bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do‐Not‐Hospitalize Orders for Individuals with Advanced Dementia: Healthcare Proxies' Perspectives
Authors: Mann Elizabeth , Goff Sarah L. , Colon‐Cartagena Wanda , Bellantonio Sandra , Rothberg Michael B. 
Published: July 2013

ObjectivesTo determine how well healthcare proxies (HCPs) understand do‐not‐hospitalize (DNH) orders and why they may or may not initiate them.DesignSemistructured qualitative interviews.SettingTwo nursing homes in western Massachusetts.ParticipantsHCPs of nursing home residents with advanced dementia.MeasurementIn‐depth interviews were audiotaped and transcribed verbatim. Data were qualitatively analyzed in an iterative process, and emergent concepts were conceptually ordered into explanatory categories. Pertinent demographic and clinical information was collected from the Minimum Data Set (MDS) and patient charts.ResultsSixteen of 31 eligible HCPs were interviewed. Major findings included barriers to and facilitators of initiating DNH orders. Barriers included a perceived lack of physician involvement in decision‐making and limited understanding of DNH orders and the resident's prognosis. Facilitators included a HCPs' personal experience in health care, understanding the prognosis of advanced dementia, and a desire to limit resident distress.ConclusionThe potential barriers to and facilitators of HCPs initiating DNH orders identified in this study suggest that HCPs may benefit from more in‐depth discussions with healthcare providers when making this decision. Interventions to address these barriers may improve the capacity of HCPs to make informed decisions about DNH orders that reflect individuals' values and wishes.
Quick‐and‐clean article figures with FigureJ
Authors: MUTTERER J. , ZINCK E. 
Published: July 2013

SummaryWe created FigureJ a new ImageJ plugin dedicated to scientific article figures preparation. Building a convincing figure is a demanding task that covers different steps ranging from content acquisition to figure assembly in editing software. Notions of image processing are required when it comes to even simple tasks such as cropping or resizing images and assembling them in a single figure. Scientific images are typically well handled in dedicated software but poorly supported in software used for laying out the final version of a figure for submission to review process.
The Effect of Variations in Translucency and Background on Color Differences in CAD/CAM Lithium Disilicate Glass Ceramics
Authors: Al Ben Ali Abdulaziz , Kang Kiho , Finkelman Matthew D. , Zandparsa Roya , Hirayama Hiroshi 
Published: July 2013

AbstractPurposeThe purpose of this study was to compare the effect of variations in translucency and background on color differences (ΔE) for different shades of computer‐aided design and computer‐aided manufacturing (CAD/CAM) lithium disilicate glass ceramics.Materials and MethodsA pilot study suggested n = 10 as an appropriate sample size for the number of lithium disilicate glass ceramic cylinders per group. High‐transparency (HT) and low‐transparency (LT) cylinders (diameter, 12 mm; length, 13 mm) were fabricated in three ceramic shades (BL1, A2, C3) using CAD/CAM technology and were cut into specimen disks (thickness, 1.2 mm; diameter, 12 mm) for placement on Natural Die (ND1 and ND4) backgrounds. Four combinations of translucency and background color were evaluated in terms of color differences for the three ceramic shades: group 1 (HT ND1, reference), group 2 (HT ND4), group 3 (LT ND1), and group 4 (LT ND4). A spectrophotometer was used to measure the color differences. Nonparametric tests (Kruskal‐Wallis tests) were used to evaluate the color differences among the tested groups, and Mann‐Whitney U tests with Bonferroni correction were used as post hoc tests. Furthermore, for each ceramic shade, the HT groups were compared to the LT groups using the Mann‐Whitney U test.ResultsSignificant differences were present among the tested groups of the same ceramic shade (p < 0.001). The highest ΔE values were observed in the HT ND4 group for BL1, while the lowest ΔE values were found in the LT ND1 group for both A2 and C3. Further, the HT groups and the groups with a darker background (ND4) showed increased ΔE values compared with the other groups (p < 0.001).ConclusionsWithin the limitations of this study, the results suggested that the translucency and background color significantly influenced the lithium disilicate glass ceramic color among the BL1, A2, and C3 ceramic shades. Changing the underlying color from a lighter background to a darker background resulted in increased color differences.
Making Linguistics Matter: Building on the Public's Interest in Language
Authors: Purnell Thomas , Raimy Eric , Salmons Joseph 
Published: July 2013

AbstractLinguists in the United States are acutely aware of the need to engage the public about their work in new and better ways. We describe here our effort to take up that challenge in Wisconsin by building a set of outreach projects that connect with communities throughout the state and that focus on issues of importance to particular audiences. Through these projects, we have become convinced that outreach, teaching, and research — treated separately and distinctly for academic evaluation — are inextricably linked, often to the point of being indistinguishable in practice.
Creole Speakers and Standard Language Education
Authors: Wigglesworth Gillian , Billington Rosey , Loakes Deborah 
Published: July 2013

AbstractSpeakers of creole languages experience educational disadvantage in schools that teach in the standard language of their region, but there remain many misconceptions about why this is the case and how best to facilitate academic improvement, despite research demonstrating that actively using creoles in the classroom leads to a range of positive outcomes for these students. This paper reviews how attitudes towards creoles influence their place in educational contexts, some of the challenges for research on creoles in education, approaches to teaching creole‐speaking children with particular reference to bilingual programs, and the ramifications of standardized testing for creole‐speaking students.
A metabolic gene cluster in Lotus japonicus discloses novel enzyme functions and products in triterpene biosynthesis
Authors: Krokida Afrodite , Delis Costas , Geisler Katrin , Garagounis Constantine , Tsikou Daniela , Peña‐Rodríguez Luis M. , Katsarou Dimitra , Field Ben , Osbourn Anne E. , Papadopoulou Kalliope K. 
Published: July 2013

Summary

Genes for triterpene biosynthetic pathways exist as metabolic gene clusters in oat and Arabidopsis thaliana plants. We characterized the presence of an analogous gene cluster in the model legume Lotus japonicus.

In the genomic regions flanking the oxidosqualene cyclase AMY2 gene, genes for two different classes of cytochrome P450 and a gene predicted to encode a reductase were identified. Functional characterization of the cluster genes was pursued by heterologous expression in Nicotiana benthamiana. The gene expression pattern was studied under different developmental and environmental conditions. The physiological role of the gene cluster in nodulation and plant development was studied in knockdown experiments.

A novel triterpene structure, dihydrolupeol, was produced by AMY2. A new plant cytochrome P450, CYP71D353, which catalyses the formation of 20‐hydroxybetulinic acid in a sequential three‐step oxidation of 20‐hydroxylupeol was characterized. The genes within the cluster are highly co‐expressed during root and nodule development, in hormone‐treated plants and under various environmental stresses. A transcriptional gene silencing mechanism that appears to be involved in the regulation of the cluster genes was also revealed.

A tightly co‐regulated cluster of functionally related genes is involved in legume triterpene biosynthesis, with a possible role in plant development.
Multilocus Sequence Typing Reveals Evidence of Homologous Recombination Linked to Antibiotic Resistance in the Genus Salinispora
Authors: Freel Kelle C. , Millán-Aguiñaga Natalie , Jensen Paul R. 
Published: July 2013

ABSTRACT

The three closely related species that currently comprise the genus
Salinispora
were analyzed using a multilocus sequence typing approach targeting 48 strains derived from four geographic locations. Phylogenetic congruence and a well-supported concatenated tree provide strong support for the delineation of the three species as currently described and the basal relationship of
Salinispora arenicola
to the more recently diverged sister taxa
S. tropica
and
S. pacifica
. The phylogeny of the initial region of the
rpoB
gene sequenced was atypical, placing the related genera
Micromonospora
and
Verrucosispora
within the
Salinispora
clade. This phylogenetic incongruence was subsequently ascribed to a homologous-recombination event in a portion of the gene associated with resistance to compounds in the rifamycin class, which target RpoB. All
S. arenicola
strains produced compounds in this class and possessed resistance-conferring amino acid changes in RpoB. The phylogeny of a region of the
rpoB
gene that is not associated with rifamycin resistance was congruent with the other housekeeping genes. The link between antibiotic resistance and homologous recombination suggests that incongruent phylogenies provide opportunities to identify the molecular targets of secondary metabolites, an observation with potential relevance for drug discovery efforts. Low ratios of interspecies recombination to mutation, even among cooccurring strains, coupled with high levels of within-species recombination suggest that the three species have been described in accordance with natural barriers to recombination.
Investigation of Malic Acid Production in Aspergillus oryzae under Nitrogen Starvation Conditions
Authors: Knuf Christoph , Nookaew Intawat , Brown Stephen H. , McCulloch Michael , Berry Alan , Nielsen Jens 
Published: July 2013

ABSTRACTMalic acid has great potential for replacing petrochemical building blocks in the future. For this application, high yields, rates, and titers are essential in order to sustain a viable biotechnological production process. Natural high-capacity malic acid producers like the malic acid producerAspergillus flavushave so far been disqualified because of special growth requirements or the production of mycotoxins. AsA. oryzaeis a very close relative or even an ecotype ofA. flavus, it is likely that its high malic acid production capabilities with a generally regarded as safe (GRAS) status may be combined with already existing large-scale fermentation experience. In order to verify the malic acid production potential, two wild-type strains, NRRL3485 and NRRL3488, were compared in shake flasks. As NRRL3488 showed a volumetric production rate twice as high as that of NRRL3485, this strain was selected for further investigation of the influence of two different nitrogen sources on malic acid secretion. The cultivation in lab-scale fermentors resulted in a higher final titer, 30.27 ± 1.05 g liter−1, using peptone than the one of 22.27 ± 0.46 g liter−1obtained when ammonium was used. Through transcriptome analysis, a binding site similar to the one of theSaccharomyces cerevisiaeyeast transcription factor Msn2/4 was identified in the upstream regions of glycolytic genes and the cytosolic malic acid production pathway from pyruvate via oxaloacetate to malate, which suggests that malic acid production is a stress response. Furthermore, the pyruvate carboxylase reaction was identified as a target for metabolic engineering, after it was confirmed to be transcriptionally regulated through the correlation of intracellular fluxes and transcriptional changes.
Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis
Authors: Russell Calum W. , Bouvaine Sophie , Newell Peter D. , Douglas Angela E. 
Published: July 2013

ABSTRACT

The symbiotic bacterium
Buchnera aphidicola
lacks key genes in the biosynthesis of five essential amino acids (EAAs), and yet its animal hosts (aphids) depend on the symbiosis for the synthesis of these EAAs (isoleucine, leucine, methionine, phenylalanine, and valine). We tested the hypothesis, derived from genome annotation, that the missing
Buchnera
reactions are mediated by host enzymes, with the exchange of metabolic intermediates between the partners. The specialized host cells bearing
Buchnera
were separated into a
Buchnera
fraction and a
Buchnera
-free host cell fraction (HF). Addition of HF to isolated
Buchnera
preparations significantly increased the production of leucine and phenylalanine, and recombinant enzymes mediating the final reactions in branched-chain amino acid and phenylalanine synthesis rescued the production of these EAAs by
Buchnera
preparations without HF. The likely precursors for the missing proximal reactions in isoleucine and methionine synthesis were identified, and they differed from predictions based on genome annotations: synthesis of 2-oxobutanoate, the aphid-derived precursor of isoleucine synthesis, was stimulated by homoserine and not threonine via threonine dehydratase, and production of the homocysteine precursor of methionine was driven by cystathionine, not cysteine, via reversal of the transsulfuration pathway. The evolution of shared metabolic pathways in this symbiosis can be attributed to host compensation for genomic deterioration in the symbiont, involving changes in host gene expression networks to recruit specific enzymes to the host cell.
Construction of a Prophage-Free Variant of Corynebacterium glutamicum ATCC 13032 for Use as a Platform Strain for Basic Research and Industrial Biotechnology
Authors: Baumgart Meike , Unthan Simon , Rückert Christian , Sivalingam Jasintha , Grünberger Alexander , Kalinowski Jörn , Bott Michael , Noack Stephan , Frunzke Julia 
Published: July 2013

ABSTRACT

The activity of bacteriophages and phage-related mobile elements is a major source for genome rearrangements and genetic instability of their bacterial hosts. The genome of the industrial amino acid producer
Corynebacterium glutamicum
ATCC 13032 contains three prophages (CGP1, CGP2, and CGP3) of so far unknown functionality. Several phage genes are regularly expressed, and the large prophage CGP3 (∼190 kbp) has recently been shown to be induced under certain stress conditions. Here, we present the construction of MB001, a prophage-free variant of
C. glutamicum
ATCC 13032 with a 6% reduced genome. This strain does not show any unfavorable properties during extensive phenotypic characterization under various standard and stress conditions. As expected, we observed improved growth and fitness of MB001 under SOS-response-inducing conditions that trigger CGP3 induction in the wild-type strain. Further studies revealed that MB001 has a significantly increased transformation efficiency and produced about 30% more of the heterologous model protein enhanced yellow fluorescent protein (eYFP), presumably as a consequence of an increased plasmid copy number. These effects were attributed to the loss of the restriction-modification system (cg1996-cg1998) located within CGP3. The deletion of the prophages without any negative effect results in a novel platform strain for metabolic engineering and represents a useful step toward the construction of a
C. glutamicum
chassis genome of strain ATCC 13032 for biotechnological applications and synthetic biology.
Comparative Proteome Analysis of Spontaneous Outer Membrane Vesicles and Purified Outer Membranes of Neisseria meningitidis
Authors: Lappann Martin , Otto Andreas , Becher Dörte , Vogel Ulrich 
Published: July 2013

ABSTRACT

Outer membrane vesicles (OMVs) of Gram-negative bacteria receive increasing attention because of various biological functions and their use as vaccines. However, the mechanisms of OMV release and selective sorting of proteins into OMVs remain unclear. Comprehensive quantitative proteome comparisons between spontaneous OMVs (SOMVs) and the outer membrane (OM) have not been conducted so far. Here, we established a protocol for metabolic labeling of neisserial proteins with
15
N. SOMV and OM proteins labeled with
15
N were used as an internal standard for proteomic comparison of the SOMVs and OMs of two different strains. This labeling approach, coupled with high-sensitivity mass spectrometry, allowed us to comprehensively unravel the proteome of the SOMVs and OMs. We quantified the relative distribution of 155 proteins between SOMVs and the OM. Complement regulatory proteins, autotransporters, proteins involved in iron and zinc acquisition, and a two-partner secretion system were enriched in SOMVs. The highly abundant porins PorA and PorB and proteins connecting the OM with peptidoglycan or the inner membrane, such as RmpM, MtrE, and PilQ, were depleted in SOMVs. Furthermore, the three lytic transglycosylases MltA, MltB, and Slt were less abundant in SOMVs. In conclusion, SOMVs are likely to be released from surface areas with a low local abundance of membrane-anchoring proteins and lytic transglycosylases. The enrichment of complement regulatory proteins, autotransporters, and trace metal binding and transport proteins needs to be explored in the context of the pathogenesis of meningococcal disease.
Ship-Based Observations of the Diurnal Cycle of Southeast Pacific Marine Stratocumulus Clouds and Precipitation
Authors: Burleyson Casey D. , de Szoeke Simon P. , Yuter Sandra E. , Wilbanks Matt , Brewer W. Alan 
Published: July 2013

Abstract
The diurnal cycle of marine stratocumulus in cloud-topped boundary layers is examined using ship-based meteorological data obtained during the 2008 Variability of American Monsoon Systems (VAMOS) Ocean–Cloud–Atmosphere–Land Study Regional Experiment (VOCALS-REx). The high temporal and spatial continuity of the ship data, as well as the 31-day sample size, allows the diurnal transition in degree of coupling of the stratocumulus-topped boundary layer to be resolved. The amplitude of diurnal variation was comparable to the magnitude of longitudinal differences between regions east and west of 80°W for most of the cloud, surface, and precipitation variables examined. The diurnal cycle of precipitation is examined in terms of areal coverage, number of drizzle cells, and estimated rain rate. East of 80°W, the drizzle cell frequency and drizzle area peaks just prior to sunrise. West of 80°W, total drizzle area peaks at 0300 local solar time (LST), 2–3 h before sunrise. Peak drizzle cell frequency is 3 times higher west of 80°W compared to east of 80°W. The waning of drizzle several hours prior to the ramp up of shortwave fluxes may be related to the higher peak drizzle frequencies in the west. The ensemble effect of localized subcloud evaporation of precipitation may make drizzle a self-limiting process where the areal density of drizzle cells is sufficiently high. The daytime reduction in vertical velocity variance in a less coupled boundary layer is accompanied by enhanced stratification of potential temperature and a buildup of moisture near the surface.
Impact of Offshore Winds on a Buoyant River Plume System
Authors: Jurisa Joseph T. , Chant Robert J. 
Published: July 2013

Abstract
Idealized numerical simulations utilizing the Regional Ocean Modeling System (ROMS) are carried out to examine the response of buoyant river plume systems to offshore-directed wind stresses. It is found that after a few inertial periods of wind forcing the plume becomes detached from the coast and reaches a steady state in terms of the plume’s offshore position, width, and plume-averaged depth, salinity, and velocity. The steady-state offshore position of the plume is a balance between the cross-shore advection driven by the estuarine outflow and the alongshore advection driven by the Ekman velocities, and is described using the ratio of the outflow Froude number and the plume Froude number. The steady-state salinity structure is maintained by a balance between the cross-shore advection of salt creating stratification, the turbulent vertical mixing, and the downstream transport of freshwater continually resetting the system. Plume mixing is also analyzed using a salinity coordinate system to track the changes in freshwater volume in salinity space and time. A dynamical plume region classification is developed with use of a Richardson number–based critical mixing salinity criterion in salinity space. This salinity class–based classification agrees well with a classification based on an alongshore analysis of the salt flux equation. For this classification the near field is dominated by large cross-shore fluxes and the midfield by a diminishing cross-shore salt flux, and in the far field there is a balance between the alongshore salt flux and turbulent mixing.
Microvascular Reconstruction after Intra‐arterial Chemotherapy with Concomitant Radiation
Authors: Valentino Joseph , Helton W. Brian , Unnikrishnan Raman , Kudrimoti Mahesh , Arnold Susanne M. , Gal T. J. 
Published: July 2013

ObjectiveWhile the success of microvascular reconstruction is well established, even in the setting of prior radiotherapy, the outcomes in the setting of prior chemoradiation are less well documented. We present our experience with microvascular reconstruction in a unique cohort of patients previously treated with concomitant hyperfractionated radiation and intra‐arterial chemotherapy (HYPERRADPLAT). Despite the observation in prior studies of minimal vessel damage in this setting, the hypothesis of this study is that in the late setting of most salvage surgical therapy, either for recurrence or osteoradionecrosis, a different, progressive level of vessel injury may be encountered.Study DesignCase series with chart review.SettingTertiary referral academic medical center practice.Subjects and MethodsEighty‐four patients received primary treatment for advanced head and neck squamous cell carcinoma with HYPERRADPLAT. Of these, 8 patients (10%) underwent free tissue transfer reconstruction and a total of 11 free flaps.ResultsWound breakdown, fistula, or both occurred postoperatively in 50% (4/8) of these patients. No complications of the venous anastomoses occurred. Fifty percent (4/8) of patients required return to surgery for arterial failure due to thrombosis of the anastomosis. Two cases of these flaps could not be salvaged.ConclusionMicrovascular reconstruction following HYPERRADPLAT appears to result in a high number of arterial related complications. This experience implies an important delayed treatment effect of HYPERRADPLAT occurs upon recipient arteries. The manner in which this effect may occur in recipient arteries in the setting of more conventional chemoradiation requires further study.