gebhart/patrepeval huggingface dataset:
Transketolase kinetics. The slow reconstitution of the holoenzyme is due to rate-limiting dimerization of the subunits. (1981)

At pH 7.6 the monomeric apoenzyme is reactivated slowly when divalent metallic cation, (M2") and thiamin-PP are added, and a lag is seen in the progress curves in the enzyme assay.The apparent Km for thiamin-PP has two values, both of which differ, depending upon whether they are determined from the steady state velocity or from v-[ for the lag, the rate constant for transition between the initial and final steady state velocities.r-' is variable and depends upon the length of preincubation of apoenzyme with thiamin-PP and M2+, as well as on the particular M2`that is used.Further, at high concentrations of thiamin-PP r- reaches a constant, limiting value, which itself depends on the concentration of the enzyme and on the particular M2, that is present; r goes to zero at high concen- trations of thiamin-PP only when the ketose substrate is also present.r-1 increases linearly with [monomer]l7, suggesting that dimerization contributes sig- nificantly to the observed lag phase.Hill coefficients obtained from a wide range of thiamin-PP concentra- tions in the presence of Mg2e or Ca21 show that there is negative cooperativity in the binding of the coenzyme to the apoenzyme.Similar results were obtained with pyruvate decarboxylase at pH 6.2 except that <-did not vary with the enzyme concentration; this suggests that an isomerization, rather than an oligomerization, is the rate limiting step that causes the lag for this enzyme under these conditions.Possible mechanisms for the binding of thiamin-PP and the influence of the substrate on the observed kinetics are discussed for both of these enzymes.A characteristic common to all thiamin-PP-requiring en- zymes studied to date is the presence of a lag in the reaction
Correspondence between different view breast X-rays using a simulation of breast deformation (2002)

We develop a method to find correspondences between a Cranio-Caudal (CC) and a Medio-Lateral Oblique (MLO) X-ray image of the same breast. Matching between such pairs of images is considered essential by radiologists for more reliable diagnosis of early breast cancer. The two images are taken while the breast is compressed between the cassette and plate of the X-ray machine, but, almost always, to a different extent in each direction. The deformations of the breast caused by the different compressions in the different directions causes corresponding points to appear far from the straight "epipolar lines" familiar from binocular stereo vision. The method developed in this paper calculates the line in a MLO image corresponding to a point in the CC image through simulation of the deformation and the projection of a 3D line (curve) corresponding to the point. Experiments using actual images show that the method gives good predictions which can be used to find exact correspondences between points in the two images.
Experimental studies of restricted protein diffusion in an agarose matrix (1992)

Abstract The diffusion of proteins in polymer matrices is an important step in the adsorptive and chromatographic processes used for protein purification, as it is often rate‐limiting. Methods for the estimation of the intraparticle diffusivity in polymer gels have been developed and were applied to the diffusion of seven model proteins in agarose particles. The intraparticle diffusivity was not affected by particle diameter. A correlation based on the restricted diffusion model of Ogston et al. (1973) and Cukier (1984) has been proposed. This correlation allows the estimation of protein diffusivity in these matrices based on the molecular weight of the protein and the polymer concentration.
Argument Extraction from News (2015)

Argument extraction is the task of identifying arguments, along with their components in text. Arguments can be usually decomposed into a claim and one or more premises justifying it. The proposed approach tries to identify segments that represent argument elements (claims and premises) on social Web texts (mainly news and blogs) in the Greek language, for a small set of thematic domains, including articles on politics, economics, culture, various social issues, and sports. The proposed approach exploits distributed representations of words, extracted from a large non-annotated corpus. Among the novel aspects of this work is the thematic domain itself which relates to social Web, in contrast to traditional research in the area, which concentrates mainly on law documents and scientific publications. The huge increase of socialwebcommunities, alongwiththeirusertendency to debate, makes the identification of arguments in these texts a necessity. In addition, a new manually annotated corpus has been constructedthatcanbeusedfreelyforresearchpurposes. Evaluation results are quite promising, suggesting that distributed representations can contributepositivelyto thetaskofargumentextraction.
Mechanical Allodynia Induced by Paclitaxel, Oxaliplatin and Vincristine: Different Effectiveness of Gabapentin and Different Expression of Voltage-Dependent Calcium Channel .ALPHA.2.DELTA.-1 Subunit (2009)

We compared the inhibitory action of gabapentin, which is used to treat neuropathic pain, on mechanical allodynia induced by chemotherapeutic agents, paclitaxel, oxaliplatin, and vincristine, in mice. Single injections of paclitaxel, oxaliplatin, and vincristine at the doses corresponding to doses clinically used caused mechanical allodynia of similar intensity. Oral administration of gabapentin (30, 100 mg/kg) produced a dose-dependent inhibition of allodynia caused by paclitaxel and oxaliplatin, but not vincristine. Intrathecal injection of gabapentin (30, 100μg/site) significantly inhibited allodynia induced by paclitaxel, but not oxaliplatin and vincristine. Intraplantar injection of gabapentin (30, 100 μg/site) did not significantly inhibit allodynia induced by paclitaxel and oxaliplatin. Paclitaxel increased the expression of mRNA of voltage-dependent calcium channel α2δ-1 subunit, an action site of gabapentin, in the dorsal spinal cord, and oxaliplatin increased it in the dorsal root ganglia. Vincristine was without effects on α2δ-1 subunit mRNA in these regions. These results suggest that the efficacy of gabapentin in the treatment of mechanical allodynia is dependent on chemotherapy agent used. It may be partly due to the distinct effects of chemotherapy agents on the expression of α2δ-1 subunit of voltage-dependent calcium channel.
An evaluation of the hot plate technique to study narcotic antagonists. (1976)

The mouse hot plate model, with slight differences from the way it is used to study narcotic analgesics, was evaluated as a method for determining the oral effectiveness, relative potency and duration of action of two standard narcotic antagonists, naloxone and naltrexone, and a new agent, 6-desoxy-6-methylene-naltrexone (ORF 11676). Naltrexone and ORF 11676 were found to be more effective orally than naloxone. Naltrexone and ORF 11676 were equipotent by 3 routes of administration and both were more potent than naloxone. Naloxone produced a significantly shorter duration of action than the other two drugs. It was concluded that the mouse hot plate method, used to detect and characterize the activity of narcotic antagonists, provides information compatible with that obtained in other species, including man.
Long‐term storage and preservation of tissue engineered articular cartilage (2015)

With limited availability of osteochondral allografts, tissue engineered cartilage grafts may provide an alternative treatment for large cartilage defects. An effective storage protocol will be critical for translating this technology to clinical use. The purpose of this study was to evaluate the efficacy of the Missouri Osteochondral Allograft Preservation System (MOPS) for room temperature storage of mature tissue engineered grafts, focusing on tissue property maintenance during the current allograft storage window (28 days). Additional research compares MOPS to continued culture, investigates temperature influence, and examines longer-term storage. Articular cartilage constructs were cultured to maturity using adult canine chondrocytes, then preserved with MOPS at room temperature, in refrigeration, or kept in culture for an additional 56 days. MOPS storage maintained desired chondrocyte viability for 28 days of room temperature storage, retaining 75% of the maturity point Young's modulus without significant decline in biochemical content. Properties dropped past this time point. Refrigeration maintained properties similar to room temperature at 28 days, but proved better at 56 days. For engineered grafts, MOPS maintained the majority of tissue properties for the 28-day window without clearly extending that period as it had for native grafts. These results are the first evaluating engineered cartilage storage.
Abnormal cortical excitability in sporadic but not homozygous D90A SOD1 ALS (2005)

A cortical inhibitory deficit in sALS was not demonstrable in a homogeneous genetic ALS population of similar disability, suggesting a distinct cortical vulnerability. (11)C-flumazenil PET demonstrated that neuronal loss/dysfunction in motor and motor association areas may underlie this difference. The corollary, that there may be relative preservation of neuronal function in these areas in the homD90A group, has implications for understanding the slower progression of disease in these patients.
The falsetto tones of the dialects in Hubei province (2012)

Falsetto phonation was applied to produce Shangsheng/Rising Tone in the early stage of Chinese tonal development (ca. 400-700 AD) and this phonation type is still in use in the tonal systems of several major Chinese dialect-groups now. In Hubei province, falsetto tones are found in three cities, Songzi , Jingmen and Jianli . In the tonal systems of these three dialects, the tone values show some noteworthy correspondences. In order to present the contemporary state of the falsetto tones and explore the tonal evolution through the synchronic field data, we conducted this research and chose Songzi as our starting point. Based on Evolutionary Phonology and the Multi-Register and Four-Level Tonal Model, three geographically connected and phonologically related dialects are found in Songzi: Weishui Type in the south, Nanhai Type in the middle, and Songzihe Type in the north. They share almost identical onset and rime systems, and their tonal systems are different but related. Weishui maintains a Rusheng/Entering Tone in falsetto or fortis voice and there are five tones in its tonal system; Rusheng has disappeared in Nanhai and four tones remain which are the same as their counterparts in Weishui; there is no Rusheng in Songzihe either, and it shares Yangping/Low Level Tone and Shangsheng with Weishui and Nanhai, but the tone values of its Yinping/High Level Tone and Qusheng/Departing Tone are involved in a tonal flip-flop These three synchronic tonal systems show a diachronic chain shift. At present, the Weishui's Rusheng which is in falsetto or fortis voice is moving down in two ways: an overall falling (the pitch falls while the contour maintains), and the lowering of the tone tail. These findings offer us the chance to detect the initial changes in the chain shift of these three tonal systems and evaluate their impact to the phonological systems.
Postnatal development- and age-related changes in DNA-methylation patterns in the human genome (2012)

Alterations in DNA methylation have been reported to occur during development and aging; however, much remains to be learned regarding post-natal and age-associated epigenome dynamics, and few if any investigations have compared human methylome patterns on a whole genome basis in cells from newborns and adults. The aim of this study was to reveal genomic regions with distinct structure and sequence characteristics that render them subject to dynamic post-natal developmental remodeling or age-related dysregulation of epigenome structure. DNA samples derived from peripheral blood monocytes and in vitro differentiated dendritic cells were analyzed by methylated DNA Immunoprecipitation (MeDIP) or, for selected loci, bisulfite modification, followed by next generation sequencing. Regions of interest that emerged from the analysis included tandem or interspersed-tandem gene sequence repeats (PCDHG, FAM90A, HRNR, ECEL1P2), and genes with strong homology to other family members elsewhere in the genome (FZD1, FZD7 and FGF17). Our results raise the possibility that selected gene sequences with highly homologous copies may serve to facilitate, perhaps even provide a clock-like function for, developmental and age-related epigenome remodeling. If so, this would represent a fundamental feature of genome architecture in higher eukaryotic organisms.
Querying by color regions using VisualSEEk content-based visual query system (1997)

VisualSEEk is a highly functional image database manipulation system that provides advanced user tools for searching, browsing and retrieving images. VisualSEEk is distinct from other content-based image query systems in that the user may query for images using both the visual properties of regions and their spatial layout. Furthermore, the image analysis for region extraction is fully automated. VisualSEEk uses a novel system for region extraction and representation based upon color sets. Through a process of color set back-projection, the system automatically extracts salient color regions from images. This paper describes the implementation of the color query system and examines its role for content-based visual query in image and video databases. The next phases of the VisualSEEk implementation will provide additional tools for querying by texture, shape, embedded text and motion features. 1. Introduction This paper describes the design, implementation and operation of the VisualS...
Hydrogen sulfide induced by nitric oxide mediates ethylene-induced stomatal closure of Arabidopsis thaliana (2011)

Pharmacological, laser scanning confocal microscopic (LSCM), real-time PCR and spectrophotographic approaches are used to study the roles of hydrogen sulfide (H2S) and nitric oxide (NO) in signaling transduction of stomatal movement response to ethylene in Arabidopsis thaliana. In the present study, inhibitors of H2S synthesis were found to block ethylene-induced stomatal closure of Arabidopsis. Treatment with ethylene induced H2S generation and increased L-/D-cysteine desulfhydrase (pyridoxalphosphate-dependent enzyme) activity in leaves. Quantitative PCR analysis showed AtL-CDes and AtD-CDes transcripts were induced by ethylene. It is suggested that ethylene-induced H2S levels and L-/D-cysteine desulfhydrase activity decreased when NO was compromised. The data clearly show that ethylene was able to induce H2S generation and stomatal closure in Atnoa1 plants, but failed in the Atnia1,nia2 mutant. Inhibitors of H2S synthesis had no effect on ethylene-induced NO accumulation and nitrate reductase (NR) activity in guard cells or leaves of Arabidopsis, whereas ethylene was able to induce NO synthesis. Therefore, we conclude that H2S and NO are involved in the signal transduction pathway of ethylene-induced stomatal closure. In Arabidopsis, H2S may represent a novel downstream indicator of NO during ethylene-induced stomatal movement.
A Framework for Transparency in Drilling Mechanics and Dynamics Measurements (2015)

Abstract The use of real-time mechanics and dynamics measurements has expanded and evolved significantly in the last thirty years, enabling the safe and reliable drilling of complex wells. Unfortunately, these measurements are poorly defined, which inhibits straightforward analysis and hinders development of models, simulators and automation applications. Adoption of open measurement guidelines will provide the transparency required to improve the value of existing measurements and accelerate the development and adoption of enhanced applications and automation. Mechanics and dynamics measurements currently can be processed and transmitted from downhole in near real-time and then merged with other surface measurements. Optimization of the drilling process uses these combined measurements for monitoring, advising and control, thereby delivering a quality borehole as planned, in a safe and reliable fashion. Processing includes real-time filtering, mathematical modeling, and simulation, which are significant parts of any systems approach. There are currently multiple methods used to quantify downhole and surface vibrations, displacements, and forces. Tools use dissimilar sensor and processing configurations, so they yield significantly different data. Regrettably, these different measurements are given the same name, and published descriptions often do not include the details required to understand and properly utilize the data. Examples of key information include sensor characteristics, sensor arrangement, bandwidth, and signal processing. Guidelines are suggested to resolve this state of confusion, including: terminology describing each drilling mechanics and dynamics sensor, configuration, and measurement; and metadata describing how a data value is derived, filtered, processed, transmitted and stored. This paper examines and defines drilling mechanics and dynamics measurements. It recommends measurement practices and good processing techniques of these measurements, with examples, and presents a recommended open measurement framework. Adoption of this framework will resolve the current state of confusion and uncertainty, enable all parties to develop monitoring, advising and control applications that use these data, and help lower well costs and improve borehole quality.
Specific in vitro anti‐tumour activity of methotrexate‐monoclonal antibody conjugates prepared using human serum albumin as an intermediary (1988)

Methotrexate (MTX) is a folic acid antagonist widely used in the treatment of cancer but, like other such agents, has non-specific toxic side effects. With the aim of reducing these toxic effects, MTX was coupled to monoclonal antibodies (MoAb) in one of two ways; either (a) directly using an active ester derivative or (b) via human serum albumin (HSA), to act as an intermediary and so increase the amount of MTX bound. The MTX coupled directly to anti-Ly-2.1 antibody had approximately 10 molecules of MTX per antibody molecule, whereas the HSA coupled material had 24 molecules of MTX per antibody molecule. After coupling MTX directly to antibody there was a loss of potency of the MTX, and MTX-MoAb conjugates were 30-fold less potent than free MTX, although the antibody-coupled material was more specific than free MTX and bound only to the antibody-reactive target cells. By contrast, the MTX-HSA-MoAb conjugates were 3.5 times less potent than free MTX and were 8.5 times more potent than MTX-MoAb conjugates. Thus, by increasing the amount of drug bound to antibody, more toxic conjugates were made--an important principle for the use of such conjugates for the treatment of cancer in man.
Neural tube defects and maternal biomarkers of folate, homocysteine, and glutathione metabolism (2006)

Increased maternal oxidative stress and decreased methylation capacity may contribute to the occurrence of NTDs. Further analysis of relevant genetic and environmental factors is required to define the basis for these observed alterations.
Altered expression of AMPAR and NMDAR subunits in hippocampal CA1 area with contextual fear memory generalization in mice (2018)

Objective
To investigate the alteration of subunit expression of AMPAR and NMDAR in hippocampal CA1 area of mice with contextual fear memory generalization.


Methods
35 male C57BL/6 mice, aged 8 weeks, were involved in the experiment.Seven mice were randomly selected as the naive group, which didn't receive the behavioral training.28 mice experienced the context fear conditioning and contextual shift task were divided into generalization group and non generalization group according to the result.Then Western blot was used to measure the expression of AMPAR and NMDAR subunits in CA1 in the naive group, non generalization group and generalization group.


Results
(1)Seven mice (discrimination ratio: 0.52±0.08) showed contextual generalization when undergoing the same stress level, while the other 21 mice (discrimination ratio: 0.75±0.07) didn’t (P 0.05). (3)NR1 subunit was similar in the three groups(P>0.05). NR2A expression was significantly increased in the non generalization group(1.11±0.20) and generalization group (1.09±0.20 ) compared with that in the naive group(0.95±0.17) (both P<0.05). The expression of NR2B was significantly increased in generalization group(1.05±0.17) compared with that in the naive group(0.83±0.19) and non generalization group(0.80±0.14 )(both P<0.05). The ratio of NR2A/NR2B was significantly increased in non generalization group(1.23±0.25) compared with that in the naive group(0.89±0.31) and generalization group (0.86±0.17)(both P<0.05).


Conclusion
(1)Only part of the individuals show contextual fear memory generalization after the same stress, and this contextual generalization progress is not related to the acquisition of context fear memory.(2)There is no significant change in expression of AMPAR subunits in CA1 of mice with the contextual generalization.The rise of NR2B and the decline of ratio of NR2A/NR2B are the main changes, suggesting that consequently the alternation of synaptic plasticity maybe one of the mechanisms of contextual fear memory generalization.


Key words: 
Contextual fear memory; Generalization; AMPA receptors; NMDA receptors
A single phylogenetic analysis of Bacillus thuringiensis strains and bacilli species inferred from 16S rRNA gene restriction fragment length polymorphism is congruent with two independent phylogenetic analyses (2002)

The combined phylogenetic study presented here, inferred from 16S rRNA gene restriction fragment length polymorphism, is congruent with two earlier independent phylogenetic studies, one on B. thuringiensis and the other on bacilli species.
Structural Transformation of Miscanthus × giganteus Lignin Fractionated under Mild Formosolv, Basic Organosolv, and Cellulolytic Enzyme Conditions (2011)

Detailed chemical structural elucidation of lignin fractions from Miscanthus × giganteus was performed by several analytical techniques. Mild formosolv, basic organosolv, and cellulolytic enzyme treatments were applied to isolate three lignin fractions (AL, BL, and CL, respectively), and their structural characterization was comparatively evaluated. Both non-destructive techniques [e.g., Fourier transform infrared (FTIR) spectroscopy, size-exclusion chromatography (SEC), and two-dimensional (2D) nuclear magnetic resonance (NMR)] and degradation methods [e.g., acidic hydrolysis, derivatization followed by reductive cleavage (DFRC), and thioacidolysis] were used. The analysis revealed that a certain amount of carbohydrates (12.8%) was associated with CL and partially led to its increased molecular weight determined by SEC before acetylation. β-O-4 linkages were determined to be the predominant interunits (82%), but also, extensively acylated structures were observed. Alkaline organosolv treatment significantly improved the purity of the lignin fraction (carbohydrate content of 1.0%) and basically kept the original structure of the lignin macromolecule. Under acidic conditions, not only the portion of aryl alkyl ether bonds were cleaved but also new carbon-carbon bonds were formed by condensation reactions, resulting in an increment of the lignin molecular weights. Guaiacyl units were more reactive toward condensation than syringyl units, which was evidenced by an increasing S/G ratio from 0.7 (CL) to 1.7 (AL).