bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation of the Cambrian Evolutionary Radiation: geochronology, evolutionary stasis of earliest Cambrian (Terreneuvian) small shelly fossil (SSF) taxa, and chronostratigraphic significance
Authors: LANDING ED , KOUCHINSKY ARTEM
Published: February 2016

Early faunas withWatsonella crosbyiwith or withoutAldanellaspp. have been equated with the Siberian Tommotian Stage (uppermost Terreneuvian) and used to define a proposed Cambrian Stage 2 base. Much earlier Terreneuvian occurrences are now shown by recovery of these micromolluscs below the I’ carbon excursion in the Siberian ‘Nemakit-Daldynian’ Stage and comparable δ13C excursions in the middle Meishucunian (China) and middle Chapel Island Formation (Avalonia). This δ13C excursion, a reliable Stage 2 marker, lies in ac. 10 Ma interval in the Cambrian Radiation in which long-ranged small shelly fossil taxa provide limited biostratigraphic resolution.
Modeling and simulation of protein–surface interactions: achievements and challenges
Authors: Ozboyaci Musa , Kokh Daria B. , Corni Stefano , Wade Rebecca C.
Published: January 2016

Understanding protein–inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein–surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein–surface interactions and discuss the successes and limitations of current approaches.
No Need to Beg China? Taiwan's Membership of the Asia-Pacific Economic Cooperation as a Contested State
Authors: Chu Ming-chin Monique
Published: January 2016

This article examines the process, causes and repercussions of the accession of Taiwan, as a contested state, together with China, to the Asia-Pacific Economic Cooperation in 1991, the first intergovernmental organization that Taipei has joined since 1971. Based on an analysis of elite interviews, primary and secondary data, the paper traces the under-explored diplomatic history of the accession. It argues that changes in Taiwan's domestic and external environments, as well as changes in the diplomatic process, account for Taipei's admission, rather than the China factor alone. The paper examines four positive effects of accession on Taiwan's international space and the implications for Taiwan's continuous survival as a contested state. By undertaking a nuanced analysis of an important yet little explored milestone in the contested state's struggle to mitigate its international isolation, the article sheds light on Taiwan's external ties against the backdrop of the sovereignty dispute between Taipei and Beijing.
Introduction: The Future of Restrictivist Scholarship on the Use of Force
Authors: KAMMERHOFER JÖRG
Published: February 2016

No international lawyer bats more than the proverbial eyelid nowadays at states intervening militarily in states which host non-state armed groups. Neither drone strikes nor what used to be called ‘invasion’ quicken the pulse of the jus ad bellum lawyer; this is now a matter for humanitarians; the ‘how’ matters much more than the ‘whether’. We have become inured to relatively small-scale military interventions. Those who remember that 20 years ago international lawyers were more likely to find such actions illegal than justified should (but do not) collectively raise an eyebrow at this rapid change.
Treatment goals and their attainment: a structured approach to assessment and evaluation
Authors: Ramnerö Jonas , Jansson Billy
Published: February 2016

Treatment goals are considered a vital part of therapeutic work, and their role is often emphasized in cognitive behavioural therapy (CBT). However, the attainment of goals is rarely accounted for in terms of treatment outcome. In this study, we set out to investigate a structured format for goal assessment and goal attainment in CBT delivered as routine care. We were especially interested in the sensitivity to change in perceived goal attainment. Patients completed a self-administered version of the Bern Inventory of Treatment Goals (BIT-C) and rated their perceived attainment on a maximum of five prioritized goals before and after 12 weeks of treatment, along with measures on anxiety, depression and health-related quality of life. The results indicated that the prioritized goals only partially correspond to disorder-specific concerns, and that perceived proximity to treatment goals is clearly associated with improvements following treatment. The results are discussed in terms of the BIT-C being a promising tool for use in clinical settings in assessing treatment goals as well as in evaluating the attainment of these goals.
Mimicking Cdk2 phosphorylation of Bcl-xL at Ser73 results in caspase activation and Bcl-xL cleavage
Authors: Seng NS , Megyesi J , Tarcsafalvi A , Price PM
Published: February 2016

Cisplatin is a widely used chemotherapeutic agent, yet its efficacy is limited by nephrotoxicity. The severity of nephrotoxicity is associated with the extent of kidney cell death. Previously, we found that cisplatin-induced kidney cell death was dependent on Cdk2 activation, and inhibition of Cdk2 protected cells from cisplatin-induced apoptosis. Using an in vitro kination assay, we showed that Cdk2 phosphorylated Bcl-xL, an anti-apoptotic member of Bcl-2 family proteins, at serine 73. We also found that this phosphorylated Bcl-xL participated in cell death, as a phosphomimetic mutant of Bcl-xL at the serine 73 site (S73D-Bcl-xL) activated caspases. We now find that S73D-Bcl-xL was cleaved at D61 and D76, which are putative caspase cleavage sites, to generate 15-kDa and 12-kDa fragments. Unlike full-length Bcl-xL, these cleavage products of Bcl-xL were previously reported to be pro-apoptotic. We sought to determine whether these Bcl-xL fragments were necessary for the induction of cell death by S73D-Bcl-xL. Mutation of these caspase cleavage sites prevented the formation of the 15-kDa and 12-kDa Bcl-xL cleavage products, but apoptosis still persisted in a S73D modified Bcl-xL. Our findings show that Cdk2 phosphorylation of Bcl-xL at Ser73, but not the Bcl-xL cleavage products, is necessary and sufficient to induce cell death.
Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction
Authors: Seitz Kiley W , Lazar Cassandre S , Hinrichs Kai-Uwe , Teske Andreas P , Baker Brett J
Published: January 2016

Marine and estuary sediments contain a variety of uncultured archaea whose metabolic and ecological roles are unknown. De novo assembly and binning of high-throughput metagenomic sequences from the sulfate–methane transition zone in estuary sediments resulted in the reconstruction of three partial to near-complete (2.4–3.9 Mb) genomes belonging to a previously unrecognized archaeal group. Phylogenetic analyses of ribosomal RNA genes and ribosomal proteins revealed that this group is distinct from any previously characterized archaea. For this group, found in the White Oak River estuary, and previously registered in sedimentary samples, we propose the name ‘Thorarchaeota’. The Thorarchaeota appear to be capable of acetate production from the degradation of proteins. Interestingly, they also have elemental sulfur and thiosulfate reduction genes suggesting they have an important role in intermediate sulfur cycling. The reconstruction of these genomes from a deeply branched, widespread group expands our understanding of sediment biogeochemistry and the evolutionary history of Archaea.
Live-cell protein labelling with nanometre precision by cell squeezing
Authors: Kollmannsperger Alina , Sharei Armon , Raulf Anika , Heilemann Mike , Langer Robert , Jensen Klavs F. , Wieneke Ralph , Tampé Robert
Published: January 2016

Live-cell labelling techniques to visualize proteins with minimal disturbance are important; however, the currently available methods are limited in their labelling efficiency, specificity and cell permeability. We describe high-throughput protein labelling facilitated by minimalistic probes delivered to mammalian cells by microfluidic cell squeezing. High-affinity and target-specific tracing of proteins in various subcellular compartments is demonstrated, culminating in photoinduced labelling within live cells. Both the fine-tuned delivery of subnanomolar concentrations and the minimal size of the probe allow for live-cell super-resolution imaging with very low background and nanometre precision. This method is fast in probe delivery (∼1,000,000 cells per second), versatile across cell types and can be readily transferred to a multitude of proteins. Moreover, the technique succeeds in combination with well-established methods to gain multiplexed labelling and has demonstrated potential to precisely trace target proteins, in live mammalian cells, by super-resolution microscopy.
Two distinct types of remapping in primate cortical area V4
Authors: Neupane Sujaya , Guitton Daniel , Pack Christopher C.
Published: February 2016

Visual neurons typically receive information from a limited portion of the retina, and such receptive fields are a key organizing principle for much of visual cortex. At the same time, there is strong evidence that receptive fields transiently shift around the time of saccades. The nature of the shift is controversial: Previous studies have found shifts consistent with a role for perceptual constancy; other studies suggest a role in the allocation of spatial attention. Here we present evidence that both the previously documented functions exist in individual neurons in primate cortical area V4. Remapping associated with perceptual constancy occurs for saccades in all directions, while attentional shifts mainly occur for neurons with receptive fields in the same hemifield as the saccade end point. The latter are relatively sluggish and can be observed even during saccade planning. Overall these results suggest a complex interplay of visual and extraretinal influences during the execution of saccades.
Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy
Authors: Johnson Douglas B. , Estrada Monica V. , Salgado Roberto , Sanchez Violeta , Doxie Deon B. , Opalenik Susan R. , Vilgelm Anna E. , Feld Emily , Johnson Adam S. , Greenplate Allison R. , Sanders Melinda E. , Lovly Christine M. , Frederick Dennie T. , Kelley Mark C. , Richmond Ann , Irish Jonathan M. , Shyr Yu , Sullivan Ryan J. , Puzanov Igor , Sosman Jeffrey A. , Balko Justin M.
Published: January 2016

Anti-PD-1 therapy yields objective clinical responses in 30–40% of advanced melanoma patients. Since most patients do not respond, predictive biomarkers to guide treatment selection are needed. We hypothesize that MHC-I/II expression is required for tumour antigen presentation and may predict anti-PD-1 therapy response. In this study, across 60 melanoma cell lines, we find bimodal expression patterns of MHC-II, while MHC-I expression was ubiquitous. A unique subset of melanomas are capable of expressing MHC-II under basal or IFNγ-stimulated conditions. Using pathway analysis, we show that MHC-II(+) cell lines demonstrate signatures of ‘PD-1 signalling’, ‘allograft rejection’ and ‘T-cell receptor signalling’, among others. In two independent cohorts of anti-PD-1-treated melanoma patients, MHC-II positivity on tumour cells is associated with therapeutic response, progression-free and overall survival, as well as CD4+and CD8+tumour infiltrate. MHC-II+tumours can be identified by melanoma-specific immunohistochemistry using commercially available antibodies for HLA-DR to improve anti-PD-1 patient selection.
Histone deacetylase 1 is required for the development of the zebrafish inner ear
Authors: He Yingzi , Tang Dongmei , Li Wenyan , Chai Renjie , Li Huawei
Published: February 2016

Histone deacetylase 1 (HDAC1) has been reported to be important for multiple aspects of normal embryonic development, but little is known about its function in the development of mechanosensory organs. Here, we first confirmed that HDAC1 is expressed in the developing otic vesicles of zebrafish by whole-mount in situ hybridization. Knockdown of HDAC1 using antisense morpholino oligonucleotides in zebrafish embryos induced smaller otic vesicles, abnormal otoliths, malformed or absent semicircular canals and fewer sensory hair cells. HDAC1 loss of function also caused attenuated expression of a subset of key genes required for otic vesicle formation during development. Morpholino-mediated knockdown of HDAC1 resulted in decreased expression of members of the Fgf family in the otic vesicles, suggesting that HDAC1 is involved in the development of the inner ear through regulation of Fgf signaling pathways. Taken together, our results indicate that HDAC1 plays an important role in otic vesicle formation.
Hybridized Phosphate with Ultrathin Nanoslices and Single Crystal Microplatelets for High Performance Supercapacitors
Authors: Zhao Yufeng , Chen Zhaoyang , Xiong Ding-Bang , Qiao Yuqing , Tang Yongfu , Gao Faming
Published: February 2016

A novel hybridized phosphate is developed through a mild hydrothermal method to construct high performance asymmetric supercapacitor. Single layered (Ni,Co)3(PO4)2·8H2O nanoslices (∼1 nm) and single crystal (NH4)(Ni,Co)PO4·0.67H2O microplatelets are obtained through a template sacrificial method and dissolution recrystallization approach respectively in one step. This unique hybridized structure delivers a maximum specific capacitance of 1128 F g−1 at current density of 0.5 A g−1. The asymmetric supercapacitor (ASC) based on the hybrid exhibits a high energy density of 35.3 Wh kg−1 at low power density and still holds 30.9 Wh kg−1 at 4400 W kg−1. Significantly, the ASC manifests very high cycling stability with 95.6% capacitance retention after 5000 cycles. Such excellent electrochemical performance could be attributed to the synergistic effect of the surface redox reaction from the ultrathin nanoslices and ion intercalation from the single crystal bulk structure. This material represents a novel kind of electrode material for the potential application in supercapacitors.
Capturing the wide variety of impaired fracture healing phenotypes in Neurofibromatosis Type 1 with eight key factors: a computational study
Authors: Carlier A. , Brems H. , Ashbourn J. M. A. , Nica I. , Legius E. , Geris L.
Published: January 2016

Congenital pseudarthrosis of the tibia (CPT) is a rare disease which normally presents itself during early childhood by anterolateral bowing of the tibia and spontaneous tibial fractures. Although the exact etiology of CPT is highly debated, 40–80% of CPT patients are carriers of a mutation in the Neurofibromatosis Type 1 (NF1) gene, which can potentially result in an altered phenotype of the skeletal cells and impaired bone healing. In this study we use a computational model of bone regeneration to examine the effect of the Nf1 mutation on bone fracture healing by altering the parameter values of eight key factors which describe the aberrant cellular behaviour of Nf1 haploinsufficient and Nf1 bi-allelically inactivated cells. We show that the computational model is able to predict the formation of a hamartoma as well as a wide variety of CPT phenotypes through different combinations of altered parameter values. A sensitivity analysis by “Design of Experiments” identified the impaired endochondral ossification process and increased infiltration of fibroblastic cells as key contributors to the degree of severity of CPT. Hence, the computational model results have added credibility to the experimental hypothesis of a genetic cause (i.e. Nf1 mutation) for CPT.
Pure electrical, highly-efficient and sidelobe free coherent Raman spectroscopy using acousto-optics tunable filter (AOTF)
Authors: Meng Zhaokai , Petrov Georgi I. , Yakovlev Vladislav V.
Published: February 2016

Fast and sensitive Raman spectroscopy measurements are imperative for a large number of applications in biomedical imaging, remote sensing and material characterization. Stimulated Raman spectroscopy offers a substantial improvement in the signal-to-noise ratio but is often limited to a discrete number of wavelengths. In this report, by introducing an electronically-tunable acousto-optical filter as a wavelength selector, a novel approach to a broadband stimulated Raman spectroscopy is demonstrated. The corresponding Raman shift covers the spectral range from 600 cm−1 to 4500 cm−1, sufficient for probing most vibrational Raman transitions. We validated the use of the new instrumentation to both coherent anti-Stokes scattering (CARS) and stimulated Raman scattering (SRS) spectroscopies.
Expression of programmed death ligand-1 on tumor cells varies pre and post chemotherapy in non-small cell lung cancer
Authors: Sheng Jin , Fang Wenfeng , Yu Juan , Chen Nan , Zhan Jianhua , Ma Yuxiang , Yang Yunpeng , Huang Yan , Zhao Hongyun , Zhang Li
Published: January 2016

The effects of treatments to programmed death ligand-1 (PD-L1) expression is unknown. The aim of this study was to investigate the impact of neoadjuvant chemotherapy (NACT) on PD-L1 expression in non-small cell lung cancer (NSCLC) patients. PD-L1 expression was detected by immunohistochemistry (IHC) method in 32 paired tumor specimens pre and post-NACT. The positivity of PD-L1 on tumor cells (TCs) changed from 75% to 37.5% after NACT (p = 0.003). Cases with IHC score of 1, 2, 3 all underwent apparent decrease (p = 0.007). However, no significant changes were observed on tumour-infiltrating immune cells (ICs) (p = 0.337). Subgroup and semiquantitative analyses all presented similar results. Moreover, patients with response to NACT presented significantly reduced PD-L1 expression on TCs (p = 0.004). Although it was not confirmed by the Cox proportional hazard regression model, there was an apparent difference in disease-free-survival (DFS) between negative-to-positive switch of PD-L1 status and the contrary group (median DFS: 9.6 versus 25.9, p = 0.005). Our data revealed that antecedent chemotherapy for NSCLC may results in inconsistency of PD-L1 expression. PD-L1 expression is suggested to be monitored around treatment and on serial samples, at least, on the latest tumor specimen.
A one-dimensional quantum walk with multiple-rotation on the coin
Authors: Xue Peng , Zhang Rong , Qin Hao , Zhan Xiang , Bian Zhihao , Li Jian
Published: January 2016

We introduce and analyze a one-dimensional quantum walk with two time-independent rotations on the coin. We study the influence on the property of quantum walk due to the second rotation on the coin. Based on the asymptotic solution in the long time limit, a ballistic behaviour of this walk is observed. This quantum walk retains the quadratic growth of the variance if the combined operator of the coin rotations is unitary. That confirms no localization exhibits in this walk. This result can be extended to the walk with multiple time-independent rotations on the coin.
Acetylome analysis reveals the involvement of lysine acetylation in biosynthesis of antibiotics in Bacillus amyloliquefaciens
Authors: Liu Lin , Wang Guangyuan , Song Limin , Lv Binna , Liang Wenxing
Published: January 2016

Lysine acetylation is a major post-translational modification that plays an important regulatory role in almost every aspects in both eukaryotes and prokaryotes. Bacillus amyloliquefaciens, a Gram-positive bacterium, is very effective for the control of plant pathogens. However, very little is known about the function of lysine acetylation in this organism. Here, we conducted the first lysine acetylome in B. amyloliquefaciens through a combination of highly sensitive immune-affinity purification and high-resolution LC−MS/MS. Overall, we identified 3268 lysine acetylation sites in 1254 proteins, which account for 32.9% of the total proteins in this bacterium. Till date, this is the highest ratio of acetylated proteins that have been identified in bacteria. Acetylated proteins are associated with a variety of biological processes and a large fraction of these proteins are involved in metabolism. Interestingly, for the first time, we found that about 71.1% (27/38) and 78.6% (22/28) of all the proteins tightly related to the synthesis of three types of pepketides and five families of lipopeptides were acetylated, respectively. These findings suggest that lysine acetylation plays a critical role in the regulation of antibiotics biosynthesis. These data serves as an important resource for further elucidation of the physiological role of lysine acetylation in B. amyloliquefaciens.
X-Linked Retinoschisis: Phenotypic Variability in a Chinese Family
Authors: Xiao Yangyan , Liu Xiao , Tang Luosheng , Wang Xia , Coursey Terry G. , Guo Xiaojian , Li Zhuo
Published: January 2016

X-linked juvenile retinoschisis (XLRS), a leading cause of juvenile macular degeneration, is characterized by a spoke-wheel pattern in the macular region of the retina and splitting of the neurosensory retina. Our study is to describe the clinical characteristics of a four generations of this family (a total of 18 members)with X-linked retinoschisis (XLRS) and detected a novel mutations of c.3G > A (p.M1?) in the initiation codon of the RS1 gene. by direct sequencing.Identification of this mutation in this family provides evidence about potential genetic or environmental factors on its phenotypic variance, as patients presented with different phenotypes regardless of having the same mutation. Importantly, OCT has proven vital for XLRS diagnosis in children.
Comparative studies on the room-temperature ferrielectric and ferrimagnetic Ni3TeO6-type A2FeMoO6 compounds (A = Sc, Lu)
Authors: Song Guang , Zhang Weiyi
Published: February 2016

First-principles calculations have been carried out to study the structural, electric and magnetic properties of Ni3TeO6-type A2FeMoO6 compounds (A = Sc, Lu). Their electric and magnetic properties behave like room-temperature ferrielectric and ferrimagnetic insulators where polarization comes from the un-cancelled antiparallel dipoles of (A(1), Fe3+) and (A(2), Mo3+) ion groups and magnetization from un-cancelled antiparallel moments of Fe3+"Equation missing" and Mo3+"Equation missing" ions. The net polarization increases with A’s ionic radius and is 7.1 and 8.7 μCcm−2 for Sc2FeMoO6 and Lu2FeMoO6, respectively. The net magnetic moment is 2 μB per formula unit. The magnetic transition temperature is estimated well above room-temperature due to the strong antiferromagnetic superexchange coupling among Fe3+ and Mo3+ spins. The estimated paraelectric to ferrielectric transition temperature is also well above room-temperature. Moreover, strong magnetoelectric coupling is also anticipated because the magnetic ions are involved both in polarization and magnetization. The fully relaxed Ni3TeO6-type A2FeMoO6 structures are free from soft-phonon modes and correspond to stable structures. As a result, Ni3TeO6-type A2FeMoO6 compounds are possible candidates for room-temperature multiferroics with large magnetization and polarization.
Tailoring the physical properties of Ni-based single-phase equiatomic alloys by modifying the chemical complexity
Authors: Jin K. , Sales B. C. , Stocks G. M. , Samolyuk G. D. , Daene M. , Weber W. J. , Zhang Y. , Bei H.
Published: February 2016

Equiatomic alloys (e.g. high entropy alloys) have recently attracted considerable interest due to their exceptional properties, which might be closely related to their extreme disorder induced by the chemical complexity. In order to understand the effects of chemical complexity on their fundamental physical properties, a family of (eight) Ni-based, face-center-cubic (FCC), equiatomic alloys, extending from elemental Ni to quinary high entropy alloys, has been synthesized and their electrical, thermal and magnetic properties are systematically investigated in the range of 4–300 K by combining experiments withab initioKorring-Kohn-Rostoker coherent-potential-approximation (KKR-CPA) calculations. The scattering of electrons is significantly increased due to the chemical (especially magnetic) disorder. It has weak correlation with the number of elements but strongly depends on the type of elements. Thermal conductivities of the alloys are largely lower than pure metals, primarily because the high electrical resistivity suppresses the electronic thermal conductivity. The temperature dependence of the electrical and thermal transport properties is further discussed and the magnetization of five alloys containing three or more elements is measured in magnetic fields up to 4 T.
An Unexpected Controlled New Oxidant: SO4.–
Authors: Bai Cui-Bing , Wang Nai-Xing , Lan Xing-Wang , Wang Yan-Jing , Xing Yalan , Wen Jia-Long , Gao Xue-Wang , Zhang Wei
Published: February 2016

A controlled new oxidant sulfate radical anion (SO4.–) was found and it can be easily prepared by mixing Na2S2O4 and TBHP with stirring. In this new metal-free oxidation system (Na2S2O4/TBHP), SO4.– can be used as a controllable oxidant to oxidize various aromatic alcohols to the corresponding aldehydes in good yields without any acid formation at room temperature. SO4.– was determined by a DMPO (5,5-dimethyl-1-pyrroline-N-oxide) spin-trapping EPR method at room temperature on a Bruker E500 spectrometer and the results suggested that SO4.– was generated in this transformation.
Matrix metalloproteinase 12 modulates high-fat-diet induced glomerular fibrogenesis and inflammation in a mouse model of obesity
Authors: Niu Honglin , Li Ying , Li Haibin , Chi Yanqing , Zhuang Minghui , Zhang Tao , Liu Maodong , Nie Lei
Published: January 2016

Obesity-induced kidney injury contributes to albuminuria, which is characterized by a progressive decline in renal function leading to glomerulosclerosis and renal fibrosis. Matrix metalloproteinases (MMPs) modulate inflammation and fibrosis by degrading a variety of extracellular matrix and regulating the activities of effector proteins. Abnormal regulation of MMP-12 expression has been implicated in abdominal aortic aneurysm, atherosclerosis and emphysema, but the underlying mechanisms remain unclear. The present study examined the function of MMP-12 in glomerular fibrogenesis and inflammation using apo E−/− or apo E−/−MMP-12−/− mice and maintained on a high-fat-diet (HFD) for 3, 6, or 9 months. MMP-12 deletion reduced glomerular matrix accumulation and downregulated the expression of NADPH oxidase 4 and the subunit-p67phox, indicating the inhibition of renal oxidative stress. In addition, the expression of the inflammation-associated molecule MCP-1 and macrophage marker-CD11b was decreased in glomeruli of apo E−/−MMP-12−/− mice fed HFD. MMP-12 produced by macrophages infiltrating into glomeruli contributed to the degradation of collagen type IV and fibronectin. Crescent formation due to renal oxidative stress in Bowman’s space was a major factor in the development of fibrogenesis and inflammation. These results suggest that regulating MMP-12 activity could be a therapeutic strategy for the treatment of crescentic glomerulonephritis and fibrogenesis.
Individual and population-level responses to ocean acidification
Authors: Harvey Ben P. , McKeown Niall J. , Rastrick Samuel P. S. , Bertolini Camilla , Foggo Andy , Graham Helen , Hall-Spencer Jason M. , Milazzo Marco , Shaw Paul W. , Small Daniel P. , Moore Pippa J.
Published: January 2016

Ocean acidification is predicted to have detrimental effects on many marine organisms and ecological processes. Despite growing evidence for direct impacts on specific species, few studies have simultaneously considered the effects of ocean acidification on individuals (e.g. consequences for energy budgets and resource partitioning) and population level demographic processes. Here we show that ocean acidification increases energetic demands on gastropods resulting in altered energy allocation, i.e. reduced shell size but increased body mass. When scaled up to the population level, long-term exposure to ocean acidification altered population demography, with evidence of a reduction in the proportion of females in the population and genetic signatures of increased variance in reproductive success among individuals. Such increased variance enhances levels of short-term genetic drift which is predicted to inhibit adaptation. Our study indicates that even against a background of high gene flow, ocean acidification is driving individual- and population-level changes that will impact eco-evolutionary trajectories.
Seasonal induction of alternative principal pathway for rose flower scent
Authors: Hirata Hiroshi , Ohnishi Toshiyuki , Tomida Kensuke , Ishida Haruka , Kanda Momoyo , Sakai Miwa , Yoshimura Jin , Suzuki Hideyuki , Ishikawa Takamasa , Dohra Hideo , Watanabe Naoharu
Published: February 2016

Ecological adaptations to seasonal changes are often observed in the phenotypic traits of plants and animals and these adaptations are usually expressed through the production of different biochemical end products. In this study, ecological adaptations are observed in a biochemical pathway without alteration of the end products. We present an alternative principal pathway to the characteristic floral scent compound 2-phenylethanol (2PE) in roses. The new pathway is seasonally induced in summer as a heat adaptation that uses rose phenylpyruvate decarboxylase (RyPPDC) as a novel enzyme. RyPPDC transcript levels and the resulting production of 2PE are increased time-dependently under high temperatures. The novel summer pathway produces levels of 2PE that are several orders of magnitude higher than those produced by the previously known pathway. Our results indicate that the alternative principal pathway identified here is a seasonal adaptation for managing the weakened volatility of summer roses.
The Quorum Sensing Inhibitor Hamamelitannin Increases Antibiotic Susceptibility of Staphylococcus aureus Biofilms by Affecting Peptidoglycan Biosynthesis and eDNA Release
Authors: Brackman Gilles , Breyne Koen , De Rycke Riet , Vermote Arno , Van Nieuwerburgh Filip , Meyer Evelyne , Van Calenbergh Serge , Coenye Tom
Published: February 2016

Treatment of Staphylococcus aureus infections has become increasingly challenging due to the rapid emergence and dissemination of methicillin-resistant strains. In addition, S. aureus reside within biofilms at the site of infection. Few novel antibacterial agents have been developed in recent years and their bacteriostatic or bactericidal activity results in selective pressure, inevitably inducing antimicrobial resistance. Consequently, innovative antimicrobials with other modes of action are urgently needed. One alternative approach is targeting the bacterial quorum sensing (QS) system. Hamamelitannin (2′,5-di-O-galloyl-d-hamamelose; HAM) was previously suggested to block QS through the TraP QS system and was shown to increase S. aureus biofilm susceptibility towards vancomycin (VAN) although mechanistic insights are still lacking. In the present study we provide evidence that HAM specifically affects S. aureus biofilm susceptibility through the TraP receptor by affecting cell wall synthesis and extracellular DNA release of S. aureus. We further provide evidence that HAM can increase the susceptibility of S. aureus biofilms towards different classes of antibiotics in vitro. Finally, we show that HAM increases the susceptibility of S. aureus to antibiotic treatment in in vivo Caenorhabditis elegans and mouse mammary gland infection models.
High-responsivity UV-Vis Photodetector Based on Transferable WS2 Film Deposited by Magnetron Sputtering
Authors: Zeng Longhui , Tao Lili , Tang Chunyin , Zhou Bo , Long Hui , Chai Yang , Lau Shu Ping , Tsang Yuen Hong
Published: January 2016

The two-dimensional layered semiconducting tungsten disulfide (WS2) film exhibits great promising prospects in the photoelectrical applications because of its unique photoelectrical conversion property. Herein, in this paper, we report the simple and scalable fabrication of homogeneous, large-size and transferable WS2 films with tens-of-nanometers thickness through magnetron sputtering and post annealing process. The produced WS2 films with low resistance (4.2 kΩ) are used to fabricate broadband sensitive photodetectors in the ultraviolet to visible region. The photodetectors exhibit excellent photoresponse properties, with a high responsivity of 53.3 A/W and a high detectivity of 1.22 × 1011 Jones at 365 nm. The strategy reported paves new way towards the large scale growth of transferable high quality, uniform WS2 films for various important applications including high performance photodetectors, solar cell, photoelectrochemical cell and so on.
A New Self-Consistent Field Model of Polymer/Nanoparticle Mixture
Authors: Chen Kang , Li Hui-shu , Zhang Bo-kai , Li Jian , Tian Wen-de
Published: February 2016

Field-theoretical method is efficient in predicting assembling structures of polymeric systems. However, it’s challenging to generalize this method to study the polymer/nanoparticle mixture due to its multi-scale nature. Here, we develop a new field-based model which unifies the nanoparticle description with the polymer field within the self-consistent field theory. Instead of being “ensemble-averaged” continuous distribution, the particle density in the final morphology can represent individual particles located at preferred positions. The discreteness of particle density allows our model to properly address the polymer-particle interface and the excluded-volume interaction. We use this model to study the simplest system of nanoparticles immersed in the dense homopolymer solution. The flexibility of tuning the interfacial details allows our model to capture the rich phenomena such as bridging aggregation and depletion attraction. Insights are obtained on the enthalpic and/or entropic origin of the structural variation due to the competition between depletion and interfacial interaction. This approach is readily extendable to the study of more complex polymer-based nanocomposites or biology-related systems, such as dendrimer/drug encapsulation and membrane/particle assembly.
Phosphorylation of serine residue modulates cotton Di19-1 and Di19-2 activities for responding to high salinity stress and abscisic acid signaling
Authors: Qin Li-Xia , Nie Xiao-Ying , Hu Rong , Li Gang , Xu Wen-Liang , Li Xue-Bao
Published: February 2016

Di19 (drought-induced protein 19) family is a novel type of Cys2/His2 zinc-finger proteins. In this study, we demonstrated that cotton Di19-1 and Di19-2 (GhDi19-1/-2) proteins could be phosphorylated in vitro by the calcium-dependent protein kinase (CDPK). Mutation of Ser to Ala in N-terminus of GhDi19-1/-2 led to the altered subcellular localization of the two proteins, but the constitutively activated form (Ser was mutated to Asp) of GhDi19-1/-2 still showed the nuclear localization. GhDi19-1/-2 overexpression transgenic Arabidopsis seedlings displayed the hypersensitivity to high salinity and abscisic acid (ABA). However, Ser site-mutated GhDi19-1(S116A) and GhDi19-2(S114A) and Ser and Thr double sites-mutated GhDi19-1(S/T-A/A) and GhDi19-2(S/T-A/A) transgenic Arabidopsis did not show the salt- and ABA-hypersensitive phenotypes. In contrast, overexpression of Thr site-mutated GhDi19-1(T114A) and GhDi19-2(T112A) in Arabidopsis still resulted in salt- and ABA-hypersensitivity phenotypes, like GhDi19-1/-2 transgenic lines. Overexpression of GhDi19-1/-2 and their constitutively activated forms in Atcpk11 background could recover the salt- and ABA-insensitive phenotype of the mutant. Thus, our results demonstrated that Ser phosphorylation (not Thr phosphorylation) is crucial for functionally activating GhDi19-1/-2 in response to salt stress and ABA signaling during early plant development and GhDi19-1/-2 proteins may be downstream targets of CDPKs in ABA signal pathway.
Correction: Corrigendum: Epidemiology study of HBV genotypes and antiviral drug resistance in multi-ethnic regions from Western China
Authors: Zhang Qi , Liao Yun , Chen Jie , Cai Bei , Su Zhenzhen , Ying Binwu , Lu Xiaojun , Tao Chuanmin , Wang Lanlan
Published: January 2016

Hepatitis B virus (HBV) infection is a critical global health issue and moderately epidemic in Western China, but HBV molecular epidemiology characteristics are still limited. We conducted this study to investigate HBV genotypes and antiviral resistant mutations in this multi-ethnic area. A total of 1316 HBV patients were recruited from four ethnic groups from 2011 to 2013. Genotypes and resistant mutations were determined by Sanger sequencing. Four genotypes (B, C, D and C/D) were identified. Genotype B and C were common in Han population, while genotype D was predominant in Uygurs. Genotype C was the major genotype in both Tibetans and Yis, and recombinant C/D was found in Tibetans only. Lamivudine resistance was common in all populations, especially in Hans with prevalence of 42.8%. Entecavir resistance was barely observed regardless of ethnicity. Genotype C isolates had higher rates of rtA181T/V than genotype B (13.5% vs. 5.1%, P < 0.001), in accordance with higher prevalence of resistance to adefovir (20.0% vs. 9.5%, P < 0.001). While incidence of resistant mutations to other drugs and clinical factors showed no difference among different genotypes. HBV genotypes and resistance-conferring mutations had different geographic and demographic distributions in Western China, which provided molecular epidemiology data for clinical management.
First airborne pathogen direct analysis system
Authors: Liu Qi , Zhang Yuxiao , Jing Wenwen , Liu Sixiu , Zhang Dawei , Sui Guodong
Published: January 2016

This is the first portable “sample to answer” system for the rapid detection of pathogenic bacteria in air.
Surface molecular imprinting on CdTe quantum dots for fluorescence sensing of 4-nitrophenol
Authors: Jiang Linye , Liu Haijian , Li Ming , Xing Yue , Ren Xueqin
Published: January 2016

The developed fluorescent sensor provides high sensitivity and selectivity and a lower detection limit than previously developed sensors.
7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein
Authors: Tokugawa Munefumi , Masaki Yoshiaki , Canggadibrata Jan Christian , Kaneko Kazuhei , Shiozawa Takashi , Kanamori Takashi , Grøtli Morten , Wilhelmsson L. Marcus , Sekine Mitsuo , Seio Kohji
Published: February 2016

7-(Benzofuran-2-yl)-7-deazadeoxyguanosine (BFdG) was synthesized and incorporated into an oligodeoxynucleotide (ODN).
Straightforward synthesis of functionalized chroman-4-ones through cascade radical cyclization-coupling of 2-(allyloxy)arylaldehydes
Authors: Zhao Jingjing , Li Pan , Li Xinjian , Xia Chungu , Li Fuwei
Published: February 2016

A novel and direct approach to synthesize a series of phosphonate, azide and hydroxy functionalized chroman-4-ones has been developed. The transformation appears to proceedviaan intramolecular addition ofin situgenerated acyl radical onto alkene, followed by a radical/radical cross coupling.
Visible-light-induced water oxidation by a hybrid photocatalyst consisting of bismuth vanadate and copper(ii) meso-tetra(4-carboxyphenyl)porphyrin
Authors: Nakashima Shu , Negishi Ryo , Tada Hiroaki
Published: February 2016

Copper(ii) meso-tetra(4-carboxyphenyl)porphyrin surface-modified monoclinic scheelite bismuth vanadate (CuTCPP/ms-BiVO4) exhibits a high level of activity for the water oxidation to oxygen (O2) under visible-light irradiation (λ > 430 nm).
Synthesis of activated 3′-amino-3′-deoxy-2-thio-thymidine, a superior substrate for the nonenzymatic copying of nucleic acid templates
Authors: Izgu Enver Cagri , Oh Seung Soo , Szostak Jack W.
Published: January 2016

We present a scalable synthesis of 3′-amino-3′-deoxy-2-thio-thymidine-5′-phosphoro-2-methylimidazolide, an activated monomer that can copy adenosine residues in nucleic acid templates rapidly without a polymerase.
Photoswitchable metal organic frameworks: turn on the lights and close the windows
Authors: Castellanos S. , Kapteijn F. , Gascon J.
Published: February 2016

Progress and challenges in the development of photo-responsive metal organic frameworks.
Formic acid-assisted synthesis of highly efficient Cu/ZnO catalysts: effect of HCOOH/Cu molar ratios
Authors: Shi Lei , Sun Dong , Wang Yuxin , Tan Yisheng , Li Jie , Yan Shirun , Fan Ronggang , Tsubaki Noritatsu
Published: February 2016

Metallic Cu/ZnO catalysts were directly prepared by a formic acid-assisted solid-state combustion method without further reduction.
Selective dehydrogenation of bioethanol to acetaldehyde over basic USY zeolites
Authors: Lari G. M. , Desai K. , Mondelli C. , Pérez-Ramírez J.
Published: January 2016

Alkali-activated zeolites are active, selective and stable catalysts for ethanol dehydrogenation to acetaldehyde. Molecular oxygen eases hydrogen abstraction from the adsorbed ethoxide intermediate boosting the catalytic performance.
Towards molecular control of elementary reactions in zeolite catalysis by advanced molecular simulations mimicking operating conditions
Authors: De Wispelaere Kristof , Bailleul Simon , Van Speybroeck Veronique
Published: February 2016

Ingeniously selecting zeolite topology and acidity, reaction temperature and guest molecule loading enables tuning the reaction mechanism of zeolite-catalyzed methylation reactions.
Achieving near-infrared emission in platinum(ii) complexes by using an extended donor–acceptor-type ligand
Authors: Zhang You-Ming , Meng Fanyuan , Tang Jian-Hong , Wang Yafei , You Caifa , Tan Hua , Liu Yu , Zhong Yu-Wu , Su Shijian , Zhu Weiguo
Published: February 2016

Three D–A-type mononuclear and dinuclear platinum(ii) complexes, (TPA-BTPy)Pt(pic), (TPA-BTPy-Fl)Pt(pic) and [Fl(TPA-BTPy)2]Pt2(pic)2, were designed and obtained.
Highly selective gas-phase oxidation of ethanol to ethyl acetate over bi-functional Pd/zeolite catalysts
Authors: Chen Hong , Dai Yihu , Jia Xinli , Yu Hao , Yang Yanhui
Published: February 2016

Zeolite supported Pd nanoparticles were demonstrated to be efficient and stable bi-functional catalysts in the selective aerobic oxidation of ethanol to ethyl acetate.
Highly selective transformation of glycerol to dihydroxyacetone without using oxidants by a PtSb/C-catalyzed electrooxidation process
Authors: Lee Seonhwa , Kim Hyung Ju , Lim Eun Ja , Kim Youngmin , Noh Yuseong , Huber George W. , Kim Won Bae
Published: January 2016

The PtSb/C catalyzed highly selective transformation of glycerol to dihydroxyacetone and H2 was achieved by controlling the applied electrode potential without using oxidants via an electrocatalytic reactor system in acidic media.
SNRFCB: sub-network based random forest classifier for predicting chemotherapy benefit on survival for cancer treatment
Authors: Shi Mingguang , He Jianmin
Published: February 2016

Adjuvant chemotherapy (CTX) should be individualized to provide potential survival benefit and avoid potential harm for cancer patients.
Reconstruction of a charge balanced genome-scale metabolic model to study the energy-uncoupled growth of Zymomonas mobilis ZM1
Authors: Motamedian E. , Saeidi M. , Shojaosadati S. A.
Published: February 2016

Zymomonas mobilisis an ethanologenic bacterium and is known to be an example microorganism with energy-uncoupled growth. The reconstructed metabolic model indicate that resistance to intracellular pH reduction could be the main reason for uncoupled growth.
Eco-friendly Suzuki–Miyaura coupling of arylboronic acids to aromatic ketones catalyzed by the oxime-palladacycle in biosolvent 2-MeTHF
Authors: Mondal Manoj , Bora Utpal
Published: January 2016

Oxime-palladacycle catalyzed aerobic cross-coupling reaction of arylboronic acids and acyl chlorides to yield aryl ketones was developed. The reaction proceeds efficiently in 2-MeTHF, which is derived from corncobs, sugar cane, and fulfils the 3rd, 5th and 7th principles of Green Chemistry.
Citrate precursor synthesis and multifunctional properties of YCrO3 nanoparticles
Authors: Ahmad Tokeer , Lone Irfan H.
Published: January 2016

Monophasic and multifunctional YCrO3 nanoparticles (22 nm) with a high surface area of 344 m2 g−1 exhibit well-defined multiferroic characteristics.
Extraordinary optical transmission in nanopatterned ultrathin metal films without holes
Authors: Peer Akshit , Biswas Rana
Published: February 2016

The gold-coated periodic nanocup structure with an ultrathin gold film at the bottom shows extraordinary optical transmission at ∼700 nm wavelength.
Porous membranes from acid decorated block copolymer nano-objects via RAFT alcoholic dispersion polymerization
Authors: Upadhyaya Lakshmeesha , Semsarilar Mona , Fernández-Pacheco Rodrigo , Martinez Gema , Mallada Reyes , Deratani André , Quemener Damien
Published: January 2016

Acid decorated diblock copolymer nano-objects were prepared by polymerization-induced self-assembly via RAFT dispersion polymerization of methyl methacrylate. Spheres were used to prepare thin film membranes.
The effect of protein concentration on the viscosity of a recombinant albumin solution formulation
Authors: Gonçalves Andrea D. , Alexander Cameron , Roberts Clive J. , Spain Sebastian G. , Uddin Shahid , Allen Stephanie
Published: January 2016

The effect of protein concentration on solution viscosity in a commercially available biopharmaceutical formulation of recombinant albumin (rAlbumin) was studied.
Effect of particle size on the surface activity of TiC–Ni composite coating via the interfacial valence electron localization
Authors: Yang Zirun , Lu Hao , Liu Ziran , Yan Xianguo , Li Dongyang
Published: January 2016

Electron work functions and open potentials of electrodeposited Ni, TiC micro- and nano-particle-reinforced Ni matrix coatings were studied to investigate the effects of TiC particle size on the surface activity and corrosion tendency of the coatings.
Explaining stability of transition metal carbides – and why TcC does not exist
Authors: Wang Qinggao , German Konstantin E. , Oganov Artem R. , Dong Huafeng , Feya Oleg D. , Zubavichus Ya. V. , Murzin V. Yu.
Published: February 2016

A simple understanding on the trend of stability for transition metal carbides.
Fabrication of a resist pattern based on plasma–polystyrene interactions
Authors: Li Ning , Feng Lei , Teng Fei , Wang Yandong , Wu Feifei , Yang Xiangchao , Lu Nan
Published: January 2016

An ultrathin resist pattern of high selectivity is fabricated based on plasma–polystyrene interaction within several minutes.