gebhart/patrepeval huggingface dataset:
Myocardial Tissue Characterization by Magnetic Resonance Imaging (2014)

Cardiac magnetic resonance (CMR) imaging is a well-established noninvasive imaging modality in clinical cardiology. Its unsurpassed accuracy in defining cardiac morphology and function and its ability to provide tissue characterization make it well suited for the study of patients with cardiac diseases. Late gadolinium enhancement was a major advancement in the development of tissue characterization techniques, allowing the unique ability of CMR to differentiate ischemic heart disease from nonischemic cardiomyopathies. Using T2-weighted techniques, areas of edema and inflammation can be identified in the myocardium. A new generation of myocardial mapping techniques are emerging, enabling direct quantitative assessment of myocardial tissue properties in absolute terms. This review will summarize recent developments involving T1-mapping and T2-mapping techniques and focus on the clinical applications and future potential of these evolving CMR methodologies.
Coronary Vasomotor Abnormalities in Insulin-Resistant Individuals (2004)

Insulin-resistant patients who do not have hypercholesterolemia or hypertension and do not smoke manifest coronary vasomotor abnormalities. Insulin-sensitizing thiazolidinedione therapy normalized these abnormalities. These results suggest an association between insulin resistance and abnormal coronary vasomotor function, a relationship that requires confirmation in larger studies.
A C <sub>35</sub> Carotenoid Biosynthetic Pathway (2003)

Upon coexpression with Erwinia geranylgeranyldiphosphate (GGDP) synthase in Escherichia coli, C(30) carotenoid synthase CrtM from Staphylococcus aureus produces novel carotenoids with the asymmetrical C(35) backbone. The products of condensation of farnesyldiphosphate and GDP, C(35) structures comprise 40 to 60% of total carotenoid accumulated. Carotene desaturases and carotene cyclases from C(40) or C(30) pathways accepted and converted the C(35) substrate, thus creating a C(35) carotenoid biosynthetic pathway in E. coli. Directed evolution to modulate desaturase step number, together with combinatorial expression of the desaturase variants with lycopene cyclases, allowed us to produce at least 10 compounds not previously described. This result highlights the plastic and expansible nature of carotenoid pathways and illustrates how combinatorial biosynthesis coupled with directed evolution can rapidly access diverse chemical structures.
Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays (2020)

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in assays, with higher sensitivity attributed to particular forms of the protein. To improve the yield of these high-sensitivity forms of RBD and support the increased demand for this antigen in serology assays, we investigated several protein expression variables including DNA elements such as promoters and signal peptides, cell culture expression parameters, and purification processes. Through this investigation, we developed a simplified and robust purification strategy that consistently resulted in high levels of the high-sensitivity form of RBD and demonstrated that a carboxyterminal tag is responsible for the increased sensitivity in the ELISA. These improved reagents and processes produce high-quality proteins which are functional in serology assays and can be used to investigate seropositivity to SARS-CoV-2 infection. Highlights: Improved yields of SARS-CoV-2 spike RBD through modification of DNA constructs and purification parametersTwo versions of RBD show different sensitivity in serology assaysYields of greater than 50 mg/l obtained under optimal conditionsMagnetic bead purification technology improves throughput of protein production.
Olefinepoxidierung mit Methyltrioxorhenium: eine Dichtefunktionalstudie zu Energetik und Mechanismen (1998)

Der Angriff des Olefins auf eine Peroxogruppe unter Bildung eines Spiroübergangszustands ist theoretischen Untersuchungen zufolge bei der Epoxidierung von Olefinen mit dem Katalysatorsystem CH3ReO3/H2O2 bevorzugt (siehe Bild). Dieser Befund wird durch Dichtefunktionalrechnungen an mehr als zehn Übergangszuständen der wahrscheinlichsten Mechanismen gestützt. Die Hydratisierung hat einen bedeutenden Einfluß auf mehrere an der Reaktion beteiligte Spezies: Sie stabilisiert Intermediate und destabilisiert, von einer Ausnahme abgesehen, die Übergangszustände.
Three Emerging Coronaviruses in Two Decades (2020)

In the past two decades, the world has seen three coronaviruses emerge and cause outbreaks that have caused considerable global health consternation Coronaviruses are enveloped, nonsegmented, single-stranded, positive-sense RNA viruses that have a characteristic appearance on electron microscopy negative staining Image 1 As a matter of fact, the characteristic electron microscopy appearance was the clue to amplify and sequence nucleic acids from Dr Urbani’s (one of the health care providers who died of severe acute respiratory syndrome [SARS] in 2003) respiratory specimen using a consensus coronavirus primer 1 The sequence of the virus was significantly different from other coronaviruses known to cause human disease at the time The virus was ultimately named SARS-CoV, as febrile patients had severe acute respiratory syndrome and could present with pneumonia and lower respiratory symptoms such as cough and dyspnea 2 The SARS-CoV outbreak started in Guangdong, China, and spread to many countries in Southeast Asia, North America, Europe, and South Africa Transmission was primarily person to person through droplets that occurred during coughing or sneezing, through personal contact (shaking hands), or by touching contaminated surfaces Of note, health professionals were particularly at risk of acquiring the disease, as transmission also occurred if isolation precautions were not followed and during certain procedures The last case of SARS-CoV occurred in September 2003, after having infected over 8,000 persons and causing 774 deaths with a case fatality rate calculated at 9 5%
Availability-aware mapping of service function chains (2017)

Network Function Virtualization (NFV) is a promising technique to greatly improve the effectiveness and flexibility of network services through a process named Service Function Chain (SFC) mapping, with which different network services are deployed over virtualized and shared platforms in data centers. However, such an evolution towards software-defined network functions introduces new challenges to network services which require high availability. One effective way of protecting the network services is to use sufficient redundancy. By doing so, however, the efficiency of physical resources may be greatly decreased. To address such an issue, this paper defines an optimal availability-aware SFC mapping problem and presents a novel online algorithm that can minimize the physical resources consumption while guaranteeing the required high availability within a polynomial time. Simulation results show that our proposed algorithm can significantly improve SFC mapping request acceptance ratio and reduce resource consumption.
Electron induced reactions of surface adsorbed tungsten hexacarbonyl (W(CO)6) (2013)

Tungsten hexacarbonyl (W(CO)(6)) is frequently used as an organometallic precursor to create metal-containing nanostructures in electron beam induced deposition (EBID). However, the fundamental electron stimulated reactions responsible for both tungsten deposition and the incorporation of carbon and oxygen atom impurities remain unclear. To address this issue we have studied the effect of 500 eV incident electrons on nanometer thick films of W(CO)(6) under Ultra-High Vacuum (UHV) conditions. Results from X-ray Photoelectron Spectroscopy, Mass Spectrometry, and Infrared Spectroscopy reveal that the initial step involves electron stimulated desorption of multiple CO ligands from parent W(CO)(6) molecules and the formation of partially decarbonylated tungsten species (W(x)(CO)(y)). Subsequent electron interactions with these W(x)(CO)(y) species lead to ligand decomposition rather than further CO desorption, ultimately producing oxidized tungsten atoms incorporated in a carbonaceous matrix. The presence of co-adsorbed water during electron irradiation increased the extent of tungsten oxidation. The electron stimulated deposition cross-section of W(CO)(6) at an incident electron energy of 500 eV was calculated to be 6.50 × 10(-16) cm(-2). When considered collectively with findings from previous precursors (MeCpPtMe(3) and Pt(PF(3))(4)), results from the present study are consistent with the idea that the electron induced reactions in EBID are initiated by low energy secondary electrons generated by primary beam-substrate interactions, rather than by the primary beam itself.
Differentially Private Multi-dimensional Time Series Release for Traffic Monitoring (2013)

Sharing real-time traffic data can be of great value to understanding many important phenomena, such as congestion patterns or popular places. To this end, private user data must be aggregated and shared continuously over time with data privacy guarantee. However, releasing time series data with standard differential privacy mechanism can lead to high perturbation error due to the correlation between time stamps. In addition, data sparsity in the spatial domain imposes another challenge to user privacy as well as utility. To address the challenges, we propose a real-time framework that guarantees differential privacy for individual users and releases accurate data for research purposes. We present two estimation algorithms designed to utilize domain knowledge in order to mitigate the effect of perturbation error. Evaluations with simulated traffic data show our solutions outperform existing methods in both utility and computation efficiency, enabling real-time data sharing with strong privacy guarantee.
Intelligent driver assist system for urban driving (2016)

Driving in an urban environment is hectic and often adventurous. Getting accurate routing instructions, finding parking spots, receiving customized information that helps individual drivers reach their destination will significantly reduce the stress of driving, save fuel and reduce unnecessary delays and pollution levels. In this paper we present a system that combines smart navigation with intelligent parking assist and driver diagnostics to considerably improve driving comfort, safety and mobility in an urban environment. The smart navigation employs an on line traffic simulator which provides traffic predictions and improves the accuracy of existing navigation systems which rely on limited traffic data. The intelligent parking assist system predicts the availability of parking at the start of the journey and these predictions get updated as the destination is approached. The system uses machine learning to understand the habits and preferences of the individual driver so that the preferred parking availability information is presented to the driver. The driver diagnostics part learns the driving characteristics of the driver i.e. whether aggressive, semi aggressive or passive, reaction times, following distances etc. and provides this information to the smart navigation and parking assist system for better estimation of travel times. In addition, it can be used to support collision warnings and other driver assist devices. The proposed system has been successfully demonstrated using an AUDI vehicle in the area of Los Angeles and San Francisco.
Silicon Nanoribbons for Electrical Detection of Biomolecules (2008)

Direct electrical detection of biomolecules at high sensitivity has recently been demonstrated using semiconductor nanowires. Here we demonstrate that semiconductor nanoribbons, in this case, a thin sheet of silicon on an oxidized silicon substrate, can approach the same sensitivity extending below the picomolar concentration regime in the biotin/streptavidin case. This corresponds to less than approximately 20 analyte molecules bound to receptors on the nanoribbon surface. The micrometer-size lateral dimensions of the nanoribbon enable optical lithography to be used, resulting in a simple and high-yield fabrication process. Electrical characterization of the nanoribbons is complemented by computer simulations showing enhanced sensitivity for thin ribbons. Finally, we demonstrate that the device can be operated both in inversion as well as in accumulation mode and the measured differences in detection sensitivity are explained in terms of the distance between the channel and the receptor coated surface with respect to the Debye screening length. The nanoribbon approach opens up for large scale CMOS fabrication of highly sensitive biomolecule sensor chips for potential use in medicine and biotechnology.
Modelling Branching Patterns on 1-year-old Trunks of Six Apple Cultivars (2002)

The structure resulting from branching on 1-year-old apple tree trunks was analysed in a set of apple cultivars with diverse branching and fruiting habits. Four different lateral types borne on successive nodes were observed when vegetative and flowering fates, as well as sylleptic and proleptic branching, were taken into account. The location and grouping of lateral types along the trunk were analysed for all cultivars, but are detailed for one cultivar only. This cultivar showed a succession of zones, each zone being characterized by its composition of lateral types. Statistical models-hidden semi-Markov chains-were built to take this structure into account and to characterize the cultivar's specific branching pattern. The models showed that most of the branching zones had a similar location in the different cultivars, even though zone composition and zone length differed among cultivars. On a more detailed scale, the nodes bearing a lateral, regardless of its type, were frequently followed by latent buds. The validity of the models and their biological interpretation are discussed with respect to parent shoot dynamics, hormonal gradients and competition between neighbouring buds.
Selective Inhibition of an Apicoplastic Aminoacyl‐tRNA Synthetase from <i>Plasmodium falciparum</i> (2013)

The resistance of malaria parasites to available drugs continues to grow, and this makes the need for new antimalarial therapies pressing. Aminoacyl-tRNA synthetases (ARSs) are essential enzymes and well-established antibacterial targets and so constitute a promising set of targets for the development of new antimalarials. Despite their potential as drug targets, apicoplastic ARSs remain unexplored. We have characterized the lysylation system of Plasmodium falciparum, and designed, synthesized, and tested a set of inhibitors based on the structure of the natural substrate intermediate: lysyl-adenylate. Here we demonstrate that selective inhibition of apicoplastic ARSs is feasible and describe new compounds that that specifically inhibit Plasmodium apicoplastic lysyl-tRNA synthetase and show antimalarial activities in the micromolar range.
GENETIC APPROACHES TO THE STUDY OF ANXIETY (2004)

Anxiety and its disorders have long been known to be familial. Recently, genetic approaches have been used to clarify the role of heredity in the development of anxiety and to probe its neurobiological underpinnings. Twin studies have shown that a significant proportion of the liability to develop any given anxiety disorder is due to genetic factors. Ongoing efforts to map anxiety-related loci in both animals and humans are underway with limited success to date. Animal models have played a large role in furthering our understanding of the genetic basis of anxiety, demonstrating that the genetic factors underlying anxiety are complex and varied. Recent advances in molecular genetic techniques have allowed increasing specificity in the manipulation of gene expression within the central nervous system of the mouse. With this increasing specificity has come the ability to ask and answer precise questions about the mechanisms of anxiety and its treatment.
COVID-19 and beyond (2021)

"COVID-19 and beyond." The Round Table, 110(1), pp. 171–172 Disclosure statementNo potential conflict of interest was reported by the author(s).
Leukocyte-Derived Myeloperoxidase Amplifies High-Glucose—Induced Endothelial Dysfunction Through Interaction With High-Glucose—Stimulated, Vascular Non—Leukocyte-Derived Reactive Oxygen Species (2004)

Vascular non-leukocyte-derived reactive oxygen species (ROS), such as superoxide and hydrogen peroxide (H(2)O(2)), have emerged as important molecules in diabetic endothelial dysfunction. In addition, leukocyte-derived myeloperoxidase (MPO) has been implicated in vascular injury, and its injury response is H(2)O(2) dependent. It is well known that MPO can use leukocyte-derived H(2)O(2); however, it is unknown whether the vascular-bound MPO can use high-glucose-stimulated, vascular non-leukocyte-derived H(2)O(2) to induce diabetic endothelial dysfunction. In the present study, we demonstrated that MPO activity is increased in vessels from diabetic rats. In high-glucose-incubated rat aortas and in carotid arteries from rats with acute hyperglycemia, vascular-bound MPO utilized high-glucose-stimulated H(2)O(2) to amplify the ROS-induced impairment of endothelium-dependent relaxation via reduction of nitric oxide bioavailability. Hypochlorous acid (HOCL)-modified LDL, a specific biomarker for the MPO/HOCL/chlorinating species pathway, was detected in LDL- and MPO-bound vessels with high-glucose-stimulated H(2)O(2). The results suggest that vascular-bound MPO could use high-glucose-stimulated H(2)O(2) to amplify high-glucose-induced injury in the vascular wall. MPO/H(2)O(2)/HOCL/chlorinating species may represent an important pathway in diabetes complications and a new mechanism in phagocyte- and systemic infection-induced exacerbation of diabetic vascular diseases.
Low Drive Voltage, 40GHz LiNbO3 Modulators (1999)

Low drive voltage, broadband modulators, with low optical insertion losses, are required for communications and signal processing applications.
Glycosylphosphonates of 2‐Amino‐2‐deoxy‐aldoses. Synthesis of a Phosphonate Analogue of Lipid X (1987)

Abstract A preparation of glycosylphosphonates ( 27 , 28 , 36 , 38 , and 39 ) from 2‐azido‐2‐deoxy‐glycoses ( 26 , 35 , and 37 ) and the synthesis of the non‐isosteric phosphonate analogue 3a of lipid X( 2 ) are described. The 2‐azido group was introduced by azidonitration. Treatment of the 1‐ O ‐acetyl‐2‐azido‐2‐deoxy‐β‐D‐galactopyranose 22 with 1.5‐3 equiv. of P(OMe) 3 and 1.2‐2.5 equiv. of TfOSiMe 3 gave mainly recovered starting material. In P(OMe) 3 as the solvent, the dimethyl phosphoramidate 24 was obtained by way of a Staudinger reaction, even in the presence of TfOSiMe 3 . Treatment of the benzylated α‐D‐ galacto ‐trichloroacetimidate 26 , however, with P(OMe) 3 and TfOSiMe 3 gave a 1:1 mixture of the α‐ and β‐D‐ galacto ‐phosphonates 27 and 28 , while the acetylated α‐D‐ gluco ‐ imidate 35 led to the α‐D‐ gluco ‐configurated phosphonate 36 . The stereoselectivity of the phosphonate formation is related to the relative ease of formation of oxonium‐ion intermediates from 26 and 35 . Starting from the phosphonate 36 , deacetylation, benzylidenation, reduction of the azido group, acylation with ( R )‐3‐(benzyloxy)tetradecanoic acid and deprotection yielded the desired compound 3a which was crystallized in the presence of 2 equiv. of (aminomethylidyne)trimethanol ( Tris. ). The structure of the phosphonates was deduced from their 1 H‐, 13 C‐, and 31 P‐NMR spectra.
A Protocol for Transcranial Photobiomodulation Therapy in Mice (2018)

Transcranial photobiomodulation is a potential innovative noninvasive therapeutic approach for improving brain bioenergetics, brain function in a wide range of neurological and psychiatric disorders, and memory enhancement in age-related cognitive decline and neurodegenerative diseases. We describe a laboratory protocol for transcranial photobiomodulation therapy (PBMT) in mice. Aged BALB/c mice (18 months old) are treated with a 660 nm laser transcranially, once daily for 2 weeks. Laser transmittance data shows that approximately 1% of the incident red light on the scalp reaches a 1 mm depth from the cortical surface, penetrating the dorsal hippocampus. Treatment outcomes are assessed by two methods: a Barnes maze test, which is a hippocampus-dependent spatial learning and memory task evaluation, and measuring hippocampal ATP levels, which is used as a bioenergetics index. The results from the Barnes task show an enhancement of the spatial memory in laser-treated aged mice when compared with age-matched controls. Biochemical analysis after laser treatment indicates increased hippocampal ATP levels. We postulate that the enhancement of memory performance is potentially due to an improvement in hippocampal energy metabolism induced by the red laser treatment. The observations in mice could be extended to other animal models since this protocol could potentially be adapted to other species frequently used in translational neuroscience, such as rabbit, cat, dog, or monkey. Transcranial photobiomodulation is a safe and cost-effective modality which may be a promising therapeutic approach in age-related cognitive impairment.
Placebo‐controlled trial of riluzole in multiple system atrophy (2006)

We performed a placebo-controlled cross-over trial of riluzole (100 mg b.i.d.) in 10 patients with probable multiple system atrophy (MSA) administering riluzole and placebo for 4 weeks each with a 4-week washout period. Outcome measures evaluated short-term anti-Parkinsonian effects using the Unified Parkinson's Disease Rating Scale (UPDRS) subscales (UPDRS-II, activities of daily living; UPDRS-III, motor examination; sum of UPDRS-II and -III) before and at the end of each treatment phase. Delta values were calculated by subtracting the UPDRS scores measured at the end of each treatment arm from those before onset of each medication phase. Riluzole was generally well tolerated. There were no significant anti-Parkinsonian effects of riluzole comparing the UPDRS delta values for both treatment arms using the Wilcoxon signed-rank test. It is unlikely that riluzole treatment could have clinically meaningful anti-Parkinsonian effects in MSA. A trial assessing the disease-modifying potential of riluzole in MSA is underway.
Spatio-temporal tracking of material shape change via multi-dimensional splines (2002)

A new method for modeling shape changes in multidimensional image sequences of deforming objects is presented. The method consists of defining an orthogonal coordinate system on the segmented object in the first image frame and then calculating the deformations of this coordinate system over time. The deformations are found by minimizing an energy functional that consists of a linear combination of a data fidelity term and a shape-change constraint term. The shape-change constraint is based on the differential geometric properties of the parametrized material coordinate system. The deforming material coordinate system models an object's shape changes both locally and globally. The mathematics is first developed for an n-dimensional sequence of images. Examples are given for both 2D and 3D image sequences of both real and synthetic images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>