bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling the embryo structure in Bromeliaceae Juss. (Poales): morphological diversity, anatomy and character evolution
Authors: de Carvalho Jordano D T , Leme Elton M C , Ramírez-Morillo Ivón M , Mariath Jorge E A 
Published: December 2024

Abstract

Background and Aims
Recent studies have documented numerous morphoanatomical variations for the seed coat in Bromeliaceae. However, the structural diversity and character evolution of the embryo within this family remain largely unexplored. Given the significance of the embryo in plant diversification, this research aims to investigate the morphology and key anatomical features of Bromeliaceae embryos, providing insights into character evolution, taxonomic applications and reproductive biology.

Methods
We analysed samples of 88 species from 50 genera representing the major lineages of Bromeliaceae, using standard plant microtechniques adapted for seeds. To determine ancestral traits, parsimony and maximum likelihood analyses were performed in a consensus supertree combining previous phylogenies.

Key Results
We identified 14 informative characters, highlighting significant differences among groups, particularly in embryo morphology, differentiation and anatomical traits. Our analysis revealed that undifferentiated embryos with a vestigial cotyledonary hyperphyll are plesiomorphic in Bromeliaceae. They have evolved multiple times into rudimentary or well-differentiated embryos, the latter exhibiting intermediate or large sizes and diverse cotyledonary hyperphyll morphologies. The cotyledonary hypophyll varies in sheath lobes and slit morphologies and is curved or expanded exclusively in representatives of Bromelioideae. Likewise, several patterns of hypocotyl/radicle constriction are unique to Tillandsioideae and plesiomorphic for this clade. Although rudimentary embryos exhibit simpler and more uniform anatomy, they are distinct from undifferentiated embryos, which lack defined organs and internal tissues. In contrast, well-differentiated embryos possess more complex anatomical structures, including a multi-layered shoot apical meristem and root cap, a broad cotyledonary sheath and often leaf primordia, the last of which have evolved independently several times only in large embryos.

Conclusions
Our findings reveal a previously unknown morphological diversity for embryos in Bromeliaceae, enhancing our understanding of the morphological evolution of their major lineages. In addition, our findings introduce new informative characters for the systematics of the family and broaden our understanding of the reproductive biology of Bromeliaceae.
Repeat competition and ecological shifts drive the evolution of the mobilome in Rhynchospora Vahl (Cyperaceae), the holocentric beaksedges
Authors: Costa Lucas , Castro Natália , Buddenhagen Christopher E , Marques André , Pedrosa-Harand Andrea , Souza Gustavo 
Published: December 2024

Abstract

Background and Aims
Genomic changes triggered by polyploidy, chromosomal rearrangements and/ or environmental stress are among factors that affect the activity of mobile elements, particularly long terminal repeat retrotransposons (LTR-RTs) and DNA transposons. Because these elements can proliferate and move throughout host genomes, altering the genetic, epigenetic and nucleotypic landscape, they have been recognized as a relevant evolutionary force. Beaksedges (Rhynchospora) stand out for their wide cosmopolitan distribution, high diversity (~400 species) and holocentric chromosomes related to high karyotypic diversity and a centromere-specific satDNA, Tyba. This makes the genus an interesting model to investigate the interactions between repetitive elements, phylogenetic relationships and ecological variables.

Methods
Here we used comparative phylogenetic methods to investigate the forces driving the evolution of the entire set of mobile elements (mobilome) in the holocentric genus Rhynchospora. We statistically tested the impact of phylogenetic relationships, abundance of holocentromeric satDNA Tyba, diversity of repeatome composition, ecological variables and chromosome number in mobile element diversification.

Key Results
Tyba abundance was found to be inversely correlated with LTR-RT content. Decrease of LTR abundance and diversity was also related to increase in chromosome number (likely due to fission events) and colonization of dry environments in the northern hemisphere. In contrast, we found constant LTR insertions throughout time in species with lower chromosome numbers in rainier environments in South America. A multivariate model showed that different traits drive LTR abundance, especially repeat diversity and Tyba abundance. Other mobile elements, such as non-LTR RTs and DNA transposons, had insufficient abundance to be included in our models.

Conclusions
Our findings suggest that LTR evolution is strongly impacted by the holocentric characteristics of Rhynchospora chromosomes, correlating with species diversification and biome shifts, and supporting a holokinetic drive model of evolution and a competitive scenario with Tyba. Altogether, our results present evidence of multi-trait influence on LTR-RT dynamics and provide a broader understanding of transposable element evolution in a macroevolutionary context.
Examining the Discrepancy between Subjective Cognitive Complaints and Processing Speed Performance in Military Personnel with Traumatic Brain Injury
Authors: Jackson Daija A , Lippa Sara M , Brickell Tracey A , French Louis M , Lange Rael T 
Published: December 2024

Abstract

Objective
To examine correlates of the discrepancy between subjective cognitive complaints and processing speed performance in a sample of military personnel with and without traumatic brain injury (TBI).

Method
About 235 U.S. military service members (31 noninjured controls [NIC], 69 injured controls [IC], 70 uncomplicated mild TBI [mTBI], and 65 complicated mild/moderate/severe TBI [sTBI]) prospectively enrolled in a longitudinal TBI study completed neuropsychological testing, performance validity tests, and self-report measures of cognitive complaints and psychological symptoms. Service members were categorized as “Accurate Estimators,” “Underestimators,” and “Overestimators” based on discrepancies between their subjective cognition and processing speed performance.

Results
The NIC group was less likely to underestimate their cognitive abilities than the mTBI group (p &lt; .05). Discrepancy groups significantly differed in processing speed scores (p &lt; .001), with underestimators demonstrating the best objective cognitive performance. Spearman correlations revealed significant positive correlations between unadjusted discrepancy scores and psychological symptoms in the NIC, IC, and sTBI groups (ps &lt; 0.05) but not the mTBI group (ps &gt; 0.05). In contrast, discrepancy scores adjusted for premorbid intelligence were consistently and positively correlated with psychological symptoms across all injury groups (ps &lt; 0.05).

Conclusions
Findings suggest that mTBI injuries may increase the likelihood of a patient underestimating their cognitive performance. Further, premorbid cognitive functioning is an important factor in evaluating discrepancies in self-reported cognitive complaints and processing speed performance.
DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering
Authors: Luo Junwei , Wang Jiaojiao , Wei Jingjing , Yan Chaokun , Luo Huimin 
Published: December 2024

Abstract
Gene polymorphism originates from single-nucleotide polymorphisms (SNPs), and the analysis and study of SNPs are of great significance in the field of biogenetics. The haplotype, which consists of the sequence of SNP loci, carries more genetic information than a single SNP. Haplotype assembly plays a significant role in understanding gene function, diagnosing complex diseases, and pinpointing species genes. We propose a novel method, DeepHapNet, for haplotype assembly through the clustering of reads and learning correlations between read pairs. We employ a sequence model called Retentive Network (RetNet), which utilizes a multiscale retention mechanism to extract read features and learn the global relationships among them. Based on the feature representation of reads learned from the RetNet model, the clustering process of reads is implemented using the SpectralNet model, and, finally, haplotypes are constructed based on the read clusters. Experiments with simulated and real datasets show that the method performs well in the haplotype assembly problem of diploid and polyploid based on either long or short reads. The code implementation of DeepHapNet and the processing scripts for experimental data are publicly available at https://github.com/wjj6666/DeepHapNet.
Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison
Authors: Heylen Dries , Pusparum Murih , Kuliesius Jurgis , Wilson Jim , Park Young-Chan , Jamiołkowski Jacek , D’Onofrio Valentino , Valkenborg Dirk , Aerts Jan , Ertaylan Gökhan , Hooyberghs Jef 
Published: December 2024

Abstract
Proteomics stands as the crucial link between genomics and human diseases. Quantitative proteomics provides detailed insights into protein levels, enabling differentiation between distinct phenotypes. OLINK, a biotechnology company from Uppsala, Sweden, offers a targeted, affinity-based protein measurement method called Target 96, which has become prominent in the field of proteomics. The SCALLOP consortium, for instance, contains data from over 70.000 individuals across 45 independent cohort studies, all sampled by OLINK. However, when independent cohorts want to collaborate and quantitatively compare their target 96 protein values, it is currently advised to include 'identical biological bridging' samples in each sampling run to perform a reference sample normalization, correcting technical variations across measurements. Such a ‘biological bridging sample’ approach requires each of the involved cohorts to resend their biological bridging samples to OLINK to run them all together, which is logistically challenging, costly and time-consuming. Hence alternatives are searched and an evaluation of the current state of the art exposes the need for a more robust method that allows all OLINK Target 96 studies to compare proteomics data accurately and cost-efficiently. To meet these goals we developed the Synthetic Plasma Pool Cohort Correction, the ‘SPOC correction’ approach, based on the use of an OLINK-composed synthetic plasma sample. The method can easily be implemented in a federated data-sharing context which is illustrated on a sepsis use case.
Foundational artificial intelligence models and modern medical practice
Authors: Medetalibeyoglu Alpay , Velichko Yury S , Hart Eric M , Bagci Ulas 
Published: December 2024

Abstract
Our opinion piece pays homage to the evolution of medical practices, tracing back to the era of Hippocrates, through significant historical milestones, and drawing parallels with the principles underpinning foundational artificial intelligence (AI) models. It emphasizes the shared ethos of both domains: a commitment to comprehensive care that values diverse data integration and individualized patient treatment. The excitement surrounding foundation models in medical imaging is understandable. However, a critical and cautious approach is crucial before widespread adoption. By addressing the present 4 major limitations (ie, data bias and generalizability, interpretability of AI models, data scarcity and diversity, and computational resources and infrastructure) and fostering a culture of rigorous research, we can unlock the true potential of these models and revolutionize medical care. This critique (opinion) paper highlights the need for a more measured approach in the field of foundation AI models for medicine in general and for medical imaging in particular. It emphasizes the importance of tackling core challenges before rushing toward clinical applications. By focusing on robust methodologies and addressing limitations, researchers can ensure the development of truly impactful and trustworthy models for the betterment of healthcare.
Definition of a disability weight for human exposure to ionizing radiation and its application to the justification of medical exposure
Authors: Kotre Colin John 
Published: December 2024

Abstract

Objectives
To establish a link between radiation dosimetry and disability-adjusted life-years (DALY) with the aim of quantifying the justification of medical exposures.

Methods
The health detriment, defined as lifetime loss of DALY at age of exposure to ionizing radiation for a US-European population was calculated. A simple model of the relationship was fitted to the results. Apart from in late life within the latency period for radiation-induced cancers, most of the relationship can be adequately fitted to a straight line of negative gradient. The gradient of this line corresponds to a loss of DALY per year following exposure to radiation and is therefore equivalent to a disability weight (DW) used in the calculation of DALY.

Results
Radiation dose-dependent DWs for radiation exposure to a US-European population are estimated as 0.020 DALY/yr/Sv for males and 0.022 DALY/yr/Sv for females.

Conclusions
By comparing a range of 66 radiological examinations in terms of the DWs of the disease or injury states with the DWs resulting from the associated radiological exposures, it is demonstrated graphically that the resulting benefit is far greater than the detriment in every case.

Advances in knowledge
The definition of a DW for ionizing radiation, proportional to effective dose as currently defined, can link radiation exposure to the existing large body of data on the DALY burden and DWs for a wide range of diseases and injuries, providing a means for the quantitative justification of the benefit-detriment balance of medical exposures.
The challenge of scaling-up social work innovations: A case study of Shared Lives schemes in England
Authors: Purcell Carl , Manthorpe Jill , Malley Juliette 
Published: December 2024

Abstract
Innovation is routinely presented as a response to pressure on public services. This article considers the development of Shared Lives (SL) schemes in English adult social care (ASC), a model of care that has been consistently promoted as innovative. SL seeks to replicate ‘ordinary family life’ for adults who need support. Evidence of positive outcomes for people supported, and of cost-effectiveness compared to other models, has attracted the attention of national policymakers and local authority (LA) ASC leaders. Most LAs now operate or commission a SL scheme. Despite this wide ‘spread’, SL remains a very small model that has not yet been ‘scaled-up’ to the extent that many have hoped. Drawing on interviews with fifty people involved in SL, including from four contrasting local schemes in 2021–2023, we highlight four interconnected sets of ‘organisational capabilities’ and resources needed for schemes to grow: (1) collaborative working with social workers; (2) leadership at different levels; (3) mechanisms to harness knowledge and evidence; and (4) investment in the workforce of scheme staff and carers. We propose these factors help schemes become locally embedded in communities. However, our study also highlights the fragility of the model to socio-economic changes and social work practice imperatives.
Global prevalence of mental health comorbidity in patients with acne: an analysis of trends from 1961 to 2023
Authors: Chen Yiran , Sun Suting , Yang Han , Fei Xiaoya , Zhang Ying , Song Jiankun , Ru Yi , Zhao Hang , Luo Ying , Kuai Le , Luo Yue , Li Bin , Xie Mengji , Fan Bin , Ding Xiaojie 
Published: December 2024

Abstract

Background
Patients with acne increasingly face mental health challenges such as anxiety, depression and suicidal thoughts. However, no global systematic analysis exists on this topic.

Objectives
To examine the prevalence of mental disorders – specifically, anxiety, depression and suicidal thoughts – among patients with acne.

Methods
An exhaustive search of six databases was conducted up to May 2023. Data analysis was performed using Python and Stata MP 17, including subgroup evaluations, metaregression and sensitivity analyses.

Results
Forty-three studies were analysed. The findings indicate that depression, anxiety and suicidal thoughts in patients with acne are prevalent at rates of 22%, 29% and 12%, respectively. Rates of depression were highest in Asia at 42%, led by India (53%) and Saudi Arabia (51%). Anxiety was also most common in Asia, at 45%, notably in Singapore (60%) and Iran (58%). Suicidal thoughts were highest in Oceania, specifically New Zealand at 24%. The study is limited by the inclusion of only Chinese- and English-language research, potentially introducing selection bias.

Conclusions
The results of this study highlight the incidence of mental health disorders coexisting with acne. This study may help to foster greater understanding and awareness among both medical professionals and patients regarding the psychological complexities tied to acne.
Bridging the Gap: Unveiling the Potential of Tanzania’s SMEs through VAT Insights
Authors: Ebrahim Amina , Castillo Sebastián , Leyaro Vincent , Swema Ezekiel , Haule Oswald 
Published: December 2024

Abstract
The collection of value added tax (VAT) is essential for achieving domestic revenue objectives, yet VAT gap estimation is rarely performed in developing countries. This study utilizes innovative tax declaration and audit data to estimate VAT misreporting in Tanzania, applying a machine learning approach to predict evasion in unaudited firms and periods. We measure the underreporting component of the compliance gap, quantifying potential revenue losses due to inaccurate reporting. Our findings indicate that firms often avoid excessive audits, leading to increased evasion, with those firms showing the largest VAT gaps. We estimate a 62% VAT gap among small and medium-sized enterprises in Tanzania. Finally, we present a cost-benefit ratio, suggesting that while auditing sectors with large VAT gaps is cost-effective, those contributing significantly to the overall VAT gap should also be prioritized for revenue generation. (JEL codes: H25, H26, and H32)
Diagnostic Accuracy of Chest X-ray Computer-Aided Detection Software for Detection of Prevalent and Incident Tuberculosis in Household Contacts
Authors: Macpherson Liana , Kik Sandra V , Quartagno Matteo , Lakay Francisco , Jaftha Marche , Yende Nombuso , Galant Shireen , Aziz Saalikha , Daroowala Remy , Court Richard , Taliep Arshad , Serole Keboile , Goliath Rene T , Davies Nashreen Omar , Jackson Amanda , Douglass Emily , Sossen Bianca , Mukasa Sandra , Thienemann Friedrich , Song Taeksun , Ruhwald Morten , Wilkinson Robert J , Coussens Anna K , Esmail Hanif ,   Imaging of TB Household Contacts Group, Barry Clifton E , Ellner Jerrold J , Flynn JoAnne L , Heinsohn Torben , Horsburgh C Robert , Jacobson Karen R , Malherbe Stephanus T , Salgame Padmini , Sheerin Dylan , Streicher Elizabeth , Tlala Mpho , Via Laura E , Walzl Gerhard , Warren Robin , Warwick James 
Published: December 2024

Abstract

Background
World Health Organization (WHO) tuberculosis (TB) screening guidelines recommend computer-aided detection (CAD) software for chest radiograph (CXR) interpretation. However, studies evaluating their diagnostic and prognostic accuracy are limited.

Methods
We conducted a prospective cohort study of household contacts of rifampicin-resistant TB in South Africa. Participants underwent baseline CXR and sputum investigation (routine [single spontaneous] and enhanced [additionally 2–3 induced]) for prevalent TB and follow-up for incident TB. Three CXR-CAD software products (CAD4TBv7.0, qXRv3.0.0, and Lunit INSIGHT v3.1.4.111) were compared. We evaluated their performance to detect routine and enhanced prevalent and incident TB, comparing performance with blood tests (Xpert MTB host-response, erythrocyte sedimentation rate, C-reactive protein, QuantiFERON) in a subgroup.

Results
483 participants were followed up for 4.6 years (median). There were 23 prevalent (7 routinely diagnosed) and 38 incident TB cases. The AUC ROCs (95% CIs) to identify prevalent TB for CAD4TBv7.0, qXRv3.0.0, and Lunit INSIGHT v3.1.4.111 were .87 (.77–.96), .88 (.79–.97), and .91 (.83–.99), respectively. More than 30% with scores above recommended CAD thresholds who were bacteriologically negative on routine baseline sputum were subsequently diagnosed by enhanced sputum investigation or during follow-up. The AUC performance of baseline CAD to identify incident cases ranged between .60 and .65. Diagnostic performance of CAD for prevalent TB was superior to blood testing.

Conclusions
Our findings suggest that the potential of CAD-CXR screening for TB is not maximized as a high proportion of those above current thresholds, but with a negative routine confirmatory sputum, have true TB disease that may benefit intervention.
Management, Outcomes, and Predictors of Mortality of Cryptococcus Infection in Patients Without Human Immunodeficiency Virus: A Multicenter Study in 46 Hospitals in Australia and New Zealand
Authors: Coussement Julien , Heath Christopher H , Roberts Matthew B , Lane Rebekah J , Spelman Tim , Smibert Olivia C , Longhitano Anthony , Morrissey C Orla , Nield Blake , Tripathy Monica , Davis Joshua S , Kennedy Karina J , Lynar Sarah A , Crawford Lucy C , Crawford Simeon J , Smith Benjamin J , Gador-Whyte Andrew P , Haywood Rose , Mahony Andrew A , Howard Julia C , Walls Genevieve B , O’Kane Gabrielle M , Broom Matthew T , Keighley Caitlin L , Bupha-Intr Olivia , Cooley Louise , O’Hern Jennifer A , Jackson Justin D , Morris Arthur J , Bartolo Caroline , Tramontana Adrian R , Grimwade Katherine C , Au Yeung Victor , Chean Roy , Woolnough Emily , Teh Benjamin W , Slavin Monica A , Chen Sharon C A ,   the Australian and New Zealand Study Group for Cryptococcosis in Patients Without HIV Infection, Alcorn Kylie , Beardsley Justin , Bloch Aaron , Crowe Amy , Doyle Wendy , England Michelle , Griffin David , Hamilton Kate , Korman Tony M , Madigan Victoria , McGann Hugh , Pratt William , Sparham Sarah , Van Hal Sebastiaan , Waters Prue , Williams Eloise 
Published: December 2024

Abstract

Background
Limited data exist regarding outcomes of cryptococcosis in patients without human immunodeficiency virus (HIV), and few studies have compared outcomes of Cryptococcus gattii versus Cryptococcus neoformans infection.

Methods
We conducted a retrospective study in 46 Australian and New Zealand hospitals to determine the outcomes of cryptococcosis in patients without HIV diagnosed between 2015 and 2019 and compared outcomes of C. gattii versus C. neoformans infections. Multivariable analysis identified predictors of mortality within 1 year.

Results
Of 426 patients, 1-year all-cause mortality was 21%. Cryptococcus gattii infection was associated with lower mortality than C. neoformans (adjusted odds ratio [OR], 0.47; 95% confidence interval [CI], .23–.95), while severe neurological symptoms at presentation were the strongest predictor of death (adjusted OR, 8.46; 95% CI, 2.99–23.98). Almost all (99.5%) patients with central nervous system (CNS) infection received induction antifungal therapy versus 27.7% with isolated pulmonary cryptococcosis. The most common regimen in CNS disease was liposomal amphotericin B with flucytosine (93.8%; mean duration, 31 ± 13 days). Among patients with CNS cryptococcosis, C. gattii infection was associated with higher risk of immune reconstitution inflammatory response (C-IRIS) than C. neoformans (21% versus 3%, P &lt; .001). Nineteen patients received amphotericin B-based re-induction therapy for suspected relapse, but none had microbiological relapse. Serum cryptococcal antigen positivity and lung imaging abnormalities resolved slowly (resolution at 1 year in 25% and 34% of patients, respectively).

Conclusions
Compared with C. neoformans, C. gattii infection demonstrated lower mortality but higher C-IRIS risk in CNS infection. Severe neurological symptoms were the strongest predictor of mortality.