gebhart/patrepeval huggingface dataset:
Uranyl Acetate Causes DNA Single Strand Breaks In Vitro in the Presence of Ascorbate (Vitamin C) (2003)

Uranium is a radioactive heavy metal with isotopes that decay on the geological time scale. People are exposed to uranium through uranium mining, processing, the resulting mine tailings, and the use of depleted uranium in the military. Acute exposures to uranium are chemically toxic to the kidney; however, little is known about chronic exposures, for example, if there is a direct chemical genotoxicity of uranium. The hypothesis that is being tested in the current work is that hexavalent uranium, as uranyl ion, may have a chemical genotoxicity similar to that of hexavalent chromium. In the current study, reactions of uranyl acetate (UA) and ascorbate (vitamin C) were observed to produce plasmid relaxation in pBluescript DNA. DNA strand breaks increased with increasing concentrations of a 1:1 reaction of UA and ascorbate but were not affected by increasing the ratio of ascorbate. Plasmid relaxation was inhibited by coincubation of reactions with catalase but not by coincubation with the radical scavengers mannitol, sodium azide, or 5,5-dimethyl-1-pyrroline-N-oxide. Reactions of UA and ascorbate monitored by (1)H NMR spectroscopy showed formation of a uranyl ascorbate complex, with no evidence of a dehydroascorbate product. A previous study inferred that hydroxyl radical formation was responsible for oxidative DNA damage in the presence of reactions of uranyl ion, hydrogen peroxide, and ascorbate [Miller et al. (2002) J. Bioinorg. Chem. 91, 246-252]. Current results, in the absence of added hydrogen peroxide, were not completely consistent with the interpretation that strand breaks were produced by a Fenton type generation of reactive oxygen species. Data were also consistent with the interpretation that a uranyl ascorbate complex was catalyzing hydrolysis of the DNA-phosphate backbone, in a manner similar to that known for the lanthanides. These data suggest that uranium may be directly genotoxic and may, like chromium, react with DNA by more than one pathway.
Vertically Stacked Multilayer Photonics on Bulk Silicon Toward Three-Dimensional Integration (2015)

Vertically stacked hydrogenated amorphous silicon (a-Si:H) and aluminum nitride (AlN) photonic circuits are fabricated on bulk silicon using complementary metal-oxide semiconductor back-end-of-line-compatible technology. The 0.5 μm × 0.22 μm a-Si:H and 1 μm × 0.4 μm AlN channel waveguides exhibit relatively low propagation losses of ∼3.8 and ∼1.4 dB/cm at 1550-nm telecom wavelengths, respectively, thus enabling the realization of various high-performance photonic devices on these two layers, such as multimode interference power splitters, waveguide ring resonators, arrayed-waveguide gratings, etc. In particular, the a-Si:H layer is suitable for ultra-compact thermo-optic (TO) devices because of its large refractive index of ∼3.5 and large TO coefficient (TOC) of ∼2.60 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−4</sup> K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1 </sup> , whereas the AlN layer is suitable for large-size temperature-insensitive devices because of its relatively small refractive index of ∼2.0 and small TOC of ∼3.56 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−5</sup> K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−1 </sup> . A cascade directional coupler structure is proposed for connection between these two layers, which provides coupling efficiency of ∼ –1.0 dB, as estimated from numerical simulations. The feasibility of stacking different photonic layers on bulk Si paves the way to realize complex 3-D photonic circuits on chip which are not possible in the conventional single-layer configuration.
A common polymorphism in the annexin V Kozak sequence (−1C>T) increases translation efficiency and plasma levels of annexin V, and decreases the risk of myocardial infarction in young patients (2002)

Annexin V has phospholipid-binding capacity and plays a potent antithrombotic role. Recently, a C to T transition has been described in the Kozak region of this gene, affecting the nucleotide preceding the initiation ATG codon. We have developed a simple method to detect this genetic change, showing by analysis of 580 Mediterranean white subjects that the −1C to T transition (−1C&gt;T) is a common polymorphism (allele frequency, 0.121). This polymorphism is in linkage disequilibrium with a new C&gt;G polymorphism located 27 bp downstream in intron 2. We show that −1C/C carriers presented significantly lower plasma levels of annexin V than −1C/T subjects (0.45 ± 0.20 ng/mL versus 0.73 ± 0.28 ng/mL, respectively;P = .02). In vitro transcription/translation experiments support that the −1T allele increases translation efficiency. The clinical relevance of the −1C&gt;T change was investigated in consecutive patients with nontraumatic spontaneous intracranial hemorrhage (n = 225), deep venous thrombosis (n = 151), and coronary heart disease (n = 101). Finally, we also studied 166 survivors of an acute myocardial infarction occurring at age of 45 or less. This polymorphism seems to have a minor effect in bleeding disorders, but to play a protective role against early myocardial infarction, reducing by 2-fold the risk of developing the disease (P = .006; odds ratio, 0.51; 95% confidence interval, 0.30-0.85).
A subset of dendritic cells induces CD4+ T cells to produce IFN-γ by an IL-12–independent but CD70-dependent mechanism in vivo (2007)

Interferon (IFN)-gamma, a cytokine critical for resistance to infection and tumors, is produced by CD4(+) helper T lymphocytes after stimulation by cultured dendritic cells (DCs) that secrete a cofactor, interleukin (IL)-12. We have identified a major IL-12-independent pathway whereby DCs induce IFN-gamma-secreting T helper (Th)1 CD4(+) T cells in vivo. This pathway requires the membrane-associated tumor necrosis family member CD70 and was identified by targeting the LACK antigen from Leishmania major within an antibody to CD205 (DEC-205), an uptake receptor on a subset of DCs. Another major DC subset, targeted with 33D1 anti-DCIR2 antibody, also induced IFN-gamma in vivo but required IL-12, not CD70. Isolated CD205(+) DCs expressed cell surface CD70 when presenting antigen to T cell receptor transgenic T cells, and this distinction was independent of maturation stimuli. CD70 was also essential for CD205(+) DC function in vivo. Detection of the IL-12-independent IFN-gamma pathway was obscured with nontargeted LACK, which was presented by both DC subsets. This in situ analysis points to CD70 as a decision maker for Th1 differentiation by CD205(+) DCs, even in Th2-prone BALB/c animals and potentially in vaccine design. The results indicate that two DC subsets have innate propensities to differentially affect the Th1/Th2 balance in vivo and by distinct mechanisms.
Increased thalamic resting‐state connectivity as a core driver of LSD‐induced hallucinations (2017)

Hallucinogenic drug effects might be provoked by facilitations of cortical excitability via thalamocortical interactions. Our findings have implications for the understanding of the mechanism of action of hallucinogenic drugs and provide further insight into the role of the 5-HT<sub>2A</sub> -receptor in altered states of consciousness.
Photochromic heteroaromatic thiofulgides and dimethoxybutanoic acid lactones (2000)

Thiofulgides 1, (X = S) cyclise on irradiation with UV light to form thermally stable photochromes 2, (X = S) that absorb at much longer wavelengths than photochromes 2, (X = O), formed from corresponding fulgides 1, (X = O), reverse reactions occur on exposure to white light; photochromic thiofulgides are prepared by reaction of fulgides with sodium hydrosulfide in hot toluene and photochromic lactones 9 and 12 are prepared by reaction of fulgides with sodium hydrosulfide in cold methanol followed by cyclisation with a carbodiimide.
2D Depiction of Protein−Ligand Complexes (2007)

A method is presented for the automated preparation of schematic diagrams for protein-ligand complexes, in which the ligand is displayed in conventional 2D form, and the interactions to and between the residues in its vicinity are summarized in a concise and information-rich manner. The structural entities are arranged to maximize aesthetic ideals and to properly convey important distance relationships. The diagram is annotated with calculated hydrogen bonds, a substitution contour, solvent exposure, chelated metals, covalently bound linkages, pi-pi and pi-cation interactions, and, for series of complexes, conserved residues and interactions. Residues, cofactors, ions, and solvent components are drawn in cartoon form as adjuncts to the ligand. The method can be applied to aligned sets which contain multiple ligands, or multiple members of a protein family, in which case the ligand orientations and protein residue placement will show consistent trends throughout the series.
Weaving the invisible thread: design of an optically invisible metamaterial fibre (2010)

We present the design of an invisible metamaterial fibre operating at optical frequencies, which could be fabricated by adapting existing fibre drawing techniques. The invisibility is realised by matching the refractive index of the metamaterial fibre with the surroundings. We present a general recipe for the fabrication of such fibres, and numerically characterise a specific example using hexagonally arranged silver nanowires in a silica background. We find that invisibility is highly sensitive to details of the metamaterial boundary, a problem that is likely to affect most invisibility and cloaking schemes.
Splitting interfaces: making trust between applications and operating systems configurable (2006)

In current commodity systems, applications have no way of limiting their trust in the underlying operating system (OS), leaving them at the complete mercy of an attacker who gains control over the OS. In this work, we describe the design and implementation of Proxos, a system that allows applications to configure their trust in the OS by partitioning the system call interface into trusted and untrusted components. System call routing rules that indicate which system calls are to be handled by the un-trusted commodity OS, and which are to be handled by a trusted private OS, are specified by the application developer. We find that rather than defining a new system call interface, routing system calls of an existing interface allows applications currently targeted towards commodity operating systems to isolate their most sensitive components from the commodity OS with only minor source code modifications.We have built a prototype of our system on top of the Xen Virtual Machine Monitor with Linux as the commodity OS. In practice, we find that the system call routing rules are short and simple -- on the order of 10's of lines of code. In addition, applications in Proxos incur only modest performance overhead, with most of the cost resulting from inter-VM context switches.
Inflammation‐induced hyperexcitability of nociceptive gastrointestinal DRG neurones: the role of voltage‐gated ion channels (2004)

Gastrointestinal (GI) inflammation modulates the intrinsic properties of nociceptive dorsal root ganglia neurones, which innervate the GI tract and these changes are important in the genesis of abdominal pain and visceral hyperalgesia neurones exhibit hyperexcitability characterized by a decreased threshold for activation and increased firing rate, and changes in voltages-gated Na(+) and K(+) channels play a major role in this plasticity. This review highlights emerging evidence that specific subsets of channels and signalling pathways are involved and their potential to provide novel selective therapeutics targets for the treatment of abdominal pain.
Development and Clinical Application of Near-Infrared Surgical Microscope: Preliminary Report (2001)

Visualization of near-infrared fluorescence through a surgical microscope can provide intraoperative information about deep-seated tissues. We studied the possibility of taking a near-infrared image through a surgical microscope after intravenous injection of indocyanine green (ICG). The surgical microscopes we used were Zeiss models OPMI MD and OPMI CS-NC. We used a halogen lamp as a light source, a band pass filter of 760 - 810 nm as an excitation filter, a laser light of 800 nm as an external light source, and a band pass filter of 820 - 920 nm as a barrier filter. Near-infrared fluorescence of vessels on the brain surface and of the dural sinus was visualized through the dura mater after intravenous injection of 25 mg ICG using a Hitachi KP-160 camera. Near-infrared fluorescence of vessels on the brain surface was observed through the dura mater. Venous images were clearer than were arterial ones. The dural sinus and the bridging veins were also clearly visualized. These results suggest that a clinical application of near-infrared fluorescence microscopy is possible. However, a stronger fluorescence emitted from ICG will be necessary for such a microscope to have practical use.
Flow-Tube Kinetics of Gas-Phase Chemical Vapor Deposition Reactions: TiN from Ti(NMe2)4 and NH3 (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFlow-Tube Kinetics of Gas-Phase Chemical Vapor Deposition Reactions: TiN from Ti(NMe2)4 and NH3Bruce H. Weiller and Brenda V. PartidoCite this: Chem. Mater. 1994, 6, 3, 260–261Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/cm00039a002https://doi.org/10.1021/cm00039a002research-articleACS PublicationsRequest reuse permissionsArticle Views97Altmetric-Citations18LEARN 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
Antibody Engineering as Opportunity for Selection and Optimization of Anti- HIV Therapeutic Agents (2010)

Since among patients who receive care for HIV-1 infection, the prevalence of antiretroviral drug resistance is 50%, clearly, new approaches to control viral replication are needed. A hundred years later the first proposal of a magic bullet by Paul Ehrlich antibody -based therapeutics currently enjoys unprecedented success. The methodologies devel- oped in these years such as antibody library, phage display, single domain antibody and the possibility to modify the al- ready well-studied antibodies in a way to render them more suitable for the specific purpose, make antibody a different and valid alternative therapy. Four human\humanized antibodies for anti HIV treatment are currently in clinical trial with some promising results. They target different antigens: the gp120 of the viral coat and the receptor or co-receptor of the virus. The development of therapeutic antibody in HIV field is progressing slowly but today, the improvement in the knowledge of antibody structure and function together with advances in protein engineering can be used to reshape anti- body molecules and devise strategies to obtain more suitable antibody for therapy.
Best Practices in Bioassay Development to Support Registration of Biopharmaceuticals (2019)

Biological activity is a critical quality attribute for biopharmaceuticals, which is accurately measured using an appropriate relative potency bioassay. Developing a bioassay is a complex, rigorous undertaking that needs to address several challenges including modelling all of the mechanisms of action associated with the biotherapeutic. Bioassay development is also an exciting and fast evolving field, not only from a scientific, medical and technological point of view, but also in terms of statistical approaches and regulatory expectations. This has led to an industry-wide discussion on the most appropriate ways to develop, validate and control the bioassays throughout the drug lifecycle.
BONE MARROW TRANSPLANTATION DEPLETED OF T CELLS FOLLOWED BY REPLETION WITH INCREMENTAL DOSES OF DONOR LYMPHOCYTES FOR RELAPSING PATIENTS WITH CHRONIC MYELOID LEUKEMIA (2000)

Escalating DLI leads to safe new molecular CR in most CML relapse patients. These results raise the possibility of using "safe" transplantation programs of T-cell depletion, that include graded DLI as prevention against disease recurrence.
The influence of optical fiber bundle parameters on the transmission of laser speckle patterns (2014)

Laser speckle imaging (LSI) techniques provide important functional information about tissue perfusion and mechanical properties. To perform LSI in vivo, laser speckle patterns are transmitted via optical fiber bundles incorporated within small-diameter endoscopes. Inter-fiber crosstalk due to mode coupling in fiber bundles can result in erroneous speckle statistics and therefore reduces the accuracy of LSI analysis. In this paper, we investigate the influence of multiple parameters that influence crosstalk between neighboring cores within optical fiber bundles and govern the modulation of transmitted laser speckle patterns. Our results show that in addition to large core-to-core separation, large refractive index contrast between core and cladding material, reduced number of propagating modes and variability in core size are essential parameters for accurate speckle pattern transmission to conduct endoscopic LSI.
Syngeneic response to SJL follicular center B cell lymphoma (reticular cell sarcoma) cells is primarily in V beta 16+ CD4+ T cells (1993)

The growth of SJL B cell lymphomas (RCS, reticulum cell sarcoma) in vivo and in vitro is known to depend on cytokine production by RCS-responsive host CD4+ T cells. The high frequency of RCS responsive cells in normal SJL lymph nodes prompted us to prepare a set of 21 RCS-specific T cell hybridomas. Like normal SJL T cells, these hybridoma cells respond to RCS, but not to normal syngeneic B cells; produce IL-2, IL-4, and IL-5; and promote growth of RCS in gamma-irradiated syngeneic hosts. A superantigen-like stimulation by RCS cells was borne out by the fact that all the RCS-specific hybridomas used V beta 16 in their TCR. RCS cells did not stimulate I-As-restricted, V beta 17a+ KLH-specific, or V beta 1+ heme-specific hybridomas, but were excellent Ag presents for these cells. Preincubation of RCS cells with high concentrations of the KM core peptide (high affinity for I-As) did not interfere with the ability of RCS to stimulate RCS-specific hybridomas. The relative representation of mRNA for V beta 1, 4, 10, 15, 16, and 17a was evaluated in RNA extracted from normal SJL lymph node cells responding to Con A or to RCS cells. Only V beta 16 was specifically enriched in the response to RCS. Moreover, the degree of responsiveness to RCS cells in lymph node cells from F1 hybrids of SJL and I-E transgenic SJL mice, corresponds to the relative abundance of V beta 16 in mRNA, but not of V beta 17a mRNA.
Using sideband transitions for two-qubit operations in superconducting circuits (2009)

We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation.
Arginase I induction in macrophages, triggered by Th2‐type cytokines, supports the growth of intracellular Leishmania parasites (2002)

Leishmania spp. are intracellular protozoan parasites that invade and replicate within macrophages. In a previous report, we have demonstrated that the growth of intracellular amastigotes could be controlled by inhibition of arginase. This enzyme, induced in host cells by Th2 cytokines, synthesizes L-ornithine which can be used by parasites to generate polyamines and proliferate. In this study, we have designed experiments to better analyse the dependence of parasite proliferation on arginase induction in infected macrophages. Treatment of Leishmania major-infected BALB/c macrophages with interleukin (IL)-4, IL-10 or transforming growth factor-beta, which are all inducers of arginase I in murine macrophages, led to a proportional increase in the number of intracellular amastigotes. Moreover, parasite proliferation and arginase activity levels in macrophages from the susceptible BALB/c mice were significantly higher than those from infected C57BL/6 cells when treated with identical doses of these cytokines, indicating that a strong correlation exist between the permissibility of host cells to L. major infection and the induction of arginase I in macrophages. Specific inhibition of arginase by N(omega)-hydroxy-nor-L-arginine (nor-LOHA) reverted growth, while L-ornithine and putrescine promoted parasite proliferation, indicating that the parasite cell division depends critically on the level of L-ornithine available in the host. Therefore, arginase induction in the context of a Th2 predominant response might be a contributor to susceptibility in leishmaniasis.
Treatment of demodicosis in dogs: 2011 clinical practice guidelines (2012)

Demodicosis can usually be diagnosed by deep skin scrapings or trichograms; in rare cases a skin biopsy may be needed for diagnosis. Immune suppression due to endoparasitism or malnutrition in young dogs and endocrine diseases, neoplasia and chemotherapy in older dogs are considered predisposing factors and should be diagnosed and treated to optimize the therapeutic outcome. Dogs with disease severity requiring parasiticidal therapy should not be bred. Secondary bacterial skin infections frequently complicate the disease and require topical and/or systemic antimicrobial therapy. There is good evidence for the efficacy of weekly amitraz rinses and daily oral macrocyclic lactones such as milbemycin oxime, ivermectin and moxidectin for the treatment of canine demodicosis. Weekly application of topical moxidectin can be useful in dogs with milder forms of the disease. There is some evidence for the efficacy of weekly or twice weekly subcutaneous or oral doramectin. Systemic macrocyclic lactones may cause neurological adverse effects in sensitive dogs, thus a gradual increase to the final therapeutic dose may be prudent (particularly in herding breeds). Treatment should be monitored with monthly skin scrapings and extended beyond clinical and microscopic cure to minimize recurrences.