gebhart/patrepeval huggingface dataset:
Degeneracy-Preserving Quantum Nondemolition Measurement of Parity-Type Observables for Cat Qubits (2017)

A central requirement for any quantum error correction scheme is the ability to perform quantum nondemolition measurements of an error syndrome, corresponding to a special symmetry property of the encoding scheme. It is in particular important that such a measurement does not introduce extra error mechanisms, not included in the error model of the correction scheme. In this Letter, we ensure such a robustness by designing an interaction with a measurement device that preserves the degeneracy of the measured observable. More precisely, we propose a scheme to perform continuous and quantum nondemolition measurement of photon-number parity in a microwave cavity. This corresponds to the error syndrome in a class of error correcting codes called the cat codes, which have recently proven to be efficient and versatile for quantum information processing. In our design, we exploit the strongly nonlinear Hamiltonian of a high-impedance Josephson circuit, coupling a high-Q cavity storage cavity mode to a low-Q readout one. By driving the readout resonator at its resonance, the phase of the reflected or transmitted signal carries directly exploitable information on parity-type observables for encoded cat qubits of the high-Q mode.
Metabolism of poly-β-hydroxybutyrate. II. Enzymic synthesis of D-(-)-β-hydroxybutyryl coenzyme A by an enoyl hydrase from Rhodospirillum rubrum (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetabolism of poly-β-hydroxybutyrate. II. Enzymic synthesis of D-(-)-β-hydroxybutyryl coenzyme A by an enoyl hydrase from Rhodospirillum rubrumGerard Jay Moskowitz and Joseph M. MerrickCite this: Biochemistry 1969, 8, 7, 2748–2755Publication Date (Print):July 1, 1969Publication History Published online1 May 2002Published inissue 1 July 1969https://pubs.acs.org/doi/10.1021/bi00835a009https://doi.org/10.1021/bi00835a009research-articleACS PublicationsRequest reuse permissionsArticle Views318Altmetric-Citations98LEARN 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
Characteristics and specificity of acquired immunologic memory to Mycobacterium tuberculosis infection. (1988)

The results herein show that mice infected with Mycobacterium tuberculosis and then exposed to a protracted course of isoniazid chemotherapy possess a heightened state of acquired resistance to subsequent challenge with the homologous organism. Our results provide the first evidence, moreover, that this resistance is mediated by a long-lived, cyclophosphamide- and irradiation-resistant L3T4+ Lyt-2- lymphocyte capable of giving rise to an accelerated re-emergence of resistance in the animal upon rechallenge. Evidence is also provided to show that triggering of this memory-immune T cell population in the re-challenged host was associated with the rapid emergence of non-specific resistance to secondary bacterial infection; however, the accelerated emergence of this population was only observed if the challenge inoculum consisted of the living organism. The relevance of this latter finding to strategies for vaccine development is discussed.
Direct Adenoviral Gene Transfer of Viral IL-10 to Rabbit Knees with Experimental Arthritis Ameliorates Disease in Both Injected and Contralateral Control Knees (1999)

Abstract IL-10, a cytokine produced primarily by macrophages, B lymphocytes, and Th2 cells, has both immunostimulatory and immunosuppressive properties. A homologue of IL-10 encoded by EBV, known as viral IL-10 (vIL-10), is also able to suppress the immune response, but may lack some of the immunostimulatory properties of IL-10. To evaluate the potential of vIL-10 to block the progression of rheumatoid arthritis, we have utilized a replication-defective adenovirus vector to deliver the gene encoding vIL-10 to the knee joints of rabbits with Ag-induced arthritis. Intraarticular expression of vIL-10 significantly reduced leukocytosis, cartilage matrix degradation, and levels of endogenous rabbit TNF-α, as well as the degree of synovitis, while maintaining high levels of cartilage matrix synthesis. Interestingly, an antiarthritic effect was also observed in opposing contralateral control knee joints that received only a marker gene. An adenoviral vector carrying the enhanced green fluorescent protein marker gene was used to demonstrate that a morphologically similar subset of cells infected in the injected knee joint are able to traffic to the uninjected contralateral knee joint. Our results suggest that direct, local intraarticular delivery of the vIL-10 gene may have polyarticular therapeutic effects.
Interleukin-1 in the pathogenesis and treatment of inflammatory diseases (2011)

More than any other cytokine family, the IL-1 family of ligands and receptors is primarily associated with acute and chronic inflammation. The cytosolic segment of each IL-1 receptor family member contains the Toll-IL-1-receptor domain. This domain is also present in each Toll-like receptor, the receptors that respond to microbial products and viruses. Since Toll-IL-1-receptor domains are functional for both receptor families, responses to the IL-1 family are fundamental to innate immunity. Of the 11 members of the IL-1 family, IL-1β has emerged as a therapeutic target for an expanding number of systemic and local inflammatory conditions called autoinflammatory diseases. For these, neutralization of IL-1β results in a rapid and sustained reduction in disease severity. Treatment for autoimmune diseases often includes immunosuppressive drugs whereas neutralization of IL-1β is mostly anti-inflammatory. Although some autoinflammatory diseases are due to gain-of-function mutations for caspase-1 activity, common diseases such as gout, type 2 diabetes, heart failure, recurrent pericarditis, rheumatoid arthritis, and smoldering myeloma also are responsive to IL-1β neutralization. This review summarizes acute and chronic inflammatory diseases that are treated by reducing IL-1β activity and proposes that disease severity is affected by the anti-inflammatory members of the IL-1 family of ligands and receptors.
Oligonucleotide Mediated Gene Targeting in Mammalian Cells (2004)

Gene targeting can be loosely defined as a process through which a specific chromosomal sequence is recognized and bound by a reagent designed for the purpose. The endpoint may be modulation of events at the target, such as transcription, or a permanent change in sequence at the site. A facile strategy for mammalian cells would have broad applications in basic and applied research, including gene therapy. Although approaches based on homologous recombination are routinely employed for transgenic animal construction, they are too laborious and inefficient for broader use. Consequently there has been a longstanding interest in developing effective synthetic reagents. Sequence recognition can be either at the level of a single strand or via the major or minor grooves, and specific approaches for each route are under development. In this review several oligonucleotide-based strategies will be discussed. These include single and double strand oligonucleotides designed to attack single strand targets, and triple helix forming olgonucleotides and peptide nucleic acids, intended for double stranded targets.
Detectable minimal residual disease before allogeneic hematopoietic stem cell transplantation predicts extremely poor prognosis in children with acute lymphoblastic leukemia (2006)

We show that MRD quantitation using clonal Ig/TCR rearrangements successfully assesses the risk in pediatric ALL patients undergoing allogeneic HSCT. As our ability to treat detectable MRD levels after HSCT is very limited, alternative strategies for MRD-positive patients prior HSCT are necessary.
DNA topoisomerase-targeting antitumor drugs can be studied in yeast. (1988)

The antitumor drugs camptothecin and an anilinoacridine, 4'-(9-acridinylamino)-methanesulfon-m-anisidide (mAMSA), which act on DNA topoisomerase I and II, respectively, are shown to inhibit the growth of Saccharomyces cerevisiae mutants selected for their permeability to other inhibitors. In addition to growth inhibition, these drugs induce high levels of homologous recombination and induce the expression of a DNA damage-inducible gene DIN3. Cytotoxicity of the drugs is more pronounced in strains that also carry a rad52 mutation. An analog of mAMSA), which is ineffective as an inhibitor of DNA topoisomerase II in mammalian cells, is also ineffective in eliciting physiological responses in these yeast strains. The physiological effects of camptothecin, but not those of mAMSA, disappear if the TOP1 gene encoding DNA topoisomerase I is disrupted. This shows that DNA topoisomerase I is the sole target of camptothecin cytotoxicity and illustrates that a nonessential enzyme can nevertheless be the target for a cytotoxic drug.
Proofreading genotyping assays and electrochemical detection of SNPs (2004)

The use of proofreading DNA polymerases in genotyping assays offers the prospect of improved performance. To this end, we have recently used compatible DNA polymerases, protected primers, and substrates to implement proofreading single base extension (P-SBE) and proofreading allele-specific extension (PRASE) assays. Key aspects of the P-SBE and related proofreading assay formats are described here. For transduction of genotyping reactions into physical signals, electrochemical SBE implementations may offer simple, inexpensive assays in electrode array or electrophoretic formats. We have developed electrochemically-labeled nucleotides and electrode detection methods with a view to these applications. Detection of electrochemically-labeled SBE products on an oligonucleotide-modified gold electrode surface is demonstrated.
Role of Oxidative Stress in Development of Complications in Diabetes (1991)

N epsilon-(carboxymethyl)lysine, N epsilon-(carboxymethyl)hydroxylysine, and the fluorescent cross-link pentosidine are formed by sequential glycation and oxidation reactions between reducing sugars and proteins. These compounds, termed glycoxidation products, accumulate in tissue collagen with age and at an accelerated rate in diabetes. Although glycoxidation products are present in only trace concentrations, even in diabetic collagen, studies on glycation and oxidation of model proteins in vitro suggest that these products are biomarkers of more extensive underlying glycative and oxidative damage to the protein. Possible sources of oxidative stress and damage to proteins in diabetes include free radicals generated by autoxidation reactions of sugars and sugar adducts to protein and by autoxidation of unsaturated lipids in plasma and membrane proteins. The oxidative stress may be amplified by a continuing cycle of metabolic stress, tissue damage, and cell death, leading to increased free radical production and compromised free radical inhibitory and scavenger systems, which further exacerbate the oxidative stress. Structural characterization of the cross-links and other products accumulating in collagen in diabetes is needed to gain a better understanding of the relationship between oxidative stress and the development of complications in diabetes. Such studies may lead to therapeutic approaches for limiting the damage from glycation and oxidation reactions and for complementing existing therapy for treatment of the complications of diabetes.
Protocol for sortase-mediated construction of DNA–protein hybrids and functional nanostructures (2014)

Recent methods in DNA nanotechnology are enabling the creation of intricate nanostructures through the use of programmable, bottom-up self-assembly. However, structures consisting only of DNA are limited in their ability to act on other biomolecules. Proteins, on the other hand, perform a variety of functions on biological materials, but directed control of the self-assembly process remains a challenge. While DNA-protein hybrids have the potential to provide the best-of-both-worlds, they can be difficult to create as many of the conventional techniques for linking proteins to DNA render proteins dysfunctional. We present here a sortase-based protocol for covalently coupling proteins to DNA with minimal disturbance to protein function. To accomplish this we have developed a two-step process. First, a small synthetic peptide is bioorthogonally and covalently coupled to a DNA oligo using click chemistry. Next, the DNA-peptide chimera is covalently linked to a protein of interest under protein-compatible conditions using the enzyme sortase. Our protocol allows for the simple coupling and purification of a functional DNA-protein hybrid. We use this technique to form oligos bearing cadherin-23 and protocadherin-15 protein fragments. Upon incorporation into a linear M13 scaffold, these protein-DNA hybrids serve as the gate to a binary nanoswitch. The outlined protocol is reliable and modular, facilitating the construction of libraries of oligos and proteins that can be combined to form functional DNA-protein nanostructures. These structures will enable a new class of functional nanostructures, which could be used for therapeutic and industrial processes.
Mollison's Blood Transfusion in Clinical Medicine (2005)

Preface to twelfth edition v Preface to eleventh edition vii Preface to first edition ix In memoriam: Professor Mollison xi 1 Blood donors and the withdrawal of blood 1 2 Transfusion of blood, blood components and plasma alternatives in oligaemia 22 3 Immunology of red cells 53 4 ABO, H, LE, P1PK, GLOB, I and FORS blood group systems 118 5 The Rh blood group system (including LW and RHAG) 167 6 Other red cell antigens 214 7 Red cell antibodies against self-antigens, bound antigens and induced antigens 259 8 Blood grouping techniques 303 9 The transfusion of red cells 356 10 Red cell incompatibility in vivo 411 11 Haemolytic transfusion reactions 458 12 Haemolytic disease of the fetus and the newborn 499 13 Immunology of leucocytes, platelets and plasma components 549 14 The transfusion of platelets, leucocytes, haematopoietic progenitor cells and plasma components 611 15 Some unfavourable effects of transfusion 660 16 Infectious agents transmitted by transfusion 696 17 Exchange transfusion and haemapheresis 764 18 Alternatives to allogeneic transfusion 800 19 Plasma fractionation and fractionation products 846 Appendices 873 Index 892 Colour plate section facing p. 148
Coupled Transcription and Translation Within Nuclei of Mammalian Cells (2001)

It is widely assumed that the vital processes of transcription and translation are spatially separated in eukaryotes and that no translation occurs in nuclei. We localized translation sites by incubating permeabilized mammalian cells with [3H]lysine or lysyl-transfer RNA tagged with biotin or BODIPY; although most nascent polypeptides were cytoplasmic, some were found in discrete nuclear sites known as transcription "factories." Some of this nuclear translation also depends on concurrent transcription by RNA polymerase II. This coupling is simply explained if nuclear ribosomes translate nascent transcripts as those transcripts emerge from still-engaged RNA polymerases, much as they do in bacteria.
VACCINIA VIRUS MEDIATED p53 GENE THERAPY FOR BLADDER CANCER IN AN ORTHOTOPIC MURINE MODEL (2005)

To our knowledge we report for the first time that recombinant vaccinia virus expressing human p53 can induce the death of MB-49 tumor cells in vivo, not only through the lytic effect of the virus, but also through expression of the death inducing p53 transgene. Further studies are needed to shed light on the mechanisms of rVV-TK-53 mediated tumor apoptosis and the antitumor immune response.
Molar Absorptivities of Glucose and other Biological Molecules in Aqueous Solutions over the First Overtone and Combination Regions of the Near-Infrared Spectrum (2004)

Molar absorptivities are measured for water, glucose, alanine, ascorbate, lactate, triacetin, and urea in the near-infrared spectral region at 37 degrees C. Values are based on the Beer-Lambert law and cover the first overtone (1550-1850 nm; 6450-5400 cm(-1)) and combination (2000-2500 nm; 4000-5000 cm(-1)) spectral windows through aqueous media. Accurate calculations demand accounting for the impact of water displacement upon dissolution of solute. In this regard, water displacement coefficients are measured and reported for each solute. First overtone absorptivities range from 2 to 7 x 10(-5) mM(-1)mm(-1) for all solutes except urea, for which absorptivity values are below 0.5 x 10(-5) mM(-1) mm(-1) across this spectral range. Molar absorptivities over the combination spectral region range from 0.8 to 3.2 x 10(-4) mM(-1) mm(-1), which is a factor of four to five greater than the first overtone absorptivities. Accuracy of the measured values is assessed by comparing calculated or modeled spectra with spectra measured from standard solutions. This comparison reveals accurately modeled spectra in terms of magnitude and position of solute absorption bands. Both actual and modeled spectra from glucose solutions reveal positive and negative absorbance values depending on the measurement wavelength. It is shown that the net absorbance of light is controlled by the magnitude of the absorptivity of glucose compared to the product of the absorptivity of water and the water displacement coefficient for glucose.
International Scoring System for Evaluating Prognosis in Myelodysplastic Syndromes (1997)

Despite multiple disparate prognostic risk analysis systems for evaluating clinical outcome for patients with myelodysplastic syndrome (MDS), imprecision persists with such analyses. To attempt to improve on these systems, an International MDS Risk Analysis Workshop combined cytogenetic, morphological, and clinical data from seven large previously reported risk-based studies that had generated prognostic systems. A global analysis was performed on these patients, and critical prognostic variables were re-evaluated to generate a consensus prognostic system, particularly using a more refined bone marrow (BM) cytogenetic classification. Univariate analysis indicated that the major variables having an impact on disease outcome for evolution to acute myeloid leukemia were cytogenetic abnormalities, percentage of BM myeloblasts, and number of cytopenias; for survival, in addition to the above, variables also included age and gender. Cytogenetic subgroups of outcome were as follows: "good" outcomes were normal, -Y alone, del(5q) alone, del(20q) alone; "poor" outcomes were complex (ie, > or = 3 abnormalities) or chromosome 7 anomalies; and "intermediate" outcomes were other abnormalities. Multivariate analysis combined these cytogenetic subgroups with percentage of BM blasts and number of cytopenias to generate a prognostic model. Weighting these variables by their statistical power separated patients into distinctive subgroups of risk for 25% of patients to undergo evolution to acute myeloid leukemia, with: low (31% of patients), 9.4 years; intermediate-1 (INT-1; 39%), 3.3 years; INT-2 (22%), 1.1 years; and high (8%), 0.2 year. These features also separated patients into similar distinctive risk groups for median survival: low, 5.7 years; INT-1, 3.5 years; INT-2, 1.2 years; and high, 0.4 year. Stratification for age further improved analysis of survival. Compared with prior risk-based classifications, this International Prognostic Scoring System provides an improved method for evaluating prognosis in MDS. This classification system should prove useful for more precise design and analysis of therapeutic trials in this disease.
A comparative study of the tolerance of skeletal muscle to ischemia. Tourniquet application compared with acute compartment syndrome. (1986)

In this study, the tolerance of skeletal muscle to tourniquet application (ischemia) and to acute compartment syndrome (ischemia and pressure) was compared. In five animals, the cuff of a pneumatic tourniquet was inflated to 350 millimeters of mercury at the level of the thigh for three hours. In five other animals, an acute experimental compartment syndrome was created in one anterolateral compartment by autologous plasma infusion. The compartment pressure (measured by wick catheter) was maintained at a level equal to the mean arterial pressure for three hours. At three hours, reperfusion was established in both groups, either by tourniquet release or by decompressive fasciotomy and epimysiotomy. During both the ischemic period and a two-hour recovery period immediately thereafter, the mean intracellular pH and high-energy phosphate profile (levels of adenosine triphosphate and phosphocreatine) of the muscles of the anterolateral compartment were monitored non-invasively by phosphorus nuclear magnetic-resonance spectroscopy. Muscle biopsies were done the following day to take specimens for electron microscopic analysis of ultrastructural cellular degeneration. During ischemia, the cellular levels of phosphocreatine decreased at an identical rate in both groups. In contrast, the levels of adenosine triphosphate diminished rapidly in the animals with the compartment syndrome, but remained unchanged in the tourniquet group. Ischemic muscle acidosis was more severe in dogs with the compartment syndrome. In the tourniquet group, the phosphocreatine, adenosine triphosphate, and pH were all normal within fifteen minutes after release of the tourniquet, but these values remained depressed even two hours after fasciotomy in the group with compartment syndrome.(ABSTRACT TRUNCATED AT 250 WORDS)