bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between symptoms of sleep apnea and problem behaviors in young adult twins and siblings
Authors: Madrid-Valero Juan J. , Barclay Nicola L. , Rowe Richard , Perach Rotem , Buysse Daniel J. , Ordoñana Juan R. , Eley Thalia C. , Gregory Alice M. 
Published: February 2020

AbstractBackgroundSleep apnea is one of the most common sleep disorders and it is related to multiple negative health consequences. Previous studies have shown that sleep apnea is influenced by genetic factors. However, studies have not investigated the genetic and environmental influences of symptoms of sleep apnea in young adults. Furthermore, the underpinnings of the relationship between apnea symptoms and internalizing/externalizing problems are unknown. The objectives of this study were to estimate the magnitude of: (1) genetic and environmental influences on self-reported apnea symptoms; (2) the relationship between self-reported apnea symptoms and internalizing/externalizing traits; (3) genetic and environmental influences on the associations between self-reported apnea symptoms, internalizing behaviors and externalizing behaviors.MethodsIn a twin/sibling study, univariate and multivariate models were fitted to estimate both individual variance and sources of covariance between symptoms of sleep apnea and internalizing/externalizing behaviors.ResultsOur results show that genetic influences account for 40% of the variance in sleep apnea symptoms. Moreover, there are modest associations between depression, anxiety and externalizing behaviors with apnea symptoms (ranging from r = 0.22–0.29). However, the origins of these associations differ. For example, whereas most of the covariation between symptoms of depression and sleep apnea can be explained by genes (95%), there was a larger role for the environment (53%) in the association between symptoms of anxiety and sleep apnea.ConclusionsGenetic factors explain a significant proportion of variance in symptoms of apnea and most of the covariance with depression.
A cubical Squier’s theorem
Authors: Lucas Maxime 
Published: February 2020

AbstractThe homotopical Squier’s theorem relates rewriting properties of a presentation of a monoid with homotopical invariants of this monoid. This theorem has since been extended by Guiraud and Malbos, yielding a so-called polygraphic resolution of a monoid starting from a presentation with suitable rewriting properties. In this article, we argue that cubical categories are a more natural setting in which to express and possibly extend Guiraud and Malbos construction. As a proof-of-concept, we give a new proof of Squier’s homotopical theorem using cubical categories.
Capacity building and mentorship among pan-Canadian early career researchers in community-based primary health care
Authors: Nicholson Kathryn , Ganann Rebecca , Bookey-Bassett Sue , Garland Baird Lisa , Garnett Anna , Marshall Zack , Khan Anum Irfan , Pirrie Melissa , Sasseville Maxime , Ben Charif Ali , Poitras Marie-Ève , Kyoon-Achan Grace , Dionne Émilie , Hassani Kasra , Stewart Moira 
Published: February 2020

AbstractAim:To describe activities and outcomes of a cross-team capacity building strategy that took place over a five-year funding period within the broader context of 12 community-based primary health care (CBPHC) teams.Background:In 2013, the Canadian Institutes of Health Research funded 12 CBPHC Teams (12-Teams) to conduct innovative cross-jurisdictional research to improve the delivery of high-quality CBPHC to Canadians. This signature initiative also aimed to enhance CBPHC research capacity among an interdisciplinary group of trainees, facilitated by a collaboration between a capacity building committee led by senior researchers and a trainee-led working group.Methods:After the committee and working group were established, capacity building activities were organized based on needs and interests identified by trainees of the CBPHC Teams. This paper presents a summary of the activities accomplished, as well as the outcomes reported through an online semistructured survey completed by the trainees toward the end of the five-year funding period. This survey was designed to capture the capacity building and mentorship activities that trainees either had experienced or would like to experience in the future. Descriptive and thematic analyses were conducted based on survey responses, and these findings were compared with the existing core competencies in the literature.Findings:Since 2013, nine webinars and three online workshops were hosted by trainees and senior researchers, respectively. Many of the CBPHC Teams provided exposure for trainees to innovative methods, CBPHC content, and showcased trainee research. A total of 27 trainees from 10 of the 12-Teams responded to the survey (41.5%). Trainees identified key areas of benefit from their involvement in this initiative: skills training, networking opportunities, and academic productivity. Trainees identified gaps in research and professional skill development, indicating areas for further improvement in capacity building programs, particularly for trainees to play a more active role in their education and preparation.
They Came From the Pacific: How Changing Arctic Currents Could Contribute to an Ecological Regime Shift in the Atlantic Ocean
Authors: Kelly S. J. , Popova E. , Aksenov Y. , Marsh R. , Yool A. 
Published: February 2020

AbstractThe Arctic Ocean is rapidly changing. With warming waters, receding sea ice, and changing circulation patterns, it has been hypothesized that previously closed ecological pathways between the Pacific and Atlantic Oceans will be opened as we move toward a seasonally ice‐free Arctic. The discovery of the Pacific diatom Neodenticula seminae in the Atlantic suggests that a tipping point may have already been reached and this “opening up” of the Arctic could already be underway. Here, we investigate how circulation connectivity between the Pacific and Atlantic Oceans has changed in recent decades, using a state‐of‐the‐art high‐resolution ocean model and a Lagrangian particle‐tracking method. We identify four main trans‐Arctic pathways and a fifth route that is sporadically available with a shorter connectivity timescale. We discuss potential explanations for the existence of this “shortcut” advective pathway, linking it to a shift in atmospheric and oceanic circulation regimes. Advective timescales associated with each route are quantified, and seasonal and interannual trends in the main four pathways are discussed, including an increase in Fram Strait outflow relative to the Canadian Archipelago. In conclusion, we note that while tipping points for ecological connectivity are species dependent, even the most direct routes require multiannual connectivity timescales.
Soil Organic Carbon Across Mexico and the Conterminous United States (1991–2010)
Authors: Guevara Mario , Arroyo Carlos , Brunsell Nathaniel , Cruz Carlos O. , Domke Grant , Equihua Julian , Etchevers Jorge , Hayes Daniel , Hengl Tomislav , Ibelles Alejandro , Johnson Kris , de Jong Ben , Libohova Zamir , Llamas Ricardo , Nave Lucas , Ornelas Jose L. , Paz Fernando , Ressl Rainer , Schwartz Anita , Victoria Arturo , Wills Skye , Vargas Rodrigo 
Published: February 2020

AbstractSoil organic carbon (SOC) information is fundamental for improving global carbon cycle modeling efforts, but discrepancies exist from country‐to‐global scales. We predicted the spatial distribution of SOC stocks (topsoil; 0–30 cm) and quantified modeling uncertainty across Mexico and the conterminous United States (CONUS). We used a multisource SOC dataset (>10 000 pedons, between 1991 and 2010) coupled with a simulated annealing regression framework that accounts for variable selection. Our model explained ~50% of SOC spatial variability (across 250‐m grids). We analyzed model variance, and the residual variance of six conventional pedotransfer functions for estimating bulk density to calculate SOC stocks. Two independent datasets confirmed that the SOC stock for both countries represents between 46 and 47 Pg with a total modeling variance of ±12 Pg. We report a residual variance of 10.4 ±5.1 Pg of SOC stocks calculated from six pedotransfer functions for soil bulk density. When reducing training data to define decades with relatively higher density of observations (1991–2000 and 2001–2010, respectively), model variance for predicted SOC stocks ranged between 41 and 55 Pg. We found nearly 42% of SOC across Mexico in forests and 24% in croplands, whereas 31% was found in forests and 28% in croplands across CONUS. Grasslands and shrublands stored 29 and 35% of SOC across Mexico and CONUS, respectively. We predicted SOC stocks >30% below recent global estimates that do not account for uncertainty and are based on legacy data. Our results provide insights for interpretation of estimates based on SOC legacy data and benchmarks for improving regional‐to‐global monitoring efforts.
The UV Spectrum of the Lyman‐Birge‐Hopfield Band System of N2 Induced by Cascading from Electron Impact
Authors: Ajello Joseph M. , Evans J. Scott , Veibell Victoir , Malone Charles P. , Holsclaw Greg M. , Hoskins Alan C. , Lee Rena A. , McClintock William E. , Aryal Saurav , Eastes Richard W. , Schneider Nicholas 
Published: February 2020

AbstractWe have measured in the laboratory the far ultraviolet (FUV: 125.0–170.0 nm) cascade‐induced spectrum of the Lyman‐Birge‐Hopfield (LBH) band system (
) of N2 excited by 30–200 eV electrons. The cascading transition begins with two processes: radiative and collision‐induced electronic transitions (CIETs) involving two states (
and w1Δu → a1Πg), which are followed by a cascade induced transition
at the single‐scattering pressures employed here. Direct excitation to the a‐state produces a confined LBH spectral glow pattern around an electron beam. We have spatially resolved the electron‐induced glow pattern from an electron beam colliding with N2 at radial distances of 0–400 mm at three gas pressures. This imaging measurement is the first to isolate spectral measurements in the laboratory of single‐scattering electron‐impact‐induced fluorescence from two LBH emission processes: direct excitation, which is strongest in emission near the electron beam axis; and cascading‐induced, which is dominant far from the electron beam axis. The vibrational populations for vibrational levels from v′ = 0–2 of the a 1Πg state are enhanced by radiative cascade and CIETs, and the emission cross sections of the LBH band system for direct and cascading‐induced excitation are provided at 40, 50, 100, and 200 eV.
Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy
Authors: Woodhouse Joyce , Nass Kovacs Gabriela , Coquelle Nicolas , Uriarte Lucas M. , Adam Virgile , Barends Thomas R. M. , Byrdin Martin , de la Mora Eugenio , Bruce Doak R. , Feliks Mikolaj , Field Martin , Fieschi Franck , Guillon Virginia , Jakobs Stefan , Joti Yasumasa , Macheboeuf Pauline , Motomura Koji , Nass Karol , Owada Shigeki , Roome Christopher M. , Ruckebusch Cyril , Schirò Giorgio , Shoeman Robert L. , Thepaut Michel , Togashi Tadashi , Tono Kensuke , Yabashi Makina , Cammarata Marco , Foucar Lutz , Bourgeois Dominique , Sliwa Michel , Colletier Jacques-Philippe , Schlichting Ilme , Weik Martin 
Published: February 2020

AbstractReversibly switchable fluorescent proteins (RSFPs) serve as markers in advanced fluorescence imaging. Photoswitching from a non-fluorescent off-state to a fluorescent on-state involves trans-to-cis chromophore isomerization and proton transfer. Whereas excited-state events on the ps timescale have been structurally characterized, conformational changes on slower timescales remain elusive. Here we describe the off-to-on photoswitching mechanism in the RSFP rsEGFP2 by using a combination of time-resolved serial crystallography at an X-ray free-electron laser and ns-resolved pump–probe UV-visible spectroscopy. Ten ns after photoexcitation, the crystal structure features a chromophore that isomerized from trans to cis but the surrounding pocket features conformational differences compared to the final on-state. Spectroscopy identifies the chromophore in this ground-state photo-intermediate as being protonated. Deprotonation then occurs on the μs timescale and correlates with a conformational change of the conserved neighbouring histidine. Together with a previous excited-state study, our data allow establishing a detailed mechanism of off-to-on photoswitching in rsEGFP2.
Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria
Authors: Garcia-Garcera Marc , Rocha Eduardo P. C. 
Published: February 2020

AbstractWe test the hypothesis that the frequency and cost of extracellular proteins produced by bacteria, which often depend on cooperative processes, vary with habitat structure and community diversity. The integration of the environmental distribution of bacteria (using 16S datasets) and their genomes shows that bacteria living in more structured habitats encode more extracellular proteins. In contrast, the effect of community diversity depends on protein function: it’s positive for proteins implicated in antagonistic interactions and negative for those involved in nutrient acquisition. Extracellular proteins are costly and endure stronger selective pressure for low cost and for low diffusivity in less structured habitats and in more diverse communities. Finally, Bacteria found in multiple types of habitats, including host-associated generalists, encode more extracellular proteins than niche-restricted bacteria. These results show that ecological variables, notably habitat structure and community diversity, shape the evolution of the repertoires of genes encoding extracellular proteins and thus affect the ability of bacteria to manipulate their environment.
Separability and geometry of object manifolds in deep neural networks
Authors: Cohen Uri , Chung SueYeon , Lee Daniel D. , Sompolinsky Haim 
Published: February 2020

AbstractStimuli are represented in the brain by the collective population responses of sensory neurons, and an object presented under varying conditions gives rise to a collection of neural population responses called an ‘object manifold’. Changes in the object representation along a hierarchical sensory system are associated with changes in the geometry of those manifolds, and recent theoretical progress connects this geometry with ‘classification capacity’, a quantitative measure of the ability to support object classification. Deep neural networks trained on object classification tasks are a natural testbed for the applicability of this relation. We show how classification capacity improves along the hierarchies of deep neural networks with different architectures. We demonstrate that changes in the geometry of the associated object manifolds underlie this improved capacity, and shed light on the functional roles different levels in the hierarchy play to achieve it, through orchestrated reduction of manifolds’ radius, dimensionality and inter-manifold correlations.
A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes
Authors: Beveridge Rebecca , Stadlmann Johannes , Penninger Josef M. , Mechtler Karl 
Published: February 2020

AbstractCrosslinking-mass spectrometry (XL-MS) serves to identify interaction sites between proteins. Numerous search engines for crosslink identification exist, but lack of ground truth samples containing known crosslinks has precluded their systematic validation. Here we report on XL-MS data arising from measuring synthetic peptide libraries that provide the unique benefit of knowing which identified crosslinks are true and which are false. The data are analysed with the most frequently used search engines and the results filtered to an estimated false discovery rate of 5%. We find that the actual false crosslink identification rates range from 2.4 to 32%, depending on the analysis strategy employed. Furthermore, the use of MS-cleavable crosslinkers does not reduce the false discovery rate compared to non-cleavable crosslinkers. We anticipate that the datasets acquired during this research will further drive optimisation and development of XL-MS search engines, thereby advancing our understanding of vital biological interactions.
Fear of Killer Whales Drives Extreme Synchrony in Deep Diving Beaked Whales
Authors: Aguilar de Soto Natacha , Visser Fleur , Tyack Peter L. , Alcazar Jesús , Ruxton Graeme , Arranz Patricia , Madsen Peter T. , Johnson Mark 
Published: February 2020

AbstractFear of predation can induce profound changes in the behaviour and physiology of prey species even if predator encounters are infrequent. For echolocating toothed whales, the use of sound to forage exposes them to detection by eavesdropping predators, but while some species exploit social defences or produce cryptic acoustic signals, deep-diving beaked whales, well known for mass-strandings induced by navy sonar, seem enigmatically defenceless against their main predator, killer whales. Here we test the hypothesis that the stereotyped group diving and vocal behaviour of beaked whales has benefits for abatement of predation risk and thus could have been driven by fear of predation over evolutionary time. Biologging data from 14 Blainville’s and 12 Cuvier’s beaked whales show that group members have an extreme synchronicity, overlapping vocal foraging time by 98% despite hunting individually, thereby reducing group temporal availability for acoustic detection by killer whales to <25%. Groups also perform a coordinated silent ascent in an unpredictable direction, covering a mean of 1 km horizontal distance from their last vocal position. This tactic sacrifices 35% of foraging time but reduces by an order of magnitude the risk of interception by killer whales. These predator abatement behaviours have likely served beaked whales over millions of years, but may become maladaptive by playing a role in mass strandings induced by man-made predator-like sonar sounds.
Empathic responses to unknown others are modulated by shared behavioural traits
Authors: Anders Silke , Beck Christian , Domin Martin , Lotze Martin 
Published: February 2020

AbstractHow empathically people respond to a stranger’s pain or pleasure does not only depend on the situational context, individual traits and intentions, but also on interindividual factors. Here we ask whether empathic responses towards unknown others are modulated by behavioural similarity as a potential marker of genetic relatedness. Participants watched two supposed human players who were modelled as having a strong (player LP) or weak (player NLP) tendency to lead in social situations executing penalty shots in a virtual reality robot soccer game. As predicted, empathic response were modulated by shared behavioural traits: participants whose tendency to lead was more similar to player LP’s tendency to lead experienced more reward, and showed stronger neural activity in reward-related brain regions, when they saw player LP score a goal, and participants whose tendency to lead was more similar to player NLP’s tendency to lead showed stronger empathic responses when they saw player NLP score a goal. These findings highlight the potentially evolutionary grounded role of phenotypic similarity for neural processes underlying human social perception.
Formate dehydrogenase, ubiquinone, and cytochrome bd-I are required for peptidoglycan recognition protein-induced oxidative stress and killing in Escherichia coli
Authors: Kashyap Des R. , Kowalczyk Dominik A. , Shan Yue , Yang Chun-Kai , Gupta Dipika , Dziarski Roman 
Published: February 2020

AbstractMammalian Peptidoglycan Recognition Proteins (PGRPs) kill bacteria through induction of synergistic oxidative, thiol, and metal stress. PGRPs induce oxidative stress in bacteria through a block in the respiratory chain, which results in decreased respiration and incomplete reduction of oxygen (O2) to hydrogen peroxide (H2O2). In this study we identify the site of PGRP-induced generation of H2O2 in Escherichia coli. Tn-seq screening of E. coli Tn10 insertion library revealed that mutants in formate dehydrogenase (FDH) genes had the highest survival following PGRP treatment. Mutants lacking functional FDH-O had abolished PGRP-induced H2O2 production and the highest resistance to PGRP-induced killing, and formate enhanced PGRP-induced killing and H2O2 production in an FDH-dependent manner. Mutants in ubiquinone synthesis (but not menaquinone and demethylmenaquinone) and cytochrome bd-I (but not cytochromes bo3 and bd-II) also had completely abolished PGRP-induced H2O2 production and high resistance to PGRP-induced killing. Because electrons in the respiratory chain flow from dehydrogenases’ substrates through quinones and then cytochromes to O2, these results imply that the site of PGRP-induced incomplete reduction of O2 to H2O2 is downstream from dehydrogenases and ubiquinone at the level of cytochrome bd-I, which results in oxidative stress. These results reveal several essential steps in PGRP-induced bacterial killing.
On the need for a new generation of coastal change models for the 21st century
Authors: Ranasinghe Roshanka 
Published: February 2020

AbstractThe combination of climate change impacts, declining fluvial sediment supply, and heavy human utilization of the coastal zone, arguably the most populated and developed land zone in the world, will very likely lead to massive socio-economic and environmental losses in the coming decades. Effective coastal planning/management strategies that can help circumvent such losses require reliable local scale (<~10 km) projections of coastal change resulting from the integrated effect of climate change driven variations in mean sea level, storm surge, waves, and riverflows. Presently available numerical models are unable to adequately fulfill this need. A new generation of multi-scale, probabilistic coastal change models is urgently needed to comprehensively assess and optimise coastal risk at local scale, enabling risk informed, climate proof adaptation measures that strike a good balance between risk and reward.
Pentatricopeptide repeat protein MID1 modulates nad2 intron 1 splicing and Arabidopsis development
Authors: Zhao Peng , Wang Fang , Li Na , Shi Dong-Qiao , Yang Wei-Cai 
Published: February 2020

AbstractAs one of the best-studied RNA binding proteins in plant, pentatricopeptide repeats (PPRs) protein are mainly targeted to mitochondria and/or chloroplasts for RNA processing to regulate the biogenesis and function of the organelles, but its molecular mechanism and role in development remain to be further revealed. Here, we identified a mitochondria-localized P-type small PPR protein, MITOCHONDRION-MEDIATED GROWTH DEFECT 1 (MID1) that is crucial forArabidopsisdevelopment. Mutation inMID1causes retarded embryo development and stunted plant growth with defects in cell expansion and proliferation. Molecular experiments showed thatMID1is required for the splicing of thenad2intron 1 in mitochondria. Consistently,mid1plants display significant reduction in the abundance and activity of mitochondrial respiration complex I, accompanied by abnormal mitochondrial morphology and energy metabolism. Furthermore, MID1 is associated with othertrans-factors involved inNICOTINAMIDE ADENINE DINUCLEOTIDE HYDROGEN(NADH)DEHYDROGENASE SUBUNIT 2(nad2) intron 1 splicing, and interacts directly with itself and MITOCHONDRIAL STABILITY FACTOR 1 (MTSF1). This suggests that MID1 most likely functions as a dimer fornad2intron 1 splicing. Together, we characterized a novel PPR protein MID1 fornad2intron 1 splicing.