bluuebunny/crossref_metadata_2025_split huggingface dataset:
Connectomic identification and three-dimensional color tuning of S-OFF midget ganglion cells in the primate retina
Authors: Wool Lauren E , Packer Orin S , Zaidi Qasim , Dacey Dennis M 
Published: February 2019

AbstractIn the trichromatic primate retina, the ‘midget’ retinal ganglion cell is the classical substrate for red-green color signaling, with a circuitry that enables antagonistic responses between long (L)- and medium (M)-wavelength sensitive cone inputs. Previous physiological studies show that some OFF midget ganglion cells may receive sparse input from short (S)-wavelength sensitive cones, but the effect of S-cone inputs on the chromatic tuning properties of such cells has been unexplored. Moreover, anatomical evidence for a synaptic pathway from S cones to OFF midget ganglion cells through OFF-midget bipolar cells remains ambiguous. In this study we address both questions for the macaque monkey retina. First, we used serial block-face electron microscopy (SBEM) to show that every S-cone in the parafoveal retina synapses principally with a single OFF-midget bipolar cell which in turn forms a private-line connection with an OFF midget ganglion cell. Second, we used patch electrophysiology to characterize the chromatic tuning of OFF midget ganglion cells in the near peripheral retina that receive combined input from L, M and S cones. These ‘S-OFF’ midget cells have a characteristic S-cone spatial signature, but demonstrate heterogeneous color properties due to variable strength of L, M, and S cone input across the receptive field. Together these findings strongly support the hypothesis that the OFF midget pathway is the major conduit for S-OFF signals in primate retina, and redefines the pathway as a chromatically complex substrate that encodes color signals beyond the classically recognized L vs. M and S vs. L+M cardinal mechanisms.Significance statementThe first step of color processing in the visual pathway of primates occurs when signals from short- (S), middle- (M) and long- (L) wavelength sensitive cone types interact antagonistically within the retinal circuitry to create color-opponent pathways. The midget (L vs. M or ‘red-green’) and small bistratified (S vs. L+M, or ‘blue-yellow’) appear to provide the physiological origin of the cardinal axes of human color vision. Here we confirm the presence of an additional S-OFF midget circuit in the macaque monkey fovea with scanning block-face electron microscopy (SBEM) and show physiologically that a subpopulation of S-OFF midget cells combine S, L and M cone inputs along non-cardinal directions of color space, expanding the retinal role in color coding.
Contrasting patterns of ERK activation in the tail of the striatum in response to aversive and rewarding signals
Authors: Gangarossa Giuseppe , Castell Laia , Castro Liliana , Tarot Pauline , Veyrunes Frederic , Vincent Pierre , Bertaso Federica , Valjent Emmanuel 
Published: February 2019

AbstractThe caudal part of the striatum, also named the tail of the striatum (TS), defines a fourth striatal domain. Determining whether rewarding, aversive and salient stimuli regulate the activity of striatal spiny projections neurons (SPNs) of the TS is therefore of a paramount importance to understand its functions, which remain largely elusive. Taking advantage of genetically encoded biosensors (AKAR3) to record PKA signals and by analyzing the distribution of D1R-and D2R/A2aR-SPNs in the TS, we characterized three evolutionary highly conserved subterritories: a D2R/A2aR-lacking area, a D1R/D2-SPNs-enriched and an D1R/D2R-intermingled area. The analysis of ERK phosphorylation in these TS subterritories in response to distinct appetitive, aversive and pharmacological stimuli revealed that SPNs of the TS are not recruited by stimuli triggering innate or learned avoidance responses, fasting, satiety or palatable signals. In contrast, D1R-SPNs of the intermingled and D2R/A2AR-lacking areas are strongly activated by both direct stimulation of D1R and psychostimulant drugs (d-amphetamine, cocaine, MDMA or methylphenidate), but not by hallucinogens. Finally, a similar pattern of ERK activation was observed by blocking selectively dopamine reuptake. Together, our results reveal that the caudal TS might participate in the processing of specific reward signals.
Allele-specific transcript abundance: A pilot study in healthy centenarians
Authors: Tindale Lauren C. , Thiessen Nina , Leach Stephen , Brooks-Wilson Angela R. 
Published: February 2019

AbstractThe genetic basis of healthy aging and longevity remains largely unexplained. One hypothesis as to why long-lived individuals do not appear to have a lower number of common-complex disease variants, is that despite carrying risk variants, they express disease-linked alleles at a lower level than the wild-type alleles. Allele-specific abundance (ASA) is the different transcript abundance of the two haplotypes of a diploid individual. We sequenced the transcriptomes of four healthy centenarians and four mid-life controls. CIBERSORT was used to estimate blood cell fractions: neutrophils were the most abundant source of RNA, followed by CD8+ T cells, resting NK cells, and monocytes. ASA variants were more common in non-coding than coding regions. Centenarians and controls had a comparable distribution of ASA variants by predicted effect, and we did not observe an overall bias in expression towards major or minor alleles. Immune pathways were most highly represented among the gene set that showed ASA. Although we found evidence of ASA in disease-associated genes and transcription factors, we did not observe any differences in the pattern of expression between centenarians and controls in this small pilot study.
Ultra-thin fluorocarbon foils optimise multiscale imaging of three-dimensional native and optically cleared specimens
Authors: Hötte Katharina , Koch Michael , Hof Lotta , Tuppi Marcel , Moreth Till , Stelzer Ernst H. K. , Pampaloni Francesco 
Published: February 2019

AbstractIn three-dimensional light microscopy, the heterogeneity of the optical density in a specimen ultimately limits the achievable penetration depth and hence the three-dimensional resolution. The most direct approach to reduce aberrations, improve the contrast, and achieve an optimal resolution is minimizing the impact of changes of the refractive index along an optical path. Many light sheet fluorescence microscopes operate with a large chamber that contains an aqueous immersion medium and an inner specimen holder that contains the specimen embedded in a possibly entirely different non-aqueous medium. In order to minimize the impact of the specimen holder on the optical quality, we use multi-facetted cuvettes fabricated with vacuum-formed ultra-thin fluorocarbon (FEP) foils The ultra-thin FEP-foil cuvettes have a wall thickness of about 12 µm. They are resilient to fluidic exchanges, durable, mechanically stable and yet flexible.We confirm the improved imaging performance of ultra-thin FEP-foil cuvettes with excellent quality images of whole organs, thick tissue sections and dense organoid clusters. The cuvettes outperform many other sample-mounting techniques in terms of full separation of the specimen from the immersion medium, compatibility with aqueous and organic clearing media, quick specimen mounting without hydrogel embedding, as well as their applicability for multiple-view imaging and automated segmentation. Additionally, we show that ultra-thin FEP foil cuvettes are suitable for seeding and growing organoids over a time period of at least ten days. The ultra-thin cuvettes allow the fixation and staining of the specimens inside the holder, preserving the delicate morphology of e.g. fragile, mono-layered three-dimensional organoids.
High prevalence of precocious menarche in Puerto Barrios, Guatemala
Authors: Torres-González Edmundo , López Griselda , Trabert Britton , Lou Hong , Guerra Sarita Polo , Orozco Anali , Garland Lisa , Florez-Vargas Oscar , Castillo Miriam , Argueta Victor , Gharzouzi Eduardo , Dean Michael , Orozco Roberto 
Published: February 2019

AbstractBackgroundAge of menarche is variable between women with a median age of 14 years old worldwide, and averages ranging from 12-13 years old in developed countries to 15-16 years old in low and middle-income countries. Precocious menarche, occurring before age 11, is rare, with a prevalence of 1.4 to 2.3% in most worldwide populations. Precocious menarche is poorly understood but is associated with early puberty and is a risk factor for pre-teen birth. In studying HPV prevalence in Latin America, we identified a community with a very high rate of precocious menarche.Objective(s)Describe the patterns of precocious menarche in Guatemala.Study DesignReproductive histories were collected from 3385 cancer-free women at the time of routine Pap smear from 4 sites in Guatemala including hospitals in Guatemala City and Puerto Barrios, Izabal. Statistical analyses included determination of the age-specific prevalence of menarche and linear regression to determine the effect of year of birth, study site, number of births and miscarriages, on the age at menarche.ResultsCompared with a low prevalence of precocious menarche observed in Guatemala City (3.1%, 88/2834), we observed a high prevalence of precocious menarche in the city of Puerto Barrios, Izabal, Guatemala (88%, 486/551). We observed a high prevalence of precocious menarche in Puerto Barrios across all age groups. In contrast in Guatemala City, the median age at menarche declined from the age of 14 in 50-60-year-old women to 13 in women under 40 years of age. Hospital records show that the occurrence of both miscarriage and pregnancy under age 14 is substantially higher in Izabal. In addition, the main public hospital in Puerto Barrios accounts for a high fraction of the early pregnancies and miscarriages seen in Guatemala.ConclusionsIn Puerto Barrios, Izabal, Guatemala, the prevalence of menarche before age 11 is dramatically elevated compared to Guatemala City and substantially higher than other worldwide populations. We observed precocious menarche in Puerto Barrios in all age groups examined, indicating that this condition has been common for decades. This finding is supported by the comparatively higher occurrence of early pregnancy and miscarriage in Puerto Barrios compared with Guatemala City. The cause is unknown, but precocious menarche is associated with adverse reproductive outcome in young women and warrants further investigation.
A NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data
Authors: Matsumoto Hirotaka , Hayashi Tetsutaro , Ozaki Haruka , Tsuyuzaki Koki , Umeda Mana , Iida Tsuyoshi , Nakamura Masaya , Okano Hideyuki , Nikaido Itoshi 
Published: February 2019

AbstractSingle-cell RNA sequencing has enabled researchers to quantify the transcriptomes of individual cells, infer cell types, and investigate differential expression among cell types, which will lead to a better understanding of the regulatory mechanisms of cell states. Transcript diversity caused by phenomena such as aberrant splicing events have been revealed, and differential expression of previously unannotated transcripts might be overlooked by annotation-based analyses.Accordingly, we have developed an approach to discover overlooked differentially expressed (DE) gene regions that complements annotation-based methods. We applied our algorithm to two datasets and discovered several intriguing DE transcripts, including a transcript related to the modulation of neural stem/progenitor cell differentiation.
GEMME: a simple and fast global epistatic model predicting mutational effects
Authors: Laine Elodie , Karami Yasaman , Carbone Alessandra 
Published: February 2019

AbstractsThe systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modeling inter-site dependencies within biological sequences. However, state-of-the-art methods require numerous highly variable sequences and remain time consuming. Here, we present GEMME (www.lcqb.upmc.fr/GEMME), a method that overcomes these limitations by explicitly modeling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. Assessed against 41 experimental high-throughput mutational scans, GEMME overall performs similarly or better than existing methods and runs faster by several orders of magnitude. It greatly improves predictions for viral sequences and, more generally, for very conserved families. It uses only a few biologically meaningful and interpretable parameters, while existing methods work with hundreds of thousands of parameters.
Maladaptive striatal plasticity and abnormal reward-learning in cervical dystonia
Authors: Gilbertson Tom , Humphries Mark , Steele J. Douglas 
Published: February 2019

AbstractIn monogenetic generalized forms of dystonia,in vitroneurophysiological recordings have demonstrated direct evidence for abnormal plasticity at the level of the cortico-striatal synapse. It is unclear whether similar abnormalities contribute to the pathophysiology of cervical dystonia, the most common type of focal dystonia. We investigated whether abnormal cortico-striatal synaptic plasticity contributes to abnormal reward-learning behavior in patients with focal dystonia. Forty patients and forty controls performed a reward-gain and loss-avoidance reversal learning task. Participant’s behavior was fitted to a computational model of the basal ganglia incorporating detailed cortico-striatal synaptic learning rules. Model comparisons were performed to assess the ability of four hypothesised receptor specific abnormalities of cortico-striatal long term potentiation (LTP) and Long Term Depression (LTD): increased or decreased D1:LTP/LTD and increased or decreased D2: LTP/LTD to explain abnormal behavior in patients. Patients were selectively impaired in the post-reversal phase of the reward task. Individual learning rates in the reward reversal task correlated with the severity of the patient’s motor symptoms. A model of the striatum with decreased D2:LTP/ LTD best explained the patient’s behavior, suggesting excessive D2 cortico-striatal synaptic depotentiation could underpin biased reward learning in patients with cervical dystonia. Reversal learning impairment in cervical dystonia may be a behavioural correlate of D2 specific abnormalities in cortico-striatal synaptic plasticity. Reinforcement learning tasks with computational modeling could allow the identification of molecular targets for novel treatments based on their ability to restore normal reward-learning behavior in these patients.
Whole Brain Polarity Regime Dynamics are Significantly Disrupted in Schizophrenia and Correlate Strongly with Network Connectivity Measures
Authors: Miller Robyn L. , Pearlson Godfrey , Calhoun Vince D. 
Published: February 2019

AbstractFrom a large clinical blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) study, we report several interrelated findings involving transient supra-network brainwide states characterized by a saturation phenomenon we are referring to as “polarization.” These are whole-brain states in which the voxelwise-normalized BOLD (vnBOLD) activation of a large proportion of voxels is simultaneously either very high or very low. The presence of such states during a resting-state fMRI (rs-fMRI) scan is significantly anti-correlated with diagnosed schizophrenia, significantly anti-correlated with connectivity between subcortical networks and auditory, visual and sensorimotor networks and also significantly anti-correlated with contemporaneous occupancy of transient functional network connectivity states featuring broad disconnectivity or strong inhibitory connections between the default mode and other networks. Conversely, the presence of highly polarized vn-BOLD states is significantly correlated with connectivity strength between auditory, visual and sensorimotor networks and with contemporaneous occupancy of transient whole-brain patterns of strongly modularized network connectivity and diffuse hyperconnectivity. Despite their consistency with well-documented effects of schizophrenia on static and time-varying functional network connectivity, the observed relationships between polarization and network connectivity are with very few exceptions unmediated by schizophrenia diagnosis. We also find that the spatial distribution of voxels most likely to contribute to the highly polarized states (polarity participation maps (PPMs)) differs with a high degree of statistical significance between schizophrenia patients and healthy controls. Finally, we report evidence suggesting the process by which the most polarized states are achieved, i.e. the ways that strongly polarized voxel regions extend, merge and recede also differs significantly between patient and control populations. Many differences observed between patients and controls are echoed within the patient population itself in the effect patterns of positive symptomology (e.g. hallucinations, delusions, grandiosity and other positive symptoms of schizophrenia). Our findings highlight a particular whole-brain spatiotemporal BOLD activation phenomenon that differs markedly between healthy subjects and schizophrenia patients, one that also strongly informs time-resolved network connectivity patterns that are associated with this serious clinical disorder.
Percentage of Foveal versus Total Macular Geographic Atrophy as a Predictor of Visual Acuity in Age-related Macular Degeneration
Authors: Bagheri Saghar , Lains Ines , Silverman Rebecca , Kim Ivana , Eliott Dean , Silva Rufino , Miller John , Husain Deeba , Miller Joan W , Saad Leonide , Vavvas Demetrios 
Published: February 2019

AbstractObjectivesTo investigate the relationship between visual acuity (VA), total area of geographic atrophy (GA) and percentage of foveal GA.MethodsMulticenter, retrospective cross-sectional study of patients with GA due to age-related macular degeneration. Demographics, VA, fundus autofluorescence (FAF) and optical coherence tomography (OCT) images were collected. Using FAF images aided by OCT, foveal sparing status, GA pattern, total GA size, and percentage of GA covering the foveal area - area within a 1.5 mm diameter circle centered on the fovea centralis - were assessed. Univariable and multiple linear regression analyses were performed.Results54 eyes (mean age 78.7 ±7.7 (SD), 60.0% female) were studied. Mean VA was 0.8 ± 0.6 logMAR, mean total GA 8.8 ± 6.7 mm2 and mean percentage of foveal GA was 71.5 ± 30.9%. Of all assessed eyes, 48.2% (n = 26) presented with multifocal GA, and 18.5% (n = 10) had foveal sparing. Multiple regression analysis revealed that, controlling for age and GA pattern, the percentage of foveal GA presented a statistically significant association with VA (ß = 0.41, P = 0.004). No significant associations were observed with mean total GA size, while controlling for the same variables (ß = 0.010, P = 0.440).ConclusionPercentage of foveal GA was significantly associated with VA impairment, while the same was not verified for total GA area. These findings suggest that percentage of foveal GA may represent a more useful tool for assessing the impact of GA on VA. Further validation is needed in larger cohorts.
Isolates from colonic spirochaetosis in humans show high genomic divergence and carry potential pathogenic features but are not detected by 16S amplicon sequencing using standard primers for the human microbiota
Authors: Thorell Kaisa , Inganäs Linn , Backhans Annette , Agréus Lars , Öst Åke , Walker Marjorie , Talley Nicholas J , Kjellström Lars , Andreasson Anna , Engstrand Lars 
Published: February 2019

AbstractColonic spirochaetosis, diagnosed based on the striking appearance in histological sections, still has an obscure clinical relevance and only few bacterial isolates from this condition have been characterized to date. In a randomized, population-based study in Stockholm, Sweden, 745 healthy individuals underwent colonoscopy with biopsy sampling. In these individuals, 17 (2.3 %) had colonic spirochaetosis, which was associated with eosinophilic infiltration and a three-fold increased risk for irritable bowel syndrome (IBS). We aimed to culture the bacteria and perform whole genome sequencing of the isolates from this unique representative population sample. From 14 out of 17 individuals with spirochaetosis we successfully isolated, cultured and performed whole genome sequencing of in total 17 isolates including theBrachyspira aalborgitype strain 513AT. Also, 16S analysis of the mucosa-associated microbiota was performed in the cases and non-spirochaetosis controls.This is the first report of whole genome analysis of clinical isolates from individuals with colonic spirochaetosis. We found one isolate to be of the speciesBrachyspira pilosicoliand all remaining isolates were of the speciesBrachyspira aalborgi. Besides displaying extensive genetic heterogeneity, the isolates harboured several mucin-degrading enzymes and other virulence-associated genes that could confer a pathogenic potential in the human colon. We also showed that 16S amplicon sequencing using standard primers for human microbiota studies fail to detectBrachyspiradue to primer incompatibility. This failure to detect colonic spirochaetosis should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings.
NMR Methods for Quantitative Isotopomer Rates in Real-Time Metabolism of Cells
Authors: Reed Michelle AC , Roberts Jennie , Gierth Peter , Kupče Ēriks , Günther Ulrich L 
Published: February 2019

AbstractTracer-based metabolism is becoming increasingly important to study metabolic mechanisms in cells. NMR offers several approaches to measure label incorporation in metabolites, including 13C and 1H-detected spectra. The latter are generally more sensitive but quantification depends on the proton carbon 1JCH coupling constant which varies significantly between different metabolites. It is therefore not possible to have one experiment optimised for all metabolites and quantification of 1H-edited spectra such as HSQCs requires precise knowledge of coupling constants. Increasing interest in tracer-based and metabolic flux analysis requires robust analyses with reasonably small acquisition times. Here we compare 13C-filtered and 13C-edited methods for quantification with a special focus towards application in real-time NMR of cancer cells under near-physiological conditions. We find an approach using a double-filter most suitable and sufficiently robust to reliably obtain 13C-incorporations from difference spectra. This is demonstrated for JJN3 multiple myeloma cells processing glucose over 24h.
Drying enhances signal intensity for global GC-MS metabolomics
Authors: Liebeke Manuel , Puskas Erik 
Published: February 2019

ABSTRACTWe report here that a straightforward change of standard derivatization procedure for GC-MS metabolomics is leading to a strong increase in metabolite signal intensity. Drying samples between methoxymation and trimethylsilylation significantly increased signals by two-to tenfold in extracts of yeast cells, plant and animal tissue and human urine. This easy step reduces the cost of sample material and the need for expensive new hardware.