gebhart/patrepeval huggingface dataset:
Prospective, randomized, endoscopic-blinded trial comparing precolonoscopy bowel cleansing methods (1994)

The smaller volume oral sodium phosphate was not associated with any clinically significant problem, caused no increase in the incidence of side effects, was preferred by patients, and was more effective in colonic cleansing. However, the hyperphosphatemia seen may limit its use in patients with impaired renal function.
Suffix trees for very large genomic sequences (2009)

A suffix tree is a fundamental data structure for string searching algorithms. Unfortunately, when it comes to the use of suffix trees in real-life applications, the current methods for constructing suffix trees do not scale for large inputs. All the existing practical algorithms perform random access to the input string, thus requiring that the input be small enough to be kept in main memory.
High-Efficient CMOS-Compatible Grating Couplers with Backside Metal Mirror (2012)

We present a grating coupler for efficient coupling between standard fibers and photonic integrated circuits realized in a CMOS fabrication process. The method introduces a backside metal mirror to the grating coupler without need of extensive wafer bonding. The structure exhibits high coupling efficiency of -1.6 dB near the wavelength 1550 nm.
Serial and Hybrid Concatenated Codes with Applications (1997)

Abstract — Analytical bounds on the performance of concatenated codes on a tree structure are obtained. Analytical results are applied to examples of parallel concatenation of two codes (turbo codes), serial concatenation of two codes, hybrid concatenation of three codes, and self concatenated codes, over AWGN and fading channels. Based on the analysis, design criteria for the selection of component codes are presented. Asymptotic results for large interleavers are extended to MPSK modulations over AWGN and Rayleigh fading channels. Simulation results are only given for examples of coded modulation and fading channels. 1.
Chance and Necessity (1973)

I have not had time to prepare a formal paper and wish to apologise for this, since I had every intention of doing so and it has only been made impossible by a combination of extremely heavy duties and being ill for several months this year. On the other hand, I understand that a number of you have either read the little essay I wrote recently [Chance and Necessity, Knopf, New York (1971)], or at least heard of it. Therefore, I hope that if those who have read it agree or disagree, you can ask me some questions after this presentation. What I would like to do here, is the following. I have taken a few notes at random, which are, of course, on various subjects that I did discuss in the book, and I would like to emphasise a few points.
A machine learning approach for filtering Monte Carlo noise (2015)

The most successful approaches for filtering Monte Carlo noise use feature-based filters (e.g., cross-bilateral and cross non-local means filters) that exploit additional scene features such as world positions and shading normals. However, their main challenge is finding the optimal weights for each feature in the filter to reduce noise but preserve scene detail. In this paper, we observe there is a complex relationship between the noisy scene data and the ideal filter parameters, and propose to learn this relationship using a nonlinear regression model. To do this, we use a multilayer perceptron neural network and combine it with a matching filter during both training and testing. To use our framework, we first train it in an offline process on a set of noisy images of scenes with a variety of distributed effects. Then at run-time, the trained network can be used to drive the filter parameters for new scenes to produce filtered images that approximate the ground truth. We demonstrate that our trained network can generate filtered images in only a few seconds that are superior to previous approaches on a wide range of distributed effects such as depth of field, motion blur, area lighting, glossy reflections, and global illumination.
Proceedings of the Second International Symposium on Dynamics of Fluids in Fractured Rock (2004)

Proceedings of the Second International Symposium on DYNAMICS OF FLUIDS IN FRACTURED ROCK Foreword Table of Contents February 10–12, 2004 Edited by Boris Faybishenko and Paul A. Witherspoon Earth Sciences Division Ernest Orlando Lawrence Berkeley National Laboratory University of California Berkeley, California 94720 U.S.A Ernest Orlando Lawrence Berkeley National Laboratory is administered for the U.S. Department of Energy by the University of California under Contract No. DE-AC03-76SF00098
Human Machine Interface Programming and Testing (2013)

Human Machine Interface (HMI) Programming and Testing is about creating graphical displays to mimic mission critical ground control systems in order to provide NASA engineers with the ability to monitor the health management of these systems in real time. The Health Management System (HMS) is an online interactive human machine interface system that monitors all Kennedy Ground Control Subsystem (KGCS) hardware in the field. The Health Management System is essential to NASA engineers because it allows remote control and monitoring of the health management systems of all the Programmable Logic Controllers (PLC) and associated field devices. KGCS will have equipment installed at the launch pad, Vehicle Assembly Building, Mobile Launcher, as well as the Multi-Purpose Processing Facility. I am designing graphical displays to monitor and control new modules that will be integrated into the HMS. The design of the display screen will closely mimic the appearance and functionality of the actual modules. There are many different field devices used to monitor health management and each device has its own unique set of health management related data, therefore each display must also have its own unique way to display this data. Once the displays are created, the RSLogix5000 application is used to write software that maps all the required data read from the hardware to the graphical display. Once this data is mapped to its corresponding display item, the graphical display and hardware device will be connected through the same network in order to test all possible scenarios and types of data the graphical display was designed to receive. Test Procedures will be written to thoroughly test out the displays and ensure that they are working correctly before being deployed to the field. Additionally, the Kennedy Ground Controls Subsystem's user manual will be updated to explain to the NASA engineers how to use the new module displays.
Effects of Blood Contamination on Microtensile Bond Strength to Dentin of Three Self-etch Adhesives (2010)

This study evaluated the effects of blood contamination and decontamination methods during different steps of bonding procedures on the microtensile bond strength of two-step self-etch adhesives to dentin. Sixty extracted human molars were ground flat to expose occlusal dentin. The 60 molars were randomly assigned to three groups, each treated with a different two-step self-etch adhesive: Clearfil SE Bond, AdheSE and Tyrian SPE. In turn, these groups were subdivided into five subgroups (n = 20), each treated using different experimental conditions as follows: control group-no contamination; contamination group 1-CG1: primer application/ contamination/primer re-application; contamination group 2-CG2: primer application/contamination/wash/dry/primer re-application; contamination group 3-CG3: primer application/adhesive application/light curing/contamination/ adhesive re-application/light curing; contamina- tion group 4-CG4: primer application/adhesive application/light curing/contamination/wash/ dry/adhesive re-application/light curing. Composite buildup was performed using Z250. After 24 hours of storage in distilled water at 37 degrees C, the bonded specimens were trimmed to an hourglass shape and serially sectioned into slabs with 0.6 mm2 cross-sectional areas. Microtensile bond strengths (MTBS) were assessed for each specimen using a universal testing machine. The data were analyzed by two-way ANOVA followed by a post hoc LSD test. SEM evaluations of the fracture modes were also performed. The contaminated specimens showed lower bond strengths than specimens in the control group (p < 0.05), with the exception of CG1 in the Clearfil SE group and CG2 and CG3 in the Tyrian SPE group. Among the three self-etch adhesives, the Tyrian SPE group exhibited a significantly lower average MTBS compared to the Clearfil SE Bond and AdheSE (p < 0.05) groups. Based on the results of the current study, it was found that blood contamination reduced the MTBS of all three self-etch adhesives to dentin, and water-rinsing was unable to overcome the effects of blood contamination.
1×11 Few-Mode Fiber Wavelength Selective Switch using Photonic Lanterns (2014)

We demonstrate an 11 port count wavelength selective switch supporting spatial superchannels of three spatial modes, based on the combination of photonic lanterns and a high-port count single-mode WSS.
Robust constrained model predictive control (2005)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2005.
Binding of Neurotrophin-3 to p75LNGFR, TrkA, and TrkB Mediated by a Single Functional Epitope Distinct from That Recognized by TrkC (1996)

Neurotrophins regulate differentiation and survival of vertebrate neurons through binding to members of the Trk family of receptor tyrosine kinases and to a common low affinity receptor, p75LNGFR. The specificity of neurotrophin action is determined by their selective interaction with the different members of the Trk family; TrkA, TrkB, and TrkC serve as cognate receptors for nerve growth factor, brain-derived neurotrophic factor, and neurotrophin-3 (NT-3), respectively. Unlike nerve growth factor and brain-derived neurotrophic factor, NT-3 can to some extent also bind and activate non-cognate TrkA and B receptors, although the physiological relevance of these interactions is unclear. Previous studies established that neurotrophins use an extended surface for binding to cognate Trk receptors, while binding to p75LNGFR is mediated by a localized cluster of positively charged residues. Here we show that the binding site of NT-3 to its non-preferred receptors TrkA and TrkB is dominated by two positively charged residues, Arg-31 and His-33, previously shown to constitute a main determinant of binding to p75LNGFR. Simultaneous mutation of these two residues into Ala completely abolished NT-3 binding and signaling through TrkA and greatly diminished binding and activation of TrkB. However, NT-3 binding and signaling through its cognate receptor TrkC was unaffected by the mutation. These results show that binding of NT-3 to p75LNGFR, TrkA, and TrkB is mediated by a common determinant, which is distinct from that recognized by TrkC and also different and more localized than the one recognized by TrkA and TrkB in their cognate ligands. Thus, although homologous regions in all neurotrophins are used for binding to Trk receptors, a given Trk may actually contact different residues in different neurotrophins. The mutant NT-3 described here may be of greater advantage than native NT-3 when a trophic activity needs to be specifically targeted to TrkC-expressing neurons and provides a monospecific neurotrophin for future therapeutic development.
Prevention of Hepatocellular Carcinoma in Patients with Chronic Hepatitis B Virus Infection (2011)

Chronic hepatitis B (CHB) accounts for approximately 50% of the underlying etiologies for the development of hepatocellular carcinoma (HCC) worldwide. We reviewed the primary, secondary, and tertiary measures for the prevention of HCC in CHB patients. First, the most effective method is preventing the acquisition of CHB through global vaccination of infants. However, in patients already chronically infected, antiviral treatment using interferon or nucleoside analogs can prevent disease progression to cirrhosis or HCC. Studies have found viral replications indicated by a HBV DNA level to be a strong predictor for cirrhosis and HCC, irrespective of other viral and biochemical factors. Additionally, periodic surveillance using ultrasonography and serum α-fetoprotein every 3-6 months for earlier detection of HCC is also important so that curative treatments can be used. Once HCC occurs, hepatic resection is the mainstay of curative treatments. To prevent tumor recurrence after resection, adjuvant interferon treatments have been tried with promising results based on the assumption that they not only suppress viral activity but also have tumoricidal, antiangiogenetic, and antiproliferative effects. Using nucleoside analogs also has its rationale for preventing de novo tumor development in remnant liver, considering that viral replications are a strong risk factor for HCC. Optimal preventive plans should be further investigated in future studies.
Understanding the Electrolyte Background for Biochemical Sensing with Ion-Sensitive Field-Effect Transistors (2012)

Silicon nanowire field-effect transistors have attracted substantial interest for various biochemical sensing applications, yet there remains uncertainty concerning their response to changes in the supporting electrolyte concentration. In this study, we use silicon nanowires coated with highly pH-sensitive hafnium oxide (HfO(2)) and aluminum oxide (Al(2)O(3)) to determine their response to variations in KCl concentration at several constant pH values. We observe a nonlinear sensor response as a function of ionic strength, which is independent of the pH value. Our results suggest that the signal is caused by the adsorption of anions (Cl(-)) rather than cations (K(+)) on both oxide surfaces. By comparing the data to three well-established models, we have found that none of those can explain the present data set. Finally, we propose a new model which gives excellent quantitative agreement with the data.
Synthesis, Characterization, and Properties of Starlike Poly(<i>n</i>-butyl acrylate)-<i>b</i>-poly(methyl methacrylate) Block Copolymers (2010)

A series of 10- and 20-arm starlike block copolymers containing inner soft poly(n-butyl acrylate) (PBA) block and outer hard poly(methyl methacrylate) (PMMA) block were synthesized by atom transfer radical polymerization (ATRP). Short macroinitiators for preparation of starlike copolymers, poly(2-bromoisobutyryloxyethyl acrylate) (PBiBEA) with degree of polymerization DP = 10 and 20, was prepared by ATRP of trimethylsilyloxyethyl acrylate (HEATMS) and subsequently esterified. Partial star coupling during the star extension with PMMA blocks was observed, and the coupling increased with increasing number of arms and arm length. Phase-separated morphologies of cylindrical hard PMMA block domains arranged in the soft PBA matrix were observed by atomic force microscopy and small-angle X-ray scattering. The mechanical and thermal properties of the copolymers were also thoroughly characterized, and their thermoplastic elastomer behavior was studied. Tensile strength of the starlike copolymers was considerably higher compared to linear and three-arm stars with similar compositions.
Improved Bilinear Pooling with CNNs (2017)

Bilinear pooling of Convolutional Neural Network (CNN) features [22, 23], and their compact variants [10], have been shown to be effective at fine-grained recognition, scene categorization, texture recognition, and visual question-answering tasks among others. The resulting representation captures second-order statistics of convolutional features in a translationally invariant manner. In this paper we investigate various ways of normalizing these statistics to improve their representation power. In particular we find that the matrix square-root normalization offers significant improvements and outperforms alternative schemes such as the matrix logarithm normalization when combined with elementwise square-root and l2 normalization. This improves the accuracy by 2-3% on a range of fine-grained recognition datasets leading to a new state of the art. We also investigate how the accuracy of matrix function computations effect network training and evaluation. In particular we compare against a technique for estimating matrix square-root gradients via solving a Lyapunov equation that is more numerically accurate than computing gradients via a Singular Value Decomposition (SVD). We find that while SVD gradients are numerically inaccurate the overall effect on the final accuracy is negligible once boundary cases are handled carefully. We present an alternative scheme for computing gradients that is faster and yet it offers improvements over the baseline model. Finally we show that the matrix square-root computed approximately using a few Newton iterations is just as accurate for the classification task but allows an order-of-magnitude faster GPU implementation compared to SVD decomposition.
Biosynthesis of the red pigment bikaverin in <i>Fusarium fujikuroi</i>: genes, their function and regulation (2009)

Fusarium secondary metabolites are structurally diverse, have a variety of activities and are generally poorly understood biosynthetically. The F. fujikuroi polyketide synthase gene bik1 was previously shown to be responsible for formation of the mycelial pigment bikaverin. Here we present the characterization of five genes adjacent to bik1 as encoding a putative FAD-dependent monooxygenase (bik2), an O-methyltransferase (bik3), an NmrA-like protein (bik4), a Zn(II)2Cys6 transcription factor (bik5) and an MFS transporter (bik6). Deletion of each gene resulted in total loss or significant reduction of bikaverin synthesis. Expression studies revealed that all bik genes are repressed by high amounts of nitrogen in an AreA-independent manner and are subject to a time- and pH-dependent regulation. Deletion of the pH regulatory gene pacC resulted in partial derepression while complementation with a dominant active allele resulted in repression of bik genes at acidic ambient pH. Transcription of all bik genes in strains lacking bik1, bik2 or bik3 was essentially eliminated, while transcription of some bik genes was detected in strains lacking bik4, bik5 or bik6. Thus, bikaverin synthesis is regulated by a complex regulatory network. Understanding how different factors influence the synthesis of this model secondary metabolite will aid understanding secondary metabolism in general.
Fusion Gains, Basic Science Takes a Hit (1999)

DOE BUDGETDespite continuing criticism of security at its weapons labs and lax worker safety controls, the Department of Energy has won from Congress a 4.3% increase in its science budget for the fiscal year that began last week. Although the 2000 budget will mean delays for several projects, including the $1.2 billion Spallation Neutron Source, and cuts in others, such as materials science, some programs come out ahead. Even more important, say supporters, is that the integrity of the science program remains intact.
14-3-3 Proteins Associate with A20 in an Isoform-specific Manner and Function Both as Chaperone and Adapter Molecules (1996)

A20, a novel zinc finger protein, is an inhibitor of tumor necrosis factor-induced apoptosis. The mechanism by which A20 exerts its protective effect is currently unknown. Several isoforms of the 14-3-3 proteins were found to interact with A20 in a yeast two-hybrid screen. A20 bound several 14-3-3 isoforms in vitro. Moreover, transfected A20 was found to preferentially bind the endogenous eta14-3-3 isoform, whereas the beta/zeta isoforms co-immunoprecipitated much less efficiently, and epsilon14-3-3 had an intermediate affinity. Importantly, c-Raf, a previously described 14-3-3-interacting protein, also preferentially bound the eta isoform. The cellular localization and subcellular fractionation of A20 was dramatically altered by co-transfected 14-3-3, providing the first experimental evidence for the notion that 14-3-3 can function as a chaperone. Furthermore, c-Raf and A20 co-immunoprecipitated in a 14-3-3-dependent manner, suggesting that 14-3-3 can function as a bridging or adapter molecule.
Lipoprotein lipase gene mutations in coronary artery disease. (1998)

In this selected population of premature CAD subjects, the prevalence of heterozygosity for defective LPL alleles was slightly higher (but not significantly so) than that in a group of healthy subjects. The LPL(Gly188-->Glu) and LPL(Asn291-->Ser) mutations may confer genetic susceptibility to premature CAD in a small number (approximately 2.4%) of patients; overall these four LPL alleles do not appear to contribute significantly to CAD risk in French Canadians.
Factors influencing product customisation (2005)

Advances in technologies are increasingly changing how consumers and firms interact. A growing type of interaction is product customisation. This paper examines factors influencing customisation. Factors investigated were the number of attributes, the presence of default values, and participants' experience with the product, the internet, and the remote shopping experiences via the internet and mail order catalogues. Also investigated were differences between gender and the amount of education of the consumer. A web-based program created specifically for this investigation empirically investigates factors simulating an experience customising products. The results identify factors influencing the customisation process. Discussed are implications and future directions for managers and researchers.
Coarse-Graining Protein Structures With Local Multivariate Features from Molecular Dynamics (2008)

A multivariate statistical theory, local feature analysis (LFA), extracts functionally relevant domains from molecular dynamics (MD) trajectories. The LFA representations, like those of principal component analysis (PCA), are low dimensional and provide a reduced basis set for collective motions of simulated proteins, but the local features are sparsely distributed and spatially localized, in contrast to global PCA modes. One key problem in the assignment of local features is the coarse-graining of redundant LFA output functions by means of seed atoms. One can solve the combinatorial problem by adding seed atoms one after another to a growing set, minimizing a reconstruction error at each addition. This allows for an efficient implementation, but the sequential algorithm does not guarantee the optimal mutual correlation of the sequentially assigned features. Here, we present a novel coarse-graining algorithm for proteins that directly minimizes the mutual correlation of seed atoms by Monte Carlo (MC) simulations. Tests on MD trajectories of two biological systems, bacteriophage T4 lysozyme and myosin II motor domain S1, demonstrate that the new algorithm provides statistically reproducible results and describes functionally relevant dynamics. The well-known undersampling of large-scale motion by short MD simulations is apparent also in our model, but the new coarse-graining offers a major advantage over PCA; converged features are invariant across multiple windows of the trajectory, dividing the protein into converged regions and a smaller number of localized, undersampled regions. In addition to its use in structure classification, the proposed coarse-graining thus provides a localized measure of MD sampling efficiency.
Analysis and evaluation of interleaving techniques in forward converters (1998)

Analysis, design and evaluation of different interleaving techniques for the forward power converter are presented. Specifically, the performance of the one-choke interleaving approach is compared with the two-choke interleaving approach. The results of the analysis are verified experimentally on two 5 V/20 A interleaved DC/DC power converters. The analysis, design and evaluation results can be extended to any number of interleaved power converters.