bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunization practices among pediatric transplant hepatologists
Authors: Feldman Amy G. , Kempe Allison , Beaty Brenda L. , Sundaram Shikha S. ,   the Studies of Pediatric Liver Transplantation (SPLIT) Research Group
Published: July 2016

AbstractVaccination of pediatric liver transplant candidates and recipients represents an opportunity to decrease infectious complications following transplant. Although vaccine recommendations exist, studies have shown that many transplant candidates and recipients are under‐immunized. The goals of this study were to assess among pediatric transplant hepatologists: (i) current immunization practices before and after transplantation, (ii) involvement of an ID physician in the transplant evaluation, and (iii) perceptions about vaccine safety and barriers to immunization. An 80‐item e‐mail survey of pediatric transplant hepatologists at centers in the United States and Canada participating in the SPLIT consortium was conducted from December 2014 to March 2015. The overall response rate was 80% (73/91), representing 97% (32/33) of SPLIT centers. Fifty percent of programs routinely involved an ID physician in the transplant evaluation. Administration of palivizumab was routinely considered by 48% of hepatologists pre‐transplant and by 41% post‐transplant. Live vaccines were recommended by 26% of hepatologists after transplant. About 10% of hepatologists reported concern that live vaccines after transplant could induce rejection. There is wide variation in immunization practices among transplant hepatologists. Specific evidence‐based protocols are needed to guide immunization practices in transplant candidates and recipients.
Decomposing mechanisms of abnormal saccade generation in schizophrenia patients: Contributions of volitional initiation, motor preparation, and fixation release
Authors: Reuter Benedikt , Elsner Björn , Möllers David , Kathmann Norbert 
Published: July 2016

AbstractClinical and theoretical models suggest deficient volitional initiation of action in schizophrenia patients. Recent research provided an experimental model of testing this assumption using saccade tasks. However, inconsistent findings necessitate a specification of conditions on which the deficit may occur. The present study sought to detect mechanisms that may contribute to poor performance. Sixteen schizophrenia patients and 16 healthy control participants performed visually guided and two types of volitional saccade tasks. All tasks varied as to whether the initial fixation stimulus disappeared (fixation stimulus offset) or continued during saccade initiation, and whether a direction cue allowed motor preparation of the specific saccade. Saccade latencies of the two groups were differentially affected by task type, fixation stimulus offset, and cueing, suggesting abnormal volitional saccade generation, fixation release, and motor preparation in schizophrenia. However, substantial performance deficits may only occur if all affected processes are required in a task.
Three‐dimensional architecture and hydrostratigraphy of cross‐cutting buried valleys using airborne electromagnetics, glaciated Central Lowlands, Nebraska, USA
Authors: Korus Jesse T. , Joeckel R. Matt , Divine Dana P. , Abraham Jared D. 
Published: July 2016

AbstractBuried valleys are characteristic features of glaciated landscapes, and their deposits host important aquifers worldwide. Understanding the stratigraphic architecture of these deposits is essential for protecting groundwater and interpreting sedimentary processes in subglacial and ice‐marginal environments. The relationships between depositional architecture, topography and hydrostratigraphy in dissected, pre‐Illinoian till sheets is poorly understood. Boreholes alone are inadequate to characterize the complex geology of buried valleys, but airborne electromagnetic surveys have proven useful for this purpose. A key question is whether the sedimentary architecture of buried valleys can be interpreted from airborne electromagnetic profiles. This study employs airborne electromagnetic resistivity profiles to interpret the three‐dimensional sedimentary architecture of cross‐cutting buried valleys in a ca 400 km2 area along the western margin of Laurentide glaciation in North America. A progenitor bedrock valley is succeeded by at least five generations of tunnel valleys that become progressively younger northward. Tunnel‐valley infills are highly variable, reflecting under‐filled and over‐filled conditions. Under‐filled tunnel valleys are expressed on the modern landscape and contain fine sediments that act as hydraulic barriers. Over‐filled tunnel valleys are not recognized in the modern landscape, but where they are present they form hydraulic windows between deep aquifer units and the land surface. The interpretation of tunnel‐valley genesis herein provides evidence of the relationships between depositional processes and glacial landforms in a dissected, pre‐Illinoian till sheet, and contributes to the understanding of the complex physical hydrology of glacial aquifers in general.
Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance
Authors: Sardi Maria , Rovinskiy Nikolay , Zhang Yaoping , Gasch Audrey P. 
Published: July 2016

ABSTRACTA major obstacle to sustainable lignocellulosic biofuel production is microbe inhibition by the combinatorial stresses in pretreated plant hydrolysate. Chemical biomass pretreatment releases a suite of toxins that interact with other stressors, including high osmolarity and temperature, which together can have poorly understood synergistic effects on cells. Improving tolerance in industrial strains has been hindered, in part because the mechanisms of tolerance reported in the literature often fail to recapitulate in other strain backgrounds. Here, we explored and then exploited variations in stress tolerance, toxin-induced transcriptomic responses, and fitness effects of gene overexpression in differentSaccharomyces cerevisiae(yeast) strains to identify genes and processes linked to tolerance of hydrolysate stressors. Using six differentS. cerevisiaestrains that together maximized phenotypic and genetic diversity, first we explored transcriptomic differences between resistant and sensitive strains to identify common and strain-specific responses. This comparative analysis implicated primary cellular targets of hydrolysate toxins, secondary effects of defective defense strategies, and mechanisms of tolerance. Dissecting the responses to individual hydrolysate components across strains pointed to synergistic interactions between osmolarity, pH, hydrolysate toxins, and nutrient composition. By characterizing the effects of high-copy gene overexpression in three different strains, we revealed the breadth of the background-specific effects of gene fitness contributions in synthetic hydrolysate. Our approach identified new genes for engineering improved stress tolerance in diverse strains while illuminating the effects of genetic background on molecular mechanisms.IMPORTANCERecent studies on natural variation withinSaccharomyces cerevisiaehave uncovered substantial phenotypic diversity. Here, we took advantage of this diversity, using it as a tool to infer the effects of combinatorial stress found in lignocellulosic hydrolysate. By comparing sensitive and tolerant strains, we implicated primary cellular targets of hydrolysate toxins and elucidated the physiological states of cells when exposed to this stress. We also explored the strain-specific effects of gene overexpression to further identify strain-specific responses to hydrolysate stresses and to identify genes that improve hydrolysate tolerance independent of strain background. This study underscores the importance of studying multiple strains to understand the effects of hydrolysate stress and provides a method to find genes that improve tolerance across strain backgrounds.
Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities
Authors: Bradley Ian M. , Pinto Ameet J. , Guest Jeremy S. 
Published: July 2016

ABSTRACT
The use of high-throughput sequencing technologies with the 16S rRNA gene for characterization of bacterial and archaeal communities has become routine. However, the adoption of sequencing methods for eukaryotes has been slow, despite their significance to natural and engineered systems. There are large variations among the target genes used for amplicon sequencing, and for the 18S rRNA gene, there is no consensus on which hypervariable region provides the most suitable representation of diversity. Additionally, it is unclear how much PCR/sequencing bias affects the depiction of community structure using current primers. The present study amplified the V4 and V8-V9 regions from seven microalgal mock communities as well as eukaryotic communities from freshwater, coastal, and wastewater samples to examine the effect of PCR/sequencing bias on community structure and membership. We found that degeneracies on the 3′ end of the current V4-specific primers impact read length and mean relative abundance. Furthermore, the PCR/sequencing error is markedly higher for GC-rich members than for communities with balanced GC content. Importantly, the V4 region failed to reliably capture 2 of the 12 mock community members, and the V8-V9 hypervariable region more accurately represents mean relative abundance and alpha and beta diversity. Overall, the V4 and V8-V9 regions show similar community representations over freshwater, coastal, and wastewater environments, but specific samples show markedly different communities. These results indicate that multiple primer sets may be advantageous for gaining a more complete understanding of community structure and highlight the importance of including mock communities composed of species of interest.

IMPORTANCE
The quantification of error associated with community representation by amplicon sequencing is a critical challenge that is often ignored. When target genes are amplified using currently available primers, differential amplification efficiencies result in inaccurate estimates of community structure. The extent to which amplification bias affects community representation and the accuracy with which different gene targets represent community structure are not known. As a result, there is no consensus on which region provides the most suitable representation of diversity for eukaryotes. This study determined the accuracy with which commonly used 18S rRNA gene primer sets represent community structure and identified particular biases related to PCR amplification and Illumina MiSeq sequencing in order to more accurately study eukaryotic microbial communities.
Humanized Monoclonal Antibody That Passively Protects Mice against Systemic and Intranasal Ricin Toxin Challenge
Authors: Van Slyke Greta , Sully Erin K. , Bohorova Natasha , Bohorov Ognian , Kim Do , Pauly Michael H. , Whaley Kevin J. , Zeitlin Larry , Mantis Nicholas J. 
Published: July 2016

ABSTRACT

PB10 is a murine monoclonal antibody against an immunodominant epitope on ricin toxin's enzymatic subunit. Here, we characterize a fully humanized version of PB10 IgG1 (hPB10) and demonstrate that it has potent
in vitro
and
in vivo
toxin-neutralizing activities. We also report the minimum serum concentrations of hPB10 required to protect mice against 10 times the 50% lethal dose of ricin when delivered by injection and inhalation.
Pleistocene onset of rapid, punctuated exhumation in the eastern Central Range of the Taiwan orogenic belt
Authors: Hsu Wei-Hao , Byrne Timothy B. , Ouimet William , Lee Yuan-Hsi , Chen Yue-Gau , Soest Matthijs van , Hodges Kip 
Published: July 2016

Abstract
The Taiwan orogenic belt is often treated as a steady, southward-propagating orogenic system with an essentially constant erosion rate of 4–6 mm/yr over the past 5 m.y. We present 4 new age-elevation transects from the Central Range based on 19 new and 86 previously published fission track and (U-Th)/He dates of completely reset detrital zircon and apatite grains. The age-elevation curves and thermal models imply slow cooling prior to ca. 2–1.5 Ma (at exhumation rates of ∼0.1 mm/yr), an increase in exhumation rates from ca. 2–1.5 Ma to ca. 0.5 Ma (2–4 mm/yr), and possibly a further acceleration in exhumation from ca. 0.5 Ma to present (4–8 mm/yr). Three transects from three different latitudes in the eastern Central Range yield similar results, each showing punctuated exhumation with progressively faster rates.
The Thor suture zone: From subduction to intraplate basin setting
Authors: Smit Jeroen , Wees Jan-Diederik van , Cloetingh Sierd 
Published: July 2016

Abstract
The crustal seismic velocity structure of northwestern Europe shows a low P-wave velocity zone (LVZ) in the lower crust along the Caledonian Thor suture zone (TSZ) that cannot be easily attributed to Avalonia or Baltica plates abutting the TSZ. The LVZ appears to correspond to a hitherto unrecognized crustal segment (accretionary complex) that separates Avalonia from Baltica, explaining well the absence of Avalonia further east. Consequently, the northern boundary of Avalonia is shifted ∼150 km southward. Our interpretation, based on analysis of deep seismic profiles, places the LVZ in a consistent crustal domain interpretation. A comparison with present-day examples of the Kuril and Cascadia subduction zones suggests that the LVZ separating Avalonia from Baltica is composed of remnants of the Caledonian accretionary complex. If so, the present-day geometry probably originates from pre-Variscan extension and eduction during Devonian–Carboniferous backarc extension. The reinterpretation of deep crustal zonation provides a crustal framework in which the northern limit of Avalonia corresponds to the southern limit of the deep North German Basin and the northern limit of prolific gas reservoirs and late Mesozoic inversion structures.
Formation of a future supercontinent through plate motion–driven flow coupled with mantle downwelling flow
Authors: Yoshida Masaki 
Published: July 2016

Abstract
Series of high-resolution numerical simulations of three-dimensional mantle convection were performed to examine the interaction between the drifting continental lithospheres and the underlying mantle structure for 250 m.y. from the present, and to predict the configuration of the future supercontinent. The density anomaly of the mantle interior was determined by the seismic velocity anomaly from global seismic tomography data sets, which contain well-resolved subducting slabs. The present-day plate motion was imposed for the first stage of the simulation as a velocity boundary condition at the top surface boundary, instead of a shear stress–free condition. The switching time from the plate motion boundary to shear stress–free conditions was taken as a free parameter. The results revealed that Australia, Eurasia, North America, and Africa will merge together in the Northern Hemisphere to form a new supercontinent within ∼250 m.y. from the present. The continental drift was assumed to be realized by plate-scale mantle flow, rather than large-scale upwelling plumes. That is, continuously moving plates at the surface for the first stage of the simulation are mechanically coupled with the subducting slabs in the mantle; this enhances the underlying mantle downwelling flow. As a result, persistent continental drift can be reproduced for long future time periods even though top surface boundary conditions may switch in response to shear stress–free conditions. The configuration of the numerically reproduced future supercontinent in this study is broadly consistent with the hypothetical model of Amasia as indicated by previous findings from geological correlations and a paleogeographic reconstruction.
Rifting under steam—How rift magmatism triggers methane venting from sedimentary basins
Authors: Berndt C. , Hensen C. , Mortera-Gutierrez C. , Sarkar S. , Geilert S. , Schmidt M. , Liebetrau V. , Kipfer R. , Scholz F. , Doll M. , Muff S. , Karstens J. , Planke S. , Petersen S. , Böttner C. , Chi W.-C. , Moser M. , Behrendt R. , Fiskal A. , Lever M.A. , Su C.-C. , Deng L. , Brennwald M.S. , Lizarralde D. 
Published: July 2016

Abstract
During opening of a new ocean, magma intrudes into the surrounding sedimentary basins. Heat provided by the intrusions matures the host rock, creating metamorphic aureoles potentially releasing large amounts of hydrocarbons. These hydrocarbons may migrate to the seafloor in hydrothermal vent complexes in sufficient volumes to trigger global warming, e.g., during the Paleocene-Eocene Thermal Maximum (PETM). Mound structures at the top of buried hydrothermal vent complexes observed in seismic data off Norway were previously interpreted as sediment volcanoes, and the amount of released hydrocarbon was estimated based on this interpretation. Here, we present new geophysical and geochemical data from the Gulf of California suggesting that such mound structures could in fact be edifices constructed by the growth of black smoker–type chimneys rather than sediment volcanoes. We have evidence for two buried and one active hydrothermal vent systems outside the rift axis. The active vent releases fluids of several hundred degrees Celsius containing abundant methane, mid-ocean ridge basalt–type helium, and precipitating solids up to 300 m high into the water column. Our observations challenge the idea that methane is emitted slowly from rift-related vents. The association of large amounts of methane with hydrothermal fluids that enter the water column at high pressure and temperature provides an efficient mechanism to transport hydrocarbons into the water column and atmosphere, lending support to the hypothesis that rapid climate change such as during the PETM can be triggered by magmatic intrusions into organic-rich sedimentary basins.
Synchronous diversification of Laurentian and Baltic rhynchonelliform brachiopods: Implications for regional versus global triggers of the Great Ordovician Biodiversification Event
Authors: Trubovitz Sarah , Stigall Alycia L. 
Published: July 2016

Abstract
The profound global impact of marine radiations during the Great Ordovician Biodiversification Event (GOBE) is widely appreciated; however, diversification varied among paleocontinents and these individual trajectories are less understood. Here we present a new species-level diversity curve for rhynchonelliform brachiopods from midcontinental Laurentia based on bed-by-bed analysis of the Simpson Group of Oklahoma (USA). Diversity and abundance data span the Dapingian through Sandbian Stages, which encompass the interval of maximum global diversification. A rapid, statistically significant increase in brachiopod diversity was observed in the early Darriwilian Histiodella holodentata Biozone. We interpret this as a biological signal because the increase cannot be explained by sampling intensity, facies types, or position along depositional gradient. Diversifications on Laurentia and Baltica were temporally synchronous at the biozone level, and cumulative diversity curves for the regions show similar patterns, suggesting a global driver for the radiations. The taxonomic composition of the brachiopod faunas, however, differs substantially, highlighting the importance of regional controls on diversification. Thus both global and local factors controlled diversity increase during the GOBE.
SCISSOR—Spinal Cord Injury Study on Small molecule-derived Rho inhibition: a clinical study protocol
Authors: Kopp Marcel A , Liebscher Thomas , Watzlawick Ralf , Martus Peter , Laufer Stefan , Blex Christian , Schindler Ralf , Jungehulsing Gerhard J , Knüppel Sven , Kreutzträger Martin , Ekkernkamp Axel , Dirnagl Ulrich , Strittmatter Stephen M , Niedeggen Andreas , Schwab Jan M 
Published: July 2016

IntroductionThe approved analgesic and anti-inflammatory drugs ibuprofen and indometacin block the small GTPase RhoA, a key enzyme that impedes axonal sprouting after axonal damage. Inhibition of the Rho pathway in a central nervous system-effective manner requires higher dosages compared with orthodox cyclooxygenase-blocking effects. Preclinical studies on spinal cord injury (SCI) imply improved motor recovery after ibuprofen/indometacin-mediated Rho inhibition. This has been reassessed by a meta-analysis of the underlying experimental evidence, which indicates an overall effect size of 20.2% regarding motor outcome achieved after ibuprofen/indometacin treatment compared with vehicle controls. In addition, ibuprofen/indometacin may also limit sickness behaviour, non-neurogenic systemic inflammatory response syndrome (SIRS), neuropathic pain and heterotopic ossifications after SCI. Consequently, ‘small molecule’-mediated Rho inhibition after acute SCI warrants clinical investigation.Methods and analysisProtocol of an investigator-initiated clinical open-label pilot trial on high-dose ibuprofen treatment after acute traumatic, motor-complete SCI. A sample of n=12 patients will be enrolled in two cohorts treated with 2400 mg/day ibuprofen for 4 or 12 weeks, respectively. The primary safety end point is an occurrence of serious adverse events, primarily gastroduodenal bleedings. Secondary end points are pharmacokinetics, feasibility and preliminary effects on neurological recovery, neuropathic pain and heterotopic ossifications. The primary safety analysis is based on the incidence of severe gastrointestinal bleedings. Additional analyses will be mainly descriptive and casuistic.Ethics and disseminationThe clinical trial protocol was approved by the responsible German state Ethics Board, and the Federal Institute for Drugs and Medical Devices. The study complies with the Declaration of Helsinki, the principles of Good Clinical Practice and all further applicable regulations. This safety and pharmacokinetics trial informs the planning of a subsequent randomised controlled trial. Regardless of the result of the primary and secondary outcome assessments, the clinical trial will be reported as a publication in a peer-reviewed journal.Trial registration numberNCT02096913; Pre-results.