bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Diverse Array of Fluvial Depositional Systems in Arabia Terra: Evidence for mid‐Noachian to Early Hesperian Rivers on Mars
Authors: Davis Joel M. , Gupta Sanjeev , Balme Matthew , Grindrod Peter M. , Fawdon Peter , Dickeson Zachary I. , Williams Rebecca M.E. 
Published: July 2019

AbstractBranching to sinuous ridges systems, hundreds of kilometers in length and comprising layered strata, are present across much of Arabia Terra, Mars. These ridges are interpreted as depositional fluvial channels, now preserved as inverted topography. Here we use high‐resolution image and topographic data sets to investigate the morphology of these depositional systems and show key examples of their relationships to associated fluvial landforms. The inverted channel systems likely comprise indurated conglomerate, sandstone, and mudstone bodies, which form a multistory channel stratigraphy. The channel systems intersect local basins and indurated sedimentary mounds, which we interpret as paleolake deposits. Some inverted channels are located within erosional valley networks, which have regional and local catchments. Inverted channels are typically found in downslope sections of valley networks, sometimes at the margins of basins, and numerous different transition morphologies are observed. These relationships indicate a complex history of erosion and deposition, possibly controlled by changes in water or sediment flux, or base‐level variation. Other inverted channel systems have no clear preserved catchment, likely lost due to regional resurfacing of upland areas. Sediment may have been transported through Arabia Terra toward the dichotomy and stored in local and regional‐scale basins. Regional stratigraphic relations suggest these systems were active between the mid‐Noachian and early Hesperian. The morphology of these systems is supportive of an early Mars climate, which was characterized by prolonged precipitation and runoff.
Two Production Stages of Coccolithophores in Winter as Revealed by Sediment Traps in the Northern South China Sea
Authors: Jin X. B. , Liu C. L. , Zhao Y. L. , Zhang Y. W. , Wen K. , Lin S. , Li J. R. , Liu Z. F. 
Published: July 2019

AbstractCoccolithophores, originating in the Late Triassic, are one of the most successful marine calcifying algae living in modern oceans. Coccoliths are the calcareous fossil remnants left in marine sediments after coccolithophores die. These calcite scales record the conditions of the surface ocean (e.g., primary productivity, seawater temperature, and carbonate chemistry) and are expected to be a promising subject in paleoceanographic and paleoclimatic studies. Hence, a comprehensive understanding of the ecology and phenology of living coccolithophores, as well as their interactions with other plankton groups, is needed to develop better constraints on their uses in paleoenvironmental studies. Here we show modern coccolithophore production through the coccolith fluxes from sediment traps at a ~500‐m water depth from 2013 to 2015 in the northern South China Sea. In addition to the expected seasonality of the coccolithophore production that occurs during winter seasons due to the strong water mixing induced by monsoon winds, a two‐stage mode for the coccolithophore production is also recognized in relatively “coastal” waters. The first stage includes the production of Gephyrocapsa oceanica in December, when the macronutrient inventory is built, and the second stage describes the growth of Emiliania huxleyi in late February with the depletion of silicate nutrients. This two‐stage mode originates from subtle differences in the nutrient assimilation ability between the two species. In addition, coccolithophore production is significantly influenced by the decadal oceanic events (i.e., El Niño) in the northern South China Sea.
Forecasting High‐Speed Solar Wind Streams Based on Solar Extreme Ultraviolet Images
Authors: Bu X. , Luo B. , Shen C. , Liu S. , Gong J. , Cao Y. , Wang H. 
Published: July 2019

AbstractHigh‐speed solar wind streams that originate from coronal holes play an important role in space weather disturbances, especially during the declining phase of the solar cycle. Space weather forecasters attempt to find good coronal hole indices that can be used to predict high‐speed streams days in advance. Several indices related to the coronal hole area, brightness, or magnetic field expansion factor have been reported in the literature. Empirical solar wind forecast models have been developed and used in operational service by several organizations by constructing prediction functions that relate the coronal hole index to the solar wind speed. In this paper, we present a new empirical modeling method and test its validity by comparing it with a previously reported method when applied to different coronal hole indices. In total, six empirical models are tested for a long period of time (2011–2018), with a 27‐day persistence model as a comparison benchmark. The results show that while all these empirical models can capture the temporal patterns of the solar wind observations well, the new modeling method and utilization of a composite coronal hole index PCH as an input parameter indeed improves the forecast accuracy. The high‐speed streams can be predicted approximately 3 days in advance, with a probability of detection of 0.78, a positive predictive value of 0.73, and a threat score of 0.61. The uncertainty of the high‐speed stream arrival time is approximately 1 day and the uncertainty of the peak speed is approximately 80 km/s.
Late Miocene to Pleistocene Source to Sink Record of Exhumation and Sediment Routing in the Gulf of Alaska From Detrital Zircon Fission‐Track and U‐Pb Double Dating
Authors: Bootes Nathaniel , Enkelmann Eva , Lease Richard 
Published: July 2019

AbstractWe investigate the late Miocene‐Pleistocene offshore sedimentary record of the Yakutat microplate to evaluate the spatial and temporal variations in rock exhumation and sediment routing patterns at the heavily glaciated and actively converging plate boundary in southeast Alaska. We present 1,456 new fission track ages and 1,372 new U‐Pb ages from double‐dated detrital zircons derived from fourteen samples collected from offshore. We integrate our results with published geochronology and thermochronology data onland and offshore in order to constrain grain provenance. We find that offshore strata deposited east of the fold and thrust belt are sourced from the rapidly exhuming areas along the entire Fairweather Fault, the northeastern part of the syntaxial region, as well as the slowly exhuming Insular superterrane. In contrast, the western strata are sourced from the emerging fold and thrust belt and the Chugach Metamorphic Complex located north of the plate boundary. In these samples we identified a change in sediment provenance, which we suggest marks the capture of the Bagley Ice Valley by the proto‐Bering Glacier at the transition from the early to late Pliocene. This implies that the modern Bagley‐Bering Glacier System is much older than previously known. Strata deposited at ~8.6 Ma suggest that extreme rapid exhumation was already ongoing in the late Miocene, which supports previous findings in deep‐sea deposits. Overall, the data help discern several stages in the evolution of sediment routing patterns in response to dynamic tectonic and surficial processes along this active convergent margin.
Synthetic modeling reveals HOXB genes are critical for the initiation and maintenance of human leukemia
Authors: Kusakabe Manabu , Sun Ann Chong , Tyshchenko Kateryna , Wong Rachel , Nanda Aastha , Shanna Claire , Gusscott Samuel , Chavez Elizabeth A. , Lorzadeh Alireza , Zhu Alice , Hill Ainsleigh , Hung Stacy , Brown Scott , Babaian Artem , Wang Xuehai , Holt Robert A. , Steidl Christian , Karsan Aly , Humphries R. Keith , Eaves Connie J. , Hirst Martin , Weng Andrew P. 
Published: July 2019

AbstractMechanistic studies in human cancer have relied heavily on cell lines and mouse models, but are limited by in vitro adaptation and species context issues, respectively. More recent efforts have utilized patient-derived xenografts; however, these are hampered by variable genetic background, inability to study early events, and practical issues with availability/reproducibility. We report here an efficient, reproducible model of T-cell leukemia in which lentiviral transduction of normal human cord blood yields aggressive leukemia that appears indistinguishable from natural disease. We utilize this synthetic model to uncover a role for oncogene-induced HOXB activation which is operative in leukemia cells-of-origin and persists in established tumors where it defines a novel subset of patients distinct from other known genetic subtypes and with poor clinical outcome. We show further that anterior HOXB genes are specifically activated in human T-ALL by an epigenetic mechanism and confer growth advantage in both pre-leukemia cells and established clones.
Motional Fock states for quantum-enhanced amplitude and phase measurements with trapped ions
Authors: Wolf Fabian , Shi Chunyan , Heip Jan C. , Gessner Manuel , Pezzè Luca , Smerzi Augusto , Schulte Marius , Hammerer Klemens , Schmidt Piet O. 
Published: July 2019

AbstractThe quantum noise of the vacuum limits the achievable sensitivity of quantum sensors. In non-classical measurement schemes the noise can be reduced to overcome this limitation. However, schemes based on squeezed or Schrödinger cat states require alignment of the relative phase between the measured interaction and the non-classical quantum state. Here we present two measurement schemes on a trapped ion prepared in a motional Fock state for displacement and frequency metrology that are insensitive to this phase. The achieved statistical uncertainty is below the standard quantum limit set by quantum vacuum fluctuations, enabling applications in spectroscopy and mass measurements.
Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology
Authors: Barrington Christopher , Georgopoulou Dimitra , Pezic Dubravka , Varsally Wazeer , Herrero Javier , Hadjur Suzana 
Published: July 2019

AbstractCohesin and CTCF are master regulators of genome topology. How these ubiquitous proteins contribute to cell-type specific genome structure is poorly understood. Here, we explore quantitative aspects of topologically associated domains (TAD) between pluripotent embryonic stem cells (ESC) and lineage-committed cells. ESCs exhibit permissive topological configurations which manifest themselves as increased inter- TAD interactions, weaker intra-TAD interactions, and a unique intra-TAD connectivity whereby one border makes pervasive interactions throughout the domain. Such ‘stripe’ domains are associated with both poised and active chromatin landscapes and transcription is not a key determinant of their structure. By tracking the developmental dynamics of stripe domains, we show that stripe formation is linked to the functional state of the cell through cohesin loading at lineage-specific enhancers and developmental control of CTCF binding site occupancy. We propose that the unique topological configuration of stripe domains represents a permissive landscape facilitating both productive and opportunistic gene regulation and is important for cellular identity.
Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
Authors: Gaublomme Jellert T. , Li Bo , McCabe Cristin , Knecht Abigail , Yang Yiming , Drokhlyansky Eugene , Van Wittenberghe Nicholas , Waldman Julia , Dionne Danielle , Nguyen Lan , De Jager Philip L. , Yeung Bertrand , Zhao Xinfang , Habib Naomi , Rozenblatt-Rosen Orit , Regev Aviv 
Published: July 2019

AbstractSingle-nucleus RNA-seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate or are frozen, and opens the way to human genetics studies, clinical trials, and precise cell atlases of large organs. However, such applications are currently limited by batch effects, processing, and costs. Here, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter recovered profiles. We develop DemuxEM, a computational tool that detects inter-sample multiplets and assigns singlets to their sample of origin, and validate its accuracy using sex-specific gene expression, species-mixing and natural genetic variation. Our approach will facilitate tissue atlases of isogenic model organisms or from multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.
Lysine/RNA-interactions drive and regulate biomolecular condensation
Authors: Ukmar-Godec Tina , Hutten Saskia , Grieshop Matthew P. , Rezaei-Ghaleh Nasrollah , Cima-Omori Maria-Sol , Biernat Jacek , Mandelkow Eckhard , Söding Johannes , Dormann Dorothee , Zweckstetter Markus 
Published: July 2019

AbstractCells form and use biomolecular condensates to execute biochemical reactions. The molecular properties of non-membrane-bound condensates are directly connected to the amino acid content of disordered protein regions. Lysine plays an important role in cellular function, but little is known about its role in biomolecular condensation. Here we show that protein disorder is abundant in protein/RNA granules and lysine is enriched in disordered regions of proteins in P-bodies compared to the entire human disordered proteome. Lysine-rich polypeptides phase separate into lysine/RNA-coacervates that are more dynamic and differ at the molecular level from arginine/RNA-coacervates. Consistent with the ability of lysine to drive phase separation, lysine-rich variants of the Alzheimer’s disease-linked protein tau undergo coacervation with RNA in vitro and bind to stress granules in cells. Acetylation of lysine reverses liquid–liquid phase separation and reduces colocalization of tau with stress granules. Our study establishes lysine as an important regulator of cellular condensation.
Orthogonal regulation of phytochrome B abundance by stress-specific plastidial retrograde signaling metabolite
Authors: Jiang Jishan , Zeng Liping , Ke Haiyan , De La Cruz Brittenny , Dehesh Katayoon 
Published: July 2019

AbstractPlant survival necessitates constant monitoring of fluctuating light and balancing growth demands with adaptive responses, tasks mediated via interconnected sensing and signaling networks. Photoreceptor phytochrome B (phyB) and plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) are evolutionarily conserved sensing and signaling components eliciting responses through unknown connection(s). Here, via a suppressor screen, we identify two phyB mutant alleles that revert the dwarf and high salicylic acid phenotypes of the high MEcPP containing mutant ceh1. Biochemical analyses show high phyB protein levels in MEcPP-accumulating plants resulting from reduced expression of phyB antagonists and decreased auxin levels. We show that auxin treatment negatively regulates phyB abundance. Additional studies identify CAMTA3, a MEcPP-activated calcium-dependent transcriptional regulator, as critical for maintaining phyB abundance. These studies provide insights into biological organization fundamentals whereby a signal from a single plastidial metabolite is transduced into an ensemble of regulatory networks controlling the abundance of phyB, positioning plastids at the information apex directing adaptive responses.
Motor dysfunction and neurodegeneration in a C9orf72 mouse line expressing poly-PR
Authors: Hao Zongbing , Liu Liu , Tao Zhouteng , Wang Rui , Ren Haigang , Sun Hongyang , Lin Zixuan , Zhang Zhixiong , Mu Chenchen , Zhou Jiawei , Wang Guanghui 
Published: July 2019

AbstractA GGGGCC hexanucleotide repeat expansion in intron 1 ofchromosome 9 open reading frame 72(C9ORF72) gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Repeat-associated non-ATG translation of dipeptide repeat proteins (DPRs) contributes to the neuropathological features of c9FTD/ALS. Among the five DPRs, arginine-rich poly-PR are reported to be the most toxic. Here, we generate a transgenic mouse line that expresses poly-PR (GFP-PR28) specifically in neurons. GFP-PR28homozygous mice show decreased survival time, while the heterozygous mice show motor imbalance, decreased brain weight, loss of Purkinje cells and lower motor neurons, and inflammation in the cerebellum and spinal cord. Transcriptional analysis shows that in the cerebellum, GFP-PR28heterozygous mice show differential expression of genes related to synaptic transmission. Our findings show that GFP-PR28transgenic mice partly model neuropathological features of c9FTD/ALS, and show a role for poly-PR in neurodegeneration.
Structural basis of Q-dependent transcription antitermination
Authors: Shi Jing , Gao Xiang , Tian Tongguan , Yu Zhaoyang , Gao Bo , Wen Aijia , You Linlin , Chang Shenghai , Zhang Xing , Zhang Yu , Feng Yu 
Published: July 2019

AbstractBacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex. The structure reveals key interactions responsible for σ-dependent pause, Q engagement, and Q-mediated transcription antitermination. The structure shows that two Q protomers (QI and QII) bind to a direct-repeat DNA site and contact distinct elements of the RNA exit channel. Notably, QI forms a narrow ring inside the RNA exit channel and renders RNAP resistant to termination signals by prohibiting RNA hairpin formation in the RNA exit channel. Because the RNA exit channel is conserved among all multisubunit RNAPs, it is likely to serve as an important contact site for regulators that modify the elongation properties of RNAP in other organisms, as well.
Transient drug-tolerance and permanent drug-resistance rely on the trehalose-catalytic shift in Mycobacterium tuberculosis
Authors: Lee Jae Jin , Lee Sun-Kyung , Song Naomi , Nathan Temitope O. , Swarts Benjamin M. , Eum Seok-Yong , Ehrt Sabine , Cho Sang-Nae , Eoh Hyungjin 
Published: July 2019

AbstractStochastic formation of Mycobacterium tuberculosis (Mtb) persisters achieves a high level of antibiotic-tolerance and serves as a source of multidrug-resistant (MDR) mutations. As conventional treatment is not effective against infections by persisters and MDR-Mtb, novel therapeutics are needed. Several approaches were proposed to kill persisters by altering their metabolism, obviating the need to target active processes. Here, we adapted a biofilm culture to model Mtb persister-like bacilli (PLB) and demonstrated that PLB underwent trehalose metabolism remodeling. PLB use trehalose as an internal carbon to biosynthesize central carbon metabolism intermediates instead of cell surface glycolipids, thus maintaining levels of ATP and antioxidants. Similar changes were identified in Mtb following antibiotic-treatment, and MDR-Mtb as mechanisms to circumvent antibiotic effects. This suggests that trehalose metabolism is associated not only with transient drug-tolerance but also permanent drug-resistance, and serves as a source of adjunctive therapeutic options, potentiating antibiotic efficacy by interfering with adaptive strategies.
Essentiality of sterol synthesis genes in the planctomycete bacterium Gemmata obscuriglobus
Authors: Rivas-Marin Elena , Stettner Sean , Gottshall Ekaterina Y. , Santana-Molina Carlos , Helling Mitch , Basile Franco , Ward Naomi L. , Devos Damien P. 
Published: July 2019

AbstractSterols and hopanoids are chemically and structurally related lipids mostly found in eukaryotic and bacterial cell membranes. Few bacterial species have been reported to produce sterols and this anomaly had originally been ascribed to lateral gene transfer (LGT) from eukaryotes. In addition, the functions of sterols in these bacteria are unknown and the functional overlap between sterols and hopanoids is still unclear. Gemmata obscuriglobus is a bacterium from the Planctomycetes phylum that synthesizes sterols, in contrast to its hopanoid-producing relatives. Here we show that sterols are essential for growth of G. obscuriglobus, and that sterol depletion leads to aberrant membrane structures and defects in budding cell division. This report of sterol essentiality in a prokaryotic species advances our understanding of sterol distribution and function, and provides a foundation to pursue fundamental questions in evolutionary cell biology.
Proof of concept of a frequency-preserving and time-invariant metamaterial-based nonlinear acoustic diode
Authors: Gliozzi A. S. , Miniaci M. , Krushynska A. O. , Morvan B. , Scalerandi M. , Pugno N. M. , Bosia F. 
Published: July 2019

AbstractAcoustic filters and metamaterials have become essential components for elastic wave control in applications ranging from ultrasonics to noise abatement. Other devices have been designed in this field, emulating their electromagnetic counterparts. One such case is an acoustic diode or rectifier, which enables one-way wave transmission by breaking the wave equation-related reciprocity. Its achievement, however, has proved to be rather problematic, and current realizations display a number of shortcomings in terms of simplicity and versatility. Here, we present the design, fabrication and characterization of a device able to work as an acoustic diode, a switch and a transistor-like apparatus, exploiting symmetry-breaking nonlinear effects like harmonic generation and wave mixing, and the filtering capabilities of metamaterials. This device presents several advantages compared with previous acoustic diode realizations, including versatility, time invariance, frequency preserving characteristics and switchability. We numerically evaluate its efficiency and demonstrate its feasibility in a preliminary experimental realization. This work may provide new opportunities for the practical realization of structural components with one-way wave propagation properties.
Glutamate levels in the anterior cingulate cortex in un-medicated first episode psychosis: a proton magnetic resonance spectroscopy study
Authors: Borgan Faith R. , Jauhar Sameer , McCutcheon Robert A. , Pepper Fiona S. , Rogdaki Maria , Lythgoe David J. , Howes Oliver D. 
Published: July 2019

AbstractConverging lines of evidence suggest that glutamatergic dysfunction may contribute to the pathophysiology of first episode psychosis. We investigated whether first episode psychosis patients free from all pharmacological treatments and illicit substances show cortical glutamatergic alterations. One-hundred and eleven volunteers including 65 healthy volunteers and 46 first episode psychosis patients free from all pharmacological treatments (28 drug naïve) underwent a proton magnetic resonance spectroscopy scan measuring glutamate levels in the bilateral anterior cingulate cortex. Symptom severity was measured using the Positive and Negative Syndrome Scale (PANSS) and cognition was measured using the Wechsler Adult Intelligence Scale (WAIS) digit symbol test. There were no differences in glutamate levels between patients and controls. These findings remained unchanged when adjusting for the effects of age, sex and ethnicity or when restricting the analyses to patients who were both medication naïve to all pharmacological treatments and illicit substances. Whilst these findings do not preclude glutamatergic alterations in psychosis, methodological advances are needed for us to investigate whether patients show alterations in other aspects of glutamate function, such as pre-synaptic glutamate or release.