gebhart/patrepeval huggingface dataset:
604. Comparative Analysis of Different Methods for Quantitative Evaluation of Neutralizing Antibody to Ebola Virus in a Biosafety Level 2 or 4 Environment (2006)

Ebola hemorrhagic fever virus can be modeled in different animal species such as mice, Guinea pigs and nonhuman primates. Several vaccine strategies were evaluated using DNA-, protein-based and/or viral vectors and found to protect mice against challenge with a lethal dose of mouse-adapted Ebola virus. However, only a few strategies involving DNA, Adenovirus or Vesicular Stomatitis virus (VSV), alone or in combination, succeeded at protecting nonhuman primates from Ebola virus aggressive replication. Ebola virus offers thus a unique disease model for the evaluation and testing of different vaccine platforms and/or strategies that can be screened in vivo in conditions of low to high stringency. One major limitation of using Ebola virus as a disease model is the requirement to manipulate the virus in a biosafety level 4 environment (BSL-4) which makes in vitro and in vivo testing less accessible and more time consuming. We compared four different methodologies to evaluate the levels of neutralizing antibody (NAB) from sera of nonhuman primates vaccinated with VSV- or Adenovirus-based vaccine expressing the Ebola envelope glycoprotein (EboGP). The first strategy evaluates neutralization of wild-type Ebola virus by immunoplaques; the second evaluates neutralization of Ebola expressing EGFP inserted as an additional gene in the viral genome; the third evaluates inhibition of plaque formation by an EboGP-pseudotyped VSV virus and the fourth evaluates neutralization of an EboGP-pseudotyped HIV vector. The first two strategies are using a replication competent Ebola virus and were thus performed in a BSL4 laboratory while the other two, using a replication competent VSV or replication defective HIV vector, were done in an enhanced BSL2 environment. Results indicate that the two methodologies using replication competent Ebola virus are slightly more sensitive than with pseudotyped VSV or HIV vector. Ebola expressing EGFP was found the method of choice in the BSL4 laboratory since it can be performed in 48 hours (instead of 6 days for immunoplaque assay) and does not depend on the sensitivity of an antibody/antigen reaction. Overall, each protocol offers advantages and inconveniences that will be discussed. James Wilson had equity in Targeted Genetics at the moment of the study.
Molten air – a new, highest energy class of rechargeable batteries (2013)

This study introduces the principles of a new class of high-energy batteries and their fundamental chemistry is demonstrated. These molten air batteries use air, a molten electrolyte, are quasi-reversible (rechargeable), have the capability for multiple electrons stored per molecule, and have the highest intrinsic electric energy storage capacities. Here we show three examples of the new battery's electron transfer chemistry. These are the metal, carbon and VB2 molten air batteries with respective intrinsic volumetric energy capacities of 10 000 (for Fe to Fe(III)), 19 000 (C to CO32−) and 27 000 W h l−1 (VB2 to B2O3 + V2O5), compared to 6200 W h l−1 for the lithium air battery. Higher energy capacity, cost effective batteries are needed for a range of electronic, transportation and greenhouse gas reduction power generation devices. Needed greenhouse gas battery reduction applications include overcoming the battery driven “range anxiety” of electric vehicles, and increased capacity energy storage for the electric grid.
Real-time mesh simplification using the GPU (2007)

Recent advances in real-time rendering have allowed the GPU implementation of traditionally CPU-restricted algorithms, often with performance increases of an order of magnitude or greater. Such gains are achieved by leveraging the large-scale parallelism of the GPU towards applications that are well-suited for these streaming architectures. By contrast, mesh simplification has traditionally been viewed as a non-interactive process not readily amenable to GPU acceleration. We demonstrate how it becomes practical for real-time use through our method, and that the use of the GPU even for offline simplification leads to significant increases in performance. Our approach for mesh decimation adopts a vertex-clustering method to the GPU by taking advantage of a new addition to the rendering pipeline - the geometry shader stage. We present a novel general-purpose data structure designed for streaming architectures called the probabilistic octree, which allows for much of the flexibility of offline implementations, including sparse encoding and variable level-of-detail. We demonstrate successful use of this data structure in our GPU implementation of mesh simplification. We can generate adaptive levels of detail by applying non-linear warping functions to the cluster map in order to improve resulting simplification quality. Our GPU-accelerated approach enables simultaneous construction of multiple levels of detail and out-of-core simplification of extremely large polygonal meshes.
Optimal Tradeoff Between Sum-Rate Efficiency and Jain's Fairness Index in Resource Allocation (2013)

The focus of this paper is on studying the tradeoff between the sum efficiency and Jain's fairness index in general resource allocation problems. Such problems are frequently encountered in wireless communication systems with M users. Among the commonly-used methods to approach these problems is the one based on the α-fair policy. Analyzing this policy, it is shown that it does not necessarily achieve the optimal Efficiency-Jain tradeoff (EJT) except for the case of M=2 users. When the number of users M>2, it is shown that the gap between the efficiency achieved by the α-fair policy and that achieved by the optimal EJT policy for the same Jain's index can be unbounded. Finding the optimal EJT corresponds to solving a family of potentially difficult non-convex optimization problems. To alleviate this difficulty, we derive sufficient conditions which are shown to be sharp and naturally satisfied in various radio resource allocation problems. These conditions provide us with a means for identifying cases in which finding the optimal EJT and the rate vectors that achieve it can be reformulated as convex optimization problems. The new formulations are used to devise computationally-efficient resource schedulers that enable the optimal EJT to be achieved for both quasi-static and ergodic time-varying communication scenarios. Analytical findings are confirmed by numerical examples.
Synthesis, Characterization, and Crystal Structure of [6]Cycloparaphenylene (2012)

Strained: [6]Cycloparaphenylene, a molecule with 97 kcal mol−1 of strain energy, was synthesized. The synthetic strategy relied on two sequential oxidative dearomatization/addition sequences and a final reductive aromatization reaction (see scheme). The optoelectronic properties of [6]cycloparaphenylene were measured, and the analysis of the X-ray crystal structure revealed a linear packing geometry reminiscent of a carbon nanotube.
Targeting Vascular and Avascular Compartments of Tumors with<i>C. novyi-NT</i>and Anti-microtubule Agents (2004)

Current approaches for treating cancer are limited, in part, by the inability of drugs to affect the poorly vascularized regions of tumors. We have found that C. novyi-NT in combination with anti-microtubule agents can cause the destruction of both the vascular and avascular compartments of tumors. The two classes of microtubule inhibitors were found to exert markedly different effects. Some agents that inhibited microtubule synthesis, such as HTI-286 and vinorelbine, caused rapid, massive hemorrhagic necrosis when used in combination with C. novyi-NT. In contrast, agents that stabilized microtubules, such as the taxanes docetaxel and MAC-321, resulted in slow tumor regressions that killed most neoplastic cells. Remaining cells in the poorly perfused regions of tumors could be eradicated by C. novyi-NT. Mechanistic studies showed that the microtubule destabilizers, but not the microtubule stabilizers, radically reduced blood flow to tumors, thereby enlarging the hypoxic niche in which C. novyi-NT spores could germinate. A single intravenous injection of C. novyi-NT plus selected anti-microtubule agents was able to cause regressions of several human tumor xenografts in nude mice in the absence of excessive toxicity.
The Development of Highly Potent Inhibitors for Porcupine (2013)

Porcupine is a member of the membrane-bound O-acyltransferase family of proteins. It catalyzes the palmitoylation of Wnt proteins, a process required for their secretion and activity. We recently disclosed a class of small molecules (IWPs) as the first reported Porcn inhibitors. We now describe the structure-activity relationship studies and the identification of subnanomolar inhibitors. We also report herein the effects of IWPs on Wnt-dependent developmental processes, including zebrafish posterior axis formation and kidney tubule formation.
Diphenylchloronitroethane Insecticides (1987)

Insecticidal activity of chloronitroalkanes was predicted on the basis of structure-activity relationships. Two series of new bis(substituted-phenyl) chloronitroalkanes were synthesized and evaluated for insecticidal activity. The synthetic pathway proceeded through phenylnitroethanols and diphenylnitroethanes as intermediates. Final products were 1,1-bis (substituted-phenyl)-2-chloro-2-nitroethanes and 1,1-bis(substituted-phenyl)-2,2-dichloro-2-nitroethanes. Aromatic substituents were selected from alkyl, alkoxy, and halogen moieties. Following purifications and confirmation of structures, the compounds were bioassayed against insects. The two series were compared for potency, as were various combinations of X and Y substituents. Adult female house flies (Musca domestica), mosquito larvae (Aedes aegypti), western corn rootworm (Diabrotica virgifera virgifera) and German cockroach (Blattella germanica) have been tested. In general, the mono-chloro series is more toxic than the di-chloro series. Five of the mono-chloro analogs are 8-10 times more potent than pyrethrins and 6-7 times more toxic than methoxychlor to the house fly.
Intra-Cavity Astigmatic Mode Converting VECSEL (2022)

We report the design and demonstration of a vertical external cavity surface emitting laser with intra-cavity astigmatic mode converters. Using a flexible optical pumping scheme Hermite-Gaussian transverse modes were excited at the gain chip and end mirror, and Laguerre-Gaussian transverse modes were observed between the two astigmatic mode converters. Adjusting the flexible pumping scheme allowed for mode order tuning while the laser was operating.
Software fault tolerance in distributed systems using controlled re-execution (2000)

Distributed applications are particularly vulnerable to synchronization faults. An important approach to tolerating synchronization faults is rollback recovery, which involves restoring a previous state and re-executing. Existing rollback recovery methods depend on chance and cannot guarantee that synchronization faults do not recur during re-execution. We propose a new rollback recovery method, controlled re-execution, based on selectively adding synchronizations during re-execution to ensure that synchronization faults do not recur. The controlled re-execution method gives rise to three interesting questions: How do we determine the synchronizations that ensure a safe re-execution? How do we monitor an application to detect faulty global conditions? How well does controlled re-execution perform in practice? 
The first part of the dissertation addresses the predicate control problem which takes a computation and a global property and adds synchronizations to the computation to maintain the property. We design efficient algorithms to solve the problem for many useful predicates, including disjunctive predicates and various types of mutual exclusion predicates. These predicates correspond to commonly encountered synchronization faults such as races. 
The second part of the dissertation investigates the predicate detection problem which involves determining whether a global property occurs in a computation. We address the problem for the useful class of conjunctive predicates and in the context of an extended model of computation that allows improved predicate detection over the conventional model. We show that, in general, the problem is NP-Complete. However, an efficient solution is demonstrated for the useful cases of receive-ordered and send-ordered computations. Further, this solution can be used to achieve an improved, though exponential, solution for the general problem. 
The third part of the dissertation involves an experimental study of the controlled re-execution method. We evaluate the controlled re-execution method in tolerating race faults and find that the extra tracing costs imposed are within tolerable limits and that it greatly enhanced the likelihood of recovery. We conclude that controlled re-execution is an effective and desirable method for tolerating races in long-running non-interactive distributed applications.
Real-Time Barcode Detection in the Wild (2015)

The linear 1D barcode is the main tagging system for billions of products sold each day. Barcodes have many advantages but require a laser scanner for fast and robust scanning. Solutions exist to read barcodes from cell phones but they assume a carefully framed image within the field of view. This undermines the true potential of barcodes in a wide range of scenarios. In this paper we present a real time technique to detect barcodes in the wild from video streams. Our technique outperforms the state-of-the-art passive techniques both in accuracy and speed. Potential commercial applications enabled by such passive scanning system are also discussed in this paper.
Clinical evaluation of a single oral dose of human‐bovine (UK) reassortant rotavirus vaccines Wa x UK (P1A[8],G6) and Wa x (DS‐1 x UK) (P1A[8],G2) (2002)

The safety, infectivity, and immunogenicity of two human-bovine reassortant rotavirus candidate vaccines were evaluated in adults, children, and infants. One of these, Wa x UK, contained a single human rotavirus gene from the Wa strain that encoded VP4 P1A specificity in a background of 10 bovine genes including the VP7 gene that encodes G6 specificity, whereas the other, Wa x (DS-1 x UK), possessed the human rotavirus VP4 gene from the Wa strain as well as the human VP7 gene from strain DS-1 that encoded G2 specificity. Each of these vaccines appeared to be well-tolerated and immunogenic in infants less than 6 months of age following a single oral dose, and therefore should be evaluated further as vaccine candidates.
Domain Structure of Hepatocyte Growth Factor/Scatter Factor (HGF/SF) (2007)

The modular structure of hepatocyte growth factor/scatter factor (HGF/SF) has facilitated structure-function analysis. Domain deletion experiments have established that the N-domain, kringle 1 and kringle 2 are essential for HGF/SF activity on target cells and that, conversely, truncated variants containing the N-domain and kringle 1 (NK1) or kringles 1 and 2 (NK2) exhibit partial agonistic or antagonistic activity depending on target cells and the presence of full length HGF/SF. The 3D structures of the six domains of HGF/SF have been modelled on the structure of homologues, offering interesting insights into putative mechanisms of domain interactions, receptor binding and activation. The predictions offered by such models are currently assessed by protein engineering techniques and will ultimately be measured against experimental structures.
Chemical development of new processes for the recovery of resource materials from coal ash (1979)

Laboratory-scale tests of methods for the recovery of aluminum and other metal values from fly ash include reported processes such as lime sinter lime-soda sinter, and the obvious direct acid leach methods, as well as two new combination sinter--dilute acid leach methods. In the first of these new methods, fly ash is sintered with a NaCl-Na/sub 2/CO/sub 3/ mixture at 1000/sup 0/C followed by successive leaches with water and 1 N NHO/sub 3/ or H/sub 2/SO/sub 4/. In the second method, fly ash is sintered with a CaSO/sub 4/--CaCO/sub 3/ mixture at 1400/sup 0/C, after which the sinter-cake is pugged with 36 N H/sub 2/SO/sub 4/ and then diluted to 4 N for a second leaching period. Aluminum recovery is increased in each method as the sintering temperature is increased; recovery is greater than 95% at the optimum sintering conditions, and a pure Al/sub 2/O/sub 3/ product can be obtained if a solvent extraction or an ion exchange circuit is included for iron and trace-metal removal. Product option flexibility is provided in that Fe, Ti, Mn, U, and Th can also be recovered.
Digital beam forming in MRI (2014)

Digital beam forming has been implemented in a 7T MRI system with a multi-channel RF coil to obtain images with optimized signal to noise ratio, and uniform intensity. Beam forming is performed by summing the complex images received at each pixel in the image plane using a weighting algorithm to optimize the signal to noise ratio. The theory developed for the algorithm is outlined and includes the RF coil element directivity. Experimental results of beam formed images are compared to the usual magnitude root sum squared (RSS) images.
ChemInform Abstract: NOVEL SYNTHESIS OF α‐SUBSTITUTED ACRYLIC ACIDS (1982)

Abstract Aus den Carbonsäuren (I) entstehen mit Dimethyl‐ethanolamin (II) bei der thermischen Cyclisierung die Oxazoline (IV) über die Amidzwischenstufen (III).
Elevated lactoferrin is associated with moderate to severe Clostridium difficile disease, stool toxin, and 027 infection (2013)

We evaluated blood and fecal biomarkers as indicators of severity in symptomatic patients with confirmed Clostridium difficile infection (CDI). Recruitment included patients with CDI based on clinical symptoms and supporting laboratory findings. Disease severity was defined by physician's assessment and blood and fecal biomarkers were measured. Toxigenic culture done using spore enrichment and toxin B detected by tissue culture were done as confirmatory tests. Polymerase chain reaction (PCR) ribotyping was performed on each isolate. There were 98 patients recruited, with 85 (87%) confirmed cases of toxigenic CDI (21 severe, 57 moderate, and seven mild), of which 68 (80%) were also stool toxin-positive. Elevated lactoferrin (p = 0.01), increased white blood cell (WBC) count (p = 0.08), and low serum albumin (p = 0.03) were all associated with the more severe cases of CDI. Ribotype 027 infection accounted for 71% of severe cases (p < 0.01) and patients with stool toxin had significantly higher lactoferrin levels and WBC counts (p < 0.05). Our findings show that elevated fecal lactoferrin, along with increased WBC count and low serum albumin, were associated with more severe CDI. In addition, patients infected with ribotype 027 and those with stool toxin had significantly higher fecal lactoferrin and WBC counts.
Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture (2008)

The crystal structure of AtPDF1B [Arabidopsis thaliana PDF (peptide deformylase) 1B; EC 3.5.1.88], a plant specific deformylase, has been determined at a resolution of 2.4 A (1 A=0.1 nm). The overall fold of AtPDF1B is similar to other peptide deformylases that have been reported. Evidence from the crystal structure and gel filtration chromatography indicates that AtPDF1B exists as a symmetric dimer. PDF1B is essential in plants and has a preferred substrate specificity towards the PS II (photosystem II) D1 polypeptide. Comparative analysis of AtPDF1B, AtPDF1A, and the type 1B deformylase from Escherichia coli, identifies a number of differences in substrate binding subsites that might account for variations in sequence preference. A model of the N-terminal five amino acids from the D1 polypeptide bound in the active site of AtPDF1B suggests an influence of Tyr(178) as a structural determinant for polypeptide substrate specificity through hydrogen bonding with Thr(2) in the D1 sequence. Kinetic analyses using a polypeptide mimic of the D1 N-terminus was performed on AtPDF1B mutated at Tyr(178) to alanine, phenylalanine or arginine (equivalent residue in AtPDF1A). The results suggest that, whereas Tyr(178) can influence catalytic activity, other residues contribute to the overall preference for the D1 polypeptide.
Development of Ti-Cu Alloy Sheets for Automobile Exhaust Systems (2014)

Titanium alloys having excellent performances at elevated temperature and good formability at room temperature for automobile exhaust systems have been developed based on the unique alloy design concept that 1 mass% Cu, together with low oxygen content, was added, and 0.5 mass% Nb was furthermore added in case oxidation resistance at temperatures up to 800˚C was necessary. They do not include any conventional alloying elements, such as Al, Si and Sn, which are often added to titanium alloys used at elevated temperatures and lower their formability. In place of them, Cu was added as a solid solution hardening element at high temperature. The oxygen content was lowered together as that in Gr.1 pure titanium(CP) to enjoy the active mechanical twinning at room temperature which is indispensable for excellent formability. The alloy, Ti-1mass%Cu(Super-TIX TM 10CU), actually has high strength and high fatigue strength (twice as high as those of Gr.2) as well as excellent creep resistance at elevated temperatures. The other alloy, Ti-1mass%Cu0.5mass%Nb(Super-TIX TM 10CUNB), has improved oxidation resistance at temperatures up to 800˚C with keeping excellent formability equivalent to that of Super-TIX TM 10CU. Recently a new Ti-Cu alloy which was added some solid solution hardening elements for higher strength at elevated temperature than the former two Ti-Cu alloys has been developed.
Effect of Dose of Calcium Salts of Conjugated Linoleic Acid (CLA) on Percentage and Fatty Acid Content of Milk Fat in Midlactation Holstein Cows (2002)

Increasing conjugated linoleic acid (CLA) content of milk fat from lactating dairy cattle has become a research interest due to the possible health benefits afforded humans consuming CLA. Dietary supplementation of CLA to lactating dairy cows is one potential method by which CLA content of milk and dairy products may be enhanced. Feeding CLA in calcium salt form could potentially deliver CLA to the lower digestive tract through prevention of biohydrogenation by rumen microbes. Milk fat depression (MFD) occurs when cows receive CLA-60, a commercially available CLA source containing numerous CLA isomers, abomasally. Our objectives were to determine the quantity of CLA as calcium salts required to elicit maximal MFD and to evaluate the effects of CLA supplementation on fatty acid composition of milk fat. Five Holstein cows at approximately 93 DIM were utilized in a 5 x 5 balanced Latin square crossover design. Periods were 14-d in length with a 5-d treatment phase and 9-d rest phase. Treatments were 5-d supplementation of 0, 12.5, 25, 50, and 100 g of CLA-60 in calcium salt form. Milk samples were collected on d 5 of CLA supplementation and analyzed for composition and fatty acid profile. Regression analysis of milk fat data suggested that MFD was not maximized over the dose levels investigated, despite delivery of 34.5 g of trans-10, cis-12 CLA in the 100-g dose of CLA. Supplementation with 50 and 100 g of CLA per day resulted in a reduction of milk fat percent of 29 and 34%, respectively. Trend analysis indicated a linear decrease in the milk fat content of caprylic, capric, and lauric acids as the dose of CLA increased. Milk fat content of cis-9, trans-11, and trans-10, cis-12 CLA increased at an increasing rate as dose increased.