bluuebunny/crossref_metadata_2025_split huggingface dataset:
Logarithmic Model Joint Inversion Method for Coseismic and Postseismic Slip: Application to the 2017 Mw 7.3 Sarpol Zahāb Earthquake, Iran
Authors: Liu Xiaoge , Xu Wenbin 
Published: October 2019

AbstractInterferometric synthetic aperture radar (InSAR) has become an important technique for studying earthquake cycle deformation. However, due to the limited satellite revisit time, it is often difficult to fully separate coseismic and postseismic slip from InSAR data. Nevertheless, accurately estimating spatiotemporal coseismic and postseismic fault slip distribution models is important for quantifying earthquake slip, understanding the kinematics of seismogenic faulting, and evaluating seismic hazards. Here, we develop a logarithmic model‐based method (LogSIM) for the joint inversion of coseismic and postseismic fault slip using InSAR data from multiple platforms in different orbits. This method considers the nature of early postseismic slip following logarithmic decay. The coseismic slip, the decay time constant, and the decay amplitude of the logarithmic model can be jointly estimated from unwrapped interferograms without the need for InSAR time series calculations, thereby reducing the number of unknown parameters and stabilizing the inversion. The robustness of LogSIM is first validated with synthetic experiments. We then apply LogSIM to invert for the coseismic and postseismic slip models of the 2017 Mw 7.3 Sarpol Zahāb earthquake. We find that the maximum afterslip value and postseismic moment release during the first four months reported in previous studies are underestimated by ~26% and ~31%, respectively, due to the unavailability of the first five days of postseismic deformation. The estimated afterslip distribution spatially overlaps with the aftershocks in the updip region of the fault plane. LogSIM could potentially be extended to integrate different space geodetic data in earthquake cycle deformation modeling.
AquaSat: A Data Set to Enable Remote Sensing of Water Quality for Inland Waters
Authors: Ross Matthew R. V. , Topp Simon N. , Appling Alison P. , Yang Xiao , Kuhn Catherine , Butman David , Simard Marc , Pavelsky Tamlin M. 
Published: October 2019

AbstractSatellite estimates of inland water quality have the potential to vastly expand our ability to observe and monitor the dynamics of large water bodies. For almost 50 years, we have been able to remotely sense key water quality constituents like total suspended sediment, dissolved organic carbon, chlorophyll a, and Secchi disk depth. Nonetheless, remote sensing of water quality is poorly integrated into inland water sciences, in part due to a lack of publicly available training data and a perception that remote estimates are unreliable. Remote sensing models of water quality can be improved by training and validation on larger data sets of coincident field and satellite observations, here called matchups. To facilitate model development and deeper integration of remote sensing into inland water science, we have built AquaSat, the largest such matchup data set ever assembled. AquaSat contains more than 600,000 matchups, covering 1984–2019, of ground‐based total suspended sediment, dissolved organic carbon, chlorophyll a, and SDDSecchi disk depth measurements paired with spectral reflectance from Landsat 5, 7, and 8 collected within ±1 day of each other. To build AquaSat, we developed open source tools in R and Python and applied them to existing public data sets covering the contiguous United States, including the Water Quality Portal, LAGOS‐NE, and the Landsat archive. In addition to publishing the data set, we are also publishing our full code architecture to facilitate expanding and improving AquaSat. We anticipate that this work will help make remote sensing of inland water accessible to more hydrologists, ecologists, and limnologists while facilitating novel data‐driven approaches to monitoring and understanding critical water resources at large spatiotemporal scales.
The interrelationship between cerebral ischemic stroke and glioma: a comprehensive study of recent reports
Authors: Ghosh Mrinal K. , Chakraborty Dipankar , Sarkar Sibani , Bhowmik Arijit , Basu Malini 
Published: October 2019

AbstractGlioma and cerebral ischemic stroke are two major events that lead to patient death worldwide. Although these conditions have different physiological incidences, ~10% of ischemic stroke patients develop cerebral cancer, especially glioma, in the postischemic stages. Additionally, the high proliferation, venous thrombosis and hypercoagulability of the glioma mass increase the significant risk of thromboembolism, including ischemic stroke. Surprisingly, these events share several common pathways, viz. hypoxia, cerebral inflammation, angiogenesis, etc., but the proper mechanism behind this co-occurrence has yet to be discovered. The hypercoagulability and presence of the D-dimer level in stroke are different in cancer patients than in the noncancerous population. Other factors such as atherosclerosis and coagulopathy involved in the pathogenesis of stroke are partially responsible for cancer, and the reverse is also partially true. Based on clinical and neurosurgical experience, the neuronal structures and functions in the brain and spine are observed to change after a progressive attack of ischemia that leads to hypoxia and atrophy. The major population of cancer cells cannot survive in an adverse ischemic environment that excludes cancer stem cells (CSCs). Cancer cells in stroke patients have already metastasized, but early-stage cancer patients also suffer stroke for multiple reasons. Therefore, stroke is an early manifestation of cancer. Stroke and cancer share many factors that result in an increased risk of stroke in cancer patients, and vice-versa. The intricate mechanisms for stroke with and without cancer are different. This review summarizes the current clinical reports, pathophysiology, probable causes of co-occurrence, prognoses, and treatment possibilities.
Reminiscent capillarity in subnanopores
Authors: Deroche Irena , Daou T. Jean , Picard Cyril , Coasne Benoit 
Published: October 2019

AbstractFluids in large and small pores display different behaviors with a crossover described through the concept of critical capillarity. Here we report experimental and simulation data for various siliceous zeolites and adsorbates that show unexpected reminiscent capillarity for such nanoporous materials. For pore sizes D exceeding the fluid molecule size, the filling pressures p are found to follow a generic behavior kBT ln p ∼ γ/ρD where γ and ρ are the fluid surface tension and density. This result is rationalized by showing that the filling chemical potential for such ultra-small pores is the sum of an adsorption energy and a capillary energy that remains meaningful even for severe confinements. A phenomenological model, based on Derjaguin’s formalism to bridge macroscopic and molecular theories for condensation in porous materials, is developed to account for the behavior of fluids confined down to the molecular scale from simple parameters.
Integrated molecular characterization of chondrosarcoma reveals critical determinants of disease progression
Authors: Nicolle Rémy , Ayadi Mira , Gomez-Brouchet Anne , Armenoult Lucile , Banneau Guillaume , Elarouci Nabila , Tallegas Matthias , Decouvelaere Anne-Valérie , Aubert Sébastien , Rédini Françoise , Marie Béatrice , Labit-Bouvier Corinne , Reina Nicolas , Karanian Marie , le Nail Louis-Romée , Anract Philippe , Gouin François , Larousserie Frédérique , de Reyniès Aurélien , de Pinieux Gonzague 
Published: October 2019

AbstractChondrosarcomas are primary cancers of cartilaginous tissue with highly contrasting prognoses. These tumors are defined by recurrent mutations in the IDH genes and other genetic alterations including inactivation of CDKN2A and COL2A1; however, these have no clinical value. Here we use multi-omics molecular profiles from a series of cartilage tumors and find an mRNA classification that identifies two subtypes of chondrosarcomas defined by a balance in tumor differentiation and cell cycle activation. The microRNA classification reveals the importance of the loss of expression of the 14q32 locus in defining the level of malignancy. Finally, DNA methylation is associated with IDH mutations. We can use the multi-omics classifications to predict outcome. We propose an mRNA-only classifier to reproduce the integrated multi-omics classification, and its application to relapsed tumor samples shows the progressive nature of the classification. Thus, it may be possible to use mRNA-based signatures to detect patients with high-risk chondrosarcomas.
How to control single-molecule rotation
Authors: Simpson Grant J. , García-López Víctor , Daniel Boese A. , Tour James M. , Grill Leonhard 
Published: October 2019

AbstractThe orientation of molecules is crucial in many chemical processes. Here, we report how single dipolar molecules can be oriented with maximum precision using the electric field of a scanning tunneling microscope. Rotation is found to occur around a fixed pivot point that is caused by the specific interaction of an oxygen atom in the molecule with the Ag(111) surface. Both directions of rotation are realized at will with 100% directionality. Consequently, the internal dipole moment of an individual molecule can be spatially mapped via its behavior in an applied electric field. The importance of the oxygen-surface interaction is demonstrated by the addition of a silver atom between a single molecule and the surface and the consequent loss of the pivot point.
Understanding resonant charge transport through weakly coupled single-molecule junctions
Authors: Thomas James O. , Limburg Bart , Sowa Jakub K. , Willick Kyle , Baugh Jonathan , Briggs G. Andrew D. , Gauger Erik M. , Anderson Harry L. , Mol Jan A. 
Published: October 2019

AbstractOff-resonant charge transport through molecular junctions has been extensively studied since the advent of single-molecule electronics and is now well understood within the framework of the non-interacting Landauer approach. Conversely, gaining a qualitative and quantitative understanding of the resonant transport regime has proven more elusive. Here, we study resonant charge transport through graphene-based zinc-porphyrin junctions. We experimentally demonstrate an inadequacy of non-interacting Landauer theory as well as the conventional single-mode Franck–Condon model. Instead, we model overall charge transport as a sequence of non-adiabatic electron transfers, with rates depending on both outer and inner-sphere vibrational interactions. We show that the transport properties of our molecular junctions are determined by a combination of electron–electron and electron-vibrational coupling, and are sensitive to interactions with the wider local environment. Furthermore, we assess the importance of nuclear tunnelling and examine the suitability of semi-classical Marcus theory as a description of charge transport in molecular devices.
Topology, landscapes, and biomolecular energy transport
Authors: Elenewski Justin E. , Velizhanin Kirill A. , Zwolak Michael 
Published: October 2019

AbstractWhile ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior that diverges from the macroscale. Here, we show that transient thermal transport reflects macromolecular energy landscape architecture through the topological characteristics of molecular contacts and the nonlinear processes that mediate dynamics. While the former determines transport pathways via pairwise interactions, the latter reflects frustration within the landscape for local conformational rearrangements. Unlike transport through small-molecule systems, such as alkanes, nonlinearity dominates over coherent processes at even quite short time- and length-scales. Our exhaustive all-atom simulations and novel local-in-time and space analysis, applicable to both theory and experiment, permit dissection of energy migration in biomolecules. The approach demonstrates that vibrational energy transport can probe otherwise inaccessible aspects of macromolecular dynamics and interactions that underly biological function.
Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection
Authors: Ulz Peter , Perakis Samantha , Zhou Qing , Moser Tina , Belic Jelena , Lazzeri Isaac , Wölfler Albert , Zebisch Armin , Gerger Armin , Pristauz Gunda , Petru Edgar , White Brandon , Roberts Charles E. S. , John John St. , Schimek Michael G. , Geigl Jochen B. , Bauernhofer Thomas , Sill Heinz , Bock Christoph , Heitzer Ellen , Speicher Michael R. 
Published: October 2019

AbstractDeregulation of transcription factors (TFs) is an important driver of tumorigenesis, but non-invasive assays for assessing transcription factor activity are lacking. Here we develop and validate a minimally invasive method for assessing TF activity based on cell-free DNA sequencing and nucleosome footprint analysis. We analyze whole genome sequencing data for >1,000 cell-free DNA samples from cancer patients and healthy controls using a bioinformatics pipeline developed by us that infers accessibility of TF binding sites from cell-free DNA fragmentation patterns. We observe patient-specific as well as tumor-specific patterns, including accurate prediction of tumor subtypes in prostate cancer, with important clinical implications for the management of patients. Furthermore, we show that cell-free DNA TF profiling is capable of detection of early-stage colorectal carcinomas. Our approach for mapping tumor-specific transcription factor binding in vivo based on blood samples makes a key part of the noncoding genome amenable to clinical analysis.
Gel electrophoresis separation and origins of light emission in fluorophores prepared from citric acid and ethylenediamine
Authors: Kokorina Alina A. , Bakal Artem A. , Shpuntova Daria V. , Kostritskiy Alexandr Yu. , Beloglazova Natalia V. , De Saeger Sarah , Sukhorukov Gleb B. , Sapelkin Andrei V. , Goryacheva Irina Yu. 
Published: October 2019

AbstractWe investigated light emission of hydrothermally treated citric acid and ethylenediamine (EDA) with various precursor ratios using gel-electrophoresis. We show that this relatively simple approach can deliver significant insights into the origins of photoluminescence. We found that products of the synthesis consist of both positively and negatively charged species and exhibit large dispersion in electrophoretic mobility (i.e. charge-to-size ratio). We observed that despite the large dispersion of the reaction products the blue light emission is confined to discrete bands clearly identifiable in the gel. We demonstrate clear evidence that this emission originates from the negatively charged light molecular fraction with the highest mobility which shows no excitation-dependent light emission. This molecular fluorophore exhibits spectral characteristics similar to previously reported 1,2,3,5-tetrahydro-5-oxo-imidazo[1,2-a]pyridine-7-carboxylic acid (IPCA). Secondary gel electrophoresis run performed on the bands extracted from the first run indicates that no further separation takes place. On the basis of our experimental results, we conclude that relatively stable binding exists between IPCA and EDA-derived product. Thus, the products of the reaction contain IPCA both in molecular form and in complexes with EDA-derived products. We conclude that excitation-dependent emission is related to the fluorophore binding to the positively charged EDA-derived products with a positive charge.
Vitamin K1 prevents diabetic cataract by inhibiting lens aldose reductase 2 (ALR2) activity
Authors: Thiagarajan R. , Varsha M. K. N. Sai , Srinivasan V. , Ravichandran R. , Saraboji K. 
Published: October 2019

AbstractThis study investigated the potential of vitamin K1 as a novel lens aldose reductase inhibitor in a streptozotocin-induced diabetic cataract model. A single, intraperitoneal injection of streptozotocin (STZ) (35 mg/kg) resulted in hyperglycemia, activation of lens aldose reductase 2 (ALR2) and accumulation of sorbitol in eye lens which could have contributed to diabetic cataract formation. However, when diabetic rats were treated with vitamin K1 (5 mg/kg, sc, twice a week) it resulted in lowering of blood glucose and inhibition of lens aldose reductase activity because of which there was a corresponding decrease in lens sorbitol accumulation. These results suggest that vitamin K1 is a potent inhibitor of lens aldose reductase enzyme and we made an attempt to understand the nature of this inhibition using crude lens homogenate as well as recombinant human aldose reductase enzyme. Our results from protein docking and spectrofluorimetric analyses clearly show that vitamin K1 is a potent inhibitor of ALR2 and this inhibition is primarily mediated by the blockage of DL-glyceraldehyde binding to ALR2. At the same time docking also suggests that vitamin K1 overlaps at the NADPH binding site of ALR2, which probably shows that vitamin K1 could possibly bind both these sites in the enzyme. Another deduction that we can derive from the experiments performed with pure protein is that ALR2 has three levels of affinity, first for NADPH, second for vitamin K1 and third for the substrate DL-glyceraldehyde. This was evident based on the dose-dependency experiments performed with both NADPH and DL-glyceraldehyde. Overall, our study shows the potential of vitamin K1 as an ALR2 inhibitor which primarily blocks enzyme activity by inhibiting substrate interaction of the enzyme. Further structural studies are needed to fully comprehend the exact nature of binding and inhibition of ALR2 by vitamin K1 that could open up possibilities of its therapeutic application.
Depletion of dietary aryl hydrocarbon receptor ligands alters microbiota composition and function
Authors: Brawner Kyle M. , Yeramilli Venkata A. , Duck Lennard W. , Van Der Pol William , Smythies Lesley E. , Morrow Casey D. , Elson Charles O. , Martin Colin A. 
Published: October 2019

AbstractThe intestinal microbiota is critical for maintaining homeostasis. Dysbiosis, an imbalance in the microbial community, contributes to the susceptibility of several diseases. Many factors are known to influence gut microbial composition, including diet. We have previously shown that fecal immunoglobulin (Ig) A levels are decreased in mice fed a diet free of aryl hydrocarbon receptor (AhR) ligands. Here, we hypothesize this IgA decrease is secondary to diet-induced dysbiosis. We assigned mice to a conventional diet, an AhR ligand-free diet, or an AhR ligand-free diet supplemented with the dietary AhR ligand indole-3-carbinol (I3C). We observed a global alteration of fecal microbiota upon dietary AhR ligand deprivation. Compared to mice on the conventional diet, familyErysipelotrichaceaewas enriched in the feces of mice on the AhR ligand-free diet but returned to normal levels upon dietary supplementation with I3C.Faecalibaculum rodentium, anErysipelotrichaceaespecies, depleted its growth media of AhR ligands. Cultured fecal bacteria from mice on the AhR ligand-free diet, but not the other two diets, were able to alter IgA levelsin vitro, as wasF.rodentiumalone. Our data point to the critical role of AhR dietary ligands in shaping the composition and proper functioning of gut microbiota.
Efficient photosynthesis in dynamic light environments: a chloroplast's perspective
Authors: Kaiser Elias , Correa Galvis Viviana , Armbruster Ute 
Published: October 2019

Abstract
In nature, light availability for photosynthesis can undergo massive changes on a very short timescale. Photosynthesis in such dynamic light environments requires that plants can respond swiftly. Expanding our knowledge of the rapid responses that underlie dynamic photosynthesis is an important endeavor: it provides insights into nature's design of a highly dynamic energy conversion system and hereby can open up new strategies for improving photosynthesis in the field. The present review focuses on three processes that have previously been identified as promising engineering targets for enhancing crop yield by accelerating dynamic photosynthesis, all three of them involving or being linked to processes in the chloroplast, i.e. relaxation of non-photochemical quenching, Calvin–Benson–Bassham cycle enzyme activation/deactivation and dynamics of stomatal conductance. We dissect these three processes on the functional and molecular level to reveal gaps in our understanding and critically discuss current strategies to improve photosynthesis in the field.
The plastid NAD(P)H dehydrogenase-like complex: structure, function and evolutionary dynamics
Authors: Strand Deserah D. , D'Andrea Lucio , Bock Ralph 
Published: October 2019

Abstract
The thylakoid NAD(P)H dehydrogenase-like (NDH) complex is a large protein complex that reduces plastoquinone and pumps protons into the lumen generating protonmotive force. In plants, the complex consists of both nuclear and chloroplast-encoded subunits. Despite its perceived importance for stress tolerance and ATP generation, chloroplast-encoded NDH subunits have been lost numerous times during evolution in species occupying seemingly unrelated environmental niches. We have generated a phylogenetic tree that reveals independent losses in multiple phylogenetic lineages, and we use this tree as a reference to discuss possible evolutionary contexts that may have relaxed selective pressure for retention of ndh genes. While we are still yet unable to pinpoint a singular specific lifestyle that negates the need for NDH, we are able to rule out several long-standing explanations. In light of this, we discuss the biochemical changes that would be required for the chloroplast to dispense with NDH functionality with regards to known and proposed NDH-related reactions.
LncRNA SNHG1 was down-regulated after menopause and participates in postmenopausal osteoporosis
Authors: Huang Shuaihao , Zhu Xiaowen , Xiao Dan , Zhuang Jianxiong , Liang Guoyan , Liang Changxiang , Zheng Xiaoqing , Ke Yuhong , Chang Yunbing 
Published: October 2019

Abstract
The functions of long (&gt;200 nt) non-coding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) have only been investigated in cancer biology. We found that plasma LncRNA SNHG1 was down-regulated in postmenopausal than in premenopausal females. Among postmenopausal females, the ones with postmenopausal osteoporosis showed much lower expression levels of plasma lncRNA SNHG1. A 6-year follow-up study on postmenopausal females revealed that plasma lncRNA SNHG1 decreased in females with postmenopausal osteoporosis but not in healthy postmenopausal females. Levels of plasma lncRNA SNHG1 at 12 months before diagnosis is sufficient to distinguish postmenopausal osteoporosis patients from healthy controls. After treatment, plasma lncRNA SNHG1 were significantly up-regulated. Therefore, lncRNA SNHG1 was down-regulated after menopause and plasma level of lncRNA SNHG1 may serve as a biomarker for the diagnosis and treatment of postmenopausal osteoporosis.