bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regional ventilation characteristics during non-invasive respiratory support in preterm infants
Authors: Thomson J , Rüegger CM , Perkins EJ , Pereira-Fantini PM , Farrell O , Owen LS , Tingay DG 
Published: August 2020

ABSTRACTObjectiveTo determine the regional ventilation characteristics during non-invasive ventilation in stable preterm infants. The secondary aims were to explore the relationship between indicators of ventilation homogeneity and other clinical measures of respiratory status.DesignProspective observational study.SettingTwo tertiary neonatal intensive care units.PatientsForty stable preterm infants born <30 weeks gestation receiving either CPAP (n=32) or nHF(n=8) if <36 weeks corrected gestation, and extubated for at least 24 hours at time of study.InterventionsContinuous electrical impedance tomography imaging of regional ventilation during 60-minutes of quiet breathing on clinician-determined non-invasive settings.Main outcome measuresGravity-dependent and right-left centre of ventilation (CoV), percentage of whole lung tidal volume by lung region, and percentage of lung unventilated were determined for 120 artefact-free breaths/infant (4770 breaths included). Oxygen saturation, heart and respiratory rates were also measured.ResultsVentilation was greater in the right lung (mean (SD) CoVRL 69.1 (14.9)%) and the gravity non-dependent lung; ideal-actual CoV 1.4 (4.5). The central third of the lung received the most tidal volume, followed by the non-dependent and dependent regions (p<0.0001 repeated measure ANOVA). Ventilation inhomogeneity was associated with worse SpO2/FiO2, (p=0.031, r2 0.12; linear regression). In those infants that later developed bronchopulmonary dysplasia (n=25) SpO2/FiO2 was worse and non-dependent ventilation inhomogeneity greater than in those that did not (both p<0.05; t test Welch correction).ConclusionsThere is high breath-by-breath variability in regional ventilation patterns during NIV in preterm infants. Ventilation favoured the gravity non-dependent lung, with ventilation inhomogeneity associated with worse oxygenation.
Seasonal climate variations promote bacterial α-diversity in soil
Authors: Zhao Xin-Feng , Shu Wen-Sheng , Hao Yi-Qi 
Published: August 2020

AbstractEcological theory suggests that temporal environmental fluctuations can contribute greatly to diversity maintenance. Given bacteria’s short generation time and rapid responses to environmental change, seasonal climate fluctuations are very likely to play an important role in maintaining the extremely high α-diversity of soil bacterial community, which has been unfortunately neglected in previous studies. Here, with in-depth analyses of two previously published soil bacterial datasets at global scale, we found that soil bacterial α-diversity was positively correlated with both seasonal variations of temperature and precipitation. Furthermore, piecewise structural equation models showed that seasonal variations of temperature or precipitation directly promoted soil bacterial α-diversity in each dataset. However, it is noteworthy that the importance of seasonal climate variations might be underestimated in the above analyses, due to the high level of environmental variations irrelevant to climate seasonality among sampling sites and the lack of sampling across seasons. Supplementary analyses of a previously published wheat cropland dataset with samples collected in both summer and winter across North China Plain was conducted. Similarly, we found that bacterial α-diversity was positively correlated with seasonal climate variations, but much stronger, though the range of seasonal climate variations was much smaller compared to the two global datasets. Collectively, these findings implied that fluctuation-dependent mechanisms of diversity maintenance presumably operate in soil bacterial communities. Based on existing evidence, we speculated that the storage effect may be the main mechanism responsible for diversity maintenance in soil bacterial community, but rigorous experimental tests are needed in the future.
Advances in mixed cell deconvolution enable quantification of cell types in spatially-resolved gene expression data
Authors: Danaher Patrick , Kim Youngmi , Nelson Brenn , Griswold Maddy , Yang Zhi , Piazza Erin , Beechem Joseph M. 
Published: August 2020

AbstractWe introduce SpatialDecon, an algorithm for quantifying cell populations defined by single cell RNA sequencing within the regions of spatially-resolved gene expression studies. It obtains cell abundance estimates that are spatially-resolved, granular, and paired with highly multiplexed gene expression data.SpatialDecon incorporates several advancements in the field of gene expression deconvolution. We propose an algorithm based in log-normal regression, attaining sometimes dramatic performance improvements over classical least-squares methods. We compile cell profile matrices for 27 tissue types. We identify genes whose minimal expression by cancer cells makes them suitable for immune deconvolution in tumors. And we provide a lung tumor dataset for benchmarking immune deconvolution methods.In a lung tumor GeoMx DSP experiment, we observe a spatially heterogeneous immune response in intricate detail and identify 7 distinct phenotypes of the localized immune response. We then demonstrate how cell abundance estimates give crucial context for interpreting gene expression results.
Different activation signatures in the primary sensorimotor and higher-level regions for haptic three-dimensional curved surface exploration
Authors: Yang Jiajia , Molfese Peter J. , Yu Yinghua , Handwerker Daniel A. , Chen Gang , Taylor Paul A. , Ejima Yoshimichi , Wu Jinglong , Bandettini Peter A. 
Published: August 2020

AbstractHaptic object perception begins with continuous exploratory contacts, and the human brain needs to accumulate sensory information continuously over time. However, it is still unclear how the primary sensorimotor cortex (PSC) interacts with these higher-level regions during haptic exploration across time. This functional magnetic resonance imaging (fMRI) study investigates time-dependent haptic object processing by examining brain activity during haptic 3D curve and roughness estimation. For this experiment, we designed sixteen haptic stimuli (4 kinds of curve × 4 kinds of roughness) for the haptic curve and roughness estimation tasks. Twenty participants were asked to move their right index and middle fingers along with the surface twice and to estimate one of the two features--roughness or curvature--dependent on the task instruction. We found that the brain activity in several higher-level regions (e.g., bilateral posterior parietal cortex) linearly increased with curvature through the haptic exploration phase. Surprisingly, we found that the contralateral PSC was parametrically modulated by the number of curves only during the late exploration phase, but not during the early exploration phase. In contrast, we found no similar parametric modulation activity patterns for haptic roughness estimation in either the contralateral PSC or in the higher-level regions. Together, our findings suggest that haptic 3D object perception is processed across the cortical hierarchy, while the contralateral PSC interacts with other higher-level regions across time in a manner that is dependent upon object features.HighlightsWe observed the brain activity of haptic object perception using parametric stimuli.Haptic curve estimation showed parametric modulation across the cortical hierarchy.Curve parametric modulation in the sensorimotor cortex showed time dependency.Roughness parametric modulation showed very little dependency in any regions of the brain.These findings reflect the nature of time-dependent haptic object processing in the brain.
Plant community associations with environmental variables in a semi-deciduous tropical forest of the Dominican Republic
Authors: Martínez Batlle José Ramón , van der Hoek Yntze 
Published: August 2020

AbstractDespite being increasingly threatened by human-induced disturbances, dry forests remain the least studied and protected forest types in the Caribbean region. In contrast to many other forest systems in the world, we have little knowledge of the site-specific variation in vegetation communities within these forests, nor understand how plant species distribution is determined by environmental variables, including among them geological attributes. Here, we assessed the associations between plant communities and habitat types in a semi-deciduous forest of the Dominican Republic. We collected vegetation data from 23 sites within the Ocoa river basin, which we classified into six groups with a Random Forest algorithm, lithology, geomorphology, topography, and last decade history of forest loss as predictor variables. We established three main clusters: one group which encompassed sites with forest over a limestone substrate, four groups of sites with forests over a marlstone substrate with varied degrees of steepness and forest loss history, and one group that gathered all sites with forest over an alluvial substrate. In order to measure the associations of plant communities with groups of sites, we used the indicator value index (IndVal), which indicates whether a plant species is found in one or multiple habitat types, and the phi coefficient of association, which measures species preferences for habitats. We found that 16 species of woody plants are significantly associated with groups of sites by means of their indices. Our findings suggest that the detection of plant species associations with our selection of environmental variables is possible using a combination of indices. We show that there is considerable variation in plant community composition within the semi-deciduous forest studied, and suggest that conservation planning should focus on protection of this variation, while considering the significance and variability of geodiversity as well. In addition, we propose that our indicator groups facilitate vegetation mapping in nearby dry forests, where it is difficult to conduct thorough vegetation or environmental surveys. In short, our analyses hold potential for the development of site-specific management and protection measures for threatened semi-deciduous forests in the Caribbean.
Social integration predicts survival in female white-faced capuchin monkeys
Authors: Kajokaite Kotrina , Whalen Andrew , Koster Jeremy , Perry Susan 
Published: August 2020

ABSTRACTAcross multiple species of social mammals, a growing number of studies have found that that individual sociality is associated with survival. In long-lived species, like primates, lifespan is one of the main components of fitness. We used 18 years of data from the Lomas Barbudal Monkey project to quantify social integration in 11 capuchin (Cebus capucinus) groups and tested whether female survivorship was associated with females’ tendencies to interact with three types of partners: (1) all group members, (2) adult females, (3) adult males. We found strong evidence that females who engaged more with other females in affiliative interactions and foraged in close proximity experienced increased survivorship. We found some weak evidence that females might also benefit from engaging in more support in agonistic contexts with other females. These benefits were evident in models that account for the females’ rank and group size. Female interactions with all group members also increased survival, but the estimates of the effects were more uncertain. In interactions with adult males, only females who provided more grooming to males survived longer. The results presented here suggest that social integration may result in survival-related benefits. Females might enjoy these benefits through exchanging grooming for other currencies, such as coalitionary support or tolerance.
A quick and easy way to estimate entropy and mutual information for neuroscience
Authors: Zbili Mickael , Rama Sylvain 
Published: August 2020

AbstractCalculations of entropy of a signal or mutual information between two variables are valuable analytical tools in the field of neuroscience. They can be applied to all types of data, capture nonlinear interactions and are model independent. Yet the limited size and number of recordings one can collect in a series of experiments makes their calculation highly prone to sampling bias. Mathematical methods to overcome this so-called “sampling disaster” exist, but require significant expertise, great time and computational costs. As such, there is a need for a simple, unbiased and computationally efficient tool for estimating the level of entropy and mutual information. In this paper, we propose that application of entropy-encoding compression algorithms widely used in text and image compression fulfill these requirements. By simply saving the signal in PNG picture format and measuring the size of the file on the hard drive, we can estimate entropy changes through different conditions. Furthermore, with some simple modifications of the PNG file, we can also estimate the evolution of mutual information between a stimulus and the observed responses through different conditions. We first demonstrate the applicability of this method using white-noise-like signals. Then, while this method can be used in all kind of experimental conditions, we provide examples of its application in patch-clamp recordings, detection of place cells and histological data. Although this method does not give an absolute value of entropy or mutual information, it is mathematically correct, and its simplicity and broad use make it a powerful tool for their estimation through experiments.
Towards A 3D Chromosome Shape Alphabet
Authors: Soto Carlos , Bryner Darshan , Neretti Nicola , Srivastava Anuj 
Published: August 2020

AbstractThe study of the 3-dimensional (3D) structure of chromosomes – the largest macromolecules in biology – is one of the most challenging to date in structural biology. Here, we develop a novel representation of chromosomes, as sequences ofshape lettersfrom a finiteshape alphabet, which provides a compact and efficient way to analyze ensembles of chromosome shape data, akin to the analysis of texts in a language by using letters. We construct aChromosome Shape Alphabet(CSA) from an ensemble of chromosome 3D structures inferred from Hi-C data – via SIMBA3D or other methods – by segmenting curves based on topologically associating domains (TADs) boundaries, and by clustering all TADs’ 3D structures into groups of similar shapes. The median shapes of these groups, with some pruning and processing, form theChromosome Shape Letters(CSLs) of the alphabet. We provide a proof-of-concept for these CSLs by reconstructing independent test curves using only CSLs (and corresponding transformations) and comparing these reconstructions with the original curves. Finally, we demonstrate how CSLs can be used to summarize the variability of shapes in an ensemble of chromosome 3D structures using generalized sequence logos.
Proteogenomic analysis unveils the HLA Class I presented immunopeptidome in melanoma and EGFR mutant lung adenocarcinoma
Authors: Qi Yue A. , Maity Tapan K. , Cultraro Constance M. , Misra Vikram , Zhang Xu , Ade Catherine , Gao Shaojian , Milewski David , Nguyen Khoa D. , Ebrahimabadi Mohammad H. , Hanada Ken-ichi , Khan Javed , Sahinalp Cenk , Yang James C. , Guha Udayan 
Published: August 2020

AbstractImmune checkpoint inhibitor and adoptive lymphocyte transfer-based therapies have shown great therapeutic potential for cancers with high tumor mutation burden (TMB). Here, we employed mass spectrometry (MS)-based proteogenomic large-scale profiling to identify potential immunogenic human leukocyte antigen (HLA) Class I-presented peptides in both melanoma, a “hot tumor” with high TMB, and EGFR mutant lung adenocarcinoma, a “cold tumor” with low TMB. We identified several classes of neopeptides, including mutated neoantigens and more than 1000 post-translationally modified peptides representing 58 different PTMs. We constructed a cancer germline (CG) antigen database with 285 antigens and identified 42 Class I-presented CG antigens. Finally, we developed a non-canonical peptide discovery pipeline to identify 44 lncRNA-derived peptides and validated Class I binding for select neopeptides. We provide direct evidence of HLA Class I presentation of a large number of neopeptides for potential vaccine or adoptive cell therapy in melanoma and mutant EGFR lung cancer.
Gut microbiome composition predicts summer core range size in a generalist and specialist ungulate
Authors: Wolf J.F. , Kriss K.D. , MacAulay K.M. , Munro K. , Patterson B.R. , Shafer A.B.A. 
Published: August 2020

AbstractThe gut microbiome of animals varies by age, diet, and habitat, and directly influences individual health. Similarly, variation in an individual’s home range can lead to differences in feeding strategies and fitness. Ungulates (hooved mammals) exhibit species-specific microbiomes and habitat use patterns: here, we combined gut microbiome and movement data to assess relationships between space use and the gut microbiome in a specialist and a generalist ungulate. We captured and GPS radiocollared 24 mountain goats (Oreamnos americanus) and 34 white-tailed deer (Odocoileus virginianus). We collected fecal samples and conducted high-throughput sequencing of the 16S rRNA gene. Using GPS data, we estimated core (50%) and home range (95%) sizes and calculated proportional use for several important habitat types. We generated metrics related to gut diversity and key bacterial ratios. We hypothesize that largerFirmicutestoBacteroidesratios confer body size or fat advantages that allow for larger home ranges, and that relationships between gut diversity and disproportionate habitat use is stronger in mountain goats due to their restricted niche relative to white-tailed deer.FirmicutestoBacteroidesratios were positively correlated with core range area in both species. Mountain goats exhibited a negative relationship between gut diversity and use of two key habitat types (treed areas and escape terrain), whereas no relationships were detected in white-tailed deer. This is the first study to relate core range size to the gut microbiome in wild ungulates and is an important proof of concept that advances the information that can be gleaned from non-invasive sampling.
Evidence for an extreme founding effect in a highly successful invasive species
Authors: Kratzer Kateryna V. , van der Marel Annemarie , Garroway Colin , López-Darias Marta , Petersen Stephen D. , Waterman Jane M. 
Published: August 2020

AbstractThe adaptive potential of invasive species is thought to decrease during founding events due to reduced genetic diversity, limiting the new population’s ability to colonize novel habitats. Barbary ground squirrels (Atlantoxerus getulus) were purportedly introduced as a single breeding pair to the island of Fuerteventura but have expanded to over a million individuals spread across the island in just over 50 years. We estimated the number of founders and measured the level of genetic diversity in this population using the mitochondrial displacement loop and microsatellite markers. Island samples (n= 19) showed no variation in the d-loop, suggesting a single founding female, while Moroccan samples (n= 6) each had unique mitochondrial haplotypes. The microsatellite data of the island population (n= 256 individuals) revealed a small effective population size, low levels of heterozygosity, and high levels of inbreeding, supporting a founding population size of two to three individuals. Our results suggest thatA. getulushas undergone an intense genetic bottleneck during their colonization of the island. They are one of the few species where introduction effort does not explain invasion success, although further investigation may explain how they have avoided the worst expected effects following an extreme genetic bottleneck.
Effect of sublethal prenatal endotoxaemia on murine placental transport systems and lipid homeostasis
Authors: Reginatto MW , Fontes KN , Monteiro VRS , Silva NL , Andrade CBV , Gomes HR , Imperio GE , Bloise FF , Kluck G , Atella GC , Matthews SG , Bloise E , Ortiga-Carvalho TM 
Published: August 2020

AbstractInfection alters the expression of transporters that mediate the placental exchange of xenobiotics, lipids and cytokines. We hypothesized that lipopolysaccharide (LPS) modifies the expression of placental transport systems and lipid homeostasis. LPS (150 μg/kg; i.p.) treatments were administered for 4 h or 24 h, animals were euthanized at gestational days (GD) 15.5 or 18.5, and maternal blood, foetuses and placentae were collected. Increased rates of foetal demise were observed at GD15.5 following LPS treatment, whereas at GD18.5, high rates of early labour occurred and were associated with distinct proinflammatory responses. LPS did not alter ABC transporter mRNA expression but decreased Fabppm at GD15.5 (LPS-4 h) and increased Fat/Cd36 lipid transporter mRNA at GD18.5 (LPS-4 h). At the protein level, breast cancer-related protein (BCRP) and Abcg1 levels were decreased in the placental labyrinth zone (Lz) at GD15.5, whereas P-glycoprotein (P-gp) and Bcrp Lz-immunostaining was decreased at GD18.5. In the placental junctional zone (Jz), P-gp, Bcrp and Abcg1 levels were higher at GD18.5. Specific maternal plasma and placental changes in triacylglycerol, free fatty acid, cholesterol, cholesterol ester and monoacylglycerol levels were detected in a gestational age-dependent manner. In conclusion, LPS-induced foetal death and early labour were associated with altered placental ABC and lipid transporter expression and deranged maternal plasma and placental lipid homeostasis. These changes likely modify foetal xenobiotic exposure and placental lipid exchange in cases of bacterial infection.