bluuebunny/crossref_metadata_2025 huggingface dataset:
Parent–Child Connectedness and Long-Term Risk for Suicidal Ideation in a Nationally Representative Sample of US Adolescents
Authors: Kuramoto-Crawford S. Janet , Ali Mir M. , Wilcox Holly C.
Published: November 2016

Abstract. Background: Few studies have addressed on the role of parent–child connectedness (PCC) on adolescents' risk for suicidal ideation from a longitudinal, developmental perspective. Aim: This study examined PCC during adolescence and risk of suicidal ideation into adulthood among a nationally representative sample of American adolescents. Method: The study includes 13,234 adolescents aged 11–18 from the National Longitudinal Study of Adolescent to Adult Health (Add Health) who were surveyed during adolescence (1994–1995) and then again in early adulthood (2008–2009). Multinomial logistic regression estimated the association between PCC during adolescence and having ideation during the adolescence period only, in adulthood only, and in both adolescence and adulthood as compared with those without suicidal ideation. Results: After adjusting for depressive symptoms and other parent and adolescent characteristics, adolescents in two-parent households who reported higher PCC during adolescence had lower relative risk of having ideation during adolescence alone and in both adolescence and adulthood. In mother-only households, higher mother connectedness was also associated with decreased risk of having adolescent ideation. Conclusion: PCC is an important modifiable target for the prevention of suicidal ideation from adolescence into adulthood.
CELF1 is a central node in post-transcriptional regulatory programmes underlying EMT
Authors: Chaudhury Arindam , Cheema Shebna , Fachini Joseph M. , Kongchan Natee , Lu Guojun , Simon Lukas M. , Wang Tao , Mao Sufeng , Rosen Daniel G. , Ittmann Michael M. , Hilsenbeck Susan G. , Shaw Chad A. , Neilson Joel R.
Published: November 2016

The importance of translational regulation in tumour biology is increasingly appreciated. Here, we leverage polyribosomal profiling to prospectively define translational regulatory programs underlying epithelial-to-mesenchymal transition (EMT) in breast epithelial cells. We identify a group of ten translationally regulated drivers of EMT sharing a common GU-rich cis-element within the 3′-untranslated region (3′-UTR) of their mRNA. These cis-elements, necessary for the regulatory activity imparted by these 3′-UTRs, are directly bound by the CELF1 protein, which itself is regulated post-translationally during the EMT program. CELF1 is necessary and sufficient for both mesenchymal transition and metastatic colonization, and CELF1 protein, but not mRNA, is significantly overexpressed in human breast cancer tissues. Our data present an 11-component genetic pathway, invisible to transcriptional profiling approaches, in which the CELF1 protein functions as a central node controlling translational activation of genes driving EMT and ultimately tumour progression.
Reprogramming mouse fibroblasts into engraftable myeloerythroid and lymphoid progenitors
Authors: Cheng Hui , Ang Heather Yin-Kuan , A. EL Farran Chadi , Li Pin , Fang Hai Tong , Liu Tong Ming , Kong Say Li , Chin Michael Lingzi , Ling Wei Yin , Lim Edwin Kok Hao , Li Hu , Huber Tara , Loh Kyle M. , Loh Yuin-Han , Lim Bing
Published: November 2016

Recent efforts have attempted to convert non-blood cells into hematopoietic stem cells (HSCs) with the goal of generating blood lineages de novo. Here we show that hematopoietic transcription factors Scl, Lmo2, Runx1 and Bmi1 can convert a developmentally distant lineage (fibroblasts) into ‘induced hematopoietic progenitors’ (iHPs). Functionally, iHPs generate acetylcholinesterase+ megakaryocytes and phagocytic myeloid cells in vitro and can also engraft immunodeficient mice, generating myeloerythoid and B-lymphoid cells for up to 4 months in vivo. Molecularly, iHPs transcriptionally resemble native Kit+ hematopoietic progenitors. Mechanistically, reprogramming factor Lmo2 implements a hematopoietic programme in fibroblasts by rapidly binding to and upregulating the Hhex and Gfi1 genes within days. Moreover the reprogramming transcription factors also require extracellular BMP and MEK signalling to cooperatively effectuate reprogramming. Thus, the transcription factors that orchestrate embryonic hematopoiesis can artificially reconstitute this programme in developmentally distant fibroblasts, converting them into engraftable blood progenitors.
Genome-wide RNAi screen reveals ALK1 mediates LDL uptake and transcytosis in endothelial cells
Authors: Kraehling Jan R. , Chidlow John H. , Rajagopal Chitra , Sugiyama Michael G. , Fowler Joseph W. , Lee Monica Y. , Zhang Xinbo , Ramírez Cristina M. , Park Eon Joo , Tao Bo , Chen Keyang , Kuruvilla Leena , Larriveé Bruno , Folta-Stogniew Ewa , Ola Roxana , Rotllan Noemi , Zhou Wenping , Nagle Michael W. , Herz Joachim , Williams Kevin Jon , Eichmann Anne , Lee Warren L. , Fernández-Hernando Carlos , Sessa William C.
Published: November 2016

In humans and animals lacking functional LDL receptor (LDLR), LDL from plasma still readily traverses the endothelium. To identify the pathways of LDL uptake, a genome-wide RNAi screen was performed in endothelial cells and cross-referenced with GWAS-data sets. Here we show that the activin-like kinase 1 (ALK1) mediates LDL uptake into endothelial cells. ALK1 binds LDL with lower affinity than LDLR and saturates only at hypercholesterolemic concentrations. ALK1 mediates uptake of LDL into endothelial cells via an unusual endocytic pathway that diverts the ligand from lysosomal degradation and promotes LDL transcytosis. The endothelium-specific genetic ablation of Alk1 in Ldlr-KO animals leads to less LDL uptake into the aortic endothelium, showing its physiological role in endothelial lipoprotein metabolism. In summary, identification of pathways mediating LDLR-independent uptake of LDL may provide unique opportunities to block the initiation of LDL accumulation in the vessel wall or augment hepatic LDLR-dependent clearance of LDL.
Classic IL-6R signalling is dispensable for intestinal epithelial proliferation and repair
Authors: Aden K , Breuer A , Rehman A , Geese H , Tran F , Sommer J , Waetzig G H , Reinheimer T M , Schreiber S , Rose-John S , Scheller J , Rosenstiel P
Published: November 2016

Inflammatory bowel disease is characterized by disturbed cytokine signalling in the mucosa. Inhibition of the proinflammatory interleukin (IL)-6 pathway is a promising new therapeutic strategy, but safety concerns arise as IL-6 signalling also contributes to epithelial repair of the intestinal mucosa. To which extent IL-6 classic or trans-signalling contributes to intestinal repair remains elusive. We tested the influence of IL-6 classic signalling on intestinal repair and proliferation. Whereas IL-6 induced STAT3 phosphorylation in the colonic cancer cell lines, primary non-malignant intestinal organoids did not respond to IL-6 classic signalling. Mice deficient in intestinal IL-6R (IL-6RΔIEC mice) did not display increased susceptibility to acute dextran sulfate sodium (DSS)-induced colitis. In the azoxymethane DSS model IL-6RΔIEC mice were not protected from inflammation-induced carcinogenesis but showed comparable tumor load to wild-type mice. These data indicate that classic signalling is not the major pathway to transduce IL-6 stimuli into the intestinal epithelium.
N-linked glycosylation at Asn152 on CD147 affects protein folding and stability: promoting tumour metastasis in hepatocellular carcinoma
Authors: Li Jiang-Hua , Huang Wan , Lin Peng , Wu Bo , Fu Zhi-Guang , Shen Hao-Miao , Jing Lin , Liu Zhen-Yu , Zhou Yang , Meng Yao , Xu Bao-Qing , Chen Zhi-Nan , Jiang Jian-Li
Published: November 2016

Cluster of differentiation 147 (CD147), also known as extracellular matrix metalloproteinase inducer, is a transmembrane glycoprotein that mediates oncogenic processes partly through N-glycosylation modifications. N-glycosylation has been demonstrated to be instrumental for the regulation of CD147 function during malignant transformation. However, the role that site-specific glycosylation of CD147 plays in its defective function in hepatocellular carcinomacells needs to be determined. Here, we demonstrate that the modification of N-glycosylation at Asn152 on CD147 strongly promotes hepatocellular carcinoma (HCC) invasion and migration. After the removal of N-glycans at Asn152, CD147 was more susceptible to degradation by ER-localized ubiquitin ligase-mediated endoplasmic reticulum-associated degradation (ERAD). Furthermore, N-linked glycans at Asn152 were required for CD147 to acquire and maintain proper folding in the ER. Moreover, N-linked glycans at Asn152 functioned as a recognition motif that was directly mediated by the CNX quality control system. Two phases in the retention-based ER chaperones system drove ER-localized CD147 trafficking to degradation. Deletion of N-linked glycosylation at Asn152 on CD147 significantly suppressed in situ tumour metastasis. These data could potentially shed light on the molecular regulation of CD147 through glycosylation and provide a valuable means of developing drugs that target N-glycans at Asn152 on CD147.
Using the virtual reality device Oculus Rift for neuropsychological assessment of visual processing capabilities
Authors: Foerster Rebecca M. , Poth Christian H. , Behler Christian , Botsch Mario , Schneider Werner X.
Published: November 2016

Neuropsychological assessment of human visual processing capabilities strongly depends on visual testing conditions including room lighting, stimuli, and viewing-distance. This limits standardization, threatens reliability, and prevents the assessment of core visual functions such as visual processing speed. Increasingly available virtual reality devices allow to address these problems. One such device is the portable, light-weight, and easy-to-use Oculus Rift. It is head-mounted and covers the entire visual field, thereby shielding and standardizing the visual stimulation. A fundamental prerequisite to use Oculus Rift for neuropsychological assessment is sufficient test-retest reliability. Here, we compare the test-retest reliabilities of Bundesen’s visual processing components (visual processing speed, threshold of conscious perception, capacity of visual working memory) as measured with Oculus Rift and a standard CRT computer screen. Our results show that Oculus Rift allows to measure the processing components as reliably as the standard CRT. This means that Oculus Rift is applicable for standardized and reliable assessment and diagnosis of elementary cognitive functions in laboratory and clinical settings. Oculus Rift thus provides the opportunity to compare visual processing components between individuals and institutions and to establish statistical norm distributions.
Sub-optimality in motor planning is retained throughout 9 days practice of 2250 trials
Authors: Ota Keiji , Shinya Masahiro , Kudo Kazutoshi
Published: November 2016

Optimality in motor planning, as well as accuracy in motor execution, is required to maximize expected gain under risk. In this study, we tested whether humans are able to update their motor planning. Participants performed a coincident timing task with an asymmetric gain function, in which optimal response timing to gain the highest total score depends on response variability. Their behaviours were then compared using a Bayesian optimal decision model. After 9 days of practicing 2250 trials, the total score increased, and temporal variance decreased. On the other hand, the participants showed consistent risk-seeking or risk-averse behaviour, preserving suboptimal motor planning. These results suggest that a human’s computational ability to calculate an optimal motor plan is limited, and it is difficult to improve it through repeated practice with a score feedback.
Correction: Corrigendum: Proteome mapping of Plasmodium: identification of the P. yoelii remodellome
Authors: Siau Anthony , Huang Ximei , Weng Mei , Sze Siu Kwan , Preiser Peter R.
Published: November 2016

Scientific Reports 6: Article number: 31055; published online: 09 August 2016; updated: 21 November 2016.
The helminth product, ES-62 modulates dendritic cell responses by inducing the selective autophagolysosomal degradation of TLR-transducers, as exemplified by PKCδ
Authors: Eason Russell J. , Bell Kara S. , Marshall Fraser A. , Rodgers David T. , Pineda Miguel A. , Steiger Christina N. , Al-Riyami Lamyaa , Harnett William , Harnett Margaret M.
Published: November 2016

We have previously shown that ES-62, a phosphorylcholine (PC)-containing glycoprotein secreted by the parasitic filarial nematode Acanthocheilonema viteae targets dendritic cell (DC) responses, specifically by suppressing TLR4 signalling to inhibit Th1/Th17-driven inflammation. We have now investigated the molecular mechanisms underpinning such immunomodulation and show here that ES-62-mediated downregulation of protein kinase C-δ (PKC-δ), a TLR4-associated signalling mediator required for full activation of LPS-driven pro-inflammatory responses, is associated with induction of a low level of autophagic flux, as evidenced by upregulation and trafficking of p62 and LC3 and their consequent autophagolysosomal degradation. By contrast, the classical TLR4 ligand LPS, strongly upregulates p62 and LC3 expression but under such canonical TLR4 signalling this upregulation appears to reflect a block in autophagic flux, with these elements predominantly degraded in a proteasomal manner. These data are consistent with autophagic flux acting to homeostatically suppress proinflammatory DC responses and indeed, blocking of PKC-δ degradation by the autophagolysosomal inhibitors, E64d plus pepstatin A, results in abrogation of the ES-62-mediated suppression of LPS-driven release of IL-6, IL-12p70 and TNF-α by DCs. Thus, by harnessing this homeostatic regulatory mechanism, ES-62 can protect against aberrant inflammation, either to promote parasite survival or serendipitously, exhibit therapeutic potential in inflammatory disease.
The transcription cofactor CRTC1 protects from aberrant hepatic lipid accumulation
Authors: Kim Hwijin
Published: November 2016

Nonalcoholic fatty liver disease (NAFLD) is a rapidly emerging global health-problem. NAFLD encompasses a range of conditions associated with hepatic steatosis, aberrant accumulation of fat in hepatocytes. Although obesity and metabolic syndrome are considered to have a strong association with NAFLD, genetic factors that predispose liver to NAFLD and molecular mechanisms by which excess hepatic lipid develops remain largely unknown. We report that the transcription cofactor CRTC1 confers broad spectrum protection against hepatic steatosis development. CRTC1 directly interferes with the expression of genes regulated by lipogenic transcription factors, most prominently liver x receptor α (LXRα). Accordingly, Crtc1 deficient mice develop spontaneous hepatic steatosis in young age. As a cyclic AMP effector, CRTC1 mediates anti-steatotic effects of calorie restriction (CR). Notably, CRTC1 also mediates anti-lipogenic effects of bile acid signaling, whereas it is negatively regulated by miR-34a, a pathogenic microRNA upregulated in a broad spectrum of NAFLD. These patterns of gene function and regulation of CRTC1 are distinct from other CR-responsive proteins, highlighting critical protective roles that CRTC1 selectively plays against NAFLD development, which in turn provides novel opportunities for selectively targeting beneficial therapeutic effects of CR.
Heat stroke internet searches can be a new heatwave health warning surveillance indicator
Authors: Li Tiantian , Ding Fan , Sun Qinghua , Zhang Yi , Kinney Patrick L.
Published: November 2016

The impact of major heatwave shocks on population morbidity and mortality has become an urgent public health concern. However, Current heatwave warning systems suffer from a lack of validation and an inability to provide accurate health risk warnings in a timely way. Here we conducted a correlation and linear regression analysis to test the relationship between heat stroke internet searches and heat stroke health outcomes in Shanghai, China, during the summer of 2013. We show that the resulting heatstroke index captures much of the variation in heat stroke cases and deaths. The correlation between heat stroke deaths, the search index and the incidence of heat stroke is higher than the correlation with maximum temperature. This study highlights a fast and effective heatwave health warning indicator with potential to be used throughout the world.
Interplay between VEGF and Nrf2 regulates angiogenesis due to intracranial venous hypertension
Authors: Li Liwen , Pan Hao , Wang Handong , Li Xiang , Bu Xiaomin , Wang Qiang , Gao Yongyue , Wen Guodao , Zhou Yali , Cong Zixiang , Yang Youqing , Tang Chao , Liu Zhengwei
Published: November 2016

Venous hypertension(VH) plays an important role in the pathogenesis of cerebral arteriovenous malformations (AVMs) and is closely associated with the HIF-1α/VEGF signaling pathway. Nuclear factor erythroid 2-related factor 2(Nrf2) significantly influences angiogenesis; however, the interplay between Nrf2 and VEGF under VH in brain AVMs remains unclear. Therefore, our study aimed to investigate the interplay between Nrf2 and VEGF due to VH in brain AVMs. Immunohistochemistry indicated that Nrf2 and VEGF were highly expressed in human brain AVM tissues. In vivo, we established a VH model in both wild-type (WT) and siRNA-mediated Nrf2 knockdown rats. VH significantly increased the expression of Nrf2 and VEGF. Loss of Nrf2 markedly inhibited the upregulation of VEGF, as determined by Western blot analysis and qRT-PCR. In vitro, primary brain microvascular endothelial cells (BMECs) were isolated from WT and Nrf2−/− mice, and a VEGF-Nrf2 positive feed-back loop was observed in BMECs. By trans well assay and angiogenesis assay, Nrf2 knockout significantly inhibited the migration and vascular tube formation of BMECs. These findings suggest that the interplay between Nrf2 and VEGF can contribute to VH-induced angiogenesis in brain AVMs pathogenesis.
Direct comparison of gluco-oligosaccharide oxidase variants and glucose oxidase: substrate range and H2O2 stability
Authors: Vuong Thu V. , Foumani Maryam , MacCormick Benjamin , Kwan Rachel , Master Emma R.
Published: November 2016

Glucose oxidase (GO) activity is generally restricted to glucose and is susceptible to inactivation by H2O2. By comparison, the Y300A variant of gluco-oligosaccharide oxidase (GOOX) from Sarocladium strictum showed broader substrate range and higher H2O2 stability. Specifically, Y300A exhibited up to 40 times higher activity on all tested sugars except glucose, compared to GO. Moreover, fusion of the Y300A variant to a family 22 carbohydrate binding module from Clostridium thermocellum (CtCBM22A) nearly doubled its catalytic efficiency on glucose, while retaining significant activity on oligosaccharides. In the presence of 200 mM of H2O2, the recombinant CtCBM22A_Y300A retained 80% of activity on glucose and 100% of activity on cellobiose, the preferred substrate for this enzyme. By contrast, a commercial glucose oxidase reported to contain ≤0.1 units catalase/ mg protein, retained 60% activity on glucose under the same conditions. GOOX variants appear to undergo a different mechanism of inactivation, as a loss of histidine instead of methionine was observed after H2O2 incubation. The addition of CtCBM22A also promoted functional binding of the fusion enzyme to xylan, facilitating its simultaneous purification and immobilization using edible oat spelt xylan, which might benefit the usage of this enzyme preparation in food and baking applications.
Erratum: Control of ADAM17 activity by regulation of its cellular localisation
Authors: Lorenzen Inken , Lokau Juliane , Korpys Yvonne , Oldefest Mirja , Flynn Charlotte M. , Künzel Ulrike , Garbers Christoph , Freeman Matthew , Grötzinger Joachim , Düsterhöft Stefan
Published: November 2016

Scientific Reports 6: Article number: 35067; published online: 12 October 2016; updated: 21 November 2016.
A new species of Trichoderma hypoxylon harbours abundant secondary metabolites
Authors: Sun Jingzu , Pei Yunfei , Li Erwei , Li Wei , Hyde Kevin D. , Yin Wen-Bing , Liu Xingzhong
Published: November 2016

Some species of Trichoderma are fungicolous on fungi and have been extensively studied and commercialized as biocontrol agents. Multigene analyses coupled with morphology, resulted in the discovery of T. hypoxylon sp. nov., which was isolated from surface of the stroma of Hypoxylon anthochroum. The new taxon produces Trichoderma- to Verticillium-like conidiophores and hyaline conidia. Phylogenetic analyses based on combined ITS, TEF1-α and RPB2 sequence data indicated that T. hypoxylon is a well-distinguished species with strong bootstrap support in the polysporum group. Chemical assessment of this species reveals a richness of secondary metabolites with trichothecenes and epipolythiodiketopiperazines as the major compounds. The fungicolous life style of T. hypoxylon and the production of abundant metabolites are indicative of the important ecological roles of this species in nature.
Crosstalk between sugarcane and a plant-growth promoting Burkholderia species
Authors: Paungfoo-Lonhienne Chanyarat , Lonhienne Thierry G. A. , Yeoh Yun Kit , Donose Bogdan C. , Webb Richard I. , Parsons Jeremy , Liao Webber , Sagulenko Evgeny , Lakshmanan Prakash , Hugenholtz Philip , Schmidt Susanne , Ragan Mark A.
Published: November 2016

Bacterial species in the plant-beneficial-environmental clade of Burkholderia represent a substantial component of rhizosphere microbes in many plant species. To better understand the molecular mechanisms of the interaction, we combined functional studies with high-resolution dual transcriptome analysis of sugarcane and root-associated diazotrophic Burkholderia strain Q208. We show that Burkholderia Q208 forms a biofilm at the root surface and suppresses the virulence factors that typically trigger immune response in plants. Up-regulation of bd-type cytochromes in Burkholderia Q208 suggests an increased energy production and creates the microaerobic conditions suitable for BNF. In this environment, a series of metabolic pathways are activated in Burkholderia Q208 implicated in oxalotrophy, microaerobic respiration, and formation of PHB granules, enabling energy production under microaerobic conditions. In the plant, genes involved in hypoxia survival are up-regulated and through increased ethylene production, larger aerenchyma is produced in roots which in turn facilitates diffusion of oxygen within the cortex. The detected changes in gene expression, physiology and morphology in the partnership are evidence of a sophisticated interplay between sugarcane and a plant-growth promoting Burkholderia species that advance our understanding of the mutually beneficial processes occurring in the rhizosphere.
Towards Functional Annotation of the Preimplantation Transcriptome: An RNAi Screen in Mammalian Embryos
Authors: Cui Wei , Dai Xiangpeng , Marcho Chelsea , Han Zhengbin , Zhang Kun , Tremblay Kimberly D. , Mager Jesse
Published: November 2016

With readily available transcriptome-wide data, understanding the role of each expressed gene is an essential next step. Although RNAi technologies allow for genome-wide screens in cell culture, these approaches cannot replace strategies for discovery in the embryo. Here we present, for the first time, a knockdown screen in mouse preimplantation embryos. Early mammalian development encompasses dynamic cellular, molecular and epigenetic events that are largely conserved from mouse to man. We assayed 712 genes for requirements during preimplantation. We identified 59 genes required for successful development or outgrowth and implantation. We have characterized each phenotype and revealed cellular, molecular, and lineage specific defects following knockdown of transcript. Induced network analyses demonstrate this as a valid approach to identify networks of genes that play important roles during preimplantation. Our approach provides a robust and efficient strategy towards identification of novel phenotypes during mouse preimplantation and facilitates functional annotation of the mammalian transcriptome.
Magnesium alloy covered stent for treatment of a lateral aneurysm model in rabbit common carotid artery: An in vivo study
Authors: Wang Wu , Wang Yong-Li , Chen Mo , Chen Liang , Zhang Jian , Li Yong-Dong , Li Ming-Hua , Yuan Guang-Yin
Published: November 2016

Magnesium alloy covered stents have rarely been used in the common carotid artery (CCA). We evaluated the long-term efficacy of magnesium alloy covered stents in a lateral aneurysm model in rabbit CCA. Magnesium alloy covered stents (group A, n = 7) or Willis covered stents (group B, n = 5) were inserted in 12 New Zealand White rabbits and they were followed up for 12 months. The long-term feasibility for aneurysm occlusion was studied through angiograms; the changes in vessel area and lumen area were assessed with IVUS. Complete aneurysmal occlusion was achieved in all aneurysms. Angiography showed that the diameter of the stented CCA in group A at 6 and 12 months was significantly greater than the diameter immediately after stent placement. On intravascular ultrasound (IVUS) examination, the mean lumen area of the stented CCA in group A was significantly greater at 6 and 12 months than that immediately after stent placement; the mean lumen area was also significantly greater in group A than in group B at the same time points. The magnesium alloy covered stents proved to be an effective approach for occlusion of lateral aneurysm in the rabbit CCA; it provides distinct advantages that are comparable to that obtained with the Willis covered stent.
Mitigating effects of ex situ application of rice straw on CH4 and N2O emissions from paddy-upland coexisting system
Authors: Wang Wei , Wu Xiaohong , Chen Anlei , Xie Xiaoli , Wang Yunqiu , Yin Chunmei
Published: November 2016

The in situ application of rice straw enhances CH4 emissions by a large margin. The ex situ application of rice straw in uplands, however, may mitigate total global warming potential (GWP) of CH4 and N2O emissions from paddy-upland coexisting systems. To evaluate the efficiency of this practice, two field trials were conducted in rice-rice-fallow and maize-rape cropping systems, respectively. Year-round measurements of CH4 and N2O emissions were conducted to evaluate the system-scaled GWP. The results showed that CH4 accounted for more than 98% of GWP in paddy. Straw removal from paddy decreased 44.7% (302.1 kg ha−1 yr−1) of CH4 emissions and 51.2% (0.31 kg ha−1 yr−1) of N2O emissions, thus decreased 44.8% (7693 kg CO2-eqv ha−1 yr−1) of annual GWP. N2O accounted for almost 100% of GWP in upland. Straw application in upland had insignificant effects on CH4 and N2O emissions, which increased GWP only by 91 kg CO2-eqv ha−1 yr−1. So, the transfer of straw from paddy to upland could decrease GWP by 7602 kg CO2-eqv ha−1 yr−1. Moreover, straw retention during late rice season contributed to 88.2% of annual GWP increment. It is recommended to transfer early rice straw to upland considering GWP mitigation, nutrient recycling and labor cost.
Motor noise is rich signal in autism research and pharmacological treatments
Authors: Torres E. B. , Denisova K.
Published: November 2016

The human body is in constant motion, from every breath that we take, to every visibly purposeful action that we perform. Remaining completely still on command is a major achievement as involuntary fluctuations in our motions are difficult to keep under control. Here we examine the noise-to-signal ratio of micro-movements present in time-series of head motions extracted from resting-state functional magnetic resonance imaging scans in 1048 participants. These included individuals with autism spectrum disorders (ASD) and healthy-controls in shared data from the Autism Brain Imaging Data Exchange (ABIDE) and the Attention-Deficit Hyperactivity Disorder (ADHD-200) databases. We find excess noise and randomness in the ASD cases, suggesting an uncertain motor-feedback signal. A power-law emerged describing an orderly relation between the dispersion and shape of the probability distribution functions best describing the stochastic properties under consideration with respect to intelligence quotient (IQ-scores). In ASD, deleterious patterns of noise are consistently exacerbated with the presence of secondary (comorbid) neuropsychiatric diagnoses, lower verbal and performance intelligence, and autism severity. Importantly, such patterns in ASD are present whether or not the participant takes psychotropic medication. These data unambiguously establish specific noise-to-signal levels of head micro-movements as a biologically informed core feature of ASD.
Interleukins 17 and 23 in patients with gastric neoplasms
Authors: Błogowski Wojciech , Madej-Michniewicz Anna , Marczuk Natalia , Dołęgowska Barbara , Starzyńska Teresa
Published: November 2016

Recently there has been heightened interest in the potential significance of interleukin (IL)-17 and IL-23 in the development/progression of human malignancies. Here, we analyzed the systemic levels of these cytokines in 75 patients with different types of gastric neoplasms (carcinoma, gastrointestinal stromal tumors, neuroendocrine neoplasms, and lymphomas) and 42 healthy volunteers. We found that patients with all types of gastric neoplasms have significantly lower IL-23 levels. However, in comparison to the levels in healthy individuals, IL-17 concentrations were lower only in patients with types of gastric neoplasms other than carcinoma. Interestingly, IL-17 levels significantly differed between patients with early and advanced gastric carcinoma. No significant associations were detected between the systemic levels of examined interleukins and TNM staging. However, peripheral levels of IL-23 were correlated with the absolute numbers of circulating populations of bone marrow-derived mesenchymal and very small embryonic/epiblast-like stem cells in patients with gastric carcinoma. ROC curve analyses demonstrated that systemic levels of IL-17 seem to meet basic criteria for consideration as a helpful diagnostic marker in the detection of gastric carcinoma. In conclusion, our study provides translational evidence confirming the clinical significance of IL-17 and IL-23 in the pathogenesis of different types of gastric neoplasms in humans.
Multiple Resource Use Efficiency (mRUE): A New Concept for Ecosystem Production
Authors: Han Juanjuan , Chen Jiquan , Miao Yuan , Wan Shiqiang
Published: November 2016

The resource-driven concept, which is an important school for investigating ecosystem production, has been applied for decades. However, the regulatory mechanisms of production by multiple resources remain unclear. We formulated a new algorithm model that integrates multiple resource uses to study ecosystem production and tested its applications on a water-availability gradient in semi-arid grassland. The result of our experiment showed that changes in water availability significantly affected the resources of light and nitrogen, and altered the relationships among multiple resource absorption rate (ε), multiple resource use efficiency (mRUE), and available resource (Ravail). The increased water availability suppressed ecosystem mRUE (i.e., “declining marginal returns”); The changes in mRUE had a negative effect on ε (i.e., “inverse feedback”). These two processes jointly regulated that the stimulated single resource availability would promote ecosystem production rather than suppress it, even when mRUE was reduced. This study illustrated the use of the mRUE model in exploring the coherent relationships among the key parameters on regulating the ecosystem production for future modeling, and evaluated the sensitivity of this conceptual model under different dataset properties. However, this model needs extensive validation by the ecological community before it can extrapolate this method to other ecosystems in the future.
Correction: Corrigendum: Efficient delivery of C/EBP beta gene into human mesenchymal stem cells via polyethylenimine-coated gold nanoparticles enhances adipogenic differentiation
Authors: Das Joydeep , Choi Yun-Jung , Yasuda Hideyo , Han Jae Woong , Park Chankyu , Song Hyuk , Bae Hojae , Kim Jin-Hoi
Published: November 2016

Scientific Reports 6: Article number: 33784; published online: 28 September 2016; updated: 21 November 2016.
Solar Output Controls Periodicity in Lake Productivity and Wetness at Southernmost South America
Authors: Pérez-Rodríguez Marta , Gilfedder Benjamin-Silas , Hermanns Yvonne-Marie , Biester Harald
Published: November 2016

Cyclic changes in total solar irradiance (TSI) during the Holocene are known to affect global climatic conditions and cause cyclic climatic oscillations, e.g., Bond events and related changes of environmental conditions. However, the processes how changes in TSI affect climate and environment of the Southern Hemisphere, especially in southernmost South America, a key area for the global climate, are still poorly resolved. Here we show that highly sensitive proxies for aquatic productivity derived from sediments of a lake near the Chilean South Atlantic coast (53 °S) strongly match the cyclic changes in TSI throughout the Holocene. Intra-lake productivity variations show a periodicity of ~200–240 years coherent with the time series of TSI-controlled cosmogenic nuclide 10Be production. In addition TSI dependent periodicity of Bond events (~1500 years) appear to control wetness at the LH site indicated by mineral matter erosion from the catchment to the lake assumingly through shifts of the position of the southern westerly wind belt. Thus, both intra-lake productivity and wetness at the southernmost South America are directly or indirectly controlled by TSI.
A Novel Role of Spred2 in the Colonic Epithelial Cell Homeostasis and Inflammation
Authors: Takahashi Sakuma , Yoshimura Teizo , Ohkura Takahiro , Fujisawa Masayoshi , Fushimi Soichiro , Ito Toshihiro , Itakura Junya , Hiraoka Sakiko , Okada Hiroyuki , Yamamoto Kazuhide , Matsukawa Akihiro
Published: November 2016

Rapid and adequate mucosal healing is important for a remission of ulcerative colitis (UC) patients. Here, we examined whether Spred2, a member of the Sprouty-related EVH1-domain-containing proteins that inhibit the Ras/Raf/ERK pathway, plays a role in colonic mucosal homeostasis and inflammation by using Spred2 knockout (KO) mice. We first detected increased epithelial cell proliferation and cadherin 1 expression in the colon of naïve Spred2 KO mice compared to wild-type mice. Interestingly, Spred2 KO mice were resistant to dextran sulfate sodium (DSS)-induced acute colitis as indicated by lower levels of body weight loss and disease activity index. Histologically, epithelial cell injury and inflammation were milder in the colonic mucosa of Spred2 KO mice on day 3 and almost undetectable by day 8. Experiments with bone chimeric mice indicated that Spred2-deficiency in non-hematopoietic cells was responsible for the reduced sensitivity to DSS. Finally, Spred2 KO mice developed significantly fewer tumors in response to azoxymethane plus DSS. Taken together, our results demonstrate, for the first time, that Spred2 plays an important role in the regulation of colonic epithelial cell proliferation and inflammation by potentially down-regulating the activation of ERK. Thus, Spred2 may be a new therapeutic target for the treatment of UC.
Autoimmune susceptibility imposed by public TCRβ chains
Authors: Zhao Yunqian , Nguyen Phuong , Vogel Peter , Li Bofeng , Jones Lindsay L. , Geiger Terrence L.
Published: November 2016

Although the TCR repertoire is highly diverse, a small fraction of TCR chains, referred to as public, preferentially form and are shared by most individuals. Prior studies indicated that public TCRβ may be preferentially deployed in autoimmunity. We hypothesized that if these TCRβ modulate the likelihood of a TCRαβ heterodimer productively engaging autoantigen, because they are widely present in the population and often high frequency within individual repertoires, they could also broadly influence repertoire responsiveness to specific autoantigens. We assess this here using a series of public and private TCRβ derived from autoimmune encephalomyelitis-associated TCR. Transgenic expression of public, but not private, disease-associated TCRβ paired with endogenously rearranged TCRα endowed unprimed T cells with autoantigen reactivity. Further, two of six public, but none of five private TCRβ provoked spontaneous early-onset autoimmunity in mice. Our findings indicate that single TCRβ are sufficient to confer on TCRαβ chains reactivity toward disease-associated autoantigens in the context of diverse TCRα. They further suggest that public TCR can skew autoimmune susceptibility, and that subsets of public TCR sequences may serve as disease- specific biomarkers or therapeutic targets.
Selection of reliable reference genes for normalization of quantitative RT-PCR from different developmental stages and tissues in amphioxus
Authors: Zhang Qi-Lin , Zhu Qian-Hua , Liao Xin , Wang Xiu-Qiang , Chen Tao , Xu Han-Ting , Wang Juan , Yuan Ming-Long , Chen Jun-Yuan
Published: November 2016

Amphioxus is a closest living proxy to the ancestor of cephalochordates with vertebrates, and key animal for novel understanding in the evolutionary origin of vertebrate body plan, genome, tissues and immune system. Reliable analyses using quantitative real-time PCR (qRT-PCR) for answering these scientific questions is heavily dependent on reliable reference genes (RGs). In this study, we evaluated stability of thirteen candidate RGs in qRT-PCR for different developmental stages and tissues of amphioxus by four independent (geNorm, NormFinder, BestKeeper and deltaCt) and one comparative algorithms (RefFinder). The results showed that the top two stable RGs were the following: (1)S20and18 Sin thirteen developmental stages, (2)EF1AandACTin seven normal tissues, (3)S20andL13in both intestine and hepatic caecum challenged with lipopolysaccharide (LPS), and (4)S20andEF1Ain gill challenged with LPS. The expression profiles of two target genes (EYAandHHEX) in thirteen developmental stages were used to confirm the reliability of chosen RGs. This study identified optimal RGs that can be used to accurately measure gene expression under these conditions, which will benefit evolutionary and functional genomics studies in amphioxus.
GeS2–In2S3–CsI Chalcogenide Glasses Doped with Rare Earth Ions for Near- and Mid-IR Luminescence
Authors: Li Legang , Bian Junyi , Jiao Qing , Liu Zijun , Dai Shixun , Lin Changgui
Published: November 2016

Chalcogenide glass has been considered as a promising host for the potential laser gain and amplifier media operating in near- and mid-IR spectral region. In this work, the IR luminescence spectra of rare earth ions (Tm3+, Er3+, and Dy3+) doped 65GeS2–25In2S3–10CsI chalcogenide glasses were measured under the excitation of an 808 nm laser diode. To the best of our knowledge, it firstly provides the luminescence spectra of a full near- and mid-IR spectral range from 1 to 4 μm in rare earth ions doped chalcogenide glasses. The results of absorption spectra, luminescence spectra, and fluorescence decay curves were obtained in these samples with singly-, co- and triply-doping behaviors of Tm3+, Er3+, and Dy3+ ions. In order to search possible efficient IR emissions, the luminescence behavior was investigated specifically with the variation of doping behaviors and dopant ions, especially in the samples co- and triply-doped active ions. The results suggest that favorable near- and mid-IR luminescence of rare earth ions can be further modified in chalcogenide glasses through an elaborated design of doping behavior and optically active ions.
Regulation of Anticancer Styrylpyrone Biosynthesis in the Medicinal Mushroom Inonotus obliquus Requires Thioredoxin Mediated Transnitrosylation of S-nitrosoglutathione Reductase
Authors: Zhao Yanxia , He Meihong , Ding Jianing , Xi Qi , Loake Gary J. , Zheng Weifa
Published: November 2016

The medicinal macrofungus Inonotus obliquus widely utilized as folk medicine in Russia and Baltic countries is a source of phenylpropanoid-derived styrylpyrone polyphenols that can inhibit tumor proliferation. Insights into the regulatory machinery that controls I. obliquus styrylpyrone polyphenol biosynthesis will enable strategies to increase the production of these molecules. Here we show that Thioredoxin (Trx) mediated transnitrosylation of S-nitrosoglutathione reductase (GSNOR) underpins the regulation of styrylpyrone production, driven by nitric oxide (NO) synthesis triggered by P. morii coculture. NO accumulation results in the S-nitrosylation of PAL and 4CL required for the synthesis of precursor phenylpropanoids and styrylpyrone synthase (SPS), integral to the production of styrylpyrone, inhibiting their activities. These enzymes are targeted for denitrosylation by Trx proteins, which restore their activity. Further, this Trx S-nitrosothiol (SNO) reductase activity was potentiated following S-nitrosylation of Trx proteins at a non-catalytic cysteine (Cys) residue. Intriguingly, this process was counterbalanced by Trx denitrosylation, mediated by Trx-dependent transnitrosylation of GSNOR. Thus, unprecedented interplay between Trx and GSNOR oxidoreductases regulates the biosynthesis of styrylpyrone polyphenols in I. obliquus.
Quantitative secretomic analysis of pancreatic cancer cells in serum-containing conditioned medium
Authors: Liu Peng , Weng Yejing , Sui Zhigang , Wu Yunhao , Meng Xiangli , Wu Mengwei , Jin Haoyi , Tan Xiaodong , Zhang Lihua , Zhang Yukui
Published: November 2016

Pancreatic cancer is a highly metastatic and chemo-resistant disease. Secreted proteins involved in cell-cell interactions play an important role in changing the tumor microenvironment. Previous studies generally focus on the secretome of cancer cell line from serum-free media, due to the serious interference of fetal bovine serum (FBS). However, serum-starvation may alter expression patterns of secreted proteins. Hence, efforts to decrease the interference of serum in proteomic analysis of serum-containing media have been hampered to quantitatively measure the tumor secretion levels. Recently, the metabolic labeling, protein equalization, protein fractionation and filter-aided sample preparation (FASP) strategy (MLEFF) has been successfully used to avoid the disturbance of serum on secretome analysis. Here, this efficient method was applied for comparative secretome analysis of two hamster pancreatic cancer cells with differentially metastatic potentials, enabling the observation of 161 differentially expressed proteins, including 106 proteins that had been previously reported and detected in plasma. By integrated analysis of our data and publicly available bioinformatics resources, we found that a combination panel consisting of CDH3, PLAU, and LFNG might improve the prognosis of overall pancreatic cancer survival. These secreted proteins may serve as a potential therapeutic targets for pancreatic cancer metastasis.
Anion-controlled dimer distance induced unique solid-state fluorescence of cyano substituted styrene pyridinium
Authors: Zhang Gaobin , Zhang Xuanjun , Kong Lin , Wang Shichao , Tian Yupeng , Tao Xutang , Yang Jiaxiang
Published: November 2016

Molecular packing arrangements play a key role in dominating the photophysical properties of luminophores in aggregated state but fine control of the molecular packing is a great challenge. This article describes a unique cyano substituted styrene pyridinium with interesting solid-state fluorescence that can be finely tuned by simple change of counteranions. The dilute solutions of the organic salts (PyCl, PyNO3, PyOTs and PyPh4B) exhibit very weak fluorescence. The crystals of the organic salts (PyCl, PyNO3, and PyOTs) show much enhanced fluorescence compared with their dilute solutions. It is interesting that the emissions changed from bluish-green to deep-blue and fluorescence quantum yields increase from 2.5% to 13.1% with the increasing of steric hindrance of the anions from chloridion, nitrate, to p-toluenesulfonate. Crystal and DFT studies reveal that the enhanced fluorescence is ascribed to the formation of dimers and bigger anions induce larger molecular separation in dimers. Tetraphenylboron anion with very large steric hindrance impedes the formation of dimers and thus results in non-fluorescent salt (PyPh4B). Meanwhile, this unique dimeric packing endows the crystal of PyNO3 with anisotropic fluorescence.
Analytical methods based on the light-scattering of plasmonic nanoparticles at the single particle level with dark-field microscopy imaging
Authors: Li Tian , Wu Xi , Liu Feng , Li Na
Published: November 2016

This minireview summarizes analytical methods based on the light-scattering of gold nanoparticles with the dark-field microscopy imaging technique at the single particle level.
Correction: In solution SERS sensing using mesoporous silica-coated gold nanorods
Authors: Gao Zhe , Burrows Nathan D. , Valley Nicholas A. , Egger Sam , Schatz George C. , Murphy Catherine J. , Haynes Christy L.
Published: November 2016

Correction for ‘In solution SERS sensing using mesoporous silica-coated gold nanorods’ by Zhe Gao, et al., Analyst, 2016, 141, 5088–5095.
Identification methods in microplastic analysis: a review
Authors: Shim Won Joon , Hong Sang Hee , Eo Soeun Eo
Published: November 2016

Microplastics have become a major global environmental issue in recent decades due to their ubiquity in the oceans, bioavailability and ability to carry toxic chemicals.
Extracting DNA from ocean microplastics: a method comparison study
Authors: Debeljak Pavla , Pinto Maria , Proietti Maira , Reisser Julia , Ferrari Francesco F. , Abbas Ben , van Loosdrecht Mark C. M. , Slat Boyan , Herndl Gerhard J.
Published: November 2016

Molecular characterization of ocean plastic biofilms can shed light on the ecological implications of plastic pollution; here we provide detailed protocols and compare different DNA extraction methods applied to marine microplastics.
Transition metal-catalyzed iodine(iii)-mediated nitrene transfer reactions: efficient tools for challenging syntheses
Authors: Darses B. , Rodrigues R. , Neuville L. , Mazurais M. , Dauban P.
Published: November 2016

The main synthetic applications of catalytic C(sp3)–H amination and alkene aziridination reactions are discussed in the context of natural product synthesis. The examples highlight that these synthetic methods now firmly belong in the organic chemist's toolbox.
Metal-catalyzed C–H functionalization involving isocyanides
Authors: Song Bingrui , Xu Bin
Published: November 2016

This review demonstrates the metal-catalyzed incorporation of isocyanides into C–H functionalization to establish complicated reactions utilizing synergistic effects.
Review of two-dimensional materials for photocatalytic water splitting from a theoretical perspective
Authors: Li Yunguo , Li Yan-Ling , Sa Baisheng , Ahuja Rajeev
Published: November 2016

Two-dimensional (2D) materials have shown extraordinary performances as photocatalysts compared to their bulk counterparts.
High-efficiency humidity-stable planar perovskite solar cells based on atomic layer architecture
Authors: Koushik Dibyashree , Verhees Wiljan J. H. , Kuang Yinghuan , Veenstra Sjoerd , Zhang Dong , Verheijen Marcel A. , Creatore Mariadriana , Schropp Ruud E. I.
Published: November 2016

An ultra-thin ALD Al2O3 architected at the CH3NH3PbI3−δClδ/Spiro-OMeTAD interface reduces hysteresis loss and stabilizes perovskite devices against humidity.
Visible-light-driven TiO2/Ag3PO4 heterostructures with enhanced antifungal activity against agricultural pathogenic fungi Fusarium graminearum and mechanism insight
Authors: Liu Bingkun , Xue Yongfei , Zhang Jingtao , Han Bing , Zhang Jie , Suo Xinying , Mu Lilong , Shi Hengzhen
Published: November 2016

TiO2/Ag3PO4 heterostructures improved the separation efficiency of electron–hole pairs and enhanced the photocatalytic disinfection efficiency for F. graminearum macroconidia.