bluuebunny/crossref_metadata_2025_split huggingface dataset:
The multifaceted roles of mitochondria in osteoblasts: from energy production to mitochondrial-derived vesicle secretion
Authors: Suh Joonho , Lee Yun-Sil 
Published: June 2024

Abstract
Mitochondria in osteoblasts have been demonstrated to play multiple crucial functions in bone formation from intracellular adenosine triphosphate production to extracellular secretion of mitochondrial components. The present review explores the current knowledge about mitochondrial biology in osteoblasts, including mitochondrial biogenesis, bioenergetics, oxidative stress generation, and dynamic changes in morphology. Special attention is given to recent findings, including mitochondrial donut formation in osteoblasts, which actively generates mitochondrial-derived vesicles (MDVs), followed by extracellular secretion of small mitochondria and MDVs. We also discuss the therapeutic effects of targeting osteoblast mitochondria, highlighting their potential applications in improving bone health.
Modified dung beetle optimizer with multi-strategy for uncertain multi-modal transport path problem
Authors: Wu Jiang , Luo Qifang , Zhou Yongquan 
Published: June 2024

Abstract
Uncertain multi-modal transport path optimization (UMTPO) is a combined optimization non-deterministic polynomial-time hard problem. Its goal is to determine a path with the lowest total transportation cost and carbon emissions from the starting point to the destination. To effectively address this issue, this article proposes a modified dung beetle optimizer (DBO) to address it. DBO is a swarm-based metaheuristic optimization algorithm that has the features of a fast convergence rate and high solution accuracy. Despite this, the disadvantages of weak global exploration capability and falling easily into local optima exist. In this article, we propose a modified DBO called MSHDBO for function optimization and to solve the UMTPO problem. However, for the vast majority of metaheuristic algorithms, they are designed for continuous problems and cannot directly solve discrete problems. Therefore, this article employs a priority based encoding and decoding method to solve the UMTPO problem. To verify the performance and effectiveness of the MSHDBO algorithm, we compared it with other improved versions of the DBO algorithm used in the literature. We confirmed the excellent performance of MSHDBO using 41 benchmark test functions from the IEEE CEC 2017 test suite and IEEE CEC 2022 test suite. Additionally, we compared the MSHDBO algorithm with 10 other state-of-the-art metaheuristic optimization algorithms through a practical UMTPO problem. The experimental results indicated that the MSHDBO algorithm achieved very good performance when solving the UMTPO problem.
Feasibility and acceptability of a telehealth intervention for improving peer relationships for adolescents with neurofibromatosis type 1: a single-arm pilot study
Authors: Glad Danielle M , Pardej Sara K , Olszewski Ellen , Klein-Tasman Bonita P 
Published: June 2024

Abstract

Objective
Elevated rates of social difficulties are evident for children and adolescents with neurofibromatosis type 1 (NF1) but the effects of social skills interventions have not been investigated for this population. The Program for the Education and Enrichment of Relational Skills (PEERS®), a widely established social skills intervention in autism spectrum disorders with expansion to other conditions, was recently modified to be offered virtually. This study examined the feasibility and acceptability of this telehealth intervention.

Methods
27 adolescents with NF1 with social skills difficulties and at least 1 caregiver enrolled in the study. 19 of those participants (Mage = 14.21 years, SD = 1.63; 7 females; 79% White) completed PEERS® via telehealth in a single-arm pilot study. Dropout rates, attendance records, helpfulness of the curriculum topics and caregiver-reported acceptability, including ratings on the Treatment Acceptability Questionnaire, were examined.

Results
Low study drop out (30% of enrolled participants; 14% of participants who began the intervention) and high attendance rates were observed. Caregivers found sessions related to common, everyday interactions most helpful. Adolescents indicated sessions related to having get-togethers and social nuances (e.g., humor) as most helpful. Caregiver ratings indicated acceptability of the intervention.

Conclusions
This investigation supported the feasibility and acceptability of telehealth PEERS®, a social skills intervention program, among adolescents with NF1 and their caregivers based on attendance patterns as well as appraisal of the curriculum and telehealth modality.
Language-based machine perception: linguistic perspectives on the compilation of captioning datasets
Authors: Hekanaho Laura , Hirvonen Maija , Virtanen Tuomas 
Published: June 2024

Abstract
Over the last decade, a plethora of training datasets have been compiled for use in language-based machine perception and in human-centered AI, alongside research regarding their compilation methods. From a primarily linguistic perspective, we add to these studies in two ways. First, we provide an overview of sixty-six training datasets used in automatic image, video, and audio captioning, examining their compilation methods with a metadata analysis. Second, we delve into the annotation process of crowdsourced datasets with an interest in understanding the linguistic factors that affect the form and content of the captions, such as contextualization and perspectivation. With a qualitative content analysis, we examine annotator instructions with a selection of eleven datasets. Drawing from various theoretical frameworks that help assess the effectiveness of the instructions, we discuss the visual and textual presentation of the instructions, as well as the perspective-guidance that is an essential part of the language instructions. While our analysis indicates that some standards in the formulation of instructions seem to have formed in the field, we also identified various reoccurring issues potentially hindering readability and comprehensibility of the instructions, and therefore, caption quality. To enhance readability, we emphasize the importance of text structure, organization of the information, consistent use of typographical cues, and clarity of language use. Last, engaging with previous research, we assess the compilation of both web-sourced and crowdsourced captioning datasets from various perspectives, discussing factors affecting the diversity of the datasets.
Pain Management in Staged Osseointegration Procedures: A Retrospective Study and Foundation for Future Optimization
Authors: McCarthy Margaret L , Ariizumi Ren M , Grajales Ana G , DeCicco Joseph , Forsberg Jonathan A , Watson Nora , Burch Robert H , Highland Krista B 
Published: June 2024

ABSTRACT

Introduction
Osseointegration is an innovative procedure to attach an external prosthetic device directly to the skeleton. The technique has been shown to improve physical function and quality of life relative to conventional socket prosthetic devices. While much of the research in osseointegration has focused on functional outcomes, less is known regarding perioperative pain management. The purpose of this study was to describe perioperative and postoperative pain management approaches received by patients undergoing osseointegration procedures at a tertiary medical center.

Materials and Methods
This retrospective study was determined to be exempt from Institutional Review Board review by the Walter Reed National Military Medical Center Department of Research Programs. Perioperative and postoperative pain management approaches received by 41 patients who underwent 76 staged osseointegration procedures from 2016 to 2021 at Walter Reed National Military Medical Center were described.

Results
Pain management approaches included perioperative ketamine (51% stage I, 55% stage II), epidurals (76% stage I, 77% stage II) with a median of 3-4 days across stages, peripheral nerve catheters (27% stage I, 16% stage II), and/or single-shot peripheral nerve block (&lt;10% across stages). The median morphine equivalent dose provided during surgery was 65 mg across both stages, with 56% and 54% of patients also requiring opioid medication in the post-anesthesia care unit. In 11 of 76 (15%) procedures, patients required an increase in the rate or concentration of epidural or peripheral nerve catheter infusion. In six (8%) unique recovery periods, patients experienced a dislodged catheter. In 27 of 76 (36%) unique recovery periods, patients experienced a significant increase in postoperative pain requiring acute pain service intervention in the form of catheter adjustment, intravenous pain medications, and/or the addition of intravenous patient-controlled analgesia. Adequate pain control was achieved with minimal epidural or peripheral nerve catheter trouble-shooting and a bolus for 24 patients (89% requiring intervention). Summed 24-hour pain scores (SPI24) did not vary across stages. SPI24 was positively correlated with opioid doses received. Patients with single, relative to multiple, limb amputations had similar SPI24 values (P &gt; .05).

Conclusions
Variability in pain management requirements calls forth opportunities to optimize osseointegration analgesia care and future research. As osseointegration becomes more accessible, the need for optimizing pain management through patient-centered research becomes more salient.
Accurate estimate of the ESPRESSO fibre-injection losses inferred from integrated field-stabilization images
Authors: Schmidt Tobias M 
Published: June 2024

ABSTRACT
Ground-based astronomy is unavoidably subject to the adverse effect of atmospheric turbulence, a.k.a. the seeing, which blurs the images and limits the achievable spatial resolution. For spectroscopic observations, it leads to slit or fibre-injection losses, since not all photons distributed over the extended seeing disc can be captured. These losses might have a very substantial impact on the overall efficiency of a spectrograph and are naturally highly variable. Assessing the fibre-injection losses requires accurate information about the image quality (IQ) delivered by the telescope to the instrument over the course of the observations, which, however, is often not directly available. ESPRESSO provides acquisition and field-stabilization images attached to the science data and thus offers the opportunity for a post-processing analysis. Here, we present a novel method to infer the IQ profile and fibre-injection losses from the integrated field-stabilization images, utilizing the spill-over light that does not get injected into the fibre. We validate these measurements against the IQ observed in the acquisition images and determine that our method delivers unbiased estimates with a scatter of 0.11 arcsec for the FWHM of the profile and $15~{{\ \rm per\ cent}}$ in terms of fibre-injection losses. This compares favourably to the estimates derived from either the differential image motion monitor or the telescope guide probe sensors and therefore represents a valuable tool to characterize the instrument efficiency and to correct raw spectra for fibre-injection losses.
Nebular dominated galaxies: insights into the stellar initial mass function at high redshift
Authors: Cameron Alex J , Katz Harley , Witten Callum , Saxena Aayush , Laporte Nicolas , Bunker Andrew J 
Published: June 2024

ABSTRACT
We identify a low-metallicity ($12+\log ({\rm O}/{\rm H})=7.59$) Ly $\alpha$-emitting galaxy at $z=5.943$ with evidence of a strong Balmer jump, arising from nebular continuum. While Balmer jumps are sometimes observed in low-redshift star-forming galaxies, this galaxy also exhibits a steep turnover in the UV continuum. Such turnovers are typically attributed to absorption by a damped Ly $\alpha$ system (DLA); however, the shape of the turnover and the high observed Ly $\alpha$ escape fraction ($f_{\rm esc,Ly\alpha }~\sim 27~{{\ \rm per\ cent}}$) is also consistent with strong nebular two-photon continuum emission. Modelling the UV turnover with a DLA requires extreme column densities ($N_{\rm HI}\,\,\gt\,\, 10^{23}$ cm$^{-2}$), and simultaneously explaining the high $f_{\rm esc,Ly\alpha }$ requires a fine-tuned geometry. In contrast, modelling the spectrum as primarily nebular provides a good fit to both the continuum and emission lines, motivating scenarios in which (a) we are observing only nebular emission or (b) the ionizing source is powering extreme nebular emission that outshines the stellar emission. The nebular-only scenario could arise if the ionizing source has ‘turned off’ more recently than the recombination time-scale ($\sim$1000 yr), hence we may be catching the object at a very specific time. Alternatively, hot stars with $T_{\rm eff}\gtrsim 10^5$ K (e.g. Wolf–Rayet or low-metallicity massive stars) produce enough ionizing photons such that the two-photon emission becomes visible. While several stellar SEDs from the literature fit the observed spectrum well, the hot-star scenario requires that the number of $\gtrsim 50~{\rm M}_\odot$ stars relative to $\sim 5\!-\!50~{\rm M}_\odot$ stars is significantly higher than predicted by typical stellar initial mass functions (IMFs). The identification of more galaxies with similar spectra may provide evidence for a top-heavy IMF at high redshift.
Reconsidering the dynamical states of galaxy clusters using PCA and UMAP
Authors: Haggar Roan , De Luca Federico , De Petris Marco , Sazonova Elizaveta , Taylor James E , Knebe Alexander , Gray Meghan E , Pearce Frazer R , Contreras-Santos Ana , Cui Weiguang , Kuchner Ulrike , Mostoghiu Paun Robert A , Power Chris 
Published: June 2024

ABSTRACT
Numerous metrics exist to quantify the dynamical state of galaxy clusters, both observationally and within simulations. Many of these correlate strongly with one another, but it is not clear whether all of these measures probe the same intrinsic properties. In this work, we use two different statistical approaches – principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) – to investigate which dynamical properties of a cluster are in fact the best descriptors of its dynamical state. We use measurements taken directly from The Three Hundred suite of galaxy cluster simulations, as well as morphological properties calculated using mock X-ray and SZ maps of the same simulated clusters. We find that four descriptions of dynamical state naturally arise, and although correlations exist between these, a given cluster can be ‘dynamically relaxed’ according to all, none, or some of these four descriptions. These results demonstrate that it is highly important for future observational and theoretical studies to consider in which sense clusters are dynamically relaxed. Cluster dynamical states are complex and multidimensional, and so it is not meaningful to classify them simply as ‘relaxed’ and ‘unrelaxed’ based on a single linear scale.
Disordered sequences of transcription factors regulate genomic binding by integrating diverse sequence grammars and interaction types
Authors: Hurieva Bohdana , Kumar Divya Krishna , Morag Rotem , Lupo Offir , Carmi Miri , Barkai Naama , Jonas Felix 
Published: June 2024

Abstract
Intrinsically disordered regions (IDRs) guide transcription factors (TFs) to their genomic binding sites, raising the question of how structure-lacking regions encode for complex binding patterns. We investigated this using the TF Gln3, revealing sets of IDR-embedded determinants that direct Gln3 binding to respective groups of functionally related promoters, and enable tuning binding preferences between environmental conditions, phospho-mimicking mutations, and orthologs. Through targeted mutations, we defined the role of short linear motifs (SLiMs) and co-binding TFs (Hap2) in stabilizing Gln3 at respiration-chain promoters, while providing evidence that Gln3 binding at nitrogen-associated promoters is encoded by the IDR amino-acid composition, independent of SLiMs or co-binding TFs. Therefore, despite their apparent simplicity, TF IDRs can direct and regulate complex genomic binding patterns through a combination of SLiM-mediated and composition-encoded interactions.
A treasure trove of 1034 actinomycete genomes
Authors: Jørgensen Tue Sparholt , Mohite Omkar S , Sterndorff Eva B , Alvarez-Arevalo Maria , Blin Kai , Booth Thomas J , Charusanti Pep , Faurdal David , Hansen Troels Ø , Nuhamunada Matin , Mourched Anna-Sophie , Palsson Bernhard Ø , Weber Tilmann 
Published: June 2024

Abstract
Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from &gt;1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus is Streptomyces with 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linear Streptomyces chromosome, and analyze the content and length of the terminal inverted repeats which are characteristic for Streptomyces. We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.
Promoter dependent RNA polymerase II bypass of the epimerizable DNA lesion, Fapy•dG and 8-Oxo-2′-deoxyguanosine
Authors: Gao Shijun , Tahara Yuki , Kool Eric T , Greenberg Marc M 
Published: June 2024

Abstract
Formamidopyrimidine (Fapy•dG) is a major lesion arising from oxidation of dG that is produced from a common chemical precursor of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-OxodGuo). In human cells, replication of single-stranded shuttle vectors containing Fapy•dG is more mutagenic than 8-OxodGuo. Here, we present the first data regarding promoter dependent RNA polymerase II bypass of Fapy•dG. 8-OxodGuo bypass was examined side-by-side. Experiments were carried out using double-stranded shuttle vectors in HeLa cell nuclear lysates and in HEK 293T cells. The lesions do not significantly block transcriptional bypass efficiency. Less than 2% adenosine incorporation occurred in cells when the lesions were base paired with dC. Inhibiting base excision repair in HEK 293T cells significantly increased adenosine incorporation, particularly from Fapy•dG:dC bypass which yielded ∼25% adenosine incorporation. No effect was detected upon transcriptional bypass of either lesion in nucleotide excision repair deficient cells. Transcriptional mutagenesis was significantly higher when shuttle vectors containing dA opposite one of the lesions were employed. For Fapy•dG:dA bypass, adenosine incorporation was greater than 85%; whereas 8-OxodGuo:dA yielded &gt;20% point mutations. The combination of more frequent replication mistakes and greater error-prone Pol II bypass suggest that Fapy•dG is more mutagenic than 8-OxodGuo.
Differential impact of quiescent non-coding loci on chromatin entropy
Authors: Wu Peiyao , Yao Mina , Wang Wei 
Published: June 2024

AbstractNon-coding regions of the human genome are important for functional regulations, but their mechanisms remain elusive. We used machine learning to guide a CRISPR screening on hubs (i.e. non-coding loci forming many 3D contacts) and significantly increased the discovery rate of hubs essential for cell growth. We found no clear genetic or epigenetic differences between essential and nonessential hubs, but we observed that some neighboring hubs in the linear genome have distinct spatial contacts and opposite effects on cell growth. One such pair in an epigenetically quiescent region showed different impacts on gene expression, chromatin accessibility and chromatin organization. We also found that deleting the essential hub altered the genetic network activity and increased the entropy of chromatin accessibility, more severe than that caused by deletion of the nonessential hub, suggesting that they are critical for maintaining an ordered chromatin structure. Our study reveals new insights into the system-level roles of non-coding regions in the human genome.
PBOX-sRNA-seq uncovers novel features of miRNA modification and identifies selected 5′-tRNA fragments bearing 2′-O-modification
Authors: Chen Susu , Cai Yuchen , Yang Huiru , Zhang Bin , Li Ning , Ren Guodong 
Published: June 2024

Abstract
The concomitant cloning of RNA degradation products is a major concern in standard small RNA-sequencing practices. This not only complicates the characterization of bona fide sRNAs but also hampers cross-batch experimental replicability and sometimes even results in library construction failure. Given that all types of plant canonical small RNAs possess the 3′ end 2′-O-methylation modification, a new small RNA sequencing (sRNA-seq) method, designated as PBOX-sRNA-seq, has been developed specifically to capture this modification. PBOX-sRNA-seq, as its name implies, relies on the sequential treatment of RNA samples with phenylboronic acid-polyacrylamide gel electrophoresis (PBA-PAGE) and sodium periodate (NaIO4) oxidation, before sRNA library construction and sequencing. PBOX-sRNA-seq outperformed separate treatments (i.e. PBA-PAGE only or NaIO4 only) in terms of the depletion of unmethylated RNA species and capture 2′-O-modified sRNAs with extra-high purity. Using PBOX-sRNA-seq, we discovered that nascent miRNA-5p/-3p duplexes may undergo mono-cytidylation/uridylation before 2′-O-methylation. We also identified two highly conserved types of 5′-tRNA fragments (tRF) bearing HEN1-independent 2′-O modification (mainly the 13-nt tRF-5aAla and the 26-nt tRF-5bGly). We believe that PBOX-sRNA-seq is powerful for both qualitative and quantitative analyses of sRNAs in plants and piRNAs in animals.
Tracking rivalry with neural rhythms: multivariate SSVEPs reveal perception during binocular rivalry
Authors: Laukkonen Ruben E , Lewis-Healey Evan , Ghigliotti Luca , Daneshtalab Nasim , Lageman Jet , Slagter Heleen A 
Published: June 2024

Abstract
The contents of awareness can substantially change without any modification to the external world. Such effects are exemplified in binocular rivalry, where a different stimulus is presented to each eye causing instability in perception. This phenomenon has made binocular rivalry a quintessential method for studying consciousness and the necessary neural correlates for awareness. However, to conduct research on binocular rivalry usually requires self-reports of changes in percept, which can produce confounds and exclude states and contexts where self-reports are undesirable or unreliable. Here, we use a novel multivariate spatial filter dubbed ‘Rhythmic Entrainment Source Separation’ to extract steady state visual evoked potentials from electroencephalography data. We show that this method can be used to quantify the perceptual switch-rate of participants during binocular rivalry and therefore may be valuable in experimental contexts where self-reports are methodologically problematic or impossible, particularly as an adjunct. Our analyses also reveal that ‘no-report’ conditions may affect the deployment of attention and thereby neural correlates, another important consideration for consciousness research.