bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential overestimation of community respiration in the western Pacific boundary ocean: What causes the putative net heterotrophy in oligotrophic systems?
Authors: Huang Yibin , Chen Bingzhang , Huang Bangqin , Zhou Hui , Yuan Yongquan 
Published: May 2019

AbstractMicrobial metabolism is of great importance in affecting the efficiency of biological pump and global carbon cycles. However, the metabolic state of the oligotrophic ocean, the largest biome on Earth, remains contentious. We examined the planktonic and bacterial metabolism using in vitro incubations along the western Pacific boundary during September and October 2016. The integrated gross primary production (GPP) of the photic zone exhibited higher values in the region of 2°–8°N along 130°E and the western Luzon Strait, which is consistent with the regional variability of nutrients in the different ocean provinces. Spatially, the community respiration (CR) was less variable than the GPP and slightly exceeded the GPP at most of the sampling stations. Overall, the in vitro incubation results suggest a prevailing heterotrophic state in this region. A comparison of the metabolic rates from the in vitro incubations with recently published biogeochemical model results in the same region shows that our observed GPP values were close to those predicted by the model, but the measured CR was approximately 30% higher than the modeled values. We also found that most of the in vitro CR estimates were higher than the upper range of the empirical CR estimated from the sum of the contributions of the main trophic groups. Conversely, the estimates of the empirical CR support the rationality of the CR predicted by the biogeochemical model. In general, the results indicate that systematic net heterotrophy is more likely a result of the overestimation of CR measured by the light–dark bottle incubation experiments, although the exact cause of the methodological problem remains unknown.
Benthic communities and their drivers: A spatial analysis off the Antarctic Peninsula
Authors: Gutt Julian , Arndt Janina , Kraan Casper , Dorschel Boris , Schröder Michael , Bracher Astrid , Piepenburg Dieter 
Published: May 2019

AbstractMultiple environmental factors control benthic community patterns, and their relative importance varies with spatial scale. Since this variation is difficult to evaluate quantitatively, extensive sampling across a broad range of spatial scales is required. Here, we present a first case study on Southern Ocean shelf benthos, in which mega‐epibenthic communities and biota‐environment relationships have been explored at multiple spatial scales. The analyses encompassed 20 seafloor, water‐column, and sea‐ice parameters, as well as abundances of 18 mega‐epibenthic taxa in a total of 2799 high‐resolution seabed images taken at 28 stations at 32–786 m depth off the northern Antarctic Peninsula. Based on a priori nesting of sampling stations into ecoregions, subregions, and habitats, analyses indicated most pronounced patchiness levels at finest (within transects among adjacent seabed photos) and largest (among ecoregions) spatial scale considered. Using an alternative approach, explicitly involving the spatial distances between the geo‐referenced data, Moran's Eigenvector mapping (MEM) classified the continuum of spatial scales into four categories: broad (> 60 km), meso (10–60 km), small (2–10 km), and fine (< 2 km). MEM analyses generally indicated an increase in mega‐epibenthic community complexity with increasing spatial scale. Moreover, strong relationships between biota and environmental drivers were found at scales of > 2 km. In contrast, few environmental variables contributed to explaining biotic structures at finer scales. These are likely rather determined by nonmeasured environmental variables, as well as biological traits and interactions that are assumed to be most effective at small spatial scales.
Landscape process domains drive patterns of CO2 evasion from river networks
Authors: Rocher‐Ros Gerard , Sponseller Ryan A. , Lidberg William , Mörth Carl‐Magnus , Giesler Reiner 
Published: May 2019

AbstractStreams are important emitters of CO2 but extreme spatial variability in their physical properties can make upscaling very uncertain. Here, we determined critical drivers of stream CO2 evasion at scales from 30 to 400 m across a 52.5 km2 catchment in northern Sweden. We found that turbulent reaches never have elevated CO2 concentrations, while less turbulent locations can potentially support a broad range of CO2 concentrations, consistent with global observations. The predictability of stream pCO2 is greatly improved when we include a proxy for soil‐stream connectivity. Catchment topography shapes network patterns of evasion by creating hydrologically linked “domains” characterized by high water‐atmosphere exchange and/or strong soil‐stream connection. This template generates spatial variability in the drivers of CO2 evasion that can strongly bias regional and global estimates. To overcome this complexity, we provide the foundations of a mechanistic framework of CO2 evasion by considering how landscape process domains regulate transfer and supply.
Transcriptome analysis identifies metallothionein as biomarkers to predict recurrence in hepatocellular cacinoma
Authors: Wang Sufang , Gribskov Michael 
Published: May 2019

AbstractBackgroundLiver cancer is the fifth most common cancer, and hepatocellular carcinoma (HCC) is the major liver tumor type seen in adults. HCC is usually caused by chronic liver disease such as hepatitis B virus or hepatitis C virus infection. One of the promising treatments for HCC is liver transplantation, in which a diseased liver is replaced with a healthy liver from another person. However, recurrence of HCC after surgery is a significant problem. Therefore, it is important to discover reliable cellular biomarkers that can predict recurrence in HCC.MethodsWe analyzed previously published HCC RNA‐Seq data that includes 21 paired tumor and normal samples, in which nine tumors were recurrent after orthotopic liver transplantation and 12 were nonrecurrent tumors with their paired normal samples. We used both the reference genome and de novo transcriptome assembly based analyses to identify differentially expressed genes (DEG) and used RandomForest to discover biomarkers.ResultsWe obtained 398 DEG using the Reference approach and 412 DEG using de novo assembly approach. Among these DEG, 258 genes were identified by both approaches. We further identified 30 biomarkers that could predict the recurrence. We used another independent HCC study that includes 50 patients normal and tumor samples. By using these 30 biomarkers, the prediction accuracy was 100% for normal condition and 98% for tumor condition. A group of Metallothionein was specifically discovered as biomarkers in both reference and de novo assembly approaches.ConclusionWe identified a group of Metallothionein genes as biomarkers to predict recurrence. The metallothionein genes were all down‐regulated in tumor samples, suggesting that low metallothionein expression may be a promoter of tumor growth. In addition, using de novo assembly identified some unique biomarkers, further confirmed the necessity of conducting a de novo assembly in human cancer study.
Determining the energy spectrum of clinical linear accelerator using an optimized photon beam transmission protocol
Authors: Choi Hyun Joon , Park Hyojun , Yi Chul Young , Kim Byoung‐Chul , Shin Wook‐Geun , Min Chul Hee 
Published: May 2019

PurposeThe complex beam delivery techniques for patient treatment using a clinical linear accelerator (linac) may result in variations in the photon spectra, which can lead to dosimetric differences in patients that cannot be accounted for by current treatment planning systems (TPSs). Therefore, precise knowledge of the fluence and energy spectrum (ES) of the therapeutic beam is very important. However, owing to the high energy and flux of the beam, the ES cannot be measured directly, and validation of the spectrum modeled in the TPS is difficult. The aim of this study is to develop an efficient beam transmission measurement procedure for accurately reconstructing the ES of a therapeutic x‐ray beam generated by a clinical linac.MethodsThe attenuation of a 6 MV photon beam from an Elekta Synergy Platform clinical linac through different thicknesses of graphite and lead was measured using an ion chamber. The response of the ion chamber as a function of photon energy was obtained using the Monte Carlo (MC) method in the Geant4 simulation code. Using the curves obtained in the photon beam transmission measurements and the ion chamber energy response, the ES was reconstructed using an iterative algorithm based on a mathematical model of the spectrum. To evaluate the accuracy of the spectrum reconstruction method, the reconstructed ES (ESrecon) was compared to that determined by the MC simulation (ESMC).ResultsThe ion chamber model in the Geant4 simulation was well validated by comparing the ion chamber perturbation factors determined by the TRS‐398 calibration protocol and EGSnrc; the differences were within 0.57%. The number of transmission measurements was optimized to 10 for efficient spectrum reconstruction according to the rate of increase in the spectrum reconstruction accuracy. The distribution of ESrecon obtained using the measured transmission curves was clearly similar to the reference, ESMC, and the dose distributions in water calculated using ESrecon and ESMC were similar within a 2% local difference. However, in a heterogeneous medium, the dose discrepancy between them was >5% when a complex beam delivery technique composed of 171 control points was used.ConclusionsThe proposed measurement procedure required a total time of approximately 1 h to obtain and analyze 20 transmission measurements. In addition, it was confirmed that the transmission curve of high‐Z materials influences the accuracy of spectrum reconstruction more than that of low‐Z materials. A well‐designed transmission measurement protocol suitable for clinical environments could be an essential tool for better dosimetric accuracy in patient treatment and for periodic verification of the beam quality.
Summary of the AAPM task group 248 report: Interoperability assessment for the commissioning of medical imaging acquisition systems
Authors: Walz‐Flannigan Alisa , Weiser John , Goode Allen R. , Junck Kevin , Tarbox Lawrence , Dave Jaydev K. , Clunie David A. , McColl Roderick W. , Langer Steve G. 
Published: May 2019

PurposeWe summarize the AAPM TG248 Task Group report on interoperability assessment for the commissioning of medical imaging acquisition systems in order to bring needed attention to the value and role of quality assurance testing throughout the imaging chain.MethodsTo guide the clinical physicist involved in commissioning of imaging systems, we describe a framework and tools for incorporating interoperability assessment into imaging equipment commissioning.ResultsWhile equipment commissioning may coincide with equipment acceptance testing, its scope may extend beyond validation of product or purchase specifications. Equipment commissioning is meant to provide assurance that a system is ready for clinical use, and system interoperability plays an essential role in the clinical use of an imaging system.ConclusionThe functionality of a diagnostic imaging system extends beyond the acquisition console and depends on interoperability with a host of other systems such as the Radiology Information System, a Picture Archive and Communication System, post‐processing software, treatment planning software, and clinical viewers.
c‐Met‐dependent phosphorylation of RhoA plays a key role in gastric cancer tumorigenesis
Authors: Liu Jianjun , Li Shun , Chen Shangxiang , Chen Shuai , Geng Qirong , Xu Dazhi 
Published: May 2019

AbstractRhoA has been identified as having a gain‐of‐function mutation in approximately 20% of diffuse gastric cancer patients. However, the carcinogenic role of RhoA mutations in gastric cancer (GC) is unclear. In the present study, we report that RhoA directly interacts with c‐Met and can be phosphorylated by c‐Met at Y42 before subsequent K48‐linked polyubiquitination and proteasome‐mediated protein degradation. Y42C‐mutated RhoA exhibits higher protein levels and promotes the proliferation and motility of GC cells. Interestingly, a c‐Met inhibitor significantly repressed the growth of GC cells transfected with WT RhoA but not RhoA mutated at Y42 in vivo and in vitro. Analyses of human GC tissues showed that the combined levels of p‐c‐Met and p‐RhoA are a better predictor for prognosis than either factor alone. Taken together, our findings unravel the mechanism by which the RhoA Y42 mutant is linked to poor prognosis in GC. Moreover, this study helps to identify a strategy for patient stratification and optimization of targeted c‐Met therapy. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Phosphoproteome Profiling of Isogenic Cancer Cell‐Derived Exosome Reveals HSP90 as a Potential Marker for Human Cholangiocarcinoma
Authors: Weeraphan Churat , Phongdara Amornrat , Chaiyawat Parunya , Diskul‐Na‐Ayudthaya Penchatr , Chokchaichamnankit Daranee , Verathamjamras Chris , Netsirisawan Pukkavadee , Yingchutrakul Yodying , Roytrakul Sittiruk , Champattanachai Voraratt , Svasti Jisnuson , Srisomsap Chantragan 
Published: May 2019

AbstractThe northeastern region of Thailand is well known to have a high incidence and mortality of cholangiocarcinoma (CCA). Protein phosphorylation status has been reported to reflect a key determinant of cellular physiology, but identification of phosphoproteins can be a problem due to the presence of phosphatase. Exosomes are stable toward circulating proteases and other enzymes in human blood and can be recognized before the onset of cancer progression. Here an in vitro metastatic model of isogenic CCA cells is used to provide insight into the phosphorylation levels of exosomal proteins derived from highly invasive cells. Gel‐based and gel‐free proteomics approaches are used to reveal the proteins differentially phosphorylated in relation to tumor cell phenotypes. Forty‐three phosphoproteins are identified with a significant change in phosphorylation level. Phos‐tag western blotting and immunohistochemistry staining are then employed to validate the candidate phosphoproteins. Heat shock protein 90 is successfully confirmed as being differentially phosphorylated in relation to tumor malignancy. Importantly, the aberrant phosphorylation of exosomal proteins might serve as a promising tool for the development of a biomarker for metastatic CCA.
The quest for a triplet ground‐state alkene: Highly twisted C═C double bonds
Authors: Wu Judy I. , van Eikema Hommes Nico J.R. , Lenoir Dieter , Bachrach Steven M. 
Published: May 2019

AbstractDensity functional theory and extrapolated CCSD(T) computations of several “anti‐Bredt” alkenes were carried to explore possible 1,2‐diyl “alkene” candidates with a triplet ground state. Ten candidates containing twisted double bonds at the bridgehead positions of bicyclic structures (1‐6) or adamantene (7‐10) derivatives were studied. Based on a combination of ring strain, rigid scaffolding, and steric crowding, four species were identified to have surprisingly low singlet‐triplet energy gaps (lower than 4 kcal/mol). A tert‐butyl substituted bicyclic structure (4) was identified to have a near‐zero singlet‐triplet energy gap, but no triplet ground‐state alkene was found. Ring strain energy (RSE) calculations, π‐orbital axis vector (POAV) analyses, and multiple linear regression models were performed to elucidate the geometric and energetic effects of double bond twisting in 1‐10. Based on our computational exploration, it appears unlikely that there is a ground‐state triplet olefin.
Pre‐NQ Manifolds and Correspondence Spaces: the Nilmanifold Example
Authors: Deser Andreas 
Published: May 2019

AbstractCourant algebroids correspond to degree‐2 symplectic differential graded manifolds or NQ‐manifolds for short. We review how a similar construction shows that locally the gauge structure of Double Field Theory corresponds to degree‐2 symplectic pre‐NQ manifolds. To illustrate first steps towards a global understanding of the pre‐NQ case, we apply the local constructions to 3‐dimensional nilmanifolds carrying an abelian gerbe. These are among prime examples where T‐duality is well‐understood and allow us to investigate classic results in the graded language.
Iterative ‐conic controller synthesis
Authors: Bridgeman Leila Jasmine , Forbes James Richard 
Published: May 2019

SummaryThis paper proposes a method to synthesize controllers that minimize an upper bound on the closed‐loop
‐norm while imposing desired controller conic bounds. An initial conic controller is synthesized and iteratively improved. Conic sectors can be used to characterize a variety of input‐output properties, such as gain, phase, and minimum gain. If such plant properties hold robustly to uncertainty present, then closed‐loop stability can be ensured robustly via the Conic Sector Theorem by imposing desired controller conic bounds. Consequently, this paper provides a versatile optimal and robust controller synthesis method. Moreover, it relies only on the solution of convex optimization problems subject to linear matrix inequality constraints, making it readily implementable.
TiO2‐Based Photopolymerized Hybrid Catalysts with Visible Light Catalytic Activity Induced by In Situ Generated Ag/Au NPs
Authors: Melinte Violeta , Buruiana Tinca , Rosca Irina , Chibac Andreea L. 
Published: May 2019

AbstractThis work describes the use of surface modified TiO2 nanoparticles in combination with photopolymerizable monomers in the achieving of hybrid photocrosslinked polymer networks for photocatalysis. The surface of TiO2 nanoparticles was functionalized by means of a silane coupling agent with acrylic sequences and quaternary ammonium units in order to attain a covalent linkage of the nanoparticles inside the photocured matrix. To increase the photocatalytic performance of TiO2 NPs and to expand its catalytic activity under visible light, Ag/Au NPs were in situ photogenerated in the acrylic matrix simultaneously with the photopolymerization process. The photopolymerization profile, diffraction patterns and nanoparticles distribution were established for the hybrid films by FTIR, XRD and TEM, respectively. Additionally, the hybrid films exhibited good antibacterial properties against Staphylococcus aureus and Escherichia coli. The photocatalytic efficiency of the hybrid coatings was tested on phenol and Congo Red photodecomposition under UV and visible light irradiation, the best results being observed for the materials incorporating Ag/Au NPs.
Recent advances in photodynamic therapy for cancer and infectious diseases
Authors: Shi Xutong , Zhang Can Yang , Gao Jin , Wang Zhenjia 
Published: May 2019

AbstractPhotodynamic therapy (PDT) is a treatment by combining light and a photosensitizer to generate reactive oxygen species (ROS) for cellular damage, and is used to treat cancer and infectious diseases. In this review, we focus on recent advances in design of new photosensitizers for increased production of ROS and in genetic engineering of biological photosensitizers to study cellular signaling pathways. A new concept has been proposed that PDT‐induced acute inflammation can mediate neutrophil infiltration to deliver therapeutics in deep tumor tissues. Combination of PDT and immunotherapies (neutrophil‐mediated therapeutic delivery) has shown the promising translation of PDT for cancer therapies. Furthermore, a new area in PDT is to treat bacterial infections to overcome the antimicrobial resistance. Finally, we have discussed the new directions of PDT for therapies of cancer and infectious diseases. In summary, we believe that rational design and innovations in nanomaterials may have a great impact on translation of PDT in cancer and infectious diseases.This article is categorized under:Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic DiseaseTherapeutic Approaches and Drug Discovery > Nanomedicine for Infectious DiseaseNanotechnology Approaches to Biology > Nanoscale Systems in Biology
Error possibility, contextualism, and bias
Authors: Buckwalter Wesley 
Published: May 2019

AbstractA central theoretical motivation for epistemic contextualism is that it can explain something that invariantism cannot. Specifically, contextualism claims that judgments about “knowledge” are sensitive to the salience of error possibilities and that this is explained by the fact that salience shifts the evidential standard required to truthfully say someone “knows” something when those possibilities are made salient. This paper presents evidence that undermines this theoretical motivation for epistemic contextualism. Specifically, it demonstrates that while error salience does sometimes impact “knowledge” judgments as contextualism predicts, it does so in ways that are consistent with invariantism and does not require positing any additional contextualist semantics to explain. These results advance our understanding of the pathways by which error possibility affects “knowledge” judgments, answer a major challenge to invariantism, and suggest several methodological improvements for the study of knowledge attribution.
COHERENT EXTENSION OF PARTIAL AUTOMORPHISMS, FREE AMALGAMATION AND AUTOMORPHISM GROUPS
Authors: SINIORA DAOUD , SOLECKI SŁAWOMIR 
Published: May 2019

AbstractWe give strengthened versions of the Herwig–Lascar and Hodkinson–Otto extension theorems for partial automorphisms of finite structures. Such strengthenings yield several combinatorial and group-theoretic consequences for homogeneous structures. For instance, we establish a coherent form of the extension property for partial automorphisms for certain Fraïssé classes. We deduce from these results that the isometry group of the rational Urysohn space, the automorphism group of the Fraïssé limit of any Fraïssé class that is the class of all ${\cal F}$-free structures (in the Herwig–Lascar sense), and the automorphism group of any free homogeneous structure over a finite relational language all contain a dense locally finite subgroup. We also show that any free homogeneous structure admits ample generics.
In the Name of Anticommunism: Chinese practices of ideological accommodation in the early Cold War Philippines
Authors: KUNG CHIEN-WEN 
Published: May 2019

AbstractThis article builds on work by social and cultural historians of the Cold War such as Heonik Kwon and Masuda Hajimu by showing how three groups of Chinese actors helped create the locally specific reality of Chinese anticommunism in the Philippines during the late 1940s and early 1950s. It argues that, in a climate thick with Sinophobia and fears of communism, but largely devoid of actual Chinese Reds, anticommunism for the Chinese was only secondarily about rooting out subversives, ideological authenticity, and supporting Chiang Kai-shek's counterattack against mainland China. As a social phenomenon, it was primarily a diverse and flexible repertoire of practices, from crime to civic associationism, that Chinese elites and their challengers employed to bolster their reputations as anticommunists, enrich themselves, and pursue vendettas against their ‘communist’ enemies. By focusing on these practices of what I call ideological accommodation, the article intervenes in scholarship on the Chinese diaspora after the Second World War by showing that anticommunism was essential to how the overseas Chinese adapted to being resident ‘aliens’ in post-colonial Philippine society.