gebhart/patrepeval huggingface dataset:
Natural DNA Sequencing by Synthesis (2011)

DNA sequencing is used in a vast array of applications including pharmacogenetics, cancer research, biodiversity studies and genotyping. With an increasing demand for faster, more accessible DNA sequencers, current next- generation technologies have made astonishing advances that promise to break the $1,000 per human genome barrier. Here we present a novel DNA sequencing strategy called Natural DNA Sequencing by Synthesis (nSBS). The key aspect of nSBS is the incorporation of a small percentage of a non-terminating fluorescently labeled nucleotide along with the natural nucleotide in the cyclic nucleotide-by- nucleotide DNA synthesis process for sequence detection. The sparse incorporation and subsequent removal of the fluorescent labels minimizes the modification of the natural structure of the extending DNA template, ensuring that subsequent DNA synthesis will be mostly natural and un-perturbed. Our platform allows scaling to high-density arrays for genome sequencing due to the decoupling of the sequencing reaction from the detection step. A theoretical model of the nSBS process has been developed, utilizing Monte Carlo simulations with random sequences from the human genome to assess the feasibility of the method. The model revealed that homopolymer stretches up to 20 bases long can be sequenced with high accuracy and Q20 (with 99% accuracy) read lengths of up to 1,000 bases can be achieved with less than 10,000 copies of DNA templates and 10% labeled incorporation. A major challenge to the implementation of nSBS was the design and construction of an automated sequencing platform. An overview of the hardware and software of this system is given. Finally, results from the implementation of nSBS are provided beginning with a study of the kinetics of the incorporation of fluorescently labeled nucleotides. In addition, we demonstrate fractional labeling of a synthetic DNA template. By combining the best proven aspects of SBS with streamlined methods for DNA amplification and high-speed fluorescence imaging, nSBS can provide a platform for inexpensive genome resequencing and de novo sequencing
ChemInform Abstract: INHIBITORS OF GLYCOLIC ACID OXIDASE. 4‐SUBSTITUTED 3‐HYDROXY‐1H‐PYRROLE‐2,5‐DIONE DERIVATIVES (1983)

Abstract Hydroxypyrroldione (III) können ausgehend von (I) in direkter Weise oder über die Nitrilketoester (V) zugänglich gemacht werden.
Cell-free nucleic acids as non-invasive biomarkers of gynecological cancers, ovarian, endometrial and obstetric disorders and fetal aneuploidy (2014)

The profiling of circulating nucleic acids, such as miRNAs and cfDNA, opens new perspectives for the diagnosis/prognosis of ovarian disorders and for the prediction of IVF outcomes, namely (embryo quality and pregnancy).
Efficient Low Dose X-ray CT Reconstruction through Sparsity-Based MAP\n Modeling (2014)

Ultra low radiation dose in X-ray Computed Tomography (CT) is an important\nclinical objective in order to minimize the risk of carcinogenesis. Compressed\nSensing (CS) enables significant reductions in radiation dose to be achieved by\nproducing diagnostic images from a limited number of CT projections. However,\nthe excessive computation time that conventional CS-based CT reconstruction\ntypically requires has limited clinical implementation. In this paper, we first\ndemonstrate that a thorough analysis of CT reconstruction through a Maximum a\nPosteriori objective function results in a weighted compressive sensing\nproblem. This analysis enables us to formulate a low dose fan beam and helical\ncone beam CT reconstruction. Subsequently, we provide an efficient solution to\nthe formulated CS problem based on a Fast Composite Splitting Algorithm-Latent\nExpected Maximization (FCSA-LEM) algorithm. In the proposed method we use\npseudo polar Fourier transform as the measurement matrix in order to decrease\nthe computational complexity; and rebinning of the projections to parallel rays\nin order to extend its application to fan beam and helical cone beam scans. The\nweight involved in the proposed weighted CS model, denoted by Error Adaptation\nWeight (EAW), is calculated based on the statistical characteristics of CT\nreconstruction and is a function of Poisson measurement noise and rebinning\ninterpolation error. Simulation results show that low computational complexity\nof the proposed method made the fast recovery of the CT images possible and\nusing EAW reduces the reconstruction error by one order of magnitude. Recovery\nof a high quality 512$\\times$ 512 image was achieved in less than 20 sec on a\ndesktop computer without numerical optimizations.\n
Bioreducible Polycations in Nucleic Acid Delivery: Past, Present, and Future Trends (2014)

Polycations that are degradable by reduction of disulfide bonds are developed for applications in delivery of nucleic acids. This Feature Article surveys methods of synthesis of bioreducible polycations and discusses current understanding of the mechanism of action of bioreducible polyplexes. Emphasis is placed on the relationship between the biological redox environment and toxicity, trafficking, transfection activity, and in vivo behavior of bioreducible polycations and polyplexes.
Unsupervised clustering approaches to color classification for color-based image code recognition (2008)

Color-vision-based applications for mobile phones has become a subject of special interest lately. It would be interesting to investigate an unsupervised, adaptive, and fast algorithm that can classify color components into color clusters. We propose a hierarchical clustering approach using a single-linkage algorithm and a k-means clustering approach to color classification for color-based image code recognition in mobile computing environments. We also measured the performance of the proposed algorithms by color channel stretch, which is a simple color-correction method. Experimental results show that the single-linkage method is more robust than previous algorithms used in experiments with varying cameras and print materials. In particular the k-means-based method with color channel stretching has the highest performance and is the most robust under varying environment conditions such as illuminants, cameras, and print materials.
The inflammasome as a therapeutic target to improve outcomes after injury to the central nervous system (135.73) (2009)

Abstract The inflammasome constitutes one of the host’s defenses against pathogens and deleterious stimuli by activating caspase-1. Inflammation with production of cytokines processed upon inflammasome activation is a crucial part of the secondary cascade of cell death induced after central nervous system (CNS) injury. The molecular mechanisms underlying trauma-induced inflammation in the CNS are poorly defined. In this study, the cellular distribution and protein association of inflammasome components were investigated in spinal cords and brains of rats subjected to moderate cervical injury and fluid-percussion brain injury, respectively. Coimmunoprecipitation experiments revealed that in the CNS, Apoptosis-Associated Speck-like protein containing a CARD (ASC) associates with caspase-1, caspase-11, NLR family, Pyrin domain containing 1 (NLRP1) and the inhibitor of apoptosis XIAP, forming the NLRP1 inflammasome. Injury to the CNS affects the composition of the inflammasome resulting in increased association of caspases-1 and -11 and NLRP1 with ASC and cleavage of XIAP. Immunohistochemistry revealed that motor neurons and cortical neurons express the NLRP1 inflammasome proteins. Therapeutic neutralization of ASC after injury inhibited inflammasome activation as shown by decreased caspase-1 activation and XIAP cleavage, resulting in reduced lesion volume and improved functional outcomes after spinal cord injury. Thus the inflammasome forms part of the innate immune response in the CNS and its inhibition may offer a novel therapeutic strategy to improve outcomes after injury and CNS inflammatory diseases. This research was supported by the NIH/NINDS and the US Army.
Path verification for robust, instantaneous loop-free routing in ad hoc networks (2005)

We present path verification routing (PVR) to enable robust, instantaneous on-demand loop-free routing of data packets based on their destination address in mobile ad hoc networks. PVR attains instantaneous loop-freedom by using a path verification technique without the necessity for sequence numbers, source-routed data packets, or nodal synchronization. The motivation for PVR is twofold. On the one hand, DSR provides loop-free routing but requires source routed data packets. On the other hand, AODV, which is based on destination-based sequence numbers, is vulnerable to the counting-to-infinity problem and has route requests that in many cases must be answered by the destinations. Simulation experiments are used to show that the performance of PVR is comparable to or better than that of AODV, AODVbis, DSR and OLSR.
A Redesigned Vancomycin Engineered for Dual <scp>d</scp> -Ala- <scp>d</scp> -Ala and <scp>d</scp> -Ala- <scp>d</scp> -Lac Binding Exhibits Potent Antimicrobial Activity Against Vancomycin-Resistant Bacteria (2011)

The emergence of bacteria resistant to vancomycin, often the antibiotic of last resort, poses a major health problem. Vancomycin-resistant bacteria sense a glycopeptide antibiotic challenge and remodel their cell wall precursor peptidoglycan terminus from d-Ala-d-Ala to d-Ala-d-Lac, reducing the binding of vancomycin to its target 1000-fold and accounting for the loss in antimicrobial activity. Here, we report [Ψ[C(═NH)NH]Tpg(4)]vancomycin aglycon designed to exhibit the dual binding to d-Ala-d-Ala and d-Ala-d-Lac needed to reinstate activity against vancomycin-resistant bacteria. Its binding to a model d-Ala-d-Ala ligand was found to be only 2-fold less than vancomycin aglycon and this affinity was maintained with a model d-Ala-d-Lac ligand, representing a 600-fold increase relative to vancomycin aglycon. Accurately reflecting these binding characteristics, it exhibits potent antimicrobial activity against vancomycin-resistant bacteria (MIC = 0.31 μg/mL, VanA VRE). Thus, a complementary single atom exchange in the vancomycin core structure (O → NH) to counter the single atom exchange in the cell wall precursors of resistant bacteria (NH → O) reinstates potent antimicrobial activity and charts a rational path forward for the development of antibiotics for the treatment of vancomycin-resistant bacterial infections.
Speech Modelingwith Magnitude-Normalized Complex Spectra and Its Application to Multisensory Speech Enhancement (2006)

A good speech model is essential for speech enhancement, but it is very difficult to build because of huge intra- and extra-speaker variation. We present a new speech model for speech enhancement, which is based on statistical models of magnitude-normalized complex spectra of speech signals. Most popular speech enhancement techniques work in the spectrum space, but the large variation of speech strength, even from the same speaker, makes accurate speech modeling very difficult because the magnitude is correlated across all frequency bins. By performing magnitude normalization for each speech frame, we are able to get rid of the magnitude variation and to build a much better speech model with only a small number of Gaussian components. This new speech model is applied to speech enhancement for our previously developed microphone headsets that combine a conventional air microphone with a bone sensor. Much improved results have been obtained
A NEW APPROACH TO MEASURE THE CONTACT ANGLE AND THE EVAPORATION RATE WITH FLOW VISUALIZATION IN A SESSILE DROP (2002)

The contact angle and the spreading process of sessile droplet are very crucial in many technological processes, such as painting and coating, material processing, film-cooling applications, lubrication, and boiling. Additionally, as it is well known that the surface free energy of polymers cannot be directly, measured for their elastic and viscous restraints. The measurements of liquid contact angle on the polymer surfaces become extremely important to evaluate the surface free energy of polymers through indirect methods linked with the contact angle data. Due to the occurrence of liquid evaporation is inevitable, the effects of evaporation on the contact angle and the spreading become very important for more complete understanding of these processes. It is of interest to note that evaporation can induce Marangoni-Benard convection in sessile drops. However, the impacts of the inside convection on the wetting and spreading processes are not clear. The experimental methods used by previous investigators cannot simultaneously measure the spreading process and visualize the convection inside. Based on the laser shadowgraphic system used by the present author, a very simple optical procedure has been developed to measure the contact angle, the spreading speed, the evaporation rate, and to visualize inside convection of a sessile drop simultaneously. Two CCD cameras were used to synchronously record the real-time diameter of the sessile drop, which is essential for determination of both spreading speed and evaporation rate, and the shadowgraphic image magnified by the sessile drop acting as a thin plano-convex lens. From the shadowgraph, the inside convection of the drop can be observed if any and the image outer diameter, which linked to the drop profile, can be measured. Simple equations have been derived to calculate the drop profile, including the instantaneous contact angle, height, and volume of the sessile drop, as well as the evaporation rate. The influence of the inside convection on the wetting and spreading processes can be figured out through comparison of the drop profiles with and without inside convection when the sessile drop is placed at different evaporation conditions.
Spectral Angle Mapper classification of fluorescence hyperspectral image for aflatoxin contaminated corn (2010)

Aflatoxin contamination in corn is a serious problem for both producers and consumers. The present study applied the Spectral Angle Mapper classification technique to classify single corn kernels into contaminated and healthy groups. Fluorescence hyperspectral images were used in the classification. Actual corn aflatoxin concentration was chemically determined using the VICAM analytical method for quantification purpose. An obvious fluorescence peak shift was observed to be associated with the aflatoxin contaminated corn. Aflatoxin classification levels were based on Food and Drug Administration's regulation, including 20 ppb (parts per billion) for human consumption and 100 ppb for feed. Classification accuracy for the 20 ppb level is 86% with a false positive rate of 15%. For the 100 ppb level, the accuracy is 88% with a false positive rate of 16%. The results indicate that the Spectral Angle Mapper method and fluorescence hyperspectral imagery have the potential to classify aflatoxin contaminated corn kernels.
Using Social Influence to Predict Subscriber Churn (2012)

The saturation of mobile phone markets has resulted in rising costs for operators to obtain new customers. These operators thus focus their energies on identifying users that will churn so they can be targeted for retention campaigns. Typical churn prediction algorithms identify churners based on service usage metrics, network performance indicators, and demographic information. Social and peer-influence to churn, however, is usually not considered. In this paper, we describe a new churn prediction algorithm that incorporates the influence churners spread to their social peers. Using data from a major service provider, we show that social influence improves churn prediction and is among the most important factors.
An efficient YUV-based image compression algorithm for wireless capsule endoscopy (2011)

The paper presents an efficient image compression algorithm for wireless capsule endoscopy application. This algorithm works in YUV colour plane and exploits some special features of human endoscopic images. Based on the nature of endoscopic images, a set of transform-quantization pair is proposed that results in high compression while keeping the reconstruction quality over 45dB. Compared to other transform-based algorithms targeted to capsule endoscopy, the proposed scheme performs strongly with a compression ratio of 90% and high reconstruction PSNR and SSIM (over 48dB and 0.999).
Fast Private Set Intersection from Homomorphic Encryption. (2017)

Private Set Intersection (PSI) is a cryptographic technique that allows two parties to compute the intersection of their sets without revealing anything except the intersection. We use fully homomorphic encryption to construct a fast PSI protocol with a small communication overhead that works particularly well when one of the two sets is much smaller than the other, and is secure against semi-honest adversaries. The most computationally efficient PSI protocols have been constructed using tools such as hash functions and oblivious transfer, but a potential limitation with these approaches is the communication complexity, which scales linearly with the size of the larger set. This is of particular concern when performing PSI between a constrained device (cellphone) holding a small set, and a large service provider (e.g. WhatsApp), such as in the Private Contact Discovery application. Our protocol has communication complexity linear in the size of the smaller set, and logarithmic in the larger set. More precisely, if the set sizes are Ny Nx, we achieve a communication overhead of O(Ny log Nx). Our running-time-optimized benchmarks show that it takes 36 seconds of online-computation, 71 seconds of non-interactive (receiver-independent) pre-processing, and only 12.5MB of round trip communication to intersect five thousand 32-bit strings with 16 million 32-bit strings. Compared to prior works, this is roughly a 38--115x reduction in communication with minimal difference in computational overhead.
History Matching and Uncertainty Quantification Assisted by Global Optimization Techniques (2006)

Ranges in production forecast provide critical information for reservoir management decisions. Well developed methodologies exist for handling subsurface uncertainties for new field developments. The task is more challenging for fields that have been produced for several years as all models need to be conditioned to available production data in order to deliver reliable predictions. The computing cost associated with the exhaustive search of models that reproduce historical data is in general prohibitive. This paper describes an efficient method that combines the strength of various techniques, including optimization algorithms, experimental design and non-linear response surfaces. It is applied to an off-shore field in the Philippines for which multiple history-matched models are obtained in a reasonable timeframe.
Abstract 19839: Annexin-a1 Tripeptide is Cardioprotective in Several Preclinical Models of Ischemia-Reperfusion Through Resolution of Myocardial Inflammation (2010)

Background: Annexin A1 is a glucocorticoid-regulated protein that plays a pivotal role as an endogenous regulator of the inflammatory response, with many of its anti-inflammatory properties retained by the N-terminal peptides. Using in vitro and in vivo models of myocardial ischemia-reperfusion (I/R) under both normo- and hyperglycemic conditions, we tested the hypothesis that a novel annexin A1 tripeptide (ANXA1sp) exerts cardioprotective effects through resolution of myocardial inflammation. Methods: In vitro simulated I/R: Adult rat ventricular cardiomyocytes were incubated in normal or high glucose (25mM), with and without ANXA1sp (30 μM) for 24h, subjected to 2h oxygen-glucose deprivation, followed by 24h reoxygenation in either normo- or hyperglycemic medium. Rat I/R: SD rats underwent 75 min of mild hypothermic cardiopulmonary bypass (CPB) with 45 min of cardioplegic arrest (CA) in 4 groups: normo- and hyperglycemic (20mM) CA, each treated with ANXA1sp (3mg/kg) or vehicle. Pig I/R: Yorkshire pigs subjected to 180 min of mild hypothermic CPB with 60 min of CA received ANXA1sp (4mg/kg) or vehicle. Efficacy endpoints assessed at 24h post-reoxygenation (ARVC), 24h (rat) and 6h (pig) post-reperfusion include markers of myonecrosis, apoptosis, myocardial inflammation, leukocyte extravasation, and pump function. Results: ANXA1sp consistently attenuated myocardial I/R injury under both glycemic conditions, which correlated with reduced activation of NF-κB pathway (Figure). Peptide treated pigs further demonstrated improved myocardial energetics and hemodynamics, none requiring inotropic or vasopressor support, which was substantial in all control animals. Conclusions: Using a translational approach and robust efficacy endpoints, we report that ANXA1sp elicits cardioprotection in vitro and in small and large animal models of surgical I/R. The effects are not blunted by hyperglycemia and involve attenuation of myocardial inflammation.
<i>Borrelia burgdorferi</i>Escape Mutants That Survive in the Presence of Antiserum to the OspA Vaccine Are Killed When Complement Is Also Present (1998)

ABSTRACT As an initial attempt to investigate the possible role of outer surface protein A (OspA) escape mutants of Borrelia burgdorferi in decreasing the efficacy of the OspA vaccine, mutants of the HB19 strain of B. burgdorferi sensu stricto were selected in vitro from an uncloned, low-passage-number isolate. The antiserum used for selection was obtained from rhesus monkeys that had been given a vaccine of the same formulation and dose, and by the same route of administration, as that given to humans in several trials. All of the mutants selected in liquid medium and subsequently cloned twice in solid medium expressed a single abundant protein of 28 to 34 kDa instead of both OspA and OspB. Depending on the mutant, this protein reacted strongly, weakly, or not detectably with the anti-OspA antibody used for selection. Analysis of the ospAB locus of each of four representatives from these three groups of mutants by PCR with oligonucleotide primers that hybridize to flanking regions of the ospAB operon, and of the corresponding phenotype with monoclonal antibodies that bind to the amino or carboxyl terminus of the OspA or OspB polypeptide, indicated that in all cases a deletion within the operon had occurred. Spirochetes from the four mutant strains chosen for further analysis could be killed in antibody-dependent, complement-mediated killing assays with the selecting anti-OspA antibody, despite their resistance to killing with this antibody in the absence of complement. Complement-mediated killing occurred at an antibody concentration higher than that required to kill wild-type spirochetes. If anti-OspA antibody acts only within the tick, where complement is probably ineffective due to tick-derived decomplementing factors, then OspA escape mutants, if infectious, could seriously diminish the efficacy of OspA vaccines. On the other hand, if the killing of B. burgdorferi with anti-OspA antibody also takes place within the human host, then our results indicate that chimeric/deletion escape mutants will be killed as well.