bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcranial recording of electrophysiological neural activity in the rodent brain in vivo using functional photoacoustic imaging of near-infrared voltage-sensitive dye
Authors: Kang Jeeun , Zhang Haichong K. , Kadam Shilpa D. , Fedorko Julie , Valentine Heather , Malla Adarsha P. , Yan Ping , Harraz Maged M. , Kang Jin U. , Rahmim Arman , Gjedde Albert , Loew Leslie M. , Wong Dean F. , Boctor Emad M. 
Published: October 2017

AbstractMinimally-invasive monitoring of electrophysiological neural activities in real-time—that enables quantification of neural functions without a need for invasive craniotomy and the longer time constants of fMRI and PET—presents a very challenging yet significant task for neuroimaging. In this paper, we present in vivo functional PA (fPA) imaging of chemoconvulsant rat seizure model with intact scalp using a fluorescence quenching-based cyanine voltage-sensitive dye (VSD) characterized by a lipid vesicle model mimicking different levels of membrane potential variation. The framework also involves use of a near-infrared VSD delivered through the blood-brain barrier (BBB), opened by pharmacological modulation of adenosine receptor signaling. Our normalized time-frequency analysis presented in vivo VSD response in the seizure group significantly distinguishable from those of the control groups at sub-mm spatial resolution. Electroencephalogram (EEG) recording confirmed the changes of severity and frequency of brain activities, induced by chemoconvulsant seizures of the rat brain. The findings demonstrate that the near-infrared fPA VSD imaging is a promising tool for in vivo recording of brain activities through intact scalp, which would pave a way to its future translation.
Galectin-3 andN-acetylglucosamine promote myogenesis and improve skeletal muscle function in themdxmodel of Duchenne muscular dystrophy
Authors: Rancourt Ann , Dufresne Sébastien , St-Pierre Guillaume , Lévesque Julie-Christine , Nakamura Haruka , Kikuchi Yodai , Satoh Masahiko S. , Frenette Jérôme , Sato Sachiko 
Published: October 2017

AbstractThe muscle membrane, sarcolemma, must be firmly attached to the basal lamina. The failure of proper attachment results in muscle injury, which is the underlying cause of Duchenne muscular dystrophy (DMD), where mutations in the dystrophin gene disrupts the firm adhesion. In DMD patients, even moderate contraction causes damage, leading to progressive muscle degeneration. The damaged muscles are repaired through myogenesis. Consequently, myogenesis is highly active in DMD patients, and the repeated activation of myogenesis leads to the exhaustion of the myogenic stem cells. Therefore, approaches to reducing the risk of the exhaustion are to develop a treatment that strengthens the interaction between the sarcolemma and the basal lamina, and increases the efficiency of myogenesis. Galectin-3 is an oligosaccharide-binding protein and known to be involved in cell-cell interactions and cell-matrix interactions. Galectin-3 is expressed in myoblasts and skeletal muscle while its function in muscle remains elusive. In this study, we found evidence that galectin-3 and the monosaccharideN-acetylglucosamine, which increases the ligands (oligosaccharides) of galectin-3, promotes myogenesisin vitro. Moreover, in themdxmouse model of DMD, treatment withN-acetylglucosamine increased the muscle force production. Our results demonstrate that treatment with N-acetylglucosamine can mitigate the burden of DMD.
Cluster Headache: Comparing Clustering Tools for 10X Single Cell Sequencing Data
Authors: Freytag Saskia , Lonnstedt Ingrid , Ng Milica , Bahlo Melanie 
Published: October 2017

AbstractThe commercially available 10X Genomics protocol to generate droplet-based single cell RNA-seq (scRNA-seq) data is enjoying growing popularity among researchers. Fundamental to the analysis of such scRNA-seq data is the ability to cluster similar or same cells into non-overlapping groups. Many competing methods have been proposed for this task, but there is currently little guidance with regards to which method offers most accuracy. Answering this question is complicated by the fact that 10X Genomics data lack cell labels that would allow a direct performance evaluation. Thus in this review, we focused on comparing clustering solutions of a dozen methods for three datasets on human peripheral mononuclear cells generated with the 10X Genomics technology. While clustering solutions appeared robust, we found that solutions produced by different methods have little in common with each other. They also failed to replicate cell type assignment generated with supervised labeling approaches. Furthermore, we demonstrate that all clustering methods tested clustered cells to a large degree according to the amount of genes coding for ribosomal protein genes in each cell.
Modification of scale-free electrophysiological activity induced by changes in excitatory-inhibitory balance is governed by the dynamics of multiple oscillatory relaxation processes
Authors: Muthukumaraswamy Suresh D , Liley David TJ 
Published: October 2017

AbstractNeurophysiological recordings are dominated by arhythmical activity whose spectra can be characterised by power-law functions, and on this basis are often referred to as reflecting scale-free brain dynamics (1/fβ). Relatively little is known regarding the neural generators and temporal dynamics of this arhythmical behaviour compared to rhythmical behaviour. Here we used Irregularly Resampled AutoSpectral Analysis (IRASA) to quantifyβ, in both the high (5-100 Hz,βhf) and low frequency bands (0.1-2.5 Hz,βlfin EEG/MEG/ECoG recordings and to separate arhythmical from oscillatory modes of activity, such as, alpha rhythms. In MEG/EEG/ECoG data, we demonstrate that oscillatory alpha power dynamically correlates over time withβhfand similarly, participants with higher rhythmical alpha power have higherβhf). In a series of MEG investigations using the GABA reuptake inhibitor tiagabine, the glutamatergic AMPA receptor antagonist perampanel, the NMDA receptor antagonist ketamine and the mixed partial serotonergic agonist LSD we reveal systematic effects of excitation-inhibition balance on bothβhfandβlf. Additionally, strong modulations ofβhfare seen in monkey ECoG data during general anaesthesia using propofol and ketamine. Surrogate data analysis demonstrates that arhythmical activity is generated by both linear and non-linear schemes, with non-linear effects emerging at critical boundaries. We develop and test a unifying model which can explain, the 1/f nature of electrophysiological spectra, their dynamic interaction with oscillatory rhythms as well as the sensitivity of 1/f activity to excitation-inhibition balance by considering electrophysiological spectra as being generated by a collection of stochastically perturbed damped oscillators having a distribution of relaxation rates.
A miniaturized threshold-triggered acceleration data-logger for recording burst movements of aquatic animals
Authors: Nishiumi Nozomi , Matsuo Ayane , Kawabe Ryo , Payne Nicholas , Huveneers Charlie , Watanabe Yuuki Y. , Kawabata Yuuki 
Published: October 2017

AbstractAnimal-borne accelerometers are effective tools for quantifying the kinematics of animal behaviors, such as swimming, running, and flying, under natural conditions. However, quantifying burst movements of small and agile aquatic animals (e.g., small teleost fish), such as during predatory behavior, or while fleeing, remains challenging. To capture the details of burst movements, accelerometers need to sample at a very high frequency, which will inevitably shorten the duration of the recording or increase the size of the device. To overcome this problem, we developed a high-frequency acceleration data-logger that can be triggered by a manually-defined acceleration threshold, thus allowing the selective measurement of animal burst movements. We conducted experiments under laboratory and field conditions to examine the performance of the logger. The laboratory experiment using red seabream (Pagrus major) showed that the new logger could measure the kinematics of their escape behaviors (i.e., body beat cycles and maximum acceleration values). The field experiment using free-swimming yellowtail kingfish (Seriola lalandi) showed that the loggers trigger correctly (i.e., of the 18 burst movements, 17 were recorded by the loggers). We suggest that this new logger can be applied to measure the burst movements of various small and agile animals, whose movements may be otherwise difficult to measure.
Mud sticks after all: Chronically implanted microelectrodes but not electrical stimulation causec-fosexpression along their trajectory
Authors: Pflüger Patrick , Pinnell Richard C. , Martini Nadja , Hofmann Ulrich G. 
Published: October 2017

ABSTRACTThe goal of CNS implanted devices is to build a stable brain-machine-interface. The brain tissue response to the foreign body limits the functionality and viability of this brain-machine connection. Notably the astrocytic glial scar formation and inflammation with resulting neuronal cell loss is considered to be responsible for the signal deterioration over time. We chronically implanted a polyimide microelectrode in the dorsolateral striatum of rats. First, we analyzed thec-fosimmunoreactivity following high frequency stimulation (HFS) of the dorsolateral striatum and second, using GFAP and ED1 immunocytochemistry, the brain tissue response. Acute as well as chronic HFS showed no significant change of neuronalc-fosexpression in the dorsolateral striatum and corresponding cortical areas. We found that the sole chronic implantation of a polyimide microelectrode leads to a reaction of the surrounding neurons, i.e.c-fosexpression, along the implantation trajectory. We also observed the formation of a glial scar around the microelectrode with a low number of inflammation cells. Histological and statistical analysis of NeuN positive cells showed no ‘kill zone’, which accompanied neuronal cell death around the implantation site.
Coral reef carbonate budgets and ecological drivers in the naturally high temperature and high alkalinity environment of the Red Sea
Authors: Roik Anna , Röthig Till , Pogoreutz Claudia , Voolstra Christian R. 
Published: October 2017

AbstractThe coral structural framework is crucial for maintaining reef ecosystem function and services. In the central Red Sea, a naturally high alkalinity is beneficial to reef growth, but rising water temperatures impair the calcification capacity of reef-building organisms. However, it is currently unknown how beneficial and detrimental factors affect the balance between calcification and erosion, and thereby the overall growth of the reef framework. To provide insight into present-day carbonate budgets and reef growth dynamics in the central Red Sea, we measuredin situnet-accretion and net-erosion rates (Gnet) by deployment of limestone blocks and estimated census-based carbonate budgets (Gbudget) in four reef sites along a cross-shelf gradient (25 km). We assessed abiotic variables (i.e., temperature, inorganic nutrients, and carbonate system variables) and biotic drivers (i.e., calcifier and bioeroder abundances). On average, total alkalinity AT(2346 - 2431 μmol kg−1), aragonite saturation state (4.5 - 5.2 Ωa), and pCO2(283 -315 μatm) were close to estimates of pre-industrial global ocean surface waters. Despite these calcification-favorable carbonate system conditions, Gnetand Gbudgetencompassed positive (offshore) and negative net-production (midshore-lagoon and exposed nearshore site) estimates. Notably, Gbudgetmaxima were lower compared to reef growth from pristine Indian Ocean sites. Yet, a comparison with historical data from the northern Red Sea suggests that overall reef growth in the Red Sea has likely remained similar since 1995. When assessing sites across the shelf gradient, ATcorrelated well with reef growth rates (ρ = 0.89), while temperature was a weaker, negative correlate (ρ = −0.71). Further, ATexplained about 65 % of Gbudgetin a best fitting distance-based linear model. Interestingly, parrotfish abundances added up to 82% of explained variation, further substantiating recent studies highlighting the importance of parrotfish to reef ecosystem function. Our study provides a baseline that will be particularly useful in assessing future trajectories of reef growth capacities in the Red Sea under continuous ocean warming and acidification.
Improved imputation of summary statistics for admixed populations
Authors: Rüeger Sina , McDaid Aaron , Kutalik Zoltán 
Published: October 2017

AbstractMotivationSummary statistics imputation can be used to infer association summary statistics of an already conducted, genotype-based meta-analysis to higher ge-nomic resolution. This is typically needed when genotype imputation is not feasible for some cohorts. Oftentimes, cohorts of such a meta-analysis are variable in terms of (country of) origin or ancestry. This violates the assumption of current methods that an external LD matrix and the covariance of the Z-statistics are identical.ResultsTo address this issue, we present variance matching, an extention to the existing summary statistics imputation method, which manipulates the LD matrix needed for summary statistics imputation. Based on simulations using real data we find that accounting for ancestry admixture yields noticeable improvement only when the total reference panel size is > 1000. We show that for population specific variants this effect is more pronounced with increasing FST.
Epidermal expression of a sterol biosynthesis gene regulates root growth by a non-cell autonomous mechanism inArabidopsis
Authors: Short Eleri , Pullen Margaret , Imriz Gul , Liu Dongbin , Cope-Selby Naomi , Smertenko Andrei , Hussey Patrick J. , Topping Jennifer F. , Lindsey Keith 
Published: October 2017

AbstractThe epidermis has been hypothesized to play a signalling role during plant development. One class of mutants showing defects in signal transduction and radial patterning are those in sterol biosynthesis. The expectation is that sterol biosynthesis is a constitutive cell-autonomous process for the maintenance of basic cellular functions. TheHYDRA1(HYD1) gene of Arabidopsis encodes an essential sterol Δ8-Δ7 isomerase, and althoughhyd1mutant seedlings are defective in radial patterning of several tissues, we show that theHYD1gene is expressed primarily in the root epidermis. Cell type-specific transgenic activation ofHYD1transcription reveals thatHYD1expression in the epidermis ofhyd1null mutants is sufficient to rescue root patterning and growth. Unexpectedly, expression ofHYD1in the vascular tissues and root meristem, though not endodermis or pericycle, also leads to phenotypic rescue. Phenotypic rescue is associated with rescued patterning of the PIN1 and PIN2 auxin efflux carriers. The importance of the epidermis is in part due to its role as a site for tissue-specific sterol biosynthesis, and auxin is a candidate for a non-cell autonomous signal.
Chromosome loss rate in cells of different ploidy can be explained by spindle self-organization
Authors: Jelenić Ivan , Selmecki Anna M. , Laan Liedewij , Pavin Nenad 
Published: October 2017

SummaryThe mitotic spindle segregates chromosomes and minimizes chromosome loss for the specific number of chromosomes present in an organism. In Saccharomyces cerevisiae, for example, haploid and diploid cells are part of the sexual life cycle and have a thousand times lower rate of chromosome loss than tetraploid cells. Currently it is unclear what constrains the number of chromosomes that can be segregated with high fidelity in an organism. Here we developed a mathematical model to study if different rates of chromosome loss in cells with different ploidy can arise from changes in (1) spindle dynamics and (2) a maximum duration of mitotic arrest, after which cells enter anaphase. Our model reveals how small increases in spindle assembly time can result in exponential differences in rate of chromosomes loss between cells of increasing ploidy and predicts the maximum duration of mitotic arrest.
Predominant Patterns of Splicing Evolution on Human, Chimpanzee, and Macaque Evolutionary Lineages
Authors: Xiong Jieyi , Jiang Xi , Ditsiou Angeliki , Gao Yang , Sun Jing , Lowenstein Elijah D. , Huang Shuyun , Khaitovich Philipp 
Published: October 2017

ABSTRACTAlthough splicing is widespread and evolves rapidly among species, the mechanisms driving this evolution, as well as its functional implications, are not yet fully understood. We analyzed the evolution of splicing patterns based on transcriptome data from five tissues of humans, chimpanzees, rhesus macaques, and mice. In total, 1,526 exons and exon sets from 1,236 genes showed significant splicing differences among primates. More than 60% of these differences represent constitutive-to-alternative exon transitions while an additional 25% represent changes in exon inclusion frequency. These two dominant evolutionary patterns have contrasting conservation, regulation, and functional features. The sum of these features indicates that, despite their prevalence, constitutive-to-alternative exon transitions do not substantially contribute to long-term functional transcriptome changes. Conversely, changes in exon inclusion frequency appear to be functionally relevant, especially for changes taking place in the brain on the human evolutionary lineage.
Reducing Pollen Dispersal using Forest Windbreaks
Authors: Meyer Thomas , Sagun Vernie , Auer Carol 
Published: October 2017

AbstractThe adoption of genetically engineered (GE) crops has created a demand for practical methods to mitigate pollen dispersal and gene flow. The goal of this project was to measure the ability of a narrow forest windbreak to reduce downwind pollen fluxes from switchgrass (Panicum virgatum L.), a North American grass and model biofuels feedstock. Switchgrass fields were established in two identical plots where one had a forest windbreak and the other was in an open (control) site. Switchgrass reproduction, pollen dispersal, wind speed, and wind direction were measured over two years. Daily release of switchgrass pollen peaked at 11:00-13:30 during a flowering period that lasted about 44 days. The best estimate for switchgrass pollen source strength (PSS) was 141 × 109 pollen/season/hectare for fields planted at commercial densities. The forest windbreak consistently decreased downwind switchgrass pollen concentrations by 333-20,000 fold compared to the control plot which had a 58-77 fold decrease due to downwind distance alone. These results suggest that forest windbreaks could be used as a barrier to reduce pollen dispersal and gene flow from switchgrass and other crops.Research HighlightA narrow forest windbreak greatly decreased downwind pollen concentrations from a switchgrass field suggesting that trees can reduce crop gene flow, enhance coexistence between farming systems, and provide ecosystem services.
Measuring Selection Across HIV Gag: Combining Physico-Chemistry and Population Genetics
Authors: Johnson Elizabeth , Gilchrist Michael A. 
Published: October 2017

AbstractWe present physico-chemical based model grounded in population genetics. Our model predicts the stationary probability of observing an amino acid residue at a given site. Its predictions are based on the physico-chemical properties of the inferred optimal residue at that site and the sensitivity of the protein’s functionality to deviation from the physico-chemical optimum at that site. We contextualize our physico-chemical model by comparing our model fit and parameters it to the more general, but less biologically meaningful entropy based metric: site sensitivity or 1/E. We show mathematically that our physico-chemical model is a more restricted form of the entropy model and how 1/Eis proportional to the log-likelihood of a parameter-wise ‘saturated’ model. Next, we fit both our physico-chemical and entropy models to sequences for subtype C’s Gag poly-protein in the LANL HIV database. Comparing our model’s site sensitivity parametersG′ to 1/Ewe find they are highly correlated. We also compare the ability ofG′, 1/E, and other indirect measures of HIV fitness to empiricalin vitroandin vivomeasures. We findG′ does a slightly better job predicting empirical fitness measures ofin vivoviral escape time andin vitrospreading rates. While our predictive gain is modest, our model can be modified to test more complex or alternative biological hypotheses. More generally, because of its explicit biological formulation, our model can be easily extended to test for stabilizing vs. diversifying selection. We conjecture that our model could also be extended include epistasis in a more realistic manner than Ising models, while requiring many fewer parameters than Potts models.
Analysis of hierarchical organization in gene expression networks reveals underlying principles of collective tumor cell dissemination and metastatic aggressiveness of inflammatory breast cancer
Authors: Tripathi Shubham , Kumar Jolly Mohit , Woodward Wendy A. , Levine Herbert , Deem Michael W. 
Published: October 2017

AbstractBackgroundClusters of circulating tumor cells (CTCs), despite being rare, may account for more than 95% of metastases. Cells in these clusters do not undergo a complete epithelial-to-mesenchymal transition (EMT) but retain some epithelial traits as compared to individually disseminating tumor cells. Determinants of single cell dissemination versus collective dissemination remain elusive. Inflammatory breast cancer (IBC), a highly aggressive breast cancer subtype that chiefly metastasizes via CTC clusters, is a promising model for studying mechanisms of collective tumor cell dissemination. Previous studies on breast cancer and adult acute myeloid leukemia, motivated by a theory that suggests physical systems with hierarchical organization tend to be more adaptable, have found that the expression of metastasis associated genes is more hierarchically organized in cases of successful metastases.MethodsWe used the cophenetic correlation coefficient (CCC) to quantify the hierarchical organization in the expression networks of two distinct gene sets, collective dissemination associated genes and IBC associated genes, in cancer cell lines and in tumor samples from breast cancer patients. Hypothesizing that a higher CCC for collective dissemination associated genes and for IBC associated genes would be associated with a more evident epithelial phenotype and with worse outcomes in breast cancer patients, we evaluated the correlation of CCC with different phenotypic groups.ResultsThe CCC of both gene networks, the collective dissemination associated gene network and the IBC associated gene network, was higher in (a) epithelial cell lines as compared to mesenchymal cell lines and (b) tumor samples from IBC patients, as compared to samples from non-IBC breast cancer patients. A higher CCC of both networks was also correlated with a higher rate of metastatic relapse in breast cancer patients. Neither the levels of CDH1 gene expression, nor gene set enrichment analysis could provide similar insights.ConclusionsThese results suggest that retention of some epithelial traits in disseminating tumor cells as IBC progresses promotes successful breast cancer metastasis to distant organs. The CCC provides additional information regarding the organizational complexity of gene expression in comparison to differential gene expression analyses. We have shown that the CCC may be a useful metric for investigating the collective dissemination phenotype and a prognostic factor for IBC.