bluuebunny/crossref_metadata_2025_split huggingface dataset:
Piece by piece—a computer-aided method for virtual re-association of commingled fragmented remains
Authors: Camine Lise Malfroy , Magnin Virginie , Soto Ruben , Bruguier Christine , Grabherr Silke , Varlet Vincent , Moghaddam Negahnaz 
Published: July 2024

Abstract

Air crashes or explosions with numerous victims may result in thousands of fragmented human remains that present a massive challenge for disaster victim identification teams. Genetic identification may present important financial and technical limits, and the physical re-association of fractured bones by forensic anthropologists may require a time-consuming phase of cleaning and drying. A virtual re-association (VRA) of fragmented human remains using postmortem computed tomography (CT)-scan images could enhance the identification process and reduce the number of genetic analyses required. Therefore, this study investigated the advantages and limitations of a VRA protocol in comparison with physical re-association (PRA) in a laboratory setting and in a real case scenario. As a first step, six porcine femurs were scanned by multi-detector CT before and after physical fragmentation. PRA of the dry bones and VRA of the 3D models of the fragments were then performed. The physically reconstructed dry bones were then once more scanned with CT. The mean distance between intact and reconstructed models, the number of re-associated fragments, and the time needed for the reconstruction were evaluated. In a second step, 87 fragmented remains resulting from a controlled pig bombing were collected, scanned, and virtually re-associated to test the feasibility of the protocol in a real context. The reconstruction of the femurs showed no difference in accuracy between PRA and VRA. Although the VRA was faster than PRA, the preparation of the material still needs to be taken into consideration. The VRA after the controlled pig bombing was limited to 8% of the total fragments. Differences in alveolar and cortical osseous structure and the presence of cartilage resulted in segmentation approximations and difficulties in the re-association itself. The explosion produced an important loss of intermediate bone elements. The VRA method still needs further evaluations with a larger sample size and different fragmentation mechanisms. However, the presented research shows promising results towards enhancing the efficiency of identifying individuals after a mass disaster.

Key points
The Psathyrostachys juncea DWARF27 gene encodes an all-trans-/9-cis-beta-carotene isomerase in the control of plant branches in Arabidopsis thaliana by strigolactones
Authors: Ren Xiaomin , Ai Qian , Li Zhen , Zhao Qiao , Yun Lan 
Published: July 2024

Abstract
Strigolactones (SLs), carotenoid-derived plant hormones, govern the growth and development of both monocotyledonous and dicotyledonous plants. DWARF27 (D27), a plastid-targeted protein located at the initiation site of the core pathway in SL synthesis, plays a crucial role in regulating plant tillering (branching). In rice (Oryza sativa) and wheat (Triticum aestivum), OsD27 and TaD27-B proteins modulate the number of plant tillers by participating in SL biosynthesis. Similarly, AtD27 in Arabidopsis thaliana is required for SL production and has a significant impact on phenotypic changes related to branching. At the same time, TaD27 in wheat has been confirmed as a functional orthologue of AtD27 in Arabidopsis, and both Psathyrostachys juncea and wheat belong to the Triticeae, so we speculate that PjD27 gene may also have the same function as AtD27 in Arabidopsis. In this study, we initially screened the PjD27 gene significantly associated with tillering regulation through transcriptome data analysis and subsequently validated its expression levels using qRT-PCR analysis. Furthermore, we conducted phylogenetic analysis using amino acid sequences from 41 species, including P. juncea, to identify closely related species of P. juncea. Here, we analyze the conservation of D27 protein among P. juncea, rice, wheat, and Arabidopsis and provide preliminary evidence suggesting that PjD27 protein is an orthologue of D27 protein in Arabidopsis. Through reverse genetics, we demonstrate the crucial role of PjD27 in regulating plant branching, establishing it as a functional orthologue of D27 in Arabidopsis. Furthermore, following transient expression in tobacco (Nicotiana tabacum), we demonstrate that the subcellular location of the PjD27 protein is consistent with the cellular location of TaD27-B in wheat. Quantitative analysis of SLs shows that PjD27 is a key gene regulating tillering (branching) by participating in SL biosynthesis. By elucidating the function of the PjD27 gene, our findings provide valuable genetic resources for new germplasm creation and improving grain yield in P. juncea.
Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence
Authors: Vakirlis Nikolaos , Acar Omer , Cherupally Vijay , Carvunis Anne-Ruxandra 
Published: July 2024

Abstract
New protein-coding genes can evolve from previously noncoding genomic regions through a process known as de novo gene emergence. Evidence suggests that this process has likely occurred throughout evolution and across the tree of life. Yet, confidently identifying de novo emerged genes remains challenging. Ancestral sequence reconstruction is a promising approach for inferring whether a gene has emerged de novo or not, as it allows us to inspect whether a given genomic locus ancestrally harbored protein-coding capacity. However, the use of ancestral sequence reconstruction in the context of de novo emergence is still in its infancy and its capabilities, limitations, and overall potential are largely unknown. Notably, it is difficult to formally evaluate the protein-coding capacity of ancestral sequences, particularly when new gene candidates are short. How well-suited is ancestral sequence reconstruction as a tool for the detection and study of de novo genes? Here, we address this question by designing an ancestral sequence reconstruction workflow incorporating different tools and sets of parameters and by introducing a formal criterion that allows to estimate, within a desired level of confidence, when protein-coding capacity originated at a particular locus. Applying this workflow on ∼2,600 short, annotated budding yeast genes (&lt;1,000 nucleotides), we found that ancestral sequence reconstruction robustly predicts an ancient origin for the most widely conserved genes, which constitute “easy” cases. For less robust cases, we calculated a randomization-based empirical P-value estimating whether the observed conservation between the extant and ancestral reading frame could be attributed to chance. This formal criterion allowed us to pinpoint a branch of origin for most of the less robust cases, identifying 49 genes that can unequivocally be considered de novo originated since the split of the Saccharomyces genus, including 37 Saccharomyces cerevisiae-specific genes. We find that for the remaining equivocal cases we cannot rule out different evolutionary scenarios including rapid evolution, multiple gene losses, or a recent de novo origin. Overall, our findings suggest that ancestral sequence reconstruction is a valuable tool to study de novo gene emergence but should be applied with caution and awareness of its limitations.
Adult Physical Function Has Roots in Early Childhood Brain Function: A Five-Decade Cohort Study
Authors: Xie J Kathy , Caspi Avshalom , Harrington HonaLee , Houts Renate , Pietrosimone Laura , Whitman Ethan T , McKinney Lauren W , Moffitt Terrie E 
Published: July 2024

Abstract

Objectives
Tests of physical function are often thought to measure functioning that is (1) musculoskeletal, and (2) newly declining in adult life. In contrast, this study aimed to: (1) add to evidence that physical-function tests also measure brain function, and (2) test the novel hypothesis that adult physical function is associated with brain function beginning in early childhood. We investigated early childhood brain function and midlife physical function in the Dunedin Study, a 5-decade longitudinal birth cohort (n = 1,037).

Methods
Brain function was measured at age 3 using 5 measures which formed a reliable composite (neurological examination, cognitive and motor tests, and temperament ratings). Physical function was measured at age 45 using 5 measures which formed a reliable composite (gait speed, step-in-place, chair stands, balance, and grip strength).

Results
Children with worse age-3 brain function had worse midlife physical function as measured by the age-45 composite, even after controlling for childhood socioeconomic status (β: 0.23; 95% CI: 0.16 to 0.30; p &lt; .001). Worse age-3 brain function significantly predicted slower gait speed, fewer steps-in-place and chair-stands, worse balance, and weaker grip strength.

Discussion
Children with poorer brain function were more likely to have poorer physical-function scores as adults. In addition to indicating recent musculoskeletal decline, physical-function tests may also provide indications of lifelong, integrated brain–body health. By reconceptualizing the meaning of physical-function scores, clinicians can orient the use of physical-function tests in a more holistic approach to health care.
National Institute on Aging’s 50th Anniversary: Advancing Cognitive Aging Research and the Cognitive Health of Older Adults
Authors: Harrell Erin R , King Jonathan W , Stoeckel Luke E , Treviño Melissa 
Published: July 2024

Abstract
In celebration of the National Institute on Aging’s (NIA) 50th anniversary, this paper highlights the significant advances in cognitive aging research and the promotion of cognitive health among older adults. Since its inception in 1974, the NIA has played a pivotal role in understanding cognitive aging, including cognitive epidemiology, interventions, and methods, for measuring cognitive change. Key milestones include the shift toward understanding cognitive impairment and Alzheimer’s disease and Alzheimer’s disease-related dementias (AD/ADRD), the development of large-scale longitudinal studies, and the incorporation of AD/ADRD-related biomarkers in cognitive aging cohorts. Additionally, NIA has championed diversifying the scientific workforce through initiatives, such as the Resource Centers for Minority Aging Research and the Butler-Williams Scholars Program. The next 50 years will continue to emphasize the importance of inclusion, innovation, and impactful research to enhance the cognitive health and well-being of older adults.
Introducing biosimilar competition for cell and gene therapy products
Authors: Canter Brian , Sussman Sabine , Colvill Stephen , Arad Nitzan , Staton Elizabeth , Rai Arti 
Published: July 2024

Abstract
This article provides an early analysis of the potential for creating future biosimilar competition for cell and gene therapies (CGTs) to lower prices and improve patient access, building on a unique set of interviews with relevant experts. Our discussion addressed regulatory, manufacturing, intellectual property, and market size challenges. Due to CGTs' complexity, meeting the regulatory requirement of ‘high similarity with no clinically meaningful differences’ will be difficult. Gene therapies are likely better candidates for biosimilar development than cell therapies. Biosimilarity should be met when gene therapy biosimilars contain the same genetic sequence as a reference product, and the variability in the vector meets the high similarity standard. Manufacturing challenges, including the lack of standardized platforms, high production costs, and complexity, pose significant obstacles. It may also be important to demonstrate biosimilarity within the manufacturing process. Intellectual property barriers, specifically patenting, trade secrecy, and regulatory exclusivity, could hinder biosimilars' ability to gain market share, although recent Supreme Court decisions limiting the breadth of patent claims could ease barriers to future CGT competition, including from biosimilars. Finally, inadequate market sizes might create hurdles, especially for curative treatments, as patient pools shrink following treatment by the reference CGT.
Japanese fathers’ work-related factors associated with involvement in childcare
Authors: Ochi Manami , Kato Tsuguhiko , Kachi Yuko , Dhungel Bibha , Nagayoshi Mako , Ichinose Yuichi , Takehara Kenji 
Published: July 2024

Abstract

Objectives
Existing studies of fathers’ involvement in childcare have focused on its impact on children’s psychosocial development and the facilitation of family functions, like marital relationships. In this study, we investigated the factors that determine paternal childcare in Japan, particularly focusing on work-related hours and environment, separately, according to mothers’ employment status.

Methods
We used data from the Longitudinal Survey of Newborns in the 21st Century (2010 cohort) conducted in Japan. We restricted the sample to 27 783 participants with working fathers and analyzed how paternal work-related factors affect fathers’ childcare involvement by mothers’ employment status using an ordered logistic regression model.

Results
In the model adjusting for all covariates, the odds ratio (OR) of spending less time with children on weekdays was higher: for fathers who worked 50 and more hours per week compared with those who worked 40-49 hours per week (OR = 1.95, 95% CI: 1.72-2.20 for 50-59 hours), for fathers whose commuting hours were longer than those commuting less than 0.5 hours per day (OR = 2.93, 95% CI: 2.34-3.69 for 1.5 or more hours), for larger workplace employee sizes than for 5-99 employee sizes (OR = 1.56, 95% CI: 1.38-1.77 for 500 or more employees). The associations between these paternal work-related variables and paternal hours spent with the children on weekdays were almost the same if the mothers were working or not working.

Conclusions
Regardless of whether the mother is working, fathers’ work environment factors, such as working hours, play a key role in their involvement in childcare.
‘Don’t educate me—move me!’ Why we need art and artists (especially films and filmmakers) to love education into existence
Authors: Frimberger Katja 
Published: July 2024

Abstract
This paper explores the anthropological and ontological conditions of our ‘educational movement’ in aesthetic experience and illustrates these through a range of examples from popular cinema/film (the Empire Strikes Back; Memento; David Lynch’s musings). For the anthropological framing of education, I enlist the help of German philosopher Hans-Georg Gadamer and his notion of ‘formation’ as it unfolds in the aesthetic appearance of the cultural world—with film’s moving images’ coming-into-form-and-meaning as my key example. For Gadamer, the artwork’s formative potential is bound up in its capacity to move our senses and intellect into an encounter with what is other to our subjectivity. Drawn into a mode of paying attention to what appears (e.g. in film’s moving images), we are called to lose ourselves and be present in a new way to familiar world objects and relations. The second part of the paper imagines the ontological conditions that make possible our formative movement in the cultural world: the mode of the beautiful. Why do certain artworks shine forth and summon us to be present to them? To pursue this question, I turn to French Catholic philosopher Jacques Maritain’s notion of Beauty and craftsmanship. He turns us (like Gadamer) to a neo-Platonic notion of Beauty rooted in St Thomas Aquinas’ notion of the mystery of B/being (i.e. God). In Maritain’s reading, our hermeneutic aesthetic experience—and with that our movement into self-formation—is held in existence through the artist’s participation in the mode of the beautiful and their loss of self in the labour of love of craftsmanship.
Application of Weak-Beam Dark-Field STEM for Dislocation Loop Analysis
Authors: Lin Yan-Ru , Li Yao , Zinkle Steven J , Arregui-Mena Jose’ D , Burke M Grace 
Published: July 2024

Abstract
Nanoscale dislocation loops formed by irradiation can significantly contribute to both irradiation hardening and embrittlement of materials when subjected to extreme nuclear reactor environments. This study explores the application of weak-beam dark-field (WBDF) scanning transmission electron microscopy (STEM) methods for quantitative irradiation-induced defect analysis in crystalline materials, with a specific focus on dislocation loop imaging and analysis. A high-purity Fe-5 wt% Cr model alloy was irradiated with 8 MeV Fe2+ ions at 450°C to a fluence of 8.8 × 1019 m−2, inducing dislocation loops for analysis. While transmission electron microscopy (TEM) has traditionally been the primary tool for dislocation imaging, recent advancements in STEM technology have reignited interest in using STEM for defect imaging. This study introduces and compares three WBDF STEM methods, demonstrating their effectiveness in suppressing background contrasts, isolating defect information for dislocation loop type classification, providing finer dislocation line images for small loop analysis, and presenting inside–outside contrast for identifying loop nature. Experimental findings indicate that WBDF STEM methods surpass traditional TEM approaches, yielding clearer and more detailed images of dislocation loops. The study concludes by discussing the potential applications of WBDF STEM techniques in defect analysis, emphasizing their adaptability across various material systems beyond nuclear materials.
Spatially resolved properties of extraplanar diffuse ionized gas in NGC 3511 and NGC 3513
Authors: Zhu Hanjue , Boettcher Erin , Chen Hsiao-Wen 
Published: July 2024

ABSTRACT
Gaseous, disc–halo interfaces are shaped by processes that are critical to galaxy evolution, including gas accretion and outflows. Extraplanar diffuse ionized gas (eDIG) layers are characterized by scale heights that largely exceed those predicted by their temperature, suggesting the presence of turbulent energy injection from star-formation feedback. However, the origin of this large-scale height remains uncertain. To explore the connection between eDIG and star-forming discs, we present a spatially resolved case study of a nearby pair of sub-$L_*$, intermediately inclined disc galaxies NGC 3511/3513. We decompose optical nebular lines observed using long-slit spectroscopy into narrow and broad velocity components. In NGC 3511, the broad component has three distinctive characteristics in comparison to the narrow component: (1) significantly higher velocity dispersions (a median $\langle \sigma \rangle _{\text{Broad}} = 24$  km s$^{-1}$compared to $\langle \sigma \rangle _{\text{Narrow}} = 13$  km s$^{-1}$), (2) elevated [N ii]$\lambda$6583/H$\alpha$ and [S ii]$\lambda$6716/H$\alpha$ line ratios, and (3) a rotational velocity lag. These characteristics support the origin of the broad component in an extraplanar, gaseous disc. In NGC 3513, the broad component reveals disc–halo circulation via localized outflows at radius $\lesssim 1$ kpc. For NGC 3511, we test a vertical hydrostatic equilibrium model with pressure support supplied by thermal and turbulent motions. Under this assumption, the eDIG velocity dispersion corresponds to a scale height $h_{z} \gtrsim 0.2 - 0.4$ kpc at $R = 3 - 5$ kpc, a factor of a few above the thermal scale height ($h_{z} \lesssim 0.1$ kpc). This highlights the importance of turbulent motions to the vertical structure of the gaseous, disc–halo interface.
Evolution and Functional Differentiation of the C-terminal Motifs of FtsZs During Plant Evolution
Authors: An Jinjie , Wang Lulu , Hong Conghao , Gao Hongbo 
Published: July 2024

Abstract
Filamentous temperature-sensitive Z (FtsZ) is a tubulin-like GTPase that is highly conserved in bacteria and plants. It polymerizes into a ring at the division site of bacteria and chloroplasts and serves as the scaffold protein of the division complex. While a single FtsZ is present in bacteria and cyanobacteria, there are two subfamilies, FtsZ1 and FtsZ2 in the green lineage, and FtsZA and FtsZB in red algae. In Arabidopsis thaliana, the C-terminal motifs of AtFtsZ1 (Z1C) and AtFtsZ2-1 (Z2C) display distinct functions in the regulation of chloroplast division. Z1C exhibits weak membrane-binding activity, whereas Z2C engages in the interaction with the membrane protein AtARC6. Here, we provide evidence revealing the distinct traits of the C-terminal motifs of FtsZ1 and FtsZ2 throughout the plant evolutionary process. In a range of plant species, the C-terminal motifs of FtsZ1 exhibit diverse membrane-binding properties critical for regulating chloroplast division. In chlorophytes, the C-terminal motifs of FtsZ1 and FtsZ2 exhibit both membrane-binding and protein interaction functions, which are similar to those of cyanobacterial FtsZ and red algal FtsZA. During the transition from algae to land plants, the functions of the C-terminal motifs of FtsZ1 and FtsZ2 exhibit differentiation. FtsZ1 lost the function of interacting with ARC6 in land plants, and the membrane-binding activity of FtsZ2 was lost in ferns. Our findings reveal the functional differentiation of the C-terminal motifs of FtsZs during plant evolution, which is critical for chloroplast division.
Varenicline Over-The-Counter Trial on Efficacy and Safety
Authors: Pearson Jennifer , Nides Mitchell A , Cataldo Alana , Martinez Marisol , Morales Jackie , Seltzer Ryan , Kurka Jonathan , Broussard Matthew , Leischow Scott J 
Published: July 2024

Abstract

Introduction
Varenicline helps people who smoke quit at rates 2–3 times greater than placebo. Currently, in the United States, varenicline is not available over the counter (OTC).

Aims and Methods
In this study, we assessed the safety and efficacy of 1 mg and 0.5 mg varenicline as an OTC medication for smoking cessation in comparison to placebo. This randomized, double-blind, placebo-controlled study was performed at two clinical sites in the United States of n = 313 people. The treatment period was 12 weeks. During the COVID pandemic, the protocol was modified to allow remote participation; verification of smoking status was via breath carbon monoxide levels for in-person visits and mailed urine cotinine kits for the remote participants.

Results
There was no difference in biologically confirmed continuous abstinence by condition between weeks 8 and 12; however, the odds of biologically confirmed point prevalence abstinence were higher for those in the 1 mg b.i.d. condition than for those in the placebo condition at week 12 (OR 3.39; 95% CI 1.49, 7.71), and were higher for those assigned to the 1.0 mg b.i.d. condition than the 0.5 mg b.i.d. condition at week 12 (OR 2.37; 95% CI 1.11, 5.05). Adverse events were modest, and as expected (vivid dreams and nausea in the medication conditions).

Conclusions
The results are suggestive that varenicline is safe and effective as an OTC medication.