gebhart/patrepeval huggingface dataset:
Low‐energy CO2 laser intestinal anastomosis: An experimental study (1988)

Intestinal anastomosis was performed in 17 Wistar rats via tissue welding by the low-energy CO2 laser. The postoperative course in the animals studied was uneventful. The integrity of the anastomosis was investigated manometrically, immediately upon completion of the anastomosis as well as 20 days later. Ten additional Wistar rats served as controls in which conventional interrupted one-layer anastomosis was performed. The results show a significant superiority of the intestinal anastomoses that were constructed by means of laser tissue welding. The time to complete the anastomosis was also significantly shorter when laser rather than manual suturing was used. Serial histological examinations for up to 90 days following surgery revealed complete healing and epithelization of the anastomotic site.
Pegnology: a review of PEG-ylated systems. (2002)

Polyethylene glycol conjugation or linking with the system is called PEGylation. Many novel drug systems are used for the delivery of drugs and bioactive substances to particular sites in a controlled or sustained manner, but various side effects or shortcomings restrict their use for the intended purpose. The shortcomings such as RES uptake, drug leakage, immunogenicity, stability, hemolytic toxicity etc. can generally be overcome by PEGylation of novel drug delivery systems such as liposomes, proteins, enzymes, drugs, nanoparticles etc. In this article the whole aspect of PEGylation starting from activation and derivatisation of poly (ethylene glycol) to the linking and designing of systems and their purification and characterization is discussed. The various properties of Pegylated systems are also discussed.
Designing Responsive Buckled Surfaces by Halftone Gel Lithography (2012)

Self-actuating materials capable of transforming between three-dimensional shapes have applications in areas as diverse as biomedicine, robotics, and tunable micro-optics. We introduce a method of photopatterning polymer films that yields temperature-responsive gel sheets that can transform between a flat state and a prescribed three-dimensional shape. Our approach is based on poly(N-isopropylacrylamide) copolymers containing pendent benzophenone units that allow cross-linking to be tuned by irradiation dose. We describe a simple method of halftone gel lithography using only two photomasks, wherein highly cross-linked dots embedded in a lightly cross-linked matrix provide access to nearly continuous, and fully two-dimensional, patterns of swelling. This method is used to fabricate surfaces with constant Gaussian curvature (spherical caps, saddles, and cones) or zero mean curvature (Enneper's surfaces), as well as more complex and nearly closed shapes.
Fc‐engineered EGF‐R antibodies mediate improved antibody‐dependent cellular cytotoxicity (ADCC) against KRAS‐mutated tumor cells (2010)

Oncogenic mutations of the KRAS gene have emerged as a common mechanism of resistance against epidermal growth factor receptor (EGF-R)-directed tumor therapy. Mutated KRAS leads to ligand-independent activation of signaling pathways downstream of EGF-R. Thereby, direct effector mechanisms of EGF-R antibodies, such as blockade of ligand binding and inhibition of signaling, are bypassed. Thus, a humanized variant of the approved EGF-R antibody Cetuximab inhibited growth of wild-type KRAS-expressing A431 cells, but did not inhibit KRAS-mutated A549 tumor cells. We then investigated whether killing of tumor cells harboring mutated KRAS can be improved by enhancing antibody-dependent cellular cytotoxicity (ADCC). Protein- and glyco-engineering of antibodies' Fc region are established technologies to enhance ADCC by increasing antibodies' affinity to activating Fcgamma receptors. Thus, EGF-R antibody variants with increased affinity for the natural killer (NK) cell-expressed FcgammaRIIIa (CD16) were generated and analyzed. These variants triggered significantly enhanced mononuclear cell (MNC)-mediated killing of KRAS-mutated tumor cells compared to wild-type antibodies. Additionally, cells transfected with mutated KRAS were killed as effectively by ADCC as vector-transfected control cells. Together, these data demonstrate that KRAS mutations are not sufficient to render tumor cells resistant to ADCC. Consequently Fc-engineered EGF-R antibodies may prove effective against KRAS-mutated tumors, which are not susceptible to signaling inhibition by EGF-R antibodies.
Nucleotide sequence and expression of a phosphate-regulated gene encoding a secreted hemolysin of Pseudomonas aeruginosa (1986)

A 3.3-kilobase-pair fragment of Pseudomonas aeruginosa DNA containing the phospholipase C (heat-labile hemolysin) gene was sequenced, and the location of the gene was determined. The gene product contains at its NH2 terminus a 38-amino acid sequence which structurally resembles the signal peptides of other secreted proteins but is unusually long and positively charged (6+). The location of the translation start codon was determined by constructing a series of plasmids in which the promoter of a transcription vector was ligated to Pseudomonas DNA containing deletions at the 5' end of the gene. The plasmids were used to transform Escherichia coli, and the resulting clones were assayed for hemolysin activity. In addition, sizes of truncated proteins produced by mutants with translation terminators introduced at specific sites were analyzed in E. coli maxicells. The gene is transcribed, starting just upstream of the hemolysin gene, as an mRNA of approximately 2,800 bases. Analysis of the nucleotide sequence, analysis of mutants in maxicells, and transcriptional studies indicate that the hemolysin is part of an operon composed of two genes. Phosphate regulation of the operon is at the transcriptional level. The location of the 5' end of the transcript was determined by S1 mapping.
Phase I trials using Sleeping Beauty to generate CD19-specific CAR T cells (2016)

National Cancer Institute, private foundations, and institutional funds. Please see Acknowledgments for details.
The Molecular Properties of Human Growth Hormone (1972)

Abstract The stability of human growth hormone to acid, alkali, and urea has been evaluated by fluorescence, absorption, and circular dichroism spectroscopy. In accord with previous studies on other growth hormones and prolactins, similar molecular transitions were observed although small shifts in parameters were found among the different proteins. It is of interest to find such a resemblance in properties between human growth hormone and ovine prolactin since the number of residues occupying identical positions is less than 20% and the longest identical sequence is a tripeptide.
A fisheye text editor for relaxed-WYSIWIS groupware (1996)

Participants in a real-time groupware conference require a sense of awareness about other people’s interactions within a large shared workspace. Fisheye views can afford this awareness by assigning a focal point to each participant. The fisheye effect around these multiple focal points provides peripheral awareness by showing people’s location in the global context, and by magnifying the area around their work to highlight interaction details. An adjustable magnification function lets people customize the awareness information to fit their collaboration needs. A fisheye text editor illustrates how this can be accomplished.
Neurocognitive dysfunction predicts postmortem findings of HIV encephalitis (2002)

Neuropsychological assessment can help select HIV-positive patients for treatment of CNS disease.
Merkel Cell Carcinoma and Multiple Primary Cancers (2006)

Merkel cell carcinoma (MCC) is an aggressive neuroendocrine tumor of the skin for which causative factors remain largely unknown. The site-specific risks of multiple primary cancers associated with MCC, which may provide insight into etiologic influences, have not been quantified in large population-based studies. We estimated the long-term risk of subsequent primary tumors after a first primary MCC (1,306 patients) and the risk of second primary MCC following other first primary cancers (2,048,739 patients) within 11 population-based cancer registries which report to the National Cancer Institute's Surveillance, Epidemiology, and End Results Program (1986-2002). Patients with first primary MCC were at significantly increased risk of developing a subsequent cancer [standardized incidence ratio (SIR), 1.22; 95% confidence intervals (95% CI), 1.01-1.45; observed (O = 122)], with significant excesses restricted to the first year after diagnosis (SIR, 1.71; 95% CI, 1.21-2.33; O = 39). Significantly elevated site-specific risks were observed for cancers of salivary gland (SIR, 11.55; 95% CI, 2.32-33.76; O = 3), biliary sites other than liver and gallbladder (SIR, 7.24; 95% CI, 1.46-21.16; O = 3), and non-Hodgkin lymphoma (SIR, 2.56; 95% CI, 1.23-4.71; O = 10). Nonsignificantly increased risks of 2-fold or higher were seen for chronic lymphocytic leukemia, and cancers of the small intestine and brain. A significantly increased 1.36-fold risk (95% CI, 1.19-1.55; O = 221) of MCC as a second primary malignancy was observed among patients with all other first primary cancers taken together. In particular, significant 3- to 7-fold excesses of MCC followed multiple myeloma (SIR, 3.70; 95% CI, 1.01-9.47; O = 4), chronic lymphocytic leukemia (SIR, 6.89; 95% CI, 3.77-11.57; O = 14), non-Hodgkin lymphoma (SIR, 3.37; 95% CI, 1.93-5.47; O = 16), and malignant melanoma (SIR, 3.05; 95% CI, 1.74-4.95; O = 16). Although enhanced medical surveillance may play a role, increased reciprocal risks suggest that MCC may share etiologic influences with other malignancies. Heightened awareness of the associations of lymphohematopoietic malignancies with MCC may facilitate early clinical recognition.
AN EPIDEMIOLOGIC STUDY OF ALTERED CLINICAL REACTIVITY TO RESPIRATORY SYNCYTIAL (RS) VIRUS INFECTION IN CHILDREN PREVIOUSLY VACCINATED WITH AN INACTIVATED RS VIRUS VACCINE (1969)

Journal Article AN EPIDEMIOLOGIC STUDY OF ALTERED CLINICAL REACTIVITY TO RESPIRATORY SYNCYTIAL (RS) VIRUS INFECTION IN CHILDREN PREVIOUSLY VACCINATED WITH AN INACTIVATED RS VIRUS VACCINE Get access ALBERT Z. KAPIKIAN, ALBERT Z. KAPIKIAN 1From the National Institutes of Health, National Institute of Allergy and Infectious Diseases, Laboratory of Viral DiseasesBethesda, Maryland 20014 Reprint request: Dr. Kapikian, Laboratory of Infectious Diseases, N.I.A.I.D.; or to the Vaccine Development Branch, N.I.A.I.D., N.I.B., Bethesda, Md. 20014 Search for other works by this author on: Oxford Academic PubMed Google Scholar REGINALD H. MITCHELL, REGINALD H. MITCHELL 2Junior Village, Department of Public WelfareWashington, D.C. Search for other works by this author on: Oxford Academic PubMed Google Scholar ROBERT M. CHANOCK, ROBERT M. CHANOCK 1From the National Institutes of Health, National Institute of Allergy and Infectious Diseases, Laboratory of Viral DiseasesBethesda, Maryland 20014 Search for other works by this author on: Oxford Academic PubMed Google Scholar RUTH A. SHVEDOFF, RUTH A. SHVEDOFF 1From the National Institutes of Health, National Institute of Allergy and Infectious Diseases, Laboratory of Viral DiseasesBethesda, Maryland 20014 Search for other works by this author on: Oxford Academic PubMed Google Scholar C. ELEANOR STEWART C. ELEANOR STEWART 1From the National Institutes of Health, National Institute of Allergy and Infectious Diseases, Laboratory of Viral DiseasesBethesda, Maryland 20014 Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 89, Issue 4, April 1969, Pages 405–421, https://doi.org/10.1093/oxfordjournals.aje.a120954 Published: 01 April 1969 Article history Received: 08 August 1968 Published: 01 April 1969
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network (2003)

Full genome sequences of prokaryotic organisms have led to reconstruction of genome-scale metabolic networks and in silico computation of their integrated functions. The first genome-scale metabolic reconstruction for a eukaryotic cell, Saccharomyces cerevisiae, consisting of 1,175 metabolic reactions and 733 metabolites, has appeared. A constraint-based in silico analysis procedure was used to compute properties of the S. cerevisiae metabolic network. The computed number of ATP molecules produced per pair of electrons donated to the electron transport system (ETS) and energy-maintenance requirements were quantitatively in agreement with experimental results. Computed whole-cell functions of growth and metabolic by-product secretion in aerobic and anaerobic culture were consistent with experimental data, and thus mRNA expression profiles during metabolic shifts were computed. The computed consequences of gene knockouts on growth phenotypes were consistent with experimental observations. Thus, constraint-based analysis of a genome-scale metabolic network for the eukaryotic S. cerevisiae allows for computation of its integrated functions, producing in silico results that were consistent with observed phenotypic functions for approximately 70-80% of the conditions considered.
PAWS: Paraphrase Adversaries from Word Scrambling (2019)

Existing paraphrase identification datasets lack sentence pairs that have high lexical overlap without being paraphrases. Models trained on such data fail to distinguish pairs like flights from New York to Florida and flights from Florida to New York. This paper introduces PAWS (Paraphrase Adversaries from Word Scrambling), a new dataset with 108,463 well-formed paraphrase and non-paraphrase pairs with high lexical overlap. Challenging pairs are generated by controlled word swapping and back translation, followed by fluency and paraphrase judgments by human raters. State-of-the-art models trained on existing datasets have dismal performance on PAWS (&lt;40% accuracy); however, including PAWS training data for these models improves their accuracy to 85% while maintaining performance on existing tasks. In contrast, models that do not capture non-local contextual information fail even with PAWS training examples. As such, PAWS provides an effective instrument for driving further progress on models that better exploit structure, context, and pairwise comparisons.
CCR8+FOXp3+Tregcells as master drivers of immune regulation (2017)

The current study identifies CCR8<sup>+</sup> regulatory T cells (T<sub>reg</sub> cells) as drivers of immunosuppression. We show that in human peripheral blood cells, more than 30% of T<sub>reg</sub> up-regulate CCR8 following activation in the presence of CCL1. This interaction induces STAT3-dependent up-regulation of FOXp3, CD39, IL-10, and granzyme B, resulting in enhanced suppressive activity of these cells. Of the four human CCR8 ligands, CCL1 is unique in potentiating T<sub>reg</sub> cells. The relevance of these observations has been extended using an experimental model of multiple sclerosis [experimental autoimmune encephalomyelitis, (EAE)] and a stabilized version of mouse CCL1 (CCL1-Ig). First, we identified a self-feeding mechanism by which CCL1 produced by T<sub>reg</sub> cells at an autoimmune site up-regulates the expression of its own receptor, CCR8, on these cells. Administration of CCL1-Ig during EAE enhanced the in vivo proliferation of these CCR8<sup>+</sup> regulatory cells while inducing the expression of CD39, granzyme B, and IL-10, resulting in the efficacious suppression of ongoing EAE. The critical role of the CCL1-CCR8 axis in T<sub>reg</sub> cells was further dissected through adoptive transfer studies using CCR8<sup>-/-</sup> mice. Collectively, we demonstrate the pivotal role of CCR8<sup>+</sup> T<sub>reg</sub> cells in restraining immunity and highlight the potential clinical implications of this discovery.
Recipient inflammation affects the frequency and magnitude of immunization to transfused red blood cells (2006)

These findings demonstrate that recipient inflammation with poly(I:C) significantly enhances humoral immunization to transfused alloantigens in a murine model. Moreover, these data suggest that the inflammatory status of human transfusion recipients may regulate the immunogenicity of transfused RBCs.
Suppression of c-jun by antisense oligonucleotides inhibits cell adhesion but not respiratory burst during phorbol ester-induced differentiation of U937 human monoblastic cells. (1996)

We studied the role of the immediate early gene c-jun in cell proliferation and phorbol 12-myristate 13-acetate (PMA)-induced differentiation in U937 human monoblastic cells, using c-jun-specific antisense (AS) phosphorothioate oligonucleotides. In selecting the most specific and potent oligonucleotide sequence, we performed extensive analyses for the binding specificity between all candidates of c-jun AS oligonucleotides and the whole sequences in GenBank database, using a computer program. Among the 20 selected oligonucleotides, two potent 15-mer AS oligonucleotides (C-JUN AS oligonucleotides) exhibited significant inhibition of cell growth in a dose-dependent manner between 2 and 10 microM. Reverse transcription-PCR and Western blot analysis demonstrated that 10 microM of C-JUN AS oligonucleotides reduced c-jun expression at both the mRNA and protein levels. More importantly, C-JUN AS oligonucleotides showed distinct effects on two markers of PMA-induced differentiation; the C-JUN AS oligonucleotides inhibited cell adhesion, whereas they did not affect another marker of differentiation, respiratory burst (measured by nitro blue tetrazolium reduction assay). These results suggest a critical role of c-jun in both cell proliferation and PMA-induced cell adhesion but not in PMA-induced respiratory burst in U937 cells.
A new restaurant guide conversational system: issues in rapid prototyping for specialized domains (2002)

We are developing a new restaurant guide domain, DINEX, which utilizes all of the same core technology as our other GALAXY conversational systems. The domain server has been adapted from our CityGuide domain within our GALAXY framework, using the same mechanisms to locate places on the map or to give directions. The system has information on several features for restaurants, such as hours, cuisine, parking availability, and an online menu. DINEX knows over 450 restaurants in the Boston area, and can also provide directions from subway stops or well-known landmarks. DINEX makes use of a relational database derived from several online sources, including a nationally known travel guide. This paper particularly emphasizes the language tools we have developed to construct the relational database semi-automatically and to derive from user queries the appropriate SQL queries for accessing the database.
Quantitative estimation of minor mRNAs by cDNA‐polymerase chain reaction (1990)

Amplification of the mRNA polymerase chain reaction is a very sensitive technique to detect low-abundance transcripts. We describe in this paper conditions necessary to make this technique quantitative. Quantification is performed in the exponential phase of the amplification process and the results are standardized with respect to those obtained with an exogenous mRNA which is co-reverse-transcribed and co-amplified in the same reaction as the analyzed transcripts. The primers are chosen in different exons to distinguish the amplification of mRNA fragments from the amplification of contaminating DNA. Analysis of the kinetics of amplification and parameters influencing this kinetics shows that: (a) in the exponential phase of amplification, the amount of amplified fragments is proportional to the initial amount of transcripts; (b) in a certain range of length fragment, the yield of amplification is inversely proportional to the length of the amplified fragments. Using this method we have demonstrated that the dystrophin gene is already activated at the myoblastic stage. A quantitative estimation of the transcript showed that the expression of this gene increases strongly in the course of in vitro myogenesis. In primary culture of mouse brain cells, the dystrophin gene was found to be more expressed in neuronal than in glial cells.
Plasmid Vectors Capable of Transferring Large DNA Fragments to Yeast (1981)

We have constructed several cloning vectors which can be used in vitro packaging and yeast transformation. These plasmids have been designed for the convenient cloning of large segments of DNA and their transfer to yeast. They contain bacterial plasmid DNA sequences for replication and selection in Escherichia coli, yeast 2-microns plasmid DNA sequences or chromosomal replicators and yeast markers necessary for replication and selection in yeast, and the cohesive ends of bacteriophage lambda which allow packaging of recombinant molecules into lambda phage heads. Large fragments (22-38 kb) of Klebsiella pneumoniae and Zea mays DNA were ligated into plasmid vector pBTI-1 to make complete genome libraries. One clone from the K. pneumoniae library was amplified in E. coli and the purified DNA used to transform yeast cells. Transformation of yeast by large DNA fragments occurred at high frequencies. The recombinant plasmid was stably maintained in yeast, provided selective pressure for Leu+ transformants was maintained. The structurally complete recombinant plasmid can be recovered from yeast by transforming E. coli to ampicillin resistance. Fewer than 5% of the recovered plasmids had undergone recombination with endogenous yeast 2-microns plasmid.
Effect of Surrounded-Channel Structure on Electrical Characteristics of $c$ -Axis Aligned Crystalline In–Ga–Zn–O Field-Effect Transistor (2015)

In this letter, we report the electrical characteristics of a crystalline oxide semiconductor, especially c-axis aligned crystalline In-Ga-Zn-O (CAAC-IGZO) field-effect transistors (FETs) having a surrounded-channel structure with 51-nm channel lengths, 11-nm equivalent oxide thicknesses of the gate insulating films, and various channel widths. The results show that the influence of the gate electrode on the sides of the channel increases as the channel width is reduced, which leads to excellent OFF-state and ON-state current characteristics of the FET with a 51-nm channel length and a 50-nm channel width. By exploiting these characteristics, low-power large-scale integration (LSI) applications become possible that would not be possible with conventional Si-LSI techniques.