gebhart/patrepeval huggingface dataset:
Unexpected property of trehalose as observed by cryo‐electron microscopy (1999)

Trehalose is an agent useful in maintaining the integrity of many biological systems submitted to various stresses. It is also presumed to improve specimen preparation for electron microscopy and to reduce beam damage. Here we study the effect of trehalose on the preparation and observation by cryo-electron microscopy of thin vitrified films of biological suspensions. We observe that trehalose, as compared to sucrose, can indeed reduce electron beam damage to biological particles, as determined from the dose necessary for the onset of bubbling. Surprisingly, we also find that the contrast of biological particles is higher in a vitrified solution of trehalose than in one of sucrose. This effect can be explained if the water evaporation during the specimen preparation is less in the presence of trehalose than with sucrose, but we do not yet understand the underlying reasons since the evaporation properties of both sugars are similar at a macroscopic level. We conclude that trehalose is truly a remarkable substance and that more investigation is needed in order to fully understand its properties, and that the addition of ca. 3-5% trehalose to biological suspensions is a simple and useful method to reduce commonly arising drying artefacts and water evaporation in the thin film vitrification method.
Flattening Technique of (551) Silicon Surface Using Xe/H<sub>2</sub> Plasma (2014)

In order to flatten Si(551) surface the thermal annealing in Ar ambience at the atmospheric pressure was performed. The surface roughness of Si(551) is very flat after annealing at 600 °C. It is considered that Si atoms on Si(551) surface easily migrate at lower temperature than Si(100). However because the very roughened spot are locally appeared, the atomically flat silicon surface cannot be obtained on Si(551) yet. Xe/H 2 plasma process is also performed at low temperature less than 600 °C At the H 2 concentration of 10 % and at the process pressure of 266 Pa, Ra of Si(551) surface has a very flat value of 0.068 nm. It is considered that the surface migration of Si atoms on Si(551) surface increasingly progresses because Si(551) surface became activated by Xe/H 2 plasma.
A New Wilt Disease of Lettuce Incited by<i>Fusarium oxysporum</i>f. sp.<i>lactucum</i>forma specialis nov. (1993)

A wilt disease was observed in the fall of 1990 in one commercial lettuce field (Lartura sativa «Empire») in Fresno County, California, and in the fall of 1991 in two nearby fields (cvs. Empire and Desert Queen). The disease is characterized by the death of some plants in the seedling stage, accompanied by a red streak through the cortex of the crown and upper root. Older affected heads show a tan-to-yellow tipburn with black streaks in the vascular system of some affected leaves, brown streaks in the vascular system of the crown, and a reddish brown discoloration of the cortex of the crown and upper root, Fusarium oxysporum was readily isolated from all affected plants, and in greenhouse inoculations this fungus caused a wilt disease of lettuce but not of any other crop species onto which it was inoculated
Purification and Characterization of Thermostable Pectate Lyase with Protopectinase Activity from Thermophilic <i>Bacillus</i> sp. TS 47 (2000)

A strain of thermophilic bacterium, Bacillus sp., with pectolytic activity has been isolated. It produced an extracellular endo-polygalacturonate trans-eliminase (PL, EC 4.2.2.1) when grown at 60 degrees C on a medium containing polygalacturonate (PGA). The PL was purified by hydrophobic, cation exchange, and size exclusion column chromatographies. The molecular mass of the enzyme was 50 kDa by SDS-PAGE. The isoelectric point of the enzyme was pH 5.3. The enzyme had a half-life of 13 and 1 h at 65 and 70 degrees C, respectively, and showed optimal activity around at 70 degrees C and pH 8.0. It had protopectinase activity, besides PL activity, on lemon protopectin and cotton fibers. The first 20 amino acids sequence of the enzyme had significant similarity with that of PL from methophilic Bacillus subtilis, with 50% identity.
Transcriptomics comparison reveals the diversity of ethylene and methyl-jasmonate in roles of TIA metabolism in Catharanthus roseus (2018)

Results presented above illustrate that ethylene has a stronger effect than MeJA on TIA induction at both transcriptional and metabolite level. Furthermore, meta-analysis reveals that ERF and BIS1 form a positive feedback loop connecting two ABC transporters respectively and are actively involved in TIAs responding to ET and MeJA in C. roseus.
<i>Na</i> <i> <sub>v</sub> </i> <i>1.1</i> mutations cause febrile seizures associated with afebrile partial seizures (2001)

Recent evidence has suggested that the neuronal voltage-gated sodium channel alpha(1)-subunit gene (Na(v)1.1: SCN1A) is responsible for generalized epilepsy with febrile seizures plus (GEFS+2). Here the authors report two novel disease mutations of Na(v)1.1 in patients with febrile seizures associated with afebrile partial seizures. One is a Val1428Ala substitution in the pore-forming region, and the other is Ala1685Val in the transmembrane helix. These results support the previous findings and contribute to the reliable diagnosis of epilepsy.
ChAcNLS, a Novel Modification to Antibody-Conjugates Permitting Target Cell-Specific Endosomal Escape, Localization to the Nucleus, and Enhanced Total Intracellular Accumulation (2016)

The design of antibody-conjugates (ACs) for delivering molecules for targeted applications in humans has sufficiently progressed to demonstrate clinical efficacy in certain malignancies and reduced systemic toxicity that occurs with standard nontargeted therapies. One area that can advance clinical success for ACs will be to increase their intracellular accumulation. However, entrapment and degradation in the endosomal-lysosomal pathway, on which ACs are reliant for the depositing of their molecular payload inside target cells, leads to reduced intracellular accumulation. Innovative approaches that can manipulate this pathway may provide a strategy for increasing accumulation. We hypothesized that escape from entrapment inside the endosomal-lysosomal pathway and redirected trafficking to the nucleus could be an effective approach to increase intracellular AC accumulation in target cells. Cholic acid (ChAc) was coupled to the peptide CGYGPKKKRKVGG containing the nuclear localization sequence (NLS) from SV-40 large T-antigen, which is termed ChAcNLS. ChAcNLS was conjugated to the mAb 7G3 (7G3-ChAcNLS), which has nanomolar affinity for the cell-surface leukemic antigen interleukin-3 receptor-α (IL-3Rα). Our aim was to determine whether 7G3-ChAcNLS increased intracellular accumulation while retaining nanomolar affinity and IL-3Rα-positive cell selectivity. Competition ELISA and cell treatment assays were performed. Cell fractionation, confocal microscopy, flow cytometry, and Western blot techniques were used to determine the level of antibody accumulation inside cells and in corresponding nuclei. In addition, the radioisotope copper-64 ((64)Cu) was also utilized as a surrogate molecular cargo to evaluate nuclear and intracellular accumulation by radioactivity counting. 7G3-ChAcNLS effectively escaped endosome entrapment and degradation resulting in a unique intracellular distribution pattern. mAb modification with ChAcNLS maintained 7G3 nM affinity and produced high selectivity for IL-3Rα-positive cells. In contrast, 7G3 ACs with the ability to either escape endosome entrapment or traffic to the nucleus was not superior to 7G3-ChAcNLS for increasing intracellular accumulation. Transportation of (64)Cu when complexed to 7G3-ChAcNLS also resulted in increased nuclear and intracellular radioactivity accumulation. Thus, ChAcNLS is a novel mAb functionalizing technology that demonstrates its ability to increase AC intracellular accumulation in target cells through escaping endosome entrapment coupled to nuclear trafficking.
On the modifier razgovetno (2004)

A problem not previously considered is whether the actual Standard Serbian vocabulary of manner adverbs coincides with the one attested in Vuk Karadzic' times. Pointing to some relevant facts concerning the co-occurrence of the speech act verbs with the manner modifier razgovetno, this paper not only delineates the differences in the expression of such a manner modification between the earlier stages of Standard Serbian and the contemporary language but also provides a novel argument for the validity of the author's claim (published in one of her previous articles) that it is theoretically as well as pragmatically important to distinguish between the partial and the total types of predicate modifiers.
Dehydration-Responsive Reversible and Irreversible Changes in the Extracellular Matrix: Comparative Proteomics of Chickpea Genotypes with Contrasting Tolerance (2011)

Dehydration is the most crucial environmental factor that limits plant growth, development, and productivity affecting agriculture throughout the world. Studies on genetic variations for dehydration tolerance in plants is crucial because divergent cultivars with contrasting traits aid the identification of key cellular components that confer better adaptability. The extracellular matrix (ECM) is a dynamic structure that serves as the repository for important signaling components and acts as a front-line defense. To better understand dehydration adaptation, a proteomic study was performed on the extracellular matrix of ICCV-2, a dehydration-susceptible genotype of chickpea. The proteome was generated with ECM-enriched fractions using two-dimensional gel electrophoresis. The LC-ESI-MS/MS analysis led to the identification of 81 dehydration-responsive proteins. The proteome was then compared with that of JG-62, a tolerant genotype. Comparative proteomics revealed genotype-specific expression of many proteins involved in a variety of cellular functions. Further, the reversible and irreversible changes in the proteomes revealed their differing ability to recover from dehydration-induced damage. We propose that cell wall restructuring and superior homeostasis, particularly the management of reactive oxygen species, may render better dehydration-adaptation. To our knowledge, this is the first report on the comprehensive comparison of dehydration-responsive organellar proteome of two genotypes with contrasting tolerance.
First-principles calculation of mechanical properties of Si⟨001⟩ nanowires and comparison to nanomechanical theory (2007)

We report the results of first-principles density functional theory calculations of the Young's modulus and other mechanical properties of hydrogen-passivated Si⟨001⟩ nanowires. The nanowires are taken to have predominantly {100} surfaces, with small {110} facets according to the Wulff shape. The Young's modulus, the equilibrium length, and the constrained residual stress of a series of prismatic beams of differing sizes are found to have size dependences that scale like the surface area to volume ratio for all but the smallest beam. The results are compared with a continuum model and the results of classical atomistic calculations based on an empirical potential. We attribute the size dependence to specific physical structures and interactions. In particular, the hydrogen interactions on the surface and the charge density variations within the beam are quantified and used both to parametrize the continuum model and to account for the discrepancies between the two models and the first-principles results.
MOLECULAR MARKER-ASSISTED SELECTION OF TWO BEAN RUST RESISTANCE GENES WITH PHENOTYPIC MASKING EFFECTS (2007)

ISHS XXVII International Horticultural Congress - IHC2006: International Symposium on Structural and Functional Genomics of Horticultural Plants MOLECULAR MARKER-ASSISTED SELECTION OF TWO BEAN RUST RESISTANCE GENES WITH PHENOTYPIC MASKING EFFECTS
Phase evolution of Na<sub>2</sub>O–Al<sub>2</sub>O<sub>3</sub>–SiO<sub>2</sub>–H<sub>2</sub>O gels in synthetic aluminosilicate binders (2016)

This study demonstrates the production of stoichiometrically controlled alkali-aluminosilicate gels ('geopolymers') via alkali-activation of high-purity synthetic amorphous aluminosilicate powders. This method provides for the first time a process by which the chemistry of aluminosilicate-based cementitious materials may be accurately simulated by pure synthetic systems, allowing elucidation of physicochemical phenomena controlling alkali-aluminosilicate gel formation which has until now been impeded by the inability to isolate and control key variables. Phase evolution and nanostructural development of these materials are examined using advanced characterisation techniques, including solid state MAS NMR spectroscopy probing (29)Si, (27)Al and (23)Na nuclei. Gel stoichiometry and the reaction kinetics which control phase evolution are shown to be strongly dependent on the chemical composition of the reaction mix, while the main reaction product is a Na2O-Al2O3-SiO2-H2O type gel comprised of aluminium and silicon tetrahedra linked via oxygen bridges, with sodium taking on a charge balancing function. The alkali-aluminosilicate gels produced in this study constitute a chemically simplified model system which provides a novel research tool for the study of phase evolution and microstructural development in these systems. Novel insight of physicochemical phenomena governing geopolymer gel formation suggests that intricate control over time-dependent geopolymer physical properties can be attained through a careful precursor mix design. Chemical composition of the main N-A-S-H type gel reaction product as well as the reaction kinetics governing its formation are closely related to the Si/Al ratio of the precursor, with increased Al content leading to an increased rate of reaction and a decreased Si/Al ratio in the N-A-S-H type gel. This has significant implications for geopolymer mix design for industrial applications.
Sound-field reproduction systems using fixed-directivity loudspeakers (2010)

Sound reproduction systems using open arrays of loudspeakers in rooms suffer from degradations due to room reflections. These reflections can be reduced using pre-compensation of the loudspeaker signals, but this requires calibration of the array in the room, and is processor-intensive. This paper examines 3D sound reproduction systems using spherical arrays of fixed-directivity loudspeakers which reduce the sound field radiated outside the array. A generalized form of the simple source formulation and a mode-matching solution are derived for the required loudspeaker weights. The exterior field is derived and expressions for the exterior power and direct to reverberant ratio are derived. The theoretical results and simulations confirm that minimum interference occurs for loudspeakers which have hyper-cardioid polar responses.
Scaling model for a speed-dependent vehicle noise spectrum (2017)

Considering the well-known features of the noise emitted by moving sources, a number of vehicle characteristics such as speed, unladen mass, engine size, year of registration, power and fuel were recorded in a dedicated monitoring campaign performed in three different places, each characterized by different number of lanes and the presence of nearby reflective surfaces. A full database of 144 vehicles (cars) was used to identify statistically relevant features. In order to compare the vehicle transit noise in different environmental condition, all 1/3-octave band spectra were normalized and analysed. Unsupervised clustering algorithms were employed to group together spectrum levels with similar profiles. Our results corroborate the well-known fact that speed is the most relevant characteristic to discriminate between different vehicle noise spectrum. In keeping with this fact, we present a new approach to predict analytically noise spectra for a given vehicle speed. A set of speed-dependent analytical functions are suggested in order to fit the normalized average spectrum profile at different speeds. This approach can be useful for predicting vehicle speed based purely on its noise spectrum pattern. The present work is complementary to the accurate analysis of noise sources based on the beamforming technique.
Construction of a vector containing a site-specific DNA double-strand break with 3-phosphoglycolate termini and analysis of the products of end-joining in CV-1 cells ' (1996)

Previous studies have shown that linearized SV40-based shuttle vectors transfected into mammalian cells are efficiently recircularized by an error-prone end-joining pathway. To determine whether and with what specificity free radical-mediated double-strand breaks are rejoined by this pathway, a structural mimic of such a break was introduced at a specific site in an SV40-based shuttle vector, by ligating purified 3'-phosphoglycolate-terminated oligonucleotides into 3' recessed ends generated in the linearized vector. These terminally blocked linear vectors were efficiently repaired and replicated when transfected into simian CV-1 cells. Sequencing across the repair joints in progeny plasmid indicated that, for a blunt-ended vector, the most frequent mechanism of rejoining was splicing at a terminal 4-base homology; however, a significant fraction of the joints retained all bases from both ends of the break, consistent with a mechanism involving simple 3'-phosphoglycolate removal, followed by blunt-end ligation. For the analogous 3'-hydroxyl terminated break, the fraction of simple blunt-end ligations was considerably higher. For a phosphoglycolate-terminated vector with cohesive ends the most frequent repair mechanism was simple ligation of the annealed cohesive ends, presumably preceded by phosphoglycolate removal. For all these substrates, the remaining repair joints showed small or large deletions from one or both of the ends, usually with apparent annealing at short (1-4-base) homologies. The results suggest that while breaks with 3'-phosphoglycolates can be repaired, these blocked termini represent a significant barrier to DNA end-joining, and can significantly alter its specificity. The presence of cohesive ends appears to improve markedly the fidelity of rejoining for terminally blocked double-strand breaks.
Self-aligned integration of 8×1 micromachined micro-Fresnel lens arrays and 8×1 vertical cavity surface emitting laser arrays for free-space optical interconnect (2002)

A novel, three-dimensional 8/spl times/1 micro-Fresnel lens array has been realized by surface micromachining technique; three-dimensional alignment blocks and supporting structures for both the micro-Fresnel lens array and the 8/spl times/1 vertical-cavity surface-emitting laser (VCSEL) array are also realized during the same process. With the help of these three-dimensional structures, self-aligned integration of the micro-Fresnel lens array and the VCSEL array are realized with passive alignment. Individual addressing of the VCSEL/micro-lens element is also successfully demonstrated. With their three-dimensional and array structural characteristics, they are very attractive for free-space optical interconnect and optoelectronic packaging.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Negative Tunneling Magnetoresistance by Canted Magnetization in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>MgO</mml:mi><mml:mo>/</mml:mo><mml:mi>NiO</mml:mi></mml:math>Tunnel Barriers (2011)

The influence of the insertion of an ultrathin NiO layer between the MgO barrier and the ferromagnetic electrodes in magnetic tunnel junctions has been investigated from measurements of the tunneling magnetoresistance and via x-ray magnetic circular dichroism (XMCD). The magnetoresistance shows a high asymmetry with respect to bias voltage, giving rise to a negative value of up to -16% at 2.8 K. We attribute this effect to the formation of noncollinear spin structures at the interface of the NiO layer as inferred from XMCD measurements. The magnetic moments of the interface Ni atoms tilt from their easy axis due to exchange coupling with the neighboring ferromagnetic electrode, and the tilting angle decreases with increasing NiO thickness. The experimental observations are further supported by noncollinear spin density functional calculations.
Complement Subcomponent C1q in Various Strains of Mice (1988)

The protein amount and the hemolytic activity of the initiating complement component (C1q) in the classical pathway, and the level of immunoglobulin G (IgG) in sera of various inbred mouse strains were measured in parallel with those in sera of closed colony mice. C1q levels were significantly high in male A/He and C57BL/10Sn mice, and conspicuously high in female C57BL/10Sn mice. In these strains and C57BL/6J mice of both sexes, IgG levels were also significantly high. IgG levels were strikingly high in female NZB mice and NZW mice of both sexes. On the other hand, both C1q and IgG levels were conspicuously low in BALB/c mice of both sexes and in male CBA mice, and surprisingly low in BALB/c-nu (nude) mice of both sexes. A significant correlation was observed between serum levels of C1q and IgG. The C1q specific activity, however, was equivalent in all serum samples with approximately 2 x 10(13) effective molecules/mg. The subunit composition of C1q analyzed by polyacrylamide gel electrophoresis was well comparable within all strains of mice tested. These results may suggest that mouse serum C1q does not have any phenotypic polymorphism.
A rigid motion correction method for helical computed tomography (CT) (2015)

We propose a method to compensate for six degree-of-freedom rigid motion in helical CT of the head. The method is demonstrated in simulations and in helical scans performed on a 16-slice CT scanner. Scans of a Hoffman brain phantom were acquired while an optical motion tracking system recorded the motion of the bed and the phantom. Motion correction was performed by restoring projection consistency using data from the motion tracking system, and reconstructing with an iterative fully 3D algorithm. Motion correction accuracy was evaluated by comparing reconstructed images with a stationary reference scan. We also investigated the effects on accuracy of tracker sampling rate, measurement jitter, interpolation of tracker measurements, and the synchronization of motion data and CT projections. After optimization of these aspects, motion corrected images corresponded remarkably closely to images of the stationary phantom with correlation and similarity coefficients both above 0.9. We performed a simulation study using volunteer head motion and found similarly that our method is capable of compensating effectively for realistic human head movements. To the best of our knowledge, this is the first practical demonstration of generalized rigid motion correction in helical CT. Its clinical value, which we have yet to explore, may be significant. For example it could reduce the necessity for repeat scans and resource-intensive anesthetic and sedation procedures in patient groups prone to motion, such as young children. It is not only applicable to dedicated CT imaging, but also to hybrid PET/CT and SPECT/CT, where it could also ensure an accurate CT image for lesion localization and attenuation correction of the functional image data.