gebhart/patrepeval huggingface dataset:
Synthesis and Characterization of Zirconium and Iron Complexes Containing Substituted Indenyl Ligands:  Evaluation of Steric and Electronic Parameters (2004)

Evaluation of the steric and electronic influence of a family of silyl- and alkyl-substituted indenyl ligands on zirconium and iron centers has been accomplished by a combination of X-ray diffraction, IR spectroscopy, solution NMR dynamics, and electrochemical measurements. Three tetrasubstituted, bis-indenyl zirconocene dichloride complexes have been characterized by X-ray diffraction and adopt a gauche ligand conformation such that the interactions between tertiary substituents on adjacent rings are minimized. Similar solid state conformations were also observed in two of the corresponding iron compounds. Evaluation of the electronic environment about each zirconium center was achieved by measurement of the CO stretching frequencies of the dicarbonyl derivatives. Simple inductive effects govern the electronic properties of each zirconocene where silyl groups are relatively electron withdrawing and alkyl groups electron donating. For the most hindered zirconocene dicarbonyl derivatives, population of three vibrationally distinct rotamers has been detected by IR spectroscopy. Independent assessment of these stereoelectronic parameters by variable-temperature NMR spectroscopy and electrochemistry with the analogous series of iron complexes provided the same relative ordering of the indenyl ligands.
Real-time modeling and 3D visualization of source dynamics and connectivity using wearable EEG (2013)

This report summarizes our recent efforts to deliver real-time data extraction, preprocessing, artifact rejection, source reconstruction, multivariate dynamical system analysis (including spectral Granger causality) and 3D visualization as well as classification within the open-source SIFT and BCILAB toolboxes. We report the application of such a pipeline to simulated data and real EEG data obtained from a novel wearable high-density (64-channel) dry EEG system.
MOS characteristics of ultra thin rapid thermal CVD ZrO/sub 2/ and Zr silicate gate dielectrics (2002)

In this paper, we report MOS characteristics of ultra thin, high quality CVD ZrO/sub 2/ and Zr silicate (Zr/sub 27/Si/sub 10/O/sub 63/) gate dielectrics deposited on Si substrates by in-situ rapid thermal processing. These high-K gate dielectrics show excellent equivalent oxide thickness (EOT) of 8.9 /spl Aring/ (ZrO/sub 2/) and 9.6 /spl Aring/ (Zr/sub 27/Si/sub 10/O/sub 63/) with extremely low leakage current of 20 mA/cm/sup 2/ and 23 mA/cm/sup 2/ @Vg=-1 V, respectively. The thermal stability of ZrO/sub 2//Si as well as the poly-Si/ZrO/sub 2/ interfaces are examined using in-situ XPS. We also investigate the conduction mechanisms and long-term reliability in these gate stacks. In addition, the effects of various gate electrode materials (Al/TiN, poly-SiGe, and poly-Si) on the electrical properties of gate stacks are studied. Finally, we also study the boron diffusion behaviors in p/sup +/-poly-Si PMOS.
Distribution and Evolution of Circular Miniproteins in Flowering Plants (2008)

Cyclotides are disulfide-rich miniproteins with the unique structural features of a circular backbone and knotted arrangement of three conserved disulfide bonds. Cyclotides have been found only in two plant families: in every analyzed species of the violet family (Violaceae) and in few species of the coffee family (Rubiaceae). In this study, we analyzed >200 Rubiaceae species and confirmed the presence of cyclotides in 22 species. Additionally, we analyzed >140 species in related plant families to Rubiaceae and Violaceae and report the occurrence of cyclotides in the Apocynaceae. We further report new cyclotide sequences that provide insights into the mechanistic basis of cyclotide evolution. On the basis of the phylogeny of cyclotide-bearing plants and the analysis of cyclotide precursor gene sequences, we hypothesize that cyclotide evolution occurred independently in various plant families after the divergence of Asterids and Rosids ( approximately 125 million years ago). This is strongly supported by recent findings on the in planta biosynthesis of cyclotides, which involves the serendipitous recruitment of ubiquitous proteolytic enzymes for cyclization. We further predict that the number of cyclotides within the Rubiaceae may exceed tens of thousands, potentially making cyclotides one of the largest protein families in the plant kingdom.
Cyclophosphamide/granulocyte colony-stimulating factor induces hematopoietic stem cells to proliferate prior to mobilization (1997)

We isolated hematopoietic stem cells (HSC) from mice treated with cyclophosphamide (CY) and granulocyte colony-stimulating factor (G-CSF). All mobilized multipotent progenitor activity was contained in two populations: Thy-1(lo) Sca-1+ Lin- Mac-1- CD4- c-kit+ long-term reconstituting progenitors and Thy-1(lo) Sca-1+ Lin- Mac-1(lo) CD4- transiently reconstituting progenitors. CY/G-CSF treatment drove both long-term and transient multipotent progenitors into cycle, leading to a more than 12-fold expansion in the number of long-term self-renewing HSC prior to mobilization. After CY and 2 days of G-CSF treatment the number of bone marrow HSC began to decline and the number of blood and splenic HSC increased. HSC continued to proliferate in the bone marrow and spleen through 8 days of G-CSF treatment, but HSC released into the blood tended to be in G0/G1 phase. Mobilized multipotent progenitors isolated from the spleen were less efficient than normal bone marrow multipotent progenitors in engrafting irradiated mice but did not differ in colony forming unit-spleen (CFU-S) activity or single cell in vitro assays of primitive progenitor activity. The data suggest that mobilized HSC isolated from the spleen are less efficient at homing to and engrafting the bone marrow of irradiated recipient mice.
Fritillaria cirrhosa, Anemarrhena asphodeloides, Lee‐Mo‐Tang and Cyclosporine a Inhibit Ovalbumin‐Induced Eosinophil Accumulation and Th2‐Mediated Bronchial Hyperresponsiveness in a Murine Model of Asthma (2007)

Asthma is a chronic inflammatory disorder of the airways characterized by excess production of Th2 cytokines and eosinophil accumulation in the lungs. Fritillaria cirrhosa, Anemarrhena asphodeloides and Lee-Mo-Tang are well-known herbs used in oriental medicine for the treatment of asthma and bronchial inflammation. To clarify the anti-asthmatic effects of Fritillaria cirrhosa bulbus, Anemarrhena rhizoma and Lee-Mo-Tang, we examined the development of pulmonary eosinophilic accumulation, control of Th2 cytokine, immunoglobulin E (IgE) and histamine productions in a murine model of asthma. Eosinophil cell proliferation was performed by [(3)H]thymidine uptake, eosinophilic accumulation. Cell counts in bronchoalveolar lavage fluid were investigated by means of fluorescence activated cell sorter analysis and control of Th2 cytokine, IgE and histamine productions were investigated by RT-PCR and ELISA. Moreover, lung tissue was histologically analysed. The suppressive effects of Fritillaria cirrhosa bulbus, Anemarrhena rhizoma and Lee-Mo-Tang on eosinophil recruitment and airway inflammation were demonstrated throughout the reduction of eosinophil numbers. This result correlated with a marked reduction IL-5, IL-13 and IL-4 levels in the bronchoalveolar lavage fluid. Ovalbumin-specific IgE levels were also decreased in serum. Fritillaria cirrhosa bulbus, Anemarrhena rhizoma and Lee-Mo-Tang have deep inhibitory effects on airway inflammation by suppression of Th2 cytokines (IL-4, IL-5 and IL-13), IgE, histamine production, reduction eosinophilic accumulation and increase of interferon-gamma production.
D6 and the atypical chemokine receptor family: Novel regulators of immune and inflammatory processes (2009)

Chemokines are key regulators of leukocyte migration and play important roles in a number of physiological and pathological immune and inflammatory contexts. In addition to the classical signalling chemokine receptors there has emerged, recently, a new subclass of atypical chemokine receptors. This subfamily is characterised by an apparent lack of signalling and, in some cases, by an ability to internalise and degrade chemokine ligands. This review describes the family of atypical chemokine receptors with particular emphasis on the D6 receptor. The in vitro and in vivo biology of D6 is described, which indicates that D6 is active as a scavenger of inflammatory CC-chemokines and appears to play essential roles in the regulation of inflammatory responses.
Regulation of WRN Helicase Activity in Human Base Excision Repair (2004)

Werner syndrome patients are deficient in the Werner protein (WRN), which is a multifunctional nuclear protein possessing 3'-5' exonuclease and ATP-dependent helicase activities. Studies of Werner syndrome cells and biochemical studies of WRN suggest that WRN plays a role in several DNA metabolic pathways. WRN interacts with DNA polymerase beta (pol beta) and stimulates pol beta strand displacement synthesis on a base excision repair (BER) intermediate in a helicase-dependent manner. In this report, we examined the effect of the major human apurinic/apyrimidinic endonuclease (APE1) and of pol beta on WRN helicase activity. The results show that WRN alone is able to unwind several single strand break BER intermediates. However, APE1 inhibits WRN helicase activity on these intermediates. This inhibition is likely due to the binding of APE1 to nicked apurinic/apyrimidinic sites, suggesting that APE1 prevents the promiscuous unwinding of BER intermediates. This inhibitory effect was relieved by the presence of pol beta. A model involving the pol beta-mediated hand-off of WRN protein is proposed based on these results.
Hepcidin, a key regulator of iron metabolism and mediator of anemia of inflammation (2003)

Human hepcidin, a 25-amino acid peptide made by hepatocytes, may be a new mediator of innate immunity and the long-sought iron-regulatory hormone. The synthesis of hepcidin is greatly stimulated by inflammation or by iron overload. Evidence from transgenic mouse models indicates that hepcidin is the predominant negative regulator of iron absorption in the small intestine, iron transport across the placenta, and iron release from macrophages. The key role of hepcidin is confirmed by the presence of nonsense mutations in the hepcidin gene, homozygous in the affected members, in 2 families with severe juvenile hemochromatosis. Recent evidence shows that deficient hepcidin response to iron loading may contribute to iron overload even in the much milder common form of hemochromatosis, from mutations in the HFE gene. In anemia of inflammation, hepcidin production is increased up to 100-fold and this may account for the defining feature of this condition, sequestration of iron in macrophages. The discovery of hepcidin and its role in iron metabolism could lead to new therapies for hemochromatosis and anemia of inflammation.
Methotrexate and Cyclosporine Compared with Cyclosporine Alone for Prophylaxis of Acute Graft versus Host Disease after Marrow Transplantation for Leukemia (1986)

We treated 93 patients who had acute nonlymphoblastic leukemia in the first remission or chronic myelocytic leukemia in the chronic phase (median age, 30 years) with high-dose cyclophosphamide and fractionated total-body irradiation, followed by infusion of marrow from an HLA-identical sibling. To evaluate postgrafting prophylaxis for graft versus host disease, we studied these patients in a sequential, prospective, randomized trial that compared the effect of a combination of methotrexate and cyclosporine (n = 43) with that of cyclosporine alone (n = 50). All patients had evidence of sustained engraftment. A significant reduction in the cumulative incidence of grades II to IV acute graft versus host disease was observed in the patients who received both methotrexate and cyclosporine (33 percent), as compared with those who were given cyclosporine alone (54 percent) (P = 0.014). Seven patients who received cyclosporine alone acquired grade IV acute graft versus host disease, as compared with none who received both methotrexate and cyclosporine. Thirty-five of the 43 patients given both methotrexate and cyclosporine and 31 of the 50 patients given cyclosporine are alive as of this writing, at 4 months to 2 years (median, 15 months); the actuarial survival rates in the two groups at 1.5 years were 80 percent and 55 percent, respectively (P = 0.042). We conclude that the combination of methotrexate and cyclosporine is superior to cyclosporine alone in the prevention of acute graft versus host disease after marrow transplantation for leukemia, and that this therapy may have a beneficial effect on long-term survival.
Studies of intraspecies heterogeneity of mycoplasma synoviae, M. meleagridis, and M. iowae with arbitrarily primed polymerase chain reaction. (1996)

Intraspecies genotypic heterogeneity among isolates and strains of M. synoviae (MS), M. iowae (MI), and M. meleagridis (MM) was demonstrated with the arbitrarily primed polymerase chain reaction (AP-PCR) method. The generated banding patterns of amplified DNA indicated a degree of genotypic heterogeneity among MS, MI, and MM isolates and strains tested, whereas isolates from common sources generated clusters with identical banding patterns. The results show that flocks infected with members of the cluster were epidemiologically associated, possibly by a common or point source of infection. This AP-PCR method may be a useful identification tool in epidemiology of mycoplasmosis in poultry.
Comparative Analysis of Regulatory and Effector T Cells in Progressively Growing versus Rejecting Tumors of Similar Origins (2006)

Although regulatory T cells (Tregs) have been detected in clinically apparent and experimentally induced tumors, the significance of their presence is obscured because past studies examined late-stage tumors that had formed in immunocompetent hosts and thus had evolved mechanisms to escape immunologic recognition and/or elimination. Herein, we report the first comparative analysis of the antitumor response to 3'-methylcholanthrene-induced tumors, which either grow progressively (progressor tumors) or are rejected by the immune system (regressor tumors). Surprisingly, we found that both progressor and regressor tumors harbored proliferating (i.e., activated) Foxp3+CD25+Tregs. However, progressor tumors contained a higher percentage of Tregs in the lymphocyte subset versus regressor tumors. The Tregs in progressor tumors were derived from peripheral CD25+ natural Tregs, accumulated early after tumor challenge and were actively proliferating, suggesting that progressor tumors recruited and/or activated endogenous Tregs as a mechanism of escaping immune destruction. To explore whether Tregs directly contributed to the progressive growth phenotype of progressor tumors, we monitored tumor outgrowth in naive wild-type recipients pretreated with either a control monoclonal antibody (mAb) or a depleting CD25-specific mAb. In mice predepleted of CD25+ cells, the tumors that subsequently developed displayed an increased accumulation of proliferating CD8+ T cells and were rejected. These results show that, although Tregs are activated in both regressor and progressor tumors, the ratio of regulatory to effector T cells is critical in determining whether the host successfully rejects the tumor or eventually succumbs to tumor outgrowth.
Phylogenetic analysis of phospholipase C genes from Clostridium perfringens types A to E and Clostridium novyi (1995)

The phylogenetic interrelationships between strains of 5 toxin types (A to E) of Clostridium perfringens were examined by analysis of differences in the nucleotide sequences of phospholipase C genes (plc genes) among 10 strains, including 3 strains for which the plc gene sequences have been previously reported. A plc gene was also cloned from a Clostridium novyi type A strain and sequenced to analyze the interspecies diversity of plc genes. Phylogenetic trees constructed by the neighbor-joining method revealed that the phylogeny of C. perfringens strains is not related to toxin typing, in agreement with the results of a comparative genome mapping study by Canard et al. (B. Canard, B. Saint-Joanis, and S. T. Cole, Mol. Microbiol. 6:1421-1429, 1992). Various C. perfringens phospholipase C enzymes were purified from cultures of Escherichia coli cells into which the encoding plc genes had been cloned. All of the enzymes showed the same specific activity. On the other hand, the level of plc transcripts differed greatly (up to 40-fold) from one C. perfringens strain to another. No significant difference in the nucleotide sequence of the plc promoter region was observed for any of the plc genes. These results suggest that the variation in phospholipase C activity among different strains is not due to mutation in the plc coding region but to that in an extragenic region. The evolution of C. perfringens phospholipase C is discussed on the basis of similarities and differences between clostridial plc genes.
Manganese‐enhanced magnetic resonance imaging (MEMRI): methodological and practical considerations (2004)

Manganese-enhanced MRI (MEMRI) is being increasingly used for MRI in animals due to the unique T1 contrast that is sensitive to a number of biological processes. Three specific uses of MEMRI have been demonstrated: to visualize activity in the brain and the heart; to trace neuronal specific connections in the brain; and to enhance the brain cytoarchitecture after a systemic dose. Based on an ever-growing number of applications, MEMRI is proving useful as a new molecular imaging method to visualize functional neural circuits and anatomy as well as function in the brain in vivo. Paramount to the successful application of MEMRI is the ability to deliver Mn2+ to the site of interest at an appropriate dose and in a time-efficient manner. A major drawback to the use of Mn2+ as a contrast agent is its cellular toxicity. Therefore, it is critical to use as low a dose as possible. In the present work the different approaches to MEMRI are reviewed from a practical standpoint. Emphasis is given to the experimental methodology of how to achieve significant, yet safe, amounts of Mn2+ to the target areas of interest.
OPS Katalog 2011 - die wichtigsten Änderungen in Kürze (2011)

Der OPS – Katalog 2011 wurde in der letzten Oktoberwoche durch das DIMDI veröffentlicht [[1]]. Die Veränderungen gegenüber dem Katalog 2010 sind nicht unerheblich. Im folgenden Beitrag sollen die Änderungen kurz skizziert werden. Es werden zuerst die übergreifenden Änderungen und im Weiteren die speziellen Änderungen innerhalb der OPS-Kodes dargestellt.
Binding Properties of Human Anti‐DNA Antibodies to Cloned Human DNA Fragments (1989)

The DNA-anti-DNA antibody immune complexes were isolated from plasma of systemic lupus erythematosus (SLE) patients and DNA fragments separated from immune complexes were subjected to molecular cloning. The resulting recombinant DNA clones showed a molecular size of 37-79 base pairs, a high guanine and cytosine content, high frequencies of CpG dinucleotides, and palindromic sequences, and also clusters of G + C- and A + T-rich segments. These clones hybridized randomly to total human DNA. The reactivity of dsDNA antibodies, both monoclonal and polyclonal, from SLE was examined with a cloned SLE antigen DNA. A competitive inhibition assay showed that human monoclonal antibodies had at least one magnitude higher affinity to the cloned DNA than to the native DNA fragments. In order to characterize the factors that were recognized by antibodies, human G + C-rich and also A + T-rich 100 bp DNA fragments were cloned, and their base sequences determined. The antibody showed a higher affinity to the G + C-rich DNA fragment (71% G + C) than to the A + T-rich DNA fragment (46% G + C). When cytosines in CpG doublets in G + C-rich fragments were methylated (mCpG), the reactivity increased up to 100-fold. The native anti-DNA antibodies from SLE patients also showed preferential binding to G + C-rich fragments. These observations suggested that human anti-dsDNA antibodies may recognize some unique structures around the G + C regions or G + C clusters of DNA.
Development of an immunodetection test for a botulinum-like neurotoxin produced by Clostridium sp. RKD. (2006)

The Clostridium sp. RKD produced a potent neurotoxin earlier shown to have novelties. A specific detection assay for the neurotoxin has been developed that may be useful both from food safety and clinical point of view.
Unwarping of images taken by misaligned omnicameras without camera calibration by curved quadrilateral morphing using quadratic pattern classifiers (2009)

A method for solving the problem of unwarping a distorted omni-image taken by a lateral-direction misaligned omni-camera with its optical axis incoincident with its mirror axis is proposed. The method does not conduct camera calibration and is based on a new concept of two-stage image mapping from the real-world space to the distorted image space. The first stage is conducted in the camera manufacturing process and includes the generation of a pano-mapping function for mapping the real-world space to an undistorted image taken by an omni-camera with its optical and mirror axes being coincident. The second stage is conducted in an in-field environment when the omni-camera becomes lateral-direction misaligned and includes the generation of a distortion-mapping function that maps undistorted image pixels to distorted ones and the generation of a misalignment adjustment table that combines the pano-mapping and distortion-mapping functions to map the real-world space to the distorted image space. The distortion mapping function is generated by a new technique of curved quadrilateral morphing using quadratic pattern classifiers. The misalignment adjustment table is last used to unwarp distorted images conveniently by table lookup. Experimental results using simulated and real-image data show the feasibility of the proposed method.
Hue image RGB colour composition. A simple technique to suppress shadow and enhance spectral signature (1990)

Abstract A hue image derived from three multi-spectral image bands by a RGB-IHS (red, green and blue to intensity, hue and saturation) transformation is shadow free because the pixel values in a hue image are independent of illumination and are related to only the shapes of the spectral signatures of the three bands. Three hue images derived from three different band triplets of a multi-spectral image, when displayed as a colour composite, form a strongly coloured, shadow-free image termed a hue red/green/blue (HRGB) colour composite image. The colours in this image are determined by the shapes of the spectral signatures of all the bands used and the spectral information of up to nine bands can be encoded into one colour image. Field checks and comparison with a published geological map have shown that geological interpretation of a HRGB image derived from a Landsat Thematic Mapper (TM) image of a semi-arid area in south east Spain accurately reveals the distribution of major rock types and hydrothermal alteration zones associated with a gold deposit.