gebhart/patrepeval huggingface dataset:
Issues in debugging sequential and concurrent programs: methods, techniques, and implementation (1992)

Ensuring program correctness is an essential but difficult task in software development. In this dissertation, we focus on issues of techniques and implementation of tools that assist programmers to locate errors in their programs. We further show that the techniques and tools described can also be applied to solve a variety of related problems.
We describe a new, dataflow approach to debugging. This approach provides a solution to the problem of collection and presentation of information about the inferior's execution to programmers, and ways for programmers to control a debugger easily and efficiently. We have implemented a prototypical debugger called Dalek for sequential programs. Furthermore, we include in Dalek a command language that is actually a general-purpose programming language. This new idea makes new debugging techniques possible and allows the debugger to be used for many other applications, such as procedure tracing, performance measurement and code profiling, and audit trails analysis. We also discuss how the dataflow approach can be extended to distributed environments.
Another notable contribution of this dissertation is the design and implementation of a dynamic linking/unlinking system. It allows compiled object modules to be added to or removed from a process anytime during its execution. This is a new idea to create programs and it combines the efficiency of executing native machine code with the flexibility of runtime program modification. Its applications include program customization, incremental program development, and most important of all, it allows a number of advanced debugging features to be implemented easily.
We describe in general what is involved in implementing a debugger, for both sequential and concurrent environments, and techniques required to overcome common implementation problems. We also present a new, layered-approach for implementing debuggers. This layered-approach separates different functionalities of a debugger into different layers, and defines clearly the interfaces between them so that different implementations of the same layer can be interchanged transparently with other layers. This approach allows new debugging and monitoring tools to be built easily by replacing only the layers involved and reusing other layers, and thus facilitates rapid prototyping and sharing of code between programs with similar functionalities.
Analysis of distribution of tumor‐ and preneoplasia‐infiltrating lymphocytes using simultaneous hoechst 33342 labeling and immunophenotyping (1992)

Hoechst 33342 in vivo staining was combined with immunofluorescent staining of cell surface antigens to quantify the distribution, relative to blood supply, of lymphocytes in a preneoplastic mammary lesion, the murine C4 hyperplastic alveolar nodule (HAN), and the C4 adenocarcinoma which develops from C4 HAN. The vascular supply to lymphocytes expressing Thy 1.2, L3T4, Ly2, and ASGM1 cell surface antigens was evaluated in both tissues. The distribution of ASGM1+ cells, which include natural killer cells, differed between the two tissues, being significantly increased in the 20% brightest Hoechst-stained lymphocyte fraction in HAN but not in C4 tumor. Distribution of T lymphocytes did not differ between the two tissues. The combination of in vivo Hoechst 33342 with in vitro immunofluorescence provides a simple method to evaluate the distribution with regard to blood supply of lymphocyte subsets in solid tumors and preneoplastic lesions.
Free-breathing pediatric MRI with nonrigid motion correction and acceleration (2014)

With the proposed methods, diagnosable high-resolution abdominal volumetric scans can be obtained from free-breathing data acquisitions.
Nanocapillarity and Chemistry in Carbon Nanotubes (1996)

Open carbon nanotubes were filled with molten silver nitrate by capillary forces. Only those tubes with inner diameters of 4 nanometers or more were filled, suggesting a capillarity size dependence as a result of the lowering of the nanotube-salt interface energy with increasing curvature of the nanotube walls. Nanotube cavities should also be less chemically reactive than graphite and may serve as nanosize test tubes. This property has been illustrated by monitoring the decomposition of silver nitrate within nanotubes in situ in an electron microscope, which produced chains of silver nanobeads separated by high-pressure gas pockets.
Arginine Grafting to Endow Cell Permeability (2007)

We report on a means to endow proteins with the ability to permeate mammalian cells without appending an exogenous domain. Our approach is to install a cationic patch on the surface of a target protein by the grafting of arginine residues. Doing so with GFP did not compromise conformational stability but enabled efficient cellular uptake that was dependent on cell-surface glycosaminoglycans. We anticipate that this cell-permeable variant of GFP, which obviates the need for transfection, will be useful for numerous applications in cell biology and that the method of arginine grafting will be broadly applicable.
Refractive surprise after toric intraocular lens implantation: Graph analysis (2014)

Dr. Alpins and Mr. Stamatelatos have a financial interest in the Assort software program used to support the planning and analysis of astigmatic correction. Dr. Ong is an employee of Assort.
Monitoring the Menstrual Cycle of Humans and Lowland Gorillas Based on Urinary Profiles of Bioactive Follicle-Stimulating Hormone and Steroid Metabolites* (1987)

A sensitive and specific in vitro granulosa cell aromatase bioassay was adapted to measure bioactive FSH (bio-FSH) levels in urine samples. Urinary levels of bio-FSH, immunoreactive LH, estrone conjugates, and pregnanediol-3-glucuronide (PdG) were measured in first morning urine samples during the menstrual cycle in six cycling women and four lowland gorillas. The cycle length of women was relatively constant [28 +/- 1 (+/- SD) days], but varied from 28-38 days for lowland gorillas; the length of the luteal phases was relatively constant for both. All subjects had a midcycle LH peak and a luteal phase elevation in PdG. In addition, urinary estrogen excretion displayed a midcycle elevation that preceded the LH peak and a luteal phase increase similar to that of PdG. The bio-FSH levels in urine of cycling women, although at almost 100-fold higher concentrations, exhibited a pattern that closely resembled that of serum bio-FSH levels reported earlier, with an early follicular phase rise and a midcycle peak. Statistical analysis indicated a highly significant correlation (r = 0.90) between serum and urinary bio-FSH levels during the human menstrual cycle and in women in several hypo- and hypergonadotropic states, including oral contraceptive pill users, hypothalamic amenorrhea, premature ovarian failure, and postmenopause. Although a midcycle bio-FSH surge was also detected in lowland gorillas, two peaks of bio-FSH levels were consistently found during the follicular phase. The late follicular phase increase in bio-FSH levels was presumably involved in follicle selection and preceded the midcycle FSH peak by about 6 days, whereas the timing of the early follicular phase peak was variable, suggesting the involvement of complex regulatory mechanisms. These findings suggest that measurement of urinary bio-FSH levels in humans reflects serum bio-FSH in subjects in several physiological and pathological states. Studies of urinary bio-FSH levels in humans and nonhuman primates are useful in monitoring menstrual cycles, and the gorillas may be a model for understanding human reproductive cycles. The urinary granulosa cell aromatase bioassay should be useful for future assessment of bio-FSH levels in situations where serum measurements are impractical or in animal species for which specific FSH RIAs are not available.
Cargo‐Towing Fuel‐Free Magnetic Nanoswimmers for Targeted Drug Delivery (2011)

Fuel-free nanomotors are essential for future in-vivo biomedical transport and drug-delivery applications. Herein, the first example of directed delivery of drug-loaded magnetic polymeric particles using magnetically driven flexible nanoswimmers is described. It is demonstrated that flexible magnetic nickel-silver nanoswimmers (5-6 μm in length and 200 nm in diameter) are able to transport micrometer particles at high speeds of more than 10 μm s(-1) (more than 0.2 body lengths per revolution in dimensionless speed). The fundamental mechanism of the cargo-towing ability of these magnetic (fuel-free) nanowire motors is modelled, and the hydrodynamic features of these cargo-loaded motors discussed. The effect of the cargo size on swimming performance is evaluated experimentally and compared to a theoretical model, emphasizing the interplay between hydrodynamic drag forces and boundary actuation. The latter leads to an unusual increase of the propulsion speed at an intermediate particle size. Potential applications of these cargo-towing nanoswimmers are demonstrated by using the directed delivery of drug-loaded microparticles to HeLa cancer cells in biological media. Transport of the drug carriers through a microchannel from the pick-up zone to the release microwell is further illustrated. It is expected that magnetically driven nanoswimmers will provide a new approach for the rapid delivery of target-specific drug carriers to predetermined destinations.
Activation of Stat-3 Is Involved in the Induction of Apoptosis After Ligation of Major Histocompatibility Complex Class I Molecules on Human Jurkat T Cells (1998)

Activation of Janus tyrosine kinases (Jak) and Signal transducers and activators of transcription (Stat) after ligation of major histocompatibility complex class I (MHC-I) was explored in Jurkat T cells. Cross-linking of MHC-I mediated tyrosine phosphorylation of Tyk2, but not Jak1, Jak2, and Jak3. In addition, the transcription factor Stat-3 was tyrosine phosphorylated in the cytoplasm and subsequently translocated to the cell nucleus. Data obtained by electrophoretic mobility shift assay suggested that the activated Stat-3 protein associates with the human serum-inducible element (hSIE) DNA-probe derived from the interferon-gamma activated site (GAS) in the c-fos promoter, a common DNA sequence for Stat protein binding. An association between hSIE and Stat-3 after MHC-I ligation was directly demonstrated by precipitating Stat-3 from nuclear extracts with biotinylated hSIE probe and avidin-coupled agarose. To investigate the function of the activated Stat-3, Jurkat T cells were transiently transfected with a Stat-3 isoform lacking the transactivating domain. This dominant-negative acting Stat-3 isoform significantly inhibited apoptosis induced by ligation of MHC-I. In conclusion, our data suggest the involvement of the Jak/Stat signal pathway in MHC-I-induced signal transduction in T cells.
Stronger Brønsted Acids (2007)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStronger Brønsted AcidsTakahiko AkiyamaView Author Information Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan Cite this: Chem. Rev. 2007, 107, 12, 5744–5758Publication Date (Web):November 6, 2007Publication History Received9 May 2007Published online6 November 2007Published inissue 1 December 2007https://pubs.acs.org/doi/10.1021/cr068374jhttps://doi.org/10.1021/cr068374jresearch-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views24675Altmetric-Citations2065LEARN 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:Brønsted acid,Catalysts,Reaction products,Stereoselectivity,Transfer reactions Get e-Alerts
Regulated gene expression in transfected primary chicken erythrocytes. (1986)

We describe a method for studying transient gene expression in primary avian erythroid cells that involves controlled osmotic shock, followed by DNA transfection using DEAE-dextran. Cells treated in this way reproducibly express high levels of chloramphenicol acetyltransferase (CAT) when transfected with a plasmid having the cat gene coupled to an appropriate viral promoter. An observed correlation between levels of CAT expression and extent of hemoglobin release during controlled shock makes it possible to choose optimum conditions for expression in erythroid cells at various stages of embryonic development. Using these techniques, we have investigated the effect on CAT expression of fusing to the cat gene various portions of the chicken adult beta-globin (beta A) gene. We show that in 9-day or 12-day embryonic erythrocytes, the promoter activity of the 5' flanking region of the beta A gene (in the absence of any viral promoters) is strongly stimulated by a downstream sequence, located in the region 110-588 base pairs on the 3' side of the poly(A) signal, that acts as an enhancer. Its activity is reduced in 5-day embryonic cells and absent in primary chicken fibroblasts and mouse L cells, suggesting that this transient expression system will be useful in studying developmentally regulated globin gene expression.
Peptide/Protein Hybrid Materials: Enhanced Control of Structure and Improved Performance through Conjugation of Biological and Synthetic Polymers (2004)

The conjugation of peptides/proteins and synthetic polymers is a useful strategy to overcome some of the limitations related to the use of the individual components. This review will highlight two aspects: enhanced structural control at the nanometer level and improved performance, in particular with respect to biomedical applications. In the former case, peptide sequences are mainly used to mediate self-assembly of synthetic polymers. In the latter case, conjugation of an appropriate synthetic polymer to a pharmaceutically active peptide/protein can, for example, prevent premature enzymatic degradation and enhance blood circulation times, which is therapeutically advantageous.
Phase I Trial of “bi-shRNAifurin/GMCSF DNA/Autologous Tumor Cell” Vaccine (FANG) in Advanced Cancer (2011)

We performed a phase I trial of FANG vaccine, an autologous tumor-based product incorporating a plasmid encoding granulocyte-macrophage colony-stimulating factor (GMCSF) and a novel bifunctional short hairpin RNAi (bi-shRNAi) targeting furin convertase, thereby downregulating endogenous immunosuppressive transforming growth factors (TGF) β1 and β2. Patients with advanced cancer received up to 12 monthly intradermal injections of FANG vaccine (1 × 10(7) or 2.5 × 10(7) cells/ml injection). GMCSF, TGFβ1, TGFβ2, and furin proteins were quantified by enzyme-linked immunosorbent assay (ELISA). Safety and response were monitored. Vaccine manufacturing was successful in 42 of 46 patients of whom 27 received ≥1 vaccine. There were no treatment-related serious adverse events. Most common grade 1, 2 adverse events included local induration (n = 14) and local erythema (n = 11) at injection site. Post-transfection mean product expression GMCSF increased from 7.3 to 1,108 pg/10(6) cells/ml. Mean TGFβ1 and β2 effective target knockdown was 93.5 and 92.5% from baseline, respectively. Positive enzyme-linked immunospot (ELISPOT) response at month 4 was demonstrated in 9 of 18 patients serially assessed and correlated with survival duration from time of treatment (P = 0.025). Neither dose-adverse event nor dose-response relationship was noted. In conclusion, FANG vaccine was safe and elicited an immune response correlating with prolonged survival. Phase II assessment is justified.
PTMD: A Database of Human Disease-Associated Post-Translational Modifications (2018)

Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM-disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of disease-associated PTM events. By reconstructing a disease-gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http://ptmd.biocuckoo.org.
Non-Hematologic Effects of Chronic Iron Deficiency (1982)

From the Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.
Gamma delta T cells in normal spleen assist immunized alpha beta T cells in the adoptive cell transfer of contact sensitivity. Effect of Bordetella pertussis , cyclophosphamide, and antibodies to determinants on suppressor cells. (1995)

Our prior studies showed that gamma delta T cells were required to assist alpha beta T cells in the successful adoptive cell transfer of contact sensitivity (CS) responsiveness. These TCR-gamma delta+ regulatory T cells in immune spleen and lymph node were CD3+, CD4-, CD8+, nonantigen-specific, and non-MHC-restricted. In the current work, experiments were conducted to determine the mechanisms of how the gamma delta T cells were required to assist the alpha beta T cells in CS. We found that similar regulatory gamma delta T cells were in the spleen of normal mice, but not in the spleen of nude nor SCID mice, suggesting that the regulatory gamma delta T cells were present before immunization and required the thymus for differentiation, and also required rearrangements of gamma delta V gene segments. Treatment of cell transfer recipient mice with Bordetella pertussis (Bp), or with a low dose of cyclophosphamide (50 mg/kg), restored the ability of alpha beta+ gamma delta- T cells to transfer CS. This and other results suggested that Bp caused the CS-assisting gamma delta T cells to leave the lymphoid organs (such as the spleen) and enter the circulation, and only then to be able to assist the TCR-alpha beta+ CS-effector T cells. This effect needed the simultaneous i.v. injection of the CS-effector alpha beta T cells and the CS-assisting gamma delta T cells. The results also suggested that treatment with cyclophosphamide inactivated suppressor T cells in the recipients that acted to inhibit the alpha beta T cell transfer of CS, and thus that the CS-assisting gamma delta T cells acted by protecting the CS-effector alpha beta T cells from this endogenous suppression. This suppression of CS transfers also was eliminated by treatment of recipients with two different mAbs to determinants on suppressor T cells. In conclusion, we have described regulatory TCR-gamma delta+ CS-assisting/protecting T cells that are non-antigen-specific, non-MHC-restricted, CD3+, CD8+ gamma delta T cells that may assist adoptive transferring CS-effector alpha beta T cells by making these effector T cells resistant to suppressor T cells in the normal recipients.
Peripheral Blood Mononuclear Cells Induce Programmed Cell Death in Human Endothelial Cells and May Prevent Repair: Role of Cytokines (1997)

Human umbilical vein endothelial cells (HUVECs) undergo programmed cell death (apoptosis) after coculture with peripheral blood mononuclear cells (PBMCs) preactivated by ionizing radiation (IR) or by bacterial endotoxin (lipopolysaccharide [LPS]). Cell-to-cell contact-mediated apoptosis could be blocked in both cases by anti-tumor necrosis factor-alpha (anti-TNF-alpha) monoclonal antibody MAK195 and also by the antagonistic cytokine interleukin-10 (IL-10). Cell-free PBMC supernatants from both preactivation treatments were sufficient to trigger endothelial apoptosis. In contrast, MAK195 and IL-10 were found to be ineffective in this system, suggesting a TNF-alpha-independent mechanism. However, N-Acetylcystein, an antioxidant, fully abrogated programmed cell death mediated by the supernatant of IR-treated PBMCs, but not of LPS-treated PBMCs. Additionally, we found that coculture and cell-free supernatants of preactivated as well as untreated PBMCs caused cell cycle arrest in proliferating EC in G(0/1), which could be relieved by IL-10, but not by anti-TNF-alpha. Further analysis showed that transforming growth factor-beta, which was constitutively expressed in the supernatant of PBMCs, namely lymphocytes, was responsible for this. These data suggest a pathophysiologic model in which preactivated PBMCs cause EC damage and may prevent blood vessel repair by arresting the proliferation of ECs. This could contribute to the understanding of various clinical endothelial complications that occur after irradiation as well as in cases of endotoxemia or related inflammatory states.
Rapid Combinatorial Synthesis and Chromatography Based Screening of Phosphorescent Iridium Complexes for Solution Processing (2012)

Abstract This work reports the combinatorial synthesis and screening of phosphorescent iridium complexes as solution processable emitters for OLEDs. The approach taken here allows for the rapid synthesis, isolation, spectroscopic characterization and identification of the libraries based on chromatographic methods. Subsequent analysis of the irradiation induced degradation provides insight on the stability of the complexes under continuous excitation. The method is versatile and can easily be applied to other metal complexes or organic dyes for various applications, e.g., in electroluminescence, photovoltaics and sensing.
Clay Gels For the Delivery of Regenerative Microenvironments (2011)

The sorptive properties of clay are harnessed to provide niches for tissue regeneration. Synthetic smectite clays self-organize into gels under physiological conditions to allow encapsulation of cells and demonstrate remarkable capacity for the localization of biological molecules without the need for complex chemical modifications.