gebhart/patrepeval huggingface dataset:
Prediction of hemorrhagic transformation after recanalization therapy using T2*‐permeability magnetic resonance imaging (2007)

Permeability images derived from pretreatment perfusion MRI source data may identify patients at risk for HT with high specificity. Our preliminary demonstration of permeability imaging based on standard perfusion data for prediction of hemorrhage merits further study with dedicated MRI BBB permeability acquisitions and multicenter validation.
Cell Culture Technology for Pharmaceutical and Cell-Based Therapies Edited by S. S. Ozturk and W.-S. Hu (Centocor, Inc. and University of Minnesota, respectively). CRC Press/Taylor & Francis, Boca Raton. 2006. xiv + 755 pp. 7 × 10 in. $179.95. ISBN 0-8247-5334-8. (2007)

ADVERTISEMENT RETURN TO ISSUEPREVBook ReviewNEXTCell Culture Technology for Pharmaceutical and Cell-Based Therapies Edited by S. S. Ozturk and W.-S. Hu (Centocor, Inc. and University of Minnesota, respectively). CRC Press/Taylor & Francis, Boca Raton. 2006. xiv + 755 pp. 7 × 10 in. $179.95. ISBN 0-8247-5334-8.Khisal AlviView Author Information Phyton Biotech East Windsor, New JerseyCite this: J. Nat. Prod. 2007, 70, 4, 712–713Publication Date (Web):March 8, 2007Publication History Published online8 March 2007Published inissue 1 April 2007https://pubs.acs.org/doi/10.1021/np078140ahttps://doi.org/10.1021/np078140abook-reviewACS PublicationsCopyright © 2007 American Chemical Society and American Society of PharmacognosyRequest reuse permissionsArticle Views614Altmetric-Citations2LEARN 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:Cell culture,Cells,Protein dynamics,Therapeutics Get e-Alerts
Pichia pastoris as a host system for transformations. (1985)

We developed a methylotrophic yeast, Pichia pastoris, as a host for DNA transformations. The system is based on an auxotrophic mutant host of P. pastoris which is defective in histidinol dehydrogenase. As a selectable marker, we isolated and characterized the P. pastoris HIS4 gene. Plasmid vectors which contained either the P. pastoris or the Saccharomyces cerevisiae HIS4 gene transformed the P. pastoris mutant host. DNA transfer was accomplished by a modified version of the spheroplast generation (CaCl2-polyethylene glycol)-fusion procedure developed for S. cerevisiae. In addition, we report the isolation and characterization of P. pastoris DNA fragments with autonomous replication sequence activity. Two fragments, PARS1 and PARS2, when present on plasmids increased transformation frequencies to 10(5)/micrograms and maintained the plasmids as autonomous elements in P. pastoris cells.
Inhibition of deoxyribonucleases by phosphorothioate groups in oligodeoxyribonucleotides (1988)

The Rp- and Sp-diastereomers of the phosphorothioate-containing oligonucleotide d[ApAp(S)ApA] have been synthesized. They and the tetramer d[ApApApA] were tested as substrates for staphylococcal nuclease, DNase II and spleen phosphodiesterase. For digestions with DNase I these oligonucleotides were converted to the 5'-phosphorylated derivates. The reactions with the nucleases were analysed by HPLC. The phosphorothioate groups of both diastereomers were resistant to the action of staphylococcal nuclease, DNase I and DNase II. While the phosphorothioate group of the Rp-diastereomer was resistant to the action of spleen phosphodiesterase, the Sp-diastereomer was hydrolysed at an estimated rate 1/100 the rate of cleavage of the unmodified tetramer. The presence of the phosphorothioate group in the center of the molecule affected the rate of hydrolysis of neighbouring phosphate groups for some enzymes. In particular, very slow release of 3'-dAMP from the Rp-diastereomer occurred on incubation with staphylococcal nuclease but the Sp-diastereomer was completely resistant. DNase II produced 3'-dAMP quite rapidly from both diastereomers of d[ApAp(S)ApA] and DNase I released 5'-dAMP from both diastereomers of d[pApAp(S)ApA] only slowly.
Air-Lift Bioreactors for Algal Growth on Flue Gas:  Mathematical Modeling and Pilot-Plant Studies (2005)

Air-lift reactors (ALRs) have great potential for industrial bioprocesses, because of the low level and homogeneous distribution of hydrodynamic shear. One growing field of application is the flue-gas treatment using algae for the absorption of CO2. In this paper, we discuss the requirements for photosynthetic biomass growth in an ALR. The effects of the operating variables are analyzed using a mathematical model [Wu, X.; Merchuk, J. C. Simulation of Algae Growth in a Bench Scale Internal Loop Airlift Reactor. Chem. Eng. Sci. 2004, 59 (14), 2899] that accounts for the effects of ALR geometry, fluid flow, and illumination on the biomass growth. On the basis of the ALR principles and the specific requirements of photosynthetic processes, we developed a “triangular” ALR configuration that is particularly suitable for algal growth. We describe the design and operation of this novel bioreactor and present the first series of experimental data obtained for two different algal species in a pilot-scale unit supplied with flue gases from a small power plant. The measured removal efficiency of CO2 was significant (82.3 ± 12.5% on sunny days and 50.1 ± 6.5% on cloudy days) and consistent with the increase in the algal biomass.
Smart body contact for SOI MOSFETs (2003)

Summary form only given. SOI MOSFETs exhibit various floating-body effects due to the lack of a contact to the channel region. These effects can show up as a kink in the saturation region of I/sub DS/-V/sub DS/ characteristics (higher drive current) and an improvement of the subthreshold slope, or can be as severe as latch-up of the SOI MOSFET at large drain biases. The easiest was to eliminate floating-body effects is to provide a contact to the channel region to deep it at or below the source potential. One problem with providing a body contact is that the increased transistor drive current due to the floating-body effects is lost even in the saturation region, where it may be desirable for high-speed circuit operation. Here, a scheme for providing a smart body contact is presented. This contact acts as a low-resistance channel contact at low gate voltages to keep the transistor off and avoid latch-up. At high-gate voltages, the resistance of this body contact becomes very high and allows the MOSFET channel to float, which increases the drain current due to both MOS body effect and bipolar action.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comprehensive molecular characterization of human colon and rectal cancer (2019)

To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase ε (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.
Mesothelin is a malignant factor and therapeutic vaccine target for pancreatic cancer (2008)

Given the high fatality rate of pancreatic cancer, an effective treatment for this devastating disease is urgently needed. We have shown that mesothelin expression was higher in human pancreatic cancer cells than in human pancreatic duct epithelial cells, and mesothelin mRNA was substantially overexpressed in 18 of 21 (86%) clinical pancreatic adenocarcinoma specimens when compared with the surrounding normal tissues. However, the biological functions of mesothelin in tumor progression are not clearly understood. Here we studied the effects of mesothelin overexpression in pancreatic cancer cell proliferation and migration in vitro and pancreatic cancer progression in vivo. We found that forced expression of mesothelin significantly increased tumor cell proliferation and migration by 90% and 300%, respectively, and increased tumor volume by 4-fold in the nude mice xenograft model when compared with the vector control cell line. Silencing of mesothelin inhibited cell proliferation and migration in pancreatic cancer cells and ablated tumor progression in vivo. Vaccination with chimeric virus-like particles that contain human mesothelin substantially inhibited tumor progression in C57BL/6J mice. The increases in mesothelin-specific antibodies and CTL activity and the decrease in regulatory T cells correlated with reduced tumor progression and prolonged survival. This study revealed novel functions of mesothelin and suggested a new therapeutic vaccine strategy whereby mesothelin is targeted to control pancreatic cancer progression.
Density of fat-free body mass: relationship with race, age, and level of body fatness (1997)

The two-compartment body composition method assumes that fat-free body mass (FFM) has a density of 1.100 kg/l. This study tested the hypothesis that FFM density is independent of race, age, and body fatness. Subjects were 703 black and white subjects, ages 20-94 yr, with body mass index (BMI) 17-35 kg/m2. Body composition was assessed using a four-compartment model based on tritium dilution volume, body density by underwater weighing, bone mineral by dual-energy X-ray absorptiometry, and body weight. No relationship was observed between FFM density and race or BMI. A tendency was observed for a lower FFM density only in older white women. The difference in percent body fat (delta fat) between the four-compartment model and underwater weighing was < 2% for all groups. Race, age, and BMI explained only 2.3 (women) and 1.4% (men) of the variance in delta fat, whereas the total body water fraction of FFM explained 77%. In contrast to current thinking, these results show that the assumption of constant FFM density is valid in black, elderly, and obese subjects.
Managing pipeline-reconfigurable FPGAs (1998)

While reconfigurable computing promises to deliver incomparable performance, it is still a marginal technology due to the high cost of developing and upgrading applications. Hardware virtualization can be used to significantly reduce both these costs. In this paper we describe the benefits of hardware virtualization, and show how it can be achieved using a combination of pipeline reconfiguration and run-time scheduling of both configuration streams and data streams. The result is PipeRench, an architecture that supports robust compilation and provides forward compatibility. Our preliminary performance analysis predicts that PipeRench will outperform commercial FPGAs and DSPs in both overall performance and in performance per mm2.
Separation of capsulate and non-capsulate Bacteroides fragilis on a discontinuous density gradient (1983)

SUMMARY A discontinuous density gradient procedure was used successfully to separate capsulate and non-capsulate cells of strains of Bacteroides fragilis. Bacteria from the capsulate fraction retained their capsules on subculture, but non-capsulate cells reverted to the mixed phenotype.
Biological and clinical relevance of the urokinase-type plasminogen activator (uPA) in breast cancer. (1991)

Tumor cell invasion and metastasis is a multifactorial process, which at each step may require the action of proteolytic enzymes such as collagenases, cathepsins, plasmin, or plasminogen activators. An enzymatically inactive proenzyme form of the urokinase-type plasminogen activator (pro-uPA) is secreted by tumor cells which may be converted to an enzymatically active two-chain uPA-molecule (HMW-uPA) by plasmin-like enzymes. Action of proteases on pro-uPA may generate the enzymatically active or inactive high-molecular-weight form of uPA (HMW-uPA). Some proteases (plasmin, cathepsin B and L, kallikrein, trypsin or thermolysin) activate pro-uPA by cleaving the peptide bond Lys158 and IIe159. Other proteases (elastase, thrombin) cleave pro-uPA at different positions to yield enzymatically inactive HMW-uPA. HMW-uPA may be split into the enzymatically active LMW-uPA and the enzymatically inactive ATF (amino terminal fragment). ATF may be cleaved between peptide sequence 20 and 40 within the receptor binding domain of uPA (GFD). Such impaired ATF does not bind to uPA-receptors. Action of the bacterial endoproteinase Asp-N from Pseudomonas fragi mutant on pro-uPA or HMW-uPA, however, generates intact ATF which efficiently competes for binding of HMW-uPA or pro-uPA to receptors on tumor cells. High uPA-antigen content (pro-uPA, HMW-uPA, or LMW-uPA) in breast cancer tissue (not in plasma) indicates an elevated risk for the patient of recurrences and shorter overall survival. Thus pro-uPA/uPA-antigen content in breast cancer tissue serves as an independent prognostic parameter for the outcome of the disease. Cathepsin D is also an independent prognostic factor for recurrences and overall survival. High content of cathepsin D in breast cancer tumors is, however, not correlated with elevated levels of pro-uPA/uPA indicating that synthesis and release of cathepsin D and pro-uPA/uPA are independent events.
Identification and concentration of soy isoflavones in commercial cat foods (2002)

Genistein and daidzein are common constituents of commercial cat foods. Predictors of isoflavone content included ingredient labeling, food type, and food cost. Soy isoflavones in some commercial cat foods were detected in amounts predicted to have a biological effect.
A MOS Transistor with self-aligned polysilicon source—drain (1986)

A new MOS transistor with self-aligned polysilicon source-drain (SAPSD) is demonstrated. Using a thin implant-doped polysilicon layer above the active channel region, a shallow source-drain junction with negligible leakage is realized. A novel lightly doped-drain (LDD) structure is also incorporated by diffusing dopants from the n+ polysilicon source-drain layer into the silicon substrate, forming the n- region. During the gate oxidation, a sidewall spacer is simultaneously formed by the oxidation of polysilicon source-drain sidewalls. The transistor layout area is saved by bringing the source-drain contacts onto the field oxide region. Experimental results of the new structure are presented.
Cloning of the Vibrio cholerae recA gene and construction of a Vibrio cholerae recA mutant (1986)

A recombinant plasmid carrying the recA gene of Vibrio cholerae was isolated from a V. cholerae genomic library, using complementation in Escherichia coli. The plasmid complements a recA mutation in E. coli for both resistance to the DNA-damaging agent methyl methanesulfonate and recombinational activity in bacteriophage P1 transductions. After determining the approximate location of the recA gene on the cloned DNA fragment, we constructed a defined recA mutation by filling in an XbaI site located within the gene. The 4-base pair insertion resulted in a truncated RecA protein as determined by minicell analysis. The mutation was spontaneously recombined onto the chromosome of a derivative of V. cholerae strain P27459 by screening for methyl methanesulfonate-sensitive variants. Southern blot analysis confirmed the presence of the inactivated XbaI site in the chromosome of DNA isolated from one of these methyl methanesulfonate-sensitive colonies. The recA V. cholerae strain was considerably more sensitive to UV light than its parent, was impaired in homologous recombination, and was deficient in induction of a temperate vibriophage upon exposure to UV light. We conclude that the V. cholerae RecA protein has activities which are analogous to those described for the RecA protein of E. coli.
Selection of non-competitive leptin antagonists using a random nanobody-based approach (2011)

The adipocyte-derived cytokine leptin acts as a metabolic switch, connecting the body's metabolism to high-energy consuming processes such as reproduction and immune responses. Accumulating evidence suggests that leptin plays a role in human pathologies, such as autoimmune diseases and cancer, thus providing a rationale for the development of leptin antagonists. In the present study, we generated and evaluated a panel of neutralizing nanobodies targeting the LR (leptin receptor). A nanobody comprises the variable domain of the naturally occurring single-chain antibodies found in members of the Camelidae family. We identified three classes of neutralizing nanobodies targeting different LR subdomains: i.e. the CRH2 (cytokine receptor homology 2), Ig-like and FNIII (fibronectin type III) domains. Only nanobodies directed against the CRH2 domain inhibited leptin binding. We could show that a nanobody that targets the Ig-like domain potently interfered with leptin-dependent regulation of hypothalamic NPY (neuropeptide Y) expression. As a consequence, daily intraperitoneal injection increased body weight, body fat content, food intake, liver size and serum insulin levels. All of these characteristics resemble the phenotype of leptin and LR-deficient animals. The results of the present study support proposed models of the activated LR complex, and demonstrate that it is possible to block LR signalling without affecting ligand binding. These nanobodies form new tools to study the mechanisms of BBB (blood-brain barrier) leptin transport and the effect of LR inhibition in disease models.
Potential Theory in Gravity and Magnetic Applications (1995)

This text bridges the gap between the classic texts on potential theory and modern books on applied geophysics. It opens with an introduction to potential theory, emphasising those aspects particularly important to earth scientists, such as Laplace's equation, Newtonian potential, magnetic and electrostatic fields, and conduction of heat. The theory is then applied to the interpretation of gravity and magnetic anomalies, drawing on examples from modern geophysical literature. Topics explored include regional and global fields, forward modeling, inverse methods, depth-to-source estimation, ideal bodies, analytical continuation, and spectral analysis. The book includes numerous exercises and a variety of computer subroutines written in FORTRAN. Graduate students and researchers in geophysics will find this book essential.
Mutational analysis of the influenza virus A/Victoria/3/75 PA protein: studies of interaction with PB1 protein and identification of a dominant negative mutant (1996)

The RNA polymerase activity and PB1 binding of influenza virus PA mutants were studied using an in vivo-reconstituted polymerase assay and a two hybrid system. Deletions covering the whole PA protein abolished polymerase activity, but the deletion of the 154 N-terminal amino acids allowed PB1 binding, indicating that the PA protein N terminus is not absolutely required for this interaction. Further internal or C-terminal deletions abolished PB1 interaction, suggesting that most of the protein is involved in this association. As a novel finding we showed that a single amino acid insertion mutant, PAI672, was responsible for a temperature-sensitive phenotype. Mutant PAS509, which had a serine insertion at position 509, bound to PB1 like wild-type PA but did not show any polymerase activity. Over-expression of PAS509 interfered with the polymerase activity of wild-type PA, identifying PAS509 as a dominant negative mutant.
Effective Plague Vaccination via Oral Delivery of Plant Cells Expressing F1-V Antigens in Chloroplasts (2008)

The chloroplast bioreactor is an alternative to fermentation-based systems for production of vaccine antigens and biopharmaceuticals. We report here expression of the plague F1-V fusion antigen in chloroplasts. Site-specific transgene integration and homoplasmy were confirmed by PCR and Southern blotting. Mature leaves showed the highest level of transgene expression on the third day of continuous illumination, with a maximum level of 14.8% of the total soluble protein. Swiss Webster mice were primed with adjuvant-containing subcutaneous (s.c.) doses of F1-V and then boosted with either adjuvanted s.c. doses (s.c. F1-V mice) or unadjuvanted oral doses (oral F1-V mice). Oral F1-V mice had higher prechallenge serum immunoglobulin G1 (IgG1) titers than s.c. F1-V mice. The corresponding serum levels of antigen-specific IgG2a and IgA were 2 and 3 orders of magnitude lower, respectively. After vaccination, mice were exposed to an inhaled dose of 1.02 x 10(6) CFU of aerosolized Yersinia pestis CO92 (50% lethal dose, 6.8 x 10(4) CFU). All control animals died within 3 days. F1-V given s.c. (with adjuvant) protected 33% of the immunized mice, while 88% of the oral F1-V mice survived aerosolized Y. pestis challenge. A comparison of splenic Y. pestis CFU counts showed that there was a 7- to 10-log reduction in the mean bacterial burden in survivors. Taken together, these data indicate that oral booster doses effectively elicit protective immune responses in vivo. In addition, this is the first report of a plant-derived oral vaccine that protected animals from live Y. pestis challenge, bringing the likelihood of lower-cost vaccines closer to reality.
Generation of interleukin-6 receptor antagonists by molecular-modeling guided mutagenesis of residues important for gp130 activation. (1994)

Interleukin-6 (IL-6) drives the sequential assembly of a receptor complex formed by the IL-6 receptor (IL-6R alpha) and the signal transducing subunit, gp130. A model of human IL-6 (hIL-6) was constructed by homology using the structure of bovine granulocyte colony stimulating factor. The modeled cytokine was predicted to interact sequentially with the cytokine binding domains of IL-6R alpha and gp130 bridging them in a way similar to that of the interaction between growth hormone and its homodimeric receptor. Several residues on helices A and C which were predicted as contact points between IL-6 and gp130 and therefore essential for IL-6 signal transduction, were subjected to site-directed mutagenesis individually or in combined form. Interestingly, while single amino acid changes never produced major alterations in IL-6 bioactivity, a subset of double mutants of Y31 and G35 showed a considerable reduction of biological activity and were selectively impaired from associating with gp130 in binding assays in vitro, while they maintained wild-type affinity towards hIL-6-R alpha. More importantly, we demonstrated the antagonistic effect of mutant Y31D/G35F versus wild-type IL-6.