bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydroacoustic, Seismic, and Bathymetric Observations of the 2014 Submarine Eruption at Ahyi Seamount, Mariana Arc
Authors: Tepp Gabrielle , Chadwick William W. , Haney Matthew M. , Lyons John J. , Dziak Robert P. , Merle Susan G. , Butterfield David A. , Young Charles W.
Published: July 2019

Ahyi seamount, a shallow submarine volcano in the Northern Mariana Islands, began erupting on 23 April 2014. Hydroacoustic eruption signals were observed on the regional Mariana seismic network and on distant hydrophones, and National Oceanic and Atmospheric Administration (NOAA) scuba divers working in the area soon after the eruption began heard and felt underwater explosion sounds. The NOAA crew observed yellow‐orange bubble mats along the shore of neighboring Farallon de Pájaros Island, but no other surface manifestations of the eruption were reported by the crew or observed in satellite data. Here, we detail the eruption chronology and its morphologic impacts through analysis of seismic and hydroacoustic recordings and repeat bathymetric mapping. Throughout the 2‐week‐long eruption, Ahyi produced several thousand short, impulsive hydroacoustic signals that we interpret as underwater explosions as well as tremor near the beginning and end of the sequence. The initial tremor, which occurred for 2 hr, is interpreted as small phreatomagmatic explosions. This tremor was followed by a 90‐min pause before the characteristic impulsive signals began. Occasional tremor (lasting up to a few minutes) during the last 1.5 days of the eruption is interpreted as more sustained eruptive activity. Bathymetric changes show that a new crater, about 150 m deep, formed near the former summit and a large landslide chute formed on the southeastern flank. Comparing to other geophysically detected submarine eruptions, we find that the signals from the 2014 Ahyi eruption were more similar to those from other shallow or at‐surface submarine eruptions than those at deep (>500 m) eruptions.
Mantle Dynamics of Western Pacific and East Asia: New Insights from P Wave Anisotropic Tomography
Authors: Ma Jincheng , Tian You , Zhao Dapeng , Liu Cai , Liu Tingting
Published: July 2019

Seismic anisotropy records past and present tectonic deformations and provides important constraints for understanding the structure and dynamics of the Earth's interior. In this work, we use tremendous amounts of high‐quality P wave arrival times from local and regional earthquakes to determine a high‐resolution tomographic model of 3‐D P wave azimuthal anisotropy down to 1,000‐km depth beneath East Asia. Our results show that trench‐parallel fast‐velocity directions (FVDs) are visible in the shallow portion of the subducting Pacific slab (<80 km), whereas the deeper portion of the Pacific slab mainly exhibits trench‐normal FVDs, except for the stagnant slab in the mantle transition zone (MTZ) where obvious NE‐SW FVDs are revealed. The FVDs in the subslab mantle change from a subduction‐parallel trend at depths of 80–400 km to a subduction‐normal trend in the MTZ. Large‐scale low‐velocity anomalies are revealed beneath the Philippine Sea plate where the FVD is NE‐SW. The FVDs along the Izu‐Bonin arc and in a slab gap exhibit a striking anticlockwise toroidal trend. All these features may reflect complex 3‐D flows in the mantle wedge due to tearing and dehydration processes of the subducting Pacific slab. The subducting Pacific slab is split at ~300‐km depth under the Bonin arc and then penetrates into the lower mantle, whereas under East Asia the Pacific slab becomes stagnant in the MTZ and reaches the North‐South Gravity Lineament in China. The intraplate volcanoes in East Asia are caused by hot and wet upwelling flows in the big mantle wedge above the stagnant Pacific slab.
SAPS in the 17 March 2013 Storm Event: Initial Results From the Coupled Magnetosphere‐Ionosphere‐Thermosphere Model
Authors: Lin Dong , Wang Wenbin , Scales Wayne A. , Pham Kevin , Liu Jing , Zhang Binzheng , Merkin Viacheslav , Shi Xueling , Kunduri Bharat , Maimaiti Maimaitirebike
Published: July 2019

Subauroral polarization stream (SAPS) is latitudinally narrow flow channels of large westward plasma drifts in the subauroral ionosphere. In this study, the global structure and dynamic evolution of SAPS are investigated by using the Coupled Magnetosphere‐Ionosphere‐Thermosphere model with ring current extension, namely, the Lyon‐Fedder‐Mobarry‐Thermosphere Ionosphere Electrodynamics General Circulation Model‐Rice Convection Model, to simulate the 2013 St. Patrick's Day storm event. This is the first time that the global distribution and temporal evolution of SAPS are investigated using first‐principle models. The model shows a strong westward ion drift channel formed equatorward of the auroral electron precipitation boundary on the duskside, which is identified as the SAPS structure. The simulated ion drift velocity and auroral electron precipitation sampled along the trajectory of the Defense Meteorological Satellite Program F18 satellite are in good agreement with the satellite measurements. SAPS initiate in the predusk sector when the interplanetary magnetic field turns southward. SAPS latitude generally decreases with magnetic local time from dusk to midnight. The SAPS channel shows wedge, inverse wedge, and crescent morphologies during the storm and becomes discontinuous when the interplanetary magnetic field is weakly southward. The SAPS mean latitude has a correlation coefficient of 0.77 with the Dst index. The mean latitude moves equatorward, and the flow channel broadens in the storm main phase. The simulation results illustrate both the global distribution and highly dynamic behavior of SAPS that are not readily apparent from the observation data.
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

Branching 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

Coccolithophores, 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

High‐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

We 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

Mechanistic 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

The 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

Cohesin 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

Single-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

Cells 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

Plant 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

A 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

Bacteriophage 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

Stochastic 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

Sterols 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

Acoustic 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

Converging 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.
Lower limb sagittal gait kinematics can be predicted based on walking speed, gender, age and BMI
Authors: Moissenet Florent , Leboeuf Fabien , Armand Stéphane
Published: July 2019

Clinical gait analysis attempts to provide, in a pathological context, an objective record that quantifies the magnitude of deviations from normal gait. However, the identification of deviations is highly dependent with the characteristics of the normative database used. In particular, a mismatch between patient characteristics and an asymptomatic population database in terms of walking speed, demographic and anthropometric parameters may lead to misinterpretation during the clinical process. Rather than developing a new normative data repository that may require considerable of resources and time, this study aims to assess a method for predicting lower limb sagittal kinematics using multiple regression models based on walking speed, gender, age and BMI as predictors. With this approach, we were able to predict kinematics with an error within 1 standard deviation of the mean of the original waveforms recorded on fifty-four participants. Furthermore, the proposed approach allowed us to estimate the relative contribution to angular variations of each predictor, independently from the others. It appeared that a mismatch in walking speed, but also age, sex and BMI may lead to errors higher than 5° on lower limb sagittal kinematics and should thus be taken into account before any clinical interpretation.
Sequencing and comparative analysis of three Chlorella genomes provide insights into strain-specific adaptation to wastewater
Authors: Wu Tian , Li Linzhou , Jiang Xiaosen , Yang Yong , Song Yanzi , Chen Liang , Xu Xun , Shen Yue , Gu Ying
Published: July 2019

Microalgal Chlorella has been demonstrated to process wastewater efficiently from piggery industry, yet optimization through genetic engineering of such a bio-treatment is currently challenging, largely due to the limited data and knowledge in genomics. In this study, we first investigated the differential growth rates among three wastewater-processing Chlorella strains: Chlorella sorokiniana BD09, Chlorella sorokiniana BD08 and Chlorella sp. Dachan, and the previously published Chlorella sorokiniana UTEX 1602, showing us that BD09 maintains the best tolerance in synthetic wastewater. We then performed genome sequencing and analysis, resulting in a high-quality assembly for each genome with scaffold N50 > 2 Mb and genomic completeness ≥91%, as well as genome annotation with 9,668, 10,240, 9,821 high-confidence gene models predicted for BD09, BD08, and Dachan, respectively. Comparative genomics study unravels that metabolic pathways, which are involved in nitrogen and phosphorus assimilation, were enriched in the faster-growing strains. We found that gene structural variation and genomic rearrangement might contribute to differential capabilities in wastewater tolerance among the strains, as indicated by gene copy number variation, domain reshuffling of orthologs involved, as well as a ~1 Mb-length chromosomal inversion we observed in BD08 and Dachan. In addition, we speculated that an associated bacterium, Microbacterium chocolatum, which was identified within Dachan, play a possible role in synergizing nutrient removal. Our three newly sequenced Chlorella genomes provide a fundamental foundation to understand the molecular basis of abiotic stress tolerance in wastewater treatment, which is essential for future genetic engineering and strain improvement.
Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes
Authors: Bradford Stephen T. , Nair Shalima S. , Statham Aaron L. , van Dijk Susan J. , Peters Timothy J. , Anwar Firoz , French Hugh J. , von Martels Julius Z. H. , Sutcliffe Brodie , Maddugoda Madhavi P. , Peranec Michelle , Varinli Hilal , Arnoldy Rosanna , Buckley Michael , Ross Jason P. , Zotenko Elena , Song Jenny Z. , Stirzaker Clare , Bauer Denis C. , Qu Wenjia , Swarbrick Michael M. , Lutgers Helen L. , Lord Reginald V. , Samaras Katherine , Molloy Peter L. , Clark Susan J.
Published: July 2019

Adipocytes support key metabolic and endocrine functions of adipose tissue. Lipid is stored in two major classes of depots, namely visceral adipose (VA) and subcutaneous adipose (SA) depots. Increased visceral adiposity is associated with adverse health outcomes, whereas the impact of SA tissue is relatively metabolically benign. The precise molecular features associated with the functional differences between the adipose depots are still not well understood. Here, we characterised transcriptomes and methylomes of isolated adipocytes from matched SA and VA tissues of individuals with normal BMI to identify epigenetic differences and their contribution to cell type and depot-specific function. We found that DNA methylomes were notably distinct between different adipocyte depots and were associated with differential gene expression within pathways fundamental to adipocyte function. Most striking differential methylation was found at transcription factor and developmental genes. Our findings highlight the importance of developmental origins in the function of different fat depots.
Carotenoids from UV-resistant Antarctic Microbacterium sp. LEMMJ01
Authors: Reis-Mansur Maria Cristina P. P. , Cardoso-Rurr Janine S. , Silva Josemar V. Maiworm Abreu , de Souza Gabriela Rodrigues , Cardoso Verônica da Silva , Mansoldo Felipe Raposo Passos , Pinheiro Yuri , Schultz Júnia , Lopez Balottin Luciene B. , da Silva Antonio Jorge Ribeiro , Lage Claudia , dos Santos Elisabete Pereira , Rosado Alexandre Soares , Vermelho Alane Beatriz
Published: July 2019

The Microbacterium sp. LEMMJ01 isolated from Antarctic soil does not belong to any of the nearest species identified in the RDP database. Under UV radiation (A, B and C wavebands) the survival fractions of Microbacterium sp. cells were much higher compared with wild-type E. coli K12A15. Especially remarkable for an Antarctic bacterium, an expressive resistance against high UV-B doses was observed. The increased survival of DNA repair-proficient E. coli grown overnight added of 0.1 mg/ml or 1 mg/ml of the whole pigment extract produced by Microbacterium sp. revealed that part of the resistance of Microbacterium sp. against UV-B radiation seems to be connected with photoprotection by its pigments. Scanning electron microscopy revealed that UV-A and UV-B ensued membrane alterations only in E. coli. The APCI-MS fingerprints revealed the diagnostic ions for neurosporene (m/z 580, 566, 522, 538, and 524) synergism for the first time in this bacterium by HPLC-MS/MS analysis. Carotenoids also were devoid of phototoxicity and cytotoxicity effects in mouse cells and in human keratinocytes and fibroblasts.
Pancreatic alpha-cell mass in the early-onset and advanced stage of a mouse model of experimental autoimmune diabetes
Authors: Bru-Tari Eva , Cobo-Vuilleumier Nadia , Alonso-Magdalena Paloma , Dos Santos Reinaldo S. , Marroqui Laura , Nadal Angel , Gauthier Benoit R. , Quesada Ivan
Published: July 2019

Most studies in type 1 diabetes (T1D) have focused on the loss of the pancreatic beta-cell population. However, despite the involvement of the alpha-cell in the aetiology and complications of T1D, little is known about the regulation of the pancreatic alpha-cell mass in this disease. The need for a better understanding of this process is further emphasized by recent findings suggesting that alpha-cells may constitute a potential reservoir for beta-cell regeneration. In this study, we characterized the pancreatic alpha-cell mass and its regulatory processes in the transgenic RIP-B7.1 mice model of experimental autoimmune diabetes (EAD). Diabetic mice presented insulitis, hyperglycaemia, hypoinsulinemia and hyperglucagonemia along with lower pancreatic insulin content. While alpha-cell mass and pancreatic glucagon content were preserved at the early-onset of EAD, both parameters were reduced in the advanced phase. At both stages, alpha-cell size, proliferation and ductal neogenesis were up-regulated, whereas apoptosis was almost negligible. Interestingly, we found an increase in the proportion of glucagon-containing cells positive for insulin or the beta-cell transcription factor PDX1. Our findings suggest that pancreatic alpha-cell renewal mechanisms are boosted during the natural course of EAD, possibly as an attempt to maintain the alpha-cell population and/or to increase beta-cell regeneration via alpha-cell transdifferentiation.
In vivo magnetic resonance imaging of treatment-induced apoptosis
Authors: Jiang Xiaoyu , McKinley Eliot T. , Xie Jingping , Li Hua , Xu Junzhong , Gore John C.
Published: July 2019

Imaging apoptosis could provide an early and specific means to monitor tumor responses to treatment. To date, despite numerous attempts to develop molecular imaging approaches, there is still no widely-accepted and reliable method for in vivo imaging of apoptosis. We hypothesized that the distinct cellular morphologic changes associated with treatment-induced apoptosis, such as cell shrinkage, cytoplasm condensation, and DNA fragmentation, can be detected by temporal diffusion spectroscopy imaging (TDSI). Cetuximab-induced apoptosis was assessed in vitro and in vivo with cetuximab-sensitive (DiFi) and insensitive (HCT-116) human colorectal cancer cell lines by TDSI. TDSI findings were complemented by flow cytometry and immunohistochemistry. Cell cycle analysis and flow cytometry detected apoptotic cell shrinkage in cetuximab-treated DiFi cells, and significant apoptosis was confirmed by histology. TDSI-derived parameters quantified key morphological changes including cell size decreases during apoptosis in responsive tumors that occurred earlier than gross tumor volume regression. TDSI provides a unique measurement of apoptosis by identifying cellular characteristics, particularly cell shrinkage. The method will assist in understanding the underlying biology of solid tumors and predict tumor response to therapies. TDSI is free of any exogenous agent or radiation, and hence is very suitable to be incorporated into clinical applications.
Afterglow, TL and OSL properties of Mn2+-doped ZnGa2O4 phosphor
Authors: Luchechko Andriy , Zhydachevskyy Yaroslav , Ubizskii Sergii , Kravets Oleh , Popov Anatoli I. , Rogulis Uldis , Elsts Edgars , Bulur Enver , Suchocki Andrzej
Published: July 2019

Zinc gallate (ZnGa2O4) spinel ceramics doped with Mn2+ ions was prepared by a solid-state reaction at 1200 °C in air. Manganese concentration was equal to 0.05 mol.% of MnO with respect to ZnO. Ceramics produced in this way show an efficient green emission at about 505 nm under UV or X-ray excitations, which is caused by Mn2+ ions. This green emission is observed also as a relatively long afterglow (visible to the naked eye in the dark for about one hour) after switching-off the X-ray excitation. Time profiles of the beginning of glow and afterglow have been studied together with thermally stimulated (TSL) and optically stimulated (OSL) luminescence. Experimental results demonstrate a presence of few types of shallow and deep traps responsible for the observed afterglow and TSL/OSL emission of the material. The possibility of pulsed optical stimulation and time-resolved OSL characteristics of ZnGa2O4: Mn2+ has been reported for the first time. The presented results suggest the ZnGa2O4: Mn2+ spinel as a promising material for further fundamental research and possibility of application as a green long-lasting phosphor or storage phosphor for TSL/OSL radiation dosimetry.
Prolonged use of noninvasive positive pressure ventilation after extubation among patients in the intensive care unit following cardiac surgery: The predictors and its impact on patient outcome
Authors: Chen Pei-Ku , Shih Chun-Che , Lin Fang-Chi , Perng Diahn-Warng , Chou Kun-Ta , Kou Yu Ru , Ko Hsin-Kuo
Published: July 2019

This retrospective, observational cohort study aimed to determine the independent risk factors and impact of prolonged non-invasive positive pressure ventilation (NIPPV) after extubation among patients in the intensive care unit following cardiac surgery. Patients who received prophylactic NIPPV after extubation were categorized into prolonged (NIPPV duration >3 days, n = 83) and non-prolonged groups (NIPPV duration ≤3 days, n = 105). The perioperative characteristics and hospital outcomes were recorded. The multivariate analyses identified the preoperative residual volume/total lung capacity (RV/TLC) ratio (adjusted odds ratio [AOR]: 1.10; 95% CI:1.01–1.19,p = 0.022) and postoperative acute kidney injury (AKI) with Kidney Disease Improving Global Outcomes (KDIGO) stage 2–3, 48 h after surgery (AOR: 3.87; 95% CI:1.21–12.37,p = 0.023) as independent predictors of prolonged NIPPV. Patients with both RV/TLC ratio > 46.5% and KDIGO stage 2–3 showed a highly increased risk of prolonged NIPPV (HR 27.17,p = 0.010), which was in turn associated with higher risk of postoperative complications and prolonged ICU and hospital stays. Preoperative RV/TLC ratio and postoperative AKI could identify patients at higher risk for prolonged NIPPV associated with poor outcomes. These findings may allow early recognition of patients who are at a higher risk for prolonged NIPPV, and help refine the perioperative management and critical care.
The development of a novel SNP genotyping assay to differentiate cacao clones
Authors: De Wever Jocelyn , Everaert Helena , Coppieters Frauke , Rottiers Hayley , Dewettinck Koen , Lefever Steve , Messens Kathy
Published: July 2019

In this study, a double-mismatch allele-specific (DMAS) qPCR SNP genotyping method has been designed, tested and validated specifically for cacao, using 65 well annotated international cacao reference accessions retrieved from the Center for Forestry Research and Technology Transfer (CEFORTT) and the International Cocoa Quarantine Centre (ICQC). In total, 42 DMAS-qPCR SNP genotyping assays have been validated, with a 98.05% overall efficiency in calling the correct genotype. In addition, the test allowed for the identification of 15.38% off-types and two duplicates, highlighting the problem of mislabeling in cacao collections and the need for conclusive genotyping assays. The developed method showed on average a high genetic diversity (He = 0.416) and information index (I = 0.601), making it applicable to assess intra-population variation. Furthermore, only the 13 most informative markers were needed to achieve maximum differentiation. This simple, effective method provides robust and accurate genotypic data which allows for more efficient resource management (e.g. tackling mislabeling, conserving valuable genetic material, parentage analysis, genetic diversity studies), thus contributing to an increased knowledge on the genetic background of cacao worldwide. Notably, the described method can easily be integrated in other laboratories for a wide range of objectives and organisms.
Aqueous copper bioavailability linked to shipwreck-contaminated reef sediments
Authors: Hartland Adam , Zitoun Rebecca , Middag Rob , Sander Sylvia , Laferriere Alix , Saeed Huma , De Luca Sharon , Ross Philip M.
Published: July 2019

Pollution from the grounding or sinking of ships can have long lasting effects on the recovery and dynamics of coastal ecosystems. Research on the impact of copper (Cu) pollution from the 2011 MV Rena shipwreck at the Astrolabe Reef (Otaiti), New Zealand, 5 years after the grounding, followed a multi-method and multi-disciplinary approach. Three independent measures of aqueous Cu using trace-element-clean-techniques substantiate the presence of high total, total dissolved (<2 µm) and elevated bioavailable Cu in the water column immediately above the aft section of the wreck where the highest sedimentary load of Cu was located. Intermittently elevated concentrations of strong Cu-binding ligands occurred in this location, and their binding strength was consistent with ligands actively produced by organisms in response to Cu induced stress. The recruitment of benthic invertebrates was modified at the high-Cu location. Taxonomic groups usually considered robust to pollution were restricted to this site (e.g. barnacles) or were the most abundant taxa present (e.g. foraminifera). Our results demonstrate that Cu-contaminated sediments can impose a persistent point source of Cu pollution in high-energy reef environments, with the potential to modify the composition and recovery of biological communities.
Maternal fever during pregnancy and offspring attention deficit hyperactivity disorder
Authors: Gustavson Kristin , Ask Helga , Ystrom Eivind , Stoltenberg Camilla , Lipkin W. Ian , Surén Pål , Håberg Siri E. , Magnus Per , Knudsen Gun Peggy , Eilertsen Espen , Bresnahan Michaeline , Aase Heidi , Mjaaland Siri , Susser Ezra S. , Hornig Mady , Reichborn-Kjennerud Ted
Published: July 2019

Maternal fever during pregnancy is associated with several adverse child outcomes. We investigated associations between maternal fever and ADHD among offspring, as well as the sub-dimensions of ADHD - inattention and hyperactivity/impulsivity. Data came from the Norwegian Mother and Child Cohort Study, including more than 114,000 children. Information about children’s ADHD diagnoses was obtained from the Norwegian Patient Register. Mothers reported on inattention and hyperactivity/impulsivity symptoms in questionnaires at 8 years. Logistic regression analysis showed that children exposed to maternal fever in the first trimester received an ADHD diagnosis more often than unexposed children (Odds Ratio (OR) = 1.31, 95% confidence interval (CI) = 1.06–1.61). For children exposed twice or more in the first trimester, the OR was 2.64 (CI = 1.36–5.14). Linear regression analysis showed elevated inattention symptoms among children exposed to fever in the first (Cohen’s d = 0.09, CI = 0.03–0.15) and second (Cohen’s d = 0.05, CI = 0.01–0.09) trimester. Results were similar whether the mother had taken acetaminophen for their fever or not. Hyperactivity/impulsivity symptoms were not related to maternal fever. The results indicate that maternal fever in early pregnancy may be a risk factor for ADHD, and particularly for inattention problems. This risk is neither mitigated nor inflated by use of acetaminophen.