bluuebunny/crossref_metadata_2025_split huggingface dataset:
Connections Between a Late Summer Snowstorm Over the Southwestern Tibetan Plateau and a Concurrent Indian Monsoon Low‐Pressure System
Authors: Dong Wenhao , Lin Yanluan , Wright Jonathon S. , Xie Yuanyu , Xu Fanghua , Yang Kun , Li Xin , Tian Lide , Zhao Xi , Cao Dianbin 
Published: December 2018

AbstractSnowstorms cause more damage to the livelihoods and livestock of more than 2 million herders (~80% of the total population) on the Tibetan Plateau than any other natural disaster. In this study, we investigate an extreme snowstorm over the southwestern Tibetan Plateau (SWTP) that occurred on 18–21 September 2008. We explore sources and transport pathways of moisture to this storm using multiple data sets and a series of regional model simulations. The results show that this snowstorm results from dynamical coupling between an upper‐level trough and a concurrent low‐pressure system over northern India. This tropical‐extratropical interaction provides the dynamical mechanism for the snowstorm to occur: the upper level trough favors southward cold advection upstream of the SWTP while the low‐pressure system over northern India provides an abundant supply of moisture. Model‐based sensitivity tests indicate that large amounts of moisture are transported over the SWTP via both the up‐and‐over and upslope transport pathways. Our findings corroborate that low‐pressure systems over northern India can deliver abundant moisture into the SWTP. The coupling of this abundant supply of moisture with an upper‐level trough further leads to the occurrence of an early snow disaster in this case, aggravating already harsh conditions and causing severe damage. Improved understanding of the interactions between these two types of synoptic systems and the climatic conditions that influence their occurrence would aid the development of effective strategies for climate change adaptation and sustainable husbandry, as well as the mitigation and relief of future snow disasters in this region.
Motility-based label-free detection of parasites in bodily fluids using holographic speckle analysis and deep learning
Authors: Zhang Yibo , Ceylan Koydemir Hatice , Shimogawa Michelle M. , Yalcin Sener , Guziak Alexander , Liu Tairan , Oguz Ilker , Huang Yujia , Bai Bijie , Luo Yilin , Luo Yi , Wei Zhensong , Wang Hongda , Bianco Vittorio , Zhang Bohan , Nadkarni Rohan , Hill Kent , Ozcan Aydogan 
Published: December 2018

AbstractParasitic infections constitute a major global public health issue. Existing screening methods that are based on manual microscopic examination often struggle to provide sufficient volumetric throughput and sensitivity to facilitate early diagnosis. Here, we demonstrate a motility-based label-free computational imaging platform to rapidly detect motile parasites in optically dense bodily fluids by utilizing the locomotion of the parasites as a specific biomarker and endogenous contrast mechanism. Based on this principle, a cost-effective and mobile instrument, which rapidly screens ~3.2 mL of fluid sample in three dimensions, was built to automatically detect and count motile microorganisms using their holographic time-lapse speckle patterns. We demonstrate the capabilities of our platform by detecting trypanosomes, which are motile protozoan parasites, with various species that cause deadly diseases affecting millions of people worldwide. Using a holographic speckle analysis algorithm combined with deep learning-based classification, we demonstrate sensitive and label-free detection of trypanosomes within spiked whole blood and artificial cerebrospinal fluid (CSF) samples, achieving a limit of detection of ten trypanosomes per mL of whole blood (~five-fold better than the current state-of-the-art parasitological method) and three trypanosomes per mL of CSF. We further demonstrate that this platform can be applied to detect other motile parasites by imaging Trichomonas vaginalis, the causative agent of trichomoniasis, which affects 275 million people worldwide. With its cost-effective, portable design and rapid screening time, this unique platform has the potential to be applied for sensitive and timely diagnosis of neglected tropical diseases caused by motile parasites and other parasitic infections in resource-limited regions.
Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil
Authors: Levy-Booth David J , Giesbrecht Ian J W , Kellogg Colleen T E , Heger Thierry J , D’Amore David V , Keeling Patrick J , Hallam Steven J , Mohn William W 
Published: December 2018

AbstractThe Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO2 flux in peat bog and net CH4 flux in bog forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH4 cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH4 fluxes (r = 0.46, p &lt; 0.0001). Phylotype functional assignments were supported by metatranscriptomic analysis. We propose that active microbial populations respond primarily to changes in hydrology, pH, and nutrient availability. The increased microbial carbon export observed over winter may have ramifications for climate–soil feedbacks in the PCTR.
Dysregulated autophagy contributes to caspase-dependent neuronal apoptosis
Authors: Chung Yuhyun , Lee Juhyung , Jung Shinae , Lee Yangsin , Cho Jin Won , Oh Young J. 
Published: December 2018

AbstractAutophagy is a regulated, intracellular degradation process that delivers unnecessary or dysfunctional cargo to the lysosome. Autophagy has been viewed as an adaptive survival response to various stresses, whereas in other cases, it promotes cell death. Therefore, both deficient and excessive autophagy may lead to cell death. In this study, we specifically attempted to explore whether and how dysregulated autophagy contributes to caspase-dependent neuronal cell death induced by the neurotoxin 6-hydroxydopamine (6-OHDA). Ultrastructural and biochemical analyses indicated that MN9D neuronal cells and primary cultures of cortical neurons challenged with 6-OHDA displayed typical features of autophagy. Cotreatment with chloroquine and monitoring autophagic flux by a tandem mRFP-EGFP-tagged LC3 probe indicated that the autophagic phenomena were primarily caused by dysregulated autophagic flux. Consequently, cotreatment with an antioxidant but not with a pan-caspase inhibitor significantly blocked 6-OHDA-stimulated dysregulated autophagy. These results indicated that 6-OHDA-induced generation of reactive oxygen species (ROS) played a critical role in triggering neuronal death by causing dysregulated autophagy and subsequent caspase-dependent apoptosis. The results of the MTT reduction, caspase-3 activation, and TUNEL assays indicated that pharmacological inhibition of autophagy using 3-methyladenine or deletion of the autophagy-related gene Atg5 significantly inhibited 6-OHDA-induced cell death. Taken together, our results suggest that abnormal induction of autophagic flux promotes apoptotic neuronal cell death, and that the treatments limiting dysregulated autophagy may have a strong neuroprotective potential.
ALDH1A3 induces mesenchymal differentiation and serves as a predictor for survival in glioblastoma
Authors: Li Guanzhang , Li Yiming , Liu Xing , Wang Zheng , Zhang Chuanbao , Wu Fan , Jiang Haoyu , Zhang Wenlong , Bao Zhaoshi , Wang Yongzhi , Cai Jinquan , Zhao Liang , Kahlert Ulf D. , Jiang Tao , Zhang Wei 
Published: December 2018

AbstractAs aldehyde dehydrogenase (ALDH) is a novel stem cell marker, increasing studies have confirmed that high ALDH activity promotes tumorigenesis and progression in cancers. Some preliminary studies have found that ALDH1A3 may play an important role in glioma malignant progression, but so far there was no conclusive conclusion. The purpose of our study was to elucidate the mechanisms by which ALDH1A3 regulated in glioma and to provide practical tools for clinical application. Aldefluor, flow cytometry sorting and qRT-PCR were performed to verify the role of ALDH1A3 in ALDH activity maintenance. Transwell, immunofluorescence, glycolytic assays, and orthotopic xenograft models were used to explore ALDH1A3 bio-functions in GBM. LASSO-COX, COX survival analysis and Kaplan–Meier analysis were used to establish the prognostic evaluation system and predict postoperative chemotherapy sensitivity of GBMs. Our integrated study found that (1) ALDH1A3 associates with mesenchymal differentiation of GBM in Eastern and Western world patients. (2) ALDH1A3 plays a critical role in ALDH activity maintenance. (3) ALDH1A3 is an activator of mesenchymal transformation in GBM. (4) ALDH1A3-derived PMT markers’ molecular signature can predict 1-, 2-, and 3-year survival rates of GBMs precisely. In conclusion, ALDH1A3 was a major contributor to ALDH activity and a key driver in triggering mesenchymal transformation in GBM. ALDH1A3-based molecular classification scheme can help to improve guidance for prognosis forecasting and individualized treatment decision making for GBM patients.
Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis
Authors: Schwartz Michael H. , Wang Haipeng , Pan Jessica N. , Clark Wesley C. , Cui Steven , Eckwahl Matthew J. , Pan David W. , Parisien Marc , Owens Sarah M. , Cheng Brian L. , Martinez Kristina , Xu Jinbo , Chang Eugene B. , Pan Tao , Eren A. Murat 
Published: December 2018

AbstractAdvances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current sequencing strategies are insufficient to reveal physiological states of microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) are core components of protein synthesis machinery, present in all living cells, and are phylogenetically tractable, which make them ideal targets to gain physiological insights into environmental microbes. Here we report a direct sequencing approach, tRNA-seq, and a software suite, tRNA-seq-tools, to recover sequences, abundance profiles, and post-transcriptional modifications of microbial tRNA transcripts. Our analysis of cecal samples using tRNA-seq distinguishes high-fat- and low-fat-fed mice in a comparable fashion to 16S ribosomal RNA gene amplicons, and reveals taxon- and diet-dependent variations in tRNA modifications. Our results provide taxon-specific in situ insights into the dynamics of tRNA gene expression and post-transcriptional modifications within complex environmental microbiomes.
Stretched and compressed exponentials in the relaxation dynamics of a metallic glass-forming melt
Authors: Wu Zhen Wei , Kob Walter , Wang Wei-Hua , Xu Limei 
Published: December 2018

AbstractThe dynamics of glass-forming systems shows a multitude of features that are absent in normal liquids, such as non-exponential relaxation and a strong temperature-dependence of the relaxation time. Connecting these dynamic properties to the microscopic structure of the system is challenging because of the presence of the structural disorder. Here we use computer simulations of a metallic glass-former to establish such a connection. By probing the temperature and wave-vector dependence of the intermediate scattering function we find that the relaxation dynamics of the glassy melt is directly related to the local arrangement of icosahedral structures: Isolated icosahedra give rise to a liquid-like stretched exponential relaxation whereas clusters of icosahedra lead to a compressed exponential relaxation that is reminiscent to the one found in a solid. Our results show that in metallic glass-formers these two types of relaxation processes can coexist and give rise to a dynamics that is surprisingly complex.
Increased nitrogen supply promoted the growth of non-N-fixing woody legume species but not the growth of N-fixing Robinia pseudoacacia
Authors: Wang Xiao , Guo Xiao , Yu Yang , Cui Han , Wang Renqing , Guo Weihua 
Published: December 2018

AbstractNitrogen (N) is an essential macronutrient for plant development and growth, and the deposition of N has increased in recent decades. Legumes that fix N can also provide N for nearby species. However, N in soil inhibits N fixation. We tested the effects of N fertilisation on one N-fixing (Robinia pseudoacacia) and two non-N-fixing (Sophora japonica and Senna surattensis) woody legume species, which were subjected to five different N levels (0, 1.5, 2.9, 5.9 and 11.4 mg N per plant day−1) under greenhouse conditions. The growth of the two non-N-fixing species was promoted by N supply, while that of R. pseudoacacia was unaffected. Among the three species, R. pseudoacacia had the largest specific leaf area and chlorophyll concentration, S. japonica had the largest root-to-shoot ratio and main root-to-lateral root ratio, and S. surattensis had the largest leaf N and phosphorus concentrations. The N-fixing species was mostly unaffected by N supply. The growth, leaf chlorophyll concentration, and leaf number in the non-N-fixing species were promoted by N supply. The N-fixing species showed better growth in low-N environments, while under increased N deposition, its growth was similar to that of the non-N-fixing species.
Magnetized plasma implosion in a snail target driven by a moderate-intensity laser pulse
Authors: Pisarczyk T. , Gus’kov S. Yu , Zaras-Szydłowska A. , Dudzak R. , Renner O. , Chodukowski T. , Dostal J. , Rusiniak Z. , Burian T. , Borisenko N. , Rosinski M. , Krupka M. , Parys P. , Klir D. , Cikhardt J. , Rezac K. , Krasa J. , Rhee Y.-J. , Kubes P. , Singh S. , Borodziuk S. , Krus M. , Juha L. , Jungwirth K. , Hrebicek J. , Medrik T. , Golasowski J. , Pfeifer M. , Skala J. , Pisarczyk P. , Korneev Ph. 
Published: December 2018

AbstractOptical generation of compact magnetized plasma structures is studied in the moderate intensity domain. A sub-ns laser beam irradiated snail-shaped targets with the intensity of about 1016 W/cm2. With a neat optical diagnostics, a sub-megagauss magnetized plasmoid is traced inside the target. On the observed hydrodynamic time scale, the hot plasma formation achieves a theta-pinch-like density and magnetic field distribution, which implodes into the target interior. This simple and elegant plasma magnetization scheme in the moderate-intensity domain is of particular interest for fundamental astrophysical-related studies and for development of future technologies.
In vivo time-harmonic ultrasound elastography of the human brain detects acute cerebral stiffness changes induced by intracranial pressure variations
Authors: Tzschätzsch Heiko , Kreft Bernhard , Schrank Felix , Bergs Judith , Braun Jürgen , Sack Ingolf 
Published: December 2018

AbstractCerebral stiffness (CS) reflects the biophysical environment in which neurons grow and function. While long-term CS changes can occur in the course of chronic neurological disorders and aging, little is known about acute variations of CS induced by intracranial pressure variations. Current gold standard methods for CS and intracranial pressure such as magnetic resonance elastography and direct pressure recordings are either expensive and slow or invasive. The study objective was to develop a real-time method forin vivoCS measurement and to demonstrate its sensitivity to physiological aging and intracranial pressure variations induced by the Valsalva maneuver in healthy volunteers. We used trans-temporal ultrasound time-harmonic elastography (THE) with external shear-wave stimulation by continuous and superimposed vibrations in the frequency range from 27 to 56 Hz. Multifrequency wave inversion generated maps of shear wave speed (SWS) as a surrogate maker of CS. On average, cerebral SWS was 1.56 ± 0.08 m/s with a tendency to reduce with age (R = −0.76, p < 0.0001) while Valsalva maneuver induced an immediate stiffening of the brain as reflected by a 10.8 ± 2.5% increase (p < 0.0001) in SWS. Our results suggest that CS is tightly linked to intracranial pressure and might be used in the future as non-invasive surrogate marker for intracranial pressure, which otherwise requires invasive measurements.
Comparison of community- and healthcare-associated methicillin-resistant Staphylococcus aureus isolates at a Chinese tertiary hospital, 2012–2017
Authors: Peng Haiying , Liu Dengtao , Ma Yuhua , Gao Wei 
Published: December 2018

AbstractThe transmission between community-associated (CA-) and healthcare-associated (HA-) methicillin-resistant Staphylococcus aureus (MRSA) has increased the challenge of infection control. To understand the clonal evolution and transmission of MRSA isolates, we compared the characteristics of 175 CA-MRSA and 660 HA-MRSA strains at a Chinese tertiary hospital in 2012–2017. Antibiotic susceptibility was performed on VITEK system, the genetic background of the isolates was characterized by SCCmec, spa, and MLST typing, while virulence determinants were screened using conventional PCR. Although more than 70% of the CA-MRSA isolates were erythromycin and clindamycin resistant, CA-MRSA was more susceptible than HA-MRSA to most of the antibiotics tested. ST239-MRSA-III-t030 (30%) was the most prevalent clone among HA-MRSA, while ST59-MRSA-IVa-t437 (28.8%) was the major clone among CA-MRSA. Notably, ST59-MRSA-IVa-t437 accounted for 6.7% of the chosen HA-MRSA isolates. Additionally, difference in virulence gene content was found between the CA- and HA-MRSA strains. In conclusion, epidemiological characteristics were largely different between CA- and HA-MRSA. Although ST239-MRSA-III-t030 is still the predominant clone among HA-MRSA, the community clone ST59-MRSA-IVa-t437 has the potential of becoming an essential part of HA-MRSA in the region tested.
Monensin inhibits cell proliferation and tumor growth of chemo-resistant pancreatic cancer cells by targeting the EGFR signaling pathway
Authors: Wang Xin , Wu Xingye , Zhang Zhonglin , Ma Chao , Wu Tingting , Tang Shengli , Zeng Zongyue , Huang Shifeng , Gong Cheng , Yuan Chengfu , Zhang Linghuan , Feng Yixiao , Huang Bo , Liu Wei , Zhang Bo , Shen Yi , Luo Wenping , Wang Xi , Liu Bo , Lei Yan , Ye Zhenyu , Zhao Ling , Cao Daigui , Yang Lijuan , Chen Xian , Haydon Rex C. , Luu Hue H. , Peng Bing , Liu Xubao , He Tong-Chuan 
Published: December 2018

AbstractPancreatic ductal adenocarcinoma (PDAC) is one of the most deadly malignancies with <5% five-year survival rate due to late diagnosis, limited treatment options and chemoresistance. There is thus an urgent unmet clinical need to develop effective anticancer drugs to treat pancreatic cancer. Here, we study the potential of repurposing monensin as an anticancer drug for chemo-resistant pancreatic cancer. Using the two commonly-used chemo-resistant pancreatic cancer cell lines PANC-1 and MiaPaCa-2, we show that monensin suppresses cell proliferation and migration, and cell cycle progression, while solicits apoptosis in pancreatic cancer lines at a low micromole range. Moreover, monensin functions synergistically with gemcitabine or EGFR inhibitor erlotinib in suppressing cell growth and inducing cell death of pancreatic cancer cells. Mechanistically, monensin suppresses numerous cancer-associated pathways, such as E2F/DP1, STAT1/2, NFkB, AP-1, Elk-1/SRF, and represses EGFR expression in pancreatic cancer lines. Furthermore, the in vivo study shows that monensin blunts PDAC xenograft tumor growth by suppressing cell proliferation via targeting EGFR pathway. Therefore, our findings demonstrate that monensin can be repurposed as an effective anti-pancreatic cancer drug even though more investigations are needed to validate its safety and anticancer efficacy in pre-clinical and clinical models.
The deubiquitylating enzyme UCHL3 regulates Ku80 retention at sites of DNA damage
Authors: Nishi Ryotaro , Wijnhoven Paul W. G. , Kimura Yusuke , Matsui Misaki , Konietzny Rebecca , Wu Qian , Nakamura Keisuke , Blundell Tom L. , Kessler Benedikt M. 
Published: December 2018

AbstractNon-homologous end-joining (NHEJ), which can promote genomic instability when dysfunctional, is a major DNA double-strand break (DSB) repair pathway. Although ubiquitylation of the core NHEJ factor, Ku (Ku70-Ku80), which senses broken DNA ends, is important for its removal from sites of damage upon completion of NHEJ, the mechanism regulating Ku ubiquitylation remains elusive. We provide evidence showing that the ubiquitin carboxyl-terminal hydrolase L3 (UCHL3) interacts with and directly deubiquitylates one of the Ku heterodimer subunits, Ku80. Additionally, depleting UCHL3 resulted in reduced Ku80 foci formation, Ku80 binding to chromatin after DSB induction, moderately sensitized cells to ionizing radiation and decreased NHEJ efficiencies. Mechanistically, we show that DNA damage induces UCHL3 phosphorylation, which is dependent on ATM, downstream NHEJ factors and UCHL3 catalytic activity. Furthermore, this phosphorylation destabilizes UCHL3, despite having no effect on its catalytic activity. Collectively, these data suggest that UCHL3 facilitates cellular viability after DSB induction by antagonizing Ku80 ubiquitylation to enhance Ku80 retention at sites of damage.
Meta-Dome for Broadband Radar Absorbing Structure
Authors: Jeong Heijun , Nguyen Toan Trung , Lim Sungjoon 
Published: December 2018

AbstractThis study focused on the radome and proposed an absorber with a meta-dome structure for ultra-wideband radar absorption using an FR-4 dielectric material on the metasurface absorber for protection. In addition to protecting the absorber, the metasurface absorber exhibited ultra-wideband frequency absorptivity from radar signals, with an absorptivity band from 4.6–12 GHz, including the C and X frequency bands of radar signals. A wide incidence angle should also be considered in addition to the absorption frequency band. Experimental results were obtained for all polarization angles at normal incidence for 5–14 GHz. Sensitivity to incident angle from 0° to 40° in the transverse electric mode and 0° to 60° in the transverse magnetic mode were observed. The proposed concept was demonstrated using full-wave simulation and experimental measurements.