gebhart/patrepeval huggingface dataset:
Chlamydial Infection Induces Pathobiotype-Specific Protein Tyrosine Phosphorylation in Epithelial Cells (2005)

Members of the genus Chlamydia are strict obligate intracellular pathogens that exhibit marked differences in host range and tissue tropism despite sharing a remarkable level of genomic synteny. These pathobiotype differences among chlamydiae are also mirrored in their early interactions with cultured mammalian host cells. Chlamydial attachment and entry is known to trigger protein tyrosine phosphorylation. In this study, we examined the kinetics and pattern of protein tyrosine phosphorylation induced by infection with a comprehensive collection of chlamydial strains exhibiting diversity in host, tissue, and disease tropisms. We report new findings showing that protein tyrosine phosphorylation patterns induced by infection directly correlate with the pathobiotype of the infecting organism. Patterns of protein tyrosine phosphorylation were induced following early infection that unambiguously categorized chlamydial pathobiotypes into four distinct groups: (i) Chlamydia trachomatis trachoma biovars (serovars A to H), (ii) C. trachomatis lymphogranuloma venereum biovars (serovars L1 to L3), (iii) C. muridarum, and (iv) C. pneumoniae and C. caviae. Notably, chlamydia-infected murine and human epithelial cells exhibited the same protein tyrosine phosphorylation patterns; this is indirect evidence suggesting that the phosphorylated protein(s) is of chlamydial origin. If our hypothesis is correct, these heretofore-uncharacterized proteins may represent a novel class of bacterial molecules that influence pathogen-host range or tissue tropism.
Immunotherapy of a murine ovarian carcinoma with Corynebacterium parvum and specific heteroantiserum. I. Activation of peritoneal cells to mediate antibody-dependent cytotoxicity. (1979)

Immunotherapy with a combination of Corynebacterium parvum and specific heteroantiserum is significantly more effective than treatment with either single agent in prolonging the survival of mice that have recevied an i.p. injection of syngeneic murine ovarian carcinoma (MOT) cells. Invitro, a combination of C. parvum-activated peritoneal cells and specific heteroantiserum has proven significantly more effective than either single component in destroying 51Cr-labeled MOT cells in the absence of complement. Activation of peritoneal cells to produce lysis of tumor in the presence specific antiserum peaked 3 to 7 days after a single injection of C. parvum and declined to baseline over 3 to 4 weeks. With repeated i.p. injections of C. parvum at appropriate intervals, activation of peritoneal cells could be prolonged and augmented. Among the routes tested, only i.p. administration of C. parvum was effective, although activation of peritoneal cells for cooperation with heteroantiserum was observed over a broad range of i.p. dosage (0.45 to 4.20 mg). These data suggest that the administration of C. parvum by appropriate doses, routes, and schedules can attract and activate a population of peritoneal effectors that mediate antibody-dependent cytotoxicity more effectively than resident peritoneal cells.
Templating methods for preparation of porous structures (2005)

This article features recent research progress towards various templating methods for preparing porous structures with prescribed structural, surface, and morphological properties. It should be noted that this is not a comprehensive review article as such reviews are available in the literature. Instead, on the basis of our own research results we attempt to provide a brief summary of recent demonstrations of how templating strategies can be used to prepare porous architectures with desired properties to meet the specific requirements of new technological applications, such as environmentally friendly technology, nanotechnology, tissue engineering, and photonics.
Imatinib Mesylate — Uncovering a Fast Track to Adaptive Immunity (2006)

Gastrointestinal stromal tumors have been shown to respond to imatinib mesylate in a manner dependent on immune-cell function. A new type of immune cell that shares characteristics with both natural killer cells and dendritic cells seems to mediate this response.
Protein Folding Simulation by Particle Swarm Optimization (2007)

This work introduces Particle Swarm Optimization (PSO) to protein structure prediction as a new field of application. Finding the global optimum in the free energy landscape of protein structures is a challenging, non-trivial task and has been subject of research for decades, resulting in many different approaches and methods until today. Here we show that a standard implementation of PSO is capable of optimizing backbone geometries and generating good solutions in refolding studies, yielding near native structures for two small sample proteins. We present a straightforward approach to include secondary structure information in the optimization process and show that results improve. Finally, a first predicted structure from ab initio folding by PSO is shown where native topology could be captured with a basic energy function, giving a promising outlook on future research.
Elliptic Curve Diffie-Hellman Random Keys Using Artificial Neural Network and Genetic Algorithm for Secure Data over Private Cloud (2016)

Background: Achieving secure communication and safeguarding sensitive data from unauthorized access over public networks are major concerns in cloud servers. Unique and random encryption keys are vital for data security. Methodology: A public key cannot be derived from a random key generator because it can allow middlemen to attack the network easily and access sensitive data. Hence, to secure both data and keys, a system should be used to generate intermediate encryption and decryption keys that are unique, mixed and random. This study investigates how much time is needed to encrypt and decrypt the Elliptic Curve Diffie-Hellman (ECDH) key between cloud users and cloud servers, which are simulated as GUI tools. Results: Findings showed that the time consumed increases as the number of text files grows. Conclusion: Thus, this experiment demonstrates good improvement in time when an Artificial Neural Network (ANN) is applied to ECDH key exchanges. When the developed ECDH with ANN is applied to genetic algorithms, a high efficiency in terms of the time consumed, performance and accuracy is achieved.
Human T-lymphocytes targeted against an established human ovarian carcinoma with a bispecific F(ab')2 antibody prolong host survival in a murine xenograft model. (1991)

A bispecific F(ab')2 fragment with anti-CD3 and antitumor specificity was used to target activated human peripheral blood lymphocytes (PBL) against OVCAR-3 human ovarian carcinoma cells growing i.p. in athymic mice. Mice were given injections of OVCAR-3 cells on day 0 and treated with i.p. injections of activated PBL coated with the [anti-CD3 (TR66) x antitumor (MOv18)] bispecific F(ab')2 on day 4, using an approximate effector:target ratio of 1:1. Treatment was evaluated for the ability either to block tumor growth at 15 days or to prolong survival of tumor-bearing mice. After 15 days, the incidence of mice with tumor growth was 20% among those given PBL coated with bispecific F(ab')2, whereas the incidence among mice untreated or treated with PBL alone or PBL with either parental antibody ranged from 80 to 94%. The mean survival time of tumor-bearing mice treated with PBL and bispecific F(ab')2 was 104 days, which was 3.5 times that of untreated mice and twice that of mice given PBL alone or PBL with either parental antibody. These results provide support for the concept that treatment of ovarian cancer patients with targeted T-cells could prove beneficial.
Protein Kinase Inhibitors as a Therapeutic Modality (2003)

Most of the signal transduction pathways are mediated by protein kinases regulating every aspect of cell function. Mutations which deregulate their expression or their function or both result in cancers. Therefore, protein kinase inhibitors has become the focus of development of new therapies for cancer. Almost all 120 protein tyrosine kinases are involved in signaling, whereas only a handful of Ser/Thr kinases are involved. Thus, most of the effort is directed toward the development of tyrosine phosphorylation inhibitors. The success of Gleevec in the treatment of chronic myeloid leukemia and of Iressa for lung cancer validates the approach.
The Base16, Base32, and Base64 Data Encodings (2006)

This document describes the commonly used base 64, base 32, and base 16 encoding schemes. It also discusses the use of line-feeds in encoded data, use of padding in encoded data, use of non-alphabet characters in encoded data, use of different encoding alphabets, and canonical encodings.
VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation in Arabidopsis (2010)

The Arabidopsis thaliana NAC domain transcription factor VASCULAR-RELATED NAC-DOMAIN7 (VND7) acts as a master regulator of xylem vessel differentiation. To understand the mechanism by which VND7 regulates xylem vessel differentiation, we used a yeast two-hybrid system to screen for proteins that interact with VND7 and identified cDNAs encoding two NAC domain proteins, VND-INTERACTING1 (VNI1) and VNI2. Binding assays demonstrated that VNI2 effectively interacts with VND7 and the VND family proteins, VND1-5, as well as with other NAC domain proteins at lower affinity. VNI2 is expressed in both xylem and phloem cells in roots and inflorescence stems. The expression of VNI2 overlaps with that of VND7 in elongating vessel precursors in roots. VNI2 contains a predicted PEST motif and a C-terminally truncated VNI2 protein, which lacks part of the PEST motif, is more stable than full-length VNI2. Transient reporter assays showed that VNI2 is a transcriptional repressor and can repress the expression of vessel-specific genes regulated by VND7. Expression of C-terminally truncated VNI2 under the control of the VND7 promoter inhibited the normal development of xylem vessels in roots and aerial organs. These data suggest that VNI2 regulates xylem cell specification as a transcriptional repressor that interacts with VND proteins and possibly also with other NAC domain proteins.
Utilization of C-C chemokine receptor 5 by the envelope glycoproteins of a pathogenic simian immunodeficiency virus, SIVmac239 (1997)

We examined chemokine receptors for the ability to facilitate the infection of CD4-expressing cells by viruses containing the envelope glycoproteins of a pathogenic simian immunodeficiency virus, SIVmac239. Expression of either human or simian C-C chemokine receptor CCR5 allowed the SIVmac239 envelope glycoproteins to mediate virus entry and cell-to-cell fusion. Thus, distantly related immunodeficiency viruses such as SIV and the primary human immunodeficiency virus type 1 isolates can utilize CCR5 as an entry cofactor.
Replicative Fitness of Protease Inhibitor-Resistant Mutants of Human Immunodeficiency Virus Type 1 (1999)

The relative replicative fitness of human immunodeficiency virus type 1 (HIV-1) mutants selected by different protease inhibitors (PIs) in vivo was determined. Each mutant was compared to wild type (WT), NL4-3, in the absence of drugs by several methods, including clonal genotyping of cultures infected with two competing viral variants, kinetics of viral antigen production, and viral infectivity/virion particle ratios. A nelfinavir-selected protease D30N substitution substantially decreased replicative capacity relative to WT, while a saquinavir-selected L90M substitution moderately decreased fitness. The D30N mutant virus was also outcompeted by the L90M mutant in the absence of drugs. A major natural polymorphism of the HIV-1 protease, L63P, compensated well for the impairment of fitness caused by L90M but only slightly improved the fitness of D30N. Multiply substituted indinavir-selected mutants M46I/L63P/V82T/I84V and L10R/M46I/L63P/V82T/I84V were just as fit as WT. These results indicate that the mutations which are usually initially selected by nelfinavir and saquinavir, D30N and L90M, respectively, impair fitness. However, additional mutations may improve the replicative capacity of these and other drug-resistant mutants. Hypotheses based on the greater fitness impairment of the nelfinavir-selected D30N mutant are suggested to explain observations that prolonged responses to delayed salvage regimens, including alternate PIs, may be relatively common after nelfinavir failure.
An improved version of the view factor method for simulating inertial confinement fusion hohlraums (1996)

A modified version of the view factor equations is proposed which improves the accuracy of the description of temporal effects in energy redistribution by thermal radiation in cavities driven by power pulses typical for inertial confinement fusion (ICF). The method is applied to analyze the process of radiative symmetrization in the simplest type of closed cylindrical hohlraums heated by two x-ray rings on the sidewall of the hohlraum case. Such hohlraums may be used in certain types of ICF targets driven by ion beams.
Lentiviral gene transfer into human and murine hematopoietic stem cells: size matters (2016)

Contemporary biomedical research increasingly depends on techniques to induce or to inhibit expression of genes in hematopoietic stem cells (HSCs) or other primary cells to assess their roles on cellular processes including differentiation, apoptosis and migration. Surprisingly little information is available to optimize lentiviral transduction of HSCs. We have therefore carefully optimized transduction of murine and human HSCs by optimizing vector design, serum-free virus production and virus quantitation. We conclude that the viral RNA length, even in relatively small vectors, is an important factor affecting the lentiviral gene transfer on the level of both the virus production and the cellular transduction efficiency. Efficient transfer of large gene sequences into difficult-to-transduce primary cells will benefit from reducing the lentiviral construct size.
Gramicidin S biosynthesis operon containing the structural genes grsA and grsB has an open reading frame encoding a protein homologous to fatty acid thioesterases (1989)

The DNA sequence of about 5.9 kilobase pairs (kbp) of the gramicidin S biosynthesis operon (grs) was determined. Three open reading frames were identified; the corresponding genes, called grsT, grsA, and grsB, were found to be organized in one transcriptional unit, not two as previously reported (M. Krause and M. A. Marahiel, J. Bacteriol. 170:4669-4674, 1988). The entire nucleotide sequence of grsA, coding for the 126.663-kilodalton gramicidin S synthetase 1, grsT, encoding a 29.191-kilodalton protein of unknown function, and 732 bp of the 5' end of grsB, encoding the gramicidin S synthetase 2, were determined. A single initiation site of transcription 81 bp upstream of the grsT initiation condon GTG was identified by high-resolution S1 mapping studies. The sequence of the grsA gene product showed a high degree of homology to the tyrocidine synthetase 1 (TycA protein), and that of grsT exhibited a significant degree of homology to vertebrate fatty acid thioesterases.
Loss of MHC class II gene and protein expression in diffuse large B-cell lymphoma is related to decreased tumor immunosurveillance and poor patient survival regardless of other prognostic factors: a follow-up study from the Leukemia and Lymphoma Molecular Profiling Project (2004)

The Leukemia and Lymphoma Molecular Profiling Project recently published results from DNA microarray analyses of 240 diffuse large B-cell lymphomas (DLBCLs). Four gene expression "signatures" were identified as correlated with patient outcome, including the major histocompatibility complex (MHC) class II genes (eg, HLA-DRA) which correlated with better survival. We further analyzed the effects of HLA-DRA on survival and correlated gene expression with protein status and tumor-infiltrating lymphocytes. The 5-year overall survival was 24% in the lowest 10% of HLA-DRA expression, 37% in the 10% to 25% group, 50% in the 25% to 50% group, and 55% for patients in the highest 50%. Further analysis demonstrated that the hazard ratio of death was a nonlinear function of HLA-DRA expression. Adjustment for the International Prognostic Index did not alter the impact of HLA-DRA on survival. Other MHC class II genes were found to predict survival similarly. Microarray HLA-DRA expression correlated with the presence or absence of human leukocyte antigen-DR (HLA-DR) protein in 20 of 22 cases assessed. Fewer tumor-infiltrating CD8(+) T cells were detected in MHC class II-negative cases compared with positive cases (2.8% versus 11.0%; P =.001), supporting the hypothesis that loss of tumor immunosurveillance has a devastating effect on patient outcome in DLBCL.
Oxidative Stress-Activated Zinc Cluster Protein Stb5 Has Dual Activator/Repressor Functions Required for Pentose Phosphate Pathway Regulation and NADPH Production (2006)

In Saccharomyces cerevisiae, zinc cluster protein Pdr1 can form homodimers as well as heterodimers with Pdr3 and Stb5, suggesting that different combinations of these proteins may regulate the expression of different genes. To gain insight into the interplay among these regulators, we performed genome-wide location analysis (chromatin immunoprecipitation with hybridization to DNA microarrays) and gene expression profiling. Unexpectedly, we observed that Stb5 shares only a few target genes with Pdr1 or Pdr3 in rich medium. Interestingly, upon oxidative stress, Stb5 binds and regulates the expression of most genes of the pentose phosphate pathway as well as of genes involved in the production of NADPH, a metabolite required for oxidative stress resistance. Importantly, deletion of STB5 results in sensitivity to diamide and hydrogen peroxide. Our data suggest that Stb5 acts both as an activator and as a repressor in the presence of oxidative stress. Furthermore, we show that Stb5 activation is not mediated by known regulators of the oxidative stress response. Integrity of the pentose phosphate pathway is required for the activation of Stb5 target genes but is not necessary for the increased DNA binding of Stb5 in the presence of diamide. These data suggest that Stb5 is a key player in the control of NADPH production for resistance to oxidative stress.
Immune Response to Capsular Polysaccharide and Surface Proteins ofStreptococcus pneumoniaein Patients with Invasive Pneumococcal Disease (2003)

The immune response to pneumococcal capsular polysaccharides (CPSs) and to the pneumococcal surface proteins cell wall-associated serine proteinase A (PrtA), pneumococcal surface protein A (PspA), and Streptococcus pneumoniae pullulanase A was evaluated in 45 patients with invasive pneumococcal disease compared with healthy adults. In serum from patients with meningitis and pneumonia, CPS antibody levels were low, compared with healthy adults; antibody levels did not differ between groups and did not change between phases. Levels of immunoglobulin G directed against the investigated pneumococcal surface proteins in patients with invasive pneumococcal disease were in the same range as in healthy adults. However, median PrtA and PspA antibody levels tended to increase during early convalescent phase. Low levels of CPS antibody, rather than of antibodies directed against the pneumococcal surface proteins, may predispose to invasive pneumococcal infection.
Micromechanical "hollow-disk" ring resonators (2004)

A vibrating polysilicon micromechanical "hollow-disk" ring resonator obtained by removing quadrants of material from a solid disk resonator, but purposely leaving intact beams of material to non-intrusively support the structure, has been demonstrated in several vibration modes spanning frequencies from HF (24.4 MHz), to VHF (72.1MHz), to UHF (1.169 GHz), with Q's as high as 67,519, 48,048, and 5,846, respectively. Furthermore, the use of notched support attachments closer to actual extensional ring nodal points raises the Q to 14,603 at 1.2 GHz, which is the highest yet achieved past 1 GHz, and which clearly illustrates the utility of notching for substantially higher Q. At 1.2 GHz, a combination of high Q and larger capacitive transducers allows the notched version to achieve an R/sub x/ of only 282 k/spl Omega/, which is 12X smaller than achieved by previous pure polysilicon surface-micromachined solid disk resonators in the GHz range.
Clinical value of monitoring eosinophil activity in asthma. (1995)

To evaluate the use of eosinophil cationic protein (ECP) in monitoring disease activity in childhood asthma, serum ECP in 175 asthmatic children was assessed. Forty five patients with cystic fibrosis, 23 with lower respiratory tract infections (LRTI), and 87 healthy children were used as controls. Serum ECP concentrations (34.3 micrograms/l v 9.8 micrograms/l) were significantly higher in children with bronchial asthma than in healthy control subjects. In symptomatic patients with asthma serum ECP concentrations were increased compared with those from asymptomatic patients (40.2 micrograms/l v 14.4 micrograms/l), irrespective of treatment modalities (that is steroids, beta 2 agonists, or sodium cromoglycate). Moreover, atopy and infection appeared to be factors enhancing eosinophil activity in bronchial asthma as measured by serum ECP (58.4 micrograms/l v 36.8 micrograms/l and 68.8 micrograms/l v 42.2 micrograms/l, respectively). In a longitudinal trial, antiasthmatic treatment modalities (that is steroids) reduced serum ECP within four weeks (42.2 micrograms/l v 19.0 micrograms/l). In conclusion, the data indicate that (1) eosinophils also play a central part in childhood asthma; (2) serum concentrations of ECP in children with bronchial asthma are related to the disease severity and may thus be used for monitoring inflammation in childhood asthma; (3) eosinophil activity appears to be enhanced by atopy and infection; and (4) longitudinal measurements of serum ECP concentrations may be useful for optimising anti-inflammatory treatment in children with bronchial asthma.
Detecting stepping stones (2000)

One widely-used technique by which network attackers attain anonymity and complicate their apprehension is by employing stepping stones: they launch attacks not from their own computer but from intermediary hosts that they previously compromised. We develop an efficient algorithm for detecting stepping stones by monitoring a site&amp;apos;s Internet access link. The algorithm is based on the distinctive characteristics (packet size, timing) of interactive traffic, and not on connection contents, and hence can be used to find stepping stones even when the traffic is encrypted. We evaluate the algorithm on large Internet access traces and find that it performs quite well. However, the success of the algorithm is tempered by the discovery that large sites have many users who routinely traverse stepping stones for a variety of legitimate reasons. Hence, stepping-stone detection also requires a significant policy component for separating allowable stepping-stone pairs from surreptitious access. 1 ...