gebhart/patrepeval huggingface dataset:
DNA polymerases with improved reverse transcriptase activity (2009)

There exists a need for enzymes with improved reverse transcriptase activity to increase the sensitivity of diagnostic assays which use RNA targets. In our lab we have produced a collection of chimeric mutant DNA polymerases with modulated proofreading activity. A mutagenized library of one of these DNA pols was screened for improved extension rates on a primed M13 template. Some of the mutants displayed the ability to perform improved RT‐PCR using either Mn2+ or Mg2+. One of the DNA pol mutations, D640G, was transferred to the parent DNA pols of the chimera, Thermatoga maritima and Thermus sp. Z05. These mutants also demonstrated the ability to perform efficient RT‐PCR with reduced RT incubation times. In Z05 the D580 position was mutated to all 19 other amino acids and the resulting proteins were purified. The D580G and K mutants were found to have improved RT activity and increased RT‐PCR sensitivity using TaqMan‐based detection. Enzymatic characterization revealed a 12.5‐fold improvement in the catalytic efficiency of Mn2+‐activated RT for Z05 D580G over wild‐type. The Z05 D580K enzyme also showed significant activity when Mn2+ was replaced by Mg2+ allowing for higher fidelity RT‐PCR.
Selective Conversion of Cellulose to Hydroxymethylfurfural in Polar Aprotic Solvents (2014)

Abstract Herein, we report a new reaction pathway to produce hydroxymethylfurfural (HMF) from cellulose under mild reaction conditions (140–190 °C; 5 m M H 2 SO 4 ) in polar aprotic solvents (i.e. THF) without the presence of water. In this system, levoglucosan is the major decomposition product of cellulose, followed by dehydration to produce HMF. Glucose, levulinic acid, and formic acid are also produced as a result of side reactions with water, which is a by‐product of dehydration. The turnover frequency for cellulose conversion increases as the water content in the solvent decreases, with conversion rates in THF being more than twenty times higher than those in water. The highest HMF yield from cellulose was 44 % and the highest combined yield of HMF and levulinic from cellulose was 53 %, which are nearly comparable to yields obtained in ionic liquids or biphasic systems. Moreover, the use of a low boiling point solvent, such as THF, facilitates recovery of HMF in downstream processes.
Load balancing for clustered web farms (2001)

We propose a scheme which attempts to optimally balance the load on the servers of a clustered web farm. Solving this performance problem is crucial to achieving minimal average response time for customer requests, and thus ultimately to achieving maximal customer throughput. This short paper gives an overview of three new mathematical contributions. First, we describe a goal setting algorithm to determine the load on each server which minimizes the average customer request response time given the possibly overlapping cluster assignments of sites to servers and the current customer request load for each site. The cluster assignments, which of necessity can only be changed relatively infrequently, have a major effect on the optimal response time in the goal setting component. So, second, we describe a static algorithm which determines good assignments of sites to servers. Third, and finally, we describe a dynamic algorithm which handles the real-time server load balancing, reacting to the fluctuating customer request load in order to come as close as possible to achieving the idealized optimal average response time. We examine the performance of the overall load balancing scheme via simulation experiments.
Single-Feed Circularly Polarized Microstrip Antenna With Bethe Holes on the Radiating Patch (2019)

A novel single-feed (SF) circularly polarized (CP) microstrip antenna with Bethe holes on the radiating patch is introduced. The proposed antenna provides a small axial ratio (AR) over a relatively large frequency range and the CP quality is good over a wide range of radiation angle. The structure is of a single layer, providing easy fabrication at low cost.
ChemInform Abstract: One‐Step Synthesis of Halogenated Carboxylic Acid Fluorides from the Free Acids. (1987)

Abstract The per‐ and polyhalogenated carboxylic acids (I) react with the trifluoromethyl‐ or difluorochloromethyl substituted aromatic compounds (II) in the presence of Lewis acids to yield the acyl fluorides (III), together with the benzoyl fluorides (IV) and the hydrogen halides (V).
Non-orthogonal Multiple Access (NOMA) with Successive Interference Cancellation for Future Radio Access (2015)

This paper presents our investigation of non-orthogonal multiple access (NOMA) as a novel and promising power-domain user multiplexing scheme for future radio access. Based on information theory, we can expect that NOMA with a successive interference canceller (SIC) applied to the receiver side will offer a better tradeoff between system efficiency and user fairness than orthogonal multiple access (OMA), which is widely used in 3.9 and 4G mobile communication systems. This improvement becomes especially significant when the channel conditions among the non-orthogonally multiplexed users are significantly different. Thus, NOMA can be expected to efficiently exploit the near-far effect experienced in cellular environments. In this paper, we describe the basic principle of NOMA in both the downlink and uplink and then present our proposed NOMA scheme for the scenario where the base station is equipped with multiple antennas. Simulation results show the potential system-level throughput gains of NOMA relative to OMA.
Adaptive Two-Dimensional Microgas Chromatography (2012)

We proposed and investigated a novel adaptive two-dimensional (2-D) microgas chromatography system, which consists of one 1st-dimensional column, multiple parallel 2nd-dimensional columns, and a decision-making module. The decision-making module, installed between the 1st- and 2nd-dimensional columns, normally comprises an on-column nondestructive vapor detector, a flow routing system, and a computer that monitors the detection signal from the detector and sends out the trigger signal to the flow routing system. During the operation, effluents from the 1st-dimensional column are first detected by the detector and, then, depending on the signal generated by the detector, routed to one of the 2nd-dimensional columns sequentially for further separation. As compared to conventional 2-D GC systems, the proposed adaptive GC scheme has a number of unique and advantageous features. First and foremost, the multiple parallel columns are independent of each other. Therefore, their length, stationary phase, flow rate, and temperature can be optimized for best separation and maximal versatility. In addition, the adaptive GC significantly lowers the thermal modulator modulation frequency and hence power consumption. Finally, it greatly simplifies the postdata analysis process required to reconstruct the 2-D chromatogram. In this paper, the underlying working principle and data analysis of the adaptive GC was first discussed. Then, separation of a mixture of 20 analytes with various volatilities and polarities was demonstrated using an adaptive GC system with a single 2nd-dimensional column. Finally, an adaptive GC system with dual 2nd-dimensional columns was employed, in conjunction with temperature ramping, in a practical application to separate a mixture of plant emitted volatile organic compounds with significantly shortened analysis time.
Autosomal dominant polycystic kidney disease: molecular analysis (1995)

Using a positional cloning approach the major autosomal dominant polycystic kidney disease (ADPKD) gene (PKD1) has been identified on chromosome 16: a disease associated chromosome translocation was instrumental in its identification. Study of the PKD1 gene has been complicated because most of the gene lies in a genomic region reiterated elsewhere on the same chromosome. The duplicate area contains three genes which share substantial homology with PKD1 and generate polyadenylated transcripts. Most PKD1 mutations have so far been detected in the single copy, 3' end of the gene, but a group of patients with deletion of PKD1 and the adjacent TSC2 gene, which have severe infantile polycystic kidney disease, have also been characterised. The full length transcript of PKD1 (approximately 14 kb) has now been cloned and is predicted to encode a protein, polycystin, of 4302/3 aa. Polycystin contains multiple extracellular domains including leucine rich repeats, a C-type lectin, immunoglobulin and fibronectin type III-like domains and has a C terminal region which is likely associated with the membrane. These homologies indicate that polycystin is a cell-cell/matrix interaction protein.
User interfaces for multimedia multiparty communications (2002)

Network control and coordination functions needed to support multimedia multiparty applications are discussed. Emphasis is placed on user interfaces for these applications. Whereas conventional, single-medium devices (such as telephones) present their users with one connection to one party during a call, these new applications make multiple network resources visible to their users. The authors' experience suggests that the user interfaces for these applications should not be built as simple additions to interfaces for conventional devices, but rather should reflect new communication models with independent controls of the network resources associated with the application. Important features of user interfaces are discussed for multimedia conferencing systems, illustrating how individual controls for network resources can be made available to the application user during a communication session. The benefits of building user interfaces as a collection of modules, in which some modules are responsible for conference conduct and others provide controls for exchange of information in each medium, are explained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Algorithms for unboundedly parallel simulations (1991)

New methods are presented for parallel simulation of discrete event systems that, when applicable, can usefully employ a number of processors much larger than the number of objects in the system being simulated, Abandoning the distributed event list approach, the simulation problem is posed using recurrence relations. We bring three algorithmic ideas to bear on parallel simulation: parallel prefix computation, parallel merging, and iterative folding. Efficient parallel simulations are given for (in turn) the G/G/l queue, a variety of queueing networks having a global first come first served structure (e.g., a series of queues with finite buffers), acyclic networks of queues, and networks of queues with feedbacks and cycles. In particular, the problem of simulating the arrival and departure times for the first N jobs to a single G/G/l queue is solved in time proportional to N/P + log P using P processors.
Massive structured data management solution (2010)

The need to analyze structured data for various business intelligence applications such as customer churn analysis, social network analysis, etc. is well known. However, the potential size to which such data will scale in future will make solutions that revolve around data warehouses hard to scale. We begin by presenting a business case that prompted us to look at building a distributed analytics platform that is leveraging the MapReduce framework pioneered by Google. We present the results of the study and highlight issues with the current structured data access techniques for MapReduce platforms. Finally, we present a distributed and scalable data platform that leverages Apache Hadoop to enable business analysts to seamlessly query archived data along with data stored in the warehouse.
Comparison of biochemical microbial effects in enhanced oil recovery (MEOR) (1992)

Experimental data dealing with the interactions between certain microbial species and crude oils indicates that these interactions are selective and occur via biochemical pathways which can be characterized by the chemical composition of the initial crude oil and that of the end products. In the studies discussed in this paper, the microbial species used were thermophilic and/or thermoadapted microorganisms which thrive in harsh environments (e.g., pH, temperature, pressure, salinity). Crude oils chosen for biotreatment represented a wide range of oils, which varied from relatively light oils to heavy, high sulfur content oils. The crude oils used have also been distinguished in terms of their geological history, i.e., heavy, because they are immature or heavy, because they have been biodegraded. The significance of ``biodegraded`` vs. ``biotreated`` crude oil in MEOR also discussed.
Permanent magnets for magnetic resonance imaging (1986)

Several permanent-magnet structures for whole-body nuclear magnetic resonance diagnostics are described and compared. All provide a field of 1.5 kOe over working volumes of about 0.9 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> without the use of electrical solenoids or bulky power supplies. A previously proposed ferrite model now weighs more than 11 tons. By using more unorthodox configurations employing rare earth permanent magnets, the same performance can be attained with as little as 3.6 tons of material.
Predicting Blood Pressure with Deep Bidirectional LSTM Network (2017)

Blood pressure (BP) has been a difficult vascular risk factor to measure continuously and precisely with a small cuffless electronic gadget. In the meantime, it is the key biomarker for control of cardiovascular diseases (CVD), the leading cause of death worldwide. In this work, we addressed the current limitation of BP prediction models by formulating BP extraction as a temporal sequence prediction problem in which both the input and target are sequential data. By incorporating both a bidirectional layer structure and a deep architecture in a standard long short term-memory (LSTM), we established a deep bidirectional LSTM (DB-LSTM) network that can adaptively discover the latent structures of different timescales in BP sequences and automatically learn such multiscale dependencies. We evaluated our proposed model on a one-day and four-day continuous BP dataset, and the results show that DB-LSTM network can effectively learn different timescale dependencies in the BP sequences and advances the state-of-the-art by achieving superior accuracy performance than other leading methods on both datasets. To the best of our knowledge, this is the first study to validate the ability of recurrent neural networks to learn the different timescale dependencies of long-term continuous BP sequence.
Introduction of Shigella flexneri 2a type and group antigen genes into oral typhoid vaccine strain Salmonella typhi Ty21a (1987)

For protection against dysentery caused by Shigella flexneri 2a, an in vivo-constructed recombinant plasmid with genes specifying the S. flexneri type and group antigens located near the pro (min 6) and his (min 44) chromosomal markers, respectively, was made and transferred to the galE Salmonella typhi strain Ty21a. Strain Ty21a carrying this recombinant plasmid was shown by immunological and biochemical analyses to express the S. flexneri 2a type and group antigens. Mice immunized with this vaccine strain were found to be protected against challenge with virulent S. flexneri 2a, but not significantly against S. typhi challenge, presumably because synthesis of the Shigella antigens interfered with expression of the typhoid antigens. Elimination of the recombinant plasmid from Ty21a allowed this strain to again express typical S. typhi O antigens. Mouse protection against both S. typhi and S. flexneri 2a challenges was achieved with a whole-cell vaccine mixture composed of equal parts of Ty21a and the Ty21a-S. flexneri 2a hybrid strain.
Projection-based approaches for model reduction of weakly nonlinear, time-varying systems (2003)

The problem of automated macromodel generation is interesting from the viewpoint of system-level design because if small, accurate reduced-order models of system component blocks can be extracted, then much larger portions of a design, or more complicated systems, can be simulated or verified than if the analysis were to have to proceed at a detailed level. The prospect of generating the reduced model from a detailed analysis of component blocks is attractive because then the influence of second-order device effects or parasitic components on the overall system performance can be assessed. In this way overly conservative design specifications can be avoided. This paper reports on experiences with extending model reduction techniques to nonlinear systems of differential-algebraic equations, specifically, systems representative of RF circuit components. The discussion proceeds from linear time-varying, to weakly nonlinear, to nonlinear time-varying analysis, relying generally on perturbational techniques to handle deviations from the linear time-invariant case. The main intent is to explore which perturbational techniques work, which do not, and outline some problems that remain to be solved in developing robust, general nonlinear reduction methods.
Experimental Demonstration of Double Moiré Structured Illumination Microscopy (2018)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text D. Shterman, B. Gjonaj, and G. Bartal, "Experimental Demonstration of Double Moiré Structured Illumination Microscopy," in Conference on Lasers and Electro-Optics, OSA Technical Digest (online) (Optica Publishing Group, 2018), paper SW4J.2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Novel C-4 Heteroaryl 13-<i>cis</i>-Retinamide Mnk/AR Degrading Agents Inhibit Cell Proliferation and Migration and Induce Apoptosis in Human Breast and Prostate Cancer Cells and Suppress Growth of MDA-MB-231 Human Breast and CWR22Rv1 Human Prostate Tumor Xenografts in Mice (2015)

The synthesis and in vitro and in vivo antibreast and antiprostate cancers activities of novel C-4 heteroaryl 13-cis-retinamides that modulate Mnk-eIF4E and AR signaling are discussed. Modifications of the C-4 heteroaryl substituents reveal that the 1H-imidazole is essential for high anticancer activity. The most potent compounds against a variety of human breast and prostate cancer (BC/PC) cell lines were compounds 16 (VNHM-1-66), 20 (VNHM-1-81), and 22 (VNHM-1-73). In these cell lines, the compounds induce Mnk1/2 degradation to substantially suppress eIF4E phosphorylation. In PC cells, the compounds induce degradation of both full-length androgen receptor (fAR) and splice variant AR (AR-V7) to inhibit AR transcriptional activity. More importantly, VNHM-1-81 has strong in vivo antibreast and antiprostate cancer activities, while VNHM-1-73 exhibited strong in vivo antibreast cancer activity, with no apparent host toxicity. Clearly, these lead compounds are strong candidates for development for the treatments of human breast and prostate cancers.
Spatial Learning Impairment, Enhanced CDK5/p35 Activity, and Downregulation of NMDA Receptor Expression in Transgenic Mice Expressing Tau-Tubulin Kinase 1 (2008)

Tau-tubulin kinase-1 (TTBK1) is involved in phosphorylation of tau protein at specific Serine/Threonine residues found in paired helical filaments, suggesting its role in tauopathy pathogenesis. We found that TTBK1 levels were upregulated in brains of human Alzheimer' disease (AD) patients compared with age-matched non-AD controls. To understand the effects of TTBK1 activation in vivo, we developed transgenic mice harboring human full-length TTBK1 genomic DNA (TTBK1-Tg). Transgenic TTBK1 is highly expressed in subiculum and cortical pyramidal layers, and induces phosphorylated neurofilament aggregation. TTBK1-Tg mice show significant age-dependent memory impairment as determined by radial arm water maze test, which is associated with enhancement of tau and neurofilament phosphorylation, increased levels of p25 and p35, both activators of cyclin-dependent protein kinase 5 (CDK5), enhanced calpain I activity, and reduced levels of hippocampal NMDA receptor types 2B (NR2B) and D. Enhanced CDK5/p35 complex formation is strongly correlated with dissociation of F-actin from p35, suggesting the inhibitory mechanism of CDK5/p35 complex formation by F-actin. Expression of recombinant TTBK1 in primary mouse cortical neurons significantly downregulated NR2B in a CDK5- and calpain-dependent manner. These data suggest that TTBK1 in AD brain may be one of the underlying mechanisms inducing CDK5 and calpain activation, NR2B downregulation, and subsequent memory dysfunction.
A Molecular MoS <sub>2</sub> Edge Site Mimic for Catalytic Hydrogen Generation (2012)

Inorganic solids are an important class of catalysts that often derive their activity from sparse active sites that are structurally distinct from the inactive bulk. Rationally optimizing activity is therefore beholden to the challenges in studying these active sites in molecular detail. Here, we report a molecule that mimics the structure of the proposed triangular active edge site fragments of molybdenum disulfide (MoS(2)), a widely used industrial catalyst that has shown promise as a low-cost alternative to platinum for electrocatalytic hydrogen production. By leveraging the robust coordination environment of a pentapyridyl ligand, we synthesized and structurally characterized a well-defined Mo(IV)-disulfide complex that, upon electrochemical reduction, can catalytically generate hydrogen from acidic organic media as well as from acidic water.
Evaluation of Instrument Dexterity and Static Resistance of Laparoendoscopic Single-Site (LESS) Surgical Ports (2012)

There is a lack of data on instrument dexterity and interface resistance with respect to the emerging surgical technology of LESS ports. A comparative analysis was conducted to characterize the force to maneuver laparoscopic instruments at various working angles within three commercially available LESS ports. A novel test fixture was created where working angles of the instruments were systematically varied in both the horizontal and sagittal plane within synthetic skin and rigid inserts. Two standard 5-mm laparoscopic graspers and a 10-mm simulated laparoscope were inserted into the trocars of the SILS™, TriPort™ and GelPOINT™ LESS ports. The positions of the laparoscope and grasper (G1) were fixed, while the working instrument’s position (G2) was systematically varied to create a range-of-motion. The static force required to maintain a specific position for G2 was measured using a digital force gauge for that range-of-motion. The resistance created by each LESS port was most noticeable at greater separation angles. The GelPOINT™ provided the least resistance to instrument movement; while the TriPort™ required the greatest amount of force at all angular positions. The 15-mm skin interface yielded lower overall resistance for all ports compared to the 30-mm skin interface. Resistance created by each LESS port increased with greater angular separation. Increased thickness and rigidity of the abdominal wall resulted in greater static forces and reduced instrument range-of-motion for all surgical ports. LESS port design and geometry heavily influenced overall instrument range-of-motion, as well as the resistance found at extreme separation angles. Surgeons should consider the degree of instrument motion required specific to the procedure being performed when selecting a LESS port.
Real-time volumetric shadows using 1D min-max mipmaps (2011)

Light scattering in a participating medium is responsible for several important effects we see in the natural world. In the presence of occluders, computing single scattering requires integrating the illumination scattered towards the eye along the camera ray, modulated by the visibility towards the light at each point. Unfortunately, incorporating volumetric shadows into this integral, while maintaining real-time performance, remains challenging.