gebhart/patrepeval huggingface dataset:
Formulation and Simulation of a 3D Mechanical Model of Embryos for Microinjection (2013)

The understanding of cell manipulation, for example in microinjection, requires an accurate model of the cells. Motivated by this important requirement, a 3D particle-based mechanical model is derived for simulating the deformation of the fish egg membrane and the corresponding cellular forces during micro robotic cell injection. The model is formulated based on the kinematic and dynamic of spring-damper configuration with multi-particle joints considering the visco-elastic fluidic properties. It simulates the indentation force feedback as well as cell visual deformation during microinjection. A preliminary simulation study is conducted with different parameter configurations. The results indicate that the proposed particle-based model is able to provide similar deformation profiles as observed from a real microinjection experiment of the zebra fish embryo published in the literature. As a generic modelling approach is adopted, the proposed model also has the potential in applications with different types of manipulation such as micropipette cell aspiration.
Development of a technique for the in vivo assessment of flatulence in dogs (2001)

The technique described in this report appears to provide sensitive, reliable, and relevant data and will enable further studies of the factors that influence flatulence in dogs. Use of this technique also has the potential to aid in investigations of colonic physiology and pathology.
Synthesis of a Pseudodisaccharide Suitable for Synthesis of Ring I Modified 4,5-2-Deoxystreptamine Type Aminoglycoside Antibiotics (2020)

To facilitate the synthesis of paromomycin and/or neomycin analogues, we describe a cleavage of ring I from paromomycin that proceeds in the presence of azides and affords a glycosyl acceptor for the installation of a modified ring I. A paromomycin 4',6'-diol is oxidized by the Dess-Martin periodinane followed by <i>m</i>-chloroperoxybenzoic acid. Base treatment then affords a protected pseudodisaccharide, which functions as a glycosyl acceptor. The method should also apply to the cleavage of pyranosyl 4,6-diols from oligosaccharides and glycoconjugates.
Broad Substrate Stereospecificity of the Mycobacterium tuberculosis 7-Keto-8-aminopelargonic Acid Synthase (2006)

Biotin is an essential enzyme cofactor required for carboxylation and transcarboxylation reactions. The absence of the biotin biosynthesis pathway in humans suggests that it can be an attractive target for the development of novel drugs against a number of pathogens. 7-Keto-8-aminopelargonic acid (KAPA) synthase (EC 2.3.1.47), the enzyme catalyzing the first committed step in the biotin biosynthesis pathway, is believed to exhibit high substrate stereospecificity. A comparative kinetic characterization of the interaction of the mycobacterium tuberculosis KAPA synthase with both L- AND D-alanine was carried out to investigate the basis of the substrate stereospecificity exhibited by the enzyme. The formation of the external aldimine with D-alanine (k = 82.63 m(-1) s(-1)) is approximately 5 times slower than that with L-alanine (k = 399.4 m(-1) s(-1)). In addition to formation of the external aldimine, formation of substrate quinonoid was also observed upon addition of pimeloyl-CoA to the preformed d-alanine external aldimine complex. However, the formation of this intermediate was extremely slow compared with the substrate quinonoid with L-alanine and pimeloyl-CoA (k = 16.9 x 10(4) m(-1) s(-1)). Contrary to earlier reports, these results clearly show that D-alanine is not a competitive inhibitor but a substrate for the enzyme and thereby demonstrate the broad substrate stereospecificity of the M. tuberculosis KAPA synthase. Further, d-KAPA, the product of the reaction utilizing D-alanine inhibits both KAPA synthase (Ki = 114.83 microm) as well as 7,8-diaminopelargonic acid synthase (IC50 = 43.9 microm), the next enzyme of the pathway.
Conductor Jetting Experiences In Deepwater Offshore Ghana - An Investigation Into Geotechnical And Operational Influences On Success, And Establishment of Future Best Practice (2012)

Nitrite inhalants, as drugs of abuse, have received a new prominence in the literature since their use has been associated with Kaposi's Sarcoma and possibly other manifestations of acquired immunodeficiency syndrome (AIDS). Changes in patterns and prevalence of use have not been investigated since the onset of the AIDS epidemic. We have examined the abuse patterns of nitrite inhalants (poppers) in several different groups. The use of poppers among drug abusers in the Baltimore-Washington, D.C. metropolitan area has remained constant over the past 5 years, with the prevalence of use being approximately 11% for recreational drug users and 22% for heavy abusers. Self-reported use by a homosexual group had decreased over the same time period. Sixty-nine percent of the homosexual sample had experience with nitrities, but only 21% had used them in the 6 months prior to being surveyed. The mean interval since last use was 25 months, and since peak use, 4.1 years. Among substance abusers, nitrites appear to be a drug whose use starts late, with the mean age of first use being 25.6 years compared to 14.6 years for glue, 17.6 years for marijuana, and 18.5 years for heroin. We found both heterosexual and homosexual groups utilize nitrites primarily to "get high," but homosexuals more often use them during overt sexual activity. Experience with amyl nitrite was much more prevalent than that with the butyl derivative in both populations. We conclude that the prevalence of nitrite abuse among drug users has not changed as a result of the AIDS epidemic, but such use appears to have decreased within the homosexual community.
A rapidly convergent expansion technique for local quantum mechanical operators (1982)

A general technique is described for efficiently expanding quantum mechanical operators. The basis is a particular set of wave functions and the expansion coefficients are physically meaningful matrix elements of the operator. Two applications to molecular properties, the transition dipole operator and the anharmonic force field, are discussed. We demonstrate that the entire force field can be expressed exactly in terms of anharmonic perturbations of the ground state, and that a great deal of information can be easily obtained from the spectroscopic frequencies. Similarly, the dipole moment matrix elements in any vibrational band are shown to be given in terms of a sum of only the R(1) matrix elements for various vibrational levels. Numerical results are presented for HCl rotational line strengths. These applications are only two examples of the potential experimental and theoretical uses of this method.
Differential expression of SNAP-25 protein isoforms during divergent vesicle fusion events of neural development. (1995)

The presynaptic plasma membrane protein SNAP-25 (synaptosome-associated protein of 25 kDa) has been implicated as one of several neural-specific components that direct constitutive fusion mechanisms to the regulated vesicle trafficking and exocytosis of neurotransmitter release. There exist two alternatively spliced isoforms of SNAP-25, a and b, which differ in a putative membrane-interacting domain. We show that these two isoforms have distinct quantitative and anatomical patterns of expression during brain development, in neurons, and in neuroendocrine cells and that the proteins localize differently in neurites of transfected PC12 pheochromocytoma cells. These findings indicate that alternative isoforms of SNAP-25 may play distinct roles in vesicular fusion events required for membrane addition during axonal outgrowth and for release of neuromodulatory peptides and neurotransmitters.
ChemInform Abstract: New Glutamic and Aspartic Derivatives with Potent CCK‐Antagonistic Activity. (1986)

Abstract 110 new derivatives of aspartic and of glutamic acid are synthesized and evaluated in vitro and in vivo for anti‐CCK activity on the guinea pig gallbladder.
DC and millimeter-wave performance of watt-level barrier-intrinsic-n/sup +/ diode-grid frequency multiplier fabricated on III-V compound semiconductors (2003)

The authors report the fabrication and millimeter-wave performance of a novel class of monolithic metal-semiconductor heterostructure devices, the barrier-intrinsic-n/sup +/ (BIN) diode-grid frequency multipliers, which are fabricated on III-V compound semiconductors. They also report the measurement of the DC and low-frequency electrical properties of the multiplier. A novel analytical model that accurately describes the structure is presented. Based on the theoretical and experimental studies presented here, the authors predict watt-level CW (continuous wave) output power at 90-180 GHz from a monolithic diode-grid multiplier design using the GaAs BIN concept.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A self-assembled lysinated perylene diimide film as a multifunctional material for neural interfacing (2016)

We report the design, synthesis and structure-property investigation of a new perylene diimide material (PDI-Lys) bearing lysine end substituents. Water processed films of PDI-Lys were prepared and their self-assembly, morphology and electrical properties in both inert and air environments were theoretically and experimentally investigated. With the aim of evaluating the potential of PDI-Lys as a biocompatible and functional neural interface for organic bioelectronic applications, its electrochemical impedance as well as the adhesion and viability properties of primary neurons on the PDI-Lys films were studied. By combining theoretical calculations and electrical measurements we show that due to conversion between neutral and zwitterionic anions, the PDI-Lys film conductivity increased significantly upon passing from air to an inert atmosphere, reaching a maximum value of 6.3 S m<sup>-1</sup>. We also show that the PDI-Lys film allows neural cell adhesion and neuron differentiation and decreases up to 5 times the electrode/solution impedance in comparison to a naked gold electrode. The present study introduces an innovative, water processable conductive film usable in organic electronics and as a putative neural interface.
New and improved Johnson-Lindenstrauss embeddings via the Restricted\n Isometry Property (2010)

Consider an m by N matrix Phi with the Restricted Isometry Property of order\nk and level delta, that is, the norm of any k-sparse vector in R^N is preserved\nto within a multiplicative factor of 1 +- delta under application of Phi. We\nshow that by randomizing the column signs of such a matrix Phi, the resulting\nmap with high probability embeds any fixed set of p = O(e^k) points in R^N into\nR^m without distorting the norm of any point in the set by more than a factor\nof 1 +- delta. Consequently, matrices with the Restricted Isometry Property and\nwith randomized column signs provide optimal Johnson-Lindenstrauss embeddings\nup to logarithmic factors in N. In particular, our results improve the best\nknown bounds on the necessary embedding dimension m for a wide class of\nstructured random matrices; for partial Fourier and partial Hadamard matrices,\nwe improve the recent bound m = O(delta^(-4) log(p) log^4(N)) appearing in\nAilon and Liberty to m = O(delta^(-2) log(p) log^4(N)), which is optimal up to\nthe logarithmic factors in N. Our results also have a direct application in the\narea of compressed sensing for redundant dictionaries.\n
Structuring processes for meat analogues (2018)

Animal-derived protein foods, such as meat, have a large impact on the environment. Meat analogues are products that replace meat in its functionality, i.e. have similar product properties and sensory attributes, which is achieved by the fibrous nature of those products. The techniques used to make fibrous products that mimic muscle meats are outlined and categorized based on their approach. The bottom-up approach refers to assembly of structural elements that are combined. The top-down approach refers to structuring of biopolymer blends using an overall force field. The strengths and weaknesses of these approaches are discussed in terms of ingredient and equipment use, (achievable) product resemblance, robustness, scalability, and resource efficiency. To enlarge the theoretical framework, the techniques with the top-down strategy are further contextualized by relating to structure formation processes of materials with other applications, and the methods to analyse the fibrous structures are further outlined. Techniques that follow the bottom-up strategy have the potential to resemble the structure of meat most closely, by structuring the proteins hierarchically through assembly of individual structural components. The top-down strategy is better scalable, is more efficient in its use of resources, but can only create the desired structure on larger length scales. Significant progress has been made on the methods to analyse structured products from the last category. Most analysis methods focussed on the (micro)structural anisotropy of the fibrous products, however there is also a need for methods that allow in situ analysis of the evolution of the structure during processing.
Phase Evolution of MHigh Speed Steel During Selective Laser Melting: Experimental Investigation and Modelling (2014)

This work studies the phase evolution in SLM where the resultant melt is considered as a moving volumetric heat source modeled as a double ellipsoidal heat source. The cooling rates and temperatures at different locations along the substrate and away from the heat source during the SLM process were simulated with the MATLAB program. Thermal gradient graphs were generated and the range of HAZ was identified from the corresponding theoretical austenitising temperature of M2 HSS. The associated HAZs were examined from their melt cross sections and validated with the simulated results. The evaluated HAZs from the experiments were found to be very close to the simulated HAZ range. The development of this model also provides the temperature distribution and cooling profiles in SLM.
Medusahead Invasion Along Unimproved Roads, Animal Trails, and Random Transects (2013)

Medusahead (Taeniatherum caput-medusae [L.] Nevski), an exotic annual grass, is rapidly spreading and causing ecological damage across the western United States. Because this exotic plant occupies vast areas and because management resources are limited, it is critical that land managers prioritize where they direct treatment and monitoring efforts. Identifying where and by what means medusahead is spreading could provide valuable information to assist in determining where prevention and control efforts should be applied. We compared medusahead invasion levels along unimproved roads, animal trails, and random transects at 6 sites in southeastern Oregon to determine where medusahead was more common and to identify potential vectors for its spread. Medusahead was more common and its cover was greater along unimproved roads than along trails and random transects. Medusahead infestations were also larger along roads. Medusahead was more common along animal trails than along random transects, but differences were less evident. Our results suggest that medusahead spreads along roads. This outcome implies, though not conclusively, that vehicles may be one of the most important vectors for medusahead spread. Our results also suggest that animals may be a vector for medusahead dispersal; however, invasions were much more concentrated near roads than trails, suggesting that medusahead management along roads should receive higher priority. Medusahead invasion is not random across the landscape, and thus, control and monitoring efforts can be prioritized, based on potential vector pathways, to manage this invasive plant.
HPLC Comparison of Tear Film Protein Pattern in Normal and Infectious Bovine Keratoconjunctivitis Affected Cattle (1994)

Purpose: This project was undertaken to establish the tear protein pattern in normal cattle and changes in the pattern at different stages of IBK, and disease of great economic importance.&#x0D; Methods: Non-stimulated tears were atraumatically collected with a 50μ1 capillary tube. The study included normal and infected animals in three stages of naturally occurring IBK. Analysis was performed with a TSK 3000 SWXL size exclusion HPLC column at a flow rate of 0.3ml/min with 0.5M NaCl, 0.1M NaH3PO4, pH 5. Quantitation was completed with computerized integration of peaks.&#x0D; Results: In all animals 7 major peaks were found at retention times of 17, 19, 21, 27, 29, 33, and 39 minutes. During the active course of the disease, peaks 1, 2, 3, 5, 6, and 7 showed various changes. Separation for different bacterial culture result within the group had statistically significant differences.&#x0D; Conclusions: The tear protein pattern in IBK affected cattle versus normal shows distinct changes. In addition to the stage of the disease changes are markedly influenced by the type of recovered organism. The first three peaks that changed in size during the course of the disease are likely to contain immunoglobulins.
Einführung (1959)

Thomasroheisen erstarrt, wenn man es in kleine Kokillen abgießt, überwiegend weiß. Man findet in seinem Gefüge nur stellenweise Graphit, der Anteil an Zementit und Phosphid ist in diesem Eisen größer als der Anteil an Ferrit. Bei einer elektrolytischen Auflösung werden, da der Ferrit zumeist vollständig von Zementit umhüllt ist, auch große Anteile des Zementits gelöst. Im Isolierrückstand findet man sie dann nach der gewählten Auflösungsart neben restlichem Zementit Phosphide, Sulfide und Oxydeinschlüsse. Für eine eingehende Untersuchung ist es wichtig, daß es gelingt, das erhaltene Isolat weiter zu zerlegen. Nach dem im Forschungsbericht Nr. 702 mitgeteilten Ergebnis schien ein Magnettrennverfahren dazu besonders geeignet, das im Rahmen dieser Untersuchung weiter entwickelt und vervollkommnet wurde.
In Vitro Susceptibility of Clinical Isolates of Aspergillus spp. to Anidulafungin, Caspofungin, and Micafungin: a Head-to-Head Comparison Using the CLSI M38-A2 Broth Microdilution Method (2009)

We determined the in vitro activities of anidulafungin, caspofungin, and micafungin against 526 isolates of Aspergillus spp. (64 A. flavus, 391 A. fumigatus, 46 A. niger, and 25 A. terreus isolates) collected from over 60 centers worldwide from 2001 through 2007. Susceptibility testing was performed according to the CLSI M38-A2 method. All three echinocandins--anidulafungin (50% minimum effective concentration [MEC50], 0.007 microg/ml; MEC90, 0.015 microg/ml), caspofungin (MEC50, 0.015 microg/ml; MEC90, 0.03 microg/ml), and micafungin (MEC50, 0.007 microg/ml; MEC90, 0.015 microg/ml)-were very active against Aspergillus spp. More than 99% of all isolates were inhibited by < or = 0.06 microg/ml of all three agents.
An electron momentum spectroscopy and density functional theory study of the outer valence electronic structure of stella-2,6-dione (2003)

We report on the first electron momentum spectroscopy (EMS) study into the outer valence electronic structure of the ground electronic state for the organic molecule stella-2,6-dione (C8H8O2). Experimentally measured binding-energy spectra are compared against a He(Iα) photoelectron spectroscopy result, while our derived momentum distributions (MDs) are compared against corresponding results from the planewave impulse approximation (PWIA) level calculations. These computations employed density functional theory (DFT) basis states at the triple zeta valence polarization (TZVP) level, with a range of exchange-correlation (XC) functionals. A detailed comparison between the experimental and PWIADFT-XC/TZVP calculatedMDs enabled us to evaluate the accuracy of the various functionals, the Becke–Perdew (BP) XC functional being found to provide the most accurate description here. The importance of the through-bondinteraction to the molecular orbitals(MOs) of stella-2,6-dione is demonstrated using the orbital imaging capability of EMS. Finally we show that the molecular geometry of this molecule, as derived from BP/TZVP, is in quite good agreement with corresponding independent experimental data.
Insights into the Substrate Promiscuity of Novel Hydroxysteroid Dehydrogenases (2020)

Abstract Hydroxysteroid dehydrogenases (HSDHs) are valuable biocatalysts for the regio‐ and stereoselective modification of steroids, bile acids and other steroid derivatives. In this work, we investigated the substrate promiscuity of this highly selective class of enzymes. In order to reach this goal, a preliminary search of HSDH homologues in in‐house or public available (meta)genomes was carried out. Eight novel NAD(H)‐dependent HSDHs, showing either 7α‐, 7β‐, or 12α‐HSDH activity, and including, for the first time, enzymes from extremophilic microorganisms, were identified, recombinantly produced, and characterized. Among the novel HSDHs, four highly active (up to 92 U mg −1 ) NAD(H)‐dependent 7β‐HSDHs showing negligible similarity towards previously described 7β‐HSDHs, were discovered. These enzymes, along with previously characterized HSDHs, were tested as biocatalysts for the stereoselective reduction of a panel of substrates including two α‐ketoesters of pharmaceutical interest and selected ketones that partially resemble the structural features of steroids. All the reactions were coupled with a suitable cofactor regeneration system. Regarding the α‐ketoesters, nearly all of the tested HSDHs showed a good activity toward the selected substrates, yielding the reduced α‐hydroxyester with up to 99% conversions and enantiomeric excesses. On the other hand, only the 7β‐HSDHs from Collinsella aerofaciens and Clostridium absonum showed appreciable activity toward more complex ketones, i. e., (±)‐trans‐1‐decalone, but with interesting as well as different selectivity. magnified image
Synthesis of Allenyl Sulfones via a TBHP/TBAI-Mediated Reaction of Propargyl Alcohols with Sulfonyl Hydrazides (2015)

A new TBHP/TBAI-mediated reaction of propargyl alcohols with sulfonyl hydrazides in the presence of HOAc has been established, in which a wide variety of allenyl sulfones were obtained in moderate to excellent yields. Mechanistic studies indicate that this transformation involves HOAc-promoted sulfonohydrazide intermediate formation, sequential C-O, C-N, and N-S bond cleavage, and C-S bond formation. Significantly, this sulfonohylation proceeds in a radical process and shows highly functional group compatibility and excellent regioselectivity, with a short reaction time and inexpensive reagents.
Cryopreservation of Mouse Adipose Tissue-Derived Stem/Progenitor Cells (2008)

Adipose tissue-derived stem/progenitor cells (ASCs) have been reported to differentiate not only into mesodermal cells such as osteoblasts, chondorocytes, and adipocytes, but also to endodermal cells such as hepatocytes and insulin-expressing cells. These stem/progenitor cells are expected to be used for variety of regenerative therapies. This study demonstrates the viability and the adipo/osteogenic potential of cryopreserved ASCs using seven cryopreservation solutions, including 10% DMSO, Cell Freezing Medium-DMSO, Cell Freezing Medium-Glycerol, Cell Banker 1, Cell Banker 1+, Cell Banker 2, and CP-1. ASCs were obtained from mouse subcutaneous adipose tissue. The viability of the cryopreserved ASCs was over 90% with Cell Banker 2 preservation, approximately 90% with Cell Banker 1, Cell Banker 1+, or CP-1 preservation, and less than 80% for 10% DMSO, Cell Freezing Medium-DMSO, or Cell Freezing Medium-Glycerol preservation. No difference in the adipo/osteogenic potential was found between cells with or without cryopreservation in Cell Banker 2. These data suggests that Cell Banker 2 is the most effective cryopreservation solution for ASCs and that cryopreserved as well as noncryopreserved ASCs could be applied for regenerative medicine.