bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Patch-Clamp Study on the Physiology of Aluminum Toxicity and Aluminum Tolerance in Maize. Identification and Characterization of Al3+-Induced Anion Channels
Authors: Piñeros Miguel A. , Kochian Leon V. 
Published: July 2002

Abstract
The presence of Al3+ in the rhizosphere induces citrate efflux from the root apex of the Al-tolerant maize (Zea mays) hybrid South American 3, consequently chelating and reducing the activity of toxic Al3+ at the root surface. Because citrate is released from root apical cells as the deprotonated anion, we used the patch-clamp technique in protoplasts isolated from the terminal 5 mm of the root to study the plasma membrane ion transporters that could be involved in Al-tolerance and Al-toxicity responses. Acidification of the extracellular environment stimulated inward K+ currents while inhibiting outward K+currents. Addition of extracellular Al3+ inhibited the remaining K+ outward currents, blocked the K+inward current, and caused the activation of an inward Cl−current (anion efflux). Studies with excised membrane patches revealed the existence of Al-dependent anion channels, which were highly selective for anions over cations. Our success in activating this channel with extracellular Al3+ in membrane patches excised prior to any Al3+ exposure indicates that the machinery required for Al3+ activation of this channel, and consequently the whole root Al3+ response, is localized to the root-cell plasma membrane. This Al3+-activated anion channel may also be permeable to organic acids, thus mediating the Al-tolerance response (i.e. Al-induced organic acid exudation) observed in intact maize root apices.
N-Acetylglucosamine and Glucosamine-Containing Arabinogalactan Proteins Control Somatic Embryogenesis
Authors: van Hengel Arjon J. , Tadesse Zewdie , Immerzeel Peter , Schols Henk , van Kammen Ab , de Vries Sacco C. 
Published: July 2002

Abstract
In plants, complete embryos can develop not only from the zygote, but also from somatic cells in tissue culture. How somatic cells undergo the change in fate to become embryogenic is largely unknown. Proteins, secreted into the culture medium such as endochitinases and arabinogalactan proteins (AGPs) are required for somatic embryogenesis. Here we show that carrot (Daucus carota) AGPs can contain glucosamine andN-acetyl-d-glucosaminyl and are sensitive to endochitinase cleavage. To determine the relevance of this observation for embryogenesis, an assay was developed based on the enzymatic removal of the cell wall from cultured cells. The resulting protoplasts had a reduced capacity for somatic embryogenesis, which could be partially restored by adding endochitinases to the protoplasts. AGPs from culture medium or from immature seeds could fully restore or even increase embryogenesis. AGPs pretreated with chitinases were more active than untreated molecules and required an intact carbohydrate constituent for activity. AGPs were only capable of promoting embryogenesis from protoplasts in a short period preceding cell wall reformation. Apart from the increase in embryogenesis, AGPs can reinitiate cell division in a subpopulation of otherwise non-dividing protoplasts. These results show that chitinase-modified AGPs are extracellular matrix molecules able to control or maintain plant cell fate.
Azospirillum brasilense and Azospirillum lipoferum Hydrolyze Conjugates of GA20 and Metabolize the Resultant Aglycones to GA1 in Seedlings of Rice Dwarf Mutants
Authors: Cassán Fabricio , Bottini Rubén , Schneider Gernot , Piccoli Patricia 
Published: July 2002

Abstract
Azospirillum species are plant growth-promotive bacteria whose beneficial effects have been postulated to be partially due to production of phytohormones, including gibberellins (GAs). In this work, Azospirillum brasilense strain Cd andAzospirillum lipoferum strain USA 5b promoted sheath elongation growth of two single gene GA-deficient dwarf rice (Oryza sativa) mutants, dy anddx, when the inoculated seedlings were supplied with [17,17-2H2]GA20-glucosyl ester or [17,17- 2H2]GA20-glucosyl ether. Results of capillary gas chromatography-mass spectrometry analysis show that this growth was due primarily to release of the aglycone [17,17-2H2]GA20 and its subsequent 3β-hydroxylation to [17,17-2H2]GA1 by the microorganism for the dy mutant, and by both the rice plant and microorganism for the dx mutant.
The Arabidopsis Cell Plate-Associated Dynamin-Like Protein, ADL1Ap, Is Required for Multiple Stages of Plant Growth and Development
Authors: Kang Byung-Ho , Busse James S. , Dickey Carrie , Rancour David M. , Bednarek Sebastian Y. 
Published: July 2002

AbstractDynamin and dynamin-like proteins are GTP-binding proteins involved in vesicle trafficking. In soybean, a 68-kD dynamin-like protein called phragmoplastin has been shown to be associated with the cell plate in dividing cells (Gu and Verma, 1996). Five ADL1 genes encoding dynamin-like proteins related to phragmoplastin have been identified in the completed Arabidopsis genome. Here we report that ADL1Ap is associated with punctate subcellular structures and with the cell plate in dividing cells. To assess the function of ADL1Ap we utilized a reverse genetic approach to isolate three separate Arabidopsis mutant lines containing T-DNA insertions inADL1A. Homozygous adl1A seeds were shriveled and mutant seedlings arrested soon after germination, producing only two leaf primordia and severely stunted roots. Immunoblotting revealed that ADL1Ap expression was not detectable in the mutants. Despite the loss of ADL1Ap, the mutants did not display any defects in cytokinesis, and growth of the mutant seedlings could be rescued in tissue culture by the addition of sucrose. Although these sucrose-rescued plants displayed normal vegetative growth and flowered, they set very few seeds. Thus, ADL1Ap is critical for several stages of plant development, including embryogenesis, seedling development, and reproduction. We discuss the putative role of ADL1Ap in vesicular trafficking, cytokinesis, and other aspects of plant growth.
Oligomerization of acidic fibroblast growth factor is not a prerequisite for its cell proliferation activity
Authors: Arunkumar Alphonse I. , Kumar Thallampuranam Krishnaswamy S. , Kathir Karuppanan Muthusamy , Srisailam Sampath , Wang Han‐Min , Leena Philominathan Sagaya Theresa , Chi Ya‐Hui , Chen Ho‐Chz , Wu Chieh‐Hsi , Wu Rong‐Tsun , Chang Gu‐Gang , Chiu Ing‐Ming , Yu Chin 
Published: July 2002

AbstractOligomerization of fibroblast growth factors (FGFs) induced on binding to heparin or heparan sulfate proteoglycan is considered to be crucial for receptor activation and initiation of biological responses. To gain insight into the mechanism of activation of the receptor by FGFs, in the present study we investigate the effect(s) of interaction of a heparin analog, sucrose octasulfate (SOS), on the structure, stability, and biological activities of a recombinant acidic FGF from Notophthalmus viridescens (nFGF‐1). SOS is found to bind to nFGF‐1 and significantly increase the thermodynamic stability of the protein. Using a variety of techniques such as size‐exclusion chromatography, sedimentation velocity, and multidimensional nuclear magnetic resonance (NMR) spectroscopy, it is shown that binding of SOS to nFGF‐1 retains the protein in its monomeric state. In its monomeric state (complexed to SOS), n‐FGF‐1 shows significant cell proliferation activity. 15N and 1H chemical shift perturbation and the intermolecular nuclear Overhauser effects (NOEs) between SOS and nFGF‐1 reveal that the ligand binds to the dense, positively charged cluster located in the groove enclosed by β‐strands 10 and 11. In addition, molecular modeling based on the NOEs observed for the SOS‐nFGF‐1 complex, indicates that SOS and heparin share a common binding site on the protein. In conclusion, the results of the present study clearly show that heparin‐induced oligomerization of nFGF‐1 is not mandatory for its cell proliferation activity.
LiveBench‐1: Continuous benchmarking of protein structure prediction servers
Authors: Bujnicki Janusz M. , Elofsson Arne , Fischer Daniel , Rychlewski Leszek 
Published: July 2002

AbstractWe present a novel, continuous approach aimed at the large‐scale assessment of the performance of available fold‐recognition servers. Six popular servers were investigated: PDB‐Blast, FFAS, T98‐lib, GenTHREADER, 3D‐PSSM, and INBGU. The assessment was conducted using as prediction targets a large number of selected protein structures released from October 1999 to April 2000. A target was selected if its sequence showed no significant similarity to any of the proteins previously available in the structural database. Overall, the servers were able to produce structurally similar models for one‐half of the targets, but significantly accurate sequence‐structure alignments were produced for only one‐third of the targets. We further classified the targets into two sets: easy and hard. We found that all servers were able to find the correct answer for the vast majority of the easy targets if a structurally similar fold was present in the server's fold libraries. However, among the hard targets—where standard methods such as PSI‐BLAST fail—the most sensitive fold‐recognition servers were able to produce similar models for only 40% of the cases, half of which had a significantly accurate sequence‐structure alignment. Among the hard targets, the presence of updated libraries appeared to be less critical for the ranking. An “ideally combined consensus” prediction, where the results of all servers are considered, would increase the percentage of correct assignments by 50%. Each server had a number of cases with a correct assignment, where the assignments of all the other servers were wrong. This emphasizes the benefits of considering more than one server in difficult prediction tasks. The LiveBench program (http://BioInfo.PL/LiveBench) is being continued, and all interested developers are cordially invited to join.
The application of frequency‐modulated continuous wave modulated thermoacoustic imaging in geological media
Authors: Liu Chang , Wang Chang , Mao Xu , Zhang Weite , Martínez‐López Raquel Isabel , Heredia‐Juesas Juan , Martinez‐Lorenzo Jose 
Published: February 2025

AbstractA thermoacoustics imaging system is investigated in this paper to enhance conventional imaging modalities in geological subsurface situational awareness applications. While thermoacoustics imaging has traditionally been used in biological scenarios like breast cancer detection, this work aims to extend thermoacoustics imaging to geophysical applications by demonstrating that water‐saturated sand can be distinguished from dry and oil‐saturated sand based on their amplitude differences. This breakthrough enables the feasibility of monitoring water distribution in these media. Moreover, to compensate for the low conversion efficiency from electromagnetic power to thermoacoustics amplitude, the signal modulation method is used by applying the frequency‐modulated continuous wave techniques. The experiment results show that the frequency‐modulated continuous wave can enhance the signal‐to‐noise ratio while maintaining a similar resolution as the pulse‐excited thermoacoustics wave. These findings pave the way for the future use of thermoacousticsimaging in subsurface sensing and imaging of fluid flow and transport in porous media.
Thermodynamics Underpinning the Microbial Community‐Level Nitrogen Energy Metabolism
Authors: Seto Mayumi , Sasaki Risa , Ooka Hideshi , Nakamura Ryuhei 
Published: February 2025

ABSTRACTNitrogen compounds often serve as crucial electron donors and acceptors in microbial energy metabolism, playing a key role in biogeochemical cycles. The energetic favorability of nitrogen oxidation–reduction (redox) reactions, driven by the thermodynamic properties of these compounds, may have shaped the evolution of microbial energy metabolism, though the extent of their influence remains unclear. This study quantitatively evaluated the similarity between energetically superior nitrogen reactions, identified from 988 theoretically plausible reactions, and the nitrogen community‐level network, reconstructed as a combination of enzymatic reactions representing intracellular to interspecies‐level reaction interactions. Our analysis revealed significant link overlap rates between these networks. Notably, composite enzymatic reactions aligned more closely with energetically superior reactions than individual enzymatic reactions. These findings suggest that selective pressure from the energetic favorability of redox reactions can operate primarily at the species or community level, underscoring the critical role of thermodynamics in shaping microbial metabolic networks and ecosystem functioning.
Voxel‐Based Dosimetry as a Means for Treatment Personalisation in Radioembolization: A Systematic Review
Authors: Schlegel R. N. , Griffin S. , Merchant A. , Ma D. , Owen A. 
Published: February 2025

ABSTRACTIntroductionRadionuclide therapy including 90Y radioembolization is an established form of brachytherapy for treatment of malignancy including hepatocellular carcinoma. Currently, there are several methods available to estimate patient absorbed dose, including voxel‐based dosimetry, that can achieve a level of personalisation in the planning and outcome assessments of radioembolization. Despite the advantages of voxel‐based dosimetry, it remains a relatively new concept in radioembolization. This study evaluates if voxel‐based dosimetry was associated with improved treatment efficacy in radioembolization planning.MethodsA systematic review was conducted by searching relevant databases (Medline Ovid, PubMed, Embase Ovid, CINAHL Complete, Cochrane Library, CENTRAL, Australian New Zealand Clinical Trials Registry, ClinicalTrials.gov, WHO International Trials Registry, Google Scholar) for literature regarding voxel‐based dosimetry in radioembolization.ResultsA total of 41 papers were included for this systematic review. Review of these studies revealed that voxel‐based dosimetry can benefit numerous aspects of radioembolization in radionuclide therapy including predicting tumour response, toxicity and patient survival. Numerous studies also indicated that voxel‐based dosimetry in radioembolization is a more accurate approach in establishing a dose‐effect relationship in targeted radionuclide therapy when compared to other methods. Despite these promising findings, these studies did not investigate or comment on the accuracy of voxel‐based dosimetry.ConclusionThe evidence from this review highlights that voxel‐based dosimetry can improve treatment efficacy in radioembolization planning. However, further studies are required to validate the accuracy and feasibility of voxel‐based dosimetry in clinical practice.
Influence of laser parameters on texturing of 3Y‐TZP and Ce‐TZP/Al2O3/SrAl12O19 composite
Authors: Fabris Douglas , Ränke Fabian , Fredel Márcio C. , Lasagni Andrés F. , Henriques Bruno 
Published: February 2025

AbstractThe development of new materials and surface functionalization processes has been extensively studied to further improve the performance of implants. This work explores the direct laser writing method as a potential alternative to produce controlled textures on the surface of traditional 3Y‐TZP and a novel high‐toughness composite (Ce‐TZP/Al2O3/SrAl12O19). A 532 nm picosecond laser source is used to produce lines in sintered samples of both materials with different values of laser fluence, repetition rate, and scanning speed. The resulting textured samples are analyzed using confocal and scanning electron microscopes. Both materials were successfully textured using the laser technique, but the groove morphology and geometry are highly dependent on the parameters used. While low energy results in shallow and irregular grooves, high energy can result in crack and resolidification layer. Overall, for the same set of parameters, the laser produced wider and deeper grooves in the nanocomposite (up to 30 µm wide and 26 µm deep) than in the 3Y‐TZP (up to 12 µm wide and 6 µm deep). Hence, this work showed the feasibility of laser texturing of traditional 3Y‐TZP and the novel Ce‐TZP/Al2O3/SrAl12O19 that can be further explored to functionalize their surfaces for biomedical applications.
An mHealth app technology to strengthen adverse event management of multi‐drug‐resistant tuberculosis in Vietnam: Protocol for a process evaluation of the V‐SMART trial
Authors: Nguyen Binh Hoa , Dang Tho T. H. , Hoang Duy Trinh , Do Thu Thuong , Van Dinh Luong , Nguyen Viet Nhung , Vu Dinh Hoa , Drabarek Dorothy , Nguyen Tram N. B. , Vu Dang , Nguyen Thu Anh , Marks Guy B. , Negin Joel , Fox Greg J. , Bernays Sarah , Yapa H. Manisha 
Published: February 2025

AbstractBackgroundDrug‐related adverse events cause poorer treatment outcomes amongst people with multi‐drug‐resistant tuberculosis, exacerbating a major global public health problem. The Harnessing new mHealth technologies to Strengthen the Management of Multi‐Drug‐Resistant Tuberculosis in Vietnam (V‐SMART) trial tests whether a mobile health (mHealth) application (app) can optimise management of drug‐related adverse events, within routine health services in Vietnam. Implementation of digital health within routine services is complex and driven by behaviour change as well as a range of health system factors. Understanding implementation is key to informing the evidence base for digital health prior to scale up, despite its potential appeal.MethodsThrough a process evaluation of the V‐SMART trial, we aim to (i) understand the multi‐drug‐resistant tuberculosis service delivery context and how trial procedures are implemented within services; (ii) describe ‘dose’ and ‘reach’ of the app; and (iii) understand health worker and patient perspectives of app implementation and identify areas for improvement.To achieve this, we will (i) conduct process maps (patient flow maps) to describe implementation of the mHealth intervention within routine multi‐drug‐resistant tuberculosis health services including adverse event management pathways at different levels of the health system; (ii) measure app usage by all participating health workers and people with multi‐drug‐resistant tuberculosis over time; and (iii) conduct a total of up to 45 semi‐structured interviews in seven provinces, with people with multi‐drug‐resistant tuberculosis, health workers, and policymakers, to identify determinants of app uptake and suggestions for future person‐centred app design. Interview topic guides are informed by the Theoretical Framework for Acceptability, Normalisation Process Theory, and the Tailored Implementation of Chronic Diseases framework respectively.DiscussionThe process evaluation will strongly complement the parent trial impact evaluation, and the economic evaluation. Moreover, it will inform future tailored approaches to scaling up digital health as part of broader health system strengthening initiatives.
Combustion Characteristics of Heavy Liquid Fuels in a Bubbling Fluidized Bed
Authors: Anthony E. J. , Lu D. Y. , Zhang J. Q. 
Published: July 2002

AbstractLiquid fuels such as bitumen, tars, and pitches are byproducts of heavy oil upgrading processes, and are usually contaminated with high sulphur and sometimes heavy metals contents as well. Fluidized bed combustion (FBC) appears to be a promising technology for the combustion of such fuels due to its inherent fuel flexibility and low emissions characteristics. The combustion of three liquid fuels, i.e., no. 6 oil, bitumen and pitch was investigated in a pilot-scale bubbling FBC unit. An efficient liquid fuel feeding system was developed and a bubbling FBC was successfully used to combust all three liquid fuels. The proportion of fuel escaping in the form of unburnt hydrocarbons in the flue gas was less than 0.4 percent and combustion efficiencies higher than 98.5 percent were achieved. However, combustion of liquid fuels tended to occur in the freeboard and, therefore, good mixing of the fuels in the bed was critical in achieving satisfactory combustion performance.
Oxygen induced adhesion degradation at metal/polyimide interface
Authors: Shih Da-Yuan , Klymko Nancy , Flitsch Richard , Paraszczak Jurij , Nunes Sharon 
Published: July 2002

The role of oxygen in affecting the adhesive bonding at the metal/polyimide (polyimide-on-metal) interface has been studied. Both pyromellitic dianhydride (PMDA) -oxydianiline (ODA) and biphenyl-tetracarboxylic dianhydride(BPDA) -p-phenylene diamine (PDA) based poly(amic acid) precursors were cast and fully imidized on metal surfaces of Cr, Cu, Ni, Co, Cu/Ni, and Cu/Co in a nitrogen atmosphere. The peel strengths at the polyimide-on-metal interface were measured, using a 90° peel test, immediately after curing, and then remeasured after annealing in either nitrogen (N2−≤100 ppm O2 ) or air (N2 –21% O2 ) at 350 °C for 1 h. Very little or no change in peel strength was measured after these samples were annealed in nitrogen, while significant adhesion degradations were measured on all metals after annealing in air. The loss of polyimide (PI) adhesion to the Cu or Co surface is attributed to metal catalyzed thermal–oxidative degradation of the PI at the metal/PI interface, as characterized by polyimide thickness reduction, Fourier transform infrared and x-ray photoelectron spectrometries. The rate of degradation of the PMDA-ODA films on Cu or Co is several times faster than that of the BPDA-PDA films.
The degradation products were characterized as CO2, CO, Cu carboxylate salts and a nitrile moiety entrapped in partially degraded PI films. The extent of degradation was found to increase with increasing oxygen content in the annealing ambient or with decreasing PI thickness, indicating that oxygen diffusion through the PI overcoating to the metal/PI interface plays a critical role in promoting degradation. On the Cr and Ni surfaces, such metal catalyzed degradation was not detected with our techniques, while some adhesion strength was still retained, a significant loss in adhesion strength was observed. This is probably due to oxidation of the metal underlayer causing debonding at the originally well adhered metal/PI interface. When all testing variables were held constant, the peel strength of a well adhered metal/PI joint is shown to increase with increasing peeling rate (crosshead speed). An increase of up to ∼40% in peel strength was measured when the crosshead speed was increased from a low speed of 0.05 mm/min to 10 mm/min. The locus of fracture of the as-cured films was cohesive, i.e., the fractured surface was located within PI, while for the thermal–oxidative degraded joint the failure mode was changed to adhesive.