gebhart/patrepeval huggingface dataset:
Pharmacological neuroprotection after perinatal asphyxia (2010)

Recent progress has provided us with several promising neuroprotective compounds to reduce perinatal hypoxic-ischemic (HI) brain injury. In the early post HI phase, therapies can be concentrated on ion channel blockage (Xenon), anti-oxidation (allopurinol, 2-iminobiotin, and indomethacin), anti-inflammation (erythropoietin [EPO], melatonin), and anti-apoptosis (nuclear factor kappa B [NF-&#x03BA;B]and c-jun N-terminal kinase [JNK] inhibitors); in the later phase, therapies should be targeted to promote neuronal regeneration by stimulation of neurotrophic properties of the neonatal brain (EPO, growth factors, stem cells transplantation). Combination of pharmacological interventions with moderate hypothermia, which is the only established therapy for post HI brain injury, is probably the next step to fight HI brain damage in the clinical setting. Further studies should be concentrated on more rational pharmacological strategies by determining the optimal time and dose to inhibit the various potentially destructive molecular pathways and/or to enhance endogenous repair meanwhile avoiding the adverse effects.
Urea-Mediated Cross-Presentation of Soluble Epstein-Barr Virus BZLF1 Protein (2008)

Soluble extracellular proteins usually do not enter the endogenous human leukocyte antigen (HLA) I-dependent presentation pathway of antigen-presenting cells, strictly impeding their applicability for the re-stimulation of protein-specific CD8(+) cytotoxic T lymphocytes (CTL). Here we present for the Epstein-Barr virus (EBV) BZLF1 a novel strategy that facilitates protein translocation into antigen-presenting cells by its solubilisation in high molar urea and subsequent pulsing of cells in presence of low molar urea. Stimulation of PBMC from HLA-matched EBV-seropositive individuals with urea-treated BZLF1 but not untreated BZLF1 induces an efficient reactivation of BZLF1-specific CTL. Urea-treated BZLF1 (uBZLF1) enters antigen-presenting cells in a temperature-dependent manner by clathrin-mediated endocytosis and is processed by the proteasome into peptides that are bound to nascent HLA I molecules. Dendritic cells and monocytes but also B cells can cross-present uBZLF1 in vitro. The strategy described here has potential for use in the development of improved technologies for the monitoring of protein-specific CTL.
Platelets induce neutrophil extracellular traps in transfusion-related acute lung injury (2012)

There is emerging evidence that platelets are major contributors to inflammatory processes through intimate associations with innate immune cells. Here, we report that activated platelets induce the formation of neutrophil extracellular traps (NETs) in transfusion-related acute lung injury (TRALI), which is the leading cause of death after transfusion therapy. NETs are composed of decondensed chromatin decorated with granular proteins that function to trap extracellular pathogens; their formation requires the activation of neutrophils and release of their DNA in a process that may or may not result in neutrophil death. In a mouse model of TRALI that is neutrophil and platelet dependent, NETs appeared in the lung microvasculature and NET components increased in the plasma. We detected NETs in the lungs and plasma of human TRALI and in the plasma of patients with acute lung injury. In the experimental TRALI model, targeting platelet activation with either aspirin or a glycoprotein IIb/IIIa inhibitor decreased NET formation and lung injury. We then directly targeted NET components with a histone blocking antibody and DNase1, both of which protected mice from TRALI. These data suggest that NETs contribute to lung endothelial injury and that targeting NET formation may be a promising new direction for the treatment of acute lung injury.
Multi-step ahead prediction using neural networks (2011)

Multimedia applications transmitted over the Internet generate a major part of the Internet traffic. The bursty characteristics of the video traffic make it difficult to fulfill the requirements for Quality of Services (QoS) of such applications. Among other procedures for traffic and congestion control bandwidth allocation is also one of the options to guarantee the specified QoS. Dynamic bandwidth allocation can be successfully performed with the use of traffic prediction. Neural networks are a vastly used tool for prediction. The multi-step ahead prediction is more difficult approach then the single-step ahead prediction, but because video time series include long-range time dependencies, the multi-step ahead prediction seems as a better approach to video traffic prediction. In this paper we present three different approaches to multi-step ahead prediction and compare the results. First we describe basic principles of two types of neural networks, which we use for all the three approaches: the multilayer perceptron and the Nonlinear AutoRegressive model with eXogeneous inputs neural network (NARX). Then we briefly describe the composition of the video trace files. In the last section we present the results for multi-step ahead video prediction.
The Extracellular Component of a Transport Metabolon (2002)

Cytosolic carbonic anhydrase II (CAII) and the cytoplasmic C-terminal tails of chloride/bicarbonate anion exchange (AE) proteins associate to form a bicarbonate transport metabolon, which maximizes the bicarbonate transport rate. To determine whether cell surface-anchored carbonic anhydrase IV (CAIV) interacts with AE proteins to accelerate the bicarbonate transport rate, AE1-mediated bicarbonate transport was monitored in transfected HEK293 cells. Expression of the inactive CAII V143Y mutant blocked the interaction between endogenous cytosolic CAII and AE1, AE2, and AE3 and inhibited their transport activity (53 +/- 3, 49 +/- 10, and 35 +/- 1% inhibition, respectively). However, in the presence of V143Y CAII, expression of CAIV restored full functional activity to AE1, AE2, and AE3 (AE1, 101 +/- 3; AE2, 85 +/- 5; AE3, 108 +/- 1%). In Triton X-100 extracts of transfected HEK293 cells, resolved by sucrose gradient ultracentrifugation, CAIV recruitment to the position of AE1 suggested a physical interaction between CAIV and AE1. Gel overlay assays showed a specific interaction between CAIV and AE1, AE2, and AE3. Glutathione S-transferase pull-down assays revealed that the interaction between CAIV and AE1 occurs on the large fourth extracellular loop of AE1. We conclude that AE1 and CAIV interact on extracellular loop 4 of AE1, forming the extracellular component of a bicarbonate transport metabolon, which accelerates the rate of AE-mediated bicarbonate transport.
Provable data possession at untrusted stores (2007)

We introduce a model for provable data possession (PDP) that allows a client that has stored data at an untrusted server to verify that the server possesses the original data without retrieving it. The model generates probabilistic proofs of possession by sampling random sets of blocks from the server, which drastically reduces I/O costs. The client maintains a constant amount of metadata to verify the proof. The challenge/response protocol transmits a small, constant amount of data, which minimizes network communication. Thus, the PDP model for remote data checking supports large data sets in widely-distributed storage system.
Alternative Approach To Modeling Bacterial Lag Time, Using Logistic Regression as a Function of Time, Temperature, pH, and Sodium Chloride Concentration (2012)

The objective of this study was to develop a probabilistic model to predict the end of lag time (λ) during the growth of Bacillus cereus vegetative cells as a function of temperature, pH, and salt concentration using logistic regression. The developed λ model was subsequently combined with a logistic differential equation to simulate bacterial numbers over time. To develop a novel model for λ, we determined whether bacterial growth had begun, i.e., whether λ had ended, at each time point during the growth kinetics. The growth of B. cereus was evaluated by optical density (OD) measurements in culture media for various pHs (5.5 ∼ 7.0) and salt concentrations (0.5 ∼ 2.0%) at static temperatures (10 ∼ 20°C). The probability of the end of λ was modeled using dichotomous judgments obtained at each OD measurement point concerning whether a significant increase had been observed. The probability of the end of λ was described as a function of time, temperature, pH, and salt concentration and showed a high goodness of fit. The λ model was validated with independent data sets of B. cereus growth in culture media and foods, indicating acceptable performance. Furthermore, the λ model, in combination with a logistic differential equation, enabled a simulation of the population of B. cereus in various foods over time at static and/or fluctuating temperatures with high accuracy. Thus, this newly developed modeling procedure enables the description of λ using observable environmental parameters without any conceptual assumptions and the simulation of bacterial numbers over time with the use of a logistic differential equation.
Regulation of Ncx1 Expression (2006)

The Na+-Ca2+ exchanger (NCX1) is up-regulated in hypertrophy and is often found up-regulated in end-stage heart failure. Studies have shown that the change in its expression contributes to contractile dysfunction. We have previously shown that the 1831-bp Ncx1 H1 (1831Ncx1) promoter directs cardiac-specific expression of the exchanger in both development and in the adult, and is sufficient for the up-regulation of Ncx1 in response to pressure overload. Here, we utilized adenoviral mediated gene transfer and transgenics to identify minimal regions and response elements that mediate Ncx1 expression in the heart. We demonstrate that the proximal 184 bp of the Ncx1 H1 (184Ncx1) promoter is sufficient for expression of reporter genes in adult cardiomyocytes and for the correct spatiotemporal pattern of Ncx1 expression in development but not for up-regulation in response to pressure overload. Mutational analysis revealed that both the -80 CArG and the -50 GATA elements were required for expression in isolated adult cardiomyocytes. Chromatin immunoprecipitation assays in adult cardiocytes demonstrate that SRF and GATA4 are associated with the proximal region of the endogenous Ncx1 promoter. Transgenic lines were established for the 1831Ncx1 promoter-luciferase containing mutations in the -80 CArG or -50 GATA element. No luciferase activity was detected during development, in the adult, or after pressure overload in any of the -80 CArG transgenic lines. The Ncx1 -50 GATA mutant promoter was sufficient for driving the normal spatiotemporal pattern of Ncx1 expression in development and for up-regulation in response to pressure overload but importantly, expression was no longer cardiac restricted. This work is the first in vivo study that demonstrates which cis elements are important for Ncx1 regulation.
Prevalence of Attempting Weight Loss and Strategies for Controlling Weight (1999)

Weight loss and weight maintenance are common concerns for US men and women. Most persons trying to lose weight are not using the recommended combination of reducing calorie intake and engaging in leisure-time physical activity 150 minutes or more per week.
Assessment of Proliferative Activity in Colorectal Carcinomas by Quantitative Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) (2001)

The monoclonal antibody Ki-67 and the isospecific monoclonal antibody MIB-1 are routinely used in oncology to assess the proliferation index of tumor cells. A more objective and sensitive method is the determination of the of Ki-67 protein-specific mRNA by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). In 25 resected colorectal adenocarcinomas of different stages and grades we determined between 0.2 and 4.4 amol (10(-18) mol) Ki-67 protein-specific mRNA per microgram total RNA (median = 0.88 amol). The corresponding Ki-67 indices (expressing the percentage of Ki-67/MIB-I positive tumor cells) ranged from 41 to 81% (median = 61%). We found a good correlation between Ki-67 index and mRNA expression (r = 0.75), a significant correlation between both data and tumor stage (primary tumor, regional nodes, metastasis [pTNM] staging classification) (p < 0.001), but not between both data and tumor grade. Both Ki-67 indices (p = 0.05) and mRNA levels (p = 0.014) correlated significantly to the patients' survival. These results demonstrate that the Ki-67 protein-specific quantitative RT-PCR is a useful method for the characterization of tumor cell proliferation.
Chapter 24 Antiglycolipid antibodies and peripheral neuropathies: links to pathogenesis (1994)

For most of the now sizable number of neuropathies in which antibodies against glycoconjugates have been reported, there are no data to support or exclude a pathogenetic role for the antibodies. This chapter examines two classes of antibodies in which there is more substantial pathogenetic information called “anti-myelin-associated glycoprotein (MAG) antibodies” and the “anti-GM1 antibodies.” In the former instance, there is good evidence that the anti-glycoconjugate antibody does cause the neuropathy, but that the nature of the epitope remains unresolved. For the anti-GM1 antibodies there is increasing evidence that at least one of the disorders associated with the antibody is immune mediated, but it is premature to conclude that the antibody causes the disease. In many settings the antibody may be a consequence of nervous system disease or may be only indirectly related. Multifocal motor neuropathy stands out as a disorder that can respond dramatically to immunotherapies, supporting the likelihood of an immune pathogenetic mechanism. The relationship of the anti-GM1 antibody to the pathogenesis remains a matter of speculation, but the anatomic and cellular distributions of GMI in the PNS make it a candidate as the molecular target.
Growth of kidney epithelial cells in culture: evidence for autocrine control (1984)

The factors that stimulate kidney growth in K+-deficient animals are unknown. Cultures of renal epithelial cells (BSC-1 line) were used to study this phenomenon because their growth is accelerated in medium containing a reduced K+ concentration. We tested the hypothesis that growth induced by low-K+ medium is mediated by factors produced by the cells; i.e., is subject to autocrine control. Low-K+ (3.2 mM) or control (5.4 mM) medium was conditioned by placing it on confluent cultures of BSC-1 cells for 1 h and was then collected. The K+ concentration of the low-K+ conditioned medium was then adjusted to the control value by addition of KCl. This conditioned medium stimulated growth of fresh cultures of cells to the same extent as did unconditioned low-K+ medium. The appearance of growth-promoting activity was maximal at a K+ concentration of 3.2 mM during conditioning of the medium. Low-K+ conditioned medium, corrected to a K+ concentration of 5.4 mM, required 6 h to commit cells to enhanced proliferation. Growth-stimulating activity in low-K+ conditioned medium was antagonized by a purified growth inhibitor produced by the cells. These observations are consistent with the hypothesis that autocrine products with opposite effects on growth can regulate proliferation of renal epithelial cells.
Transfer of the human NaI symporter gene enhances iodide uptake in hepatoma cells. (2001)

The transduction of the hNIS gene per se is sufficient to induce 125I transport in Morris hepatoma cells in vitro and in vivo. With regard to a therapeutic application, however, additional conditions need to be defined that inhibit the iodide efflux from the tumor cells.
How labor markets and imperfect competition affect tariff policy (1993)

Labor market institutions provide a rationale for the difference between the &amp;quot;corporatist &amp;quot; consensus on free trade and the &amp;quot;popu-list &amp;quot; resistance to trade liberalizatior. PolicyRc anhWoingPapendiuinatthefings ofwo&amp;amp;inppmsandmneougetheecangeofidasammgBank staffmnd all otheas ined in dowdopmant heanpapers, distzibu edby theResehAdvisoy Staff.carry thenam!-&amp;apos;1 ho0Mxdlect onlydyeirviews.andshouldbeusedandcitedaccordingly.Tlefindings.interpretations.andconclusions ethes,-c- &amp;amp;h dsould nct bo atuibuted to thc Wodd Bank. its Bord of Dieos, its mbnageman, or any of its manbercountries. Pu bl ic Di sc lo su re A ut ho riz ed Pu bl ic Di sc lo su re A ut ho riz ed Pu bl ic Di sc lo su re A ut ho riz ed Pu bl ic Di sc lo su re A ut ho riz ed
Oxidative Stress and Neurotoxicity (2007)

There is increasing awareness of the ubiquitous role of oxidative stress in neurodegenerative disease states. A continuing challenge is to be able to distinguish between oxidative changes that occur early in the disease from those that are secondary manifestations of neuronal degeneration. This perspective highlights the role of oxidative stress in Alzheimer's, Parkinson's, and Huntington's diseases, amyotrophic lateral sclerosis, and multiple sclerosis, neurodegenerative and neuroinflammatory disorders where there is evidence for a primary contribution of oxidative stress in neuronal death, as opposed to other diseases where oxidative stress more likely plays a secondary or by-stander role. We begin with a brief review of the biochemistry of oxidative stress as it relates to mechanisms that lead to cell death, and why the central nervous system is particularly susceptible to such mechanisms. Following a review of oxidative stress involvement in individual disease states, some conclusions are provided as to what further research should hope to accomplish in the field.
Outcomes with daptomycin in the treatment of Staphylococcus aureus infections with a range of vancomycin MICs (2010)

In this diverse population, daptomycin was associated with similar outcomes for patients, regardless of whether the vancomycin MIC was categorized as <2 or >or=2 mg/L. Further studies are warranted.
Mutant rab8 Impairs Docking and Fusion of Rhodopsin-bearing Post-Golgi Membranes and Causes Cell Death of TransgenicXenopusRods (2001)

Rab8 is a GTPase involved in membrane trafficking. In photoreceptor cells, rab8 is proposed to participate in the late stages of delivery of rhodopsin-containing post-Golgi membranes to the plasma membrane near the base of the connecting cilium. To test the function of rab8 in vivo, we generated transgenic Xenopus laevis expressing wild-type, constitutively active (Q67L), and dominant negative (T22N) forms of canine rab8 in their rod photoreceptors as green fluorescent protein (GFP) fusion proteins. Wild-type and constitutively active GFP-rab8 proteins were primarily associated with Golgi and post-Golgi membranes, whereas the dominant negative protein was primarily cytoplasmic. Expression of wild-type GFP-rab8 had minimal effects on cell survival and intracellular structures. In contrast, GFP-rab8T22N caused rapid retinal degeneration. In surviving peripheral rods, tubulo-vesicular structures accumulated at the base of the connecting cilium. Expression of GFP-rab8Q67L induced a slower retinal degeneration in some tadpoles. Transgene effects were transmitted to F1 offspring. Expression of the GFP-rab8 fusion proteins appears to decrease the levels of endogenous rab8 protein. Our results demonstrate a role for rab8 in docking of post-Golgi membranes in rods, and constitute the first report of a transgenic X. laevis model of retinal degenerative disease.
The estradiol-stimulated lipoprotein receptor of rat liver. A binding site that membrane mediates the uptake of rat lipoproteins containing apoproteins B and E. (1980)

Hepatic catabolism of lipoproteins containing apolipoproteins B or E is enhanced in rats treated with pharmacologic doses of 17 alpha-ethinyl estradiol. Liver membranes prepared from these rats exhibit an increased number of receptor sites that bind 125I-labeled human low density lipoproteins (LDL) in vitro. In the present studies, this estradiol-stimulated hepatic receptor was shown to recognize the following rat lipoproteins: LDL, very low density lipoproteins obtained from liver perfusates (hepatic VLDL), and VLDL-remnants prepared by intravenous injection of hepatic VLDL into functionally eviscerated rats. The receptor also recognized synthetic lamellar complexes of lecithin and rat apoprotein E as well as canine high density lipoproteins containing apoprotein E (apo E-HDLc). It did not recognize human HDL or rat HDL deficient in apoprotein E. Much smaller amounts of this high affinity binding site were also found on liver membranes from untreated rats, the number of such sites increasing more than 10-fold after the animals were treated with estradiol. Each of the rat lipoproteins recognized by this receptor was taken up more rapidly by perfused livers from estrogen-treated rats. In addition, enrichment of hepatic VLDL with C-apoproteins lowered the ability of these lipoproteins to bind to the estradiol-stimulated receptor and diminished their rate of uptake by the perfused liver of estrogen-treated rats, just as it did in normal rats. The current data indicate that under the influence of pharmacologic doses of estradiol the liver of the rat contains increased amounts of a functional lipoprotein receptor that binds lipoproteins containing apoproteins B and E. This hepatic lipoprotein receptor appears to mediate the uptake and degradation of lipoproteins by the normal liver as well as the liver of estradiol-treated rats. The hepatic receptor bears a close functional resemblance to the LDL receptor previously characterized on extrahepatic cells.
Hybrid NOrec (2011)

Transactional memory (TM) is a promising synchronization mechanism for the next generation of multicore processors. Best-effort Hardware Transactional Memory (HTM) designs, such as Sun's prototype Rock processor and AMD's proposed Advanced Synchronization Facility (ASF), can efficiently execute many transactions, but abort in some cases due to various limitations. Hybrid TM systems can use a compatible software TM (STM) in such cases.
Quantitative role of LAL, NPC2, and NPC1 in lysosomal cholesterol processing defined by genetic and pharmacological manipulations (2011)

Lipoprotein cholesterol taken up by cells is processed in the endosomal/lysosomal (E/L) compartment by the sequential action of lysosomal acid lipase (LAL), Niemann-Pick C2 (NPC2), and Niemann-Pick C1 (NPC1). Inactivation of NPC2 in mouse caused sequestration of unesterified cholesterol (UC) and expanded the whole animal sterol pool from 2,305 to 4,337 mg/kg. However, this pool increased to 5,408 and 9,480 mg/kg, respectively, when NPC1 or LAL function was absent. The transport defect in mutants lacking NPC2 or NPC1, but not in those lacking LAL, was reversed by cyclodextrin (CD), and the ED₅₀ values for this reversal varied from ~40 mg/kg in kidney to >20,000 mg/kg in brain in both groups. This reversal occurred only with a CD that could interact with UC. Further, a CD that could interact with, but not solubilize, UC still overcame the transport defect. These studies showed that processing and export of sterol from the late E/L compartment was quantitatively different in mice lacking LAL, NPC2, or NPC1 function. In both npc2(-/-) and npc1(-/-) mice, the transport defect was reversed by a CD that interacted with UC, likely at the membrane/bulk-water interface, allowing sterol to move rapidly to the export site of the E/L compartment.