gebhart/patrepeval huggingface dataset:
Evolutionary Acquisition and Loss of Saxitoxin Biosynthesis in Dinoflagellates: the Second “Core” Gene, <i>sxtG</i> (2013)

Saxitoxin and its derivatives are potent neurotoxins produced by several cyanobacteria and dinoflagellate species. SxtA is the initial enzyme in the biosynthesis of saxitoxin. The dinoflagellate full mRNA and partial genomic sequences have previously been characterized, and it appears that sxtA originated in dinoflagellates through a horizontal gene transfer from a bacterium. So far, little is known about the remaining genes involved in this pathway in dinoflagellates. Here we characterize sxtG, an amidinotransferase enzyme gene that putatively encodes the second step in saxitoxin biosynthesis. In this study, the entire sxtG transcripts from Alexandrium fundyense CCMP1719 and Alexandrium minutum CCMP113 were amplified and sequenced. The transcripts contained typical dinoflagellate spliced leader sequences and eukaryotic poly(A) tails. In addition, partial sxtG transcript fragments were amplified from four additional Alexandrium species and Gymnodinium catenatum. The phylogenetic inference of dinoflagellate sxtG, congruent with sxtA, revealed a bacterial origin. However, it is not known if sxtG was acquired independently of sxtA. Amplification and sequencing of the corresponding genomic sxtG region revealed noncanonical introns. These introns show a high interspecies and low intraspecies variance, suggesting multiple independent acquisitions and losses. Unlike sxtA, sxtG was also amplified from Alexandrium species not known to synthesize saxitoxin. However, amplification was not observed for 22 non-saxitoxin-producing dinoflagellate species other than those of the genus Alexandrium or G. catenatum. This result strengthens our hypothesis that saxitoxin synthesis has been secondarily lost in conjunction with sxtA for some descendant species.
Abstract 2921: Genome-wide Association Reveals Sequence Variants on 4q25 that Affect the Risk of Atrial Fibrillation and Stroke (2007)

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia in man and is characterized by chaotic electrical activity of the atria. It affects one in ten individuals over eighty, causes significant morbidity, and is an independent predictor of mortality. We have carried out a genome-wide scan using 316,000 SNPs on an Illumina beadchip to genotype a large atrial fibrillation cohort in Iceland. We found two common sequence variants (SNPs) within the same LD block on chromosome 4q25 near the PITX2 gene which increase the risk of AF substantially (by 1.72 and 1.39 per copy, respectively). An even higher risk was observed in individuals with typical atrial flutter. The association was replicated in Swedish, American, and Chinese populations. These variants do not associate with known risk factors for AF and thus provide an independent predictor of risk. The variants have a stronger effect in individuals younger than 80 but the risk in males and females is indistinguishable. As expected, given that AF is the primary cause of cardiogenic stroke, we found significant correlation to cardiogenic stroke in multiple cohorts. We have now followed up this initial study by combining these two variants to define a test to predict the risk of AF and show its characteristics in a meta-analysis of about 4500 AF patients from four European and American Caucasian cohorts. We demonstrate the effect of age on prediction. About 30% of the general population is positive for this test and has an OR of 1.8 for atrial fibrillation in individuals younger than 80. Such a test may be useful in recently diagnosed ischemic stroke and TIA patients to help decide which patients may benefit from ambulatory cardiac monitoring and perhaps provide a higher yield of detection of asymptomatic intermittent AF that is not discovered during the standard 24 to 48 hour monitoring within the hospital. This may be particularly important given that secondary stroke prevention strategies of antiplatelet agents and statins widely used for atherosclerosis-related strokes are much less effective for preventing strokes caused by AF.
A Systems Approach to Ionospheric Delay Compensation (2006)

Dual-frequency and single frequency ionospheric delay compensation algorithms are fundamental GPS receiver methods that attempt to remove the signal delay that occurs when NAVSTAR satellites' transmissions pass through the ionosphere. Dual-frequency algorithms normally provide higher accuracy navigation solutions than single-frequency compensation algorithms, but environmental factors and signal conditions may adversely impact the performance of the dual- frequency algorithms. Receiver noise and frequency-dependent multi-path are two terms that often lead to dual-frequency ionospheric delay compensation errors. An alternative ionospheric delay compensation algorithm has been designed, implemented, and tested that moves the dual- frequency compensation algorithm from the GPS receiver into a Kalman filter that serves as the fundamental integration component in a tightly-coupled or ultra-tightly-coupled GPS- aided Inertial Navigation System (INS) integration. This ionospheric delay algorithm adds a number of dedicated states to the Kalman filter. One of these states represents a normalized global ionospheric delay that models the ionospheric delay that is common to all satellites. An additional Kalman filter state is allocated to each tracked satellite to model the normalized component of ionospheric delay error unique to that satellite. An obliquity factor, that describes the distance that the GPS signal passes through ionosphere, scales the normalized delay estimated by the filter to attain the actual estimate of ionospheric delay for each satellite. Using a Kalman filter to estimate the ionospheric delays is particularly beneficial when the received GPS signal is attenuated by environmental factors such as foliage, when receiver noise is high, or when simultaneous track of L1 and L2 frequencies is not possible. This Kalman filter design has become a common component of Boeing's GPS-aided INS design. Significant laboratory and flight test data have demonstrated the benefits of this design and have substantiated inertial navigation simulation predictions.
Conjugated Dendrimers for Colour Control in Light-emitting Diodes (1998)

We report a novel molecular engineering approach to organic materials for LEDs based on dendrimers. The molecules consist of a conjugated core, conjugated linkers, and surface groups, as illustrated schematically in figure 1. The conjugated core and linkers control the electronic properties, whilst the surface groups control the processing properties. This is a very attractive feature as it should enable electronic and processing properties to be optimised independently, in contrast to linear polymers where substitution can affect both.
Detecting dominant locations from search queries (2005)

Accurately and effectively detecting the locations where search queries are truly about has huge potential impact on increasing search relevance. In this paper, we define a search query's dominant location (QDL) and propose a solution to correctly detect it. QDL is geographical location(s) associated with a query in collective human knowledge, i.e., one or few prominent locations agreed by majority of people who know the answer to the query. QDL is a subjective and collective attribute of search queries and we are able to detect QDLs from both queries containing geographical location names and queries not containing them. The key challenges to QDL detection include false positive suppression (not all contained location names in queries mean geographical locations), and detecting implied locations by the context of the query. In our solution, a query is recursively broken into atomic tokens according to its most popular web usage for reducing false positives. If we do not find a dominant location in this step, we mine the top search results and/or query logs (with different approaches discussed in this paper) to discover implicit query locations. Our large-scale experiments on recent MSN Search queries show that our query location detection solution has consistent high accuracy for all query frequency ranges.
Measuring High Temperatures In Ceramic-Fiber Blankets (1996)

Thermocouple assemblies devised specifically for measuring temperatures at fixed locations within insulating blankets made of such ceramic fibers as alumina, silicon carbide, and/or aluminoborosilicate. Thermocouples measure temperatures from 100 to 3,200 degrees F in oxidizing atmospheres. Wires enclosed in alumina sheath for protection against hot oxidation and mechanical damage.
Photonic reservoir computing: A new approach to optical information processing (2010)

Despite ever increasing computational power, recognition and classification problems remain challenging to solve. Recently advances have been made by the introduction of the new concept of reservoir computing. This is a methodology coming from the field of machine learning and neural networks and has been successfully used in several pattern classification problems, like speech and image recognition. The implementations have so far been in software, limiting their speed and power efficiency. Photonics could be an excellent platform for a hardware implementation of this concept because of its inherent parallelism and unique nonlinear behaviour. We propose using a network of coupled Semiconductor Optical Amplifiers (SOA) and show in simulation that it could be used as a reservoir by comparing it on a benchmark speech recognition task to conventional software implementations. In spite of several differences, they perform as good as or better than conventional implementations. Moreover, a photonic implementation offers the promise of massively parallel information processing with low power and high speed. We will also address the role phase plays on the reservoir performance.
Field-testing UV disinfection of drinking water (1997)

A recently invented device, “UV Waterworks,” uses ultraviolet (UV) light to disinfect drinking water. Its novel features are: low cost, robust design, rapid disinfection (12 seconds), low electricity use (40W), low maintenance (every 6 months), high flow rate (15 l/min) and ability to\nwork with unpressurized water sources. The device could service a community of 1000 persons, at an annual total cost of less than 10 cents US per person. UV Waterworks has been successfully tested in the laboratory. Limited field\ntrials of an early version of the device were conducted in India in 1994-95. Insights from these trials led to the present design. Extended field trials of UV Waterworks, initiated in South Africa in February 1997, will be coordinated by the South African Centre for Essential Community Services (SACECS), with technical and organizational support from Lawrence Berkeley National Laboratory (LBNL) and the Natural Resources Defence Council (both USA). The first of the eight planned sites of the year long trial is an AIDS hospice near Durban. Durban Metro Water and LBNL lab-tested a UV Waterworks unit prior to installing it at the hospice in August, 1997. We describe the field test plans and preliminary results from Durban.
Effect of Process and Layout on Strain Enhancement from Dual Stress Liners (2006)

Tensile and compressive stressed nitride liners have been used to increase the carrier mobility in n-channel and p-channel silicon transistors respectively. Simulations indicate how much of the stress in the film is transferred to the channel region and the magnitude of the stress in different directions. A simple bulk piezoresistive model was used to estimate the effect on carrier mobility. It is shown in the case of the n-channel transistors that the enhancement is due to the vertical stress component whereas in the case of p-channel devices the enhancement is due to the in-plane stresses. The effect of different process conditions such as film stress, thickness and method of deposition, on mobility enhancement, was also characterized. It is shown that the enhancement saturates with increasing nitride thickness but scales proportionally with the film stress. Detailed studies of the effect of the circuit layout on the final channel stress allow the critical layout parameters to be identified. The variation of device performance with the layout parameters is quantified and can be used to define design rules as well as equations to modify the device characteristics based on layout.
Galactooligosaccharides (GOS) Inhibit Vibrio cholerae Toxin Binding to Its GM1 Receptor (2009)

It is widely reported that cholera toxin (Ctx) remains a significant cause of gastrointestinal disease globally, particularly in developing countries where access to clean drinking water is at a premium. Vaccines are prohibitively expensive and have shown only short-term protection. Consequently, there is scope for continued development of novel treatment strategies. One example is the use of galactooligosaccharides (GOS) as functional mimics for the cell-surface toxin receptor (GM1). In this study, GOS fractions were fractionated using cation exchange chromatography followed by structural characterization using a combination of hydrophilic interaction liquid chromatography (HILIC) and electrospray ionization mass spectrometry (ESI-MS) such that their molecular weight profiles were known. Each profile was correlated against biological activity measured using a competitive inhibitory GM1-linked ELISA. GOS fractions containing >5% hexasaccharides (DP(6)) exhibited >90% binding, with EC(50) values between 29.27 and 56.04 mg/mL. Inhibition by GOS DP(6) was dose dependent, with an EC(50) value of 5.10 mg/mL (5.15 microM MW of 990 Da). In removing low molecular weight carbohydrates that do possess prebiotic, nutraceutical, and/or biological properties and concentrating GOS DP(5) and/or DP(6), Ctx antiadhesive activity per unit of (dry) weight was improved. This could be advantageous in the manufacture of pharmaceutical or nutraceutical formulations for the treatment or prevention of an acute or chronic disease associated with or caused by the adhesion and/or uptake of a Ctx or HLT.
Emphasis on the Properties of Metal‐Containing Zeolites Operating Outside the Comfort Zone of Current Heterogeneous Catalytic Reactions (2020)

Abstract The development of catalysts that can operate under exceptionally harsh and unconventional conditions is of critical importance for the transition of the energy and chemicals industries to low‐emission and renewable chemical feedstocks. In this review we will highlight materials and more specifically metal‐containing zeolite catalysts that have been tested under harsh reaction conditions such as high temperature light alkane conversion and biomass valorization. Particular attention will be given to studies that explore the stability and recyclability of metal‐containing zeolite catalysts operating in continuous modes. Metal‐containing zeolites are considered as an important class of catalysts operating outside the comfort zone of current heterogeneous catalytic reactions in both gas and liquid phase reactions. The relationship between the properties of the metal‐containing zeolite and catalytic performance will be explored.
Transform Domain Motion Estimation (1979)

This paper introduces an algorithm for estimating the displacement of moving objects in a television scene from spatial transform coefficients of successive frames. The algorithm works recursively in such a way that the displacement estimates are updated from coefficient to coefficient. A promising application of this algorithm is in motion-compensated interframe hybrid transform- dpcm image coding. We give a statistical analysis of the transform domain displacement estimation algorithm and prove its convergence under certain realistic conditions. An analytical derivation is presented that gives sufficient conditions for the rate of convergence of the algorithm to be independent of the transform type. This result is supported by a number of simulation examples using Hadamard, Haar, and Slant transforms. We also describe an extension of the algorithm that adaptively updates displacement estimation according to the local features of the moving objects. Simulation results demonstrate that the adaptive displacement estimation algorithm has good convergence properties in estimating displacement even for very noisy images.
(Invited) New Paradigms for Cost-Effective III-V Photovoltaic Technology (2013)

In this paper, we discuss two new paradigms for enabling cost-effective III-V solar cell photovoltaics using (i) our novel layer transfer technology, called controlled spalling and (ii) new solar cell device structures. First, we present the application of the controlled spalling for making high-efficiency thin-film multi-junction solar cells. Finally, a novel GaAs heterojunction solar cell structure is described, consisting of thin hydrogenated amorphous silicon stack deposited directly on the GaAs surface at 200ºC, aiming to eliminate the III-V epitaxy. This feature in conjunction with a kerf-less removal of GaAs using the controlled spalling technique offers a viable pathway for realizing low cost high-efficiency III-V photovoltaic technology.
Extracorporeal circulation for port-access cardiac surgery (1997)

Minimally invasive techniques for cardiac surgery are a new approach in performing some cardiac operations. Minimally invasive surgery may minimize patient discomfort, length of stay in the hospital and postoperative rehabilitation. These procedures utilize a small thoracotomy for direct visualization of the heart. However, without the use of cardiopulmonary bypass, this approach is limited to some epicardial procedures such as coronary bypass grafting, where the heart rate is pharmacologically reduced. Port-access cardiac surgery is a new approach which provides all the benefits of minimally invasive surgery without sacrificing the advantages of cardiopulmonary bypass and myocardial preservation. Port-access cardiac surgery uses an anterior mediastinotomy and thoracic ports in conjunction with a specially designed set of endovascular catheters. These catheters provide a mode to arrest, preserve and vent the heart through an endoaortic occlusion balloon positioned in the ascending aorta. A pulmonary artery vent and coronary sinus cardioplegia catheter can also be used. These endovascular catheters, integrated with a modified heart-lung machine, provide complete cardiopulmonary support through extrathoracic cannulae inserted in a femoral artery and vein. Maintenance and monitoring of this endovascular cardiopulmonary bypass system requires the use of a kinetic pump in the venous drainage line to augment return to the heart-lung machine. Special guidelines and management parameters exist to optimize bypass with this catheter system. Using this system, port-access, minimally invasive surgery can be applied to a wider range of both epicardial and intracardiac procedures.
Design and characterization of a magneto-rheological series elastic actuator for a lower extremity exoskeleton (2017)

In this paper, an innovative actuator named magneto-rheological series elastic actuator (MRSEA) is designed for the knee joints of a lower extremity exoskeleton CUHK-EXO. MRSEA is designed to reduce the mechanical impedance of the exoskeleton and filter out unwanted collisions. It can also provide large controllable braking torque with low power, and hence improve the system energy efficiency. A description of CUHK-EXO developed to help paraplegic patients regain the mobility to stand up, sit down and walk is firstly introduced, followed by the mechanical design of MRSEA and simulation of the torsion spring pack (TSP) and magneto-rheological (MR) brake of MRSEA. Prototype of MRSEA is fabricated. Preliminary tests are performed to investigate the characteristics of the TSP and MR brake, and walking experiments with a paraplegic patient are performed to evaluate the performance of MRSEA. Experimental results of MRSEA match the modeling and simulation. As compared with the electric motor, the energy efficiency of the innovative MRSEA is improved by 52.8% during a gait cycle.
Abstract 15053: New Insights into the Development of the Protease Proprotein Convertase Subtilisin-Like Kexin Type 9 Antagonists (2016)

Protease proprotein convertase subtilisin-like kexin type 9 (PCSK9) is an important target for the treatment of hypercholesterolemia. PCSK9 is synthesized as a zymogen that undergoes autocatalytic ...
Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes (2011)

Potent HaeIII-like DNA restriction activity was detected in cell-free extracts of Caldicellulosiruptor bescii DSM 6725 using plasmid DNA isolated from Escherichia coli as substrate. Incubation of the plasmid DNA in vitro with HaeIII methyltransferase protected it from cleavage by HaeIII nuclease as well as cell-free extracts of C. bescii. The gene encoding the putative restriction enzyme was cloned and expressed in E. coli with a His-tag at the C-terminus. The purified protein was 38 kDa as predicted by the 981-bp nucleic acid sequence, was optimally active at temperatures between 75°C and 85°C, and was stable for more than 1 week when stored at 35°C. The cleavage sequence was determined to be 5'-GG/CC-3', indicating that CbeI is an isoschizomer of HaeIII. A search of the C. bescii genome sequence revealed the presence of both a HaeIII-like restriction endonuclease (Athe 2438) and DNA methyltransferase (Athe 2437). Preliminary analysis of other Caldicellulosiruptor species suggested that this restriction/modification activity is widespread in this genus. A phylogenetic analysis based on sequence alignment and conserved motif searches identified features of CbeI distinct from other members of this group and classified CbeI as a member of a novel subfamily of HaeIII-like enzymes.
Next‐Generation Cobalt‐Free Cathodes – A Prospective Solution to the Battery Industry's Cobalt Problem (2022)

Abstract Lithium‐ion batteries are overreliant on cobalt containing cathodes. Current projections estimate that hundreds of millions of electric vehicles (EVs) will be on the road by 2050, and this ever‐growing demand threatens to deplete global cobalt reserves at an alarming rate. Moreover, cobalt supply chain issues have significantly increased cobalt prices throughout the last decade. As such, energy storage research and development need to reduce the reliance on cobalt to meet ever‐growing demand for lithium‐ion batteries. The present review summarizes the science and technology gaps and potential of numerous cobalt‐free Li‐ion cathodes including layered, spinel, olivine, and disordered rock‐salt systems. Despite the promising performance of these Co‐free cathodes, scale‐up and manufacturing bottlenecks associated with these materials must also be addressed to enable widespread adoption in commercial batteries. Overall, this review broadly highlights the enormous promise of “zero‐cobalt” Li‐ion batteries to enable sustainable production of EVs in the coming decades.
Pathogenicity of Steinernema scapterisci to Selected Invertebrates. (1991)

Steinernema scapterisci was more pathogenic to insects tested in the order Orthoptera than to those in the orders Lepidoptera or Hymenoptera; it was not pathogenic to earthworms. The nematode also infected and killed the mole crickets Scapteriscus acletus and S. vicinus when released four successive times at 10-day intervals in containers of soil infested with the nematode.
Substituted 2‐Phenyl‐benzimidazole Derivatives: Novel Compounds that Suppress Key Markers of Allergy. (2006)

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