gebhart/patrepeval huggingface dataset:
Antitumor 1,3-.BETA.-Glucan from Cultured Fruit Body of Sparassis crispa. (2000)

Sparassis crispa is an edible mushroom recently cultivable in Japan. Polysaccharide fractions were prepared from the cultured S. crispa by repeated extraction with hot water (SCHWE), cold NaOH (SCCA), and then hot NaOH (SCHA). HWE was further separated by 1 volume (SCHWE1v) or 4 volumes (SCHWE4v) of ethanol-precipitable fractions. By chemical, enzymic, and NMR analyses, the primary structures of SCHWE1v, SCCA, and SCHA were 6-branched 1,3-beta-glucan, having one branch in approximately every third mainchain unit. All of these fractions showed antitumor activity to the solid form of Sarcoma 180 in ICR mice with strong vascular dilation and hemorrhage reaction. These fractions also showed enhanced hematopoietic response to cyclophosphamide induced leukopenic mice following intraperitoneal or peroral administration.
A community overlap strategy reveals central genes and networks in heart failure (2016)

Heart failure is one of the leading causes of mortality worldwide, but its underlying molecular mechanisms are poorly understood. To obtain a systems view of the molecular networks that underlie heart failure, we harvested 1352 samples from 313 healthy and failing hearts directly from transplant operating rooms and obtained left-ventricular whole-genome gene expression and genotype measurements. From these data, we built directed regulatory gene networks and gene communities using an approach that combines network and community inference in one framework. Differences in co-expression and global and local centrality parameters pinpointed changes in the molecular interaction network associated with heart failure, as well as its network-wise genetic determinants. Connectivity of one gene, PPP1R3A, previously unassociated with heart failure, changed significantly between healthy and diseased states. Perturbation of in vitro and in vivo systems via time series transcriptome sequencing and murine cardiovascular phenotyping revealed that ablation of PPP1R3A alters disease progression.
Computed Tomography and Magnetic Resonance Imaging for Noninvasive Coronary Angiography and Plaque Imaging (2002)

A therothrombosis is a systemic disease of the vessel wall that causes distinct clinical manifestations, depending on the affected circulatory bed and the characteristics of the individual lesions. 1 These lesions may be quite heterogeneous.
이벤트기업의 재무구조관리에 관한 연구 - C,K 기업을 사례로 - (2005)

The enterprises have faced with turbulent environmental changes. Therefore event enterprises have exerted all possible efforts to raise the real value of a event enterprise than the growth in quantity of assets. The purpose of this study was to find out the problem on financial structure and present the improvement plan of financial structure management on the basis of financial statement analysis of event enterprises. This study was conducted by case analysis focusing on C and K enterprises in the field of PR and mega-events. Financial structure analysis of C and K enterprises had assets composition, stability, leverage ratio, profitability, growth rates. As a result of financial structure analysis, the findings indicated that C enterprises have stabilities of financial structure because leverage ratio is low and assets ratio is high. Then C enterprises is well worth investment. But K enterprises have unstabilities because leverage ratio is high and profitability ratio is very low as well as high financial rates change. The problem of C enterprises are found to financial structure ratios are growing down and especially profitability ratios. Therefore, suggests that need financial structure management bases on enlarging net worth to assets and profitability ratio.
Identification and genetic analysis of the APOSPORY locus in Hypericum perforatum L. (2010)

The introduction of apomixis - seed formation without fertilization - into crop plants is a long-held goal of breeding research, since it would allow for the ready fixation of heterozygosity. The genetic basis of apomixis, whether of the aposporous or the diplosporous type, is still only poorly understood. Hypericum perforatum (St John's wort), a plant with a small genome and a short generation time, can be aposporous and/or parthenogenetic, and so represents an interesting model dicot for apomixis research. Here we describe a genetic analysis which first defined and then isolated a locus (designated HAPPY for Hypericum APOSPORY) associated with apospory. Amplified fragment length polymorphism (AFLP) profiling was used to generate a cleaved amplified polymorphic sequence (CAPS) marker for HAPPY which co-segregated with apospory but not with parthenogenesis, showing that these two components of apomixis are independently controlled. Apospory was inherited as a dominant simplex gene at the tetraploid level. Part of the HAPPY sequence is homologous to the Arabidopsis thaliana gene ARI7 encoding the ring finger protein ARIADNE7. This protein is predicted to be involved in various regulatory processes, including ubiquitin-mediated protein degradation. While the aposporous and sexual alleles of the HAPPY component HpARI were co-expressed in many parts of the plant, the gene product of the apomict's allele is truncated. Cloning HpARI represents the first step towards the full characterization of HAPPY and the elucidation of the molecular mechanisms underlying apomixis in H. perforatum.
Effect of interleukin-6 blockade on tissue factor-induced coagulation in human endotoxemia (2004)

IL-6 does not appear to mediate early-phase lipopolysaccharide-induced coagulation activation in humans.
Mutations in the A subunit affect yield, stability, and protease sensitivity of nontoxic derivatives of heat-labile enterotoxin (1996)

Heat-labile toxin (LT) is a protein related to cholera toxin, produced by enterotoxigenic Escherichia coli strains, that is organized as an AB5 complex. A number of nontoxic derivatives of LT, useful for new or improved vaccines against diarrheal diseases or as mucosal adjuvants, have been constructed by site-directed mutagenesis. Here we have studied the biochemical properties of the nontoxic mutants LT-K7 (Arg-7-->Lys), LT-D53 (Val-53-->Asp), LT-K63 (Ser-63-->Lys), LT-K97 (Val-97-->Lys), LT-K104 (Tyr-104-->Lys), LT-K114 (Ser-114-->Lys), and LT-K7/K97 (Arg-7-->Lys and Val-97-->Lys). We have found that mutations in the A subunit may have profound effects on the ability to form the AB5 structure and on the stability and trypsin sensitivity of the purified proteins. Unstable mutants, during long-term storage at 4 degrees C, showed a decrease in the amount of the assembled protein in solution and a parallel appearance of soluble monomeric B subunit. This finding suggests that the stability of the B pentamer is influenced by the A subunit which is associated with it. Among the seven nontoxic mutants tested, LT-K63 was found to be efficient in AB5 production, extremely stable during storage, resistant to proteolytic attack, and very immunogenic. In conclusion, LT-K63 is a good candidate for the development of antidiarrheal vaccines and mucosal adjuvants.
Transcriptional regulation of the Enterococcus faecium BM4147 vancomycin resistance gene cluster by the VanS-VanR two-component regulatory system in Escherichia coli K-12 (1997)

An Escherichia coli K-12 model system was developed for studying the VanS-VanR two-component regulatory system required for high-level inducible vancomycin resistance in Enterococcus faecium BM4147. Our model system is based on the use of reporter strains with lacZ transcriptional and translational fusions to the PvanR or PvanH promoter of the vanRSHAX gene cluster. These strains also express vanR and vanS behind the native PvanR promoter, the arabinose-inducible ParaB promoter, or the rhamnose-inducible PrhaB promoter. Our reporter strains have the respective fusions stably recombined onto the chromosome in single copy, thereby avoiding aberrant regulatory effects that may occur with plasmid-bearing strains. They were constructed by using allele replacement methods or a conditionally replicative attP plasmid. Using these reporter strains, we demonstrated that (i) the response regulator VanR activates PvanH, but not PvanR, expression upon activation (phosphorylation) by the partner kinase VanS, the noncognate kinase PhoR, or acetyl phosphate, indicating that phospho-VanR (P-VanR) is a transcriptional activator; (ii) VanS interferes with activation of VanR by PhoR or acetyl phosphate, indicating that VanS also acts as a P-VanR phosphatase; and (iii) the conserved, phosphate-accepting histidine (H164) of VanS is required for activation (phosphorylation) of VanR but not for deactivation (dephosphorylation) of P-VanR. Similar reporter strains may be useful in new studies on these and other interactions of the VanS-VanR system (and other systems), screening for inhibitors of these interactions, and deciphering the molecular logic of the signal(s) responsible for activation of the VanS-VanR system in vivo. Advantages of using an E. coli model system for in vivo studies on VanS and VanR are also discussed.
TDP-43 mutant transgenic mice develop features of ALS and frontotemporal lobar degeneration (2009)

Frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative diseases that show considerable clinical and pathologic overlap, with no effective treatments available. Mutations in the RNA binding protein TDP-43 were recently identified in patients with familial amyotrophic lateral sclerosis (ALS), and TDP-43 aggregates are found in both ALS and FTLD-U (FTLD with ubiquitin aggregates), suggesting a common underlying mechanism. We report that mice expressing a mutant form of human TDP-43 develop a progressive and fatal neurodegenerative disease reminiscent of both ALS and FTLD-U. Despite universal transgene expression throughout the nervous system, pathologic aggregates of ubiquitinated proteins accumulate only in specific neuronal populations, including layer 5 pyramidal neurons in frontal cortex, as well as spinal motor neurons, recapitulating the phenomenon of selective vulnerability seen in patients with FTLD-U and ALS. Surprisingly, cytoplasmic TDP-43 aggregates are not present, and hence are not required for TDP-43-induced neurodegeneration. These results indicate that the cellular and molecular substrates for selective vulnerability in FTLD-U and ALS are shared between mice and humans, and suggest that altered DNA/RNA-binding protein function, rather than toxic aggregation, is central to TDP-43-related neurodegeneration.
Free energy calculations in rational drug design (2001)

1. Historical Overview and Future Challenges J.A. McCammon. Section One: Theory. 2. Free Energy Calculations: Methods for Estimating Ligand Binding Affinities D.A. Pearlman. 3. Molecular Mechanics Force Field Development and Applications P.M. Todebush, J.P. Bowen. Section Two: Molecular Properties. 4. Solvation Thermodynamics and the Treatment of Equilibrium and Nonequilibrium Solvation Effects by Models Based on Collective Solvent Coordinates C.J. Cramer, D.G. Truhlar. 5. Relative Solvation Free Energies Calculated Using Explicit Solvent A. Agarwal, et al. 6. Tautomerism and Ionisation Studies Using Free Energy Methods G.A. Worth, P.M. King. Section Three: Ligand Binding. 7. Free Energy Calculations on Enzyme-Inhibitor Complexes: Studies of Thermolysin and Rhizopus Pepsin B.G. Rao. 8. Free Energy Calculations on DNA: Ligand Complexes S.B. Singh, P.A. Kollman. Section Four: Ligand Design and Analysis. 9. The Linear Interaction Energy Method for Computation of Ligand Binding Affinities J. Aqvist, J. Marelius. 10. New Free Energy Based Methods for Ligand Binding from Detailed Structure-Function to Multiple-Ligand Screening S. Banba, et al. 11. Ligand Interaction Scanning Using Free Energy Calculations M.D. Erion, M.R. Reddy. 12. MM-PBSA Applied to Computer-Assisted Ligand Design B. Kuhn, et al. 13. Reaction Free Energy Profiles Using Free Energy Perturbation and Coordinate Coupling Methodologies: Analysis of the Dihydrofolate Reductase Catalytic Mechanism U.C. Singh, et al. Section Five: Drug Design Case Studies. 14. Fructose 1,6-Bisphosphatase: Use of Free Energy Calculations in the Design and Optimization of AMP Mimetics M.R. Reddy, M.D. Erion. 15. COX-2, SRC SH2 Domain, HIV Reverse Transcriptase, and Thrombin: Computational Approaches to Protein-Ligand Binding W.L. Jorgensen, et al. 16. HIV-1 Protease: Structure-Based Drug Design Using the Free Energy Perturbation Approach M.R. Reddy, K. Appelt. 17. Thymidylate Synthase: Free Energy Calculations for Estimating Inhibitor Binding Affinities T.-S. Lee, P.A. Kollman. 18. Dihydrofolate Reductase: Free Energy Calculations for the Design of Mechanism-Based Inhibitors J.E. Gready, P.L. Cummins. 19. Adenosine Deaminase: Calculation of Relative Hydration Free Energy Differences M.D. Erion, M.R. Reddy. Index.
Standard methods for toxicology research inApis mellifera (2013)

Modern agriculture often involves the use of pesticides to protect crops. These substances are harmful to target organisms (pests and pathogens). Nevertheless, they can also damage non-target animals, such as pollinators and entomophagous arthropods. It is obvious that the undesirable side effects of pesticides on the environment should be reduced to a minimum. Western honey bees (Apis mellifera) are very important organisms from an agricultural perspective and are vulnerable to pesticide-induced impacts. They contribute actively to the pollination of cultivated crops and wild vegetation, making food production possible. Of course, since Apis mellifera occupies the same ecological niche as many other species of pollinators, the loss of honey bees caused by environmental pollutants suggests that other insects may experience a similar outcome. Because pesticides can harm honey bees and other pollinators, it is important to register pesticides that are as selective as possible. In this manuscript, we describe a selection of methods used for studying pesticide toxicity/selectiveness towards Apis mellifera. These methods may be used in risk assessment schemes and in scientific research aimed to explain acute and chronic effects of any target compound on Apis mellifera.
Construction and Characterization of Recombinant VLPs and Semliki-Forest Virus Live Vectors for Comparative Evaluation in the SHIV Monkey Model (1999)

For testing of recombinant virus-like particles (VLPs) in the SHIV monkey model, SIVmac239 Pr56gag precursor-based pseudovirions were modified by HIV-1 gp160 derived peptides. First, well-characterized epitopes from the HIV-1 envelope glycoprotein were inserted into the Pr56gag precursor by replacing defined regions that were shown to be dispensable for virus particle formation. Expression of these chimeric proteins in a baculovirus expression system resulted in efficient assembly and release of non-infectious, hybrid VLPs. In a second approach the HIV-1IIIB external glycoprotein gp120 was covalently linked to an Epstein-Barr virus derived transmembrane domain. Coexpression of the hybrid envelope derivative with the Pr56gag precursor yielded recombinant SIV derived Pr56gag particles with the HIV-1 gp120 firmly anchored on the VLP surface. Immunization of rhesus monkeys with either naked VLPs or VLPs adsorbed to alum induced substantial serum antibody titers and promoted both T helper cell and cytotoxic T lymphocyte responses. Furthermore, priming macaques with the corresponding set of recombinant Semliki-Forest viruses tended to enhance the immunological outcome. Challenge of the immunized monkeys with chimeric SHIV resulted in a clearly accelerated reduction of the plasma viremia as compared to control animals.
The MD4 Message Digest Algorithm (2007)

The MD4 message digest algorithm takes an input message of arbitrary length and produces an output 128-bit “fingerprint” or “message digest”, in such a way that it is (hopefully) computationally infeasible to produce two messages having the same message digest, or to produce any message having a given prespecified target message digest. The MD4 algorithm is thus ideal for digital signature applications: a large file can be securely “compressed” with MD4 before being signed with (say) the RSA public-key cryptosystem.The MD4 algorithm is designed to be quite fast on 32-bit machines. For example, on a SUN Sparc station, MD4 runs at 1,450,000 bytes/second (11.6 Mbit/sec). In addition, the MD4 algorithm does not require any large substitution tables; the algorithm can be coded quite compactly.The MD4 algorithm is being placed in the public domain for review and possible adoption as a standard.
CRYPTO RANSOMWARE ANALYSIS AND DETECTION USING PROCESS MONITOR (2017)

Ransomware is a faster growing threat that encrypts user’s files and locks the computer and holds the key required to decrypt the files for ransom. Over the past few years, the impact of ransomware has increased exponentially. There have been several reported high profile ransomware attacks, such as CryptoLocker, CryptoWall, WannaCry, Petya and Bad Rabbit which have collectively cost individuals and companies well over a billion dollars according to FBI. As the threat of ransomware has become more prevalent, security companies and researchers have begun proposing new approaches for detection and prevention of ransomware. However, these approaches generally lack dynamicity and are either prone to a high false positive rate, or they detect ransomware after some amount of data loss has occurred. \n\nThis research represents a dynamic approach to ransomware analysis and is specifically developed to detect ransomware on the user’s data. It starts by generating an artificial user environment using Cuckoo Sandbox and monitoring system behavior using Process Monitor to analyze ransomware in its early stages before it interacts with the user’s files. By utilizing a Cuckoo sandbox with Process Monitor, I can generate a detailed report of system activities from which ransomware behavior is analyzed. This model also keeps a record of file access rates and other file-related details in order to track potentially malicious behavior. In this paper, I demonstrate the ability of the model to identify Ransomware by providing a training set that consist of known ransomware families and samples listed on VirusTotal.
Inhibition of BMP Receptor Synthesis by Antisense Oligonucleotides Attenuates OP-1 Action in Primary Cultures of Fetal Rat Calvaria Cells (1998)

Osteogenic protein-1 (OP-1 or bone morphogenetic protein-7 [BMP-7]) stimulates osteoblast differentiation in vitro and induces bone formation in vivo. BMPs exert their effects through complex formation with a heterodimeric receptor composed of a type I and a type II polypeptide. In the present study, mRNAs for three BMP subtype I receptors (ActR-I, BMPR-IA, and BMPR-IB) and one BMPR-II receptor were detected by Northern analysis in two human osteosarcoma cell lines (SaOS-2 and TE85) and in the primary cultures of fetal rat calvaria (FRC) cells. OP-1 affected the steady-state mRNA levels of these receptors differently among these cell types. To study the role of each receptor type in OP-1 action in FRC cells, receptor synthesis was inhibited by antisense oligonucleotides. Inhibition of receptor synthesis was confirmed by immunoprecipitation of radiolabeled cellular proteins with specific antibodies. The osteogenic action of OP-1 was measured by alkaline phosphatase (ALP) activity and mineralized bone nodule formation in FRC cells. Results showed that inhibition of synthesis of a single subtype I receptor alone did not affect significantly the OP-1-stimulated ALP activity. Inhibition of BMPR-II synthesis reduced the OP-1-stimulated ALP activity by about 50%. Inhibition of synthesis of any one of the type I receptor plus the BMPR-II receptor did not reduce the OP-1-stimulated ALP activity significantly beyond that observed by inhibition of BMPR-II alone. Under these conditions, nodule formation was affected similarly, thus supporting the observations made with the ALP measurements. The present results suggest that the ActR-I, BMPR-IA, and BMPR-IB receptors and the BMPR-II receptor are expressed and functional for OP-1 in FRC cells and that regulation of synthesis of these receptors may be a mechanism by which a specific cell type responds to OP-1. The turnover rate of these receptor proteins might be relatively long and another type II receptor(s) for OP-1 might be functional in FRC cells.
Handbook of heterocyclic chemistry (2011)

Heterocyclic compounds play a vital role in the metabolism of living cells. Their practical applications range from extensive clinical use to fields as diverse as agriculture, photography, biocide formulation and polymer science. Written by leading scholars and industry experts, the Handbook of Heterocyclic Chemistry is thoroughly updated with over 50% new content. It has been rewritten with a new expanded author team, who have carefully distilled essential information on the reactivity, structure and synthesis of heterocycles from the 2008 major reference work Comprehensive Heterocyclic Chemistry III. To bring the work up to date the author team have also added new synthetic examples and structures, key applications and new references from 2008-2010. Contains more than 1500 clearly drawn structures and reactions. The highly systematic coverage given to the subject makes this one of the most authoritative single-volume accounts of modern heterocyclic chemistry available and should be useful reference for those teaching a heterocyclic course. -Covers the structure, reactivity and synthesis of all heterocyclic compounds as distilled from the larger 15-volume reference work -Saves researchers time when they require important information on heterocycles--speeding them to thousands of clearly drawn chemical structures and pertinent reviews by leading experts -Features 35% new material to compliment the completely revised text
Effects of Growth Hormone–Releasing Hormone on Cognitive Function in Adults With Mild Cognitive Impairment and Healthy Older Adults (2012)

clinicaltrials.gov Identifier: NCT00257712
Detection of HLA-G by a specific sandwich ELISA using monoclonal antibodies G233 and 56B (2002)

Human leukocyte antigen (HLA)-G, which is mainly expressed at the maternal-fetal interface, may play a role in the immune tolerance of the semi-allogenic fetus by the mother. Functional studies have shown that HLA-G is indeed a potential modulator of different immune responses. Therefore, it is of interest to study the level of expression of soluble HLA-G in several biological fluids derived from women with and without fertility problems. In order to measure soluble HLA-G, a reliable and sensitive HLA-G specific sandwich ELISA is required. Here, we describe such an ELISA in which G233 is used as the coating antibody and 56B as the detecting antibody. In comparison with two other assays, this assay shows highest responses to recombinant HLA-G and native HLA-G in primary trophoblast culture supernatant and high responses to HLA-G in amniotic fluid. No HLA-G in follicular fluid or preimplantation embryo culture supernatant could be detected.
Artificial lotus leaf structures from assembling carbon nanotubes and their applications in hydrophobic textiles (2006)

Artificial lotus leaf structures were fabricated on cotton substrates via the controlled assembly of carbon nanotubes onto the surface of cotton substrates. Both pristine carbon nanotubes (CNTs) and surface modified carbon nanotubes (PBA-g-CNTs) were used as building blocks to biomimic the surface microstructures of lotus leaves at the nanoscale. Cotton fabrics, which otherwise have perfect water absorbabilities, have been endowed with super-hydrophobic properties—water contact angles greater than 150° were measured. The method provides a bionic route to create hydrophobic textiles. Furthermore, considering the novel mechanical and electric properties of carbon nanotubes, these carbon nanotubes coated cotton fabrics will find potential application in sensing, conducting and special textiles.