bluuebunny/crossref_metadata_2025_split huggingface dataset:
Projected climate change impacts in rainfall erosivity over Brazil
Authors: Almagro André , Oliveira Paulo Tarso S. , Nearing Mark A. , Hagemann Stefan 
Published: August 2017

AbstractThe impacts of climate change on soil erosion may bring serious economic, social and environmental problems. However, few studies have investigated these impacts on continental scales. Here we assessed the influence of climate change on rainfall erosivity across Brazil. We used observed rainfall data and downscaled climate model output based on Hadley Center Global Environment Model version 2 (HadGEM2-ES) and Model for Interdisciplinary Research On Climate version 5 (MIROC5), forced by Representative Concentration Pathway 4.5 and 8.5, to estimate and map rainfall erosivity and its projected changes across Brazil. We estimated mean values of 10,437 mm ha−1 h−1 year−1 for observed data (1980–2013) and 10,089 MJ mm ha−1 h−1 year−1 and 10,585 MJ mm ha−1 h−1 year−1 for HadGEM2-ES and MIROC5, respectively (1961–2005). Our analysis suggests that the most affected regions, with projected rainfall erosivity increases ranging up to 109% in the period 2007–2040, are northeastern and southern Brazil. Future decreases of as much as −71% in the 2071–2099 period were estimated for the southeastern, central and northwestern parts of the country. Our results provide an overview of rainfall erosivity in Brazil that may be useful for planning soil and water conservation, and for promoting water and food security.
Structural characterization of CAS SH3 domain selectivity and regulation reveals new CAS interaction partners
Authors: Gemperle Jakub , Hexnerová Rozálie , Lepšík Martin , Tesina Petr , Dibus Michal , Novotný Marian , Brábek Jan , Veverka Václav , Rosel Daniel 
Published: August 2017

AbstractCAS is a docking protein downstream of the proto-oncogene Src with a role in invasion and metastasis of cancer cells. The CAS SH3 domain is indispensable for CAS-mediated signaling, but structural aspects of CAS SH3 ligand binding and regulation are not well understood. Here, we identified the consensus CAS SH3 binding motif and structurally characterized the CAS SH3 domain in complex with ligand. We revealed the requirement for an uncommon centrally localized lysine residue at position +2 of CAS SH3 ligands and two rather dissimilar optional anchoring residues, leucine and arginine, at position +5. We further expanded the knowledge of CAS SH3 ligand binding regulation by manipulating tyrosine 12 phosphorylation and confirmed the negative role of this phosphorylation on CAS SH3 ligand binding. Finally, by exploiting the newly identified binding requirements of the CAS SH3 domain, we predicted and experimentally verified two novel CAS SH3 binding partners, DOK7 and GLIS2.
Delivery of large transgene cassettes by foamy virus vector
Authors: Sweeney Nathan Paul , Meng Jinhong , Patterson Hayley , Morgan Jennifer E. , McClure Myra 
Published: August 2017

AbstractViral vectors are effective tools in gene therapy, but their limited packaging capacity can be restrictive. Larger clinically-relevant vectors are needed. Foamy viruses have the largest genomes among mammalian retroviruses and their vectors have shown potential for gene therapy in preclinical studies. However, the effect of vector genome size on titre has not been determined. We inserted increasing lengths of the dystrophin open reading frame in a foamy virus vector and quantified packaged vector RNA and integrated DNA. For both measures, a semi-logarithmic reduction in titre was observed as genome size increased. Concentrated titres were reduced 100-fold to approximately 106 transducing units per ml when vector genomes harboured a 12 kb insert, approximately twice that reported for lentivirus vectors in a comparable study. This potential was applied by optimising foamy virus vectors carrying the full-length dystrophin open-reading frame for transduction of human muscle derived cells. Full-length dystrophin protein was expressed and transduced cells remained able to form myotubes in vitro. Foamy virus vectors are well-suited for stable delivery of large transgene cassettes and warrant further investigation for development as a therapy for Duchenne or Becker muscular dystrophy.
Adaptive simulations, towards interactive protein-ligand modeling
Authors: Lecina Daniel , Gilabert Joan F. , Guallar Victor 
Published: August 2017

AbstractModeling the dynamic nature of protein-ligand binding with atomistic simulations is one of the main challenges in computational biophysics, with important implications in the drug design process. Although in the past few years hardware and software advances have significantly revamped the use of molecular simulations, we still lack a fast and accurateab initiodescription of the binding mechanism in complex systems, available only for up-to-date techniques and requiring several hours or days of heavy computation. Such delay is one of the main limiting factors for a larger penetration of protein dynamics modeling in the pharmaceutical industry. Here we present a game-changing technology, opening up the way for fast reliable simulations of protein dynamics by combining an adaptive reinforcement learning procedure with Monte Carlo sampling in the frame of modern multi-core computational resources. We show remarkable performance in mapping the protein-ligand energy landscape, being able to reproduce the full binding mechanism in less than half an hour, or the active site induced fit in less than 5 minutes. We exemplify our method by studying diverse complex targets, including nuclear hormone receptors and GPCRs, demonstrating the potential of using the new adaptive technique in screening and lead optimization studies.
Symmetry in the open-system dynamics of quantum correlations
Authors: Lyyra Henri , Karpat Göktuğ , Li Chuan-Feng , Guo Guang-Can , Piilo Jyrki , Maniscalco Sabrina 
Published: August 2017

AbstractWe study the symmetry properties in the dynamics of quantum correlations for two-qubit systems in one-sided noisy channels, with respect to a switch in the location of noise from one qubit to the other. We consider four different channel types, namely depolarizing, amplitude damping, bit-flip, and bit-phase-flip channel, and identify the classes of initial states leading to symmetric decay of entanglement, non-locality and discord. Our results show that the symmetric decay of quantum correlations is not directly linked to the presence or absence of symmetry in the initial state, while it does depend on the type of correlation considered as well as on the type of noise. We prove that asymmetric decay can be used to infer, in certain cases, characteristic properties of the channel. We also show that the location of noise may lead to dramatic changes in the persistence of phenomena such as entanglement sudden death and time-invariant discord.
Associations between serum homocysteine levels and anxiety and depression among children and adolescents in Taiwan
Authors: Chung Kuo-Hsuan , Chiou Hung-Yi , Chen Yi-Hua 
Published: August 2017

AbstractAlthough evidence suggests that homocysteine levels are elevated in severe mental illness in children, findings regarding homocysteine levels in youth with anxiety and depression are scarce. Therefore, this study examined the association of homocysteine levels with anxiety and depression in a community sample of students aged 6–13 years. In total, 649 students were selected from the first, fourth, and seventh grades of schools in Taipei, Taiwan, in 2010. These students completed a hospital-based health examination, which included physical examination, blood sample collection, and questionnaire administration. The data were analysed through multiple linear regression. Among the seventh-grade boys, both depression (adjusted β = 0.044, 95% confidence interval (CI) = 0.004–0.084) and anxiety (adjusted β = 0.052, 95% CI = 0.013–0.091) were independently associated with increased homocysteine levels. In further dichotomisation, compared with students with low anxiety levels, those with moderate to high anxiety levels were significantly positively associated with elevated serum homocysteine levels (adjusted β = 0.091, 95% CI = 0.003–0.180). Our results suggest that increased depression and anxiety may be positively associated with higher serum homocysteine levels in older boys. Our results provide essential data on the biological aspects underlying anxiety and depression in the studied population.
A new horned and long-necked herbivorous stem-archosaur from the Middle Triassic of India
Authors: Sengupta Saradee , Ezcurra Martín D. , Bandyopadhyay Saswati 
Published: August 2017

AbstractThe early evolution of archosauromorphs (bird- and crocodile-line archosaurs and stem-archosaurs) represents an important case of adaptive radiation that occurred in the aftermath of the Permo-Triassic mass extinction. Here we enrich the early archosauromorph record with the description of a moderately large (3–4 m in total length), herbivorous new allokotosaurian, Shringasaurus indicus, from the early Middle Triassic of India. The most striking feature of Shringasaurus indicus is the presence of a pair of large supraorbital horns that resemble those of some ceratopsid dinosaurs. The presence of horns in the new species is dimorphic and, as occurs in horned extant bovid mammals, these structures were probably sexually selected and used as weapons in intraspecific combats. The relatively large size and unusual anatomy of Shringasaurus indicus broadens the morphological diversity of Early–Middle Triassic tetrapods and complements the understanding of the evolutionary mechanisms involved in the early archosauromorph diversification.
NLRP3 inflammasome activation results in liver inflammation and fibrosis in mice infected with Schistosoma japonicum in a Syk-dependent manner
Authors: Lu Ya-Qi , Zhong Shan , Meng Nan , Fan Yin-Ping , Tang Wang-Xian 
Published: August 2017

AbstractGranulomatous and fibrosing inflammation in response to soluble egg antigen (SEA) from Schistosoma japonicum (S. japonicum) is the main pathological process of S. japonicum infection. Inflammasome activation has recently been implicated in the pathogenesis of liver disease. However, the role of inflammasome activation in schistosomiasis-associated liver fibrosis (SSLF) has not been extensively studied. In this study, it is demonstrated that the NLRP3 inflammasome is markedly activated in mouse HSCs both in vivo and in vitro during S. japonicum infection. Furthermore, it is demonstrated that inhibition of NLRP3 inflammasome significantly alleviates the liver inflammation and collagen deposition that are induced by infection with S. japonicum. The mechanism of SEA-induced NLRP3 inflammasome activation is studied in isolated, cultured mouse HSCs and it is shown that SEA-induced NLRP3 inflammasome activation in HSCs is dependent upon the activities of spleen tyrosine kinase (Syk), an enzyme usually associated with a pathogen recognition receptor for fungal pathogens. Moreover, it is demonstrated that Dectin-1 and JNK signaling are also involved in SEA-induced NLRP3 inflammasome activation in HSCs. These data shed new light on the mechanisms of NLRP3 inflammasome activation during an infection with S. japonicum, and further characterize its role in schistosomiasis-associated liver fibrosis (SSLF).
Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology
Authors: Kwambana-Adams Brenda , Hanson Blake , Worwui Archibald , Agbla Schadrac , Foster-Nyarko Ebenezer , Ceesay Fatima , Ebruke Chinelo , Egere Uzochukwu , Zhou Yanjiao , Ndukum Maze , Sodergren Erica , Barer Michael , Adegbola Richard , Weinstock George , Antonio Martin 
Published: August 2017

AbstractThere is growing concern that interventions that alter microbial ecology can adversely affect health. We characterised the impact of the seven-valent pneumococcal conjugate vaccine (PCV7) on pneumococcal carriage and the bacterial component of the nasopharyngeal microbiome during infancy. Newborns were recruited into three groups as follows: Group1 (n = 33) was the control group and comprised infants who received PCV7 after 6 months and came from unvaccinated communities. Group 2 (n = 30) came from unvaccinated communities and Group 3 (n = 39) came from vaccinated communities. Both group 2 and 3 received PCV7 at 2, 3 and 4 months. Culture and 16 S rRNA gene sequencing were performed on nasopharyngeal specimens collected at regular intervals from infants. Nasopharyngeal carriage of PCV7 serotypes in Group 1 was significantly higher than in Group 2 and 3 (p < 0.01). However, pneumococcal carriage remained comparable due to an expansion of non-vaccine serotypes in Groups 2 and 3. Determination of phylogenetic dis(similarities) showed that the bacterial community structures were comparable across groups. A mixed effects model showed no difference in community richness (p = 0.15) and Shannon α-diversity (p = 0.48) across the groups. Immediate replacement of pneumococcal vaccine serotypes with non-vaccine serotypes may mitigate the impact of PCV7 on nasopharyngeal bacterial community structure and ecology.
Magnetic microsphere-based portable solid phase extraction device for on-site pre-concentration of organics from large-volume water samples
Authors: Yao Zhijian , Zhao Qingqing , Ma Yan , Wang Wei , Zhou Qing , Li Aimin 
Published: August 2017

AbstractIn this research a new magnetic material called M88 was fully synthetized and characterized for the extraction of pharmaceutical and personal care products in water samples. In addition, a portable prototype of magnetic solidphase extraction (MSPE) device was developed for the onsite preconcentration. The MSPE coupling with high performance liquid chromatography-Diode array detector (HPLC-DAD) method was developed and validated for simultaneous analysis of 11 PPCPs (mefenamic acid, chloroamphenicol, ketoprofen, clofibric acid, indometacin, acetylsalicylic acid, bisphenol A, phenylphenol, gemfibrozil, triclosan, and ibuprofen) in environmental water samples. Experimental parameters affecting the extraction efficiencies, such as the amount of M88, desorption solvent, extraction time, and solution pH and sample volume were investigated. Under the optimal conditions, the limits of detection (LODs, S/N = 3) for the selected PPCPs were found to be in the range of 0.7–9.4 ng/L, with good linear correlation coefficients. It is also shown that the extraction efficiency of M88 was comparable to that of the commercial Oasis HLB and was evidently higher than that of the C18 cartridge. The optimised method was further verified by performing spiking experiments in water samples from Taihu Lake, with good recovery and reproducibility for all the compounds.
Gait Speed rather than Dynapenia Is a Simple Indicator for Complex Care Needs: A Cross-sectional Study Using Minimum Data Set
Authors: Huang Tzu-Ya , Liang Chih-Kuang , Shen Hsiu-Chu , Chen Hon-I , Liao Mei-Chen , Chou Ming-Yueh , Lin Yu-Te , Chen Liang-Kung 
Published: August 2017

AbstractThe impact of dynapenia on the complexity of care for residents of long-term care facilities (LTCF) remains unclear. The present study evaluated associations between dynapenia, care problems and care complexity in 504 residents of Veterans Care Homes (VCHs) in Taiwan. Subjects with dynapenia, defined as low muscle strength (handgrip strength <26 kg), were older adults with lower body mass index (BMI), slow gait speed, and higher numbers of Resident Assessment Protocol (RAP) triggers. After adjusting for age, education, BMI, and Charlson’s comorbidity index (CCI), only age, education, BMI and gait speed were independently associated with higher numbers of RAP triggers, but not dynapenia or handgrip strength (kg). Dividing subjects into groups based on quartiles of gait speed, those with gait speed ≤0.803 m/s were significantly associated with higher complexity of care needs (defined as ≥4 RAP triggers) compared to the reference group (gait speed >1 m/s). Significantly slow gait speed was associated with RAP triggers, including cognitive loss, poor communication ability, rehabilitation needs, urinary incontinence, depressed mood, falls, pressure ulcers, and use of psychotropic drugs. In conclusion, slow gait speed rather than dynapenia is a simple indicator for higher complexity of care needs of older male LTCF residents.
The linear artifact in enhanced depth imaging spectral domain optical coherence tomography
Authors: Zuo Chengguo , Mi Lan , Yang Shasha , Guo Xinxing , Xiao Hui , Liu Xing 
Published: August 2017

AbstractOptical coherence tomography (OCT) is a valuable ancillary test in the diagnosis and management of chorioretinal disease. The evaluation of choroid thickness using OCT has become the focus of clinical applications. We report a linear artifact that acts as a confounding factor in choroidal thickness measurements by enhanced depth imaging OCT. We found that the linear artifact is located stably at a depth of 485 μm beneath the retinal pigment epithelium in 81.88% of subjects. The study suggested that the linear artifact was a confounding factor in assessing choroidal thickness and that caution should be used in the interpretation of the choroidal thickness, especially when it is approximately 485 μm.
Surveillance Bias in Cancer Risk After Unrelated Medical Conditions: Example Urolithiasis
Authors: Hemminki Kari , Hemminki Otto , Försti Asta , Sundquist Kristina , Sundquist Jan , Li Xinjun 
Published: August 2017

AbstractWe analysed cancer risks in patients with urinary tract stones but some features of the generated results alarmed us about possible surveillance bias, which we describe in this report. We used nationwide Swedish hospital records to identify patients with urinary tract stones (N = 211,718) and cancer registration data for cancer patients for years 1987 to 2012. Standardized incidence ratios (SIRs) for cancer were calculated after the last medical contact for urinary tract stones. All cancers were increased after kidney (SIR 1.54, 95%CI: 1.50–1.58), ureter (1.44, 1.42–1.47), mixed (1.51, 1.44–1.58) and bladder stones (1.63, 1.57–1.70). The risk of kidney cancer was increased most of all cancers after kidney, ureter and mixed stones while bladder cancer was increased most after bladder stones. All SIRs decreased steeply in the course of follow-up time. Tumour sizes were smaller in kidney cancer and in situ colon cancers were more common in patients diagnosed after urinary tract stones compared to all patients. The results suggest that surveillance bias influenced the result which somewhat surprisingly appeared to extend past 10 years of follow-up and include cancers at distant anatomical sites. Surveillance bias may be difficult to avoid in the present type of observational studies in clinical settings.
The Us2 Gene Product of Herpes Simplex Virus 2 modulates NF-κB activation by targeting TAK1
Authors: Lu Xuan , Huang Changjing , Zhang Yi , Lin Yong , Wang Xueyu , Li Qian , Liu Shi , Tang Jingfeng , Zhou Li 
Published: August 2017

AbstractHSV-2 is one of the most common sexually transmitted pathogens worldwide and HSV-2 infection triggers cytokine and chemokine production. However, little is known about which HSV-2 genes engage in the regulation of NF-κB signaling and what mechanisms are involved. In a screen of the unique short (Us) regions of HSV-2, we observed that HSV-2 Us2 activates NF-κB signaling. We additionally indicated that deficiencies of Us2 decrease HSV-2 WT mediated NF-κB activation and cytokine and chemokine production, and overexpression of Us2 showed opposite effects. Co-immunoprecipitations indicated that Us2 interacted with TGF-β activated kinase 1 (TAK1), a serine/threonine kinase essential for NF-κB activation, and Us2 has the ability to regulate the TAK1-mediated pathway and induces TAK1 downstream signaling. Further studies verified that Us2 induced the phosphorylation of TAK1, resulting in the activation of TAK1 mediated downstream signaling. The role of Us2 in HSV-2 induced NF-κB pathways was also confirmed in the Us2-deficient mutant and HSV-2 WT infected mice. Our results indicate that HSV-2 Us2 gene product binds to TAK1 to positively regulate NF-κB signaling and, for the first time, provide insights into the molecular mechanism.
Genetic polymorphisms of lncRNA-p53 regulatory network genes are associated with concurrent chemoradiotherapy toxicities and efficacy in nasopharyngeal carcinoma patients
Authors: Wang Youhong , Guo Zhen , Zhao Yu , Jin Yi , An Liang , Wu Bin , Liu Zhaoqian , Chen Xiaoping , Chen Xiang , Zhou Honghao , Wang Hui , Zhang Wei 
Published: August 2017

AbstractThe relevance of the transcription factor p53 in cancer is inarguable, and numerous lncRNAs are involved in the p53 regulatory network as either regulators or effectors, triggering a transcriptional response that causes either cell arrest or apoptosis following DNA damage in a p53-dependent manner. Despite the fact that the therapeutic response is improved in NPC, heterogeneity among people remains with regard to the susceptibility of adverse effects and the efficacy of treatments. Therefore, we analysed eight potentially functional SNPs of five genes in the lncRNA-p53 regulatory network in a discovery cohort of 505 NPC patients. By performing multivariate logistic regression, the impact of genetic variations on the efficacy and risk of CRT-induced toxicities was investigated. The most dramatic finding was that the MEG3 rs10132552 CC genotype had a greater than three-fold increased risk of developing grade 3–4 anaemia (OR = 3.001, 95%CI = 1.355–6.646, P = 0.007). Furthermore, the rs10132552 CT genotype had a better response to treatment (OR = 0.261, 95%CI = 0.089–0.770, P = 0.015). Individuals carrying LINC-ROR rs2027701 with one or two variant alleles had significant associations with a reduced risk of neutropaenia (OR = 0.503, 95%CI = 0.303–0.835, P = 0.008). In conclusion, our results suggested that genetic polymorphisms of the lncRNA-p53 regulatory network could play a potential role in reducing treatment-related toxicities and improving outcomes for NPC patients.
Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert
Authors: Idris Hamidah , Goodfellow Michael , Sanderson Roy , Asenjo Juan A. , Bull Alan T. 
Published: August 2017

AbstractThe Atacama Desert is the most extreme non-polar biome on Earth, the core region of which is considered to represent the dry limit for life and to be an analogue for Martian soils. This study focused on actinobacteria because they are keystone species in terrestrial ecosystems and are acknowledged as an unrivalled source of bioactive compounds. Metagenomic analyses of hyper-arid and extreme hyper-arid soils in this desert revealed a remarkable degree of actinobacterial ‘dark matter’, evidenced by a detected increase of 34% in families against those that are validly published. Rank-abundance analyses indicated that these soils were high-diversity habitats and that the great majority of designated ‘rare’ genera (up to 60% of all phylotypes) were always rare. These studies have enabled a core actinobacterial microbiome common to both habitats to be defined. The great majority of detected taxa have not been recovered by culture dependent methods, neither, with very few exceptions, has their functional ecology been explored. A microbial seed bank of this magnitude has significance not just for Atacama soil ecosystem resilience but represents an enormous untapped resource for biotechnology discovery programmes in an era where resistance to existing antibiotics is rapidly becoming a major threat to global health.