gebhart/patrepeval huggingface dataset:
Furfural to 1,4‐Butanediol/Tetrahydrofuran – A Detailed Catalyst and Process Design (2020)

The feasibility to convert furan, a direct derivative of furfural, to a mixture of 1,4-butanediol (BDO) and tetrahydrofuran (THF) is demonstrated with industrially acceptable performances using mm-sized pellets of a carbon-supported RePd catalyst for 2000 h of operation. The reaction schemes were unraveled by spiking potential reaction intermediates and a full kinetic model was developed. Finally, we developed a comprehensive process flow scheme that integrates the conversion of furfural to furan, the recovery and purification of furan, its reductive hydration to BDO/THF as well as the recovery and purification of BDO and THF. This process concept appears economically viable at current furfural, BDO and THF market prices.
An Automated Microfluidic Multiplexer for Fast Delivery of C. elegans Populations from Multiwells (2013)

Automated biosorter platforms, including recently developed microfluidic devices, enable and accelerate highthroughput and/or high-resolution bioassays on small animal models. However, time-consuming delivery of different organism populations to these systems introduces a major bottleneck to executing large-scale screens. Current population delivery strategies rely on suction from conventional well plates through tubing periodically exposed to air, leading to certain disadvantages: 1) bubble introduction to the sample, interfering with analysis in the downstream system, 2) substantial time drain from added bubble-cleaning steps, and 3) the need for complex mechanical systems to manipulate well plate position. To address these concerns, we developed a multiwell-format microfluidic platform that can deliver multiple distinct animal populations from on-chip wells using multiplexed valve control. This Population Delivery Chip could operate autonomously as part of a relatively simple setup that did not require any of the major mechanical moving parts typical of plate-handling systems to address a given well. We demonstrated automatic serial delivery of 16 distinct C. elegans worm populations to a single outlet without introducing any bubbles to the samples, causing cross-contamination, or damaging the animals. The device achieved delivery of more than 90% of the population preloaded into a given well in 4.7 seconds; an order of magnitude faster than delivery modalities in current use. This platform could potentially handle other similarly sized model organisms, such as zebrafish and drosophila larvae or cellular micro-colonies. The device's architecture and microchannel dimensions allow simple expansion for processing larger numbers of populations.
New markers for minimal residual disease detection in acute lymphoblastic leukemia (2011)

To identify new markers for minimal residual disease (MRD) detection in acute lymphoblastic leukemia (ALL), we compared genome-wide gene expression of lymphoblasts from 270 patients with newly diagnosed childhood ALL to that of normal CD19⁺CD10⁺ B-cell progenitors (n = 4). Expression of 30 genes differentially expressed by ≥ 3-fold in at least 25% of cases of ALL (or 40% of ALL subtypes) was tested by flow cytometry in 200 B-lineage ALL and 61 nonleukemic BM samples, including samples containing hematogones. Of the 30 markers, 22 (CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, CD49f) were differentially expressed in up to 81.4% of ALL cases; expression of some markers was associated with the presence of genetic abnormalities. Results of MRD detection by flow cytometry with these markers correlated well with those of molecular testing (52 follow-up samples from 18 patients); sequential studies during treatment and diagnosis-relapse comparisons documented their stability. When incorporated in 6-marker combinations, the new markers afforded the detection of 1 leukemic cell among 10(5) BM cells. These new markers should allow MRD studies in all B-lineage ALL patients, and substantially improve their sensitivity.
Human bone sialoprotein. Deduced protein sequence and chromosomal localization. (1990)

A cDNA encoding the human bone sialoprotein was isolated from a lambda Zap expression library (made from cultured human bone cell poly(A)+ RNA) using radiolabeled rat bone sialoprotein cDNA (Oldberg, A., and Heinegard, D. (1988) J. Biol. Chem. 263, 19430-19432) as a probe. A 5' 1-kilobase EcoRI fragment of the purified 3-kilobase clone was sequenced and found to contain the entire protein-encoding region. The deduced protein sequence revealed a 317-amino acid protein (34,982 Da) containing a 16-amino acid hydrophobic signal sequence and a 33,352-Da protein destined to undergo extensive post-translational modifications before being secreted from the cell. A comparison of the human and rat protein sequences showed extensive (greater than 70%) amino acid identities including the Arg-Gly-Asp (RGD) tripeptide thought to confer the cell attachment activity observed previously for this protein. Also conserved were three regions rich in acidic amino acids and three regions rich in tyrosine. While all three tyrosine-rich regions appear to be composed of a nominal repeat structure, only the two carboxyl-terminal regions that flank the RGD sequence fit all three of the requirements for extensive tyrosine sulfation. Interestingly, human bone sialoprotein, whose final secreted product is approximately 50% carbohydrate, contains no cystines. Northern analysis showed that while bone cells are the major source of bone sialoprotein message production, other tissues may contain trace amounts of this message. Southern hybridization of DNA from human-rodent somatic cell hybrids that have segregated human chromosomes indicated that the gene is located on human chromosome 4. The human bone sialoprotein gene is a single copy gene unlikely to exceed 11.1 kilobases in length. No restriction fragment length polymorphisms were observed with 12 different restriction enzymes in 10 normal individuals.
Camera tracking for augmented reality media (2002)

The paper presents a camera tracking system for the spatial stabilization of augmented reality (AR) media. Our approach integrates both artificial landmarks (fiducials) and natural features for camera tracking. Artificial landmarks are used for system initialization and computation of initial camera pose. Robust and extendible tracking is achieved by dynamically calibrating the 3D positions of a priori uncalibrated natural features. Analysis and experimental results demonstrate the effectiveness of this approach for presenting stabilized AR media in long camera-motion video sequences.
Improved Surface Layer Wind Modeling for Autonomous Parafoils in a Maritime Environment (2011)

This paper investigates the use of atmospheric boundary layer theory to produce more accurate wind estimates for guiding an autonomous parafoil during the last portion of its flight before touchdown. The problem of wind estimation for a prototype autonomous parafoil aerial delivery system is first explained, followed by the simple assumptions for wind estimation that its guidance algorithm makes. A logarithmic wind profile model in the atmospheric surface layer is then introduced. The parameters and limitations of this model are discussed, along with the characteristics of this model that make it especially useful over the surface of the ocean. Finally, the incorporation of this model into the guidance algorithm of the prototype aerial delivery system is discussed, and subsequently evaluated in flight tests against the original algorithm that did not include the logarithmic surface layer wind model.
Water‐soluble C60 fullerene prevents degeneration of articular cartilage in osteoarthritis via down‐regulation of chondrocyte catabolic activity and inhibition of cartilage degeneration during disease development (2007)

The results indicate that C60 fullerene is a potential therapeutic agent for the protection of articular cartilage against progression of OA.
The Tübingen approach: identification, selection and validation of tumor-associated HLA peptides for cancer therapy (2004)

There is substantial need for molecularly defined tumor antigens to prime cytotoxic T cells in vivo for cancer immunotherapy, especially in the case of tumor entities for which only a few tumor antigens have been defined so far. In this review, we present the “Tubingen approach” to identify, select, and validate large numbers of MHC/HLA class I–associated peptides derived from tumor-associated antigens. Step 1 is the identification of naturally presented HLA-associated peptides directly from primary tumor cells. Step 2 is selection of tumor-associated peptides from step 1 by differential gene expression analysis and data mining. Step 3 is validation of selected candidates by monitoring in vivo T-cell responses in the context of patient-individualized immunizations. Our approach combines methods from genomics, proteomics, bioinformatics, and T-cell immunology. The aim is to develop effective immunotherapeutics consisting of multiple tumor-associated epitopes in order to induce a broad and specific immune response against cancer cells.
Privacy-Preserving Outlier Detection for Data Streams (2017)

In cyber-physical systems sensors data should be anonymized at the source. Local data perturbation with differential privacy guarantees can be used, but the resulting utility is often (too) low. In this paper we contribute an algorithm that combines local, differentially private data perturbation of sensor streams with highly accurate outlier detection. We evaluate our algorithm on synthetic data. In our experiments we obtain an accuracy of 80% with a differential privacy value of $$\epsilon = 0.1$$ for well separated outliers.
Quantitative phase analysis using observed integrated intensities and chemical composition data of individual crystalline phases: quantification of materials with indefinite chemical compositions (2017)

In a previous report, a new method for quantitative phase analysis (QPA) of multi-component mixtures using a conventional X-ray powder diffractometer was proposed. The formula for deriving weight fractions of individual crystalline phases presented therein includes sets of observed integrated intensities measured in a wide 2\theta range, chemical formula weights and sums of squared numbers of electrons belonging to atoms in respective chemical formula units [Toraya (2016). J. Appl. Cryst . 49 , 1508–1516]. The latter two parameters required to perform QPA could be calculated from only the information of chemical formulae of individual phases. In the present study, these two parameters are replaced with a single parameter in the form new parameter = (chemical formula weight)/(sum of squared numbers of electrons). As will be expected from this definition, the parameter has nearly equal values for groups of materials consisting of similar kinds of atoms, and its value becomes identical for polytypes or polymorphs having the same chemical composition. That characteristic of this parameter makes it possible to estimate the parameter value not only directly from the chemical composition of the target material itself but also from database-stored chemical analysis data sorted on the basis of mineral or chemical composition. The parameter value is also hardly changed as a result of small compositional variations of the target component material. Therefore, the present method can be applied to QPA of materials not only of definite chemical compositions but also of indefinite chemical compositions without degrading the accuracy of the analysis. This is expected to widen the application to QPA of, for example, natural products containing many kinds of trace elements, industrial materials with complex substitutional replacement of atoms, nonstoichiometric compounds etc . The theory and some examples of applications are presented. A procedure for quantifying unknown material is also proposed.
Probing Structure-Property Relationships in a Family of Aryloxyphenoxy Propionate Herbicides Using Single Crystal X-Ray Diffraction Techniques (1991)

Aryloxyphenoxy propionates are a widely manufactured class of highly active grass-selective herbicides for use in various crops. Examples include VERDICT (1a), FUSILADE (1b), WHIP (1c), and ASSURE (1d). Figure 1 shows the general structure of aryloxyphenoxy propionates. All of these compounds contain a chiral center and each enantiomer of the optical pair exhibits significantly different herbicidal activity. The optically active isomers can be prepared by reacting the corresponding substituted phenoxyphenol with the S-(-)methyl lactate sulfonate ester (2). However, the optical yield from this type of reaction is usually less than 85%. Optical purification can be achieved by control of the crystallization.
Fabrication of Anisotropic Super Hydrophobic/Hydrophilic Nanoporous Membranes by Plasma Polymerization of C[sub 4]F[sub 8] on Anodic Aluminum Oxide (2004)

Freestanding anodic aluminum oxide (AAO) membranes were fabricated using a two-step anodization procedure, voltage reduction method, and inductively coupled plasma polymerization. The fabrication process was monitored with electrochemical and spectroscopic ellipsometry measurements, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and scanning electron microscopy. Static contact angle measurements demonstrated that the two surfaces of the fabricated AAO membranes have dramatically different degrees of hydrophobicity. The contact angle of water on the side modified with the fluorocarbon film was 150°, whereas the contact angle on the hydrophilic side, which was initially attached to the aluminum substrate, was less than 5°. The fabricated freestanding AAO membranes with only one hydrophobic surface are expected to find applications in the design of new systems for separation and filtration and as gas and liquid transport devices such as gas-diffusion electrodes for miniature power sources and sensors. © 2004 The Electrochemical Society. All rights reserved.
Automatically organizing digital photographs using time and content (2004)

We present similarity-based methods to cluster digital photos by time and image content. This approach is general, unsupervised, and makes minimal assumptions regarding the structure or statistics of the photo collection. We describe versions of the algorithm using temporal similarity with and without content-based similarity, and compare the algorithms with existing techniques, measured against ground-truth clusters created by humans.
A New Tooth Finishing Method with CBN Abrasive Wheel for Involute Internal Spline. Improvement of Tooth Accuracy with Slant Traverse Feeding. (1997)

To improve shift feeling is required for automobile transmission parts. For this purpose, it is important to increase an accuracy of involute spline. That is to make profile modifications for a pair of teeth in mesh and to improve roughness as well. Although a technique to use honing is effective for the above requirements, it has not been sufficiently studied. A new tooth finishing experiment with CBN abrasive wheel for the involute internal spline is made. It is clear that the best tooth accuracy can be obtained by the slant traverse feeding, reducing a speed ratio between revolutions and feed. Maximum finishing roughness is improved approximately by half to compare with that of before honing, until now. With a speed ratio of ψ=1, roughness is obtained at 4.8 μmRz in tooth profile direction and at 0.8 μmRz in tooth lead direction. At a revolution load torque of 3 N·m and a machining time of 20 seconds, chips are smoothly exhausted and honing is effective. In conclusion, it is now clear why the proper tooth accuracy and roughness can be obtained.
Evaluation of Truncated NhhA Protein as a Candidate Meningococcal Vaccine Antigen (2013)

NhhA (Neisseria hia homologue) is an outer membrane protein from Neisseria meningitidis, the causative agent of meningococcal disease. The protein is surface exposed and its expression in a wide range of meningococcal strains suggests it is a promising vaccine candidate. In addition, immunization of mice with outer membrane vesicles of strains that overexpress NhhA in conjunction with one of TbpA, Omp85 or NspA results in synergistic bactericidal responses. We previously showed that the NhhA sequence is highly conserved between strains, with the majority of the differences localized to four distinct variable regions located in the amino-terminal region of the mature protein. In this study, N. meningitidis strains were constructed that over-express wild-type NhhA. Strains expressing truncated versions of NhhA, with deletions from the amino-terminal region that removed the most variable regions, were also made. These expression strains were also modified so that immunodominant, phase- and antigenically-variable outer membrane proteins were not expressed, truncated lipooligosaccharide (LOS) expression was genetically fixed (no phase variability), and capsular polysaccharide expression abolished. Outer membrane vesicles derived from these strains were used to immunize mice. As previously observed, a synergistic effect involving another antigen, TbpA, was required to demonstrate bactericidal activity. The highest bactericidal response against a heterologous strain was obtained with a truncated variant of NhhA. These results indicate that removal of (a) variable region(s) does not reduce bactericidal responses against NhhA, and that bactericidal targets exist in regions other than the variable N-teminus. This provides the basis for future examination of responses against truncated NhhA in protecting against heterologous NhhA strains, and further evaluation of truncated NhhA as a candidate for inclusion in a vaccine against all serogroups of N. meningitidis.
Treatment of Murine Colitis by <i>Lactococcus lactis</i> Secreting Interleukin-10 (2000)

The cytokine interleukin-10 (IL-10) has shown promise in clinical trials for treatment of inflammatory bowel disease (IBD). Using two mouse models, we show that the therapeutic dose of IL-10 can be reduced by localized delivery of a bacterium genetically engineered to secrete the cytokine. Intragastric administration of IL-10-secreting Lactococcus lactis caused a 50% reduction in colitis in mice treated with dextran sulfate sodium and prevented the onset of colitis in IL-10(-/-) mice. This approach may lead to better methods for cost-effective and long-term management of IBD in humans.
Norton Equivalent Circuit for Pulsed Photoconductive Antennas–Part I: Theoretical Model (2018)

A novel equivalent circuit for pulsed photoconductive sources is introduced for describing the coupling between the photoconductive gap and the antenna. The proposed circuit effectively describes the mechanism of feeding the antenna by the semiconductor when this latter is illuminated by a laser operating in a pulsed mode. Starting from the classical continuity equation, which models the free carriers' density with respect to the laser power pump and the semiconductor features, a Norton equivalent circuit in the frequency domain is derived. According to the Norton theorem, the equivalent source representation is decoupled from the antenna. In particular, for photoconductive antennas (PCAs), the Norton circuit takes into account of the electrical and optical properties of the semiconductor material, the features of the laser excitation, as well as the geometrical dimensions of the gap. The presence of the electrodes around the gap is part of the antenna and, therefore, it is taken into account in the antenna impedance. The proposed circuit allows the analysis of the coupling between the photoconductive source and the antenna, providing a tool to analyze and design PCAs.
La<sub>2</sub>Zr<sub>2</sub>O<sub>7</sub> Nanoparticle-Mediated Synthesis of Porous Al-Doped Li<sub>7</sub>La<sub>3</sub>Zr<sub>2</sub>O<sub>12</sub> Garnet (2021)

In this work, we modified the reaction pathway to quickly (minutes) incorporate lithium and stabilize the ionic conducting garnet phase by decoupling the formation of a La-Zr-O network from the addition of lithium. To do this, we synthesized La<sub>2</sub>Zr<sub>2</sub>O<sub>7</sub> (LZO) nanoparticles to which LiNO<sub>3</sub> was added. This method is a departure from typical solid-state synthesis methods that require high-energy milling to promote mixing and intimate particle-particle contact and from sol-gel syntheses as a unique porous microstructure is obtained. We show that the reaction time is limited by the rate of nitrate decomposition and that this method produces a porous high-Li-ion-conducting cubic phase, within an hour, that may be used as a starting structure for a composite electrolyte.
Visualizing myocardial function using HARP MRI (2000)

Harmonic phase magnetic resonance imaging (HARP) is a new technique for measuring the motion of the left ventricle of the heart. HARP uses magnetic resonance tagging, Fourier filtering and special processing algorithms to calculate key indices of myocardial motion including Eulerian and Lagrangian strain. This paper presents several new methods for visualizing myocardial motion based on HARP. Quantities that are computed and visualized include motion grids, velocity fields, strain rates, pathlines, tracked Eulerian strain, and contraction angle. The computations are fast and fully automated and have the potential for clinical application.
Aptasensor for diabetes mellitus detection and monitoring (2015)

DNA aptamers against GHSA, which is protein marker for diabetes mellitus, were selected and modified. In combination properties of modified GHSA binding aptamer and fluorescence quenching of GO, we develop simple and sensitive platform for detection of GHSA in both PBS and human serum with the LOD of 50 μg/mL. We envision that our GO-aptamer platform has a potential to be GHSA detection for screening and monitoring diabetes mellitus.
Inhibiting the Initiation of<i>Clostridium difficile</i>Spore Germination using Analogs of Chenodeoxycholic Acid, a Bile Acid (2010)

To cause disease, Clostridium difficile spores must germinate in the host gastrointestinal tract. Germination is initiated upon exposure to glycine and certain bile acids, e.g., taurocholate. Chenodeoxycholate, another bile acid, inhibits taurocholate-mediated germination. By applying Michaelis-Menten kinetic analysis to C. difficile spore germination, we found that chenodeoxycholate is a competitive inhibitor of taurocholate-mediated germination and appears to interact with the spores with greater apparent affinity than does taurocholate. We also report that several analogs of chenodeoxycholate are even more effective inhibitors. Some of these compounds resist 7α-dehydroxylation by Clostridium scindens, a core member of the normal human colonic microbiota, suggesting that they are more stable than chenodeoxycholate in the colonic environment.