bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Sea Level Variability Due to Seasonal River Discharge: A Preliminary Global Ocean Model Study
Authors: Piecuch Christopher G. , Wadehra Riley 
Published: February 2020

AbstractRiver discharge
is an important driver of the coastal ocean circulation. However, the influence of variable
effects on large‐scale sea level
related to ocean dynamics is not well understood. We perform numerical experiments using a coarse (
°) global ocean state estimate to quantify
effects on the seasonal cycle in dynamic
over the global ocean. Forcing by
drives substantial dynamic
signals (
cm) on regional scales around major rivers (e.g., Amazon, Ganges, Brahmaputra, Irrawaddy, Ob, Lena, and Yenisei). Modeled
changes largely reflect halosteric (salinity) effects, which are partly affected by transport processes involving planetary waves and advection. The modeled
response to
is informative for interpreting
observations from satellite altimetry and tide gauges, explaining 10–20% of the regional‐scale seasonal data variance around some major rivers. Future
studies should consider finer‐resolution models and
forcing on nonseasonal time scales of relevance to climate.
Future Interactions Between Sea Level Rise, Tides, and Storm Surges in the World's Largest Urban Area
Authors: De Dominicis Michela , Wolf Judith , Jevrejeva Svetlana , Zheng Peng , Hu Zhan 
Published: February 2020

AbstractThe Pearl River Delta contains the world's largest urban area in both size and population. It is a low‐lying flood‐prone coastal environment exposed to sea level rise (SLR) and extreme water levels caused by typhoons. A Finite Volume Community Ocean Model implementation for the South China Sea and the Pearl River Delta is used to understand how future SLR, tides, and typhoon storm surges will interact and affect coastal inundation. The SLR signal and extreme surge levels provide the major contributions to flooding; however, amplification of tides could exceed 0.5 m for 2.1 m SLR and should be considered when planning future coastal defences. On the other hand, if typhoons like Hato or Mangkhut, the latest and strongest ones hitting the area, were to happen in the future, a surge level reduction up to 0.5 m could be expected in coastal areas.
Timing of exercise for muscle strength and physical function in men initiating ADT for prostate cancer
Authors: Newton Robert U. , Galvão Daniel A. , Spry Nigel , Joseph David , Chambers Suzanne K. , Gardiner Robert A. , Hayne Dickon , Taaffe Dennis R. 
Published: February 2020

Abstract
Background
Androgen deprivation therapy (ADT) in men with prostate cancer (PCa) results in adverse effects, including reduced muscle strength and physical function, potentially compromising daily functioning. We examined whether it was more efficacious to commence exercise at the onset of ADT rather than later in treatment to counter declines in strength and physical function.

Methods
One-hundred-and-four men with PCa (68.3 ± 7.0 years) initiating ADT were randomised to immediate exercise (IMX, n = 54) or delayed exercise (DEL, n = 50) for 12 months. IMX comprised 6 months of supervised resistance/aerobic/impact exercise initiated at the onset of ADT with a 6-month follow-up. DEL comprised 6 months of usual care followed by 6 months of resistance/aerobic/impact exercise. Upper and lower body muscle strength and physical function were assessed at baseline, 6 and 12 months.

Results
There was a significant difference for all strength measures at 6 months favouring IMX (P < 0.001), with net differences in leg press, seated row and chest press strength of 19.9 kg (95% CI, 12.3–27.5 kg), 5.6 kg (3.8–7.4 kg) and 4.3 kg (2.7–5.8 kg), respectively. From 7 to 12 months, DEL increased in all strength measures (P < 0.001), with no differences between groups at 12 months. Similarly, physical function improved (P < 0.001) in IMX compared with DEL at 6 months for the 6-m fast walk (−0.2, 95% CI −0.3 to −0.1 s), 400-m walk (−9.7, −14.8 to −4.6 s), stair climb (−0.4, −0.6 to −0.2 s) and chair rise (−1.0, −1.4 to −0.7 s), with no differences between groups by 12 months, except for the 6-m fast walk (P < 0.001).

Conclusion
Exercise either at the onset or after 6 months of ADT preserves/enhances muscle strength and physical function. However, to avoid initial treatment-related adverse effects on strength and function, exercise therapy should be implemented with initiation of ADT.
Organizing genome engineering for the gigabase scale
Authors: Bartley Bryan A. , Beal Jacob , Karr Jonathan R. , Strychalski Elizabeth A. 
Published: February 2020

AbstractGenome-scale engineering holds great potential to impact science, industry, medicine, and society, and recent improvements in DNA synthesis have enabled the manipulation of megabase genomes. However, coordinating and integrating the workflows and large teams necessary for gigabase genome engineering remains a considerable challenge. We examine this issue and recommend a path forward by: 1) adopting and extending existing representations for designs, assembly plans, samples, data, and workflows; 2) developing new technologies for data curation and quality control; 3) conducting fundamental research on genome-scale modeling and design; and 4) developing new legal and contractual infrastructure to facilitate collaboration.
Human large-scale cooperation as a product of competition between cultural groups
Authors: Handley Carla , Mathew Sarah 
Published: February 2020

AbstractA fundamental puzzle of human evolution is how we evolved to cooperate with genetically unrelated strangers in transient interactions. Group-level selection on culturally differentiated populations is one proposed explanation. We evaluate a central untested prediction of Cultural Group Selection theory, by assessing whether readiness to cooperate between individuals from different groups corresponds to the degree of cultural similarity between those groups. We documented the normative beliefs and cooperative dispositions of 759 individuals spanning nine clans nested within four pastoral ethnic groups of Kenya—the Turkana, Samburu, Rendille and Borana. We find that cooperation between groups is predicted by how culturally similar they are, suggesting that norms of cooperation in these societies have evolved under the influence of group-level selection on cultural variation. Such selection acting over human evolutionary history may explain why we cooperate readily with unrelated and unfamiliar individuals, and why humans’ unprecedented cooperative flexibility is nevertheless culturally parochial.
Nitric oxide orchestrates metabolic rewiring in M1 macrophages by targeting aconitase 2 and pyruvate dehydrogenase
Authors: Palmieri Erika M. , Gonzalez-Cotto Marieli , Baseler Walter A. , Davies Luke C. , Ghesquière Bart , Maio Nunziata , Rice Christopher M. , Rouault Tracey A. , Cassel Teresa , Higashi Richard M. , Lane Andrew N. , Fan Teresa W.-M. , Wink David A. , McVicar Daniel W. 
Published: February 2020

AbstractProfound metabolic changes are characteristic of macrophages during classical activation and have been implicated in this phenotype. Here we demonstrate that nitric oxide (NO) produced by murine macrophages is responsible for TCA cycle alterations and citrate accumulation associated with polarization.13C tracing and mitochondrial respiration experiments map NO-mediated suppression of metabolism to mitochondrial aconitase (ACO2). Moreover, we find that inflammatory macrophages reroute pyruvate away from pyruvate dehydrogenase (PDH) in an NO-dependent and hypoxia-inducible factor 1α (Hif1α)-independent manner, thereby promoting glutamine-based anaplerosis. Ultimately, NO accumulation leads to suppression and loss of mitochondrial electron transport chain (ETC) complexes. Our data reveal that macrophages metabolic rewiring, in vitro and in vivo, is dependent on NO targeting specific pathways, resulting in reduced production of inflammatory mediators. Our findings require modification to current models of macrophage biology and demonstrate that reprogramming of metabolism should be considered a result rather than a mediator of inflammatory polarization.
Spatiotemporal functional organization of excitatory synaptic inputs onto macaque V1 neurons
Authors: Ju Niansheng , Li Yang , Liu Fang , Jiang Hongfei , Macknik Stephen L. , Martinez-Conde Susana , Tang Shiming 
Published: February 2020

AbstractThe integration of synaptic inputs onto dendrites provides the basis for neuronal computation. Whereas recent studies have begun to outline the spatial organization of synaptic inputs on individual neurons, the underlying principles related to the specific neural functions are not well understood. Here we perform two-photon dendritic imaging with a genetically-encoded glutamate sensor in awake monkeys, and map the excitatory synaptic inputs on dendrites of individual V1 superficial layer neurons with high spatial and temporal resolution. We find a functional integration and trade-off between orientation-selective and color-selective inputs in basal dendrites of individual V1 neurons. Synaptic inputs on dendrites are spatially clustered by stimulus feature, but functionally scattered in multidimensional feature space, providing a potential substrate of local feature integration on dendritic branches. Furthermore, apical dendrite inputs have larger receptive fields and longer response latencies than basal dendrite inputs, suggesting a dominant role for apical dendrites in integrating feedback in visual information processing.
DNA unwinding mechanism of a eukaryotic replicative CMG helicase
Authors: Yuan Zuanning , Georgescu Roxana , Bai Lin , Zhang Dan , Li Huilin , O’Donnell Michael E. 
Published: February 2020

AbstractHigh-resolution structures have not been reported for replicative helicases at a replication fork at atomic resolution, a prerequisite to understanding the unwinding mechanism. The eukaryotic replicative CMG (Cdc45, Mcm2-7, GINS) helicase contains a Mcm2-7 motor ring, with the N-tier ring in front and the C-tier motor ring behind. The N-tier ring is structurally divided into a zinc finger (ZF) sub-ring followed by the oligosaccharide/oligonucleotide-binding (OB) fold ring. Here we report the cryo-EM structure of CMG on forked DNA at 3.9 Å, revealing that parental DNA enters the ZF sub-ring and strand separation occurs at the bottom of the ZF sub-ring, where the lagging strand is blocked and diverted sideways by OB hairpin-loops of Mcm3, Mcm4, Mcm6, and Mcm7. Thus, instead of employing a specific steric exclusion process, or even a separation pin, unwinding is achieved via a “dam-and-diversion tunnel” mechanism that does not require specific protein-DNA interaction. The C-tier motor ring contains spirally configured PS1 and H2I loops of Mcms 2, 3, 5, 6 that translocate on the spirally-configured leading strand, and thereby pull the preceding DNA segment through the diversion tunnel for strand separation.
Deep learning approach based on dimensionality reduction for designing electromagnetic nanostructures
Authors: Kiarashinejad Yashar , Abdollahramezani Sajjad , Adibi Ali 
Published: February 2020

AbstractIn this paper, we demonstrate a computationally efficient new approach based on deep learning (DL) techniques for analysis, design and optimization of electromagnetic (EM) nanostructures. We use the strong correlation among features of a generic EM problem to considerably reduce the dimensionality of the problem and thus, the computational complexity, without imposing considerable errors. By employing the dimensionality reduction concept using the more recently demonstrated autoencoder technique, we redefine the conventional many-to-one design problem in EM nanostructures into a one-to-one problem plus a much simpler many-to-one problem, which can be simply solved using an analytic formulation. This approach reduces the computational complexity in solving both the forward problem (i.e., analysis) and the inverse problem (i.e., design) by orders of magnitude compared to conventional approaches. In addition, it provides analytic formulations that, despite their complexity, can be used to obtain intuitive understanding of the physics and dynamics of EM wave interaction with nanostructures with minimal computation requirements. As a proof-of-concept, we applied such an efficacious method to design a new class of on-demand reconfigurable optical metasurfaces based on phase-change materials (PCMs). The experimental results of the fabricated devices are in good agreement with those predicted by the proposed approach. We envision that the integration of such a DL-based technique with full-wave commercial software packages offers a powerful toolkit to facilitate the analysis, design, and optimization of the EM nanostructures as well as explaining, understanding, and predicting the observed responses in such structures. It will thus enable to solve complex design problems that could not be solved with existing techniques.
Flexible inorganic bioelectronics
Authors: Chen Ying , Zhang Yingchao , Liang Ziwei , Cao Yu , Han Zhiyuan , Feng Xue 
Published: February 2020

AbstractFlexible inorganic bioelectronics represent a newly emerging and rapid developing research area. With its great power in enhancing the acquisition, management and utilization of health information, it is expected that these flexible and stretchable devices could underlie the new solutions to human health problems. Recent advances in this area including materials, devices, integrated systems and their biomedical applications indicate that through conformal and seamless contact with human body, the measurement becomes continuous and convenient with yields of higher quality data. This review covers recent progresses in flexible inorganic bio-electronics for human physiological parameters’ monitoring in a wearable and continuous way. Strategies including materials, structures and device design are introduced with highlights toward the ability to solve remaining challenges in the measurement process. Advances in measuring bioelectrical signals, i.e., the electrophysiological signals (including EEG, ECoG, ECG, and EMG), biophysical signals (including body temperature, strain, pressure, and acoustic signals) and biochemical signals (including sweat, glucose, and interstitial fluid) have been summarized. In the end, given the application property of this topic, the future research directions are outlooked.
Quantum computing with exciton-polariton condensates
Authors: Ghosh Sanjib , Liew Timothy C. H. 
Published: February 2020

AbstractExciton-polariton condensates have attractive features for quantum computation, e.g., room temperature operation, high dynamical speed, ease of probe, and existing fabrication techniques. Here, we present a complete theoretical scheme of quantum computing with exciton-polariton condensates formed in semiconductor micropillars. Quantum fluctuations on top of the condensates are shown to realize qubits, which are externally controllable by applied laser pulses. Quantum tunneling and nonlinear interactions between the condensates allow SWAP, square-root-SWAP and controlled-NOT gate operations between the qubits.
A chromosome-scale reference genome for Giardia intestinalis WB
Authors: Xu Feifei , Jex Aaron , Svärd Staffan G. 
Published: February 2020

AbstractGiardia intestinalis is a protist causing diarrhea in humans. The first G. intestinalis genome, from the WB isolate, was published more than ten years ago, and has been widely used as the reference genome for Giardia research. However, the genome is fragmented, thus hindering research at the chromosomal level. We re-sequenced the Giardia genome with Pacbio long-read sequencing technology and obtained a new reference genome, which was assembled into near-complete chromosomes with only four internal gaps at long repeats. This new genome is not only more complete but also better annotated at both structural and functional levels, providing more details about gene families, gene organizations and chromosomal structure. This near-complete reference genome will be a valuable resource for the Giardia community and protist research. It also showcases how a fragmented genome can be improved with long-read sequencing technology completed with optical maps.
Simultaneous downregulation of miR-21 and upregulation of miR-7 has anti-tumor efficacy
Authors: Bhere Deepak , Arghiani Nahid , Lechtich Esther Revai , Yao Yizheng , Alsaab Sarah , Bei Fengfeng , Matin Maryam M. , Shah Khalid 
Published: February 2020

AbstractDysregulation of miRNA expression has been implicated in cancer. Numerous strategies have been explored to modulate miR but sub-optimal delivery and inability to concurrently target multiple pathways involved in tumor progression have limited their efficacy. In this study, we explored the potential co-modulation of upregulated miR-21 and downregulated miR-7 to enhance therapeutic outcomes in heterogenic tumor types. We first engineered lentiviral (LV) and adeno-associated viral (AAV) vectors that preferentially express anti-sense miR against miR-21(miRzip-21) and show that modulating miR-21 via miRzip extensively targets tumor cell proliferation, migration and invasion in vitro in a broad spectrum of cancer types and has therapeutic efficacy in vivo. Next, we show a significantly increased expression of caspase-mediated apoptosis by simultaneously downregulating miR-21 and upregulating miR-7 in different tumor cells. In vivo co-treatment with AAV-miRzip-21 and AAV-miR-7 in mice bearing malignant brain tumors resulted in significantly decreased tumor burden with a corresponding increase in survival. To our knowledge, this is the first study that demonstrates the therapeutic efficacy of simultaneously upregulating miR-7 and downregulating miR-21 and establishes a roadmap towards clinical translation of modulating miRs for various cancer types.
CDX-301: a novel medical countermeasure for hematopoietic acute radiation syndrome in mice
Authors: Satyamitra Merriline , Cary Lynnette , Dunn Dylan , Holmes-Hampton Gregory P. , Thomas Lawrence J. , Ghosh Sanchita P. 
Published: February 2020

AbstractBone marrow failure and hematopoietic damage is one of the major consequences of irradiation-induced lethality. There is an immediate need to develop medical countermeasures (MCMs) to combat irradiation-induced lethality. We tested the efficacy of CDX-301, developed by Celldex Therapeutics Inc., in mice exposed to Co-60 gamma total body irradiation (TBI). The drug demonstrated its efficacy both as a prophylactic countermeasure and a mitigator in CD2F1 mice exposed to TBI. A single dose of CDX-301 administered 24 h prior to 24 h post–exposure conferred significant survival. Accelerated recovery from irradiation-induced peripheral blood cytopenia, bone marrow damage as well as apoptosis in sternum was observed in mice pre-treated with CDX-301. Analysis of splenocytes revealed alterations in T cell profiles that were dependent on the time of drug administration. Prophylactic treatment of CDX-301 resulted in increased splenic CD3+ T cells, specifically CD4+T helper cells, compared to splenocytes from non-irradiated mice. These results indicate that CDX-301 is a promising radiation countermeasure and demonstrate its capability to protect cells within hematopoietic organs. These data support potential use of CDX-301, both pre- and post-radiation, against hematopoietic acute radiation syndrome with a broad window for medical management in a radiological or nuclear event.
Multimodal X-ray imaging of nanocontainer-treated macrophages and calcium distribution in the perilacunar bone matrix
Authors: Stachnik Karolina , Warmer Martin , Mohacsi Istvan , Hennicke Vincent , Fischer Pontus , Meyer Jan , Spitzbart Tobias , Barthelmess Miriam , Eich Jacqueline , David Christian , Feldmann Claus , Busse Björn , Jähn Katharina , Schaible Ulrich E. , Meents Alke 
Published: February 2020

AbstractStudies of biological systems typically require the application of several complementary methods able to yield statistically-relevant results at a unique level of sensitivity. Combined X-ray fluorescence and ptychography offer excellent elemental and structural imaging contrasts at the nanoscale. They enable a robust correlation of elemental distributions with respect to the cellular morphology. Here we extend the applicability of the two modalities to higher X-ray excitation energies, permitting iron mapping. Using a long-range scanning setup, we applied the method to two vital biomedical cases. We quantified the iron distributions in a population of macrophages treated with Mycobacterium-tuberculosis-targeting iron-oxide nanocontainers. Our work allowed to visualize the internalization of the nanocontainer agglomerates in the cytosol. From the iron areal mass maps, we obtained a distribution of antibiotic load per agglomerate and an average areal concentration of nanocontainers in the agglomerates. In the second application we mapped the calcium content in a human bone matrix in close proximity to osteocyte lacunae (perilacunar matrix). A concurrently acquired ptychographic image was used to remove the mass-thickness effect from the raw calcium map. The resulting ptychography-enhanced calcium distribution allowed then to observe a locally lower degree of mineralization of the perilacunar matrix.
Phylogenomic Perspective on a Unique Mycobacterium bovis Clade Dominating Bovine Tuberculosis Infections among Cattle and Buffalos in Northern Brazil
Authors: Conceição Marília Lima da , Conceição Emilyn Costa , Furlaneto Ismari Perini , Silva Sandro Patroca da , Guimarães Arthur Emil dos Santos , Gomes Pedro , Boschiroli María Laura , Michelet Lorraine , Kohl Thomas Andreas , Kranzer Katharina , Francez Loreno da Costa , Lima Luana Nepomuceno Gondim Costa , Portugal Isabel , Perdigão João , Lima Karla Valéria Batista 
Published: February 2020

AbstractLack of routine surveillance in countries endemic for bovine tuberculosis (TB) and limited laboratory support contributes to the inability to differentiate theMycobacterium tuberculosisComplex species, leading to an underestimated burden of the disease. Here, Whole-Genome Sequencing ofMycobacterium bovisisolated from tissues with TB-like lesions obtained from cattle and buffalos at Marajó Island, Brazil, demonstrates that recent transmission ofM. bovisis ongoing at distinct sites. Moreover, theM. bovisepidemiology in this setting is herein found to be dominated by an endemic and unique clade composed of strains evolved from a common ancestor that are now genetically differentiated from otherM. bovisclades. Additionally, envisioning a rapid strain differentiation and tracing across multiple settings, 28 globally validated strain-specific SNPs were identified, three of which considered as robust markers for theM. bovisMarajó strain. In conclusion, this study contributes with data regarding the identification of a novelM. bovisphylogenetic clade responsible for ongoing transmission events in both cattle and buffalo species in Brazil, provides a framework to investigate the dissemination of this highly prevalent strain and, holds the potential to inform TB control strategies that may help to prevent the spread of bovine and zoonotic TB.