bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opportune cell culture conditions permit transfer of the neurosphere paradigm to cells of the cerebellar granule cell lineage by being permissive to sonic hedgehog signaling
Authors: Heil Constantin 
Published: December 2016

AbstractThein vitrostudy of neural progenitors is based around the idea that defined culture conditions can emulate an environment which maintains an undifferentiated state and self-renewal capability of explanted progenitor cells, culminating in the growth of neurospheres. Neurosphere culture systems are used to study cells of physiological origin as well as transformed cells. In the case of the cerebellar granule cell lineage, neurosphere cultures have been produced from medulloblastoma tumors, while non-transformed granule progenitors are reported to be transientin vitro.SHH signaling is a key signaling pathway with roles in morphogenesis and cell proliferation in the central nervous system, in particular, involved in mitogenic signaling within the context of postnatal cerebellar granule cell expansion. In this paper, I demonstrate that in addition to commonly used mitogens such as EGF and bFGF, the SHH pathway agonist SAG, as well as genetic activation of SHH signaling by PTCH1 deletion, can lead to the growth of neurospheres from postnatal day 7 (p7) cerebellar explants.I also show that these neurosphere adhere to the cerebellar GCP lineage.. Strikingly, mSS cells can be maintained indefinitely in culture, as demonstrated by extensive clonogenic capability, assayed over a period of 10 weeks. In the context of self-renewal, I assay gene expression of POU3f2, POU5f1, NANOG, and SOX2, genes associated with neural progenitors, which I find expressed in mSS cells. Importantly, mSS cultures are continuously dependent on SAG for their clonogenic potential and SHH pathway activation, assayed by expression of GLI1, PTCH1 and NMYC. In addition to the aforementioned extensive self-renewal capability, mSS neurosphere cultures also maintain the ability to differentiate.In vitrodifferentiation leads to formation of cells with typical granule cell morphology and which are positive for beta3-tubulin and express GABRA6.Overall, my work demonstrates that by applying culture conditions which are tailored towards biological characteristics of specific regions of the central nervous system the paradigm of the neurosphere can be expanded to include lineages not previously studied in this way. In particular, I apply this principle to unmask the property of cells from the GCP lineage as having extensive self-renewal capabilityin vitro.
DNAlogo: a smart mini application for generating DNA sequence logos
Authors: Guo Yabin 
Published: December 2016

AbstractSequence logos are frequently used for presenting consensus sequences and motifs of nucleic acids and proteins. WebLogo of UC Berkeley is the most popular tool for creating sequence logos, whereas, it is often restricted by the internet speed in some developing countries and no graphic interface for its stand-alone version. Here, the author generated an application, DNAlogo, using VB.net, which runs in Windows system. DNAlogo is small and convenient. It creates both bitmap and vector map. Beside the classic sequence logo function, DNAlogo introduced compensated logo to generate consensus sequences considering different GC contents of different genomes. DNAlogo provides a simple way for researchers without programming knowledge to create DNA sequence logos.
Super-resolution Imaging of Synaptic and Extra-synaptic Pools of AMPA Receptors with Different-sized Fluorescent Probes
Authors: Lee Sang Hak , Jin Chaoyi , Cai En , Ge Pinghua , Ishitsuka Yuji , Teng Kai Wen , Thomaz Andre A. de , Nall Duncan , Baday Murat , Jeyifous Okunola , Demonte Daniel , Dundas Christopher M. , Park Sheldon , Green William N. , Selvin Paul R. 
Published: December 2016

AbstractWhether AMPA receptors (AMPARs) enter into neuronal synapses, by exocytosis from an internal pool, or by diffusion from an external membrane-bound pool, is hotly contested. 3D super-resolution fluorescent nanoscopy to measure the dynamics and placement of AMPAR is a powerful method for addressing this issue. However, probe size and accessibility to tightly packed spaces can be limiting. We have therefore labeled AMPARs with differently sized fluorophores: small organic fluorescent dyes (~ 4 nm), small quantum dots (sQD, ~10 nm in diameter), or big (commercial) quantum dots (bQD, ~ 20 nm in diameter). We then compared their diffusion rate, trajectories, and placement with respect to a postsynaptic density (PSD) protein, Homer 1c. Labeled with the small probes of sQDs or organic fluorophores, we find that AMPARs are located largely within PSDs (~73-93%), and generally reside in “nanodomains” with constrained diffusion. In contrast, when labeled with bQDs, only 5-10% of AMPARs are within PSDs. The results can be explained by relatively free access, or lack thereof, to synaptic clefts of the AMPARs when labeled with small or big probes, respectively. This implies that AMPARs primarily enter PSDs soon after their exocytosis and not from a large diffusive pool of extrasynaptic AMPARs.
Dealing with many correlated covariates in capture-recapture models
Authors: Gimenez Olivier , Barbraud Christophe 
Published: December 2016

SummaryCapture-recapture models for estimating demographic parameters allow covariates to be incorporated to better understand population dynamics. However, high-dimensionality and multicollinearity can hamper estimation and inference. Principal component analysis is incorporated within capture-recapture models and used to reduce the number of predictors into uncorrelated synthetic new variables. Principal components are selected by sequentially assessing their statistical significance. We provide an example on seabird survival to illustrate our approach. Our method requires standard statistical tools, which permits an efficient and easy implementation using standard software.
Frequency‐ and angle‐dependent poroelastic seismic analysis for highly attenuating reservoirs
Authors: Zhao Luanxiao , Yao Qiuliang , Han De‐hua , Zhou Rui , Geng Jianhua , Li Hui 
Published: December 2016

ABSTRACTWe extend the frequency‐ and angle‐dependent poroelastic reflectivity to systematically analyse the characteristic of seismic waveforms for highly attenuating reservoir rocks. It is found that the mesoscopic fluid pressure diffusion can significantly affect the root‐mean‐square amplitude, frequency content, and phase signatures of seismic waveforms. We loosely group the seismic amplitude‐versus‐angle and ‐frequency characteristics into three classes under different geological circumstances: (i) for Class‐I amplitude‐versus‐angle and ‐frequency, which corresponds to well‐compacted reservoirs having Class‐I amplitude‐versus‐offset characteristic, the root‐mean‐square amplitude at near offset is boosted at high frequency, whereas seismic energy at far offset is concentrated at low frequency; (ii) for Class‐II amplitude‐versus‐angle and ‐frequency, which corresponds to moderately compacted reservoirs having Class‐II amplitude‐versus‐offset characteristic, the weak seismic amplitude might exhibit a phase‐reversal trend, hence distorting both the seismic waveform and energy distribution; (iii) for Class‐III amplitude‐versus‐angle and ‐frequency, which corresponds to unconsolidated reservoir having Class‐III amplitude‐versus‐offset characteristic, the mesoscopic fluid flow does not exercise an appreciable effect on the seismic waveforms, but there exists a non‐negligible amplitude decay compared with the elastic seismic responses based on the Zoeppritz equation.
Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers
Authors: Lindh Markus V. , Sjöstedt Johanna , Ekstam Börje , Casini Michele , Lundin Daniel , Hugerth Luisa W. , Hu Yue O. O. , Andersson Anders F. , Andersson Agneta , Legrand Catherine , Pinhassi Jarone 
Published: December 2016

SummaryMetapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy‐frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.
The molecular response of the white‐rot fungus Dichomitus squalens to wood and non‐woody biomass as examined by transcriptome and exoproteome analyses
Authors: Rytioja Johanna , Hildén Kristiina , Di Falco Marcos , Zhou Miaomiao , Aguilar‐Pontes Maria Victoria , Sietiö Outi‐Maaria , Tsang Adrian , de Vries Ronald P. , Mäkelä Miia R. 
Published: December 2016

SummaryThe ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post‐)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well‐adapted to the prevailing substrate. White‐rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white‐rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non‐woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non‐woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.
Oscillospira and related bacteria – From metagenomic species to metabolic features
Authors: Gophna Uri , Konikoff Tom , Nielsen Henrik Bjørn 
Published: December 2016

SummaryOscillospira is an under‐studied anaerobic bacterial genus from Clostridial cluster IV that has resisted cultivation for over a century since the first time it was observed. In recent years its 16S rRNA gene was identified in several human gut microbiota studies where it was often associated with interesting traits, especially leanness. However, very little is known about its metabolism or physiology. Here we used nearly complete genomes derived from shot‐gun metagenomic data from the human gut to analyze Oscillospira and related bacteria. We used sequence similarity, gene neighbourhood information and manual metabolic pathway curation to decipher key metabolic features of this intriguing bacterial genus. We infer that Oscillospira species are butyrate producers, and at least some of them have the ability to utilize glucuronate, a common animal‐derived sugar that is both produced by the human host and consumed by that host in diets rich in animal products. These findings could help explain diet‐related inter‐individual variation in faecal Oscillospira levels as well as the observation that the presence of this genus is reduced in diseases that involve inflammation.
Gestational diabetes alters the fetal heart rate variability during an oral glucose tolerance test: a fetal magnetocardiography study
Authors: Fehlert E , Willmann K , Fritsche L , Linder K , Mat‐Husin H , Schleger F , Weiss M , Kiefer‐Schmidt I , Brucker S , Häring H‐U , Preissl H , Fritsche A 
Published: December 2016

ObjectiveGestational diabetes mellitus (GDM) potentially harms the child before birth. We previously found GDM to be associated with developmental changes in the central nervous system. We now hypothesise that GDM may also impact on the fetal autonomic nervous system under metabolic stress like an oral glucose tolerance test (OGTT).DesignWe measured heart rate variability (HRV) of mothers and fetuses during a three‐point OGTT using fetal magnetocardiography (fMCG).SettingMeasurements were performed in the fMEG Centre in Tübingen.PopulationAfter exclusion of 23 participants, 13 pregnant women with GDM and 36 pregnant women with normal glucose tolerance were examined.MethodsAll women underwent the same examination setting with OGTT during which fMCG was recorded three times.Main outcome measure(s)Parameters of heart rate variability were measured.ResultsCompared with mothers with normal glucose regulation, mothers with GDM showed increased heart rate but no significant differences of maternal HRV. In contrast, HRV in fetuses of mothers with GDM differed from those in the metabolically healthy group regarding standard deviation normal to normal beat (SDNN) (P = 0.012), low‐frequency band (P = 0.008) and high‐frequency band (P = 0.031). These HRV parameters exhibit a decrease only in GDM fetuses during the second hour of the OGTT.ConclusionsThese results show an altered response of the fetal autonomic nervous system to metabolic stress in GDM‐complicated pregnancies. Hence, disturbances in maternal glucose metabolism might not only impact on the central nervous system of the fetus but may also affect the fetal autonomic nervous system.Tweetable abstractMetabolic stress reveals a different response of fetal autonomic nervous system in GDM‐complicated pregnancies.
Decreasing mortality during pregnancy and for a year after while mortality after termination of pregnancy remains high: a population‐based register study of pregnancy‐associated deaths in Finland 2001–2012
Authors: Karalis E , Ulander V‐M , Tapper A‐M , Gissler M 
Published: December 2016

ObjectiveTo investigate mortality in the non‐pregnant fertile female population, and mortality during pregnancy and up to 1 year after the end of pregnancy, in Finland from 2001 to 2012 and compare the results with those of 1987–2000.DesignRetrospective cohort study.SettingFinland.Population10 427 deceased women of reproductive age (15–49).MethodsPregnancy outcomes were categorised into: ongoing pregnancy or birth, miscarriage or ectopic pregnancy and termination of pregnancy. Mortality was calculated per 100 000 pregnancies. The mortality rate of the non‐pregnant female population of fertile age was calculated per 100 000 person‐years, and the results were compared with those of 1987–2000.Main outcome measuresPregnancy‐associated mortality during pregnancy and up to 1 year after the end of pregnancy. Mortality of non‐pregnant, fertile‐age, female population.ResultsThe age‐adjusted mortality rate during pregnancy and within 1 year after the end of pregnancy was 28.4/100 000 pregnancies, and it had significantly decreased compared with the period 1987–2000 [risk ratio (RR) 0.75 (95% CI, 0.65–0.88)]. Mortality in non‐pregnant fertile‐age females was 48.1/100 000 person‐years. Mortality for diseases and medical conditions during and after pregnancy decreased by 26% [RR 0.74 (95% CI, 0.59–0.92)] and for external causes by 23% [RR 0.77 (95% CI, 0.62–0.95)]. The mortality rate for suicides was 3.3/100 000 in ongoing pregnancies and pregnancies ending in birth while it was 21.8/100 000 after termination of pregnancy and 10.2/100 000 among non‐pregnant women.ConclusionsIn comparison with earlier decades, pregnancy‐associated mortality has decreased in Finland.Tweetable abstractMortality decreases among pregnant women and within 1 year after pregnancy in Finland.
Sex‐ and Size‐Related Patterns of Carrion Visitation inNecrodes littoralis(Coleoptera: Silphidae) andCreophilus maxillosus(Coleoptera: Staphylinidae)
Authors: Mądra‐Bielewicz Anna , Frątczak‐Łagiewska Katarzyna , Matuszewski Szymon 
Published: December 2016

AbstractThe estimation of postmortem interval (PMI) based on successional patterns of adult insects is largely limited, due to the lack of potentialPMImarkers. Sex and size of adult insects could be easily used for such estimation. In this study, sex‐ and size‐related patterns of carrion attendance by adult insects were analyzed inNecrodes littoralis(Coleoptera: Silphidae) andCreophilus maxillosus(Coleoptera: Staphylinidae). For both species, abundance of males and females changed similarly during decomposition. A slightly female‐biased sex ratio was recorded inN. littoralis. Females ofN. littoralisstarted visiting carcasses, on average, one day earlier than males. There was a rise in size of males ofN. littoralisat the end of decomposition, whereas for females of both species and males ofC. maxillosus, no size‐related patterns of carrion visitation were found. Current results demonstrate that size and sex of adult carrion beetles are poor indicators ofPMI.
How do groups of red imported fire ants (Hymenoptera: Formicidae) feed on a droplet of sugar water?
Authors: Wang Cai , Chen Xuan , Hooper‐Bùi Linda M. , Strecker Rachel , Wen Yu‐Zhen , Qin Wen‐Quan , Ma Tao , Sun Zhao‐Hui , Chen Xiao‐Yang , Wen Xiu‐Jun 
Published: December 2016

AbstractMany previous studies have focused on the foraging behaviors and strategies of the red imported fire ants, Solenopsis invicta Buren on solid food or granular bait; little attention has been paid to how liquid sugar is fed upon. In the present study, behavioral responses of S. invicta to 25% sucrose water droplets were observed. Five foraging patterns were identified in S. invicta colonies under laboratory conditions: (i) no feeding, no sucrose water feeding was observed; (ii) surround feeding, ants surrounded and fed along the edge of the sucrose droplet; (iii) stacked feeding, ants stacked and fed along the edge of the sucrose droplet; (iv) droplet‐break feeding, ants broke the liquid droplet and sucked sucrose water that spread on surface of the substance or soil particles previously transported by ants; and (v) cover feeding, whole surface of the sucrose droplet was covered by layers of feeding ants. This is the first time cover feeding in S. invicta has been reported, which obviously requires more ants compared to the other patterns. In addition, individual ants were tracked in videos under laboratory conditions, and behavioral repertoires that led to stacking, covering and droplet‐breaking were identified and described. The field investigation showed that surround feeding was most frequently performed by S. invicta foragers; however, cover feeding was not observed under field conditions during this study. Both laboratory and field studies showed colony‐level variations in sugar‐water feeding.
Recurrence of Helicobacter pylori infection and the affecting factors: A follow‐up study
Authors: Zhou Li Ya , Song Zhi Qiang , Xue Yan , Li Xiao , Li Yan Qing , Qian Jia Ming 
Published: December 2016

ObjectiveRecurrence of Helicobacter pylori (H. pylori) infection weakens the protective effect and long‐term prognosis of eradication. With the widespread therapies, decreasing prevalence of H. pylori infection and improvement in living conditions, the recurrence of H. pylori infection may present with new features. We conducted this prospective, large‐scale, multicenter follow‐up study to determine the recurrence rate of H. pylori infection and its affecting factors.MethodsA total of 827 patients receiving successful H. pylori eradication in our previous randomized controlled trial were enrolled. 13
C‐urea breath test (UBT) was repeated one year after the eradication therapy to determine its recurrence. Moreover, a questionnaire survey was performed to explore the potential factors affecting the recurrence.ResultsA total of 743 patients completed 13C‐UBT (follow‐up rate 89.8%), and the result was positive in 13 patients one year after eradication therapy, with an annual recurrence rate of 1.75% (95% confidence interval [CI] 0.81–2.69%). Six hundred and ninety‐two patients (13 with recurrence and 679 without recurrence) returned their questionnaires, with a response rate of >80%. Multivariate analysis revealed that peptic ulcer (odds ratio [OR] 3.385, 95% CI 1.016–11.274), close contact with individuals having H. pylori infection (OR 4.231, 95% CI 1.201–14.911), and hospitalization (OR 9.302, 95% CI 2.441–35.440) were independent risk factors of H. pylori infection recurrence.ConclusionsThe recurrence of H. pylori infection one year after eradication therapy is low in urban population of China. Peptic ulcer, contact history with individuals having H. pylori infection and hospitalization are risk factors.
RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al. (2016)
Authors: McKinney Garrett J. , Larson Wesley A. , Seeb Lisa W. , Seeb James E. 
Published: December 2016

AbstractIn their recently corrected manuscript, “Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation”, Lowry et al. argue that genome scans using RADseq will miss many loci under selection due to a combination of sparse marker density and low levels of linkage disequilibrium in most species. We agree that marker density and levels of LD are important considerations when designing a RADseq study; however, we dispute that RAD‐based genome scans are as prone to failure as Lowry et al. suggest. Their arguments ignore the flexible nature of RADseq; the availability of different restriction enzymes and capacity for combining restriction enzymes ensures that a well‐designed study should be able to generate enough markers for efficient genome coverage. We further believe that simplifying assumptions about linkage disequilibrium in their simulations are invalid in many species. Finally, it is important to note that the alternative methods proposed by Lowry et al. have limitations equal to or greater than RADseq. The wealth of studies with positive impactful findings that have used RAD genome scans instead supports the argument that properly conducted RAD genome scans are an effective method for gaining insight into ecology and evolution, particularly for non‐model organisms and those with large or complex genomes.