bluuebunny/crossref_metadata_2025_split huggingface dataset:
Joint Effects of Extrinsic Biophysical Fluxes and Intrinsic Hydrodynamics on the Formation of Hypoxia West off the Pearl River Estuary
Authors: Lu Zhongming , Gan Jianping , Dai Minhan , Liu Hongbin , Zhao Xiaozheng 
Published: August 2018

AbstractUsing field measurements and a process‐oriented three‐dimensional coupled physical‐biogeochemical numerical model, we investigated the physical and biogeochemical processes governing the bottom hypoxic zone west off the Pearl River estuary. The intensity and area of the hypoxia grew with increasing total nutrient input from the Pearl River that has increased continuously in recent decades. The hypoxic zone was formed and maintained largely associated with the stable water column where the stability was provided simultaneously by wind stress and freshwater discharge, favorable local hydrodynamics for flow convergence, and westward organic matter transport. Wind stress altered the stratification, while freshwater discharge changed the stratification and baroclinic velocity shear simultaneously. Two‐layered flow with a cyclonically rotating current around a coastal salient edge of the western shelf off the estuary hydrodynamically enhanced the local convergence, allowing sufficient residence time in the bottom for the remineralization of organic matter produced in the hypoxic zone and organic matter transported into the region. Our results suggest that a combination of unique local hydrodynamic feature and decomposition of organic matter in water column (and possibly in the sediment) are the cause of the formation and maintenance of the bottom hypoxia on the western shelf of the estuary during summer.
Longitudinal and Seasonal Variability of Equatorial Ionospheric Irregularities and Electrodynamics
Authors: Yizengaw Endawoke , Groves Keith M. 
Published: August 2018

AbstractOver the past decades significant progresses have been done to understand the origin of seeding mechanisms of ionospheric irregularities. However, characterization of the global ionospheric irregularities as a function of local time, longitude, and season is still a challenge for the modeling community. In this review paper, using multiinstrument observations, we investigated the global irregularity distribution and its possible drivers that control the longitudinal and seasonal dependences. We demonstrated that forcing from lower thermosphere, like the localized tropospheric gravity waves seeding, may be responsible for the formation of strong longitudinal dependence of irregularity distribution. The location of Intertropical Convergence Zone that generate forceful thunderstorms and become favorable location for the launch of localized gravity waves may play an important role in the longitudinal dependence of irregularity distribution. Hence, incorporating the Intertropical Convergence Zone location into density irregularity modeling effort may provide important information to understand and characterize the longitudinal variability of irregularity distributions.
Revealing circadian mechanisms of integration and resilience by visualizing clock proteins working in real time
Authors: Mori Tetsuya , Sugiyama Shogo , Byrne Mark , Johnson Carl Hirschie , Uchihashi Takayuki , Ando Toshio 
Published: August 2018

AbstractThe circadian clock proteins KaiA, KaiB, and KaiC reconstitute a remarkable circa-24 h oscillation of KaiC phosphorylation that persists for many days in vitro. Here we use high-speed atomic force microscopy (HS-AFM) to visualize in real time and quantify the dynamic interactions of KaiA with KaiC on sub-second timescales. KaiA transiently interacts with KaiC, thereby stimulating KaiC autokinase activity. As KaiC becomes progressively more phosphorylated, KaiA’s affinity for KaiC weakens, revealing a feedback of KaiC phosphostatus back onto the KaiA-binding events. These non-equilibrium interactions integrate high-frequency binding and unbinding events, thereby refining the period of the longer term oscillations. Moreover, this differential affinity phenomenon broadens the range of Kai protein stoichiometries that allow rhythmicity, explaining how the oscillation is resilient in an in vivo milieu that includes noise. Therefore, robustness of rhythmicity on a 24-h scale is explainable by molecular events occurring on a scale of sub-seconds.
Diverse Cretaceous larvae reveal the evolutionary and behavioural history of antlions and lacewings
Authors: Badano Davide , Engel Michael S. , Basso Andrea , Wang Bo , Cerretti Pierfilippo 
Published: August 2018

AbstractMyrmeleontiformia are an ancient group of lacewing insects characterized by predatory larvae with unusual morphologies and behaviours. Mostly soil dwellers with a soft cuticle, their larvae fossilize only as amber inclusions, and thus their fossil record is remarkably sparse. Here, we document a disparate assemblage of myrmeleontiform larvae from the mid-Cretaceous amber (99 Ma) of Myanmar, evidence of a considerable diversification. Our cladistic analysis integrating extant and extinct taxa resolves the fossils as both stem- and crown-groups. Similarities between extinct and extant species permit inferences of larval ethology of the fossil species through statistical correlation analyses with high support, implying that morphological disparity matched behavioural diversity. An improved understanding of the evolutionary history of antlions and relatives supports the conclusion that hunting strategies, such as camouflage and fossoriality, were acquired early within the lineage.
Gating mechanism of the extracellular entry to the lipid pathway in a TMEM16 scramblase
Authors: Lee Byoung-Cheol , Khelashvili George , Falzone Maria , Menon Anant K. , Weinstein Harel , Accardi Alessio 
Published: August 2018

AbstractMembers of the TMEM16/ANO family of membrane proteins are Ca2+-activated phospholipid scramblases and/or Cl− channels. A membrane-exposed hydrophilic groove in these proteins serves as a shared translocation pathway for ions and lipids. However, the mechanism by which lipids gain access to and permeate through the groove remains poorly understood. Here, we combine quantitative scrambling assays and molecular dynamic simulations to identify the key steps regulating lipid movement through the groove. Lipid scrambling is limited by two constrictions defined by evolutionarily conserved charged and polar residues, one extracellular and the other near the membrane mid-point. The region between these constrictions is inaccessible to lipids and water molecules, suggesting that the groove is in a non-conductive conformation. A sequence of lipid-triggered reorganizations of interactions between these residues and the permeating lipids propagates from the extracellular entryway to the central constriction, allowing the groove to open and coordinate the headgroups of transiting lipids.
Spatially similar surface energy flux perturbations due to greenhouse gases and aerosols
Authors: Persad Geeta G. , Ming Yi , Shen Zhaoyi , Ramaswamy V. 
Published: August 2018

AbstractDespite distinct geographic distributions of top-of-the-atmosphere radiative forcing, anthropogenic greenhouse gases and aerosols have been found to produce similar patterns of climate response in atmosphere-and-ocean coupled climate model simulations. Understanding surface energy flux changes, a crucial pathway by which atmospheric forcing is communicated to the ocean, is a vital bridge to explaining the similar full atmosphere-and-ocean responses to these disparate forcings. Here we analyze the fast, atmosphere-driven change in surface energy flux caused by present-day greenhouse gases vs aerosols to elucidate its role in shaping the subsequent slow, coupled response. We find that the surface energy flux response patterns achieve roughly two-thirds of the anti-correlation seen in the fully coupled response, driven by Rossby waves excited by symmetric changes to the land–sea contrast. Our results suggest that atmosphere and land surface processes are capable of achieving substantial within-hemisphere homogenization in the climate response to disparate forcers on fast, societally-relevant timescales.
Confined small-sized cobalt catalysts stimulate carbon-chain growth reversely by modifying ASF law of Fischer–Tropsch synthesis
Authors: Cheng Qingpeng , Tian Ye , Lyu Shuaishuai , Zhao Na , Ma Kui , Ding Tong , Jiang Zheng , Wang Lihua , Zhang Jing , Zheng Lirong , Gao Fei , Dong Lin , Tsubaki Noritatsu , Li Xingang 
Published: August 2018

AbstractFischer–Tropsch synthesis (FTS) is a promising technology to convert syngas derived from non-petroleum-based resources to valuable chemicals or fuels. Selectively producing target products will bring great economic benefits, but unfortunately it is theoretically limited by Anderson–Schulz–Flory (ASF) law. Herein, we synthesize size-uniformed cobalt nanocrystals embedded into mesoporous SiO2 supports, which is likely the structure of water-melon seeds inside pulps. We successfully tune the selectivity of products from diesel-range hydrocarbons (66.2%) to gasoline-range hydrocarbons (62.4%) by controlling the crystallite sizes of confined cobalt from 7.2 to 11.4 nm, and modify the ASF law. Generally, larger Co crystallites increase carbon-chain growth, producing heavier hydrocarbons. But here, we interestingly observe a reverse phenomenon: the uniformly small-sized cobalt crystallites can strongly adsorb active C* species, and the confined structure will inhibit aggregation of cobalt crystallites and escape of reaction intermediates in FTS, inducing the higher selectivity towards heavier hydrocarbons.
The tyrosine phosphatase SHP2 controls TGFβ-induced STAT3 signaling to regulate fibroblast activation and fibrosis
Authors: Zehender Ariella , Huang Jingang , Györfi Andrea-Hermina , Matei Alexandru-Emil , Trinh-Minh Thuong , Xu Xiaohan , Li Yi-Nan , Chen Chih-Wei , Lin Jianping , Dees Clara , Beyer Christian , Gelse Kolja , Zhang Zhong-Yin , Bergmann Christina , Ramming Andreas , Birchmeier Walter , Distler Oliver , Schett Georg , Distler Jörg H. W. 
Published: August 2018

AbstractUncontrolled activation of TGFβ signaling is a common denominator of fibrotic tissue remodeling. Here we characterize the tyrosine phosphatase SHP2 as a molecular checkpoint for TGFβ-induced JAK2/STAT3 signaling and as a potential target for the treatment of fibrosis. TGFβ stimulates the phosphatase activity of SHP2, although this effect is in part counterbalanced by inhibitory effects on SHP2 expression. Stimulation with TGFβ promotes recruitment of SHP2 to JAK2 in fibroblasts with subsequent dephosphorylation of JAK2 at Y570 and activation of STAT3. The effects of SHP2 on STAT3 activation translate into major regulatory effects of SHP2 on fibroblast activation and tissue fibrosis. Genetic or pharmacologic inactivation of SHP2 promotes accumulation of JAK2 phosphorylated at Y570, reduces JAK2/STAT3 signaling, inhibits TGFβ-induced fibroblast activation and ameliorates dermal and pulmonary fibrosis. Given the availability of potent SHP2 inhibitors, SHP2 might thus be a potential target for the treatment of fibrosis.
The Streptococcus pyogenes fibronectin/tenascin-binding protein PrtF.2 contributes to virulence in an influenza superinfection
Authors: Herrera Andrea L. , Faal Haddy , Moss Danielle , Addengast Leslie , Fanta Lauren , Eyster Kathleen , Huber Victor C. , Chaussee Michael S. 
Published: August 2018

AbstractInfluenza A virus (IAV) and Streptococcus pyogenes (the group A Streptococcus; GAS) are important contributors to viral-bacterial superinfections, which result from incompletely defined mechanisms. We identified changes in gene expression following IAV infection of A549 cells. Changes included an increase in transcripts encoding proteins with fibronectin-type III (FnIII) domains, such as fibronectin (Fn), tenascin N (TNN), and tenascin C (TNC). We tested the idea that increased expression of TNC may affect the outcome of an IAV-GAS superinfection. To do so, we created a GAS strain that lacked the Fn-binding protein PrtF.2. We found that the wild-type GAS strain, but not the mutant, co-localized with TNC and bound to purified TNC. In addition, adherence of the wild-type strain to IAV-infected A549 cells was greater compared to the prtF.2 mutant. The wild-type strain was also more abundant in the lungs of mice 24 hours after superinfection compared to the mutant strain. Finally, all mice infected with IAV and the prtF.2 mutant strain survived superinfection compared to only 42% infected with IAV and the parental GAS strain, indicating that PrtF.2 contributes to virulence in a murine model of IAV-GAS superinfection.
A rock physics modelling algorithm for simulating the elastic parameters of shale using well logging data
Authors: Wang Bing , Chen Yurong , Lu Jing , Jin Wujun 
Published: August 2018

AbstractAs a high-resolution geophysical method employed by the oil and gas industry, well logging can be used to accurately investigate reservoirs. Challenges associated with shale gas reservoir exploration increase the importance of applying elastic parameters or velocity at the logging scale. An efficient shale rock physics model is the foundation for the successful application of this method. We propose a procedure for modelling shale rock physics in which an appropriate modelling method is applied for different compositions of shale rock. The stiffnesses of the kerogen and fluid (oil, gas or water) mixture are obtained with the Kuster-Toksöz model, which assumes that the fluid is included in the kerogen matrix. A self-consistent approximation method is used to model clay, where the clay pores are filled with formation water. The Backus averaging model is then used to simulate the influence of laminated clay and laminated kerogen. Elastic parameter simulations using well logging data show the importance of treating the volume fractions of laminated clay and kerogen carefully. A comparison of the measured compressional slowness and modelled compressional slowness shows the efficiency of the proposed modelling procedure.
Electrochemical metallization cell with solid phase tunable Ge2Sb2Te5 electrolyte
Authors: Zhang Ziyang , Wang Yaoyuan , Wang Guanghan , Mu Jiaming , Ma Mingyuan , He Yuhan , Yang Rongrong , Li Huanglong 
Published: August 2018

AbstractElectrochemical metallization (ECM) cell kinetics are strongly determined by the electrolyte and can hardly be altered after the cell has been fabricated. Solid-state property tunable electrolytes in response to external stimuli are therefore desirable to introduce additional operational degree of freedom to the ECM cells, enabling novel applications such as multistate memory and reconfigurable computation. In this work, we use Ge2Sb2Te5(GST) as the electrolyte material whose solid state is switched from the amorphous(a) to the crystalline(c) phase thermally. Electrical heating too is readily achievable. The resistive switching characteristics of the cells with different GST phases are examined. The magnitude of the high resistance, the SET voltage and the on/off ratio are found to be considerably affected by the solid phase of GST, whereas the magnitude of the low resistance is least affected. Moreover, a transition from volatile to nonvolatile SET switching is only observed for c-GST based cell under prolonged voltage sweep, but not for a-GST based cell. This work provides a springboard for more studies on the manipulation of the ECM cell kinetics by tunable electrolyte and the resulting unprecedented device functionalities.
Multi-marker metabarcoding approach to study mesozooplankton at basin scale
Authors: Stefanni Sergio , Stanković David , Borme Diego , de Olazabal Alessandra , Juretić Tea , Pallavicini Alberto , Tirelli Valentina 
Published: August 2018

AbstractZooplankton plays a pivotal role in marine ecosystems and the characterisation of its biodiversity still represents a challenge for marine ecologists. In this study, mesozooplankton composition from 46 samples collected in summer along the western Adriatic Sea, was retrieved by DNA metabarcoding analysis. For the first time, the highly variable fragments of the mtDNA COI and the V9 region of 18S rRNA genes were used in a combined matrix to compile an inventory of mesozooplankton at basin scale. The number of sequences retrieved after quality filtering were 824,148 and 223,273 for COI and 18S (V9), respectively. The taxonomical assignment against reference sequences, using 95% (for COI) and 97% (for 18S) similarity thresholds, recovered 234 taxa. NMDS plots and cluster analysis divided coastal from offshore samples and the most representative species of these clusters were distributed according to the dominant surface current pattern of the Adriatic for the summer period. For selected sampling sites, mesozooplankton species were also identified under a stereo microscope providing insights on the strength and weakness of the two approaches. In addition, DNA metabarcoding was shown to be helpful for the monitoring of non-indigenous marine metazoans and spawning areas of commercial fish species. We defined pros and cons of applying this approach at basin scale and the benefits of combining the datasets from two genetic markers.
Laplace-domain diffuse optical measurement
Authors: Hasnain Ali , Mehta Kalpesh , Zhou Xiaowei , Li Hongsheng , Chen Nanguang 
Published: August 2018

AbstractTime-domain diffuse optical measurement systems determine depth-resolved absorption changes by using the time of flight distribution of the detected photons. It is well known that certain feature data, such as the Laplace transform of the temporal point spread function, is sufficient for image reconstruction and diffuse optical sensing. Conventional time-domain systems require the acquisition of full temporal profiles of diffusive photons and then numerically compute the feature dataset, for example, Laplace transformed intensities for imaging applications. We have proposed a novel method for directly obtaining the Laplace transform data. Our approach can significantly improve the data acquisition speed for time-domain diffuse optical imaging. We also demonstrated that the use of negative Laplace parameters can provide enhanced sensitivity to perturbations located in deep regions.
A cancer vaccine approach for personalized treatment of Lynch Syndrome
Authors: Majumder Snigdha , Shah Rakshit , Elias Jisha , Manoharan Malini , Shah Priyanka , Kumari Anjali , Chakraborty Papia , Kode Vasumathi , Mistry Yogesh , Coral Karunakaran , Mittal Bharti , SM Sakthivel Murugan , Mahadevan Lakshmi , Gupta Ravi , Chaudhuri Amitabha , Khanna-Gupta Arati 
Published: August 2018

AbstractLynch syndrome (LS) is a cancer predisposition disorder wherein patients have a 70–80% lifetime risk of developing colorectal cancers (CRC). Finding germline mutations in predisposing genes allows for risk assessment of CRC development. Here we report a germline heterozygous frame-shift mutation in the mismatch repair MLH1 gene which was identified in members of two unrelated LS families. Since defects in DNA mismatch repair genes generate frame-shift mutations giving rise to highly immunogenic neoepitopes, we postulated that vaccination with these mutant peptide antigens could offer promising treatment options to LS patients. To this end we performed whole-exome and RNA seq analysis on the blood and tumour samples from an LS-CRC patient, and used our proprietary neoepitope prioritization pipeline OncoPeptVAC to select peptides, and confirm their immunogenicity in an ex vivo CD8+ T cell activation assay. Three neoepitopes derived from the tumour of this patient elicited a potent CD8+ T cell response. Furthermore, analysis of the tumour-associated immune infiltrate revealed CD8+ T cells expressing low levels of activation markers, suggesting mechanisms of immune suppression at play in this relapsed tumour. Taken together, our study paves the way towards development of a cancer vaccine to treat or delay the onset/relapse of LS-CRC.
Immunoproteomic Identification and Characterization of Leishmania Membrane Proteins as Non-Invasive Diagnostic Candidates for Clinical Visceral Leishmaniasis
Authors: Ejazi Sarfaraz Ahmad , Bhattacharyya Anirban , Choudhury Somsubhra Thakur , Ghosh Sneha , Sabur Abdus , Pandey Krishna , Das Vidya Nand Ravi , Das Pradeep , Rahaman Mehebubar , Goswami Rama Prosad , Ali Nahid 
Published: August 2018

AbstractVisceral leishmaniasis (VL), a potentially fatal disease is an outcome of infection caused by the parasiteLeishmania donovani. The clinical diagnostic tests for this disease are still related to invasive tissue aspiration or serological immunochromatography. Advancements in immunoproteomics such as two-dimensional gel electrophoresis, mass spectrometry, B cell epitope prediction, and peptide synthesis have enabled researchers to discover newer biomarkers for disease diagnosis. In this study, we have screened several urine-reactive leishmanial membrane proteins as potential biomarker candidates. In the immunoblot assay, three proteins 51, 55 and 63 kDa showed 100% reactivity to the urine of 47 VL patients and nonreactive to 18 healthy and other diseases. Mass spectrometry revealed the identity of 51, 55 and 63 kDa proteins as elongation factor 1α (EF1-α), α-tubulin, and glycoprotein 63, respectively. B cell reactive epitopes of these proteins were mapped through bioinformatic tools and one epitope from each protein that had the highest score were synthesized. All the three native electroeluted proteins and their corresponding synthetic peptides were tested through ELISA for reactivity with VL and control urine samples. While all three demonstrated good reactivity, the diagnostic performance of EF1-α was the best. Our findings illustrate the use of urine-based proteomic approach for biomarker discovery in non-invasive clinical diagnosis of VL.
Statistical Evidence for the Role of Southwestern Indian Ocean Heat Content in the Indian Summer Monsoon Rainfall
Authors: Venugopal T. , Ali M. M. , Bourassa M. A. , Zheng Y. , Goni G. J. , Foltz G. R. , Rajeevan M. 
Published: August 2018

AbstractThis study examines the benefit of using Ocean Mean Temperature (OMT) to aid in the prediction of the sign of Indian Summer Monsoon Rainfall (ISMR) anomalies. This is a statistical examination, rather than a process study. The thermal energy needed for maintaining and intensifying hurricanes and monsoons comes from the upper ocean, not just from the thin layer represented by sea surface temperature (SST) alone. Here, we show that the southwestern Indian OMT down to the depth of the 26 °C isotherm during January–March is a better qualitative predictor of the ISMR than SST. The success rate in predicting above- or below-average ISMR is 80% for OMT compared to 60% for SST. Other January–March mean climate indices (e.g., NINO3.4, Indian Ocean Dipole Mode Index, El Niño Southern Oscillation Modoki Index) have less predictability (52%, 48%, and 56%, respectively) than OMT percentage deviation (PD) (80%). Thus, OMT PD in the southwestern Indian Ocean provides a better qualitative prediction of ISMR by the end of March and indicates whether the ISMR will be above or below the climatological mean value.