bluuebunny/crossref_metadata_2025 huggingface dataset:
Brain age predicted using graph convolutional neural network explains developmental trajectory in preterm neonates
Authors: Liu Mengting , Kim Sharon , Duffy Ben , Yuan Shiyu , Cole James H. , Toga Arthur W. , Jahanshad Neda , Barkovich Anthony James , Xu Duan , Kim Hosung
Published: May 2021

Dramatic alterations in brain morphology, such as cortical thickness and sulcal folding, occur during the 3rd trimester of gestation which overlaps with the period of premature births. Here, we investigated the ability of the graph convolutional network (GCN) to predict brain age for preterm neonates by accounting for morphometrics measured on the cortical surface and the surface mesh topology as a sparse graph. Our findings demonstrate that GCN-based age prediction of preterm neonates (n=170; mean absolute error [MAE]: 1.06 weeks) outperformed conventional machine learning algorithms and deep learning methods that did not use topological information. We further evaluated how predicted brain age (PBA) emerges as a biologically meaningful index that characterizes the current status of brain development at the time of imaging. We hypothesized that the relative brain age (RBA; PBA minus chronological age) at scan reflects a combination of perinatal clinical factors, including preterm birth, birthweight, perinatal brain injuries, exposure to postnatal steroids, etc. We also hypothesized that RBA of neonatal scans may be associated with brain functional development in the future. To validate these hypotheses, we used general linear models. Furthermore, we established structural equation models (SEM) to determine the structural relationship between preterm birth (as a latent variable of birthweight and birth age), perinatal injuries (as a latent variable of three leading brain injuries), postnatal factors (as a latent variable of six clinical conditions), RBA at scan, and neurodevelopmental scores at 30 months. Our results suggest that low birthweight, chronic lung disease, and exposure to postnatal steroids impair cortical growth, as low RBA was significantly associated with these risks. Furthermore, RBA was associated with cognitive and language scores at 30 months. SEM analysis indicated that RBA mediated the influences of preterm birth and postnatal clinical factors, but not perinatal brain injuries, toward brain functional development at 30 months. The left middle cingulate cortex showed the most accurate prediction of brain age (MAE: 1.19 weeks), followed by left posterior and right middle cingulate cortices (1.21 weeks). These cingulate regions presented faster growth than others. RBAs of several frontal cortices significantly correlated with cognitive abilities at 30 months of age (n=50). Whereas, RBA of left Broca’s area, which is important for language production and comprehension, was associated with language functional scores. Overall, our results demonstrate the potential of the GCN in both predicting brain age and localizing regional growth that relates to postnatal factors and future neurodevelopmental outcome.
Exosomes from adipose-derived stem cells alleviate myocardial infarction via microRNA-31/FIH1/HIF-1α pathway
Authors: Zhu Dihan , Wang Yang , Thomas Miracle , McLaughlin KeAsiah , Oguljahan Babayewa , Henderson Joshua , Yang Qinglin , Chen Y. Eugene , Liu Dong
Published: May 2021

Our previous study has revealed that exosomes from adipose-derived stem cells (ASCs) promote angiogenesis in subcutaneously transplanted gels by delivery of microRNA-31 (miR-31) which targets factor inhibiting hypoxia-inducible factor-1 (FIH1) in recipient cells. Here we hypothesized that ASC exosomes alleviate ischemic diseases through miR-31/FIH1/hypoxia-inducible factor-1α (HIF-1α) signaling pathway. Exosomes from ASCs were isolated by sequential centrifugations, and were characterized with nanoparticle tracking analysis, transmission electron microscopy, and immunoblotting analysis for exosomal markers. Results from laser imaging of ischemic mouse hindlimb revealed that exosomes enhanced the blood perfusion, and this enhancement was impaired when using miR-31-depleted exosomes. Immunohistochemistry analysis showed that administration of exosomes resulted in a higher arteriole density and larger CD31+ area in ischemic hindlimb than miR-31-delpleted exosomes. Similarly, knockdown of miR-31 in exosomes reduced the effects of the exosomes on increasing ventricular fraction shortening and CD31+ area, and on decreasing infarct size. Exosomes promoted endothelial cell migration and tube formation. These changes were attenuated when miR-31 was depleted in the exosomes or when FIH1 was overexpressed in the endothelial cells. Furthermore, the results from co-immunoprecipitation and luciferase reporter assay demonstrated that the effects of exosomes on elevating the binding of HIF-1α with co-activator p300 and enhancing HIF-1α activity were decreased when miR-31 was depleted in the exosomes or FIH1 was overexpressed. Our findings provide evidence that exosomes from ASCs promote angiogenesis in both mouse ischemic hindlimb and heart through transport of miR-31 which targets FIH1 and therefore triggers HIF-1α transcriptional activation.
A pipeline for systematic comparison of model levels and parameter inference settings applied to negative feedback gene regulation
Authors: Coulier Adrien , Singh Prashant , Sturrock Marc , Hellander Andreas
Published: May 2021

Quantitative stochastic models of gene regulatory networks are important tools for studying cellular regulation. Such models can be formulated at many different levels of fidelity. A practical challenge is to determine what model fidelity to use in order to get accurate and representative results. The choice is important, because models of successively higher fidelity come at a rapidly increasing computational cost. In some situations, the level of detail is clearly motivated by the question under study. In many situations however, many model options could qualitatively agree with available data, depending on the amount of data and the nature of the observations. Here, an important distinction is whether we are interested in inferring the true (but unknown) physical parameters of the model or if it is sufficient to be able to capture and explain available data. The situation becomes complicated from a computational perspective because inference and model selection need to be approximate. Most often it is based on likelihood-free Approximate Bayesian Computation (ABC) and here determining which summary statistics to use, as well as how much data is needed to reach the desired level of accuracy, are difficult tasks. Ultimately, all of these aspects - the model fidelity, the available data, and the numerical choices for inference and model selection - interplay in a complex manner. In this paper we develop a computational pipeline designed to systematically evaluate inference accuracy for a wide range of true known parameters. We then use it to explore inference settings for negative feedback gene regulation. In particular, we compare a spatial stochastic model, a coarse-grained multiscale model, and a simple well-mixed model for several data-scenarios and for multiple numerical options for parameter inference. Practically speaking, this pipeline can be used as a preliminary step to guide modelers prior to gathering experimental data. By training Gaussian processes to approximate the distance metric, we are able to significantly reduce the computational cost of running the pipeline.
Environmental DNA (eDNA) metabarcoding surveys extend the range of invasion for non-indigenous freshwater species in Eastern Europe
Authors: Jeunen Gert-Jan , Lipinskaya Tatsiana , Gajduchenko Helen , Golovenchik Viktoriya , Moroz Michail , Rizevsky Viktor , Semenchenko Vitaliy , Gemmell Neil J.
Published: May 2021

Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e., an ichthyological, hydrobiological, and eDNA survey, whereby DNA was extracted from 500 mL surface water samples and amplified with two 16S rRNA primer assays targeting the fish and macro-invertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous sediment-living macro-invertebrates were detected by traditional surveys, while seven NIS eDNA signals were picked up, including four fish, one aquatic and two sediment-living macro-invertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey could be attributed to (i) preferential amplification of aquatic over sediment-living macro-invertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximize the probability of early detection of non-native organisms.
TAPIOCA: Topological Attention and Predictive Inference of Chromatin Arrangement Using Epigenetic Features
Authors: Highsmith Max , Cheng Jianlin
Published: May 2021

Chromatin conformation is an important characteristic of the genome which has been repeatedly demonstrated to play vital roles in many biological processes. Chromatin can be characterized by the presence or absence of structural motifs called topologically associated domains. The de facto strategy for determination of topologically associated domains within a cell line is the use of Hi-C sequencing data. However Hi-C sequencing data can be expensive or otherwise unavailable. Various epigenetic features have been hypothesized to contribute to the determination of chromatin conformation. Here we present TAPIOCA, a self-attention based deep learning transformer algorithm for the prediction of chromatin topology which circumvents the need for labeled Hi-C data and makes effective predictions of chromatin conformation organization using only epigenetic features. TAPIOCA outperforms prior art in established metrics of TAD prediction, while generalizing across cell lines beyond those used in training.

Availability

the source code of TAPIOCA and training and test datasets are available at https://github.com/Max-Highsmith/TAPIOCA

Author Summary

In this paper we outline a machine learning approach for predicting the topological organization of chromosomes using epigenetic track data as features. By utilizing an architecture inspired by the sequence transduction transformer network we are able to effectively predict multiple metrics used to characterize topologically associated domains. Our experimental results demonstrate that once trained our algorithm can effectively predict topological organization on novel cell lines all without any exposure to original Hi-C data in test datasets.
Decoding explicit and implicit representations of health and taste attributes of foods in the human brain
Authors: Schubert Elektra , Rosenblatt Daniel , Eliby Djamila , Kashima Yoshihisa , Hogendoorn Hinze , Bode Stefan
Published: May 2021

Obesity has become a significant problem word-wide and is strongly linked to poor food choices. Even in healthy individuals, taste perceptions often drive dietary decisions more strongly than healthiness. This study tested whether health and taste representations can be directly decoded from brain activity, both when explicitly considered, and when implicitly processed for decision-making. We used multivariate support vector regression for event-related potentials (as measured by the electroencephalogram) occurring in the first second of food cue processing to predict ratings of tastiness and healthiness. In Experiment 1, 37 healthy participants viewed images of various foods and explicitly rated their tastiness and healthiness, whereas in Experiment 2, 89 healthy participants indicated their desire to consume snack foods, with no explicit instruction to consider tastiness or healthiness. In Experiment 1 both attributes could be decoded, with taste information being available earlier than health. In Experiment 2, both dimensions were also decodable, and their significant decoding preceded the decoding of decisions (i.e., desire to consume the food). However, in Experiment 2, health representations were decodable earlier than taste representations. These results suggest that health information is activated in the brain during the early stages of dietary decisions, which is promising for designing obesity interventions aimed at quickly activating health awareness.
HOXB7induces STAT3-mediated transformation and lung metastasis in immortalized mammary gland NMuMG cells
Authors: Azuma Kazushi , Sakamoto Mai , Katayama Shota , Matsui Atsuka , Nakamichi Kazuya , Goshima Naoki , Watanabe Shinya , Nakayama Jun , Semba Kentaro
Published: May 2021

The homeobox family genes are often dysregulated in a various cancer type. ParticularlyHOXB7amplification and overexpression correlate with poor prognosis in various cancer such as gastric, pancreatic, and lung cancers. Moreover,HOXB7is known to contribute to cancer progression by promoting epithelial to mesenchymal transition, anti-cancer drug resistance, and angiogenesis. In this study, we show thatHOXB7is coamplified withERBB2in a subset of breast cancer patients and HOXB7 expression correlates with poor prognosis in HER2-positive breast cancer patients. This clinical observation is supported by the following results:HOXB7overexpression in an immortalized murine mammary gland epithelial cell line NMuMG induces cellular transformationin vitro, tumorigenesis and lung metastasis through the activation of JAK-STAT signaling.
Impaired α-tubulin re-tyrosination leads to synaptic dysfunction and is a feature of Alzheimer’s disease
Authors: Peris Leticia , Qu Xiaoyi , Soleilhac Jean-Marc , Parato Julie , Lanté Fabien , Kumar Atul , Pero Maria Elena , Martínez-Hernández José , Corrao Charlotte , Falivelli Giulia , Payet Floriane , Gory-Fauré Sylvie , Bosc Christophe , Blanca Ramírez Marian , Sproul Andrew , Brocard Jacques , Di Cara Benjamin , Delagrange Philippe , Buisson Alain , Goldberg Yves , Moutin Marie-Jo , Bartolini Francesca , Andrieux Annie
Published: May 2021

In neurons, dynamic microtubules play regulatory roles in neurotransmission and synaptic plasticity. While stable microtubules contain detyrosinated tubulin, dynamic microtubules are composed of tyrosinated tubulin, suggesting that the tubulin tyrosination/detyrosination (Tyr/deTyr) cycle modulates microtubule dynamics and synaptic function. In the Tyr/deTyr cycle, the C-terminal tyrosine of α-tubulin is re-added by tubulin-tyrosine-ligase (TTL). Here we show that TTL+/− mice exhibit decreased tyrosinated microtubules, synaptic plasticity and memory deficits, and that reduced TTL expression is a feature of sporadic and familial Alzheimer’s disease (AD), with human APPV717I neurons having less dynamic microtubules. We find that spines visited by dynamic microtubules are more resistant to Amyloidβ1-42 and that TTL, by promoting microtubule entry into spines, prevents Aβ1-42-induced spine pruning. Our results demonstrate that the Tyr/deTyr cycle regulates synaptic plasticity, is protective against spine injury, and that tubulin re-tyrosination is lost in AD, providing evidence that a defective Tyr/deTyr cycle may contribute to neurodegeneration.
Source range phylogenetic community structure can predict the outcome of avian introductions
Authors: Maitner Brian S. , Park Daniel S. , Enquist Brian J , Dlugosch Katrina M
Published: May 2021

Competing phylogenetic models have been proposed to explain the success of species introduced to other communities. Here, we present a study predicting the establishment success of birds introduced to Florida, Hawaii, and New Zealand using several alternative models, considering species’ phylogenetic relatedness to source and recipient range taxa, propagule pressure, and traits. We find consistent support for the predictive ability of source region phylogenetic structure. However, we find that the effects of recipient region phylogenetic structure vary in sign and magnitude depending on inclusion of source region phylogenetic structure, delineation of the recipient species pool, and the use of phylogenetic correction in the models. We argue that tests of alternative phylogenetic hypotheses including the both source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure, are likely to be critical for identifying general phylogenetic patterns in introduction success, predicting future invasions, and for stimulating further exploration of the underlying mechanisms of invasibility.
The sugar-responsive enteroendocrine neuropeptide F regulates lipid metabolism through glucagon-like and insulin-like hormones inDrosophila melanogaster
Authors: Yoshinari Yuto , Kosakamoto Hina , Kamiyama Takumi , Hoshino Ryo , Matsuoka Rena , Kondo Shu , Tanimoto Hiromu , Nakamura Akira , Obata Fumiaki , Niwa Ryusuke
Published: May 2021

The enteroendocrine cell (EEC)-derived incretins play a pivotal role in regulating the secretion of glucagon and insulins in mammals. Although glucagon-like and insulin-like hormones have been found across animal phyla, incretin-like EEC-derived hormones have not yet been characterised in invertebrates. Here, we show that the midgut-derived hormone, Neuropeptide F (NPF), acts as the sugar-responsive, incretin-like hormone in the fruit fly,Drosophila melanogaster. Secreted NPF is received by NPF receptor in the corpora cardiaca and in insulin-producing cells. NPF-NPFR signalling resulted in the suppression of the glucagon-like hormone production and the enhancement of the insulin-like peptide secretion, eventually promoting lipid anabolism. Similar to the loss of incretin function in mammals, loss of midgut NPF led to significant metabolic dysfunction, accompanied by lipodystrophy, hyperphagia, and hypoglycaemia. These results suggest that enteroendocrine hormones regulate sugar-dependent metabolism through glucagon-like and insulin-like hormones not only in mammals but also in insects.
Disrupting the CD177:proteinase 3 membrane complex reduces anti-PR3 antibody-induced neutrophil activation
Authors: Marino Stephen F. , Jerke Uwe , Rolle Susanne , Daumke Oliver , Kettritz Ralph
Published: May 2021

CD177 is a neutrophil-specific receptor presenting proteinase 3 (PR3) autoantigen on the neutrophil surface. CD177 expression is restricted to a neutrophil subset resulting in CD177pos/mPR3highand CD177neg/mPR3lowpopulations. The size of the CD177pos/mPR3highsubset has implications for anti-neutrophil cytoplasmic autoantibody (ANCA)-associated autoimmune vasculitis (AAV) where patients harbor PR3-specific ANCA that activate neutrophils. We generated high affinity anti-CD177 monoclonal antibodies, some of which interfered with PR3 binding to CD177 (PR3 “blockers”) as determined by surface plasmon resonance spectroscopy, and used them to test the effect of competing PR3 from the surface of CD177posneutrophils. Because intact anti-CD177 antibodies also caused neutrophil activation, we prepared non-activating Fab fragments of a PR3 blocker and non-blocker that bound specifically to CD177posneutrophils by flow cytometry. We observed that Fab blocker clone 40, but not non-blocker clone 80, dose-dependently reduced anti-PR3 antibody binding to CD177posneutrophils. Importantly, preincubation with clone 40 significantly reduced respiratory burst in primed neutrophils challenged either with monoclonal antibodies to PR3 or PR3-ANCA IgG from AAV patients. After separating the two CD177/mPR3 neutrophil subsets from individual donors by magnetic sorting, we found that PR3-ANCA provoked significantly more superoxide production in CD177pos/mPR3highthan in CD177neg/mPR3lowneutrophils, and that anti-CD177 Fab clone 40 reduced the superoxide production of CD177poscells to the level of the CD177negcells. Our data demonstrate the importance of the CD177:PR3 membrane complex in maintaining a high ANCA epitope density and thereby underscore the contribution of CD177 to the severity of PR3-ANCA diseases.
Synergism between Chromatin Dynamics and Gene Transcription Enhances Robustness and Stability of Epigenetic Cell Memory
Authors: Wang Zihao , Luo Songhao , Chen Meiling , Zhou Tianshou , Zhang Jiajun
Published: May 2021

Apart from carrying hereditary information inherited from their ancestors and being able to pass on the information to their descendants, cells can also inherit and transmit information that is not stored as changes in their genome sequence. Such epigenetic cell memory, which is particularly important in multicellular organisms, involves multiple biochemical modules mainly including chromatin organization, epigenetic modification and gene transcription. The synergetic mechanism among these three modules remains poorly understood and how they collaboratively affect the robustness and stability of epigenetic memory is unclear either. Here we developed a multiscale model to address these questions. We found that the chromatin organization driven by long-range epigenetic modifications can significantly enhance epigenetic cell memory and its stability in contrast to that driven by local interaction and that chromatin topology and gene activity can promptly and simultaneously respond to changes in nucleosome modifications while maintaining the robustness and stability of epigenetic cell memory over several cell cycles. We concluded that the synergism between chromatin dynamics and gene transcription facilitates the faithful inheritance of epigenetic cell memory across generations.
T Cell Receptor Beta Germline Variability is Revealed by Inference From Repertoire Data
Authors: Omer Aviv , Peres Ayelet , Rodriguez Oscar L , Watson Corey T , Lees William , Polak Pazit , Collins Andrew M , Yaari Gur
Published: May 2021

Background

T and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Understanding the genetic factors influencing the composition and dynamics of these repertoires is of major scientific and clinical importance. The chromosomal loci encoding for the variable regions of TCRs and BCRs are challenging to decipher due to repetitive elements and undocumented structural variants.

Methods

To confront this challenge, AIRR-seq-based methods have recently been developed for B cells, enabling genotype and haplotype inference and discovery of undocumented alleles. However, this approach relies on complete coverage of the receptors’ variable regions, whereas most T cell studies sequence a small fraction of that region. Here, we adapted a B cell pipeline for undocumented alleles, genotype, and haplotype inference for full and partial TCR sequences. The pipeline also deals with gene assignment ambiguities, which is especially important in the analysis of data-sets of partial sequences.

Results

We identified 39 undocumented polymorphisms in T cell receptor Beta V (TRBV) and 31 undocumented 5’ UTR sequences. A subset of these inferences was also observed using independent genomic approaches. We found that a single nucleotide polymorphism differentiating between the two documented T cell receptor Beta D2 (TRBD2) alleles is strongly associated with dramatic changes in the expressed repertoire.

Conclusions

We reveal a rich picture of germline variability, and demonstrate how a single nucleotide polymorphism dramatically affects the composition of the whole repertoire. Our findings provide a basis for annotation of TCR repertoires for future basic and clinical studies.
Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics
Authors: Gondal Mahnoor Naseer , Chaudhary Safee Ullah
Published: May 2021

Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built on top of this data have the potential to provide specific insights into complex multifactorial aberrations underpinning tumor initiation, development, and metastasis. Furthermore, the annotation of these single- or multi-scale models with patient data can additionally assist in designing personalized therapeutic interventions as well as aid in clinical decision-making. Here, we have systematically reviewed the emergence and evolution of (i) repositories with scale-specific and multiscale biomolecular cancer data, (ii) systems biology models developed using this data, (iii) associated simulation software for development of personalized cancer therapeutics, and (iv) translational attempts to pipeline multi-scale panomics data for data-drivenin silicoclinical oncology. The review concludes by highlighting that the absence of a generic, zero-code, panomics-based multi-scale modeling pipeline and associated software framework, impedes the development and seamless deployment of personalizedin silicomulti-scale models in clinical settings.
The time course of molecular acclimation to seawater in a euryhaline fish
Authors: Bonzi Lucrezia C. , Monroe Alison A. , Lehmann Robert , Berumen Michael L. , Ravasi Timothy , Schunter Celia
Published: May 2021

The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Red Sea populations have been found to receive migrants from desert ponds that are flushed out to sea during flash floods, requiring rapid acclimation to a greater than 40 ppt change in salinity. To investigate the molecular pathways of salinity acclimation during such colonization events, a Red Sea coastal lagoon and a desert pond population were sampled, with the latter exposed to a rapid increase in water salinity. Changes in branchial gene expression were investigated via genome-wide transcriptome measurements over time from 6 hours to 21 days. The two natural populations displayed basal differences in genes related to ion transport, osmoregulation and immune system functions. These mechanisms were also differentially regulated in seawater transferred fish, revealing their crucial role in long-term adaptation. Other processes were only transiently activated shortly after the salinity exposure, including cellular stress response mechanisms, such as molecular chaperone synthesis and apoptosis. Tissue remodeling processes were also identified as transient, but took place later in the timeline, suggesting their importance to long-term acclimation as they likely equip the fish with lasting adaptations to their new environment. The alterations in branchial functional pathways displayed by Arabian pupfish in response to salinity increases are diverse. These reveal a large toolkit of molecular processes important for adaptation to hyperosmolarity that allow for successful colonization to a wide variety of different habitats.
How to describe and measure phenology? An investigation on the diversity of metrics using phenology of births in large herbivores
Authors: Thel Lucie , Chamaillé-Jammes Simon , Bonenfant Christophe
Published: May 2021

Proposed in 1849 by Charles Morren to depict periodical phenomena governed by seasons, the term “phenology” has spread in many fields of biology. With the wide adoption of the concept of phenology flourished a large number of metrics with different meaning and interpretation. Here, we first a priori classified 52 previously published metrics used to characterise the phenology of births in large herbivores according to four biological characteristics of interest: timing, synchrony, rhythmicity and regularity of births. We then applied each metric retrieved on simulation data, considering normal and non-normal distributions of births, and varying distributions of births in time. We then evaluated the ability of each metric to capture the variation of the four phenology characteristics via a sensitivity analysis. Finally, we scored each metric according to eight criteria we considered important to describe phenology correctly. The high correlation we found among the many metrics we retrieved suggests that such diversity of metrics is unnecessary. We further show that the best metrics are not the most commonly used, and that simpler is often better. Circular statistics with the mean vector orientation and mean vector length seems, respectively, particularly suitable to describe the timing and synchrony of births in a wide range of phenology patterns. Tests designed to compare statistical distributions, like Mood and Kolmogorov-Smirnov tests, allow a first and easy quantification of rhythmicity and regularity of birth phenology respectively. By identifying the most relevant metrics our study should facilitate comparative studies of phenology of births or of any other life-history event. For instance, comparative studies of the phenology of mating or migration dates are particularly important in the context of climate change.
Alcohol Use Disrupts Age-Appropriate Cortical Thinning in Adolescence: A Data Driven Approach
Authors: Sun Delin , Adduru Viraj R. , Phillips Rachel D. , Bouchard Heather C. , Sotiras Aristeidis , Michael Andrew M. , Baker Fiona C. , Tapert Susan F. , Brown Sandra A. , Clark Duncan B. , Goldston David , Nooner Kate B. , Nagel Bonnie J. , Thompson Wesley K. , De Bellis Michael , Morey Rajendra A.
Published: May 2021

Objective

Cortical thickness changes dramatically during development and is influenced by adolescent drinking. However, previous findings have been inconsistent and limited by region-of-interest approaches that are underpowered because they do not conform to the underlying heterogeneity from the effects of alcohol.

Methods

Adolescents (n=657; 12-22 years at baseline) from the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA) who endorsed little to no alcohol use at baseline were assessed with structural MRI and followed longitudinally at four yearly intervals. Seven unique spatially covarying patterns of cortical thickness were obtained from the baseline scans by applying a novel data-driven method called non-negative matrix factorization (NMF). The cortical thickness maps of all participants’ longitudinal scans were projected onto vertex-level cortical patterns to obtain participant-specific coefficients for each pattern. Linear mixed-effects models were fit to each pattern to investigate longitudinal effects of alcohol consumption on cortical thickness.

Results

In most NMF-derived cortical thickness patterns, the longitudinal rate of decline in no/low drinkers was similar for all age cohorts, among moderate drinkers the decline was faster in the younger cohort and slower in the older cohort, among heavy drinkers the decline was fastest in the younger cohort and slowest in the older cohort (FDR corrected p-values < 0.01).

Conclusions

The NMF method can delineate spatially coordinated patterns of cortical thickness at the vertex level that are unconstrained by anatomical features. Age-appropriate cortical thinning is more rapid in younger adolescent drinkers and slower in older adolescent drinkers.
The role of Cyp19a1 in female pathway of a freshwater turtle (Mauremys reevesii) with temperature-dependent sex determination
Authors: Wu Peng-fei , Wang Xi-feng , Gao Fei , Du Wei-guo
Published: May 2021

The molecular mechanism of temperature-dependent sex determination (TSD) in reptiles has been drawn great interest from biologists for several decades. However, which genetic factors are essential for TSD remain elusive, especially for the female sex determination process. Cyp19a1, encodes an enzyme of aromatase catalyzing the conversion of testosterone to estrogen, has been confirmed to modulate steroid hormones involved in the sexual differentiation of many species, but whether it has a critical role in determining the gonadal sexual fate in TSD is still to be elucidated. Here, we identified that Cyp19a1 expression exhibited a temperature-dependent, sexually dimorphic expression pattern, preceding gonadal sex differentiation in a TSD turtle Mauremys reevesii. Cyp19a1 expression in gonads increased dramatically when embryos developed at high female-producing temperatures (FPT), but were extremely low throughout embryogenesis at low male-producing temperatures (MPT). Cyp19a1 expression increased rapidly in response to the temperature shift from MPT to FPT in developing gonads. The sexual phenotype of turtles was successfully reversed by aromatase inhibitor treatment at FPT, and by estrogen treatment at MPT, accompanied with the rapid upregulation of Cyp19a1. These results demonstrate that Cyp19a1 is essential for the female sex determination process in M. reevesii, indicating its vital role in the female pathway of TSD.
The 3′ end of the human norovirus antigenomic sequence is required for its genomic RNA synthesis by RNA-dependent RNA polymerase
Authors: Shimoike Takashi , Hayashi Tsuyoshi , Oka Tomoichiro , Muramatsu Masamichi
Published: May 2021

Norovirus genome is a single-stranded positive-strand RNA. To reveal the mechanism underlying the initiation of the norovirus genomic RNA synthesis by its RNA-dependent RNA polymerase (RdRp), we used an in vitro assay to detect the complementary RNA synthesis activity. Results showed that the purified recombinant RdRp synthesized the complementary positive-sense RNA from the 100 nt template corresponding to the 3′ end region of the viral antisense genome sequence, but that RdRp did not synthesize the antisense genomic RNA from the 100 nt template, corresponding to the 5′ end region of the positive-sense genome sequence. The 31 nt region at the 3′ end of the RNA antisense template was then predicted to form the stem-loop structure. Its deletion resulted in the loss of complementary RNA synthesis by RdRp. The connection of the 31 nt to the 3′ end of the positive-sense RNA template allowed to be recognized by the RdRp. Similarly, an electrophoretic mobility shift assay further revealed that RdRp bound to the antisense RNA specifically, but the 31 nt deletion at the 3′ end lost the binding to RdRp. Therefore, combining this observation with further deletion and mutation analysis, we concluded that the predicted stem-loop structure in the 31 nt and region close to the antisense viral genomic stem sequences are important for initiating the positive-sense human norovirus genomic RNA synthesis by its RdRp.
Bis(2-nitrophenyl) selenide, bis(2-aminophenyl) selenide and bis(2-aminophenyl) telluride: structural and theoretical analysis
Authors: Saravanan Raju , Singh Harkesh B. , Butcher Ray J.
Published: May 2021

Three organoselenium and organotellurium compounds containing ortho substitutents, namely, bis(2-nitrophenyl) selenide, C12H8N2O4Se, 2, bis(2-aminophenyl) selenide, C12H12N2Se, 3, and bis(2-aminophenyl) telluride, C12H12N2Te, 7, have been investigated by both structural and theoretical methods. In the structures of all three compounds, there are intramolecular contacts between both Se and Te with the ortho substituents. In the case of 2, this is achieved by rotation of the nitro group from the arene plane. For 3, both amino groups exhibit pyramidal geometry and are involved in intramolecular N—H...Se interactions, with one also participating in intermolecular N—H...N hydrogen bonding. While 3 and 7 are structurally similar, there are some significant differences. In addition to both intramolecular N—H...Te interactions and intermolecular N—H...N hydrogen bonding, 7 also exhibits intramolecular N—H...N hydrogen bonding. In the packing of these molecules, for 2, there are weak intermolecular C—H...O contacts and these, along with the O...N interactions mentioned above, link the molecules into a three-dimensional array. For 3, in addition to the N—H...N and N—H...Se interactions, there are also weak intermolecular C—H...Se interactions, which also link the molecules into a three-dimensional array. On the other hand, 7 shows intermolecular N—H...N interactions linking the molecules into R
2
2(16) centrosymmetric dimers. In the theoretical studies, for compound 2, AIM (atoms in molecules) analysis revealed critical points in the Se...O interactions with values of 0.017 and 0.026 a.u. These values are suggestive of weak interactions present between Se and O atoms. For 3 and 7, the molecular structures displayed intramolecular, as well as intermolecular, hydrogen-bond interactions of the N—H...N type. The strength of this hydrogen-bond interaction was calculated by AIM analysis. Here, the intermolecular (N—H...N) hydrogen bond is stronger than the intramolecular hydrogen bond. This was confirmed by the electron densities for 3 and 7 [ρ(r) = 0.015 and 0.011, respectively].
Accounting and accountability practices in times of crisis: a Foucauldian perspective on the UK government's response to COVID-19 for England
Authors: Ahrens Thomas , Ferry Laurence
Published: May 2021

Purpose

This paper considers the accounting and accountability practices of the UK government’s response to COVID-19 for England, focussing on the first wave of the pandemic in 2020.

Design/methodology/approach

Based on a close reading of the news media and official reports from government departments, Parliament select committees and the National Audit Office, among others, this paper frames the UK government's uses of accounting and accountability in its response to COVID-19. This is by using the categories of “apparatuses of security”, Foucault's schematic of government for economising on the uses of state power.

Findings

The paper shows that an important role for accounting is in the process of enabling the government to gauge the extent of the crisis and produce calculations to underpin its response, what Foucault called “normalisation”. This role was unlike statistics and economics. The government relied most on monthly statistical reporting and budgeting flexibilities. By contrast, the multi-year Spending Review and financial reporting were not timely enough. That said, financial reporting fed into financial sustainability projections and enabled audit that could provide potential accountability regarding regularity, probity, value for money and fairness. The authors’ findings suggest that, conceptually, accountability should be added to the object–subject element of Foucault's apparatuses of security because of its significance for governments' ability to pursue crisis objectives that require popular assent.

Practical implications

In view of the ongoing uncertainty, with the crisis extending over longer budget and financial reporting periods, a Spending Review is becoming ever more necessary for better planning, without limiting, however, the budget flexibilities that have proven so useful for rapid government responses. Moreover, the government should continue its accounting reforms post COVID-19 so that improved accountability and audit can contribute to enhanced future financial resilience.

Originality/value

This is the first paper to apply Foucault's notion of apparatuses of security to an analysis of government accounting and accountability practices.
Tolerance, governance and happiness (in)equality: cross-country evidence
Authors: Salahodjaev Raufhon
Published: May 2021

Purpose

The purpose of this study is to extend related literature on life satisfaction. In particular, the author explores the link between tolerance, governance and life satisfaction inequality in a sample of 81 countries. While studies have shown that tolerance and governance are separately linked to subjective well-being, no study has shown their mutual relationship to life satisfaction inequality.

Design/methodology/approach

Considering the existing link between tolerance and quality of institutions, in this study, the author explores the relationship between tolerance and life satisfaction inequality and the mediating role of governance. This research could be embedded in the framework of ballooning research exploring the effect of societal values on institutions and life satisfaction.

Findings

The empirical findings suggest more tolerant societies are more likely to have more even levels of life satisfaction, but this correlation is completely mediated by governance. Quality of institutions thus seem to be one of the core channels by which societies that value tolerance achieve more equal distribution of happiness. The author also finds that while GDP per capita evens out happiness, income inequality increases the gap in life satisfaction within society.

Originality/value

To the best of the author’s knowledge, this study is the first that relies on most up-to-date cross-country data to explore a novel channel through which tolerance may be linked to subjective well-being. In particular, in this study, the author posits that tolerance may have been linked to subjective well-being indirectly via its impact on quality of institutions (governance).
An analysis of students' perspectives on e-learning participation – the case of COVID-19 pandemic
Authors: Nikou Shahrokh , Maslov Ilia
Published: May 2021

Purpose

During the COVID-19 pandemic, educational institutions were forced to shut down, causing massive disruption of the education system. This paper aims to determine the critical factors for the intention to participate in e-learning during COVID-19.

Design/methodology/approach

Data were collected by surveying 131 university students and structural equation modelling technique using PLS-SEM was employed to analysis the data.

Findings

The results showed that the COVID-19 related factors such as perceived challenges and COVID-19 awareness not only directly impact students' intention but also such effects are mediated through perceived usefulness and perceived ease of use of e-learning systems. However, the results showed that the educational institution's preparedness does not directly impact the intention of students to participate in e-learning during COVID-19. The results also showed that the gender and length of the use of e-learning systems impact students' e-learning systems use.

Originality/value

These results demonstrated that, regardless of how well the educational institutions are prepared to promote the use of e-learning systems, other COVID-19-related challenges play a crucial role in forming the intention of students to participate in e-learning during the COVID-19 pandemic. Theoretical and practical implications are provided.
Review of Saudi Arabia company law reforms and its implications on corporate governance framework- an evidence from emerging market
Authors: Rizvi Lubna Javed , Hussain Zahid
Published: May 2021

Purpose

This paper aims to review the literature of CG regime in Saudi Arabia, an emerging market for several compelling reasons. Most of the earlier literature on corporate governance subjects mainly aimed at large emerging economies. To date, there is a lack of studies examining the following: authorities and obligations, subcommittees and the regulatory system in Saudi Arabia. Therefore, this paper is an attempt to bridge this gap by reviewing the current laws, regulation, trends and key reforms in corporate governance framework in the country as the current amended laws focused to offer more competence and precision to the regulatory setting in line with the development of the Saudi Arabian stock market and the influx of foreign reserves.

Design/methodology/approach

The current paper has espoused a content analysis approach in which relevant literature was deliberated and studied.

Findings

The amended CG rules include some developments into corporate governance and substitutes the earlier version of the long overdue regulation of 1965. The new 2017 implemented Code will reinforce the implication of good governance as a condition model for accomplishing good financial management in the country. This study has provided an overview of the evolution and development of corporate governance in Saudi Arabia by highlighting the key reforms.

Research limitations/implications

This study has implications for the policymakers and institutional bodies to review the current developments and progress in the country’s overall corporate governance framework in an attempt to attract more foreign direct investment. Saudi Arabia is among the nations that have a potential for huge foreign investments due to its plan of expanding its economy “Vision 2030.” Therefore, this paper will aid foreign investors in deciding to invest in the country after reviewing the current developments in an attempt to implement vision 2030.

Originality/value

This study contributes to existing literature by examining the current trends in CG, with the discussion on the development of company law in Saudi Arabia which emphasizes on sections that borders on corporate governance.
Sustainability excellence: the interactions of lean production, internal green practices and green product innovation
Authors: Afum Ebenezer , Zhang Ran , Agyabeng-Mensah Yaw , Sun Zhuo
Published: May 2021

Purpose

This study aims to investigate the interactions between lean production, internal green practices, green product innovation and sustainable performance metrics. The study further looks at the mediation effect of internal green practices and green product innovation between lean production and sustainable performance dimensions.

Design/methodology/approach

The questionnaire was used to glean data from 209 manufacturing firms. All the hypothesized relationships were processed by using partial least square-structural equation modelling.

Findings

The results suggest that lean production significantly leads to the implementation of internal green practices and the production of quality products with eco-oriented features that meet customers’ needs. Further, while lean production and internal green practices were found to significantly influence sustainability performance, green product innovation significantly influences only financial performance. Besides, the mediation analysis shows that internal green practices mediate the relationship between lean production and sustainable performance dimensions but green product innovation mediates the relationship between lean production and financial performance only.

Research limitations/implications

The study is limited to firms from Ghana, a developing country; hence, the results cannot be imported to reflect other geographical contexts.

Practical implications

The results of the study provide sufficient justifications for managers, (especially Ghanaian managers and those from other similar environs) to commit their financial resources towards implementing lean production and internal green practices so as to achieve sustainability excellence.

Originality/value

This study magnifies and provides new insight on lean and green literature by developing a comprehensive research model that concurrently tests the direct and indirect effects between lean production, internal green practices, green product innovation and sustainable performance dimensions.