gebhart/patrepeval huggingface dataset:
Structured Topic Models for Language (2008)

This thesis introduces new methods for statistically modelling text using topic models. Topic models have seen many successes in recent years, and are used in a variety of applications, including analysis of news articles, topic-based search interfaces and navigation tools for digital libraries. Despite these recent successes, the field of topic modelling is still relatively new and there remains much to be explored. One noticeable absence from most of the previous work on topic modelling is consideration of language and document structure—from low-level structures, including word order and syntax, to higher-level structures, such as relationships between documents. The focus of this thesis is therefore structured topic models—models that combine latent topics with information about document structure, ranging from local sentence structure to inter-document relationships. These models draw on techniques from Bayesian statistics, including hierarchical Dirichlet distributions and processes, Pitman-Yor processes, and Markov chain Monte Carlo methods. Several methods for estimating the parameters of Dirichlet-multinomial distributions are also compared. The main contribution of this thesis is the introduction of three structured topic models. The first is a topic-based language model. This model captures both word order and latent topics by extending a Bayesian topic model to incorporate n-gram statistics. A bigram version of the new model does better at predicting future words than either a topic model or a trigram language model. It also provides interpretable topics. The second model arises from a Bayesian reinterpretation of a classic generative dependency parsing model. The new model demonstrates that parsing performance can be substantially improved by a careful choice of prior and by sampling hyperparameters. Additionally, the generative nature of the model facilitates the inclusion of latent state variables, which act as specialised part-of-speech tags or “syntactic topics”. The third is a model that captures high-level relationships between documents. This model uses nonparametric Bayesian priors and Markov chain Monte Carlo methods to infer topic-based document clusters. The model assigns a higher probability to unseen test documents than either a clustering model without topics or a Bayesian topic model without document clusters. The model can be extended to incorporate author information, resulting in finer-grained clusters and better predictive performance.
Flexible, Aligned Carbon Nanotube/Conducting Polymer Electrodes for a Lithium-Ion Battery (2007)

We present here an approach for preparing a nanostructured “free-standing” ACNT/PEDOT/PVDF membrane electrode that is lightweight, flexible, highly electroactive and conductive, and mechanically robust. It could be directly and easily fabricated into a rechargeable lithium-ion battery as the anode material without using a metal substrate or binder.
CXCL16/SR-PSOX Is an Interferon-γ–Regulated Chemokine and Scavenger Receptor Expressed in Atherosclerotic Lesions (2004)

We demonstrate a novel role of IFN-gamma in foam cell formation through upregulation of CXCL16/SR-PSOX. CXCR6 expression in the plaque confirms the presence of cells able to respond to CXCL16. Therefore, this chemokine/scavenger receptor could serve as a molecular link between lipid metabolism and immune activity in the atherosclerotic lesion.
ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data (2018)

The accurate detection of ultralow allele frequency variants in DNA samples is of interest in both research and medical settings, particularly in liquid biopsies where cancer mutational status is monitored from circulating DNA. Next-generation sequencing (NGS) technologies employing molecular barcoding have shown promise but significant sensitivity and specificity improvements are still needed to detect mutations in a majority of patients before the metastatic stage. To address this we present analytical validation data for ERASE-Seq (Elimination of Recurrent Artifacts and Stochastic Errors), a method for accurate and sensitive detection of ultralow frequency DNA variants in NGS data. ERASE-Seq differs from previous methods by creating a robust statistical framework to utilize technical replicates in conjunction with background error modeling, providing a 10 to 100-fold reduction in false positive rates compared to published molecular barcoding methods. ERASE-Seq was tested using spiked human DNA mixtures with clinically realistic DNA input quantities to detect SNVs and indels between 0.05% and 1% allele frequency, the range commonly found in liquid biopsy samples. Variants were detected with greater than 90% sensitivity and a false positive rate below 0.1 calls per 10,000 possible variants. The approach represents a significant performance improvement compared to molecular barcoding methods and does not require changing molecular reagents.
Inducible overexpression of the FUM1 gene in Saccharomyces cerevisiae: localization of fumarase and efficient fumaric acid bioconversion to L-malic acid (1990)

Cloning of the Saccharomyces cerevisiae FUM1 gene downstream of the strong GAL10 promoter resulted in inducible overexpression of fumarase in the yeast. The overproducing strain exhibited efficient bioconversion of fumaric acid to L-malic acid with an apparent conversion value of 88% and a conversion rate of 80.4 mmol of fumaric acid/h per g of cell wet weight, both of which are much higher than parameters known for industrial bacterial strains. The only product of the conversion reaction was L-malic acid, which was essentially free of the unwanted by-product succinic acid. The GAL10 promoter situated upstream of a promoterless FUM1 gene led to production and correct distribution of the two fumarase isoenzyme activities between cytosolic and mitochondrial subcellular fractions. The amino-terminal sequence of fumarase contains the mitochondrial signal sequence since (i) 92 of 463 amino acid residues from the amino terminus of fumarase are sufficient to localize fumarase-lacZ fusions to mitochondria and (ii) fumarase and fumarase-lacZ fusions lacking the amino-terminal sequence are localized exclusively in the cytosol. The possibility that both mitochondrial and cytosolic fumarases are derived from the same initial translation product is discussed.
Anti-chaperone behavior of BiP during the protein disulfide isomerase-catalyzed refolding of reduced denatured lysozyme. (1994)

Folding catalysts of the endoplasmic reticulum (ER), such as protein disulfide isomerase (PDI), accelerate the slow chemical steps, such as disulfide bond formation, that accompany protein folding. Molecular chaperones of the ER, notably the heavy chain-binding protein, BiP (grp78), bind and release unfolded proteins in an ATP-dependent fashion. In vitro, the fate of reduced, denatured lysozyme is dependent on whether the substrate interacts first with BiP or PDI. Depending on the ratio of PDI to substrate and order in which the components of the reaction are mixed, PDI can exhibit a foldase/chaperone activity, which increases the rate and extent of lysozyme refolding, or it can function as an anti-chaperone that promotes the formation of inactive, disulfide-linked lysozyme aggregates (Puig, A., and Gilbert, H.F. (1994) J. Biol. Chem. 269, 7764-7771). Reduced, denatured lysozyme, but not the native protein, interacts with BiP and efficiently stimulates its peptide-dependent ATPase activity. When present at substoichiometric amounts, BiP, like PDI, facilitates the formation of large, inactive lysozyme aggregates that are non-covalently associated with BiP. BiP and PDI compete for a limited number of sites in these insoluble aggregates. If BiP is present at a high molar excess, the chaperone binds unfolded lysozyme and inhibits its aggregation by maintaining it in a soluble, yet inactive, conformation, both in the presence or absence of ATP. Increasing concentrations of BiP decrease the extent, but not the initial rate, of refolding, suggesting that BiP and PDI compete for unfolded lysozyme and that the BiP-lysozyme complex is not a very good substrate for PDI either in the presence or absence of ATP. Depending on the BiP and PDI concentrations, unfolded lysozyme may either be efficiently refolded into the native conformation in a PDI-catalyzed reaction, or it may form both soluble and insoluble BiP-lysozyme complexes. In vitro, PDI- and BiP-facilitated aggregation, as well as the competition of the two proteins for substrate, reproduces many of the features of the quality control system of the ER.
Molecular Docking of Carbohydrate Ligands to Antibodies: Structural Validation against Crystal Structures (2009)

Cell surface glycoproteins play vital roles in cellular homeostasis and disease. Antibody recognition of glycosylation on different cells and pathogens is critically important for immune surveillance. Conversely, adverse immune reactions resulting from antibody-carbohydrate interactions have been implicated in the development of autoimmune diseases and impact areas such as xenotransplantation and cancer treatment. Understanding the nature of antibody-carbohydrate interactions and the method by which saccharides fit into antibody binding sites is important in understanding the recognition process. In silico techniques offer attractive alternatives to experimental methods (X-ray crystallography and NMR) for the study of antibody-carbohydrate complexes. In particular, molecular docking provides information about protein-ligand interactions in systems that are difficult to study with experimental techniques. Before molecular docking can be used to investigate antibody-carbohydrate complexes, validation of an appropriate docking method is required. In this study, four popular docking programs, Glide, AutoDock, GOLD, and FlexX, were assessed for their ability to accurately dock carbohydrates to antibodies. Comparison of top ranking poses with crystal structures highlighted the strengths and weaknesses of these programs. Rigid docking, in which the protein conformation remains static, and flexible docking, where both the protein and ligand are treated as flexible, were compared. This study has revealed that generally molecular docking of carbohydrates to antibodies has been performed best by Glide.
Isolation by Differential and Zonal Centrifugation of Minicells Segregated by Escherichia coli (1979)

Minicells segregated from Escherichia coli chi925 carrying a drug-resistance plasmid were separated from nucleated cells by differential centrifugation and purified by rate-zonal centrifugation in sucrose gradients. Minicells purified in this way were capable of donating the plasmid to nucleated cells. They also incorporated thymidine, uridine and methionine into macromolecules. Methods are described for purification of plasmid-containing minicells on a scale large enough to allow isolation of DNA, DNA polymerase and RNA polymerase in sufficient quantities for studies of enzymes involved in replication and transcription of plasmid DNA.
Growth and characterization of Bi, Pr- and Bi, Sc-substituted lutetium iron garnet films with planar magnetization for magneto-optic visualization (2001)

The series of epitaxial garnet films of general composition Lu3-x-yBixPryFe5-zAlzO12 and Lu3-xBixFe5-y-zScyAlzO12 were grown on (111) oriented GGG (gadolinium gallium garnet) substrates by the liquid phase epitaxy. Their magnetic and magneto-optical properties were studied using both experimental techniques and modelling. All obtained films demonstrated generally a magnetic anisotropy close to the easy-plane type. The Pr-containing films exhibited large negative uniaxial anisotropy and significant cubic anisotropy. The latter causes a distortion of magnetization curves in samples magnetized in a direction normal to the film plane, especially at low temperatures. The large negative uniaxial anisotropy of Pr-substituted iron garnets allows us to increase the saturation field up to 0.5 T at liquid nitrogen temperature. The Sc-doped films displayed small positive uniaxial anisotropy that did not exceed the shape anisotropy. The magnetization curves of these films did not show any distortion due to the cubic anisotropy. The suitability of Pr- and Sc-doped garnets that meet the requirements for indicator layers for magneto-optic visualization at liquid nitrogen temperature is discussed.
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia (2020)

Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet clear.
Environmental Exposure of Aquatic and Terrestrial Biota to Triclosan and Triclocarban1 (2009)

The synthetic biocides triclosan (5-chloro-2-(2,4-dichlorophenoxy)phenol) and triclocarban (3,4,4'-trichlorocarbanilide) are routinely added to a wide array of antimicrobial personal care products and consumer articles. Both compounds can persist in the environment and exhibit toxicity toward a number of biological receptors. Recent reports of toxicological effects in wildlife, human cell cultures, and laboratory animals have heightened the interest in the occurrence of these biocide and related toxic effects. The present study aimed to summarize published environmental concentrations of biocides and contrast them with toxicity threshold values of susceptible organisms. Environmental occurrences and toxicity threshold values span more than six orders of magnitude in concentration. The highest biocide levels, measured in the mid parts-per-million range, were determined to occur in aquatic sediments and in municipal biosolids destined for land application. Crustacea and algae were identified as the most sensitive species, susceptible to adverse effects from biocide exposures in the parts-per-trillion range. An overlap of environmental concentrations and toxicity threshold values was noted for these more sensitive organisms, suggesting potential adverse ecological effects in aquatic environments. Affirmative evidence for this is lacking, however, since studies examining environmental occurrences of biocides vis-à-vis the health and diversity of aquatic species have not yet been conducted.
A Strategy for Annotating the Human Milk Glycome (2006)

Oligosaccharides in human milk represent a group of bioactive molecules that have evolved to be an abundant and diverse component of human milk, even though they have no direct nutritive value to the infant. A recent hypothesis proposes that they could be substrates for the development of the intestinal microflora and the mucosal immune system. The inability to determine the exact composition of these oligosaccharides limits research and the ability to understand their biological functions. Oligosaccharides isolated from the lipids and proteins of individual human milk samples were analyzed by a combination of techniques including microchip liquid chromatography mass spectrometry (HPLC-Chip/MS) and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT ICR MS). Accurate mass measurements obtained using an orthogonal time-of-flight (o-TOF) mass spectrometry provided oligosaccharide composition for approximately 200 individual molecular species. Comparison of HPLC-Chip/MS profiles from five different women revealed variations in milk oligosaccharide compositions. HPLC-Chip/MS profiling provides a method for routinely identifying milk oligosaccharides. Tandem MS in combination with exoglycosidase digestion provides unambiguous differentiation of structural isomers.
Fiber-optic immunosensor for measurement of myoglobin (1997)

Abstract A self-contained fiber-optic immunosensor was developed to measure the 16 500-Da protein myoglobin. The sensing element was constructed by entrapment of Cascade Blue-labeled antibody within polyacrylamide gel at the distal face of an optical fiber 300 μm in core diameter. The polyacrylamide gel composition was optimized to allow diffusion of myoglobin but to exclude hemoglobin and higher-molecular-mass proteins from the sensing area. The analytical signal was derived from fluorescence energy transfer between Cascade Blue and the heme group of myoglobin. Fluorescence quenching occurred when myoglobin bound to labeled antibody. The total amount of fluorescence quench was dependent on the antibody labeling conditions and the amount of antibody incorporated in the sensor gel matrix. Myoglobin concentrations &amp;gt;5 nmol/L (83 μg/L) were measurable with response times of 15 to 130 min limited by diffusion into the sensing element. This report demonstrates the technical feasibility for a self-contained immunosensor to measure a protein analyte.
Visual detection of distant objects (2002)

Taking an autonomous road vehicle as an example, approaches and methods for object detection (this being the first step of obstacle recognition) are discussed. Vision, using a single passive camera as the primary sensor and a real-time vision system for analyzing the resulting image sequence, is found to be the best approach. Results obtained in real-world experiments with such a system are reported: large obstacles have been detected in distances up to 716 m; all relevant objects that were encountered during a prolonged test on a highway were detected; the cycle time of the detection process was below 100 ms, and less than one false alarm occurred per minute.
Selection of high‐producing CHO cells using NPT selection marker with reduced enzyme activity (2005)

We developed an expression system that aimed to increase the proportion of high producers in a transfected cell population in order to reduce the effort in clone screening. The principle is based on the impairment of the selection marker. Twelve single-point mutations in more or less conserved domains of the resistance marker gene neomycin-phosphotransferase (NPT) resulted in different degrees of reduced enzyme activity, depending on the amino acid conservation and the kind of amino acid exchange. In all transfected, mutant-NPT bearing CHO-DG44 cell pools surviving the selection with G418, the ratio of high-producing cells to total cell number was higher than in pools selected with wildtype-NPT. Furthermore, these pools showed, in comparison to wildtype-NPT selected pools, not only higher NPT-RNA levels but also increased specific productivities and higher titers of a coexpressed biopharmaceutically relevant product. Elevated productivity could be ascribed to higher gene copy numbers, integration into chromatin regions with higher transcriptional activity, or a combination of both effects. Thus, the use of NPT-mutants as selection markers is suitable for the enrichment of high producers in a transfected CHO-DG44 cell population, since cell survival is achieved only if the enzymatic impairment of the cointegrated resistance marker is compensated by a higher expression level.
Paralex: an environment for parallel programming in distributed systems. Interim report (1991)

Using protein AG in an enzyme-linked immunosorbent assay (ELISA), we tried to detect antibodies against parapoxvirus in 9 species of wild animals in Japan: the Japanese badger (Meles meles anakuma), Japanese black bear (Ursus thibetanus japonicus), Japanese deer (Cervus nippon centralis), Japanese monkey (Macaca fuscata), Japanese raccoon dog (Nyctereutes procyonoides viverrinus), Japanese serow (Capricornis crispus), Japanese wild boar (Sus scrofa leucomystax), masked palm civet (Paguma larvata), and nutria (Myocastor coypus). A total of 272 serum samples were collected over the period from 1984 to 1995 and were tested by the protein AG-ELISA, the agar gel immunodiffusion test, and an indirect immunofluorescence assay. The protein AG-ELISA was effective in a serological survey for parapoxvirus in wild animals, and antibodies were detected only in Japanese serows. A total of 24 of 66 (36.4%) Japanese serows reacted positively, and they were found in almost all prefectures in all years tested. These results suggest that epizootic cycles of parapoxvirus exist widely in Japanese serows and that they could be reservoirs for the virus in the field in Japan. Moreover, it is probable that they might carry the virus to domestic animals such as cattle, sheep, and goats.
The Behavioral Phenotype in Fragile X: Symptoms of Autism in Very Young Children with Fragile X Syndrome, Idiopathic Autism, and Other Developmental Disorders (2001)

This study was designed to explore the behavioral phenotype of autism in a group of young children with fragile X syndrome (FXS). Twenty-four children with FXS, ages 21 to 48 months, were compared with two well-matched groups: 27 children with autism (AD) and 23 children with other developmental delays (DD), on two standardized autism instruments, as well as on measures of development and adaptive behavior. Two FXS subgroups emerged. One subgroup (n = 16) did not meet study criteria for autism. Their profiles on the autism instruments and the developmental instruments were virtually identical to the other DD group. The other FXS subgroup (n = 8, or 33% of the total FXS group) met study criteria for autism. Their profiles on the autism instruments were virtually identical to the group with autism. The finding of two FXS subgroups raises a hypothesis of additional genetic influences in the FXS autism group, warranting further genetic studies.
Crystalline tungsten sulfide thin films by atomic layer deposition and mild annealing (2019)

Tungsten disulfide (WS2) is a semiconducting 2D material, which is gaining increasing attention in the wake of graphene and MoS2 owing to its exciting properties and promising performance in a multitude of applications. Herein, the authors deposited WSx thin films by atomic layer deposition using W2(NMe2)6 and H2S as precursors. The films deposited at 150 °C were amorphous and sulfur deficient. The amorphous films crystallized as WS2 by mild postdeposition annealing in H2S/N2 atmosphere at 400 °C. Detailed structural characterization using Raman spectroscopy, x-ray diffraction, and transmission electron microscopy revealed that the annealed films consisted of small (&amp;lt;10 nm) disordered grains. The approach proposed by the authors enables deposition of continuous and smooth WS2 films down to a thickness of a few monolayers while retaining a low thermal budget compatible with potential applications in electronics as well as energy production and storage, for example.
Summarizing Spatial Data Streams Using ClusterHulls (2006)

We consider the following problem: given an on-line, possibly unbounded stream of two-dimensional points, how can we summarize its spatial distribution or shape using a small, bounded amount of memory? We propose a novel scheme, called ClusterHull, which represents the shape of the stream as a dynamic collection of convex hulls, with a total of at most m vertices, where m is the size of the memory. The algorithm dynamically adjusts both the number of hulls and the number of vertices in each hull to best represent the stream using its fixed memory budget. This algorithm addresses a problem whose importance is increasingly recognized, namely the problem of summarizing real-time data streams to enable on-line analytical processing. As a motivating example, consider habitat monitoring using wireless sensor networks. The sensors produce a steady stream of geographic data, namely, the locations of objects being tracked. In order to conserve their limited resources (power, bandwidth, storage), the sensors can compute, store, and exchange ClusterHull summaries of their data, without losing important geometric information. We are not aware of other schemes specifically designed for capturing shape information in geometric data streams, and so we compare ClusterHull with some of the best general-purpose clustering schemes such as CURE, k-median, and LSEARCH. We show through experiments that ClusterHull is able to represent the shape of two-dimensional data streams more faithfully and flexibly than the stream versions of these clustering algorithms.