bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategic and non-strategic semantic expectations hierarchically modulate neural processing
Authors: Vidal-Gran Consuelo , Sokoliuk Rodika , Bowman Howard , Cruse Damian 
Published: June 2020

AbstractPerception is facilitated by a hierarchy of expectations generated from context and prior knowledge. In auditory processing, violations of local (within-trial) expectations elicit a mismatch negativity, while violations of global (across-trial) expectations elicit a later positive component (P300). This result is taken as evidence of prediction errors ascending through the expectation hierarchy. However, in language comprehension, there is no evidence that violations of semantic expectations across local-global levels similarly elicit a sequence of hierarchical error signals – thus drawing into question the putative link between event-related potentials and prediction errors. We investigated the neural basis of such hierarchical expectations of semantics in a word-pair priming paradigm. By manipulating the overall proportion of related or unrelated word-pairs across the task, we created two global contexts that differentially encouraged strategic use of primes. Across two experiments, we replicated behavioural evidence of greater priming in the high validity context, reflecting strategic expectations of upcoming targets based on ‘global’ context. In our pre-registered EEG analyses, we observed a ‘local’ prediction error ERP effect (i.e. semantic priming) approximately 250ms post-target, which, in exploratory analyses, was followed 100ms later by a signal that interacted with the global context. However, the later effect behaved in an apredictive manner - i.e. was most extreme for fulfilled expectations, rather than violations. Our results are consistent with interpretations of early ERPs as reflections of prediction error and later ERPs as processes related to conscious access and in support of task demands.Significance statementSemantic expectations have been associated with the ERP N400 component, which is modulated by semantic prediction errors across levels of the hierarchy. However, there is no evidence of a two-stage profile that reflects violations of semantic expectations at a single level of the hierarchy, such as the MMN and P3b observed in the local-global paradigm, which are elicited by violations of local and global expectations, respectively. In the present study, we provided evidence of an early ERP effect that reflects violations of local semantic expectations, followed by an apredictive signal that interacted with the global context. Thus, these results support the notion of early ERPs as prediction errors and later ERPs reflecting conscious access and strategic use of context.
Latent effects of winter warming on Olympia oyster reproduction and larval viability
Authors: Spencer Laura H , Horkan Erin , Crim Ryan , Roberts Steven B 
Published: June 2020

AbstractFor ectothermic marine invertebrates living in temperate regions, impacts of ocean warming will vary considerably by season. In many species, reproductive and metabolic processes are tightly linked to the seasonal change from winter to spring, yet we know little about how these processes will shift as winters become milder. This study examined latent effects of winter warming on spring reproduction in the Olympia oyster,Ostrea lurida. Adults were collected in autumn from central Puget Sound, WA, USA, and exposed to two winter temperatures (7°C, 10°C) in the presence of food limited (5k algal cells/mL) and food abundant (50k algal cells/mL) environments. Following treatments, adults exposed to elevated winter temperature contained larger oocytes regardless of feeding regime, and those also fed abundant food contained more developed sperm. Adults then spawned in common conditions, and larvae were reared through settlement to assess carryover effects of winter conditions on larval viability. Adults previously exposed to elevated winter temperature (10°C) produced larger larvae, particularly if they were also fed high food levels. More developed gametes and larger larvae suggest that gametogenesis occurred at low levels throughout the winter, possibly resulting in increased maternal provisioning to influence larval size. Interestingly, winter temperature did not impact larval survival, or the timing or magnitude of larval production. In the wild, more developed gametes and larger larvae following milder winters could greatly impact recruitment patterns, possibly benefittingO. luridapopulations. In the hatchery setting, larval production and survival is not contingent upon winter conditions, and larval survival does not correlate with oocyte and larval size. Our results suggest thatO. luridareproduction is resilient to winter warming. Furthermore, as global temperature continues to rise, winter conditions should not be overlooked when examining reproductive cycles ofO. luridaand other temperate marine invertebrates with similar reproductive cycles.Highlights of the manuscriptElevated winter temperature resulted in more developedO. luridasperm, larger oocytes, and larger larvae.In experimental settings,O. luridaoocyte and larval size upon release did not predict larval survival, but in the wild where rearing conditions are more challenging, winter warming could benefit wild populations by increasing recruitment.Winter temperature did not affect larval production timing or magnitude, indicating thatO. luridareproductive capacity is relatively resilient to increasing winter temperatures.
The Autonomic Nervous System Differentiates Between Levels of Motor Intent and Hand Dominance
Authors: Ryu Jihye , Torres Elizabeth 
Published: June 2020

AbstractWhile attempting to bridge motor control and cognitive science, the nascent field of embodied cognition has primarily addressed intended, goal-oriented actions. Less explored however, have been unintended motions. Such movements tend to occur largely beneath awareness, while contributing to the spontaneous control of redundant degrees of freedom across the body in motion. We posit that the consequences of such unintended actions implicitly contribute to our autonomous sense of action ownership and agency. We question whether biorhythmic activities from these motions are separable from those which intentionally occur. Here we find that fluctuations in the biorhythmic activities of the nervous systems can unambiguously differentiate across levels of intent. More important yet, this differentiation is remarkable when we examine the fluctuations in biorhythmic activity from the autonomic nervous systems. We find that when the action is intended, the heart signal leads the body kinematics signals; but when the action segment spontaneously occurs without instructions, the heart signal lags the bodily kinematics signals. We posit that such differentiation within the nervous system, may be necessary to acquire the sense of action ownership, which in turn, contributes to the sense of agency. We discuss our results while considering their potential translational value.
Modeling the long-term dynamics of tropical forests: from leaf traits to whole-tree growth patterns
Authors: Petter Gunnar , Kreft Holger , Ong Yongzhi , Zotz Gerhard , Cabral Juliano Sarmento 
Published: June 2020

AbstractTropical forests are the most diverse terrestrial ecosystems and home to numerous tree species with diverse ecological strategies competing for resources in space and time. Functional traits influence the ecophysiological performance of tree species, yet the relationship between traits and emergent long-term growth pattern is poorly understood. Here, we present a novel 3D forest stand model in which growth patterns of individual trees and forest stands are emergent properties of leaf traits. Individual trees are simulated as 3D functional-structural tree models (FSTMs), considering branches up to the second order and leaf dynamics at a resolution of one m3. Each species is characterized by a set of leaf traits that corresponds to a specific position on the leaf economic spectrum and determines light-driven carbon assimilation, respiration and mortality rates. Applying principles of the pipe model theory, these leaf scale-processes are coupled with within-tree carbon allocation, i.e., 3D tree growth emerges from low-level processes. By integrating these FSTMs into a dynamic forest stand model, we go beyond modern stand models to integrate structurally-detailed internal physiological processes with interspecific competition, and interactions with the environment in diverse tree communities. For model calibration and validation, we simultaneously compared a large number of emergent patterns at both the tree and forest levels in a pattern-oriented modeling framework. At the tree level, varying specific leaf area and correlated leaf traits determined the maximum height and age of a tree, as well as its size-dependent growth rate and shade tolerance. Trait variations along the leaf economic spectrum led to a continuous transition from fast-growing, short-lived and shade-intolerant to slow-growing, long-lived and shade-tolerant trees. These emerging patterns resembled well-known functional tree types, indicating a fundamental impact of leaf traits on long-term growth patterns. At the forest level, a large number of patterns taken from lowland Neotropical forests were reproduced, indicating that our forest model simulates structurally realistic forests over long time spans. Our ecophysiological approach improves the understanding of how leaf level processes scale up to the tree and the stand level, and facilitates the development of next-generation forest models for species-rich forests in which tree performance emerges directly from functional traits.
Muscle fiber type differences in nitrate and nitrite storage and nitric oxide signaling in rats
Authors: Long Gary M. , Gray Derrick A. , Troutman Ashley D. , Fisher Amanda , Brown Mary Beth , Coggan Andrew R. 
Published: June 2020

AbstractRecent studies have emphasized the importance of the nitric oxide synthase (NOS)-independent, nitrate (NO3−) → nitrite (NO2−) → nitric oxide (NO) pathway in skeletal muscle. In particular, it has been hypothesized that this pathway is especially active in type II, or fast-twitch, muscle fibers, necessitating greater NO3−and NO2−storage. We therefore measured NO3−and NO2−concentrations in the predominantly fast-twitch vastus lateralis and predominantly slow-twitch soleus muscles of rats. Contrary to the above hypothesis, we found that NO3−and NO2−concentrations were 3.4-fold and 1.8-fold higher, respectively, in the soleus. On the other hand, NO signaling (i.e., cyclic guanosine monophosphate (cGMP) level) was comparable in the two muscles. Although the physiological significance of these observations remains to be determined, we speculate that NO production via the NO3−→ NO2−→ NO pathway is normally higher in slow-twitch muscles, thus helping compensate for their inherently lower NOS activity.
A domestic cat whole exome sequencing resource for trait discovery
Authors: Rodney Alana R. , Buckley Reuben M. , Fulton Robert S. , Fronick Catrina , Richmond Todd , Helps Christopher R. , Pantke Peter , Trent Dianne J. , Lyons Leslie A. , Warren Wesley C. 
Published: June 2020

AbstractOver 94 million domestic cats are considered pets, who, as our companions, are also susceptible to cancers, common and rare diseases. Whole exome sequencing (WES) is a cost-effective strategy to study their putative disease-causing variants. Presented is ~35.8 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. WES was conducted on 41 cats from various breeds with known and unknown diseases and traits, including 10 cats with prior whole genome sequence (WGS) data available, to test WES capture probe performance. A WES and WGS comparison was completed to understand variant discovery capability of each platform. At ~80x exome coverage, the percent of on-target base coverage >20x was 96.4% with an average of 10.4% off-target. For variant discovery, greater than 98% of WGS SNPs were also discovered by WES. Platform specific variants were mainly restricted to a small number of sex chromosome and olfactory receptor genes. Within the 41 cats with ~31 diseases and normal traits, 45 previously known disease or trait causal variants were observed, such as Persian progressive retinal degeneration and hydrocephalus. Novel candidate variants for polycystic kidney disease and atrichia in the Peterbald breed were also identified as well as a new cat patient with a known variant for cystinuria. These results show the discovery potential of deep exome sequencing to validate existing disease gene models and identify novel gene candidate alleles for many common and rare diseases in cats.
Dihydroceramide desaturase regulates the compartmentalization of Rac1 for neuronal oxidative stress
Authors: Tzou Fei-Yang , Su Tsu-Yi , Yu Yu-Lian , Yeh Yu-Han , Liu Chung-Chih , Huang Shu-Yi , Chan Chih-Chiang 
Published: June 2020

SummaryDisruption of sphingolipid homeostasis has been shown to cause neurological disorders. How specific sphingolipid species modulate the pathogenesis remains unknown. The last step of sphingolipidde novosynthesis is the conversion of dihydroceramide to ceramide catalyzed by dihydroceramide desaturase (human DEGS1;DrosophilaIfc). Loss ofifcleads to dihydroceramide accumulation and oxidative stress, resulting in photoreceptors degeneration, whileDEGS1variants were associated with leukodystrophy and neuropathy. Here, we demonstrated thatifcregulates Rac1 compartmentalization in fly photoreceptors and further showed that dihydroceramide alters the association of active Rac1 to membranes mimicking specific organelles. We also revealed that the major source of ROS originated from Rac1 and NADPH oxidase (NOX) in the cytoplasm, as the NOX inhibitor apocynin ameliorated the oxidative stress and functional defects in both flyifc-KO photoreceptors and human neuronal cells with disease-associated variantDEGS1H132R. Therefore,DEGS1/ifcdeficiency causes dihydroceramide accumulation, resulting in Rac1 translocation and NOX-dependent neurodegeneration.Graphical AbstractADEGS1/ifcconverts dihydroceramide to ceramide in neuronal cells, and the endolysosomal NOX complex is not activated.BDihydroceramide accumulates without functionalDEGS1/ifcand causes alterations in membrane microdomains and recruits active Rac1 to endolysosomes. The activation of endolysosomal Rac1-NOX complex elevates cytosolic ROS levels, causing neurodegeneration.In Brief (eTOC blurb)Deficiency in dihydroceramide desaturase causes oxidative stress-mediated neurological disorders. Tzou and Su et al. show that increased dihydroceramide causes the relocalization of active Rac1, whilst inhibition of the Rac1-NOX ameliorates the oxidative stress and neuronal defects. NOX inhibitor apocynin may provide new direction of treatments for patients withDEGS1variants.HighlightsDeficiency in dihydroceramide (dhCer) desaturase induces cytoplasmic ROS elevationdhCer alters the binding of active Rac1 to reconstituted organelle membranesActive Rac1 is enriched in endolysosomes inifc-KO neurons for ROS genesisRac1-NADPH oxidase elicits ROS, degenerating leukodystrophy-related neuronal cells
A humanTSC1mutation screening platform in GABAergic cortical interneurons for Genotype to Phenotype assessments
Authors: Wundrach Dean , Martinetti Luis E , Stafford April M , Bilinovich Stephanie M , Angara Kartik , Crandall Shane R , Vogt Daniel 
Published: June 2020

AbstractTuberous Sclerosis Complex is a complex syndrome that affects multiple organs and is caused by dysfunction of either theTSC1orTSC2genes. One of the least understood features of TSC is the impact ofTSC1&2variants on brain phenotypes, including elevated rates of autism spectrum disorder and seizures. Moreover, while a great deal of work has uncovered how loss of either gene can alter various neural cell types, the impact of many variants in TSC and on these cell types is poorly understood. In particular, missense variants that cause minor changes in the proteins are expected to cause functional changes that differ from a complete loss of the protein. Herein, we examined how some missense variants inTSC1impacted the development of cortical inhibitory interneurons, a cell type whose molecular, cellular and physiological properties are known to be altered after loss of mouseTsc1. Importantly, we found that most missense variants complemented phenotypes caused by loss ofTsc1and resulting in elevated MTOR activity as well as several cell intrinsic physiological properties. However, distinct variants showed deficits in complementing an increase in parvalbumin levels, which is observed after loss ofTsc1and demonstrated smaller amplitudes of after hyperpolarizations. These data suggest subtle but sensitive phenotypes can be detected by someTSC1missense variants and provide anin vivosystem in which to better assess TSC variants.
Limbal Niche Cells in Three-Dimensional Matrigel Induced Dedifferentiation of Mature Corneal Epithelial Cells toward a Progenitor State
Authors: Zhu Hui , Wang Wei , Xu Lingjuan , Jiang Menglin , Tan Yongyao , Wang Yunming , Meir Yaa-Jyuhn James , Li Guigang 
Published: June 2020

ABSTRACTPurposeTo investigate the possibility and the key factors of stably committed mature corneal epithelial cells dedifferentiate into corneal epithelial stem cellsin vitro.MethodsMature cornea epithelia cell (MCEC) sheets or limbal epithelial progenitor cell (LEPC) sheets were isolated from central corneas or limbal segments by Dispase II and further digested with 0.25% trypsin/1 mM EDTA (T/E) to yield single cells. Limbal niche cells (LNC) were isolated from the limbal stroma by collagenase A and expanded on 5% Matrigel coated plastic. Single MCECs were seeded on 50% Matrigel with or without LNC culturing for 10 days, regarding as three-dimensional MCEC (3D-MCEC) group or three-dimensional MCEC+LNC (3D-MCEC+LNC) group. Expression of CK12, p63α, PCK, Vimentin were analyzed with immunofluorescence staining.ResultsThe expression of mature cornea epithelial marker (CK12) in MCEC was higher than that in LEPC (P=0.020) but epithelial stem cell marker (p63α) was lower than that in LEPC (P=0.000). When seeded in 3D Matrigel, single MCEC cells could form spheres within 72 hours, and the expression of CK12 reduced (P=0.005) and the expression of p63α also reduced to zero (P=0.000) compared to MCEC. Serial passages of LNC which were expanded in coated Matrigel could form spheres in 3D Matrigel. After mixing MCECs with LNC, rounder spheres emerged within 24 hours which consisted of both epithelia cells (PCK+/Vim-) and LNC (PCK-/Vim+). Moreover, epithelia cells in 3D-MCEC+LNC group expressed less CK12 and more p63α than those in MCEC group (P=0.043, 0.000). Besides, the diameter of spheres in 3D-MCEC+LNC group were larger than that in 3D-MCEC group (P=0.000).ConclusionHuman LNC and three-dimensional Matrigel could induce the dedifferentiation of mature corneal epithelial cells into corneal epithelial stem cells.
Partitiviruses infectingDrosophila melanogasterandAedes aegyptiexhibit efficient biparental vertical transmission
Authors: Cross Shaun T. , Maertens Bernadette L. , Dunham Tillie J. , Rodgers Case P. , Brehm Ali L. , Miller Megan R. , Williams Alissa M. , Foy Brian D. , Stenglein Mark D. 
Published: June 2020

AbstractPartitiviruses are segmented, multipartite dsRNA viruses that until recently were only known to infect fungi, plants, and protozoans. Metagenomic surveys have revealed that partitivirus-like sequences are also commonly associated with arthropods. One arthropod-associated partitivirus, galbut virus, is extraordinarily common in wild populations ofDrosophila melanogasterfruit flies. To begin to understand the processes that underlie this virus’s high global prevalence, we established colonies of wild-caught infected flies. Infection remained at stably high levels over three years, with between 63-100% of individual flies infected. Galbut virus infects fly cells and replicates in tissues throughout infected adults, including reproductive tissues and the gut epithelium. We detected no evidence of horizontal transmission via ingestion but vertical transmission from either infected females or infected males was ~100% efficient. Vertical transmission of a related partitivirus, verdadero virus, that we discovered in a laboratory colony ofAedes aegyptimosquitoes was similarly efficient. This suggests that efficient biparental vertical transmission may be a feature of at least a subset of insect-infecting partitiviruses. To study the impact of galbut virus infection free from the confounding effect of other viruses, we generated an inbred line of flies with galbut virus as the only detectable virus infection. We were able to transmit infection experimentally via microinjection of homogenate from these galbut-only flies. This sets the stage for experiments to understand the biological impact and possible utility of partitiviruses infecting important model organisms and disease vectors.ImportanceGalbut virus is a recently discovered partitivirus that is extraordinarly common in wild populations of the model organismDrosophila melanogaster. Like most viruses discovered through metagenomics, most of the basic biological questions about this virus remain unanswered. We found that galbut virus, along with a closely related partitivirus found inAedes aegyptimosquitoes, is transmitted from infected females or males to offspring with ~100% efficiency and can be maintained in laboratory colonies over years. This represents one of the most efficient means of virus transmission described, and likely underlies the successful spread of these viruses through insect populations. We createdDrosophilalines that contained galbut virus as the only virus infection and showed that these flies can be used as a source for experimental infections. This provides insight into how arthropod-infecting partitiviruses may be maintained in nature and sets the stage for exploration of their biology and potential utility.
Collecting data on HIV-related mortality during household surveys: a randomized validation study in Malawi
Authors: Amoah Abena , Brumfield Sarah , Crampin Amelia C. , Dube Albert N. , Helleringer Stéphane , McLean Estelle , Reniers Georges 
Published: June 2020

ABSTRACTBackgroundIn many African countries, there are limited representative data on HIV/AIDS mortality. We tested whether such data could be collected during household surveys periodically conducted in most African countries.MethodsWe added HIV questions to the module on adult and maternal mortality used in Demographic and Health Surveys. We conducted a validation study of the data generated by these questions in northern Malawi. We randomly assigned men and women aged 15–59 years old to a face-to-face interview or audio computer-assisted self-interviewing (ACASI). We compared survey reports of adult deaths to prospective data on mortality and HIV collected by the Karonga Health and Demographic Surveillance Site. We calculated the sensitivity and specificity of survey data in recording the HIV status of deceased siblings of respondents. We adjusted for partial verification bias using multiple imputations.ResultsWe interviewed 535 participants, who reported 885 deaths at ages 15 and older. The added HIV questions yielded largely complete data on the HIV status of respondents’ deceased siblings, particularly those who died recently. The adjusted sensitivity of survey data on HIV status of the deceased was high in both study groups (0.78–0.82). There were few false positive reports of the HIV status of deceased siblings (specificity = 0.96–0.98). ACASI did not improve the accuracy of survey data, but it required more time to collect mortality reports. Asking the HIV questions only took 0.4 minute (≈25 seconds) per deceased sibling in face-to-face interviews.ConclusionsAdding HIV questions to mortality questionnaires used in household surveys yields accurate data on the HIV status of deceased adults. These new data could aid in tracking progress towards global HIV elimination targets.MEIRU – LSHTM – JHU Partnership for improving adult mortality data1,2