gebhart/patrepeval huggingface dataset:
Heteroepitaxial growth of Pt and Au thin films on MgO single crystals by bias-assisted sputtering (2016)

The crystallographic orientation of a metal affects its surface energy and structure, and has profound implications for surface chemical reactions and interface engineering, which are important in areas ranging from optoelectronic device fabrication to catalysis. However, it can be very difficult and expensive to manufacture, orient, and cut single crystal metals along different crystallographic orientations, especially in the case of precious metals. One approach is to grow thin metal films epitaxially on dielectric substrates. In this work, we report on growth of Pt and Au films on MgO single crystal substrates of (100) and (110) surface orientation for use as epitaxial templates for thin film photovoltaic devices. We develop bias-assisted sputtering for deposition of oriented Pt and Au films with sub-nanometer roughness. We show that biasing the substrate decreases the substrate temperature necessary to achieve epitaxial orientation, with temperature reduction from 600 to 350 °C for Au, and from 750 to 550 °C for Pt, without use of transition metal seed layers. In addition, this temperature can be further reduced by reducing the growth rate. Biased deposition with varying substrate bias power and working pressure also enables control of the film morphology and surface roughness.
Using Bayesian networks to find relevant context features for HMM-based speech synthesis (2012)

Speech units are highly context-dependent, so taking contextual features into account is essential for speech modelling. Context is employed in HMM-based Text-to-Speech speech synthesis systems via context-dependent phone models. A very wide context is taken into account, represented by a large set of contextual factors. However, most of these factors probably have no significant influence on the speech, most of the time. To discover which combinations of features should be taken into account, decision tree-based context clustering is used. But the space of context-dependent models is vast, and the number of contexts seen in the training data is only a tiny fraction of this space, so the task of the decision tree is very hard: to generalise from observations of a tiny fraction of the space to the rest of the space, whilst ignoring uninformative or redundant context features. The structure of the context feature space has not been systematically studied for speech synthesis. In this paper we discover a dependency structure by learning a Bayesian Network over the joint distribution of the features and the speech. We demonstrate that it is possible to discard the majority of context features with minimal impact on quality, measured by a perceptual test.
RACBVHs: Random-Accessible Compressed Bounding Volume Hierarchies (2009)

We present a novel compressed bounding volume hierarchy (BVH) representation, random-accessible compressed bounding volume hierarchies (RACBVHs), for various applications requiring random access on BVHs of massive models. Our RACBVH representation is compact and transparently supports random access on the compressed BVHs without decompressing the whole BVH. To support random access on our compressed BVHs, we decompose a BVH into a set of clusters. Each cluster contains consecutive bounding volume (BV) nodes in the original layout of the BVH. Also, each cluster is compressed separately from other clusters and serves as an access point to the RACBVH representation. We provide the general BVH access API to transparently access our RACBVH representation. At runtime, our decompression framework is guaranteed to provide correct BV nodes without decompressing the whole BVH. Also, our method is extended to support parallel random access that can utilize the multicore CPU architecture. Our method can achieve up to a 12:1 compression ratio, and more importantly, can decompress 4.2 M BV nodes ({=}135 {\rm MB}) per second by using a single CPU-core. To highlight the benefits of our approach, we apply our method to two different applications: ray tracing and collision detection. We can improve the runtime performance by more than a factor of 4 as compared to using the uncompressed original data. This improvement is a result of the fast decompression performance and reduced data access time by selectively fetching and decompressing small regions of the compressed BVHs requested by applications.
Molecular Mechanisms and Pathophysiology of Necrotic Cell Death (2008)

Necrotic cell death has long been considered an accidental and uncontrolled mode of cell death. But recently it has become clear that necrosis is a molecularly regulated event that is associated with pathologies such as ischemia-reperfusion (IR) injury, neurodegeneration and pathogen infection. The serine/threonine kinase receptor-interacting protein 1 (RIP1) plays a crucial role during the initiation of necrosis induced by ligand-receptor interactions. On the other hand, ATP depletion is an initiating factor in ischemia-induced necrotic cell death. Common players in necrotic cell death irrespective of the stimulus are calcium and reactive oxygen species (ROS). During necrosis, elevated cytosolic calcium levels typically lead to mitochondrial calcium overload, bioenergetics effects, and activation of proteases and phospholipases. ROS initiates damage to lipids, proteins and DNA and consequently results in mitochondrial dysfunction, ion balance deregulation and loss of membrane integrity. Membrane destabilization during necrosis is also mediated by other factors, such as acid-sphingomyelinase (ASM), phospholipase A(2) (PLA(2)) and calpains. Furthermore, necrotic cells release immunomodulatory factors that lead to recognition and engulfment by phagocytes and the subsequent immunological response. The knowledge of the molecular mechanisms involved in necrosis has contributed to our under-standing of necrosis-associated pathologies. In this review we will focus on the intracellular and intercellular signaling events in necrosis induced by different stimuli, such as oxidative stress, cytokines and pathogen-associated molecular patterns (PAMPs), which can be linked to several pathologies such as stroke, cardiac failure, neurodegenerative diseases, and infections.
Simultaneous multislice rapid magnetic resonance elastography of the liver (2020)

To design and validate a rapid Simultaneous Multi-slice (SMS) Magnetic Resonance Elastography technique (MRE), which combines SMS acquisition, in-plane undersampling and an existing rapid Magnetic Resonance Elastography (MREr) scheme to allow accelerated data acquisition in healthy volunteers and comparison against MREr. SMS-MREr sequence was developed by incorporating SMS acquisition scheme into an existing MREr sequence that accelerates MRE acquisition by acquiring data during opposite phases of mechanical vibrations. The MREr sequence accelerated MRE acquisition by acquiring data during opposite phases of mechanical vibrations. Liver MRE was performed on 23 healthy subjects using MREr and SMS-MREr sequences, and mean stiffness values were obtained for manually drawn regions of interest. Linear correlation and agreement between MREr- and SMS-MREr-based stiffness values were investigated. SMS-MREr reduced the scan time by half relative to MREr, and allowed acquisition of four-slice MRE data in a single 17-second breath-hold. Visual comparison suggested agreement between MREr and SMS-MREr elastograms. A Pearson's correlation of 0.93 was observed between stiffness values derived from MREr and SMS-MREr. Bland-Altman analysis demonstrated good agreement, with -0.08 kPa mean bias and narrow limits of agreement (95% CI: 0.23 to -0.39 kPa) between stiffness values obtained using MREr and SMS-MREr. SMS can be combined with other fast MRE approaches to achieve further acceleration. This pushes the limit on the acceleration that can be achieved in MRE acquisition, and makes it possible to conduct liver MRE exams in a single breath-hold.
Methods for enhancing carrier phase GNSS positioning and attitude determination performance. (2010)

University of Minnesota Ph.D. dissertation. May 2010. Major: Aerospace Engineering and Mechanics. Advisor:Demoz Gebre-Egziabher. 1 computer file (PDF); ix, 173 pages, appendix A.
Computing geometry-aware handle and tunnel loops in 3D models (2008)

Many applications such as topology repair, model editing, surface parameterization, and feature recognition benefit from computing loops on surfaces that wrap around their 'handles' and 'tunnels'. Computing such loops while optimizing their geometric lengths is difficult. On the other hand, computing such loops without considering geometry is easy but may not be very useful. In this paper we strike a balance by computing topologically correct loops that are also geometrically relevant. Our algorithm is a novel application of the concepts from topological persistence introduced recently in computational topology. The usability of the computed loops is demonstrated with some examples in feature identification and topology simplification.
Differential wax–wane focus servo (1993)

We describe a differential wax-wane focus servo technique for use in optical data storage. A combination of scalar diffraction modeling and experiment is used to quantify performance. Our results indicate that the differential technique is superior to the single-detector wax-wane technique with respect to gain, linearity, and lock-on range. We present modeling results that show the effects of aberrations and detector misalignment. The differential system was found to be robust. It can also reject many common pattern noise effects such as tracking cross talk, which was reduced from 0.7 µm in a single channel to < 0.1 µm in the optimized differential channel.
Fibromyalgia syndrome: a review. (1996)

Fibromyalgia syndrome includes symptoms of widespread, chronic musculoskeletal aching and stiffness and soft tissue tender points. It is frequently accompanied by fatigue and sleep disturbance. Fibromyalgia is more common in women than in men, and it occurs at a mean age of 49 years. Differential diagnosis includes myofascial pain syndrome and chronic fatigue syndrome. Fibromyalgia is a multifactorial problem and no universal treatment guidelines apply to all cases. Pharmacologic therapy may incude tricyclic antidepressants. In addition to commonly used pharmacologic therapies, patient education, reassurance and an exercise program can each play an important role in relieving the symptoms associated with this common musculoskeletal syndrome.
The Early Pathogenesis of Foot-and-Mouth Disease in Cattle After Aerosol Inoculation (2010)

To characterize the early events of foot-and-mouth disease virus (FMDV) infection in cattle subsequent to simulated natural exposure, 16 steers were aerosol inoculated with FMDV and euthanized at various times. Samples were collected from each steer antemortem (serum, nasal swabs, and oral swabs) and postmortem (up to 40 tissues per animal) and screened for FMDV by virus isolation and for FMDV RNA by real-time reverse transcription polymerase chain reaction. Tissues that tested positive for FMDV or viral RNA were examined by immunohistochemistry and multichannel immunofluorescence microscopy. In previremic steers, FMDV was most consistently localized to nasopharyngeal tissues, thereby indicating this region as the most important site of primary viral replication. The earliest site of microscopic localization of FMDV antigens was the lymphoid follicle-associated epithelium of the pharyngeal mucosa-associated lymphoid tissue of the nasopharynx at 6 hours postaerosolization. At early time points after aerosol inoculation, viral antigens colocalized with cytokeratin-positive pharyngeal epithelial cells; intraepithelial FMDV-negative, MHCII/CD11c-double-positive dendritic cells were present in close proximity to FMDV-positive cells. Onset of viremia coincided with marked increase of viral loads in pulmonary tissues and with substantial decrease of viral detection in nasopharyngeal tissues. These data indicate that subsequent to aerogenous exposure to FMDV, the temporally defined critical pathogenesis events involve (1) primary replication in epithelial cells of the pharyngeal mucosa-associated lymphoid tissue crypts and (2) subsequent widespread replication in pneumocytes in the lungs, which coincides with (3) the establishment of sustained viremia.
Catching the Long-Tail: Extracting Local News Events from Twitter (2021)

Twitter, used in 200 countries with over 250 milliontweets a day, is a rich source of local news from aroundthe world. Many events of local importance are first reportedon Twitter, including many that never reach newschannels. Further, there are often only a few tweetsreporting each such event, in contrast with the largervolumes that follow events of wider significance. Eventhough such events may be primarily of local importance,they can also be of critical interest to some specificbut possibly far flung entities: For example, a firein a supplier’s factory half-way around the world maybe of interest even from afar. In this paper we describehow this ‘long tail’ of events can be detected in spite oftheir sparsity.We then extract and correlate informationfrom multiple tweets describing the same event. Ourgeneric architecture for converting a tweet-stream intoevent-objects uses locality sensitive hashing, classification,boosting, information extraction and clustering.Our results, based on millions of tweets monitored overmany months, appear to validate our approach and architecture:We achieved success-rates in the 80% rangefor event detection and 76% on event-correlation; we also reduced tweet-comparisons by 80% using LSH.
Dosage Compensation of the Sex Chromosomes (2012)

Differentiated sex chromosomes evolved because of suppressed recombination once sex became genetically controlled. In XX/XY and ZZ/ZW systems, the heterogametic sex became partially aneuploid after degeneration of the Y or W. Often, aneuploidy causes abnormal levels of gene expression throughout the entire genome. Dosage compensation mechanisms evolved to restore balanced expression of the genome. These mechanisms include upregulation of the heterogametic chromosome as well as repression in the homogametic sex. Remarkably, strategies for dosage compensation differ between species. In organisms where more is known about molecular mechanisms of dosage compensation, specific protein complexes containing noncoding RNAs are targeted to the X chromosome. In addition, the dosage-regulated chromosome often occupies a specific nuclear compartment. Some genes escape dosage compensation, potentially resulting in sex-specific differences in gene expression. This review focuses on dosage compensation in mammals, with comparisons to fruit flies, nematodes, and birds.
Diagnosis and Monitoring of Clostridium difficile Infections with the Polymerase Chain Reaction (1993)

Toxigenic Clostridium difficile is the etiologic agent of pseudomembranous colitis. We have developed an assay system for the rapid direct detection of toxigenic C. difficile in human stool samples. After DNA extraction, polymerase chain reaction (PCR) amplification is undertaken with primers targeting specific sequences in the C. difficile 16S rRNA gene. Next, toxigenic strains of C. difficile are distinguished from nontoxigenic strains by PCR amplification of toxin A and/or B gene sequences. This study included 12 patients with C. difficile colitis, seven of whom had clinical relapses after discontinuation of vancomycin therapy. We detected toxigenic C. difficile in stools from four (57%) of these seven patients before relapse--at a time when no toxin B was detectable in stools and results of anaerobic culture were negative. The PCR assay is 100-fold more sensitive than anaerobic culture methods. The course of the infection in one patient (both during and after therapy) was monitored by the PCR technique. The multigene analysis approach permitted the detection of colonization with a nontoxigenic strain when this patient's relapses had cleared. This clinically applicable assay allows earlier detection of infection with toxigenic C. difficile. The result is more timely therapeutic intervention.
Near-Optimal Algorithms for Minimax Optimization (2020)

This paper resolves a longstanding open question pertaining to the design of near-optimal first-order algorithms for smooth and strongly-convex-strongly-concave minimax problems. Current state-of-the-art first-order algorithms find an approximate Nash equilibrium using $\tilde{O}(κ_{\mathbf x}+κ_{\mathbf y})$ or $\tilde{O}(\min\{κ_{\mathbf x}\sqrt{κ_{\mathbf y}}, \sqrt{κ_{\mathbf x}}κ_{\mathbf y}\})$ gradient evaluations, where $κ_{\mathbf x}$ and $κ_{\mathbf y}$ are the condition numbers for the strong-convexity and strong-concavity assumptions. A gap still remains between these results and the best existing lower bound $\tildeΩ(\sqrt{κ_{\mathbf x}κ_{\mathbf y}})$. This paper presents the first algorithm with $\tilde{O}(\sqrt{κ_{\mathbf x}κ_{\mathbf y}})$ gradient complexity, matching the lower bound up to logarithmic factors. Our algorithm is designed based on an accelerated proximal point method and an accelerated solver for minimax proximal steps. It can be easily extended to the settings of strongly-convex-concave, convex-concave, nonconvex-strongly-concave, and nonconvex-concave functions. This paper also presents algorithms that match or outperform all existing methods in these settings in terms of gradient complexity, up to logarithmic factors.
PLDA in the i-supervector space for text-independent speaker verification (2014)

In this paper, we advocate the use of the uncompressed form of i-vector and depend on subspace modeling using probabilistic linear discriminant analysis (PLDA) in handling the speaker and session (or channel) variability. An i-vector is a low-dimensional vector containing both speaker and channel information acquired from a speech segment. When PLDA is used on an i-vector, dimension reduction is performed twice: first in the i-vector extraction process and second in the PLDA model. Keeping the full dimensionality of the i-vector in the i-supervector space for PLDA modeling and scoring would avoid unnecessary loss of information. We refer to the uncompressed i-vector as the i-supervector. The drawback in using the i-supervector with PLDA is the inversion of large matrices in the estimation of the full posterior distribution, which we show can be solved rather efficiently by portioning large matrices into smaller blocks. We also introduce the Gaussianized rank-norm, as an alternative to whitening, for feature normalization prior to PLDA modeling. We found that the i-supervector performs better during normalization. A better performance is obtained by combining the i-supervector and i-vector at the score level. Furthermore, we also analyze the computational complexity of the i-supervector system, compared with that of the i-vector, at four different stages of loading matrix estimation, posterior extraction, PLDA modeling, and PLDA scoring.
High-performance parallel programming in Java: exploiting native libraries (1998)

With most of today's fast scientific software written in Fortran and C, Java has a lot of catching up to do. In this paper we discuss how new Java programs can capitalize on high-performance libraries for other languages. With the help of a tool we have automatically created Java bindings for several standard libraries: MPI, BLAS, BLACS, PBLAS and ScaLAPACK. The purpose of the additional software layer introduced by the bindings is to resolve the interface problems between different programming languages such as data type mapping, pointers, multidimensional arrays, etc. For evaluation, performance results are presented for Java versions of two benchmarks from the NPB and PARKBENCH suites on the IBM SP2 using JDK and IBM's high-performance Java compiler, and on the Fujitsu AP3000 using Toba – a Java-to-C translator. The results confirm that fast parallel computing in Java is indeed possible. © 1998 John Wiley & Sons, Ltd.
Cloning and linkage analysis of Neisseria gonorrhoeae DNA methyltransferases (1992)

We have cloned DNA methyltransferases (MTases) from various strains of Neisseria gonorrhoeae. Each of these clones represents a single specificity, indicating that the multiple gonococcal MTase specificities are encoded by monospecific MTases. The DNAs of five strains (FA5100, F62, MS11, Pgh3-2, and WR302) were digested with NheI, SpeI, or NheI plus SpeI and subjected to pulsed-field gel electrophoresis. The DNA MTase clones were used to probe Southern blots of these pulsed-field gels to determine whether the MTase genes are linked and whether there are strain-to-strain differences. The results indicate that none of these genes are closely linked, but variable hybridization patterns indicate that there exist restriction fragment length polymorphisms between the strains tested. Most of the chromosomal regions containing these restriction fragment length polymorphisms are clustered in regions containing gonococcal genes known or suspected to antigenically vary via genetic recombination.
GST-PRIME: a genome-wide primer design software for the generation of gene sequence tags (2001)

The availability of sequenced genomes has generated a need for experimental approaches that allow the simultaneous analysis of large, or even complete, sets of genes. To facilitate such analyses, we have developed GST-PRIME, a software package for retrieving and assembling gene sequences, even from complex genomes, using the NCBI public database, and then designing sets of primer pairs for use in gene amplification. Primers were designed by the program for the direct amplification of gene sequence tags (GSTs) from either genomic DNA or cDNA. Test runs of GST-PRIME on 2000 randomly selected Arabidopsis and Drosophila genes demonstrate that 93 and 88% of resulting GSTs, respectively, fulfilled imposed length criteria. GST-PRIME primer pairs were tested on a set of 1900 Arabidopsis genes coding for chloroplast-targeted proteins: 95% of the primer pairs used in PCRs with genomic DNA generated the correct amplicons. GST-PRIME can thus be reliably used for large-scale or specific amplification of intron-containing genes of multicellular eukaryotes.
LMX1B transactivation and expression in nail-patella syndrome (2000)

Lmx1b, a member of the LIM homeodomain protein family, is essential for the specification of dorsal limb fates at the zeugopodal and autopodal level in vertebrates. We and others have shown that a skeletal dysplasia, nail-patella syndrome (NPS), results from mutations in LMX1B. While it is a unique mesenchymal determinant of dorsal limb patterning during vertebrate development, the mechanism by which LMX1B mutations generate the NPS phenotype has not been addressed at a transcriptional level or correlated with its spatial pattern of gene expression. In this study, in situ hybridizations of Lmx1b on murine limb sections reveal strong expression in dorsal mesenchymal tissues (precursors of muscle, tendons, joints and patella) and, interestingly, also in anterior structures of the limb, explaining the anterior to posterior gradient of joint and nail dysplasia observed in NPS patients. Transfection studies showed that both the LIM domain-interacting protein, LDB1, and the helix-loop-helix protein, E47/shPan1, can regulate LMX1B action. While co--transfections of E47/shPan1 with LMX1B result in a synergistic effect on reporter activity, LDB1 down-regulated LMX1B-mediated transactivation irrespective of E47/shPan1. Mutant LMX1B proteins containing human mutations affecting each of the helices or the N-terminal arm of the homeodomain abolished transactivation, while LIM B and truncation mutations retained residual activity. These mutations fail to act in a dominant-negative manner on wild-type LMX1B in mixing studies, thereby supporting haploinsufficiency as the mechanism underlying NPS pathogenesis.