bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust method for identification of prognostic gene signatures from gene expression profiles
Authors: Sim Woogwang , Lee Jungsul , Choi Chulhee 
Published: November 2017

AbstractIn the last decade, many attempts have been made to use gene expression profiles to identify prognostic genes for various types of cancer. Previous studies evaluating the prognostic value of genes suffered by failing to solve the critical problem of classifying patients into different risk groups based on specific gene expression threshold levels. Here, we present a novel method, called iterative patient partitioning (IPP), which was inspired by the receiver operating characteristic (ROC) curve, is based on the log-rank test and overcomes the threshold decision problem. We applied IPP to analyze datasets pertaining to various subtypes of breast cancer. Using IPP, we discovered both novel and well-studied prognostic genes related to cell cycle/proliferation or the immune response. The novel genes were further analyzed using copy-number alteration and mutation data, and these results supported their relationship with prognosis.
Effect of different organic fertilizers application on growth and environmental risk of nitrate under a vegetable field
Authors: Li Shuyan , Li Jijin , Zhang Bangxi , Li Danyang , Li Guoxue , Li Yangyang 
Published: November 2017

AbstractThe effect of chicken manure after different disposal methods (water-logged composting, GOF; anaerobic digestion, BR; thermophilic composting, ROF) on vegetable growth and environmental risk was investigated under the tomato-celery-tomato field. Results showed that organic fertilizers significantly increased vegetable yield and quality, but with inappropriate application may cause serious environmental risk such as nitrate pollution. Maximum vegetable yield of 80.9, 68.3, 112.7 t·ha−1 (first, second and third rotation crop, respectively) with best vegetable quality was obtained in ROF treatment. The highest N use efficiency with the least nitrate enrichment in soil was also found in ROF treatment. Moreover, under this fertilization way, nitrate concentration in soil leachate dropped to 6.4 mg·L−1, which satisfied the threshold (<10 mg·L−1) for drinking water set by the US Environmental Protection Agency. Thus, ROF was suggested to be the optimal fertilizer with the best yield, quality and the least environmental risk under the “tomato-celery” rotation system.
Fabrication and characterization of reversible thermochromic wood veneers
Authors: Zhu Xiaodong , Liu Yu , Dong Ningwen , Li Zhao 
Published: November 2017

AbstractLeuco dyes are widely used as functional materials for their thermosensitive chromogenic nature. The influences of thermochromic compounds and impregnation processing conditions on thermochromic wood veneer properties were investigated in this paper. The thermochromic compounds included thermochromic dye (ODB-2), color developer (bisphenol A) and solvent (1-tetradecanol). To achieve the maximum color change, the optimum mixing ratio of ODB-2 to bisphenol A to 1-tetradecanol was 1:2:60. Juglans mandshurica veneers were ultrasonically impregnated with reversible thermochromic compound suspensions. Analysis of variance showed that the influences of impregnation parameters on veneer color change were significant at the 0.05 level. The optimum thermochromic wood veneer can be obtained by impregnating with a thermochromic compound suspension for 2.0 min at 65 °C. In this paper, the thermochromic properties of wood veneers were evaluated, and functional thermochromic veneers exhibited excellent properties and thermostability.
The orientation and stability of the GPCR-Arrestin complex in a lipid bilayer
Authors: Wang Dali , Yu Hua , Liu Xiangdong , Liu Jianqiang , Song Chen 
Published: November 2017

AbstractG protein-coupled receptors (GPCRs) constitute a large family of membrane proteins that plays a key role in transmembrane signal transduction and draw wide attention since it was discovered. Arrestin is a small family of proteins which can bind to GPCRs, block G protein interactions and redirect signaling to G-protein-independent pathways. The detailed mechanism of how arrestin interacts with GPCR remains elusive. Here, we conducted molecular dynamics simulations with coarse-grained (CG) and all-atom (AA) models to study the complex structure formed by arrestin and rhodopsin, a prototypical GPCR, in a POPC bilayer. Our results indicate that the formation of the complex has a significant impact on arrestin which is tightly anchored onto the bilayer surface, while has a minor effect on the orientation of rhodopsin in the lipid bilayer. The formation of the complex induces an internal change of conformation and flexibility in both rhodopsin and arrestin, mainly at the binding interface. Further investigation on the interaction interface identified the hydrogen bond network, especially the long-lived hydrogen bonds, and the key residues at the contact interface, which are responsible for stabilizing the complex. These results help us to better understand how rhodopsin interacts with arrestin on membranes, and thereby shed lights on arrestin-mediated signal transduction through GPCRs.
Inhibitory effects of curcumin and cyclocurcumin in 1-methyl-4-phenylpyridinium (MPP+) induced neurotoxicity in differentiated PC12 cells
Authors: Chakraborty Sandeep , Karmenyan Artashes , Tsai Jin-Wu , Chiou Arthur 
Published: November 2017

AbstractDevelopment and progression of neurodegenerative diseases like Parkinson’s disease (PD) involve multiple pathways. Thus, effective therapeutic treatments should intervene to address all these pathways simultaneously for greater success. Most of the current pharmacotherapeutic approaches just supplement striatal dopamine. Hence, natural extracts of plants with therapeutic potential have been explored. Curcuminoids belong to one such group of polyphenol which show immense therapeutic effects. Here, we have used intracellular reactive oxygen species (ROS) measurement, and two-photon fluorescence lifetime imaging microscopy (2P-FLIM) of cellular autofluorescent co-enzyme reduced nicotinamide adenine dinucleotide (NADH) to study the inhibitory effects of curcumin and cyclocurcumin in alleviating PD like neurotoxicity of 1-methyl-4-phenylpyridinium (MPP+) in neuronal growth factor (NGF) induced differentiated PC12 cells. Our results showed that both cyclocurcumin and curcumin reduced the level of ROS caused by MPP+ treatment. Moreover, a significant increase in the free, protein-bound, and average NADH fluorescence lifetimes along with a decrease in the relative contribution of free- vs. protein-bound NADH components in curcuminoids treated cells (pretreated with MPP+) were observed compared with those treated with MPP+ only. This study, which indicates that cyclocurcumin offers higher neuronal protection than curcumin, may initiate further studies of these compounds in the cure of neurodegenerative diseases.
Na+ entry through heteromeric TRPC4/C1 channels mediates (−)Englerin A-induced cytotoxicity in synovial sarcoma cells
Authors: Muraki Katsuhiko , Ohnishi Kaori , Takezawa Akiho , Suzuki Hiroka , Hatano Noriyuki , Muraki Yukiko , Hamzah Nurasyikin , Foster Richard , Waldmann Herbert , Nussbaumer Peter , Christmann Mathias , Bon Robin S. , Beech David J. 
Published: November 2017

AbstractThe sesquiterpene (−)Englerin A (EA) is an organic compound from the plant Phyllanthus engleri which acts via heteromeric TRPC4/C1 channels to cause cytotoxicity in some types of cancer cell but not normal cells. Here we identified selective cytotoxicity of EA in human synovial sarcoma cells (SW982 cells) and investigated the mechanism. EA induced cation channel current (Icat) in SW982 cells with biophysical characteristics of heteromeric TRPC4/C1 channels. Inhibitors of homomeric TRPC4 channels were weak inhibitors of the Icat and EA-induced cytotoxicity whereas a potent inhibitor of TRPC4/C1 channels (Pico145) strongly inhibited Icat and cytotoxicity. Depletion of TRPC1 converted Icat into a current with biophysical and pharmacological properties of homomeric TRPC4 channels and depletion of TRPC1 or TRPC4 suppressed the cytotoxicity of EA. A Na+/K+-ATPase inhibitor (ouabain) potentiated EA-induced cytotoxicity and direct Na+ loading by gramicidin-A caused Pico145-resistant cytotoxicity in the absence of EA. We conclude that EA has a potent cytotoxic effect on human synovial sarcoma cells which is mediated by heteromeric TRPC4/C1 channels and Na+ loading.
Possible function of the second RecJ-like protein in stalled replication fork repair by interacting with Hef
Authors: Nagata Mariko , Ishino Sonoko , Yamagami Takeshi , Simons Jan-Robert , Kanai Tamotsu , Atomi Haruyuki , Ishino Yoshizumi 
Published: November 2017

AbstractRecJ was originally identified in Escherichia coli and plays an important role in the DNA repair and recombination pathways. Thermococcus kodakarensis, a hyperthermophilic archaeon, has two RecJ-like nucleases. These proteins are designated as GAN (GINS-associated nuclease) and HAN (Hef-associated nuclease), based on the protein they interact with. GAN is probably a counterpart of Cdc45 in the eukaryotic CMG replicative helicase complex. HAN is considered mainly to function with Hef for restoration of the stalled replication fork. In this study, we characterized HAN to clarify its functions in Thermococcus cells. HAN showed single-strand specific 3′ to 5′ exonuclease activity, which was stimulated in the presence of Hef. A gene disruption analysis revealed that HAN was non-essential for viability, but the ΔganΔhan double mutant did not grow under optimal conditions at 85 °C. This deficiency was not fully recovered by introducing the mutant han gene, encoding the nuclease-deficient HAN protein, back into the genome. These results suggest that the unstable replicative helicase complex without GAN performs ineffective fork progression, and thus the stalled fork repair system including HAN becomes more important. The nuclease activity of HAN is required for the function of this protein in T. kodakarensis.
Functional and spatial segregation within the inferior frontal and superior temporal cortices during listening, articulation imagery, and production of vowels
Authors: Rampinini Alessandra Cecilia , Handjaras Giacomo , Leo Andrea , Cecchetti Luca , Ricciardi Emiliano , Marotta Giovanna , Pietrini Pietro 
Published: November 2017

AbstractClassical models of language localize speech perception in the left superior temporal and production in the inferior frontal cortex. Nonetheless, neuropsychological, structural and functional studies have questioned such subdivision, suggesting an interwoven organization of the speech function within these cortices. We tested whether sub-regions within frontal and temporal speech-related areas retain specific phonological representations during both perception and production. Using functional magnetic resonance imaging and multivoxel pattern analysis, we showed functional and spatial segregation across the left fronto-temporal cortex during listening, imagery and production of vowels. In accordance with classical models of language and evidence from functional studies, the inferior frontal and superior temporal cortices discriminated among perceived and produced vowels respectively, also engaging in the non-classical, alternative function – i.e. perception in the inferior frontal and production in the superior temporal cortex. Crucially, though, contiguous and non-overlapping sub-regions within these hubs performed either the classical or non-classical function, the latter also representing non-linguistic sounds (i.e., pure tones). Extending previous results and in line with integration theories, our findings not only demonstrate that sensitivity to speech listening exists in production-related regions and vice versa, but they also suggest that the nature of such interwoven organisation is built upon low-level perception.
Interaction of Complement Defence Collagens C1q and Mannose-Binding Lectin with BMP-1/Tolloid-like Proteinases
Authors: Lacroix Monique , Tessier Agnès , Dumestre-Pérard Chantal , Vadon-Le Goff Sandrine , Gout Evelyne , Bruckner-Tuderman Leena , Kiritsi Dimitra , Nyström Alexander , Ricard-Blum Sylvie , Moali Catherine , Hulmes David J. S. , Thielens Nicole M. 
Published: November 2017

AbstractThe defence collagens C1q and mannose-binding lectin (MBL) are immune recognition proteins that associate with the serine proteinases C1r/C1s and MBL-associated serine proteases (MASPs) to trigger activation of complement, a major innate immune system. Bone morphogenetic protein-1 (BMP-1)/tolloid-like proteinases (BTPs) are metalloproteinases with major roles in extracellular matrix assembly and growth factor signalling. Despite their different functions, C1r/C1s/MASPs and BTPs share structural similarities, including a specific CUB-EGF-CUB domain arrangement found only in these enzymes that mediates interactions with collagen-like proteins, suggesting a possible functional relationship. Here we investigated the potential interactions between the defence collagens C1q and MBL and the BTPs BMP-1 and mammalian tolloid-like-1 (mTLL-1). C1q and MBL bound to immobilized BMP-1 and mTLL-1 with nanomolar affinities. These interactions involved the collagen-like regions of the defence collagens and were inhibited by pre-incubation of C1q or MBL with their cognate complement proteinases. Soluble BMP-1 and mTLL-1 did not inhibit complement activation and the defence collagens were neither substrates nor inhibitors of BMP-1. Finally, C1q co-localized with BMP-1 in skin biopsies following melanoma excision and from patients with recessive dystrophic epidermolysis bullosa. The observed interactions provide support for a functional link between complement and BTPs during inflammation and tissue repair.
Sauber und gründlich
Authors: Bürkert Susanne S. 
Published: November 2017

SummaryDie Colon-Hydro-Therapie (CHT) ist eine saubere und geruchsfreie Art der Darmspülung. Ziel ist es, eine Regeneration des Darms auf natürliche Weise zu erreichen, indem Kotreste und Giftstoffe aus dem Darm gespült werden. Mithilfe der CHT, einer Ernährungsumstellung, der Substitution von Mikronährstoffen und Probiotika kann sich der Darm erholen und regenerieren.
Mikrovaskuläre Kehlkopfrekonstruktion nach totaler Laryngektomie
Authors: Hackenberg Stephan , Kleinsasser Norbert , Scherzad Agmal , Kraus Fabian , Hagen Rudolf 
Published: November 2017

ZusammenfassungDie totale Laryngektomie stellt nach wie vor ein Standardverfahren zur Therapie fortgeschrittener Larynx- und Hypopharynxkarzinome dar. Der
Verlust des stimmbildenden Organs schränkt die Lebensqualität der Betroffenen maßgeblich ein. Die am häufigsten eingesetzte Technik zur
Stimmrehabilitation ist die tracheoösophageale Punktion mit Einsatz eines Stimmventils. Zu den chirurgischen Verfahren der
Stimmrehabilitation gehört unter anderem die Larynxrekonstruktion mit einem Unterarmlappen. Im Rahmen dieser monozentrischen retrospektiven
Analyse wurden Patienten betrachtet, die zwischen 2006 und 2015 nach totaler Laryngektomie mit einer solchen sogenannten Laryngoplastik
versorgt wurden. Fokus der Untersuchung lag auf der Beurteilung von funktionellen Langzeitergebnissen und Komplikationen. Insgesamt konnten
39 Patienten in die Studie eingeschlossen werden, von denen bei 77 % eine dauerhafte Phonation über das Transplantat möglich war, bei 62 %
sogar fingerfrei. Nach Ausschluss adjuvant bestrahlter Patienten lag die Rate der erfolgreichen Stimmrehabilitation bei 91 % (20 / 22). Das
postoperative Halshämatom war mit 15 % die häufigste Frühkomplikation, Lappennekrosen traten nicht auf. Die häufigste Spätkomplikation war
die Stenosierung des Laryngoplastiklumens, welche in der Regel als Folge einer Radiatio auftrat. Im Vergleich zu Daten aus der Literatur ist
die Rate erfolgreich stimmrehabilitierter Patienten annähernd gleichwertig zur Versorgung mit einem Stimmventil, allerdings mit qualitativ
besseren Ergebnissen. Komplikationen, die durch das Stimmventil bedingt sind und in seltenen Fällen schwerwiegend sein können, treten bei
Laryngoplastikpatienten nicht auf. Die lebenslange Notwendigkeit zum regelmäßigen Stimmventilwechsel entfällt. Bei korrekter
Indikationsstellung ist die Laryngoplastik eine suffiziente Methode zur Stimmrehabilitation nach Laryngektomie.
Expressivism, meaning, and allthat
Authors: Köhler Sebastian 
Published: November 2017

AbstractIt has recently been suggested that meta-normative expressivism is best seen as a meta-semantic, rather than a semantic view. One strong motivation for this is that expressivism becomes, thereby, compatible with truth-conditional semantics. While this approach is promising, however, many of its details are still unexplored. One issue that still needs to be explored in particular, is what accounts of propositional contents are open to meta-semantic expressivists. This paper makes progress on this issue by developing an expressivist-friendly deflationary account of such contents.
Impact of land cover change on a mountain ecosystem and its services: case study from the Phobjikha valley, Bhutan
Authors: Chaudhary Sunita , Tshering Dago , Phuntsho Tshering , Uddin Kabir , Shakya Bandana , Chettri Nakul 
Published: November 2017

ABSTRACT

Introduction:
Mountains occupy 24% of the global land surface and are home to 12% of the world’s population; they host the world’s principal biomes and supply a diverse array of ecosystem services. But they are also highly sensitive to both natural and human induced changes, which can affect service provision meant for one third of humanity. Systematic research on impacts of land cover change from mountains at the local scale are limited, especially in developing countries, which poses a barrier to informed planning for sustainable management. Bhutan being in the forefront as contributor towards global conservation goals, a case study following a systematic research framework considering quantitative, qualitative and geospatial tools was experimented.

Outcome:
Respondents identified and ranked 24 ecosystem services, among which the provisioning services were the most important, followed by cultural, regulating, and supporting services. Forest was the most important land cover type for services, followed by marsh, scrub, water bodies, and agriculture. The area of forest declined by 2% and marsh by 7% over the 32-year period, suggesting a potential decrease in ecosystem services, which was also observed by the local community.

Discussion:
It was observed that 80% of the local people are still directly dependent on the diverse ecosystems for services. Though subtle, the decrease in land cover has implications for livelihoods of the people and the rich biodiversity of the area. Aspiring communities for local development needs guidance for identifying trade-offs in land cover types in sustainable management. An integrated and holistic approach focusing on both conservation and community development should be used to manage and develop the valley and the region sustainably.

Conclusion:
We recommend diversifying the limited livelihood strategies (potato farming and livestock grazing) to reduce the potential vulnerability of the local community and reduce the pressure on forest and marsh. Proper land use planning in the valley would be beneficial to maintain and regulate land uses in an effective way and avoid possible conflicts between settlement, agriculture, forest, and marsh.
Marsh persistence under sea-level rise is controlled by multiple, geologically variable stressors
Authors: Mitchell M. , Herman J. , Bilkovic D. M. , Hershner C. 
Published: November 2017

ABSTRACT

Introduction:
Marshes contribute to habitat and water quality in estuaries and coastal bays. Their importance to continued ecosystem functioning has led to concerns about their persistence.

Outcomes:
Concurrent with sea-level rise, marshes are eroding and appear to be disappearing through ponding in their interior; in addition, in many places, they are being replaced with shoreline stabilization structures. We examined the changes in marsh extent over the past 40 years within a subestuary of Chesapeake Bay, the largest estuary in the United States, to better understand the effects of sea-level rise and human pressure on marsh coverage.

Discussion:
Approximately 30 years ago, an inventory of York River estuary marshes documented the historic extent of marshes. Marshes were resurveyed in 2010 to examine shifts in tidal marsh extent and distribution. Marsh change varied spatially along the estuary, with watershed changes between a 32% loss and an 11% gain in marsh area. Loss of marsh was apparent in high energy sections of the estuary while there was marsh gain in the upper/riverine section of the estuary and where forested hummocks on marsh islands have become inundated. Marshes showed little change in the small tributary creeks, except in the creeks dominated by fringing marshes and high shoreline development.

Conclusions:
Differential resilience to sea-level rise and spatial variations in erosion, sediment supply, and human development have resulted in spatially variable changes in specific marsh extents and are predicted to lead to a redistribution of marshes along the estuarine gradient, with consequences for their unique communities.
circlncRNAnet: an integrated web-based resource for mapping functional networks of long or circular forms of noncoding RNAs
Authors: Wu Shao-Min , Liu Hsuan , Huang Po-Jung , Chang Ian Yi-Feng , Lee Chi-Ching , Yang Chia-Yu , Tsai Wen-Sy , Tan Bertrand Chin-Ming 
Published: November 2017

Abstract

Background
Despite their lack of protein-coding potential, long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. These noncoding RNA transcripts are known to affect expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation. Given their widespread target spectrum, as well as extensive modes of action, a complete understanding of their biological relevance will depend on integrative analyses of systems data at various levels.

Findings
While a handful of publicly available databases have been reported, existing tools do not fully capture, from a network perspective, the functional implications of lncRNAs or circRNAs of interest. Through an integrated and streamlined design, circlncRNAnet aims to broaden the understanding of ncRNA candidates by testing in silico several hypotheses of ncRNA-based functions, on the basis of large-scale RNA-seq data. This web server is implemented with several features that represent advances in the bioinformatics of ncRNAs: (1) a flexible framework that accepts and processes user-defined next-generation sequencing–based expression data; (2) multiple analytic modules that assign and productively assess the regulatory networks of user-selected ncRNAs by cross-referencing extensively curated databases; (3) an all-purpose, information-rich workflow design that is tailored to all types of ncRNAs. Outputs on expression profiles, co-expression networks and pathways, and molecular interactomes, are dynamically and interactively displayed according to user-defined criteria.

Conclusions
In short, users may apply circlncRNAnet to obtain, in real time, multiple lines of functionally relevant information on circRNAs/lncRNAs of their interest. In summary, circlncRNAnet provides a “one-stop” resource for in-depth analyses of ncRNA biology. circlncRNAnet is freely available at http://app.cgu.edu.tw/circlnc/.