gebhart/patrepeval huggingface dataset:
Mapping Protein Domains Involved in Macromolecular Interactions: A Novel Protein Footprinting Approach (1994)

A novel direct approach, analogous to DNA footprinting, for mapping protein domains involved in macromolecular interactions is presented in this paper and applied to cAMP receptor protein (CRP) interactions with the allosteric ligand (cAMP) and DNA. In this approach, a protein-macromolecule complex is subjected to a nonspecific cleavage by Fe-EDTA. The cleavage products are resolved by SDS-PAGE and transferred to a PVDF membrane. Transferred polypeptides are visualized by immunostaining with antibodies specific to the N-terminal peptide of the protein. The mobility of the bands visualized in such a way is directly proportional to the distance of the cleavage sites from the N-terminus, and thus the positions of the sites protected from cleavage by a bound macromolecule can be determined. Thus, protein domains involved in macromolecular interactions can be mapped. In the case of CRP, the cleavage conditions were established which resulted in, on the average, less than one cleavage event/protein molecule and which preserved satisfactory levels of protein and DNA activity. When applied to CRP-DNA interactions, the protein footprinting approach correctly identified domains of CRP that were known to be involved in the recognition of DNA. The obtained results showed also that the binding of CRP to the DNA binding site perturbed the region of CRP involved in intersubunit interactions. An allosteric ligand (cAMP) appeared to perturb the same region of CRP. This stresses out the importance of intersubunit interactions in cAMP modulation of protein DNA binding affinity. The protein footprinting methodology presented in this paper should be broadly generalizable to any protein-macromolecule system.
Synthesis of New Mero- and Asymmetrical Pyrazolo-Monomethine Cyanine Dyes. (1977)

Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt, A.R.E. <em>Manuscript received 29 November 1976, accepted 17 May 1977</em> New isatylidine mero cyanioe dyes (II) were prepared through the reaction of lsatin (I) With 2-methyl quaterrnary salts in presence of a basic catalyst. Interaction of 3-methyl-1-phenyl-5-pyrazolone derivatives (lll) with \(\alpha\)-picoline- and quioaldine-ethiodides in presence of triethylamine afforded the asymmetrical pyrazolo-2'-monomethioe cyanioes (V). Meanwhile, the use of piperldine gave the aldol intermediate (IV), which dehydrated to the corresponding cyanioe dye (V). Structural configurations were identified by i.r. and v.s. spectral determination.
Immune Reconstitution/Immunocompetence in Recipients of Kidney Plus Hematopoietic Stem/Facilitating Cell Transplants (2015)

Nineteen subjects have more than 18 months' follow-up in a phase IIb tolerance protocol in HLA-mismatched recipients of living donor kidney plus facilitating cell enriched hematopoietic stem cell allografts (FCRx). Reduced intensity conditioning preceded a kidney allograft, followed the next day by FCRx. Twelve have achieved stable donor chimerism and have been successfully taken off immunosuppression (IS). We prospectively evaluated immune reconstitution and immunocompetence. Return of CD4 and CD8 T central and effector memory cell populations was rapid. T-cell receptor (TCR) Excision Circle analysis showed a significant proportion of chimeric cells produced were being produced de novo. The TCR repertoires posttransplant in chimeric subjects were nearly as diverse as pretransplant donors and recipients, and were comparable to subjects with transient chimerism who underwent autologous reconstitution. Subjects with persistent chimerism developed few serious infections when off IS. The majority of infectious complications occurred while subjects were still on conventional IS. BK viruria and viremia resolved after cessation of IS and no tissue-invasive cytomegalovirus infections occurred. Notably, although 2 of 4 transiently or nonchimeric subjects experienced recurrence of their underlying autoimmune disorders, none of the chimeric subjects have, suggesting that self-tolerance is induced in addition to tolerance to alloantigen. No persistently chimeric subject has developed donor-specific antibody, and renal function has remained within normal limits. Patients were successfully vaccinated per The American Society for Blood and Marrow Transplantation guidelines without loss of chimerism or rejection. Memory for hepatitis vaccination persisted after transplantation. Chimeric subjects generated immune responses to pneumococcal vaccine. These data suggest that immune reconstitution and immunocompetence are maintained in persistently chimeric subjects.
Cerebral Blood Volume Calculated by Dynamic Susceptibility Contrast-Enhanced Perfusion MR Imaging: Preliminary Correlation Study with Glioblastoma Genetic Profiles (2013)

We found that glioblastomas with aggressive genetic alterations tended to have a high nTBV in the present study. Thus, we believe that DSC-enhanced perfusion MR imaging could be helpful in predicting genetic alterations that are crucial in predicting the prognosis of and selecting tailored treatment for glioblastoma patients.
Endophytes and their role in phytoremediation (2012)

Many endophytes have been found to be resistant to heavy metals and/or capable of degrading organic contaminants, and endophyte-assisted phytoremediation has been documented as a promising technology for in situ remediation of contaminated soils. During the phytoremediation of heavy metals, the heavy-metal-resistant endophytes can enhance plant growth, decrease metal phytotoxicity, and affect metal translocation and accumulation in plants. For the phytoremediation of organic contaminants, endophytes can produce various enzymes to degrade organic contaminants and reduce both the phytotoxicity and evapotranspiration of volatile contaminants. This paper reviews the diversity of contaminant-resistant/degrading endophytes and their role in phytoremediation and discusses some issues that have been raised surrounding this area of research.
The HLA-B14 peptide binding site can accommodate peptides with different combinations of anchor residues. (1994)

Most peptides that bind to a particular major histocompatibility complex class I molecule share amino acid residues important for binding at one or two positions. Sequence analyses of peptides bound to HLA-B14 revealed at least four candidates for these so-called anchor residues: Arg at P2, Tyr at P3, Arg at P5, and Leu at P9. Combinations of any three of these amino acids sufficed for binding to HLA-B14 in vitro. Using this information, we identified an antigenic peptide critical for cytotoxic T lymphocyte recognition of virus-infected cells. Molecular models of HLA-B14 peptide complexes were constructed to investigate how the potential anchor residues might function. By using binding data to calculate the contribution to binding of each amino acid at anchor positions and predicting the stability of all possible nonapeptide complexes that could be formed from antigenic proteins, we estimate that three known antigenic nonapeptides are in the highest affinity cohort of peptides. Thus, even when multiple combinations of anchor residues contribute to binding, antigenic peptides are routinely identifiable.
Structural and Functional Heterogeneity of Nuclear Bodies (1999)

The nuclear body is a cellular structure that appears to be involved in the pathogenesis of acute promyelocytic leukemia and viral infection. In addition, the nuclear body is a target of autoantibodies in patients with the autoimmune disease primary biliary cirrhosis. Although the precise function of the nuclear body in normal cellular biology is unknown, this structure may have a role in the regulation of gene transcription. In a previous investigation, we identified a leukocyte-specific, gamma interferon (IFN-gamma)-inducible autoantigen designated Sp140. The objectives of the present study were to investigate the cellular location of Sp140 with respect to the nuclear-body components PML and Sp100 and to examine the potential role of Sp140 in the regulation of gene transcription. We used adenovirus-mediated gene transfer to express Sp140 in human cells and observed that the protein colocalized with PML and Sp100 in resting cells and associated with structures containing PML during mitosis. In cells infected with the adenovirus expressing Sp140 and incubated with IFN-gamma, the number of PML-Sp100 nuclear bodies per cell increased but immunoreactive Sp140 was not evenly distributed among the nuclear bodies. Sp140 associated with a subset of IFN-gamma-induced PML-Sp100 nuclear bodies. To examine the potential effect of Sp140 on gene transcription, a plasmid encoding Sp140 fused to the DNA-binding domain of GAL4 was cotransfected into COS cells with a chloramphenicol acetyltransferase (CAT) reporter gene containing five GAL4-binding sites and a simian virus 40 enhancer region. The GAL4-Sp140 fusion protein increased the expression of the reporter gene. In contrast, Sp100 fused to the GAL4 DNA-binding domain inhibited CAT activity in transfected mammalian cells. The results of this study demonstrate that Sp140 associates with a subset of PML-Sp100 nuclear bodies in IFN-gamma-treated cells and that Sp140 may activate gene transcription. Taken together, these observations suggest that the nuclear bodies within a cell may be heterogeneous with respect to both composition and function.
Paclitaxel (Taxol®) - a guide to administration (1996)

The introduction of a new chemotherapeutic agent has implications for nursing care. Paclitaxel (Taxol) chemotherapy is now being used throughout Europe for treatment of patients with ovarian cancer who have previously failed a platinum-containing chemotherapy regimen, and in many countries to treat metastatic breast cancer. Nurses need to be equipped to care for these patients receiving Paclitaxel. This paper introduces nurses to Paclitaxel, the history of its development, its mechanism of action, potential side-effects and administration. Paclitaxel's side-effects include hypersensitivity reactions, neutropaenia, peripheral neuropathy, asymptomatic bradycardia, alopecia, malaise, myalgias and arthralgias. Administration guidelines will be discussed because Paclitaxel leaches plasticizer from polyvinyl chloride (PVC) intravenous-giving sets normally used to administer chemotherapy, hence an alternative delivery system is required.
[A preliminary study on immune complexes in myasthenia gravis]. (1989)

The levels of circulating immune complex from 43 patients with myasthenia gravis (MG) and 50 normal controls were detected by using ELISA based on bovine conglutinin. The levels of circulating immune complex in MG patients were higher than those in normal controls (P less than 0.01). Although the levels of circulating immune complex in generalized type MG were higher than those in ocular type MG, the difference showed no statistically significant. It was found that the levels of circulating immune complex, both generalized type MG and ocular type MG, were higher than those in normal controls respectively (P less than 0.01).
High-Avidity CTL Exploit Two Complementary Mechanisms to Provide Better Protection Against Viral Infection Than Low-Avidity CTL (2001)

Previously, we observed that high-avidity CTL are much more effective in vivo than low-avidity CTL in elimination of infected cells, but the mechanisms behind their superior activity remained unclear. In this study, we identify two complementary mechanisms: 1) high-avidity CTL lyse infected cells earlier in the course of a viral infection by recognizing lower Ag densities than those distinguished by low-avidity CTL and 2) they initiate lysis of target cells more rapidly at any given Ag density. Alternative mechanisms were excluded, including: 1) the possibility that low-avidity CTL might control virus given more time (virus levels remained as high at 6 days following transfer as at 3 days) and 2) that differences in efficacy might be correlated with homing ability. Furthermore, adoptive transfer of high- and low-avidity CTL into SCID mice demonstrated that transfer of a 10-fold greater amount of low-avidity CTL could only partially compensate for their decreased ability to eliminate infected cells. Thus, we conclude that high-avidity CTL exploit two complementary mechanisms that combine to prevent the spread of virus within the animal: earlier recognition of infected cells when little viral protein has been made and more rapid lysis of infected cells.
Targeting Clostridium difficile Surface Components to Develop Immunotherapeutic Strategies Against Clostridium difficile Infection (2018)

New therapies are needed to prevent and treat <i>Clostridium difficile</i> infection and to limit the rise in antibiotic resistance. Besides toxins, several surface components have been characterized as colonization factors and have been shown as immunogenic. This review will focus on passive and active immunization strategies targeting <i>C. difficile</i> surface components to combat <i>C. difficile</i>. Concerning passive immunization, the first strategies used antisera raised against the entire bacterium to prevent infection in the hamster model. Then, surface components such as the flagellin and the S-layer proteins were used for immunization and the passive transfer of antibodies was protective in animal models. Passive immunotherapy with polyvalent immunoglobulins was used in humans and bovine immunoglobulin concentrates were evaluated in clinical trials. Concerning active immunization, vaccine assays targeting surface components were tested mainly in animal models, mouse models of colonization and hamster models of infection. Bacterial extracts, spore proteins and surface components of vegetative cells such as cell wall proteins, flagellar proteins, and polysaccharides were used as vaccine targets. Vaccine assays were performed by parenteral and mucosal routes of immunization. Both gave promising results and pave the way to development of new vaccines.
The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population (1943)

Part 1. It is shown that in a large collection of Lepidoptera captured in Malaya the frequency of the number of species represented by different numbers of individuals fitted somewhat closely to a hyperbola type of curve, so long as only the rarer species were considered. The data for the commoner species was not so strictly `randomized', but the whole series could be closely fitted by a series of the logarithmic type as described by Fisher in Part 3. Other data for random collections of insects in the field were also shown to fit fairly well to this series. Part 2. Extensive data on the capture of about 1500 Macrolepidoptera of about 240 species in a light-trap at Harpenden is analysed in relation to Fisher's mathematical theory and is shown to fit extremely closely to the calculations. The calculations are applied first to the frequency of occurrence of species represented by different numbers of individuals--and secondly to the number of species in samples of different sizes from the same population. The parameter ` alpha ', which it is suggested should be called the `index of diversity', is shown to have a regular seasonal change in the case of the Macrolepidoptera in the trap. In addition, samples from two traps which overlooked somewhat different vegetation are shown to have ` alpha ' values which are significantly different. It is shown that, provided the samples are not small, ` alpha ' is the increase in the number of species obtained by increasing the size of a sample by e (2.718). A diagram is given (Fig. 8) from which any one of the values, total number of species, total number of individuals and index of diversity (alpha), can be obtained approximately if the other two are known. The standard error of alpha is also indicated on the same diagram. Part 3. A theoretical distribution is developed which appears to be suitable for the frequencies with which different species occur in a random collection, in the common case in which many species are so rare that their chance of inclusion is small. The relationships of the new distribution with the negative binomial and the Poisson series are established. Numerical processes are exhibited for fitting the series to observations containing given numbers of species and individuals, and for estimating the parameter alpha representing the richness in species of the material sampled; secondly, for calculating the standard error of alpha, and thirdly, for testing whether the series exhibits a significant deviation from the limiting form used. Special tables are presented for facilitating these calculations.
Noise in current-commutating CMOS mixers (1999)

A noise analysis of current-commutating CMOS mixers, such as the widely used CMOS Gilbert cell, is presented. The contribution of all internal and external noise sources to the output noise is calculated. As a result, the noise figure can be rapidly estimated by computing only a few parameters or by reading them from provided normalized graphs. Simple explicit formulas for the noise introduced by a switching pair are derived, and the upper frequency limit of validity of the analysis is examined. Although capacitive effects are neglected, the results are applicable up to the gigahertz frequency range for modern submicrometer CMOS technologies. The deviation of the device characteristics from the ideal square law is taken into account, and the analysis is verified with measurements.
Induction of Th1 response by dendritic cells pulsed with autologous melanoma apoptotic bodies. (2000)

MAB-pulsed DCs are capable of stimulating Th1-directed autologous effector T cells. Pulsing DCs with autologous MABs may be a novel approach in future DC-based immunotherapeutic trials.
Subjective Sexual Response to Testosterone Replacement Therapy Based on Initial Serum Levels of Total Testosterone (2006)

These preliminary data suggest that men with sexual symptoms of hypogonadism respond well to TRT across a wide range of initial TT values, including men with low-normal TT levels. These men may have low bioavailable levels of testosterone that are not reflected in TT values.
Facile synthesis of homogeneous artificial proteins (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFacile synthesis of homogeneous artificial proteinsKeith RoseCite this: J. Am. Chem. Soc. 1994, 116, 1, 30–33Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/ja00080a004https://doi.org/10.1021/ja00080a004research-articleACS PublicationsRequest reuse permissionsArticle Views1886Altmetric-Citations367LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The distinct leukocyte integrins of mouse spleen dendritic cells as identified with new hamster monoclonal antibodies. (1990)

Hybridoma fusions with hamster hosts were undertaken to generate mAbs to mouse spleen dendritic cells. Two mAb were obtained and used to uncover the distinct integrins of these APC. One, 2E6, bound a determinant common to all members of the CD11/CD18 family, most likely the shared 90 kD CD18 beta chain. 2E6 immunoprecipitated the characteristic beta 2 integrin heterodimers from lymphocytes (p180, 90; CD11a) and macrophages (p170,90; CD11b), but from dendritic cells, a p150,90 (presumably CD11c) integrin was the predominant species. 2E6 inhibited the binding function of the CD11a and CD11b integrins on B cells and macrophages in appropriate assays, but 2E6 exerted little or no inhibition on the clustering of dendritic cells to T cells early in primary MLR, suggesting a CD11/CD18-independent mechanism for this binding. The second mAb, N418, precipitated a 150, 90 kD heterodimer that shared the 2E6 CD18 epitope. This N418 epitope may be the murine homologue of the previously characterized human CD11c molecule, but the epitope was only detected on dendritic cells. N418 did not react with peritoneal macrophages, anti-Ig-induced spleen B blasts, or bulk lymph node cells. When used to stain sections of spleen, N418 stained dendritic cells in the T-dependent areas, much like anti-class II mAbs that were also generated in these fusions. In addition, N418 revealed nests of dendritic cells that punctuated the rim of marginal zone macrophages between red and white pulp. This localization positioned most dendritic cells at regions where arterial vessels and T cells enter the white pulp. We conclude that the p150, 90 heterodimer is the major beta 2 integrin of spleen dendritic cells, and we speculate that it may function to localize these APC at sites that permit access to the recirculating pool of resting T cells.
Design and performance evaluation of vertical shafts: rational shaft design method and verification of design method (1988)

Ground deformations around axisymmetric shafts cannot be determined with the design approaches currently available, which are mostly based on plasticity methods. The convergence–confinement method (usually applied to tunnels), with consideration of gravitational effects and the three-dimensional conditions near a shaft, is proposed as a tool to predict formation pressure on a shaft and radial ground displacements. It is shown that the behaviour of a shaft is governed by (1) the mode of yield initiation dominated by the in situ stress state and the soil strength parameters and (2) the extent of the yield zone that develops if wall displacements are allowed to occur during construction.Closed-form solutions are presented to approximate the pressure–displacement relationship for cohesionless and cohesive soils. Results from this approach compare well with those obtained by finite element analyses. The conventional design methods that provide the minimum support pressures required to maintain stability are not conservative. These pressures are generally less than those actually encountered if ground movements during construction are restricted with good ground control. Key words: shaft, design method, support, interaction, yielding, stress, displacement, earth pressure, arching.
Demodulated low frequency currents from electrosurgical procedures. (1984)

Low frequency currents produced incidental to electrosurgical procedures are usually only a minor threat unless they are coupled directly into the heart through a catheter or a thoracic surgical procedure. However, should the low frequency blocking capacitors in the electrosurgical generator fail in the conducting state, extremely dangerous low frequency currents of many milliamperes may flow into the patient. Even with properly functioning capacitors, low frequencies up to several milliamperes may be produced by some generators. The results of this study show that the coagulation mode of operation produces greater amounts of low frequency currents than the "pure cutting" mode at the same power setting. These results also demonstrate that the higher the generator power output, the higher the magnitude of the low frequency currents.