bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold plasma treatment to release dormancy and improve growth in grape buds: a promising alternative to natural chilling and rest breaking chemicals
Authors: Mujahid Z. , Tounekti T. , Khemira H. 
Published: February 2020

AbstractWinter dormancy of temperate zone perennial plant species is commonly released by chilling temperature. If the duration of the cold weather is not adequate, plant growth becomes disorganized leading to reduced growth, spread out flowering and fruit maturation and often reduced yield. In mild-winter regions, growers commonly resort to spraying their trees with chemicals such as hydrogen cyanamide to compensate for the lack of chilling to ensure good growth and yield. Although effective, most of these chemicals are highly toxic; unfortunately, there is no effective and environmentally friendly alternative which can be used to release dormancy. In this work, we present a cold plasma treatment-based method which can effectively release the dormancy of grape buds. We have found that exposing grape buds to plasma provides improvement of several growth parameters including higher, faster and more synchronous budbreak and more vigorous vegetative growth, comparatively similar to or better than natural chilling. Biochemical analyses of bud tissue suggest that the plasma treatment triggered a marked transient oxidative stress as indicated by the increase in the concentrations of free proline, malondialdehyde (MDA) and hydrogen peroxide (H2O2). Proline appears to have played a key role; as a compatible osmolyte, it may have protected cellular structures against free radicals and as a signaling molecule, it may have induced the events leading to dormancy release. We anticipate that our work will provide a starting point for the development of novel plasma-based tools and methods to treat dormant plants. The plasma treatment method may allow higher agricultural production in several regions of the world at risk of becoming marginal for the cultivation of certain crops due to global warming.
Extract from used Xpert MTB/RIF Ultra cartridges is useful for accurate second-line drug-resistant tuberculosis diagnosis with minimal rpoB-amplicon cross-contamination risk
Authors: Venter Rouxjeane , Minnies Stephanie , Derendinger Brigitta , Tshivhula Happy , de Vos Margaretha , Dolby Tania , Ruiters Ashley , Warren Robin M. , Theron Grant 
Published: February 2020

AbstractXpert MTB/RIF Ultra (Ultra) detects Mycobacterium tuberculosis and rifampicin resistance. Follow-on drug susceptibility testing (DST) requires additional sputum. Extract from the diamond-shaped chamber of the cartridge (dCE) of Ultra’s predecessor, Xpert MTB/RIF (Xpert), is useful for MTBDRsl-based DST but this is unexplored with Ultra. Furthermore, whether CE from non-diamond compartments is useful, the performance of FluoroType MTBDR (FT) on CE, and rpoB cross-contamination risk associated with the extraction procedure are unknown. We tested MTBDRsl, MTBDRplus, and FT on CEs from chambers from cartridges (Ultra, Xpert) tested on bacilli dilution series. MTBDRsl on Ultra dCE on TB-positive sputa (n = 40) was also evaluated and, separately, rpoB amplicon cross-contamination risk . MTBDRsl on Ultra dCE from dilutions ≥103 CFU/ml (CTmin <25, >“low semi-quantitation”) detected fluoroquinolone (FQ) and second-line injectable (SLID) susceptibility and resistance correctly (some SLIDs-indeterminate). At the same threshold (at which ~85% of Ultra-positives in our setting would be eligible), 35/35 (100%) FQ and 34/35 (97%) SLID results from Ultra dCE were concordant with sputa results. Tests on other chambers were unfeasible. No tubes open during 20 batched extractions had FT-detected rpoB cross-contamination. False-positive Ultra rpoB results was observed when dCE dilutions ≤10−3 were re-tested. MTBDRsl on Ultra dCE is concordant with isolate results. rpoB amplicon cross-contamination is unlikely. These data mitigate additional specimen collection for second-line DST and cross-contamination concerns.
Appraising the potential of Zr-based biomedical alloys to reduce magnetic resonance imaging artifacts
Authors: Suzuki Anderson Kiyoshi , Campo Kaio Niitsu , Fonseca Eduardo Bertoni , Araújo Luana Caldeira , Gandra Flávio César Guimarães , Lopes Éder Sócrates Najar 
Published: February 2020

AbstractThis study compared Zr-Mo alloys with commercial metallic biomaterials. It was observed that the Zr-Mo alloys exhibited favourable mechanical properties, particularly the Zr-10Mo alloy, which showed the highest strength to Young’s modulus ratio among all evaluated metals. These alloys also exhibited the lowest magnetic susceptibilities, which are important for magnetic resonance imaging (MRI). However, both Zr- and Ti-based metals yielded comparable artifacts. It was concluded that the magnetic susceptibility must differ considerably to afford significantly improved MRI quality owing to the increased importance of non-susceptibility-related artifacts when comparing materials with relatively similar magnetic susceptibilities.
Fractional Anisotropy changes in Parahippocampal Cingulum due to Alzheimer’s Disease
Authors: Dalboni da Rocha Josué Luiz , Bramati Ivanei , Coutinho Gabriel , Tovar Moll Fernanda , Sitaram Ranganatha 
Published: February 2020

AbstractCurrent treatments for Alzheimer’s disease are only symptomatic and limited to reduce the progression rate of the mental deterioration. Mild Cognitive Impairment, a transitional stage in which the patient is not cognitively normal but do not meet the criteria for specific dementia, is associated with high risk for development of Alzheimer’s disease. Thus, non-invasive techniques to predict the individual’s risk to develop Alzheimer’s disease can be very helpful, considering the possibility of early treatment. Diffusion Tensor Imaging, as an indicator of cerebral white matter integrity, may detect and track earlier evidence of white matter abnormalities in patients developing Alzheimer’s disease. Here we performed a voxel-based analysis of fractional anisotropy in three classes of subjects: Alzheimer’s disease patients, Mild Cognitive Impairment patients, and healthy controls. We performed Support Vector Machine classification between the three groups, using Fisher Score feature selection and Leave-one-out cross-validation. Bilateral intersection of hippocampal cingulum and parahippocampal gyrus (referred as parahippocampal cingulum) is the region that best discriminates Alzheimer’s disease fractional anisotropy values, resulting in an accuracy of 93% for discriminating between Alzheimer’s disease and controls, and 90% between Alzheimer’s disease and Mild Cognitive Impairment. These results suggest that pattern classification of Diffusion Tensor Imaging can help diagnosis of Alzheimer’s disease, specially when focusing on the parahippocampal cingulum.
A Novel in situ Approach to Studying Detrusor Smooth Muscle Cells in Mice
Authors: Serdinšek Tamara , Lipovšek Saša , Leitinger Gerd , But Igor , Stožer Andraž , Dolenšek Jurij 
Published: February 2020

AbstractThe aim of our study was to develop a novel approach to investigating mouse detrusor smooth muscle cell (SMC) physiological activity, utilizing an acute tissue dissection technique and confocal calcium imaging. The bladder of a sacrificed adult female NMRI mouse was dissected. We used light and transmission electron microscopy to assess morphology of SMCs within the tissue. Calcium imaging in individual SMCs was performed using confocal microscopy during stimulation with increasing concentrations of carbamylcholine (CCh). SMCs were identified according to their morphology and calcium activity. We determined several parameters describing the SMC responses: delays to response, recruitment, relative activity, and contraction of the tissue. CCh stimulation revealed three different SMC phenotypes: spontaneously active SMCs with and without CCh-enhanced activity and SMCs with CCh-induced activity only. SMCs were recruited into an active state in response to CCh-stimulation within a narrow range (1–25 µM); causing activation of virtually all SMCs. Maximum calcium activity of SMCs was at about 25 µM, which coincided with a visible tissue contraction. Finally, we observed shorter time lags before response onsets with higher CCh concentrations. In conclusion, our novel in situ approach proved to be a robust and reproducible method to study detrusor SMC morphology and physiology.
Evaluating thyroid hormone disruption: investigations of long-term neurodevelopmental effects in rats after perinatal exposure to perfluorohexane sulfonate (PFHxS)
Authors: Ramhøj Louise , Hass Ulla , Gilbert Mary E. , Wood Carmen , Svingen Terje , Usai Diana , Vinggaard Anne Marie , Mandrup Karen , Axelstad Marta 
Published: February 2020

AbstractThyroid hormones are critical for mammalian brain development. Thus, chemicals that can affect thyroid hormone signaling during pregnancy are of great concern. Perfluorohexane sulfonate (PFHxS) is a widespread environmental contaminant found in human serum, breastmilk, and other tissues, capable of lowering serum thyroxine (T4) in rats. Here, we investigated its effects on the thyroid system and neurodevelopment following maternal exposure from early gestation through lactation (0.05, 5 or 25 mg/kg/day PFHxS), alone or in combination with a mixture of 12 environmentally relevant endocrine disrupting compounds (EDmix). PFHxS lowered thyroid hormone levels in both dams and offspring in a dose-dependent manner, but did not change TSH levels, weight, histology, or expression of marker genes of the thyroid gland. No evidence of thyroid hormone-mediated neurobehavioral disruption in offspring was observed. Since human brain development appear very sensitive to low T4 levels, we maintain that PFHxS is of potential concern to human health. It is our view that current rodent models are not sufficiently sensitive to detect adverse neurodevelopmental effects of maternal and perinatal hypothyroxinemia and that we need to develop more sensitive brain-based markers or measurable metrics of thyroid hormone-dependent perturbations in brain development.
Dynamic chiral magnetic effect and anisotropic natural optical activity of tilted Weyl semimetals
Authors: Dey Urmimala , Nandy S. , Taraphder A. 
Published: February 2020

AbstractWe study the dynamic chiral magnetic conductivity (DCMC) and natural optical activity in an inversion-broken tilted Weyl semimetal (WSM). Starting from the Kubo formula, we derive the analytical expressions for the DCMC for two different directions of the incident electromagnetic wave. We show that the angle of rotation of the plane of polarization of the transmitted wave exhibits remarkable anisotropy and is larger along the tilt direction. This striking anisotropy of DCMC results in anisotropic optical activity and rotary power, which can be experimentally observed as a topological magneto-electric effect of inversion-broken tilted WSMs. Finally, using the low energy Hamiltonian, we show that the DCMC follows the universal $$\frac{{\bf{1}}}{{{\boldsymbol{\omega }}}^{{\bf{2}}}}$$

1

ω

2

decay in the high frequency regime. In the low frequency regime, however, the DCMC shows sharp peaks at the tilt dependent effective chemical potentials of the left-handed and right-handed Weyl points. This can serve as a signature to distinguish between the type-I and type-II Weyl semimetals.
Single-molecular real-time deep sequencing reveals the dynamics of multi-drug resistant haplotypes and structural variations in the hepatitis C virus genome
Authors: Yamashita Taiki , Takeda Haruhiko , Takai Atsushi , Arasawa Soichi , Nakamura Fumiyasu , Mashimo Yoichi , Hozan Miyuki , Ohtsuru Shigeru , Seno Hiroshi , Ueda Yoshihide , Sekine Akihiro 
Published: February 2020

AbstractWhile direct-acting antivirals (DAAs) for hepatitis C virus (HCV) have dramatically progressed, patients still suffer from treatment failures. For the radical eradication of HCV, a deeper understanding of multiple resistance-associated substitutions (RASs) at the single-clone level is essential. To understand HCV quasispecies and their dynamics during DAA treatment, we applied single-molecule real-time (SMRT) deep sequencing on sera from 12 patients with genotype-1b HCV infections with DAA treatment failures, both pre- and post-treatment. We identified >3.2 kbp sequences between NS3 and NS5A genes of 187,539 clones in total, classifying into haplotype codes based on the linkage of seven RAS loci. The number of haplotype codes during the treatment, per sample, significantly decreased from 14.67 ± 9.12 to 6.58 ± 7.1, while the number of nonsynonymous codons on the seven RAS loci, per clone, significantly increased from 1.50 ± 0.92 to 3.64 ± 0.75. In five cases, the minority multi-drug resistant haplotypes at pre-treatment were identical to the major haplotypes at relapse. Moreover, various structural variations (SVs) were detected and their dynamics analysed. These results suggest that SMRT deep sequencing is useful for detecting minority haplotypes and SVs, and to evaluate the dynamics of viral genomes at the single-clone level.
Impact of pulsed electric fields and mechanical compressions on the permeability and structure of Chlamydomonas reinhardtii cells
Authors: Bensalem Sakina , Pareau Dominique , Cinquin Bertrand , Français Olivier , Le Pioufle Bruno , Lopes Filipa 
Published: February 2020

AbstractCurrent research findings clearly reveal the role of the microalga’s cell wall as a key obstacle to an efficient and optimal compound extraction. Such extraction process is therefore closely related to the microalga species used. Effects of electrical or mechanical constraints on C. reinhardtii’s structure and particularly its cell wall and membrane, is therefore investigated in this paper using a combination of microscopic tools. Membrane pores with a radius between 0.77 and 1.59 nm were determined for both reversible (5 kV∙cm−1) and irreversible (7 kV∙cm−1) electroporation with a 5 µs pulse duration. Irreversible electroporation with longer pulses (10 µs) lead to the entry of large molecules (at least 5.11 nm). Additionally, for the first time, the effect of pulsed electric fields on the cell wall was observed. The combined electrical and mechanical treatment showed a significant impact on the cell wall structure as observed under Transmission Electron Microscopy. This treatment permits the penetration of larger molecules (at least 5.11 nm) within the cell, shown by tracking the penetration of dextran molecules. For the first time, the size of pores on the cell membrane and the structural changes on the microalgae cell wall induced by electrical and mechanical treatments is reported.
Globe thermometer free convection error potentials
Authors: Teitelbaum Eric , Chen Kian Wee , Meggers Forrest , Guo Hongshan , Houchois Nicholas , Pantelic Jovan , Rysanek Adam 
Published: February 2020

AbstractFor thermal comfort research, globe thermometers have become the de facto tool for mean radiant temperature,tr, measurement. They provide a quick means to survey the radiant environment in a space with nearly a century of trials to reassure researchers. However, as more complexity is introduced to built environments, we must reassess the accuracy of globe measurements. In particular, corrections for globe readings taking wind into account rely on a forced convection heat transfer coefficient. In this study, we investigate potential errors introduced by buoyancy driven flow, or free convection, induced by radiant forcing of a black globe’s surface to a temperature different from the air. We discovered this error in an experimental radiant cooling system with high separation of air to radiant temperature. Empirical simulations and the data collected in a radiant cooling setup together demonstrate the influence of free convection on the instrument’s readings. Initial simulation and data show thattrmeasurements neglecting free convection when calculatingtrfrom air temperatures of 2 K abovetrcould introduce a mechanism for globe readings to incorrectly track air temperatures. The experimental data constructed to test this hypothesis showed the standard correction readings are 1.94 ± 0.90 °C higher than the ground truth readings for all measurements taken in the experiment. The proposed mixed convection correction is 0.51 ± 1.07 °C higher than the ground truth, and is most accurate at low air speeds, within 0.25 ± 0.60 °C. This implies a potential systematic error in millions of measurements over the past 30 years of thermal comfort research. Future work will be carried out to experimentally validate this framework in a controlled climate chamber environment, examining the tradeoffs between accuracy and precision with globe thermometer measurements.
What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein
Authors: Welte Hannah , Zhou Tiankun , Mihajlenko Xenia , Mayans Olga , Kovermann Michael 
Published: February 2020

AbstractFluorine labelling represents one promising approach to study proteins in their native environment due to efficient suppressing of background signals. Here, we systematically probe inherent thermodynamic and structural characteristics of the Cold shock protein B from Bacillus subtilis (BsCspB) upon fluorine labelling. A sophisticated combination of fluorescence and NMR experiments has been applied to elucidate potential perturbations due to insertion of fluorine into the protein. We show that single fluorine labelling of phenylalanine or tryptophan residues has neither significant impact on thermodynamic stability nor on folding kinetics compared to wild type BsCspB. Structure determination of fluorinated phenylalanine and tryptophan labelled BsCspB using X-ray crystallography reveals no displacements even for the orientation of fluorinated aromatic side chains in comparison to wild type BsCspB. Hence we propose that single fluorinated phenylalanine and tryptophan residues used for protein labelling may serve as ideal probes to reliably characterize inherent features of proteins that are present in a highly biological context like the cell.
N-terminal domain of the architectural protein CTCF has similar structural organization and ability to self-association in bilaterian organisms
Authors: Bonchuk Artem , Kamalyan Sofia , Mariasina Sofia , Boyko Konstantin , Popov Vladimir , Maksimenko Oksana , Georgiev Pavel 
Published: February 2020

AbstractCTCF is the main architectural protein found in most of the examined bilaterian organisms. The cluster of the C2H2 zinc-finger domains involved in recognition of long DNA-binding motif is only part of the protein that is evolutionarily conserved, while the N-terminal domain (NTD) has different sequences. Here, we performed biophysical characterization of CTCF NTDs from various species representing all major phylogenetic clades of higher metazoans. With the exception of Drosophilides, the N-terminal domains of CTCFs show an unstructured organization and absence of folded regions in vitro. In contrast, NTDs of Drosophila melanogaster and virilis CTCFs contain unstructured folded regions that form tetramers and dimers correspondingly in vitro. Unexpectedly, most NTDs are able to self-associate in the yeast two-hybrid and co-immunoprecipitation assays. These results suggest that NTDs of CTCFs might contribute to the organization of CTCF-mediated long-distance interactions and chromosomal architecture.
Comprehensive biophysical and functional study of ziv-aflibercept: characterization and forced degradation
Authors: Hermosilla Jesús , Pérez-Robles Raquel , Salmerón-García Antonio , Casares Salvador , Cabeza Jose , Bones Jonathan , Navas Natalia 
Published: February 2020

AbstractAflibercept (AFL) is an Fc fusion protein used in the treatment of colorectal cancers and different ophthalmological diseases. There are two medicines in which AFL is the active substance: Zaltrap and Eylea, referred as ziv-AFL and AFL respectively. No proper accelerated degradation studies were published on either AFL or ziv-AFL. These studies are essential during research, development and manufacturing stages. Here, we characterized ziv-AFL and submitted it to different stress conditions: light, 60 °C, freeze-thaw cycles, changes in pH, high hypertonic solution and strong denaturing conditions. We used an array of techniques to detect aggregation (SE-HPLC/DAD and DLS), changes in secondary structure (Far-UV circular dichroism), changes in conformation or tertiary structure (Intrinsic tryptophan fluorescence) and alterations in functionality (ELISA). Results indicate that aggregation is common degradation pathway. Two different types of aggregates were detected: dimers and high molecular weight aggregates attributed to β-amyloid-like structures. Secondary structure was maintained in most of the stress tests, while conformation was altered by almost all the tests except for the freeze-thaw cycles. Functionality, evaluated by its immunochemical reaction with VEGF, was found to be stable but with decrease when exposed to light and with likely partial inactivation of the drug when pH was altered.
RETRACTED ARTICLE: Inhibition of autophagic flux differently modulates cannabidiol-induced death in 2D and 3D glioblastoma cell cultures
Authors: Ivanov Vladimir N. , Grabham Peter W. , Wu Cheng-Chia , Hei Tom K. 
Published: February 2020

AbstractRadiotherapy combined with chemotherapy is the major treatment modality for human glioblastoma multiforme (GBM). GBMs eventually relapse after treatment and the average survival of GBM patients is less than two years. There is some evidence that cannabidiol (CBD) can induce cell death and increases the radiosensitivity of GBM by enhancing apoptosis. Beside initiation of death, CBD has been demonstrated as an inducer of autophagy. In the present study, we address the question whether CBD simultaneously induces a protective effect in GBM by upregulating autophagy. Addition of chloroquine that suppressed autophagic flux to 2D GBM cultures increased CBD-induced cell death, presenting proof for the protective autophagy. Blockage of autophagy upregulated radiation-induced cytotoxicity but only modestly affected the levels of cell death in CBD- or CBD/γ-irradiated 3D GBM cultures. Furthermore, CBD enhanced the pro-apoptotic activities of JNK1/2 and MAPK p38 signaling cascades while partially downregulated the pro-survival PI3K-AKT cascade, thereby changing a balance between cell death and survival. Suppression of JNK activation partially reduced CBD-induced cell death in 3D GBM cultures. In contrast, co-treatment of CBD-targeted cells with inhibitors of PI3K-AKT-NF-κB, IKK-NF-κB or JAK2-STAT3 pathways killed surviving GBM cells in both 2D and 3D cultures, potentially improving the therapeutic ratio of GBM.