gebhart/patrepeval huggingface dataset:
A trace-driven analysis of the UNIX 4.2 BSD file system (1985)

We analyzed the UNIX 4.2 BSD file system by recording user-level activity in trace files and writing programs to analyze the traces. The tracer did not record individual read and write operations, yet still provided tight bounds on what information was accessed and when. The trace analysis shows that the average file system bandwidth needed per user is low (a few hundred bytes per second). Most of the files accessed are open only a short time and are accessed sequentially. Most new information is deleted or overwritten within a few minutes of its creation. We also wrote a simulator that uses the traces to predict the performance of caches for disk blocks. The moderate-sized caches used in UNIX reduce disk traffic for file blocks by about 50%, but larger caches (several megabytes) can eliminate 90% or more of all disk traffic. With those large caches, large block sizes (16 kbytes or more) result in the fewest disk accesses.
Preliminary Investigation of Bio-carriers Using Magnetotactic Bacteria (2006)

This paper proposes a novel micro-carrier based on magnetotactic bacteria (MTB). To confirm the feasibility of such carriers, the thrust force of the bacteria is evaluated. By measuring the swimming speed of MC-1 bacteria in an unbounded medium, a thrust of 4 pN generated by a single MC-1 bacterium is found. The effects on the MTB's swimming speed under the control of micro-electromagnets and influenced by the wall effects when each MTB is attached to a microbead are investigated.
High affinity ligands from in vitro selection: Complex targets (1998)

Human red blood cell membranes were used as a model system to determine if the systematic evolution of ligands by exponential enrichment (SELEX) methodology, an in vitro protocol for isolating high-affinity oligonucleotides that bind specifically to virtually any single protein, could be used with a complex mixture of potential targets. Ligands to multiple targets were generated simultaneously during the selection process, and the binding affinities of these ligands for their targets are comparable to those found in similar experiments against pure targets. A secondary selection scheme, deconvolution-SELEX, facilitates rapid isolation of the ligands to targets of special interest within the mixture. SELEX provides high-affinity compounds for multiple targets in a mixture and might allow a means for dissecting complex biological systems.
Vasoactive Factors and Diabetic Retinopathy: Vascular Endothelial Growth Factor, Cycoloxygenase-2 and Nitric Oxide (2004)

The pathogenetic agents involved in the development of diabetic retinopathy are diverse. In the setting of hyperglycaemia and retinal hypoxia a number of vasoactive factors may interact to promote pathology in a variety of cell types including the microvasculature, neurons and glia. Vascular endothelial growth factor (VEGF) is universally accepted as a primary factor in the regulation of vessel patency in vascular networks throughout the body and including the retina. There is considerable evidence that the VEGF system in disturbed early in diabetes and interacts with other pathways and vasoactive factors to stimulate breakdown of the blood retinal barrier (BRB) and eventually promote angiogenesis, the hallmark feature of proliferative diabetic retinopathy (PDR). There is a distinct relationship between VEGF and the prostaglandin-cyclooxygenase system. Prostaglandins influence retinal blood flow, are important in inflammation and are also pro-angiogenic. Recent evidence suggests that cyclooxygenase-2 (COX-2) modulates angiogenesis by interacting with the VEGF system. Like prostaglandins, nitric oxide (NO) is a vasodilator and is implicated in VEGF mediated vascular permeability and angiogenesis. Emerging evidence indicates that COX-2 also interacts with NO and that these two systems have reciprocal effects on each other. There is little doubt that the interactions between these three vasoactive systems are complex and requires further study in the context of retinal vascular permeability, angiogenesis and neurodegeneration. This review will explore experimental and clinical evidence that VEGF, COX-2 and NO promote retinal pathology in diabetes and other ischemic-induced retinopathies.
Recent Methodologies for the Estimation of N-Octanol / Water Partition Coefficients and their Use in the Prediction of Membrane Transport Properties of Drugs (2005)

The lipophilicity of drug molecules (represented as the logarithm of the n-octanol/water partition coefficient) often strongly correlates with their pharmacological and toxic activities. It is therefore, not surprising that there is considerable interest in developing mathematical models capable to accurately predict their value for new drug candidates. In this review, current major approaches for estimating partition coefficients are described and some of their advantages and disadvantages are discussed. Recent uses of these partition coefficient algorithms in the development of membrane transport models are also discussed.
The Java™ Class Libraries, Volume 2: java.applet, java.awt, java.beans (1997)

From the Publisher:
This volume provides comprehensive reference documentation for the development of applets, user interfaces, and Java beans. The information is presented in an easy-to-use, dictionary-like format. The packages covered in Volume 2 are:
java.applet		java.awt.image	java.awt		java.awt.peer	java.awt.datatransfer		java.beans	java.awt.event	
The extensive class and member descriptions contain details crucial for developing robust and professional applets and applications. Each description is supplemented by an example that demonstrates the class or member in a relevant context. The 20,000 lines of code in over 350 examples facilitate learning-by-example and provide useful code fragments for your projects. Each class description includes:

a class hierarchy diagram showing its connection to related classes a detailed overview describing its purpose and key concepts a convenient member summary that briefly describes each member and arranges the members into related groups an example demonstrating the class in a real-world context comprehensive descriptions and an example for each member
Binding of Human Plasminogen toBifidobacterium (2007)

Bifidobacteria constitute up to 3% of the total microbiota and represent one of the most important health-promoting bacterial groups of the human intestinal microflora. The presence of Bifidobacterium in the human gastrointestinal tract has been directly related to several health-promoting activities; however, to date, no information about the specific mechanisms of interaction with the host is available. In order to provide some insight into the molecular mechanisms involved in the interaction with the host, we investigated whether Bifidobacterium was able to capture human plasminogen on the cell surface. By using flow cytometry, we demonstrated a dose-dependent human plasminogen-binding activity for four strains belonging to three bifidobacterial species: Bifidobacterium lactis, B. bifidum, and B. longum. The binding of human plasminogen to Bifidobacterium was dependent on lysine residues of surface protein receptors. By using a proteomic approach, we identified five putative plasminogen-binding proteins in the cell wall fraction of the model strain B. lactis BI07. The data suggest that plasminogen binding to B. lactis is due to the concerted action of a number of proteins located on the bacterial cell surface, some of which are highly conserved cytoplasmic proteins which have other essential cellular functions. Our findings represent a step forward in understanding the mechanisms involved in the Bifidobacterium-host interaction.
Application of a first-pass effect model to characterize the pharmacokinetic disposition of venlafaxine after oral administration to human subjects. (1997)

Venlafaxine (VEN), a drug used in the treatment of depression, undergoes significant first-pass metabolism after oral dosing to O-desmethylvenlafaxine (ODV), a metabolite with comparable therapeutic activity to that of parent drug. The pharmacokinetic disposition of VEN was characterized using a "first-pass" model that incorporates a presystemic compartment (liver) to account for the first-pass metabolism of VEN to ODV. A series of differential equations were simultaneously fitted to plasma concentrations of parent and metabolite. A good fit of the model to observed data was demonstrated, generating estimates for the following parameters: ka (1.31 +/- 0.009 hr-1), VVEN (252 +/- 87.6 liters), CLint (65.8 +/- 39.7 liters/hr), RL (liver:plasma partition coefficient, 29.6 +/- 18. 3), VODV (181 +/- 84.1 liters), and CLODV (23.5 +/- 12.5 liters/hr). Parameter estimates correlated closely with those obtained through noncompartmental methods. These results indicate that the time-course disposition of a compound undergoing first-pass hepatic metabolism after oral dosing can be successfully modeled.
Expression of a tumor necrosis factor-alpha transgene in murine lung causes lymphocytic and fibrosing alveolitis. A mouse model of progressive pulmonary fibrosis. (1995)

The murine TNF-alpha gene was expressed under the control of the human surfactant protein SP-C promoter in transgenic mice. A number of the SP-C TNF-alpha mice died at birth or after a few weeks with very severe lung lesions. Surviving mice transmitted a pulmonary disease to their offspring, the severity and evolution of which was related to the level of TNF-alpha mRNA in the lung; TNF-alpha RNA was detected in alveolar epithelium, presumably in type II epithelial cells. In a longitudinal study of two independent mouse lines, pulmonary pathology, at 1-2 mo of age, consisted of a leukocytic alveolitis with a predominance of T lymphocytes. Leukocyte infiltration was associated with endothelial changes and increased levels of mRNA for the endothelial adhesion molecule VCAM-1. In the following months, alveolar spaces enlarged in association with thickening of the alveolar walls due to an accumulation of desmin-containing fibroblasts, collagen fibers, and lymphocytes. Alveolar surfaces were lined by regenerating type II epithelial cells, and alveolar spaces contained desquamating epithelial cells in places. Platelet trapping in the damaged alveolar capillaries was observed. Pulmonary pathology in the SP-C TNF-alpha mice bears a striking resemblance to human idiopathic pulmonary fibrosis, in which increased expression of TNF-alpha in type II epithelial cells has also been noted. These mice provide a valuable animal model for understanding the pathogenesis of pulmonary fibrosis and exploring possible therapeutic approaches.
Peripheral Neurostimulation for the Treatment of Chronic, Disabling Transformed Migraine (2003)

These results raise the possibility that C1 through C3 peripheral nerve stimulation can help improve transformed migraine symptoms and disability. A controlled study is required to confirm these results.
Effect of tocotrienols on the growth of a human breast cancer cell line in culture (1995)

The tocotrienol-rich fraction (TRF) of palm oil consists of tocotrienols and some alpha-tocopherol (alpha-T). Tocotrienols are a form of vitamin E having an unsaturated side-chain, rather than the saturated side-chain of the more common tocopherols. Because palm oil has been shown not to promote chemically-induced mammary carcinogenesis, we tested effects of TRF and alpha-T on the proliferation, growth, and plating efficiency (PE) of the MDA-MB-435 estrogen-receptor-negative human breast cancer cells. TRF inhibited the proliferation of these cells with a concentration required to inhibit cell proliferation by 50% of 180 microgram/mL whereas alpha-T had no effect at concentrations up to 1000 microgram/mL as measured by incorporation of [3H]thymidine. The effects of TRF and alpha-T also were tested in longer-term growth experiments, using concentrations of 180 and 500 microgram/mL. We found that TRF inhibited the growth of these cells by 50%, whereas alpha-T did not. Their effect on the ability of these cells to form colonies also was studied, and it was found that TRF inhibited PE, whereas alpha T had no effect. These results suggest that the inhibition is due to the presence of tocotrienols in TRF rather than alpha T.
Abstract 5390: The TRK inhibitor RXDX-101 enhances the efficacy of temozolomide and irinotecan in a xenograft model of neuroblastoma (2015)

Abstract Purpose: Neuroblastoma (NB) is one of the most common and deadly solid tumors of childhood. The Trk family of neurotrophin receptors plays an important role in clinical behavior of NBs. Overexpression of TrkB and its ligand, BDNF, is associated with poor prognosis. We wanted to determine if RXDX-101, an oral pan-TRK, ROS1 and ALK inhibitor, would be effective in our NB xenograft model, either alone or in combination with conventional chemotherapy. Experimental Design: We tested the in vitro effects of RXDX-101 as a single agent, or in combination with the chemotherapeutic agents irinotecan and temozolomide (Irino-TMZ), using a subclone of the SH-SY5Y NB cell line transfected with TrkB. We also examined in vivo growth inhibition of TrkB-expressing NB xenografts with RXDX-101 alone or in combination with Irino-TMZ. Results: RXDX-101 significantly inhibited growth of TrkB-expressing NB cells in vitro. Enhanced in vitro inhibition was observed when RXDX-101 was used in combination with Irino-TMZ. Single agent therapy with RXDX-101 resulted in significant tumor growth inhibition compared to control animals [p&amp;lt;0.0001 for event-free survival (EFS)]. The addition of RXDX-101 to Irino-TMZ also significantly improved the EFS of animals compared to vehicle or Irino-TMZ treated animals (p&amp;lt;0.0001 for combination vs. control, p = 0.0012 for combination vs. Irino-TMZ). Conclusions: We show that RXDX-101 inhibits growth of TrkB expressing NB cells in vitro and in vivo. Furthermore, RXDX-101 cotreatment enhanced the efficacy of conventional chemotherapy in our NB xenograft model. Our data suggest that RXDX-101 has potential for incorporation in clinical trials for NB and other Trk expressing tumors. Citation Format: Radhika Iyer, Rebecca L. Golden, Koumudi Naraparaju, Jamie L. Croucher, Peng Guan, Gang Li, Zachary Hornby, Garrett M. Brodeur. The TRK inhibitor RXDX-101 enhances the efficacy of temozolomide and irinotecan in a xenograft model of neuroblastoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5390. doi:10.1158/1538-7445.AM2015-5390
Enhanced magnetoresistance of semiconductor-metal hybrid structures (2005)

Semiconductor‐metal hybrid structures can show a large magnetoresistance effect, the extraordinary magnetoresistance (EMR) effect. In this work, we study theoretically the influence of the voltage probe configuration on the magnetoresistance of such hybrid structures. We find a configuration, in which the current sensitivity of the device is enhanced considerably if compared to the probe configuration discussed so far in the literature. We argue that this enhancement is due to the combination of the EMR effect and the Hall effect in the hybrid structure.
The UCSC Genome Browser database: 2018 update (2017)

The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.
Biosensing with Nanofluidic Diodes (2009)

Recently reported nanofluidic diodes with highly nonlinear current-voltage characteristics offer a unique possibility to construct different biosensors. These sensors are based on local changes of the surface charge on walls of single conical nanopores induced by binding of an analyte. The analyte binding can be detected as a change of the ion-current rectification of single nanopores defined as a ratio of currents for voltages of one polarity, and currents for voltages of the opposite polarity. In this article, we provided both modeling and experimental studies of various biosensing routes based on monitoring changes of the rectification degree in nanofluidic diodes used as a biosensing platform. A prototype of a sensor for the capsular poly gamma-D-glutamic acid (gammaDPGA) from Bacillus anthracis is presented. The nanopore used for the sensing was locally modified with the monoclonal antibody for gammaDPGA. The proof of principle of the rectification degree-based sensing was further shown by preparation of sensors for avidin and streptavidin. Our devices also allowed for determination of the isoelectric point of the minute amounts of proteins immobilized on the surface.
Investigation of Carbon Metabolism in “ Dehalococcoides ethenogenes ” Strain 195 by Use of Isotopomer and Transcriptomic Analyses (2009)

Members of the genus "Dehalococcoides" are the only known microorganisms that can completely dechlorinate tetrachloroethene and trichloroethene to the innocuous end product, ethene. This study examines the central metabolism in "Dehalococcoides ethenogenes" strain 195 via (13)C-labeled tracer experiments. Supported by the genome annotation and the transcript profile, isotopomer analysis of key metabolites clarifies ambiguities in the genome annotation and identifies an unusual biosynthetic pathway in strain 195. First, the (13)C-labeling studies revealed that strain 195 contains complete amino acid biosynthesis pathways, even though current genome annotation suggests that several of these pathways are incomplete. Second, the tricarboxylic acid cycle of strain 195 is confirmed to be branched, and the Wood-Ljungdahl carbon fixation pathway is shown to not be functionally active under our experimental conditions; rather, CO(2) is assimilated via two reactions, conversion of acetyl-coenzyme A (acetyl coenzyme A [acetyl-CoA]) to pyruvate catalyzed by pyruvate synthase (DET0724-0727) and pyruvate conversion to oxaloacetate via pyruvate carboxylase (DET0119-0120). Third, the (13)C-labeling studies also suggested that isoleucine is synthesized from acetyl-CoA and pyruvate via citramalate synthase (CimA, EC 2.3.1.182), rather than from the common pathway via threonine ammonia-lyase (EC 4.3.1.19). Finally, evidence is presented that strain 195 may contain an undocumented citrate synthase (>95% Re-type stereospecific), i.e., a novel Re-citrate synthase that is apparently different from the one recently reported in Clostridium kluyveri.
THE PREPARATION OF 1,1'- AND 3,3'-BIISOQUINOLINE1 (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE PREPARATION OF 1,1'- AND 3,3'-BIISOQUINOLINE1FRANCIS H. CASECite this: J. Org. Chem. 1952, 17, 3, 471–472Publication Date (Print):March 1, 1952Publication History Published online1 May 2002Published inissue 1 March 1952https://pubs.acs.org/doi/10.1021/jo01137a021https://doi.org/10.1021/jo01137a021research-articleACS PublicationsRequest reuse permissionsArticle Views437Altmetric-Citations16LEARN 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 Get e-Alerts
Human CD4+ T Cells Recognize an Epitope within α-Fetoprotein Sequence and Develop into TGF-β-Producing CD4+ T Cells (2008)

There is limited information on the influence of tumor growth on the expansion of tumor-specific TGF-beta-producing CD4(+) T cells in humans. alpha-Fetoprotein (AFP) is an oncofetal Ag and has intrinsic immunoregulatory properties. In this study, we report the identification and characterization of subsets of CD4(+) T cells that recognize an epitope within the AFP sequence (AFP(46-55)) and develop into TGF-beta-producing CD4(+) T cells. In a peptide-specific and dose-dependent manner, AFP(46-55) CD4(+) T cells produce TGF-beta, GM-CSF, and IL-2 but not Th1-, Th2-, Th17-, or Tr1-type cytokines. These cells express CTLA-4 and glucocorticoid-induced TNR receptor and inhibit T cell proliferation in a contact-dependent manner. In this study, we show that the frequency of AFP(46-55) CD4(+) T cells is significantly higher (p = 001) in patients with hepatocellular carcinoma than in healthy donors, suggesting that these cells are expanded in response to tumor Ag. In contrast, tumor necrosis-inducing treatments that are shown to improve survival rate can shift the Th1/TGF-beta-producing CD4(+) T cell balance in favor of Th1 responses. Our data demonstrate that tumor Ags may contain epitopes which activate the expansion of inducible regulatory T cells, leading to evasion of tumor control.
Alternating Copolymerization of Carbon Dioxide and Cyclohexene Oxide and Their Terpolymerization with Lactide Catalyzed by Zinc Complexes of N,N Ligands (2006)

Abstract For the alternating copolymerization of CO 2 and cyclohexene oxide, a variety of zinc acetate complexes with new aminoimidoacrylate ligands has been synthesized and tested as catalysts. All complexes catalyzed the reaction and structure‐activity investigations revealed that the highest activities and selectivities were reached when the ligand’s aromatic rings were 2,6‐substituted by alkyl groups of different size (isopropyl versus methyl) and when the ligand backbone embodied an electron‐withdrawing cyano group. Furthermore, these complexes catalyzed the terpolymerization of CO 2 , cyclohexene oxide and lactide to give poly(cyclohexyl carbonate‐ co ‐lactide) and the composition of the polymer was adjustable by the monomer feed.