gebhart/patrepeval huggingface dataset:
Use of nude mouse xenografts as preclinical drug screens: in vivo activity of established chemotherapeutic agents against melanoma and ovarian carcinoma xenografts. (1987)

To evaluate the utility of nude mouse xenografts as preclinical drug screens, the activity of ten established chemotherapeutic agents was evaluated against seven melanoma and three ovarian carcinoma xenografts. Xenografts were established using primary explants from patients who had not received chemotherapy and serially passaged as sc tumors in nude mice. In vivo drug activities for dactinomycin, carmustine, vinblastine, melphalan, amsacrine, cisplatin, bleomycin, mitomycin, doxorubicin, and etoposide were evaluated by 4 weekly ip injections of 10% less than LD10 doses. Plots of relative tumor growth versus time were nearly log-linear. Analysis of in vivo activity was performed using percent control growth (treated/control tumor volume) and by calculation of a novel growth delay index obtained by fitting growth curves to a quadratic regression model. Both modes of data analysis identified alkylating agents (melphalan, carmustine, and mitomycin) as the most active drugs against human melanomas. Melphalan, mitomycin, and cisplatin showed the greatest activity against ovarian xenografts. However, complete tumor regressions were noted only with melphalan, mitomycin, and cisplatin against a single ovarian tumor xenograft. Correlation analysis suggested xenograft tumor growth rate was an important determinant of drug response. These results suggest that preclinical, new-drug screening with melanoma xenografts would identify drugs such as alkylating agents as active, and may not provide an advantage over murine leukemia screens. However, screening with ovarian xenografts may more closely reflect clinical drug activity. Criteria for detecting active drugs in such systems are discussed.
Petroleum Expulsion Part 1. Theory of Kerogen Swelling in Multicomponent Solvents (2006)

An extended Flory−Rehner and Regular Solution Theory model framework has been developed for interpreting the swelling behavior of kerogen toward solvents. Thermodynamic parameters controlling the swelling response of kerogen are the solubility parameter, the cross-link density, and the volume fraction of the kerogen network veq that minimizes its elastic strain energy, termed “native swelling”. These parameters are obtained by optimizing the match between theoretical predictions and experimental swelling data of kerogen for neat solvents. A good match between theory and experiment is obtained for Draupne Type II kerogen. These results imply that this kerogen behaves like a cross-linked elastomer network and that the interaction with the solvents used involves nonspecific interactions. This model framework enables prediction of the kerogen's response to solvent mixtures. This is an important step toward modeling hydrocarbon expulsion from kerogen during petroleum generation. If the composition of the mixture is made to resemble the primary products of kerogen maturation, it should be possible to predict the equilibrium composition of molecules retained in kerogen with those in the proximate fluid.
[The preliminary study of metallic stent implantation in combination with three-dimensional conformal radiation therapy in the treatment of hepatocellular carcinoma patients with portal vein tumor thrombus]. (2009)

Stent implantation combined with three-dimensional conformal radiation therapy is a good treatment for hepatocellular carcinoma with portal vein tumor thrombus and causes less damage to liver.
Efficacy of an Herbal Extract on the Microbiological Quality of Broiler Carcasses During a Simulated Chill (2000)

Protecta II, an herbal extract on an NaCl carrier, was evaluated in a 30-min, 1 C simulated chill for its effectiveness of lowering microbial counts on broiler carcasses. Eighteen broiler carcasses were obtained from a local processing plant after final wash but before chill, placed into an insulated container, and transported to the research facility for treatment. Six plant run controls (PRC) were immediately bagged on return to the pilot plant, and a whole-carcass rinse was performed. The remaining carcasses were subjected to a 30-min chill (1 C) in tap water or a 2% solution of Protecta II, (n = 6 per treatment). After treatment, carcasses were rinsed with tap water and subjected to the whole-carcass rinse procedure. All rinse diluents were microbiologically analyzed for total aerobes, coliforms, generic Escherichia coli, and Campylobacter. Six replications were analyzed on 6 different d for a total 36 carcasses per treatment and 36 PRC. The PRC carcasses had 3.7, 2.5, 2.1, and 2.0 log10 cfu/mL for total aerobes, coliforms, generic E. coli, and Campylobacter. Water treatment significantly reduced counts (2.6, 1.4, 0.7, and 0.9 log10 cfu/mL, respectively) when compared with the PRC. Protecta II treatment significantly reduced counts (P < 0.01) even further to counts of 0.06, 0.04, 0.01, and 0.00 log10 cfu/mL for total aerobes, coliforms, Campylobacter, and E. coli, respectively. Detectable levels of the monitored organisms were 1 cell/mL (log10 0) for the E. coli, coliforms, and total counts and 10 cells/mL (log10 1) for the Campylobacter. Microbial counts for carcasses treated with Protecta II would be considered too low to be detected (<1 cell/mL).
Dexmedetomidine decreases emergence agitation in pediatric patients after sevoflurane anesthesia without surgery (2006)

We concluded that a 1 microg x kg(-1) dose of i.v. dexmedetomidine reduces EA after sevoflurane anesthesia in children undergoing MRI.
Diagnosis of bladder cancer by urine survivin, an inhibitor of apoptosis: a preliminary report. (2006)

Urine survivin seems to have a higher sensitivity than urine cytology, especially in low-grade bladder cancer. The quantitative measurement of survivin in urine by advanced techniques may provide a better diagnostic and prognostic tool. However, the clinical use of survivin and its association with different stages and grades of TCC still requires more studies.
A novel cold‐inducible zinc finger protein from soybean, SCOF‐1, enhances cold tolerance in transgenic plants (2001)

Cold stress on plants induces changes in the transcription of cold response genes. A cDNA clone encoding C2H2-type zinc finger protein, SCOF-1, was isolated from soybean. The transcription of SCOF-1 is specifically induced by low temperature and abscisic acid (ABA) but not by dehydration or high salinity. Constitutive overexpression of SCOF-1 induced cold-regulated (COR) gene expression and enhanced cold tolerance of non-acclimated transgenic Arabidopsis and tobacco plants. SCOF-1 localized to the nucleus but did not bind directly to either C-repeat/dehydration (CRT/DRE) or ABA responsive element (ABRE), cis-acting DNA regulatory elements present in COR gene promoters. However, SCOF-1 greatly enhanced the DNA binding activity of SGBF-1, a soybean G-box binding bZIP transcription factor, to ABRE in vitro. SCOF-1 also interacted with SGBF-1 in a yeast two-hybrid system. The SGBF-1 transactivated the beta-glucuronidase reporter gene driven by the ABRE element in Arabidopsis leaf protoplasts. Furthermore, the SCOF-1 enhanced ABRE-dependent gene expression mediated by SGBF-1. These results suggest that SCOF-1 may function as a positive regulator of COR gene expression mediated by ABRE via protein-protein interaction, which in turn enhances cold tolerance of plants.
Signalling molecules and growth factors for tissue engineering of cartilage-what can we learn from the growth plate? (2009)

Modern tissue engineering concepts integrate cells, scaffolds, signalling molecules and growth factors. For the purposes of regenerative medicine, fetal development is of great interest because it is widely accepted that regeneration recapitulates in part developmental processes. In tissue engineering of cartilage the growth plate of the long bone represents an interesting, well-organized developmental structure with a spatial distribution of chondrocytes in different proliferation and differentiation stages, embedded in a scaffold of extracellular matrix components. The proliferation and differentiation of these chondrocytes is regulated by various hormonal and paracrine factors. Thus, members of the TGFbeta superfamily, the parathyroid hormone-related peptide-Indian hedgehog loop and a number of transcription factors, such as Sox and Runx, are involved in the regulation of chondrocyte proliferation and differentiation. Furthermore, adhesion molecules, homeobox genes, metalloproteinases and prostaglandins play a role in the complex regulation mechanisms. The present paper summarizes the morphological organization of the growth plate and provides a short but not exhaustive overview of the regulation of growth plate development, giving interesting insights for tissue engineering of cartilage.
G PROTEIN MECHANISMS: Insights from Structural Analysis (1997)

This review is concerned with the structures and mechanisms of a superfamily of regulatory GTP hydrolases (G proteins). G proteins include Ras and its close homologs, translation elongation factors, and heterotrimeric G proteins. These proteins share a common structural core, exemplified by that of p21ras (Ras), and significant sequence identity, suggesting a common evolutionary origin. Three-dimensional structures of members of the G protein superfamily are considered in light of other biochemical findings about the function of these proteins. Relationships among G protein structures are discussed, and factors contributing to their low intrinsic rate of GTP hydrolysis are considered. Comparison of GTP- and GDP-bound conformations of G proteins reveals how specific contacts between the gamma-phosphate of GTP and the switch II region stabilize potential effector-binding sites and how GTP hydrolysis results in collapse (or reordering) of these surfaces. A GTPase-activating protein probably binds to and stabilizes the conformation of its cognate G protein that recognizes the transition state for hydrolysis, and may insert a catalytic residue into the G protein active site. Inhibitors of nucleotide release, such as the beta gamma subunit of a heterotrimeric G protein, bind selectively to and stabilize the GDP-bound state. Release factors, such as the translation elongation factor, Ts, also recognize the switch regions and destabilize the Mg(2+)-binding site, thereby promoting GDP release. G protein-coupled receptors are expected to operate by a somewhat different mechanism, given that the GDP-bound form of many G protein alpha subunits does not contain bound Mg2+.
Synergistic enhancement of globin gene expression by activator protein-1-like proteins. (1990)

DNA sequences corresponding to the four major DNase I hypersensitive sites upstream of the beta-globin gene cluster are essential for the achievement of high levels of globin gene expression and development regulation. In this study, we focused on one of these sites, hypersensitive site 2, which behaves as a powerful enhancer in transient expression and transgenic mouse experiments. We identified a tandem repeat of the activator protein 1 (AP-1) consensus sequence that binds AP-1-like proteins from nuclear extracts of K562 and HeLa cells. These proteins have the same binding properties as HeLa AP-1 but differ in the electrophoretic mobility and in functional assays. Transient-expression experiments in K562 of various deletion and point mutation constructs derived from hypersensitive site 2 indicate that the enhancer activity and the inducibility of a linked gamma-globin promoter are dependent upon the synergistic action of proteins bound to the tandem AP-1 repeat.
Multi-version Concurrency via Timestamp Range Conflict Management (2012)

A database supporting multiple versions of records may use the versions to support queries of the past or to increase concurrency by enabling reads and writes to be concurrent. We introduce a new concurrency control approach that enables all SQL isolation levels including serializability to utilize multiple versions to increase concurrency while also supporting transaction time database functionality. The key insight is to manage a range of possible timestamps for each transaction that captures the impact of conflicts that have occurred. Using these ranges as constraints often permits concurrent access where lock based concurrency control would block. This can also allow blocking instead of some aborts that are common in earlier multi-version concurrency techniques. Also, timestamp ranges can be used to conservatively find deadlocks without graph based cycle detection. Thus, our multi-version support can enhance performance of current time data access via improved concurrency, while supporting transaction time functionality.
Synthesis of Oligo(thiophene)-Coated Star-Shaped ROMP Polymers: Unique Emission Properties by the Precise Integration of Functionality (2012)

A facile synthesis of oligo(thiophene)-modified (coated) "soluble" star (ball)-shaped polymers has been achieved via sequential living ring-opening metathesis polymerization (ROMP) of norbornene and a cross-linking reagent using Mo(CHCMe(2)Ph)(N-2,6-(i)Pr(2)C(6)H(3))(O(t)Bu)(2) as the initiator and oligo(thiophene) carboxaldehydes for termination. The resultant star-shaped ROMP polymers containing ter- and tetrathiophene moieties exhibit unique emission properties due to an integration of the ROMP polymers (arranged functionalities): the blue emission was tuned to the white emission upon addition of 2-[2-[(E)-4-(dimethylamino)styryl]-6-methyl-4H-pyran-4-ylidene]malononitrile.
Metal Cation Micelle Mediated Hydrolysis of Phosphonic Acid Esters (1998)

p-Nitrophenyl methylphosphonate (PNPMP, 3) and p-nitrophenyl phenylphosphonate (PNPPP, 4) are rapidly hydrolyzed in acidic solutions (pH 3.5−6.0) at 37 °C by excess Zr4+, Ce4+, or Th4+ cations. Brij-35 micelles are employed in the Ce4+ and Th4+ cases. Second-order rate constants (M-1 s-1) with PNPMP are 115 (Zr4+), 53.9 (Ce4+), and 16.9 (Th4+), while for PNPPP they are, respectively, 76.8, 16.1, and 13.1. Relative to water (k2 = 3.6 × 10-11 M-1 s-1 at 30 °C, pH 7.6), kinetic advantages with Zr4+ or Ce4+ exceed 1012.
Integrating region growing and edge detection (1990)

A method that combines region growing and edge detection for image segmentation is presented. The authors start with a split-and merge algorithm wherein the parameters have been set up so that an over-segmented image results. Region boundaries are then eliminated or modified on the basis of criteria that integrate contrast with boundary smoothness, variation of the image gradient along the boundary, and a criterion that penalizes for the presence of artifacts reflecting the data structure used during segmentation (quadtree in this case). The algorithms were implemented in the C language on a Sun 3/160 workstation running under the Unix operating system. Simple tool images and aerial photographs were used to test the algorithms. The impression of human observers is that the method is very successful on the tool images and less so on the aerial photograph images. It is thought that the success in the tool images is because the objects shown occupy areas of many pixels, making it is easy to select parameters to separate signal information from noise.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Type III Secretion Machines: Bacterial Devices for Protein Delivery into Host Cells (1999)

Several Gram-negative pathogenic bacteria have evolved a complex protein secretion system termed type III to deliver bacterial effector proteins into host cells that then modulate host cellular functions. These bacterial devices are present in both plant and animal pathogenic bacteria and are evolutionarily related to the flagellar apparatus. Although type III secretion systems are substantially conserved, the effector molecules they deliver are unique for each bacterial species. Understanding the biology of these devices may allow the development of novel prevention and therapeutic approaches for several infectious diseases.
Protein Kinase B Regulates T Lymphocyte Survival, Nuclear Factor κb Activation, and Bcl-XL Levels in Vivo (2000)

The serine/threonine kinase protein kinase B (PKB)/Akt mediates cell survival in a variety of systems. We have generated transgenic mice expressing a constitutively active form of PKB (gag-PKB) to examine the effects of PKB activity on T lymphocyte survival. Thymocytes and mature T cells overexpressing gag-PKB displayed increased active PKB, enhanced viability in culture, and resistance to a variety of apoptotic stimuli. PKB activity prolonged the survival of CD4+CD8+ double positive (DP) thymocytes in fetal thymic organ culture, but was unable to prevent antigen-induced clonal deletion of thymocytes expressing the major histocompatibility complex class I–restricted P14 T cell receptor (TCR). In mature T lymphocytes, PKB can be activated in response to TCR stimulation, and peptide-antigen–specific proliferation is enhanced in T cells expressing the gag-PKB transgene. Both thymocytes and T cells overexpressing gag-PKB displayed elevated levels of the antiapoptotic molecule Bcl-XL. In addition, the activation of peripheral T cells led to enhanced nuclear factor (NF)-κB activation via accelerated degradation of the NF-κB inhibitory protein IκBα. Our data highlight a physiological role for PKB in promoting survival of DP thymocytes and mature T cells, and provide evidence for the direct association of three major survival molecules (PKB, Bcl-XL, and NF-κB) in vivo in T lymphocytes.
In-place differential file compression of non-aligned files with applications to file distribution, backups, and string similarity (2004)

We consider in-place differential file compression; that is, compressing a file T of size n with respect to an existing file S of size m, where decompression is in-place by overwriting S with T, using at most MAX(m,n)+O(1) space. In previous work we presented the IPSW algorithm (in-place sliding window). IPSW is fast and the compression achieved compares well with other existing methods, including those that are not in-place. IPSW is most effective when S and T are reasonably well aligned (most large common substrings occur in approximately the same order). Here we present a preprocessing step for string alignment that can be employed when the encoder determines significant gains will be achieved.
Association of an Increase in CD8+ T Cells with the Presence of Trypanosoma cruzi Antigens in Chronic, Human, Chagasic Myocarditis (1997)

The role of Trypanosoma cruzi in the pathogenesis of myocarditis in the chronic phase of Chagas' disease is still controversial, with autoimmune mechanisms frequently being proposed. In the present work, we demonstrate that higher numbers of CD8+ T cells are correlated with the presence of parasite antigens, suggesting an important role for the parasite in the development of myocardial inflammation. Quantification of the mean numbers of CD8+ and CD4+ T cells per 400x microscopic field was performed in myocardial specimens from 33 chronic chagasic patients with heart failures (nine biopsies and 24 necropsies), using an immunoperoxidase technique. The cases were grouped according to a semiquantitative score of the relative amounts of T. cruzi antigens: group 1 = absent (14 cases); group 2 = scarce extracellular or intramacrophagic antigens (12 cases); group 3 = many extracellular or intramacrophagic antigens plus T. cruzi intramyocytic pseudocysts (seven cases). The mean numbers of CD8+ and CD4+ T cells in groups 1,2, and 3 were 6.94 and 3.79, 13.89 and 6.24, and 17.91 and 5.97, respectively. The numbers of CD8+ T cells in groups 2 and 3 were significantly higher compared with group 1 (no T. cruzi antigens), but were not different from each other. Scarce, extramyocytic T. cruzi antigens were associated with an intense inflammatory infiltrate, suggesting that delayed-type hypersensitivity immune mechanism is induced by the parasite; intact myocardiocytes containing parasites did not show an inflammatory reaction around them. A poor inflammatory response was frequently associated with many extramyocytic antigens and myocardial parasite pseudocysts, suggesting that active proliferation and dissemination of the parasites occur when the immunologic response is diminished. The number of CD4+ T cells did not vary significantly among the three groups. We conclude that the CD8+ T cell is the main cell type responsible for immune activation in chronic, human, chagasic myocarditis and is probably activated by the presence of T. cruzi antigens associated with internal myocytic host antigens. The absence of a significant member of CD4+ T cells in the presence of T. cruzi antigens suggests inhibition of CD4+ T cell activation or the lack of a class II major histocompatibility complex molecule presentation mechanism.
Passivating chemical vapor deposited graphene with metal oxides for transfer and transistor fabrication processes (2013)

The dependence of the spectroscopic and electrical transport characteristics of graphene grown by chemical vapor deposition on oxide-passivations was investigated. We found that in graphene transfer and transistor fabrication processes, Al2O3- and Cr2O3-passivations are effective to suppress the extrinsic p-type doping into graphene due to surface contamination. TiO2- and NiO-passivations are not suitable because p–d hybridization between graphene π (pz) and metal (Ti or Ni) d orbitals occurs at the interfaces, resulting in deteriorated transport properties.
Somatic gene transfer in the development of an animal model for primary hyperparathyroidism (1992)

The overproduction of hormones is associated with a variety of endocrinological disorders. We have used somatic cell gene transfer of human PTH (hPTH) to develop an animal model of hypercalcemia and osteoclastic skeletal resorption. Recombinant retroviruses were used to transduce a functional hPTH gene into cultured rat fibroblasts. The recombinant-derived preproparathyroid hormone peptide was appropriately processed in this ectopic cell, and intact hPTH (1-84) was secreted at a high level (2-5 ng/10(6) cells/24 h). Transplantation of the PTH-secreting cells into syngeneic rat recipients was associated with the development of hypercalcemia mediated by increasing serum concentrations of hPTH. Thyroparathyroidectomy in these hypercalcemic rats producing hPTH did not result in hypocalcemia and tetany, which was observed in control animals undergoing thyroparathyroidectomy. Chronic overproduction of hPTH (60 days) was associated with severe hypercalcemia, metastatic calcification, and histological changes of osteoclastic resorption of bone. This animal model will be useful in studying the pathophysiology of severe hyperparathyroidism in humans and should help in the evaluation of new medical therapies for hypercalcemia.