bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can artificial intelligence-driven cephalometric analysis replace manual tracing? A systematic review and meta-analysis
Authors: Hendrickx Julie , Gracea Rellyca Sola , Vanheers Michiel , Winderickx Nicolas , Preda Flavia , Shujaat Sohaib , Jacobs Reinhilde 
Published: June 2024

Abstract

Objectives
This systematic review and meta-analysis aimed to investigate the accuracy and efficiency of artificial intelligence (AI)-driven automated landmark detection for cephalometric analysis on two-dimensional (2D) lateral cephalograms and three-dimensional (3D) cone-beam computed tomographic (CBCT) images.

Search methods
An electronic search was conducted in the following databases: PubMed, Web of Science, Embase, and grey literature with search timeline extending up to January 2024.

Selection criteria
Studies that employed AI for 2D or 3D cephalometric landmark detection were included.

Data collection and analysis
The selection of studies, data extraction, and quality assessment of the included studies were performed independently by two reviewers. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. A meta-analysis was conducted to evaluate the accuracy of the 2D landmarks identification based on both mean radial error and standard error.

Results
Following the removal of duplicates, title and abstract screening, and full-text reading, 34 publications were selected. Amongst these, 27 studies evaluated the accuracy of AI-driven automated landmarking on 2D lateral cephalograms, while 7 studies involved 3D-CBCT images. A meta-analysis, based on the success detection rate of landmark placement on 2D images, revealed that the error was below the clinically acceptable threshold of 2 mm (1.39 mm; 95% confidence interval: 0.85–1.92 mm). For 3D images, meta-analysis could not be conducted due to significant heterogeneity amongst the study designs. However, qualitative synthesis indicated that the mean error of landmark detection on 3D images ranged from 1.0 to 5.8 mm. Both automated 2D and 3D landmarking proved to be time-efficient, taking less than 1 min. Most studies exhibited a high risk of bias in data selection (n = 27) and reference standard (n = 29).

Conclusion
The performance of AI-driven cephalometric landmark detection on both 2D cephalograms and 3D-CBCT images showed potential in terms of accuracy and time efficiency. However, the generalizability and robustness of these AI systems could benefit from further improvement.

Registration
PROSPERO: CRD42022328800.
In silico design and analysis of a multiepitope vaccine against Chlamydia
Authors: Tanner Tayhlor , Medhavi F N U , Richardson Shakyra , Omosun Yusuf O , Eko Francis O 
Published: June 2024

Abstract
Chlamydia trachomatis (Ct) is the most common sexually transmitted bacterial infection worldwide, potentially leading to severe pathologies including pelvic inflammatory disease, ectopic pregnancy, and tubal infertility if left untreated. Current strategies, including screening and antibiotics, have limited effectiveness due to high rates of asymptomatic cases and logistical challenges. A multiepitope prophylactic vaccine could afford long-term protection against infection. Immunoinformatic analyses were employed to design a multiepitope Chlamydia vaccine antigen. B- and T-cell epitopes from five highly conserved and immunogenic Ct antigens were predicted and selected for the vaccine design. The final construct, adjuvanted with cholera toxin A1 subunit (CTA1), was further screened for immunogenicity. CTA1-MECA (multiepitope Chlamydia trachomatis antigen) was identified as antigenic and nonallergenic. A tertiary structure was predicted, refined, and validated as a good quality model. Molecular docking exhibited strong interactions between the vaccine and toll-like receptor 4 (TLR4). Additionally, immune responses consistent with protection including IFN-γ, IgG + IgM antibodies, and T- and B-cell responses were predicted following vaccination in an immune simulation. Expression of the construct in an Escherichia coli expression vector proved efficient. To further validate the vaccine efficacy, we assessed its immunogenicity in mice. Immunization with CTA1-MECA elicited high levels of Chlamydia-specific antibodies in mucosal and systemic compartments.
DNA Methylation at C-Reactive Protein-Associated CpG Sites May Mediate the Pathway Between Educational Attainment and Cognition
Authors: Stoldt Meike , Ammous Farah , Lin Lisha , Ratliff Scott M , Ware Erin B , Faul Jessica D , Zhao Wei , Kardia Sharon L R , Smith Jennifer A 
Published: June 2024

Abstract
Growing evidence has linked inflammatory processes to cognitive decline and dementia. This work examines whether an epigenetic marker of C-reactive protein (CRP), a common clinical inflammatory biomarker, may mediate the relationship between educational attainment and cognition. We first evaluated whether 53 previously reported CRP-associated DNA methylation sites (CpGs) are associated with CRP, both individually and aggregated into a methylation risk score (MRSCRP), in 3 298 participants from the Health and Retirement Study (HRS, mean age = 69.7 years). Forty-nine CpGs (92%) were associated with the natural logarithm of CRP in HRS after adjusting for age, sex, smoking, BMI, genetic ancestry, and white blood cell counts (p &lt; .05), and each standard deviation increase in MRSCRP was associated with a 0.38 unit increase in lnCRP (p = 4.02E-99). In cross-sectional analysis, for each standard deviation increase in MRSCRP, total memory score and total cognitive score decreased, on average, by 0.28 words and 0.43 items, respectively (p &lt; .001). Further, MRSCRP mediated 6.9% of the relationship between high school education and total memory score in a model adjusting for age, sex, and genetic ancestry (p &lt; .05); this was attenuated to 2.4% with additional adjustment for marital status, APOE ε4 status, health behaviors, and comorbidities (p &lt; .05). Thus, CRP-associated methylation may partially mediate the relationship between education and cognition at older ages. Further research is warranted to determine whether DNA methylation at these sites may improve current prediction models for cognitive impairment in older adults.
Characteristics and Effectiveness of Physical Therapist-Supervised Exercise Interventions for Nursing Home Residents With Dementia: A Systematic Review
Authors: Boer Dennis , Schmidt Charlotte , Sterke Shanty , Schoones Jan , Elbers Roy , Vliet Vlieland Thea 
Published: June 2024

Abstract

Background and Objectives
Although physical therapy, in particular exercise therapy, is widely used in nursing home residents with dementia, the literature on this topic is relatively scarce. This systematic review aimed to summarize the literature on the characteristics and effectiveness of exercise interventions supervised by physical therapists in nursing home residents with dementia.

Research Design and Methods
Six electronic databases were systematically searched for relevant studies up to August 17, 2022. Randomized controlled trials (RCTs) comparing exercise interventions supervised by a physical therapist to any other form of intervention or usual care in nursing home residents with dementia were selected. Data were narratively analyzed and forest plots visualizing exercise effects were created.

Results
From the 1 377 records retrieved and screened, 6 RCTs, reported in 11 papers, met the selection criteria. Included studies used multimodal or aerobic exercise interventions, with the frequency, duration and intensity varying across studies. Three of the 6 studies were at high risk of bias. Due to inconsistency in the findings and variety in outcome measures, results on the effectiveness of the interventions are inconclusive.

Discussion and Implications
Our review emphasizes the need for more robust studies to offer understanding of the efficacy of exercise interventions supervised by physical therapists for nursing home residents with dementia.
What explains the provision of health insurance by Indonesian employers? A trend analysis of the National Labour Force Survey 2018-2022
Authors: Khoe Levina Chandra , Mansyur Muchtaruddin , Wiseman Virginia , Asante Augustine 
Published: June 2024

Abstract
Indonesian laws mandate that every employer should provide health insurance and work accident insurance to their employees. Nevertheless, there is a significant gap in the coverage of employer-sponsored insurance among Indonesian workers. This study examines the coverage of employer-sponsored insurance and work accident insurance and analyses the characteristics of the uninsured working population in Indonesia. We analysed nationally representative cross-sectional data from the National Labour Force Survey (NLFS) conducted between 2018 and 2022. The primary dependent variable was the provision of health insurance and work accident insurance by employers. The independent variables included having any physical disabilities, number of working hours, duration of employment, labour union membership, earning at least the provincial minimum wage, having a written contract and working in high risk jobs. Logistic regression was employed using the R statistical software. The findings indicate that coverage of employer-sponsored health insurance is low in Indonesia—ranging from 36.1% in 2018 to 38.4% in 2022. Workers with a written contract, earning at least the provincial minimum wage, were members of a labour union, employed for at least 5 years and working more than 40 hours a week were more likely to be insured. By contrast, workers who had physical disabilities or were employed in high-risk jobs were less likely to be insured. Our study concludes that having a written employment contract is the single most influential factor that explains the provision of employer-sponsored health insurance in Indonesia. The country’s labour laws should therefore formalize the provision of written employment contracts for all workers regardless of the type and nature of work. The existing laws on health insurance and work accident insurance should be enforced to ensure that employers meet their constitutionally mandated obligation of providing these types of insurance to their workers, particularly those engaged in high risk jobs.
Optimal Gearing of Musculoskeletal Systems
Authors: Polet Delyle T , Labonte David 
Published: June 2024

Synopsis
Movement is integral to animal life, and most animal movement is actuated by the same engine: striated muscle. Muscle input is typically mediated by skeletal elements, resulting in musculoskeletal systems that are geared: at any instant, the muscle force and velocity are related to the output force and velocity only via a proportionality constant G, the “mechanical advantage”. The functional analysis of such “simple machines” has traditionally centered around this instantaneous interpretation, such that a small vs large G is thought to reflect a fast vs forceful system, respectively. But evidence is mounting that a comprehensive analysis ought to also consider the mechanical energy output of a complete contraction. Here, we approach this task systematically, and deploy the theory of physiological similarity to study how gearing affects the flow of mechanical energy in a minimalist model of a musculoskeletal system. Gearing influences the flow of mechanical energy in two key ways: it can curtail muscle work output, because it determines the ratio between the characteristic muscle kinetic energy and work capacity; and it defines how each unit of muscle work is partitioned into different system energies, that is, into kinetic vs “parasitic” energy such as heat. As a consequence of both effects, delivering maximum work in minimum time and with maximum output speed generally requires a mechanical advantage of intermediate magnitude. This optimality condition can be expressed in terms of two dimensionless numbers that reflect the key geometric, physiological, and physical properties of the interrogated musculoskeletal system, and the environment in which the contraction takes place. Illustrative application to exemplar musculoskeletal systems predicts plausible mechanical advantages in disparate biomechanical scenarios, yields a speculative explanation for why gearing is typically used to attenuate the instantaneous force output ($G_{\text{opt}} \lt 1)$, and predicts how G needs to vary systematically with animal size to optimize the delivery of mechanical energy, in superficial agreement with empirical observations. A many-to-one mapping from musculoskeletal geometry to mechanical performance is identified, such that differences in G alone do not provide a reliable indicator for specialization for force vs speed—neither instantaneously, nor in terms of mechanical energy output. The energy framework presented here can be used to estimate an optimal mechanical advantage across variable muscle physiology, anatomy, mechanical environment, and animal size, and so facilitates investigation of the extent to which selection has made efficient use of gearing as a degree of freedom in musculoskeletal “design.”
The Causes and Consequences of Public Misunderstanding of Shark Conservation
Authors: Shiffman D S 
Published: June 2024

Synopsis
Sharks and their relatives face serious conservation challenges. In addition to more effective implementation of regulations already on the books, they need more and stronger conservation and management policies to prevent the extinction of many species, which would have associated negative ecological and economic consequences. Many members of the public are aware of and concerned by shark conservation challenges, but there is widespread misunderstanding of the threats to sharks and the available policy solutions to address those threats. Such misunderstanding has been spread by both well-intentioned but uninformed shark enthusiasts (i.e., people who care and want to help but have limited or incorrect knowledge of key facts and evidence) and also by extremist activist organizations (i.e., those far outside of mainstream norms). Specifically, many members of the public incorrectly believe that the practice of shark finning (and associated demand for shark fins) is the largest or only threat to sharks. In general, the public is far less familiar with widely used and effective tools such as sustainable fisheries management as a solution to shark conservation threats. Many members of the public incorrectly believe that banning the 1% of the global shark fin trade that is the most sustainable will be a major victory for shark conservation. Many members of the public are heavily influenced by information from uninformed extremists rather than from experts. These misunderstandings result in suboptimal policy outcomes, and even conflict between stakeholder groups that ostensibly share goals or desired outcomes. This perspective summarizes a decade of work attempting to understand the causes and consequences of widespread misunderstanding about shark conservation threats and solutions, mapping each along the Science-Policy Interface. It also proposes solutions focusing on sharing our hard-earned expertise with the interested public in an accessible format.
Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages
Authors: Cook Ryan , Telatin Andrea , Bouras George , Camargo Antonio Pedro , Larralde Martin , Edwards Robert A , Adriaenssens Evelien M 
Published: June 2024

Abstract
The majority of bacteriophage diversity remains uncharacterized, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and its subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome Catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokka-gv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome median) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased median coding capacity from 66.8% to 90.0% and from 69.0% to 89.8% for UHGV and INPHARED sequences predicted to use translation table 15. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.
CDP-DAG synthesis by peripheral membrane-bound Tam41-type enzymes
Authors: Okamoto Koji 
Published: June 2024

Abstract
Cytidine diphosphate diacylglycerol (CDP-DAG) is a critical intermediate that is converted to multiple phospholipids in prokaryotes and eukaryotes. In budding yeast, CDP-DAG synthesis from cytidine triphosphate (CTP) and phosphatidic acid (PA) is catalyzed by the membrane-integrated protein Cds1 in the endoplasmic reticulum and the peripheral membrane-bound protein Tam41 in mitochondria. Although a recent study revealed that the fission yeast SpTam41 consists of a nucleotidyltransferase domain and a winged helix domain, forming an active-site pocket for CTP binding between the two domains together with a C-terminal amphipathic helix for membrane association, how CTP and Mg 2+, a most-favoured divalent cation, are accommodated with PA remains obscure. A more recent report by Kimura et al. (J. Biochem. 2022; 171:429–441) solved the crystal structure of FbTam41, a functional ortholog from a Firmicutes bacterium, with CTP-Mg 2+, successfully providing a detailed molecular view of CDP-DAG synthesis. In this commentary, our current understanding of Tam41-mediated reaction is discussed.
A Scoping Review of PTSD and Depression in Adult Burn Patients: A Call for Standardized Screening and Intervention Research
Authors: Wang Sarah , Cannata Brigette , Vallurupalli Medha , Yenikomshian Haig A , Gillenwater Justin , Stoycos Sarah A 
Published: June 2024

Abstract
Despite the growing incidence of burn injuries globally and the advancements in physical recovery, the psychological aspect of burn trauma recovery remains inadequately addressed. This review aims to consolidate existing literature on posttraumatic stress disorder (PTSD) and depression in adult burn survivors, recognizing the need for a holistic approach to burn recovery that encompasses both physical and mental health. The comprehensive analysis of 156 studies revealed significant variations in methodological approaches, leading to challenges in creating standardized protocols for mental health assessment in burn care. Key findings include the identification of a wide range of psychological assessment tools and a substantial research gap in low- and middle-income countries, where the majority of burn injuries occur. Only 7.0% of the studies assessed interventions for PTSD or depression, indicating a lack of focus on treatment modalities. The studies identified demographic factors, patient history, psychosocial factors, burn injury characteristics, and treatment course as risk factors for PTSD and depression postburn injury. The review highlights the need for early screening, intervention, and attention to subjective experiences related to burn injury, as these are strong predictors of long-term psychological distress. It also emphasizes the complexity of addressing psychological distress in burn survivors and the need for more standardized practices in assessing PTSD and depression specific to this population.
Seasonal Dynamics in Burn Profiles: A Comprehensive Retrospective Analysis at the Burn Care Centre, PIMS, Islamabad (2016–2022)
Authors: Qayyum Kashaf , Rehan Muhammad , Arshad Zunera , Iqbal Tariq , Sarwar Muhammad Asad , Mahmood Rabia 
Published: June 2024

Abstract
Seasons have a major impact on the frequency and characteristics of burn injuries; in warmer months, thermal burns from outdoor activities are more common, while in cooler months, incidents involving heating sources and fires are more common. It is essential to comprehend these trends in order to customize safety precautions and awareness initiatives. Studies on the impact of seasonal variations help burn centers allocate resources more effectively in order to prepare for variations in patient volume and severity. Data from January 2016 to December 2022, with an emphasis on burn types excluding nonburn cases, were analyzed retrospectively over a 7-year period at the Burn Care Centre in Pakistan Institute of Medical Sciences, Islamabad. The research examined hospital stays, demographics, burn causes, admissions, total burned surface area, and death rates while dividing the years into winter and summer seasons for analysis. With 4014 admitted patients, the study found that winter admissions increased by 11.007%, with winter admissions accounting for 55.503% of all admissions and summer admissions for 44.496%. The gender distribution stayed the same, with 54.59% of the population being male and 45.99% being female. Hospital stays were longer for summer admissions (16.428) than for winter admissions (11.285). Summertime saw a rise in electric burn cases (307 cases), with a 43 case fatality rate. With 1699 cases, flame burns predominated in the epidemiology of burns, followed by scald burns with 1384 cases. In conclusion, seasonal differences have a substantial impact on burn profiles, with winter seeing a marked rise in occurrences. Men are also more likely to sustain electric burns, particularly in the summer. Effective management and prevention techniques depend on an understanding of these patterns.
Literacy and signing deaf students: a multi-national scoping review
Authors: Dostal Hannah , Scott Jessica , Gediel Ana , Vilhalva Shirley , Gasparin Camila 
Published: June 2024

Abstract
Many literature reviews or other types of reviews (e.g., meta-analyses, scoping reviews) in deaf education research are focused upon primarily or exclusively research that is performed in U.S. contexts or English-speaking contexts only. However, research that is conducted in non-English-speaking, non-U.S. settings that may be more likely to be multilingual, has value for our understanding of how deaf students using multiple languages may develop literacy skills. The objective of this review was to explore the literature on literacy development with deaf learners conducted outside of English-speaking contexts that has been published in English, Portuguese, or Spanish. We identified 13 English-language articles, 9 Portuguese-language articles, and 0 Spanish articles that met inclusion criteria. From these articles, we glean important insights into the reading process, including the teaching of subskills of reading, writing instruction, early literacy experiences, and the potential relationship between signed languages and literacy. We also note the need for multiple, converging sources of evidence and the value of an asset-driven approach to understanding deaf learners.