bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments
Authors: Xu Meiying , Zhang Qin , Xia Chunyu , Zhong Yuming , Sun Guoping , Guo Jun , Yuan Tong , Zhou Jizhong , He Zhili 
Published: March 2014

Abstract
Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.
Carbon Nanotube Chemiresistor for Wireless pH Sensing
Authors: Gou Pingping , Kraut Nadine D. , Feigel Ian M. , Bai Hao , Morgan Gregory J. , Chen Yanan , Tang Yifan , Bocan Kara , Stachel Joshua , Berger Lee , Mickle Marlin , Sejdić Ervin , Star Alexander 
Published: March 2014

AbstractThe ability to accurately measure real-time pH fluctuations in-vivo could be highly advantageous. Early detection and potential prevention of bacteria colonization of surgical implants can be accomplished by monitoring associated acidosis. However, conventional glass membrane or ion-selective field-effect transistor (ISFET) pH sensing technologies both require a reference electrode which may suffer from leakage of electrolytes and potential contamination. Herein, we describe a solid-state sensor based on oxidized single-walled carbon nanotubes (ox-SWNTs) functionalized with the conductive polymer poly(1-aminoanthracene) (PAA). This device had a Nernstian response over a wide pH range (2–12) and retained sensitivity over 120 days. The sensor was also attached to a passively-powered radio-frequency identification (RFID) tag which transmits pH data through simulated skin. This battery-less, reference electrode free, wirelessly transmitting sensor platform shows potential for biomedical applications as an implantable sensor, adjacent to surgical implants detecting for infection.
Super-resolution microscopy reveals decondensed chromatin structure at transcription sites
Authors: Wang Yejun , Maharana Shovamayee , Wang Michelle D. , Shivashankar G. V. 
Published: March 2014

AbstractRemodeling of the local chromatin structure is essential for the regulation of gene expression. While a number of biochemical and bioimaging experiments suggest decondensed chromatin structures are associated with transcription, a direct visualization of DNA and transcriptionally active RNA polymerase II (RNA pol II) at super-resolution is still lacking. Here we investigate the structure of chromatin isolated from HeLa cells using binding activatable localization microscopy (BALM). The sample preparation method preserved the structural integrity of chromatin. Interestingly, BALM imaging of the chromatin spreads revealed the presence of decondensed chromatin as gap structures along the spreads. These gaps were enriched with phosphorylated S5 RNA pol II and were sensitive to the cellular transcriptional state. Taken together, we could visualize the decondensed chromatin regions together with active RNA pol II for the first time using super-resolution microscopy.
A small-molecule benzimidazole derivative that potently activates AMPK to increase glucose transport in skeletal muscle: comparison with effects of contraction and other AMPK activators
Authors: Lai Yu-Chiang , Kviklyte Samanta , Vertommen Didier , Lantier Louise , Foretz Marc , Viollet Benoît , Hallén Stefan , Rider Mark H. 
Published: March 2014

AMPK (AMP-activated protein kinase) is an attractive therapeutic drug target for treating metabolic disorders. We studied the effects of an AMPK activator developed by Merck (ex229 from patent application WO2010036613), comparing chemical activation with contraction in intact incubated skeletal muscles. We also compared effects of ex229 with those of the Abbott A769662 compound and AICAR (5-amino-4-imidazolecarboxamide riboside). In rat epitrochlearis muscle, ex229 dose-dependently increased AMPK activity of α1-, α2-, β1- and β2-containing complexes with significant increases in AMPK activity seen at a concentration of 50 μM. At a concentration of 100 μM, AMPK activation was similar to that observed after contraction and importantly led to an ~2-fold increase in glucose uptake. In AMPK α1-/α2-catalytic subunit double-knockout myotubes incubated with ex229, the increases in glucose uptake and ACC (acetyl-CoA carboxylase) phosphorylation seen in control cells were completely abolished, suggesting that the effects of the compound were AMPK-dependent. When muscle glycogen levels were reduced by ~50% after starvation, ex229-induced AMPK activation and glucose uptake were amplified in a wortmannin-independent manner. In L6 myotubes incubated with ex229, fatty acid oxidation was increased. Furthermore, in mouse EDL (extensor digitorum longus) and soleus muscles, ex229 increased both AMPK activity and glucose uptake at least 2-fold. In summary, ex229 efficiently activated skeletal muscle AMPK and elicited metabolic effects in muscle appropriate for treating Type 2 diabetes by stimulating glucose uptake and increasing fatty acid oxidation.
T-cell co-stimulation through the CD2 and CD28 co-receptors induces distinct signalling responses
Authors: Skånland Sigrid S. , Moltu Kristine , Berge Torunn , Aandahl Einar M. , Taskén Kjetil 
Published: March 2014

Full T-cell activation critically depends on the engagement of the TCR (T-cell receptor) in conjunction with a second signal by co-stimulatory receptors that boost the immune response. In the present study we have compared signalling patterns induced by the two co-receptors CD2 and CD28 in human peripheral blood T-cells. These co-receptors were previously suggested to be redundant in function. By a combination of multi-parameter phosphoflow cytometry, phosphokinase arrays and Western blot analyses, we demonstrate that CD2 co-stimulation induces phosphorylation of the TCR-proximal signalling complex, whereas CD28 activates distal signalling molecules, including the transcription factors NF-κB (nuclear factor κB), ATF (activating transcription factor)-2, STAT3/5 (signal transducer and activator of transcription 3/5), p53 and c-Jun. These signalling patterns were conserved in both naïve and effector/memory T-cell subsets. We show that free intracellular Ca2+ and signalling through the PI3K (phosphoinositide 3-kinase)/Akt pathway are required for proper CD28-induced NF-κB activation. The signalling patterns induced by CD2 and CD28 co-stimulation lead to distinct functional immune responses in T-cell proliferation and cytokine production. In conclusion, CD2 and CD28 co-stimulation induces distinct signalling responses and functional outcomes in T-cells.
Exploring the limit of accuracy for density functionals based on the generalized gradient approximation: Local, global hybrid, and range-separated hybrid functionals with and without dispersion corrections
Authors: Mardirossian Narbe , Head-Gordon Martin 
Published: March 2014

The limit of accuracy for semi-empirical generalized gradient approximation (GGA) density functionals is explored by parameterizing a variety of local, global hybrid, and range-separated hybrid functionals. The training methodology employed differs from conventional approaches in 2 main ways: (1) Instead of uniformly truncating the exchange, same-spin correlation, and opposite-spin correlation functional inhomogeneity correction factors, all possible fits up to fourth order are considered, and (2) Instead of selecting the optimal functionals based solely on their training set performance, the fits are validated on an independent test set and ranked based on their overall performance on the training and test sets. The 3 different methods of accounting for exchange are trained both with and without dispersion corrections (DFT-D2 and VV10), resulting in a total of 491 508 candidate functionals. For each of the 9 functional classes considered, the results illustrate the trade-off between improved training set performance and diminished transferability. Since all 491 508 functionals are uniformly trained and tested, this methodology allows the relative strengths of each type of functional to be consistently compared and contrasted. The range-separated hybrid GGA functional paired with the VV10 nonlocal correlation functional emerges as the most accurate form for the present training and test sets, which span thermochemical energy differences, reaction barriers, and intermolecular interactions involving lighter main group elements.
Students’ experiences of school suspension
Authors: Quin Daniel , Hemphill Sheryl A. 
Published: March 2014

Issue addressedSchool inclusion and academic attainment are key social determinants of health. Students who have been suspended from school are more likely to disengage from school and consequently not receive the health promoting benefits of social inclusion and academic achievement. This study sought to explore the experiences of students who have been previously suspended (i.e. had experienced school exclusion).MethodsSeventy‐four previously suspended adolescents from five schools in the state of Victoria, Australia, completed a written questionnaire. Students reported their understanding of the process of being suspended; what they did and with whom they spent the day(s) of suspension; and their perceptions of their return to school post‐suspension.ResultsWhile suspended, a minority of suspended students received adult supervision and most suspended students participated in benign leisure activities. Upon return to school, students reported diminished teacher assistance and found that suspension did not help resolve the underlying issues that lead to the suspension.ConclusionsRemoval of a student displaying problem behaviours from the classroom may provide temporary relief to the school community but suspended students report minimal benefits from suspension. Suspension removes the potential pro‐social normative influences of school and provides an opportunity to establish antisocial peer networks. Suspended students appear to perceive a stigma upon their return to school, further diminishing an already tenuous school relationship.So what?School suspension exposes disadvantaged students to several negative social determinants of health. Students displaying problem behaviours would benefit from interventions that maintain the student's relationship with school. Should suspension be necessary, schools could assist by ensuring that suspended students receive appropriate adult supervision and a formal reintegration to school to promote social inclusion and academic attainment, two recognised key determinants of health.
α-Catenin is an inhibitor of transcription
Authors: Daugherty Rebecca L. , Serebryannyy Leonid , Yemelyanov Alex , Flozak Annette S. , Yu Hui-Jun , Kosak Steven T. , deLanerolle Primal , Gottardi Cara J. 
Published: March 2014

Significance
Recent studies have shown that actin-binding and -regulating proteins, originally characterized in the context of cytoskeletal events, can also modify gene expression through directly impacting actin-dependent transcription. This study shows α-catenin (α-cat), an actin-binding protein that is essential for cell–cell adhesion and contact-dependent growth inhibition, can antagonize Wnt/β-catenin–mediated transcription and impact nuclear actin properties, suggesting that these events may be related. These findings establish α-cat as one of a growing list of actin-binding proteins that can modulate transcription, possibly by controlling actin dynamics in the nucleus.
Cell-type–based model explaining coexpression patterns of genes in the brain
Authors: Grange Pascal , Bohland Jason W. , Okaty Benjamin W. , Sugino Ken , Bokil Hemant , Nelson Sacha B. , Ng Lydia , Hawrylycz Michael , Mitra Partha P. 
Published: March 2014

Significance
Neuroanatomy is experiencing a renaissance due to the study of gene-expression data covering the entire mouse brain and the entire genome that have been recently released (the Allen Atlas). On the other hand, some cell types extracted from the mouse brain have been characterized by their genetic activity. However, given a cell type, it is not known in which brain regions it can be found. We propose a computational model using the Allen Atlas to solve this problem, thus estimating previously unidentified cell-type–specific maps of the mouse brain. The model can be used to define brain regions through genetic data.
Global and time-resolved monitoring of crop photosynthesis with chlorophyll fluorescence
Authors: Guanter Luis , Zhang Yongguang , Jung Martin , Joiner Joanna , Voigt Maximilian , Berry Joseph A. , Frankenberg Christian , Huete Alfredo R. , Zarco-Tejada Pablo , Lee Jung-Eun , Moran M. Susan , Ponce-Campos Guillermo , Beer Christian , Camps-Valls Gustavo , Buchmann Nina , Gianelle Damiano , Klumpp Katja , Cescatti Alessandro , Baker John M. , Griffis Timothy J. 
Published: March 2014

SignificanceGlobal food and biofuel production and their vulnerability in a changing climate are of paramount societal importance. However, current global model predictions of crop photosynthesis are highly uncertain. Here we demonstrate that new space-based observations of chlorophyll fluorescence, an emission intrinsically linked to plant biochemistry, enable an accurate, global, and time-resolved measurement of crop photosynthesis, which is not possible from any other remote vegetation measurement. Our results show that chlorophyll fluorescence data can be used as a unique benchmark to improve our global models, thus providing more reliable projections of agricultural productivity and climate impact on crop yields. The enormous increase of the observational capabilities for fluorescence in the very near future strengthens the relevance of this study.
Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1
Authors: Tamir Sagi , Rotem-Bamberger Shahar , Katz Chen , Morcos Faruck , Hailey Kendra L. , Zuris John A. , Wang Charles , Conlan Andrea R. , Lipper Colin H. , Paddock Mark L. , Mittler Ron , Onuchic José N. , Jennings Patricia A. , Friedler Assaf , Nechushtai Rachel 
Published: March 2014

Significance
Misregulation of cell growth and proliferation leads to the onset of various diseases, including cancer. Two proteins crucial for proper cellular control that were recently shown to affect cellular proliferation are Bcl-2, well-known for its role in programmed cell death, and the newly identified iron-sulfur protein NAF-1, localized near the mitochondrial outer membrane. In this report, we use a strategy utilizing a combination of experimental and computational techniques that provides valuable information to enable us to determine a molecular picture of the NAF-1–Bcl-2 interaction interface that is more complete than that obtained from any one technique alone. This interaction interface provides the basis from which novel drugs can be developed for the treatment of diseases such as cancer.
Is Diet Quality Improving? Distributional Changes in the United States, 1989–2008
Authors: Beatty Timothy K. M. , Lin Biing-Hwan , Smith Travis A. 
Published: March 2014

AbstractThis article measures changes in the distribution of dietary quality among adults in the United States over the period 1989–2008. Diet quality is a direct input to health, is often used as a proxy for well‐being, and is an outcome variable for a wide variety of economic interventions. For the population as a whole, we find significant improvements across all levels of diet quality. Further, we find improvements for both low‐income and higher‐income individuals alike. Counterfactual distributions of dietary quality are constructed to investigate the extent to which observed improvements can be attributed to changes in the nutritional content of foods and to changes in population characteristics. We find that 63% of the improvement for all adults can be attributed to changes in food formulation and demographics. Changes in food formulation account for a substantially larger percentage of the dietary improvement within the lower‐income population (19.6%) vs. the higher‐income population (6.4%).
Chloroplast DNA in Mature and Senescing Leaves: A Reappraisal
Authors: Golczyk Hieronim , Greiner Stephan , Wanner Gerhard , Weihe Andreas , Bock Ralph , Börner Thomas , Herrmann Reinhold G. 
Published: March 2014

AbstractThe fate of plastid DNA (ptDNA) during leaf development has become a matter of contention. Reports on little change in ptDNA copy number per cell contrast with claims of complete or nearly complete DNA loss already in mature leaves. We employed high-resolution fluorescence microscopy, transmission electron microscopy, semithin sectioning of leaf tissue, and real-time quantitative PCR to study structural and quantitative aspects of ptDNA during leaf development in four higher plant species (Arabidopsis thaliana, sugar beet [Beta vulgaris], tobacco [Nicotiana tabacum], and maize [Zea mays]) for which controversial findings have been reported. Our data demonstrate the retention of substantial amounts of ptDNA in mesophyll cells until leaf necrosis. In ageing and senescent leaves of Arabidopsis, tobacco, and maize, ptDNA amounts remain largely unchanged and nucleoids visible, in spite of marked structural changes during chloroplast-to-gerontoplast transition. This excludes the possibility that ptDNA degradation triggers senescence. In senescent sugar beet leaves, reduction of ptDNA per cell to ∼30% was observed reflecting primarily a decrease in plastid number per cell rather than a decline in DNA per organelle, as reported previously. Our findings are at variance with reports claiming loss of ptDNA at or after leaf maturation.
Fast Retrograde Signaling in Response to High Light Involves Metabolite Export, MITOGEN-ACTIVATED PROTEIN KINASE6, and AP2/ERF Transcription Factors in Arabidopsis
Authors: Vogel Marc Oliver , Moore Marten , König Katharina , Pecher Pascal , Alsharafa Khalid , Lee Justin , Dietz Karl-Josef 
Published: March 2014

Abstract
Regulation of the expression of nuclear genes encoding chloroplast proteins allows for metabolic adjustment in response to changing environmental conditions. This regulation is linked to retrograde signals that transmit information on the metabolic state of the chloroplast to the nucleus. Transcripts of several APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERF-TFs) were found to respond within 10 min after transfer of low-light-acclimated Arabidopsis thaliana plants to high light. Initiation of this transcriptional response was completed within 1 min after transfer to high light. The fast responses of four AP2/ERF genes, ERF6, RRTF1, ERF104, and ERF105, were entirely deregulated in triose phosphate/phosphate translocator (tpt) mutants. Similarly, activation of MITOGEN-ACTIVATED PROTEIN KINASE6 (MPK6) was upregulated after 1 min in the wild type but not in the tpt mutant. Based on this, together with altered transcript regulation in mpk6 and erf6 mutants, a retrograde signal transmission model is proposed starting with metabolite export through the triose phosphate/phosphate translocator with subsequent MPK6 activation leading to initiation of AP2/ERF-TF gene expression and other downstream gene targets. The results show that operational retrograde signaling in response to high light involves a metabolite-linked pathway in addition to previously described redox and hormonal pathways.
Constructing an information science resource ontology based on the Chinese Social Science Citation Index
Authors: Qiu Junping , Lou Wen 
Published: March 2014

Purpose
– The purpose of this study is to construct a Chinese information science resource ontology and to explore a new method for semiautomatic ontology construction.

Design/methodology/approach
– More than 8,290 articles indexed in the Chinese Social Science Citation Index (CSSCI), covering the years 2001 to 2010, were included in this study. Statistical analysis, co-occurrence analysis, and semantic similarity methods were applied to the selected articles. The ontology was built using existing construction principles and methods, as well as categories and hierarchy definitions based on CSSCI indexing fields.

Findings
– Seven categories were found to be relevant for the Chinese information science resource ontology, which, in this study, consists of a three-tier architecture, 78,291 instances, and 182,109 pairs of semantic relations. These results indicate the following: further improvements are required in ontology construction methods; resource ontology is a breakthrough concept in ontology studies; the combination of semantic similarities and co-occurrence analysis can quantitatively describe relationships between concepts.

Originality/value
– This study pioneers the resource ontology concept. It is one of the first to combine informetric methods with semantic similarity to reveal deep relationships in textual data.
Real estate ownership and closely-held firm value
Authors: Edward Graham John , Galbraith Craig , Stiles Curt 
Published: March 2014

Purpose– The authors aim to measure the value of leasing, versus owning, business locations for the closely-held firm.Design/methodology/approach– The authors examine the sales transactions of small businesses in the USA – those with revenues of less than $20 million per year – between 1995 and 2010. The authors contrast the values of firms that own, and do not own, their real estate.Findings– In general, the authors find negative relationships between closely-held firm values and real estate ownership. Nowhere did the authors observe firm value being enhanced by property ownership.Research limitations/implications– The data set may be limited by the accuracy of the data provided by business brokers. Compared to the capital markets, the small business “exchange” is less efficient, but it is the only source of unlisted business sales data.Practical implications– The findings are important to the small-business broker and the investor. The broker might better advise the buyer and seller with the findings. Business owners, private equity investors, and their advisors, are all reminded to focus on the core business strategy and avoid getting “locked into” real estate ownership in a business investment.Originality/value– The impact of real estate on the valuations of closely-held firms is a largely unexamined area. And there is a lack of consistency on publicly-held company valuations as a function of real estate ownership; these public company findings and the dearth of work on the privately-held company's real estate attract the attention in this study.