gebhart/patrepeval huggingface dataset:
Characterization of the Aspergillus nidulans transporters for the siderophores enterobactin and triacetylfusarinine C (2003)

The filamentous ascomycete Aspergillus nidulans produces three major siderophores: fusigen, triacetylfusarinine C, and ferricrocin. Biosynthesis and uptake of iron from these siderophores, as well as from various heterologous siderophores, is repressed by iron and this regulation is mediated in part by the transcriptional repressor SREA. Recently we have characterized a putative siderophore-transporter-encoding gene ( mirA ). Here we present the characterization of two further SREA- and iron-regulated paralogues (mirB and mirC ), including the chromosomal localization and the complete exon/intron structure. Expression of mirA and mirB in a Saccharomyces cerevisiae strain, which lacks high affinity iron transport systems, showed that MIRA transports specifically the heterologous siderophore enterobactin and that MIRB transports exclusively the native siderophore triacetylfusarinine C. Construction and analysis of an A. nidulans mirA deletion mutant confirmed the substrate specificity of MIRA. Phylogenetic analysis of the available sequences suggests that the split of the species A. nidulans and S. cerevisiae predates the divergence of the paralogous Aspergillus siderophore transporters.
Dreaming More Data: Class-dependent Distributions over Diffeomorphisms for Learned Data Augmentation (2015)

Data augmentation is a key element in training high-dimensional models. In this approach, one synthesizes new observations by applying pre-specified transformations to the original training data; e.g.~new images are formed by rotating old ones. Current augmentation schemes, however, rely on manual specification of the applied transformations, making data augmentation an implicit form of feature engineering. With an eye towards true end-to-end learning, we suggest learning the applied transformations on a per-class basis. Particularly, we align image pairs within each class under the assumption that the spatial transformation between images belongs to a large class of diffeomorphisms. We then learn a class-specific probabilistic generative models of the transformations in a Riemannian submanifold of the Lie group of diffeomorphisms. We demonstrate significant performance improvements in training deep neural nets over manually-specified augmentation schemes. Our code and augmented datasets are available online.
<i>Meis1</i> is an essential and rate-limiting regulator of <i>MLL</i> leukemia stem cell potential (2007)

Oncogenic mutations of the MLL histone methyltransferase confer an unusual ability to transform non-self-renewing myeloid progenitors into leukemia stem cells (LSCs) by mechanisms that remain poorly defined. Misregulation of Hox genes is likely to be critical for LSC induction and maintenance but alone it does not recapitulate the phenotype and biology of MLL leukemias, which are clinically heterogeneous--presumably reflecting differences in LSC biology and/or frequency. TALE (three-amino-acid loop extension) class homeodomain proteins of the Pbx and Meis families are also misexpressed in this context, and we thus employed knockout, knockdown, and dominant-negative genetic techniques to investigate the requirements and contributions of these factors in MLL oncoprotein-induced acute myeloid leukemia. Our studies show that induction and maintenance of MLL transformation requires Meis1 and is codependent on the redundant contributions of Pbx2 and Pbx3. Meis1 in particular serves a major role in establishing LSC potential, and determines LSC frequency by quantitatively regulating the extent of self-renewal, differentiation arrest, and cycling, as well as the rate of in vivo LSC generation from myeloid progenitors. Thus, TALE proteins are critical downstream effectors within an essential homeoprotein network that serves a rate-limiting regulatory role in MLL leukemogenesis.
A friction apparatus for measuring the normal displacement of a sliding body (1980)

An apparatus is described in which the sliding friction between a small rider and a flat surface was accomplished. Normal load was applied to the rider without mechanical contact by an electromagnetic loading system. Friction force, normal displacement of the rider and electric contact resistance could be measured simultaneously. The apparatus may be used widely to study the dynamic motion of sliding bodies under miscellaneous frictional conditions.
Minimal Hepatic Encephalopathy Is Associated with Motor Vehicle Crashes (2009)

Patients with cirrhosis and MHEICT have a significantly higher crash rate over the preceding year and on prospective follow-up compared to patients without MHE. ICT, but not SPT performance is significantly associated with prior and future crashes and violations. There was an excellent agreement between self- and DOT-reports.
Computer-aided determination of crystal-lattice orientation from electron channeling patterns in the SEM (1989)

The paper presents the major steps of a mathematical procedure that permits the simulation of Electron Channeling Pattern @CP) maps of any mineral species for which unit-cell constants, the atomic species and their equivalent positions are known. The basis of calculation is the Bragg equation, the structure factor d and the atomic scattering factors of the atomic species. Simulated spherical ECP maps for chromite and quartz are presented and compared to traditional ECP maps, which were constructed from ECP photomicrographs, good results. The fraction of the ECP sphere that covers all possible orientations of a crystal is discussed for all 32 point groups. It is shown that Lauegroup symmetry is the determining factor, which results in a loss of resolution in certain point groups. The ECP simulation leads to the creation of a software package CHANNEL, which permits rapid ECP-pattern recognition and lattice-orientation determination, in principle without the need for previous construction of an ECP map.
Asymmetric Enzymatic Synthesis of Allylic Amines: A Sigmatropic Rearrangement Strategy (2016)

Sigmatropic rearrangements, while rare in biology, offer opportunities for the efficient and selective synthesis of complex chemical motifs. A "P411" serine-ligated variant of cytochrome P450(BM3) has been engineered to initiate a sulfimidation/[2,3]-sigmatropic rearrangement sequence in whole E. coli cells, a non-natural function for any enzyme, providing access to enantioenriched, protected allylic amines. Five mutations in the enzyme substantially enhance its activity toward this new function, demonstrating the evolvability of the catalyst toward challenging nitrene transfer reactions. The evolved catalyst additionally performs the highly enantioselective imidation of non-allylic sulfides.
Assessment of lipoxygenase activity in seed extracts from 35 plant species (1995)

Lipoxygenase activity in 35 seed extracts was determined on the basis of hydroperoxide synthesis using linoleic acid as substrate. The results referring to the extracted protein content show that several species of Vigna (V. unguiculata, V. radiata and V. mungo) and one of Trifolium exhibit stronger lipoxygenase activity than soybean enzyme extracts. The pH activity relationship was also established for 4 very active samples. GC-MS analysis revealed equal amounts of 9- and 13- hydroperoxides of linoleic acid in these seed extracts, indicating no enzyme positional specificity.
Assessment of Markers for Identifying Patients at Risk for Life‐Threatening Arrhythmic Events in Brugada Syndrome (2005)

Regarding risk stratification for identifying high-risk patients in Brugada syndrome, only LP by SAECG was shown to be useful, suggesting the importance of RMS40 in predicting the history of life-threatening arrhythmic events and the recurrence of VF.
Synthesis of Intermediates by Rhodium‐Catalyzed Hydroformylation (1980)

Abstract The reaction of olefins with carbon monoxide and hydrogen to give aldehydes is referred to as hydroformylation (oxo reaction). As catalyst for this reaction rhodium is about three to four orders of magnitude more active than the more commonly employed cobalt. With special rhodium compounds, e.g. di‐ν‐chlorobis(ν‐1,5‐cyclooctadiene)dirhodium [RhCl(C 8 H 12 )] 2 , in the presence of chiral phosphanes, even asymmetric hydroformylations can be achieved; however, the enantiomeric purity of the products (20–30%) is not high enough for industrial‐scale syntheses.
[A new orthotopic retinoblastoma model expressing green fluorescent protein]. (2004)

The established orthotopic RB model expressing GFP via injection of human RB cells into the subretinal space of nude mice provides a new approach to exploring the growth and metastasis processes of RB in natural situations.
Electrochemical properties of magnesium electrolyte with organic solvent (2007)

Three kinds of electrolytes are investigated to find out the proper electrolyte for magnesium battery. Propylene carbonate electrolyte using magnesium salt of Mg(ClO4)2 shows a higher ionic conductivity than that of dimethyl carbonate and tri(ethyleneglycol dimethyl)ether (TRGDME) but low decomposition potential. The TRGDME electrolyte with 0.5 M Mg(ClO4)2 has a higher ionic conductivity of 6 × 10−4 S cm−1 than that of dimethyl carbonate, but the decomposition voltage of the electrolyte is over 3.0 V which can be used for Mg/S cell.
A Novel Method for Blind Source Separation (2011)

A novel blind source separation algorithm is proposed which can separate the mixture of super- and sub-Gaussian sources. one novel method is proposed to estimate the probability density function of super and sub-Gaussian sources respectively. In the framework of natural gradient, the parameters of two models are adaptively manipulated by online kurtosis learning. Applied to the speeches, experiments give good performance of proposed algorithm.
Thieno[3,2-<i>b</i>]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 1: High-Throughput Screening and Preliminary Exploration (2017)

Lysine specific demethylase 1 KDM1A (LSD1) regulates histone methylation and it is increasingly recognized as a potential therapeutic target in oncology. We report on a high-throughput screening campaign performed on KDM1A/CoREST, using a time-resolved fluorescence resonance energy transfer (TR-FRET) technology, to identify reversible inhibitors. The screening led to 115 hits for which we determined biochemical IC<sub>50</sub>, thus identifying four chemical series. After data analysis, we have prioritized the chemical series of N-phenyl-4H-thieno[3, 2-b]pyrrole-5-carboxamide for which we obtained X-ray structures of the most potent hit (compound 19, IC<sub>50</sub> = 2.9 μM) in complex with the enzyme. Initial expansion of this chemical class, both modifying core structure and decorating benzamide moiety, was directed toward the definition of the moieties responsible for the interaction with the enzyme. Preliminary optimization led to compound 90, which inhibited the enzyme with a submicromolar IC<sub>50</sub> (0.162 μM), capable of inhibiting the target in cells.
Effects of Re-finishing of Terminations by Solder-Dipping on Plastic Quad Flatpack Electronic Parts (2006)

Tin whiskering is a concern with high tin finishes on electronic part terminations. Solder-dipping is being used as a method for replacing the original finish with eutectic tin-lead solder, as a tin whisker risk mitigation method. The solder-dipping process however, may expose the electronic parts to additional risks due to the the finish quality and thermal shock produced by the dipping process. This paper presents the effects of solder-dipping as a refinishing technique on quality and reliability on three, 0.5 mm pitch, plastic quad flatpack (PQFP) parts. The paper discusses issues concerning quality of the new dipped finish and thermo-mechanical damage at critical package interfaces
Photoamplification and Multiple Tag Release in a Linear Peptide‐Based Array of Dithiane Adducts (2007)

Binary encoding and amplification can be achieved in linear polypeptide-based scaffolds of photoactive dithiane adducts. QA masked sensitizer is tethered to lysine and incorporated in a peptide chain terminated with a sensitizer (see picture). When illuminated, the sensitizer induces fragmentation, thus unmasking more sensitizer and resulting in a linear domino photoamplification effect.
Engineering of Flexible Loops in Enzymes (2014)

ADVERTISEMENT RETURN TO ISSUEPREVViewpointNEXTEngineering of Flexible Loops in EnzymesBettina M. Nestl and Bernhard Hauer*View Author Information Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany*E-mail: [email protected]Cite this: ACS Catal. 2014, 4, 9, 3201–3211Publication Date (Web):August 8, 2014Publication History Received12 March 2014Published online19 August 2014Published inissue 5 September 2014https://pubs.acs.org/doi/10.1021/cs500325phttps://doi.org/10.1021/cs500325peditorialACS PublicationsCopyright © 2014 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views7599Altmetric-Citations132LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (4 MB) Get e-AlertscloseSUBJECTS:Catalysis,Conformational transitions,Genetics,Monomers,Peptides and proteins Get e-Alerts
Monosialoganglioside Containing Cationic Liposomes with a Cationic Cholesterol Derivative Promote the Efficiency of Gene Transfection in Mammalian Culture Cells. (2000)

We have studied the effects of monosialoganglioside (GM1)-containing cationic liposomes with a cationic cholesterol on the liposome-mediated gene transfection into mammalian culture cells. The results showed that both cationic liposomes with either a cationic cholesterol derivative of a hydrophobic amino head group (I) and a hydrophilic amino head group (II) promoted the transfection of luciferase plasmids (pGL3) into HeLa and CHO-K1 cells more than the control cationic liposomes without GM1. In addition, we found that cationic liposomes with a cationic cholesterol derivative (II) were about ten times as effective as that by commercially available cationic liposome Lipofectin. Confocal fluorescence microscopy showed that the liposome/DNA complex was transferred more efficiently into the target cells by the GM1-containing liposomes than by the liposomes without GM1. In proportion to the above results, free antisense DNAs were also more efficiently transferred into the nucleus of the target cells by the GM1-containing liposomes. When there was 100 mM galactose in the transfection medium, the luciferase activity by the GM1-containing liposomes was reduced to the level of the control liposomes. The results suggest that GM1-containing cationic liposomes with a cationic cholesterol derivative of a hydrophobic amino head group or a hydrophilic amino head group should significantly increase the transfection efficiency of plasmid DNAs and antisense DNAs by galactose receptor-mediated endocytosis. This means that the GM1-containing liposomes described here should be very promising for gene transfection in vitro.
Virtual logistics (1998)

Describes concepts for a method of organising logistics systems termed “virtual logistics”. With virtual logistics, the physical and information aspects of logistics operations are treated independently from each other. In such operations, ownership and control of resources is effected through Internet (or intranet) applications rather than direct physical control and resources can, thereby, be owned and utilised remotely. Goes on to describe the means through which virtual logistics systems can be realised, and it also provides examples of where virtual logistics concepts are already being employed. The article concludes by suggesting the most likely initial implementations of virtual logistics and suggests that, in the long term, the application of such concepts could allow for the efficiency of many logistics operations to be greatly increased and for lead times to be significantly reduced. It is also suggested that there could be distinct environmental benefits due to better coordinated goods flows, particularly in city centres.
Predicting mobile network bandwidth fluctuation to enhance video stream service quality (2013)

Due to the very nature of modern day Smartphone's and tablets, users of such devices will often travel from an area with strong mobile signal to a weaker area. Travelling from a Strong Signal Area (SSA) to a Weak Signal Area (WSA) causes a significant drop in the mobile network bandwidth available to the device. This causes Quality of Service (QoS) problems for video streams over mobile networks. For a completely pause-less video stream, the average stream download rate must be consistently equal to, or greater than, the video bit-rate. A sudden bandwidth drop often causes the stream to rapidly become starved of buffered data, causing a pause in playback whilst the client attempts further buffering - posing a QoS problem. This paper proposes a solution that helps counter this mobility problem by attempting to foresee a user entering a WSA, and dynamically rate-limiting other nearby best-case users to increase available bandwidth to said user. Predictions are based on active user location information, and Mobile Network Coverage Map (MNCM) queries. Best-case user determination and dynamic rate-limit algorithms are described in this paper. Through mathematical proofing with two unique test scenarios, the proposed solution is proven to significantly improve QoS of a video stream to a user entering a WSA.
Vectorial Phase Retrieval for Linear Characterization of Attosecond Pulses (2011)

The waveforms of attosecond pulses produced by high-harmonic generation carry information on the electronic structure and dynamics in atomic and molecular systems. Current methods for the temporal characterization of such pulses have limited sensitivity and impose significant experimental complexity. We propose a new linear and all-optical method inspired by widely used multidimensional phase retrieval algorithms. Our new scheme is based on the spectral measurement of two attosecond sources and their interference. As an example, we focus on the case of spectral polarization measurements of attosecond pulses, relying on their most fundamental property-being well confined in time. We demonstrate this method numerically by reconstructing the temporal profiles of attosecond pulses generated from aligned CO(2) molecules.
Third-order optical nonlinearities and their ultrafast response in Bi_2O_3–B_2O_3–SiO_2 glasses (1999)

Nonresonant-type homogeneous Bi2O3–B2O3–SiO2 glasses were prepared by melting. The third-order optical nonlinear susceptibility χ(3), which was determined by measurement of third-harmonic generation, increased with increasing concentrations of Bi2O3 in the glass. The maximum χ(3) estimated was 9.3×10-12 esu in glass that contained 92 wt. % of Bi2O3.χ(3) values of these glasses were enhanced by the small optical bandgap. These glasses also exhibited an ultrafast response time, less than 200 fs, when a degenerate four-wave mixing method with a femtosecond laser was used, indicating that the nonlinearity of these glasses originated mainly from pure electronic polarization.
Investigation into thermoformability of hot compacted polypropylene sheet (2000)

This paper describes an investigation into the thermoformability of a new class of oriented polymeric material recently developed, namely hot compacted polypropylene sheet. Exploitation of any new material requires an intimate understanding of a whole range of factors, amongst which thermoformability is pre-eminent. This is particularly true for oriented polymeric materials, for while the preferred molecular alignment gives enhanced properties such as stiffness, strength, and resistance to impact, the downside is that the stretched molecular chains tend to limit further flow under stress, making thermoforming difficult. The aim of the present study was to establish the critical parameters for successful thermoforming of hot compacted polypropylene sheet.Elevated temperature tensile tests were used to investigate the stress–strain behaviour of the compacted materials. The crucial parameters were found to be the post-yield modulus, which gives a measure of the resistance of the material to large scale deformation, and the strain to failure, which gives the upper limit on deformation. The post-yield modulus was found to be significantly affected by the test temperature and the high strain hardening behaviour of the material confirmed that significant force is required to thermoform the compacted polypropylene sheets. A hemispherical mould, with built-in gripping plate, was used to carry out a study of the thermoforming behaviour of the compacted sheets, and the results were found broadly to confirm the conclusions of the tensile tests. A linear relationship was found between the tensile force and the postforming force, reinforcing the synergy between the two tests. In addition the forming tests showed that the best temperatures to use were either side of the melting point of the melted and recrystallised phase, depending on the amount of postforming deformation required. Different gripping arrangements were investigated both in which the sheet was fully gripped and in which the sheet was allowed to flow into the mould during forming. The different schemes were found to control whether a successful component could be produced under different conditions and at different ultimate strains. Finally, the tests with the hemispherical mould showed that thermoforming this shape requires significant interlaminar shear deformation, and above 15% strain this resulted in destruction of the interlayer bond. For strains greater than this, successful thermoforming could only be achieved by allowing the material to flow into the mould.
PVT-invariant single-to-differential data converter with minimum skew and duty-ratio distortion (2008)

This paper proposes PVT-invariant single-to-differential signal converter (SDQ applicable to the output circuitry of high-speed DDR SDRAM. The proposed SDC generates PVT-invariant differential-output sampling clock using a phase interpolation technique and a symmetric structure, and improves the aperture window of output data in source synchronous DDR SDRAM. The proposed SDC was simulated using 1.8-V 80-nm DRAM technology. The comparison result indicates that the differential clocks generated by the proposed SDC achieve 80.6% reduction of skew, 76.6% reduction of duty-cycle distortion, 61.7% of reduction of delay variation, and 8.5% reduction of maximum current for a given process, voltage, and temperature (PVT) variations, as compared to conventional SDCs. The I/O interface of a source-synchronous DDR SDRAM designed using the proposed SDC, which is operating at 1.0-Gbps/pin data rate has aperture window increased by 15.3% and ISI improved by 67.7% in comparison to conventional I/O interface.