bluuebunny/crossref_metadata_2025_split huggingface dataset:
Item recognition and lure discrimination in younger and older adults are supported by alpha/beta desynchronization
Authors: Karlsson Anna E. , Wehrspaun Claudia C. , Sander Myriam C. 
Published: April 2020

AbstractOur episodic memories vary in their specificity, ranging from a mere sense of familiarity to detailed recollection of the initial experience. Recent work suggests that alpha/beta desynchronization promotes information flow through the cortex, tracking the richness in detail of recovered memory representations. At the same time, as we age, memories become less vivid and detailed, which may be reflected in age-related reductions in alpha/beta desynchronization during retrieval. To understand age differences in the specificity of episodic memories, we investigated differences in alpha/beta desynchronization between younger (18–26 years,n= 31) and older (65–76 years,n= 27) adults during item recognition and lure discrimination.Alpha/beta desynchronization increased linearly with the demand for memory specificity, i.e., the requirement to retrieve details for an accurate response, across retrieval situations (correct rejections < item recognition < lure discrimination). Stronger alpha/beta desynchronization was related to memory success, as indicated by reliable activation differences between correct and incorrect memory responses. In line with the assumption of a loss of mnemonic detail in older age, older adults had more difficulties than younger adults to discriminate lures from targets. Importantly, they also showed a reduced modulation of alpha/beta desynchronization across retrieval demands. Together, these results extend previous findings by demonstrating that alpha/beta desynchronization dissociates between item recognition and the retrieval of highly detailed memories as required in lure discrimination, and that age-related impairments in episodic retrieval are accompanied by attenuated modulations in the alpha/beta band. Thus, we provide novel findings suggesting that alpha/beta desynchronization tracks mnemonic specificity and that changes in these oscillatory mechanisms may underlie age-related declines in episodic memory.
Obtaining leaner deep neural networks for decoding brain functional connectome in a single shot
Authors: Gupta Sukrit , Chan Yi Hao , Rajapakse Jagath C. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2020

AbstractNeuroscientific knowledge points to the presence of redundancy in the correlations of brain’s functional activity. These redundancies can be removed to mitigate the problem of overfitting when deep neural network (DNN) models are used to classify neuroimaging datasets. We propose an algorithm that removes insignificant nodes of DNNs in a layerwise manner and then adds a subset of correlated features in a single shot. When performing experiments with functional MRI datasets for classifying patients from healthy controls, we were able to obtain simpler and more generalizable DNNs. The obtained DNNs maintained a similar performance as the full network with only around 2% of the initial trainable parameters. Further, we used the trained network to identify salient brain regions and connections from functional connectome for multiple brain disorders. The identified biomarkers were found to closely correspond to previously known disease biomarkers. The proposed methods have cross-modal applications in obtaining leaner DNNs that seem to fit the data better. The corresponding code is available athttps://github.com/SCSE-Biomedical-Computing-Group/LEAN_CLIP.
Common brain networks between major depressive disorder and symptoms of depression that are validated for independent cohorts
Authors: Yamashita Ayumu , Sakai Yuki , Yamada Takashi , Yahata Noriaki , Kunimatsu Akira , Okada Naohiro , Itahashi Takashi , Hashimoto Ryuichiro , Mizuta Hiroto , Ichikawa Naho , Takamura Masahiro , Okada Go , Yamagata Hirotaka , Harada Kenichiro , Matsuo Koji , Tanaka Saori C , Kawato Mitsuo , Kasai Kiyoto , Kato Nobumasa , Takahashi Hidehiko , Okamoto Yasumasa , Yamashita Okito , Imamizu Hiroshi 
Published: April 2020

AbstractMany studies have highlighted the difficulty inherent to the clinical application of fundamental neuroscience knowledge based on machine learning techniques. It is difficult to generalize machine learning brain markers to the data acquired from independent imaging sites, mainly due to large site differences in functional magnetic resonance imaging. We address the difficulty of finding a generalizable major depressive disorder (MDD) brain network markers which would distinguish patients from healthy controls (a classifier) or would predict symptom severity (a prediction model) based on resting state functional connectivity patterns. For the discovery dataset with 713 participants from 4 imaging sites, we removed site differences using our recently developed harmonization method and developed a machine learning MDD brain network markers. The classifier achieved 70% generalization accuracy, and the prediction model moderately well predicted symptom severity for an independent validation dataset with 449 participants from 4 different imaging sites. Finally, we found common 2 functional connections between those related to MDD diagnosis and those related to depression symptoms. The successful generalization to the perfectly independent dataset acquired from multiple imaging sites is novel and ensures scientific reproducibility and clinical applicability.
Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism
Authors: Horne Christopher R. , Venugopal Hariprasad , Panjikar Santosh , Henrickson Amy , Brookes Emre , North Rachel A. , Murphy James M. , Friemann Rosmarie , Griffin Michael D.W. , Ramm Georg , Demeler Borries , Dobson Renwick C.J. 
Published: April 2020

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. TheEscherichia coliGntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Truncation of an N-terminal extension abolishes cooperative binding. The effector,N-acetylneuraminate, binds NanR and attenuates DNA binding. Crystal structure data show thatN-acetylneuraminate binding to NanR causes a domain rearrangement that locks the protein in a conformation that prevents DNA binding. Single-particle cryo-electron microscopy structures of NanR bound to DNA reveal the DNA binding domain is reorganized to engage DNA, while the three dimers assemble in close proximity across the (GGTATA)3-repeat operator allowing protein-protein interactions to formviathe N-terminal extensions. Our data provides a molecular basis for the regulation of bacterial sialic acid metabolism.
Autonomic activity during a daytime nap facilitates working memory improvement
Authors: Chen Pin-Chun , Whitehurst Lauren N. , Mednick Sara C. 
Published: April 2020

AbstractRecent investigations have implicated the parasympathetic branch of the autonomic nervous system (ANS) in higher-order executive functions. These actions are purported to occur through ANS’s modulation of the prefrontal cortex, with parasympathetic activity during wake associated with working memory ability (WM). Compared with wake, sleep is a period with substantially greater parasympathetic tone. Recent work has reported that sleep may also contribute to improvement in WM. Here, we examined the role of cardiac parasympathetic activity during sleep on WM improvement in healthy young adults. Participants were tested in an operation span task (OSpan) in the morning and evening, and during the inter-test period subjects either experienced a nap or wake. We measured high frequency heart rate variability (HF HRV) as an index of cardiac, parasympathetic activity during both wake and sleep. Participants showed the expected boost in parasympathetic activity during nap, compared with wake, as well as greater WM improvement after a nap compared with an equivalent period awake. Furthermore, parasympathetic activity during sleep, but not wake, was significantly correlated with WM improvement. Together these results indicate that the natural boost in parasympathetic activity during sleep has substantial benefits to gains in prefrontal executive function in young adults. We present a conceptual model illustrating the interaction between sleep, autonomic activity, and prefrontal brain function, and highlight open research questions that will facilitate understanding of the factors that contribute to executive abilities in young adults, as well as in cognitive aging.Significance StatementRecently, the neurovisceral integration model has implicated activity on the parasympathetic branch of the autonomic nervous system (ANS) during wake in executive functioning. Parasympathetic activity peaks during deep sleep, and sleep has been shown to facilitate executive functioning. Yet, the role of parasympathetic activity during sleep for executive functioning is not known. Herein, participants demonstrated increased parasympathetic activity during deep sleep, sleep-dependent WM improvement, and associations between performance gains and parasympathetic activity in sleep, not wake. Our conceptual model illustrates the interaction between sleep, autonomic activity, and prefrontal brain function that may contribute to executive abilities in young adults and to cognitive aging.
Diurnal metabolic regulation of isoflavones and soyasaponins in soybean roots
Authors: Matsuda Hinako , Nakayasu Masaru , Aoki Yuichi , Yamazaki Shinichi , Nagano Atsushi J. , Yazaki Kazufumi , Sugiyama Akifumi 
Published: April 2020

AbstractIsoflavones and soyasaponins are major specialized metabolites accumulated in soybean roots and secreted into the rhizosphere. Unlike the biosynthetic pathway, the transporters involved in metabolite secretion remain unknown. The developmental regulation of isoflavone and soyasaponin secretions has been recently reported, but the diurnal regulation of their biosynthesis and secretion still needs to be further studied. To address these challenges, we conducted transcriptome and metabolite analysis using hydroponically grown soybean plants at 6-hour intervals for 48 hours in a 12-h-light/12-h-dark condition. Isoflavone and soyasaponin biosynthetic genes showed opposite patterns in the root tissues; that is, the former genes are highly expressed in daytime, while the latter ones are strongly induced at nighttime.GmMYB176encoding a transcription factor of isoflavone biosynthesis was upregulated from ZT0 (6:00 am) to ZT6 (12:00 am), followed by the induction of isoflavone biosynthetic genes at ZT6. The isoflavone aglycone content in the roots accordingly increased from ZT6 to ZT18 (0:00 am), accompanied by an increase in glucoside levels that peaked at ZT0. The isoflavone aglycone content in root exudates was kept consistent throughout the day, whereas that of glucosides increased at ZT6, which reflected the decreased expression of the gene encoding beta-glucosidase involved in the hydrolysis of apoplast-localized isoflavone conjugates. Co-expression analysis revealed that those isoflavone and soyasaponin biosynthetic genes formed separate clusters, which exhibited a correlation to ABC and MATE transporter genes. As summary, the results in this study indicated the diurnal regulation of isoflavone biosynthesis in soybean roots and the putative transporter genes responsible for isoflavone and soyasaponin transport.
Clinical genetics lacks standard definitions and protocols for the collection and use of diversity measures
Authors: Popejoy Alice B. , Crooks Kristy R. , Fullerton Stephanie M. , Hindorff Lucia A. , Hooker Gillian W. , Koenig Barbara A. , Pino Natalie , Ramos Erin M. , Ritter Deborah I. , Wand Hannah , Wright Matt W. , Yudell Michael , Zou James Y. , Plon Sharon E. , Bustamante Carlos D. , Ormond Kelly E. 
Published: April 2020

AbstractGenetics researchers and clinical professionals rely on diversity measures such as race, ethnicity, and ancestry (REA) to stratify study participants and patients for a variety of applications in research and precision medicine. However, there are no comprehensive, widely accepted standards or guidelines for collecting and using such data in either setting. Two NIH-funded research consortia, the Clinical Genome Resource (ClinGen) and Clinical Sequencing Evidence-generating Research (CSER), have partnered to address this issue and report how REA are currently collected, conceptualized, and used. Surveying clinical genetics professionals and researchers (N=448), we found heterogeneity in the way REA are perceived, defined, and measured, with variation in the perceived importance of REA in both clinical and research settings. The majority of respondents (>55%) felt that REA are at least somewhat important for clinical variant interpretation, ordering genetic tests, and communicating results to patients. However, there was no consensus on the relevance of REA, including how each of these measures should be used in different scenarios and what information they can convey in the context of human genetics. A lack of common definitions and applications of REA across the precision medicine pipeline may contribute to inconsistencies in data collection, missing or inaccurate classifications, and misleading or inconclusive results. Thus, our findings support the need for standardization and harmonization of REA data collection and use in clinical genetics and precision health research.
Modeling the Effective Control Strategy for the Transmission Dynamics of Global Pandemic COVID-19
Authors: Biswas M. H. A. , Khatun M. S. , Paul A. K. , Khatun M. R. , Islam M. A. , Samad S. A. , Ghosh U. 
Published: April 2020

AbstractThe novel coronavirus disease (namely COVID-19) has taken attention because of its deadliness across the globe, causing a massive death as well as critical situation around the world. It is an infectious disease which is caused by newly discovered coronavirus. Our study demonstrates with a nonlinear model of this devastating COVID-19 which narrates transmission from human-to-human in the society. Pontryagin’s Maximum principle has also been applied in order to obtain optimal control strategies where the maintenance of social distancing is the major control. The target of this study is to find out the most fruitful control measures of averting coronavirus infection and eventually, curtailed of the COVID-19 transmission among people. The model is investigated analytically by using most familiar necessary conditions of Pontryagin’s maximum principle. Furthermore, numerical simulations have been performed to illustrate the analytical results. The analysis reveals that implementation of educational campaign, social distancing and developing human immune system are the major factors which can be able to plunge the scenario of becoming infected.
Mosquito densoviruses: the revival of a biological control agent against urbanAedesvectors of arboviruses
Authors: Perrin Aurélie , Gosselin-Grenet Anne-Sophie , Rossignol Marie , Ginibre Carole , Scheid Bethsabée , Lagneau Christophe , Chandre Fabrice , Baldet Thierry , Ogliastro Mylène , Bouyer Jérémy 
Published: April 2020

ABSTRACTUrbanAedesmosquitoes are vectors of many viruses affecting human health such as Dengue, Chikungunya and Zika viruses. Insecticide resistance and environmental toxicity risks hamper the effectiveness of chemical control against these mosquito vectors. Alternative control methods, such as the use of mosquito-specific entomopathogenic viruses should be explored. Numerous studies have focused on evaluating the potential of different densoviruses species as biological control agent. However, knowledge on the extent of inter- and intra-specific variations in the susceptibility ofAedesmosquitoes to infection by different densoviruses remains insufficient. In this study, we compared infection and mortality rates induced by the Aedes albopictus densovirus 2 in different strains ofAedes albopictusandAedes aegyptimosquitoes. The twoAedesspecies were different in terms of susceptibility to viral infection. Under laboratory conditions, Aedes albopictus densovirus 2 appeared more virulent for the different strains ofAedes aegyptitested than for those ofAedes albopictus. In addition, we also found significant intra-specific variation in infection and mortality rates. Thus, although even if Aedes albopictus densoviruses could be powerful biocontrol agents used in the management of urbanAedespopulations, our results also call into question the use of single viral isolate as biocontrol agents.
Impacts of the 1918 flu on survivors’ nutritional status: a double quasi-natural experiment
Authors: Palloni Alberto , McEniry Mary , Huangfu Yiyue , Beltran-Sanchez Hiram 
Published: April 2020

ABSTRACTA unique set of events that took place in Puerto Rico during 1918-1919 generated conditions of a “double “quasi-natural experiment. We exploit these conditions to empirically identify effects of exposure to the 1918 flu pandemic, those of the devastation left by an earthquake-tsunami that struck the island in 1918, and those associated with the joint occurrence of these events. We use geographic variation to identify the effects of the quake and timing of birth variation to identify those of the flu. In addition, we use markers of nutritional status gathered in a nationally representative sample of individuals aged 75 and older in 2002. This unique data set enables to make two distinct contributions. First, unlike most fetal-origins research that singles out early nutritional status as adeterminant of adult health, we test the hypothesis that the 1918 flu had deleterious effects on the nutritional status on adult survivors who at the time of the flu werein uteroor infants. Second, and unlike most research on the effects of the flu, we focus on markers of nutritional status set when the adult survivors were children or adolescents. We find that estimates of effects of the pandemic are sizeable primarily among females and among those who, in addition to the flu,were exposed to the earthquake-tsunami.We argue that these findings constitute empirical evidence supporting the conjecture that effects of the 1918 flu alone and the combined effects of the flu and the earthquake are associated not just with damage experienced during the fetal period but also postnatally.
Potential short-term negative versus positive effects of olive mill-derived biochar on nutrient availability in a calcareous loamy sandy soil
Authors: Alazzaz Azzaz , Usman Adel R. A. , Ahmad Munir , Elfaki Jamal , Sallam Abdelazeem S. , Ibrahim Hesham , Akanji Mutair A. , Al-Wabel Mohammad I. 
Published: April 2020

AbstractIn this study, a greenhouse pot experiment with maize (Zea mays L.) was conducted using treatments consisting of a control (CK), inorganic fertilizer of NPK (INF), and 1% and 3% (wt/wt) of olive mill solid waste (OMSW)-derived biochar (BC) at various pyrolytic temperatures (300–700 °C). The goal was to investigate potential negative versus positive effects of BC on pH, electrical conductivity (EC), and nutrient (P, K, Na, Ca, Mg, Fe, Mn, Zn, and Cu) availability in a calcareous loamy sandy soil. The results showed that application of OMSW-derived BC, especially with increasing pyrolysis temperature and/or application rate, significantly increased soil pH, EC, NH4OAc-extractable K, Na, Ca, and Mg, and ammonium bicarbonate-diethylenetriaminepentaacetic acid (AB-DTPA)-extractable Fe and Zn, while AB-DTPA-extractable Mn decreased. The application of 1% and 3% BC, respectively, increased the NH4OAc-extractable K by 2.5 and 5.2-fold for BC300, by 3.2 and 8.0-fold for BC500, and by 3.3 and 8.9-fold for BC700 compared with that of untreated soil. The results also showed significant increases in shoot content of K, Na, and Zn, while there were significant decreases in shoot content of P, Ca, Mg, and Mn. Furthermore, no significant effects were observed for growth of maize plants as a result of biochar BC addition. In conclusion, OMSW-derived BC can potentially have positive effects on the enhancement of soil K availability and its plant content but it reduced shoot nutrients, specifically P, Ca, Mg, and Mn; therefore, application of OMSW-derived BC to calcareous soil might be restricted.
Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens
Authors: Bezstarosti Karel , Lamers Mart M. , Doff Wouter A.S. , Wever Peter , Thai Khoa , van Kampen Jeroen J. A. , Haagmans Bart L. , Demmers Jeroen A. A. 
Published: April 2020

ABSTRACTThe rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry based (MS) proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.
Postnatal mechanical loading drives adaptation of tissues primarily through modulation of the non-collagenous matrix
Authors: Zamboulis D. E. , Thorpe C. T. , Kharaz Y. Ashraf , Birch H. L. , Screen H. R. C. , Clegg P. D. 
Published: April 2020

AbstractMature connective tissues demonstrate highly specialised properties, remarkably adapted to meet their functional requirements. Tissue adaptation to environmental cues can occur throughout life and poor adaptation commonly results in injury. However, the temporal nature and drivers of functional adaptation remain undefined. Here, we explore functional adaptation and specialisation of mechanically loaded tissues using tendon; a simple aligned biological composite, in which the collagen (fibre phase) and surrounding predominantly non-collagenous matrix (matrix phase) can be interrogated independently. Using an equine model of late development, we report the first phase-specific analysis of biomechanical, structural and compositional changes seen in functional adaptation, demonstrating adaptation occurs postnatally, following mechanical loading, and is almost exclusively localised to the non-collagenous matrix phase. These novel data redefine adaptation in connective tissue, highlighting the fundamental importance of non-collagenous matrix and suggesting that regenerative medicine strategies should change focus from the fibrous to the non-collagenous matrix phase of tissue.