Miracle-dz/UniFAR-FTUs huggingface dataset:
Gain of C-Ala enables AlaRS to target the L-shaped tRNAAla

Abstract Unlike many other aminoacyl-tRNA synthetases, alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout biology. While Caenorhabditis elegans cytoplasmic AlaRS (CeAlaRSc) retains the prototype structure, its mitochondrial counterpart (CeAlaRSm) contains only a residual C-terminal domain (C-Ala). We demonstrated herein that the C-Ala domain from CeAlaRSc robustly binds both tRNA and DNA. It bound different tRNAs but preferred tRNAAla. Deletion of this domain from CeAlaRSc sharply reduced its aminoacylation activity, while fusion of this domain to CeAlaRSm selectively and distinctly enhanced its aminoacylation activity toward the elbow-containing (or L-shaped) tRNAAla. Phylogenetic analysis showed that CeAlaRSm once possessed the C-Ala domain but later lost most of it during evolution, perhaps in response to the deletion of the T-arm (part of the elbow) from its cognate tRNA. This study underscores the evolutionary gain of C-Ala for docking AlaRS to the L-shaped tRNAAla.
Esthetic complications in implant dentistry.

Esthetic complications in implant dentistry have become a significant consideration for patients and practitioners. This review presents an appraisal on the current knowledge of the physiological peri-implant soft-tissue dimensions and factors that may compromise peri-implant tissue esthetics. Factors such as papilla fill adjacent to the implant and midfacial mucosal height are critical parameters that determine the esthetic success of implant-supported restorations. Papilla fill adjacent to a single dental implant appears to depend upon the clinical attachment level of the neighboring tooth. A horizontal inter-implant distance of at least 3 mm is necessary to ensure optimal interproximal mucosal embrasure between two adjacent implants in the anterior maxilla. In cases where implants cannot be placed at least 3 mm apart, a single implant with a cantilever bridge should be considered. Buccolingual implant positioning plays a major role in midfacial mucosal height. Soft-tissue volume grafting following immediate implant placement in the presence of a thin soft-tissue phenotype or simultaneous to surgical peri-implantitis therapy might help to overcome facial mucosa recession.
Promoting Resilience and Well-being Through Co-design (The PRIDE Project): Protocol for the Development and Preliminary Evaluation of a Prototype Resilience-Based Intervention for Sexual and Gender Minority Youth

Background Sexual and gender minority youth (SGMY) are at an increased risk of a range of mental health problems. However, few evidence-informed interventions have been developed specifically to support their mental well-being. Interventions that are evidence-informed for the general population and are fine-tuned specifically with SGMY in mind proffer considerable potential. A particular opportunity lies in the delivery of engaging interventions on the web, where the focus is on enhancing the coping skills and building the resilience of SGMY, in a way that is directly relevant to their experiences. On the basis of earlier work related to an intervention called Rainbow SPARX (Smart, Positive, Active, Realistic, X-factor thoughts), we seek to create a new resource, especially for SGMY in the United Kingdom. Objective This project has 3 main objectives. First, together with SGMY as well as key adult experts, we aim to co-design a media-rich evidence-informed web-based SGMY well-being prototype toolkit aimed at those aged between 13 and 19 years. Second, we will explore how the web-based toolkit can be used within public health systems in the United Kingdom by SGMY and potentially other relevant stakeholders. Third, we aim to conduct a preliminary evaluation of the toolkit, which will inform the design of a future effectiveness study. Methods The first objective will be met by conducting the following: approximately 10 interviews with SGMY and 15 interviews with adult experts, a scoping review of studies focused on psychosocial coping strategies for SGMY, and co-design workshops with approximately 20 SGMY, which will inform the creation of the prototype toolkit. The second objective will be met by carrying out interviews with approximately 5 selected adult experts and 10 SGMY to explore how the toolkit can be best used and to determine the parameters and user-generated standards for a future effectiveness trial. The final objective will be met with a small-scale process evaluation, using the think out loud methodology, conducted with approximately 10 SGMY. Results The study commenced on September 1, 2021, and data gathering for phase 1 began in October 2021. Conclusions A considerable body of work has described the issues faced by the SGMY. However, there is a dearth of research seeking to develop interventions for SGMY so that they can thrive. This project aims to co-design such an intervention. Trial Registration Research Registry Reference researchregistry6815; https://www.researchregistry. com/browse-the-registry#home/registrationdetails/609e81bda4a706001c94b63a/ International Registered Report Identifier (IRRID) PRR1-10.2196/31036
DIOR: Deep Iterative Optimization-Based Residual-Learning for Limited-Angle CT Reconstruction

Limited-angle CT is a challenging problem in real applications. Incomplete projection data will lead to severe artifacts and distortions in reconstruction images. To tackle this problem, we propose a novel reconstruction framework termed Deep Iterative Optimization-based Residual-learning (DIOR) for limited-angle CT. Instead of directly deploying the regularization term on image space, the DIOR combines iterative optimization and deep learning based on the residual domain, significantly improving the convergence property and generalization ability. Specifically, the asymmetric convolutional modules are adopted to strengthen the feature extraction capacity in smooth regions for deep priors. Besides, in our DIOR method, the information contained in low-frequency and high-frequency components is also evaluated by perceptual loss to improve the performance in tissue preservation. Both simulated and clinical datasets are performed to validate the performance of DIOR. Compared with existing competitive algorithms, quantitative and qualitative results show that the proposed method brings a promising improvement in artifact removal, detail restoration and edge preservation.
STUDY ON THE LCA EVALUATION OF WASTEWATER TREATMENT

本研究はインフラ施設の計画及び設計段階へのライフサイクルアセスメント (以下「LCA」という) の適用を考慮して, その一連の作業に必要なデータや手法の整備を行ったものである. まず, 10種の環境負荷項目を選定し, ライフサイクルでの環境負荷の定量化 (インベントリー段階) に必要な原単位情報の整備を行った. 次に, 多数の環境カテゴリーを評価対象とする影響評価を行うために, 環境負荷量について相違する環境カテゴリーを同一の次元で比較できる評価指標を導入した. この評価指標を利用可能とするためにケース・スタディとして実施した排水処理施設でのインベントリー分析結果を用いて, 代表的排水処理方式での比較参考値となる値を提示するとともに, その適用事例によってその有用性を示した.
Molecular mechanisms controlling age‐associated B cells in autoimmunity *

Age‐associated B cells (ABCs) have emerged as critical components of immune responses. Their inappropriate expansion and differentiation have increasingly been linked to the pathogenesis of autoimmune disorders, aging‐associated diseases, and infections. ABCs exhibit a distinctive phenotype and, in addition to classical B cell markers, often express the transcription factor T‐bet and myeloid markers like CD11c; hence, these cells are also commonly known as CD11c+T‐bet+ B cells. Formation of ABCs is promoted by distinctive combinations of innate and adaptive signals. In addition to producing antibodies, these cells display antigen‐presenting and proinflammatory capabilities. It is becoming increasingly appreciated that the ABC compartment exhibits a high degree of heterogeneity, plasticity, and sex‐specific regulation and that ABCs can differentiate into effector progeny via several routes particularly in autoimmune settings. In this review, we will discuss the initial insights that have been obtained on the molecular machinery that controls ABCs and we will highlight some of the unique aspects of this control system that may enable ABCs to fulfill their distinctive role in immune responses. Given the expanding array of autoimmune disorders and pathophysiological settings in which ABCs are being implicated, a deeper understanding of this machinery could have important and broad therapeutic implications for the successful, albeit daunting, task of targeting these cells.
The Usefulness of Trabecular CT Attenuation Measurement at L4 Level to Predict Screw Loosening After Degenerative Lumbar Fusion Surgery

L4 t-ROI CT attenuation, number of fused levels, and postoperative sagittal balance were associated with screw loosening in lumbar fusion surgery. L4 t-ROI CT attenuation considering number of fused levels and postoperative sagittal balance is an accurate measurement method for predicting screw loosening. Study Design. Retrospective study. Objective. To evaluate the absolute value of L4 trabecular region-of-interest (t-ROI) computed tomography (CT) attenuation, which can predict pedicle screw loosening, and determine the changes in value according to number of fused levels and sagittal balance in patients undergoing lumbar fusion surgery. Summary of Background Data. Although osteoporosis was not diagnosed in spinal dual x-ray absorptiometry preoperatively, we encountered several cases of screw loosening within 1 year of lumbar fusion surgery. Methods. We enrolled 478 patients and analyzed factors related to screw loosening. We evaluated the association between L4 t-ROI CT attenuation and screw loosening and determined the best cutoff value of t L4 t-ROI CT attenuation for predicting screw loosening. Results. The number of fused levels, postoperative C7-S1 sagittal vertical axis (SVA), and L4 t-ROI CT attenuation were independently correlated with screw loosening. According to number of fused level and postoperative C7-T1 SVA (≥36.9 mm or <36.9 mm), in patients with one-level fusion and C7-S1 SVA less than 36.9 mm, the optimal cutoff point of the L4 t-ROI CT attenuation predicting screw loosening was 106.5 Hounsfield unit (HU). L4 t-ROI attenuation did not change until two-level fusions. In patients with three-level fusions and C7-S1 SVA less than 36.9 mm, the optimal cutoff point of the L4 t-ROI CT attenuation predicting screw loosening was 159.0 HU. The optimal cutoff point of L4 t-ROI CT attenuation in patients with three-level fusions and C7-S1 SVA more than or equal to 36.9 mm was 191.0 HU. Conclusion. L4 t-ROI CT attenuation value considering number of fused levels and sagittal balance is an accurate measurement method to predict screw loosening. Spine surgeons should be aware of the L4 t-ROI attenuation before surgery to improve the fusion rate and reduce instrument-related complications of lumbar spine surgery in osteoporotic patients. Level of Evidence. 3
Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data

Abstract Translation Complex Profile Sequencing (TCP-seq), a protocol that was developed and implemented on Saccharomyces cerevisiae, provides the footprints of the small subunit (SSU) of the ribosome (with additional factors) across the entire transcriptome of the analyzed organism. In this study, based on the TCP-seq data, we developed for the first-time a predictive model of the SSU density and analyzed the effect of transcript features on the dynamics of the SSU scan in the 5′UTR. Among others, our model is based on novel tools for detecting complex statistical relations tailored to TCP-seq. We quantitatively estimated the effect of several important features, including the context of the upstream AUG, the upstream ORF length and the mRNA folding strength. Specifically, we suggest that around 50% of the variance related to the read counts (RC) distribution near a start codon can be attributed to the AUG context score. We provide the first large scale direct quantitative evidence that shows that indeed AUG context affects the small sub-unit movement. In addition, we suggest that strong folding may cause the detachment of the SSU from the mRNA. We also identified a number of novel sequence motifs that can affect the SSU scan; some of these motifs affect transcription factors and RNA binding proteins. The results presented in this study provide a better understanding of the biophysical aspects related to the SSU scan along the 5′UTR and of translation initiation in S. cerevisiae, a fundamental step toward a comprehensive modeling of initiation.
The impacts of mangrove range expansion on wetland ecosystem services in the southeastern United States: Current understanding, knowledge gaps, and emerging research needs

Climate change is transforming ecosystems and affecting ecosystem goods and services. Along the Gulf of Mexico and Atlantic coasts of the southeastern United States, the frequency and intensity of extreme freeze events greatly influence whether coastal wetlands are dominated by freeze‐sensitive woody plants (mangrove forests) or freeze‐tolerant grass‐like plants (salt marshes). In response to warming winters, mangroves have been expanding and displacing salt marshes at varying degrees of severity in parts of north Florida, Louisiana, and Texas. As winter warming accelerates, mangrove range expansion is expected to increasingly modify wetland ecosystem structure and function. Because there are differences in the ecological and societal benefits that salt marshes and mangroves provide, coastal environmental managers are challenged to anticipate the effects of mangrove expansion on critical wetland ecosystem services, including those related to carbon sequestration, wildlife habitat, storm protection, erosion reduction, water purification, fisheries support, and recreation. Mangrove range expansion may also affect wetland stability in the face of extreme climatic events and rising sea levels. Here, we review the current understanding of the effects of mangrove range expansion and displacement of salt marshes on wetland ecosystem services in the southeastern United States. We also identify critical knowledge gaps and emerging research needs regarding the ecological and societal implications of salt marsh displacement by expanding mangrove forests. One consistent theme throughout our review is that there are ecological trade‐offs for consideration by coastal managers. Mangrove expansion and marsh displacement can produce beneficial changes in some ecosystem services, while simultaneously producing detrimental changes in other services. Thus, there can be local‐scale differences in perceptions of the impacts of mangrove expansion into salt marshes. For very specific local reasons, some individuals may see mangrove expansion as a positive change to be embraced, while others may see mangrove expansion as a negative change to be constrained.
Daam2 Regulates Myelin Structure and the Oligodendrocyte Actin Cytoskeleton through Rac1 and Gelsolin

Myelin is essential to neuronal health and CNS function, and oligodendrocytes (OLs) undergo a complex process of cytoskeletal remodeling to form compact myelin sheaths. We previously discovered that a formin protein, Dishevelled associated activator of morphogenesis 2 (Daam2), suppresses OL differentiation through Wnt signaling; however, its role in cytoskeletal control remains unknown. To investigate this, we used OL-specific Daam2 conditional knockout (Daam2 cKO) mice of either sex and found myelin decompaction during an active period of myelination in postnatal development and motor coordination deficits in adulthood. Using primary OL cultures, we found Daam2-depleted OLs showed morphologic dysregulation during differentiation, suggesting that Daam2 regulates the OL cytoskeleton. In vivo screening identified the actin regulators Rac1 and Gelsolin as possible effectors in Daam2-deficient OL cytoskeletal regulation. Using gain-of-function and loss-of-function (LOF) experiments in primary OLs, we found that Rac1 and Gelsolin operate downstream of Daam2 in OL differentiation, with Gelsolin and Daam2 promoting and inhibiting membrane spreading during late differentiation, respectively. In vivo experiments using Daam2 cKO mice revealed increased protein levels of Gelsolin in the developing white matter with no change in RNA levels, suggesting that Daam2 acts in a posttranslational manner to suppress Gelsolin levels. In vitro biochemical studies show Daam2 induces Gelsolin ubiquitination and degradation in OLs. Together, our studies show Daam2 is essential for formation of functional myelin through modulation of Gelsolin levels to regulate the OL cytoskeleton. These findings further demonstrate the critical role of cytoskeletal dynamics in myelination and reveal novel avenues for treatment of a variety of white matter diseases. SIGNIFICANCE STATEMENT Proper myelin formation is essential to CNS function, and oligodendrocytes (OLs) require extensive changes in the actin cytoskeleton to form myelin sheaths. Here, we show that the formin protein Dishevelled associated activator of morphogenesis 2 (Daam2) is necessary for myelin compaction during development and motor learning in adulthood. Further, we demonstrate that Daam2 regulates OL differentiation and morphology through actin regulators Rac1 and Gelsolin. Lastly, we find that Daam2 may control myelin compaction by modulating the ubiquitination and degradation of Gelsolin through recruitment of the E3 ubiquitin ligase Nedd4. These findings reveal novel pathways for regulating myelin structure and function during white matter development.
Protection of Quiescence and Longevity of IgG Memory B Cells by Mitochondrial Autophagy

Key Points Nix and Bnip3 regulate mitochondrial homeostasis by autophagy in memory B cells. Mitochondrial autophagy is required for metabolic quiescence in memory B cells. Uncontrolled metabolic function increases cell death in memory B cells. The development of long-lived immune memory cells against pathogens is critical for the success of vaccines to establish protection against future infections. However, the mechanisms governing the long-term survival of immune memory cells remain to be elucidated. In this article, we show that the maintenance mitochondrial homeostasis by autophagy is critical for restricting metabolic functions to protect IgG memory B cell survival. Knockout of mitochondrial autophagy genes, Nix and Bnip3, leads to mitochondrial accumulation and increases in oxidative phosphorylation and fatty acid synthesis, resulting in the loss of IgG+ memory B cells in mice. Inhibiting fatty acid synthesis or silencing necroptosis gene Ripk3 rescued Nix−/−Bnip3−/− IgG memory B cells, indicating that mitochondrial autophagy is important for limiting metabolic functions to prevent cell death. Our results suggest a critical role for mitochondrial autophagy in the maintenance of immunological memory by protecting the metabolic quiescence and longevity of memory B cells.
Using financial incentives to support service engagement of adults experiencing homelessness and mental illness: A qualitative analysis of key stakeholder perspectives

Homelessness and mental illness are associated with poor service engagement, health and health service use outcomes. Existing literature suggests that financial incentives may effectively support service engagement of this population, but studies investigating key stakeholder perspectives are lacking. This study aimed to elicit, using qualitative methods, nuanced service user and provider experiences by using financial incentives to support service engagement among adults experiencing homelessness and mental illness.
Identifying regional environmental factors driving differences in climatic niche overlap in Peromyscus mice

Different groups of taxa exhibit varying degree of climatic niche conservatism or divergence due to evolutionary constraints imposed on taxa and distributional relationships among them. Herein, we explore to what extent regional environmental conditions that taxa occupy affect climatic niche overlap between pairs of congeneric species of Peromyscus mice exhibiting allopatric, parapatric, or sympatric distributions. We used Bayesian generalized linear mixed models to identify environmental variables that best explain differences in climatic niche overlap between species. Our results suggest that regional environmental conditions explain 13–44% of variation in climatic niche overlap. Specifically, allopatric and parapatric species pairs are more likely to occupy similar climatic niches in areas that are topographically less complex but with more complex habitats. Sympatric species are more likely to occupy similar climatic niches in areas that promote local niche partitioning (topographically less complex, warmer winter temperatures, higher precipitation, and higher habitat complexity on a local scale). By understanding the relationship between regional environmental conditions and niche overlap, we highlight how differences in geography can contribute to shaping niches of congeneric species.
Concurrent Product Design Based on Simultaneous Processing of Design and Manufacturing Information by Utility Analysis.

A methodology of concurrent design of machine products based on simultaneous processing of design and manufacturing information is proposed for obtaining better product designs from a global viewpoint, according to the concept of concurrent engineering. In this method, an integrated higher-rank decision-making utility function is formulated using the satisfactory level functions of product design and manufacturing divisions by utility analysis. Then, on the Pareto optimum solution curves of multiobjective optimization problems of the maximization of the product performance and the minimization of the product manufacturing cost, the values of the integrated satisfactory levels are obtained for alternative product designs and the most preferable design solution is selected. An applied example of the concurrent design procedures is given for demonstrating the effectiveness of the proposed method in comparison to conventional design method procedures.
Perception of economic inequality: concepts, associated factors and prospects of a burgeoning research agenda (Percepción de desigualdad económica: conceptos, factores asociados y proyecciones de una agenda creciente de investigación)

Abstract Perceptions of economic inequality have become a topic of growing interest in research from different social science disciplines. This article presents an up-to-date literature review of studies on this topic, stressing aspects related to its conceptualization and measurement, as well as psychosocial, socioeconomic and contextual factors associated with the perception of inequality. This review ends by pointing out some consequences of perception of inequality and identifying some pathways for future research agendas
What is the Current and Future Status of Digital Mental Health Interventions?

Abstract The prevalence of mental disorders continues to increase, especially with the advent of the COVID-19 pandemic. Although we have evidence-based psychological treatments to address these conditions, most people encounter some barriers to receiving this help (e.g., stigma, geographical or time limitations). Digital mental health interventions (e.g., Internet-based interventions, smartphone apps, mixed realities -virtual and augmented reality) provide an opportunity to improve accessibility to these treatments. This article summarizes the main contributions of the different types of digital mental health solutions. It analyzes their limitations (e.g., drop-out rates, lack of engagement, lack of personalization, lack of cultural adaptations) and showcases the latest sophisticated and innovative technological advances under the umbrella of precision medicine (e.g., digital phenotyping, chatbots, or conversational agents). Finally, future challenges related to the need for real world implementation of these interventions, the use of predictive methodology, and hybrid models of care in clinical practice, among others, are discussed.