bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D characterisation and quantification of an offshore freshened groundwater system in the Canterbury Bight
Authors: Micallef Aaron , Person Mark , Haroon Amir , Weymer Bradley A. , Jegen Marion , Schwalenberg Katrin , Faghih Zahra , Duan Shuangmin , Cohen Denis , Mountjoy Joshu J. , Woelz Susanne , Gable Carl W. , Averes Tanita , Kumar Tiwari Ashwani 
Published: March 2020

AbstractAlthough offshore freshened groundwater (OFG) systems have been documented in numerous continental margins worldwide, their geometry, controls and emplacement dynamics remain poorly constrained. Here we integrate controlled-source electromagnetic, seismic reflection and borehole data with hydrological modelling to quantitatively characterise a previously unknown OFG system near Canterbury, New Zealand. The OFG system consists of one main, and two smaller, low salinity groundwater bodies. The main body extends up to 60 km from the coast and a seawater depth of 110 m. We attribute along-shelf variability in salinity to permeability heterogeneity due to permeable conduits and normal faults, and to recharge from rivers during sea level lowstands. A meteoric origin of the OFG and active groundwater migration from onshore are inferred. However, modelling results suggest that the majority of the OFG was emplaced via topographically-driven flow during sea level lowstands in the last 300 ka. Global volumetric estimates of OFG will be significantly revised if active margins, with steep coastal topographies like the Canterbury margin, are considered.
A signaling hub of insulin receptor, dystrophin glycoprotein complex and plakoglobin regulates muscle size
Authors: Eid Mutlak Yara , Aweida Dina , Volodin Alexandra , Ayalon Bar , Dahan Nitsan , Parnis Anna , Cohen Shenhav 
Published: March 2020

AbstractSignaling through the insulin receptor governs central physiological functions related to cell growth and metabolism. Here we show by tandem native protein complex purification approach and super-resolution STED microscopy that insulin receptor activity requires association with the fundamental structural module in muscle, the dystrophin glycoprotein complex (DGC), and the desmosomal component plakoglobin (γ-catenin). The integrity of this high-molecular-mass assembly renders skeletal muscle susceptibility to insulin, because DGC-insulin receptor dissociation by plakoglobin downregulation reduces insulin signaling and causes atrophy. Furthermore, low insulin receptor activity in muscles from transgenic or fasted mice decreases plakoglobin-DGC-insulin receptor content on the plasma membrane, but not when plakoglobin is overexpressed. By masking β-dystroglycan LIR domains, plakoglobin prevents autophagic clearance of plakoglobin-DGC-insulin receptor co-assemblies and maintains their function. Our findings establish DGC as a signaling hub, and provide a possible mechanism for the insulin resistance in Duchenne Muscular Dystrophy, and for the cardiomyopathies seen with plakoglobin mutations.
A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas
Authors: Cazares Adrian , Moore Matthew P. , Hall James P.  J. , Wright Laura L. , Grimes Macauley , Emond-Rhéault Jean-Guillaume , Pongchaikul Pisut , Santanirand Pitak , Levesque Roger C. , Fothergill Joanne L. , Winstanley Craig 
Published: March 2020

AbstractMultidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.
Tactile sensory coding and learning with bio-inspired optoelectronic spiking afferent nerves
Authors: Tan Hongwei , Tao Quanzheng , Pande Ishan , Majumdar Sayani , Liu Fu , Zhou Yifan , Persson Per O. Å. , Rosen Johanna , van Dijken Sebastiaan 
Published: March 2020

AbstractThe integration and cooperation of mechanoreceptors, neurons and synapses in somatosensory systems enable humans to efficiently sense and process tactile information. Inspired by biological somatosensory systems, we report an optoelectronic spiking afferent nerve with neural coding, perceptual learning and memorizing capabilities to mimic tactile sensing and processing. Our system senses pressure by MXene-based sensors, converts pressure information to light pulses by coupling light-emitting diodes to analog-to-digital circuits, then integrates light pulses using a synaptic photomemristor. With neural coding, our spiking nerve is capable of not only detecting simultaneous pressure inputs, but also recognizing Morse code, braille, and object movement. Furthermore, with dimensionality-reduced feature extraction and learning, our system can recognize and memorize handwritten alphabets and words, providing a promising approach towards e-skin, neurorobotics and human-machine interaction technologies.
Predicting gene expression using morphological cell responses to nanotopography
Authors: Cutiongco Marie F. A. , Jensen Bjørn Sand , Reynolds Paul M. , Gadegaard Nikolaj 
Published: March 2020

AbstractCells respond in complex ways to their environment, making it challenging to predict a direct relationship between the two. A key problem is the lack of informative representations of parameters that translate directly into biological function. Here we present a platform to relate the effects of cell morphology to gene expression induced by nanotopography. This platform utilizes the ‘morphome’, a multivariate dataset of cell morphology parameters. We create a Bayesian linear regression model that uses the morphome to robustly predict changes in bone, cartilage, muscle and fibrous gene expression induced by nanotopography. Furthermore, through this model we effectively predict nanotopography-induced gene expression from a complex co-culture microenvironment. The information from the morphome uncovers previously unknown effects of nanotopography on altering cell–cell interaction and osteogenic gene expression at the single cell level. The predictive relationship between morphology and gene expression arising from cell-material interaction shows promise for exploration of new topographies.
Thermodynamics of continuous non-Markovian feedback control
Authors: Debiossac Maxime , Grass David , Alonso Jose Joaquin , Lutz Eric , Kiesel Nikolai 
Published: March 2020

AbstractFeedback control mechanisms are ubiquitous in science and technology, and play an essential role in regulating physical, biological and engineering systems. The standard second law of thermodynamics does not hold in the presence of measurement and feedback. Most studies so far have extended the second law for discrete, Markovian feedback protocols; however, non-Markovian feedback is omnipresent in processes where the control signal is applied with a non-negligible delay. Here, we experimentally investigate the thermodynamics of continuous, time-delayed feedback control using the motion of an optically levitated, underdamped microparticle. We test the validity of a generalized second law which bounds the energy extracted from the system, and study the breakdown of feedback cooling for very large time delays.
Horizontal transfer and evolution of transposable elements in vertebrates
Authors: Zhang Hua-Hao , Peccoud Jean , Xu Min-Rui-Xuan , Zhang Xiao-Gu , Gilbert Clément 
Published: March 2020

AbstractHorizontal transfer of transposable elements (HTT) is an important process shaping eukaryote genomes, yet very few studies have quantified this phenomenon on a large scale or have evaluated the selective constraints acting on transposable elements (TEs) during vertical and horizontal transmission. Here we screen 307 vertebrate genomes and infer a minimum of 975 independent HTT events between lineages that diverged more than 120 million years ago. HTT distribution greatly differs from null expectations, with 93.7% of these transfers involving ray-finned fishes and less than 3% involving mammals and birds. HTT incurs purifying selection (conserved protein evolution) on all TEs, confirming that producing functional transposition proteins is required for a TE to invade new genomes. In the absence of HTT, DNA transposons appear to evolve neutrally within genomes, unlike most retrotransposons, which evolve under purifying selection. This selection regime indicates that proteins of most retrotransposon families tend to process their own encoding RNA (cis-preference), which helps retrotransposons to persist within host lineages over long time periods.
Bisphosphonate nanoclay edge-site interactions facilitate hydrogel self-assembly and sustained growth factor localization
Authors: Kim Yang-Hee , Yang Xia , Shi Liyang , Lanham Stuart A. , Hilborn Jons , Oreffo Richard O. C. , Ossipov Dmitri , Dawson Jonathan I. 
Published: March 2020

AbstractNanoclays have generated interest in biomaterial design for their ability to enhance the mechanics of polymeric materials and impart biological function. As well as their utility as physical cross-linkers, clays have been explored for sustained localization of biomolecules to promote in vivo tissue regeneration. To date, both biomolecule-clay and polymer-clay nanocomposite strategies have utilised the negatively charged clay particle surface. As such, biomolecule-clay and polymer-clay interactions are set in competition, potentially limiting the functional enhancements achieved. Here, we apply specific bisphosphonate interactions with the positively charged clay particle edge to develop self-assembling hydrogels and functionalized clay nanoparticles with preserved surface exchange capacity. Low concentrations of nanoclay are applied to cross-link hyaluronic acid polymers derivatised with a pendant bisphosphonate to generate hydrogels with enhanced mechanical properties and preserved protein binding able to sustain, for over six weeks in vivo, the localized activity of the clinically licensed growth factor BMP-2.
Non-stationary statistics and formation jitter in transient photon condensation
Authors: Walker Benjamin T. , Rodrigues João D. , Dhar Himadri S. , Oulton Rupert F. , Mintert Florian , Nyman Robert A. 
Published: March 2020

AbstractWhile equilibrium phase transitions are easily described by order parameters and free-energy landscapes, for their non-stationary counterparts these quantities are usually ill-defined. Here, we probe transient non-equilibrium dynamics of an optically pumped, dye-filled microcavity. We quench the system to a far-from-equilibrium state and find delayed condensation close to a critical excitation energy, a transient equivalent of critical slowing down. Besides number fluctuations near the critical excitation energy, we show that transient phase transitions exhibit timing jitter in the condensate formation. This jitter is a manifestation of the randomness associated with spontaneous emission, showing that condensation is a stochastic, rather than deterministic process. Despite the non-equilibrium character of this phase transition, we construct an effective free-energy landscape that describes the formation jitter and allows, in principle, its generalization to a wider class of processes.
A highly CMOS compatible hafnia-based ferroelectric diode
Authors: Luo Qing , Cheng Yan , Yang Jianguo , Cao Rongrong , Ma Haili , Yang Yang , Huang Rong , Wei Wei , Zheng Yonghui , Gong Tiancheng , Yu Jie , Xu Xiaoxin , Yuan Peng , Li Xiaoyan , Tai Lu , Yu Haoran , Shang Dashan , Liu Qi , Yu Bing , Ren Qiwei , Lv Hangbing , Liu Ming 
Published: March 2020

AbstractMemory devices with high speed and high density are highly desired to address the ‘memory wall’ issue. Here we demonstrated a highly scalable, three-dimensional stackable ferroelectric diode, with its rectifying polarity modulated by the polarization reversal of Hf0.5Zr0.5O2 films. By visualizing the hafnium/zirconium lattice order and oxygen lattice order with atomic-resolution spherical aberration-corrected STEM, we revealed the correlation between the spontaneous polarization of Hf0.5Zr0.5O2 film and the displacement of oxygen atom, thus unambiguously identified the non-centrosymmetric Pca21 orthorhombic phase in Hf0.5Zr0.5O2 film. We further implemented this ferroelectric diode in an 8 layers 3D array. Operation speed as high as 20 ns and robust endurance of more than 109 were demonstrated. The built-in nonlinearity of more than 100 guarantees its self-selective property that eliminates the need for external selectors to suppress the leakage current in large array. This work opens up new opportunities for future memory hierarchy evolution.
The RNA-binding protein DAZL functions as repressor and activator of mRNA translation during oocyte maturation
Authors: Yang Cai-Rong , Rajkovic Gabriel , Daldello Enrico Maria , Luong Xuan G. , Chen Jing , Conti Marco 
Published: March 2020

AbstractDeleted in azoospermia-like (DAZL) is an RNA-binding protein critical for gamete development. In full-grown oocytes, the DAZL protein increases 4-fold during reentry into the meiotic cell cycle. Here, we have investigated the functional significance of this accumulation at a genome-wide level. Depletion of DAZL causes a block in maturation and widespread disruption in the pattern of ribosome loading on maternal transcripts. In addition to decreased translation, DAZL depletion also causes translational activation of a distinct subset of mRNAs both in quiescent and maturing oocytes, a function recapitulated with YFP-3′UTR reporters. DAZL binds to mRNAs whose translation is both repressed and activated during maturation. Injection of recombinant DAZL protein in DAZL-depleted oocytes rescues the translation and maturation to MII. Mutagenesis of putative DAZL-binding sites in these mRNAs mimics the effect of DAZL depletion. These findings demonstrate that DAZL regulates translation of maternal mRNAs, functioning both as the translational repressor and activator during oocyte maturation.
Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity
Authors: Carnesecchi Julie , Sigismondo Gianluca , Domsch Katrin , Baader Clara Eva Paula , Rafiee Mahmoud-Reza , Krijgsveld Jeroen , Lohmann Ingrid 
Published: March 2020

AbstractTranscription factors (TFs) control cell fates by precisely orchestrating gene expression. However, how individual TFs promote transcriptional diversity remains unclear. Here, we use the Hox TF Ultrabithorax (Ubx) as a model to explore how a single TF specifies multiple cell types. Using proximity-dependent Biotin IDentification in Drosophila, we identify Ubx interactomes in three embryonic tissues. We find that Ubx interacts with largely non-overlapping sets of proteins with few having tissue-specific RNA expression. Instead most interactors are active in many cell types, controlling gene expression from chromatin regulation to the initiation of translation. Genetic interaction assays in vivo confirm that they act strictly lineage- and process-specific. Thus, functional specificity of Ubx seems to play out at several regulatory levels and to result from the controlled restriction of the interaction potential by the cellular environment. Thereby, it challenges long-standing assumptions such as differential RNA expression as determinant for protein complexes.
An engineered oncolytic virus expressing PD-L1 inhibitors activates tumor neoantigen-specific T cell responses
Authors: Wang Guan , Kang Xi , Chen Katherine S. , Jehng Tiffany , Jones Lindsey , Chen Jie , Huang Xue F. , Chen Si-Yi 
Published: March 2020

AbstractOncolytic viruses offer an in situ vaccination approach to activate tumor-specific T cell responses. However, the upregulation of PD-L1 expression on tumor cells and immune cells leads to tumor resistance to oncolytic immunotherapy. In this study, we generate an engineered oncolytic virus that coexpresses a PD-L1 inhibitor and GM-CSF. We find that the oncolytic virus is able to secrete the PD-L1 inhibitor that systemically binds and inhibits PD-L1 on tumor cells and immune cells. Importantly, the intratumoral injection with the oncolytic virus overcomes PD-L1-mediated immunosuppression during both the priming and effector phases, provokes systemic T cell responses against dominant and subdominant neoantigen epitopes derived from mutations, and leads to an effective rejection of both virus-injected and distant tumors. In summary, this engineered oncolytic virus is able to activate tumor neoantigen-specific T cell responses, providing a potent, individual tumor-specific oncolytic immunotherapy for cancer patients, especially those resistant to PD-1/PD-L1 blockade therapy.
Plant Raf-like kinases regulate the mRNA population upstream of ABA-unresponsive SnRK2 kinases under drought stress
Authors: Soma Fumiyuki , Takahashi Fuminori , Suzuki Takamasa , Shinozaki Kazuo , Yamaguchi-Shinozaki Kazuko 
Published: March 2020

AbstractSNF1-related protein kinases 2 (SnRK2s) are key regulators governing the plant adaptive responses to osmotic stresses, such as drought and high salinity. Subclass III SnRK2s function as central regulators of abscisic acid (ABA) signalling and orchestrate ABA-regulated adaptive responses to osmotic stresses. Seed plants have acquired other types of osmotic stress-activated but ABA-unresponsive subclass I SnRK2s that regulate mRNA decay and promote plant growth under osmotic stresses. In contrast to subclass III SnRK2s, the regulatory mechanisms underlying the rapid activation of subclass I SnRK2s in response to osmotic stress remain elusive. Here, we report that three B4 Raf-like MAP kinase kinase kinases (MAPKKKs) phosphorylate and activate subclass I SnRK2s under osmotic stress. Transcriptome analyses reveal that genes downstream of these MAPKKKs largely overlap with subclass I SnRK2-regulated genes under osmotic stress, which indicates that these MAPKKKs are upstream factors of subclass I SnRK2 and are directly activated by osmotic stress.
GIS- Based Screening Model of Coastal City Karachi for Plantation of Biofuel Source
Authors: Khan Muhammad Jahangir , Hasan Syeda Ailya 
Published: March 2020

AbstractGeospatial techniques are mediating in decision making, diversified data management and critical analysis. Jatropha Curcas. is a biodiesel crop and friendly to the regions of saline water environment. This study focuses to map the suitable plantation sites for biodiesel energy crop by using meteorological parameters and satellite imageries of ASTER GDEM and Landsat 8. The thematic layers of soil adjacent to existing vegetation, topographical elevation, slope, land surface temperature, and humidity are created and analyzed with soil types, bareness index and stream orders. Suitability of sites for plantation is a function of these variables which are found to be favorable in the study area. It should be taken into consideration that Jatropha Curcas plantation in Karachi which may contribute in local economic prosperity and support in maintaining heat-sink for the industrialized city.
LC-HRMS based approach to identify novel sphingolipid biomarkers in breast cancer patients
Authors: Bhadwal Priyanka , Dahiya Divya , Shinde Dhananjay , Vaiphei Kim , Math Raviswamy G. H. , Randhawa Vinay , Agnihotri Navneet 
Published: March 2020

AbstractPerturbations in lipid metabolic pathways to meet the bioenergetic and biosynthetic requirements is a principal characteristic of cancer cells. Sphingolipids (SPLs) are the largest class of bioactive lipids associated to various aspects of tumorigenesis and have been extensively studied in cancer cell lines and experimental models. The clinical relevance of SPLs in human malignancies however is still poorly understood and needs further investigation. In the present study, we adopted a UHPLC-High resolution (orbitrap) Mass spectrometry (HRMS) approach to identify various sphingolipid species in breast cancer patients. A total of 49 SPLs falling into 6 subcategories have been identified. Further, integrating the multivariate analysis with metabolomics enabled us to identify an elevation in the levels of ceramide phosphates and sphingosine phosphates in tumor tissues as compared to adjacent normal tissues. The expression of genes involved in the synthesis of reported metabolites was also determined in local as well as TCGA cohort. A significant upregulation in the expression of CERK and SPHK1 was observed in tumor tissues in local and TCGA cohort. Sphingomyelin levels were found to be high in adjacent normal tissues. Consistent with the above findings, expression of SGMS1 in tumor tissues was downregulated in TCGA cohort only. Clinical correlations of the selected metabolites and their performance as biomarkers was also evaluated. Significant ROC and positive correlation with Ki67 index highlight the diagnostic potential and clinical relevance of ceramide phosphates in breast cancer.
Bubble-mediated transport of benthic microorganisms into the water column: Identification of methanotrophs and implication of seepage intensity on transport efficiency
Authors: Jordan Sebastian F. A. , Treude Tina , Leifer Ira , Janßen René , Werner Johannes , Schulz-Vogt Heide , Schmale Oliver 
Published: March 2020

AbstractBenthic microorganisms transported into the water column potentially influence biogeochemical cycles and the pelagic food web structure. In the present study six gas-releasing vent sites in the Coal Oil Point seep field (California) were investigated, and the dislocation of microorganisms from the sediment into the water column via gas bubbles released from the seabed was documented. It was found that the methanotrophs transport efficiency was dependent on the volumetric gas flow, with the highest transport rate of 22.7 × 103 cells mLgas−1 at a volumetric gas flow of 0.07 mLgas s−1, and the lowest rate of 0.2 × 103 cells mLgas−1 at a gas flow of 2.2 mLgas s−1. A simple budget approach showed that this bubble-mediated transport has the potential to maintain a relevant part of the water-column methanotrophs in the seep field. The bubble-mediated link between the benthic and pelagic environment was further supported by genetic analyses, indicating a transportation of methanotrophs of the family Methylomonaceae and oil degrading bacteria of the genus Cycloclasticus from the sediment into the water column. These findings demonstrate that the bubble-mediated transport of microorganisms influences the pelagic microbial abundance and community composition at gas-releasing seep sites.