gebhart/patrepeval huggingface dataset:
ChemInform Abstract: A Ruthenium‐Catalyzed Alkylative Cycloetherification. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Quantitative evaluation of heartbeat interval time series using Poincaré analysis reveals distinct patterns of heart rate dynamics during cycles of vagus nerve stimulation in patients with heart failure (2017)

Optimization of stimulation parameters is essential to maximizing therapeutic efficacy and minimizing side effects. The ANTHEM-HF study enrolled patients with heart failure who received chronic autonomic regulation therapy (ART) with an implantable vagus nerve stimulation (VNS) system on either the right (n = 30) or left side (n = 29). Acute effects of continuously cycling VNS on R-R interval dynamics were evaluated using post hoc Poincaré analysis of ECG recordings collected during multiple titration sessions over an 8–12 week period. During each titration session, VNS intensity associated with maximum tolerable dose was determined. Poincaré plots of R-R interval time series were created for epochs when VNS cycled from OFF to ON at varying intensity levels. VNS produced an immediate, relatively small change in beat-to-beat distribution of R-R intervals during the 14-sec ON time, which was correlated with stimulation current amplitude (r = 0.85, p = 0.05). During titration of right-sided stimulation, there was a strong correlation (r = 0.91, p = 0.01) between stimulus intensity and the Poincaré parameter of standard deviation, SD1, which is associated with high-frequency heart rate variability. The effect of VNS on instantaneous heart rate was indicated by a shift in the centroid of the beat-to-beat cloud distribution demarcated by the encircling ellipse. As anticipated, left-sided stimulation did not alter any Poincaré parameter except at high stimulation intensities (≥ 2 mA). Quantitative Poincaré analysis reveals a tight coupling in beat-to-beat dynamics during VNS ON cycles that is directly related to stimulation intensity, providing a useful measurement for confirming autonomic engagement.
YeeO fromEscherichia coliexports flavins (2014)

Multidrug and toxic compound extrusion (MATE) proteins help maintain cellular homeostasis by secreting metabolic wastes. Flavins may occur as cellular waste products, with their production and secretion providing potential benefit for industrial applications related to biofuel cells. Here we find that MATE protein YeeO from Escherichia coli exports both flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Significant amounts of flavins were trapped intracellularly when YeeO was produced indicating transport limits secretion of flavins. Wild-type E. coli secreted 3 flavins (riboflavin, FMN, and FAD), so E. coli likely produces additional flavin transporters.
Chapter 1. Translational Motion of Water in Biological Tissues – A Brief Primer (2020)

As an introduction to the rigorous treatment of diffusion encoding in the rest of the book, this chapter gives simple non-mathematical explanations of the relations between the properties of biological tissues and the translational motion of the tissue water with the aim of conveying an intuitive feel of the relevant time and length scales and the level of detail of the information that can be obtained. The influence of biomembranes and macromolecules on water dynamics is reviewed from both molecular and cellular scale perspectives. The potentially complex motion patterns are decomposed into short-time diffusivity, restriction, anisotropy, flow, and exchange, which can be independently assessed and correlated with advanced diffusion encoding methods in MRI.
Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial (2020)

Antibodies (Abs) specific for CD4-induced envelope (Env) epitopes within constant region 1 and 2 (C1/C2) were induced in the RV144 vaccine trial, where antibody-dependent cellular cytotoxicity (ADCC) correlated with reduced risk of HIV-1 infection. We combined X-ray crystallography and fluorescence resonance energy transfer-fluorescence correlation spectroscopy to describe the molecular basis for epitopes of seven RV144 Abs and compared them to A32 and C11, C1/C2 Abs induced in HIV infection. Our data indicate that most vaccine Abs recognize the 7-stranded β-sandwich of gp120, a unique hybrid epitope bridging A32 and C11 binding sites. Although primarily directed at the 7-stranded β-sandwich, some accommodate the gp120 N terminus in C11-bound 8-stranded conformation and therefore recognize a broader range of CD4-triggered Env conformations. Our data also suggest that Abs of RV144 and RV305, the RV144 follow-up study, although likely initially induced by the ALVAC-HIV prime encoding full-length gp120, matured through boosting with truncated AIDSVAX gp120 variants.<b>IMPORTANCE</b> Antibody-dependent cellular cytotoxicity (ADCC) correlated with a reduced risk of infection from HIV-1 in the RV144 vaccine trial, the only HIV-1 vaccine trial to date to show any efficacy. Antibodies specific for CD4-induced envelope (Env) epitopes within constant region 1 and 2 (cluster A region) were induced in the RV144 trial and their ADCC activities were implicated in the vaccine efficacy. We present structural analyses of the antigen epitope targets of several RV144 antibodies specific for this region and C11, an antibody induced in natural infection, to show what the differences are in epitope specificities, mechanism of antigen recognition, and ADCC activities of antibodies induced by vaccination and during the course of HIV infection. Our data suggest that the truncated AIDSVAX gp120 variants used in the boost of the RV144 regimen may have shaped the vaccine response to this region, which could also have contributed to vaccine efficacy.
Repurposing tin mesoporphyrin as a novel immune checkpoint therapy in the treatment of cancer: A preclinical evaluation. (2018)

e15129 Background: Unprecedented clinical outcomes have been achieved in a variety of cancers by targeting the immune checkpoint molecules PD-1 and CTLA-4. However, as a significant number of patients is unresponsive, or only responds transiently to current therapies, it suggests that further important immune regulators in the tumor microenvironment exist. Heme oxygenase-1 (HO-1) is an enzyme that is responsible for the breakdown of heme to generate biliverdin, ferrous iron and the immune suppressive molecule carbon monoxide. In this preclinical study we evaluate HO-1 as an innate immune checkpoint target. An HO-1 inhibitor, tin mesoporphyrin (SnMP), has previously demonstrated tolerability and efficacy in the clinic for the treatment of hyperbilirubinemia, and we evaluate repurposing SnMP as a novel immune checkpoint therapeutic. Methods: We studied HO-1 in an aggressive spontaneous murine model of mammary adenocarcinoma (MMTV-PyMT) using chemotherapy to stimulate an anti-tumor immune response. We use patient survival data and RNA-sequencing analyses to support the clinical relevance of our conclusions. Results: In MMTV-PyMT mice, inhibiting HO-1 using SnMP synergized with chemotherapy to permit immunological control of tumor growth. HO-1 was primarily expressed by tumor associated macrophages, and genetic inactivation of the gene in myeloid cells paralleled the observations of SnMP treatment with chemotherapy. We discovered a striking clinical parallel, where high HO-1 expression was associated with poor prognosis in cancer patients receiving chemotherapy. Single-cell RNA sequencing analysis of a breast cancer patient dataset also suggested that the myeloid lineage was a significant source of HO-1 expression in human cancer, and was co-expressed with the immune checkpoints PD-L1/2. We compared the efficacy of PD-1 blockade to that of SnMP, and in the MMTV-PyMT model, SnMP was more efficacious than PD-1 blockade alongside chemotherapy, highlighting the potential importance of HO-1 as an immune checkpoint target. Conclusions: Our data support the clinical evaluation of SnMP as a novel immune checkpoint therapeutic in cancer within chemotherapy regimens.
Severe Combined Immunodeficiency Mice Engrafted With Human T Cells, B Cells, and Myeloid Cells After Transplantation With Human Fetal Bone Marrow or Liver Cells and Implanted With Human Fetal Thymus: A Model for Studying Human Gene Therapy (1997)

To develop an in vivo model wherein human hematopoiesis occurs, we transplanted severe combined immunodeficiency (SCID) mice with either human fetal bone marrow (HFBM) or human fetal liver (HFL). After transplantation of SCID mice with cultured HFBM (BM-SCID-hu mice) or HFL cells (Liv-SCID-hu mice), significant engraftment of the mouse bone marrow (BM) and population of the peripheral blood with human leukocytes was detected. Human colony-forming unit–granulocyte macrophage and burst forming unit-erythroid were detected in the BM of the BM-SCID-hu and Liv-SCID-hu mice up to 8 months after transplantation. When the HFBM or HFL cells were transduced with a retroviral vector before transplantation, integrated retroviral sequences were detected in human precursor cells present in the SCID mouse BM and in leukocytes circulating in the peripheral blood (PB) up to 7 months after transplantation. The PB of the BM-SCID-hu mice also became populated with human T cells after implantation with human thymic tissue, which provided a human microenvironment wherein human pre-T cells from the BM could mature. When the HFBM was retrovirally transduced before transplantation, integrated retrovirus was detected in sorted CD4+CD8+ double positive and CD4+ single positive cells from the thymic implant and CD4+ cells from the PB. Taken together, these data indicated that the BM of our BM-SCID-hu and Liv-SCID-hu mice became engrafted with retrovirally transduced human hematopoietic precursors that undergo the normal human hematopoietic program and populate the mouse PB with human cells containing integrated retroviral sequences. In addition to being a model for studying in vivo human hematopoiesis, these mice should also prove to be a useful model for investigating in vivo gene therapy using human stem/precursor cells.
The analytic Cauchy problem with singular data (1972)

I left Marlboro College and went back to Brandeis in 1969 to complete my Ph.D. At that time, I intended to study and write a thesis in mathematical physics. However, I wound up doing a thesis in pure mathematics, on analytic partial differential equations. I learned nothing about analytic partial differential equations except what was needed for my thesis research, and I have never looked at them since then. The thesis itself was a small, solid piece of very classical math. Had Cauchy arisen from the grave to read it, he would have found nothing unfamiliar in the mathematics.
A high performance continuously tunable top-emitting VCSEL (2002)

In conclusion, we report the first high performance, micromechanical tunable top-emitting AlGaAs DBR VCSEL laser that continuously tunes over 20 nm, has threshold current between 0.76 mA-1.9 mA and output power 0.92 mW-1.9 mW throughout the entire tuning range. Such a top-emitting tunable structure is highly desirable for easy optical and electrical packaging and for integration with other devices. The achieved high performance of low threshold and high power renders its practical implementation extremely feasible.
Cellular compartments cause multistability in biochemical reaction\n networks and allow cells to process more information (2012)

Many biological, physical, and social interactions have a particular\ndependence on where they take place. In living cells, protein movement between\nthe nucleus and cytoplasm affects cellular response (i.e., proteins must be\npresent in the nucleus to regulate their target genes). Here we use recent\ndevelopments from dynamical systems and chemical reaction network theory to\nidentify and characterize the key-role of the spatial organization of\neukaryotic cells in cellular information processing. In particular the\nexistence of distinct compartments plays a pivotal role in whether a system is\ncapable of multistationarity (multiple response states), and is thus directly\nlinked to the amount of information that the signaling molecules can represent\nin the nucleus. Multistationarity provides a mechanism for switching between\ndifferent response states in cell signaling systems and enables multiple\noutcomes for cellular-decision making. We find that introducing species\nlocalization can alter the capacity for multistationarity and mathematically\ndemonstrate that shuttling confers flexibility for and greater control of the\nemergence of an all-or-none response.\n
Influence of screw type and length on fixation of anterior glenoid bone grafts (2017)

The present study demonstrates that common screw types resist physiological shear loads in a bicortical configuration. However, the 3.75 mm screws incurred significant displacements at 200 N in the unicortical configurations. These findings have implications regarding hardware selection for bone-grafting procedures.
Probing the Osteoinductive Effect of Calcium Phosphate by Using an In Vitro Biomimetic Model (2010)

The use of calcium phosphate (CaP)-based carriers in bone engineering is a promising approach to induce in vivo bone formation. However, the exact mechanism of osteoinduction by CaP is not known. Here, by mimicking the in vivo Ca(2+) and P(i)-enriched environment in an in vitro model, we assessed the effects of these ions on human periosteum-derived cells. We observed a significant Ca(2+) and P(i)-induced cell proliferation, which was found to be through the modulation of cell cycle progression, in a dose- and time-dependent manner. In addition, Ca(2+), P(i), and combined Ca-P upregulated osteogenic gene expression in a dose- and time-dependent manner. Encouragingly, both ions administered individually or in combination persistently and dose dependently upregulated bone morphogenetic protein-2 gene expression. This suggested a potential osteoinductive effect through an autonomous activation of the bone morphogenetic protein signaling pathway by released Ca(2+) and P(i), which may serve as an autocrine/paracrine osteoinduction loop that drives the cellularized CaP constructs toward effective bone formation in vivo. In conclusion, through an in vitro biomimetic model, we have partially probed the roles of the released Ca(2+) and P(i) on the osteoinductivity of CaP-based biomaterials.
Incidence and Mortality of Second Primary Cancers in Danish Patients With Retinoblastoma, 1943-2013 (2020)

The findings of this study suggest that the incidence and mortality associated with SPC were significantly higher in patients with heritable retinoblastoma vs patients with nonheritable retinoblastoma. The largest increases in risk were noted for sarcoma and malignant melanoma. External radiotherapy did not appear to increase the risk. These findings are relevant when treating patients with retinoblastoma to manage the risk for SPC.
<title>Photorefractivity in polymer-stabilized nematic liquid crystals</title> (1998)

Polymer-stabilized liquid crystals, consisting of low concentrations of a polymeric electron acceptor, are shown to exhibit significantly enhanced photorefractive properties. The charge generation and transport properties of these composite systems are strongly modified from nematic liquid crystals doped with electron donors and acceptors. The new composites are produced by polymerizing a small quantity of a 1,4:5,8-naphthalenediimide electron acceptor functionalized with an acrylate group in an aligned nematic liquid crystal. Photopolymerization creates an anisotropic gel-like medium in which the liquid crystal is free to reorient in the presence of a space charge field, while maintaining charge trapping sites in the polymerized regions of the material. The presence of these trapping sites results in the observation of longer lived, higher resolution holographic gratings in the polymer-stabilized liquid crystals than observed in nematic liquid crystals alone. These gratings display Bragg regime diffraction. Asymmetric beam coupling, photo-conductivity, and four-wave mixing experiments are performed to characterize the photophysics of these novel materials.
The Development of Biologically Important Spirooxindoles as New Antimicrobial Agents (2018)

This review highlights the importance of spirooxindoles as potential antimicrobial agents. The antimicrobial activity of spirooxindoles against different types of bacteria is less studied, mainly centering on primary antimicrobial assessment, some of these compounds have showed interesting antimicrobial activity. However, the current study is only limited to primary antimicrobial assessment, no detailed modes of action are investigated.
Multifunctional on-chip storage at telecommunication wavelength for quantum networks (2020)

Quantum networks will enable a variety of applications, from secure communication and precision measurements to distributed quantum computing. Storing photonic qubits and controlling their frequency, bandwidth, and retrieval time are important functionalities in future optical quantum networks. Here we demonstrate these functions using an ensemble of erbium ions in yttrium orthosilicate coupled to a silicon photonic resonator and controlled via on-chip electrodes. Light in the telecommunication C-band is stored, manipulated, and retrieved using a dynamic atomic frequency comb protocol controlled by linear DC Stark shifts of the ion ensemble’s transition frequencies. We demonstrate memory time control in a digital fashion in increments of 50 ns, frequency shifting by more than a pulse width ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>±</mml:mo> </mml:mrow> <mml:mn>39</mml:mn> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="normal">M</mml:mi> <mml:mi mathvariant="normal">H</mml:mi> <mml:mi mathvariant="normal">z</mml:mi> </mml:mrow> </mml:math> ), and a bandwidth increase by a factor of 3, from 6 to 18 MHz. Using on-chip electrodes, electric fields as high as 3 kV/cm were achieved with a low applied bias of 5 V, making this an appealing platform for rare-earth ions, which experience Stark shifts of the order of 10 kHz/(V/cm).
Copy of a plan made by Alexander Anderson in 1845 of that portion of the northern part of Lot 11 sold at various times for land taxes (1909)

Copy of a plan made by Alexander Anderson in 1845 of that portion of the northern part of Lot 11 sold at various times for land taxes. Plan shows property bought by David Ramsay at a Sheriff's sale. The map shows lots, residents, acreage, and water.
Power-efficient ASIC synthesis of cryptographic sboxes (2004)

In this paper we present a novel methodology that can be used to design efficient hardware structures for a certain class of combinatorial functions. The methodology is primarily intended to achieve low-power synthesis of non-linear one-to-one functions on ASIC technology libraries and fits well for the synthesis of small cryptographic substitution box (Sbox) functional components; the latter are found in most secret key cryptographic algorithms, and usually represent their most relevant part in terms of required computational power. We also describe an extension that allows us to apply the method to general vectorial Boolean functions.
Immunoprecipitation of adenylate cyclase with an antibody to a carboxyl-terminal peptide from Gs.alpha. (1990)

An antibody (RM) raised against the carboxyl-terminal decapeptide of the alpha subunit of the stimulatory guanine nucleotide regulatory protein (Gs alpha) has been used to study the interaction of Gs alpha with bovine brain adenylate cyclase [ATP pyrophosphate-lyase (cyclizing), EC 4.6.1.1]. RM antibody immunoprecipitated about 60% of the solubilized adenylate cyclase preactivated with either GTP-gamma-S or AlF4-. In contrast, RM antibody immunoprecipitated about 5% of the adenylate cyclase not preactivated (control) and 15% of the adenylate cyclase pretreated with forskolin. Adenylate cyclase solubilized from control membranes or GTP-gamma-S preactivated membranes was partially purified by using forskolin-agarose affinity chromatography. The amount of Gs alpha protein in the partially purified preparations was determined by immunoblotting with RM antibody. There was 3-fold more Gs alpha detected in partially purified adenylate cyclase from preactivated membranes than in the partially purified adenylate cyclase from control membranes. Partially purified adenylate cyclase from preactivated membranes was immunoprecipitated with RM antibody and the amount of adenylate cyclase activity immunoprecipitated (65% of total) corresponded to the amount of Gs alpha protein immunoprecipitated. Only 15% of the partially purified adenylate cyclase from control membranes was immunoprecipitated. The presence of other G proteins in the partially purified preparations of adenylate cyclase was investigated by using specific antisera that detect Go alpha, Gi alpha, and G beta. The G beta protein was the only subunit detected in the partially purified preparations of adenylate cyclase and the amount of G beta was about the same in adenylate cyclase from preactivated membranes and from control membranes.(ABSTRACT TRUNCATED AT 250 WORDS)
Roles of lymphatic endothelial cells expressing peripheral tissue antigens in CD4 T-cell tolerance induction (2015)

Lymphatic endothelial cells (LECs) directly express peripheral tissue antigens and induce CD8 T-cell deletional tolerance. LECs express MHC-II molecules, suggesting they might also tolerize CD4 T cells. We demonstrate that when β-galactosidase (β-gal) is expressed in LECs, β-gal-specific CD8 T cells undergo deletion via the PD-1/PD-L1 and LAG-3/MHC-II pathways. In contrast, LECs do not present endogenous β-gal in the context of MHC-II molecules to β-gal-specific CD4 T cells. Lack of presentation is independent of antigen localization, as membrane-bound haemagglutinin and I-Eα are also not presented by MHC-II molecules. LECs express invariant chain and cathepsin L, but not H2-M, suggesting that they cannot load endogenous antigenic peptides onto MHC-II molecules. Importantly, LECs transfer β-gal to dendritic cells, which subsequently present it to induce CD4 T-cell anergy. Therefore, LECs serve as an antigen reservoir for CD4 T-cell tolerance, and MHC-II molecules on LECs are used to induce CD8 T-cell tolerance via LAG-3.
Dynamics of the Simplest Reaction of a Carbon Atom in a Tetrahedral Environment (2003)

Die Abstraktionsreaktion H+CD4→CD3+HD wurde bei einer Kollisionsenergie von ca. 2 eV unter Einzelstoß-Bedingungen untersucht (siehe Schema). Der überwiegende Anteil der Energie wird in die Translation der CD3-Produktmoleküle übertragen, die seitlich und rückwärts zur Einfallsrichtung der H-Atome gestreut werden. Dieses Verhalten ist im Widerspruch zu gängigen Atom-Diatom-Modellen.