bluuebunny/crossref_metadata_2025_split huggingface dataset:
A U‐Th Dating Approach to Understanding Past Coral Reef Dynamics and Geomorphological Constraints on Future Reef Growth Potential; Mazie Bay, Southern Great Barrier Reef
Authors: Leonard Nicole D. , Lepore Mauro L. , Zhao Jian‐xin , Rodriguez‐Ramirez Alberto , Butler Ian , Clark Tara R. , Roff George , McCook Laurence , Nguyen Ai D. , Feng Yuexing , Pandolfi John M. 
Published: February 2020

AbstractReconstructing coral reef histories provides a window of understanding into reef response to changing environmental and climatic conditions over various temporal scales. Here we present the results of 117 U‐Th dates from emergent reef flat and slope cores and surface death assemblages, combined with previously published fossil microatoll data, to capture the entire sequence of reef growth at Mazie Bay, inshore Southern Great Barrier Reef (GBR). Coral U‐Th dates indicate that Mazie Bay reef initiated ~6,900 years before present (yr. BP) quickly filling accommodation space. While rates of vertical reef accretion (5.3 ± 1.0 mm year−1) were comparable to the GBR average during the mid‐Holocene (~5.0 mm year−1), reef flat progradation occurred at a rate 1.5‐ to 6‐fold previous GBR rates until 5,100 yr. BP (~70.4 cm year−1). Average progradation slowed to ~7.1 cm year−1 in the subsequent ~4,000 years and reef slope cores indicate this reef had largely “turned‐off” by 400 yr. BP, with modern coral communities existing as a veneer over the largely senescent framework. Death assemblage dates highlight coral disturbance and recovery regimes in response to increased cyclone activity 1960–1985 AD and recent extreme sea surface temperature and flood events post 2000 AD. U‐Th dating of mid‐Holocene to modern coral deposits from Mazie Bay reef provides a unique insight into past reef development, response to recent disturbance regimes, and potential for future reef growth. In the case of Mazie Bay, our data suggest limited accommodation space and increased occurrence of sea surface temperature extremes will restrict future reef growth at this site.
Spin Transition of Iron in δ‐(Al,Fe)OOH Induces Thermal Anomalies in Earth's Lower Mantle
Authors: Hsieh Wen‐Pin , Ishii Takayuki , Chao Keng‐Hsien , Tsuchiya Jun , Deschamps Frédéric , Ohtani Eiji 
Published: February 2020

AbstractSeismic anomalies observed in Earth's deep mantle are conventionally considered to be associated with thermal and compositional anomalies, and possibly partial melt of major lower‐mantle phases. However, through deep water cycle, impacts of hydrous minerals on geophysical observables and on the deep mantle thermal state and geodynamics remain poorly understood. Here we precisely measured thermal conductivity of δ‐(Al,Fe)OOH, an important water‐carrying mineral in Earth's deep interior, to lowermost mantle pressures at room temperature. The thermal conductivity varies drastically by twofold to threefold across the spin transition of iron, resulting in an exceptionally low thermal conductivity at the lowermost mantle conditions. As δ‐(Al,Fe)OOH is transported to the lowermost mantle, its exceptionally low thermal conductivity may serve as a local thermal insulator, promoting high‐temperature anomalies and the formation of partial melt and thermal plumes at the base of the mantle, strongly influencing thermo‐chemical profiles in the region and fate of Earth's deep water cycle.
Dissecting the role of crosstalk between glioblastoma subpopulations in tumor cell spreading
Authors: Jubran Maria R. , Rubinstein Ariel M. , Cojocari Irina , Adejumobi Ibukun Adesoji , Mogilevsky Maxim , Tibi Sama , Sionov Ronit V. , Verreault Maïté , Idbaih Ahmed , Karni Rotem , Kravchenko-Balasha Nataly 
Published: February 2020

AbstractGlioblastoma (GBM) is a highly infiltrative brain cancer, which is thus difficult to operate. GBM cells frequently harbor Epidermal Growth Factor Receptor amplification (EGFRwt) and/or activating mutation (EGFRvIII), generating at least two different cellular subpopulations within the tumor. We examined the relationship between the diffusive architectures of GBM tumors and the paracrine interactions between those subpopulations. Our aim was to shed light on what drives GBM cells to reach large cell–cell distances, and whether this characteristic can be manipulated. We established a methodology that quantifies the infiltration abilities of cancer cells through computation of cell–cell separation distance distributions in 3D. We found that aggressive EGFRvIII cells modulate the migration and infiltrative properties of EGFRwt cells. EGFRvIII cells secrete HGF and IL6, leading to enhanced activity of Src protein in EGFRwt cells, and rendering EGFRwt cells higher velocity and augmented ability to spread. Src inhibitor, dasatinib, at low non-toxic concentrations, reduced the infiltrative properties of EGFRvIII/EGFRwt neurospheres. Furthermore, dasatinib treatment induced compact multicellular microstructure packing of EGFRvIII/EGFRwt cells, impairing their ability to spread. Prevention of cellular infiltration or induction of compact microstructures may assist the detection of GBM tumors and tumor remnants in the brains and improve their surgical removal.
Reversal of CYLD phosphorylation as a novel therapeutic approach for adult T-cell leukemia/lymphoma (ATLL)
Authors: Xu Xin , Kalac Matko , Markson Michael , Chan Mark , Brody Joshua D. , Bhagat Govind , Ang Rosalind L. , Legarda Diana , Justus Scott J. , Liu Feng , Li Qingshan , Xiong Huabao , Ting Adrian T. 
Published: February 2020

AbstractAdult T-cell leukemia/lymphoma (ATLL) is a malignancy of mature T cells associated with chronic infection by human T-cell lymphotropic virus type-1 (HTLV-1). ATLL patients with aggressive subtypes have dismal outcomes. We demonstrate that ATLL cells co-opt an early checkpoint within the tumor necrosis factor receptor 1 (TNFR1) pathway, resulting in survival advantage. This early checkpoint revolves around an interaction between the deubiquitinase CYLD and its target RIPK1. The status of RIPK1 K63-ubiquitination determines cell fate by creating either a prosurvival signal (ubiquitinated RIPK1) or a death signal (deubiquitinated RIPK1). In primary ATLL samples and in cell line models, an increased baseline level of CYLD phosphorylation was observed. We therefore tested the hypothesis that this modification of CYLD, which has been reported to inhibit its deubiquitinating function, leads to increased RIPK1 ubiquitination and thus provides a prosurvival signal to ATLL cells. CYLD phosphorylation can be pharmacologically reversed by IKK inhibitors, specifically by TBK1/IKKε and IKKβ inhibitors (MRT67307 and TPCA). Both of the IKK sub-families can phosphorylate CYLD, and the combination of MRT67307 and TPCA have a marked effect in reducing CYLD phosphorylation and triggering cell death. ATLL cells overexpressing a kinase-inactive TBK1 (TBK1-K38A) demonstrate lower CYLD phosphorylation and subsequently reduced proliferation. IKK blockade reactivates CYLD, as evidenced by the reduction in RIPK1 ubiquitination, which leads to the association of RIPK1 with the death-inducing signaling complex (DISC) to trigger cell death. In the absence of CYLD, RIPK1 ubiquitination remains elevated following IKK blockade and it does not associate with the DISC. SMAC mimetics can similarly disrupt CYLD phosphorylation and lead to ATLL cell death through reduction of RIPK1 ubiquitination, which is CYLD dependent. These results identify CYLD as a crucial regulator of ATLL survival and point to its role as a potential novel target for pharmacologic modification in this disease.
Using remarkability to define coastal flooding thresholds
Authors: Moore Frances C. , Obradovich Nick 
Published: February 2020

AbstractCoastal flooding is increasingly common in many areas. However, the degree of inundation and associated disruption depend on local topography as well as the distribution of people, infrastructure and economic activity along the coast. Local measures of flooding that are comparable over large areas are difficult to obtain. Here we use the remarkability of flood events, measured by flood-related posts on social media, to estimate county-specific flood thresholds for shoreline counties along the east coast of the United States. While thresholds in most counties are statistically-indistinguishable from minor flood thresholds of nearby tide gauges, we find evidence that several areas experience noticeable flooding at tide heights lower than existing flood thresholds. These 22 counties include several major cities such as Miami, New York, and Boston, with a total population over 13 million. Our analysis implies that large populations might currently be exposed to nuisance flooding not identified via standard measures.
Inhibition of vascular calcification by inositol phosphates derivatized with ethylene glycol oligomers
Authors: Schantl Antonia E. , Verhulst Anja , Neven Ellen , Behets Geert J. , D’Haese Patrick C. , Maillard Marc , Mordasini David , Phan Olivier , Burnier Michel , Spaggiari Dany , Decosterd Laurent A. , MacAskill Mark G. , Alcaide-Corral Carlos J. , Tavares Adriana A. S. , Newby David E. , Beindl Victoria C. , Maj Roberto , Labarre Anne , Hegde Chrismita , Castagner Bastien , Ivarsson Mattias E. , Leroux Jean-Christophe 
Published: February 2020

AbstractMyo-inositol hexakisphosphate (IP6) is a natural product known to inhibit vascular calcification (VC), but with limited potency and low plasma exposure following bolus administration. Here we report the design of a series of inositol phosphate analogs as crystallization inhibitors, among which 4,6-di-O-(methoxy-diethyleneglycol)-myo-inositol-1,2,3,5-tetrakis(phosphate), (OEG2)2-IP4, displays increased in vitro activity, as well as more favorable pharmacokinetic and safety profiles than IP6 after subcutaneous injection. (OEG2)2-IP4 potently stabilizes calciprotein particle (CPP) growth, consistently demonstrates low micromolar activity in different in vitro models of VC (i.e., human serum, primary cell cultures, and tissue explants), and largely abolishes the development of VC in rodent models, while not causing toxicity related to serum calcium chelation. The data suggest a mechanism of action independent of the etiology of VC, whereby (OEG2)2-IP4 disrupts the nucleation and growth of pathological calcification.
Identification of a Zeb1 expressing basal stem cell subpopulation in the prostate
Authors: Wang Xue , Xu Haibo , Cheng Chaping , Ji Zhongzhong , Zhao Huifang , Sheng Yaru , Li Xiaoxia , Wang Jinming , Shu Yu , He Yuman , Fan Liancheng , Dong Baijun , Xue Wei , Wai Chua Chee , Wu Dongdong , Gao Wei-Qiang , He Zhu Helen 
Published: February 2020

AbstractThe basal cell compartment in many epithelial tissues is generally believed to serve as an important pool of stem cells. However, basal cells are heterogenous and the stem cell subpopulation within basal cells is not well elucidated. Here we uncover that the core epithelial-to-mesenchymal transition (EMT) inducer Zeb1 is expressed in a prostate basal cell subpopulation. The Zeb1+ prostate epithelial cells are multipotent prostate basal stem cells (PBSCs) that can self-renew and generate functional prostatic glandular structures at the single-cell level. Genetic ablation studies reveal an indispensable role for Zeb1 in prostate basal cell development. Utilizing unbiased single-cell transcriptomic analysis of over 9000 mouse prostate basal cells, we confirm the existence of the Zeb1+ basal cell subset. Moreover, Zeb1+ epithelial cells can be detected in mouse and human prostate tumors. Identification of the PBSC and its transcriptome profile is crucial to advance our understanding of prostate development and tumorigenesis.
ProtCID: a data resource for structural information on protein interactions
Authors: Xu Qifang , Dunbrack Roland L. 
Published: February 2020

AbstractStructural information on the interactions of proteins with other molecules is plentiful, and for some proteins and protein families, there may be 100s of available structures. It can be very difficult for a scientist who is not trained in structural bioinformatics to access this information comprehensively. Previously, we developed the Protein Common Interface Database (ProtCID), which provided clusters of the interfaces of full-length protein chains as a means of identifying biological assemblies. Because proteins consist of domains that act as modular functional units, we have extended the analysis in ProtCID to the individual domain level. This has greatly increased the number of large protein-protein clusters in ProtCID, enabling the generation of hypotheses on the structures of biological assemblies of many systems. The analysis of domain families allows us to extend ProtCID to the interactions of domains with peptides, nucleic acids, and ligands. ProtCID provides complete annotations and coordinate sets for every cluster.
High-throughput identification of synthetic riboswitches by barcode-free amplicon-sequencing in human cells
Authors: Strobel Benjamin , Spöring Maike , Klein Holger , Blazevic Dragica , Rust Werner , Sayols Sergi , Hartig Jörg S. , Kreuz Sebastian 
Published: February 2020

AbstractSynthetic riboswitches mediating ligand-dependent RNA cleavage or splicing-modulation represent elegant tools to control gene expression in various applications, including next-generation gene therapy. However, due to the limited understanding of context-dependent structure–function relationships, the identification of functional riboswitches requires large-scale-screening of aptamer-effector-domain designs, which is hampered by the lack of suitable cellular high-throughput methods. Here we describe a fast and broadly applicable method to functionally screen complex riboswitch libraries (~1.8 × 104 constructs) by cDNA-amplicon-sequencing in transiently transfected and stimulated human cells. The self-barcoding nature of each construct enables quantification of differential mRNA levels without additional pre-selection or cDNA-manipulation steps. We apply this method to engineer tetracycline- and guanine-responsive ON- and OFF-switches based on hammerhead, hepatitis-delta-virus and Twister ribozymes as well as U1-snRNP polyadenylation-dependent RNA devices. In summary, our method enables fast and efficient high-throughput riboswitch identification, thereby overcoming a major hurdle in the development cascade for therapeutically applicable gene switches.
Deep tissue space-gated microscopy via acousto-optic interaction
Authors: Jang Mooseok , Ko Hakseok , Hong Jin Hee , Lee Won Kyu , Lee Jae-Seung , Choi Wonshik 
Published: February 2020

AbstractTo extend the imaging depth of high-resolution optical microscopy, various gating operations—confocal, coherence, and polarization gating—have been devised to filter out the multiply scattered wave. However, the imaging depth is still limited by the multiply scattered wave that bypasses the existing gating operations. Here, we present a space gating method, whose mechanism is independent of the existing methods and yet effective enough to complement them. Specifically, we reconstruct an image only using the ballistic wave that is acousto-optically modulated at the object plane. The space gating suppresses the multiply scattered wave by 10–100 times in a highly scattering medium, and thus enables visualization of the skeletal muscle fibers in whole-body zebrafish at 30 days post fertilization. The space gating will be an important addition to optical-resolution microscopy for achieving the ultimate imaging depth set by the detection limit of ballistic wave.
Controlling solid-liquid interfacial energy anisotropy through the isotropic liquid
Authors: Wang Lei , Hoyt Jeffrey J. , Wang Nan , Provatas Nikolas , Sinclair Chad W. 
Published: February 2020

AbstractAlthough the anisotropy of the solid-liquid interfacial free energy for most alloy systems is very small, it plays a crucial role in the growth rate, morphology and crystallographic growth direction of dendrites. Previous work posited a dendrite orientation transition via compositional additions. In this work we examine experimentally the change in dendrite growth behaviour in the Al-Sm (Samarium) system as a function of solute concentration and study its interfacial properties using molecular dynamics simulations. We observe a dendrite growth direction which changes from $$\langle 100\rangle$$
⟨
100
⟩
to $$\langle 110\rangle$$
⟨
110
⟩
as Sm content increases. The observed change in dendrite orientation is consistent with the simulation results for the variation of the interfacial free energy anisotropy and thus provides definitive confirmation of a conjecture in previous works. In addition, our results provide physical insight into the atomic structural origin of the concentration dependent anisotropy, and deepen our fundamental understanding of solid-liquid interfaces in binary alloys.
CMOS-based bio-image sensor spatially resolves neural activity-dependent proton dynamics in the living brain
Authors: Horiuchi Hiroshi , Agetsuma Masakazu , Ishida Junko , Nakamura Yusuke , Lawrence Cheung Dennis , Nanasaki Shin , Kimura Yasuyuki , Iwata Tatsuya , Takahashi Kazuhiro , Sawada Kazuaki , Nabekura Junichi 
Published: February 2020

AbstractRecent studies have shown that protons can function as neurotransmitters in cultured neurons. To further investigate regional and neural activity-dependent proton dynamics in the brain, the development of a device with both wide-area detectability and high spatial-ltemporal resolution is necessary. Therefore, we develop an image sensor with a high spatial-temporal resolution specifically designed for measuring protons in vivo. Here, we demonstrate that spatially deferent neural stimulation by visual stimulation induced distinct patterns of proton changes in the visual cortex. This result indicates that our biosensor can detect micrometer and millisecond scale changes of protons across a wide area. Our study demonstrates that a CMOS-based proton image sensor with high spatial and temporal precision can be used to detect pH changes associated with biological events. We believe that our sensor may have broad applicability in future biological studies.
Association between low estrogen receptor positive breast cancer and staining performance
Authors: Caruana Dennis , Wei Wei , Martinez-Morilla Sandra , Rimm David L. , Reisenbichler Emily S. 
Published: February 2020

AbstractEstrogen receptor (ER) expression in breast carcinomas, determined by immunohistochemistry, indicates statistically significant benefit to endocrine therapy in patients with tumors expressing ER in ≥1% of tumor cells. Rare cases with low ER expression (1–10%) lead to the dilemma of treating these tumors as ER positive or negative. We hypothesize that low ER positive result from poor staining performance and that we may detect this artefact by assessing the average dynamic range of normal ducts adjacent to low ER positive tumors. Using quantitative tools, we compare the dynamic range of normal background ER expression in patients with low (1–10%) ER tumors to dynamic range of ER expression in normal epithelium from control patient populations, to determine if low ER cases are accompanied by decreased dynamic range. Low ER cases were infrequent (1% of invasive breast carcinomas). Twenty-one cases with low ER staining and two control cohorts, including a tissue microarray (TMA) of 10 benign breast sections and a group of 34 control breast carcinomas (reported as ER negative or >10% ER positive) with normal background epithelium, were digitally scanned. QuPath was utilized to quantify ER staining for each cell as the mean optical density of nuclear DAB staining. The dynamic range of ER expression in normal epithelium surrounding low ER tumors was significantly lower (range 2–240, median 16.5) than that of the benign epithelium in the control tumors (range 3–475, median 30.8; p < 0.001) and benign TMA sections (range 38–212, median 114; p < 0.001) suggesting inconsistent stainer performance.
Bio-inspired self-folding strategy to break the trade-off between strength and ductility in carbon-nanoarchitected materials
Authors: Jia Xiangzheng , Liu Ze , Gao Enlai 
Published: February 2020

AbstractGraphene possesses extraordinary mechanical, electronic, and thermal properties, thus making it one of the most promising building blocks for constructing macroscopic high performance and multifunctional materials. However, the common material strength–ductility paradox also appears in the carbon-nanoarchitected materials and some of the key mechanical performance, for example, the tensile strength of graphene-based materials, are still far lower than that of graphene. Inspired by the exceptional mechanical performance of silk protein benefiting from the conformations of folded structures as well as their transitions, this work proposed a topological strategy to yield graphene-based materials with ultrahigh ductility while maintaining decent tensile strength by self-folding graphene sheets. This drastically improved mechanical performance of graphene-based materials is attributed to the exploitation of shearing, sliding, and unfolding deformation at the self-folded interface. Molecular dynamics simulations show that both modulating self-folded length and engineering interface interaction can effectively control the strength, ductility, and the ductile failure of van der Waals interfaces among the self-folded structures, where interfacial shearing, sliding, and unfolding open channels to dissipate mechanical energy. Based on the insights into the atomic-scale deformation by molecular dynamics simulations, the underlying mechanism of deformation and failure of these materials is finally discussed with a continuum mechanics-based model. Our findings bring perceptive insights into the microstructure design of strong-yet-ductile materials for load-bearing engineering applications.
A PDM-based 128-Gb/s PAM4 fibre-FSO convergent system with OBPFs for polarisation de-multiplexing
Authors: Wu Hsiao-Wen , Li Chung-Yi , Lu Hai-Han , Huang Qi-Ping , Tu Shi-Cheng , Huang Yong-Cheng 
Published: February 2020

AbstractA polarisation-division-multiplexing (PDM)-based four-level pulse amplitude modulation (PAM4) fibre-free-space optical (FSO) convergent system with optical band-pass filters (OBPFs) for polarisation de-multiplexing is feasibly demonstrated for the first time. In a PDM scenario with PAM4 modulation, the transmission capacity of fibre-FSO convergent systems is enhanced four times with an aggregate channel capacity of 128 Gb/s (64 Gb/s PAM4/polarisation × 2 polarisations). With an OBPF, polarisation-tracking free de-multiplexing is attained by eliminating other optical carrier with orthogonal polarisation. An OBPF is a simple polarisation de-multiplexing scheme in which the polarisation-orthogonal carrier can be effectively de-multiplexed and the cross-polarisation interference can be nearly eliminated. Compared with traditional PDM-based fibre-FSO convergent systems with sophisticated polarisation-tracking mechanism and elaborate digital signal processing (DSP) approach, it reveals a noteworthy one with the advantage of simplicity. Through 25 km single-mode fibre transport and 500 m FSO link, sufficiently low bit error rate and qualified PAM4 eye diagrams are attained. This proposed polarisation-tracking free PDM-based fibre-FSO convergent system is notable because it not only incorporates the fibre backbone and optical wireless feeder, but it also simplifies the framework since complicated polarisation-tracking mechanism and DSP approach are not involved.