gebhart/patrepeval huggingface dataset:
Diversity in GeneticIn VivoMethods for Protein-Protein Interaction Studies: from the Yeast Two-Hybrid System to the Mammalian Split-Luciferase System (2012)

The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
Lessons learned from the experiences and perspectives of frontline healthcare workers on the COVID-19 response (2023)

Abstract Background During the COVID-19 pandemic, healthcare systems and healthcare workers (HCWs) faced significant demands and unique challenges. In this qualitative study, we explore the effects of the COVID-19 public health policies on British Columbia’s frontline HCWs, describe what worked in the management of the pandemic, and elucidate the lessons learned that could be applied to future pandemic preparedness, recovery and response. Methods This qualitative descriptive study is part of a larger, national multi-case study on pandemic policy communication and uptake. Semi-structured interviews were conducted from November 2020- June 2021 with fourteen HCWs working in long-term care (LTC), acute care and public health settings. Data were inductively coded, and analyzed following a resilience framework for public health emergency preparedness, which emphasizes the essential elements of a public health system, vital to all phases of health emergency management, readiness, response and recovery. Results HCWs experienced confusion, frustration, uncertainty, anxiety, fatigue and stress, during the pandemic and detailed challenges that affected policy implementation. This included communication and coordination inconsistencies between the province and regional health authorities; lack of involvement of frontline staff in pandemic planning; inadequate training and support; inadequate personal protective equipment resource capacity and mobilization; and staffing shortages. HCWs recommended increased collaboration between frontline staff and policy makers, investment in preparing and practicing pandemic plans, and the need for training in emergency management and infection prevention and control. Conclusions Pandemic planning, response and recovery should include inputs from actors/key stakeholders at the provincial, regional and local levels, to facilitate better coordination, communication and outcomes. Also, given the critical roles of frontline HCWs in policy implementation, they should be adequately supported and consideration must be given to how they interpret and act on policies. Bi-directional communication channels should be incorporated between policymakers and frontline HCWs to verify the appropriate adoption of policies, reflective learning, and to ensure policy limitations are being communicated and acted upon by policy makers.
SATURN (2018)

We demonstrate the design, fabrication, evaluation, and use of a self-powered microphone that is thin, flexible, and easily manufactured. Our technology is referred to as a Self-powered Audio Triboelectric Ultra-thin Rollable Nanogenerator (SATURN) microphone. This acoustic sensor takes advantage of the triboelectric nanogenerator (TENG) to transform vibrations into an electric signal without applying an external power source. The sound quality of the SATURN mic, in terms of acoustic sensitivity, frequency response, and directivity, is affected by a set of design parameters that we explore based on both theoretical simulation and empirical evaluation. The major advantage of this audio material sensor is that it can be manufactured simply and deployed easily to convert every-day objects and physical surfaces into microphones which can sense audio. We explore the space of potential applications for such a material as part of a self-sustainable interactive system.
Statistical Signal Integrity Analysis and Diagnosis Methodology for High-Speed Systems (2004)

This paper discusses an efficient statistical analysis methodology for system-level signal integrity analysis. In the proposed method, statistical variations of the design and operational parameters are mapped to system performance through simulations based on orthogonal Taguchi arrays. Using the sensitivity functions derived from these simulations, statistical distributions of the performance measures are computed. The sensitivity functions and probability distributions of the design parameters are utilized as a diagnosis tool to estimate the design parameters of a system for a given measured performance. The statistical methodology is applied for design space exploration to improve system performance. For demonstrating the concept, a source synchronous memory bus and a peripheral input-output (I/O) bus have been analyzed under design and operational variations.
Hypertension in mice lacking the CXCR3 chemokine receptor (2009)

The CXC chemokine receptor 3 (CXCR3) has been linked to autoimmune and inflammatory disease, allograft rejection, and ischemic nephropathy. CXCR3 is expressed on endothelial and smooth muscle cells. Although a recent study posited that antagonizing of CXCR3 function may reduce atherosclerosis, the role of CXCR3 in controlling physiological vascular functions remains unclear. This study demonstrates that disruption of CXCR3 leads to elevated mean arterial pressures in anesthetized and conscious mice, respectively. Stimulation of isolated resistance vessels with various vasoconstrictors showed increased contractibility in CXCR3-/- mice in response to angiotensin II (ANG II) and a decreased vasodilatation in response to acetylcholine (ACh). The increased contractibility was related to higher ANG II type 1 receptor (AT1R) expression, whereas the decreased vasodilatation was related to lower M3-ACh receptor expression in the mesenteric arteries of CXCR3-/- mice compared with wild-type mice. The vasodilatatory response to ACh could be antagonized by the nonselective ACh receptor antagonist atropine and the selective M3 receptor antagonist 4-DAMP, but not by M1, M2, and M4 receptor antagonists. Additionally, EMSA studies revealed that transcription factors SP-1 and EGR-1 interact as a complex with the murine AT1R promoter region. Furthermore, we could show increased expression of SP-1 in CXCR3-/- mice indicating an imbalanced SP-1 and EGR-1 complex formation which causes increased AT1R expression and hypertension. The data indicate that CXCR3 receptor is important in vascular contractility and hypertension, possibly through upregulated AT1R expression.
Mass and charge transport relevant to the formation of toroidal lithium peroxide nanoparticles in an aprotic lithium-oxygen battery: An experimental and theoretical modeling study (2017)

The discharge and charge mechanisms of rechargeable Li-O2 batteries have been the subject of extensive investigation recently. However, they are not fully understood yet. Here we report a systematic study of the morphological transition of Li2O2 from a single crystalline structure to a toroid like particle during the discharge–charge cycle, with the help of a theoretical model to explain the evolution of the Li2O2 at different stages of this process. The model suggests that the transition starts in the first monolayer of Li2O2, and is subsequently followed by a transition from particle growth to film growth if the applied current exceeds the exchange current for the oxygen reduction reaction in a Li-O2 cell. Furthermore, a sustainable mass transport of the diffusive active species (e.g., O2 and Li+) and evolution of the underlying interfaces are critical to dictate desirable oxygen reduction (discharge) and evolution (charge) reactions in the porous carbon electrode of a Li-O2 cell.
Perchlorination of Polychlorinated Biphenyls (1974)

Abstract A simple and efficient method for the perchlorination of polychlorinated biphenyls (PCBs) to decachlorobiphenyl, using antimony pentachloride, is described. Average yields of decachlorobiphenyl from 3 individual samples of Aroclors 1016 and 1254 were 85 and 104%, respectively. Bromine was identified as a contaminant in certain lots of antimony pentachloride. PCB perchlorinations with bromide-contaminated antimony pentachloride resulted in significant amounts of bromononachlorobiphenyl.
Role of Molecular Surface Passivation in Electrical Transport Properties of InAs Nanowires (2007)

The existence of large densities of surface states on InAs pins the surface Fermi level above the conduction band and also degrades the electron mobility in thin films and nanowires. Field effect transistors have been fabricated and characterized in the "as fabricated" state and after surface passivation with 1-octadecanethiol (ODT). Electrical characterization of the transistors shows that the subthreshold slope and electron mobility in devices passivated with ODT are superior to the respective values in unpassivated devices. An X-ray photoelectron spectroscopy study of ODT passivated undoped InAs nanowires indicates that sulfur from ODT is bonded to In on the InAs nanowires. Simulations using a two-dimensional device simulator (MEDICI) show that the improvements in device performance after ODT passivation can be quantified in terms of a decrease of interface trap electron donor states, shifts in fixed interfacial charge, and changes in body and surface mobilities.
(Invited) Impact of Stress and Defects on Advanced Junction Leakage (2010)

Comparison of relative strengths of different leakage mechanisms in stress-free vs stressed, defect-free vs full-of-defects, planar MOSFET vs FinFET is performed. First, all major junction leakage mechanisms are analyzed using numerical models in a stress-free and defect-free 30 nm planar bulk NMOSFET. Then, the impact of stress on silicon bandgap is described along with the appropriate modeling guidelines. The magnitude and the current flow patterns for different leakage mechanisms affected by mechanical stress and by crystal defects are systematically analyzed. Junction leakage increase of 30 times under 2 GPa compressive stress is expected according to both the models and the available measurements. Junction leakage increase ranges from 10 pA to 100 pA per trap depending on the particular trap location relative to the drain junction. Based on results of this analysis, suggestions are given for finding the best trade-offs in designing transistors with stress engineering and occasional defects.
IP-Optical Interaction during Traffic Restoration (2013)

We analyze the required interaction between the optical and IP layers to enable restoration of IP links in the optical layer. Significant interaction is needed to achieve a cost effective process that minimizes traffic impact.
Biotransformation of Vinclozolin by the Fungus Cunninghamella elegans (2000)

This study investigated the biotransformation of the dicarboximide fungicide vinclozolin [3-(3,5-dichlorophenyl)-5-methyl-5-vinyl-1,3-oxazolidine-2,4-dione] by the fungus Cunninghamella elegans. Experiments with phenyl-[U-ring-14C]vinclozolin showed that after 96 h incubation, 93% had been transformed to four major metabolites. Metabolites were separated by HPLC and characterized by mass and NMR spectroscopy. Biotransformation occurred predominantly on the oxazolidine-2,4-dione portion of vinclozolin. The metabolites were identified as the 3R- and 3S- isomers of 3',5'-dichloro-2,3,4-trihydroxy-2-methylbutyranilide, N-(2-hydroxy-2-methyl-1-oxobuten-3-yl)-3,5-dichlorophenyl-1-carbamic acid, and 3',5'-dichloro-2-hydroxy-2-methylbut-3-enanilide. The enanilide compound has been reported previously as a plant and mammalian metabolite and is implicated to contain antiandrogenic activity. The 3R- and 3S- isomers of 3',5'-dichloro-2,3,4-trihydroxy-2-methylbutyranilide are novel metabolites.
A 174 W high-efiiciency GaN HEMT power amplifier for W-CDMA base station applications (2003)

AIGaN/GaN high electron mobility transistors (HEMTs) have been developed for current-collapse-free operation at high drain bias voltages. The newly designed single-chip GaN HEW amplifier for W-CDMA he station applications achieves a record CW output power of 150 W with a high power-added efficiency (F'AE) of 54% at 2.1 GHz. The amplifier, combined with a digital pre-distortion (DPD) system, also demonstrates a state of the art efficiency of 40% with an adjacent channel leakage power ratio (ACLR) of less than -50 dBc for 44ei W-CDMA signals and reaches the saturated peak power level of 174 W with a drain supply voltage of 63 V. We prove for the first time that the AIGaN/GaN HEMT amplifier can completely fulfills the W-CDMA system requirement.
Pyrazoleamides in Catalytic Asymmetric Reactions: Recent Advances (2021)

Abstract Pyrazoleamides are a class of compounds which have received significant attention in the last years in asymmetric catalysis as more reactive and practical surrogates of esters or amides. These readily available reagents have served in a variety of diastereo‐ and enantioselective metal‐ and organocatalytic transformations, spanning from simple carbon‐carbon or carbon‐heteroatom bond formation to cascade and rearrangement reactions, to produce valuable classes of heterocyclic compounds. More recently, pyrazoleamides have proved to be pertinent reagents in asymmetric catalysis merged with photoredox catalysis, and in more challenging stereoselective bond‐forming reactions, occurring directly from a visible‐light activated substrate/catalyst complex without any charge separation. Both strategies enable new activation concepts useful for the production of difficult‐to‐access intermediates and pharmaceuticals. In this review, an overview of the progress achieved in asymmetric catalytic reactions of pyrazoleamides from 2015 up to middle 2020, is illustrated. magnified image
Smart kindergarten (2001)

Despite enormous progress in networking and computing technologies, their application has remained restricted to conventional person-to-person and person-to-computer communication. However, continual reduction in cost and form factor is now making it possible to imbed networking - even wireless networking - and computing capabilities not just in our PCs and laptops but also other objects. Further, a marriage of these ever tinier and cheaper processors and wireless network interfaces with emerging micro-sensors based on MEMS technology is allowing cheap sensing, processing, and communication capabilities to be unobtrusively embedded in familiar physical objects. The result is an emerging paradigm shift where the primary role of information technology would be to enhance or assist in "person to physical world communication via familiar physical objects with embedded (a) micro-sensors to react to external stimuli, and (b) wireless networking and computing engines for tetherless communication with compute servers and other networked embedded objects. In this paper we present the application of sensor-based wireless networks to a "Smart Kindergarten that we are developing to target developmental problem-solving environments for early childhood education. This is a natural application as young children learn by exploring and interacting with objects such as toys in their environment. Our envisioned system would enhance the education process by providing a childhood learning environment that is individualized to each child, adapts to the context, coordinates activities of multiple children, and allows continual unobtrusive evaluation of the learning process by the teacher. This would be done by wirelessly-networked, sensor-enhanced toys and other classroom objects with back-end middleware services and database techniques. We explore wireless networking, middleware, and data management technologies for realizing this application, and describe challenges arising from ad hoc distributed structure, unreliable sensing, large scale/density, and novel sensor data types that are characteristic of such deeply instrumented environments with inter-networked physical objects.
Side chain hydroxylation of aromatic hydrocarbons by fungi. Part 2. Isotope effects and mechanism (1988)

The benzylic hydroxylation of ethylbenzene, p-diethylbenzene, tetralin, indane, and toluene by the fungi Mortierella isabellina, Cunninghamella echinulata, and Helminthosporium species has been investigated by the use of deuterium-labelled substrates. An intermolecular primary isotope effect kH/kD 1.04 ± 0.05 was observed for conversion of ethylbenzene into 1-phenylethanol. The secondary deuterium isotope effect for this conversion was large and positive (kH/kD averaging 1.27 ± 0.05). p-Diethylbenzene, tetralim, and indane were hydroxylated at the benzylic position with an intramolecular primary deuterium isotope effect averaging 2.6 ± 0.2. The use of R-(–)- and S-(+)-1-deuterioethylbenzenes as substrates with the fungus M. isabellina show that hydrogen removal is specific for the pro-R position of substrate. Toluene is converted into benzyl alcohol by the fungi Mortierella isabellina and Helminthosporium species; in the latter case, the product is further metabolized. [α-2H]-, [αα-2H2]-, and [ααα-2H3]-toluene have been used with M. isabellina in a series of experiments to determine both primary and secondary deuterium kinetic isotope effects for the enzymic benzylic hydroxylation reaction. The values obtained, intermolecular primary kH/kD= intramolecular primary kH/kD= 1.02 ± 0.05, and secondary kH/kD= 1.37 ± 0.05, lead to the suggestion of a mechanism for benzylic hydroxylation involving benzylic proton removal from a radical-cation intermediate in a non-symmetrical transition state.
STUDY OF ION IMPLANTED COPPER LASER MIRRORS BY SPECTROSCOPIC ELLIPSOMETRY. (1987)

Implantation with 400 keV Ag or Cu ions improves the near-surface microstructural quality and reflectance of diamond turned and mechanically polished flat copper laser mirrors. Spectroscopic ellipsometry is sensitive to changes in either the microscopic surface roughness, or in the nearsurface substrate void fraction, and both parameters are observed to change upon implantation. Substrate density as a function of ion fluence peaks at about 5 × 1015cm-2. Low energy (300 eV) Ar ion implantation can cause either a reduction or increase in microscopic surface roughness, depending on fluence.
A high-throughput effector screen identifies a novel small molecule scaffold for inhibition of ten-eleven translocation dioxygenase 2 (2022)

Ten-eleven translocation dioxygenases (TETs) are the erasers of 5-methylcytosine (mC), the central epigenetic regulator of mammalian DNA. TETs convert mC to three oxidized derivatives with unique physicochemical properties and inherent regulatory potential, and it initializes active demethylation by the base excision repair pathway. Potent small molecule inhibitors would be useful tools to study TET functions by conditional control. To facilitate the discovery of such tools, we here report a high-throughput screening pipeline and its application to screen and validate 31.5k compounds for inhibition of TET2. Using a homogenous fluorescence assay, we discover a novel quinoline-based scaffold that we further validate with an orthogonal semi-high throughput MALDI-MS assay for direct monitoring of substrate turnover. Structure-activity relationship (SAR) studies involving >20 derivatives of this scaffold led to the identification of optimized inhibitors, and together with computational studies suggested a plausible model for its mode of action.
Rearrangement of 4-Perfluoroalkyl Quinols (1991)

Abstract Treatment of 4-perfluoroalkyl-4-hydroxy-2,5-hexadien-1-one (4-perfluoroalkyl-4-quinol), prepared from the reaction of 1,4-benzoquinone with perfluoroalkyllithium, with acetic anhydride–sulfuric acid gave a mixture of 2,4-diacetoxy-1-perfluoroalkylbenzene and 1,2-diacetoxy-4-perfluoroalkylbenzene in a comparable ratio. When 4-perfluoroalkyl-4-quinols bearing a methyl group ortho to the perfluoroalkyl group were subjected to the rearrangement, acetoxymethyl compounds were obtained in addition to diacetoxybenzene derivatives. Only 1,3-migration was observed in the cases of 2,4-di-t-butyl-4-perfluorooctyl-4-quinol and 4-hydroxy-4-perfluoroalkyl-1(4H)-naphthalenone, while the reaction of 2,6-dimethyl and 2-methoxy derivatives gave only 1,2-shift products. Reaction routes to the apparent 1,2- and 1,3-acetoxyl migration products are discussed.
#10: Tropism, Susceptibility, and Infectivity of Differentiated Human Tonsillar Epithelial Cells by Different Influenza Viruses (2021)

Abstract Introduction Influenza viruses cause significant socioeconomic impact due to annual outbreaks and pandemic risks. Human tonsil epithelium cells (HTEC) are a heterogeneous group of actively differentiating epithelia comprising stratified squamous epithelium and reticulated crypt cells with abundant keratin expression. Hypothesis We hypothesized that the tonsils are a primary site for influenza infection and sustained viral replication. Methods and Results Primary HTEC (ScienCell Research Laboratories) were grown using an air-liquid interface and infected apically with different influenza viruses at various MOIs to measure viral growth kinetics. These cells were highly differentiated, with subpopulations of cells including ciliated, non-ciliated cells and specialized cells with secretory functions. There was a heterogenous distribution of both human-like (α2,6-linked) and avian-like (α2,3-linked) sialic acid receptors. The HTEC surface and crypts were lined with pseudostratified columnar ciliated cells possessing both α2,6-linked and α2,3-linked sialic acid receptors that were interrupted by patches of reticular epithelial cells. The HTEC epithelial cells were permissive for growth of influenza A and B viruses. A subset of cells, mostly ciliated cells, underwent apoptosis while others including non-ciliated cells remained intact despite being positive for influenza virus nucleoprotein. Interestingly, differences were seen between subtypes with colocalization of H3N2 virus and non-ciliated cells while H1N1 virus mostly associated with ciliated cells. Conclusion Our results implicated human tonsillar crypt epithelium as a site for influenza virus replication. The tonsil epithelium cell culture differentiated system provides a valuable in vitro model for studying cellular tropism, infectivity, cytokines immune response and the pathogenesis of influenza viruses for better development of effective universal vaccine and therapies against different strains of influenza viruses.
ChemInform Abstract: On Steroids. Part 330. Alternative Syntheses of 2α,3α,17β‐Trihydroxy‐7‐oxa‐B‐homo‐5α‐androstan‐6‐one and Some Androstane Brassinolide Analogs. (1987)

Abstract The title compound (VIc) is synthesized starting from the steroids (I) or (III) via the alkene (II).