gebhart/patrepeval huggingface dataset:
Engineering Botulinum Toxins to Improve and Expand Targeting and SNARE Cleavage Activity (2018)

Botulinum neurotoxins (BoNTs) are highly successful protein therapeutics. Over 40 naturally occurring BoNTs have been described thus far and, of those, only 2 are commercially available for clinical use. Different members of the BoNT family present different biological properties but share a similar multi-domain structure at the molecular level. In nature, BoNTs are encoded by DNA in producing clostridial bacteria and, as such, are amenable to recombinant production through insertion of the coding DNA into other bacterial species. This, in turn, creates possibilities for protein engineering. Here, we review the production of BoNTs by the natural host and also recombinant production approaches utilised in the field. Applications of recombinant BoNT-production include the generation of BoNT-derived domain fragments, the creation of novel BoNTs with improved performance and enhanced therapeutic potential, as well as the advancement of BoNT vaccines. In this article, we discuss site directed mutagenesis, used to affect the biological properties of BoNTs, including approaches to alter their binding to neurons and to alter the specificity and kinetics of substrate cleavage. We also discuss the target secretion inhibitor (TSI) platform, in which the neuronal binding domain of BoNTs is substituted with an alternative cellular ligand to re-target the toxins to non-neuronal systems. Understanding and harnessing the potential of the biological diversity of natural BoNTs, together with the ability to engineer novel mutations and further changes to the protein structure, will provide the basis for increasing the scope of future BoNT-based therapeutics.
Investigating the correlation of muscle function tests and sarcomere organization in C. elegans (2021)

Abstract Background Caenorhabditis elegans has been widely used as a model to study muscle structure and function due to many genes having human homologs. Its body wall muscle is functionally and structurally similar to vertebrate skeletal muscle with conserved molecular pathways contributing to sarcomere structure, and muscle function. However, a systematic investigation of the relationship between muscle force and sarcomere organization is lacking. Here, we investigate the contribution of various sarcomere proteins and membrane attachment components to muscle structure and function to introduce C. elegans as a model organism to study the genetic basis of muscle strength. Methods We employ two recently developed assays that involve exertion of muscle forces to investigate the correlation of muscle function to sarcomere organization. We utilized a microfluidic pillar-based platform called NemaFlex that quantifies the maximum exertable force and a burrowing assay that challenges the animals to move in three dimensions under a chemical stimulus. We selected 20 mutants with known defects in various substructures of sarcomeres and compared the physiological function of muscle proteins required for force generation and transmission. We also characterized the degree of sarcomere disorganization using immunostaining approaches. Results We find that mutants with genetic defects in thin filaments, thick filaments and M-lines are generally weaker, and our assays are successful in detecting the functional changes in response to each sarcomere location tested. We find that the NemaFlex and burrowing assays are functionally distinct informing on different aspects of muscle physiology. Specifically, the burrowing assay has a larger bandwidth in phenotyping muscle mutants, because it could pick ten additional mutants impaired while exerting normal muscle force in NemaFlex. This enabled us to combine their readouts to develop an integrated muscle function score that was found to correlate with the score for muscle structure disorganization. Conclusions Our results highlight the suitability of NemaFlex and burrowing assays for evaluating muscle physiology of C. elegans . Using these approaches, we discuss the importance of the studied sarcomere proteins for muscle function and structure. The scoring methodology we have developed lays the foundation for investigating the contribution of conserved sarcomere proteins and membrane attachment components to human muscle function and strength.
Colloquium 15: Role of the Protease‐Activated Receptors in Neural Development, Degeneration and Trauma. Expression and regulation of PARs in brain and spinal cord (2002)

Glutamate carboxypeptidase II (GCPII, EC 3.4.17.21) is a membrane peptidase expressed in a number of tissues such as kidney, prostate and brain. The brain form of GCPII (also known as N‐acetylated‐α‐linked‐acidic dipeptidase, NAALADase) cleaves N‐acetyl‐aspartyl glutamate to yield free glutamate. Animal model experiments show that inhibition of GCPII prevents neuronal cell death during experimental ischaemia. GCPII thus represents an important target for the treatment of neuronal damage caused by excess glutamate. We report the mapping of the entire coding region of GCPII and identification of the region sufficient and necessary for the production of active recombinant protein. Extracellular portion of human glutamate carboxypeptidase II (amino acids 44–750) was expressed in Drosophila Schneider's cells and purified to homogeneity. A novel assay for hydrolytic activity of GCPII, based on fluorimetric detection of released alpha‐amino groups was established, and used for enzymological characterization of GCPII. The potential of this assay for high‐throughput inhibitor testing was evaluated and pH dependence for the enzymatic activity have been analysed. Using a complete set of protected dipeptides, substrate specificity of recombinant GCPII was elucidated. Ac‐Glu‐Met, Ac‐Asp‐Met and surprisingly Ac‐Ala‐Met were identified as novel substrates for GCPII. The glycosylation has been found indispensable for the activity of the enzyme. A series of point mutants of the enzyme has been expressed and purified and the glycosylation sites critical for the proteolytic activity have been identified.
2,3:6,7-Di-O-diethylidene-D-glycero-L-talo-heptono-1,4-lactone (2006)

The title compound, C17H28O7, was prepared from protected d-glycero-d-gulo-heptono-1,4-lactone by tandem SN2 displacements. The relative configuration of the crystal structure establishes that two stereocentres have been inverted; the absolute configuration was determined by the use of d-glucose as the starting material. There are three independent mol­ecules in the asymmetric unit (Z′=3).
ChemInform Abstract: The Synthesis and Evaluation of Temperature Sensitive Tubulin Toxins. (1999)

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.
Protein Conformational Change Is Essential for Reductive Activation of Lytic Polysaccharide Monooxygenase by Cellobiose Dehydrogenase (2020)

Large-scale protein domain dynamics and electron transfer are often associated. However, as protein motions span a broad range of time and length scales, it is often challenging to identify and thus link functionally relevant dynamic changes to electron transfer in proteins. It is hypothesized that large-scale domain motions direct electrons through a FAD and a heme <i>b</i> cofactor of the fungal cellobiose dehydrogenase (CDH) enzymes to the type-II copper center (T2Cu) of the polysaccharide-degrading lytic polysaccharide monooxygenases (LPMOs). However, as of yet, domain motions in CDH have not been linked formally to enzyme-catalyzed electron transfer reactions. The detailed structural features of CDH, which govern the functional conformational landscapes of the enzyme, have only been partially resolved. Here, we use a combination of pressure, viscosity, ionic strength, and temperature perturbation stopped-flow studies to probe the conformational landscape associated with the electron transfer reactions of CDH. Through the use of molecular dynamics simulations, potentiometry, and stopped-flow spectroscopy, we investigated how a conserved Tyr99 residue plays a key role in shaping the conformational landscapes for both the interdomain electron transfer reactions of CDH (from FAD to heme) and the delivery of electrons from the reduced heme cofactor to the LPMO T2Cu. Our studies show how motions gate the electron transfer within CDH and from CDH to LPMO and illustrate the conformational landscape for interdomain and interprotein electron transfer in this extracellular fungal electron transfer chain.
Rationally Designed PEGDA–LLZTO Composite Electrolyte for Solid-State Lithium Batteries (2021)

A novel composite electrolyte is rationally designed with a polyethylene glycol diacrylate (PEGDA) polymer and a garnet-type fast lithium-ion conductor (Li<sub>6.4</sub>La<sub>3</sub>Zr<sub>1.4</sub>Ta<sub>0.6</sub>O<sub>12</sub>, LLZTO) for solid-state lithium batteries. The LLZTO ceramic phase is incorporated into the PEGDA polymeric matrix as nanoparticles. The ionic conductivity of the composite is further optimized with a succinonitrile plasticizer. The solid composite membranes are synthesized via a tape casting process followed by a UV curing procedure. The resulting solid-state composite electrolyte delivers a room-temperature Li<sup>+</sup>-ion conductivity of 3.1 × 10<sup>-4</sup> S cm<sup>-1</sup> and can sustain an electrochemical polarization potential up to 4.6-4.7 V (vs Li<sup>+</sup>/Li). The compositing approach harnesses the advantages of both polymeric PEGDA and ceramic LLZTO. In addition to enhancing the ionic conductivity, the LLZTO ceramic filler can suppress Li dendrites. The polymeric phase of PEGDA facilitates good interfacial contact between the solid electrolyte and the electrodes. The solid-state cells fabricated with the composite solid electrolyte, lithium-metal anode, and LiNi<sub>0.8</sub>Mn<sub>0.1</sub>Co<sub>0.1</sub>O<sub>2</sub> (NMC 811) cathode show long cyclability.
Catechin Glucosides: Occurrence, Synthesis, and Stability (2010)

Catechins are flavonoids with suggested health benefits, but are unstable during storage, processing and, after ingestion, during gut transit. We hypothesized that catechin glucosides, which occur in various plants, could be more stable than unsubstituted catechin, and additionally be deglucosylated in the gut and so act to deliver catechin in a form able to be absorbed. (+)-Catechin O-glucosides from various sources have been used in the course of this investigation. (+)-Catechin 3'-O-beta-D-glucopyranoside (C3'G), (+)-catechin 5-O-beta-D-glucopyranoside (C5G), and (+)-catechin 3-O-beta-D-glucopyranoside (C3G) were chemically synthesized. (+)-Catechin 4'-O-beta-D-glucopyranoside (C4'G) and (+)-catechin 7-O-beta-D-glucopyranoside (C7G) were prepared enzymically using preparations from lentil and barley. In general, but with some exceptions, the (+)-catechin glucosides were more stable between pH 4 and 8 than (+)-catechin, with C3'G exhibiting greatest stability. The intestinal metabolism of (+)-catechin and all (+)-catechin glucosides in the gut was determined by perfusion of rat intestine in vivo. C3'G and C5G were extensively deglycosylated in the gut, and C3'G showed greatest apparent "absorption" as calculated by the difference between effluent and influent. The results show the potential of catechin glucosides, especially C3'G, as more stable prescursors of catechin.
Low-noise-figure photonic links without pre-amplification (2009)

Using optical fiber to retrieve signals from remote sensors has several advantages compared to remoting by means of metallic waveguides such as coaxial cable. Fiber-optic retrieval of an RF signal can be achieved by down-converting and digitizing the signal for conveyance by a digital fiber-optic link, or it can be achieved by conveying the RF signal over an analog fiber-optic link before digitization. The latter approach can be realized with a minimum of hardware and dc power required at the sensing site, provided that the analog fiber-optic link has a sufficiently low noise figure without a pre-amplifier. Early demonstrations of ldquoamplifierlessrdquo analog fiber-optic links typically reported very high noise figures-in excess of 30 dB. In the last decade or so, several techniques have been developed to improve this situation. We describe five such techniques and show that they have resulted in much lower measured noise figures for amplifierless links. One technique, for example, has yielded noise figures < 5 dB for amplifierless links at frequencies of up to 10 GHz. The existence of amplifierless links with such low noise figures may enable remote sensing of signals in situations where the size, weight, and power (SWAP) of the remote hardware is of primary concern.
Lithography simulation system for total CD control from design to manufacturing (2005)

Systematic design for manufacturability ( DfM ) scheme including triple gates for hot spot elimination under the low-k<sub>1</sub> lithography condition is proposed and efficient approaches to the hot spot elimination at each development stage in the DfM scheme are discussed in view of the actual situation under the concurrent development of design rule ( DR ), layout, process, optical proximity correction ( OPC ) and resolution enhancement technique ( RET ) technologies. Integrated-type lithography simulation system with OPC tool is much available for the fast processing at the initial stage and promising to be complementarily used for the verification of chip-level layout with conventional-type one at the final development stage. Low order of the lithography empirical model originating moderate prediction accuracy for all kinds of patterns is hopeful to be used at the initial development stage because it is difficult to obtain a lot of reliable experimental data for making the accurate empirical lithography model due to frequent improvement of the process, OPC and RET technologies. At the final development stage, sufficient and reliable experimental data for device pattern variations allow us to implement the higher order of the empirical model. The DfM scheme with efficient approaches in view of the actual situation under the concurrent development is found to be promising for the robust pattern formation under the low-k<sub>1</sub> lithography condition.
A Framework for Training-Based Estimation in Arbitrarily Correlated Rician MIMO Channels With Rician Disturbance (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, we create a framework for training-based channel estimation under different channel and interference statistics. The minimum mean square error (MMSE) estimator for channel matrix estimation in Rician fading multi-antenna systems is analyzed, and especially the design of mean square error (MSE) minimizing training sequences. By considering Kronecker-structured systems with a combination of noise and interference and arbitrary training sequence length, we collect and generalize several previous results in the framework. We clarify the conditions for achieving the optimal training sequence structure and show when the spatial training power allocation can be solved explicitly. We also prove that spatial correlation improves the estimation performance and establish how it determines the optimal training sequence length. The analytic results for Kronecker-structured systems are used to derive a heuristic training sequence under general unstructured statistics. </para>
Androgens in the maternal and fetal circulation: association with insulin resistance (2012)

Our results demonstrate a possible association between fetal and maternal androgen concentrations in relationship with insulin resistance.
Assessment of cerebral lesions by rapid sequential scintiphotography. (1968)

Until the advent of rapid sequential scintiphotog raphy, information regarding regional cerebral blood flow has been obtained by monitoring the passage of radioisotope tracer injected via the internal carotid artery with several large or many small scintillation detectors (1 ) . Radioactivity from each of the areas is recorded on magnetic tape from which it is graphically read out as a clearance curve. Consider able time and computation is necessary for the mathematical analysis of the temporal and spatial relationships between these multiple curves in order to determine whether a region of altered blood flow exists within the brain. Accuracy of these calcula tions is dependent upon adequate collimation and minimum overlap of adjacent regions. The Ter-Pogossian scintillation camera, on the other hand, can visualize the whole hemisphere at all times; variations of the radioisotope tracer dis tribution are seen on the television monitor. These data are also permanently recorded on video tape for playback on Polaroid film as pictures of a single 1/30th of a second frame or of integrated frames for any specific time interval. Initial studies with the camera were performed on three baboons to determine the parameters for the radioisotope dose and for the anatomical orienta tion (2,3) . O9mTc@1abeled albumin microaggregates (OOmTcAA),1â€”8 microns in size, and OOniTc.pertech.. : netate, each in a high-specific-activity bolus, were injected into the internal carotid artery. In brief, visualization of the passage of these agents through the circulation is as follows: the area of the Circle of Willisin less than0.1 5cc, the insulain 0.2 see, the jugular bulb in 3 sec and the superior sagittal sinus in 4 sec. The radioisotopes disappear from the venous circulation within 10â€”12 sec after injec ton.
P4BFT: Hardware-Accelerated Byzantine-Resilient Network Control Plane (2019)

Byzantine Fault Tolerance (BFT) enables correct operation of distributed, i.e., replicated applications in the face of malicious take-over and faulty/buggy individual instances. Recently, BFT designs have gained traction in the context of Software Defined Networking (SDN). In SDN, controller replicas are distributed and their state replicated for high availability purposes. Malicious controller replicas, however, may destabilize the control plane and manipulate the data plane, thus motivating the BFT requirement. Nonetheless, deploying BFT in practice comes at a disadvantage of increased traffic load stemming from replicated controllers, as well as a requirement for proprietary switch functionalities, thus putting strain on switches' control plane where particular BFT actions must be executed in software. P4BFT leverages an optimal strategy to decrease the total amount of messages transmitted to switches that are the configuration targets of SDN controllers. It does so by means of message comparison and deduction of correct messages in the determined optimal locations in the data plane. In terms of the incurred control plane load, our P4-based data plane extensions outperform the existing solutions by ~33.2% and ~40.2% on average, in random 128-switch and Fat-Tree/Internet2 topologies, respectively. To validate the correctness and performance gains of P4BFT, we deploy bmv2 and Netronome Agilio SmartNIC-based topologies. The advantages of P4BFT can thus be reproduced both with software switches and "commodity" P4-enabled hardware. A hardware- accelerated controller packet comparison procedure results in an average 96.4% decrease in processing delay per request compared to existing software approaches.
Value and Limitations of Formaldehyde for Hatch Cabinet Applications: The Search for Alternatives (2022)

Pioneer colonization by beneficial microorganisms promote a shift in the composition of the gut microbiota, excluding opportunistic pathogens. Commercially, the horizontal transmission of both apathogenic and pathogenic organisms is common during the hatching phase. The microbial bloom occurs as the humidity rises during hatch, exposing naïve chicks to a plethora of potentially harmful microbes. Horizontal transmission or introduction of pathogens may occur as infected chicks hatch or during handling after hatch pull. Moreover, contaminated infertile or non-viable embryonated eggs can serve as reservoirs for pathogenic organisms and even rupture during incubation. The organisms within the contents of these eggs can penetrate the shell of the embryonated eggs and subsequently contaminate the entire cabinet. Formaldehyde fumigation is commonly applied during the hatching phase to control the microbial bloom in the environment, but does not penetrate the eggshell prior to hatch. Additionally, this fumigation technique eliminates microbial organisms in the environment at hatch, including beneficial species. Furthermore, prolonged exposure to formaldehyde can damage the tracheal epithelia of neonatal chicks increasing susceptibility to infection by opportunistic microbes. Laboratory challenge models that mimic the microbial bloom that occurs in commercial hatch cabinets can be used to evaluate effective alternatives to control the microbial bloom and promote colonization by beneficial bacteria without the use of formaldehyde fumigation.
A Chicken Chorioallantoic Membrane Assay for the Evaluation of the Androgen Responsiveness of Prostatic Tissue (1986)

A biological assay using the chorioallantoic membrane (CAM) of the chicken egg as an in vitro culture system has been developed and standardized in order to assess the androgen responsiveness of normal and abnormal prostatic tissue. In this assay, test tissue is implanted onto the CAM of chicken eggs in the presence or absence of exogenous testosterone treatment, with subsequent serum levels of 45 ng./dl. and greater than 5,000 ng./dl., respectively. The responsiveness of test tissue to low versus high androgen levels was evaluated in this CAM assay using both cellular morphology and mitotic index as response criteria. Both androgen responsive and unresponsive tissues from the rat were grown on the CAM and demonstrated appropriate morphologic and proliferative responses to the presence and absence of testosterone supplementation. Human prostatic adenocarcinoma and benign hyperplastic tissues were also grown successfully on the CAM. Documentation of human tissue survival was performed by immunocytochemical analysis for prostate specific antigen and prostate specific acid phosphatase. The human prostatic adenocarcinomas studied demonstrated a two to four-fold increase in mitotic index with androgen augmentation. In conclusion, the ability of this assay to determine androgen responsiveness as measured by morphologic and proliferative criteria has been documented in rat tissues. Human prostatic adenocarcinoma has been grown consistently on the chick chorioallantoic membrane for the first time using newly developed techniques. Therefore, this technique shows promise in the clinical application for the determination of the androgen responsiveness of human prostatic carcinomas.
Power factor simulation of focus quadrupole DC power supply of white circuit system with MATLAB simulink (2002)

The focus quadrupole DC power supply used at white circuit system of booster ring of Synchrotron Radiation Research Center (SRRC) is a 19.2kW unit, but an AC power source to measure the power factor of such a power supply with built-in power factor measuring function is very expensive. Power factor simulation of this power supply with MATLAB Simulink software is economic and the simulated results may be used to find some efficient ways to correct this parameter if necessary. The results from the simulation model will be compared with the results of power factor monitored from direct measurement on AC mains. The model of quadrupole DC power supply is constructed and provided for better understanding for further modification.