bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of differentiation of the acute myeloid leukemia cell line (HL-60) by a securinine dimer
Authors: Hou Wen , Wang Zhen-Ya , Lin Jing , Chen Wei-Min 
Published: November 2020

AbstractDifferentiation therapy has been successfully applied clinically in cases of acute promyelocytic leukemia (APL), but few differentiation-induction agents other than all-trans retinoic acid (ATRA) have been discovered clinically. Based on our previously reported neuritogenic differentiation activity of synthetic dimeric derivatives of securinine, we explored the leukemia differentiation-induction activity of such as compound, SN3-L6. It was found that SN3-L6 induces transdifferentiation of both acute myeloid leukemia (AML) and chronic myelogenous leukemia (CML) cells but unexpectedly, a new transdifferentiation pathway from APL cells to morphologically and immunologically normal megakaryocytes and platelets were discovered. SN3-L6 fails to induce transdifferentiation of ATRA–produced mature granulocytes into megakaryocytes, indicating its selectivity between mature and immature cells. SN3-L6 induces CML K562 cells to transdifferentiate into apoptotic megakaryocytes but without platelet formation, indicating a desirable selectivity between different leukemia cells. Our data illuminate a differentiation gap between AML cells and platelets, and promises applications in leukemia differentiation therapy strategy.
PTRH2: an adhesion regulated molecular switch at the nexus of life, death, and differentiation
Authors: Corpuz Austin D. , Ramos Joe W. , Matter Michelle L. 
Published: November 2020

AbstractPeptidyl-tRNA hydrolase 2 (PTRH2; Bit-1; Bit1) is an underappreciated regulator of adhesion signals and Bcl2 expression. Its key roles in muscle differentiation and integrin-mediated signaling are central to the pathology of a recently identified patient syndrome caused by a cluster of Ptrh2 gene mutations. These loss-of-function mutations were identified in patients presenting with severe deleterious phenotypes of the skeletal muscle, endocrine, and nervous systems resulting in a syndrome called Infantile-onset Multisystem Nervous, Endocrine, and Pancreatic Disease (IMNEPD). In contrast, in cancer PTRH2 is a potential oncogene that promotes malignancy and metastasis. PTRH2 modulates PI3K/AKT and ERK signaling in addition to Bcl2 expression and thereby regulates key cellular processes in response to adhesion including cell survival, growth, and differentiation. In this Review, we discuss the state of the science on this important cell survival, anoikis and differentiation regulator, and opportunities for further investigation and translation. We begin with a brief overview of the structure, regulation, and subcellular localization of PTRH2. We discuss the cluster of gene mutations thus far identified which cause developmental delays and multisystem disease. We then discuss the role of PTRH2 and adhesion in breast, lung, and esophageal cancers focusing on signaling pathways involved in cell survival, cell growth, and cell differentiation.
Individual differences among deep neural network models
Authors: Mehrer Johannes , Spoerer Courtney J. , Kriegeskorte Nikolaus , Kietzmann Tim C. 
Published: November 2020

AbstractDeep neural networks (DNNs) excel at visual recognition tasks and are increasingly used as a modeling framework for neural computations in the primate brain. Just like individual brains, each DNN has a unique connectivity and representational profile. Here, we investigate individual differences among DNN instances that arise from varying only the random initialization of the network weights. Using tools typically employed in systems neuroscience, we show that this minimal change in initial conditions prior to training leads to substantial differences in intermediate and higher-level network representations despite similar network-level classification performance. We locate the origins of the effects in an under-constrained alignment of category exemplars, rather than misaligned category centroids. These results call into question the common practice of using single networks to derive insights into neural information processing and rather suggest that computational neuroscientists working with DNNs may need to base their inferences on groups of multiple network instances.
Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale
Authors: Zhuang Wei , Yu Xiaoli , Hu Ruiwen , Luo Zhiwen , Liu Xingyu , Zheng Xiafei , Xiao Fanshu , Peng Yisheng , He Qiang , Tian Yun , Yang Tony , Wang Shanquan , Shu Longfei , Yan Qingyun , Wang Cheng , He Zhili 
Published: November 2020

AbstractMangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56–74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.
Evidence for different behaviors of atmospheric glass alteration as a function of glass composition
Authors: Alloteau Fanny , Majérus Odile , Valbi Valentina , Biron Isabelle , Lehuédé Patrice , Caurant Daniel , Charpentier Thibault , Seyeux Antoine 
Published: November 2020

AbstractThe glass composition is a determining parameter that influences the glass chemical durability, particularly in atmospheric conditions (defined by the relative humidity, RH, < 100%). This is obvious in the field of the cultural heritage (CH), where some glass compositions qualified as unstable show advanced signs of degradation under atmosphere, while others seem, on the contrary, stable. This study investigates the differences between stable and unstable glass compositions regarding the phenomenology of the atmospheric glass alteration, by means of accelerated ageing of three glass replicas followed by the characterization of their alteration layers at different scales. Over the same ageing period and experimental conditions, the two glass compositions qualified as unstable develop thick hydrated layers and a thin top layer of carbonate precipitates. Their hydrated layers are depolymerized, and they remarkably retain alkalis and non-bridging oxygens in a dense network of hydrogen bonds, as demonstrated by 29Si and 1H MAS NMR. On the contrary, the stable glass composition shows a considerably thinner hydrated layer and, relatively, a higher amount of carbonates on the surface. In unstable glasses, the retention of a significant proportion of alkalis and NBOs, probably by maintaining a basic character to the hydrated layer, seems comparatively a destabilizing factor sustaining hydration by fast network hydrolysis.
Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs
Authors: Marin Egor , Luginina Aleksandra , Gusach Anastasiia , Kovalev Kirill , Bukhdruker Sergey , Khorn Polina , Polovinkin Vitaly , Lyapina Elizaveta , Rogachev Andrey , Gordeliy Valentin , Mishin Alexey , Cherezov Vadim , Borshchevskiy Valentin 
Published: November 2020

AbstractStructural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acquired from lipidic cubic phase (LCP) grown microcrystals of two human GPCRs, Cysteinyl leukotriene receptors 1 and 2 (CysLT1R and CysLT2R), in complex with various antagonists. Five datasets were collected using small-wedge synchrotron crystallography (SWSX) at the European Synchrotron Radiation Facility with multiple crystals under cryo-conditions. Two datasets were collected using X-ray free electron laser (XFEL) serial femtosecond crystallography (SFX) at the Linac Coherent Light Source, with microcrystals delivered at room temperature into the beam within LCP matrix by a viscous media microextrusion injector. All seven datasets have been deposited in the open-access databases Zenodo and CXIDB. Here, we describe sample preparation and annotate crystallization conditions for each partial and full datasets. We also document full processing pipelines and provide wrapper scripts for SWSX and SFX data processing.A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00759-w
Knockdown lncRNA NEAT1 regulates the activation of microglia and reduces AKT signaling and neuronal apoptosis after cerebral ischemic reperfusion
Authors: Ni Xunran , Su Qian , Xia Wenbo , Zhang Yanli , Jia Kejuan , Su Zhiqiang , Li Guozhong 
Published: November 2020

AbstractAcute cerebral ischaemia may lead to serious consequences, including brain injury caused by uncontrolled reperfusion, which occurs when circulation is re-established. The long non-coding RNA (lncRNA) nuclear enriched abundant transcript 1 (NEAT1) plays an important role in the immune system. However, the potential roles and underlying molecular mechanisms of NEAT1 in cerebral ischaemia/reperfusion (I/R) injury remain unclear. The aim of the present study was to investigate the function of the lncRNA NEAT1 in cerebral I/R injury and its potential beneficial effects on neurons. In our study, oxygen–glucose deprivation (OGD)/reoxygenation (OGD/R) was induced in vitro to mimic cerebral I/R injury. Cholecystokinin-octopeptide (CCK-8) was used to measure cell viability, and flow cytometry was used to measure cell apoptosis. Real-time quantitative PCR (qRT-PCR) was used to measure the expression of phenotypic markers of classically activated (M1) and alternatively activated (M2) microglia, and western blotting was performed to detect the levels of proteins related to the AKT/STAT3 pathway. The expression of the lncRNA NEAT1 was significantly upregulated in patients with ischaemic stroke, and knockdown of the lncRNA NEAT1 alleviated OGD/R-induced apoptosis and increased neuronal viability. Furthermore, the lncRNA NEAT1 may inhibit microglial polarization towards the M1 phenotype to reduce the damage caused by OGD/R and reduce the activity of the AKT/STAT3 pathway. In conclusion, the lncRNA NEAT1 may be a potential target for new therapeutic interventions for cerebral I/R.
Brain potentials reveal reduced attention and error-processing during a monetary Go/No-Go task in procrastination
Authors: Michałowski Jarosław M. , Wiwatowska Ewa , Weymar Mathias 
Published: November 2020

AbstractProcrastination is a self-regulatory problem of voluntarily and destructively delaying intended and necessary or personally important tasks. Previous studies showed that procrastination is associated with executive dysfunctions that seem to be particularly strong in punishing contexts. In the present event-related potential (ERP) study a monetary version of the parametric Go/No-Go task was performed by high and low academic procrastinators to verify the influence of motivational context (reward vs. punishment expectation) and task difficulty (easy vs. hard) on procrastination-related executive dysfunctions. The results revealed increased post-error slowing along with reduced P300 and error-related negativity (ERN) amplitudes in high (vs. low) procrastination participants—effects that indicate impaired attention and error-related processing in this group. This pattern of results did not differ as a function of task difficulty and motivation condition. However, when the task got more difficult executive attention deficits became even more apparent at the behavioral level in high procrastinators, as indexed by increased reaction time variability. The findings substantiate prior preliminary evidence that procrastinators show difficulties in certain aspects of executive functioning (in attention and error processing) during execution of task-relevant behavior, which may be more apparent in highly demanding situations.
An earth system model shows self-sustained thawing of permafrost even if all man-made GHG emissions stop in 2020
Authors: Randers Jorgen , Goluke Ulrich 
Published: November 2020

AbstractThe risk of points-of-no-return, which, once surpassed lock the world into new dynamics, have been discussed for decades. Recently, there have been warnings that some of these tipping points are coming closer and are too dangerous to be disregarded. In this paper we report that in the ESCIMO climate model the world is already past a point-of-no-return for global warming. In ESCIMO we observe self-sustained thawing of the permafrost for hundreds of years, even if global society stops all emissions of man-made GHGs immediately. We encourage other model builders to explore our discovery in their (bigger) models, and report on their findings. The thawing (in ESCIMO) is the result of a continuing self-sustained rise in the global temperature. This warming is the combined effect of three physical processes: (1) declining surface albedo (driven by melting of the Arctic ice cover), (2) increasing amounts of water vapour in the atmosphere (driven by higher temperatures), and (3) changes in the concentrations of the GHG in the atmosphere (driven by the absorption of CO2 in biomass and oceans, and emission of carbon (CH4 and CO2) from thawing permafrost). This self-sustained, in the sense of no further GHG emissions, thawing process (in ESCIMO) is a causally determined, physical process that evolves over time. It starts with the man-made warming up to the 1950s, leading to a rise in the amount of water vapour in the atmosphere—further lifting the temperature, causing increasing release of carbon from thawing permafrost, and simultaneously a decline in the surface albedo as the ice and snow covers melts. To stop the self-sustained warming in ESCIMO, enormous amounts of CO2 have to be extracted from the atmosphere.
Metabolomics profiling of plasma, urine and saliva after short term training in young professional football players in Saudi Arabia
Authors: Alzharani Mansour A. , Alshuwaier Ghareeb O. , Aljaloud Khalid S. , Al-Tannak Naser F. , Watson David G. 
Published: November 2020

AbstractMetabolomics profiling was carried out to observe the effect of short-term intensive physical activity on the metabolome of young Saudi professional football players. Urine, plasma and saliva were collected on 2 days pre- and post-training. An Orbitrap Exactive mass spectrometer was used to analyze the samples. A reversed-phase (RP) column was used for the analysis of non-polar plasma metabolites, and a ZIC-pHILIC column was used for the analysis of plasma, saliva and urine. mzMine was used to extract the data, and the results were modelled using Simca-P 14.1 software. There was no marked variation in the metabolite profiles between pre day 1 and 2 or between post day 1 and 2 according to principal components analysis (PCA). When orthogonal partial least squares (OPLSDA) modelling was also used, and then models could be fitted based on a total number of metabolites of 75, 16 and 32 for urine, plasma and saliva using hydrophilic interaction chromatography (HILIC) and 6 for analysis of plasma with reversed-phase (RP) chromatography respectively. The present study concludes that acylcarnitine may increase post-exercise in football players suggesting that they may burn fat rather than glucose. The levels of carnitine metabolites in plasma post-exercise could provide an important indicator of fitness.
Accelerated ethanol elimination via the lungs
Authors: Klostranec Jesse M. , Vucevic Diana , Crawley Adrian P. , Venkatraghavan Lashmi , Sobczyk Olivia , Duffin James , Sam Kevin , Holmes Royce , Fedorko Ludwik , Mikulis David J. , Fisher Joseph A. 
Published: November 2020

AbstractEthanol poisoning is endemic the world over. Morbidity and mortality depend on blood ethanol levels which in turn depend on the balance between its rates of absorption and clearance. Clearance of ethanol is mostly at a constant rate via enzymatic metabolism. We hypothesized that isocapnic hyperpnea (IH), previously shown to be effective in acceleration of clearance of vapour anesthetics and carbon monoxide, would also accelerate the clearance of ethanol. In this proof-of-concept pilot study, five healthy male subjects were brought to a mildly elevated blood ethanol concentration (~ 0.1%) and ethanol clearance monitored during normal ventilation and IH on different days. IH increased elimination rate of ethanol in proportion to blood levels, increasing the elimination rate more than three-fold. Increased veno-arterial ethanol concentration differences during IH verified the efficacy of ethanol clearance via the lung. These data indicate that IH is a nonpharmacologic means to accelerate the elimination of ethanol by superimposing first order elimination kinetics on underlying zero order liver metabolism. Such kinetics may prove useful in treating acute severe ethanol intoxication.
Partial synchronisation of glycolytic oscillations in yeast cell populations
Authors: Weber André , Zuschratter Werner , Hauser Marcus J. B. 
Published: November 2020

AbstractThe transition between synchronized and asynchronous behaviour of immobilized yeast cells of the strain Saccharomyces carlsbergensis was investigated by monitoring the autofluorescence of the coenzyme NADH. In populations of intermediate cell densities the individual cells remained oscillatory, whereas on the level of the cell population both a partially synchronized and an asynchronous state were accessible for experimental studies. In the partially synchronized state, the mean oscillatory frequency was larger than that of the cells in the asynchronous state. This suggests that synchronisation occurred due to entrainment by the cells that oscillated more rapidly. This is typical for synchronisation due to phase advancement. Furthermore, the synchronisation of the frequency of the glycolytic oscillations preceded the synchronisation of their phases. However, the cells did not synchronize completely, as the distribution of the oscillatory frequencies only narrowed but did not collapse to a unique frequency. Cells belonging to spatially denser clusters showed a slightly enhanced local synchronisation during the episode of partial synchronisation. Neither the clusters nor a transition from partially synchronized glycolytic oscillations to travelling glycolytic waves did substantially affect the degree of partial synchronisation. Chimera states, i.e., the coexistence of a synchronized and an asynchronous part of the population, could not be found.
Search strategy in a complex and dynamic environment: the MH370 case
Authors: Ivić Stefan , Crnković Bojan , Arbabi Hassan , Loire Sophie , Clary Patrick , Mezić Igor 
Published: November 2020

AbstractSearch and detection of objects on the ocean surface is a challenging task due to the complexity of the drift dynamics and lack of known optimal solutions for the path of the search agents. This challenge was highlighted by the unsuccessful search for Malaysian Flight 370 (MH370) which disappeared on March 8, 2014. In this paper, we propose an improvement of a search algorithm rooted in the ergodic theory of dynamical systems which can accommodate complex geometries and uncertainties of the drifting search areas on the ocean surface. We illustrate the effectiveness of this algorithm in a computational replication of the conducted search for MH370. We compare the algorithms using many realizations with random initial positions, and analyze the influence of the stochastic drift on the search success. In comparison to conventional search methods, the proposed algorithm leads to an order of magnitude improvement in success rate over the time period of the actual search operation. Simulations of the proposed search control also indicate that the initial success rate of finding debris increases in the event of delayed search commencement. This is due to the existence of convergence zones in the search area which leads to local aggregation of debris in those zones and hence reduction of the effective size of the area to be searched.
The importance of feature aggregation in radiomics: a head and neck cancer study
Authors: Fontaine Pierre , Acosta Oscar , Castelli Joël , De Crevoisier Renaud , Müller Henning , Depeursinge Adrien 
Published: November 2020

AbstractIn standard radiomics studies the features extracted from clinical images are mostly quantified with simple statistics such as the average or variance per Region of Interest (ROI). Such approaches may smooth out any intra-region heterogeneity and thus hide some tumor aggressiveness that may hamper predictions. In this paper we study the importance of feature aggregation within the standard radiomics workflow, which allows to take into account intra-region variations. Feature aggregation methods transform a collection of voxel values from feature response maps (over a ROI) into one or several scalar values that are usable for statistical or machine learning algorithms. This important step has been little investigated within the radiomics workflows, so far. In this paper, we compare several aggregation methods with standard radiomics approaches in order to assess the improvements in prediction capabilities. We evaluate the performance using an aggregation function based on Bags of Visual Words (BoVW), which allows for the preservation of piece-wise homogeneous information within heterogeneous regions and compared with standard methods. The different models are compared on a cohort of 214 head and neck cancer patients coming from 4 medical centers. Radiomics features were extracted from manually delineated tumors in clinical PET-FDG and CT images were analyzed. We compared the performance of standard radiomics models, the volume of the ROI alone and the BoVW model for survival analysis. The average concordance index was estimated with a five fold cross-validation. The performance was significantly better using the BoVW model 0.627 (95% CI: 0.616–0.637) as compared to standard radiomics0.505 (95% CI: 0.499–0.511), mean-var. 0.543 (95% CI: 0.536–0.549), mean0.547 (95% CI: 0.541–0.554), var.0.530 (95% CI: 0.524–0.536) or volume 0.577 (95% CI: 0.571–0.582). We conclude that classical aggregation methods are not optimal in case of heterogeneous tumors. We also showed that the BoVW model is a better alternative to extract consistent features in the presence of lesions composed of heterogeneous tissue.