gebhart/patrepeval huggingface dataset:
Self-organization of gold nanoclusters on hexagonal SiC and SiO2 surfaces (2007)

Very thin Au layers were deposited on SiC hexagonal and SiO2 substrates by sputtering. The Au surface diffusion, clustering, and self-organization of Au nanoclusters on these substrates, induced by thermal processes, were investigated by Rutherford backscattering spectrometry, atomic force microscopy, scanning electron microscopy, and transmission electron microscopy. On both types of substrates, clustering is shown to be a ripening process of three-dimensional structures controlled by surface diffusion and the application of the ripening theory allowed us to derive the surface diffusion coefficient and all other parameters necessary to describe the entire process. The system Au nanoclusters/SiC and Au nanoclusters/SiO2 are proposed as nanostructured materials for nanoelectronic and nanotechnology applications.
Background charge noise in metallic single-electron tunneling devices (1996)

With the help of two single-electron tunneling transistors whose islands were positioned about 100 nm apart, a low-frequency charge noise generated in the ${\mathrm{Al}}_{2}$${\mathrm{O}}_{3}$ substrate has been measured. The signals detected by these electrometers have shown a 10--20 % correlation in power in the 1--10-Hz range. Using a simple model we show that the charge noise sources (fluctuating traps) can be distributed either in thin dielectric layers (including the barriers) adjacent to the islands or, alternatively but more likely, in a volume of the substrate. \textcopyright{} 1996 The American Physical Society.
Neuropsychiatric Symptoms Associated With Hepatitis C and Interferon Alpha: A Review (2000)

Psychiatrists should become familiar with the clinical spectrum associated with hepatitis C virus infection as well as the neuropsychiatric symptoms related to hepatitis C and IFN-alpha treatment. More studies are necessary to define the neuropsychiatric syndromes associated with this population and to find possible effective treatments. Furthermore, research is needed so that patients with psychiatric problems are not excluded from effective treatments for this growing medical problem.
Rapid mobilization of functional donor hematopoietic cells without G-CSF using AMD3100, an antagonist of the CXCR4/SDF-1 interaction (2008)

Allografts from HLA-matched sibling donors were mobilized and collected without granulocyte colony-stimulating factor (G-CSF) using AMD3100, a direct antagonist of CXCR4/stromal-derived factor 1 (SDF-1/CXCL12). Donors (N = 25) were treated with AMD3100 at a dose of 240 mug/kg by subcutaneous injection, and leukapheresis was then initiated just 4 hours later. Two-thirds of the donors collected an allograft with a CD34(+) cell dose sufficient for transplantation after just one dose of AMD3100. No donor experienced more than grade 1 toxicity. After a myeloablative regimen, 20 patients with hematologic malignancies received allografts collected after AMD3100 alone. All patients engrafted neutrophils (median day 10) and platelets (median day 12) promptly. Acute graft-versus-host disease (GVHD) grades 2 through 4 occurred in 35% of patients. One patient died due to complications related to acute GVHD. No unexpected adverse events were observed in any of the recipients. All 14 patients surviving in remission have robust trilineage hematopoiesis and are transfusion-free with a median follow-up of 277 days (range, 139-964 days). Direct antagonism of CXCR4 by AMD3100 may provide a more rapid and possibly less toxic and cumbersome alternative to traditional G-CSF-based mobilization in normal donors. This trial was registered as no. NCT00241358 at www.ClinicalTrials.gov.
Adverse effects associated with the intrathecal administration of ziconotide (2000)

The omega-conopeptide, ziconotide, is an N-type calcium-channel blocker that has been shown to produce antinociception in animals using formalin and hot-plate tests. Initial reports of intrathecal administration of ziconotide in cancer and AIDS patients whose pain was unrelieved with opioids demonstrated analgesic efficacy. Although adverse effects were reported, these appeared to be easily managed through dose reduction or symptomatic treatment. This clinical report describes the experiences of three patients with serious adverse effects associated with intrathecal ziconotide.
Characteristics of microfabricated rectangular coax in the Ka band (2004)

Abstract Miniature rectangular coaxial transmission line (with a 300 × 300 μm outer conductor) is simulated, fabricated, and tested up to the Ka band. It is made by the electrochemical fabrication (EFAB™) of nickel such that the center conductor is supported primarily by ≈λ/4 stubs that also establish a resonant passband. The minimum insertion loss of a 1.67‐cm‐long test structure is found to be 1.74 dB at the passband center of 29 GHz. This is within 0.57 dB of the lowest insertion loss predicted by full‐wave numerical simulations, indicative of the high precision and smooth surface morphology of the EFAB process. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 40: 365–368, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.11383
ETS-related Transcription Factors ETV4 and ETV5 Are Involved in Proliferation and Induction of Differentiation-associated Genes in Embryonic Stem (ES) Cells (2015)

The pluripotency and self-renewal capacity of embryonic stem (ES) cells is regulated by several transcription factors. Here, we show that the ETS-related transcription factors Etv4 and Etv5 (Etv4/5) are specifically expressed in undifferentiated ES cells, and suppression of Oct3/4 results in down-regulation of Etv4/5. Simultaneous deletion of Etv4 and Etv5 (Etv4/5 double knock-out (dKO)) in ES cells resulted in a flat, epithelial cell-like appearance, whereas the morphology changed into compact colonies in a 2i medium (containing two inhibitors for GSK3 and MEK/ERK). Expression levels of self-renewal marker genes, including Oct3/4 and Nanog, were similar between wild-type and dKO ES cells, whereas proliferation of Etv4/5 dKO ES cells was decreased with overexpression of cyclin-dependent kinase inhibitors (p16/p19, p15, and p57). A differentiation assay revealed that the embryoid bodies derived from Etv4/5 dKO ES cells were smaller than the control, and expression of ectoderm marker genes, including Fgf5, Sox1, and Pax3, was not induced in dKO-derived embryoid bodies. Microarray analysis demonstrated that stem cell-related genes, including Tcf15, Gbx2, Lrh1, Zic3, and Baf60c, were significantly repressed in Etv4/5 dKO ES cells. The artificial expression of Etv4 and/or Etv5 in Etv4/5 dKO ES cells induced re-expression of Tcf15 and Gbx2. These results indicate that Etv4 and Etv5, potentially through regulation of Gbx2 and Tcf15, are involved in the ES cell proliferation and induction of differentiation-associated genes in ES cells.
Stereoselective induction of an axiel chirality by Suzuki cross coupling of tricarbonyl(arene)chromium complexes with arylboronic acids (1994)

Tricarbonyl(2,6-disubstituted-1-bromobenzene)chromium was treated with ortho-substituted phenylboronic acids in the presence of a palladium(0) catalyst to give mono-Cr(CO)3 complexes of biphenyl componds with a complementary axial chirality depending upon the nature of ortho-substituent of the phenylboronic acids
Fifty Years of Molecular (DNA/RNA) Diagnostics (2005)

As the journal Clinical Chemistry celebrates its 50th birthday and enters its 51st year, we reflect on recent advances in nucleic acid diagnostics. Although the structure of DNA was also described ∼50 years ago, only 20 years have past since a practical method of amplifying DNA for the clinical laboratory appeared, well known today as the PCR. Since the advent of PCR, growth in nucleic acid diagnostics has been extraordinary and is the fastest growing segment of many clinical laboratories. Clinical Chemistry is now subtitled The International Journal of Molecular Diagnostics and Laboratory Medicine in recognition of the importance of DNA/RNA diagnostics.

In this review, we offer personal perspectives on five key advances in molecular diagnostics by some of the pioneers in the field. Russ Higuchi reviews real-time PCR, which is an elegant solution for nucleic acid quantification in research and the clinical laboratory. Carl Wittwer describes DNA melting analysis as a simple and surprisingly powerful tool that can be seamlessly appended to PCR. Tom Gingeras reviews the increasing power of array technology, with feature density rivaling microelectronics miniaturization. Progress on integrated devices that combine cell separation, sample preparation, amplification, and analysis is described by Larry Kricka. Finally, the field of circulating nucleic acids is reviewed by Dennis Lo, with a myriad of clinical applications enabled by a new understanding of the biology of extracellular DNA and RNA.

Many early advances in molecular diagnostics have been highlighted in Clinical Chemistry . With DNA/RNA diagnostics becoming ever more important in the 21st century, the Journal serves as an advanced window into the future of molecular clinical chemistry.

—Russ Higuchi

When late in 1986 I joined Cetus, the birthplace of PCR, “closed-tube” PCR using a thermostable DNA polymerase had just been achieved (1)(2). Before this, the thermolabile polymerase had to …
Irradiation Induces Upregulation of CD31 in Human Endothelial Cells (1999)

Radiation-induced vascular injury is believed to be a major factor contributing to parenchymal atrophy, fibrosis and necrosis in normal tissue after radiotherapy. In this study irradiation of human umbilical vein endothelial cells (HUVECs) significantly increased adherence of U-937 cells in a time-dependent manner. Given the potential multifunctional role of CD31 in the vasculature we have examined the possible effects of irradiation on levels of CD31 expression in HUVECs. Irradiation upregulated CD31 expression on HUVECs, independently of initial plating density and radiation-induced changes such as cell number, cell cycle stage, or cell size. CD31 mRNA levels were raised in irradiated HUVECs relative to controls. Both CD31 mRNA and surface protein showed similar changes, suggesting that the increase in mRNA in irradiated HUVECs is responsible for the elevation in cell surface protein. A semi-quantitative study of tissue specimens from patients who had received radiotherapy indicated that CD31 staining in the blood vessels from irradiated tissues was increased compared with controls. Endothelial CD31 is important in the transmigration of leukocytes. We have demonstrated that the incorporation of monoclonal antibody to CD31 significantly inhibited the transmigration of human peripheral blood leukocytes through a monolayer of irradiated HUVECs. Taken together these data strongly suggest that irradiation induces a marked increase in CD31 expression on endothelial cells as part of a general response to irradiation. Its upregulation may play an important role in the development of radiation-induced normal tissue damage and thus is a possible target for therapeutic intervention.
The reaction of the hydroxyl radical with glutathione in neutral and alkaline aqueous solution. (1982)

SJOBERG, L., ERIKSEN, T. E., AND REVESZ, L. The Reaction of the Hydroxyl Radical with Glutathione in Neutral and Alkaline Aqueous Solution. Radiat. Res. 89, 255-263 (1982). The reaction of OH with glutathione (y-glu-cys-gly) in neutral and alkaline aqueous solutions has been studied by pulse radiolysis. In addition to the sulfur-centered GS.(GSSG-.) radical formed by electron transfer or hydrogen abstraction from GS- (GSH), at least one carbon-centered radical is formed with pH-dependent yield by hydrogen abstraction from the y carbon or the amino group on the 'y-glutamyl moiety. The latter radical is transformed in a first-order reaction most probably to a carbon-centered radical on the cysteine group. No evidence for the formation of carbon-centered radicals was found in comparable experiments with cysteine and 2-mercaptopropionylglycine.
A COMPARISON OF IVHS PROGRESS IN THE UNITED STATES, EUROPE, AND JAPAN (1993)

Related Projects in Japan In order to successfully launch the info-mobility or IVHS/RTI systems in the society, many advanced technologies could be properly utilized with necessary R&D and related activities. The realizations of the info-mobility related systems also require relatively long time range from concept and R&D stages to final realization of the systems. How to efficiently coordi- nate these different stages ranging many years could be one of the important and difficult problems we face today to successfully launch the systems in the society. This paper describes the follow- ing items with some examples of the past and presently on-going info-mobility related projects in Japan, i.e., roles of public organizations, phases of activities, cooperations between public and private sectors, etc. TOTAL NUMBER OF THE AUTOMOBLIES in use in Japan has reached to a level of 58 million units in 1990, meaning that one of two people owns an automobile in the total population of 120 million. Whereas the road infrastructures satisfying the auto- mobile traffic are not well established compared with the US and Europe. * Numbers in parentheses designate references at end of paper. Hironao Kawashima Keio University Haruki Fujii Assn. of Electronic Tech. for Auto. Traffic and Driving (JSK) Kozo Kitoh JSK Info-Mobility Res. Committee The expressway extension per 1000 vehicles accounts for ca. one fifth and one third of those in the US and Germany, respectively, i.e., high density traffic with extended expressways of 5200km. As for normal road, the situations are similar to those of expressways. Narrow and small flat area of Japan makes also difficult to construct the road network. Under these circumstances, National Police Agency and Ministry of Construction have been making their respective invest- ments for the constructions of traffic control system and road traffic information providing-device continuously rather from early days. Presently, the traffic control systems are already introduced in 74 cities across the nation. As for the domestic market of auto- mobiles, the auto manufacturers have been placed under severe competitive conditions in terms of launching new models especially equipped with new features favorable for consumers. In these regards, the intensive uses of micro-electronics and communication technology are strongly acknowledged as the market trend compared with those of the US and Europe, enabling the launch of auto- mobile navigation system. Beside these typical Japanese back- grounds above, those problems, such as increasing traffic accidents, growing number of elderly people, global environ- mental problems, etc., have come out. In order to meet the existing and newly coming out problems Japan faces today, extensive use of information technology, moreover the integration of automobile and road funct- ions, i.e., the realization of the info-
Vectorizing Face Images by Interleaving Shape and Texture Computations (1995)

The correspondence problem in computer vision is basically a matching task between two or more sets of features. Computing feature correspondence is of great importance in computer vision, especially in the subfields of object recognition, stereo, and motion. In this paper, weintroduce a vectorized image representation, which is a feature-based representation where correspondence has been established with respect to a reference image. The representation consists of two image measurements made at the feature points: shape and texture. Feature geometry, or shape, is represented using the (x# y) locations of features relative to the some standard reference shape. Image grey levels, or texture, are represented by mapping image grey levels onto the standard reference shape. Computing this representation is essentially a correspondence task, and in this paper we explore an automatic technique for &amp;quot;vectorizing&amp;quot; face images.
Ultraviolet Light and Osmotic Stress: Activation of the JNK Cascade Through Multiple Growth Factor and Cytokine Receptors (1996)

Exposure of mammalian cells to ultraviolet (UV) light or high osmolarity strongly activates the c-Jun amino-terminal protein kinase (JNK) cascade, causing induction of many target genes. Exposure to UV light or osmotic shock induced clustering and internalization of cell surface receptors for epidermal growth factor (EGF), tumor necrosis factor (TNF), and interleukin-1 (IL-1). Activation of the EGF and TNF receptors was also detected biochemically. Whereas activation of each receptor alone resulted in modest activation of JNK, coadministration of EGF, IL-1, and TNF resulted in a strong synergistic response equal to that caused by exposure to osmotic shock or UV light. Inhibition of clustering or receptor down-regulation attenuated both the osmotic shock and UV responses. Physical stresses may perturb the cell surface or alter receptor conformation, thereby subverting signaling pathways normally used by growth factors and cytokines.
Solution Redox Chemistry of Carbon Nanotubes (2004)

UV/vis/NIR absorbance spectra were used to monitor electron transfer between small-molecule redox reagents and carbon nanotubes (CNTs). The oxidation of (6, 5)-enriched nanotubes in water with K(2)Ir(Cl)(6) reveals a valence electron density of 0.2-0.4 e(-)/100 carbon atoms and a reduction potential of approximately 800 mV versus NHE. The reduction potential of CNTs is found to increase with increasing band gap and to decrease with the introduction of an anionic dispersant. In light of this newly revealed redox chemistry of CNTs, we propose that the previously observed bleaching of the CNT absorbance spectrum at low pH is most likely a consequence of the oxidation of the nanotubes by oxygen. These results demonstrate facile oxidation and reduction of CNTs, provide a way to quantify the population of valence electrons, and point to possible applications of CNT in the catalysis of redox reactions.
Antibody-Drug Conjugates for Cancer Therapy (2008)

The antibody-drug conjugate (ADC) concept is to use an antibody to deliver a cytotoxic drug selectively to a target such as a tumor-associated antigen. Such conjugates represent a broadly applicable approach to enhance the antitumor activity of antibodies and improve the tumor-to-normal tissue selectivity of chemotherapy. Critical parameters for ADC development include target antigen selection, conjugate internalization by tumor cells, drug potency and stability of the linker between drug and antibody. Other important considerations include the conjugation methods, drug-to-antibody ratio, and the effects of drug conjugation on antibody properties. Highly potent drugs with more stable linkers have been attached to a new generation of antibodies to create conjugates with pronounced antitumor activities in preclinical studies and encouraging results in early stage clinical trials. This review details these advances, discusses some of the remaining challenges, and overviews ADCs currently in clinical trials for cancer therapy.
Gene therapy with a single chain interleukin 12 fusion protein induces T cell-dependent protective immunity in a syngeneic model of murine neuroblastoma (1998)

A major goal of tumor immunotherapy is the effective eradication of established metastases associated with the induction of a T cell-mediated protective immunity. We achieved this in a poorly immunogenic murine neuroblastoma model by gene therapy with a single chain interleukin 12 (scIL-12) fusion protein that assures equal expression of its p35 and p40 subunits. Thus, NXS2 hybrid neuroblastoma cells (C1300 x dorsal root ganglion cells), which form experimental bone marrow and liver metastases in syngeneic A/J mice, were transduced with a gene encoding murine interleukin 12, monomerized by introduction of a protein linker between the p35 and p40 protein chains of this heterodimeric cytokine. We demonstrate for the first time that subcutaneous vaccination with these transduced cells induces a protective immunity, as indicated by the complete absence of liver and bone marrow metastasis after challenge with NXS2 wild-type tumor cells. Furthermore, vaccination of animals with established liver and bone marrow metastases completely eradicated liver metastases and suppressed bone marrow metastases. The local and systemic immune response against scIL-12-transduced NXS2 cells is largely dependent on CD8(+) T cells. This was demonstrated in vivo by depletion of immunocompetent A/J mice with monoclonal anti-CD4 and anti-CD8 antibodies and in vitro by specific major histocompatibility complex, class I-restricted CD8(+) T cell-mediated killing of NXS2 and their parental C1300 neuroblastoma cells. In conclusion, we demonstrate successful anti-tumor immunotherapy with an scIL-12 fusion protein that could facilitate clinical application of interleukin 12 gene therapy.
Cloning and Biological Activity of Epigen, a Novel Member of the Epidermal Growth Factor Superfamily (2001)

High throughput sequencing of a mouse keratinocyte library was used to identify an expressed sequence tag with homology to the epidermal growth factor (EGF) family of growth factors. We have named the protein encoded by this expressed sequence tag Epigen, for epithelial mitogen. Epigen encodes a protein of 152 amino acids that contains features characteristic of the EGF superfamily. Two hydrophobic regions, corresponding to a putative signal sequence and transmembrane domain, flank a core of amino acids encompassing six cysteine residues and two putative N-linked glycosylation sites. Epigen shows 24-37% identity to members of the EGF superfamily including EGF, transforming growth factor alpha, and Epiregulin. Northern blotting of several adult mouse tissues indicated that Epigen was present in testis, heart, and liver. Recombinant Epigen was synthesized in Escherichia coli and refolded, and its biological activity was compared with that of EGF and transforming growth factor alpha in several assays. In epithelial cells, Epigen stimulated the phosphorylation of c-erbB-1 and mitogen-activated protein kinases and also activated a reporter gene containing enhancer sequences present in the c-fos promoter. Epigen also stimulated the proliferation of HaCaT cells, and this proliferation was blocked by an antibody to the extracellular domain of the receptor tyrosine kinase c-erbB-1. Thus, Epigen is the newest member of the EGF superfamily and, with its ability to promote the growth of epithelial cells, may constitute a novel molecular target for wound-healing therapy.
High Pressure Behavior ofZrW2O8: Grüneisen Parameter and Thermal Properties (2000)

High pressure Raman spectroscopic studies are carried out on negative thermal expansion material ZrW2O8. The system exhibits amorphization at 2.2+/-0.3 GPa via an intermediate orthorhombic phase. In the cubic phase most modes below 50 meV are found to have negative Gruneisen parameter. Using the reported phonon density of states thermal properties are calculated and compared with the reported results. In contrast to the earlier belief, the present results show that modes of energies much higher than 10 meV also contribute substantially to the negative thermal expansion.
A Salmonella typhimurium virulence protein is similar to a Yersinia enterocolitica invasion protein and a bacteriophage lambda outer membrane protein (1991)

The phoP-phoQ-regulated pagC locus is essential for full virulence and survival within macrophages of Salmonella typhimurium. The protein product, DNA sequence, and transcript of pagC were determined. The pagC locus encodes a single 188-amino-acid membrane protein that is similar to the ail-encoded eucaryotic cell invasion protein of Yersinia enterocolitica and the lom-encoded protein of bacteriophage lambda. The similarity of PagC and Ail to Lom leads us to hypothesize that Lom is a virulence protein and that bacteriophage gene transfer and lysogeny could have led to the development of proteins essential to survival within macrophages and eucaryotic cell invasion.