bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gravity Currents Facilitate Formation of High‐Frequency Internal Solitons and Bores at the Base of the Fraser Delta in the Southern Strait of Georgia
Authors: Thomson Richard E. , Spear David J. 
Published: October 2020

AbstractWe use velocity and acoustic backscatter records from downward looking acoustic Doppler current profilers moored 47 m above the seafloor, 20 km apart in water depths of 100 and 240 m to examine internal wave dynamics near the seabed in the southern Strait of Georgia. The observations reveal that the lower layer of the strait becomes a seasonal (wintertime) waveguide for energetic internal “solibores”—internal bores trailed by large‐amplitude internal solitons—that propagate up the flank of the Fraser Delta. The rotor‐like bores have shoreward bottom velocities of 0.2 m s−1 and vertical velocities of 0.05 m s−1; the trailing wave trains attain amplitudes of tens of meters, periods as short as 10 min and durations of several hours. Establishment of the seabed waveguide required to support the high‐frequency internal motions begins in summer, when gravity currents originating from the shallow (~100 m) Skipjack‐Java sill in neighboring Boundary Pass, descend deep into the strait at monthly intervals. During the ensuing winter, lower‐density gravity currents form over the sill and subsequently override the denser bottom layer in the strait, increasing the buoyancy frequency of the guide. Based on the direction of solibore propagation, we speculate that the winter gravity currents also initiate generation of the internal waves during their descent over the rapidly deepening seafloor leading to the central strait. We further propose that the solibores are contributing to the formation and/or shoreward propagation of the O(10) m‐high sediment waves found on the delta foreslope.
Secure optical communication using a quantum alarm
Authors: Gong Yupeng , Kumar Rupesh , Wonfor Adrian , Ren Shengjun , Penty Richard V. , White Ian H. 
Published: October 2020

AbstractOptical fibre networks are advancing rapidly to meet growing traffic demands. Security issues, including attack management, have become increasingly important for optical communication networks because of the vulnerabilities associated with tapping light from optical fibre links. Physical layer security often requires restricting access to channels and periodic inspections of link performance. In this paper, we report how quantum communication techniques can be utilized to detect a physical layer attack. We present an efficient method for monitoring the physical layer security of a high-data-rate classical optical communication network using a modulated continuous-variable quantum signal. We describe the theoretical and experimental underpinnings of this monitoring system and the monitoring accuracy for different monitored parameters. We analyse its performance for both unamplified and amplified optical links. The technique represents a novel approach for applying quantum signal processing to practical optical communication networks and compares well with classical monitoring methods. We conclude by discussing the challenges facing its practical application, its differences with respect to existing quantum key distribution methods, and its usage in future secure optical transport network planning.
The mammalian target of rapamycin (mTOR) kinase mediates haloperidol-induced cataleptic behavior
Authors: Ramírez-Jarquín Uri Nimrod , Shahani Neelam , Pryor William , Usiello Alessandro , Subramaniam Srinivasa 
Published: October 2020

AbstractThe mammalian target of rapamycin (mTOR) is a ubiquitously expressed serine/threonine kinase protein complex (mTORC1 or mTORC2) that orchestrates diverse functions ranging from embryonic development to aging. However, its brain tissue-specific roles remain less explored. Here, we have identified that the depletion of the mTOR gene in the mice striatum completely prevented the extrapyramidal motor side effects (catalepsy) induced by the dopamine 2 receptor (D2R) antagonist haloperidol, which is the most widely used typical antipsychotic drug. Conversely, a lack of striatal mTOR in mice did not affect catalepsy triggered by the dopamine 1 receptor (D1R) antagonist SCH23390. Along with the lack of cataleptic effects, the administration of haloperidol in mTOR mutants failed to increase striatal phosphorylation levels of ribosomal protein pS6 (S235/236) as seen in control animals. To confirm the observations of the genetic approach, we used a pharmacological method and determined that the mTORC1 inhibitor rapamycin has a profound influence upon post-synaptic D2R-dependent functions. We consistently found that pretreatment with rapamycin entirely prevented (in a time-dependent manner) the haloperidol-induced catalepsy, and pS6K (T389) and pS6 (S235/236) signaling upregulation, in wild-type mice. Collectively, our data indicate that striatal mTORC1 blockade may offer therapeutic benefits with regard to the prevention of D2R-dependent extrapyramidal motor side effects of haloperidol in psychiatric illness.
Polygenic risk score, psychosocial environment and the risk of attention-deficit/hyperactivity disorder
Authors: Østergaard Søren D. , Trabjerg Betina B. , Als Thomas D. , Climent Clara Albiñana , Privé Florian , Vilhjálmsson Bjarni Jóhann , Bækvad-Hansen Marie , Bybjerg-Grauholm Jonas , Hougaard David M. , Nordentoft Merete , Werge Thomas , Demontis Ditte , Mortensen Preben B. , Børglum Anders D. , Mors Ole , Agerbo Esben 
Published: October 2020

AbstractThe objective of the present study was to investigate whether the polygenic liability for attention-deficit/hyperactivity disorder (ADHD) and the psychosocial environment impact the risk of ADHD in interaction or independently of each other. We conducted a register- and biobank-based cohort study of 13,725 individuals with ADHD and 20,147 randomly drawn population-based controls. These 33,872 cohort members were genotyped on the Infinium PsychChip v1.0 array (Illumina). Subsequently, we calculated the polygenic risk score (PRS) for ADHD and extracted register data regarding the following risk factors pertaining to the psychosocial environment for each cohort member at the time of birth: maternal/paternal history of mental disorders, maternal/paternal education, maternal/paternal work status, and maternal/paternal income. We used logistic regression analyses to assess the main effects of the PRS for ADHD and the psychosocial environment on the risk of ADHD. Subsequently, we evaluated whether the effect of the PRS and the psychosocial environment act independently or in interaction upon the risk of ADHD. We found that ADHD was strongly associated with the PRS (odds ratio: 6.03, 95%CI: 4.74–7.70 for highest vs. lowest 2% liability). All risk factors pertaining to the psychosocial environment were associated with an increased risk of ADHD. These associations were only slightly attenuated after mutual adjustments. We found no statistically significant interaction between the polygenic liability and the psychosocial environment upon the risk of ADHD. In conclusion, we found main effects of both polygenic liability and risk factors pertaining to the psychosocial environment on the risk of ADHD—in the expected direction.
Epigenetic silencing of CDKN1A and CDKN2B by SNHG1 promotes the cell cycle, migration and epithelial-mesenchymal transition progression of hepatocellular carcinoma
Authors: Li Bei , Li Ang , You Zhen , Xu Jingchang , Zhu Sha 
Published: October 2020

AbstractEnhanced SNHG1 (small nucleolar RNA host gene 1) expression has been found to play a critical role in the initiation and progression of hepatocellular carcinoma (HCC) with its detailed mechanism largely unknown. In this study, we show that SNHG1 promotes the HCC progression through epigenetically silencing CDKN1A and CDKN2B in the nucleus, and competing with CDK4 mRNA for binding miR-140-5p in the cytoplasm. Using bioinformatics analyses, we found hepatocarcinogenesis is particularly associated with dysregulated expression of SNHG1 and activation of the cell cycle pathway. SNHG1 was upregulated in HCC tissues and cells, and its knockdown significantly inhibited HCC cell cycle, growth, metastasis, and epithelial–mesenchymal transition (EMT) both in vitro and in vivo. Chromatin immunoprecipitation and RNA immunoprecipitation assays demonstrate that SNHG1 inhibit the transcription of CDKN1A and CDKN2B through enhancing EZH2 mediated-H3K27me3 in the promoter of CDKN1A and CDKN2B, thus resulting in the de-repression of the cell cycle. Dual-luciferase assay and RNA pulldown revealed that SNHG1 promotes the expression of CDK4 by competitively binding to miR-140-5p. In conclusion, we propose that SNHG1 formed a regulatory network to confer an oncogenic function in HCC and SNHG1 may serve as a potential target for HCC diagnosis and treatment.
Real-world data from a molecular tumor board demonstrates improved outcomes with a precision N-of-One strategy
Authors: Kato Shumei , Kim Ki Hwan , Lim Hyo Jeong , Boichard Amelie , Nikanjam Mina , Weihe Elizabeth , Kuo Dennis J. , Eskander Ramez N. , Goodman Aaron , Galanina Natalie , Fanta Paul T. , Schwab Richard B. , Shatsky Rebecca , Plaxe Steven C. , Sharabi Andrew , Stites Edward , Adashek Jacob J. , Okamura Ryosuke , Lee Suzanna , Lippman Scott M. , Sicklick Jason K. , Kurzrock Razelle 
Published: October 2020

AbstractNext-generation sequencing (NGS) can identify novel cancer targets. However, interpreting the molecular findings and accessing drugs/clinical trials is challenging. Furthermore, many tumors show resistance to monotherapies. To implement a precision strategy, we initiated a multidisciplinary (basic/translational/clinical investigators, bioinformaticians, geneticists, and physicians from multiple specialties) molecular tumor board (MTB), which included a project manager to facilitate obtaining clinical-grade biomarkers (blood/tissue NGS, specific immunohistochemistry/RNA expression including for immune-biomarkers, per physician discretion) and medication-acquisition specialists/clinical trial coordinators/navigators to assist with medication access. The MTB comprehensively reviewed patient characteristics to develop N-of-One treatments implemented by the treating physician’s direction under the auspices of a master protocol. Overall, 265/429 therapy-evaluable patients (62%) were matched to ≥1 recommended drug. Eighty-six patients (20%) matched to all drugs recommended by MTB, including combinatorial approaches, while 38% received physician’s choice regimen, generally with unmatched approach/low degree of matching. Our results show that patients who receive MTB-recommended regimens (versus physician choice) have significantly longer progression-free (PFS) and overall survival (OS), and are better matched to therapy. High (≥50%) versus low (<50%) Matching Score therapy (roughly reflecting therapy matched to ≥50% versus <50% of alterations) independently correlates with longer PFS (hazard ratio [HR], 0.63; 95% confidence interval [CI], 0.50–0.80;P < 0.001) and OS (HR, 0.67; 95% CI, 0.50–0.90;P = 0.007) and higher stable disease ≥6 months/partial/complete remission rate (52.1% versus 30.4%P < 0.001) (all multivariate). In conclusion, patients who receive MTB-based therapy are better matched to their genomic alterations, and the degree of matching is an independent predictor of improved oncologic outcomes including survival.
Exploiting two-dimensional morphology of molybdenum oxycarbide to enable efficient catalytic dry reforming of methane
Authors: Kurlov Alexey , Deeva Evgeniya B. , Abdala Paula M. , Lebedev Dmitry , Tsoukalou Athanasia , Comas-Vives Aleix , Fedorov Alexey , Müller Christoph R. 
Published: October 2020

AbstractThe two-dimensional morphology of molybdenum oxycarbide (2D-Mo2COx) nanosheets dispersed on silica is found vital for imparting high stability and catalytic activity in the dry reforming of methane. Here we report that owing to the maximized metal utilization, the specific activity of 2D-Mo2COx/SiO2 exceeds that of other Mo2C catalysts by ca. 3 orders of magnitude. 2D-Mo2COx is activated by CO2, yielding a surface oxygen coverage that is optimal for its catalytic performance and a Mo oxidation state of ca. +4. According to ab initio calculations, the DRM proceeds on Mo sites of the oxycarbide nanosheet with an oxygen coverage of 0.67 monolayer. Methane activation is the rate-limiting step, while the activation of CO2 and the C–O coupling to form CO are low energy steps. The deactivation of 2D-Mo2COx/SiO2 under DRM conditions can be avoided by tuning the contact time, thereby preventing unfavourable oxygen surface coverages.
Solid state chemistry for developing better metal-ion batteries
Authors: Abakumov Artem M. , Fedotov Stanislav S. , Antipov Evgeny V. , Tarascon Jean-Marie 
Published: October 2020

AbstractMetal-ion batteries are key enablers in today’s transition from fossil fuels to renewable energy for a better planet with ingeniously designed materials being the technology driver. A central question remains how to wisely manipulate atoms to build attractive structural frameworks of better electrodes and electrolytes for the next generation of batteries. This review explains the underlying chemical principles and discusses progresses made in the rational design of electrodes/solid electrolytes by thoroughly exploiting the interplay between composition, crystal structure and electrochemical properties. We highlight the crucial role of advanced diffraction, imaging and spectroscopic characterization techniques coupled with solid state chemistry approaches for improving functionality of battery materials opening emergent directions for further studies.
Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera
Authors: Song Hojun , Béthoux Olivier , Shin Seunggwan , Donath Alexander , Letsch Harald , Liu Shanlin , McKenna Duane D. , Meng Guanliang , Misof Bernhard , Podsiadlowski Lars , Zhou Xin , Wipfler Benjamin , Simon Sabrina 
Published: October 2020

AbstractAcoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific and dynamic patterns of evolution for hearing and sound producing organs. In the suborder Ensifera, we infer that forewing-based stridulation and tibial tympanal ears co-evolved, but in the suborder Caelifera, abdominal tympanal ears first evolved in a non-sexual context, and later co-opted for sexual signalling when sound producing organs evolved. However, we find little evidence that the evolution of hearing and sound producing organs increased diversification rates in those lineages with known acoustic communication.
A compendium of DNA-binding specificities of transcription factors in Pseudomonas syringae
Authors: Fan Ligang , Wang Tingting , Hua Canfeng , Sun Wenju , Li Xiaoyu , Grunwald Lucas , Liu Jingui , Wu Nan , Shao Xiaolong , Yin Yimeng , Yan Jian , Deng Xin 
Published: October 2020

AbstractPseudomonas syringae is a Gram-negative and model pathogenic bacterium that causes plant diseases worldwide. Here, we set out to identify binding motifs for all 301 annotated transcription factors (TFs) of P. syringae using HT-SELEX. We successfully identify binding motifs for 100 TFs. We map functional interactions between the TFs and their targets in virulence-associated pathways, and validate many of these interactions and functions using additional methods such as ChIP-seq, electrophoretic mobility shift assay (EMSA), RT-qPCR, and reporter assays. Our work identifies 25 virulence-associated master regulators, 14 of which had not been characterized as TFs before.
Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides
Authors: Tani Kazutoshi , Kanno Ryo , Makino Yuki , Hall Malgorzata , Takenouchi Mizuki , Imanishi Michie , Yu Long-Jiang , Overmann Jörg , Madigan Michael T. , Kimura Yukihiro , Mizoguchi Akira , Humbel Bruno M. , Wang-Otomo Zheng-Yu 
Published: October 2020

AbstractThe light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption for any bacteriochlorophyll (BChl) a-containing species. Here we present a cryo-EM structure of the strain 970 LH1-RC complex at 2.82 Å resolution. The LH1 forms a closed ring structure composed of sixteen pairs of the αβ-polypeptides. Sixteen Ca ions are present in the LH1 C-terminal domain and are coordinated by residues from the αβ-polypeptides that are hydrogen-bonded to BChl a. The Ca2+-facilitated hydrogen-bonding network forms the structural basis of the unusual LH1 redshift. The structure also revealed the arrangement of multiple forms of α- and β-polypeptides in an individual LH1 ring. Such organization indicates a mechanism of interplay between the expression and assembly of the LH1 complex that is regulated through interactions with the RC subunits inside.
D-serine mitigates cell loss associated with temporal lobe epilepsy
Authors: Beesley Stephen , Sullenberger Thomas , Crotty Kathryn , Ailani Roshan , D’Orio Cameron , Evans Kimberly , Ogunkunle Emmanuel O. , Roper Michael G. , Kumar Sanjay S. 
Published: October 2020

AbstractTemporal lobe epilepsy (TLE) is the most common type of drug-resistant epilepsy in adults, with an unknown etiology. A hallmark of TLE is the characteristic loss of layer 3 neurons in the medial entorhinal area (MEA) that underlies seizure development. One approach to intervention is preventing loss of these neurons through better understanding of underlying pathophysiological mechanisms. Here, we show that both neurons and glia together give rise to the pathology that is mitigated by the amino acid D-serine whose levels are potentially diminished under epileptic conditions. Focal administration of D-serine to the MEA attenuates neuronal loss in this region thereby preventing epileptogenesis in an animal model of TLE. Additionally, treatment with D-serine reduces astrocyte counts in the MEA, alters their reactive status, and attenuates proliferation and/or infiltration of microglia to the region thereby curtailing the deleterious consequences of neuroinflammation. Given the paucity of compounds that reduce hyperexcitability and neuron loss, have anti-inflammatory properties, and are well tolerated by the brain, D-serine, an endogenous amino acid, offers new hope as a therapeutic agent for refractory TLE.
A defect-resistant Co–Ni superalloy for 3D printing
Authors: Murray Sean P. , Pusch Kira M. , Polonsky Andrew T. , Torbet Chris J. , Seward Gareth G. E. , Zhou Ning , Forsik Stéphane A. J. , Nandwana Peeyush , Kirka Michael M. , Dehoff Ryan R. , Slye William E. , Pollock Tresa M. 
Published: October 2020

AbstractAdditive manufacturing promises a major transformation of the production of high economic value metallic materials, enabling innovative, geometrically complex designs with minimal material waste. The overarching challenge is to design alloys that are compatible with the unique additive processing conditions while maintaining material properties sufficient for the challenging environments encountered in energy, space, and nuclear applications. Here we describe a class of high strength, defect-resistant 3D printable superalloys containing approximately equal parts of Co and Ni along with Al, Cr, Ta and W that possess strengths in excess of 1.1 GPa in as-printed and post-processed forms and tensile ductilities of greater than 13% at room temperature. These alloys are amenable to crack-free 3D printing via electron beam melting (EBM) with preheat as well as selective laser melting (SLM) with limited preheat. Alloy design principles are described along with the structure and properties of EBM and SLM CoNi-base materials.
Early prediction of disease progression in COVID-19 pneumonia patients with chest CT and clinical characteristics
Authors: Feng Zhichao , Yu Qizhi , Yao Shanhu , Luo Lei , Zhou Wenming , Mao Xiaowen , Li Jennifer , Duan Junhong , Yan Zhimin , Yang Min , Tan Hongpei , Ma Mengtian , Li Ting , Yi Dali , Mi Ze , Zhao Huafei , Jiang Yi , He Zhenhu , Li Huiling , Nie Wei , Liu Yin , Zhao Jing , Luo Muqing , Liu Xuanhui , Rong Pengfei , Wang Wei 
Published: October 2020

AbstractThe outbreak of coronavirus disease 2019 (COVID-19) has rapidly spread to become a worldwide emergency. Early identification of patients at risk of progression may facilitate more individually aligned treatment plans and optimized utilization of medical resource. Here we conducted a multicenter retrospective study involving patients with moderate COVID-19 pneumonia to investigate the utility of chest computed tomography (CT) and clinical characteristics to risk-stratify the patients. Our results show that CT severity score is associated with inflammatory levels and that older age, higher neutrophil-to-lymphocyte ratio (NLR), and CT severity score on admission are independent risk factors for short-term progression. The nomogram based on these risk factors shows good calibration and discrimination in the derivation and validation cohorts. These findings have implications for predicting the progression risk of COVID-19 pneumonia patients at the time of admission. CT examination may help risk-stratification and guide the timing of admission.
Bacterial nanotubes as a manifestation of cell death
Authors: Pospíšil Jiří , Vítovská Dragana , Kofroňová Olga , Muchová Katarína , Šanderová Hana , Hubálek Martin , Šiková Michaela , Modrák Martin , Benada Oldřich , Barák Imrich , Krásný Libor 
Published: October 2020

AbstractBacterial nanotubes are membranous structures that have been reported to function as conduits between cells to exchange DNA, proteins, and nutrients. Here, we investigate the morphology and formation of bacterial nanotubes using Bacillus subtilis. We show that nanotube formation is associated with stress conditions, and is highly sensitive to the cells’ genetic background, growth phase, and sample preparation methods. Remarkably, nanotubes appear to be extruded exclusively from dying cells, likely as a result of biophysical forces. Their emergence is extremely fast, occurring within seconds by cannibalizing the cell membrane. Subsequent experiments reveal that cell-to-cell transfer of non-conjugative plasmids depends strictly on the competence system of the cell, and not on nanotube formation. Our study thus supports the notion that bacterial nanotubes are a post mortem phenomenon involved in cell disintegration, and are unlikely to be involved in cytoplasmic content exchange between live cells.