bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Novel Chondroprotective Mediators in Resolving Inflammatory Exudates
Authors: Kaneva Magdalena K. , Greco Karin V. , Headland Sarah E. , Montero-Melendez Trinidad , Mori Prashant , Greenslade Kevin , Pitzalis Costantino , Moore Adrian , Perretti Mauro 
Published: February 2017

Abstract
We hypothesized that exudates collected at the beginning of the resolution phase of inflammation might be enriched for tissue protective molecules; thus an integrated cellular and molecular approach was applied to identify novel chondroprotective bioactions. Exudates were collected 6 h (inflammatory) and 24 h (resolving) following carrageenan-induced pleurisy in rats. The resolving exudate was subjected to gel filtration chromatography followed by proteomics, identifying 61 proteins. Fractions were added to C28/I2 chondrocytes, grown in micromasses, ions with or without IL-1β or osteoarthritic synovial fluids for 48 h. Three proteins were selected from the proteomic analysis, α1-antitrypsin (AAT), hemopexin (HX), and gelsolin (GSN), and tested against catabolic stimulation for their effects on glycosaminoglycan deposition as assessed by Alcian blue staining, and gene expression of key anabolic proteins by real-time PCR. In an in vivo model of inflammatory arthritis, cartilage integrity was determined histologically 48 h after intra-articular injection of AAT or GSN. The resolving exudate displayed protective activities on chondrocytes, using multiple readouts: these effects were retained in low m.w. fractions of the exudate (46.7% increase in glycosaminoglycan deposition; ∼20% upregulation of COL2A1 and aggrecan mRNA expression), which reversed the effect of IL-1β. Exogenous administration of HX, GSN, or AAT abrogated the effects of IL-1β and osteoarthritic synovial fluids on anabolic gene expression and increased glycosaminoglycan deposition. Intra-articular injection of AAT or GSN protected cartilage integrity in mice with inflammatory arthritis. In summary, the strategy for identification of novel chondroprotective activities in resolving exudates identified HX, GSN and AAT as potential leads for new drug discovery programs.
Multitasking Immune Sp185/333 Protein, rSpTransformer-E1, and Its Recombinant Fragments Undergo Secondary Structural Transformation upon Binding Targets
Authors: Lun Cheng Man , Bishop Barney M. , Smith L. Courtney 
Published: February 2017

AbstractThe purple sea urchin, Strongylocentrotus purpuratus, expresses a diverse immune response protein family called Sp185/333. A recombinant Sp185/333 protein, previously called rSp0032, shows multitasking antipathogen binding ability, suggesting that the protein family mediates a flexible and effective immune response to multiple foreign cells. Bioinformatic analysis predicts that rSp0032 is intrinsically disordered, and its multiple binding characteristic suggests structural flexibility to adopt different conformations depending on the characteristics of the target. To address the flexibility and structural shifting hypothesis, circular dichroism analysis of rSp0032 suggests that it transforms from disordered (random coil) to α helical structure. This structural transformation may be the basis for the strong affinity between rSp0032 and several pathogen-associated molecular patterns. The N-terminal Gly-rich fragment of rSp0032 and the C-terminal His-rich fragment show unique transformations by either intensifying the α helical structure or changing from α helical to β strand depending on the solvents and molecules added to the buffer. Based on these results, we propose a name change from rSp0032 to rSpTransformer-E1 to represent its flexible structural conformations and its E1 element pattern. Given that rSpTransformer-E1 shifts its conformation in the presence of solvents and binding targets and that all Sp185/333 proteins are predicted to be disordered, many or all of these proteins may undergo structural transformation to enable multitasking binding activity toward a wide range of targets. Consequently, we also propose an overarching name change for the entire family from Sp185/333 proteins to SpTransformer proteins.
Cyanobacterial endobionts within a major marine planktonic calcifier (Globigerina bulloides, Foraminifera) revealed by 16S rRNA metabarcoding
Authors: Bird Clare , Darling Kate F. , Russell Ann D. , Davis Catherine V. , Fehrenbacher Jennifer , Free Andrew , Wyman Michael , Ngwenya Bryne T. 
Published: February 2017

Abstract. We investigated the possibility of bacterial symbiosis in Globigerina bulloides, a palaeoceanographically important, planktonic foraminifer. This marine protist is commonly used in micropalaeontological investigations of climatically sensitive subpolar and temperate water masses as well as wind-driven upwelling regions of the world's oceans. G. bulloides is unusual because it lacks the protist algal symbionts that are often found in other spinose species. In addition, it has a large offset in its stable carbon and oxygen isotopic compositions compared to other planktonic foraminifer species, and also that predicted from seawater equilibrium. This is suggestive of novel differences in ecology and life history of G. bulloides, making it a good candidate for investigating the potential for bacterial symbiosis as a contributory factor influencing shell calcification. Such information is essential to evaluate fully the potential response of G. bulloides to ocean acidification and climate change. To investigate possible ecological interactions between G. bulloides and marine bacteria, 18S rRNA gene sequencing, fluorescence microscopy, 16S rRNA gene metabarcoding and transmission electron microscopy (TEM) were performed on individual specimens of G. bulloides (type IId) collected from two locations in the California Current. Intracellular DNA extracted from five G. bulloides specimens was subjected to 16S rRNA gene metabarcoding and, remarkably, 37–87 % of all 16S rRNA gene sequences recovered were assigned to operational taxonomic units (OTUs) from the picocyanobacterium Synechococcus. This finding was supported by TEM observations of intact Synechococcus cells in both the cytoplasm and vacuoles of G. bulloides. Their concentrations were up to 4 orders of magnitude greater inside the foraminifera than those reported for the California Current water column and approximately 5 % of the intracellular Synechococcus cells observed were undergoing cell division. This suggests that Synechococcus is an endobiont of G. bulloides type IId, which is the first report of a bacterial endobiont in the planktonic foraminifera. We consider the potential roles of Synechococcus and G. bulloides within the relationship and the need to determine how widespread the association is within the widely distributed G. bulloides morphospecies. The possible influence of Synechococcus respiration on G. bulloides shell geochemistry is also explored.
An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples
Authors: Clusa Laura , Ardura Alba , Fernández Sara , Roca Agustín A. , García-Vázquez Eva 
Published: February 2017

BackgroundSalmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow troutOncorhynchus mykiss, Atlantic salmonSalmo salar, brown troutSalmo trutta, brook troutSalvelinus fontinalis, and lake troutSalvelinus namaycush. In contrast, other salmonids are endangered in their native settings.MethodsHere we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples.ResultsThe method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain).DiscussionThis new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms.
Comparison of full and empirical Bayes approaches for inferring sea‐level changes from tide‐gauge data
Authors: Piecuch Christopher G. , Huybers Peter , Tingley Martin P. 
Published: February 2017

AbstractTide‐gauge data are one of the longest instrumental records of the ocean, but these data can be noisy, gappy, and biased. Previous studies have used empirical Bayes methods to infer the sea‐level field from tide‐gauge records but have not accounted for uncertainty in the estimation of model parameters. Here we compare to a fully Bayesian method that accounts for uncertainty in model parameters, and demonstrate that empirical Bayes methods underestimate the uncertainty in sea level inferred from tide‐gauge records. We use a synthetic tide‐gauge data set to assess the skill of the empirical and full Bayes methods. The empirical‐Bayes credible intervals on the sea‐level field are narrower and less reliable than the full‐Bayes credible intervals: the empirical‐Bayes 95% credible intervals are 42.8% narrower on average than are the full‐Bayes 95% credible intervals; full‐Bayes 95% credible intervals capture 95.6% of the true field values, while the empirical‐Bayes 95% credible intervals capture only 77.1% of the true values, showing that parameter uncertainty has an important influence on the uncertainty of the inferred sea‐level field. Most influential are uncertainties in model parameters for data biases (i.e., tide‐gauge datums); letting data‐bias parameters vary along with the sea‐level process, but holding all other parameters fixed, the 95% credible intervals capture 92.8% of the true synthetic‐field values. Results indicate that full Bayes methods are preferable for reconstructing sea‐level estimates in cases where complete and accurate estimates of uncertainty are warranted.
Pediatric Critical Event Debriefing in Emergency Medicine Training: An Opportunity for Educational Improvement
Authors: Nocera Mariann , Merritt Chris 
Published: February 2017

AbstractIntroductionIn the emergency department (ED), critical events, including death and severe illness, are not uncommon. Critical events involving children, while less frequent, may be especially distressing. Debriefing following a critical event may serve several purposes: review of team performance, education, identification of errors, emotional support, and planning for future events. Debriefing skills and habits learned during training may be carried forward throughout an emergency physician's career. This study evaluates how educators in emergency medicine (EM) view debriefing after pediatric critical events and identifies barriers to use of debriefing in postgraduate training programs.MethodsIn this cross‐sectional observational study, we surveyed program directors (PDs) from EM residency and pediatric emergency medicine (PEM) fellowship programs via e‐mail listserv. A panel of PEM experts and survey methodologists designed the survey, which was reviewed for content validity by an independent panel of EM educators. We obtained data on current debriefing practices following pediatric critical events, PDs’ perceptions of ideal debriefing practices, and barriers to implementation. Data were analyzed using descriptive statistics.ResultsA total of 109 PDs completed the survey (45% overall response rate). All respondents feel that debriefing pediatric critical events is useful. The majority of debriefings are initiated and led by emergency physicians as informal meetings shortly following a critical event. Debriefings are most commonly held following a patient death, although PDs feel that debriefings should also occur for other specific patient scenarios (e.g., child abuse). Barriers to debriefing include timing, scheduling, location, discomfort with debriefing, participant buy‐in, and leader buy‐in.ConclusionsProgram leaders in both EM and PEM believe that debriefing after pediatric critical events is important for training. Barriers to debriefing specific to the ED setting should be explored to optimize the implementation of this practice.
The development and testing of a tool to assess joint health and safety committee functioning and effectiveness
Authors: Nichol Kathryn , Kudla Irena , Robson Lynda , Hon Chun‐Yip , Eriksson Jonas , Holness D. Linn 
Published: February 2017

BackgroundConcern regarding functioning and effectiveness of joint health and safety committees (JHSCs) in Ontario hospitals was raised following the Severe Acute Respiratory Syndrome outbreak in 2003. A subsequent literature review revealed a lack of studies focused within the healthcare sector.MethodsA tool to measure JHSC effectiveness was developed by a panel of occupational health and safety experts based on a framework from the healthcare sector. Usability testing was conducted in two phases with members of five hospital JHSCs before, during and after a committee meeting.ResultsUsability of the tool was scored high overall with an average of > 4 on a 5 point scale across twelve items. Downward adjustment of self‐assessment scores was reported following JHSC meetings.ConclusionFindings demonstrated that the tool was easy to use, effective in supporting discussion and in assisting participants in reaching consensus on rating a large number of JHSC characteristics. Am. J. Ind. Med. 60:368–376, 2017. © 2017 Wiley Periodicals, Inc.
Möbius Aromatic [28]Hexaphyrin Germanium(IV) and Tin(IV) Complexes: Efficient Formation of Triplet Excited States
Authors: Izawa Mondo , Kim Taeyeon , Ishida Shin‐ichiro , Tanaka Takayuki , Mori Tadashi , Kim Dongho , Osuka Atsuhiro 
Published: February 2017

Abstract[28]Hexaphyrin GeIV and SnIV complexes were synthesized in high yields by reactions of [28]hexaphyrin with GeCl4 or SnCl4 in the presence of triethylamine. Both complexes display distinct 28π Möbius aromatic character and possess a trigonal bipyramidal geometry at the central GeIV or SnIV atom. The equatorial hydroxy group of the GeIV complex was smoothly exchanged with neutral nucleophiles, such as phenol derivatives and thiophenol, with retention of configuration. In the SnIV complex, intersystem crossing to the T1 state is remarkably enhanced owing to the effective heavy‐atom effect, thus allowing the formation of the T1 state in high yield. The T1 states of the GeIV and SnVI complexes were found to be antiaromatic on the basis of the transient absorption features in line with the Baird rule.
Reconstruction of a Palaeosurface and Archaeological Site Location in an Anthropogenic Drift Sand Area
Authors: Schneider Anna , Hirsch Florian , Wechler Klaus‐Peter , Raab Alexandra , Raab Thomas 
Published: February 2017

AbstractKnowledge of the position of archaeological remains in the surface relief provides important basic information for archaeological survey design and interpretation. Geomorphological processes in (pre)history may have resulted in a modification of the local relief around archaeological sites, especially in areas that are prone to sediment erosion and relocation, such as sheet sand and dune landscapes. In this study, we reconstructed and analysed the palaeorelief of an archaeological excavation site in an inland dune area in southern Brandenburg, Germany. The remains of two Mesolithic sites were documented in the archaeological excavations and found to be associated with a buried soil horizon. To gather information on the relief of the buried soil surface, we used a combination of sedimentological and pedological profile descriptions along archaeological survey trenches and geophysical prospection with ground penetrating radar supplemented with microdrone photography and photogrammetry, global positioning system (GPS) surveys, and analysis of LiDAR‐based elevation models. A digital elevation model of the buried surface was generated and analysed using a geographical information system (GIS). A comparison of the palaeosurface model with the recent surface elevation model shows that sand remobilization resulted in a considerable reshaping of the relief. Further, an analysis of the buried surface model shows that the relief position of the two archaeological sites in the study area was considerably more prominent in relation to the corresponding buried soil surface than in relation to the recent surface morphology. The results affirm the significance of Holocene sediment relocation for the local surface morphology and the importance of considering such relief modifications in archaeological surveys. Copyright © 2017 John Wiley & Sons, Ltd.
Exo‐exo synergy between Cel6A and Cel7A from Hypocrea jecorina: Role of carbohydrate binding module and the endo‐lytic character of the enzymes
Authors: Badino Silke F. , Christensen Stefan J. , Kari Jeppe , Windahl Michael S. , Hvidt Søren , Borch Kim , Westh Peter 
Published: February 2017

ABSTRACTSynergy between cellulolytic enzymes is essential in both natural and industrial breakdown of biomass. In addition to synergy between endo‐ and exo‐lytic enzymes, a lesser known but equally conspicuous synergy occurs among exo‐acting, processive cellobiohydrolases (CBHs) such as Cel7A and Cel6A from Hypocrea jecorina. We studied this system using microcrystalline cellulose as substrate and found a degree of synergy between 1.3 and 2.2 depending on the experimental conditions. Synergy between enzyme variants without the carbohydrate binding module (CBM) and its linker was strongly reduced compared to the wild types. One plausible interpretation of this is that exo‐exo synergy depends on the targeting role of the CBM. Many earlier works have proposed that exo‐exo synergy was caused by an auxiliary endo‐lytic activity of Cel6A. However, biochemical data from different assays suggested that the endo‐lytic activity of both Cel6A and Cel7A were 103–104 times lower than the common endoglucanase, Cel7B, from the same organism. Moreover, the endo‐lytic activity of Cel7A was 2–3‐fold higher than for Cel6A, and we suggest that endo‐like activity of Cel6A cannot be the main cause for the observed synergy. Rather, we suggest the exo‐exo synergy found here depends on different specificities of the enzymes possibly governed by their CBMs. Biotechnol. Bioeng. 2017;114: 1639–1647. © 2017 Wiley Periodicals, Inc.
Concentration of Nitric Acid Strongly Influences Chemical Composition of Graphite Oxide
Authors: Jankovský Ondřej , Nováček Michal , Luxa Jan , Sedmidubský David , Boháčová Marie , Pumera Martin , Sofer Zdeněk 
Published: February 2017

AbstractGraphite oxide is the most widely used precursor for the synthesis of graphene through top‐down methods. We demonstrate a significant influence of nitric acid concentration on the structure and composition of the graphite oxide prepared by graphite oxidation. In general, two main chlorate‐based oxidation methods are currently used for graphite oxide synthesis: the Staudenmaier method using 98 wt % nitric acid, and the Hofmann method with 68 wt % nitric acid. However, a gradual change in nitric acid concentration allows a continuous change in the graphite oxide composition. The prepared samples are thoroughly characterised by microscopic techniques as well as various spectroscopic and analytical methods. Lowering the nitric acid concentration leads to an increase in oxidation degree, and in particular, to the concentration of epoxy and hydroxyl groups. This knowledge is not only useful for the large‐scale synthesis of graphite oxide with tuneable size and chemical composition, but the use of nitric acid in lower concentrations can also reduce the overall cost of the synthesis significantly.
Validity and utility of the DSM‐5 severity specifier for binge‐eating disorder
Authors: Dakanalis Antonios , Colmegna Fabrizia , Riva Giuseppe , Clerici Massimo 
Published: February 2017

AbstractObjectiveTo test both the concurrent and predictive significance of the new DSM‐5 severity specifier for binge‐eating disorder (BED) in adult outpatients.MethodExisting data from 195 adults with DSM‐5 BED who received evidence‐based treatment (manual‐based cognitive‐behavioral therapy) in an outpatient setting were re‐analysed to examine whether these patients sub‐grouped according to the DSM‐5 severity levels, defined by the frequency of binge‐eating (BE) episodes, would show meaningful differences in a range of variables of clinical interest assessed at pre‐treatment and end‐of treatment abstinence from BE.ResultsParticipants categorized with mild (33.3% of the sample), moderate (35.4%), severe (15.9%), and extreme (15.4%) severity of BED, based on their pre‐treatment clinician‐rated frequency of BE episodes, differed significantly from each other in physical characteristics (body mass index) and another sixteen variables of clinical interest assessed at pre‐treatment regarding eating disorder psychopathology and putative maintenance factors, lifetime and current psychiatric disorder comorbidity, general psychiatric distress, and psychosocial impairment. The four DSM‐5 severity groups were statistically indistinguishable in demographics or age‐of‐BED onset. However, significant between‐group differences were observed in the treatment outcome, i.e., abstinence from BE, achieved by 98.5%, 66.7%, 38.7% and 6.7% of participants categorized with mild, moderate, severe, and extreme severity respectively. The outcome analyses repeated in the completer sample (n = 187) yielded the same pattern of the aforementioned intent‐to‐treat (N = 195) results.DiscussionThe findings provide support for the severity specifier for BED introduced in the DSM‐5 as a means of addressing within‐group variability in severity.