bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications of Deep Learning to Ocean Data Inference and Subgrid Parameterization
Authors: Bolton Thomas , Zanna Laure 
Published: January 2019

AbstractOceanographic observations are limited by sampling rates, while ocean models are limited by finite resolution and high viscosity and diffusion coefficients. Therefore, both data from observations and ocean models lack information at small and fast scales. Methods are needed to either extract information, extrapolate, or upscale existing oceanographic data sets, to account for or represent unresolved physical processes. Here we use machine learning to leverage observations and model data by predicting unresolved turbulent processes and subsurface flow fields. As a proof of concept, we train convolutional neural networks on degraded data from a high‐resolution quasi‐geostrophic ocean model. We demonstrate that convolutional neural networks successfully replicate the spatiotemporal variability of the subgrid eddy momentum forcing, are capable of generalizing to a range of dynamical behaviors, and can be forced to respect global momentum conservation. The training data of our convolutional neural networks can be subsampled to 10–20% of the original size without a significant decrease in accuracy. We also show that the subsurface flow field can be predicted using only information at the surface (e.g., using only satellite altimetry data). Our results indicate that data‐driven approaches can be exploited to predict both subgrid and large‐scale processes, while respecting physical principles, even when data are limited to a particular region or external forcing. Our in‐depth study presents evidence for the successful design of ocean eddy parameterizations for implementation in coarse‐resolution climate models.
Niche-directed evolution modulates genome architecture in freshwater Planctomycetes
Authors: Andrei Adrian-Ştefan , Salcher Michaela M , Mehrshad Maliheh , Rychtecký Pavel , Znachor Petr , Ghai Rohit 
Published: January 2019

Abstract
Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche).
Combining carfilzomib and panobinostat to treat relapsed/refractory multiple myeloma: results of a Multiple Myeloma Research Consortium Phase I Study
Authors: Kaufman Jonathan L. , Mina Roberto , Jakubowiak Andrzej J. , Zimmerman Todd L. , Wolf Jeffrey J. , Lewis Colleen , Gleason Charise , Sharp Cathy , Martin Thomas , Heffner Leonard T. , Nooka Ajay K. , Harvey R. Donald , Lonial Sagar 
Published: January 2019

AbstractProteasome (PIs) and hystone deacetylase inhibitors (HDACis) have previously shown synergistic activity in the treatment of relapesed/refractory multiple myeloma (RRMM) patients. In this phase 1 study, we combined carfilzomib, a second generation PI, with panobinostat, a HDACi, to determine the maximum tolerated dose (MTD) of the combination (CarPan) and assess safety and efficacy among RRMM patients. Thirty-two patients (median of 4 prior lines of therapy) were enrolled. The MTD was carfilzomib 36 mg/m2 (on days 1, 2, 8, 9, 15, and 16) and panobinostat 20 mg (TIW, 3 weeks on/1 week off, every 28 days), administered until progression. At the MTD, the most common grade 3/4, treatment-related adverse events were thrombocytopenia (41%), fatigue (17%), and nausea/vomiting (12%). The objective response rate (ORR) and clinical benefit rate were 63% and 68%, respectively. Median progression-free survival (PFS) and overall survival (OS) for the entire population were 8 and 23 months, respectively. No differences in terms of ORR (55% vs. 57%), median PFS (months 8 vs. 7 months) and OS (24 vs. 22 months) were observed between bortezomib-sensitive and -refractory patients. CarPan proved to be a safe and effective steroid-sparing regimen in a heavily pre-treated population of MM patients. (Trial registered at ClinicalTrial.gov: NCT01549431)
Oil palm expansion and deforestation in Southwest Cameroon associated with proliferation of informal mills
Authors: Ordway Elsa M. , Naylor Rosamond L. , Nkongho Raymond N. , Lambin Eric F. 
Published: January 2019

AbstractOil palm expansion resulted in 2 million hectares (Mha) of forest loss globally in 2000–2010. Despite accounting for 24% (4.5 Mha) of the world’s total oil palm cultivated area, expansion dynamics in sub-Saharan Africa have been overlooked. We show that in Southwest Cameroon, a top producing region of Africa, 67% of oil palm expansion from 2000–2015 occurred at the expense of forest. Contrary to the publicized narrative of industrial-scale expansion, most oil palm expansion and associated deforestation is occurring outside large agro-industrial concessions. Expansion and deforestation carried out by non-industrial producers is occurring near low-efficiency informal mills, unconstrained by the location of high-efficiency company-owned mills. These results highlight the key role of a booming informal economic sector in driving rapid land use change. High per capita consumption and rising palm oil demands in sub-Saharan Africa spotlight the need to consider informal economies when identifying regionally relevant sustainability pathways.
A disinhibitory mechanism biases Drosophila innate light preference
Authors: Zhao Weiqiao , Zhou Peipei , Gong Caixia , Ouyang Zhenhuan , Wang Jie , Zheng Nenggan , Gong Zhefeng 
Published: January 2019

AbstractInnate preference toward environmental conditions is crucial for animal survival. Although much is known about the neural processing of sensory information, how the aversive or attractive sensory stimulus is transformed through central brain neurons into avoidance or approaching behavior is largely unclear. Here we show that Drosophila larval light preference behavior is regulated by a disinhibitory mechanism. In the disinhibitory circuit, a pair of GABAergic neurons exerts tonic inhibition on one pair of contralateral projecting neurons that control larval reorientation behavior. When a larva enters the light area, the reorientation-controlling neurons are disinhibited to allow reorientation to occur as the upstream inhibitory neurons are repressed by light. When the larva exits the light area, the inhibition on the downstream neurons is restored to repress further reorientation and thus prevents the larva from re-entering the light area. We suggest that disinhibition may serve as a common neural mechanism for animal innate preference behavior.
Long-term functional and structural preservation of precision-cut human myocardium under continuous electromechanical stimulation in vitro
Authors: Fischer Carola , Milting Hendrik , Fein Evelyn , Reiser Elisabeth , Lu Kun , Seidel Thomas , Schinner Camilla , Schwarzmayr Thomas , Schramm Rene , Tomasi Roland , Husse Britta , Cao-Ehlker Xiaochun , Pohl Ulrich , Dendorfer Andreas 
Published: January 2019

AbstractIn vitro models incorporating the complexity and function of adult human tissues are highly desired for translational research. Whilst vital slices of human myocardium approach these demands, their rapid degeneration in tissue culture precludes long-term experimentation. Here, we report preservation of structure and performance of human myocardium under conditions of physiological preload, compliance, and continuous excitation. In biomimetic culture, tissue slices prepared from explanted failing human hearts attain a stable state of contractility that can be monitored for up to 4 months or 2000000 beats in vitro. Cultured myocardium undergoes particular alterations in biomechanics, structure, and mRNA expression. The suitability of the model for drug safety evaluation is exemplified by repeated assessment of refractory period that permits sensitive analysis of repolarization impairment induced by the multimodal hERG-inhibitor pentamidine. Biomimetic tissue culture will provide new opportunities to study drug targets, gene functions, and cellular plasticity in adult human myocardium.
Post-exposure immunotherapy for two ebolaviruses and Marburg virus in nonhuman primates
Authors: Brannan Jennifer M. , He Shihua , Howell Katie A. , Prugar Laura I. , Zhu Wenjun , Vu Hong , Shulenin Sergey , Kailasan Shweta , Raina Henna , Wong Gary , Rahim Md Niaz , Banadyga Logan , Tierney Kevin , Zhao Xuelian , Li Yuxing , Holtsberg Frederick W. , Dye John M. , Qiu Xiangguo , Aman M. Javad 
Published: January 2019

AbstractThe 2013–2016 Ebola virus (EBOV) disease epidemic demonstrated the grave consequences of filovirus epidemics in the absence of effective therapeutics. Besides EBOV, two additional ebolaviruses, Sudan (SUDV) and Bundibugyo (BDBV) viruses, as well as multiple variants of Marburg virus (MARV), have also caused high fatality epidemics. Current experimental EBOV monoclonal antibodies (mAbs) are ineffective against SUDV, BDBV, or MARV. Here, we report that a cocktail of two broadly neutralizing ebolavirus mAbs, FVM04 and CA45, protects nonhuman primates (NHPs) against EBOV and SUDV infection when delivered four days post infection. This cocktail when supplemented by the anti-MARV mAb MR191 exhibited 100% efficacy in MARV-infected NHPs. These findings provide a solid foundation for clinical development of broadly protective immunotherapeutics for use in future filovirus epidemics.
Bifurcation-based embodied logic and autonomous actuation
Authors: Jiang Yijie , Korpas Lucia M. , Raney Jordan R. 
Published: January 2019

AbstractMany plants autonomously change morphology and function in response to environmental stimuli or sequences of stimuli. In contrast with the electronically-integrated sensors, actuators, and microprocessors in traditional mechatronic systems, natural systems embody these sensing, actuation, and control functions within their compositional and structural features. Inspired by nature, we embody logic in autonomous systems to enable them to respond to multiple stimuli. Using 3D printable fibrous composites, we fabricate structures with geometries near bifurcation points associated with a transition between bistability and monostability. When suitable stimuli are present, the materials swell anisotropically. This forces a key geometric parameter to pass through a bifurcation, triggering rapid and large-amplitude self-actuation. The actuation time can be programmed by varying structural parameters (from 0.6 to 108 s for millimeter-scale structures). We demonstrate this bioinspired control strategy with examples that respond to their environment according to their embodied logic, without electronics, external control, or tethering.
Phase self-aligned continuous-variable measurement-device-independent quantum key distribution
Authors: Yin Hua-Lei , Zhu Wei , Fu Yao 
Published: January 2019

AbstractContinuous-variable measurement-independent-device quantum key distribution (CV-MDI-QKD) can offer high secure key rate at metropolitan distance and remove all side channel loopholes of detection as well. However, there is no in-field experimental demonstration of CV-MDI-QKD due to the remote distance phase-locking techniques challenge. Here, we present a new optical scheme to overcome this difficulty and also removes the requirement of two identical independent lasers. Furthermore, we give an alternate but detailed proof of the minimized key rate condition to extract the secure key rate. We anticipate that our new scheme can be used to demonstrate the in-field CV-MDI-QKD experiment and build the CV-MDI-QKD network with untrusted source.
Pangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them
Authors: Abreo Eduardo , Altier Nora 
Published: January 2019

AbstractSerratia marcescensis a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-based approach, based on publicly available genomes, to apply whole genome multilocus sequence type schemes to assess whether there is an association between source and genotype, aiming at differentiating between isolates from nosocomial sources and the environment, and between strains reported as PGPR from other environmental strains. Most genomes from a nosocomial setting and environmental origin could be assigned to the proposed nosocomial or environmental MLSTs, which is indicative of an association between source and genotype. The fact that a few genomes from a nosocomial source showed an environmental MLST suggests that a minority of nosocomial strains have recently derived from the environment. PGPR strains were assigned to different environmental types and clades but only one clade comprised strains accumulating a low number of known virulence and antibiotic resistance determinants and was exclusively from environmental sources. This clade is envisaged as a group of promissory MLSTs for selecting prospective PGPR strains.
Induced cross-resistance of BRAFV600E melanoma cells to standard chemotherapeutic dacarbazine after chronic PLX4032 treatment
Authors: Erdmann Sarah , Seidel Diana , Jahnke Heinz-Georg , Eichler Marie , Simon Jan-Christoph , Robitzki Andrea A. 
Published: January 2019

AbstractThe maximum response and 10-year survival rate for metastatic melanoma patients treated with standardised chemotherapy is still less than 15% and 10%, respectively. In contrast, oncogene targeting was found a promising tool for killing of BRAFV600 mutated melanoma cells. Nevertheless, despite improved response and survival rates, resistance acquisition remains an ongoing problem. In this context, the impact of chronic BRAF inhibition on the efficacy of commonly applied cytostatics is still unknown. In our study, human melanoma cells with BRAFV600E mutation were treated with chemotherapeutics and a BRAF inhibitor. Resistance patterns were analysed by microelectrode array-based impedance spectroscopy, XTT and flow cytometric apoptosis/proliferation assay. BRAFV600E melanoma cells acquired a time- and concentration-dependent desensitisation up to 100-fold towards oncogene-specific PLX4032 and chemotherapeutic dacarbazine after twelve months treatment. The impact of multiple drug insensitivity on molecular melanoma characteristics was elaborated via mRNA and protein quantification. Following BRAFV600E targeting, melanoma cells developed an increasingly aggressive, dacarbazine-insensitive phenotype. Thereby, hyperactivated canonical alternative MAPK and bypass PI3K/AKT signalling caused cross-resistance of differently acting drugs. With these results, we are the first to show that long-term melanoma therapy with BRAF inhibitors can prevent further therapeutic success with dacarbazine due to acquisition of cross-resistance.
Nickel-catalyzed remote and proximal Wacker-type oxidation
Authors: Liu Binbin , Hu Penghui , Xu Fangning , Cheng Lu , Tan Mingxi , Han Wei 
Published: January 2019

AbstractWacker oxidation chemistry is widely applied to oxidation of olefins to carbonyls in the synthesis of pharmaceuticals, natural products, and commodity chemicals. However, in this chemistry efficient oxidation of internal olefins and highly selective oxidation of unbiased internal olefins without reliance upon suitable coordinating groups have remained significant challenges. Here we report a nickel-catalyzed remote Wacker-type oxidation where reactions occur at remote and less-reactive sp3 C–H sites in the presence of a priori more reactive ones through a chain-walking mechanism with excellent regio- and chemo- selectivity. This transformation has attractive features including the use of ambient air as the sole oxidant, naturally-abundant nickel as the catalyst, and polymethylhydrosiloxane as the hydride source at room temperature, allowing for effective oxidation of challenging olefins. Notably, this approach enables direct access to a broad array of complex, medicinally relevant molecules from structurally complex substrates and chemical feedstocks.
FBXL19-AS1 exerts oncogenic function by sponging miR-431-5p to regulate RAF1 expression in lung cancer
Authors: Jiang Qian , Cheng Li , Ma Daiyuan , Zhao Yanli 
Published: January 2019

Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide, characterized by uncontrolled proliferation and metastasis of lung cancer cells. Tumor angiogenesis plays a key role in proliferation and metastasis in cancers, and is an essential component in microenvironment. It has been reported that long non-coding RNA FBXL19-AS1 plays an oncogenic role in colorectal cancer. However, the molecular mechanism of FBXL19-AS1 in lung cancer has not been fully elucidated. In the present study, we found that FBXL19-AS1 expression was up-regulated in lung cancer tissues and cell lines. FBXL19-AS1 knockdown inhibited cell proliferation, migration, invasion, and angiogenesis in lung cancer cells. Molecular mechanism exploration uncovered that FBXL19-AS1 acted as a molecular sponge of miR-431-5p and that RAF1 was a downstream target of miR-431-5p in lung cancer. Moreover, there was a negative association between miR-431-5p expression and FBXL19-AS1 or RAF1 expression in tumor tissues. Through rescue experiments, we discovered that overexpression of RAF1 partially rescued FBXL19-AS1 knockdown-mediated inhibition of angiogenesis and progression in lung cancer. Together, these results indicated that FBXL19-AS1 was involved in progression and angiogenesis in lung cancer by targeting miR-431-5p/RAF1 axis, which provided a new insight into the therapeutic strategies of lung cancer.
Circularly polarised antenna with wide harmonics suppression by two angled C‐shaped structures
Authors: Oh J.E. , Sung Y. 
Published: January 2019

In this Letter, a circularly polarised (CP) antenna is proposed. The proposed antenna is realised by combining two angled C‐shaped structures. By setting different widths (WL and WR) for the left and right angled C‐shaped structures, respectively, an asymmetric structure is obtained. Therefore, the proposed antenna exhibits CP characteristics. From repeated simulation results, the authors find that the optimum ratio WL: WR to make the proposed structure operate as a CP antenna is 5: 8. Moreover, the measured reflection coefficient is lower than −2.4 dB within a stopband up to 12 GHz. This means that wide harmonics suppression (up to the fifth harmonic) is successfully achieved.
Enabling on‐aircraft visible‐light communications in low‐light conditions
Authors: Tagliaferri D. , Capsoni C. 
Published: January 2019

Visible‐light communications (VLCs) are emerging as a valid alternative to radio‐frequency systems for the provision of Internet connectivity to aircraft passengers through the LED reading lamps. In this Letter, the authors investigate the minimum required level of emitted flux in order to support the communication with the users' terminals. A VLC system employing 1 lm of flux is able to achieve an average per‐user capacity comparable with the one currently in use for 4G (6 bit/s/Hz) over an electrical bandwidth of 10 MHz, which is sufficient to support the latest multimedia services (40 Mb/s for Blu‐ray video streaming).
BBPD with wide input phase range
Authors: Kossel M. , Francese P. , Morf T. , Brändli M. , Khatri V. , Yonar S. , Dazzi M. , Khaddam‐Aljameh R. 
Published: January 2019

Wireline communication circuits often include serialisers/deserialisers using multiphase signals for multiplexing or sampling. From a power efficiency viewpoint, configurations are desired in which a single differential clock at frequency f is distributed to decentralised multiphase generators as opposed to distribution at 2f with local frequency dividers. A bang–bang phase detector (BBPD) is presented for such a multiphase generator operated from 4 to 16 GHz. Owing to the 2‐octave frequency range, a wide input phase range is required for which the BBPD may not generate false locks. This is achieved by an implementation in which down pulses at the output of a fully symmetrical set/reset latch are stretched via pulse‐width extension circuitries. A sampling pulse generated from one of the input phases can then easily capture the extended down pulses across a wide input phase range to unambiguously indicate phase leading or phase lagging to the control logic of the multiphase generator. The proposed circuitry has been implemented in a 7 nm CMOS technology. A comparison to alternative BBPD approaches implemented in the same technology shows that the proposed architecture outperforms them in terms of achievable input phase range.
Dual‐band dual‐polarised microstrip antenna with improved inter‐port isolation
Authors: Chakrabarti S. , Chakraborty A. 
Published: January 2019

This Letter presents the development of a dual linearly polarised microstrip antenna for S‐ and C‐band with improved isolation and bandwidth. The antenna is dual linearly polarised at each of the bands. The S‐band patch is proximity coupled to two orthogonal feed lines, whereas the C‐band patches are aperture coupled to other two mutually orthogonal feed lines. The antenna results in an impedance bandwidth ≥ 3.65% with an isolation ≥ 26 dB at the S‐band ports. At the C‐band ports, it also displays an isolation ≥ 45 dB over the entire operating bandwidth of ≥ 21%. All these results are improved compared to the earlier reported investigations.
Forage silica and water content control dental surface texture in guinea pigs and provide implications for dietary reconstruction
Authors: Winkler Daniela E. , Schulz-Kornas Ellen , Kaiser Thomas M. , De Cuyper Annelies , Clauss Marcus , Tütken Thomas 
Published: January 2019

Significance
Ingesta leave characteristic wear features on the tooth surface, which enable us to reconstruct the diet of extant and fossil vertebrates. However, whether dental wear is caused by internal (phytoliths) or external (mineral dust) silicate abrasives is controversially debated in paleoanthropology and biology. To assess this, we fed guinea pigs plant forages of increasing silica content (lucerne < grass < bamboo) without any external abrasives, both in fresh and dried state. Abrasiveness and enamel surface wear increased with higher forage phytolith content. Additionally, water loss altered plant material properties. Dental wear of fresh grass feeding was similar to lucerne browsing, while dried grass caused more grazer-like wear. Fresh grass grazing could be confounded with browsing, being a major pitfall for paleodietary reconstructions.