gebhart/patrepeval huggingface dataset:
Dynamic syslog mining for network failure monitoring (2005)

Syslog monitoring technologies have recently received vast attentions in the areas of network management and network monitoring. They are used to address a wide range of important issues including network failure symptom detection and event correlation discovery. Syslogs are intrinsically dynamic in the sense that they form a time series and that their behavior may change over time. This paper proposes a new methodology of dynamic syslog mining in order to detect failure symptoms with higher confidence and to discover sequential alarm patterns among computer devices. The key ideas of dynamic syslog mining are 1) to represent syslog behavior using a mixture of Hidden Markov Models, 2) to adaptively learn the model using an on-line discounting learning algorithm in combination with dynamic selection of the optimal number of mixture components, and 3) to give anomaly scores using universal test statistics with a dynamically optimized threshold. Using real syslog data we demonstrate the validity of our methodology in the scenarios of failure symptom detection, emerging pattern identification, and correlation discovery.
PLGA micro/nanosphere synthesis by droplet microfluidic solvent evaporation and extraction approaches (2010)

In this paper, we present two approaches for the synthesis of poly(lactide-co-glycolide) (PLGA) micro/nanospheres using non-toxic organic solvents in droplet-based microfluidic platforms. Solvent evaporation and solvent extraction methods were employed to enable the controlled generation of monodisperse PLGA particles that range from 70 nanometres to 30 microns in diameter. Determination of particle size was carried out with dynamic light scattering (DLS) and image analysis to show less than 2% variation in particle size. Sizes of the PLGA microspheres were controlled by the PLGA concentration in solvent and by the relative flow rates of oil and aqueous phases in the system. A penetration imaging assay was performed to determine the depth of diffusion of a model drug molecule fluorescein, out of the PLGA nanoparticles into corneal tissue. With the ability to prepare high quality, monodisperse, biodegradable particles, our methods have great potential to benefit drug delivery applications.
From 2000 to Mid-2010: A Fruitful Decade for the Synthesis of Pyrazoles (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTFrom 2000 to Mid-2010: A Fruitful Decade for the Synthesis of PyrazolesSantos Fustero*†‡, María Sánchez-Roselló‡, Pablo Barrio†, and Antonio Simón-Fuentes*†View Author Information† Departamento de Química Orgánica, Universidad de Valencia, 46100-Burjassot (Valencia), Spain‡ Laboratorio de Moléculas Orgánicas, Centro de Investigación Príncipe Felipe, 46012-Valencia, SpainE-mail: [email protected], [email protected]. Phone: 34-963544279. Fax: 34-963544939.Cite this: Chem. Rev. 2011, 111, 11, 6984–7034Publication Date (Web):August 1, 2011Publication History Received3 February 2011Published online1 August 2011Published inissue 9 November 2011https://pubs.acs.org/doi/10.1021/cr2000459https://doi.org/10.1021/cr2000459review-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views15879Altmetric-Citations907LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Anions,Condensation,Cross coupling reaction,Cyclization,Reaction products Get e-Alerts
Differentiation of human bone marrow osteogenic stromal cells in vitro: induction of the osteoblast phenotype by dexamethasone. (1994)

Human bone marrow stromal cells were examined for their osteogenic potential in an in vitro cell culture system. Dexamethasone (Dex) treatment induced morphological transformation of these cells from an elongated to a more cuboidal shape, increased their alkaline phosphatase activity and cAMP responses to PTH and prostaglandin E2, and was essential for mineralization of the extracellular matrix. Dex-induced differentiation of human bone marrow stromal cells was apparent after 2-3 days of treatment and reached a maximum at 7-14 days, as judged by alkaline phosphatase activity, although induction of osteocalcin by 1,25-dihydroxyvitamin D3 was attenuated by Dex. Withdrawal of Dex resulted in an enhancement of the 1,25-dihydroxyvitamin D3-induced secretion of osteocalcin, whereas alkaline phosphatase activity and the cAMP response to PTH remained at prewithdrawal levels. The steady state mRNA level of osteonectin was not affected by Dex. Our results, which demonstrate that Dex conditions the differentiation of human bone marrow osteogenic stromal cells into osteoblast-like cells, support the hypothesis of a permissive effect of glucocorticoids in ensuring an adequate supply of mature osteoblast populations. Furthermore, the established human bone marrow stromal cell culture provides a good model of an in vitro system to study the regulation of differentiation of human bone osteoprogenitor cells.
Concentration of, and SDS Removal from Proteins Isolated from Multiple two‐Dimensional Electrophoresis Gels (1997)

We have developed a gel electrophoresis system that can concentrate proteins from spots cut out of up to 50 two-dimensional electrophoresis gels. During protein concentration, SDS is substituted with a non-ionic detergent (octyl beta-glucopyranoside) which allows digestion and MS analysis of the protein directly extracted from the gel without fixation or staining. The system avoids the problems associated with the digestion of dilute protein in multiple bands by (a) greatly reducing the gel volume for digestion and thus the amount of protease required, hence lowering contamination by autodigestion products, (b) reducing the volume of solvent required for extraction of protein from the gel, thus minimising loss of material to container surfaces, and (c) removing SDS which interferes with subsequent MS or HPLC analysis. The efficiency of protein recovery ranges between an average of 80% for proteins from silver stained two-dimensional gels to 90% for fluorescence and Coomassie-blue-stained gels. The method is compatible with MS analysis of very low amounts of protein from any staining system, but appears not to be useful for Edman sequencing of silver-stained or fluorescent-stained proteins since the amount of N-terminal blockage appears to increase as the amount of protein isolated from the two-dimensional gel decreases.
Effect of Culture Media on In Vitro Development of Cloned Mouse Embryos (2001)

The effect of simple and sequential embryo culture media on the preimplantation development of mouse nuclear transfer (NT) embryos reconstructed with cumulus cell nuclei using a mechanical NT technique was studied. Blastocyst formation rate was evaluated using CZB medium and the sequential media G1/G2 and KSOM/G2. Arrested two- and three-cell NT embryos were Hoechst-stained to check for nuclear abnormalities. Nonmanipulated and sham-manipulated parthenogenetic embryos served as controls for, respectively, the medium and the handling technique. Rates of blastocyst formation for medium and handling control embryos were similar in CZB (58% and 61%), in G1/G2 (94% and 85%), and in KSOM/G2 (88% and 84%). Development of NT embryos was significantly impaired from the two-cell stage onwards, reaching the blastocyst stage at a rate of 5% in CZB, 14% in G1/G2, and 28% in KSOM/G2. Arrested two- and three-cell stage NT embryos showed a high rate of binucleation. These data demonstrate not only that NT embryos are more sensitive to in vitro culture conditions than parthenogenetic control embryos but also that selection of culture media can influence the preimplantation development of NT embryos.
Changes of serum iron transferrin and copper ceruloplasmin in rats given Cu(II)2 (acetylsalicylate)4 during acute inflammation. (1989)

Modifications of serum levels of iron transferrin and copper ceruloplasmin after acute inflammation by carrageenan and treatment with acetyl salicylic acid [ASA] or Cu(II)2(acetylsalicylate)4 [Cu(II)2(AS)4] were studied in the rat by EPR spectroscopy. Furthermore, the ulcerogenic potential of the two drugs was investigated after a single high oral dose. Our results indicate that Cu(II)2(AS)4 is more effective than ASA in limiting the inflammation provoked by the phlogogen. In these conditions the iron(III) non-heme and copper(II) ceruloplasmin concentration in serum was modified either during inflammation or after treatment with antiphlogistic agents: in carrageenan-injected rats the level of serum iron(III) non-heme was found to be very low, while the copper(II) ceruloplasmin concentration was partially reduced. On the other hand, after the pharmacological treatments, no changes of iron transferrin were observed and the concentration of copper ceruloplasmin was increased. With regard to their ulcerogenic effect, ASA appeared to be more irritating for gastric mucosa than Cu(II)2(AS)4.
Characteristics of endogenous peptides eluted from the class I MHC molecule HLA-B7 determined by mass spectrometry and computer modeling. (1993)

Microcapillary HPLC electrospray ionization tandem mass spectrometry was used to sequence 15 peptides eluted from HLA-B7. Sequence alignment implicated four peptide positions in specific interactions with the class I molecule, and their importance was confirmed using synthetic peptides. Because no crystal structure for HLA-B7 was available, computer-assisted modeling was used to understand novel aspects of peptide binding specificity and to accurately predict the effect of defined changes in peptide structure. The results demonstrate that mass-spectrometric sequencing coupled with computer-assisted modeling can be used in the absence of a crystal structure to make accurate predictions concerning requirements for peptide binding to class I molecules. These techniques may be valuable to predict or engineer T cell epitopes.
Optical tomography: forward and inverse problems (2009)

This is a review of recent mathematical and computational advances in optical tomography. We discuss the physical foundations of forward models for light propagation on microscopic, mesoscopic and macroscopic scales. We also consider direct and numerical approaches to the inverse problems that arise at each of these scales. Finally, we outline future directions and open problems in the field.
Cross-Coupling of Remote meta-C–H Bonds Directed by a U-Shaped Template (2013)

meta-C-H arylation and methylation of 3-phenylpropanoic acid and phenolic derivatives were developed using an easily removable nitrile template. The combination of a weakly coordinating U-shaped template and mono-protected amino acid ligand was crucial for the cross-coupling of C-H bonds with organoborons.
Islet transplantation: where do we stand now? (2003)

After many years of limited success in islet transplantation, researchers developing this procedure have made great strides, and several centers have now reported that islet transplantation can result in long-term insulin independence for patients with type 1 diabetes mellitus. The improved quality of life achieved in some islet allograft recipients suggests that this important line of investigation should proceed. Yet, several factors limit the technique and these hurdles must be overcome before it can be considered a practical treatment for the millions of individuals with diabetes, be it type 1 or type 2. Most obvious is the gross disparity between the number of islets available for clinical transplantation and the number of patients with diabetes who might benefit. Other important limitations, too often lost in the discussion, include complications associated with the technique itself, the toxicity of currently available immunosuppressive drugs, and the imperfect glycemia control achieved in most patients. In fact, our ongoing analysis as to whether transplantation-based therapy improves survival for patients with type 1 diabetes suggests that, for many at least, the opposite may be true. Two variables, as yet undefined, also need to be considered: (1) can the procedure, when done well, prevent or reverse diabetes-associated complications and (2) what are the long-term consequences of intrahepatic islets?
Retinal Stem Cells Transplanted into Models of Late Stages of Retinitis Pigmentosa Preferentially Adopt a Glial or a Retinal Ganglion Cell Fate (2006)

These results show that the grafted cells preferentially integrate into the GCL and IPL and express ganglion cell or glial markers, thus exhibiting migratory and differentiation preferences when injected subretinally. It also appears that the retina, whether partially degenerated or already degenerated, does not provide signals to induce massive differentiation of RSCs into photoreceptors. This observation suggests that a predifferentiation of RSCs into photoreceptors before transplantation may be necessary to obtain graft integration in the ONL.
PAF-Induced Furin and MT1-MMP Expression Is Independent of MMP-2 Activation in Corneal Myofibroblasts (2005)

PAF, through a receptor-mediated mechanism, induces a specific pattern of furin, MMP, and TIMP-2 expression in corneal myofibroblasts. MMP-2 activity was unchanged by PAF treatment. These results suggest that in response to the inflammatory mediator PAF, induction of MT1-MMP is independent of MMP-2 activity in corneal myofibroblasts. Thus, PAF-mediated changes in extracellular matrix composition surrounding the myofibroblasts could be important in regulating the corneal scarring process. Moreover, PAF antagonists could be useful in maintaining corneal transparency.
Indium incorporation during the growth of (100)Si by molecular beam epitaxy: Surface segregation and reconstruction (1984)

The In incorporation probability σIn in (100) Si grown by molecular beam epitaxy was found, using secondary ion mass spectrometry (SIMS), to decrease from essentially unity at film growth temperatures Ts of ∼500 °C to &amp;lt;10−4 at 840 °C. SIMS depth profiles of both uniformly doped and modulation-doped samples showed evidence of strong surface segregation with the amount of profile broadening directly related to σIn(Ts). A combination of in situ electron diffraction and Auger electron spectroscopy was used to show that the surface segregation rate was sufficient over a wide range in Ts and In to Si flux ratios to cause the initial (2×1)-(100) Si surface reconstruction to transform to (3×4) due to the formation of an ordered In surface layer. The In surface coverage in the (3×4) state was ∼0.05–0.1 monolayer even though the bulk In concentration was ≤2×1017 cm3. The (2×1) to (3×4) surface phase transition was reversible by either terminating film growth and reevaporating the excess surface In or terminating the In flux while continuing Si film growth.
Full-Length GB Virus C (Hepatitis G Virus) RNA Transcripts Are Infectious in Primary CD4-Positive T Cells (2000)

GB virus C (GBV-C or hepatitis G virus) is a recently described flavivirus which frequently leads to chronic viremia in humans. Although GBV-C is associated with acute posttransfusion hepatitis, it is not clear if the virus is pathogenic for humans. We constructed a full-length cDNA from the plasma of a person with chronic GBV-C viremia. Peripheral blood mononuclear cells (PBMCs) transfected with full-length RNA transcripts from this GBV-C clone resulted in viral replication. This was demonstrated by serial passage of virus from cell culture supernatants, detection of increasing concentrations of positive- and negative-sense GBV-C RNA over time, and the detection of the GBV-C E2 antigen by confocal microscopy. In addition, two types of GBV-C particles were identified in cell lysates; these particles had buoyant densities of 1.06 and 1.12 to 1.17 g/ml in sucrose gradients. PBMCs sorted for expression of CD4 contained 100-fold-more GBV-C RNA than CD4-negative cells. Taken together, these data demonstrate that RNA transcripts from GBV-C full-length cDNA are infectious in primary CD4-positive T cells. In contrast, RNA transcripts from an infectious hepatitis C virus clone did not replicate in the same cell culture system. Infectious RNA transcripts from GBV-C cDNA should prove useful for studying viral replication and may allow identification of differences between GBV-C and hepatitis C virus cultivation in vitro.
Thomas Schlich, The Origins of Organ Transplantation: Surgery and Laboratory Science 1880-1930 (2012)

Bodies break and their organs fail. Often a little. Sometimes severely. Once terminally. The causes for this are legion and it is the medical practitioners' job to prevent, repair and reverse this process. It sounds like the oldest trick in the book, an ‘ancient dream of mankind’ (p. 3) and of medicine, to replace diseased or failed organs or their function. In his book, The Origins of Organ Transplantation, Thomas Schlich challenges this notion by tackling the history of organ transplantation both as a concept and set of practices. As the title betrays, however, his history does not begin with the ancients, and Schlich makes it rather clear that organ transplantation and organ replacement therapy are the products of a very precise social and professional context. The story started during the last decades of the nineteenth century, with its focus on nervous function being developed through the emergence of the hormone concept and endocrinology, and was largely left abandoned in the interwar period, before once again gaining momentum after the Second World War.
α-Synuclein impairs macroautophagy: implications for Parkinson’s disease (2010)

Parkinson's disease (PD) is characterized pathologically by intraneuronal inclusions called Lewy bodies, largely comprised of α-synuclein. Multiplication of the α-synuclein gene locus increases α-synuclein expression and causes PD. Thus, overexpression of wild-type α-synuclein is toxic. In this study, we demonstrate that α-synuclein overexpression impairs macroautophagy in mammalian cells and in transgenic mice. Our data show that α-synuclein compromises autophagy via Rab1a inhibition and Rab1a overexpression rescues the autophagy defect caused by α-synuclein. Inhibition of autophagy by α-synuclein overexpression or Rab1a knockdown causes mislocalization of the autophagy protein, Atg9, and decreases omegasome formation. Rab1a, α-synuclein, and Atg9 all regulate formation of the omegasome, which marks autophagosome precursors.
T cell immunomonitoring and tumor responses in patients immunized with a complex of cholesterol-bearing hydrophobized pullulan (CHP) and NY-ESO-1 protein. (2007)

We recently showed that vaccination with a complex of cholesterol-bearing hydrophobized pullulan and NY-ESO-1 protein (CHP-NY-ESO-1) elicited antibody responses in 9 of 9 patients vaccinated in a clinical trial. In this study, we performed T cell immunomonitoring and analyzed tumor responses in these patients. To evaluate CD4 and CD8 T cell responses, an IFN-gamma secretion assay was used. The assay showed low background and was sensitive for detecting antigen-specific T cells. An increase in the CD4 T cell response was observed in 2 of 2 initially sero-positive and 5 of 7 initially sero-negative patients after vaccination. An increase in the CD8 T cell response was also observed in 2 of 2 sero-positive and 5 of 7 sero-negative patients after vaccination. Analysis of peptides recognized by CD4 and CD8 T cells revealed two dominant NY-ESO-1 regions, 73-114 and 121-144. Tumor responses were observed in 3 esophageal cancer patients and a malignant melanoma patient. In 3 of 4 prostate cancer patients, prostate-specific antigen (PSA) values stabilized during the course of vaccination. The use of whole protein, containing multiple CD4 and CD8 epitopes, may be beneficial for cancer vaccines to prevent tumors from evading the immune response.
Pharmacologic profile of zoledronic acid: A highly potent inhibitor of bone resorption (2002)

Abstract Bisphosphonates are effective in treating benign and malignant skeletal diseases characterized by enhanced osteoclastic bone resorption (i.e., osteoporosis, Paget’s disease, tumor‐induced osteolysis). The nitrogen‐containing bisphosphonate pamidronate is currently the standard treatment for hypercalcemia of malignancy (HCM) and skeletal complications of bone metastases. Zoledronic acid, a novel nitrogen‐containing bisphosphonate with an imidazole substituent, has demonstrated more potent inhibition of osteoclast‐mediated bone resorption than all other bisphosphonates, including pamidronate, in both in vitro and in vivo preclinical models. Zoledronic acid inhibited ovariectomy‐induced bone loss in adult monkeys and rats, and long‐term treatment prevented skeletal turnover and subsequent bone loss, reduced cortical porosity, and increased mechanical strength. Zoledronic acid also significantly inhibited bone loss associated with arthritis, bone metastases, and prosthesis loosening. The increased potency of zoledronic acid vs. pamidronate has been demonstrated clinically: zoledronic acid (4 or 8 mg iv) was superior to pamidronate (90 mg iv) in normalizing corrected serum calcium in patients with HCM. In patients with bone metastases, low doses of zoledronic acid (≤ 2 mg) suppressed bone resorption markers ≤ 50% below baseline, whereas pamidronate 90 mg yielded only 20 to 30% suppression. Importantly, the increased potency of zoledronic acid is not associated with an increased incidence of local (bone) or systemic adverse events. Zoledronic acid does not impair bone mineralization and, compared with pamidronate, has a greater renal and intestinal tolerability therapeutic index. Thus, based on preclinical assays and clinical data, zoledronic acid is the most potent bisphosphonate tested to date. Given its potency and excellent safety profile, zoledronic acid is now poised to become the new standard of treatment for HCM and metastatic bone disease. Drug Dev. Res. 55:210–224, 2002. © 2002 Wiley‐Liss, Inc.
Increased levels of a TH2-type CC chemokine thymus and activation-regulated chemokine (TARC) in serum and induced sputum of asthmatics (2002)

The elevated TARC levels in asthmatics might be involved in the pathophysiology of asthma.
Crystallization of 70 S ribosomes and 30 S ribosomal subunits from Thermus thermophilus (1987)

Well‐ordered three‐dimensional crystals of 70 S ribosomes and 30 S ribosomal subunits from extremely thermophilic bacteria Thermus thermophilus have been obtained. Positively stained thin sections of the crystals have been analyzed by electron microscopy. Redissolved crystalline ribosomes and small ribosomal subunits reveal sedimentation constants of 70 S and 30 S, respectively, and are functionally active in the poly(U)‐system.