bluuebunny/crossref_metadata_2025 huggingface dataset:
Biologically based neural circuit modelling for the study of fear learning and extinction
Authors: Nair Satish S , Paré Denis , Vicentic Aleksandra
Published: November 2016

The neuronal systems that promote protective defensive behaviours have been studied extensively using Pavlovian conditioning. In this paradigm, an initially neutral-conditioned stimulus is paired with an aversive unconditioned stimulus leading the subjects to display behavioural signs of fear. Decades of research into the neural bases of this simple behavioural paradigm uncovered that the amygdala, a complex structure comprised of several interconnected nuclei, is an essential part of the neural circuits required for the acquisition, consolidation and expression of fear memory. However, emerging evidence from the confluence of electrophysiological, tract tracing, imaging, molecular, optogenetic and chemogenetic methodologies, reveals that fear learning is mediated by multiple connections between several amygdala nuclei and their distributed targets, dynamical changes in plasticity in local circuit elements as well as neuromodulatory mechanisms that promote synaptic plasticity. To uncover these complex relations and analyse multi-modal data sets acquired from these studies, we argue that biologically realistic computational modelling, in conjunction with experiments, offers an opportunity to advance our understanding of the neural circuit mechanisms of fear learning and to address how their dysfunction may lead to maladaptive fear responses in mental disorders.
Correction: Corrigendum: Safety and anti-hyperglycemic efficacy of various tea types in mice
Authors: Han Manman , Zhao Guangshan , Wang Yijun , Wang Dongxu , Sun Feng , Ning Jingming , Wan Xiaochun , Zhang Jinsong
Published: November 2016

Scientific Reports 6: Article number: 31703; published online: 17 August 2016; updated: 08 November 2016.
Cost-effectiveness Analysis of Fluorouracil, Leucovorin, and Irinotecan versus Epirubicin, Cisplatin, and Capecitabine in Patients with Advanced Gastric Adenocarcinoma
Authors: Wen Feng , Zheng Hanrui , Wu Yifan , Wheeler John , Zeng Xiaoxi , Fu Ping , Li Qiu
Published: November 2016

No standard treatment has been accepted widely for the first-/second-line therapy for advanced gastric cancer (AGC). The current study aimed to determine a preferred strategy between FOLFIRI (fluorouracil, leucovorin, and irinotecan) and ECX (epirubicin, cisplatin,and capecitabine) for AGC from the cost-effectiveness perspective. According to a French intergroup study, two groups (ECX arm and FOLFIRI arm) and three health states (progression-free survival (PFS), progressive disease (PD) and death) were analyzed in the current Markov model. All the medical costs were calculated from a Chinese societal perspective. Although FOLFIRI was an acceptable first-line therapy in the treatment of AGC with a better time-to treatment failure (TTF) compared to ECX, ECX arm (ECX followed by FOLFIRI) gained 0.08 quality-adjusted life months (QALMs) more effectiveness benefit compared with FOLFIRI arm (FOLFIRI followed by ECX). Additionally, a lower cost was found in ECX arm ($23,813.13 versus $24,983.70). Hence, the strategy of FOLFIRI arm is dominated by ECX arm ($4,125.8 per QALM in FOLIRI arm; $3,879.724 per QALM in ECX arm). ECX followed by FOLFIRI was a preferred strategy with more effectiveness and lower cost compared with FOLFIRI followed by ECX for the treatment of AGC.
Normal incidence filters using symmetry-protected modes in dielectric subwavelength gratings
Authors: Cui Xuan , Tian Hao , Du Yan , Shi Guang , Zhou Zhongxiang
Published: November 2016

We investigate narrowband transmission filters based on subwavelength-grating reflectors at normal incidence. Computational results show that the filtering is realized through symmetry-protected mode coupling. The guided mode resonances introduced by the slab layer allow flexible control of the filter frequencies. The quality factor of the filters could exceed 106. Dielectric gratings can be used over the entire range of electromagnetic waves, owing to their scale-invariant operations. Owing to the high refraction index and low index dispersion of semiconductors in the infrared range, these filters can be applied over a broad range from near infrared to terahertz frequencies.
Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils
Authors: Dai Zhongmin , Hu Jiajie , Xu Xingkun , Zhang Lujun , Brookes Philip C. , He Yan , Xu Jianming
Published: November 2016

Sensitive responses among bacterial and fungal communities to pyrogenic organic matter (PyOM) (biochar) addition in rhizosphere and bulk soils are poorly understood. We conducted a pot experiment with manure and straw PyOMs added to an acidic paddy soil, and identified the sensitive “responders” whose relative abundance was significantly increased/decreased among the whole microbial community following PyOM addition. Results showed that PyOMs significantly (p < 0.05) increased root growth, and simultaneously changed soil chemical parameters by decreasing soil acidity and increasing biogenic resource. PyOM-induced acidity and biogenic resource co-determined bacterial responder community structure whereas biogenic resource was the dominant parameter structuring fungal responder community. Both number and proportion of responders in rhizosphere soil was larger than in bulk soil, regardless of PyOM types and microbial domains, indicating the microbial community in rhizosphere soil was sensitive to PyOM addition than bulk soil. The significant increased root biomass and length caused by PyOM addition, associated with physiological processes, e.g. C exudates secretion, likely favored more sensitive responders in rhizosphere soil than in bulk soil. Our study identified the responders at fine taxonomic resolution in PyOM amended soils, improved the understanding of their ecological phenomena associated with PyOM addition, and examined their interactions with plant roots.
Evolution of Mass Movements near Epicentre of Wenchuan Earthquake, the First Eight Years
Authors: Zhang Shuai , Zhang Limin , Lacasse Suzanne , Nadim Farrokh
Published: November 2016

It is increasingly clear that landslides represent a major cause of economic costs and deaths in earthquakes in mountains. In the Wenchuan earthquake case, post-seismic cascading landslides continue to represent a major problem eight years on. Failure to anticipate the impact of cascading landslides could lead to unexpected losses of human lives and properties. Previous studies tended to focus on separate landslide processes, with little attention paid to the quantification of long-term evolution of multiple processes or the evolution of mass movements. The very active mass movements near the epicentre of the Wenchuan earthquake provided us a unique opportunity to understand the complex processes of the evolving cascading landslides after a strong earthquake. This study budgets the mass movements on the hillslopes and in the channels in the first eight years since the Wenchuan earthquake and verify a conservation in mass movements. A system illustrating the evolution and interactions of mass movement after a strong earthquake is proposed.
Superparamagnetic Fe3O4-PEG2K-FA@Ce6 Nanoprobes for in Vivo Dual-mode Imaging and Targeted Photodynamic Therapy
Authors: Yin Ting , Huang Peng , Gao Guo , Shapter Joseph G. , Shen Yulan , Sun Rongjin , Yue Caixia , Zhang Chunlei , Liu Yanlei , Zhou Sui , Cui Daxiang
Published: November 2016

The development of targeted nanoprobes is a promising approach to cancer diagnostics and therapy. In the present work, a novel multifunctional photo/magnet-diagnostic nanoprobe (MNPs-PEG2K-FA@Ce6) has been developed. This nanoprobe is built using folic acid (FA), bifunctional polyethylene glycol (PEG2K) and photosensitizer chlorin e6 (Ce6). The MNPs-PEG2K-FA@Ce6 nanoprobes are superparamagnetic, can be synthesized on a large scale by a one-pot hydrothermal process without further surface modification and are stable in an aqueous environment for eight months. Compared with free Ce6 nanoprobes in vitro studies, the MNPs-PEG2K-FA@Ce6 nanoprobes significantly enhance cellular uptake efficiency and promote the effectiveness of photodynamic therapy (PDT) with the assistance of 633 nm laser irradiation. The unique nanoprobes show superior penetration and a retention time of more than six days with less accumulation in the liver allowing highly effective tumor recognition and monitoring. Additionally, there was little damage to healthy organs or tissues. These exciting new nanoprobes could be potential building blocks to develop new clinical therapies and translational medicine.
Systematic Analysis of Drug Targets Confirms Expression in Disease-Relevant Tissues
Authors: Kumar Vinod , Sanseau Philippe , Simola Daniel F. , Hurle Mark R. , Agarwal Pankaj
Published: November 2016

It is commonly assumed that drug targets are expressed in tissues relevant to their indicated diseases, even under normal conditions. While multiple anecdotal cases support this hypothesis, a comprehensive study has not been performed to verify it. We conducted a systematic analysis to assess gene and protein expression for all targets of marketed and phase III drugs across a diverse collection of normal human tissues. For 87% of gene-disease pairs, the target is expressed in a disease-affected tissue under healthy conditions. This result validates the importance of confirming expression of a novel drug target in an appropriate tissue for each disease indication and strengthens previous findings showing that targets of efficacious drugs should be expressed in relevant tissues under normal conditions. Further characterization of the remaining 13% of gene-disease pairs revealed that most genes are expressed in a different tissue linked to another disease. Our analysis demonstrates the value of extensive tissue specific expression resources.both in terms of tissue and cell diversity as well as techniques used to measure gene expression.
Lycium barbarum polysaccharide attenuates high-fat diet-induced hepatic steatosis by up-regulating SIRT1 expression and deacetylase activity
Authors: Jia Li , Li Wang , Li Jianning , Li Yan , Song Hui , Luan Yansong , Qi Hui , Ma Lirong , Lu Xiaohong , Yang Yi
Published: November 2016

In this study, we aimed to investigate the protective effects and underlying mechanism of Lycium barbarum polysaccharide (LBP) on high-fat-induced nonalcoholic fatty liver disease (NAFLD). Recently, sirtuin 1 (SIRT1) has been shown to play an important role in the regulation of hepatocellular lipid metabolism. Here, we demonstrated that LBP up-regulates SIRT1 deacetylase activity and protein expression by enhancing the NAD+/NADH ratio. Subsequently, LBP promoted LKB1 deacetylation and AMPK phosphorylation via SIRT1-dependent signalling. We also found that LBP increases acetyl-CoA carboxylase (ACC) phosphorylation and adipose triglyceride lipase (ATGL) protein expression and decreases fatty acid synthase (FAS) by activating the SIRT1/LKB1/AMPK pathway in vitro and in vivo. However, SIRT1 small interfering RNA (siRNA)-mediated knockdown reversed the LBP-mediated effects on ACC, FAS and ATGL. Moreover, LBP elevated carnitine palmitoyltransferase-1 alpha (CPT-1α) expression by suppressing malonyl-CoA accumulation. Taken together, our data indicate that LBP plays a vital role in the regulation of hepatic lipid metabolism and that pharmacological activation of SIRT1 by LBP may be a strategy for the prevention of NAFLD.
The nucleolar protein GLTSCR2 is required for efficient viral replication
Authors: Wang Peng , Meng Wen , Han Shi-Chong , Li Cui-Cui , Wang Xiao-Jun , Wang Xiao-Jia
Published: November 2016

Glioma tumor suppressor candidate region gene 2 protein (GLTSCR2) is a nucleolar protein. In the investigation of the role of GLTSCR2 that played in the cellular innate immune response to viral infection, we found GLTSCR2 supported viral replication of rhabdovirus, paramyxovirus, and coronavirus in cells. Viral infection induced translocation of GLTSCR2 from nucleus to cytoplasm that enabled GLTSCR2 to attenuate type I interferon IFN-β and support viral replication. Cytoplasmic GLTSCR2 was able to interact with retinoic acid-inducible gene I (RIG-I) and the ubiquitin-specific protease 15 (USP15), and the triple interaction induced USP15 activity to remove K63-linked ubiquitination of RIG-I, leading to attenuation of RIG-I and IFN-β. Blocking cytoplasmic translocation of GLTSCR2, by deletion of its nuclear export sequence (NES), abrogated its ability to attenuate IFN-β and support viral replication. GLTSCR2-mediated attenuation of RIG-I and IFN-β led to alleviation of host cell innate immune response to viral infection. Our findings suggested that GLTSCR2 contributed to efficient viral replication, and GLTSCR2 should be considered as a potential target for therapeutic control of viral infection.
Lake Ontario salmon (Salmo salar) were not migratory: A long-standing historical debate solved through stable isotope analysis
Authors: Guiry Eric J. , Needs-Howarth Suzanne , Friedland Kevin D. , Hawkins Alicia L. , Szpak Paul , Macdonald Rebecca , Courtemanche Michelle , Holm Erling , Richards Michael P.
Published: November 2016

Lake Ontario once supported a large complex of Atlantic Salmon (Salmo salar) populations that became extinct prior to scientific study. Since the 1860s, research efforts to conserve and reintroduce a sustainable population of Atlantic Salmon have focused on determining whether Lake Ontario’s original salmon populations had migrated to the Atlantic Ocean as part of their lifecycle (anadromy), stayed in the lake year-round (potamodromy), or both. We used stable carbon, nitrogen, and sulfur isotope analyses of archaeological bones and historical museum-archived salmon scales to show that the original salmon populations from Lake Ontario completed their entire lifecycle without migrating to the Atlantic Ocean. With a time depth of more than 500 years, our findings provide a unique baseline with significant potential for informing modern restocking and conservation efforts.
27 years of benthic and coral community dynamics on turbid, highly urbanised reefs off Singapore
Authors: Guest J. R. , Tun K. , Low J. , Vergés A. , Marzinelli E. M. , Campbell A. H. , Bauman A. G. , Feary D. A. , Chou L. M. , Steinberg P. D.
Published: November 2016

Coral cover on reefs is declining globally due to coastal development, overfishing and climate change. Reefs isolated from direct human influence can recover from natural acute disturbances, but little is known about long term recovery of reefs experiencing chronic human disturbances. Here we investigate responses to acute bleaching disturbances on turbid reefs off Singapore, at two depths over a period of 27 years. Coral cover declined and there were marked changes in coral and benthic community structure during the first decade of monitoring at both depths. At shallower reef crest sites (3–4 m), benthic community structure recovered towards pre-disturbance states within a decade. In contrast, there was a net decline in coral cover and continuing shifts in community structure at deeper reef slope sites (6–7 m). There was no evidence of phase shifts to macroalgal dominance but coral habitats at deeper sites were replaced by unstable substrata such as fine sediments and rubble. The persistence of coral dominance at chronically disturbed shallow sites is likely due to an abundance of coral taxa which are tolerant to environmental stress. In addition, high turbidity may interact antagonistically with other disturbances to reduce the impact of thermal stress and limit macroalgal growth rates.
MEG3, HCN3 and linc01105 influence the proliferation and apoptosis of neuroblastoma cells via the HIF-1α and p53 pathways
Authors: Tang Weitao , Dong Kuiran , Li Kai , Dong Rui , Zheng Shan
Published: November 2016

The purpose of this study was to investigate the differential expression and functional roles of long non-coding RNAs (lncRNAs) in neuroblastoma tissue. LncRNA microarrays were used to identify differentially expressed lncRNAs between tumor and para-tumor tissues. In total, in tumor tissues, 3,098 and 1,704 lncRNAs were upregulated and downregulated, respectively. HCN3 and linc01105 exhibited the higher expression (P < 0.05; P < 0.01, respectively) in neuroblastoma tissue, whereas MEG3 displayed the lower expression (P < 0.01). HIF-1α expression was negatively correlated with cell proliferation in the linc01105 KD group. In addition, Noxa and Bid expression was positively correlated with cell apoptosis. Moreover, linc01105 knockdown promoted cell proliferation, whereas MEG3 overexpression inhibited proliferation. Finally, linc01105 knockdown, MEG3 overexpression and HCN3 knockdown all increased apoptosis. The correlation coefficients between those three lncRNAs and the International Neuroblastoma Staging System (INSS) stage were −0.48, −0.58 and −0.55, respectively. In conclusion, we have identified lncRNAs that are differentially expressed in neuroblastoma tissues. The lncRNAs HCN3, linc01105, and MEG3 may be important in biological behaviors of neuroblastoma through mechanisms involving p53 pathway members such as HIF-1α, Noxa, and Bid. The expressions of MEG3, HCN3 and linc01105 are all negatively correlated with the INSS stage.
Serological diagnosis of pneumocystosis: production of a synthetic recombinant antigen for immunodetection of Pneumocystis jirovecii
Authors: Tomás A. L. , Cardoso F. , Esteves F. , Matos O.
Published: November 2016

Diagnosis of Pneumocystis pneumonia (PcP) relies on the detection of P. jirovecii in respiratory specimens obtained by invasive techniques. Thus, the development of a serological test is urgently needed as it will allow the diagnosis of PcP using blood, an inexpensive and non-invasive specimen. This study aims to combine the production of a multi-epitope synthetic recombinant antigen (RSA) and an ELISA test for detection of anti-P. jirovecii antibodies, in order to develop a new approach for PcP diagnosis. The RSA was selected and designed based on the study of the immunogenicity of the carboxyl-terminal domain of the major surface glycoprotein. This antigen was purified and used as an antigenic tool in an ELISA technique for detection of Ig, IgG and IgM antibodies anti-P. jirovecii (patent-pending no. PT109078). Serum specimens from 88 patients previously categorized in distinct clinical subgroups and 17 blood donors, were analysed. The IgM anti-P. jirovecii levels were statistically increased in patients with PcP (p = 0.001) and the ELISA IgM anti-P. jirovecii test presented a sensitivity of 100% and a specificity of 80.8%, when associated with the clinical diagnosis criteria. This innovative approach, provides good insights about what can be done in the future serum testing for PcP diagnosis.
Identification of a New Broadly Cross-reactive Epitope within Domain III of the Duck Tembusu Virus E Protein
Authors: Li Chenxi , Bai Xiaofei , Meng Runze , Shaozhou Wulin , Zhang Qingshan , Hua Ronghong , Liu Jyung-Hurng , Liu Ming , Zhang Yun
Published: November 2016

In 2010, a pathogenic flavivirus termed duck Tembusu virus (DTMUV) caused widespread outbreak of egg-drop syndrome in domesticated ducks in China. Although the glycoprotein E of DTMUV is an important structural component of the virus, the B-cell epitopes of this protein remains uncharacterized. Using phage display and mutagenesis, we identified a minimal B-cell epitope, 374EXE/DPPFG380, that mediates binding to a nonneutralizing monoclonal antibody. DTMUV-positive duck serum reacted with the epitope, and amino acid substitutions revealed the specific amino acids that are essential for antibody binding. Dot-blot assays of various flavivirus-positive sera indicated that EXE/DPPFG is a cross-reactive epitope in most flaviviruses, including Zika, West Nile, Yellow fever, dengue, and Japanese encephalitis viruses. These findings indicate that the epitope sequence is conserved among many strains of mosquito-borne flavivirus. Protein structure modeling revealed that the epitope is located in domain III of the DTMUV E protein. Together, these results provide new insights on the broad cross-reactivity of a B-cell binding site of the E protein of flaviviruses, which can be exploited as a diagnostic or therapeutic target for identifying, studying, or treating DTMUV and other flavivirus infections.
Oncometabolite D-2-Hydroxyglurate Directly Induces Epithelial-Mesenchymal Transition and is Associated with Distant Metastasis in Colorectal Cancer
Authors: Colvin Hugh , Nishida Naohiro , Konno Masamitsu , Haraguchi Naotsugu , Takahashi Hidekazu , Nishimura Junichi , Hata Taishi , Kawamoto Koichi , Asai Ayumu , Tsunekuni Kenta , Koseki Jun , Mizushima Tsunekazu , Satoh Taroh , Doki Yuichiro , Mori Masaki , Ishii Hideshi
Published: November 2016

Deranged metabolism is a hallmark of cancer, playing a significant role in driving the disease process. One such example is the induction of carcinogenesis by the oncometabolite D-2 hydroxyglutarate (D-2HG), which is produced by the mutated enzyme isocitrate dehydrogenase (IDH) occurring in subsets of leukaemias and brain tumours. The oncogenic property of D-2HG appears to stem from its ability to interfere with the activities of α-ketoglutarate-dependent dioxygenases, including the Jumonji family histone demethylases. Here, we find in colorectal cancer cells that even in the absence of IDH mutation, the levels of D-2HG and its enantiomer L-2HG were elevated through glutamine anaplerosis. D-2HG, but not L-2HG, increased the trimethylation of histone H3 lysine 4 of the promoter region of ZEB1, a master regulator of epithelial-mesenchymal transition (EMT), and increased the expression of the ZEB1 gene to directly induce EMT in colorectal cancer cells. EMT promotes the ability of cancer cells to invade the local tissue and enter into the bloodstream, leading to distant organ metastasis. D-2HG levels were elevated in colorectal cancer specimens, particularly in those associated with distant metastasis, supporting the observations in vitro and implicating the contribution of D-2HG in metastasis, the major cause of death in this disease.
Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size
Authors: Pathak Ashish K. , Singh Sudhir P. , Gupta Yogesh , Gurjar Anoop K. S. , Mantri Shrikant S. , Tuli Rakesh
Published: November 2016

Litchi chinensis is a subtropical fruit crop, popular for its nutritional value and taste. Fruits with small seed size and thick aril are desirable in litchi. To gain molecular insight into gene expression that leads to the reduction in the size of seed in Litchi chinensis, transcriptomes of two genetically closely related genotypes, with contrasting seed size were compared in developing ovules. The cDNA library constructed from early developmental stages of ovules (0, 6, and 14 days after anthesis) of bold- and small-seeded litchi genotypes yielded 303,778,968 high quality paired-end reads. These were de-novo assembled into 1,19,939 transcripts with an average length of 865 bp. A total of 10,186 transcripts with contrast in expression were identified in developing ovules between the small- and large- seeded genotypes. A majority of these differences were present in ovules before anthesis, thus suggesting the role of maternal factors in seed development. A number of transcripts indicative of metabolic stress, expressed at higher level in the small seeded genotype. Several differentially expressed transcripts identified in such ovules showed homology with Arabidopsis genes associated with different stages of ovule development and embryogenesis.
Three-waveform bidirectional pumping of single electrons with a silicon quantum dot
Authors: Tanttu Tuomo , Rossi Alessandro , Tan Kuan Yen , Mäkinen Akseli , Chan Kok Wai , Dzurak Andrew S. , Möttönen Mikko
Published: November 2016

Semiconductor-based quantum dot single-electron pumps are currently the most promising candidates for the direct realization of the emerging quantum standard of the ampere in the International System of Units. Here, we discuss a silicon quantum dot single-electron pump with radio frequency control over the transparencies of entrance and exit barriers as well as the dot potential. We show that our driving protocol leads to robust bidirectional pumping: one can conveniently reverse the direction of the quantized current by changing only the phase shift of one driving waveform with respect to the others. We anticipate that this pumping technique may be used in the future to perform error counting experiments by pumping the electrons into and out of a reservoir island monitored by a charge sensor.
Genomic continuity of Argentinean Mennonites
Authors: Pardo-Seco Jacobo , Llull Cintia , Berardi Gabriela , Gómez Andrea , Andreatta Fernando , Martinón-Torres Federico , Toscanini Ulises , Salas Antonio
Published: November 2016

Mennonites are Anabaptist communities that originated in Central Europe about 500 years ago. They initially migrated to different European countries, and in the early 18th century they established their first communities in North America, from where they moved to other American regions. We aimed to analyze an Argentinean Mennonite congregation from a genome-wide perspective by way of investigating >580.000 autosomal SNPs. Several analyses show that Argentinean Mennonites have European ancestry without signatures of admixture with other non-European American populations. Among the worldwide datasets used for population comparison, the CEU, which is the best-subrogated Central European population existing in The 1000 Genome Project, is the dataset showing the closest genome affinity to the Mennonites. When compared to other European population samples, the Mennonites show higher inbreeding coefficient values. Argentinean Mennonites show signatures of genetic continuity with no evidence of admixture with Americans of Native American or sub-Saharan African ancestry. Their genome indicates the existence of an increased endogamy compared to other Europeans most likely mirroring their lifestyle that involve small communities and historical consanguineous marriages.
Photoswitchable non-fluorescent thermochromic dye-nanoparticle hybrid probes
Authors: Harrington Walter N. , Haji Mwafaq R. , Galanzha Ekaterina I. , Nedosekin Dmitry A. , Nima Zeid A. , Watanabe Fumiya , Ghosh Anindya , Biris Alexandru S. , Zharov Vladimir P.
Published: November 2016

Photoswitchable fluorescent proteins with controllable light–dark states and spectral shifts in emission in response to light have led to breakthroughs in the study of cell biology. Nevertheless, conventional photoswitching is not applicable for weakly fluorescent proteins and requires UV light with low depth penetration in bio-tissue. Here we introduce a novel concept of photoswitchable hybrid probes consisting of thermochromic dye and absorbing nanoparticles, in which temperature-sensitive light–dark states and spectral shifts in absorption can be switched through controllable photothermal heating of doped nanoparticles. The proof-of-concept is demonstrated through the use of two different types of temperature-sensitive dyes doped with magnetic nanoparticles and reversibly photoswitched by a near-infrared laser. Photoacoustic imaging revealed the high contrast of these probes, which is sufficient for their visualization in cells and deep tissue. Our results suggest that these new photoswitchable multicolour probes can be used for multimodal cellular diagnostics and potentially for magnetic and photothermal therapy.
Can microbes compete with cows for sustainable protein production - A feasibility study on high quality protein
Authors: Vestergaard Mike , Chan Siu Hung Joshua , Jensen Peter Ruhdal
Published: November 2016

An increasing population and their increased demand for high-protein diets will require dramatic changes in the food industry, as limited resources and environmental issues will make animal derived foods and proteins, gradually more unsustainable to produce. To explore alternatives to animal derived proteins, an economic model was built around the genome-scale metabolic network of E. coli to study the feasibility of recombinant protein production as a food source. Using a novel model, we predicted which microbial production strategies are optimal for economic return, by capturing the tradeoff between the market prices of substrates, product output and the efficiency of microbial production. A case study with the food protein, Bovine Alpha Lactalbumin was made to evaluate the upstream economic feasibilities. Simulations with different substrate profiles at maximum productivity were used to explore the feasibility of recombinant Bovine Alpha Lactalbumin production coupled with market prices of utilized materials. We found that recombinant protein production could be a feasible food source and an alternative to traditional sources.
Thymic exosomes promote the final maturation of thymocytes
Authors: Lundberg Vanja , Berglund Martin , Skogberg Gabriel , Lindgren Susanne , Lundqvist Christina , Gudmundsdottir Judith , Thörn Karolina , Telemo Esbjörn , Ekwall Olov
Published: November 2016

Extensive knowledge has been gained the last years concerning mechanisms underlying the selection of single positive thymocytes in the thymic medulla. Less is known regarding other important processes in the thymic medulla such as the regulation of late stage thymocyte maturation. We have previously reported that exosomes are abundant in the thymus with a phenotype that indicates an epithelial cell origin and immunoregulatory properties. In this study we use an in vitro system to investigate the effects of thymic exosomes on the maturation of single positive thymocytes as well as effects on nTreg formation. We show that thymic exosomes promote the maturation of single positive CD4+CD25− cells into mature thymocytes with S1P1+Qa2+ and CCR7+Qa2+ phenotypes. Furthermore, we show that thymic exosomes reduce the formation of CD4+CD25+FoxP3+ thymocytes and that these exosome effects are independent of dendritic cell co-stimulation but require intact exosomal RNA content and surface proteins. An efficient direct uptake of exosomes by both thymocytes and thymic DC’s is also demonstrated. In conclusion, this study demonstrates that exosomes may represent a new route of communication within the thymus.
LRBA is Essential for Allogeneic Responses in Bone Marrow Transplantation
Authors: Park Mi Young , Sudan Raki , Srivastava Neetu , Neelam Sudha , Youngs Christie , Wang Jia-Wang , Engelman Robert W. , Kerr William G.
Published: November 2016

The PH-BEACH-WD40 (PBW) protein family members play a role in coordinating receptor signaling and intracellular vesicle trafficking. LPS-Responsive-Beige-like Anchor (LRBA) is a PBW protein whose immune function remains elusive. Here we show that LRBA-null mice are viable, but exhibit compromised rejection of allogeneic, xenogeneic and missing self bone-marrow grafts. Further, we demonstrate that LRBA-null Natural Killer (NK) cells exhibit impaired signaling by the key NK activating receptors, NKp46 and NKG2D. However, induction of IFN-γ by cytokines remains intact, indicating LRBA selectively facilitates signals by receptors for ligands expressed on the surface of NK targets. Surprisingly, LRBA limits immunoregulatory cell numbers in tissues where GvHD is primed or initiated, and consistent with this LRBA-null mice also demonstrate resistance to lethal GvHD. These findings demonstrate that LRBA is redundant for host longevity while being essential for both host and donor-mediated immune responses and thus represents a unique and novel molecular target in transplant immunology.
Fibroblast miR-210 overexpression is independently associated with clinical failure in Prostate Cancer – a multicenter (in situ hybridization) study
Authors: Andersen Sigve , Richardsen Elin , Moi Line , Donnem Tom , Nordby Yngve , Ness Nora , Holman Marte Eilertsen , Bremnes Roy M. , Busund Lill-Tove
Published: November 2016

There is a need for better prognostication in prostate cancer (PC). “The micromanager of hypoxia”, microRNA-210 (miR-210) is directly linked to hypoxia, is overexpressed in PC and has been implied in tumor cell-fibroblast crosstalk. We investigated the prognostic impact of miR-210 in tumor cells and fibroblasts in PC. Tumor and stromal samples from a multicenter PC cohort of 535 prostatectomy patients were inserted into tissue microarrays. To investigate the expression of miR-210, we used in situ hybridization and two pathologists semiquantitatively scored its expression. Overexpression of miR-210 in tumor cells was not associated to biochemical failure-free survival (BFFS, p = 0.85) or clinical failure-free survival (CFFS, p = 0.09). However, overexpression of miR-210 in fibroblasts was significantly associated to a poor CFFS (p = 0.001), but not BFFS (p = 0.232). This feature was validated in both cohorts. Overexpression of miR-210 was independently associated with a reduced CFFS (HR = 2.76, CI 95% 1.25–6.09, p = 0.012). Overexpression of miR-210 in fibroblasts is independently associated with a poor CFFS. This highlights the importance of fibroblasts and cellular compartment crosstalk in PC. miR-210 is a candidate prognostic marker and potential therapeutic target in PC.
Evidences for redox reaction driven charge transfer and mass transport in metal-assisted chemical etching of silicon
Authors: Kong Lingyu , Dasgupta Binayak , Ren Yi , Mohseni Parsian K. , Hong Minghui , Li Xiuling , Chim Wai Kin , Chiam Sing Yang
Published: November 2016

In this work, we investigate the transport processes governing the metal-assisted chemical etching (MacEtch) of silicon (Si). We show that in the oxidation of Si during the MacEtch process, the transport of the hole charges can be accomplished by the diffusion of metal ions. The oxidation of Si is subsequently governed by a redox reaction between the ions and Si. This represents a fundamentally different proposition in MacEtch whereby such transport is understood to occur through hole carrier conduction followed by hole injection into (or electron extraction from) Si. Consistent with the ion transport model introduced, we showed the possibility in the dynamic redistribution of the metal atoms that resulted in the formation of pores/cracks for catalyst thin films that are ≲30 nm thick. As such, the transport of the reagents and by-products are accomplished via these pores/cracks for the thin catalyst films. For thicker films, we show a saturation in the etch rate demonstrating a transport process that is dominated by diffusion via metal/Si boundaries. The new understanding in transport processes described in this work reconcile competing models in reagents/by-products transport, and also solution ions and thin film etching, which can form the foundation of future studies in the MacEtch process.
Infliximab and Dexamethasone Attenuate the Ductular Reaction in Mice
Authors: Verhulst Stefaan , Best Jan , Syn Wing-Kin , Reynaert Hendrik , Hellemans Karine H. , Canbay Ali , Dolle Laurent , van Grunsven Leo A.
Published: November 2016

Chronic hepatic injury is accompanied by a ductular response that is strongly correlated with disease severity and progression of fibrosis. To investigate whether anti-inflammatory drugs can modulate the ductular response, we treated mice suffering from a steatotic or cholestatic injury with anti-TNF-α antibodies (Infliximab) or glucocorticoids (Dexamethasone). We discovered that Dexamethasone and Infliximab can both modulate the adaptive remodeling of the biliary architecture that occurs upon liver injury and limit extracellular matrix deposition. Infliximab treatment, at least in these steatotic and cholestatic mouse models, is the safer approach since it does not increase liver injury, allows inflammation to take place but inhibits efficiently the ductular response and extracellular matrix deposition. Infliximab-based therapy could, thus, still be of importance in multiple chronic liver disorders that display a ductular response such as alcoholic liver disease or sclerosing cholangitis.
Conspecific injury raises an alarm in medaka
Authors: Mathuru Ajay S.
Published: November 2016

In the late 1930s, Karl von Frisch reported that semiochemicals released upon injury, act as alarm substances (Schreckstoff) in fish. In Ostariophysi species, club cells in the epidermis are believed to contain cues related to alarm substance; however, the function of club cells, primarily as reservoirs of alarm substance has been debated. Here, I describe an alarm response in the Japanese rice fishOryzias latipes(medaka), a member of the order Beloniformes. The response to alarm substance (Schreckreaction) in medaka is characterized by bouts of immobility and an increase in cortisol levels within minutes of exposure to conspecific skin extract. Histological analysis, however, suggests that club cells are either rare or absent in the medaka epidermis. In addition to describing an uncharacterized behavior in a vertebrate popular for genetic and developmental studies, these results support the hypothesis that the primary function of epidermal club cells may be unrelated to a role as alarm substance cells. The existence of similar behavioral responses in two evolutionarily distant but well established laboratory models, the zebrafish and the medaka, offers the possibility of comparative analyses of neural circuits encoding innate fear.
Laser Printing of Superhydrophobic Patterns from Mixtures of Hydrophobic Silica Nanoparticles and Toner Powder
Authors: Ngo Chi-Vinh , Chun Doo-Man
Published: November 2016

In this work, a new and facile dry printing method was developed for the direct fabrication of superhydrophobic patterns based on silica nanoparticles. Mixtures of hydrophobic fumed silica nanoparticles and toner powder were printed on paper and polymer sheets using a commercial laser printer to produce the superhydrophobic patterns. The mixing ratio of the toner powder (for the laser printer) to hydrophobic silica was also investigated to optimize both the printing quality and the superhydrophobicity of the printed areas. The proper mixing ratio was then used to print various superhydrophobic patterns, including triangular, square, circular, and complex arrangements, to demonstrate that superhydrophobic surfaces with different patterns can be fabricated in a few seconds without any post-processing. The superhydrophobicity of each sample was evaluated by contact angle measurements, and all printed areas showed contact angles greater than 150°. The research described here opens the possibility of rapid production of superhydrophobic surfaces with various patterns. Ultimately, the obtained findings may have a significant impact on applications related to self-cleaning, control of water geometry and position, fluid mixing and fluid transport.
Mechanism of Adsorption on Nanomaterials
Authors: Bushra Rani , Ahmed Anees , Shahadat Mohammad
Published: November 2016

The disposal of large amounts of wastewater containing organic, inorganic and biological pollutants has become a serious issue today. Many technologies have been established for pollutant removal, including chemical oxidation/reduction, biological treatment, coagulation/flocculation, adsorption, membrane separation, and ion exchange. The most effective among them is the adsorption process because it is simple, highly efficient, and easy to operate. Adsorption is a surface phenomenon that takes place by physical forces but sometimes, weak chemical bonding also participates in the adsorption process. Different models, like Langmuir, Freundlich, Halsey, Henderson, intraparticle diffusion, and Lagergren, are used to explain the results of adsorption. A thermodynamic study is carried out to determine the feasibility of the process by interpreting the values of enthalpy, free energy, entropy, and energy of activation. Recently, a great deal of attention has been focused on the application of nanostructured materials as sorbents to remove toxic and harmful substances from aquatic media. Nanostructure sorbents, which include metal nanoparticles, carbon nanomaterials and dendrimers, as compared to traditional materials have exhibited much higher efficiency and faster rates in water treatment with enhanced redox and photocatalytic properties.
Enzyme-free fluorescent biosensor for miRNA-21 detection based on MnO2 nanosheets and catalytic hairpin assembly amplification
Authors: Ouyang Wenjun , Liu ZhenHua , Zhang GuiFeng , Chen Zheng , Guo Longhua , Lin Zhenyu , Qiu Bin , Chen Guonan
Published: November 2016

MicroRNAs (miRNAs) have attracted enormous interest due to their involvement in complex regulatory functions and for being closely linked to some cancers.
Classification of individual cotton seeds with respect to variety using near-infrared hyperspectral imaging
Authors: Carreiro Soares Sófacles Figueredo , Medeiros Everaldo Paulo , Pasquini Celio , de Lelis Morello Camilo , Harrop Galvão Roberto Kawakami , Ugulino Araújo Mário César
Published: November 2016

This paper proposes the use of Near Infrared Hyperspectral Imaging (NIR-HSI) as a new strategy for fast and non-destructive classification of cotton seeds with respect to variety.
A database on the stability of silver and gold nanostructures for applications in biology and biomolecular sciences
Authors: Weerasekera Hasitha de Alwis , Silvero María Jazmín , Regis Correa da Silva Daliane , Scaiano Juan C.
Published: November 2016

A useful library on the stability and properties of gold/silver nanomaterials with potential biological applications.
Receptor clustering and activation by multivalent interaction through recognition peptides presented on exosomes
Authors: Nakase I. , Ueno N. , Katayama M. , Noguchi K. , Takatani-Nakase T. , Kobayashi N. B. , Yoshida T. , Fujii I. , Futaki S.
Published: November 2016

A system for inducing clustering of cell surface receptorsviarecognition peptide segments displayed on exosomes, leading to receptor activation.
Exploring the mechanochemical cycle of dynein motor proteins: structural evidence of crucial intermediates
Authors: Dutta Mandira , Jana Biman
Published: November 2016

Exploration of the biologically relevant pathways of dynein's mechanochemical cycle using structure based models.
Peeling the astronomical onion
Authors: Rosu-Finsen Alexander , Marchione Demian , Salter Tara L. , Stubbing James W. , Brown Wendy A. , McCoustra Martin R. S.
Published: November 2016

This work presents a study of water mobility on interstellar dust grain analogues at temperatures as low as 18 K. The work indicates that water forms pure domains rather than covering the entire grain, thereby leaving bare dust grain surfaces available on which other molecules can adsorb as well as themselves providing surfaces for further adsorption from the interstellar gas.
DNA ionogel: Structure and self-assembly
Authors: Pandey Pankaj Kumar , Rawat Kamla , Aswal V. K. , Kohlbrecher J. , Bohidar H. B.
Published: November 2016

DNA dissolved in ionic liquid (IL) solution showed a transition to the gel phase ([DNA] ≥ 1% (w/v)).
Thermally induced phase separation in levitated polymer droplets
Authors: Pathak Binita , Xavier Priti , Bose Suryasarathi , Basu Saptarshi
Published: November 2016

A modified technique for phase separation in polymer blends for high throughput in shorter processing timescales.
Conductance and activation energy for electron transport in series and parallel intramolecular circuits
Authors: Hsu Liang-Yan , Wu Ning , Rabitz Herschel
Published: November 2016

We investigate electron transport through series and parallel intramolecular circuits in the framework of the multi-level Redfield theory.
The inside-out supercapacitor: induced charge storage in reduced graphene oxide
Authors: Martin Samuel T. , Akbari Abozar , Chakraborty Banerjee Parama , Neild Adrian , Majumder Mainak
Published: November 2016

By turning the standard supercapacitor geometry inside out, an ionic capacitor is made for use in ionic circuits.
Mechanistic insights into excited state intramolecular proton transfer in isolated and metal chelated supramolecular chemosensors
Authors: Karsili Tolga N. V. , Marchetti Barbara , Ashfold Michael N. R.
Published: November 2016

Mechanistic studies of the excited state intramolecular proton transfer in a series of related and progressively more complex supramolecular chromophores.
Blocked isocyanates: from analytical and experimental considerations to non-polyurethane applications
Authors: Rolph Marianne S. , Markowska Anna L. J. , Warriner Colin N. , O'Reilly Rachel K.
Published: November 2016

In this review we aim to provide an introductory guide to blocked isocyanates, through discussion on different examples of blocking groups, along with experimental considerations for their application.
The synergistic effect during biphasic SET-LRP in ethanol–nonpolar solvent–water mixtures
Authors: Enayati Mojtaba , Smail Rauan B. , Grama Silvia , Jezorek Ryan L. , Monteiro Michael J. , Percec Virgil
Published: November 2016

Adding a nonpolar solvent to ethanol–water reaction mixtures transforms SET-LRP of BA from triphasic to biphasic exhibiting a synergistic effect.
A Cu(ii) metal–organic framework as a recyclable catalyst for ARGET ATRP
Authors: Lee Hui-Chun , Antonietti Markus , Schmidt Bernhard V. K. J.
Published: November 2016

A Cu(ii) MOF can serve as an comprehensive catalyst for activators regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) in the synthesis of benzyl methacrylate, styrene, isoprene and 4-vinylpyridine.
Cobalt-catalyzed C–H activation and regioselective intermolecular annulation with allenes
Authors: Li Tianlei , Zhang Chao , Tan Yonghua , Pan Weidong , Rao Yu
Published: November 2016

An efficient Co(ii)-catalyzed intermolecular annulation of N-(quinolin-8-yl)benzamide with allenes for the synthesis of novel isoquinolin-1(2H)-one scaffolds has been developed.
Copper-assisted azide–alkyne cycloaddition chemistry as a tool for the production of emissive boron difluoride 3-cyanoformazanates
Authors: Barbon Stephanie M. , Novoa Samantha , Bender Desiree , Groom Hilary , Luyt Leonard G. , Gilroy Joe B.
Published: November 2016

Emissive BF2 complexes of 3-cyanoformazanates produced using CuAAC chemistry are described. Highlights include ferrocene-substituted derivatives with ‘turn-on’ fluorescence upon oxidation and a water soluble derivative with application as a cell-imaging agent.
Achievement of linear response for competitive bioaffinity assays of ligands: criteria of optimized interaction systems
Authors: Pu J. , Hu X. L. , Liao J. , Li Y. W. , Qin J. L. , Xie Y. L. , Zhan C.-G. , Yang X. L. , Liao F.
Published: November 2016

For a linear response, an optimized competitive bioaffinity assay of a ligand requiresCRT> 3 ×CPT,CPT> 50 ×KdR, andKdR> 260 ×KdX(CRTandCPTare concentrations of the probe and protein whileKdXandKdRareKdfor the ligand and probe, respectively).
Combination of homogenous liquid–liquid extraction and dispersive liquid–liquid microextraction for extraction and preconcentration of amantadine from biological samples followed by its indirect determination by flame atomic absorption spectrometry
Authors: Sorouraddin S. M. , Farajzadeh M. A. , Hassanyani A. , Afshar Mogaddam M. R.
Published: November 2016

A new and simple procedure has been developed for the indirect determination of amantadine in biological samples.
Rationalization of liquid assisted grinding intercalation yields of organic molecules into layered double hydroxides by multivariate analysis
Authors: Conterosito E. , Milanesio M. , Palin L. , Gianotti V.
Published: November 2016

PCA, coupled to molecular descriptors, proved to be an effective tool to rationalize the mechanochemical intercalation yields of layered materials.
Remarkably durable platinum cluster supported on multi-walled carbon nanotubes with high performance in an anhydrous polymer electrolyte fuel cell
Authors: Yang Zehui , Yu Xinxin , Zhang Yunfeng , Xu Guodong
Published: November 2016

Reducing platinum (Pt) usage in the polymer electrolyte fuel cells (PEFCs) has become one of the main issues in the global commercialization of PEFCs.