bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of an optimal method for extracting RNA from human skin biopsy, using domestic pig as a model system
Authors: Reimann Ene , Abram Kristi , Kõks Sulev , Kingo Külli , Fazeli Alireza 
Published: December 2019

AbstractTo evaluate skin tissue gene expression patterns correctly, extracting sufficient quantities of good quality RNA is essential. However, RNA extraction from skin tissue is challenging, as the hyaluronic acid-collagen matrix is extremely difficult to homogenize. Although there are multiple ways to extract RNA from skin, there are no comparative studies that identify the most critical steps, e.g. sample collection, storage and homogenization. We analysed the various steps involved in RNA extraction (i.e. biopsy collection as dry biopsy or into nucleotide stabilizing reagents, different storage conditions, enzymatic digestion, stator-rotor and bead motion-based homogenizing combined with column-based RNA purification). We hypothesised that domestic pig skin is applicable as a model for human skin studies. Altogether twenty different workflows were tested on pig skin and the four most promising workflows were tested on human skin samples. The optimal strategy for extracting human skin RNA was to collect, store and homogenize the sample in RLT lysis buffer from the RNeasy Fibrous Tissue Kit combined with beta-mercaptoethanol. Both stator-rotor and bead motion-based homogenizing were found to result in high quality and quantity of extracted RNA. Our results confirmed that domestic pig skin can be successfully used as a model for human skin RNA studies.
Stepped vitrification technique for human ovarian tissue cryopreservation
Authors: Leonel Ellen Cristina Rivas , Corral Ariadna , Risco Ramon , Camboni Alessandra , Taboga Sebastião Roberto , Kilbride Peter , Vazquez Marina , Morris John , Dolmans Marie-Madeleine , Amorim Christiani A. 
Published: December 2019

AbstractThe advantage of stepped vitrification (SV) is avoiding ice crystal nucleation, while decreasing the toxic effects of high cryoprotectant concentrations. We aimed to test this method for human ovarian tissue cryopreservation. Ovarian cortex was taken from 7 fertile adult women. Samples were subjected to an SV protocol performed in an automatic freezer, which allowed sample transfer to ever higher concentrations of dimethyl sulfoxide (DMSO) as the temperature was reduced. Histological evaluation of the vitrified-warmed tissue showed large numbers of degenerated follicles after 24 hours of in vitro culture. We therefore evaluated DMSO perfusion rates by X-ray computed tomography, ice crystal formation by freeze-substitution, and cell toxicity by transmission electron microscopy, seeking possible reasons why follicles degenerated. Although cryoprotectant perfusion was considered normal and no ice crystals were formed in the tissue, ultrastructural analysis detected typical signs of DMSO toxicity, such as mitochondria degeneration, alterations in chromatin condensation, cell vacuolization and extracellular matrix swelling in both stromal and follicular cells. The findings indicated that the method failed to preserve follicles due to the high concentrations of DMSO used. However, adaptations can be made to avoid toxicity to follicles caused by elevated levels of cryoprotectants.
Chest Movement and Respiratory Volume both Contribute to Thoracic Bioimpedance during Loaded Breathing
Authors: Blanco-Almazán Dolores , Groenendaal Willemijn , Catthoor Francky , Jané Raimon 
Published: December 2019

AbstractBioimpedance has been widely studied as alternative to respiratory monitoring methods because of its linear relationship with respiratory volume during normal breathing. However, other body tissues and fluids contribute to the bioimpedance measurement. The objective of this study is to investigate the relevance of chest movement in thoracic bioimpedance contributions to evaluate the applicability of bioimpedance for respiratory monitoring. We measured airflow, bioimpedance at four electrode configurations and thoracic accelerometer data in 10 healthy subjects during inspiratory loading. This protocol permitted us to study the contributions during different levels of inspiratory muscle activity. We used chest movement and volume signals to characterize the bioimpedance signal using linear mixed-effect models and neural networks for each subject and level of muscle activity. The performance was evaluated using the Mean Average Percentage Errors for each respiratory cycle. The lowest errors corresponded to the combination of chest movement and volume for both linear models and neural networks. Particularly, neural networks presented lower errors (median below 4.29%). At high levels of muscle activity, the differences in model performance indicated an increased contribution of chest movement to the bioimpedance signal. Accordingly, chest movement contributed substantially to bioimpedance measurement and more notably at high muscle activity levels.
A systems biology approach reveals neuronal and muscle developmental defects after chronic exposure to ionising radiation in zebrafish
Authors: Murat El Houdigui Sophia , Adam-Guillermin Christelle , Loro Giovanna , Arcanjo Caroline , Frelon Sandrine , Floriani Magali , Dubourg Nicolas , Baudelet Emilie , Audebert Stéphane , Camoin Luc , Armant Olivier 
Published: December 2019

AbstractContamination of the environment after the Chernobyl and Fukushima Daiichi nuclear power plant (NPP) disasters led to the exposure of a large number of humans and wild animals to radioactive substances. However, the sub-lethal consequences induced by these absorbed radiological doses remain understudied and the long-term biological impacts largely unknown. We assessed the biological effects of chronic exposure to ionizing radiation (IR) on embryonic development by exposing zebrafish embryo from fertilization and up to 120 hours post-fertilization (hpf) at dose rates of 0.5 mGy/h, 5 mGy/h and 50 mGy/h, thereby encompassing the field of low dose rates defined at 6 mGy/h. Chronic exposure to IR altered larval behaviour in a light-dark locomotor test and affected cardiac activity at a dose rate as low as 0.5 mGy/h. The multi-omics analysis of transcriptome, proteome and transcription factor binding sites in the promoters of the deregulated genes, collectively points towards perturbations of neurogenesis, muscle development, and retinoic acid (RA) signaling after chronic exposure to IR. Whole-mount RNA in situ hybridization confirmed the impaired expression of the transcription factors her4.4 in the central nervous system and myogenin in the developing muscles of exposed embryos. At the organ level, the assessment of muscle histology by transmission electron microscopy (TEM) demonstrated myofibers disruption and altered neuromuscular junctions in exposed larvae at 5 mGy/h and 50 mGy/h. The integration of these multi-level data demonstrates that chronic exposure to low dose rates of IR has an impact on neuronal and muscle progenitor cells, that could lead to motility defects in free swimming larvae at 120 hpf. The mechanistic understanding of these effects allows us to propose a model where deregulation of RA signaling by chronic exposure to IR has pleiotropic effects on neurogenesis and muscle development.
Mn-TAT PTD-Ngb attenuates oxidative injury by an enhanced ROS scavenging ability and the regulation of redox signaling pathway
Authors: Zhang Cui , Hao Xuehui , Chang Jiaying , Geng Zhirong , Wang Zhilin 
Published: December 2019

AbstractNeurological diseases have a close relationship to excessive reactive oxygen species (ROS). Neuroglobin (Ngb), an intrinsic protective factor, protected cells from hypoxic/ischemic injury. In the present, we reported a novel neuroprotective manganese porphyrin reconstituted metal protein, Mn-TAT PTD-Ngb, consisting of a HIV Tat protein transduction domain sequence (TAT PTD) attached to the N-terminal of apo-Ngb. Mn-TAT PTD-Ngb had a stronger ROS scavenging ability than that of TAT PTD-Ngb, and reduced intracellular ROS production and restored the function of the mitochondria and inhibited the mitochondria-dependent apoptosis. Besides, Mn-TAT PTD-Ngb activated the phosphoinositide-3 kinase (PI3K)/Akt signaling pathway, which up-regulated the expression of nuclear factor E2-related factor 2 (Nrf2), Heme oxygenase-1 (HO-1), superoxide dismutase (SOD), catalase (CAT). The results showed that the redox chemistry of Mn-TAT PTD-Ngb and redox regulation of multiple signaling pathways attenuated the oxidative injury.
The Relation between Alpha/Beta Oscillations and the Encoding of Sentence induced Contextual Information
Authors: Terporten René , Schoffelen Jan-Mathijs , Dai Bohan , Hagoort Peter , Kösem Anne 
Published: December 2019

AbstractPre-stimulus alpha (8–12 Hz) and beta (16–20 Hz) oscillations have been frequently linked to the prediction of upcoming sensory input. Do these frequency bands serve as a neural marker of linguistic prediction as well? We hypothesized that if pre-stimulus alpha and beta oscillations index language predictions, their power should monotonically relate to the degree of predictability of incoming words based on past context. We expected that the more predictable the last word of a sentence, the stronger the alpha and beta power modulation. To test this, we measured neural responses with magnetoencephalography of healthy individuals during exposure to a set of linguistically matched sentences featuring three levels of sentence context constraint (high, medium and low constraint). We observed fluctuations in alpha and beta power before last word onset, and modulations in M400 amplitude after last word onset. The M400 amplitude was monotonically related to the degree of context constraint, with a high constraining context resulting in the strongest amplitude decrease. In contrast, pre-stimulus alpha and beta power decreased more strongly for intermediate constraints, followed by high and low constraints. Therefore, unlike the M400, pre-stimulus alpha and beta dynamics were not indexing the degree of word predictability from sentence context.
The effect of ligand amount, affinity and internalization on PSMA-targeted imaging and therapy: A simulation study using a PBPK model
Authors: Begum Nusrat J. , Glatting Gerhard , Wester Hans-Jürgen , Eiber Matthias , Beer Ambros J. , Kletting Peter 
Published: December 2019

AbstractThe aim of this work was to investigate the effect of ligand amount, affinity and internalization of prostate-specific membrane antigen (PSMA)-specific ligands on the activity concentrations for PET/CT imaging and on the absorbed doses for therapy. A physiologically-based pharmacokinetic (PBPK) model for PSMA-specific ligands was implemented. Thirteen virtual patients with metastatic castration-resistant prostate cancer were analysed. Simulations were performed for different combinations of association rates kon (0.1–0.01 L/nmol/min), dissociation rates koff (0.1–0.0001 min−1), internalization rates λint (0.01–0.0001 min−1) and ligand amounts (1–1000 nmol). For imaging the activity was normalized to volume and injected activity (68Ga-PSMA at 1 h). For therapy the absorbed dose was calculated for 7.3 ± 0.3 GBq 177Lu-PSMA. The effect of the investigated parameters on therapy were larger compared to imaging. For imaging, the combination of properties leading to the highest tumour uptake was kon = 0.1 L/nmol/min, koff = 0.01 min−1 for typical ligand amounts (1–10 nmol). For therapy, the higher the internalization rate, the larger was the required ligand amount for optimal tumour-to-kidney ratios. The higher the affinity, the more important was the choice of the optimal ligand amount. PBPK modelling provides insight into the pharmacokinetics of PSMA-specific ligands. Further in silico and in vivo studies are required to verify the influence of the analysed parameters.
An improved simple method for the identification of Mycobacteria by MALDI-TOF MS (Matrix-Assisted Laser Desorption- Ionization mass spectrometry)
Authors: Alcolea-Medina Adela , Fernandez M. T. Cabezas , Montiel N. , García M. P. Luzón , Sevilla C. Delamo , North Nathan , Lirola M. J. Martínez , Wilks Mark 
Published: December 2019

AbstractThe aim of this study was to establish a simple method for the rapid identification of Mycobacteria species by MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass spectrometry) using the Bruker MALDI-TOF Biotyper system (Bruker Daltonik, Bremen, Germany). A multicentre, prospective, and single blind study was performed in three European Hospitals, two Spanish and one UK hospital from May to August 2018. The BD BACTEC MGIT (Becton Dickinson, Berks, UK) liquid culture system was used in all three centres for the growth of Mycobacteria. When signal positive, tubes were removed from the analyser and in addition to standard laboratory procedures were subcultured on blood agar plates for MALDI-TOF analysis. Plates were incubated aerobically for 1 to 7 days at 37 °C and inspected every day. Once any growth was visible, it was transferred to the steel target plate, overlaid with 1 μl of neat formic acid and 1 μl HCCA matrix (alpha hydroxyl 4 cinnamic acid), and analysed in a Bruker Biotyper MALDI-TOF. Results given by MALDI-TOF were compared with the reference methods used for identification in the different centres. At two Spanish hospitals, identification by MALDI-TOF was only attempted on presumptive non-tuberculosis mycobacteria (NTM) and the results were initially compared with the results obtained by a commercial reverse hybridisation assay, GenoType CM/AS (Hain Lifescience, Tübingen, Germany). At the UK Hospital, identification of any presumptive mycobacteria was attempted and compared with the results obtained by whole genome sequencing (WGS). Overall in 142/167 (85%) of cases the identifications obtained were concordant; all Mycobacterium tuberculosis (MTB) isolates 43/43 (100%), 57/76 (75%) of the rapid growing nontuberculous mycobacteria (NTM), and 42/48 (85%) slow growing NTM tested were identified correctly. We report a new, easy, cheap and quick method for isolation and identification of Mycobacterium spp. without the need for additional steps or equipment and this method is in routine used in all three centres.
Experimental evidence of mechanical lumpy skin disease virus transmission by Stomoxys calcitrans biting flies and Haematopota spp. horseflies
Authors: Sohier C. , Haegeman A. , Mostin L. , De Leeuw I. , Campe W. Van , De Vleeschauwer A. , Tuppurainen E. S. M. , van den Berg T. , De Regge N. , De Clercq K. 
Published: December 2019

AbstractLumpy skin disease (LSD) is a devastating disease of cattle characterized by fever, nodules on the skin, lymphadenopathy and milk drop. Several haematophagous arthropod species like dipterans and ticks are suspected to play a role in the transmission of LSDV. Few conclusive data are however available on the importance of biting flies and horseflies as potential vectors in LSDV transmission. Therefore an in vivo transmission study was carried out to investigate possible LSDV transmission by Stomoxys calcitrans biting flies and Haematopota spp. horseflies from experimentally infected viraemic donor bulls to acceptor bulls. LSDV transmission by Stomoxys calcitrans was evidenced in 3 independent experiments, LSDV transmission by Haematopota spp. was shown in one experiment. Evidence of LSD was supported by induction of nodules and virus detection in the blood of acceptor animals. Our results are supportive for a mechanical transmission of the virus by these vectors.
Normal GCAPs partly compensate for altered cGMP signaling in retinal dystrophies associated with mutations in GUCA1A
Authors: Dell’Orco Daniele , Dal Cortivo Giuditta 
Published: December 2019

AbstractMissense mutations in the GUCA1A gene encoding guanylate cyclase-activating protein 1 (GCAP1) are associated with autosomal dominant cone/cone-rod (CORD) dystrophies. The nature of the inheritance pattern implies that a pool of normal GCAP proteins is present in photoreceptors together with the mutated variant. To assess whether human GCAP1 and GCAP2 may similarly regulate the activity of the retinal membrane guanylate cyclase GC-1 (GC-E) in the presence of the recently discovered E111V-GCAP1 CORD-variant, we combined biochemical and in silico assays. Surprisingly, human GCAP2 does not activate GC1 over the physiological range of Ca2+ whereas wild-type GCAP1 significantly attenuates the dysregulation of GC1 induced by E111V-GCAP1. Simulation of the phototransduction cascade in a well-characterized murine system, where GCAP2 is able to activate the GC1, suggests that both GCAPs can act in a synergic manner to mitigate the effects of the CORD-mutation. We propose the existence of a species-dependent compensatory mechanism. In murine photoreceptors, slight increases of wild-type GCAPs levels may significantly attenuate the increase in intracellular Ca2+ and cGMP induced by E111V-GCAP1 in heterozygous conditions. In humans, however, the excess of wild-type GCAP1 may only partly attenuate the mutant-induced dysregulation of cGMP signaling due to the lack of GC1-regulation by GCAP2.
Zebrafish structural development in Mueller-matrix scanning microscopy
Authors: Le Gratiet Aymeric , d’Amora Marta , Duocastella Marti , Marongiu Riccardo , Bendandi Artemi , Giordani Silvia , Bianchini Paolo , Diaspro Alberto 
Published: December 2019

AbstractZebrafish are powerful animal models for understanding biological processes and the molecular mechanisms involved in different human diseases. Advanced optical techniques based on fluorescence microscopy have become the main imaging method to characterize the development of these organisms at the microscopic level. However, the need for fluorescence probes and the consequent high light doses required to excite fluorophores can affect the biological process under observation including modification of metabolic function or phototoxicity. Here, without using any labels, we propose an implementation of a Mueller-matrix polarimeter into a commercial optical scanning microscope to characterize the polarimetric transformation of zebrafish preserved at different embryonic developmental stages. By combining the full polarimetric measurements with statistical analysis of the Lu and Chipman mathematical decomposition, we demonstrate that it is possible to quantify the structural changes of the biological organization of fixed zebrafish embryos and larvae at the cellular scale. This convenient implementation, with low light intensity requirement and cheap price, coupled with the quantitative nature of Mueller-matrix formalism, can pave the way for a better understanding of developmental biology, in which label-free techniques become a standard tool to study organisms.
High degree of polyclonality hinders somatic mutation calling in lung brush samples of COPD cases and controls
Authors: Thun Gian-Andri , Derdak Sophia , Castro-Giner Francesc , Apunte-Ramos Katherine , Águeda Lidia , Wjst Matthias , Boland Anne , Deleuze Jean-François , Kolsum Umme , Heiss-Neumann Marion S. , Nowinski Adam , Gorecka Dorota , Hohlfeld Jens M. , Welte Tobias , Brightling Christopher E. , Parr David G. , Prasse Antje , Müller-Quernheim Joachim , Greulich Timm , Stendardo Mariarita , Boschetto Piera , Barta Imre , Döme Balázs , Gut Marta , Singh Dave , Ziegler-Heitbrock Loems , Gut Ivo G. 
Published: December 2019

AbstractChronic obstructive pulmonary disease (COPD) is induced by cigarette smoking and characterized by inflammation of airway tissue. Since smokers with COPD have a higher risk of developing lung cancer than those without, we hypothesized that they carry more mutations in affected tissue. We called somatic mutations in airway brush samples from medium-coverage whole genome sequencing data from healthy never and ex-smokers (n = 8), as well as from ex-smokers with variable degrees of COPD (n = 4). Owing to the limited concordance of resulting calls between the applied tools we built a consensus, a strategy that was validated with high accuracy for cancer data. However, consensus calls showed little promise of representing true positives due to low mappability of corresponding sequence reads and high overlap with positions harbouring known genetic polymorphisms. A targeted re-sequencing approach suggested that only few mutations would survive stringent verification testing and that our data did not allow the inference of any difference in the mutational load of bronchial brush samples between former smoking COPD cases and controls. High polyclonality in airway brush samples renders medium-depth sequencing insufficient to provide the resolution to detect somatic mutations. Deep sequencing data of airway biopsies are needed to tackle the question.
Eye lens radiation exposure in paediatric interventional treatment of retinoblastoma
Authors: Obesso A. , Alejo L. , Huerga C. , Sánchez-Muñoz F. , Corredoira E. , Fernández-Prieto A. , Frutos R. , Marín B. , Garzón G. , Peralta J. , Ubeda C. , Guibelalde E. 
Published: December 2019

AbstractRetinoblastoma represents 3% of cancers in children under fifteen years of age. The standard paediatric treatment for saving the affected eye is supraselective intra-arterial chemotherapy performed in interventional rooms. In order to address the radiation toxicity due to the angiography, the aim of this study was to determine the typical dose value corresponding to the procedure, estimate the paediatric patients’ eye lens dose and study the relationship between dose indicators and dose to the lens. An automatic dose management software was installed in two interventional rooms to obtain the distribution of the dose indicators kerma-area product and reference-point air kerma, getting a typical value 16 Gy·cm2 and 130 mGy, respectively (n = 35). The eye lens dose estimates were obtained with photoluminescent dosimeters placed on the patient’s eyelids. In the left eye, the entrance surface air kerma was 44.23 ± 2.66 mGy, and 12.72 ± 0.89 mGy in the right eye (n = 10). There was a positive correlation between dose to the lens per procedure and dose indicators, with R2 > 0.65 for both eyes. Based on this information, the threshold for the onset of radiation-induce cataracts (500 mGy) will be exceeded if the treatment is performed for more than 8 sessions.
Relation between platelet coagulant and vascular function, sex-specific analysis in adult survivors of childhood cancer compared to a population-based sample
Authors: Panova-Noeva Marina , Wagner Bianca , Nagler Markus , Arnold Natalie , Prochaska Jürgen H. , Eckerle Susan , Spronk Henri M. , Merzenich Hiltrud , Wingerter Arthur , Schneider Astrid , Danckwardt Sven , ten Cate Hugo , Faber Jörg , Wild Philipp S. 
Published: December 2019

AbstractFemale sex is a risk factor for long-term adverse outcome in cancer survivors, however very little is known for the underlying pathophysiological mechanisms rendering the increased risk. This study investigated sex-specifically the relation between thrombin generation (TG) with and without presence of platelets and vascular function in 200 adult survivors of a childhood cancer compared to 335 population-based control individuals. TG lag time, peak height and endogenous thrombin potential (ETP) measured in presence and absence of platelets were correlated to reflection index (RI) and stiffness index (SI). A sex-specific correlation analysis showed a negative relation in female survivors for platelet-dependent peak height and/or ETP and RI only. An age adjusted linear regression model confirmed the negative association between RI and platelet-dependent ETP (beta estimate: −6.85, 95% confidence interval: −12.19,−1.51) in females. Adjustment for cardiovascular risk factors resulted in loss of the association, whereby arterial hypertension and obesity showed the largest effects on the observed association. No other relevant associations were found in male and female cancer survivors and all population-based controls. This study demonstrates a link between platelet coagulant and vascular function of resistance vessels, found in female cancer survivors, potentially mediated by the presence of arterial hypertension and obesity.