gebhart/patrepeval huggingface dataset:
Large-Scale Analysis of Gene Expression Profiles during Early Stages of Root Nodule Formation in a Model Legume, Lotus japonicus (2004)

Gene expression profiles during early stages of formation of symbiotic nitrogen-fixing nodules in a model legume Lotus japonicus were analyzed by means of a cDNA array of 18,144 non-redundant expressed sequence tags (ESTs) isolated from L. japonicus. Expression of a total of 1,076 genes was significantly accelerated during the successive stages that represent infection of Mesorhizobium loti, nodule primordium initiation, nodule organogenesis, and the onset of nitrogen fixation. These include 32 nodulin and nodulinhomolog genes as well as a number of genes involved in the catabolism of photosynthates and assimilation of fixed nitrogen that were previously known to be abundantly expressed in root nodules of many legumes. We also identified a large number of novel nodule-specific or enhanced genes, which include genes involved in many cellular processes such as membrane transport, defense responses, phytohormone synthesis and responses, signal transduction, cell wall synthesis, and transcriptional regulation. Notably, our data indicate that the gene expression profile in early steps of Rhizobium-legume interactions is considerably different from that in subsequent stages of nodule development. A number of genes involved in the defense responses to pathogens and other stresses were induced abundantly in the infection process, but their expression was suppressed during subsequent nodule formation. The results provide a comprehensive data source for investigation of molecular mechanisms underlying nodulation and symbiotic nitrogen fixation.
Micropatterning of Monodisperse Spherical Particles by Electrophoretic Deposition Process Using Interdigitated Microarray Electrode (2006)

Micrometer wire consisting of microbeads was successfully fabricated onto a patterned conductive electrode substrate by an electrophoretic deposition (EPD) process with precise control of electric field distribution generated in the colloidal suspension. Monodisperse polystyrene microspheres with 320 nm in diameter and an interdigitated microarray Au electrode having 10 μm in width and 5 μm in spacing were used in this EPD system. A micropattern of polystyrene particles with two dimensional arrays was formed onto the patterned electrode by the EPD process with two electrode system using an electrostatic interaction between the electrodes and the charged particles in the suspension.
Preparation and characterization of LiFePO4 /Ag composite for Li-ion batteries (2004)

Ag is introduced to the surface of LiFePO4 prepared from liquid phase and heated at different temperatures. SEM, XRD and electrochemical characterization are used to compare the differences between LiFePO4 and LiFePO4/Ag. The results are discussed from the viewpoint of impedance of the cathode composite. With increase of the particle size, Ag shows stronger function as conductor in the composites.
Evolutionary aspects of self- and world consciousness in vertebrates (2015)

Although most aspects of world and self-consciousness are inherently subjective, neuroscience studies in humans and non-human animals provide correlational and causative indices of specific links between brain activity and representation of the self and the world. In this article we review neuroanatomic, neurophysiological and neuropsychological data supporting the hypothesis that different levels of self and world representation in vertebrates rely upon (i) a "basal" subcortical system that includes brainstem, hypothalamus and central thalamic nuclei and that may underpin the primary (or anoetic) consciousness likely present in all vertebrates; and (ii) a forebrain system that include the medial and lateral structures of the cerebral hemispheres and may sustain the most sophisticated forms of consciousness [e.g., noetic (knowledge based) and autonoetic, reflective knowledge]. We posit a mutual, bidirectional functional influence between these two major brain circuits. We conclude that basic aspects of consciousness like primary self and core self (based on anoetic and noetic consciousness) are present in many species of vertebrates and that, even self-consciousness (autonoetic consciousness) does not seem to be a prerogative of humans and of some non-human primates but may, to a certain extent, be present in some other mammals and birds.
Elastic windows: design, implementation, and evaluation of multi‐window operations (1998)

Most windowing systems follow the independent overlapping windows approach, which emerged as an answer to the needs of early computer users. Due to advances in computers, display technology, and increased information needs, modern users demand more functionality from window management systems. We propose Elastic Windows with improved spatial layout and rapid multi-window operations as an alternative to current window management strategies. In this approach, multi-window operations are achieved by issuing operations on window groups hierarchically organized in a space-filling tiled layout similar to TreeMaps.1 Sophisticated multi-window operations have been developed to handle fast task-switching and to structure the work environment of users to their rapidly changing needs. We claim that these multi-window operations and the tiled spatial layout dynamics decrease the cognitive load on users by decreasing the number of window operations. This paper describes the Elastic Windows interface in detail and then presents a user study conducted to compare the performance of 12 users with Elastic Windows and traditional Independent Overlapping Windows. User performance was measured in terms of task environment setup, switching, and task execution for 2, 6, and 12 window situations. Elastic Windows users had statistically significantly faster performance for all tasks in 6 and 12 window situations. These results suggest promising possibilities for multiple window operations and hierarchical nesting, which can be applied to the next generation of tiled as well as overlapped window managers. © 1998 John Wiley & Sons, Ltd.
Gas-Phase Reactions of O- and OH-Containing Cr Cluster Ions with Ethylene Molecules:  Isolation of Reaction Sites of Cr-Containing Catalysts for Ethylene Polymerization (2004)

Reactions of ethylene molecules on Crn+ (n = 1−4), CrnO+ (n = 1−4), and CrnOH+ (n = 1, 2) were studied in a tandem mass spectrometer equipped with a reaction cell. The mass spectra of the product ions showed that (1) under a single collision condition, oxidation of ethylene and chromium pickup (Cr-pickup) by ethylene take place on Crn+ (n = 2−4), CrnO+ (n = 2−4), and CrnOH+ (n = 2), and (2) under a multiple collision condition, two ethylene molecules are chemisorbed exclusively on CrO+ and CrOH+; the ethylene molecules seem to be dimerized in comparison with our preliminary density functional theory calculation. Size and collision-energy dependences of the reaction cross sections lead us to conclude that the Cr-pickup reaction proceeds via an intermediate in which C2H4 is chemisorbed on a parent ion. The preferential ethylene dimerization on CrO+ and CrOH+ implies that, on a silica-supported chromium catalyst (Philips catalyst), ethylene polymerization proceeds preferentially on active centers consisting of atomic chromium bonded to O or OH of the substrate.
Solid state dimerisation of β-nitrostyrene: a disordered photoreactive crystal (1989)

G. R. Desiraju and V. R. Pedireddi, J. Chem. Soc., Chem. Commun., 1989, 1112 DOI: 10.1039/C39890001112
Multiply resonant photonic crystal nanocavities for nonlinear frequency conversion (2011)

We describe a photonic crystal nanocavity with multiple spatially overlapping resonances that can serve as a platform for nonlinear frequency conversion. We show nonlinear characterization of structures with two resonances nearly degenerate in frequency. We also demonstrate structures with resonances separated by up to 523 nm.
ReproZip: 1.1 (2021)

(reprounzip-vistrails didn't change) Bugfixes:<br> * Fix possible crash reading `docker inspect` output<br> * Fix reprozip-jupyter on more recent Tornado<br> * Fix failure in reprounzip-docker upload if `/bin/sh` is missing<br> * Have `reprounzip directory` execute with the correct interpreter (e.g. packed `ld-linux.so`)<br> * Fix "invalid cross-device link" errors in vagrant download if the destination is not on the same device as the unpacked directory Enhancements:<br> * Add PyQt5 compatibility to reprounzip-qt<br> * reprounzip-docker: Keep ownership of uploaded files<br> * Add a new certificate to download parameters, valid through 2121 (previous expires 2024)<br> * Always show full path of executed files in `reprozip testrun`<br> * Improved merging of pack on top of base image in reprounzip-docker<br> * Made sure the root is a mountpoint in reprounzip-vagrant, as some applications expect it (e.g. Elasticsearch)<br> * Disable unpacker options that won't work in reprounzip-qt (e.g. 'directory' and 'chroot' on non-Linux)
Network Biology editorial 2013 (2013)

The guest editors introduce the Network Biology themed issue.
Supplementary Table 1 from Substrate Overlap between Mrp4 and Abcg2/Bcrp Affects Purine Analogue Drug Cytotoxicity and Tissue Distribution (2023)

Supplementary Table 1 from Substrate Overlap between Mrp4 and Abcg2/Bcrp Affects Purine Analogue Drug Cytotoxicity and Tissue Distribution
Poly-L-Ornithine-Mediated Transformation of Mammalian Cells (1987)

Poly-L-ornithine has been used to introduce DNA and RNA into mammalian cells in culture. Ornithine-mediated DNA transfer has several interesting and potentially useful properties. The procedure is technically straightforward and is easily applied to either small or large numbers of recipient cells. The efficiency of transformation is high. Under optimal conditions, 1 to 2% of recipient mouse L cells take up and continue to express selectable marker genes. DNA content of transformants can be varied reproducibly, yielding cells with just one or two copies of the new gene under one set of conditions, while under a different set of conditions 25 to 50 copies are acquired. Cotransformation and expression of physically unlinked genes occur at high efficiency under conditions favoring multiple-copy transfer. Polyornithine promotes gene transfer into cell lines other than L cells. These include Friend erythroleukemia cells and NIH 3T3 cells. Both are transformed about 1 order of magnitude more efficiently by this procedure than by standard calcium phosphate products. However, the method does not abolish the large transformation efficiency differences between these cell lines that have been observed previously by other techniques. (vi) mRNA synthesized in vitro was also introduced into cells by this method. The RNA was translated resulting in a transient accumulation of the protein product.
Partial CT for in situ bridge NDE with 950 keV/3.95 MeV X-band linac source (2014)

Computed tomography system for in situ NDE of degradation bridges is under development, with portable 950 keV/3.95 MeV X-band linac as x-ray source. Collimator is adopted to reduce scattered X-ray noise and 3D model can be built from sectional images so that it becomes possible to evaluate mechanical characters of bridges referring to structural analysis with reduced stiffness. Furthermore, considering limitation of projection angle range during in situ scanning, reconstruction technique with incomplete projection data is studied with experimental data.
STM Analysis of Cytochrome<i>c</i>Adsorbed Hetero-LB Film using Bridging Molecules (2001)

Abstract Ferrocene(1-1′-ferrocene-N-dioctadecyl carboxamide), flavin(7,8-dimethly-10-dodecylisoalloxazine), viologen [N-allyl-N7′-[3-propylamidoN″,N″-di(n-octadecyl)]-4,4′bipyridiumdibromide), and cytochrome c were used as an electron donor (D), sensitize (S), the first electron acceptor (A1), and the second electron acceptor (A2), respectively in fabricating molecular device. Malonic acid or poly-L-aspartic acid were used as a bridging molecule for the adsorption of A2 molecules onto A1 layers. In order to confirm the electron transfer, Scanning tunneling microscopy(STM) investigation was performed.
Depression patient-derived cortical neurons reveal potential biomarkers for antidepressant response (2021)

Major depressive disorder is highly prevalent worldwide and has been affecting an increasing number of people each year. Current first line antidepressants show merely 37% remission, and physicians are forced to use a trial-and-error approach when choosing a single antidepressant out of dozens of available medications. We sought to identify a method of testing that would provide patient-specific information on whether a patient will respond to a medication using in vitro modeling. Patient-derived lymphoblastoid cell lines from the Sequenced Treatment Alternatives to Relieve Depression study were used to rapidly generate cortical neurons and screen them for bupropion effects, for which the donor patients showed remission or non-remission. We provide evidence for biomarkers specific for bupropion response, including synaptic connectivity and morphology changes as well as specific gene expression alterations. These biomarkers support the concept of personalized antidepressant treatment based on in vitro platforms and could be utilized as predictors to patient response in the clinic.
A Novel Macroinitiator for the Synthesis of Triblock Copolymers via Atom Transfer Radical Polymerization: Polystyrene‐<i>block</i>‐poly(bisphenol A carbonate)‐<i>block</i>‐polystyrene and Poly(methyl methacrylate)‐<i>block</i>‐poly(bisphenol A carbonate)‐<i>block</i>‐poly(methyl methacrylate) (2004)

Abstract Summary: Bis(hydroxy)telechelic bisphenol A polycarbonate (PC) was prepared via melt polycondensation of bisphenol A (BPA) and diphenyl carbonate (DPC) using lanthanum( III ) acetylacetonate as a catalyst for transesterification. Subsequently, the polycarbonate was converted to a bifunctional macroinitiator for atom transfer radical polymerization (ATRP) with the reagent, α ‐chlorophenylacetyl chloride. The macroinitiator was used for the polymerization of styrene (S) and methyl methacrylate (MMA) to give PS‐ block ‐PC‐ block ‐PS and PMMA‐ block ‐PC‐ block ‐PMMA triblock copolymers. These block copolymers were characterized by NMR and GPC. When styrene and methyl methacrylate were used in large excess, significant shifts toward high molecular weights were observed with quantitative consumption of the macroinitiator. Several ligands were studied in combination with CuCl as the ATRP catalyst. Kinetic studies reveal the controlled nature of the polymerization reaction for all the ligands used. Formation of a bifunctional ATRP macroinitiator by esterification of bis(hydroxy)telechelic PC with α ‐chlorophenylacetyl chloride. image Formation of a bifunctional ATRP macroinitiator by esterification of bis(hydroxy)telechelic PC with α ‐chlorophenylacetyl chloride.
Computational analysis of binding of P1 variants to trypsin (2001)

The binding of P1 variants of bovine pancreatic trypsin inhibitor (BPTI) to trypsin has been investigated by means of molecular dynamics simulations. The specific interaction formed between the amino acid at the primary binding (P1) position of the binding loop of BPTI and the specificity pocket of trypsin was estimated by use of the linear interaction energy (LIE) method. Calculations for 13 of the naturally occurring amino acids at the P1 position were carried out, and the results obtained were found to correlate well with the experimental binding free energies. The LIE calculations rank the majority of the 13 variants correctly according to the experimental association energies and the mean error between calculated and experimental binding free energies is only 0.38 kcal/mole, excluding the Glu and Asp variants, which are associated with some uncertainties regarding protonation and the possible presence of counter-ions. The three-dimensional structures of the complex with three of the P1 variants (Asn, Tyr, and Ser) included in this study have not at present been solved by any experimental techniques and, therefore, were modeled on the basis of experimental data from P1 variants of similar size. Average structures were calculated from the MD simulations, from which specific interactions explaining the broad variation in association energies were identified. The present study also shows that explicit treatment of the complex water-mediated hydrogen bonding network at the protein-protein interface is of crucial importance for obtaining reliable binding free energies. The successful reproduction of relative binding energies shows that this type of methodology can be very useful as an aid in rational design and redesign of biologically active macromolecules.
Incorporation of the electrode–electrolyte interface into finite-element models of metal microelectrodes (2007)

An accurate description of the electrode-electrolyte interfacial impedance is critical to the development of computational models of neural recording and stimulation that aim to improve understanding of neuro-electric interfaces and to expedite electrode design. This work examines the effect that the electrode-electrolyte interfacial impedance has upon the solutions generated from time-harmonic finite-element models of cone- and disk-shaped platinum microelectrodes submerged in physiological saline. A thin-layer approximation is utilized to incorporate a platinum-saline interfacial impedance into the finite-element models. This approximation is easy to implement and is not computationally costly. Using an iterative nonlinear solver, solutions were obtained for systems in which the electrode was driven at ac potentials with amplitudes from 10 mV to 500 mV and frequencies from 100 Hz to 100 kHz. The results of these simulations indicate that, under certain conditions, incorporation of the interface may strongly affect the solutions obtained. This effect, however, is dependent upon the amplitude of the driving potential and, to a lesser extent, its frequency. The solutions are most strongly affected at low amplitudes where the impedance of the interface is large. Here, the current density distribution that is calculated from models incorporating the interface is much more uniform than the current density distribution generated by models that neglect the interface. At higher potential amplitudes, however, the impedance of the interface decreases, and its effect on the solutions obtained is attenuated.
PROXIMA: Improving Measurement-Based Timing Analysis through Randomisation and Probabilistic Analysis (2016)

The use of increasingly complex hardware and software platforms in response to the ever rising performance demands of modern real-time systems complicates the verification and validation of their timing behaviour, which form a time-and-effort-intensive step of system qualification or certification. In this paper we relate the current state of practice in measurement-based timing analysis, the predominant choice for industrial developers, to the proceedings of the PROXIMA (Probabilistic real-time control of mixed-criticality multicore systems) project in that very field. We recall the difficulties that the shift towards more complex computing platforms causes in that regard. Then we discuss the probabilistic approach proposed by PROXIMA to overcome some of those limitations. We present the main principles behind the PROXIMA approach as well as the changes it requires at hardware or software level underneath the application. We also present the current status of the project against its overall goals, and highlight some of the principal confidence-building results achieved so far.
Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism (2020)

DNA methylation is a widespread epigenetic mark that contributes to transcriptome reprogramming during plant-pathogen interactions. However, the distinct role of DNA methylation in establishing resistant and susceptible responses remains largely unexplored. Here, we developed and used a pair of near-isogenic lines (NILs) to characterize DNA methylome landscapes of soybean roots during the susceptible and resistant interactions with soybean cyst nematode (SCN; Heterodera glycines). We also compared the methylomes of the NILs and their parents to identify introduced and stably inherited methylation variants. The genomes of the NILs were substantially differentially methylated under uninfected conditions. This difference was associated with differential gene expression that may prime the NIL responses to SCN infection. In response to SCN infection, the susceptible line exhibited reduced global methylation levels in both protein-coding genes and transposable elements, whereas the resistant line showed the opposite response, increased global methylation levels. Heritable and novel nonparental differentially methylated regions overlapping with genes associated with soybean response to SCN infection were identified and validated using transgenic hairy root system. Our analyses indicate that DNA methylation patterns associated with the susceptible and resistant interactions are highly specific and that novel and stably inherited methylation variants are of biological significance.
ChemInform Abstract: 3H‐Pyrroles from Ketoximes and Acetylene: Synthesis, Stability and Quantum‐Chemical Insight. (2015)

Abstract The one‐pot procedure provides access to rare nonaromatic 2‐aryl‐3,3‐dialkylsubstituted 3H‐pyrroles.
Tissue Engineering: Fluorinated Graphene for Promoting Neuro‐Induction of Stem Cells (Adv. Mater. 31/2012) (2012)

Surfaces with good biocompatibility and tissue-specific inductive capabilities are highly desirable in various tissue engineering and cell therapeutic applications. On page 4285, K. P. Loh, C. T. Lim, and co-workers show that mesenchymal stem cells (MSCs) can be controllably patterned on fluorinated graphene, triggering alignment-induced neuronal differentiation. Their results point to a large-scale and rapid strategy to align MSCs and the ability to induce neuronal lineage in the absence of chemical inducer.