bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical interaction mechanism of 10-MDP with zirconia
Authors: Nagaoka Noriyuki , Yoshihara Kumiko , Feitosa Victor Pinheiro , Tamada Yoshiyuki , Irie Masao , Yoshida Yasuhiro , Van Meerbeek Bart , Hayakawa Satoshi 
Published: March 2017

AbstractCurrently, the functional monomer 10-methacryloyloxy-decyl-dihydrogen-phosphate (10-MDP) was documented to chemically bond to zirconia ceramics. However, little research has been conducted to unravel the underlying mechanisms. This study aimed to assess the chemical interaction and to demonstrate the mechanisms of coordination between 10-MDP and zirconium oxide using 1H and 31P magic angle spinning (MAS) nuclear magnetic resonance (NMR) and two dimensional (2D) 1H → 31P heteronuclear correlation (HETCOR) NMR. In addition, shear bond-strength (SBS) tests were conducted to determine the effect of 10-MDP concentration on the bonding effectiveness to zirconia. These SBS tests revealed a 10-MDP concentration-dependent SBS with a minimum of 1-ppb 10-MDP needed. 31P-NMR revealed that one P-OH non-deprotonated of the PO3H2 group from 10-MDP chemically bonded strongly to zirconia. 1H-31P HETCOR NMR indicated that the 10-MDP monomer can be adsorbed onto the zirconia particles by hydrogen bonding between the P=O and Zr-OH groups or via ionic interactions between partially positive Zr and deprotonated 10-MDP (P-O−). The combination of 1H NMR and 2D 1H-31P HETCOR NMR enabled to describe the different chemical states of the 10-MDP bonds with zirconia; they not only revealed ionic but also hydrogen bonding between 10-MDP and zirconia.
Noise characteristics of the new converter transformer under DC bias
Authors: Liu Junhua , Luo Longfu 
Published: March 2017

Harmonic magnetic fluxes in transformer's core and harmonic currents in grid‐side winding can be restrained via the inductive filtering technology, and running noise of the transformer is reduced at the source. The A‐weighted sound levels of the measuring points are measured under DC bias. The noise test results verify this theory. When the fully‐tuned filters matched with the new converter transformer are inputted and not inputted, the noise response curves of the measured points are compared. The fitting coefficients of the noise values at 1250 and 1600 Hz with the unbalance degrees of the trigger angle are obtained.
BCL6 promotes glioma and serves as a therapeutic target
Authors: Xu Liang , Chen Ye , Dutra-Clarke Marina , Mayakonda Anand , Hazawa Masaharu , Savinoff Steve E. , Doan Ngan , Said Jonathan W. , Yong William H. , Watkins Ashley , Yang Henry , Ding Ling-Wen , Jiang Yan-Yi , Tyner Jeffrey W. , Ching Jianhong , Kovalik Jean-Paul , Madan Vikas , Chan Shing-Leng , Müschen Markus , Breunig Joshua J. , Lin De-Chen , Koeffler H. Phillip 
Published: March 2017

Significance
Glioblastoma (GBM) is the most lethal brain malignancy lacking effective treatment. In this study, we demonstrate that BCL6 is a prognostic marker and a targetable GBM-promoting factor. Silencing of BCL6 inhibits the malignant phenotype of GBM cells and triggers cellular senescence. We also identify AXL as an important BCL6 transcriptional target, the expression of which is also regulated positively by NCoR, a BCL6 cofactor. Either silencing of BCL6 or targeted disruption of the BCL6/NCoR complex diminishes AXL expression and inhibits GBM growth. This study elucidates a crucial BCL6-mediated signaling pathway in GBM biology. More importantly, our results highlight the promise and merit of targeting BCL6 for treating this deadly disease.
Towards a life of poverty and uncertainty? The livelihood strategies of Gécamines workers after retrenchment in the DRC
Authors: Rubbers Benjamin 
Published: March 2017

ABSTRACTIn 2003, with the support of the World Bank, the Congolese state-owned enterprise Gécamines implemented a voluntary departure programme for 10,000 employees with more than 25 years of service. These employees were asked to regard their severance pay as a capital to be invested in new activities. Based on ethnographic research, this article explores how ex-Gécamines workers made a living in the phase of their ‘reintegration’. In doing so, it develops a sociological approach to popular economic practices that attempts to move beyond the phenomenology of uncertainty recently advocated by several Africanist scholars.
Adsorption and diffusion of mono, di, and trivalent ions on two-dimensional TiS2
Authors: Samad Abdus , Shafique Aamir , Shin Young-Han 
Published: March 2017

Abstract
A comparative study of the monovalent (Li, Na, and K) and multivalent (Be, Mg, Ca, and Al) metal ion adsorption and diffusion on an electronically semi-metallic two-dimensional nanosheet of 1T structured TiS2 is presented here to contribute to the search for abundant, cheap, and nontoxic ingredients for efficient rechargeable metal ion batteries. The total formation energy of the metal ion adsorption and the Bader charge analysis show that the divalent Mg and Ca ions can have a charge storage density double that of the monovalent Li, Na, and K ions, while the Be and Al ions form metallic clusters even at a low adsorption density because of their high bulk energies. The adsorption of Mg ions shows the lowest averaged open circuit voltage (0.13 V). The activation energy barriers for the diffusion of metal ions on the surface of the monolayer successively decrease from Li to K and Be to Ca. Mg and Ca, being divalent, are capable of storing a higher power density than Li while K and Na have a higher rate capability than the Li ions. Therefore, rechargeable Li ion batteries can be totally or partially replaceable by Mg ion batteries, where high power density and high cell voltage are required, while the abundant, cheap, and fast Na ions can be used for green grid applications.
Fabrication of fluorescent composite hydrogel using in situ synthesis of upconversion nanoparticles
Authors: Dong Yuqing , Lin Min , Jin Guorui , Il Park Yong , Qiu Mushu , Zhao Ying , Yang Hui , Li Ang , Jian Lu Tian 
Published: March 2017

Abstract
Fluorescent composite hydrogels have found widespread applications, especially in spatial and temporal monitoring of in vivo hydrogel behaviors via the emitting optical signal. However, most existing fluorescent composite hydrogels suffer from limited capability of deep tissue imaging and complicated fabrication routes. We herein report a facile method for fabricating fluorescent composite hydrogels based on the in situ synthesis of NaYF4:Yb, Er upconversion nanoparticles (UCNPs). This approach employs polyacrylamide (PAAm) hydrogels as a template, where the interconnected pores within the hydrogel act as nanoreactors to confine the growth of nanocrystals. We then obtained a fluorescent composite hydrogel exhibiting upconversion fluorescence and enhanced mechanical properties. The fluorescence spectra show that the fluorescence intensity decreases with decreasing size of the UCNPs. We investigated the relationship between the optical properties of the fluorescent composite hydrogel and the incorporated UCNPs based on the morphology, size, and distribution of the UCNPs by using scanning electron microscopy and transmission electron microscopy. In addition, we demonstrated the applicability of the synthesized hydrogel for deep tissue imaging through an in vitro tissue penetration experiment. Compressive and dynamic rheological testing reveal enhanced mechanical properties with increasing UCNP concentration. The fabricated upconversion fluorescent composite hydrogel may pave the way for monitoring the in vivo behavior of biomimetic materials via deep tissue imaging.
Cavernous Malformation Associated With Arterialized Developmental Venous Anomaly: A Case Report
Authors: Nakase Kenta , Motoyama Yasushi , Nakai Tokiko , Takeshima Yasuhiro , Nakagawa Ichiro , Park Young-Su , Ohbayashi Chiho , Nakase Hiroyuki 
Published: March 2017

Abstract

BACKGROUND AND IMPORTANCE: Formation of cavernous malformations (CMs) has been recognized to be associated with developmental venous anomaly (DVA) by many authors. Hemodynamic stress due to venous outflow restriction could be hypothesized as a cause. On the other hand, a rare subgroup of DVA with an arterial component has been reported as likely to hemorrhage or be symptomatic. Cases of arterialized DVAs reported previously have not been associated with the presence of CM.

CLINICAL PRESENTATION: We present herein a case report of arterialized DVA in the brainstem with repeated cerebellar hemorrhage. The 49-year-old patient was treated with surgical evacuation of hematoma. A surgical specimen from the hematoma cavity demonstrated CMs on histological examination.

CONCLUSION: To the best of our knowledge, this represents the first report of CM associated with an arterialized DVA. In addition to venous congestion due to outflow obstruction, bleeding from the arterial component of the DVA might be considered as a cause of CM formation.
Histomorphometric Comparison of Bone Regeneration in Critical-Sized Bone Defects Using Demineralized Bone Matrix, Platelet-Rich Fibrin, and Hyaluronic Acid as Bone Substitutes
Authors: Sindel Alper , Dereci Ömür , Toru Havva Serap , Tozoğlu Sinan 
Published: March 2017

Aim:
To compare bone regeneration in the critical-sized bone defects grafted with demineralized bone matrix, platelet-rich fibrin, and hyaluronic acid in rats.

Materials and Methods:
Forty Wistar Albino rats allocated into 4 experimental groups: platelet-rich fibrin (PRF) group, noncross-linked hyaluronic acid gel (HA) group, demineralized bone matrix in putty form (DBM) group, and control group. A critical-sized defect of 8 mm was formed involving the sagittal suture for each rat under anesthetic induction. All animals were sacrificed at 21st day after surgery and histomorphometric parameters of total horizontal length (THL) and total vertical length (TVL) of newly produced bone and longest bone trabecula (LBT) were measured in the histologic slides. The difference between experimental groups for these parameters was analyzed.

Results:
There was statistically significant difference in THL and LBT but not in TVL. Total horizontal length was significantly increased in DBM group compared with control and HA groups (P < 0.05). There was also statistically significant increase in THL in PRF group compared with control group (P < 0.05). Longest bone trabecula significantly increased in DBM group compared with HA group (P < 0.05). There was also statistically significant increase in HA group compared with control group (P < 0.05) and LBT significantly increased in PRF group compared with HA group (P < 0.05).

Conclusion:
The sole usage of HA does not effectively increase bone regeneration when compared with DBM and PRF. The DBM and PRF do not have superiority to each other in the bone regeneration while they are superior to HA.
COULD PLANTS BE SENTIENT?
Authors: Calvo Paco , Sahi Vaidurya , Trewavas Anthony 
Published: March 2017

AbstractFeelings in humans are mental states representing groups of physiological functions that usually have defined behavioural objectives or purpose. Feelings are thought to be coordinated in the brain stem of animals and are evolutionarily ancient. One function of the brain is to prioritise between competing mental states, and thus groups of physiological functions and in turn behaviour. Anger, fear or pain call for immediate action whereas hunger, or thirst, signify longer term needs and a requirement for search. Plants use groups of coordinated physiological activities to deal with defined environmental situations but currently have no known mental state to prioritise any order of response. Plants do have a nervous system based on phloem which is highly cross linked. Its potential for forming a mental state is unknown but it could be used to distinguish between different and even contradictory signals and thus determine a priority of response. The vascular nervous system stretches throughout the whole plant providing the potential for assessment in all parts and commensurate with its self-organising, phenotypically plastic behaviour.
Genetic Variation in Adaptability and Pleiotropy in Budding Yeast
Authors: Jerison Elizabeth R. , Kryazhimskiy Sergey , Mitchell James , Bloom Joshua S. , Kruglyak Leonid , Desai Michael M. 
Published: March 2017

AbstractEvolution can favor organisms that are more adaptable, provided that genetic variation in adaptability exists. Here, we quantify this variation among 230 offspring of a cross between diverged yeast strains. We measure the adaptability of each offspring genotype, defined as its average rate of adaptation in a specific environmental condition, and analyze the heritability, predictability, and genetic basis of this trait. We find that initial genotype strongly affects adaptability and can alter the genetic basis of future evolution. Initial genotype also affects the pleiotropic consequences of adaptation for fitness in a different environment. This genetic variation in adaptability and pleiotropy is largely determined by initial fitness, according to a rule of declining adaptability with increasing initial fitness, but several individual QTLs also have a significant idiosyncratic role. Our results demonstrate that both adaptability and pleiotropy are complex traits, with extensive heritable differences arising from naturally occurring variation.
Methomyl Injury to Carbon Exchange Rates and Related Processes in Cotton
Authors: Salem C.E. , Cothren J.T. , Benedict C.R. 
Published: March 2017

AbstractSome insecticides have the potential to cause varying levels of phytotoxicity. This study examined 1) the time courses of photosynthetic injury in cotton (Gossypium hirsutisms L.) leaves treated with methomyl [S-methyl-N-[(methyl carbamoyl)oxy]-thioacetimidate] and 2) the relationships between carbon exchange rate (CER), stomatal conductance, the chlorophyll fluorescence parameter FX/FP, and ribulose-1,5-bisphosphate carboxylase/ oxygenase (rubisco) activity. Plots were sprayed with either 0 or 0.84 kg methomyl·ha-1 when cotton was in mid-reproductive growth. Starting on the day of spraying, CER, stomatal conductance, FX/FP, and rubisco activity were measured daily for five consecutive days [4, 28, 52, 76 and 100 hours after spraying (HAS)]. In methomyl-treated leaves, CER decreased within hours after spraying, reached their lowest point at 28 HAS in experiment I and 76 HAS in experiment II, then recovered near-control levels by 100 HAS. At their lowest points, CER of methomyl-treated leaves decreased from 20 to 50% compared to controls. Stomatal conductance, FX/FP, and rubisco activity followed similar patterns to CER. Stomatal conductance was more closely related to CER than were FX/FP and rubisco activity. Chlorophyll fluorescence recovered more quickly than did CER. Rubisco activity did not decrease till after CER. From the parameters measured in this study, stomatal conductance appeared to be the major factor influencing methomyl-induced changes in CER, although all three parameters may be involved in the process of CER change.AbbreviationsCERcarbon exchange raterubiscoribulose-1,5-bisphosphate carboxylase/ oxygenaseDATdays after treatmentHAShours after spraying
Methylation guide RNA evolution in archaea: structure, function, and genomic organization of 110 C/D box sRNA families across sixPyrobaculumspecies
Authors: Lui Lauren M , Uzilov Andrew V. , Bernick David L. , Corredor Andrea , Lowe Todd M. , Dennis Patrick P. 
Published: March 2017

ABSTRACTArchaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2′-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genusPyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches, and comparative genomics, we analyzed 526PyrobaculumC/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.
Canvas SPW: callingde novocopy number variants in pedigrees
Authors: Ivakhno Sergii , Roller Eric , Colombo Camilla , Tedder Philip , Cox Anthony J. 
Published: March 2017

AbstractMotivationWhole genome sequencing is becoming a diagnostics of choice for the identification of rare inherited andde novocopy number variants in families with various pediatric and late-onset genetic diseases. However, joint variant calling in pedigrees is hampered by the complexity of consensus breakpoint alignment across samples within an arbitrary pedigree structure.ResultsWe have developed a new tool, Canvas SPW, for the identification of inherited andde novocopy number variants from pedigree sequencing data. Canvas SPW supports a number of family structures and provides a wide range of scoring and filtering options to automate and streamline identification ofde novovariants.AvailabilityCanvas SPW is available for download fromhttps://github.com/Illumina/canvas.Contactsivakhno@illumina.comSupplementary informationSupplementary data are available atBioinformaticsonline.
patternize:AnRpackage for quantifying color pattern variation
Authors: Van Belleghem Steven M. , Papa Riccardo , Ortiz-Zuazaga Humberto , Hendrickx Frederik , Jiggins Chris D. , Owen McMillan W. , Counterman Brian A. 
Published: March 2017

SummaryThe use of image data to quantify, study and compare variation in the colors and patterns of organisms requires the alignment of images to establish homology, followed by color-based segmentation of images. Here we describe anRpackage for image alignment and segmentation that has applications to quantify color patterns in a wide range of organisms.patternizeis anRpackage that quantifies variation in color patterns obtained from image data.patternizefirst defines homology between pattern positions across specimens either through manually placed homologous landmarks or automated image registration. Pattern identification is performed by categorizing the distribution of colors using an RGB threshold,k-means clustering or watershed transformation.We demonstrate thatpatternizecan be used for quantification of the color patterns in a variety of organisms by analyzing image data for butterflies, guppies, spiders and salamanders. Image data can be compared between sets of specimens, visualized as heatmaps and analyzed using principal component analysis (PCA).patternizehas potential applications for fine scale quantification of color pattern phenotypes in population comparisons, genetic association studies and investigating the basis of color pattern variation across a wide range of organisms.
A systematic atlas of chaperome deregulation topologies across the human cancer landscape
Authors: Esfahani Ali Hadizadeh , Sverchkova Angelina , Saez-Rodriguez Julio , Schuppert Andreas A , Brehme Marc 
Published: March 2017

AbstractProteome balance is safeguarded by the proteostasis network (PN), an intricately regulated network of conserved processes that evolved to maintain native function of the diverse ensemble of protein species, ensuring cellular and organismal health. Proteostasis imbalances and collapse are implicated in a spectrum of human diseases, from neurodegeneration to cancer. The characteristics of PN disease alterations however have not been assessed in a systematic way. Zooming in on the chaperome as a central PN component we turned to a curated functional ontology of the human chaperome that we connect in a high-confidence physical protein-protein interaction network. Challenged by the lack of a systems-level understanding of proteostasis alterations in the heterogeneous spectrum of human cancers, we assessed gene expression across more than 10,000 patient biopsies covering 22 solid cancers. We derived a novel customized Meta-PCA dimension reduction approach yielding M-scores as quantitative indicators of disease expression changes to condense the complexity of cancer transcriptomics datasets into quantitative functional network topographies. We confirm upregulation of the HSP90 family and also highlight HSP60s, Prefoldins, HSP100s, ER- and mitochondria-specific chaperones as pan-cancer enriched. Our analysis also reveals a surprisingly consistent strong downregulation of small heat shock proteins (sHSPs) and we stratify two cancer groups based on the preferential upregulation of ATP-dependent chaperones. Strikingly, our analysis highlight similarities between stem cell and cancer proteostasis, and diametrically opposed chaperome deregulation between cancers and neurodegenerative diseases. We developed a web-based Proteostasis Profiler tool (Pro2) enabling intuitive analysis and visual exploration of proteostasis disease alterations using gene expression data. Our study showcases a comprehensive profiling of chaperome shifts in human cancers and sets the stage for a systematic global analysis of PN alterations across the human diseasome towards novel hypotheses for therapeutic network re-adjustment in proteostasis disorders.
EMT and MET: necessary or permissive for metastasis?
Authors: Jolly Mohit Kumar , Ware Kathryn E , Gilja Shivee , Somarelli Jason A , Levine Herbert 
Published: March 2017

ABSTRACTEpithelial-to-mesenchymal transition (EMT) and its reverse mesenchymal-to-epithelial transition (MET) have been often suggested to play crucial roles in metastatic dissemination of carcinomas. Recent studies have revealed that neither of these processes is binary. Instead, carcinoma cells often exhibit a spectrum of epithelial/mesenchymal phenotype(s). While epithelial-mesenchymal plasticity has been observed pre-clinically and clinically, whether any of these phenotypic transitions are indispensable for metastatic outgrowth remains an unanswered question. Here, we focus on epithelial-mesenchymal plasticity in metastatic dissemination and propose alternative mechanisms for successful dissemination and metastases beyond the traditional EMT-MET view. We highlight multiple hypotheses that can help reconcile conflicting observations, and outline the next set of key questions that can offer valuable insights into mechanisms of metastasis in multiple tumor models.