gebhart/patrepeval huggingface dataset:
Association between avian necrotic enteritis andClostridium perfringensstrains expressing NetB toxin (2009)

A novel toxin, NetB, has recently been identified in virulent avian Clostridium perfringens isolates and shown to be an essential virulence factor in a clinical necrotic enteritis isolate. To assess whether NetB is more generally associated with avian necrotic enteritis isolates we have screened a range of C. perfringens strains from geographically diverse locations for both the presence and expression of the netB gene. Forty-four isolates were derived from necrotic enteritis disease cases from Australia, Belgium, Denmark and Canada and 55 isolates from healthy chickens from Australia and Belgium. The majority of strains isolated from necrotic enteritis-affected birds were netB positive (70%) and there was an absolute correlation between the presence of netB and in vitro expression of the NetB protein. Only two of the C. perfringens isolates from healthy chickens carried netB. Sequencing of the netB gene from 23 positive isolates showed that NetB is highly conserved, with only one predicted amino acid (A168T) difference, in six isolates, compared to the published sequence. This change did not alter the in vitro activity of the NetB toxin. The gene encoding the recently discovered TpeL toxin was also screened using PCR and only found in a small proportion of NetB-positive isolates from diseased birds. A selection of NetB-negative isolates, originating from diseased birds, was unable to cause disease in a necrotic enteritis induction model. This study provides further evidence that NetB is important in pathogenesis and advances our current understanding of C. perfringens virulence factors in avian necrotic enteritis.
Vaccination with Novel Immunostimulatory Adjuvants against Blood-Stage Malaria in Mice (2003)

An important aspect of malaria vaccine development is the identification of an appropriate adjuvant which is both capable of stimulating a protective immune response and safe for use by humans. Here, we investigated the feasibility of using novel immunostimulatory molecules as adjuvants combined with a crude antigen preparation and coadsorbed to aluminum hydroxide (alum) as a vaccine against blood-stage Plasmodium chabaudi AS malaria. Prior to challenge infection, immunization of genetically susceptible A/J mice with the combination of malaria antigen plus recombinant interleukin-12 (IL-12) in alum induced a Th1 immune response with production of high levels of gamma interferon (IFN-gamma) and diminished IL-4 levels by spleen cells stimulated in vitro with parasite antigen compared to mice immunized with antigen alone, antigen in alum, or antigen plus IL-12. Mice immunized with malaria antigen plus recombinant IL-12 in alum had high levels of total malaria-specific antibody and immunoglobulin G2a. Compared to unimmunized mice, immunization with antigen plus IL-12 in alum induced the highest level of protective immunity against challenge infection with P. chabaudi AS, which was evident as a significantly decreased peak parasitemia level and 100% survival. Protective immunity was dependent on CD4(+) T cells, IFN-gamma, and B cells and was long-lasting. Replacement of IL-12 as an adjuvant by synthetic oligodeoxynucleotides (ODN) containing CpG motifs induced a similar level of vaccine-induced protection against challenge infection with P. chabaudi AS. These results illustrate that it is possible to enhance the potency of a crude malaria antigen preparation delivered in alum by inclusion of immunostimulatory molecules, such as IL-12 or CpG-ODN.
Selective toxicity of rhodamine 123 in carcinoma cells in vitro. (1983)

The study of mitochondria in situ has recently been facilitated through the use of rhodamine 123, a mitochondrial-specific fluorescent dye. It has been found to be nontoxic when applied for short periods to a variety of cell types and has thus become an invaluable tool for examining mitochondrial morphology and function in the intact living cell. In this report, however, we demonstrate that with continuous exposure, rhodamine 123 selectively kills carcinoma as compared to normal epithelial cells grown in vitro. At doses of rhodamine 123 which were toxic to carcinoma cells, the conversion of mitochondrial-specific to cytoplasmic-nonspecific localization of the drug was observed prior to cell death. At 10 microgram/ml, greater than 50% cell death occurred within 7 days in all nine of the carcinoma cell types and lines of different origin studied, while six of six normal epithelial cell types and lines remained unaffected. Cotreating carcinoma cells with 2-deoxyglucose and rhodamine 123 enhanced the inhibition of growth by rhodamine 123 alone in clonogenic survival assays. The observation of the selective toxicity of rhodamine 123 appears to be unique in view of the absence of selective toxicity reported in vitro for the various antitumor agents currently in clinical use. Preliminary results with rhodamine 123 in animal tumor systems indicate antitumor activity for carcinomas.
Unique G-Rich Oligonucleotides Which Inhibit the Growth of Prostatic Carcinoma Cells. (1999)

Abstract : This proposal was based on our original observation that certain G-rich oligonucleotides (GROs) inhibited the growth of cultured prostate cancer cells. The sequences of the active oligonucleotides led us to hypothesize that GROs could form G-quartet containing structures that bind to specific cellular proteins. The overall goal of this proposal was to characterize the structure and mechanism of these novel oligonucleotides. In the first half of this study, the hypotheses regarding G-quartet formation and protein binding were confirmed, and a protein called nucleolin was identified as the tentative target of GROs. During the current reporting period, we have completed the remaining studies in the Phase I proposal. Key results in this period include the following: (1) Structure determination of an active GRO by molecular modeling supported by biophysical data, (2) Demonstration of apoptosis induction in GRO-treated prostate cancer cells, (3) Confirmation of nucleolin as a GRO binding protein and extension of the correlation between GRO activity and ability to bind to nucleolin, and (4) Completion of TRAP assays showing the inability of GROs to inhibit telomerase. In summary, all of the studies proposed in Phase I have been successfully completed or addressed by alternative approaches. This study has produced considerable data to support GROs as potential therapeutic agents for prostate cancer.
Qubits as parafermions (2002)

Qubits are neither fermions nor bosons. A Fock space description of qubits leads to a mapping from qubits to parafermions: particles with a hybrid boson-fermion quantum statistics. We study this mapping in detail, and use it to provide a classification of the algebras of operators acting on qubits. These algebras in turn classify the universality of different classes of physically relevant qubit-qubit interaction Hamiltonians. The mapping is further used to elucidate the connections between qubits, bosons, and fermions. These connections allow us to share universality results between the different particle types. Finally, we use the mapping to study the quantum computational power of certain anisotropic exchange Hamiltonians. In particular, we prove that the XY model with nearest-neighbor interactions only is not computationally universal. We also generalize previous results about universal quantum computation with encoded qubits to codes with higher rates.
Biochemistry and applications of aprotinin, the kallikrein inhibitor from bovine organs. (1983)

The basic proteinase inhibitor from bovine organs, aprotinin (active ingredient of Trasylol) has been extensively studied with respect to its chemical, physical and biochemical properties and its inhibitory mechanism of action. It is widely used as a valuable tool for studying protein/protein interactions and protein conformation at the molecular level. There are numerous examples of the usefulness of aprotinin in biochemical and biomedical research. It has also become a valuable drug for the treatment of various diseases like, e.g. hyperfibrinolytic hemorrhage and traumatic-hemorrhagic shock. The purpose of this paper is threefold. It summarizes our present knowledge of the subject in various disciplines; it provides the active scientist with basic data for his experimental work; and above all it points the way to future directions of aprotinin research.
RNA fingerprints provide direct evidence for the inhibitory role of TGFβ and PD-1 on CD4+ T cells in Hodgkin lymphoma (2007)

A hallmark of various human malignancies is the expression of immunoinhibitory factors within the tumor microenvironment. There is indirect evidence based on in vitro experiments that tumor-infiltrating T cells in human malignancies are suppressed by such factors. Still, direct evidence of the influence of individual inhibitory factors on immune cells in human cancer in vivo is lacking. To address this question, we used Hodgkin lymphoma (HL) as a model because histopathological characteristics of HL are thought to be due mostly to the effects of a wide variety of cytokines, including TGFbeta or membrane-bound receptors such as PD-1 that are suspected to contribute to immune evasion of tumor cells. Using a genome-wide transcriptional approach, we established specific RNA fingerprints of TGFbeta and PD-1 signaling in human T cells in vitro. Applying these specific fingerprints, we directly demonstrate that CD4+ T cells in HL--but not in follicular lymphoma (FL)--are under the inhibitory influence of both TGFbeta and PD-1 in vivo. This approach can be easily generalized to provide direct evidence of the impact of any given soluble or cell-bound factor on any cell type within diseased tissue.
Electrically tailored resistance switching in silicon oxide (2012)

Resistive switching in a metal-free silicon-based material offers a compelling alternative to existing metal oxide-based resistive RAM (ReRAM) devices, both in terms of ease of fabrication and of enhanced device performance. We report a study of resistive switching in devices consisting of non-stoichiometric silicon-rich silicon dioxide thin films. Our devices exhibit multi-level switching and analogue modulation of resistance as well as standard two-level switching. We demonstrate different operational modes that make it possible to dynamically adjust device properties, in particular two highly desirable properties: nonlinearity and self-rectification. This can potentially enable high levels of device integration in passive crossbar arrays without causing the problem of leakage currents in common line semi-selected devices. Aspects of conduction and switching mechanisms are discussed, and scanning tunnelling microscopy (STM) measurements provide a more detailed insight into both the location and the dimensions of the conductive filaments.
Microbial Adhesion to Poly(ethylene oxide) Brushes:  Influence of Polymer Chain Length and Temperature (2004)

Glass surfaces were modified by end-grafting poly(ethylene oxide) (PEO) chains having molecular weights of 526, 2000, or 9800 Da. Characterization using water contact angles, ellipsometry, and X-ray photoelectron spectroscopy confirmed the presence of the PEO brushes on the surface with estimated lengths in water of 2.8-, 7.5-, and 23.7-nm, respectively. Adhesion of two bacterial (Staphylococcus epidermidis and Pseudomonas aeruginosa) and two yeast (Candida albicans and Candida tropicalis) strains to these brushes was studied and compared to their adhesion to bare glass. For the bacterium P. aeruginosa and the yeast C. tropicalis, adhesion to the 2.8-nm brush was comparable to their adhesion on bare glass, whereas adhesion to the 7.5- and 23.7-nm brushes was greatly reduced. For S. epidermidis, adhesion was only slightly higher to the 2.8-nm brush than that to the longer brushes. Adhesion of the yeast C. albicans to the PEO brushes was lower than that to glass, but no differences in adhesion were found between the three brush lengths. After passage of an air bubble, nearly all microorganisms adhering to a brush were removed, irrespective of brush length, whereas retention of the adhering organisms on glass was much higher. No significant differences were found in adhesion nor retention between experiments conducted at 20 and those conducted at 37 degrees C.
Identification of a specific self-reactive IgM antibody that initiates intestinal ischemia/reperfusion injury (2004)

Reperfusion injury of ischemic tissue represents an acute inflammatory response that can cause significant morbidity and mortality. The mechanism of injury is not fully elucidated, but recent studies indicate an important role for natural antibody and the classical pathway of complement. To test the hypothesis that injury is initiated by specific IgM, we have screened a panel of IgM-producing hybridomas prepared from peritoneal cells enriched in B-1 cells. One clone, CM22, was identified that could restore pathogenic injury in RAG-1(-/-) mice in an intestinal model of ischemia/reperfusion (I/R). In situ activation of the classical pathway of complement was evident by deposition of IgM, complement C4, and C3 in damaged tissue after passive transfer of CM22 IgM. Sequence analysis of CM22 Ig heavy and light chains showed germ-line configurations with high homology to a V(H) sequence from the B-1 repertoire and a V(K) of a known polyreactive natural IgM. These data provide definitive evidence that I/R injury can be initiated by clonally specific natural IgM that activates the classical pathway of complement. This finding opens an avenue for identification of I/R-specific self-antigen(s) and early prevention of injury.
Mechanism of the Palladium-Catalyzed Homocoupling of Arylboronic Acids:  Key Involvement of a Palladium Peroxo Complex (2006)

The mechanism of the palladium-catalyzed homocoupling of arylboronic acids ArB(OH)(2) (Ar = 4-Z-C(6)H(4) with Z = MeO, H, CN) in the presence of dioxygen, leading to symmetrical biaryls, has been fully elucidated. The peroxo complex (eta(2)-O(2))PdL(2) (L = PPh(3)), generated in the reaction of dioxygen with the Pd(0) catalyst, was found to play a crucial role. Indeed, it reacts with the arylboronic acid to generate an adduct (coordination of one oxygen atom of the peroxo complex to the oxophilic boron atom of the arylboronic acid) characterized by (31)P NMR spectroscopy and ab initio calculations. This adduct reacts with a second molecule of arylboronic acid to generate trans-ArPd(OH)L(2) complexes. A transmetalation by the arylboronic acid gives trans-ArPdArL(2) complexes. The biaryl is then released in a reductive elimination. This reaction is at the origin of the formation of biaryls as byproducts in palladium-catalyzed Suzuki-Miyaura reactions when they are not conducted under oxygen-free atmosphere.
High-speed data transmission on an optical fiber using a byte-wide WDM system (1988)

The advantages and problems of using wavelength division multiplexing (WDM) to transmit byte-wide data in parallel through a single-mode optical fiber are studied. The principle problem which is particular to byte-wide transmission is shown to be bit skew caused by group delays of the different transmission wavelengths. The aggregate bit rate of the byte-wide link is shown to be equal to the aggregate bit rate of the serial link for all byte sizes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Microwave catheter ablation of myocardium in vitro. Assessment of the characteristics of tissue heating and injury. (1994)

Microwave ablation has the potential to directly heat a greater volume of tissue than RF ablation but only with efficient MW antennas. The primary mechanism of tissue injury for both MW and RF ablation appears to be thermal.
Layered metal sulfides: Exceptionally selective agents for radioactive strontium removal (2008)

In this article, we report the family of robust layered sulfides K(2x)Mn(x)Sn(3-x)S(6) (x = 0.5-0.95) (KMS-1). These materials feature hexagonal [Mn(x)Sn(3-x)S(6)](2x-) slabs of the CdI(2) type and contain highly mobile K(+) ions in their interlayer space that are easily exchangeable with other cations and particularly strontium. KMS-1 display outstanding preference for strontium ions in highly alkaline solutions containing extremely large excess of sodium cations as well as in acidic environment where most alternative adsorbents with oxygen ligands are nearly inactive. The implication of these results is that simple layered sulfides should be considered for the efficient remediation of certain nuclear wastes.
A novel iron-regulated metal transporter from plants identified by functional expression in yeast. (1996)

Iron is an essential nutrient for virtually all organisms. The IRT1 (iron-regulated transporter) gene of the plant Arabidopsis thaliana, encoding a probable Fe(II) transporter, was cloned by functional expression in a yeast strain defective for iron uptake. Yeast expressing IRT1 possess a novel Fe(II) uptake activity that is strongly inhibited by Cd. IRT1 is predicted to be an integral membrane protein with a metal-binding domain. Data base comparisons and Southern blot analysis indicated that IRT1 is a member of a gene family in Arabidopsis. Related sequences were also found in the genomes of rice, yeast, nematodes, and humans. In Arabidopsis, IRT1 is expressed in roots, is induced by iron deficiency, and has altered regulation in plant lines bearing mutations that affect the iron uptake system. These results provide the first molecular insight into iron transport by plants.
Importance of Timing of Preprandial Subcutaneous Insulin Administration in the Management of Diabetes Mellitus (1983)

Since little is known regarding the appropriate time for preprandial insulin administration, we compared the effects of 30-min subcutaneous insulin infusions started 60 min, 30 min, and immediately before meal ingestion on postprandial plasma glucose and insulin profiles in eight subjects with insulin-dependent diabetes mellitus. Of these three regimens, administration of insulin 60 min before meal ingestion provided plasma glucose and insulin profiles closest to normal and permitted less insulin to be used. Our results suggest that adjustments in the timing as well as in the amount of insulin administered preprandially may be used in the management of diabetes and that prolonging the interval between administration of insulin and meal ingestion may reduce insulin requirements and thus decrease the hyperinsulinemia usually associated with insulin therapy.
CLONING OF FIBRINOGEN GENES AND THEIR cDNA* (1983)

Cross-species hybridizations have enabled us to isolate and clone the gene for the beta chain of human fibrinogen. Highlights of the gene for the beta chain revealed by nucleotide sequence analyses, particularly in areas that have a direct bearing on defining the overall organization of the gene, have been presented. Nucleotide sequence determination has confirmed the presence of seven intervening sequences. The positions where several of these intervening sequences interrupt the coding region appear to be related to the functional domains of the polypeptide. A putative signal peptide has been identified. Studies on the cDNA for the human alpha chain indicate that the alpha chain polypeptide may be synthesized in a precursor form with a COOH-terminal extension of 15 amino acids as compared to the alpha chain present in the mature molecule found in plasma. We are in the process of isolating the genes for the alpha and gamma chains by a similar approach. We are hopeful that these studies will provide information as to how they are regulated and how they have undergone changes in the course of evolution.
Magnetic resonance myocardial fiber-orientation mapping with direct histological correlation (1998)

Functional properties of the myocardium are mediated by the tissue structure. Consequently, proper physiological studies and modeling necessitate a precise knowledge of the fiber orientation. Magnetic resonance (MR) diffusion tensor imaging techniques have been used as a nondestructive means to characterize tissue fiber structure; however, the descriptions so far have been mostly qualitative. This study presents a direct, quantitative comparison of high-resolution MR fiber mapping and histology measurements in a block of excised canine myocardium. Results show an excellent correspondence of the measured fiber angles not only on a point-by-point basis (average difference of -2.30 +/- 0.98 degrees, n = 239) but also in the transmural rotation of the helix angles (average correlation coefficient of 0.942 +/- 0.008 with average false-positive probability of 0.004 +/- 0.001, n = 24). These data strongly support the hypothesis that the eigenvector of the largest MR diffusion tensor eigenvalue coincides with the orientation of the local myocardial fibers and underscore the potential of MR imaging as a noninvasive, three-dimensional modality to characterize tissue fiber architecture.
Energy metabolism of monocytic Ehrlichia. (1989)

We investigated if the monocytic Ehrlichia are totally dependent on their host cells for energy, or, as Rickettsia, are capable of some ATP synthesis in vitro. The Miyayama strain of Ehrlichia sennetsu and the Maryland and Illinois strains of Ehrlichia risticii were cultivated in a mouse macrophage cell line, separated from host cell constituents by procedures that included Renografin or Percoll gradient centrifugation, and tested after cryopreservation. Cells incubated without a metabolizing substrate contained little, if any, ATP. When the Ehrlichia cells were incubated for 1 hr at 34 degrees C with glutamine, significant amounts of ATP were detected. The amounts of ATP attained with glutamine were decreased in some instances by the addition of atractyloside, an inhibitor of adenine nucleotide translocase in mitochondria, and were decreased consistently and to a greater extent by 2,4-dinitrophenol. When ATP, instead of glutamine, was added to the ehrlichiae, upon incubation the amount of ATP was markedly decreased. Comparable responses under all these conditions were obtained with Rickettsia typhi, although the final ATP levels were higher. Control preparations derived from uninfected mouse macrophages or from the discards of the Ehrlichia purification procedures contained negligible amounts of ATP, which were not increased by incubation with glutamine. We conclude that with respect to ATP metabolism, the monocytic Ehrlichia resemble Rickettsia more closely than Chlamydia, even though Ehrlichia resemble Chlamydia in their intracellular location in the phagosomes and in possibly having a developmental cycle.
Effect of Amines on Single-Walled Carbon Nanotubes in Organic Solvents: Control of Bundle Structures (2002)

We have investigated the control of bundle structures of single-walled carbon nanotubes (SWNTs) in organic solvents using atomic force microscopy (AFM) and transmission electron microscopy (TEM). We have reported herein that organic amines are effective in untangling the bundled SWNTs in N,N-dimethylformamide (DMF). When Bucky paper was sonicated in DMF with 1% organic amine for 1 h, AFM images clearly showed mainly individual SWNTs. The time-dependent TEM observation revealed that the role of amine is to prevent rebundling of SWNTs in organic solvents.