bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of viscoelastic bonding layer on performance of piezoelectric actuator attached to elastic structure
Authors: Ali Ibrahim A , Alazwari Mashhour A , Eltaher Mohamed A , Abdelrahman Alaa A
Published: March 2022

In the context of the finite elements analysis, the mechanical performance of viscoelastically bonded smart structures is investigated and analyzed. Three different models are considered and compared. In the 1st model, the actuator is glued to the host structure. On the other hand, in the two other models the actuator is glued to the bonding layer which is glued to the host structures. To explore the effect of the bonding layer characteristics on the mechanical behavior of the host structure, both elastic and viscoelastic layers are considered. The Prony’s series are utilized to simulate the viscoelastic constitutive response. The mathematical formulation of the coupled problem is presented and the dynamic finite elements equations of motion of the coupled electromechanical systems are introduced. The proposed methodology is verified by comparing the obtained results with the available results in the literature and good consentience is observed. Both static and dynamic vibration behaviors are studied incorporating the interfacial shear stresses between the bonding layer and the host structure as well as the displacements as a comparison criterion to determine the performance controlling function of the host structure. Parametric study of piezoelectric properties showed that permittivity is required in solving such systems but does not affect the performance. On the other hand, the piezoelectric characteristics have significant effects on the mechanical performance of smart structures and can be used in the optimum selection of combination just like mechanical properties and geometry. Additionally, the obtained results show that the model with viscoelastic bonding layer has an overall static performance nearly half of elastic bonding layer model while it has a slight effect on the dynamic behavior compared with the corresponding elastic bonding layer. The proposed methodology with the obtained results is supportive in the applications of structure health monitoring and dynamics of smart structural systems. The proposed procedure could be extended in a future work to include the coupled electromagnetic effects on the dynamic behavior of smart structures in hygrothermal environment.
Differentially expressed genes prediction by multiple self-attention on epigenetics data
Authors: Huang Zimo , Wang Jun , Yan Zhongmin , Guo Maozu
Published: March 2022

Predicting differentially expressed genes (DEGs) from epigenetics signal data is the key to understand how epigenetics controls cell functional heterogeneity by gene regulation. This knowledge can help developing ‘epigenetics drugs’ for complex diseases like cancers. Most of existing machine learning-based methods suffer defects in prediction accuracy, interpretability or training speed. To address these problems, in this paper, we propose a Multiple Self-Attention model for predicting DEGs on Epigenetic data (Epi-MSA). Epi-MSA first uses convolutional neural networks for neighborhood bins information embedding, and then employs multiple self-attention encoders on different input epigenetics factors data to learn which locations of genes are important for predicting DEGs. Next it trains a soft attention module to pick out which epigenetics factors are significant. The attention mechanism makes the model interpretable, and the pure matrix operation of self-attention enables the model to be parallel calculated and speeds up the training. Experiments on datasets from the Roadmap Epigenome Project and BluePrint Data Analysis Portal (BDAP) show that the performance of Epi-MSA is better than existing competitive methods, and Epi-MSA also has a smaller standard deviation, which shows that Epi-MSA is effective and stable. In addition, Epi-MSA has a good interpretability, this is confirmed by referring its attention weight matrix with existing biological knowledge.
Variomes: a high recall search engine to support the curation of genomic variants
Authors: Pasche Emilie , Mottaz Anaïs , Caucheteur Déborah , Gobeill Julien , Michel Pierre-André , Ruch Patrick
Published: March 2022

Motivation

Identification and interpretation of clinically actionable variants is a critical bottleneck. Searching for evidence in the literature is mandatory according to ASCO/AMP/CAP practice guidelines; however, it is both labor-intensive and error-prone. We developed a system to perform triage of publications relevant to support an evidence-based decision. The system is also able to prioritize variants. Our system searches within pre-annotated collections such as MEDLINE and PubMed Central.

Results

We assess the search effectiveness of the system using three different experimental settings: literature triage; variant prioritization and comparison of Variomes with LitVar. Almost two-thirds of the publications returned in the top-5 are relevant for clinical decision-support. Our approach enabled identifying 81.8% of clinically actionable variants in the top-3. Variomes retrieves on average +21.3% more articles than LitVar and returns the same number of results or more results than LitVar for 90% of the queries when tested on a set of 803 queries; thus, establishing a new baseline for searching the literature about variants.

Availability and implementation

Variomes is publicly available at https://candy.hesge.ch/Variomes. Source code is freely available at https://github.com/variomes/sibtm-variomes. SynVar is publicly available at https://goldorak.hesge.ch/synvar.

Supplementary information

Supplementary data are available at Bioinformatics online.
Decreased homotopic functional connectivity in traumatic brain injury
Authors: Raizman Reut , Itzhaki Nofar , Sirkin Johanna , Meningher Inbar , Tsarfaty Galia , Keren Ofer , Zibli Zion , Silberg Tamar , Pick Chaim G , Livny Abigail
Published: March 2022

Introduction

Homotopic functional connectivity (HoFC), the synchrony in activity patterns between homologous brain regions, is a fundamental characteristic of resting-state functional connectivity (RsFC).

Methods

We examined the difference in HoFC, computed as the correlation between atlas-based regions and their counterpart on the opposite hemisphere, in 16 moderate–severe traumatic brain injury patients (msTBI) and 36 healthy controls. Regions of decreased HoFC in msTBI patients were further used as seeds for examining differences between groups in correlations with other brain regions. Finally, we computed logistic regression models of regional HoFC and fractional anisotropy (FA) of the corpus callosum (CC).

Results

TBI patients exhibited decreased HoFC in the middle and posterior cingulate cortex, thalamus, superior temporal pole, and cerebellum III. Furthermore, decreased RsFC was found between left cerebellum III and right parahippocampal cortex and vermis, between superior temporal pole and left caudate and medial left and right frontal orbital gyri. Thalamic HoFC and FA of the CC discriminate patients as msTBI with a high accuracy of 96%.

Conclusion

TBI is associated with regionally decreased HoFC. Moreover, a multimodality model of interhemispheric connectivity allowed for a high degree of accuracy in disease discrimination and enabled a deeper understanding of TBI effects on brain interhemispheric reorganization post-TBI.
Systematic Review: The Impact and Importance of Body Composition in Inflammatory Bowel Disease
Authors: Ding Nik Sheng , Tassone Daniel , Al Bakir Ibrahim , Wu Kyle , Thompson Alexander J , Connell William R , Malietzis George , Lung Phillip , Singh Siddharth , Choi Chang-ho Ryan , Gabe Simon , Jenkins John T , Hart Ailsa
Published: March 2022

Background and Aims

Alterations in body composition are common in inflammatory bowel disease [IBD] and have been associated with differences in patient outcomes. We sought to consolidate knowledge on the impact and importance of body composition in IBD.

Methods

We performed a systematic search of MEDLINE, EMBASE and conference proceedings by combining two key research themes: inflammatory bowel disease and body composition.

Results

Fifty-five studies were included in this review. Thirty-one focused on the impact of IBD on body composition with a total of 2279 patients with a mean age 38.4 years. Of these, 1071 [47%] were male. In total, 1470 [64.5%] patients had Crohn’s disease and 809 [35.5%] had ulcerative colitis. Notably, fat mass and fat-free mass were reduced, and higher rates of sarcopaenia were observed in those with active IBD compared with those in clinical remission and healthy controls. Twenty-four additional studies focused on the impact of derangements in body composition on IBD outcomes. Alterations in body composition in IBD are associated with poorer prognoses including higher rates of surgical intervention, post-operative complications and reduced muscle strength. In addition, higher rates of early treatment failure and primary non-response are seen in patients with myopaenia.

Conclusions

Patients with IBD have alterations in body composition parameters in active disease and clinical remission. The impacts of body composition on disease outcome and therapy are broad and require further investigation. The augmentation of body composition parameters in the clinical setting has the potential to improve IBD outcomes in the future.
Development and Validation of the Disability Index Among Older Adults
Authors: Zhang Xuxi , Lin Lizi , Sun Xinying , Lei Xiaoyan , Liu Gordon G , Raat Hein , Zeng Yi
Published: March 2022

Background

With the rapid population aging, the challenge to provide care for disabled older adults is becoming bigger. This study aims to develop the Disability Index (DI) to assess disability to indicate care needs, and we evaluated the reliability and validity of the DI among older adults aged 65–105.

Methods

A total of 12 559 older adults (54.0% women; mean age = 84.3; SD = 11.2) from 22 provinces in China were investigated in 2017–2018. We developed the 21-item DI covering 4 subdomains, including Activities of Daily Living (ADL), Instrumental Activities of Daily Living (IADL), physical performance, and cognitive function. Cronbach’s alpha was used to determine internal consistency. The convergent and divergent validity were assessed by Spearman rank order correlation coefficients and Pearson correlation coefficients. The known-group validity was assessed by Mann–Whitney U tests. The concurrent validity was assessed by the area under the receiver operating characteristic curve (AUC).

Results

In the total sample, the internal consistency of the full DI and its subdomains were satisfactory with Cronbach’s alpha ≥0.70; the convergent and divergent validity of the 4 subdomains were supported by all the alternative measures; the known-group validity of the full DI and its subdomains were supported by clear discriminative ability; and the concurrent validity of the full DI was supported with all the AUCs ≥0.70. The reliability and validity of the full DI and its subdomains were additionally supported by age subgroups and sex subgroups.

Conclusions

The DI is a reliable and valid instrument to assess disability status among older adults.
Health Equity in an Age-Friendly Health System: Identifying Potential Care Gaps
Authors: Morgan Emily , De Lima Bryanna , Pleet Anna , Eckstrom Elizabeth
Published: March 2022

Background

The Age-Friendly Health Systems (AFHS) initiative uses a 4Ms framework—What Matters, Mentation, Medication, and Mobility—to encourage patient-centered care for older adults. Many health systems have implemented the core elements of AFHS with the goal to uniformly apply them to all patients 65 years and older. However, equity in AFHS delivery has not yet been examined.

Methods

Five health equity factors—gender, race, ethnicity, preferred language, and electronic patient portal (MyChart) activation—were cross-sectionally analyzed against the 4Ms framework for patients in an academic internal medicine clinic seen between April 2020 and April 2021 (N = 3 370). Bivariate analysis and multiple logistic regression models analyzed the relationship of health equity variables to the 4Ms metrics and were represented with odds ratios and 95% confidence intervals.

Results

Preferred language, gender, and MyChart activation yielded significant 4M metric pairings. Females were 1.22 times more likely than males, and English-speaking patients were 2.27 times more likely than non-English-speaking patients to receive advance care planning (p < .01). Females and patients with MyChart activation were about 2 times more likely to have a high-risk medication on their medication list compared to males and patients without MyChart activation (p < .01). Patients with MyChart activation were 2.08 times more likely than patients without MyChart activation to get cognitive screening (p < .001).

Conclusion

This study, the first to incorporate demographic data into AFHS outcomes, suggests a need to develop best practices for equitable Age-Friendly care at the clinical team and institutional policy levels.
How Does Aging Affect Social Attention? A Test of Competing Theories Using Multilevel Meta-Analysis
Authors: McKay Kate T , Talipski Louisa A , Grainger Sarah A , Alister Manikya , Henry Julie D
Published: March 2022

Objectives

The present study provides a meta-analytic assessment of how gaze-cued attention—a core social-cognitive process—is influenced by normal adult aging.

Methods

A multilevel meta-analysis of standardized mean changes was conducted on gaze-cueing effects. Age effects were quantified as standardized mean differences in gaze-cueing effect sizes between young and older adult samples.

Results

We identified 82 gaze-cueing effects (k = 26, N = 919 participants). Of these, 37 were associated with young adults (k = 12, n = 438) and 45 with older adults (k = 14, n = 481). Relative to younger adults, older adults had a reduced gaze-cueing effect overall, g = −0.59, with this age effect greater when the cues were predictive, g = −3.24, rather than nonpredictive, g = −0.78.

Discussion

These results provide the clearest evidence to date that adult aging is associated with a reduction in gaze-cued attention. The results also speak to potential mechanisms of this age effect. In line with cognitive decline models of aging, it was demonstrated that when gaze cues were predictive, only younger adults seem to benefit, suggesting that older adults exhibit a particularly reduced capacity to use gaze cues volitionally.
MiR-29a regulates cardiomyocyte apoptosis by targeting Bak1 in diabetic cardiomyopathy
Authors: Wang Xiaoyan , Zhang Zhitao , Wang Mei
Published: March 2022

This study sought to investigate the association between microRNA-29a (miR-29a) and cardiomyocyte apoptosis in diabetic cardiomyopathy (DCM). DCM rat model was established by treating rats with streptozotocin (STZ), followed by injection of NC or miR-29a-3p mimics into the myocardium of rats. High glucose (HG)-treated H9c2 cells were transfected with NC and miR-29a-3p mimics. DCM rats presented elevated levels of blood glucose, HbA1c, blood pressure, urine output, decreased body weight and cardiac contractile function after modeling. MiR-29a was lowly expressed in STZ-treated rats and HG-treated H9c2 cells. Upregulation of miR-29a improved cardiac structure and function and attenuated, alleviated myocardial histological abnormalities and fibrosis and lowered cardiomyocyte apoptosis in DCM rats. Meanwhile, HG promoted H9c2 cell apoptosis, while miR-29a overexpression attenuated the function of HG. Compared with control group, the protein expression of Bax, cleaved-caspase3 and Bak1 in DCM and HG groups were significantly upregulated, and the expression of Bcl-2 and Mcl-1 was downregulated, while miR-29a overexpression exerted opposite effect. Bioinformatics prediction method and western blot revealed that miR-29a directly targeted Bak1 and downregulated Bak1 expression. Overall, miR-29a regulated STZ- and HG-induced cardiomyocyte apoptosis by targeting Bak1, providing a novel understanding of the pathogenesis of DCM.
Trapping of Crucifer-Feeding Flea Beetles (Phyllotreta spp.) (Coleoptera: Chrysomelidae) With Pheromones and Plant Kairomones
Authors: Weber Donald C , Konstantinov Alexander S , Khrimian Ashot , Bier Alexander D , Lubenow Lesley A , Knodel Janet J , Haber Ariela I , Wallingford Anna K , Mason James A C , Kuhar Thomas P
Published: March 2022

Flea beetles (Coleoptera: Chrysomelidae) of the genus Phyllotreta are major pests of cole crops, canola, and related crops in the mustard family (Brassicaceae). Adults may damage seedlings or larger crop plants, impairing crop growth, rendering crops unmarketable, or killing seedlings outright. The two major North American crucifer pest species, Phyllotreta striolata (F.) and Phyllotreta cruciferae (Goeze), have male-produced pheromones attractive to both female and male adults. We tested the racemic synthetic pheromones, himachaladiene and hydroxyhimachalanone, as well as the host-plant-produced allyl isothiocyanate, alone and in combination, with experimental trapping in Maryland, Virginia, and North Dakota, using clear and yellow sticky traps and the ground-based ‘rocket’ trap (modified from boll weevil trap). Phyllotreta striolata was consistently attracted to the hydroxyketone, and captures were often enhanced by allyl isothiocyanate (AITC), but its response to pheromones, AITC, and trap color were variable from state to state. Phyllotreta cruciferae was strongly attracted to AITC, but its response to pheromone components varied by state, and this species was found rarely at the Maryland site. Phyllotreta bipustulata (F.) was attracted to the diene component, a new finding for this species. Several other genera of flea beetles were captured, some showing response to the semiochemicals and/or color. Results will be helpful in monitoring and possibly population suppression; however, further research is necessary to develop more efficient syntheses, optimal lure loadings, combinations, and controlled release methods.
Arthroscopic hip surgery offers better early patient-reported outcome measures than targeted physiotherapy programs for the treatment of femoroacetabular impingement syndrome: a systematic review and meta-analysis of randomized controlled trials
Authors: Mahmoud Samer S S , Takla Amir , Meyer Denny , Griffin Damian , O’Donnell John
Published: March 2022

Targeted physiotherapy programs (TPP), and surgery, using either open surgical hip dislocation or hip arthroscopy (HA), are the treatment modalities available for femoroacetabular impingement syndrome (FAIS). Randomized controlled trials have recently been performed to compare these treatment options. This review was performed to provide a focused synthesis of the available evidence regarding the relative value of treatment options. A systematic search was performed of Medline, Embase, Cochrane Library and ClinicalTrials.gov databases. Inclusion criteria were randomized controlled trials comparing treatment methods. The Cochrane Risk of Bias assessment tool (RoB2) was used to assess the selected studies. A meta-analysis was performed between homogenous studies. Four trials were identified including 749 patients (392 males). The mean ages of the cohorts ranged between 30.1 and 36.2 years old. Three hundred thirty-five patients underwent HA by 46 surgeons among all trials. Fifty-two patients crossed over from the TPP to the HA group. One of the trials was found to have a high risk of bias, while the other three were between low risk and some concerns. The iHOT-33 was the most commonly used patient-reported outcome measure followed by the HOS ADL and EQ-5D-5L. Others scores were also identified. Scores from two trials could be pooled together for meta-analysis. Apart from SF-12 and GRC, all other scores have shown significantly better outcomes with HA in comparison to TPP at 8- and 12-months follow-up points. HA offers better patient-reported outcomes than TPP for management of FAIS at 8- and 12-months follow-up.
Rare case of ruptured muscular ventricular septal aneurysm due to silent myocardial ischemia in adult
Authors: Kawahira Toshihiro , Miyashita Fumihiro , Suzuki Tomoaki
Published: March 2022

Interventricular septal aneurysm of muscular type is uncommon in adult, to say nothing of membranous type. Acute or subacute left-to-right shunt (LR shunt) in a ventricular septum is mostly critical and usually shows severe symptoms. Therefore, ruptured muscular ventricular septal aneurysm (VSA) with LR shunt of unknown onset in adult is highly rare. A 70-year-old man was suffered from mild dyspnea and chest oppression. A muscular VSA was detected at the center of the ventricular septum and LR shunt of unknown onset in it had induced congestive heart failure. The sandwich patch technique through a right ventricular approach was simultaneously performed with coronary artery bypass grafting and the postoperative course was uneventful. In addition, concomitant myocardial biopsy of VSA wall during the surgery could reveal histopathologic evidence of acute or subacute myocardial infarction with old myocardial infarction as silent myocardial ischemia.
The Charlemont Library, the Sotheby Warehouse Fire of 1865, and the Vexed Provenance of British Library MS Egerton 1994
Authors: Freeman Arthur , Freeman Janet Ing
Published: March 2022

This article discusses the book collection of James Caulfeild (1728–1799), first earl of Charlemont in the Irish peerage, with particular reference to his holdings of early English drama and poetry. After the death of Charlemont’s son the library was consigned to Sotheby’s for anonymous sale in July 1865, but was in large part destroyed in the Sotheby warehouse fire of 19 June. The second part of the article explores the provenance of one surviving item, a volume of fifteen manuscript plays composed over four or five decades before 1644, now British Library, MS Egerton 1994. It is among the most interesting survivals known from the slender corpus of pre-Restoration English stage documents. Charlemont’s principal London agent for early English books, the Shakespeare editor Edmond Malone (1741–1812), has long been viewed as the source of the volume. The history of this speculation is traced and disproved.
Guest Editors’ Introduction—Visionary Praxis: Paule Marshall’s, Ntozake Shange’s, and Toni Morrison’s Foresight concerning Sick Violence and Violent Sickness
Authors: Brooks Robin , Yates-Richard Meina
Published: March 2022

This introduction provides an overview of the special issue that focuses on the interconnections of Black women’s literary studies with the crises of COVID-19 and ongoing anti-Black violence. More specifically, it considers how the work of three renowned writers, Paule Marshall, Ntozake Shange, and Toni Morrison—which collectively spans over fifty years—offers models for how to reimagine our current circumstances and create more just futures in our national and global communities. The essay identifies and expounds on the overarching question of the special issue: how does the work of Marshall, Shange, and Morrison speak to contemporary affairs and concerns? By engaging this question, this collection of essays offers new insights about these women’s writing in particular and expands the corpus of scholarship on Black women’s writing in general. In the aftermath of the passing of these writers, a collective reappraisal of their oeuvres is a timely and fitting tribute, as each of their bodies of work reveals that they long have engaged concerns about Black people’s encounters with systemic barriers that have laid the foundation for the current twinned crises of anti-Black violence and the disproportionate impact of COVID-19.
The mitogenome of the sunken wood limpetNotocrater youngi: insights into mitogenome evolution in Lepetellida (Gastropoda: Vetigastropoda)
Authors: Uribe Juan E , Sei Makiri , Harasewych M G
Published: March 2022

The complete mitochondrial genome of the pseudococculinid limpet Notocrater youngi was determined using Illumina sequencing and found to be a double-stranded circular molecule 15,915 bp in length. It contains the usual 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes, although with a gene order that differs from those of all other presently known Vetigastropoda, and that is derived within Lepetellida. Phylogenetic analyses based on amino acid sequences join the three pseudococculinid species in a clade and confirm the well-supported clade Scissurelloidea + (Lepetelloidea + Lepetodriloidea) but not a monophyletic Lepetellida as currently understood. Patterns of gene order rearrangements are concordant with these findings.
Apparently Imperfect: On the Analytical Issues of the IAC
Authors: Zhang Xieyi (Abby)
Published: March 2022

This article examines the analytical nuances of the imperfect authentic cadence (IAC). Whereas the cadential hierarchy currently in use in most North American textbooks suggests in no uncertain terms that it is stronger than the half cadence (HC) and weaker than the perfect authentic cadence (PAC), its appearances in the musical literature have often been far more nuanced, as illustrated by the frequency with which the IAC functions in a manner that contradicts the standard theoretical formulation. The IAC’s ability to engage with these alternative functions results in a range of cadential strengths, giving rise to possibilities for ambiguities, reinterpretations, and conflicts that in turn may set the stage for fascinating expressive and narrative twists.
Dysregulated RNA polyadenylation contributes to metabolic impairment in non-alcoholic fatty liver disease
Authors: Jobbins Andrew M , Haberman Nejc , Artigas Natalia , Amourda Christopher , Paterson Helen A B , Yu Sijia , Blackford Samuel J I , Montoya Alex , Dore Marian , Wang Yi-Fang , Sardini Alessandro , Cebola Inês , Zuber Johannes , Rashid Sheikh Tamir , Lenhard Boris , Vernia Santiago
Published: March 2022

Pre-mRNA processing is an essential mechanism for the generation of mature mRNA and the regulation of gene expression in eukaryotic cells. While defects in pre-mRNA processing have been implicated in a number of diseases their involvement in metabolic pathologies is still unclear. Here, we show that both alternative splicing and alternative polyadenylation, two major steps in pre-mRNA processing, are significantly altered in non-alcoholic fatty liver disease (NAFLD). Moreover, we find that Serine and Arginine Rich Splicing Factor 10 (SRSF10) binding is enriched adjacent to consensus polyadenylation motifs and its expression is significantly decreased in NAFLD, suggesting a role mediating pre-mRNA dysregulation in this condition. Consistently, inactivation of SRSF10 in mouse and human hepatocytes in vitro, and in mouse liver in vivo, was found to dysregulate polyadenylation of key metabolic genes such as peroxisome proliferator-activated receptor alpha (PPARA) and exacerbate diet-induced metabolic dysfunction. Collectively our work implicates dysregulated pre-mRNA polyadenylation in obesity-induced liver disease and uncovers a novel role for SRSF10 in this process.
Molecular basis for human mitochondrial tRNA m3C modification by alternatively spliced METTL8
Authors: Huang Meng-Han , Peng Gui-Xin , Mao Xue-Ling , Wang Jin-Tao , Zhou Jing-Bo , Zhang Jian-Hui , Chen Meirong , Wang En-Duo , Zhou Xiao-Long
Published: March 2022

METTL8 has recently been identified as the methyltransferase catalyzing 3-methylcytidine biogenesis at position 32 (m3C32) of mitochondrial tRNAs. METTL8 also potentially participates in mRNA methylation and R-loop biogenesis. How METTL8 plays multiple roles in distinct cell compartments and catalyzes mitochondrial tRNA m3C formation remain unclear. Here, we discovered that alternative mRNA splicing generated several isoforms of METTL8. One isoform (METTL8-Iso1) was targeted to mitochondria via an N-terminal pre-sequence, while another one (METTL8-Iso4) mainly localized to the nucleolus. METTL8-Iso1-mediated m3C32 modification of human mitochondrial tRNAThr (hmtRNAThr) was not reliant on t6A modification at A37 (t6A37), while that of hmtRNASer(UCN) critically depended on i6A modification at A37 (i6A37). We clarified the hmtRNAThr substrate recognition mechanism, which was obviously different from that of hmtRNASer(UCN), in terms of requiring a G35 determinant. Moreover, SARS2 (mitochondrial seryl-tRNA synthetase) interacted with METTL8-Iso1 in an RNA-independent manner and modestly accelerated m3C modification activity. We further elucidated how nonsubstrate tRNAs in human mitochondria were efficiently discriminated by METTL8-Iso1. In summary, our results established the expression pattern of METTL8, clarified the molecular basis for m3C32 modification by METTL8-Iso1 and provided the rationale for the involvement of METTL8 in tRNA modification, mRNA methylation or R-loop biogenesis.
Human TDP1, APE1 and TREX1 repair 3′-DNA–peptide/protein cross-links arising from abasic sites in vitro
Authors: Wei Xiaoying , Wang Zhishuo , Hinson Caroline , Yang Kun
Published: March 2022

Histones and many other proteins react with abundant endogenous DNA lesions, apurinic/apyrimidinic (abasic, AP) sites and/or 3′-phospho-α,β-unsaturated aldehyde (3′-PUA), to form unstable but long-lived Schiff base DNA–protein cross-links at 3′-DNA termini (3′-PUA–protein DPCs). Poly (ADP-ribose) polymerase 1 (PARP1) cross-links to the AP site in a similar manner but the Schiff base is reduced by PARP1’s intrinsic redox capacity, yielding a stable 3′-PUA–PARP1 DPC. Eradicating these DPCs is critical for maintaining the genome integrity because 3′-hydroxyl is required for DNA synthesis and ligation. But how they are repaired is not well understood. Herein, we chemically synthesized 3′-PUA-aminooxylysine-peptide adducts that closely resemble the proteolytic 3′-PUA–protein DPCs, and found that they can be repaired by human tyrosyl-DNA phosphodiesterase 1 (TDP1), AP endonuclease 1 (APE1) and three-prime repair exonuclease 1 (TREX1). We characterized these novel repair pathways by measuring the kinetic constants and determining the effect of cross-linked peptide length, flanking DNA structure, and the opposite nucleobase. We further found that these nucleases can directly repair 3′-PUA–histone DPCs, but not 3′-PUA–PARP1 DPCs unless proteolysis occurs initially. Collectively, we demonstrated that in vitro 3′-PUA–protein DPCs can be repaired by TDP1, APE1, and TREX1 following proteolysis, but the proteolysis is not absolutely required for smaller DPCs.
Substantial transition to clean household energy mix in rural China
Authors: Shen Guofeng , Xiong Rui , Tian Yanlin , Luo Zhihan , Jiangtulu Bahabaike , Meng Wenjun , Du Wei , Meng Jing , Chen Yuanchen , Xue Bing , Wang Bin , Duan Yonghong , Duo Jia , Fan Fenggui , Huang Lei , Ju Tianzhen , Liu Fenggui , Li Shunxin , Liu Xianli , Li Yungui , Wang Mu , Nan Ying , Pan Bo , Pan Yanfang , Wang Lizhi , Zeng Eddy , Zhan Chao , Chen Yilin , Shen Huizhong , Cheng Hefa , Tao Shu
Published: March 2022

The household energy mix has significant impacts on human health and climate, as it contributes greatly to many health- and climate-relevant air pollutants. Compared to the well-established urban energy statistical system, the rural household energy statistical system is incomplete and is often associated with high biases. Via a nationwide investigation, this study revealed high contributions to energy supply from coal and biomass fuels in the rural household energy sector, while electricity comprised ∼20%. Stacking (the use of multiple sources of energy) is significant, and the average number of energy types was 2.8 per household. Compared to 2012, the consumption of biomass and coals in 2017 decreased by 45% and 12%, respectively, while the gas consumption amount increased by 204%. Increased gas and decreased coal consumptions were mainly in cooking, while decreased biomass was in both cooking (41%) and heating (59%). The time-sharing fraction of electricity and gases (E&G) for daily cooking grew, reaching 69% in 2017, but for space heating, traditional solid fuels were still dominant, with the national average shared fraction of E&G being only 20%. The non-uniform spatial distribution and the non-linear increase in the fraction of E&G indicated challenges to achieving universal access to modern cooking energy by 2030, particularly in less-developed rural and mountainous areas. In some non-typical heating zones, the increased share of E&G for heating was significant and largely driven by income growth, but in typical heating zones, the time-sharing fraction was <5% and was not significantly increased, except in areas with policy intervention. The intervention policy not only led to dramatic increases in the clean energy fraction for heating but also accelerated the clean cooking transition. Higher income, higher education, younger age, less energy/stove stacking and smaller family size positively impacted the clean energy transition.
Does the evidence support a relationship between higher levels of nut consumption, lower risk of depression, and better mood state in the general population? A systematic review
Authors: Fernández-Rodríguez Rubén , Jiménez-López Estela , Garrido-Miguel Miriam , Martínez-Ortega Isabel A , Martínez-Vizcaíno Vicente , Mesas Arthur Eumann
Published: March 2022

Context

Dietary patterns play a key role in mental health, depression, and mood state. However, the evidence concerning specific foods highly recommended for mental health, such as nuts, has not yet been synthesized.

Objective

The objective of this review was to synthesize the evidence for a relationship between higher levels of nut consumption, lower risk of depression, and better mood state in the general population.

Data Sources

The MEDLINE, Scopus, Cochrane Central, Web of Science, and PsycInfo databases were systematically searched from each database’s inception to March 2021.

Data Extraction

Randomized clinical trials (RCTs) and observational studies exploring the association between nut consumption, level of depression, and mood state in the general population were included. The quality of the studies was measured through the Joanna Briggs Institute tool (cross-sectional studies), the NIH Quality Assessment Tool (cohort studies), and the Cochrane Risk-of-Bias tool (RCTs). The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed.

Data Analysis

A total of 10 studies involving 66 418 individuals were included, of which 3 were cross-sectional, 3 were cohort studies, and 4 were RCTs. In studies concerned with depression (n = 6 studies), a higher level of nut consumption was associated with a lower risk of depression in 2 cross-sectional studies and 1 cohort study, while a similar but nonsignificant association was found in another cohort and in two RCTs. In studies concerned with mood state (n = 4), 1 cohort study reported an association between higher nut consumption and significant improvement in mood state, whereas (nonsignificant) associations between higher nut consumption and increased negative feelings were reported in a cross-sectional study and two RCTs.

Conclusion

Despite the small number of studies and the limitations related to them, such as reverse causation bias, overall, the available literature suggests that higher nut consumption could be associated with a lower risk of depression, fewer depressive symptoms, and better mood state in the general population.

Systematic Review Registration

PROSPERO registration no. CRD42021241070.
Passive spiral galaxies deeply captured by Subaru Hyper Suprime-Cam
Authors: Shimakawa Rhythm , Tanaka Masayuki , Bottrell Connor , Wu Po-Feng , Chang Yu-Yen , Toba Yoshiki , Ali Sadman
Published: March 2022

This paper presents a thousand passive spiral galaxy samples at z = 0.01–0.3 based on a combined analysis of the Third Public Data Release of the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP PDR3) and the GALEX–SDSS–WISE Legacy Catalog (GSWLC-2). Among 54871 gri galaxy cutouts taken from the HSC-SSP PDR3 over 1072 deg2, we conducted a search with deep-learning morphological classification for candidates of passive spirals below the star-forming main sequence derived by ultraviolet to mid-infrared spectral energy distribution fitting in the GSWLC-2. We then classified the candidates into 1100 passive spirals and 1141 secondary samples based on visual inspections. Most of the latter cases are considered to be passive ringed S0 or pseudo-ringed galaxies. The remaining secondary samples have ambiguous morphologies, including two peculiar objects with diamond-shaped stellar wings. The selected passive spirals have a similar distribution to the general quiescent galaxies on the EWHδ–Dn4000 diagram and concentration indices. Moreover, we detected an enhanced passive fraction of spiral galaxies in X-ray clusters. Passive spirals in galaxy clusters are preferentially located in the midterm or late infall phase on the phase–space diagram, supporting the ram pressure scenario, which has been widely advocated in previous studies. The source catalog and gri-composite images are available on the HSC-SSP PDR3 website 〈https://hsc.mtk.nao.ac.jp/ssp/data-release/〉. Future updates, including integration with a citizen science project dedicated to the HSC data, will achieve more effective and comprehensive classifications.
The power of classic maize mutants: Driving forward our fundamental understanding of plants
Authors: Richardson Annis E , Hake Sarah
Published: March 2022

Since Mendel, maize has been a powerhouse of fundamental genetics research. From testing the Mendelian laws of inheritance, to the first genetic and cytogenetic maps, to the use of whole-genome sequencing data for crop improvement, maize is at the forefront of genetics advances. Underpinning much of this revolutionary work are the classic morphological mutants; the “freaks” that stood out in the field to even the untrained eye. Here we review some of these classic developmental mutants and their importance in the history of genetics, as well as their key role in our fundamental understanding of plant development.
Seeing the forest for the trees through metabolic scaling
Authors: Volkov Igor , Tovo Anna , Anfodillo Tommaso , Rinaldo Andrea , Maritan Amos , Banavar Jayanth R
Published: March 2022

We demonstrate that when power scaling occurs for an individual tree and in a forest, there is great resulting simplicity notwithstanding the underlying complexity characterizing the system over many size scales. Our scaling framework unifies seemingly distinct trends in a forest and provides a simple yet promising approach to quantitatively understand a bewilderingly complex many-body system with imperfectly known interactions. We show that the effective dimension, Dtree, of a tree is close to 3, whereas a mature forest has Dforest approaching 1. We discuss the energy equivalence rule and show that the metabolic rate–mass relationship is a power law with an exponent D/(D + 1) in both cases leading to a Kleiber’s exponent of 3/4 for a tree and 1/2 for a forest. Our work has implications for understanding carbon sequestration and for climate science.
How did extinct giant birds and pterosaurs fly? A comprehensive modeling approach to evaluate soaring performance
Authors: Goto Yusuke , Yoda Ken , Weimerskirch Henri , Sato Katsufumi
Published: March 2022

The largest extinct volant birds (Pelagornis sandersi and Argentavis magnificens) and pterosaurs (Pteranodon and Quetzalcoatlus) are thought to have used wind-dependent soaring flight, similar to modern large birds. There are 2 types of soaring: thermal soaring, used by condors and frigatebirds, which involves the use of updrafts to ascend and then glide horizontally; and dynamic soaring, used by albatrosses, which involves the use of wind speed differences with height above the sea surface. Previous studies have suggested that P. sandersi used dynamic soaring, while A. magnificens and Quetzalcoatlus used thermal soaring. For Pteranodon, there is debate over whether they used dynamic or thermal soaring. However, the performance and wind speed requirements of dynamic and thermal soaring for these species have not yet been quantified comprehensively. We quantified these values using aerodynamic models and compared them with that of extant birds. For dynamic soaring, we quantified maximum travel speeds and maximum upwind speeds. For thermal soaring, we quantified the animal's sinking speed circling at a given radius and how far it could glide losing a given height. Our results confirmed those from previous studies that A. magnificens and Pteranodon used thermal soaring. Conversely, the results for P. sandersi and Quetzalcoatlus were contrary to those from previous studies. P. sandersi used thermal soaring, and Quetzalcoatlus had a poor ability both in dynamic and thermal soaring. Our results demonstrate the need for comprehensive assessments of performance and required wind conditions when estimating soaring styles of extinct flying species.
Exploration of immunological responses underpinning severe fever with thrombocytopenia syndrome virus infection reveals IL-6 as a therapeutic target in an immunocompromised mouse model
Authors: Bryden Steven R , Dunlop James I , Clarke Andrew T , Fares Mazigh , Pingen Marieke , Wu Yan , Willett Brian J , Patel Arvind H , Gao George F , Kohl Alain , Brennan Benjamin
Published: March 2022

Dabie bandavirus (previously severe fever with thrombocytopenia syndrome virus; SFTSV), is an emerging tick-borne bunyavirus responsible for severe fever with thrombocytopenia syndrome (SFTS), a disease with high case fatality that is characterized by high fever, thrombocytopenia, and potentially lethal hemorrhagic manifestations. Currently, neither effective therapeutic strategies nor approved vaccines exist for SFTS. Therefore, there remains a pressing need to better understand the pathogenesis of the disease and to identify therapeutic strategies to ameliorate SFTS outcomes. Using a type I interferon (IFN)-deficient mouse model, we investigated the viral tropism, disease kinetics, and the role of the virulence factor nonstructural protein (NSs) in SFTS. Ly6C+ MHCII+ cells in the lymphatic tissues were identified as an important target cell for SFTSV. Advanced SFTS was characterized by significant migration of inflammatory leukocytes, notably neutrophils, into the lymph node and spleen, however, these cells were not required to orchestrate the disease phenotype. The development of SFTS was associated with significant upregulation of proinflammatory cytokines, including high levels of IFN-γ and IL-6 in the serum, lymph node, and spleen. Humoral immunity generated by inoculation with delNSs SFTSV was 100% protective. Importantly, NSs was critical to the inhibition of the host IFNɣ response or downstream IFN-stimulated gene production and allowed for the establishment of severe disease. Finally, therapeutic but not prophylactic use of anti-IL-6 antibodies significantly increased the survival of mice following SFTSV infection and, therefore, this treatment modality presents a novel therapeutic strategy for treating severe SFTS.
Self-Fulfilling Asset Prices
Authors: Zentefis Alexander K
Published: March 2022

This paper explains that anticipated market liquidity is an important concern for arbitrageurs considering entry into a market, a concern that can generate self-fulfilling asset prices. In the model, fixed investment costs turn a market illiquid and generate an arbitrage opportunity. The worst-case return on pledged collateral constrains arbitrageurs’ leverage. The interaction between this return and arbitrageurs’ capital makes entry decisions complementary and can create multiple equilibria. When arbitrageurs enter with capital, the market becomes more liquid; the worst-case return rises; and more arbitrageurs enter with capital. When arbitrageurs withhold capital, the market stays illiquid; the worst-case return falls; and other arbitrageurs stay out. (JEL D84, G11, G12)

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Early Origins of Divergent Patterns of Morphological Evolution on the Mammal and Reptile Stem-Lineages
Authors: Brocklehurst Neil , Ford David P , Benson Roger B J
Published: March 2022

The origin of amniotes 320 million years ago signaled independence from water in vertebrates and was closely followed by divergences within the mammal and reptile stem lineages (Synapsida and Reptilia). Early members of both groups had highly similar morphologies, being superficially “lizard-like” forms with many plesiomorphies. However, the extent to which they might have exhibited divergent patterns of evolutionary change, with the potential to explain the large biological differences between their living members, is unresolved. We use a new, comprehensive phylogenetic dataset to quantify variation in rates and constraints of morphological evolution among Carboniferous–early Permian amniotes. We find evidence for an early burst of evolutionary rates, resulting in the early origins of morphologically distinctive subgroups that mostly persisted through the Cisuralian. Rates declined substantially through time, especially in reptiles. Early reptile evolution was also more constrained compared with early synapsids, exploring a more limited character state space. Postcranial innovation in particular was important in early synapsids, potentially related to their early origins of large body size. In contrast, early reptiles predominantly varied the temporal region, suggesting disparity in skull and jaw kinematics, and foreshadowing the variability of cranial biomechanics seen in reptiles today. Our results demonstrate that synapsids and reptiles underwent an early divergence of macroevolutionary patterns. This laid the foundation for subsequent evolutionary events and may be critical in understanding the substantial differences between mammals and reptiles today. Potential explanations include an early divergence of developmental processes or of ecological factors, warranting cross-disciplinary investigation. [Amniote; body size; constraint; phylogeny; rate.]
The Impacts of Digital Technologies on Successful Aging in Non-Work and Work Domains: An Organizing Taxonomy
Authors: Sheng Nan , Fang Yanran , Shao Yiduo , Alterman Valeria , Wang Mo
Published: March 2022

Digital technology, broadly defined as all the electronic tools, automatic systems, technological devices, and resources that generate, process, or store information in the form of binary code (Shah, Nogueras, Van Woerden, & Kiparoglou, 2019), has brought great changes to almost all aspects of human life. In particular, the development and the application of various digital technologies have great potential to facilitate successful aging by helping individuals effectively cope with different forms of age-related challenges, though an organizing framework is lacking from the literature. In this paper, we derive a taxonomy for understanding the impacts of digital technology on successful aging by considering the intersections between digital technology types and the age-related applied settings. Based on this taxonomy, we map different types of digital technology to different functions and successful aging outcomes in both non-work and work domains. We also discuss the implications of our taxonomy to research inquiries and practical applications.