bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aspartate‐containing neurons of the brainstem and rostral spinal cord of the sea lamprey Petromyzon marinus: Distribution and comparison with γ‐aminobutyric acid
Authors: Villar‐Cerviño Verona , Fernández‐López Blanca , Celina Rodicio María , Anadón Ramón 
Published: November 2013

ABSTRACTThe amino acid L‐aspartate (ASP) is one of the most abundant excitatory neurotransmitters in the mammalian brain, but its distribution in other vertebrates has not yet been well characterized. We investigated the distribution of ASP in the brainstem and rostral spinal cord of the adult sea lamprey by using ASP immunohistochemistry. Our results indicate that ASP is accumulated in specific neurons, but not in glia (tanycytes). ASP‐immunoreactive neuronal populations were rather similar as the glutamatergic populations reported in the adult sea lamprey (Villar‐Cerviño et al. [2013] J Comp Neurol 521:522–557), although some important differences were noted. Characteristically, the largest reticular neurons of the lamprey brainstem (Müller cells) showed ASP immunoreactivity in perikarya and processes, in contrast to the absence or faint glutamate immunoreactivity reported in these perikarya. We also compared the distribution of ASP and γ‐aminobutyric acid (GABA) in brainstem neurons by using double immunofluorescence methods. In regions such as the midbrain tectum, dorsal isthmus, and motor nuclei, ASP and GABA immunoreactivity was mostly located in different neurons, whereas in other nuclei (torus semicircularis, octavolateralis area, parvocellular reticular formation), many of the ASP‐immunonegative neurons displayed colocalization with GABA. These results, together with those of our previous studies of colocalization of glutamate and GABA, suggest that some lamprey neurons may co‐release both excitatory and inhibitory neurotransmitters. Further investigation is needed to elucidate the pathways of uptake and release of ASP by ASP‐immunoreactive neurons. Our results indicate that ASP is a neurotransmitter in the central nervous system representative of agnathans, the earliest vertebrate group. J. Comp. Neurol. 522:1209–1231, 2014. © 2013 Wiley Periodicals, Inc.
Trigeminal intersubnuclear neurons: Morphometry and input‐dependent structural plasticity in adult rats
Authors: Martin Yasmina B. , Negredo Pilar , Villacorta‐Atienza Jose A. , Avendaño Carlos 
Published: November 2013

ABSTRACTIntersubnuclear neurons in the caudal division of the spinal trigeminal nucleus that project to the principal nucleus (Pr5) play an active role in shaping the receptive fields of other neurons, at different levels in the ascending sensory system that processes information originating from the vibrissae. By using retrograde labeling and digital reconstruction, we investigated the morphometry and topology of the dendritic trees of these neurons and the changes induced by long‐term experience‐dependent plasticity in adult male rats. Primary afferent input was either eliminated by transection of the right infraorbital nerve (IoN), or selectively altered by repeated whisker clipping on the right side. These neurons do not display asymmetries between sides in basic metric and topologic parameters (global number of trees, nodes, spines, or dendritic ends), although neurons on the left tend to have longer terminal segments. Ipsilaterally, both deafferentation (IoN transection) and deprivation (whisker trimming) reduced the density of spines, and the former also caused a global increase in total dendritic length and a relative increase in more complex arbors. Contralaterally, deafferentation reduced more complex dendritic trees, and caused a moderate decline in dendritic length and spatial reach, and a loss of spines in number and density. Deprivation caused a similar, but more profound, effect on spines. Our findings provide original quantitative descriptions of a scarcely known cell population, and show that denervation‐ or deprivation‐derived plasticity is expressed not only by neurons at higher levels of the sensory pathways, but also by neurons in key subcortical circuits for sensory processing. J. Comp. Neurol. 522:1597–1617, 2014. © 2013 Wiley Periodicals, Inc.
What do the data show? Knowledge map development for comprehensive environmental assessment
Authors: Painter Kyle , McConnell Emma R , Sahasrabudhe Samir , Burgoon Lyle , Powers Christina M 
Published: November 2013

Abstract
Environmental and human health risk assessments benefit from using data that cross multiple scientific domains. Although individual data points may often be readily understood, the total picture can be difficult to envision. This is especially true with gaps in the data (e.g., with emerging substances such as engineered nanomaterials [ENM]), such that simply presenting only known information can result in a skewed picture. This study describes a method for building knowledge maps (KM) to visually summarize factors relevant to risk assessment in a relatively easy to interpret format. The KMs were created in the context of the comprehensive environmental assessment (CEA) approach for research planning and risk management of environmental contaminants. Recent applications of CEA to emerging substances such as engineered nanomaterials that have numerous data gaps have suggested that a more visually based depiction of information would improve the approach. We developed KM templates as a pilot project, to represent pertinent aspects of conceptual domains, and to highlight gaps in available information for one particular portion of a specific CEA application: the comparison of environmental transport, transformation, and fate of multiwalled carbon nanotubes (MWCNTs) and decabromodiphenyl ether as flame retardants. The results are 3 KM templates representing Physical Properties, Transport, and Transformation. The 3 templates were applied to both substances, resulting in a total of 6 KMs. In addition to presenting the KMs, this paper details the process used to generate them, to aid KM development for other sections of CEA applied to MWCNTs, or to apply the process to new CEA applications. Integr Environ Assess Manag 2014;10:37–47. © 2013 SETAC
The effect of graphene substrate on osteoblast cell adhesion and proliferation
Authors: Aryaei Ashkan , Jayatissa Ahalapitiya H. , Jayasuriya Ambalangodage C. 
Published: November 2013

AbstractUnderstanding the effect of graphene substrate on graphene–cell interaction is important for considering graphene as a potential candidate for biomedical applications. In this article, biocompatibility of few layers of graphene film transferred to different substrates was evaluated using osteoblasts. The substrates were oxidized silicon wafer (SiO2/Si stack), soda lime glass, and stainless steel. Chemical vapor deposition method was employed to synthesize graphene on copper substrate using methane and hydrogen as precursors. The quality and the thickness of graphene films on different substrates were estimated by Raman spectra, whereas the thickness of graphene film was confirmed by reflectance and transmittance spectroscopy. The study was also focused on cell attachment and morphology at two time points. The results show that graphene does not have any toxic effect on osteoblasts. The cell adhesion improves with graphene coated substrate than the substrate alone. It seems that graphene substrate properties play a dominant role in cell adhesion. The result of this study suggests that a layer of graphene on bone implants will be beneficial for osteoblast attachment and proliferation. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 3282–3290, 2014.
Effect of a hospitalist‐run postdischarge clinic on outcomes
Authors: Burke Robert E. , Whitfield Emily , Prochazka Allan V. 
Published: November 2013

BACKGROUNDNew post‐discharge strategies to reduce adverse events are needed.OBJECTIVETo determine whether follow‐up in a hospitalist‐run post‐discharge clinic (PDC) decreases post‐discharge adverse events when compared to follow‐up in a primary care clinic (PCP) or urgent care clinic (UC).DESIGNRetrospective cohort study using propensity scoring in multivariate analysis.PATIENTSConsecutive Veterans discharged home after a nonscheduled admission seen in PDC, UC, or PCP within 30 days of discharge.INTERVENTIONSRecently discharged patients are seen by housestaff who cared for them during the index admission and staffed with a rotating hospitalist in PDC; UC and PCP patients are seen by housestaff or attending ambulatory physicians.MAIN MEASURESThe primary outcome was a composite of hospital readmissions, Emergency Department visits, and mortality 30 days after discharge.KEY RESULTS5085 patients met criteria; 538 followed up in PDC (10.6%), 1848 with their PCP (36.3%), and 2699 in UC (53.1%). Patients following up in PDC were older and had a higher comorbidity burden. ICU exposure was similar between groups. Patients seen in PDC had shorter length of stay (LOS) (PDC, 3.8 days, UC, 5.0 days, PCP, 6.2 days; p = 0.04) and time to first post‐discharge visit (PDC, 5.0 days, UC, 9.4 days, PCP, 13.7 days; p < 0.01). There were no differences between groups in the primary outcome in unadjusted or propensity‐adjusted multivariate analysis.CONCLUSIONSPatients seen in a hospitalist‐run PDC had similar 30‐day post‐discharge adverse outcome rates despite a 2.4‐day shorter LOS compared to patients seen by their PCP. Prospective testing of PDCs is warranted. Journal of Hospital Medicine 2014;9:7–12. © 2013 Society of Hospital Medicine
Large scale screening of human sera for HCV RNA and GBV‐C RNA
Authors: Keys Jessica R. , Leone Peter A. , Eron Joseph J. , Alexander Kelcie , Brinson Myra , Swanstrom Ronald 
Published: November 2013

AbstractNorth Carolina locates acute HIV cases by pooled nucleic acid testing of HIV‐antibody negative serum samples. Here, 224 pools of 80 HIV‐negative samples (N = 17,920) were screened for viral RNA from HCV, GBV‐C, and influenza A. No evidence of influenza A was found, but HCV and GBV‐C were common (1.2% and 1.7% prevalence, respectively), demonstrating the utility of pooled testing in locating individuals that may remain undiagnosed otherwise. By sequencing positive pools, potential transmission clusters may be located as well. J. Med. Virol. 86:473–477, 2014. © 2013 Wiley Periodicals, Inc.
Proteomics methods to study methionine oxidation
Authors: Ghesquière Bart , Gevaert Kris 
Published: November 2013

AbstractThe oxidation and consequent reduction of protein‐bound methionine residues is of great interest in understanding different aspects of how oxidative stress affects protein functions and cellular signaling. To date, few technologies are available for the study of methionine sulfoxides. And, especially the absence of highly specific antibodies has impeded the field in understanding the exact role of methionine oxidation on a proteome‐wide level. Nonetheless, the different models where the responsible enzymes for repair of the oxidized methionines have been studied show that there is an important role for this modification in a cellular context. We here review different mass spectrometry based and proteomics methods for characterizing in vivo methionine oxidation. © 2013 Wiley Periodicals, Inc. Mass Spec Rev 33: 147–156, 2014.
Whole‐body magnetic resonance imaging (WB‐MRI) as surveillance for subsequent malignancies in survivors of hereditary retinoblastoma: A pilot study
Authors: Friedman Danielle Novetsky , Lis Eric , Sklar Charles A. , Oeffinger Kevin C. , Reppucci Marina , Fleischut Megan Harlan , Francis Jasmine H. , Marr Brian , Abramson David H , Dunkel Ira J 
Published: November 2013

BackgroundIndividuals with hereditary retinoblastoma (RB) are at very high risk of developing subsequent malignant neoplasms (SMNs) of which osteosarcoma (OS) is one of the most common. We hypothesized that annual surveillance using whole‐body magnetic resonance imaging (WB‐MRI) in asymptomatic survivors of hereditary RB would detect SMN of the bone and soft tissues at an early stage.ProcedureRetrospective review of the results of a WB‐MRI screening program in hereditary RB survivors from February 2008 to August 2012. The primary outcome was to determine the sensitivity and specificity of WB‐MRI in detecting SMNs.ResultsTwenty‐five patients had at least one WB‐MRI performed (range: 1–5). First WB‐MRI was performed at a median age of 16 years (range: 8–25 years). WB‐MRI detected new osseous abnormalities suspicious for malignancy in five patients: two were diagnosed with localized high‐grade OS of the extremity and three were found to have benign osseous abnormalities after dedicated imaging (n = 5/5) and/or biopsy (n = 3/5). One patient was diagnosed with secondary OS 3 months after a normal screening WB‐MRI exam. Among a total of 41 WB‐MRI screening tests performed in survivors of hereditary RB, the sensitivity of detecting SMN was 66.7% and the specificity was 92.1%.ConclusionsPreliminary results suggest that annual WB‐MRI surveillance detects SMN in survivors of hereditary RB, but with modest sensitivity. Further study is needed to assess the performance of annual surveillance WB‐MRIs and whether this modality decreases SMN‐related mortality in RB survivors. Pediatr Blood Cancer 2014; 61:1440–1444. © 2013 Wiley Periodicals, Inc.
Transient dispersion regimes
Authors: Holleman Rusty C. , Stacey Mark T. 
Published: November 2013

AbstractCharacterizing scalar dispersion is a key concern in a wide variety of applications, including both steady-state and time-dependent studies of wastewater outfalls, salinity distribution in estuaries, and the spreading of pollutants from industrial spills. As the size of a scalar plume grows with respect to the size of the containing water body, the effective dispersion varies, from the well-known ${ \sigma }_{x}^{2} \sim {t}^{3} $ behaviour for a plume enveloped in a region of linear shear, to the ${ \sigma }_{x}^{2} \sim t$ behaviour at the limit of a laterally well-mixed plume. We introduce an additional regime in which the plume extends across the full range of the available shear, but is not significantly affected by the lateral bounds of the water body. Through an analytic treatment we show that this regime exhibits a ${ \sigma }_{x}^{2} \sim {t}^{2} $ behaviour, independent of lateral mixing coefficient. Particle tracking results in an idealized, tidal channel–shoal basin demonstrate this regime as particle clouds straddle the channel–shoal interface. Quantitative analysis of spatial moments as plumes transition between regimes show good correlation between the observed parameters and parameters predicted by the analytic framework.
Food restriction by intermittent fasting induces diabetes and obesity and aggravates spontaneous atherosclerosis development in hypercholesterolaemic mice
Authors: Dorighello Gabriel G. , Rovani Juliana C. , Luhman Christopher J. F. , Paim Bruno A. , Raposo Helena F. , Vercesi Anibal E. , Oliveira Helena C. F. 
Published: November 2013

Different regimens of food restriction have been associated with protection against obesity, diabetes and CVD. In the present study, we hypothesised that food restriction would bring benefits to atherosclerosis- and diabetes-prone hypercholesterolaemic LDL-receptor knockout mice. For this purpose, 2-month-old mice were submitted to an intermittent fasting (IF) regimen (fasting every other day) over a 3-month period, which resulted in an overall 20 % reduction in food intake. Contrary to our expectation, epididymal and carcass fat depots and adipocyte size were significantly enlarged by 15, 72 and 68 %, respectively, in the IF mice compared with thead libitum-fed mice. Accordingly, plasma levels of leptin were 50 % higher in the IF mice than in thead libitum-fed mice. In addition, the IF mice showed increased plasma levels of total cholesterol (37 %), VLDL-cholesterol (195 %) and LDL-cholesterol (50 %). As expected, in wild-type mice, the IF regimen decreased plasma cholesterol levels and epididymal fat mass. Glucose homeostasis was also disturbed by the IF regimen in LDL-receptor knockout mice. Elevated levels of glycaemia (40 %), insulinaemia (50 %), glucose intolerance and insulin resistance were observed in the IF mice. Systemic inflammatory markers, TNF-α and C-reactive protein, were significantly increased and spontaneous atherosclerosis development were markedly increased (3-fold) in the IF mice. In conclusion, the IF regimen induced obesity and diabetes and worsened the development of spontaneous atherosclerosis in LDL-receptor knockout mice. Although being efficient in a wild-type background, this type of food restriction is not beneficial in the context of genetic hypercholesterolaemia.
Offspring death and subsequent psychiatric morbidity in bereaved parents: addressing mechanisms in a total population cohort
Authors: Ljung T. , Sandin S. , Långström N. , Runeson B. , Lichtenstein P. , Larsson H. 
Published: November 2013

BackgroundIt is unclear if psychiatric morbidity among parents bereaved of a child is related to major loss in general or if the cause of death matters. Whether such a link is consistent with a causal explanation also remains uncertain.MethodWe identified 3 114 564 parents through linkage of Swedish nationwide registers. Risk of psychiatric hospitalization was assessed with log-linear Poisson regression and family-based analyses were used to explore familial confounding.ResultsA total of 3284 suicides and 14 095 any-cause deaths were identified in offspring between 12 and 25 years of age. Parents exposed to offspring suicide had considerably higher risk of subsequent psychiatric hospitalization than unexposed parents [relative risk (RR) 1.90, 95% confidence interval (CI) 1.72–2.09], higher than parents exposed to offspring non-suicide death relative to controls (RR 1.18, 95% CI 1.11–1.26). We found no risk increase among stepfathers differentially exposed to biologically unrelated stepchildren's death or suicide, and the relative risk was notably lower among full siblings differentially exposed to offspring death or suicide.ConclusionsParental psychiatric hospitalization following offspring death was primarily found in offspring suicide. Familial (e.g. shared genetic) effects seemed important, judging from both lack of psychiatric hospitalization in bereaved stepfathers and attenuated risk when bereaved parents were contrasted to their non-bereaved siblings. We conclude that offspring suicide does not ‘cause’ psychiatric hospitalization in bereaved parents.
pyGCluster, a novel hierarchical clustering approach
Authors: Jaeger Daniel , Barth Johannes , Niehues Anna , Fufezan Christian 
Published: November 2013

Abstract
Summary: pyGCluster is a clustering algorithm focusing on noise injection for subsequent cluster validation. The reproducibility of a large amount of clusters obtained with agglomerative hierarchical clustering is assessed. Furthermore, a multitude of different distance-linkage combinations are evaluated. Finally, highly reproducible clusters are meta-clustered into communities. Graphical illustration of the results as node and expression maps is implemented.
Availability and implementation: pyGCluster requires Python 2.7, it is freely available at http://pyGCluster.github.io and published under MIT license. Dependencies are NumPy, SciPy and optionally fastcluster and rpy2.
Contact: christan@fufezan.net
Supplementary information: Supplementary data is available at Bioinformatics online and at http://pyGCluster.github.io
The explosion of supernova 2011fe in the frame of the core-degenerate scenario
Authors: Soker Noam , García-Berro Enrique , Althaus Leandro G. 
Published: November 2013

Abstract
We argue that the properties of the Type Ia supernova (SN Ia) SN 2011fe can be best explained within the frame of the core-degenerate (CD) scenario. In the CD scenario, a white dwarf (WD) merges with the core of an asymptotic giant branch (AGB) star and forms a rapidly rotating WD, with a mass close to and above the critical mass for explosion. Rapid rotation prevents immediate collapse and/or explosion. Spinning down over a time of 0-1010 yr brings the WD to explosion. A very long delayed explosion to post-crystallization phase, which lasts for about 2 × 109 yr, leads to the formation of a highly carbon-enriched outer layer. This can account for the carbon-rich composition of the fastest-moving ejecta of SN 2011fe. In reaching the conclusion that the CD scenario best explains the observed properties of SN 2011fe, we consider both its specific properties, like a very compact exploding object and carbon-rich composition of the fastest-moving ejecta, and the general properties of SNe Ia.
Disrupting Autophagy Restores Peroxisome Function to anArabidopsis lon2Mutant and Reveals a Role for the LON2 Protease in Peroxisomal Matrix Protein Degradation
Authors: Farmer Lisa M. , Rinaldi Mauro A. , Young Pierce G. , Danan Charles H. , Burkhart Sarah E. , Bartel Bonnie 
Published: November 2013

AbstractPeroxisomes house critical metabolic reactions that are essential for seedling development. As seedlings mature, metabolic requirements change, and peroxisomal contents are remodeled. The resident peroxisomal protease LON2 is positioned to degrade obsolete or damaged peroxisomal proteins, but data supporting such a role in plants have remained elusive. Arabidopsis thaliana lon2 mutants display defects in peroxisomal metabolism and matrix protein import but appear to degrade matrix proteins normally. To elucidate LON2 functions, we executed a forward-genetic screen for lon2 suppressors, which revealed multiple mutations in key autophagy genes. Disabling core autophagy-related gene (ATG) products prevents autophagy, a process through which cytosolic constituents, including organelles, can be targeted for vacuolar degradation. We found that atg2, atg3, and atg7 mutations suppressed lon2 defects in auxin metabolism and matrix protein processing and rescued the abnormally large size and small number of lon2 peroxisomes. Moreover, analysis of lon2 atg mutants uncovered an apparent role for LON2 in matrix protein turnover. Our data suggest that LON2 facilitates matrix protein degradation during peroxisome content remodeling, provide evidence for the existence of pexophagy in plants, and indicate that peroxisome destruction via autophagy is enhanced when LON2 is absent.
The Evolutionarily Conserved Iron-Sulfur Protein INDH Is Required for Complex I Assembly and Mitochondrial Translation in Arabidopsis
Authors: Wydro Mateusz M. , Sharma Pia , Foster Jonathan M. , Bych Katrine , Meyer Etienne H. , Balk Janneke 
Published: November 2013

Abstract
The assembly of respiratory complexes is a multistep process, requiring coordinate expression of mitochondrial and nuclear genes and cofactor biosynthesis. We functionally characterized the iron-sulfur protein required for NADH dehydrogenase (INDH) in the model plant Arabidopsis thaliana. An indh knockout mutant lacked complex I but had low levels of a 650-kD assembly intermediate, similar to mutations in the homologous NUBPL (nucleotide binding protein-like) in Homo sapiens. However, heterozygous indh/+ mutants displayed unusual phenotypes during gametogenesis and resembled mutants in mitochondrial translation more than mutants in complex I. Gradually increased expression of INDH in indh knockout plants revealed a significant delay in reassembly of complex I, suggesting an indirect role for INDH in the assembly process. Depletion of INDH protein was associated with decreased 35S-Met labeling of translation products in isolated mitochondria, whereas the steady state levels of several mitochondrial transcripts were increased. Mitochondrially encoded proteins were differentially affected, with near normal levels of cytochrome c oxidase subunit2 and Nad7 but little Nad6 protein in the indh mutant. These data suggest that INDH has a primary role in mitochondrial translation that underlies its role in complex I assembly.