gebhart/patrepeval huggingface dataset:
Binding of <i>Clostridium difficile</i> Surface Layer Proteins to Gastrointestinal Tissues (2002)

Clostridium difficile is the etiological agent of antibiotic-associated diarrhea, a potentially serious condition frequently affecting elderly hospitalized patients. While tissue damage is primarily induced by two toxins, the mechanism of gut colonization, and particularly the role of bacterial adherence to the mucosa, remains to be clarified. Previous studies have shown binding of C. difficile whole cells to cultured cell lines and suggested the existence of multiple adhesins, only one of which has been molecularly characterized. In this paper, we have investigated tissue binding of C. difficile surface layer proteins (SLPs), which are the predominant outer surface components and are encoded by the slpA gene. The adherence of C. difficile to HEp-2 cells was studied by enzyme-linked immunosorbent assay and fluorescence-activated cell sorter analysis, which showed that antibodies to the high-molecular-weight (MW) SLP inhibited adherence. Immunohistochemical analysis of human gastrointestinal tissue sections revealed strong binding both to the surface epithelium lining the digestive cavities and to the subjacent lamina propria, while glands were negative. A similar pattern was observed in the mouse. By using purified recombinant SLPs, we show that binding is largely mediated by the high-MW SLP. By Western blotting analysis, we have identified two potential ligands of the C. difficile SLPs, one of which may be specific to the gut. By using purified extracellular matrix components immobilized on nitrocellulose, we also show SLP binding to collagen I, thrombospondin, and vitronectin, but not to collagen IV, fibronectin, or laminin. These results raise the possibility that the SLPs play a role both in the initial colonization of the gut by C. difficile and in the subsequent inflammatory reaction.
A method for measuring the activation volumes of fast reversible reactions. Ferric thiocyanate complex (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA method for measuring the activation volumes of fast reversible reactions. Ferric thiocyanate complexK. R. BrowerCite this: J. Am. Chem. Soc. 1968, 90, 20, 5401–5403Publication Date (Print):September 1, 1968Publication History Published online1 May 2002Published inissue 1 September 1968https://doi.org/10.1021/ja01022a012RIGHTS & PERMISSIONSArticle Views501Altmetric-Citations34LEARN 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 InReddit PDF (365 KB) Get e-Alertsclose Get e-Alerts
Comparison of Clinical and Microbiological Response to Treatment of<i>Clostridium difficile</i>–Associated Disease with Metronidazole and Vancomycin (2008)

In an observational study with a limited number of subjects, a majority of patients with C. difficile-associated disease responded to therapy with metronidazole or vancomycin. Failure with metronidazole treatment may be attributable to a slower and less consistent microbiological response than that with oral vancomycin treatment.
Killing of Trypanosomes by the Human Haptoglobin-Related Protein (1995)

African trypanosomes cause disease in humans and animals. Trypanosoma brucei brucei affects cattle but not humans because of its sensitivity to a subclass of human high density lipoproteins (HDLs) called trypanosome lytic factor (TLF). TLF contains two apolipoproteins that are sufficient to cause lysis of T. b. brucei in vitro. These proteins were identified as the human haptoglobin-related protein and paraoxonase-arylesterase. An antibody to haptoglobin inhibited TLF activity. TLF was shown to exhibit peroxidase activity and to be inhibited by catalase. These results suggest that TLF kills trypanosomes by oxidative damage initiated by its peroxidase activity.
Genetic engineering of immunotoxins. (1996)

Immunotoxins, composed of both targeting mechanisms and toxins, hold great promise for the treatment of some cancers and other pathological conditions. Research and manufacture of these drugs use various techniques of molecular biology, some of which are described in this article. A considerable amount of research has focused on ricin, a plant toxin, and its immunoconjugates. Areas currently under evaluation by our laboratory include structure-function studies based on mutational analysis, enhancement of intracellular trafficking, genetic fusion of the targeting and toxic moieties, and the expression of toxin in plant cell culture.
Nonhuman primates as models for studies of prostate specific antigen and prostatic diseases (2008)

Cynomolgus macaques and rhesus macaques are promising animal models for PSA biology studies.
Ruthenium Dihydride RuH<sub>2</sub>(PPh<sub>3</sub>)<sub>2</sub>((<i>R</i>,<i>R</i>)-cyclohexyldiamine) and Ruthenium Monohydride RuHCl(PPh<sub>3</sub>)<sub>2</sub>((<i>R</i>,<i>R</i>)-cyclohexyldiamine):  Active Catalyst and Catalyst Precursor for the Hydrogenation of Ketones and Imines (2000)

The new monohydride RuHCl(PPh3)2(R,R-cydn), with base added, and dihydride RuH2(PPh3)2(R,R-cydn), in the absence of base, catalyze the hydrogenation of a wide variety of ketones and some imines at 3 atm of H2 and 20 °C with high turnover numbers. The mechanism is thought to involve the concerted dihydrogen transfer from cis hydride and N−H groups to the substrate followed by heterolytic dihydrogen splitting.
米ヘリテージ財団R.フィッシャー上席研究員講演要旨--中国の兵器輸入および人民解放軍の近代化 (1999)

Thermostable enzymes are a field of growing interest in bioremediation, pharmaceuticals, food industry etc., due to their ability to catalyze bio reactions at high temperatures. This review aims to provide an overview on extremophiles with a special focus on thermophiles and enzymes produced from extremophilic bacteria. Novel thermostable catalysts, used in producing commercially important chemicals, are discussed in this review. Various classes of enzymes produced by microbes, synthesis of thermozymes and comparison with enzymes produced at optimal conditions are critically discussed. A detailed discussion on immobilized enzymes in comparisons with free enzymes, produced by extremozymes, is included. Different parameters which affect enzyme production are also discussed. The current industrial trends along with the future of biocatalysts in the production of chemicals using efficient methods are also discussed.
Embryonic lethality in mice homozygous for a targeted disruption of the N-myc gene. (1992)

The N-myc gene encodes a putative transcription factor that is thought to function in the regulation of gene expression during cell differentiation and/or growth. To examine the role of N-myc during development, we have used targeted mutagenesis in embryonic stem cells to produce a mouse line that carries an N-myc null allele. Mice homozygous for the mutation died between 10.5 and 12.5 days of gestation. Histological analysis of mutant embryos revealed that organs and tissues expected at these stages of development were present. However, multiple defects were observed, primarily in tissues and organs that normally express N-myc. In particular, mutant hearts were underdeveloped, often retaining the S-shape more typical of 9-day-old embryos. In addition, cranial and spinal ganglia were reduced in size and/or cellularity. Most of the noted defects were more consistent with a role of N-myc in proliferation of precursor populations than with a block in differentiation per se, at least at these early stages. These results demonstrate that N-myc plays an essential role during development and clearly confirm that N-myc has a physiological function that is distinct from that of the other myc-family genes.
Two types of extrajunctional L‐glutamate receptors in locust muscle fibres. (1976)

L-glutamate applied iontophoretically to the extrajunctional membrane of locust muscle produced a biphasic response, depolarization followed by hyperpolarization (i.e. DH-response). Applying L-glutamate and DL-ibotenate from multibarrel micropipettes allowed comparison of their extrajunctional responses. While glutamate produced a two component response, ibotenate produced a single component H-response. 2. The equilibrium values for the H-responses to L-glutamate and DL-ibotenate applied at the same extrajunctional site were very similar. The equilibrium value was 59-5 +/- 5-4 mV indicating an increased Cl- conductance. The H-response was reversed and abolished in Cl- free medium. Picrotoxin 10(-3) M selectively blocked the H-component of the DH-response in a reversible manner. 3. The possibility that the D- and H-responses arose from the activation of two distinct types of extrajunctional glutamate receptors was investigated. Desensitization of the glutamate H-response by ibotenate and vice versa indicated the presence of an extrajunctional H-receptor sensitive to glutamate and ibotenate and an extrajunctional D-receptor sensitive to glutamate and insensitive to ibotenate. The junctional depolarizing response to glutamate was insensitive to ibotenate. 4. The presence of junctionally occurring H-receptors could not be discounted, although, if present, they were not measurably activated by the excitatory transmitter. 5. Double logarithmic plots (coulomb dose vs. response) for the actions of glutamate and ibotenate on H-receptors had values of 0-75, indicating that both drugs act on the same receptors with similar mechanisms. The value for the action of glutamate on the D-receptors was 1-5. 6. While the extrajunctional D-receptors show analogies to the extrajunctional ACh receptors in vertebrate muscle, the significance of the extrajunctional H-receptors remains speculative.
Fibre Bragg gratings tuned and chirped using magneticfields (1997)

The authors report on the use of magnetic fields in conjunction with magnetostrictive materials for tuning and chirping optical fibre Bragg gratings. The Bragg wavelength shifts as a consequence of the strain induced in the fibre by a magnetostrictive rod when a magnetic field is applied. A tuning range of 1.1 nm has been achieved by a magnetic field of 103 mT and the grating has been chirped by applying non-uniform magnetic fields.
Adenocarcinoma of the Canine Prostate: Immunohistochemical Examination for Secretory Antigens (1988)

No AccessJournal of Urology1 Apr 1988Adenocarcinoma of the Canine Prostate: Immunohistochemical Examination for Secretory Antigens M. McEntee, W. Isaacs, and C. Smith M. McEnteeM. McEntee More articles by this author , W. IsaacsW. Isaacs More articles by this author , and C. SmithC. Smith More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)42674-7AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Adenocarcinoma of the Canine Prostate: Immunohistochemical Examination for Secretory Antigens." The Journal of Urology, 139(4), p. 878 © 1988 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 139Issue 4April 1988Page: 878 Advertisement Copyright & Permissions© 1988 by The American Urological Association Education and Research, Inc.MetricsAuthor Information M. McEntee More articles by this author W. Isaacs More articles by this author C. Smith More articles by this author Expand All Advertisement PDF downloadLoading ...
Interactive Character Animation using Simulated Physics (2011)

Physics simulation offers the possibility of truly responsive and realistic animation. Despite wide adoption of physics simulation for the animation of passive phenomena, such as rigid objects, fluids, cloths and rag-doll characters, commercial applications still resort to kinematics-based approaches for the animation of actively controlled characters. However, in recent years, research on interactive character animation using simulated physics has resulted in tremendous improvements in controllability, robustness, visual quality and usability. In this review, we present a structured evaluation of relevant aspects, approaches and techniques regarding interactive character animation using simulated physics, based on over two decades of research. We conclude by pointing out some open research areas and possible future directions.
Macromolecule-small molecule interactions. Strong binding and cooperativity in a model synthetic polymer (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMacromolecule-small molecule interactions. Strong binding and cooperativity in a model synthetic polymerIrving M. Klotz, Garfield P. Royer, and A. R. SloniewskyCite this: Biochemistry 1969, 8, 12, 4752–4756Publication Date (Print):December 1, 1969Publication History Published online1 May 2002Published inissue 1 December 1969https://pubs.acs.org/doi/10.1021/bi00840a015https://doi.org/10.1021/bi00840a015research-articleACS PublicationsRequest reuse permissionsArticle Views396Altmetric-Citations122LEARN 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
RF and Microwave Photonic techniques in biomedical applications (2009)

This invited paper addresses various "microwave photonics" techniques developed for biomedical applications. The first application is using RF photonics technique for calibration of ultrasound transducers operating at high-frequencies without spatial field averaging compromise. In particular a broadband fiber-optic based hydrophone probe is reported for measurements of acoustic fields at the frequencies up to 100 MHz. In another application of microwave photonics, tissue spectroscopy is performed using multi-wavelength absorption and scattering in near infrared. A high speed and high power laser driver is designed with a flat frequency response using RC speed up circuits in high power lasers. Phantom experiments are performed to extract optical parameters. Multi-frequency data fitting algorithm is performed to extract optical parameters of the phantom model simulating a breast tissue. The optical parameters (mua, mus') are extracted with a very good accuracy. These low cost techniques are replacement for other expensive sub-centimeter spatial resolution medical imaging methods.
Three-Dimensional Structure of the Fab′ Fragment of a Human Immunoglobulin at 2.8-Å Resolution (1973)

The structure of the Fab' fragment of a human myeloma immunoglobulin was determined by x-ray crystallographic analysis at 2.8-A resolution. The Fourier map of the electron density was correlated with the aminoacid sequence to obtain a three-dimensional model. Four globular subunits, which correspond to the homology regions of the light and heavy chains, are arranged in a tetrahedral configuration. These subunits closely resemble each other, sharing a basic pattern of polypeptide chain folding. In each subunit, long sequences of tightly packed, hydrogen bonded polypeptide chain run parallel to the major axis of the subunit. No helical conformation can be seen. Different patterns of interchain disulfide linkage and unusual intrachain disulfide bonds that have been observed in other immunoglobulins can be explained with this model. The regions of hypervariable sequences in the light and heavy chains occur at one end of the molecule, in close spatial proximity.
Supercoils in human dna (1975)

The three-dimensional structure of a double-stranded DNA molecule may be described by distinguishing the helical turns of the DNA duplex from any superhelical turns that might be superimposed upon the duplex turns. There are characteristic changes in the hydrodynamic properties of superhelical DNA molecules when they interact with intercalating agents. The hydrodynamic properties of nuclear structures released by gently lysing human cells are changed by intercalating agents in this characteristic manner. The characteristic changes are abolished by irradiating the cells with gamma-rays but may be restored by incubating the cells at 37 degrees C after irradiation. These results are interpreted as showing that human DNA is supercoiled. A model for the structure of the chromosome is suggested.
Ultralong Single-Crystal Metallic Ni<sub>2</sub>Si Nanowires with Low Resistivity (2007)

Ultralong, single-crystal Ni2Si nanowires sheathed with amorphous silicon oxide were synthesized on a large scale by a chemical vapor transport (CVT) method, using iodine as the transport reagent and Ni2Si powder as the source material. Structural characterization using powder X-ray diffraction, electron microscopy, and energy-dispersive spectroscopy shows that the nanowires have Ni2Si-SiOx core-shell structure with single-crystal Ni2Si core and amorphous silicon oxide shell. The oxide shell is electrically insulating and can be removed by HF etching. Four-terminal electrical measurements show that the single-crystal nanowire has extremely low resistivity of 21 muOmega.cm and is capable of supporting remarkably high failure current density >108 A/cm2. These unique Ni2Si nanowires are very attractive nanoscale building blocks for interconnects and fully silicided (FUSI) gate applications in nanoelectronics.
Impact of Estrogen Receptor β on Gene Networks Regulated by Estrogen Receptor α in Breast Cancer Cells (2006)

Two subtypes of the estrogen receptor (ER), ERalpha and ERbeta, mediate the actions of estrogens, and although 70% of human breast cancers express ERbeta along with ERalpha, little is known about the possible comodulatory effects of these two ERs. To investigate this, we have used adenoviral gene delivery to produce human breast cancer (MCF-7) cells expressing different levels of ERbeta, along with their endogenous ERalpha, and have examined the effects of ERbeta and receptor occupancy, using ER subtype selective ligands, on genome-wide gene expression by microarray and pathway network analysis. ERbeta had diverse effects on gene expression, enhancing or counteracting ERalpha regulation for distinct subsets of estrogen target genes. Strikingly, ERbeta in the absence of estradiol (E2), elicited the stimulation or suppression of many genes that were normally only regulated by ERalpha with E2. In addition, ERbeta plus E2 elicited the expression of a unique group of genes that were not regulated by ERalpha plus E2 alone. The expression of genes in many functional categories were modulated by ERbeta, with the greatest numbers associated with transcription factors and signal transduction pathways. Regulation of multiple components in the TGFbeta and semaphorin pathways, and of genes controlling cell cycle progression and apoptosis, may contribute to the suppression of cell proliferation observed with ERbeta. Our observations suggest that the relative levels of ERbeta and ERalpha in breast cancers are likely to impact cell proliferation and the activities of diverse signaling pathways and their response to ER ligands and endocrine therapies.
The Q-linker: a class of interdomain sequences found in bacterial multidomain regulatory proteins (1989)

Evidence is presented that establishes a novel class of interdomain linkers, named Q-linkers, as a defined element of protein structure. Q-linkers occur at the boundaries of functionally distinct domains in a widespread set of bacterial regulatory and sensory transduction proteins, typified by the nitrogen regulatory proteins, NtrB, NtrC, NifA and NifL. Q-linkers are not strongly conserved in sequence in otherwise homologous proteins, are approximately 15-25 residues long and relatively rich in glutamine, arginine, glutamate, serine and proline, and are assigned as 'coil', with a very low probability of alpha or beta structure, by eight secondary structure prediction methods. Hydrophobic amino acids are spaced with a periodicity of approximately 4-5 residues in the C-terminal 15 residues of these sequences. A pattern discriminator is presented that incorporates these properties and is used to predict segments resembling Q-linkers in sequence databases. Insertions of four and eight amino acids, constructed in the Q-linker sequences of NtrC and NifA, were found to have no effect on the function of the proteins in signal transduction and transcriptional activation. However, when NtrC was expressed as two separate polypeptides, consisting of the domains normally joined by the Q-linker, the construct failed to function. These results suggest that the Q-linker serves a simple but essential role in tethering the structurally-distinct but interacting domains of the protein. Q-linkers are therefore potentially applicable as domain fusion junctions for engineered chimaeric multidomain proteins expressed in enteric bacterial systems.
Non Cell-Autonomous Reprogramming of Adult Ocular Progenitors: Generation of Pluripotent Stem Cells without Exogenous Transcription Factors (2009)

Direct reprogramming of differentiated cells to induced pluripotent stem (iPS) cells by ectopic expression of defined transcription factors (TFs) represents a significant breakthrough towards the use of stem cells in regenerative medicine (Takahashi and Yamanaka Cell 2006;126:663-676). However, the virus-mediated expression of exogenous transcription factors could be potentially harmful and, therefore, represents a barrier to the clinical use of iPS cells. Several approaches, ranging from plasmid-mediated TF expression to introduction of recombinant TFs (Yamanaka Cell 2009;137:13-17; Zhou, Wu, Joo et al. Cell Stem Cell 2009;4:381-384), have been reported to address the risk associated with viral integration. We describe an alternative strategy of reprogramming somatic progenitors entirely through the recruitment of endogenous genes without the introduction of genetic materials or exogenous factors. To this end, we reprogrammed accessible and renewable progenitors from the limbal epithelium of adult rat eye by microenvironment-based induction of endogenous iPS cell genes. Non cell-autonomous reprogramming generates cells that are pluripotent and capable of differentiating into functional neurons, cardiomyocytes, and hepatocytes, which may facilitate autologous cell therapy to treat degenerative diseases.
Organoimido-polyoxometalates as polymer pendants (2000)

The p-styrenyl substituent borne by the organoimido ligand in the Lindqvist derivative [NBu4]2[Mo6O18(NC6- H4CHCH2)] 1 allows the polyoxometalate complex to be introduced as a pendant group in polystyrene compositions via conventional free radical-induced copolymerization.