gebhart/patrepeval huggingface dataset:
Inhibition of vascular endothelial growth factor reduces angiogenesis and modulates immune cell infiltration of orthotopic breast cancer xenografts (2009)

Vascular endothelial growth factor (VEGF) is a primary stimulant of angiogenesis and is a macrophage chemotactic protein. Inhibition of VEGF is beneficial in combination with chemotherapy for some breast cancer patients. However, the mechanism by which inhibition of VEGF affects tumor growth seems to involve more than its effect on endothelial cells. In general, increased immune cell infiltration into breast tumors confers a worse prognosis. We have shown previously that 2C3, a mouse monoclonal antibody that prevents VEGF from binding to VEGF receptor 2 (VEGFR2), decreases tumor growth, angiogenesis, and macrophage infiltration into pancreatic tumors and therefore hypothesized that r84, a fully human IgG that phenocopies 2C3, would similarly affect breast tumor growth and immune cell infiltration. In this study, we show that anti-VEGF therapy with bevacizumab, 2C3, or r84 inhibits the growth of established orthotopic MDA-MB-231 breast tumors in severe combined immunodeficiency (SCID) mice, reduces tumor microvessel density, limits the infiltration of tumor-associated macrophages, but is associated with elevated numbers of tumor-associated neutrophils. In addition, we found that treatment with r84 reduced the number of CD11b(+)Gr1(+) double-positive cells in the tumor compared with tumors from control-treated animals. These results show that selective inhibition of VEGFR2 with an anti-VEGF antibody is sufficient for effective blockade of the protumorigenic activity of VEGF in breast cancer xenografts. These findings further define the complex molecular interactions in the tumor microenvironment and provide a translational tool that may be relevant to the treatment of breast cancer.
Verifiable Computation with Massively Parallel Interactive Proofs (2012)

As the cloud computing paradigm has gained prominence, the need for verifiable computation has grown increasingly urgent. The concept of verifiable computation enables a weak client to outsource difficult computations to a powerful, but untrusted, server. Protocols for verifiable computation aim to provide the client with a guarantee that the server performed the requested computations correctly, without requiring the client to perform the computations herself. By design, these protocols impose a minimal computational burden on the client. However, existing protocols require the server to perform a large amount of extra bookkeeping in order to enable a client to easily verify the results. Verifiable computation has thus remained a theoretical curiosity, and protocols for it have not been implemented in real cloud computing systems. Our goal is to leverage GPUs to reduce the server-side slowdown for verifiable computation. To this end, we identify abundant data parallelism in a state-of-the-art general-purpose protocol for verifiable computation, originally due to Goldwasser, Kalai, and Rothblum, and recently extended by Cormode, Mitzenmacher, and Thaler. We implement this protocol on the GPU, obtaining 40-120x server-side speedups relative to a state-of-the-art sequential implementation. For benchmark problems, our implementation reduces the slowdown of the server to factors of 100-500x relative to the original computations requested by the client. Furthermore, we reduce the already small runtime of the client by 100x. Similarly, we obtain 20-50x server-side and client-side speedups for related protocols targeted at specific streaming problems. We believe our results demonstrate the immediate practicality of using GPUs for verifiable computation, and more generally that protocols for verifiable computation have become sufficiently mature to deploy in real cloud computing systems.
Inhibition of Adrenal Corticosteroid Synthesis by Aminoglutethimide: Studies of the Mechanism of Action1 (1967)

Amino-glutethimide inhibits corticosterone synthesis by the rat adrenal cortex both in vivo and in vitro. In intact rats the decrease in corticosterone production is accompanied by an increase in plasma ACTH. In the presence of endogenous or exogenous ACTH, amino-glutethimide causes marked accumulation of adrenal cholesterol. These observations, plus the fact that amino-glutethimide does not impair the conversion of pregnenolone to corticosterone, indicate that the drug inhibits the conversion of cholesterol to pregnenolone. Aminoglutethimide administration results in adrenal enlargement, an effect that appears to be partly due to cholesterol accumulation and partly due to the adrenal growth-promoting effect of increased endogenous ACTH.
Mesengenic Potential and Future Clinical Perspective of Human Processed Lipoaspirate Cells (2003)

The use of stem cells is promising for future cell-based therapy such as tissue regeneration and engineering. Although Embryonic Stem Cells (ESCs) are theoretically highly beneficial, there are some potential limitations of cell regulations and ethical consideration. Mesenchymal Stem Cells (MSCs) isolated from bone marrow stroma have been shown to possess adipogenic, osteogenic, chondrogenic, myogenic and neurogenic potential in vitro. However, bone marrow procurement is severely painful for donors and often requires general anesthesia. Moreover, only small numbers of cells can be harvested. We previously hypothesized that human adipose tissue obtained from liposuction procedures also contains the same cell population as MSCs, because adipose tissue is mesenchymal in origin, like bone marrow stroma. Subsequent studies revealed that: (1) cell population (which we termed Processed Lipoaspirate [PLA] cells), observed by indirect immunofluorescence study of adipose tissue, consist of cells of mesenchymal origin that have little contamination with endothelial cells, smooth muscle cells and pericytes; (2) these PLA cells exhibit low levels of cell senescence even after multiple passage, as demonstrated by beta-galactosidase staining assay; and (3) PLA cells can differentiate into adipogenic, osteogenic, chondrogenic and myogenic cells in vitro in lineage-specific culture media. These findings suggest that human PLA might have a mesodermal stem cell population. Since human adipose tissue is plentiful, easily harvested in large quantity under local anesthesia with little patient discomfort, it may be an alternative stem cell source for mesenchymal tissue regeneration and engineering. This review highlights our previous research work on PLA cells and future clinical perspectives, particularly in the field of plastic and reconstructive surgery.
Electronic global shutter CMOS image sensor using oxide semiconductor FET with extremely low off-state current (2011)

A novel CMOS image sensor including a pixel with a hybrid structure of an oxide semiconductor FET (OS-FET) and Si(SOI)-FETs has been developed. The OS-FET has an extremely low off-state current, and thus can form a highly insulating charge storage node in combination with SOI. We have therefore applied the OS-FET to an electronic global shutter CMOS image sensor and confirmed improvement in imaging quality.
Microvessels That Predict Axillary Lymph Node Metastases in Patients With Breast Cancer (2000)

The odds of a patient with breast cancer having axillary lymph node metastasis increased substantially as the proportion of putative lymphatic microvessels increased and the relative proportion of blood microvessels in angiogenic hot spots decreased (log likelihood = 14.6; chi2 = 53.4; P<.001; area under the receiver operation characteristic curve = 0.97).
Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months (2013)

These findings advance our understanding of the gut microbiota in healthy infants. They also provide new evidence for the effects of delivery mode and infant diet as determinants of this essential microbial community in early life.
Unusual chromatin in human telomeres. (1994)

We report that human telomeres have an unusual chromatin structure characterized by diffuse micrococcal nuclease patterns. The altered chromatin manifested itself only in human telomeres that are relatively short (2 to 7 kb). In contrast, human and mouse telomeres with telomeric repeat arrays of 14 to 150 kb displayed a more canonical chromatin structure with extensive arrays of tightly packed nucleosomes. All telomeric nucleosomes showed a shorter repeat size than bulk nucleosomes, and telomeric mononucleosomal particles were found to be hypersensitive to micrococcal nuclease. However, telomeric nucleosomes were similar to bulk nucleosomes in the rate at which they sedimented through sucrose gradients. We speculate that mammalian telomeres have a bipartite structure with unusual chromatin near the telomere terminus and a more canonical nucleosomal organization in the proximal part of the telomere.
Substrate specificity of the protease that processes human interleukin-1 beta. (1990)

The substrate specificity of the protease which generates mature human interleukin-1 beta (IL-1 beta) from pro-interleukin-1 beta was investigated using synthetic peptide substrates and recombinant pro-IL-1 beta. The requirement of an L-aspartate in the P-1 position was confirmed together with the need for a small hydrophobic residue in the P-1' position (Gly or Ala). It was shown that the enzyme can tolerate conservative substitutions in the P-2 and P-2' positions. We found little difference in the enzyme's ability to cleave denatured and native pro-IL-1 beta, indicating that tertiary structure recognition is not involved in binding. The enzyme did, however, require a peptide of more than six amino acids for cleavage to occur. These results conclusively demonstrate the unusual specificity of this protease.
Growing Self-Organizing Mini-Guts from a Single Intestinal Stem Cell: Mechanism and Applications (2013)

Recent examples have highlighted how stem cells have the capability to initiate morphogenesis in vitro; that is, to generate complex structures in culture that closely parallel their in vivo counterparts. Lgr5, the receptor for the Wnt-agonistic R-spondins, marks stem cells in multiple adult organs of mice and humans. In R-spondin-based three-dimensional cultures, these Lgr5 stem cells can grow into ever-expanding epithelial organoids that retain their original organ identity. Single Lgr5 stem cells derived from the intestine can be cultured to build epithelial structures that retain hallmarks of the in vivo epithelium. Here, we review the mechanisms that support this notable example of self-organization and discuss applications of this technology for stem cell research, disease modeling (e.g., for colorectal cancer and cystic fibrosis), and regenerative medicine.
Rearrangements in Amination by Alkali Amides in Liquid Ammonia and by Lithium Dialkylamides in Ether (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRearrangements in Amination by Alkali Amides in Liquid Ammonia and by Lithium Dialkylamides in EtherHenry Gilman and Robert H. KyleCite this: J. Am. Chem. Soc. 1952, 74, 12, 3027–3029Publication Date (Print):June 1, 1952Publication History Published online1 May 2002Published inissue 1 June 1952https://pubs.acs.org/doi/10.1021/ja01132a023https://doi.org/10.1021/ja01132a023research-articleACS PublicationsRequest reuse permissionsArticle Views235Altmetric-Citations15LEARN 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
Crohn’s disease-Defect in innate defence (2008)

Crohn's disease may principally involve the whole gastrointestinal tract. Most commonly, the inflammation occurs in the small intestine and/or in the colon with stable disease location over the years. The pathogenesis of both disease phenotypes is complex, the likely primary defect lies in the innate rather than adaptive immunity, particularly in the chemical antimicrobial barrier of the mucosa. Crohn's ileitis is associated with a reduced expression of the Wnt signalling pathway transcription factor T-cell factor 4 (TCF4), which is regulating Paneth cell differentiation. As a result, the alpha-defensins and principal Paneth cell products HD5 and HD6 are deficiently expressed in ileal disease, independent of current inflammation. In contrast, Crohn's colitis is typically associated with an impaired induction of the beta-defensins HBD2 and HBD3 caused by fewer gene copy numbers in the gene locus of the beta-defensins on chromosome 8. This ileal and colonic defect in innate defence mediated by a deficiency of the protective alpha- and beta-defensins may enable the luminal microbes to invade the mucosa and trigger the inflammation. A better understanding of the exact molecular mechanisms behind ileal and colonic Crohn's disease may give rise to new therapeutic strategies based on a stimulation of the protective innate immune system.
Options available for labelling nucleic acid samples in DNA microarray-based detection methods (2012)

DNA microarrays are considered by many researchers to be the platform of choice for the high-throughput analysis of nucleic acids. Since the past two decades, they have been used constantly as powerful tools in differential gene expression, SNP genotyping, DNA sequencing, gene discovery, disease diagnostic and pathways reconstruction. Several methods have been developed to enable samples of limited amounts of RNA to be quantified. Here we evaluate classical and up-to-date assays made available for labelling those samples. This review also sheds light on the recently developed strategies that ensure high sensitivity such as sample and signal amplification, quantum dot, surface plasmom resonance, nanoparticles and cationinc polythiophenes.
Modern Optical Engineering: The Design of Optical Systems (1966)

Chapter 1. Optics Overview Chapter 2. Gaussian Optics: The Cardinal Points Chapter 3. Paraxial Optics and Calculations Chapter 4. Optical System Considerations Chapter 5. The Primary Aberrations Chapter 6. Third-Order Aberration Theory and Calculation Chapter 7. Prism and Mirror Systems Chapter 8. Characteristics of the Human Eye Chapter 9. Stops, Apertures, Pupils and Diffraction Chapter 10. Optical Materials Chapter 11. Optical Coatings Chapter 12. Principles of Radiometry and Photometry Chapter 13. Optical System Layout Chapter 14. Case Studies in System Layout Chapter 15. Wave-Front Aberrations and MTF Chapter 16. The Basics of Lens Design Chapter 17. Lens Design for Eyepieces, Microscopes, Cameras, etc. Chapter 18. Design of Mirror and Catadioptric Systems Chapter 19. Selected Lens Designs, Analyzed and Annotated Chapter 20. The Practice of Optical Engineering Chapter 21. Getting the Most Out of Stock Lenses Appendix A. Raytracing and Aberration Calculation Appendix B. Some Standard Dimensions Glossary Index
When Cycles are Cheap, Some Tables Can Be Huge (2018)

Computer Science Department
Relationship of USDA Maturity Groups to Palatability of Cooked Beef (1982)

ABSTRACT In comparison to carcasses of B, C or E maturity, carcasses of A maturity produced broiled steaks which: (a) had higher (P &lt; 0.05) palatability ratings in 62 to 86% of comparisons, (b) were decidedly less variable (C.V.), (c) were more likely to be assigned high (≥ 6.00) and less likely to be assigned low (≤ 2.99) sensory panel ratings, and (d) were more likely to have low (≤ 3.63 kg) and less likely to have high (≥ 6.35 kg) shear force values. Position within the A or A + B maturity group(s) explained 0–4% (loin steaks) and 10–18% (round steaks) of the observed variation in overall palatability ratings and/or shear force values.
Seizures in Alzheimer Disease (2009)

Unprovoked seizures are uncommon in AD, but they do occur more frequently than in the general population. Younger age is a risk factor for seizures in AD.
Genes required for cellulose synthesis in Agrobacterium tumefaciens (1995)

A region of the chromosome of Agrobacterium tumefaciens 11 kb long containing two operons required for cellulose synthesis and a part of a gene homologous to the fixR gene of Bradyrhizobium japonicum has been sequenced. One of the cellulose synthesis operons contained a gene (celA) homologous to the cellulose synthase (bscA) gene of Acetobacter xylinum. The same operon also contained a gene (celC) homologous to endoglucanase genes from A. xylinum, Cellulomonas uda, and Erwinia chrysanthemi. The middle gene of this operon (celB) and both the genes of the other operon required for cellulose synthesis (celDE) showed no significant homology to genes contained in the databases. Transposon insertions showed that at least the last gene of each of these operons (celC and celE) was required for cellulose synthesis in A. tumefaciens.
Crystallographic Studies of Savinase, a Subtilisin‐like Proteinase, at pH 10.5 (1994)

The effect of high pH (pH 10.5) on Savinase, a subtilisin-like serine proteinase, has been investigated using X-ray crystallography. The structures of two Savinase mutants were determined at two different pH values, namely pH 6.0, where the enzyme is inactive (this is the pH at which most of the structural work has been carried out on other serine proteinases), and pH 10.5, where Savinase is active. Comparison of these high resolution (0.16 nm) structures showed four related sets of changes between the two pH values. First, the difference in protonation state of the active-site histidine leads to a change in conformation of the active-site triad. Secondly, there are resulting changes in the water structure around this histidine residue with much increased mobility of the water in the active-site at pH 10.5. Thirdly, the two substrate-binding loops on either side of the binding site are less well linked by ordered water molecules at pH 10.5 and show substantially increased flexibility. Finally, the first substrate-binding loop, residues at positions 99-104, moves slightly so as to widen the substrate channel.
Quantitative RT-PCR Measurement of Cytochromes p450 1A1, 1B1, and 2B7, Microsomal Epoxide Hydrolase, and NADPH Oxidoreductase Expression in Lung Cells of Smokers and Nonsmokers (1997)

Bronchial epithelial cells (BEC) are the progenitors of bronchogenic carcinomas and are exposed to polycyclic aromatic hydrocarbon (PAH) procarcinogens through inhalation of combustion products. PAH are converted to carcinogenic molecules through a combination of monoxygenation by cytochrome p450 (CYP) enzymes in the presence of NADPH oxidoreductase (OR) and hydrolysis by microsomal epoxide hydrolase (mEH). In artificial systems, the relative expression of these genes determines whether carcinogenic or noncarcinogenic species are generated during metabolism. This relationship was explored in humans by using quantitative competitive reverse transcriptase polymerase chain reaction amplification to determine the range of expression of CYP1A1, CYP1B1, mEH, and NADPH OR in BEC recovered from 10 nonsmokers and 9 smokers. CYP2B7 expression was evaluated because, although little is known of its substrate specificity, it is expressed at high levels in human lung tissue. CYP1A1 and CYP1B1 were expressed in BEC at significantly different levels (P < 0.05) in the 9 smokers at 1.4 +/- 2.3 x 10(4) and 2.4 +/- 3.2 x 10(3) molecules/10(6) beta-actin molecules (mean +/- STD), respectively, but each was measurable in only one of the 10 nonsmokers. There was significant inter-individual variation (P < 0.05) in both CYP1A1 and CYP1B1 expression among the subjects for whom sufficient data were obtained. The inducibility of human BEC CYP1A1 gene by PAH exposure was confirmed in vitro by incubating cultured immortalized human BEC with beta-naphthoflavone and observing a > 6-fold induction of CYP1A1 after 24 h. In contrast to BEC, alveolar macrophages expressed CYP1A1 at low (30-70 molecules/10(6) beta-actin molecules) to unmeasurable levels in both smokers and nonsmokers. There was no significant difference in expression of mEH, CYP2B7, or NADPH OR in smokers compared with nonsmokers. The inter-individual variation in absolute and relative expression of PAH metabolism enzymes in BEC reported here supports the hypothesis that inter-individual variation in ability to activate/inactivate inhaled PAH carcinogens accounts for at least some of the inter-individual variation in risk for bronchogenic carcinoma.
Lanthanide Luminescence for Biomedical Analyses and Imaging (2010)

LCSL
Anti-tumor necrosis factor antibody therapy fails to prevent lethality after cecal ligation and puncture or endotoxemia (1992)

Cytokines have been studied intensively to delineate their role in the altered pathophysiology observed in septic shock. We studied the role of TNF in the lethality of two well characterized models of septic shock by inhibiting TNF's activity with a specific antibody. In the first model, sepsis was induced by cecal ligation and puncture (CLP), and in the second model sepsis was induced by either an i.p. or i.v. injection of LPS. After CLP, plasma endotoxin was detectable within 4 h and reached a peak at 8 h (136 +/- 109 ng/ml). TNF bioactivity peaked at 12 h (528 +/- 267 pg/ml) at a significantly higher level than sham-operated control mice (64 +/- 31 pg/ml). After i.p. LPS, TNF peaked much more quickly (90 min) compared with CLP and at a significantly higher level (107,900 +/- 25,000 pg/ml). Another cytokine studied in septic shock, IL-6, peaked at 12 h after CLP at 1011 +/- 431 pg/ml, and at 90 min after lethal LPS at 16,300 +/- 3,700 pg/ml. Mice were treated with an anti-TNF antibody that has been shown previously to inhibit in vivo TNF activity. Antibody treatment of mice subjected to CLP significantly reduced TNF bioactivity but did not reduce mortality or pulmonary neutrophilic infiltration. In the i.v. LPS model, anti-TNF antibody treatment concomitant with LPS injection reduced plasma TNF activity from 80,000 +/- 20,000 pg/ml to undetectable levels. However, anti-TNF treatment immediately before either i.v. or i.p. LPS did not reduce mortality. Additionally, when the antibody was administered 4 h before the lethal i.v. LPS, there was no reduction in lethality. These data show that in two separate models of septic shock blockade of TNF biologic activity will not prevent lethality.
Handbook of Statistical Analyses Using Stata (2006)

With each new release of Stata, a comprehensive resource is needed to highlight the improvements as well as discuss the fundamentals of the software. Fulfilling this need, A Handbook of Statistical Analyses Using Stata, Fourth Edition has been fully updated to provide an introduction to Stata version 9. This edition covers many