bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of various concentrations of superabsorbent polymers on soil particle-size distribution and evaporation with sand mulching
Authors: Zhao Wenju , Cao Taohong , Dou Pinxin , Sheng Jie , Luo Minqiang 
Published: March 2019

AbstractSuperabsorbent polymers (SAPs) are type of hydrogels capable to swell and absorb a large amount of water, but easily decomposed and oxidized by the air. We used electron-microscopic imaging in an indoor simulation with sand mulching to test the effects of various SAP concentrations on controlling evaporation and salt formation. The treatments were sand-mulched columns containing 0, 0.1, 0.2, 0.5 and 1.0% SAP. The soil particle pores were from dense to sparse and the corresponding fractal dimension decreased as SAP concentration increased. SAP concentration was correlated negatively with fractal dimension, clay-particle fraction and silt-volume fraction. And it showed a positive correlation with sand volume fraction. SAP concentration significantly affected the particle-size distribution. Water-storage capacity increased in each column layer (five 8-cm layers) at the same infiltration depth. Evaporation decreased the water content of each layer. Sand mulching combined with the SAP decreased evaporation in each layer relative to the control, which retained more water and decreased the accumulation of surface salt in the order 1.0% > 0.5% > 0.2% > 0.1% > 0. Salt migrated at 0–30 cm with sand mulching but 0–25 cm with sand mulching and SAP amendment. The decrease in salt accumulation was most effective at a SAP concentration of 0.2%.
A note on retrograde gene transfer efficiency and inflammatory response of lentiviral vectors pseudotyped with FuG-E vs. FuG-B2 glycoproteins
Authors: Tanabe Soshi , Uezono Shiori , Tsuge Hitomi , Fujiwara Maki , Miwa Miki , Kato Shigeki , Nakamura Katsuki , Kobayashi Kazuto , Inoue Ken-ichi , Takada Masahiko 
Published: March 2019

AbstractPseudotyped lentiviral vectors give access to pathway-selective gene manipulation via retrograde transfer. Two types of such lentiviral vectors have been developed. One is the so-called NeuRet vector pseudotyped with fusion glycoprotein type E, which preferentially transduces neurons. The other is the so-called HiRet vector pseudotyped with fusion glycoprotein type B2, which permits gene transfer into both neurons and glial cells at the injection site. Although these vectors have been applied in many studies investigating neural network functions, it remains unclear which vector is more appropriate for retrograde gene delivery in the brain. To compare the gene transfer efficiency and inflammatory response of the NeuRet vs. HiRet vectors, each vector was injected into the striatum in macaque monkeys, common marmosets, and rats. It was revealed that retrograde gene delivery of the NeuRet vector was equal to or greater than that of the HiRet vector. Furthermore, inflammation characterized by microglial and lymphocytic infiltration occurred when the HiRet vector, but not the NeuRet vector, was injected into the primate brain. The present results indicate that the NeuRet vector is more suitable than the HiRet vector for retrograde gene transfer in the primate and rodent brains.
A permeability-increasing drug synergizes with bacterial efflux pump inhibitors and restores susceptibility to antibiotics in multi-drug resistant Pseudomonas aeruginosa strains
Authors: Ferrer-Espada Raquel , Shahrour Hawraa , Pitts Betsey , Stewart Philip S. , Sánchez-Gómez Susana , Martínez-de-Tejada Guillermo 
Published: March 2019

AbstractResistance to antibiotics poses a major global threat according to the World Health Organization. Restoring the activity of existing drugs is an attractive alternative to address this challenge. One of the most efficient mechanisms of bacterial resistance involves the expression of efflux pump systems capable of expelling antibiotics from the cell. Although there are efflux pump inhibitors (EPIs) available, these molecules are toxic for humans. We hypothesized that permeability-increasing antimicrobial peptides (AMPs) could lower the amount of EPI necessary to sensitize bacteria to antibiotics that are efflux substrates. To test this hypothesis, we measured the ability of polymyxin B nonapeptide (PMBN), to synergize with antibiotics in the presence of EPIs. Assays were performed using planktonic and biofilm-forming cells of Pseudomonas aeruginosa strains overexpressing the MexAB-OprM efflux system. Synergy between PMBN and EPIs boosted azithromycin activity by a factor of 2,133 and sensitized P. aeruginosa to all tested antibiotics. This reduced several orders of magnitude the amount of inhibitor needed for antibiotic sensitization. The selected antibiotic-EPI-PMBN combination caused a 10 million-fold reduction in the viability of biofilm forming cells. We proved that AMPs can synergize with EPIs and that this phenomenon can be exploited to sensitize bacteria to antibiotics.
Two-year observation of the occlusal vertical dimension after bite raising via cone-beam computerized tomography: A preliminary study
Authors: Liu Chuanzi , Huang Dan , Zhou Lizhi , Liu Guochen , Wang Yining , Jiang Tao 
Published: March 2019

AbstractVariation of the occlusal vertical dimension (OVD) has been discussed empirically for decades, but it has not been thoroughly explored with experimental data. In the present study, cone-beam computerized tomography (CBCT) of six selected patients was conducted to evaluate the bones of the lower facial structures. The anterior lower facial heights (ALFHs), alveolar process heights (APHs), vertical facial pattern (VFP), occluding dentition height (ODH) and condyle space (CS), which were evaluated by three-dimensional (3D) and two-dimensional (2D) lateral cephalometry derived from CBCT, were compared before and two years after the OVD increased full mouth rehabilitation. Consistent significant increases in ALFHs and the VFP indicated the OVD increase, while a significant decrease in the ΔODH indicated compressed dentition. In addition, 55 of the 56 sites (98.21%) of APH measurement illustrated no significant difference before and after treatment. The findings indicated that the increased OVD did not relapse to baseline and was sufficiently tolerated, with mostly constant APHs and an altered ODH after two years of observation in the six patients.
CRISPR/Cas9 targeted CAPTURE of mammalian genomic regions for characterization by NGS
Authors: Slesarev Alexei , Viswanathan Lakshmi , Tang Yitao , Borgschulte Trissa , Achtien Katherine , Razafsky David , Onions David , Chang Audrey , Cote Colette 
Published: March 2019

AbstractThe robust detection of structural variants in mammalian genomes remains a challenge. It is particularly difficult in the case of genetically unstable Chinese hamster ovary (CHO) cell lines with only draft genome assemblies available. We explore the potential of the CRISPR/Cas9 system for the targeted capture of genomic loci containing integrated vectors in CHO-K1-based cell lines followed by next generation sequencing (NGS), and compare it to popular target-enrichment sequencing methods and to whole genome sequencing (WGS). Three different CRISPR/Cas9-based techniques were evaluated; all of them allow for amplification-free enrichment of target genomic regions in the range from 5 to 60 fold, and for recovery of ~15 kb-long sequences with no sequencing artifacts introduced. The utility of these protocols has been proven by the identification of transgene integration sites and flanking sequences in three CHO cell lines. The long enriched fragments helped to identify Escherichia coli genome sequences co-integrated with vectors, and were further characterized by Whole Genome Sequencing (WGS). Other advantages of CRISPR/Cas9-based methods are the ease of bioinformatics analysis, potential for multiplexing, and the production of long target templates for real-time sequencing.
Inhibition of avian-origin influenza A(H7N9) virus by the novel cap-dependent endonuclease inhibitor baloxavir marboxil
Authors: Taniguchi Keiichi , Ando Yoshinori , Nobori Haruaki , Toba Shinsuke , Noshi Takeshi , Kobayashi Masanori , Kawai Makoto , Yoshida Ryu , Sato Akihiko , Shishido Takao , Naito Akira , Matsuno Keita , Okamatsu Masatoshi , Sakoda Yoshihiro , Kida Hiroshi 
Published: March 2019

AbstractHuman infections with avian-origin influenza A(H7N9) virus represent a serious threat to global health; however, treatment options are limited. Here, we show the inhibitory effects of baloxavir acid (BXA) and its prodrug baloxavir marboxil (BXM), a first-in-class cap-dependent endonuclease inhibitor, against A(H7N9), in vitro and in vivo. In cell culture, BXA at four nanomolar concentration achieved a 1.5–2.8 log reduction in virus titers of A(H7N9), including the NA-R292K mutant virus and highly pathogenic avian influenza viruses, whereas NA inhibitors or favipiravir required approximately 20-fold or higher concentrations to achieve the same levels of reduction. A(H7N9)-specific amino acid polymorphism at position 37, implicated in BXA binding to the PA endonuclease domain, did not impact on BXA susceptibility. In mice, oral administration of BXM at 5 and 50 mg/kg twice a day for 5 days completely protected from a lethal A/Anhui/1/2013 (H7N9) challenge, and reduced virus titers more than 2–3 log in the lungs. Furthermore, the potent therapeutic effects of BXM in mice were still observed when a higher virus dose was administered or treatment was delayed up to 48 hours post infection. These findings support further investigation of BXM for A(H7N9) treatment in humans.
Interpretation of EBV infection in pan-cancer genome considering viral life cycle: LiEB (Life cycle of Epstein-Barr virus)
Authors: Song Hyojin , Lim Yoojoo , Im Hogune , Bae Jeong Mo , Kang Gyeong Hoon , Ahn Junhak , Baek Daehyun , Kim Tae-You , Yoon Sung-Soo , Koh Youngil 
Published: March 2019

AbstractWe report a novel transcriptomic analysis workflow called LiEB (Life cycle of Epstein-Barr virus) to characterize distributions of oncogenic virus, Epstein-Barr virus (EBV) infection in human tumors. We analyzed 851 The Cancer Genome Atlas whole-transcriptome sequencing (WTS) data to investigate EBV infection by life cycle information using three-step LiEB workflow: 1) characterize virus infection generally; 2) align transcriptome sequences against a hybrid human-EBV genome, and 3) quantify EBV gene expression. Our results agreed with EBV infection status of public cell line data. Analysis in stomach adenocarcinoma identified EBV-positive cases involving PIK3CA mutations and/or CDKN2A silencing with biologically more determination, compared to previous reports. In this study, we found that a small number of colorectal adenocarcinoma cases involved with EBV lytic gene expression. Expression of EBV lytic genes was also observed in 3% of external colon cancer cohort upon WTS analysis. Gene set enrichment analysis showed elevated expression of genes related to E2F targeting and interferon-gamma responses in EBV-associated tumors. Finally, we suggest that interpretation of EBV life cycle is essential when analyzing its infection in tumors, and LiEB provides high capability of detecting EBV-positive tumors. Observation of EBV lytic gene expression in a subset of colon cancers warrants further research.
In-situ localization and biochemical analysis of bio-molecules reveals Pb-stress amelioration in Brassica juncea L. by co-application of 24-Epibrassinolide and Salicylic Acid
Authors: Kohli Sukhmeen Kaur , Bali Shagun , Tejpal Ruchi , Bhalla Vandana , Verma Vinod , Bhardwaj Renu , Alqarawi A. A. , Abd_Allah Elsayed Fathi , Ahmad Parvaiz 
Published: March 2019

AbstractLead (Pb) toxicity is a major environmental concern affirming the need of proper mitigation strategies. In the present work, potential of combined treatment of 24-Epibrassinolide (24-EBL) and Salicylic acid (SA) against Pb toxicity to Brassica juncea L. seedlings were evaluated. Seedlings pre-imbibed in EBL (0.1 mM) and SA (1 mM) individually and in combination, were sown in Pb supplemented petri-plates (0.25, 0.50 and 0.75 mM). Various microscopic observations and biochemical analysis were made on 10 days old seedlings of B. juncea. The toxic effects of Pb were evident with enhancement in in-situ accumulation of Pb, hydrogen peroxide (H2O2), malondialdehyde (MDA), nuclear damage, membrane damage, cell death and polyamine. Furthermore, free amino acid were lowered in response to Pb toxicity. The levels of osmoprotectants including total carbohydrate, reducing sugars, trehalose, proline and glycine betaine were elevated in response to Pb treatment. Soaking treatment with combination of 24-EBL and SA led to effective amelioration of toxic effects of Pb. Reduction in Pb accumulation, reactive oxygen content (ROS), cellular damage and GSH levels were noticed in response to treatment with 24-EBL and SA individual and combined levels. The contents of free amino acid, amino acid profiling as well as in-situ localization of polyamine (spermidine) was recorded to be enhanced by co-application of 24-EBLand SA. Binary treatment of 24-EBL and SA, further elevated the content of osmoprotectants. The study revealed that co-application of combined treatment of 24-EBL and SA led to dimination of toxic effects of Pb in B. juncea seedlings.
Consequences of delays and imperfect implementation of isolation in epidemic control
Authors: Young Lai-Sang , Ruschel Stefan , Yanchuk Serhiy , Pereira Tiago 
Published: March 2019

AbstractFor centuries isolation has been the main control strategy of unforeseen epidemic outbreaks. When implemented in full and without delay, isolation is very effective. However, flawless implementation is seldom feasible in practice. We present an epidemic model called SIQ with an isolation protocol, focusing on the consequences of delays and incomplete identification of infected hosts. The continuum limit of this model is a system of Delay Differential Equations, the analysis of which reveals clearly the dependence of epidemic evolution on model parameters including disease reproductive number, isolation probability, speed of identification of infected hosts and recovery rates. Our model offers estimates on minimum response capabilities needed to curb outbreaks, and predictions of endemic states when containment fails. Critical response capability is expressed explicitly in terms of parameters that are easy to obtain, to assist in the evaluation of funding priorities involving preparedness and epidemics management.
pyPhotometry: Open source Python based hardware and software for fiber photometry data acquisition
Authors: Akam Thomas , Walton Mark E. 
Published: March 2019

AbstractFiber photometry is the process of recording bulk neural activity by measuring fluorescence changes in activity sensitive indicators such as GCaMP through an optical fiber. We present a system of open source hardware and software for fiber photometry data acquisition consisting of a compact, low cost, data acquisition board built around the Micropython microcontroller, and a cross platform graphical user interface (GUI) for controlling acquisition and visualising signals. The system can acquire two analog and two digital signals, and control two external LEDs via built in LED drivers. Time-division multiplexed illumination allows independent readout of fluorescence evoked by different excitation wavelengths from a single photoreceiver signal. Validation experiments indicate this approach offers better signal to noise for a given average excitation light intensity than sinusoidally-modulated illumination. pyPhotometry is substantially cheaper than commercial hardware filling the same role, and we anticipate, as an open source and comparatively simple tool, it will be easily adaptable and therefore of broad interest to a wide range of users.
Acute kidney injury in cancer patients: A nationwide survey in China
Authors: Jin Juan , Wang Yafang , Shen Quanquan , Gong Jianguang , Zhao Li , He Qiang 
Published: March 2019

AbstractCancer patients have a high risk for acute kidney injury (AKI); however, the incidence, severity, and risk factors of malignancy-related AKI (MR-AKI) are unclear. This study aimed to assess MR-AKI risk factors and provide reliable data for AKI prevention, diagnosis, and management in China. This cross-sectional study analysed data from 44 academic and local hospitals in China. AKI patients were identified based on 2 screening criteria: the 2012 Kidney Disease: Improving Global Outcomes-AKI definition and the expanded screening criteria for patients with no repeated serum creatinine (SCr) test within 7 days and those who recovered from AKI. Patients whose SCr level increased or decreased by 50% during hospitalization, compared with that at admission, were considered to have AKI according to the expanded criteria. A total of 7,604 AKI patients were enrolled (1,418 with MR-AKI). Patient characteristics were compared between the MR-AKI and non-MR-AKI groups. Multivariate logistic models were used to statistically assess risk factors. The proportions of MR-AKI patients in academic and local hospitals were 20.2% and 14.1%, respectively. The incidence of MR-AKI was higher in mid-China (the affluent region), elderly patients, and groups with higher per capita gross domestic product. Among MR-AKI cases, gastrointestinal cancer (50.1%) was the most common malignancy, followed by cancers of the reproductive (15.3%), haematological (13.1%), respiratory (11.8%), and other systems (8.3%), and cancers of unknown classification (1.4%). Of 268 hospital deaths, respiratory, haematological, gastrointestinal, reproductive, other system, and unknown classification cancers accounted for 29.3%, 18.8%, 18.6%, 12.9%, 16.9%, and 20.0%, respectively. Increased age, advanced AKI stage at peak, level of per capita gross domestic product, geographic region, and renal replacement therapy indication were risk factors for hospital mortality in patients with gastrointestinal MR-AKI, whereas cardiovascular disease history, AKI stage at peak, and geographic region were risk factors for mortality in patients with reproductive MR-AKI. The incidence and mortality of MR-AKI vary by hospital, economic level, age, geographic region, and malignancy type. High MR-AKI incidence was associated with gastrointestinal cancers and higher level of medical care provided by academic hospitals in affluent regions such as Beijing, Shanghai, and other provincial-level cities. Elderly patients with advanced gastrointestinal cancer in mid-China showed the highest incidence of MR-AKI and in-hospital mortality, and thus require special attention.
Naturally available wild pollination services have economic value for nature dependent smallholder crop farms in Tanzania
Authors: Tibesigwa Byela , Siikamäki Juha , Lokina Razack , Alvsilver Jessica 
Published: March 2019

AbstractDespite the importance of naturally available wild pollination ecosystem services in enhancing sub-Saharan African smallholder farms’ productivity, their values to actual farming systems remain unknown. We develop a nationally representative empirical assessment by integrating nationally representative plot level panel data with spatially and temporally matched land cover maps to identify the contribution of wild pollinators to crop revenue. Our estimation results reveal distinct and robust contributions by natural habitats of wild pollinators - forests - to plot-level crop revenue, where habitats in near proximity to plots contribute much more value than those farther away. When contrasting between pollinator-dependent and pollinator-independent crops, we find that the positive effects emerge only for pollinator-dependent crops, while pollinator-independent crops show no benefits. We conclude the empirical assessment by using our estimates to evaluate changes in crop revenue associated with the actual habitat reduction during 2008–2013. We find that this change in the natural habitats of wild pollinators has reduced crop revenue possibly by as much as 29% (mean) and 4% (median). To our knowledge, this is the first empirical assessment to use nationally representative smallholder farms to assess the value of naturally available wild pollination ecosystem services. Our results magnify the documented benefits of forest conservation, as this preserves pollinators’ natural habitats, and by extension its inhabitants, who play an important role in boosting crop yields of nature dependent smallholder farms.
Distinguishing Lipid Subtypes by Amplifying Contrast from J-Coupling
Authors: Uche Ifeanyi K. , Galiana Gigi 
Published: March 2019

AbstractPrevious work has highlighted the complicated and distinctive dynamics that set signal evolution during a train of spin echoes, especially with nonuniform echo spacing applied to complex molecules like fats. The work presented here regards those signal patterns as codes that can be used as a contrast mechanism, capable of distinguishing mixtures of molecules with an imaging sequence, sidestepping many challenges of spectroscopy. For particular arrays of echo spacings, non-monotonic and distinctive signal evolution can be enhanced to improve contrast between target species. This work presents simulations that show how contrast between two molecules: (a) depends on the specific sequence of echo spacing, (b) is directly linked to the presence of J-coupling, and (c) can be relatively insensitive to variations in B0, T2 and B1. Imaging studies with oils demonstrate this phenomenon experimentally and also show that spin echo codes can be used for quantification. Finally, preliminary experiments apply the method to human liver in vivo, verifying that the presence of fat can lead to nonmonotonic codes like those seen in vitro. In summary, nonuniformly spaced echo trains introduce a new approach to molecular imaging of J-coupled species, such as lipids, which may have implications diagnosing metabolic diseases.
Volcaniclastic tide-modulated tempestite in a coastal tuff ring, Jeju Island, Korea
Authors: Sohn Chanwoo , Sohn Young Kwan 
Published: March 2019

AbstractThe need for more accurate and extensive records of storm activity is increasing because of growing population and infrastructure in coastal areas. Records of past storm activity have consequently been sought from diverse sedimentary proxies in marginal marine environments, as well as historical documents. In this paper, we introduce a unique record of a 3.7 ka BP storm event preserved in a coastal tuff ring on Jeju Island, Korea. The tuff ring formed mostly above high tide level by primary volcanic processes, but contains three interbeds of horizontally laminated to hummocky/swaly cross-stratified deposits with intervening mud drapes up to an altitude of ~4.6 m above high tide level. These interbeds were formed by wave activity in a swash to surf zone when the sea level rose several meters above normal high-tide level during a storm event, and the triple intercalation of the wave-worked deposits reflects three tidal cycles during a storm event that lasted 1.5 day. Jeju Island contains the most complete record of an ancient storm event ever reported in the tuff ring, and highlights the significance of coastal volcanoes in the study of extreme depositional events in coastal areas, such as storms and tsunamis.