bluuebunny/crossref_metadata_2025_split huggingface dataset:
Versatile and efficient chromatin pull-down methodology based on DNA triple helix formation
Authors: Isogawa Asako , Fuchs Robert P. , Fujii Shingo 
Published: April 2018

AbstractThe goal of present paper is to develop a reliable DNA-based method for isolation of protein complexes bound to DNA (Isolation of DNA Associated Proteins: IDAP). We describe a robust and versatile procedure to pull-down chromatinized DNA sequences-of-interest by formation of a triple helix between a sequence tag present in the DNA and a complementary triple helix forming oligonucleotide (TFO) coupled to a desthiobiotin residue. Following optimization to insure efficient recovery of native plasmids via TFO probe in vitro, the procedure is shown to work under various experimental situations. For instance, it allows capture proteins associated to plasmids hosted in E. coli, and is also successfully applied to recovering nucleosomes in vitro opening many possibilities to study post translational modifications of histones in a genuine nucleosome context. Incubation in human nuclear extracts of a plasmid carrying a NF-κB model promoter is shown to pull-down a specific transcription factor. Finally, isolation of a specific locus from human genomic chromatin has been successfully achieved (Chromatin-of-Interest Fragment Isolation: CoIFI). In conclusion, the methodology can be implemented for capturing proteins that specifically bind to any sequence-of-interest, DNA adduct or secondary structure provided a short sequence tag for triple helix formation is located nearby.
In-vivo turnover frequency of the cyanobacterial NiFe-hydrogenase during photohydrogen production outperforms in-vitro systems
Authors: Gutekunst Kirstin , Hoffmann Dörte , Westernströer Ulrike , Schulz Rüdiger , Garbe-Schönberg Dieter , Appel Jens 
Published: April 2018

AbstractCyanobacteria provide all components for sunlight driven biohydrogen production. Their bidirectional NiFe-hydrogenase is resistant against low levels of oxygen with a preference for hydrogen evolution. However, until now it was unclear if its catalytic efficiency can keep pace with the photosynthetic electron transfer rate. We identified NikKLMQO (sll0381-sll0385) as a nickel transporter, which is required for hydrogen production. ICP-MS measurements were used to quantify hydrogenase molecules per cell. We found 400 to 2000 hydrogenase molecules per cell depending on the conditions. In-vivo turnover frequencies of the enzyme ranged from 62 H2/s in the wild type to 120 H2/s in a mutant during photohydrogen production. These frequencies are above maximum in-vivo photosynthetic electron transfer rates of 47 e−/s (equivalent to 24 H2/s). They are also above those of existing in-vitro systems working with unlimited electron supply and show that in-vivo photohydrogen production is limited by electron delivery to the enzyme.
Comparison of the life-history parameters and competition outcome with Moina macrocopa between two morphs of Brachionus forficula
Authors: Ge Ya-Li , Luo Tong , Ge Cui-Cui , Zhan Rong , Yu Jin-Hang , Xi Yi-Long , Zhang Gen 
Published: April 2018

AbstractIn rotifers, the costs of morphological defenses, especially the development of long spines, have been investigated for several decades. However, the obtained results were inconsistent and the underlying reasons were complicated. Investigations on more species might be helpful to find out the reasons. In the present study, Brachionus forficula was selected as the model organism. The differences in developmental durations, life-table demography, starvation resistant time and the competitive ability with Moina macrocopa were compared between B. forficula with long (LPS) and short (SPS) posterior spines. The results showed that LPS showed relatively longer durations of juvenile stage at 1.0 × 106, 2.0 × 106 and 4.0 × 106 cells/ml Scenedesmus obliquus, and longer embryo stage at 2.0 × 106 cells/ml S. obliquus than SPS. The intrinsic rate of population increase and net reproduction rate were lower in LPS than SPS, suggesting the energy input to reproduction decreased. The starvation resistant time was also reduced in LPS, in comparison to SPS, further supporting that LPS consumed more energy, which might be directed to the development of long spines. All these results revealed that LPS spent more energy for individual growth than SPS, which might be used to develop long spines. Moreover, the maximum population density and population growth rate of LPS were always lower than those of SPS, suggesting that LPS might have a weaker competition ability with M. macrocope than SPS.
Low serum levels of vitamin D are associated with anxiety in children and adolescents with dialysis
Authors: Han Bin , Zhu Fu-Xiang , Yu Hai-Feng , Liu Si , Zhou Jun-Liang 
Published: April 2018

AbstractAnxiety is a frequent and serious complication of children and adolescents receiving dialysis. Low serum vitamin D levels have been associated with anxiety in non-pediatric patients. This study sought to examine the possible association between serum vitamin D levels and the presence of anxiety in children and adolescents with dialysis in China. A total of 156 pediatric patients who were on hemodialysis or peritoneal dialysis and 100 healthy controls were included in the current study. Serum 25-hydroxyvitamin D [25(OH)D] levels were measured by using a competitive protein-binding assay. Anxiety was assessed by using the Chinese version of the Screen for Child Anxiety Related Emotional Disorders (SCARED, = 25 as cutoff). Among 156 patients, 110 had a current anxiety (70.5%) and 46 did not (29.5%). Serum levels of 25(OH)D were significantly lower in patients with anxiety than in normal controls (19.4 ± 10.3 vs. 38.6 ± 15.5 ng/ml, P < 0.001). Serum 25(OH)D levels (≤15.0 ng/ml) were independently associated with the existent of anxiety in children and adolescents receiving dialysis (OR 4.650, 95% CI 1.663–13.001, P = 0.003). Our research demonstrates that low serum levels of vitamin D are independently associated with anxiety among children and adolescents on dialysis, which needs to be confirmed in future experimental and clinical studies.
Spin-orbit torques associated with ferrimagnetic order in Pt/GdFeCo/MgO layers
Authors: Kim JongHyuk , Lee DongJoon , Lee Kyung-Jin , Ju Byeong-Kwon , Koo Hyun Cheol , Min Byoung-Chul , Lee OukJae 
Published: April 2018

AbstractWe investigate spin orbit torque (SOT) efficiencies and magnetic properties of Pt/GdFeCo/MgO multilayers by varying the thicknesses of GdFeCo and MgO layers. Our studies indicate that the ferrimagnetism in the GdFeCo alloy is considerably influenced by both thicknesses due to the diffusion of Gd atoms toward the MgO layer. Comparing to conventional Pt/ferromagnet/MgO structures, the Pt/GdFeCo/MgO exhibits a lower efficiency of SOTs associated with ferrimagnetic order and a similar magnitude of magnetic damping. The previous models that have been developed for rigid ferromagnets are inappropriate to analyze our experimental data, leading to an unphysical consequence of spin transmission larger than unity. Our results imply that the heavy-metal/ferrimagnet system is quite different from heavy-metal/ferromagnet systems in terms of magnetic dynamical modes, spin angular momentum transfer, and relaxation processes.
Tranilast inhibits the expression of genes related to epithelial-mesenchymal transition and angiogenesis in neurofibromin-deficient cells
Authors: Harigai Ritsuko , Sakai Shigeki , Nobusue Hiroyuki , Hirose Chikako , Sampetrean Oltea , Minami Noriaki , Hata Yukie , Kasama Takashi , Hirose Takanori , Takenouchi Toshiki , Kosaki Kenjiro , Kishi Kazuo , Saya Hideyuki , Arima Yoshimi 
Published: April 2018

AbstractNeurofibromatosis type 1 (NF1) is caused by germline mutations in theNF1gene and is characterized by café au lait spots and benign tumours known as neurofibromas.NF1encodes the tumour suppressor protein neurofibromin, which negatively regulates the small GTPase Ras, with the constitutive activation of Ras signalling resulting fromNF1mutations being thought to underlie neurofibroma development. We previously showed that knockdown of neurofibromin triggers epithelial-mesenchymal transition (EMT) signalling and that such signalling is activated in NF1-associated neurofibromas. With the use of a cell-based drug screening assay, we have now identified the antiallergy drug tranilast (N-(3,4-dimethoxycinnamoyl) anthranilic acid) as an inhibitor of EMT and found that it attenuated the expression of mesenchymal markers and angiogenesis-related genes inNF1-mutated sNF96.2 cells and in neurofibroma cells from NF1 patients. Tranilast also suppressed the proliferation of neurofibromin-deficient cellsin vitromore effectively than it did that of intact cells. In addition, tranilast inhibited sNF96.2 cell migration and proliferationin vivo. Knockdown of type III collagen (COL3A1) also suppressed the proliferation of neurofibroma cells, whereas expression ofCOL3A1andSOX2was increased in tranilast-resistant cells, suggesting that COL3A1 and the transcription factor SOX2 might contribute to the development of tranilast resistance.
Automatic gain control of neural coupling during cooperative hand movements
Authors: Thomas F. A. , Dietz V. , Schrafl-Altermatt M. 
Published: April 2018

AbstractCooperative hand movements (e.g. opening a bottle) are controlled by a task-specific neural coupling, reflected in EMG reflex responses contralateral to the stimulation site. In this study the contralateral reflex responses in forearm extensor muscles to ipsilateral ulnar nerve stimulation was analyzed at various resistance and velocities of cooperative hand movements. The size of contralateral reflex responses was closely related to the level of forearm muscle activation required to accomplish the various cooperative hand movement tasks. This indicates an automatic gain control of neural coupling that allows a rapid matching of corrective forces exerted at both sides of an object with the goal ‘two hands one action’.
hTERT gene knockdown enhances response to radio- and chemotherapy in head and neck cancer cell lines through a DNA damage pathway modification
Authors: Barczak Wojciech , Sobecka Agnieszka , Golusinski Pawel , Masternak Michal M. , Rubis Blazej , Suchorska Wiktoria M. , Golusinski Wojciech 
Published: April 2018

AbstractThe aim of the study was to analyze the effect of hTERT gene knockdown in HNSCC cells by using novel in vitro models of head and neck cancer (HNSCC), as well as improving its personalized therapy. To obtain the most efficient knockdown siRNA, shRNA-bearing lentiviral vectors were used. The efficiency of hTERT silencing was verified with qPCR, Western blot, and immunofluorescence staining. Subsequently, the type of cell death and DNA repair mechanism induction after hTERT knockdown was assessed with the same methods, followed by flow cytometry. The effect of a combined treatment with hTERT gene knockdown on Double-Strand Breaks levels was also evaluated by flow cytometry. Results showed that the designed siRNAs and shRNAs were effective in hTERT knockdown in HNSCC cells. Depending on a cell line, hTERT knockdown led to a cell cycle arrest either in phase G1 or phase S/G2. Induction of apoptosis after hTERT downregulation with siRNA was observed. Additionally, hTERT targeting with lentiviruses, followed by cytostatics administration, led to induction of apoptosis. Interestingly, an increase in Double-Strand Breaks accompanied by activation of the main DNA repair mechanism, NER, was also observed. Altogether, we conclude that hTERT knockdown significantly contributes to the efficacy of HNSCC treatment.
Long-Term Coffee Monoculture Alters Soil Chemical Properties and Microbial Communities
Authors: Zhao Qingyun , Xiong Wu , Xing Yizhang , Sun Yan , Lin Xingjun , Dong Yunping 
Published: April 2018

AbstractLong-term monoculture severely inhibits coffee plant growth, decreases its yield and results in serious economic losses in China. Here, we selected four replanted coffee fields with 4, 18, 26 and 57 years of monoculture history in Hainan China to investigate the influence of continuous cropping on soil chemical properties and microbial communities. Results showed long-term monoculture decreased soil pH and organic matter content and increased soil EC. Soil bacterial and fungal richness decreased with continuous coffee cropping. Principal coordinate analysis suggested monoculture time was a major determinant of bacterial and fungal community structures. Relative abundances of bacterial Proteobacteria, Bacteroidetes and Nitrospira and fungal Ascomycota phyla decreased over time. At genus level, potentially beneficial microbes such as Nitrospira and Trichoderma, significantly declined over time and showed positive relationships with coffee plant growth in pots. In conclusion, continuous coffee cropping decreased soil pH, organic matter content, potentially beneficial microbes and increased soil EC, which might lead to the poor growth of coffee plants in pots and decline of coffee yields in fields. Thus, developing sustainable agriculture to improve soil pH, organic matter content, microbial activity and reduce the salt stress under continuous cropping system is important for coffee production in China.
The neural encoding of information prediction errors during non-instrumental information seeking
Authors: Brydevall Maja , Bennett Daniel , Murawski Carsten , Bode Stefan 
Published: April 2018

AbstractIn a dynamic world, accurate beliefs about the environment are vital for survival, and individuals should therefore regularly seek out new information with which to update their beliefs. This aspect of behaviour is not well captured by standard theories of decision making, and the neural mechanisms of information seeking remain unclear. One recent theory posits that valuation of information results from representation of informative stimuli within canonical neural reward-processing circuits, even if that information lacks instrumental use. We investigated this question by recording EEG from twenty-three human participants performing a non-instrumental information-seeking task. In this task, participants could pay a monetary cost to receive advance information about the likelihood of receiving reward in a lottery at the end of each trial. Behavioural results showed that participants were willing to incur considerable monetary costs to acquire early but non-instrumental information. Analysis of the event-related potential elicited by informative cues revealed that the feedback-related negativity independently encoded both an information prediction error and a reward prediction error. These findings are consistent with the hypothesis that information seeking results from processing of information within neural reward circuits, and suggests that information may represent a distinct dimension of valuation in decision making under uncertainty.
Nuclear versus integrated spectroscopy of galaxies in the Herschel Reference Survey
Authors: Gavazzi G. , Consolandi G. , Belladitta S. , Boselli A. , Fossati M. 
Published: April 2018

Context. The determination of the relative frequency of active galactic nuclei (AGN) versus other spectral classes, for example, HII region-like (HII), transition objects (TRAN), passive (PAS), and retired (RET), in a complete set of galaxies in the local Universe is of primary importance to discriminate the source of ionization in the nuclear region of galaxies (e.g., supermassive black holes vs. young and old stars).
Aims. Here we aim to provide a spectroscopic characterization of the nuclei of galaxies belonging to the Herschel Reference Survey (HRS), a volume and magnitude limited sample representative of the local Universe, which has become a benchmark for local and high-z studies, for semianalytical models and cosmological simulations. The comparison between the nuclear spectral classification and the one determined on the global galactic scale provides information about how galaxy properties change from the nuclear to the outer regions. Moreover, the extrapolation of the global star formation (SF) properties from the SDSS fiber spectroscopy compared to the one computed by Hα photometry can be useful for testing the method based on aperture correction for determining the global star formation rate for local galaxies.
Methods. By collecting the existing nuclear spectroscopy available from the literature, complemented with new observations obtained using the Loiano 1.52 m telescope, we analyze the 322 nuclear spectra of HRS galaxies; their integrated spectroscopy is available from the literature as well.
Results. Using two diagnostic diagrams (the BPT and the WHAN) we provide a nuclear and an integrated spectral classification for the HRS galaxies. The BPT and the WHAN methods for nuclei consistently give a frequency of 53–64% HII, around 21–27% AGNs (including TRAN), and 15–20% of PAS (including RET), whereas for integrated spectra they give 69–84% HII, 4–11% of AGNs and 12–20% PAS. Solely among late-type galaxies (LTGs) do the nuclear percentages become 67–77% HII, 22–27% AGNs (including TRAN), and only 1–7% of PAS. For the integrated spectra these frequencies become: 80–85% HII, 9–11% AGNs and 4–9% PAS.
Conclusions. We find that the fraction of HII region-like spectra is strongly anticorrelated with the stellar mass. On the contrary the frequency of AGNs increases significantly with stellar mass, such that at M* > 1010.0 M⊙~ 66% of the LTGs are AGNs or TRAN. Moreover there is not a significant dependence of the frequency of AGNs as a function of environment: AGNs+TRAN above 109.0 M⊙ are consistent with ~30% irrespective of their membership to the Virgo cluster, suggesting that the AGNs population is not sensitive to the environment. Finally, extrapolation of the global SF properties from the nuclear spectroscopy including aperture corrections leads to underestimates with respect to values derived from direct integrated Hα photometry.
Die Schuleingangsuntersuchung: Ein kritischer Blick auf Historie und Status quo
Authors: Wattjes Anja , Karathana Maria , Krackhardt Bernhard , Heudorf Ursel 
Published: April 2018

ZusammenfassungIn Deutschland wurde bereits Ende des 19. Jahrhunderts die Untersuchung der Schulanfänger, die Schuleingangsuntersuchung, etabliert. Lag zunächst der Fokus auf dem Ausschluss von Infektionserkrankungen und Gesundheitsproblemen, die den Schulbesuch erschweren könnten bzw. sich im Lauf des Schulbesuchs verschlechtern könnten, trat Mitte des 20. Jahrhunderts das Konzept der Schulreife in den Vordergrund. Dabei wurden unterschiedliche „Schulreife-Konzepte“ angewandt, die inzwischen wieder verlassen wurden, da sie einer Evaluation nicht standhielten. Inzwischen wurde auch das Konzept der „Schulreife“ durch das Konzept der „Schulfähigkeit“ ersetzt. Es stellt sich nicht mehr die Frage, ob, sondern mit welchen Hilfen und welcher Förderung ein Kind einzuschulen ist. Heute umfasst die Schuleingangsuntersuchung in praktisch allen Bundesländern neben einer Anamnese die Erfassung des Vorsorge- und des Impfstatus, einen Seh- und Hörtest sowie als besonderen Schwerpunkt die Beurteilung der Entwicklung der Kinder und des individuellen Förderbedarfs– insbesondere im Bereich der Visuomotorik, der Kognition und der Sprache. In fast allen Bundesländern macht die Schuleingangsuntersuchung einen Großteil der Arbeit des Kinder- und Jugendärztlichen Dienstes aus und bindet erhebliche Ressourcen. In der vorliegenden Arbeit wird dies kritisch diskutiert und ein Diskurs angeregt, ob diese Ressourcen nicht zielführender im Sinne der Kindergesundheit eingesetzt werden sollten angesichts geänderter gesellschaftlicher Bedingungen wie der in vielen Bundesländern verpflichtenden Wahrnehmung der Kinder-Vorsorgeuntersuchungen, der Zunahme von Seiteneinsteigenden aus anderen Ländern, insbesondere auch von Asylsuchenden, oder der Inklusion mit Schließung der Förderschulen und den damit verbundenen großen Herausforderungen in den Regelschulen.
Widespread changes in transcriptome profile of human mesenchymal stem cells induced by two-dimensional nanosilicates
Authors: Carrow James K. , Cross Lauren M. , Reese Robert W. , Jaiswal Manish K. , Gregory Carl A. , Kaunas Roland , Singh Irtisha , Gaharwar Akhilesh K. 
Published: April 2018

Significance
We demonstrate the use of next-generation sequencing technology (RNA-seq) to understand the effect of a two-dimensional nanomaterial on human stem cells at the whole-transcriptome level. Our results identify more than 4,000 genes that are significantly affected, and several biophysical and biochemical pathways are triggered by nanoparticle treatment. We expect that this systematic approach to understand widespread changes in gene expression due to nanomaterial exposure is key to develop new bioactive materials for biomedical applications.
Effect of Lime Stabilization on Vertical Deformation of Laterite Halmahera Soil
Authors: Saing Zubair , Djainal Herry 
Published: April 2018

Abstract
In this paper, the study was conducted to determine the lime effect on vertical deformation of road base physical model of laterite Halmahera soil. The samples of laterite soil were obtained from Halmahera Island, North Maluku Province, Indonesia. Soil characteristics were obtained from laboratory testing, according to American Standard for Testing and Materials (ASTM), consists of physical, mechanical, minerals, and chemical. The base layer of physical model testing with the dimension; 2m of length, 2m of width, and 1.5m of height. The addition of lime with variations of 3, 5, 7, an 10%, based on maximum dry density of standard Proctor test results and cured for 28 days. The model of lime treated laterite Halmahera soil with 0,1m thickness placed on subgrade layer with 1,5m thickness. Furthermore, the physical model was given static vertical loading. Some dial gauge is placed on the lime treated soil surface with distance interval 20cm, to read the vertical deformation that occurs during loading. The experimentals data was analyzed and validated with numerical analysis using finite element method. The results showed that the vertical deformation reduced significantly on 10% lime content (three times less than untreated soil), and qualify for maximum deflection (standard requirement L/240) on 7-10% lime content.
The Cellular Second Fundamental Theorem of Invariant Theory for Classical Groups
Authors: Bowman Christopher , Enyang John , Goodman Frederick M 
Published: April 2018

AbstractWe construct explicit integral bases for the kernels and the images of diagram algebras (including the symmetric groups, orthogonal and symplectic Brauer algebras) acting on tensor space. We do this by providing an axiomatic framework for studying quotients of diagram algebras.