bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct and legacy effects of plant-traits control litter decomposition in a deciduous oak forest in Mexico
Authors: Chávez-Vergara Bruno , Merino Agustín , González-Rodríguez Antonio , Oyama Ken , García-Oliva Felipe 
Published: June 2018

Background
Litter decomposition is a key process in the functioning of forest ecosystems, because it strongly controls nutrient recycling and soil fertility maintenance. The interaction between the litter chemical composition and the metabolism of the soil microbial community has been described as the main factor of the decomposition process based on three hypotheses: substrate-matrix interaction (SMI), functional breadth (FB) and home-field advantage (HFA). The objective of the present study was to evaluate the effect of leaf litter quality (as a direct plant effect, SMI hypothesis), the metabolic capacity of the microbial community (as a legacy effect, FB hypothesis), and the coupling between the litter quality and microbial activity (HFA hypothesis) on the litter decomposition of two contiguous deciduous oak species at a local scale.

Methods
To accomplish this objective, we performed a litterbag experiment in the field for 270 days to evaluate mass loss, leaf litter quality and microbial activity in a complete factorial design for litter quality and species site.

Results
The litter of Quercus deserticola had higher rate of decomposition independently of the site, while the site of Quercus castanea promoted a higher rate of decomposition independently of the litter quality, explained by the specialization of the soil microbial community in the use of recalcitrant organic compounds. The Home-Field Advantage Index was reduced with the decomposition date (22% and 4% for 30 and 270 days, respectively).

Discussion
We observed that the importance of the coupling of litter quality and microbial activity depends on decomposition stage. At the early decomposition stage, the home-advantage hypothesis explained the mass loss of litter; however, in the advanced decomposition stage, the litter quality and the metabolic capacity of the microbial community can be the key drivers.
Resveratrol reduces the inflammatory response in adipose tissue and improves adipose insulin signaling in high-fat diet-fed mice
Authors: Ding Shibin , Jiang Jinjin , Wang Zhe , Zhang Guofu , Yin Jianli , Wang Xiaoya , Wang Sui , Yu Zengli 
Published: June 2018

Background
Obesity-induced glucose metabolism disorder is associated with chronic, low-grade, systemic inflammation and is considered a risk factor for diabetes and metabolic syndrome. Resveratrol (RES), a natural anti-inflammatory compound, is observed to improve glucose tolerance and insulin sensitivity in obese rodents and humans. This study aimed to test the effects of RES administration on insulin signaling and the inflammatory response in visceral white adipose tissue (WAT) caused by a high-fat diet (HFD) in mice.

Methods
A total of 40 wild-type C57BL/6 male mice were divided into four groups (10 in each group): the standard chow diet (STD) group was fed a STD; the HFD group was fed a HFD; and the HFD-RES/L and HFD-RES/H groups were fed a HFD plus RES (200 and 400 mg/kg/day, respectively). The L and H in RES/L and RES/H stand for low and high, respectively. Glucose tolerance, insulin sensitivity, circulating inflammatory biomarkers and lipid profile were determined. Quantitative PCR and Western blot were used to determine the expression of CC-chemokine receptor 2 (CCR2), other inflammation markers, glucose transporter 4 (GLUT4), insulin receptor substrate 1 (IRS-1) and pAkt/Akt and to assess targets of interest involving glucose metabolism and inflammation in visceral WAT.

Results
HFD increased the levels of total cholesterol, triglycerides, low-density lipoprotein cholesterol and proinflammatory cytokines in serum, decreased the high-density lipoprotein cholesterol level in serum, and induced insulin resistance and WAT inflammation in mice. However, RES treatment alleviated insulin resistance, increased the expressions of pAkt, GLUT4 and IRS-1 in WAT, and decreased serum proinflammatory cytokine levels, macrophage infiltration and CCR2 expression in WAT.

Conclusion
Our results indicated that WAT CCR2 may play a vital role in macrophage infiltration and the inflammatory response during the development of insulin resistance in HFD-induced obesity. These data suggested that administration of RES offers protection against abnormal glucose metabolism and inflammatory adaptations in visceral WAT in mice with HFD-induced obesity.
Automated data mining of a plan‐check database and example application
Authors: Dunn Leon , Jolly David 
Published: June 2018

AbstractPurposeThe aim of this work was to present the development and example application of an automated data mining software platform that preforms bulk analysis of results and patient data passing through the 3D plan and deliveryQAsystem, Mobius3D.MethodsPython,matlab,and Java were used to create an interface that reads JavaScript Object Notation (JSON) created for every approved Mobius3D pre‐treatment plan‐check. The aforementionedJSONfiles contain all the information for every pre‐treatmentQAcheck performed by Mobius3D, including all 3D dose,CT, structure set information, as well as all plan information and patient demographics. Two Graphical User Interfaces (GUIs) were created, the first is called Mobius3D‐Database (M3D‐DB) and presents the check results in both filterable tabular and graphical form. These data are presented for all patients and includes mean dose differences, 90% coverage, 3D gamma pass rate percentages, treatment sites, machine, beam energy, Multi‐Leaf Collimator (MLC) mode, treatment planning system (TPS), plan names, approvers, dates and times. Group statistics and statistical process control levels are then calculated based on filter settings. The secondGUI, called Mobius3D organ at risk (M3DOAR), analyzes dose‐volume histogram data for all patients and all Organs‐at‐Risk (OAR). The design of the software is such that all treatment parameters and treatment site information are able to be filtered and sorted with the results, plots, and statistics updated.ResultsThe M3D‐DBsoftware can summarize and filter large numbers of plan‐checks from Mobius3D. The M3DOARsoftware is also able to analyze large amounts of dose‐volume data for patient groups which may prove useful in clinical trials, whereOARdoses for large numbers of patients can be compared and correlated. TargetDVHs can also be analyzedenmass.ConclusionsThis work demonstrates a method to extract the large amount of treatment data for every patient that is stored by Mobius3D but not easily accessible. With scripting, it is possible to mine this data for research and clinical trials as well as patient andTPS QA.
Independent evaluation of the effectiveness of IsoCal in improving image center accuracy on Varian TrueBeam and Clinac machines
Authors: Du Weiliang , Gao Song , Jiang Wei , Kudchadker Rajat J. 
Published: June 2018

AbstractModern medical linear accelerators (linacs) are often equipped with image guidance systems that are capable of megavolt (MV), kilovolt (kV), planar, or volumetric imaging. On Varian TrueBeam linacs, the isocenter accuracies of the imaging systems are calibrated with a procedure named IsoCal. On Clinac series linacs from Varian, installation of IsoCal is optional and the effects of IsoCal on the imaging systems can be turned on or off after the IsoCal procedure is performed. In this study, we report on the effectiveness of IsoCal in improving the coincidence of the image centers with the radiation isocenter, using an independent Winston‐Lutz (WL) method to locate the radiation isocenter. A ball‐bearing phantom was imaged with 2D MV, 2D kV, and cone beam computed radiography systems on two TrueBeam and two Clinac machines. Using the same phantom, digital WL tests with 16 combinations of gantry and collimator angles were performed to locate the radiation isocenter. The offsets between the IsoCal‐calibrated image centers and the WL radiation isocenter were found to be within 0.4 mm on the four linacs in this study. When IsoCal was turned off, the maximal offsets of the image centers were greater than 1.0 mm on the two Clinac machines. The method developed in this study can be used as a vendor‐independent quality assurance tool to assess the isocentricity of the image centers and radiation central axes.
Genome Editing for the Production of Natural Products in Escherichia coli
Authors: Zebec Ziga , Scrutton Nigel S. 
Published: June 2018

AbstractNatural products such as secondary metabolites (e.g., plant terpenoids) are found to be a major source of bioactive compounds. These natural products accumulate as complex mixtures with other related compounds and this chemical complexity adds cost to the downstream recovery and purification of natural products from plant biomass. One aim of synthetic biology and metabolic engineering programmes is to produce such compounds from synthetic gene clusters in heterologous hosts and thereby achieve more targeted and affordable production. Both fungi and bacteria are common hosts for metabolic engineering in industry. Fungal hosts include Penicillium chrysogenum, Saccharomyces cerevisiae, Aspergillus niger and the bacterial hosts Escherichia coli, Bacillus subtilis, Corynebacterium glutamicum. E. coli is often selected as a host given the ease of its genetic manipulation and the long history of using this organism in laboratory‐based bioengineering. The bioengineering of E. coli extends also to feedstock pathways to interface and optimize the production of high value compounds from widely available and inexpensive carbon sources. Genome editing is important in these microbial bioengineering programmes and is needed to isolate stable strains and to optimize production. Herein, this review discusses frequently used methods for genome editing in E. coli in relation to the production of natural compounds and chemicals.
Tin Nanoparticles–Enhanced Optical Transportation in Branched CdS Nanowire Waveguides
Authors: Guo Shuai , Liu Ruibin , Niu Chunhui , Weller Dieter , Hao Yan , Zhang Min , Li An , Liang Liang , Wang Xiaoxia , Wang Xiao , Yang Bin , Li Zi‐An , Pan Anlian 
Published: June 2018

AbstractHigh‐efficiency multichannel waveguiding components are desirable for integrated photonic systems to realize optical information processing and communication interconnection. Although different branched micro‐/nanostructures have been used as nanoscale multichannel waveguides, the propagation losses from their junctions are very high, which limits their applications in on‐chip photonic systems. Here, a new cadmium sulfide (CdS) nanowire branched heterostructure, with tin (Sn) nanoparticles implanted in its junctions, is achieved via a single‐step vapor deposition method. The self‐organized formation process of this structure is well investigated, through step‐by‐step observations during the growth. The implanted Sn nanoparticles in the junctions can act as strong light‐scattering centers, greatly improving the optical transportation from the backbone to the branches of the structure. Contrasting experiments demonstrate that the light‐guiding efficiency in the heterostructured nanowire branch waveguide is 20 times higher than that of the branched structures without Sn nanoparticles. Theoretical simulations further demonstrate the existence of Sn nanoparticles can greatly enhance the light scattering at the junctions and improve the light‐guiding performance. This kind of Sn‐CdS nanowire branched heterostructures may find promising applications for integrated photonic devices and systems.
Allenylphosphine Oxides as Starting Materials for the Synthesis of Conjugated Enynes: Boosting the Catalytic Performance by MOF Encapsulated Palladium Nanoparticles
Authors: Wang Xiao‐Dong , Wu Jin‐Jin , Sun Xue , Yang Wen‐Chao , Zhu Jie , Wu Lei 
Published: June 2018

AbstractA direct coupling of allenylphosphine oxides and alkynes is disclosed here mediated by MOF encapsulated palladium nanocatalysts. The methodology using α‐allenyl ethers as starting materials provides a heterogeneous approach to generate tri‐conjugated enynes with medium to excellent yields. The reaction tolerates a variety of functional groups to afford a range of structurally diverse substituted conjugated enynes. MOF served as support plays a significant role in dispersing and stabilizing the Pd nanoparticles. When compared with the homogeneous system, the advantage is also witnessed exhibiting a steady and high TOF value as well as the efficient reusability. A remarkable pore‐control effect of the MOF catalysts was also revealed, depending on the dimension of MOF, molecular size of allenylphosphine oxides, alkynes and enynes respectively. Benefitting from the heterogeneous manner, successful recycling of the MOF catalyst was further achieved with high reaction efficiency maintained.magnified image
Local environment, not local adaptation, drives leaf‐out phenology in common gardens along an elevational gradient in Acadia National Park, Maine
Authors: McDonough MacKenzie Caitlin , Primack Richard B. , Miller‐Rushing Abraham J. 
Published: June 2018

Premise of the StudyClimate‐driven changes in phenology are substantially affecting ecological relationships and ecosystem processes. The role of variation among species has received particular attention; for example, variation among species’ phenological responses to climate can disrupt trophic interactions and can influence plant performance. Variation within species in phenological responses to climate, however, has received much less attention, despite its potential role in ecological interactions and local adaptation to climate change.MethodsWe constructed three common gardens across an elevation gradient on Cadillac Mountain in Acadia National Park, Maine, to test population‐level responses in leaf‐out phenology in a reciprocal transplant experiment. The experiment included three native species: low bush blueberry (Vaccinium angustifolium), sheep's laurel (Kalmia angustifolia), and three‐toothed cinquefoil (Sibbaldiopsis tridentata).Key ResultsEvidence for local adaptation of phenological response to temperature varied among the species, but was weak for all three. Rather, variation in phenological response to temperature appeared to be driven by local microclimate at each garden site and year‐to‐year variation in temperature.ConclusionsPopulation‐level adaptations in leaf‐out phenology appear to be relatively unimportant for these species in Acadia National Park, perhaps a reflection of strong genetic mixing across elevations, or weak differences in selection on phenological response to spring temperatures at different elevations. These results concur with other observational data in Acadia and highlight the utility of experimental approaches to understand the importance of annual and local site variation in affecting phenology both among and within plant species.
Peroxisome‐targeted Supramolecular Nanoprobes Assembled with Pyrene‐labelled Peptide Amphiphiles
Authors: Kim Inhye , Bang Woo‐Young , Kim Sooyong , Jin Seon‐Mi , Hyun Ju‐Yong , Han Eun Hee , Lee Eunji 
Published: June 2018

AbstractDespite the versatile metabolic functions of peroxisomes such as lipid synthesis and fatty acid oxidation and their relevance to genetically inherited diseases, namely, peroxisome biogenesis disorders and peroxisomal enzyme deficiency, there is not much research on peroxisome‐targeting therapeutics. Herein we present supramolecular nanostructured probes based on the self‐assembly of peptide amphiphiles (PAs) having peroxisome‐targeting ability in mammalian cells. The PA was designed to include the peroxisome‐targeting tripeptide (SKL) and a fluorescent dye (pyrene). It was revealed that the presence of the SKL‐appended carboxyl terminal group of PA, the extent of α‐helical nature of the peptide block, and the fibrillar morphology of nano‐assemblies affected the targeting efficiency of PA supramolecular nanoprobe. The simple modification of PAs by the peroxisome‐targeting strength prediction showed an enhanced peroxisome specificity, as expected. This work provides important insights into designing subcellular organelle‐targeting nanoparticles for next‐generation nanomedicines.
MicroRNA‐34a‐5p inhibits liver fibrosis by regulating TGF‐β1/Smad3 pathway in hepatic stellate cells
Authors: Feili Xiao , Wu Shuang , Ye Weiwei , Tu Juncai , Lou Lianqing 
Published: June 2018

AbstractLiver fibrosis is a major cause of morbidity and mortality worldwide, and the outcome of various chronic liver diseases. Recent studies suggest that aberrant expression of miR‐34 is involved in the progression of various liver diseases including hepatocellular carcinoma (HCC). However, it is still poorly understood whether miR‐34 mediates the pathogenesis of liver fibrosis. Here, we found that the expression of microRNA‐34a‐5p (miR‐34a‐5p) was significantly decreased in patients with hepatitis B virus (HBV)‐activated liver fibrosis and HCC, as well as in CC14 (Carbon tetrachloride Tetrachloromethane) induced liver fibrosis model mice. The TGF‐β1/Smad3 (Transforming growth factor‐β1/Smad3) pathway were significantly augmented in CC14 induced mice compared with normal control, whereas inhibitor of TGF‐β1 (SB431542) significantly attenuated liver fibrosis and TGF‐β1/Smad3 activation. Administration of the miR‐34a‐5p mimic de‐activated TGF‐β1/Smad3 pathway in human hepatic stellate cells (HSC), LX‐2. Moreover, the target gene for miR‐34a‐5p, Smad4, was predicted and verified in LX‐2 cells. Taken together, these data demonstrated that overexpression of miR‐34 in HSCs ameliorated the development and progression of liver fibrosis by targeting Smad4 and regulating TGF‐β1/Smad3 pathway. Strategies targeting miR‐34a‐5p may be of benefit in the treatment of liver fibrosis.
Monitoring of the Discharge Process of Bulk Material in Silos Using Electrical Capacitance Tomography
Authors: Zurovec David , Hlosta Jakub , Rozbroj Jiri , Necas Jan , Zegzulka Jiri 
Published: June 2018

AbstractMonitoring the bulk material discharge from silos using electrical capacitance tomography (ECT) is an effective way to supervise dynamic flow profiles within silos. In this case, bulk materials such as wheat and corn are used. These materials are typical crops in the agricultural industry. The basic differences of these materials are shape and size. The material properties are the main factors influencing the optimal discharge processes. The ECT method is used to determine the flow profile during the discharge of each material from the silo. ECT is a non‐destructive and contactless method for measuring the inner space of the silo. The results demonstrate that the monitoring of discharge processes from the silo by applying ECT is an innovative online monitoring method with a wide application.
Radial Diffusers – Simulation of Three‐Dimensional Flow Effects with CFD (Part 3)
Authors: Findeisen Fabian , Urbaneck Thorsten , Platzer Bernd 
Published: June 2018

AbstractRadialdiffusoren dienen der Be‐ und Entladung von thermischen Speichern und beeinflussen signifikant die Ausbildung der thermischen Schichtung. Die Veröffentlichungsreihe behandelt dreidimensionale Strömungseffekte. Über den Umfang des Radialdiffusorauslasses kann eine ungleich verteilte Ausströmung auftreten, die mit einer stärkeren Vermischung als bei einer rotationssymmetrischen Ausströmung bzw. Modellierung einhergeht. Der Beitrag diskutiert Maßnahmen zur Vermeidung dieses asymmetrischen Ausströmens.
Stanniocalcin 2 expression is associated with a favourable outcome in male breast cancer
Authors: Coulson‐Gilmer Camilla , Humphries Matthew P , Sundara Rajan Sreekumar , Droop Alastair , Jackson Sharon , Condon Alexandra , Cserni Gabor , Jordan Lee B , Jones Louise J , Kanthan Rani , Di Benedetto Anna , Mottolese Marcella , Provenzano Elena , Kulka Janina , Shaaban Abeer M , Hanby Andrew M , Speirs Valerie 
Published: June 2018

AbstractBreast cancer can occur in either gender; however, it is rare in men, accounting for <1% of diagnosed cases. In a previous transcriptomic screen of male breast cancer (MBC) and female breast cancer (FBC) occurrences, we observed that Stanniocalcin 2 (STC2) was overexpressed in the former. The aim of this study was to confirm the expression of STC2 in MBC and to investigate whether this had an impact on patient prognosis. Following an earlier transcriptomic screen, STC2 gene expression was confirmed by RT‐qPCR in matched MBC and FBC samples as well as in tumour‐associated fibroblasts derived from each gender. Subsequently, STC2 protein expression was examined immunohistochemically in tissue microarrays containing 477 MBC cases. Cumulative survival probabilities were calculated using the Kaplan–Meier method and multivariate survival analysis was performed using the Cox hazard model. Gender‐specific STC2 gene expression showed a 5.6‐fold upregulation of STC2 transcripts in MBC, also supported by data deposited in Oncomine™. STC2 protein expression was a positive prognostic factor for disease‐free survival (DFS; Log‐rank; total p = 0.035, HR = 0.49; tumour cells p = 0.017, HR = 0.44; stroma p = 0.030, HR = 0.48) but had no significant impact on overall survival (Log‐rank; total p = 0.23, HR = 0.71; tumour cells p = 0.069, HR = 0.59; stroma p = 0.650, HR = 0.87). Importantly, multivariate analysis adjusted for patient age at diagnosis, node staging, tumour size, ER, and PR status revealed that total STC2 expression as well as expression in tumour cells was an independent prognostic factor for DFS (Cox regression; p = 0.018, HR = 0.983; p = 0.015, HR = 0.984, respectively). In conclusion, STC2 expression is abundant in MBC where it is an independent prognostic factor for DFS.
Improved estimates of net primary production, growth, and standing crop of Macrocystis pyrifera in Southern California
Authors: Rassweiler Andrew , Reed Daniel C. , Harrer Shannon L. , Nelson J. Clint 
Published: June 2018

AbstractThe giant kelp Macrocystis pyrifera forms subtidal forests on shallow reefs in temperate regions of the world. It is one of the fastest‐growing multicellular autotrophs on Earth and its high productivity supports diverse marine food webs. In 2008, we published a method for estimating biomass and net primary production (NPP) of giant kelp along with five years of data, to provide a more integrated measure of NPP than those yielded by previous methods. Our method combines monthly field measurements of standing crop and loss rates with a model of kelp biomass dynamics to estimate instantaneous mass‐specific growth rates and NPP for each season of each year. We have since improved our approach to account for several previously unresolved sources of biomass loss. These improvements have led to a near doubling of our prior estimates of growth and NPP. At our site with the most persistent stand of giant kelp, NPP averages ~5.2 kg dry mass·m−2·yr−1 and results from the rapid growth (~3.5% per d) of a relatively small standing biomass (~0.4 kg dry mass/m2 on average) that turns over ~12 times annually. Here we provide revised estimates of seasonal biomass, growth, and NPP for the five years covered by our previous publication (2002–2006), along with more than a decade of additional data (2007–2017). We also present updated relationships for predicting giant kelp biomass and NPP from much more easily obtained measurements of frond density. These data can be used to understand the mechanisms that drive variation in giant kelp NPP at a wide range of temporal scales. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.