bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous fNIRS and thermal infrared imaging during cognitive task reveal autonomic correlates of prefrontal cortex activity
Authors: Pinti Paola , Cardone Daniela , Merla Arcangelo 
Published: December 2015

AbstractFunctional Near Infrared-Spectroscopy (fNIRS) represents a powerful tool to non-invasively study task-evoked brain activity. fNIRS assessment of cortical activity may suffer for contamination by physiological noises of different origin (e.g. heart beat, respiration, blood pressure, skin blood flow), both task-evoked and spontaneous. Spontaneous changes occur at different time scales and, even if they are not directly elicited by tasks, their amplitude may result task-modulated. In this study, concentration changes of hemoglobin were recorded over the prefrontal cortex while simultaneously recording the facial temperature variations of the participants through functional infrared thermal (fIR) imaging. fIR imaging provides touch-less estimation of the thermal expression of peripheral autonomic. Wavelet analysis revealed task-modulation of the very low frequency (VLF) components of both fNIRS and fIR signals and strong coherence between them. Our results indicate that subjective cognitive and autonomic activities are intimately linked and that the VLF component of the fNIRS signal is affected by the autonomic activity elicited by the cognitive task. Moreover, we showed that task-modulated changes in vascular tone occur both at a superficial and at larger depth in the brain. Combined use of fNIRS and fIR imaging can effectively quantify the impact of VLF autonomic activity on the fNIRS signals.
A new sensitizer DVDMS combined with multiple focused ultrasound treatments: an effective antitumor strategy
Authors: Xiong Wenli , Wang Pan , Hu Jianmin , Jia Yali , Wu Lijie , Chen Xiyang , Liu Quanhong , Wang Xiaobing 
Published: December 2015

AbstractSonodynamic therapy (SDT) was developed as a promising noninvasive approach. The present study investigated the antitumor effect of a new sensitizer (sinoporphyrin sodium, referred to as DVDMS) combined with multiple ultrasound treatments on sarcoma 180 both in vitro and in vivo. The combined treatment significantly suppressed cell viability, potentiated apoptosis and markedly inhibited angiogenesis in vivo. In vivo, the tumor weight inhibition ratio reached 89.82% fifteen days after three sonication treatments plus DVDMS. This effect was stronger than one ultrasound alone (32.56%) and than one round of sonication plus DVDMS (59.33%). DVDMS combined with multiple focused ultrasound treatments initiated tumor tissue destruction, induced cancer cell apoptosis, inhibited tumor angiogenesis, suppressed cancer cell proliferation and decreased VEGF and PCNA expression levels. Moreover, the treatment did not show obvious signs of side effects or induce a drop in body weight. These results indicated that DVDMS combined with multiple focused ultrasounds may be a promising strategy against solid tumor.
Optimizing antibody expression by using the naturally occurring framework diversity in a live bacterial antibody display system
Authors: Lombana T. Noelle , Dillon Michael , Bevers III Jack , Spiess Christoph 
Published: December 2015

AbstractRapid identification of residues that influence antibody expression and thermostability is often needed to move promising therapeutics into the clinic. To establish a method that can assess small expression differences, we developed a Bacterial Antibody Display (BAD) system that overcomes previous limitations, enabling the use of full-length formats for antibody and antigen in a live cell setting. We designed a unique library of individual framework variants using natural diversity introduced by somatic hypermutation and screened half-antibodies for increased expression using BAD. We successfully identify variants that dramatically improve expression yields and in vitro thermostability of two therapeutically relevant antibodies in E. coli and mammalian cells. While we study antibody expression, bacterial display can now be expanded to examine the processes of protein folding and translocation. Additionally, our natural library design strategy could be applied during antibody humanization and library design for in vitro display methods to maintain expression and formulation stability.
Classification of octet AB-type binary compounds using dynamical charges: A materials informatics perspective
Authors: Pilania G. , Gubernatis J. E. , Lookman T. 
Published: December 2015

AbstractThe role of dynamical (or Born effective) charges in classification of octet AB-type binary compounds between four-fold (zincblende/wurtzite crystal structures) and six-fold (rocksalt crystal structure) coordinated systems is discussed. We show that the difference in the dynamical charges of the fourfold and sixfold coordinated structures, in combination with Harrison’s polarity, serves as an excellent feature to classify the coordination of 82sp–bonded binary octet compounds. We use a support vector machine classifier to estimate the average classification accuracy and the associated variance in our model where a decision boundary is learned in a supervised manner. Finally, we compare the out-of-sample classification accuracy achieved by our feature pair with those reported previously.
Shortfalls in the global protected area network at representing marine biodiversity
Authors: Klein Carissa J. , Brown Christopher J. , Halpern Benjamin S. , Segan Daniel B. , McGowan Jennifer , Beger Maria , Watson James E.M. 
Published: December 2015

AbstractThe first international goal for establishing marine protected areas (MPAs) to conserve the ocean’s biodiversity was set in 2002. Since 2006, the Convention on Biological Diversity (CBD) has driven MPA establishment, with 193 parties committed to protecting >10% of marine environments globally by 2020, especially ‘areas of particular importance for biodiversity’ (Aichi target 11). This has resulted in nearly 10 million km2 of new MPAs, a growth of ~360% in a decade. Unlike on land, it is not known how well protected areas capture marine biodiversity, leaving a significant gap in our understanding of existing MPAs and future protection requirements. We assess the overlap of global MPAs with the ranges of 17,348 marine species (fishes, mammals, invertebrates) and find that 97.4% of species have <10% of their ranges represented in stricter conservation classes. Almost all (99.8%) of the very poorly represented species (<2% coverage) are found within exclusive economic zones, suggesting an important role for particular nations to better protect biodiversity. Our results offer strategic guidance on where MPAs should be placed to support the CBD’s overall goal to avert biodiversity loss. Achieving this goal is imperative for nature and humanity, as people depend on biodiversity for important and valuable services.
Middle East respiratory syndrome coronavirus ORF4b protein inhibits type I interferon production through both cytoplasmic and nuclear targets
Authors: Yang Yang , Ye Fei , Zhu Na , Wang Wenling , Deng Yao , Zhao Zhengdong , Tan Wenjie 
Published: December 2015

AbstractMiddle East respiratory syndrome coronavirus (MERS-CoV) is a novel and highly pathogenic human coronavirus and has quickly spread to other countries in the Middle East, Europe, North Africa and Asia since 2012. Previous studies have shown that MERS-CoV ORF4b antagonizes the early antiviral alpha/beta interferon (IFN-α/β) response, which may significantly contribute to MERS-CoV pathogenesis; however, the underlying mechanism is poorly understood. Here, we found that ORF4b in the cytoplasm could specifically bind to TANK binding kinase 1 (TBK1) and IκB kinase epsilon (IKKε), suppress the molecular interaction between mitochondrial antiviral signaling protein (MAVS) and IKKε and inhibit IFN regulatory factor 3 (IRF3) phosphorylation and subsequent IFN-β production. Further analysis showed that ORF4b could also inhibit IRF3 and IRF7-induced production of IFN-β, whereas deletion of the nuclear localization signal of ORF4b abrogated its ability to inhibit IRF3 and IRF7-induced production of IFN-β, but not IFN-β production induced by RIG-I, MDA5, MAVS, IKKε and TBK-1, suggesting that ORF4b could inhibit the induction of IFN-β in both the cytoplasm and nucleus. Collectively, these results indicate that MERS-CoV ORF4b inhibits the induction of type I IFN through a direct interaction with IKKε/TBK1 in the cytoplasm and also in the nucleus with unknown mechanism. Viruses have evolved multiple strategies to evade or thwart a host’s antiviral responses. A novel human coronavirus (HCoV), Middle East respiratory syndrome coronavirus (MERS-CoV), is distinguished from other coronaviruses by its high pathogenicity and mortality. However, virulence determinants that distinguish MERS-CoV from other HCoVs have yet to be identified. MERS-CoV ORF4b antagonizes the early antiviral response, which may contribute to MERS-CoV pathogenesis. Here, we report the identification of the interferon (IFN) antagonism mechanism of MERS-CoV ORF4b. MERS-CoV ORF4b inhibits the production of type I IFN through a direct interaction with IKKε/TBK1 in the cytoplasm and also in the nucleus with unknown mechanism. These findings provide a rationale for the novel pathogenesis of MERS-CoV as well as a basis for developing a candidate therapeutic against this virus.
Leveraging a Multi-Omics Strategy for Prioritizing Personalized Candidate Mutation-Driver Genes: A Proof-of-Concept Study
Authors: Ding Keyue , Wu Songfeng , Ying Wantao , Pan Qi , Li Xiaoyuan , Zhao Dachun , Li Xianyu , Zhao Qing , Zhu Yunping , Ren Hong , Qian Xiaohong 
Published: December 2015

AbstractThe expression of mutant forms of proteins (e.g., oncogenes and tumor suppressors) has implications in cancer biology and clinical practice. Initial efforts have been made to characterize the transcription of tumor-mutated alleles; however, few studies have been reported to link tumor-mutated alleles to proteomics. We aimed to characterize the transcriptional and translational patterns of tumor-mutated alleles. We performed whole-exome sequencing, RNA-seq and proteome profiling in a hyper-mutated patient of hepatocellular carcinoma. Using the patient as a model, we show that only a small proportion of tumor-mutated alleles were expressed. In this case, 42% and 3.5% of the tumor-mutated alleles were identified to be transcribed and translated, respectively. Compared with genes with germline variations or without mutations, somatic mutations significantly reduced protein expression abundance. Using the transcriptional and translational patterns of tumor-mutated alleles, we classified the mutations into four types and only one type may be associated with the liver cancer and lead to hepatocarcinogenesis in the patient. Our results demonstrate how tumor-mutated alleles are transcribed and translated and how the expression enables the classification of somatic mutations that cause cancer. Leveraging multiple ‘omics’ datasets provides a new avenue for understanding patient-specific mutations that underlie carcinogenesis.
A preliminary study of ALPPS procedure in a rat model
Authors: Shi Huawen , Yang Guangchao , Zheng Tongsen , Wang Jiabei , Li Lulu , Liang Yingjian , Xie Changming , Yin Dalong , Sun Boshi , Sun Jing , Wang Huanlai , Pan Shangha , Jiang Hongchi , Lau WanYee , Liu Lianxin 
Published: December 2015

AbstractAssociating Liver Partition and Portal vein ligation for Staged hepatectomy (ALPPS) has been reported to be a novel surgical technique that provides fast and effective growth of liver remnant. Despite occasional reports on animal studies, the mechanisms of rapid liver regeneration in ALPPS remains unclear. In the present study, we intend to develop a reproducible rat model to mimick ALPPS and to explore the underlying mechanisms. Rats assigned to the portal vein ligation (PVL), left lateral lobe (LLL) resection, transection and sham groups served as controls. Results indicated that the regeneration rate in the remnant liver after ALPPS was two times relative to PVL, whereas rats with transection alone showed minimal volume increase. The expression levels of Ki-67 and PCNA were about ten-fold higher after ALPPS compared with the transection and LLL resection groups and four-fold higher compared with the PVL group. The levels of TNF-α, IL-6 and HGF in the regenerating liver remnant were about three-fold higher after ALPPS than the controls. There was a more significant activation of NF-κB p65, STAT3 and Yap after ALPPS, suggesting synergistic activation of the pathways by PVL and transection, which might play an important role in liver regeneration after ALPPS.
TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer
Authors: Chapman Christopher G. , Mariani Christopher J. , Wu Feng , Meckel Katherine , Butun Fatma , Chuang Alice , Madzo Jozef , Bissonnette Marc B. , Kwon John H. , Godley Lucy A. 
Published: December 2015

AbstractThe formation of differentiated cell types from pluripotent progenitors involves epigenetic regulation of gene expression. DNA hydroxymethylation results from the enzymatic oxidation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) by the ten-eleven translocation (TET) 5-mC dioxygenase enzymes. Previous work has mapped changes in 5-mC during differentiation of intestinal stem cells. However, whether or not 5-hmC regulates colonocyte differentiation is unknown. Here we show that 5-hmC regulates gene expression during colonocyte differentiation and controls gene expression in human colon cancers. Genome-wide profiling of 5-hmC during in vitro colonic differentiation demonstrated that 5-hmC is gained at highly expressed and induced genes and is associated with intestinal transcription factor binding sites, including those for HNF4A and CDX2. TET1 induction occurred during differentiation and TET1 knockdown altered gene expression and inhibited barrier formation of colonocytes. We find that the 5-hmC distribution in primary human colonocytes parallels the distribution found in differentiated cells in vitro and that gene-specific 5-hmC changes in human colon cancers are directly correlated with changes in gene expression. Our results support a model in which 5-hmC regulates differentiation of adult human intestine and 5-hmC alterations contribute to the disrupted gene expression in colon cancer.
The Y137H mutation of VvCYP51 gene confers the reduced sensitivity to tebuconazole in Villosiclava virens
Authors: Wang Fei , Lin Yang , Yin Wei-Xiao , Peng You-Liang , Schnabel Guido , Huang Jun-Bin , Luo Chao-Xi 
Published: December 2015

AbstractManagement of rice false smut disease caused by Villosiclava virens is dependent on demethylation inhibitor (DMI) fungicides. Investigation of molecular mechanisms of resistance is therefore of upmost importance. In this study the gene encoding the target protein for DMI fungicides (VvCYP51) was cloned and investigated. The VvCYP51 gene in the resistant mutant revealed both a change from tyrosine to histidine at position 137 (Y137H) and elevated gene expression compared to the parental isolate. In order to determine which of these mechanisms was responsible for the reduced sensitivity to DMI fungicide tebuconazole, transformants expressing the mutated or the wild type VvCYP51 gene were generated. Transformants carrying the mutated gene were more resistant to tebuconazole compared to control transformants lacking the mutation, but the expression of the VvCYP51 gene was not significantly correlated with EC50 values. The wild type VvCYP51 protein exhibited stronger affinity for tebuconazole compared to the VvCYP51/Y137H in both molecular docking analysis and experimental binding assays. The UV-generated mutant as well as transformants expressing the VvCYP51/Y137H did not exhibit significant fitness penalties based on mycelial growth and spore germination, suggesting that isolates resistant to DMI fungicides based on the Y137H mutation may develop and be competitive in the field.
Organochlorine pesticides (OCPs) in wetland soils under different land uses along a 100-year chronosequence of reclamation in a Chinese estuary
Authors: Bai Junhong , Lu Qiongqiong , Zhao Qingqing , Wang Junjing , Gao Zhaoqin , Zhang Guangliang 
Published: December 2015

AbstractSoil profiles were collected at a depth of 30 cm in ditch wetlands (DWs), riverine wetlands (RiWs) and reclaimed wetlands (ReWs) along a 100-year chronosequence of reclamation in the Pearl River Delta. In total, 16 OCPs were measured to investigate the effects of wetland reclamation and reclamation history on OCP levels. Our results showed that average ∑DDTs, HCB, MXC and ∑OCPs were higher in surface soils of DWs compared to RiWs and ReWs. Both D30 and D20 soils contained the highest ∑OCP levels, followed by D40 and D100 soils; lower ∑OCP levels occurred in D10 soils. Higher ∑OCP levels were observed in the younger RiWs than in the older ones and surface soils exhibited higher ∑OCP concentrations in the older ReWs compared with younger ReWs. The predominant percentages of γ-HCH in ∑HCHs (>42%) and aldrin in ∑DRINs (>46%) in most samples reflected the recent use of lindane and aldrin. The presence of dominant DDT isomers (p,p’-DDE and p,p’-DDD) indicated the historical input of DDT and significant aerobic degradation of the compound. Generally, DW soils had a higher ecotoxicological risk of OCPs than RiW and ReW soils and the top 30 cm soils had higher ecotoxicological risks of HCHs than of DDTs.
Decoding the view expectation during learned maze navigation from human fronto-parietal network
Authors: Shikauchi Yumi , Ishii Shin 
Published: December 2015

AbstractHumans use external cues and prior knowledge about the environment to monitor their positions during spatial navigation. View expectation is essential for correlating scene views with a cognitive map. To determine how the brain performs view expectation during spatial navigation, we applied a multiple parallel decoding technique to functional magnetic resonance imaging (fMRI) when human participants performed scene choice tasks in learned maze navigation environments. We decoded participants’ view expectation from fMRI signals in parietal and medial prefrontal cortices, whereas activity patterns in occipital cortex represented various types of external cues. The decoder’s output reflected participants’ expectations even when they were wrong, corresponding to subjective beliefs opposed to objective reality. Thus, view expectation is subjectively represented in human brain and the fronto-parietal network is involved in integrating external cues and prior knowledge during spatial navigation.
Neural substrate of quality of life in patients with schizophrenia: a magnetisation transfer imaging study
Authors: Faget-Agius Catherine , Boyer Laurent , Wirsich Jonathan , Ranjeva Jean-Philippe , Richieri Raphaelle , Soulier Elisabeth , Confort-Gouny Sylviane , Auquier Pascal , Guye Maxime , Lançon Christophe 
Published: December 2015

AbstractThe aim of this study was to investigate the neural substrate underlying quality of life (QoL) and to demonstrate the microstructural abnormalities associated with impaired QoL in a large sample of patients with schizophrenia, using magnetisation transfer imaging. A total of 81 right-handed men with a diagnosis of schizophrenia and 25 age- and sex-similar healthy controls were included and underwent a 3T MRI with magnetization transfer ratio (MTR) to detect microstructural abnormalities. Compared with healthy controls, patients with schizophrenia had grey matter (GM) decreased MTR values in the temporal lobe (BA21, BA37 and BA38), the bilateral insula, the occipital lobe (BA17, BA18 and BA19) and the cerebellum. Patients with impaired QoL had lower GM MTR values relative to patients with preserved QoL in the bilateral temporal pole (BA38), the bilateral insula, the secondary visual cortex (BA18), the vermis and the cerebellum. Significant correlations between MTR values and QoL scores (p < 0.005) were observed in the GM of patients in the right temporal pole (BA38), the bilateral insula, the vermis and the right cerebellum. Our study shows that QoL impairment in patients with schizophrenia is related to the microstructural changes in an extensive network, suggesting that QoL is a bio-psychosocial marker.
Laser propulsion of nanobullets by adiabatic compression of surface plasmon polaritons
Authors: Folli Viola , Ruocco Giancarlo , Conti Claudio 
Published: December 2015

AbstractLaser propulsion and guide of nanosized objects is fundamental for a wide number of applications. These applications are often limited by the fact that the optical forces acting on nanoparticles are almost negligible even in the favorable case of metallic particles and hence large laser powers are needed to accelerate and guide nanosize devices in practical applications. Furthermore, metallic nanoparticles exhibit strong absorption bands and scattering and this makes more difficult controlling nanopropulsion. Thus, finding some mechanism enhancing the optomechanical interaction at the nanoscale controlled by laser is specifically challenging and pivotal. Here, we demonstrate a novel physical effect where the well-known adiabatic localization of the enhanced plasmonic surface field on the apex of metallic nanocones produces a significant optical pressure employable as a propulsive mechanism. The proposed method gives the possibility to develop new photonics devices to accelerate metallic nanobullets over long distances for a variety of applications.
Re-engineering cellular physiology by rewiring high-level global regulatory genes
Authors: Fitzgerald Stephen , Dillon Shane C. , Chao Tzu-Chiao , Wiencko Heather L. , Hokamp Karsten , Cameron Andrew D. S. , Dorman Charles J. 
Published: December 2015

AbstractKnowledge of global regulatory networks has been exploited to rewire the gene control programmes of the model bacterium Salmonella enterica serovar Typhimurium. The product is an organism with competitive fitness that is superior to that of the wild type but tuneable under specific growth conditions. The paralogous hns and stpA global regulatory genes are located in distinct regions of the chromosome and control hundreds of target genes, many of which contribute to stress resistance. The locations of the hns and stpA open reading frames were exchanged reciprocally, each acquiring the transcription control signals of the other. The new strain had none of the compensatory mutations normally associated with alterations to hns expression in Salmonella; instead it displayed rescheduled expression of the stress and stationary phase sigma factor RpoS and its regulon. Thus the expression patterns of global regulators can be adjusted artificially to manipulate microbial physiology, creating a new and resilient organism.
Self-Growth of Centimeter-Scale Single Crystals by Normal Sintering Process in Modified Potassium Sodium Niobate Ceramics
Authors: Ahn Cheol-Woo , Lee Ho-Yong , Han Guifang , Zhang Shujun , Choi Si-Young , Choi Jong-Jin , Kim Jong-Woo , Yoon Woon-Ha , Choi Joon-Hwan , Park Dong-Soo , Hahn Byung-Dong , Ryu Jungho 
Published: December 2015

AbstractIn this manuscript, an interesting phenomenon is reported. That is the self-growth of single crystals in Pb-free piezoelectric ceramics. These crystals are several centimeters in size. They are grown without any seed addition through a normal sintering process in modified potassium sodium niobate ceramics. It has been achieved by the composition designed to compensate the Na+loss which occurs during the liquid phase sintering. The composition of the crystals is (K0.4925Na0.4925−xBa0.015+x/2)Nb0.995+xO3[x is determined by the Na+loss, due to Na2O volatilization]. These crystals have high piezoelectric voltage coefficients (g33, 13110−3Vm/N), indicating that they are good candidates for piezoelectric sensors and energy harvesting devices. We hope that this report can offer the opportunity for many researchers to have an interest in these crystals.