bluuebunny/crossref_metadata_2025_split huggingface dataset:
Falsification‐Oriented Signature‐Based Evaluation for Guiding the Development of Land Surface Models and the Enhancement of Observations
Authors: Zheng Hui , Yang Zong‐Liang , Lin Peirong , Wu Wen‐Ying , Li Lingcheng , Xu Zhongfeng , Wei Jiangfeng , Zhao Long , Bian Qingyun , Wang Shu 
Published: November 2020

AbstractWe develop a novel framework for rigorously evaluating land surface models (LSMs) against observations by recognizing the asymmetry between verification‐ and falsification‐oriented approaches. The former approach cannot completely verify LSMs even though it exhausts every case of consistency between the model predictions and observations, whereas the latter only requires a single case of inconsistency to reveal that there must be something wrong. We argue that it is such an inconsistency that stimulates further development of the models and enhancement of the observations. We therefore propose a falsification‐oriented signature‐based evaluation framework to identify cases of inconsistency between model predictions and observations by extracting signatures based on a set of key assumptions. We apply this framework to evaluate an ensemble of simulations from the Noah‐MP LSM against observations over the continental United States under the three assumptions of water mass conservation, no lateral water flow, and a sufficiently long period of time. Regions showing inconsistencies between the Noah‐MP ensemble simulations and the observations are located in the western mountainous areas, the Yellowstone river basin, the lower Floridan aquifer, the Niobrara river basin at the north tip of the Ogallala aquifer, and the basins downstream of the Balcones fault zones in Texas. These regions coincide with the sites where both advances in theoretical modeling and new observational data (e.g., from the Critical Zone Observatories) have emerged.
Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed
Authors: Bernard Jared , Wall Christopher B , Costantini Maria S , Rollins Randi L , Atkins Melissa L , Cabrera Feresa P , Cetraro Nicolas D , Feliciano Christian K J , Greene Austin L , Kitamura Philip K , Olmedo-Velarde Alejandro , Sirimalwatta Vithanage N S , Sung Helen W , Thompson Leah P M , Vu Huong T , Wilhite Chad J , Amend Anthony S 
Published: November 2020

Abstract
Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. These scales are seldom considered simultaneously, despite their potential to interact. Here, we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across a steep, but short, environmental gradient within a single Hawaiian watershed. At each location, we sampled eight microhabitats: leaves, petioles, axils, stems, roots, and litter from the plant, as well as surrounding air and soil. The composition of bacterial communities is better explained by microhabitat, while location better predicted compositional variance for fungi. Fungal community compositional dissimilarity increased more rapidly along the gradient than did bacterial composition. Additionally, the rates of fungal community compositional dissimilarity along the gradient differed among plant parts, and these differences influenced the distribution patterns and range size of individual taxa. Within plants, microbes were compositionally nested such that aboveground communities contained a subset of the diversity found belowground. Our findings indicate that both environmental context and microhabitat contribute to microbial compositional variance in our study, but that these contributions are influenced by the domain of microbe and the specific microhabitat in question, suggesting a complicated and potentially interacting dynamic.
YTHDC1 mitigates ischemic stroke by promoting Akt phosphorylation through destabilizing PTEN mRNA
Authors: Zhang Zhaolong , Wang Qiuhan , Zhao Xiaolong , Shao Liming , Liu Guoping , Zheng Xuan , Xie Lingling , Zhang Yan , Sun Chengjian , Xu Rui 
Published: November 2020

AbstractYTH Domain Containing 1 (YTHDC1) is one of the m6A readers that is essential for oocyte development and tumor progression. The role of YTHDC1 in neuronal survival and ischemic stroke is unknown. Here, we found that YTHDC1 was unregulated in the early phase of ischemic stroke. Knockdown of YTHDC1 exacerbated ischemic brain injury and overexpression of YTHDC1 protected rats against brain injury. Mechanistically, YTHDC1 promoted PTEN mRNA degradation to increase Akt phosphorylation, thus facilitating neuronal survival in particular after ischemia. These data identify YTHDC1 as a novel regulator of neuronal survival and modulating m6A reader YTHDC1 may provide a potential therapeutic target for ischemic stroke.
Spatiotemporal dynamics of 53BP1 dimer recruitment to a DNA double strand break
Authors: Lou Jieqiong , Priest David G. , Solano Ashleigh , Kerjouan Adèle , Hinde Elizabeth 
Published: November 2020

AbstractTumor suppressor p53-binding protein 1 (53BP1) is a DNA repair protein essential for the detection, assessment, and resolution of DNA double strand breaks (DSBs). The presence of a DSB is signaled to 53BP1 via a local histone modification cascade that triggers the binding of 53BP1 dimers to chromatin flanking this type of lesion. While biochemical studies have established that 53BP1 exists as a dimer, it has never been shown in a living cell when or where 53BP1 dimerizes upon recruitment to a DSB site, or upon arrival at this nuclear location, how the DSB histone code to which 53BP1 dimers bind regulates retention and self-association into higher-order oligomers. Thus, here in live-cell nuclear architecture we quantify the spatiotemporal dynamics of 53BP1 oligomerization during a DSB DNA damage response by coupling fluorescence fluctuation spectroscopy (FFS) with the DSB inducible via AsiSI cell system (DIvA). From adopting this multiplexed approach, we find that preformed 53BP1 dimers relocate from the nucleoplasm to DSB sites, where consecutive recognition of ubiquitinated lysine 15 of histone 2A (H2AK15ub) and di-methylated lysine 20 of histone 4 (H4K20me2), leads to the assembly of 53BP1 oligomers and a mature 53BP1 foci structure.
Optocapillarity-driven assembly and reconfiguration of liquid crystal polymer actuators
Authors: Hu Zhiming , Fang Wei , Li Qunyang , Feng Xi-Qiao , Lv Jiu-an 
Published: November 2020

AbstractRealizing programmable assembly and reconfiguration of small objects holds promise for technologically-significant applications in such fields as micromechanical systems, biomedical devices, and metamaterials. Although capillary forces have been successfully explored to assemble objects with specific shapes into ordered structures on the liquid surface, reconfiguring these assembled structures on demand remains a challenge. Here we report a strategy, bioinspired by Anurida maritima, to actively reconfigure assembled structures with well-defined selectivity, directionality, robustness, and restorability. This approach, taking advantage of optocapillarity induced by photodeformation of floating liquid crystal polymer actuators, not only achieves programmable and reconfigurable two-dimensional assembly, but also uniquely enables the formation of three-dimensional structures with tunable architectures and topologies across multiple fluid interfaces. This work demonstrates a versatile approach to tailor capillary interaction by optics, as well as a straightforward bottom-up fabrication platform for a wide range of applications.
Multipolar lasing modes from topological corner states
Authors: Kim Ha-Reem , Hwang Min-Soo , Smirnova Daria , Jeong Kwang-Yong , Kivshar Yuri , Park Hong-Gyu 
Published: November 2020

AbstractTopological photonics provides a fundamental framework for robust manipulation of light, including directional transport and localization with built-in immunity to disorder. Combined with an optical gain, active topological cavities hold special promise for a design of light-emitting devices. Most studies to date have focused on lasing at topological edges of finite systems or domain walls. Recently discovered higher-order topological phases enable strong high-quality confinement of light at the corners. Here, we demonstrate lasing action of corner states in nanophotonic topological structures. We identify several multipole corner modes with distinct emission profiles via hyperspectral imaging and discern signatures of non-Hermitian radiative coupling of leaky topological states. In addition, depending on the pump position in a large-size cavity, we generate selectively lasing from either edge or corner states within the topological bandgap. Our studies provide the direct observation of multipolar lasing and engineered collective resonances in active topological nanostructures.
Architecture of the flexible tail tube of bacteriophage SPP1
Authors: Zinke Maximilian , Sachowsky Katrin A. A. , Öster Carl , Zinn-Justin Sophie , Ravelli Raimond , Schröder Gunnar F. , Habeck Michael , Lange Adam 
Published: November 2020

AbstractBacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.
All atom insights into the impact of crowded environments on protein stability by NMR spectroscopy
Authors: Köhn Birgit , Kovermann Michael 
Published: November 2020

AbstractThe high density of macromolecules affecting proteins due to volume exclusion has been discussed in theory but numerous in vivo experiments cannot be sufficiently understood taking only pure entropic stabilization into account. Here, we show that the thermodynamic stability of a beta barrel protein increases equally at all atomic levels comparing crowded environments with dilute conditions by applying multidimensional high-resolution NMR spectroscopy in a systematic manner. Different crowding agents evoke a pure stabilization cooperatively and do not disturb the surface or integrity of the protein fold. The here developed methodology provides a solid base that can be easily expanded to incorporate e.g. binding partners to recognize functional consequences of crowded conditions. Our results are relevant to research projects targeting soluble proteins in vivo as it can be anticipated that their thermodynamic stability increase comparably and has consequently to be taken into account to coherently understand intracellular processes.
Acquired dysregulation of dopamine homeostasis reproduces features of Parkinson’s disease
Authors: Bucher Meghan L. , Barrett Caitlyn W. , Moon Connor J. , Mortimer Amanda D. , Burton Edward A. , Greenamyre J. Timothy , Hastings Teresa G. 
Published: November 2020

AbstractThe catecholamine neurotransmitter dopamine has the potential to act as an endogenous neurotoxin when its vesicular sequestration is dysregulated. Despite postmortem analyses from patients with Parkinson’s disease that demonstrate decreased vesicular sequestration of dopamine with a corresponding increase in dopamine metabolism, dopamine’s contribution to nigrostriatal dopaminergic degeneration in Parkinson’s disease has been debated. Here, we present a new in vivo model demonstrating the induction of Parkinson’s disease-associated pathogenic mechanisms of degeneration resulting from acquired dysregulation of dopamine sequestration in nigrostriatal dopaminergic neurons in adult rats. Utilizing adeno-associated virus (serotype 2), viral-mediated small-hairpin RNA interference of endogenous vesicular monoamine transporter 2 (VMAT2) expression resulted in a loss of VMAT2 protein expression in transduced dopaminergic cell bodies in the substantia nigra with a corresponding loss of VMAT2 protein within the striatal terminals. The loss of VMAT2 resulted in an accumulation of cytosolic dopamine and subsequent increased dopamine metabolism, deficits in dopamine-mediated behaviors, and degeneration of nigrostriatal dopaminergic neurons that was rescued through reintroduction of exogenous VMAT2, demonstrating that the toxicity was specific to the loss of VMAT2. Analysis of parkinsonian pathogenic mechanisms of degeneration identified oxidative damage, activation of Parkinson’s disease-associated kinase LRRK2, and the formation of aberrant α-synuclein. This model demonstrates that a progressive acquired loss of VMAT2 expression in adulthood is sufficient to induce Parkinson’s disease-associated pathogenic mechanisms of degeneration and provides a new model to further investigate the consequences of cytosolic dopamine.
Reduced astrocytic reactivity in human brains and midbrain organoids with PRKN mutations
Authors: Kano Masayoshi , Takanashi Masashi , Oyama Genko , Yoritaka Asako , Hatano Taku , Shiba-Fukushima Kahori , Nagai Makiko , Nishiyama Kazutoshi , Hasegawa Kazuko , Inoshita Tsuyoshi , Ishikawa Kei-ichi , Akamatsu Wado , Imai Yuzuru , Bolognin Silvia , Schwamborn Jens Christian , Hattori Nobutaka 
Published: November 2020

AbstractParkin (encoded by PRKN) is a ubiquitin ligase that plays an important role in cellular mitochondrial quality control. Mutations in PRKN cause selective dopaminergic cell loss in the substantia nigra and are presumed to induce a decrease in mitochondrial function caused by the defective clearance of mitochondria. Several studies have demonstrated that parkin dysfunction causes mitochondrial injury and astrocytic dysfunction. Using immunohistochemical methods, we analyzed astrocytic changes in human brains from individuals with PRKN mutations. Few glial fibrillary acidic protein- and vimentin-positive astrocytes were observed in the substantia nigra in PRKN-mutated subjects compared with subjects with idiopathic Parkinson’s disease. We also differentiated patient-specific induced pluripotent stem cells into midbrain organoids and confirmed decreased numbers of glial fibrillary acidic protein-positive astrocytes in PRKN-mutated organoids compared with age- and sex-matched controls. Our study reveals PRKN-mutation-induced astrocytic alteration and suggests the possibility of an astrocyte-related non-autonomous cell death mechanism for dopaminergic neurons in brains of PRKN-mutated patients.
Longitudinal stability of retinal blood flow regulation in response to flicker stimulation and systemic hyperoxia in mice assessed with laser speckle flowgraphy
Authors: Hanaguri Junya , Yokota Harumasa , Watanabe Masahisa , Kuo Lih , Yamagami Satoru , Nagaoka Taiji 
Published: November 2020

AbstractThis study aimed to evaluate longitudinal changes in retinal blood flow in response to flicker stimulation and systemic hyperoxia in mice using a laser speckle flowgraphy (LSFG-Micro). The retinal blood flow in vascular area surrounding the optic nerve head was measured in 8-week-old male mice every 2 weeks until age 20-week. The coefficient of variation of retinal blood flow under resting condition was analyzed every 2 weeks to validate the consistency of the measurement. On day 1 of the experiment, retinal blood flow was assessed every 20 s for 6 min during and after 3 min flicker light (12 Hz) stimulation; on day 2, retinal blood flow was measured every minute for 20 min during and after 10 min systemic hyperoxia; and on day 3, electroretinography (ERG) was performed. Body weight, systemic blood pressure, and ocular perfusion pressure increased significantly with age, but the resting retinal blood flow and ERG parameters remained unchanged. Retinal blood flow significantly increased with flicker stimulation and decreased with systemic hyperoxia, independent of age. The LSFG-Micro provides consistent and reproducible retinal blood flow measurement in adult mice. Longitudinal assessments of retinal blood flow in response to flicker stimulation and systemic hyperoxia may be useful indexes for noninvasive monitoring of vascular function in retinas.
Bio-process performance, evaluation of enzyme and non-enzyme mediated composting of vegetable market complex waste
Authors: Murugesan V. , Amarnath D. Joshua 
Published: November 2020

AbstractVegetable Market have become major sources of organic waste. Some of such waste when being diverted to landfills not only increase the landfill loading but also contribute to increase greenhouse gas emission. Of the many technologies available in handling such hugely generated waste, composting has proven very effective for decades. Enzyme and non-enzyme mediated aerobic composting of vegetable market complex waste (VMCW) have been investigated. Conventional composting technique though being capable of handling large quantum of waste are found to consume more time. Proven to be disadvantages factor. In the present investigation, the pre-cultured seed inoculums used for vegetable market complex waste, shortened the typical composting period from 45 to 9 days for the first time. Also, rapid size and volume reduction of VMCW was witnessed. The organic degradation of VMCW was observed as 42% (82 ± 2.83% to 40.82 ± 0.61%), with a volume reduction from 0.012m3 to 0.003 m3 within 9 days. An enriched nutrients NPK level of compost bio-fertilizer was recorded as 0.91% w/w, 0.5% w/w and 1.029% w/w respectively. Compost maturity observed through the X-ray diffraction (XRD) analysis of the manure confirmed the conversion of the crystal structure of the compost particle to amorphous form and the mineralization of organic matter during the composting. Thus, the fermented pre-cultured seed inoculums favored an enhanced nutrients level with shortened composting time.
Effects of set cathode potentials on microbial electrosynthesis system performance and biocathode methanogen function at a metatranscriptional level
Authors: Ragab Ala’a , Shaw Dario Rangel , Katuri Krishna P. , Saikaly Pascal E. 
Published: November 2020

AbstractMicrobial electrosynthesis exploits the catalytic activity of microorganisms to utilize a cathode as an electron donor for reducing waste CO2 to valuable fuels and chemicals. Electromethanogenesis is the process of CO2 reduction to CH4 catalyzed by methanogens using the cathode directly as a source of electrons or indirectly via H2. Understanding the effects of different set cathode potentials on the functional dynamics of electromethanogenic communities is crucial for the rational design of cathode materials. Replicate enriched electromethanogenic communities were subjected to different potentials (− 1.0 V and − 0.7 V vs. Ag/AgCl) and the potential-induced changes were analyzed using a metagenomic and metatranscriptomic approach. The most abundant and transcriptionally active organism on the biocathodes was a novel species of Methanobacterium sp. strain 34x. The cathode potential-induced changes limited electron donor availability and negatively affected the overall performance of the reactors in terms of CH4 production. Although high expression of key genes within the methane and carbon metabolism pathways was evident, there was no significant difference in transcriptional response to the different set potentials. The acetyl-CoA decarbonylase/synthase (ACDS) complex were the most highly expressed genes, highlighting the significance of carbon assimilation under limited electron donor conditions and its link to the methanogenesis pathway.
Cocaine, cardiomyopathy, and heart failure: a systematic review and meta-analysis
Authors: Arenas Daniel J. , Beltran Sourik , Zhou Sara , Goldberg Lee R. 
Published: November 2020

AbstractAlthough the cardiotoxic effects of cocaine are universally recognized, the association between cocaine and cardiomyopathy and/or heart failure is poorly understood. To conduct a comprehensive review and meta-analysis on the association between cocaine, heart failure, and cardiomyopathy, we first conducted a broad-term search in PubMed, Embase, Web of Science, and Scopus for human studies containing primary data on the relationship between cocaine and heart failure or cardiomyopathy. We were interested in studies with data beyond acute coronary syndromes. Retrieved studies were grouped into different categories based on possible hypotheses to test by meta-analysis. A second search with specific terms was then conducted. For grouped studies with sufficient clinical and methodological homogeneity, effect sizes were calculated and combined for meta-analysis by the Random Effects model. There is in general a need for more primary data studies that investigate heart failure and/or cardiomyopathy in cocaine users for mechanisms independent of ischemia. There were, however, enough studies to combine by meta-analyses that showed that chronic cocaine use is associated with anatomical and functional changes more consistent with diastolic heart failure instead of the commonly taught dilated cardiomyopathy pathway. In patients without a history of ACS, chronic cocaine use was not associated with significantly reduced EF. The few studies on acute cocaine had conflicting results on whether single-dose intravascular cocaine results in acute heart failure. Studies identified that included beta-blockade therapy in cocaine users with cardiac disease suggest that beta-blockers are not unsafe and that may be effective in the treatment of cocaine-associated heart failure. Chronic cocaine use is associated with anatomical and physiological changes of the heart muscle that are potentially reversible with beta-blockade therapy.
Aldosterone-to-renin ratio is related to arterial stiffness when the screening criteria of primary aldosteronism are not met
Authors: Kokko Eeva , Nevalainen Pasi I. , Choudhary Manoj Kumar , Koskela Jenni , Tikkakoski Antti , Huhtala Heini , Niemelä Onni , Viukari Marianna , Mustonen Jukka , Matikainen Niina , Pörsti Ilkka 
Published: November 2020

AbstractAldosterone-to-renin ratio (ARR) is a screening tool for primary aldosteronism (PA), but the significance of ARR when the PA criteria are not met remains largely unknown. In this cross-sectional study we investigated the association of ARR with haemodynamic variables in 545 normotensive and never-medicated hypertensive subjects (267 men, 278 women, age range 19–72 years) without suspicion of PA. Supine haemodynamic data was recorded using whole-body impedance cardiography and radial tonometric pulse wave analysis. In sex-adjusted quartiles of ARR, determined as serum aldosterone to plasma renin activity ratio, the mean values were 282, 504, 744 and 1467 pmol/µg of angiotensin I/h, respectively. The only difference in haemodynamic variables between the ARR quartiles was higher pulse wave velocity (PWV) in the highest quartile versus other quartiles (p = 0.004), while no differences in blood pressure (BP), heart rate, wave reflections, cardiac output or systemic vascular resistance were observed between the quartiles. In linear regression analysis with stepwise elimination, ARR was an independent explanatory factor for PWV (β = 0.146, p < 0.001, R2 of the model 0.634). In conclusion, ARR was directly and independently associated with large arterial stiffness in individuals without clinical suspicion of PA. Therefore, ARR could serve as a clinical marker of cardiovascular risk.Trial registration: ClinicalTrails.gov: NCT01742702.