bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autophagy Activation in Zebrafish Heart Regeneration
Authors: Chávez Myra N. , Morales Rodrigo A. , López-Crisosto Camila , Roa Juan Carlos , Allende Miguel L. , Lavandero Sergio 
Published: February 2020

AbstractAutophagy is an evolutionarily conserved process that plays a key role in the maintenance of overall cellular health. While it has been suggested that autophagy may elicit cardioprotective and pro-survival modulating functions, excessive activation of autophagy can also be detrimental. In this regard, the zebrafish is considered a hallmark model for vertebrate regeneration, since contrary to adult mammals, it is able to faithfully regenerate cardiac tissue. Interestingly, the role that autophagy may play in zebrafish heart regeneration has not been studied yet. In the present work, we hypothesize that, in the context of a well-established injury model of ventricular apex resection, autophagy plays a critical role during cardiac regeneration and its regulation can directly affect the zebrafish regenerative potential. We studied the autophagy events occurring upon injury using electron microscopy, in vivo tracking of autophagy markers, and protein analysis. Additionally, using pharmacological tools, we investigated how rapamycin, an inducer of autophagy, affects regeneration relevant processes. Our results show that a tightly regulated autophagic response is triggered upon injury and during the early stages of the regeneration process. Furthermore, treatment with rapamycin caused an impairment in the cardiac regeneration outcome. These findings are reminiscent of the pathophysiological description of an injured human heart and hence put forward the zebrafish as a model to study the poorly understood double-sword effect that autophagy has in cardiac homeostasis.
The peripheral origin of tap-induced muscle contraction revealed by multi-electrode surface electromyography in human vastus medialis
Authors: Botter Alberto , Vieira Taian M. , Geri Tommaso , Roatta Silvestro 
Published: February 2020

AbstractIt is well established that muscle percussion may lead to the excitation of muscle fibres. It is still debated, however, whether the excitation arises directly at the percussion site or reflexively, at the end plates. Here we sampled surface electromyograms (EMGs) from multiple locations along human vastus medialis fibres to address this issue. In five healthy subjects, contractions were elicited by percussing the distal fibre endings at different intensities (5–50 N), and the patellar tendon. EMGs were detected with two 32-electrode arrays, positioned longitudinally and transversally to the percussed fibres, to detect the origin and the propagation of action potentials and their spatial distribution across vastus medialis. During muscle percussion, compound action potentials were first observed at the electrode closest to the tapping site with latency smaller than 5 ms, and spatial extension confined to the percussed strip. Conversely, during tendon tap (and voluntary contractions), action potentials were first detected by electrodes closest to end plates and at a greater latency (mean ± s.d., 28.2 ± 1.7 ms, p < 0.001). No evidence of reflex responses to muscle tap was observed. Multi-electrode surface EMGs allowed for the first time to unequivocally and quantitatively describe the non-reflex nature of the response evoked by a muscle tap.
Enhanced cortical responsiveness during natural sleep in freely behaving mice
Authors: Matsumoto Sumire , Ohyama Kaoru , Díaz Javier , Yanagisawa Masashi , Greene Robert W. , Vogt Kaspar E. 
Published: February 2020

AbstractCortical networks exhibit large shifts in spontaneous dynamics depending on the vigilance state. Waking and rapid eye movement (REM) sleep are characterized by ongoing irregular activity of cortical neurons while during slow wave sleep (SWS) these neurons show synchronous alterations between silent (OFF) and active (ON) periods. The network dynamics underlying these phenomena are not fully understood. Additional information about the state of cortical networks can be obtained by evaluating evoked cortical responses during the sleep-wake cycle. We measured local field potentials (LFP) and multi-unit activity (MUA) in the cortex in response to repeated brief optogenetic stimulation of thalamocortical afferents. Both LFP and MUA responses were considerably increased in sleep compared to waking, with larger responses during SWS than during REM sleep. The strongly increased cortical response in SWS is discussed within the context of SWS-associated neuro-modulatory tone that may reduce feedforward inhibition. Responses to stimuli were larger during SWS-OFF periods than during SWS-ON periods. SWS responses showed clear daily fluctuation correlated to light-dark cycle, but no reaction to increased sleep need following sleep deprivation. Potential homeostatic synaptic plasticity was either absent or masked by large vigilance-state effects.
Chronic irradiation of human cells reduces histone levels and deregulates gene expression
Authors: Lowe Donna J. , Herzog Mareike , Mosler Thorsten , Cohen Howard , Felton Sarah , Beli Petra , Raj Ken , Galanty Yaron , Jackson Stephen P. 
Published: February 2020

AbstractOver the past decades, there have been huge advances in understanding cellular responses to ionising radiation (IR) and DNA damage. These studies, however, were mostly executed with cell lines and mice using single or multiple acute doses of radiation. Hence, relatively little is known about how continuous exposure to low dose ionising radiation affects normal cells and organisms, even though our cells are constantly exposed to low levels of radiation. We addressed this issue by examining the consequences of exposing human primary cells to continuous ionising γ-radiation delivered at 6–20 mGy/h. Although these dose rates are estimated to inflict fewer than a single DNA double-strand break (DSB) per hour per cell, they still caused dose-dependent reductions in cell proliferation and increased cellular senescence. We concomitantly observed histone protein levels to reduce by up to 40%, which in contrast to previous observations, was not mainly due to protein degradation but instead correlated with reduced histone gene expression. Histone reductions were accompanied by enlarged nuclear size paralleled by an increase in global transcription, including that of pro-inflammatory genes. Thus, chronic irradiation, even at low dose-rates, can induce cell senescence and alter gene expression via a hitherto uncharacterised epigenetic route. These features of chronic radiation represent a new aspect of radiation biology.
PlantPepDB: A manually curated plant peptide database
Authors: Das Durdam , Jaiswal Mohini , Khan Fatima Nazish , Ahamad Shahzaib , Kumar Shailesh 
Published: February 2020

AbstractPlants produce an array of peptides as part of their innate defense mechanism against pathogens. The potential use of these peptides for various therapeutic purposes is increasing per diem. In order to excel in this research, the community requires web repositories that provide reliable and accurate information about these phyto-peptides. This work is an attempt to bridge the gaps in plant-based peptide research. PlantPepDB is a manually curated database that consists of 3848 plant-derived peptides among which 2821 are experimentally validated at the protein level, 458 have experimental evidence at the transcript level, 530 are predicted and only 39 peptides are inferred from homology. Incorporation of physicochemical properties and tertiary structure into PlantPepDB will help the users to study the therapeutic potential of a peptide, thus, debuts as a powerful resource for therapeutic research. Different options like Simple, Advanced, PhysicoChem and AA composition search along with browsing utilities are provided in the database for the users to execute dynamic search and retrieve the desired data. Interestingly, many peptides that were considered to possess only a single property were found to exhibit multiple properties after careful curation and merging the duplicate data that was collected from published literature and already available databases. Overall, PlantPepDB is the first database comprising detailed analysis and comprehensive information of phyto-peptides from a broad functional range which will be useful for peptide-based applied research. PlantPepDB is freely available at http://www.nipgr.ac.in/PlantPepDB/.
Suggested Case of Langerhans Cell Histiocytosis in a Cretaceous dinosaur
Authors: Rothschild Bruce M. , Tanke Darren , Rühli Frank , Pokhojaev Ariel , May Hila 
Published: February 2020

AbstractSusceptibility to diseases is common to humans and dinosaurs. Since much of the biological history of every living creature is shaped by its diseases, recognizing them in fossilized bone can furnish us with important information on dinosaurs’ physiology and anatomy, as well as on their daily activities and surrounding environment. In the present study, we examined the vertebrae of two humans from skeletal collections with Langerhans Cell Histiocytosis (LCH), a benign osteolytic tumor-like disorder involving mainly the skeleton; they were diagnosed in life, along with two hadrosaur vertebrae with an apparent lesion. Macroscopic and microscopic analyses of the hadrosaur vertebrae were compared to human LCH and to other pathologies observed via an extensive pathological survey of a human skeletal collection, as well as a three-dimensional reconstruction of the lesion and its associated blood vessels from a µCT scan. The hadrosaur pathology findings were indistinguishable from those of humans with LCH, supporting that diagnosis. This report suggests that hadrosaurids had suffered from larger variety of pathologies than previously reported. Furthermore, it seems that LCH may be independent of phylogeny.
Exploring the familial role of social responsiveness differences between savant and non-savant children with autism
Authors: Daniel Edan , Menashe Idan 
Published: February 2020

AbstractSavant syndrome is a phenomenon whereby individuals with cognitive impairments have one or more outstanding abilities, inconsistent with their general intellectual functioning. Approximately 50% of savant individuals have autism spectrum disorder (ASD), and 10–30% of people with ASD have savant skills. To shed additional light on this considerable overlap, we compared autistic traits as measured by the Social-Responsiveness-Scale (SRS) between 712 children with at least one reported savant skill, as determined by designated questions from the ADI-R questionnaire (savant group), and 2,032 non-savant children from the Simons-Simplex-Collection (SSC) database. We also examined SRS scores of the parents of these children and compared parent-child differences in SRS scores between the savant and non-savant groups. Savant children had significantly lower SRS scores (less deficiencies) compared to non-savant children (P < 0.05), while no such differences were observed among their parents. Further intra-familial analyses revealed weak pairwise-correlations (r = −0.015–0.141) between SRS scores of parents and their children, and significantly larger parent-child differences in standardized SRS scores within savant families (P < 0.05). These findings suggest that the less severe autistic traits among savant children with ASD compared to other people with ASD is not likely to be a familial trait.
Physicochemical characterization of Pseudomonas stutzeri UFV5 and analysis of its transcriptome under heterotrophic nitrification/aerobic denitrification pathway induction condition
Authors: Silva Lívia Carneiro Fidélis , Lima Helena Santiago , Mendes Tiago Antônio de Oliveira , Sartoratto Adilson , Sousa Maira Paula , de Souza Rodrigo Suhett , de Paula Sérgio Oliveira , de Oliveira Valéria Maia , Silva Cynthia Canedo 
Published: February 2020

AbstractBiological ammonium removal via heterotrophic nitrification/aerobic denitrification (HN/AD) presents several advantages in relation to conventional removal processes, but little is known about the microorganisms and metabolic pathways involved in this process. In this study, Pseudomonas stutzeri UFV5 was isolated from an activated sludge sample from oil wastewater treatment station and its ammonium removal via HN/AD was investigated by physicochemical and molecular approaches to better understand this process and optimize the biological ammonium removal in wastewater treatment plants. Results showed that P. stutzeri UFV5 removed all the ammonium in 48–72 hours using pyruvate, acetate, citrate or sodium succinate as carbon sources, C/N ratios 6, 8, 10 and 12, 3–6% salinities, pH 7–9 and temperatures of 20–40 °C. Comparative genomics and PCR revealed that genes encoding the enzymes involved in anaerobic denitrification process are present in P. stutzeri genome, but no gene that encodes enzymes involved in autotrophic nitrification was found. Furthermore, transcriptomics showed that none of the known enzymes of autotrophic nitrification and anaerobic denitrification had their expression differentiated and an upregulation of the biosynthesis machinery and protein translation was observed, besides several genes with unknown function, indicating a non-conventional mechanism involved in HN/AD process.
Sperm enrichment from poor semen samples by double density gradient centrifugation in combination with swim-up for IVF cycles
Authors: Dai Xiuliang , Wang Yufeng , Cao Fang , Yu Chunmei , Gao Tingting , Xia Xiyang , Wu Jun , Chen Li 
Published: February 2020

AbstractSperm preparation in IVF cycles using density gradient centrifugation (DGC) in combination with swim-up (SU) has been widely adopted in reproductive centres worldwide. It is a fact that the sperm recovery rate following one DGC from poor semen samples (showing liquefaction defects/containing too many unresolvable clots or rare sperm) is relatively low. Our results showed that double DGC (DDGC) is effective at increasing the sperm recovery rate from poor semen samples. However, DDGC may increase the mechanical stress of sperm, thereby potentially impairing embryo development. Therefore, it is necessary to evaluate the safety of using sperm prepared by DDGC/SU for IVF cycles. In this study, we retrospectively analysed the data generated from a total of 529 IVF cycles (from June 2017 to June 2018), and these IVF cycles contributed 622 transfer cycles (from June 2017 to December 2018) in Changzhou Maternal and Child Health Care Hospital. Of them, 306 IVF cycles and the related 355 transfer cycles (normal semen samples prepared by DGC/SU) were set as the normal group, while 223 IVF cycles and the related 267 transfer cycles (poor semen prepared by DDGC/SU) were set as the observation group. The main outcome measures, including the normal fertilization rate, top D3 embryo formation rate, blastocyte formation rate, clinical pregnancy rate and live birth rate, birth weight and duration of pregnancy, were compared between the two groups. Compared to semen in the DGC/SU group, semen in the DDGC/SU group showed increased levels of the DNA fragmentation index (DFI) and reduced sperm concentration, percentage of progressive motility (PR) sperm, and percentage of normal morphology sperm. The indicators reflecting in vitro embryo development and clinical outcomes were similar in the DGC/SU group and DDGC/SU group, including the normal fertilization rate, top D3 embryo formation rate, blastocyte formation rate, pregnancy rate, implantation rate, spontaneous abortion rate, live birth rate, birth weight and duration of pregnancy. Furthermore, we found that the 1PN zygote formation rate was significantly lower in the DDGC/SU group than that in the DGC/SU group. We concluded that oocytes fertilized by sperm from poor semen samples separated by DDGC/SU achieved the same outcomes as oocytes fertilized by sperm from normal semen separated by DGC/SU, suggesting that DDGC/SU is an effective and safe method of sperm enrichment for poor semen samples in IVF. The main contribution of the present study is the verification of the effectiveness of DDGC/SU in improving sperm recovery from poor semen samples and the safety of using sperm prepared by DDGC/SU for IVF.
Uncertainty span for relative permeability and capillary pressure by varying wettability and spatial flow directions utilizing pore scale modelling
Authors: Ramstad Thomas , Kristoffersen Anders , Ebeltoft Einar 
Published: February 2020

Relative permeability and capillary pressure are key properties within special core analysis and provide crucial information for full field simulation models. These properties are traditionally obtained by multi-phase flow experiments, however pore scale modelling has during the last decade shown to add significant information as well as being less time-consuming to obtain.
Pore scale modelling has been performed by using the lattice-Boltzmann method directly on the digital rock models obtained by high resolution micro-CT images on end-trims available when plugs are prepared for traditional SCAL-experiments. These digital rock models map the pore-structure and are used for direct simulations of two-phase flow to relative permeability curves.
Various types of wettability conditions are introduced by a wettability map that opens for local variations of wettability on the pore space at the pore level. Focus have been to distribute realistic wettabilities representative for the Norwegian Continental Shelf which is experiencing weakly-wetting conditions and no strong preference neither to water nor oil. Spanning a realistic wettability-map and enabling flow in three directions, a large amount of relative permeability curves is obtained. The resulting relative permeabilities hence estimate the uncertainty of the obtained flow properties on a spatial but specific pore structure with varying, but realistic wettabilities.
The obtained relative permeability curves are compared with results obtained by traditional SCAL-analysis on similar core material from the Norwegian Continental Shelf. The results are also compared with the SCAL-model provided for full field simulations for the same field. The results from the pore scale simulations are within the uncertainty span of the SCAL models, mimic the traditional SCAL-experiments and shows that pore scale modelling can provide a time- and cost-effective tool to provide SCAL-models with uncertainties.
High-Resolution Inline Density Measurements: Insight on Multiphase Flow and Transport Phenomena in Porous Media
Authors: Falat Jelayne , Fehr Adam , Telmadarreie Ali , Bryant Steven 
Published: February 2020

Understanding fluid flow in porous media is essential with complex and multiphase fluid flow. We demonstrate that high-resolution in-line density measurements are a valuable tool in this regard. An in-line densitometer is used in fluid flow in porous media applications to quantify fluid production and obtain quantitative and qualitative information such as breakthrough times, emulsion/foam generation, and steam condensation.
In order to determine the potential applications for in-line densitometry for fluid flow in porous media, a series of sand pack floods were performed with a densitometer placed at the outlet of a sand pack. All fluids passed through the measurement cell at experiential temperatures and pressures. An algorithm was developed and applied to the density data to provide a quantitative determination of oil and water production. The second series of tests were performed at high temperature and pressure, with a densitometer placed at the inlet and outlet of a sand pack, for steam applications. In both series of experiments, data acquisition was collected at 1 hertz and the analyzed density data was compared to results from the conventional effluent analysis, including Dean-Stark, toluene separations, magnetic susceptibility measurement, and flash calculations where applicable.
The high-resolution monitoring of effluent from a flow experiment through porous media in a system with two phases of known densities enables two-phase production to be accurately quantified in the case of both light and heavy oil. The frequency of measurements results in a high-resolution history of breakthrough times and fluid behavior. In the case of monitoring steam injection processes, reliable laboratory tests show that in-line density measurements enable the determination of steam quality at the inlet and outlet of a sand pack and qualitative determination of steam condensation monitoring
The use of in-line densitometry provides insight on the monitoring of complex fluid flow in porous media, which typical bulk effluent analysis is not able to do. The ability to measure produced fluids at high resolution and extreme temperatures reduces mass balance error associated with the effluent collection and broadens our understanding of complex fluid flow in porous media.
Towards Relative Permeability Measurements in Tight Gas Formations
Authors: Dzhafarov Denis , Nicot Benjamin 
Published: February 2020

Relative permeability is a concept used to convey the reduction in flow capability due to the presence of multiple fluids. Relative permeability governs the multiphase flow, therefore it has a significant importance in understanding the reservoir behavior. These parameters are routinely measured on conventional rocks, however their measurement becomes quite challenging for low permeability rocks such as tight gas formations.
This study demonstrates a methodology for relative permeability measurements on tight gas samples. The gas permeability has been measured by the Step Decay method and two different techniques have been used to vary the saturations: steady state flooding and vapor desorption.
Series of steady-state gas/water simultaneous injection have been performed on a tight gas sample. After stabilization at each injection ratio, NMR T2, NMR Saturation profile and low pressure Step Decay gas permeability have been measured. In parallel, progressive desaturation by vapor desorption technique has been performed on twin plugs. After stabilization at each relative humidity level the NMR T2 and Step Decay gas permeability have been measured in order to compare and validate the two approaches.
The techniques were used to gain insight into the tight gas two phase relative permeability of extremely low petrophysical properties (K<100 nD, phi < 5 pu) of tight gas samples of Pyrophyllite outcrop.
The two methods show quite good agreement. Both methods demonstrate significant permeability degradation at water saturation higher than irreducible. NMR T2 measurements for both methods indicates bimodal T2-distributions, and desaturation first occurs on low T2 signal (small pores).
Comparison of humidity drying and steady-state desaturation technique has shown a 12-18 su difference between critical water saturation (Swc) measured in gas/water steady-state injection and irreducible saturation (Swirr) measured by vapor desorption.