gebhart/patrepeval huggingface dataset:
Live migration of virtual machines (2005)

Migrating operating system instances across distinct physical hosts is a useful tool for administrators of data centers and clusters: It allows a clean separation between hard-ware and software, and facilitates fault management, load balancing, and low-level system maintenance.By carrying out the majority of migration while OSes continue to run, we achieve impressive performance with minimal service downtimes; we demonstrate the migration of entire OS instances on a commodity cluster, recording service downtimes as low as 60ms. We show that that our performance is sufficient to make live migration a practical tool even for servers running interactive loads.In this paper we consider the design options for migrating OSes running services with liveness constraints, focusing on data center and cluster environments. We introduce and analyze the concept of writable working set, and present the design, implementation and evaluation of high-performance OS migration built on top of the Xen VMM.
Enantioselective Michael Addition of Nitromethane to α,β-Enones Catalyzed by Chiral Quaternary Ammonium Salts. A Simple Synthesis of (R)-Baclofen (2000)

[reaction:see text] Enantioselective Michael addition of nitromethane to an alpha, beta-enone is a key step in the synthesis of (R)-baclofen.
Probiotics for irritable bowel syndrome: a light in the darkness? (2001)

Probiotics have been used with apparent success for several gut disorders, so it is not surprising they have been tried in the treatment of irritable bowel syndrome (IBS). However, the pathogenesis of this disease is unknown, and opinions about how probiotics might work are speculative. Nevertheless, two small trials suggest they might benefit patients with IBS, particularly those suffering from pain and bloating. This possibility deserves further study. It is important though, that future trials employ criteria-identified subjects, be sufficiently powered and strictly double blind, and select a suitable outcome measure. Until state-of-the-art trials of probiotics are available, their use should remain in the experimental arena.
Chromosomal Spread Preparation of Human Embryonic Stem Cells for Karyotyping (2009)

Although human embryonic stem cells (hESC) have been shown to present a stable diploid karyotype, many studies have reported that depending on culture conditions they become prone to acquire chromosomal anomalies such as addition of whole or parts of chromosomes. Indeed, during long-term culture, karyotypic alterations are observed when enzymatic or chemical dissociation are used, while manual dissection of colonies for passaging retains a stable karyotype. Besides, changes in the environment such as the removal of feeder cells also seem to compromise the genetic integrity of hESC. Once chromosomal alterations could affect cellular physiology, the characterization of the genetic integrity of hESC in vitro is crucial considering hESC as an essential tool in embryogenesis studies and drug testing. Furthermore, for future therapeutic purposes chromosomal changes are a real concern as it is frequently associated to carcinogenesis. Here we show a simple and useful method to obtain high quality chromosome spreads for subsequent analysis of chromosome set by G-banding, FISH, SKY or CGH techniques. We recommend checking the chromosomal status routinely with intervals of 5 passages in order to monitor the appearance of translocations and aneuploidies.
1H‐NMR study of endothelin, sequence‐specific assignment of the spectrum and a solution structure (1989)

The solution conformation of the recently discovered bi-cyclic, 21 amino acid vasoconstrictor peptide, Endothelin I, has been examined by 1H-NMR in deuterated dimethyl sulphoxide. A full sequential assignment has been achieved. In addition, 19 long range NOEs were detected which were employed as distance constraints in molecular dynamics calculations to yield a possible solution structure for this new peptide.
Effect of dietary energy restriction on glucose production and substrate utilization in type 2 diabetes. (2000)

A total of 8 obese subjects with type 2 diabetes were studied while on a eucaloric diet and after reduced energy intake (25 and then 75% of requirements for 10 days each). Weight loss was 2, 3, and 3 kg after 5, 10, and 20 days, respectively; all of the weight lost was body fat. Fasting blood glucose (FBG) levels fell from 11.9 +/- 1.4 at baseline to 8.9 +/- 1.6, 7.9 +/- 1.4, and 8.8 +/- 1.3 mmol/l at days 5, 10, and 20, respectively (P < 0.05, baseline vs. 5, 10, and 20 days). Endogenous glucose production (EGP) was 22 +/- 2, 18 +/- 2, 17 +/- 2, and 22 +/- 2 pmol x kg(-1) lean body mass (LBM) x min(-1) (P < 0.05, days 5 and 10 vs. baseline). Gluconeogenesis measured by mass isotopomer distribution analysis provided 31 +/- 4, 41 +/- 5, 40 +/- 4, and 33 +/- 4%, respectively, of the EGP (NS); absolute glycogenolytic contribution to the EGP was 15 +/- 2, 11 +/- 2, 11 +/- 2, and 15 +/- 2 pmol x kg(-1) LBM x min(-1), respectively (P < 0.001, baseline vs. days 5 and 10 and day 10 vs. day 20). The blood glucose clearance rate increased significantly at day 20 (P < 0.05). Neither lipolysis nor flux of plasma nonesterified fatty acids were altered compared with baseline. In conclusion, severe energy restriction per se independent of major changes in body composition reduces both FBG concentration and EGP in type 2 diabetes, the reduction in EGP results entirely from a reduction of glycogenolytic input into blood glucose, and the duration of reduced glycogenolysis is short-lived after relaxation of energy restriction even without weight gain, but effects on plasma glucose clearance persist and partially maintain the improvement in fasting glycemia.
Development of nucleic acid vaccines: use of self-amplifying RNA in lipid nanoparticles (2014)

Self-amplifying RNA or RNA replicon is a form of nucleic acid-based vaccine derived from either positive-strand or negative-strand RNA viruses. The gene sequences encoding structural proteins in these RNA viruses are replaced by mRNA encoding antigens of interest as well as by RNA polymerase for replication and transcription. This kind of vaccine has been successfully assayed with many different antigens as vaccines candidates, and has been shown to be potent in several animal species, including mice, nonhuman primates, and humans. A key challenge to realizing the broad potential of self-amplifying vaccines is the need for safe and effective delivery methods. Ideally, an RNA nanocarrier should provide protection from blood nucleases and extended blood circulation, which ultimately would increase the possibility of reaching the target tissue. The delivery system must then be internalized by the target cell and, upon receptor-mediated endocytosis, must be able to escape from the endosomal compartment into the cell cytoplasm, where the RNA machinery is located, while avoiding degradation by lysosomal enzymes. Further, delivery systems for systemic administration ought to be well tolerated upon administration. They should be safe, enabling the multiadministration treatment modalities required for improved clinical outcomes and, from a developmental point of view, production of large batches with reproducible specifications is also desirable. In this review, the concept of self-amplifying RNA vaccines and the most promising lipid-based delivery systems are discussed.
Reduction of Serum Cholesterol in Heterozygous Patients with Familial Hypercholesterolemia (1983)

We studied the effects of the bile acid sequestrant cholestyramine, alone and in combination with the experimental agent compactin (ML-236B), a competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase, on serum levels of lipoproteins in 10 heterozygous patients with familial hypercholesterolemia. After cholestyramine treatment alone for 2 to 16 months, serum total and low-density lipoprotein cholesterol decreased by 20 and 28 per cent, respectively. With the addition of compactin for 12 weeks there was a 39 per cent total decrease in serum cholesterol from the control value--from 356 +/- 14 to 217 +/- 10 mg per deciliter (9.27 +/- 0.36 to 5.64 +/- 0.26 mmol per liter [mean +/- S.E.M.]; P less than 0.001)--and a 53 per cent decrease in low-density lipoprotein cholesterol--from 263 +/- 13 to 125 +/- 10 mg per deciliter (6.84 +/- 0.34 to 3.25 +/- 0.26 mmol per liter; P less than 0.001). High-density lipoprotein cholesterol, which had increased during cholestyramine treatment, remained at its higher level. No adverse effects were observed. If long-term safety can be demonstrated, the compactin-cholestyramine regimen may prove useful in heterozygous familial hypercholesterolemia. prove useful in heterozygous familial hypercholesterolemia.
Inhibitory effect of probiotic Escherichia coli strain Nissle 1917 on adhesion to and invasion of intestinal epithelial cells by adherent–invasive E. coli strains isolated from patients with Crohn's disease (2003)

As strong and significant inhibitory effects on adherent-invasive E. coli adhesion and invasion were observed in co-infection and pre-infection experiments, E. coli Nissle 1917 could be efficient for preventive or curative probiotic therapy in patients with Crohn's disease.
Diffusing-wave spectroscopy with dynamic contrast variation: disentangling the effects of blood flow and extravascular tissue shearing on signals from deep tissue (2010)

We investigate the effects of blood flow and extravascular tissue shearing on diffusing-wave spectroscopy (DWS) signals from deep tissue, using an ex vivo porcine kidney model perfused artificially at controlled arterial pressure and flow. Temporal autocorrelation functions g((1))(τ) of the multiply scattered light field show a decay which is described by diffusion for constant flow, with a diffusion coefficient scaling linearly with volume flow rate. Replacing blood by a non-scattering fluid reveals a flow-independent background dynamics of the extravascular tissue. For a sinusoidally driven perfusion, field autocorrelation functions g((1))(τ, t') depend on the phase t' within the pulsation cycle and are approximately described by diffusion. The effective diffusion coefficient D(eff)(t') is modulated at the driving frequency in the presence of blood, showing coupling with flow rate; in the absence of blood, D(eff)(t') is modulated at twice the driving frequency, indicating shearing of extravascular tissue as the origin of the DWS signal. For both constant and pulsatile flow the contribution of extravascular tissue shearing to the DWS signal is small.
In vivo incisional wound healing augmented by platelet-derived growth factor and recombinant c-sis gene homodimeric proteins. (1988)

Human platelet-derived growth factor (hPDGF) is likely to be important in stimulating tissue repair, based upon its in vivo chemotactic and stimulatory activities for inflammatory cells and fibroblasts and upon the presence of PDGF and related proteins in platelets, macrophages, and activated fibroblasts, cell types that make up the milieu of the healing wound. Recombinant human c-sis (rPDGF-B), homodimers of the B chain of PDGF, were compared with hPDGF in vitro. rPDGF-B was immunologically similar to hPDGF and, at identical concentrations, similar to hPDGF in stimulating fibroblast mitogenesis and chemotaxis of polymorphonuclear leukocytes, monocytes, and fibroblasts. Purified hPDGF and rPDGF-B were also tested in vivo for potency in a model of tissue repair using a linear incision wound through rat dermis. A single application of hPDGF or rPDGF-B (2-20 micrograms/wound) in a slow release vehicle at the time of wounding resulted in a dose-dependent, statistically highly significant increase of breaking strength of treated wounds. Wound healing in animals treated with rPDGF-B was 170% stronger and accelerated by 2 d during the first week over control wounds and by 4-6 d over the next 2 wk. Histologic evaluation of growth factor-treated wounds correlated the in vitro chemotactic activity and the accelerated healing of wounds with a striking inflammatory cell infiltrate early after wounding, markedly increased formation of granulation tissue by 4-d, and increased fibrosis by 14 d in comparison to control wounds. The results thus demonstrate that rPDGF-B is fully active in in vitro tests of mitogenesis and chemotaxis and, for the first time, demonstrate directly that PDGF significantly advances wound healing in incisional wounds of experimental animals.
A Symmetric Carrier Technique of CRPWM for Voltage Balance Method of Flying-Capacitor Multilevel Inverter (2005)

This paper presents a simple carrier symmetric method for the voltage balance of flying capacitors in flying-capacitor multilevel inverters. The carrier-redistribution pulsewidth-modulation (CRPWM) method was reported as a solution for the voltage balance but it has a drawback at the transition of voltage level. To achieve the voltage balance of flying capacitors, the utilization of each carrier must be balanced during a half-cycle of the switching period such as phase-shifted PWM. However, the CRPWM method causes the fluctuation of flying-capacitor voltages because the balanced utilization of carriers is not achieved. Moreover, it does not consider that the load current change has an influence on flying-capacitor voltages by assuming that the current flows into the load. Therefore, the charging and discharging quantities of flying-capacitor voltages do not become zero during the switching period. To overcome the drawbacks of CRPWM, it is modified by the technique where carriers of each band are disposed of symmetrically at every fundamental period. Firstly, the CRPWM method is reviewed and the theory on voltage balance of flying capacitors is analyzed. The proposed method is introduced and is verified through simulation and experimental results.
Online Learning Asymmetric Boosted Classifiers for Object Detection (2007)

We present an integrated framework for learning asymmetric boosted classifiers and online learning to address the problem of online learning asymmetric boosted classifiers, which is applicable to object detection problems. In particular, our method seeks to balance the skewness of the labels presented to the weak classifiers, allowing them to be trained more equally. In online learning, we introduce an extra constraint when propagating the weights of the data points from one weak classifier to another, allowing the algorithm to converge faster. In compared with the Online Boosting algorithm recently applied to object detection problems, we observed about 0-10% increase in accuracy, and about 5-30% gain in learning speed.
Patient-derived xenograft models of breast cancer and their predictive power (2015)

Despite advances in the treatment of patients with early and metastatic breast cancer, mortality remains high due to intrinsic or acquired resistance to therapy. Increased understanding of the genomic landscape through massively parallel sequencing has revealed somatic mutations common to specific subtypes of breast cancer, provided new prognostic and predictive markers, and highlighted potential therapeutic targets. Evaluating new targets using established cell lines is limited by the inexact correlation between responsiveness observed in cell lines versus that elicited in the patient. Patient-derived xenografts (PDXs) generated from fresh tumor specimens recapitulate the diversity of breast cancer and reflect histopathology, tumor behavior, and the metastatic properties of the original tumor. The high degree of genomic preservation evident across primary tumors and their matching PDXs over serial passaging validate them as important preclinical tools. Indeed, there is accumulating evidence that PDXs can recapitulate treatment responses of the parental tumor. The finding that tumor engraftment is an independent and poor prognostic indicator of patient outcome represents the first step towards personalized medicine. Here we review the utility of breast cancer PDX models to study the clonal evolution of tumors and to evaluate novel therapies and drug resistance.
Demonstration of the technical viability of PLC systems on medium- and low-voltage lines in the United States (2003)

Several companies in the United States are interested in applying power line communications for broadband Internet access. This article provides an in-depth report of one specific end-to-end PLC trial carried out in the United States. This article includes useful information on the various devices utilized to construct the network, the applications demonstrated, and the performance characteristics of the particular field trial selected as emblematic. Insight into the main components and challenges involved in the testing activity is also given.
Protection and antibody responses in different strains of mouse immunized with plasmid DNAs encoding influenza virus haemagglutinin, neuraminidase and nucleoprotein (1999)

Protection against influenza virus infection and antibody responses in mice vaccinated with plasmid DNAs encoding haemagglutinin (HA), neuraminidase (NA) and nucleoprotein (NP) were compared among BALB/c (H-2d), B10 (H-2b) and C3H (H-2k) mice. Mice were inoculated with each DNA construct twice, 3 weeks apart, at a dose of 1 microg per mouse by particle-mediated DNA transfer (gene gun) to the epidermis. They were challenged with a lethal dose of the homologous virus 7 days after the second vaccination. NA-DNA provided significant protection in all strains of mouse, whereas HA-DNA afforded significant protection only in BALB/c mice. The serum antibody titres against NA or HA molecules in BALB/c, C3H and B10 mice were high, intermediate and low, respectively. NP-DNA failed to provide protection in any strain of mouse, and elicited low titres of anti-NP antibodies. These results suggest that NA-DNA can be used as a vaccine component to provide effective protection against influenza virus infection in various strains of mouse.
Novel Functional Biodegradable Polymer II:  Fibroblast Growth Factor-2 Activities of Poly(γ-glutamic acid)-sulfonate (2004)

Basic fibroblast growth factor (FGF-2) mitogenic activities of sulfonated poly(γ-glutamic acid) (γ-PGA-S) were investigated with chlorate-treated L929 fibroblast culture tests. When 72% of the carboxyl groups in γ-PGA were sulfonated (γ-PGA-S72), cell numbers reached a maximum. The activity of γ-PGA-S72 was higher than that of γ-PGA and synthetic heparinoids and was almost comparable to that of heparin. Cytotoxicity of γ-PGA-S72 was not observed, regardless of the degree of sulfonation. FGF-2-protective effects of γ-PGA-S72 against acid and thermal inactivation were also evaluated, and γ-PGA-S72 showed higher FGF-2-protective effects in comparison to nonsulfonated γ-PGA. The steric structures of various sulfonated γ-PGA-Ss were analyzed by molecular modeling (molecular orbital method (MOPAC)) and indicated that γ-PGA-Ss are helical in vacuo. Results from MOPAC and the molecular mechanics method (MM2) demonstrated that electrostatic interactions can take place between sulfonic and carboxyl groups of γ-PGA-S and basic amino acid residues in FGF-2. γ-PGA-S72 can interact with FGF-2 strongly.
Fibroblasts Derive from Hepatocytes in Liver Fibrosis via Epithelial to Mesenchymal Transition (2007)

Activated fibroblasts are key contributors to the fibrotic extracellular matrix accumulation during liver fibrosis. The origin of such fibroblasts is still debated, although several studies point to stellate cells as the principal source. The role of adult hepatocytes as contributors to the accumulation of fibroblasts in the fibrotic liver is yet undetermined. Here, we provide evidence that the pro-fibrotic growth factor, TGF-beta1, induces adult mouse hepatocytes to undergo phenotypic and functional changes typical of epithelial to mesenchymal transition (EMT). We perform lineage-tracing experiments using AlbCre. R26RstoplacZ double transgenic mice to demonstrate that hepatocytes which undergo EMT contribute substantially to the population of FSP1-positive fibroblasts in CCL(4)-induced liver fibrosis. Furthermore, we demonstrate that bone morphogenic protein-7 (BMP7), a member of the TGFbeta superfamily, which is known to antagonize TGFbeta signaling, significantly inhibits progression of liver fibrosis in these mice. BMP7 treatment abolishes EMT-derived fibroblasts, suggesting that the therapeutic effect of BMP7 was at least partially due to the inhibition of EMT. These results provide direct evidence for the functional involvement of adult hepatocytes in the accumulation of activated fibroblasts in the fibrotic liver. Furthermore, our findings suggest that EMT is a promising therapeutic target for the attenuation of liver fibrosis.
A Novel Anti-Histone H1 Monoclonal Antibody, SSV Monoclonal Antibody, Improves Lung Injury and Survival in a Mouse Model of Lipopolysaccharide-Induced Sepsis-Like Syndrome (2015)

SSV mAb is shown to have anti-inflammatory activity and organ-protective effects, highlighting the importance of controlling histone H1 as well as H3 and H4 levels during inflammation.
Control of structure and properties of compound semiconductor interfaces by Si interface control layer (2002)

The authors review the current status of recent attempts to control the structure and properties of compound semiconductor interfaces by an ultrathin Si interface control layer. Surface and interface states in the energy gap cause many unwanted effects including the so-called Fermi level pinning phenomenon, which is discussed. Control of insulator-semiconductor, metal-semiconductor, and semiconductor-semiconductor interfaces are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Integration column: microwell arrays for mammalian cell culture (2009)

Microwell arrays have emerged as robust and versatile alternatives to conventional mammalian cell culture substrates. Using standard microfabrication processes, biomaterials surfaces can be topographically patterned to comprise high-density arrays of micron-sized cavities with desirable geometry. Hundreds to thousands of individual cells or cell colonies with controlled size and shape can be trapped in these cavities by simple gravitational sedimentation. Efficient long-term cell confinement allows for parallel analyses and manipulation of cell fate during in vitro culture. These live-cell arrays have already found applications in cell biology, for example to probe the effect of cell colony size on embryonic stem cell differentiation, to dissect the heterogeneity in single cell proliferation kinetics of neural or hematopoietic stem/progenitor cell populations, or to elucidate the role of cell shape on cell function. Here, we highlight the key applications of these platforms, hopefully inspiring biologists to apply these systems for their own studies.