gebhart/patrepeval huggingface dataset:
Small Molecule–Protein Hybrid for Voltage Imaging via Quenching of Bioluminescence (2021)

We report a small-molecule enzyme pair for optical voltage sensing via quenching of bioluminescence. This quenching bioluminescent voltage indicator, or Q-BOLT, pairs the dark absorbing, voltage-sensitive dipicrylamine with membrane-localized bioluminescence from the luciferase NanoLuc (NLuc). As a result, bioluminescence is quenched through resonance energy transfer (QRET) as a function of membrane potential. Fusion of HaloTag to NLuc creates a two-acceptor bioluminescence resonance energy transfer (BRET) system when a tetramethylrhodamine (TMR) HaloTag ligand is ligated to HaloTag. In this mode, Q-BOLT is capable of providing direct visualization of changes in membrane potential in live cells via three distinct readouts: change in QRET, BRET, and the ratio between bioluminescence emission and BRET. Q-BOLT can provide up to a 29% change in bioluminescence (ΔBL/BL) and >100% ΔBRET/BRET per 100 mV change in HEK 293T cells, without the need for excitation light. In cardiac monolayers derived from human-induced pluripotent stem cells (hiPSCs), Q-BOLT readily reports on membrane potential oscillations. Q-BOLT is the first example of a hybrid small molecule-protein voltage indicator that does not require excitation light and may be useful in contexts where excitation light is limiting.
Organic Spectroscopic Analysis (2004)

This introduction to organic spectroscopic analysis aims to provide the reader with a basic understanding of how nuclear magnetic resonance (NMR), infrared (IR) and ultraviolet-visible (UV-Vis) spectroscopy, and mass spectrometry (MS) give rise to spectra, and how these spectra can be used to determine the structure of organic molecules. The text aims to lead the reader to an appreciation of the information available from each form of spectroscopy and an ability to use spectroscopic information in the identification of organic compounds. Aimed at undergraduate students, Organic Spectroscopic Analysis is a unique textbook containing large numbers of spectra, problems and marginal notes, specifically chosen to highlight the points being discussed. Ideal for the needs of undergraduate chemistry students, Tutorial Chemistry Texts is a major series consisting of short, single topic or modular texts concentrating on the fundamental areas of chemistry taught in undergraduate science courses. Each book provides a concise account of the basic principles underlying a given subject, embodying an independent-learning philosophy and including worked examples.
Multinuclear Cobalt(II)-Containing Heteropolytungstates: Structure, Magnetism, and Electrochemistry (2014)

Interaction of the trilacunary Keggin polyanions [A-α-XW9O34](10-) (X = Si(IV), Ge(IV)) with Co(II) and phosphate ions in aqueous, basic media and under mild heating leads to the formation of the tetrameric, Co16-containing heteropolytungstates [{Co4(OH)3PO4}4(A-α-XW9O34)4](32-) (X = Si(IV), Ge(IV)). Both polyanions were characterized in the solid state by single-crystal X-ray diffraction, IR spectroscopy, and thermogravimetric and elemental analyses. Furthermore, the electrochemical and magnetic properties of these isostructural polyanions were investigated.
Optical Amplifiers (1999)

Abstract The sections in this article are Historical Perspective Basic Concepts Photoabsorption and Photoemission SNR Background in Generic Optical Systems Amplifier Gain and Noise Semiconductor Amplifiers Erbium‐doped Fiber Amplifiers Multiple‐Wavelength Systems Applications to Solitons Future Trends
GaN microwave varactors with insulated electrodes (2014)

Abstract We report on GaN microwave varactors with capacitively coupled isolated electrodes. Metal‐insulator‐semiconductor (MIS) varactors have 4–5 orders of magni‐tude lower leakage currents than similar devices with Schottky contacts. Low leakage capacitively coupled contacts enable microwave switches and power limiters with low loss, high RF power and excellent temperature stability up to at least 200 °C. (© 2014 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
pyKNEEr: An image analysis workflow for open and reproducible research on femoral knee cartilage (2019)

Abstract Transparent research in musculoskeletal imaging is fundamental to reliably investigate diseases such as knee osteoarthritis (OA), a chronic disease impairing femoral knee cartilage. To study cartilage degeneration, researchers have developed algorithms to segment femoral knee cartilage from magnetic resonance (MR) images and to measure cartilage morphology and relaxometry. The majority of these algorithms are not publicly available or require advanced programming skills to be compiled and run. However, to accelerate discoveries and findings, it is crucial to have open and reproducible workflows. We present pyKNEEr , a framework for open and reproducible research on femoral knee cartilage from MR images. pyKNEEr is written in python, uses Jupyter notebook as a user interface, and is available on GitHub with a GNU GPLv3 license. It is composed of three modules: 1) image preprocessing to standardize spatial and intensity characteristics, 2) femoral knee cartilage segmentation for intersubject, multimodal, and longitudinal acquisitions, and 3) analysis of cartilage morphology and relaxometry. Each module contains one or more Jupyter notebooks with narrative, code, visualizations, and dependencies to reproduce computational environments. pyKNEEr facilitates transparent image-based research of femoral knee cartilage because of its ease of installation and use, and its versatility for publication and sharing among researchers. Finally, due to its modular structure, pyKNEEr favors code extension and algorithm comparison. We tested our reproducible workflows with experiments that also constitute an example of transparent research with pyKNEEr . We provide links to executed notebooks and executable environments for immediate reproducibility of our findings.
Regulation of the Versican Promoter by the β-Catenin-T-cell Factor Complex in Vascular Smooth Muscle Cells (2005)

The proteoglycan versican is pro-atherogenic and central to vascular injury and repair events. We identified the signaling pathways and promoter elements involved in regulation of versican expression in vascular smooth muscle cells. Phosphatidylinositol 3-kinase inhibitor, LY294002, significantly decreased versican-luciferase (Luc) promoter activity and endogenous mRNA levels. We further examined the roles of protein kinase B and glycogen synthase kinase (GSK)-3beta, downstream effectors of phosphatidylinositol 3-kinase, in the regulation of versican transcription. Co-transfection of dominant negative and constitutively active protein kinase B constructs with a versican-Luc construct decreased and increased promoter activity, respectively. Inhibition of GSK-3beta activity by LiCl augmented accumulation of beta-catenin and caused induction of versican-Luc activity as well as versican mRNA levels. Beta-catenin has no DNA binding domain, therefore it cannot directly induce transcription of the versican promoter. Software analysis of the versican promoter revealed two potential binding sites for T-cell factors (TCFs), proteins that confer transcriptional activation of beta-catenin. Electrophoretic mobility shift and supershift assays revealed specific binding of human TCF-4 and beta-catenin to oligonucleotides corresponding to a potential TCF binding site in the versican promoter. In addition to binding assays, we directly assessed the dependence of versican promoter activity on TCF binding sites. Site-directed mutagenesis of the TCF site located -492 bp relative to the transcription start site markedly diminished versican-Luc activity. Co-transfection of TCF-4 with versican-Luc did not increase promoter activity, but addition of beta-catenin and TCF-4 significantly stimulated basal versican promoter activity. Our findings suggest that versican transcription is predominantly mediated by the GSK-3beta pathway via the beta-catenin-TCF transcription factor complex in smooth muscle cells, wherein such regulation contributes to the normal or aberrant formation of provisional matrix in vascular injury and repair events.
Structural Variations of N‐Acetylneuraminic Acid, 11, Synthesis of the 4‐Methylumbelliferyl 2α‐Glycosides of 7‐Epi‐, 8‐Epi‐, and 7,8‐Bis(epi)‐N‐acetylneuraminic Acids, as well as of 7‐Deoxy‐, 8‐Deoxy‐, 9‐Deoxy‐, and 4,7‐Dideoxy‐N‐acetylneuraminic Acids and Their Behaviour Towards Sialidase from Vibrio cholerae (1989)

Abstract The methyl esters of 7‐epi‐Neu5Ac ( 1a ), 8‐epi‐Neu5Ac ( 2a ), 7,8‐bis(epi)‐Neu5Ac ( 3a ), 7‐deoxy‐Neu5Ac ( 4a ), 8‐deoxy‐Neu5Ac ( 5a ), 9‐deoxy‐Neu5Ac ( 6a ), and 4,7‐dideoxy‐Neu5Ac ( 7a ) were transformed into their peracetylated mixtures of the α‐anomers 1b–7b and β‐anomers 1c–7c . In the next step the 2‐Cl derivatives were prepared with acetyl chloride/HCl which yielded in the following Königs‐Knorr reaction with 4‐methylumbelliferone (MU) the corresponding methylumbelliferyl 2α‐glycosides 7‐epi‐Neu4,5,7,8,9Ac 5 1Me‐αMU ( 1d ), 8‐epi‐Neu4,5,7,8,9Ac 5 1Me‐αMU ( 2d ), 7,8‐bis(epi)‐Neu4,5,7,8,9Ac 5 1Me‐αMU ( 3d ), 7‐deoxy‐Neu‐4,5,8,9Ac 4 1Me‐αMU ( 4d ), 8‐deoxy‐Neu4,5,7,9Ac 4 1Me‐αMU ( 5d ), 9‐deoxy‐Neu4,5,7,8A 4 1Me‐αMU ( 6d ), and 4,7‐dideoxy‐Neu‐5,8,9Ac 3 1Me‐αMU ( 7d ). In the last case also the β‐anomer of 4,7‐dideoxy‐Neu5,8,9Ac 3 1Me‐βMU ( 7d′ ) was formed. Zemplen saponification followed by hydrolysis of the ester group with sodium hydroxide, resulted in the sodium salts of the sialic acid MU 2α‐glycosides 7‐epi‐, 8‐epi‐, 7,8‐bis(epi)‐, 8‐deoxy‐, 9‐deoxy‐ and 4,7‐dideoxy‐Neu5Ac‐MU 1e–7e . The enzymatic hydrolysis of these compounds with sialidase from Vibrio cholerae showed only for 3e and 7e significantly reduced rates of cleavage, which is in agreement with the inhibitor constants K i of the related 2,3‐didehydro sialic acids 7,8‐bis(epi)‐Neu5Ac2en and 4,7‐dideoxy‐Neu5Ac2en 1,15) .
Pharmacokinetics of placental protein 13 after intravenous and subcutaneous administration in rabbits (2018)

This study shows that the concentration of total PP13 released into the maternal circulation during pregnancy might be much higher than previously estimated.
Single-Molecule Combinatorial Therapeutics for Treating Obesity and Diabetes (2017)

It will soon be 100 years since Frederick G. Banting, Charles Best, James Collip, and John J.R. Macleod in 1921 demonstrated that extracts of the pancreas had breathtaking beneficial effects to restore the health of patients with diabetes (1,2). While their breakthrough revolutionized the medical management of diabetes, the disease continues today to spread worldwide (3) along with a global increase in obesity. Novel unimolecular gut hormone polyagonists have shown unique potential to reverse obesity and diabetes in animal models and are currently being assessed in multiple clinical trials for their efficacy and safety (4).

Insulin replacement therapy currently remains a central pillar of diabetes management while additional antidiabetes medicines enhance production, secretion, and action of insulin to improve disease management and enhance patient care. Enormous progress has been made in the precise and continuous quantification of blood glucose, which, together with next-generation insulin pumps, has enabled closed-loop delivery systems, a sizable step forward in the direction of automatized insulin therapy. The cure still remains elusive, and prevalence of the disease continues to rise across the globe, frighteningly so at an accelerated pace in some of the most populous countries. How can it be that a century after the discovery of insulin, the occurrence of disease is increasing with no cure to stem the epidemic in sight?

The vast majority of diabetes worldwide is constituted of what was traditionally characterized as adult-onset, type 2 diabetes (T2D). This form of diabetes is clearly driven by another pandemic—that of obesity—and to an increasing extent is no longer an adult-onset disease. While the specific molecular mechanisms by which obesity is promoting the diabetes epidemic remain unclear, there is no controversy that in the absence of obesity, the magnitude of the diabetes problem would be far less significant and more manageable. …
Micro-ribonucleic acid-155 is a direct target of Meis1, but not a driver in acute myeloid leukemia (2017)

Micro-ribonucleic acid-155 (miR-155) is one of the first described oncogenic miRNAs. Although multiple direct targets of miR-155 have been identified, it is not clear how it contributes to the pathogenesis of acute myeloid leukemia. We found miR-155 to be a direct target of Meis1 in murine Hoxa9/Meis1 induced acute myeloid leukemia. The additional overexpression of miR-155 accelerated the formation of acute myeloid leukemia in Hoxa9 as well as in Hoxa9/Meis1 cells <i>in vivo</i> However, in the absence or following the removal of miR-155, leukemia onset and progression were unaffected. Although miR-155 accelerated growth and homing in addition to impairing differentiation, our data underscore the pathophysiological relevance of miR-155 as an accelerator rather than a driver of leukemogenesis. This further highlights the complexity of the oncogenic program of Meis1 to compensate for the loss of a potent oncogene such as miR-155. These findings are highly relevant to current and developing approaches for targeting miR-155 in acute myeloid leukemia.
Correlates of the country differences in the infection and mortality rates during the first wave of the COVID-19 pandemic: evidence from Bayesian model averaging (2022)

The COVID-19 pandemic resulted in great discrepancies in both infection and mortality rates between countries. Besides the biological and epidemiological factors, a multitude of social and economic criteria also influenced the extent to which these discrepancies appeared. Consequently, there is an active debate regarding the critical socio-economic and health factors that correlate with the infection and mortality rates outcome of the pandemic. Here, we leverage Bayesian model averaging techniques and country level data to investigate whether 28 variables, which describe a diverse set of health and socio-economic characteristics, correlate with the final number of infections and deaths during the first wave of the coronavirus pandemic. We show that only a few variables are able to robustly correlate with these outcomes. To understand the relationship between the potential correlates in explaining the infection and death rates, we create a Jointness Space. Using this space, we conclude that the extent to which each variable is able to provide a credible explanation for the COVID-19 infections/mortality outcome varies between countries because of their heterogeneous features.
Design of PIFA With Metamaterials for Body-SAR Reduction in Wearable Applications (2016)

This letter proposes a planar inverted-F antenna (PIFA) with an artificial magnetic conductor (AMC) structure for body specific absorption rate (SAR) reduction in a wideband-code-division-multiple-access band. As wireless devices such as wearable phones and smart watches become more common, health risks originating from electromagnetic waves generated by devices worn on the body have become an important issue. AMC structures are a type of metamaterial that can act as a perfect magnetic conductor and control the radiation pattern of an antenna. Thus, an antenna with an AMC structure is capable of preventing hazardous electromagnetic fields being emitted in the direction of the body. The S-parameters, radiation patterns, total radiated power values, and SAR values of such a designed structure are presented. The results demonstrate a 43.3% reduction in the SAR value at the center frequency. Thus, the human body can be protected from electromagnetic waves using metamaterials.
Grain Boundary Sliding as a Significant Mechanism of Low Temperature Plastic Deformation in ECAP Aluminum (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Transport Network Architecture (2018)

This chapter focuses on the description of transport network architecture suitable for 5G in terms of both user plane (UP) and control plane (CP). The 5G UP architecture considers converged optical and wireless network domains in a common 5G infrastructure supporting both transport and access. Given the great degree of technology heterogeneity in the transport network, special emphasis was given to technology integration and interfacing aspects. The chapter provides an overview of the various technologies and protocols and the associated interfaces that can be used in support of both fronthaul (FH) and backhaul (BH) services, and addresses self-backhauling. The concept of self-backhauling offers a flexible and cost-effective approach to address both BH and access requirements by dynamically sharing the radio resources between BH and access links. The chapter discusses framing protocol adaption and interfacing aspects. It presents a discussion on transport network optimization and performance evaluation.
Mice deficient in endothelial α5 integrin are profoundly resistant to experimental ischemic stroke (2015)

Stroke is a disease in dire need of better therapies. We have previously shown that a fragment of the extracellular matrix proteoglycan, perlecan, has beneficial effects following cerebral ischemia via the α5β1 integrin receptor. We now report that endothelial cell selective α5 integrin deficient mice (α5 KO) are profoundly resistant to ischemic infarct after transient middle cerebral artery occlusion. Specifically, α5 KOs had little to no infarct 2-3 days post-stroke, whereas controls had an increase in mean infarct volume over the same time period as expected. Functional outcome is also improved in the α5 KOs compared with controls. Importantly, no differences in cerebrovascular anatomy or collateral blood flow were noted that could account for this difference in ischemic injury. Rather, we demonstrate that α5 KOs have increased blood-brain barrier integrity (increased expression of claudin-5, and absent brain parenchymal IgG extravasation) after stroke compared with controls, which could explain their resistance to ischemic injury. Additionally, inhibition of α5 integrin in vitro leads to decreased permeability of brain endothelial cells following oxygen-glucose deprivation. Together, these findings indicate endothelial cell α5 integrin plays an important role in stroke outcome and blood-brain barrier integrity, suggesting that α5 integrin could be a novel therapeutic target for stroke.
Fabrication of self-assembled photonic-crystal structures by centrifugation and spin coating (2003)

We have developed a simple, low-cost process for the fabrication of high-quality three-dimensional artificial-opal and inverse-opal photonic crystals. The process is based on the self-assembly of a template from a uniform suspension of polystyrene microspheres, which is sintered for added strength and subsequently back-filled with high-index material. The template formation is assisted by a combination of centrifugation and spin-annealing, which requires relatively short process times and inexpensive laboratory equipment. The process has been used to fabricate polycrystalline photonic crystals with photonic stop gaps in the mid-IR portion of the spectrum. Details of the fabrication process and fabricated samples will be presented. In addition, Fourier-transform IR reflection spectroscopy has been used to characterize the samples; the results are shown to be in excellent agreement with band structure diffraction calculations.
Second Spine: Upper Body Assistive Device for Human Load Carriage (2014)

This study presents the development of second spine, an upper body assistive device for human load carriage. The motivation comes from reducing musculoskeletal injuries caused by carrying a heavy load on the upper body. Our aim was to design a wearable upper body device that can prevent musculoskeletal injuries during human load carriage by providing a secondary load pathway—second spine—to transfer the loads from shoulders to pelvis while also allowing a good range of torso motion to the wearer. Static analysis of the backpack and the second spine was first performed to investigate the feasibility of our concept design. The development of second spine had two considerations: load distribution between shoulders and pelvis, and preserving the range of torso motion. The design was realized using load bearing columns between the shoulder support and hip belt, comprising multiple segments interconnected by cone-shaped joints. The performance of second spine was evaluated through experimental study, and its biomechanical effects on human loaded walking were also assessed. Based on the findings from second spine evaluation, we proposed the design of a motorized second spine which aims to compensate the inertia force of a backpack induced by human walking through active load modulation. This was achieved by real-time sensing of human motion and actuating the motors in a way that the backpack motion is kept nearly inertially fixed. Simulation study was carried out to determine the proper actuation of motors in response to the human walking kinematics. The performance of motorized second spine was evaluated through an instrumented test-bed using Instron machine. Results showed a good agreement with simulation. It was shown that the backpack motion can be made nearly stationary with respect to the ground which can further enhance the effectiveness of the device in assisting human load carriage.
The Abacus Switch (2006)

This chapter contains sections titled: Basic Architecture Multicast Contention Resolution Algorithm Implementation of Input Port Controller Performance ATM Routing and Concentration (ARC) Chip Enhanced Abacus Switch Abacus Switch for Packet Switching
Multidatabase management in Pegasus (1991)

Pegasus is an object-oriented multidatabase system being developed at Hewlett-Packard Laboratories. The goal of the system is to provide facilities for multidatabase applications for accessing and manipulating multiple autonomous heterogeneous object-oriented, relational and other databases. This paper gives an overview of the architecture, describes the common object model and gives the justification for adapting the model for a multidatabase system. It describes the database environment of the system, discusses how to manage schemas consisting of types and functions from multiple databases. It briefly describes the features of the data language and gives an example. It discusses a method for dealing with object identification issues in a multidatabase system, reviews schema integration issues and briefly mentions schema mapping to relational models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tricyclic Alkaloid Core Structures Assembled by a Cyclotrimerization−Coupled Intramolecular Nucleophilic Substitution Reaction (2010)

A facile approach to tricyclic alkaloid core structures was developed by sequencing a pyridine-forming [2 + 2 + 2] cyclotrimerization reaction with an intramolecular nucleophilic substitution. This methodology enabled the facile assembly of the spiroindolinone framework of citrinadins A and B, and cyclopiamine B.