gebhart/patrepeval huggingface dataset:
Utilization of Metal-Organic Frameworks for the Management of Gases Used in Ion Implantation (2016)

Metal-Organic Frameworks (MOFs) are porous extended crystalline structures comprised of organic ligands and metal units. By changing the identity of the organic ligand and metal unit utilized in the MOF synthesis, the structure, surface area, pore size, and reactivity of the MOF can be modulated. This structural flexibility means that MOFs can potentially be used in a wide range of storage, separation, and catalytic applications. There is a high level of interest in the storage, delivery, capture, and purification of ultra high-purity hazardous gases used in electronics manufacturing (electronic gases). This paper will discuss the use of MOFs as an ideal platform for product and process innovation in the electronic gas sector.
The DNA methylation locus<i>DDM1</i> is required for maintenance of gene silencing in <i>Arabidopsis</i> (1998)

To investigate the relationship between cytosine methylation and gene silencing in Arabidopsis, we constructed strains containing the ddm1 hypomethylation mutation and a methylated and silenced PAI2 tryptophan biosynthetic gene (MePAI2) that results in a blue fluorescent plant phenotype. The ddm1 mutation had both an immediate and a progressive effect on PAI gene silencing. In the first generation, homozygous ddm1 MePAI2 plants displayed a weakly fluorescent phenotype, in contrast to the strongly fluorescent phenotype of the DDM1 MePAI2 parent. After two generations of inbreeding by self-pollination, the ddm1/ddm1 lines became nonfluorescent. The progressive loss of fluorescence correlated with a progressive loss of methylation from the PAI2 gene. These results indicate that methylation is necessary for maintenance of PAI gene silencing and that intermediate levels of DNA methylation are associated with intermediate gene silencing. The results also support our earlier hypothesis that ddm1 homozygotes act as "epigenetic mutators" by accumulating heritable changes in DNA methylation that can lead to changes in gene expression.
Müllerian inhibiting substance preferentially inhibits stem/progenitors in human ovarian cancer cell lines compared with chemotherapeutics (2010)

Cancer stem cells are proposed to be tumor-initiating cells capable of tumorigenesis, recurrence, metastasis, and drug resistance, and, like somatic stem cells, are thought to be capable of unlimited self-renewal and, when stimulated, proliferation and differentiation. Here we select cells by expression of a panel of markers to enrich for a population with stem cell-like characteristics. A panel of eight was initially selected from 95 human cell surface antigens as each was shared among human ovarian primary cancers, ovarian cancer cell lines, and normal fimbria. A total of 150 combinations of markers were reduced to a panel of three--CD44, CD24, and Epcam--which selected, in three ovarian cancer cell lines, those cells which best formed colonies. Cells expressing CD44, CD24, and Epcam exhibited stem cell characteristics of shorter tumor-free intervals in vivo after limiting dilution, and enhanced migration in invasion assays in vitro. Also, doxorubicin, cisplatin, and paclitaxel increased this enriched population which, conversely, was significantly inhibited by Müllerian inhibiting substance (MIS) or the MIS mimetic SP600125. These findings demonstrate that flow cytometry can be used to detect a population which shows differential drug sensitivity, and imply that treatment of patients can be individualized to target both stem/progenitor cell enriched and nonenriched subpopulations. The findings also suggest that this population, amenable to isolation by flow cytometry, can be used to screen for novel treatment paradigms, including biologic agents such as MIS, which will improve outcomes for patients with ovarian cancer.
Gaussian Conditional Random Field Network for Semantic Segmentation (2016)

In contrast to the existing approaches that use discrete Conditional Random Field (CRF) models, we propose to use a Gaussian CRF model for the task of semantic segmentation. We propose a novel deep network, which we refer to as Gaussian Mean Field (GMF) network, whose layers perform mean field inference over a Gaussian CRF. The proposed GMF network has the desired property that each of its layers produces an output that is closer to the maximum a posteriori solution of the Gaussian CRF compared to its input. By combining the proposed GMF network with deep Convolutional Neural Networks (CNNs), we propose a new end-to-end trainable Gaussian conditional random field network. The proposed Gaussian CRF network is composed of three sub-networks: (i) a CNN-based unary network for generating unary potentials, (ii) a CNN-based pairwise network for generating pairwise potentials, and (iii) a GMF network for performing Gaussian CRF inference. When trained end-to-end in a discriminative fashion, and evaluated on the challenging PASCALVOC 2012 segmentation dataset, the proposed Gaussian CRF network outperforms various recent semantic segmentation approaches that combine CNNs with discrete CRF models.
Fabry-Perot Interferometer Spectral Engines for Imaging Applications (2013)

Fabry-Perot Interferometers are powerful tools for many spectroscopic measurements. This paper presents their utilization in modern miniaturized spectral imaging systems. Several realized devices are introsuced and measurements results presented.
Total Syntheses of Vancomycin-Related Glycopeptide Antibiotics and Key Analogues (2017)

A review of efforts that have provided total syntheses of vancomycin and related glycopeptide antibiotics, their agylcons, and key analogues is provided. It is a tribute to developments in organic chemistry and the field of organic synthesis that not only can molecules of this complexity be prepared today by total synthesis but such efforts can be extended to the preparation of previously inaccessible key analogues that contain deep-seated structural changes. With the increasing prevalence of acquired bacterial resistance to existing classes of antibiotics and with the emergence of vancomycin-resistant pathogens (VRSA and VRE), the studies pave the way for the examination of synthetic analogues rationally designed to not only overcome vancomycin resistance but provide the foundation for the development of even more powerful and durable antibiotics.
Engineered nanointerfaces for microfluidic isolation and molecular profiling of tumor-specific extracellular vesicles (2018)

Extracellular vesicles (EVs) carry RNA, DNA, proteins, and lipids. Specifically, tumor-derived EVs have the potential to be utilized as disease-specific biomarkers. However, a lack of methods to isolate tumor-specific EVs has limited their use in clinical settings. Here we report a sensitive analytical microfluidic platform (<sup>EV</sup>HB-Chip) that enables tumor-specific EV-RNA isolation within 3 h. Using the <sup>EV</sup>HB-Chip, we achieve 94% tumor-EV specificity, a limit of detection of 100 EVs per μL, and a 10-fold increase in tumor RNA enrichment in comparison to other methods. Our approach allows for the subsequent release of captured tumor EVs, enabling downstream characterization and functional studies. Processing serum and plasma samples from glioblastoma multiforme (GBM) patients, we can detect the mutant EGFRvIII mRNA. Moreover, using next-generation RNA sequencing, we identify genes specific to GBM as well as transcripts that are hallmarks for the four genetic subtypes of the disease.
Microfluidic Sorting System Based on Waveguide Integration and Diode Laser Bar Trapping (2006)

We demonstrate integrated optical particle sorting in microfluidic structures. Fluorescent particles are excited using an integrated waveguide network and manipulated with a diode laser bar trapping scheme that sorts based upon their fluorescence.
Dim ultraviolet light as a means of deterring activity by the Hawaiian hoary bat Lasiurus cinereus semotus (2015)

Widespread bat fatalities at industrial wind turbines are a conservation issue with the potential to inhibit efficient use of an abundant source of energy. Bat fatalities can be reduced by altering turbine operations, but such curtailment decreases turbine efficiency. If additional ways of reducing bat fatalities at wind turbines were available such tradeoffs might not be needed. Based on the facts that bats perceive distant objects primarily through vision and can see in very dim lighting conditions, and the possibility that bats might interact with turbines after approaching them as they would trees, we propose a novel method of reducing bat activity at wind turbines: illumination of the structure with dim light. As a first step toward assessing this approach, we illuminated trees with dim flickering ultraviolet (UV) light in areas frequented by Hawaiian hoary bats Lasiurus cinereus semotus, an endangered subspecies affected by wind turbines. We used a repeated-measures design to quantify bat activity near trees with acoustic detectors and thermal video cameras in the presence and absence of UV illumination, while concurrently monitoring insect numbers. Results indicate that dim UV reduces bat activity despite an increase in insect numbers. Experimental treatment did not completely inhibit bat activity near trees, nor did all measures of bat activity show statistically significant differences due to high variance in bat activity among sites. However, the observed decreases in bat activity with dim UV illumination justify further testing of this method as a means to reduce bat fatalities at wind turbines.
Effects of an Antioxidant-enriched Multivitamin in Cystic Fibrosis. A Randomized, Controlled, Multicenter Clinical Trial (2018)

Antioxidant supplementation was safe and well tolerated, resulting in increased systemic antioxidant concentrations and modest reductions in systemic inflammation after 4 weeks. Antioxidant treatment was also associated with a lower risk of first pulmonary exacerbation. Clinical trial registered with www.clinicaltrials.gov (NCT01859390).
Synthesis and characterization of polyimides containing 4,4'-hexafluoroisopropylidene-bisphthalic (1999)

This paper presents the synthesis and characterization of polyimides, which contain a 4,4'-hexafluoroisopropylidene-bisphthalic anhydride (6FDA) unit in the backbone. These polyimides are a result of the use of the traditional method of "one step". The reactions occur between equimolar of a dianhydride and an aromatic diamine in presence of the solvent dimethylacetamide (DMAc), then cyclo-dehydrided by adding the acetic anhydride and pyridine. In this work, the 6FDA was used as the dianhydride and four different diamines were investigated: 3,3',5,5'-Tetramethyl-2,2- bis[4-( 4-aminophenoxy) phenyl] propane; 2,2-bis[4-(4-aminophenoxy)-phenyl] hexafluoropropane; 1,3-bis(4-aminophenoxy)benzene and 2,2'-dimethyl-4,4'-bis(4-aminophenoxy)biphenyl. The four polyimides (PA, PB, PC and PD) were characterized by tensile strength, infrared, inherent viscosity, Differential Scanning Calorimeter (DSC) to get the glassy transition temperature (Tg) and Gel Permeation Chromatograph (GPC) to obtain the average molecular weight (Mn).
Strongly nondegenerate parametric oscillations in a whispering gallery mode resonator (2007)

We demonstrate optical continuous wave parametric oscillations in crystalline whispering gallery mode (WGM) resonators fabricated with LiNb03. The required phase matching is achieved by geometrical confinement of the WGMs.
Endoplasmic Reticulum Chaperone GRP94 Subunit Assembly Is Regulated through a Defined Oligomerization Domain (1996)

GRP94 is an abundant, resident glycoprotein of the mammalian endoplasmic reticulum lumen and member of the hsp90 family of molecular chaperones. To identify the structure/function relationships which define the molecular basis of GRP94 activity, we have performed a structural analysis of native GRP94 and identified a discrete domain, representing amino acids 676-719, which regulates dimerization and displays autonomous oligomerization activity. Velocity sedimentation and gel filtration chromatography were used to identify native GRP94 as a dimer with an extended, rod-like shape. Limited proteolysis resulted in the loss of approximately 16 kDa from the C-terminus and disassembly into monomers, implicating the C-terminus as the site of assembly. An assembly function for the C-terminal domain was established by analysis of the quaternary structure of C-terminal constructs synthesized either in vitro or through recombinant expression. In vitro translation was used to demonstrate that a C-terminal 20 kDa domain was both necessary and sufficient for dimerization. Structural studies of recombinant fusion protein constructs yielded identification of a 44 amino acid domain that displayed autonomous dimerization activity and conferred a highly elongated structure, characteristic of native GRP94, to the fusion protein. These data, combined with molecular dimensions obtained from rotary shadowing electron microscopy, provide a structural model of GRP94 and identify the molecular basis of GRP94 self-assembly.
Peripheral markers of brain damage and blood-brain barrier dysfunction (2003)

Thus, S100beta in serum is an early marker of BBB openings that may precede neuronal damage and may influence therapeutic strategies. Secondary, massive elevations in S100beta are indicators of prior brain damage and bear clinical significance as predictors of poor outcome or diagnostic means to differentiate extensive damage from minor, transient impairment.
Intraluminal ultrasonic probe for volumetric monitoring of liquid gastroesophageal reflux (2012)

Methods for volumetric monitoring of liquid gastroesophageal reflux (GER) are still lacking. The aim of this study was to develop an automated intraluminal measurement technique which allows ambulatory volumetric quantification of liquid GER utilizing a minimum-cost intraluminal ultrasonic probe. This probe consists of two 2 MHz ultrasonic crystals longitudinally assembled along a multi-channel intraluminal impedance (MII) catheter. The proposed probe was initially tested with tubular phantoms of different diameters. Measurements of the cross-sectional areas of the phantoms showed high correlation with the actual areas (R(2) = 0.99). Subsequently, two in-vivo human tests were performed. For each human test the catheter assembly was inserted transnasally and the ultrasonic probe was placed in the area of the lower esophageal sphincter. Multiple liquid swallows of different volumes were invoked using electrolyte drinks. Sectional luminal volume (SLV) in the esophagus between the two ultrasonic crystals was obtained. Results of the swallows demonstrated that measured SLVs correlated with the actual swallowed liquid volume. The ultrasonic probe was combined with a MII catheter to discriminate between antegrade and retrograde bolus transit. Increases of SLVs during liquid GER episodes could be utilized to evaluate GER volume in the vicinity of the ultrasonic probe.
Low Cost and Highly Reactive Biobased Polyols: A Co‐Product of the Emerging Biorefinery Economy (2008)

Abstract Over several billion pounds of petroleum‐derived polyols are consumed in the U.S. annually in many polyurethane applications, e. g., foams, coatings and adhesives. There is an increasing need and interest to develop alternate polyols based on renewable, resource‐based raw materials that offer reduced price volatility with a more favorable environmental footprint compared to current petroleum‐derived polyols. A novel process is developed for the economical production of high quality biobased polyols by the ozonolysis of mixtures of vegetable oils, e. g., soybean oil and primary polyols such as glycerin. High performance coatings and both rigid and flexible foams have been prepared from these polyols.
Partitioning the feature space of a classifier with linear hyperplanes (1999)

We describe the design and use of linear hyperplanes to partition the feature space of a classifier. The objective of the partitioning is to minimize the average entropy of the class distribution in the final partitions. The hyperplanes are characterized by a vector /spl nu//sub n/ and scalar h/sub n/, which are computed with the objective of maximizing the mutual information associated with the partitioning. We show that the problem of designing the /spl nu//sub n/ can be simplified to an approximately equivalent problem, the solution of which, interestingly enough, turns out to be the linear discriminant of the data. We also describe a decision-tree based technique that partitions the feature space in a hierarchical fashion where each node in the decision tree represents a linear hyperplane that further partitions the feature space into two regions. The end result of the tree-growing process is that the entire feature space is partitioned into nonoverlapping regions where each region is bounded by a number of hyperplanes. As the criterion for the design of the hyperplanes is the minimization of the average class entropy of the regions, each region is characterized by the occurrence of only a small number of classes. The partitioning information provided by the decision-tree can then be used to eliminate a number of classes from being considered, and hence simplifies the job of the classifier. We show the application of the decision-tree as a preprocessor to a classifier in the speech recognition problem. Here the classes are modeled with mixtures of tens to hundreds of thousands of Gaussians, and the use of the partitioning information reduces the computation associated with the classification process by factors larger than 20 with negligible degradation in the word error rate (note, however, that the overall decoding process comprises other steps in addition to the classification-the computational speedup mentioned above does not affect the computation of these other steps). We also compare the performance of this quantization scheme with standard Gaussian clustering schemes and show that the decision-tree based quantization provides better performance in most cases.
An Antiviral Sesquiterpene Hydroquinone from the Marine Sponge Strongylophora hartmani (1991)

A new sesquiterpene hydroquinone 1, which we call strongylin A, was isolated from the marine sponge Strongylophora hartmani. Its structure was determined through spectroscopic methods, including 2D-13C homonuclear correlation spectroscopy (INADEQUATE). Both 1 and its acetate derivative are active in in vitro assays against the P-388 tumor cell line and influenza strain PR-8.
An Automated Learning-Based Procedure for Large-scale Vehicle Dynamics Modeling on Baidu Apollo Platform (2019)

In the autonomous driving industry, vehicle dynamic models are important to control-in-the-loop simulations. For current commercial self-driving simulators, vehicle dynamic models are expressed explicitly by sophisticated analytical equations, which are accurate but difficult to build and expensive to scale to fleets of vehicles of different brands. In this paper, we introduce a highly automated learning-based vehicle dynamic modeling procedure, which has been deployed on Baidu Apollo self-driving platform, to support cross-vehicle data-driven applications on a large scale. Compared with our previous analytical models, the end-to-end learning-based dynamic models can achieve high accuracy with significantly reduced re-development effort.
Alpha model based mixed pixel processing for view synthesis (2010)

The commercial success and acceptability of 3D technology will critically depend on the overall visual quality of the rendered images. Therefore, view synthesis techniques like Depth Image Based Rendering (DIBR) are crucial components of the 3D system chain. In this paper, we propose a fast α-model based approach that enables high quality DIBR. Given an image and depth map, a point based representation of the scene is obtained, where each point is associated with color, transparency and depth. A low complexity method estimates these attributes, making the system suitable for deployment in consumer electronics.
New Alleles in the “RN gene” Associated with Low Glycogen Content in Pig Skeletal Muscle and Improved Meat Quality (2002)

Several quantitative trait loci (QTL) affecting muscle glycogen content and related meat quality traits were mapped to pig chromosome 15 (SSC 15) by using a three-generation intercross between Berkshire x Yorkshire pigs. Based on the QTL location, the PRKAG3 (protein kinase AMPactivated, γ3 subunit) or the RN (Rendement Napole) gene, as it is popularly known, was considered to be a good candidate for the observed effects. Differences in the PRKAG3 gene sequences of the founder animals of the intercross were analyzed. The RN- mutation previously reported was not present in the cross but three missense substitutions (changes affecting proteins) were identified. To test the hypothesis that at least one of these mutations was associated with differences in meat quality, more than 1,800 animals from several unrelated commercial lines were genotyped for the candidate gene differences and an association study was performed. The results provide strong support for the presence of new economically important alleles (gene forms) of the PRKAG3 gene affecting the glycogen content in the muscle and the resulting meat quality. Because of their prevalence in the more common commercial breeds, the potential implications for the pig industry and consumers are probably more important than the original discovery of the RN- mutation.
Boron nitride nanotube: synthesis and applications (2014)

Scientists have predicted that carbon’s immediate neighbors on the periodic chart, boron and nitrogen, may also form perfect nanotubes, since the advent of carbon nanotubes (CNTs) in 1991. First proposed then synthesized by researchers at UC Berkeley in the mid 1990’s, the boron nitride nanotube (BNNT) has proven very difficult to make until now. Herein we provide an update on a catalyst-free method for synthesizing highly crystalline, small diameter BNNTs with a high aspect ratio using a high power laser under a high pressure and high temperature environment first discovered jointly by NASA/NIA/JSA. Progress in purification methods, dispersion studies, BNNT mat and composite formation, and modeling and diagnostics will also be presented. The white BNNTs offer extraordinary properties including neutron radiation shielding, piezoelectricity, thermal oxidative stability (> 800°C in air), mechanical strength, and toughness. The characteristics of the novel BNNTs and BNNT polymer composites and their potential applications are discussed.
Study of feline leukemia virus immunity (1991)

Fifteen specific-pathogen-free cats were experimentally infected with FeLV; 8 cats recovered after transient or nondetectable viremia, and 7 cats became persistently viremic. Four additional cats served as noninfected controls. Antibodies to whole FeLV (ELISA and immunoblot [western] analysis), antibodies to fixed FeLV-infected cells, and virus-neutralizing antibodies were monitored for as long as 3 years after infection. As a group, cats that recovered after acute infection developed higher titer of these various antibodies than did cats that became persistently viremic. However, specific combination or titer of antibodies was not always found in recovered cats or in persistently viremic cats. Six cats that had recovered from acute FeLV infection nearly 3 years earlier were reinfected with the same virus. Three of the cats appeared to be resistant to reinfection, 2 cats became transiently viremic, and 1 cat became persistently viremic. Slight and transient anamnestic ELISA-detectable antibody response to whole virus was seen after reinfection; immunofluorescence- and western blot-detectable responses were not greatly enhanced. Five FeLV-recovered cats were monitored for 2 years; FeLV infection spontaneously recurred in 1 cat.