bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcription factor calcium‐response factor limitsNMDAreceptor‐dependent transcription in the developing brain
Authors: Lyons Michelle R. , Chen Liang‐Fu , Deng Jie V. , Finn Caitlin , Pfenning Andreas R. , Sabhlok Aditi , Wilson Kelli M. , West Anne E. 
Published: January 2016

AbstractNeuronal activity sculpts brain development by inducing the transcription of genes such as brain‐derived neurotrophic factor (Bdnf) that modulate the function of synapses. Sensory experience is transduced into changes in gene transcription via the activation of calcium signaling pathways downstream of both L‐type voltage‐gated calcium channels (L‐VGCCs) andNMDA‐type glutamate receptors (NMDARs). These signaling pathways converge on the regulation of transcription factors including calcium‐response factor (CaRF). Although CaRFis dispensable for the transcriptional induction ofBdnffollowing the activation of L‐VGCCs, here we show that the loss of CaRFleads to enhancedNMDAR‐dependent transcription ofBdnfas well asArc. We identify theNMDARsubunit‐encoding geneGrin3aas a regulatory target of CaRF, and we show that expression of bothCarfandGrin3ais depressed by the elevation of intracellular calcium, linking the function of this transcriptional regulatory pathway to neuronal activity. We find that light‐dependent activation ofBdnfandArctranscription is enhanced in the visual cortex of young CaRFknockout mice, suggesting a role for CaRF‐dependent dampening ofNMDAR‐dependent transcription in the developing brain. Finally, we demonstrate that enhancedBdnfexpression in CaRF‐lacking neurons increases inhibitory synapse formation. Taken together, these data reveal a novel role for CaRFas an upstream regulator ofNMDAR‐dependent gene transcription and synapse formation in the developing brain.imageNMDARs promote brain development by inducing the transcription of genes, including brain‐derived neurotrophic factor (BDNF). We show that the transcription factor calcium‐response factor (CaRF) limits NMDAR‐dependent BDNF induction by regulating expression of the NMDAR subunit GluN3A. Loss of CaRF leads to enhanced BDNF‐dependent GABAergic synapse formation indicating the importance of this process for brain development. Our observation that both CaRF and GluN3A are down‐regulated by intracellular calcium suggests that this may be a mechanism for experience‐dependent modulation of synapse formation.
An innovative regenerative treatment of scars with dermal micrografts
Authors: Svolacchia Fabiano , De Francesco Francesco , Trovato Letizia , Graziano Antonio , Ferraro Giuseppe A. 
Published: January 2016

SummaryBackgroundPathological scars occur following injuries and are often considered esthetically unattractive. Several strategies have been attempted to improve these types of scars using both surgical and nonsurgical methods. The most common treatments include cryotherapy, intralesional corticosteroid injections, 5‐fluorouracil, bleomycin, interferon, and verapamil.AimsIn this study, we aim to investigate the effectiveness of dermal autologous micrografts in the treatment of pathological scars resulting from burns, trauma, or any iatrogenic source.MethodsWe used a new clinical practice called Rigenera Protocol to obtain autologous micrografts which were in turn injectable in the patients.ResultsA significant improvement was observed in appearance and texture of the exaggerated scars in all cases following already 4 months of autologous micrograft treatment We have also shown that these micrografts are composed of mesenchymal stem cells and in addition, histological evaluation verified restoration of the structural layers immediately below the epidermis and a horizontal realignment of collagen fibers in the papillary dermis.ConclusionOur results clearly demonstrate the optimal outcomes obtained following treatment with dermal micrografts on exaggerated scars with different etiologies. However, further studies are required to confirm the efficacy of this new technique.
Effect of dietary Schizochytrium microalga oil on selected markers of low‐grade inflammation in rats
Authors: Komprda T. , Sládek Z. , Škultéty O. , Křížková S. , Rozíková V. , Němcová B. , Šustrová T. , Valová M. 
Published: January 2016

SummaryThe objective of the present study was to evaluate a potential of Schizochytrium microalga oil to alleviate possible negative effects of high‐fat‐high‐energy diets. Forty adult male rats (Wistar Albino) were fed 7 weeks the diet containing beef tallow + evaporated sweetened milk (diet T) intended to cause mild obesity and low‐grade systemic inflammation. Consequently, the animals were divided into four groups by 10 animals each and fed either the T‐diet (control) or the diet containing 6% of safflower oil (S), 6% of fish oil (F) and 6% of Schizochytrium microalga oil (A), respectively, for another 7 weeks. The A‐diet decreased (p < 0.05) live weight to 86% and glycaemia to 85% of control, respectively; an effect of the S‐ and F‐diet on these markers was insignificant (p > 0.05). In comparison with control, higher (p < 0.05) deposition of eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA) in the epididymal adipose tissue (EAT) of the A‐rats correlated with increased (p < 0.05) plasma adiponectin concentration, but it was without the effect (p > 0.05) on cellular adiponectin content in the EAT. Higher (p < 0.05) EPA+DHA deposition in the liver of the A‐rats correlated with higher expression (149% of control; p < 0.05) of the gene coding for peroxisome proliferator‐activated receptor gamma, and with lower expression (82% and 66%; p < 0.05) of the genes coding for adiponectin receptors AdipoR1 and AdipoR2; no relationship to the expression of receptor GPR120 was found. The A‐diet did not affect amount of the nuclear fraction of the nuclear factor kappa B in the liver, but increased plasma level of anti‐inflammatory cytokine TGF‐β1 (p < 0.05). The presented data agree with results of other in vivo rodent and human studies, but not with literature data regarding in vitro experiments: it can be concluded that the effects of dietary oils on inflammatory markers need further investigation.
Sleep and academic performance in later adolescence: results from a large population‐based study
Authors: Hysing Mari , Harvey Allison G. , Linton Steven J. , Askeland Kristin G. , Sivertsen Børge 
Published: January 2016

SummaryThe aim of the current study was to assess the association between sleep duration and sleep patterns and academic performance in 16–19 year‐old adolescents using registry‐based academic grades. A large population‐based study from Norway conducted in 2012, the youth@hordaland‐survey, surveyed 7798 adolescents aged 16–19 years (53.5% girls). The survey was linked with objective outcome data on school performance. Self‐reported sleep measures provided information on sleep duration, sleep efficiency, sleep deficit and bedtime differences between weekday and weekend. School performance [grade point average (GPA)] was obtained from official administrative registries. Most sleep parameters were associated with increased risk for poor school performance. After adjusting for sociodemographic information, short sleep duration and sleep deficit were the sleep measures with the highest odds of poor GPA (lowest quartile). Weekday bedtime was associated significantly with GPA, with adolescents going to bed between 22:00 and 23:00 hours having the best GPA. Also, delayed sleep schedule during weekends was associated with poor academic performance. The associations were somewhat reduced after additional adjustment for non‐attendance at school, but remained significant in the fully adjusted models. In conclusion, the demonstrated relationship between sleep problems and poor academic performance suggests that careful assessment of sleep is warranted when adolescents are underperforming at school. Future studies are needed on the association between impaired sleep in adolescence and later functioning in adulthood.
Beta EEG reflects sensory processing in active wakefulness and homeostatic sleep drive in quiet wakefulness
Authors: Grønli Janne , Rempe Michael J. , Clegern William C. , Schmidt Michelle , Wisor Jonathan P. 
Published: January 2016

SummaryMarkers of sleep drive (<10 Hz; slow‐wave activity and theta) have been identified in the course of slow‐wave sleep and wakefulness. So far, higher frequencies in the waking electroencephalogram have not been examined thoroughly as a function of sleep drive. Here, electroencephalogram dynamics were measured in epochs of active wake (wake characterized by high muscle tone) or quiet wake (wake characterized by low muscle tone). It was hypothesized that the higher beta oscillations (15–35 Hz, measured by local field potential and electroencephalography) represent fundamentally different processes in active wake and quiet wake. In active wake, sensory stimulation elevated beta activity in parallel with gamma (80–90 Hz) activity, indicative of cognitive processing. In quiet wake, beta activity paralleled slow‐wave activity (1–4 Hz) and theta (5–8 Hz) in tracking sleep need. Cerebral lactate concentration, a measure of cerebral glucose utilization, increased during active wake whereas it declined during quiet wake. Mathematical modelling of state‐dependent dynamics of cortical lactate concentration was more precisely predictive when quiet wake and active wake were included as two distinct substates rather than a uniform state of wakefulness. The extent to which lactate concentration declined in quiet wake and increased in active wake was proportionate to the amount of beta activity. These data distinguish quiet wake from active wake. Quiet wake, particularly when characterized by beta activity, is permissive to metabolic and electrophysiological changes that occur in slow‐wave sleep. These data urge further studies on state‐dependent beta oscillations across species.
Genomic and functional approaches reveal a case of adaptive introgression fromPopulus balsamifera(balsam poplar) inP. trichocarpa(black cottonwood)
Authors: Suarez‐Gonzalez Adriana , Hefer Charles A. , Christe Camille , Corea Oliver , Lexer Christian , Cronk Quentin C. B. , Douglas Carl J. 
Published: January 2016

AbstractNatural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies inPopulus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister speciesPopulus balsamiferaand identified candidate genes for local adaptation. Here, we explored the patterns of introgression and signals of local adaptation inP. trichocarpaandP. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixedP. trichocarparevealed a telomeric region in chromosome 15 withP. balsamiferaancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g.PRR5,COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular or cassette‐like variation intoP. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo‐ or subfunctionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association betweenP. balsamiferaintrogressed alleles with the expression of adaptive traits inP. trichocarpasupports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.
Frequency and mitotic heritability of epimutations in Schistosoma mansoni
Authors: Roquis David , Rognon Anne , Chaparro Cristian , Boissier Jerome , Arancibia Nathalie , Cosseau Celine , Parrinello Hugues , Grunau Christoph 
Published: January 2016

AbstractSchistosoma mansoni is a parasitic platyhelminth responsible for intestinal bilharzia. It has a complex life cycle, infecting a freshwater snail of the Biomphalaria genus, and then a mammalian host. Schistosoma mansoni adapts rapidly to new (allopatric) strains of its intermediate host. To study the importance of epimutations in this process, we infected sympatric and allopatric mollusc strains with parasite clones. ChIP‐Seq was carried out on four histone modifications (H3K4me3, H3K27me3, H3K27ac and H4K20me1) in parallel with genomewide DNA resequencing (i) on parasite larvae shed by the infected snails and (ii) on adult worms that had developed from the larvae. No change in single nucleotide polymorphisms and no mobilization of transposable elements were observed, but 58–105 copy number variations (CNVs) within the parasite clones in different molluscs were detected. We also observed that the allopatric environment induces three types of chromatin structure changes: (i) host‐induced changes on larvae epigenomes in 51 regions of the genome that are independent of the parasites’ genetic background, (ii) spontaneous changes (not related to experimental condition or genotype of the parasite) at 64 locations and (iii) 64 chromatin structure differences dependent on the parasite genotype. Up to 45% of the spontaneous, but none of the host‐induced chromatin structure changes were transmitted to adults. In our model, the environment induces epigenetic changes at specific loci but only spontaneous epimutations are mitotically heritable and have therefore the potential to contribute to transgenerational inheritance. We also show that CNVs are the only source of genetic variation and occur at the same order of magnitude as epimutations.
Detecting hybridization using ancient DNA
Authors: Schaefer Nathan K. , Shapiro Beth , Green Richard E. 
Published: January 2016

AbstractIt is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high‐coverage genome sequences for a growing diversity of organisms, including many that are extinct. Thanks to the development of new statistical approaches for detecting and quantifying admixture from genomic data, genomes from extinct populations have proven useful both in revealing previously unknown hybridization events and informing the study of hybridization between living organisms. Here, we review some of the key recent statistical innovations for detecting ancient hybridization using genomewide sequence data and discuss how these innovations have revised our understanding of human evolutionary history.
Three magnitude 7 earthquakes on a single fault in central Italy in 1400 years, evidenced by new palaeoseismic results
Authors: Galli Paolo , Giaccio Biagio , Messina Paolo , Peronace Edoardo 
Published: January 2016

AbstractNew palaeoseismic trenching across the main splay of the Fucino fault system provides evidence for a High Middle Age surface‐faulting episode conceivably associated with a disruptive earthquake, similar to the one that occurred in 1915 (Mw 7.0). The existence of this event, which has already been suggested by some previous studies, implies a shortening of the recurrence interval for Mw 7.0 earthquakes with respect to current knowledge. If we assume that the palaeoseismic Holocene record is complete, this shortening is focused in the historical period, when the Fucino structure sourced three strong earthquakes in only 1.4 ka. A similar clustering of energy release in the recent past is consistent with both palaeoseismological studies on other faults affecting the Apennine divide, and the high GPS strain rates observed in the same chain sectors.
Reducing the risk of transfusion‐transmitted cytomegalovirus infection: a systematic review and meta‐analysis
Authors: Mainou Maria , Alahdab Fares , Tobian Aaron A.R. , Asi Noor , Mohammed Khaled , Murad M. Hassan , Grossman Brenda J. 
Published: January 2016

BACKGROUNDLeukoreduced (LR) or cytomegalovirus (CMV)‐seronegative cellular blood components are commonly used to reduce the risk of transfusion‐transmitted CMV infection in high‐risk patients.STUDY DESIGN AND METHODSWe performed a systematic review and meta‐analysis to evaluate the evidence for the use of LR cellular blood components with or without concurrent CMV testing of donor units in patients undergoing chemotherapy or solid organ and hematopoietic stem cell transplantation, in pregnant women, in very‐low‐birthweight infants, and in patients with primary immunodeficiency. We searched MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Scopus from 1980 through February 2015. Studies were included if they had a comparison group. Two independent reviewers selected and appraised studies. Meta‐analysis was performed when appropriate.RESULTSOf 457 studies screened, 11 were eligible. One study was excluded from the meta‐analysis because the comparison performed differed significantly from the others. Meta‐analysis of five studies that compared leukoreduction to transfusing CMV‐untested blood components showed no significant difference in clinical CMV infection (relative risk [RR], 0.26; 95% confidence interval [CI], 0.04‐1.57) or laboratory CMV infection (RR, 0.33; 95% CI, 0.08‐1.37). Meta‐analysis of three studies that compared leukoreduction to transfusing CMV‐seronegative cellular components showed no significant difference in laboratory CMV infection (RR, 2.18; 95% CI, 0.96‐4.98). Meta‐analysis of two studies that compared adding CMV testing to leukoreduction (vs. leukoreduction alone) showed no significant difference in clinical or laboratory CMV infection. The certainty in estimates was low for all comparisons.CONCLUSIONAt present, the scientific evidence does not favor a single strategy for reducing the risk of transfusion‐related CMV infection in high‐risk patients.
Evaluation of Faecal Salmonella Shedding Among Dogs at Seven Animal Shelters across Texas
Authors: Leahy A. M. , Cummings K. J. , Rodriguez‐Rivera L. D. , Rankin S. C. , Hamer S. A. 
Published: January 2016

SummaryEstimates of prevalence of faecal Salmonella shedding among dogs in the United States have varied widely. Surveillance among shelter dogs has been limited, although dogs in animal shelters may be at elevated risk of Salmonella infection because of their previous exposure history as well as factors inherent to shelter environments. Our objectives were to estimate the prevalence of Salmonella shedding among shelter dogs across Texas, to identify risk factors for shedding and to characterize the isolates. Using a repeated cross‐sectional study design, we collected faecal samples from dogs on two or three visits to each of seven Texas animal shelters between May 2013 and December 2014. Standard bacteriologic culture methods were used to isolate Salmonella from samples, and isolates were characterized via serotyping and anti‐microbial susceptibility testing. The prevalence of faecal Salmonella shedding among sampled dogs was 4.9% (27/554), and within‐shelter prevalence ranged from 1.9% to 8.3%. There was a marginal association (P = 0.09) between watery faecal samples and positive Salmonella status, as estimated by a logistic regression model that controlled for shelter as a random effect. However, over 60% of Salmonella‐positive dogs had grossly normal faeces. Salmonella prevalence did not vary significantly by age group or sex. The most common serovars were Newport (22%) and Javiana (15%), both of which were widespread among shelters. Resistance to anti‐microbial agents was uncommon. The prevalence of faecal Salmonella shedding among shelter dogs in Texas appears to be comparable to that seen among pet dogs in general.
Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices
Authors: Pellissier Loïc , Oppliger Anne , Hirzel Alexandre H. , Savova-Bianchi Dessislava , Mbayo Guilain , Mascher Fabio , Kellenberger Stefan , Niculita-Hirzel Hélène 
Published: January 2016

ABSTRACT

Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km
2
along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO
3
concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities.
Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea
Authors: Bennett Kristen , Sadler Natalie C. , Wright Aaron T. , Yeager Chris , Hyman Michael R. 
Published: January 2016

ABSTRACT

Nitrosomonas europaea
is an aerobic nitrifying bacterium that oxidizes ammonia (NH
3
) to nitrite (NO
2
−
) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH
4
+
-dependent O
2
uptake by
N. europaea
by 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, and
de novo
protein synthesis was required to reestablish this activity after cells were exposed to 17OD. Cells were reacted with Alexa Fluor 647 azide using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) (click) reaction, solubilized, and analyzed by SDS-PAGE and infrared (IR) scanning. A fluorescent 28-kDa polypeptide was observed for cells previously exposed to 17OD but not for cells treated with either allylthiourea or acetylene prior to exposure to 17OD or for cells not previously exposed to 17OD. The fluorescent polypeptide was membrane associated and aggregated when heated with β-mercaptoethanol and SDS. The fluorescent polypeptide was also detected in cells pretreated with other diynes, but not in cells pretreated with structural homologs containing a single ethynyl functional group. The membrane fraction from 17OD-treated cells was conjugated with biotin-azide and solubilized in SDS. Streptavidin affinity-purified polypeptides were on-bead trypsin-digested, and amino acid sequences of the peptide fragments were determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Peptide fragments from AmoA were the predominant peptides detected in 17OD-treated samples. In-gel digestion and matrix-assisted laser desorption ionization–tandem time of flight (MALDI-TOF/TOF) analyses also confirmed that the fluorescent 28-kDa polypeptide was AmoA.