveness as vaccine adjuvants.
Dynamics of HIV-Specific CD8+ T Lymphocytes with Changes in Viral Load (2000)

The influence of HIV burden variations on the frequencies of Ag-specific CD8+ T cell responses was evaluated before and during highly active antiretroviral therapy by analyzing the number, diversity, and function of these cells. The frequencies of HLA-A2-restricted CD8+ PBL binding HLA-A2/HIV-epitope tetramers or producing IFN-gamma were below 1%. A panel of 16 CTL epitopes covering 15 HLA class I molecules in 14 patients allowed us to test 3.8 epitopes/patient and to detect 2.2 +/- 1.8 HIV epitope-specific CD8+ subsets per patient with a median frequency of 0.24% (0.11-4. 79%). During the first month of treatment, viral load rapidly decreased and frequencies of HIV-specific CD8 PBL tripled, eight new HIV specificities appeared of 11 undetectable at entry, while CMV-specific CD8+ PBL also appeared. With efficient HIV load control, all HIV specificities decayed involving a reduction of the CD8+CD27+CD11ahigh HIV-specific effector subset. Virus rebounds triggered by scheduled drug interruptions or transient therapeutic failures induced four patterns of epitope-specific CD8+ lymphocyte dynamics, i.e., peaks or disappearance of preexisting specificities, emergence of new specificities, or lack of changes. The HIV load rebounds mobilized both effector/memory HIV- and CMV-specific CD8+ lymphocytes. Therefore, frequencies of virus-specific CD8 T cells appear to be positively correlated to HIV production in most cases during highly active antiretroviral therapy, but an inverse correlation can also be observed with rapid virus changes that might involve redistribution, sequestration, or expansion of these Ag-specific CD8 T cells. Future strategies of therapeutic interruptions should take into account these various HIV-specific cell dynamics during HIV rebounds.
Migrastatin, a Novel 14-Membered Ring Macrolide, Inhibits Anchorage-independent Growth of Human Small Cell Lung Carcinoma Ms-1 Cells. (2001)

In a previous study, we reported a novel 14-membered ring macrolide, migrastatin isolated from culture broth of Streptomyces sp. MK929-43F1 as an inhibitor of tumor cell migration1). Recently, however, we found that our original migrastatin isolate contained teleocidin-related compounds which display strong inhibitory activity against tumor cell migration. In this report, we describe the effects of teleocidin-free migrastatin on tumor cell migration and on
Photodynamic therapy vs. photochemical internalization: the surgical margin (2011)

Controlling tumour margins in head and neck surgery is of the utmost importance in preventing loco-regional spread and distant metastasis, which will ultimately lead to a significant reduction in morbidity and mortality. We comment on the surgical margins in photodynamic therapy and photochemical internalization.
Acute Stimulation of Corpus Luteum Cells by Gonadotrophin or Adenosine 3′,5′-Monophosphate Causes Accumulation of a Phosphoprotein Concurrent with Acceleration of Steroid Synthesis* (1988)

A protein (ib), which we have detected previously in peptide hormone or cAMP-stimulated corpus luteum cells, is shown to be a phosphoprotein and to be posttranslationally converted into a more acidic phosphoprotein (ia). Phosphorylation is demonstrated by two types of experiments, both using two-dimensional gel electrophoresis. In the first type, gels from [35S]methionine-labeled solubilized cell extracts are compared to gels from such extracts treated with alkaline phosphatase. This in vitro phosphatase treatment converts protein ib quantitatively into protein pb, which is synthesized in vivo only in unstimulated cells. Similarly, ia is converted into pa, the posttranslational product of pb. The second type of experiment demonstrates 32P label incorporation into proteins with the same electrophoretic mobilities as proteins ib and ia. Limited proteolytic digestion of all four proteins from phosphatase-treated and untreated corpus luteum cells shows that the newly detected acidic products, ia and pa, give rise to cleavage patterns similar to those of ib and pb. Further, these patterns resemble those produced by all four such proteins from the adrenal. These findings suggest that in both stimulated corpus luteum and adrenal, a similar protein ib, which accumulates with kinetics and stimulant dose response paralleling those of steroid hormone biosynthesis, is phosphorylated during its synthesis and is degraded by conversion to another phosphoprotein (ia).
Clinical Neuroimaging in Psychiatry (1995)

The practical aspects of contemporary neuroimaging techniques relevant to clinical psychiatry are reviewed. In particular, the structural imaging modalities of computed axial tomography (CT) and magnetic resonance imaging (MRI) are described and compared. Likewise, functional neuroimaging modalities including the nuclear imaging techniques of positron emission tomography (PET) and single photon emission computed tomography (SPECT), as well as the newer magnetic resonance techniques of functional magnetic resonance imaging (fMRI) and magnetic resonance spectroscopy (MRS), are reviewed. Although structural imaging techniques are most useful for ruling out medical etiologies of mental status disturbances, functional neuroimaging techniques currently have an adjunctive role in the evaluation of dementia and seizure disorders and show promise for the evaluation of primary psychiatric disorders in the future. Specific guidelines are suggested regarding the use of these neuroimaging studies.
The histone H3 and H4 mRNAs are polyadenylated in maize (1988)

Northern blot analysis revealed that the histone H3 and H4 mRNAs are of unusual large size in germinating maize embryos. S1-mapping experiments show that the 3'-untranslated regions of the mRNAs transcribed from 3 H3 and 2 H4 maize genes previously described are much longer than in the non-polyadenylated histone mRNAs which represent a major class in animals. Moreover, oligo d(T) cellulose fractionation of RNAs isolated at different developmental stages indicates that more than 99% of the maize H3 and H4 mRNAs are polyadenylated. A putative polyadenylation signal is present in all five genes 17 to 27 nucleotides before the 3'-ends of the mRNAs.
Automated determination of seven phenolic compounds in mainstream tobacco smoke (2008)

Exposure to hydroxyl-substituted arenes, commonly referred to as phenols or phenolic compounds, can have serious health consequences. Select phenols present in tobacco smoke are cardiovascular toxins, act as tumor co-promoters and show genotoxic activity. To examine the mainstream smoke levels of these compounds, we developed and applied a method for quantitative analysis of seven phenols (phenol, o-cresol, m-cresol, p-cresol, catechol, resorcinol, and hydroquinone) in mainstream smoke. Total mainstream smoke particulate matter was collected on a Cambridge filter pad and spiked with an isotopically labeled internal standard solution. This pad underwent an automated phenol derivatization procedure to increase analyte volatility and enhance detection. Following the derivatization step, phenols from the particulate matter were sampled using solid-phase microextraction with subsequent gas chromatography/mass spectrometric detection. Sensitivity, selectivity, accuracy, and reproducibility were more than adequate for routine detection of phenols in mainstream smoke. Detection limits ranged from 0.04-0.57 microg, with a quantification range of 0.1-710 microg. Higher sensitivity and sample throughput were achieved compared with previously described methods. Mainstream smoke from 28 brands of domestic commercial cigarettes was evaluated to assess typical levels, and reference cigarettes containing single tobacco blends were examined to ascertain the phenolic profile from different types of tobaccos. As expected under machine smoking conditions using the Federal Trade Commission parameters, full-flavored cigarettes deliver more phenols than the light varieties, followed by the ultra light varieties. Differences were seen in relative levels of phenolic compounds in the mainstream smoke from unfiltered cigarettes made with a single type of tobacco.
Privacy-preserving authentication solutions - best practices for implementation and EU regulatory perspectives (2014)

Privacy-preserving authentication solutions minimize the use of personal data of a user in an authentication process and can best be implemented with attribute-based credentials, in short: Privacy-ABCs. This technology allows not only for a reduction of personal data processed, but also conditional identification and the revocation of credentials. In order to fully benefit from their potential, implementation must be centered on the users' rights. Even though this can already be achieved, Privacy-ABCs are not explicitly taken into account in the current legal framework on identification and authentication, in particular the forthcoming eIDAS Regulation. Nevertheless, their potential to enhance current eID solutions can still be harnessed and should be incorporated increasingly in future legislation. For employment as best practice solutions, privacy-preserving authentication solutions have to be embedded in a suitable process framework within the organization as exemplarily sketched in this contribution.
Biophysical and Molecular Mechanisms of Shaker Potassium Channel Inactivation (1990)

The potassium channels encoded by the Drosophila Shaker gene activate and inactivate rapidly when the membrane potential becomes more positive. Site-directed mutagenesis and single-channel patch-clamp recording were used to explore the molecular transitions that underlie inactivation in Shaker potassium channels expressed in Xenopus oocytes. A region near the amino terminus with an important role in inactivation has now been identified. The results suggest a model where this region forms a cytoplasmic domain that interacts with the open channel to cause inactivation.
Changing the Course of Alzheimer's Disease (2007)

Discovery of safe and effective disease-modifying therapies will usher in a new age of Alzheimer's disease treatment.
Usefulness of Equilibrium Parameters of Adhesion in Predicting the Outcome of Competition for Bacterial Receptor Sites on Respiratory Epithelial Cells byPseudomonas aeruginosaStrains of Heterologous Pilus Type (1990)

The adhesion of Pseudomonas aeruginosa strain O(PAO) to human buccal epithelial cells (BECs) was analysed by an equilibrium analysis of binding and the equilibrium parameters of adhesion determined. PAO bound to a maximum of 159±28 receptor sites per BEC with an apparent association constant (Ka) of 2.89(± 1.76) ± 10−8 ml/CFU. As P.aeruginosa strain K(PAK) employs pili to adhere to BECs and there is substantial homology between the PAK pilin gene and the PAO pilin gene, the potential for competition for receptor sites on the BEC surface was investigated. PAO and PAK competed for receptor sites in a reciprocal manner, although PAO was ∼ 10 fold more effective in competing for receptor sites than was PAK. Purified pili inhibited the adhesion of the heterologous strain, PAO pili being ∼ 10 fold more effective than PAK pili in this heterologous inhibition. The difference in effectiveness of PAO and PAO pili in competing with PAK and PAK pili for receptor sites reflected the difference in the Kas of the two strains.
The mutagenic chain reaction: A method for converting heterozygous to homozygous mutations (2015)

An organism with a single recessive loss-of-function allele will typically have a wild-type phenotype, whereas individuals homozygous for two copies of the allele will display a mutant phenotype. We have developed a method called the mutagenic chain reaction (MCR), which is based on the CRISPR/Cas9 genome-editing system for generating autocatalytic mutations, to produce homozygous loss-of-function mutations. In Drosophila, we found that MCR mutations efficiently spread from their chromosome of origin to the homologous chromosome, thereby converting heterozygous mutations to homozygosity in the vast majority of somatic and germline cells. MCR technology should have broad applications in diverse organisms.
Spatio-temporal-spectral imaging of non-repeatable dissipative soliton dynamics (2020)

Dissipative solitons (DSs) are multi-dimensionally localized waves that arise from complex dynamical balances in far-from-equilibrium nonlinear systems and widely exist in physics, chemistry and biology. Real-time observations of DS dynamics across many dimensions thus have a broad impact on unveiling various nonlinear complexities in different fields. However, these observations are challenging as DS transitions are stochastic, non-repeatable and often strongly coupled across spatio-temporal-spectral (STS) domains. Here we report multi-dimensional (space xy + discrete time t + wavelength λ) DS dynamics imaged by STS compressed ultrafast photography, enabling imaging at up to trillions of frames per second. Various transient and random phenomena of multimode DSs are revealed, highlighting the importance of real-time multi-dimensional observation without the need for event repetition in decomposing the complexities of DSs.