bluuebunny/crossref_metadata_2025_split huggingface dataset:
OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow
Authors: Xu Gang , Luo Zhenwei , Zhou Ruhong , Wang Qinghua , Ma Jianpeng 
Published: October 2023

Abstract
For refining and designing protein structures, it is essential to have an efficient protein folding and docking framework that generates a protein 3D structure based on given constraints. In this study, we introduce OPUS-Fold3 as a gradient-based, all-atom protein folding and docking framework, which accurately generates 3D protein structures in compliance with specified constraints, such as a potential function as long as it can be expressed as a function of positions of heavy atoms. Our tests show that, for example, OPUS-Fold3 achieves performance comparable to pyRosetta in backbone folding and significantly better in side-chain modeling. Developed using Python and TensorFlow 2.4, OPUS-Fold3 is user-friendly for any source-code level modifications and can be seamlessly combined with other deep learning models, thus facilitating collaboration between the biology and AI communities. The source code of OPUS-Fold3 can be downloaded from http://github.com/OPUS-MaLab/opus_fold3. It is freely available for academic usage.
MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome
Authors: Zhang Quanbao , Cao Lei , Song Hongtao , Lin Kui , Pang Erli 
Published: October 2023

Abstract
Alternative splicing (AS) is an essential post-transcriptional mechanism that regulates many biological processes. However, identifying comprehensive types of AS events without guidance from a reference genome is still a challenge. Here, we proposed a novel method, MkcDBGAS, to identify all seven types of AS events using transcriptome alone, without a reference genome. MkcDBGAS, modeled by full-length transcripts of human and Arabidopsis thaliana, consists of three modules. In the first module, MkcDBGAS, for the first time, uses a colored de Bruijn graph with dynamic- and mixed- kmers to identify bubbles generated by AS with precision higher than 98.17% and detect AS types overlooked by other tools. In the second module, to further classify types of AS, MkcDBGAS added the motifs of exons to construct the feature matrix followed by the XGBoost-based classifier with the accuracy of classification greater than 93.40%, which outperformed other widely used machine learning models and the state-of-the-art methods. Highly scalable, MkcDBGAS performed well when applied to Iso-Seq data of Amborella and transcriptome of mouse. In the third module, MkcDBGAS provides the analysis of differential splicing across multiple biological conditions when RNA-sequencing data is available. MkcDBGAS is the first accurate and scalable method for detecting all seven types of AS events using the transcriptome alone, which will greatly empower the studies of AS in a wider field.
Lineage diversification of the Sky Island treefrog Scinax curicica (Anura, Hylidae) in the Espinhaço Mountain Range
Authors: Santana Diego J , Ragalzi Eric , Koroiva Ricardo , Mângia Sarah , Ceron Karoline , Leite Felipe S F , Shepard Donald B 
Published: October 2023

Abstract
Sky Islands present unique landscapes for organismal evolution because they comprise high mountain peaks separated by low valleys with vastly different environmental conditions. The Espinhaço Mountain Range in eastern Brazil is formed of groups of Sky Islands in the states of Minas Gerais and Bahia. Several phylogeographic studies have discovered strong genetic structure among populations of organisms occupying the campo rupestre (rupestrian fields) in the mountains of the Espinhaço. In this study, we aimed to test the hypothesis of spatio-temporal structuring of populations of Scinax curicica in the campo rupestre of the Espinhaço. We recovered three lineages of S. curicica: one lineage occurs in the north portion of the Espinhaço (North Lineage) in an area called Chapada Diamantina, and other two occur in the south portion of the Espinhaço (South 1 and South 2 Lineages) in Minas Gerais. All three lineages showed stable population sizes through time, probably due to the climatic stability of mountaintop areas, which was supported by ecological niche modelling.
A picture is worth a thousand dollars: a photographic approach to studying colour in anoles
Authors: Jacobs Jake A , Salazar Jhan C , Winchell Kristin M 
Published: October 2023

Abstract
Colours relay information to conspecifics and predators unique to an environment and are shaped by natural selection favouring colours that enable higher fitness. For decades, ecologists have grappled with various methods of quantifying colour. Spectrophotometers offer precise and accurate data, but their high price limits accessibility. Here we test the validity of an accessible method of quantifying colour. We analysed photographs from four species of Anolis lizards from urban and forest habitats. We compared dewlap colour in order to determine if photographic analysis can detect inter- and intraspecific differences with the same power as a spectrophotometer. We hypothesized that photographs would capture colour data comparable to a spectrophotometer within the visible light range, and that habitat divergence would be associated with intraspecific differences in dewlap. We demonstrate, as hypothesized, that photographic colour data are consistent with spectrophotometer data and capable of differentiating dewlap variation within the visible light spectrum. Differences in colour between urban and forest populations were significant for some but not all species, and the part of the colour spectrum that shifted was not consistent across species. Our results support photographic analysis as an alternative for quantifying colour to study both inter- and intraspecific variation in visible colour.
Rise and fall of a continental mesic radiation in Australia: spine evolution, biogeography, and diversification of Cryptandra (Rhamnaceae: Pomaderreae)
Authors: Nge Francis J , Kellermann Jürgen , Biffin Ed , Thiele Kevin R , Waycott Michelle 
Published: October 2023

Abstract
The Australian continent has experienced progressive aridification since the Miocene, spurring recent radiations of arid-adapted lineages and the likely decline of mesic biotic groups. While examples of the former have been relatively well-documented, post-Miocene declines of non-arid sclerophyllous floras are less well understood. Here, we present a well-sampled time-calibrated nuclear phylogeny (140 accessions representing 60/65 species) of an Australian plant genus (Cryptandra Sm.: Rhamnaceae) and using ancestral range reconstructions and diversification analyses, elucidate its evolutionary history through space and time. We used high-throughput sequencing to recover 30 orthologous nuclear loci and BioGeoBEARS to infer ancestral areas. We show that the present-day distribution of Cryptandra can be explained by multiple vicariance events followed by in situ diversification with little exchange between regions. All diversification models show a speciation rate decline in Cryptandra after its radiation in the Miocene (c. 23 Mya). This coincides with aridification episodes across Australia and indicates that diversification of this genus has been negatively affected by the expansion of aridity. We also show that there were no significant differences in diversification rates between spinescent and non-spinescent Cryptandra lineages, suggesting that spinescent lineages may be the legacies of selection from extinct megaherbivores.
Seed morphology of the Eriostemon–Phebalium clade (Rutaceae–Zanthoxyloideae) and implications for systematics
Authors: Choi Bokyung , Duretto Marco F , Hong Suk-Pyo 
Published: October 2023

Abstract
The Eriostemon–Phebalium clade (Rutaceae) includes c. 200 species across 16 genera, and is distributed in Australia (including Tasmania), New Caledonia, New Hebrides, New Zealand, and New Guinea. Phylogenetic analyses based on DNA sequences have consistently shown that the Eriostemon–Phebalium group is robustly monophyletic. However, despite this, taxonomy within the group is still uncertain: relationships between the genera are not well understood, and the genus Philotheca is polyphyletic. Seed morphological characters can be useful in taxonomy in angiosperms, and in this study, 21 seed morphological characters for 29 taxa of all the 16 genera circumscribed in the Eriostemon–Phebalium clade were examined using stereo and scanning electron microscopy. Seed morphological traits such as testa type and hilum were informative for some of the robustly supported clades in molecular phylogenetic studies, and a combination of seed characters could be useful for species identification. This study highlights the potential of seed morphological traits for the systematics.
Dermatoscopic shiny white structures in benign cutaneous tumours
Authors: Lallas Aimilios , Toloza Claudio , Morales Juan Pablo , Santos-Ortiz María Fernanda , Lallas Konstantinos , Nikolaidou Christina , Sakellaropoulou Stella , Papageorgiou Chryssoula , Vakirlis Efstratios , Sotiriou Elena , Apalla Zoe 
Published: October 2023

Abstract
The dermatoscopic characteristics of shiny white structures (SWS) in malignant skin tumours are well described, but data on benign skin neoplasms are scarce. To evaluate the dermatoscopic features of SWS in common benign tumours, we reviewed our database for histopathologically confirmed cases. Dermatoscopic images were evaluated for the presence of any type of SWS. Images with SWS were further analysed for their quantity, distribution and shape. Of 2420 evaluated benign tumours, 357 (14.8%) displayed SWS. The highest frequencies were observed in pyogenic granuloma (n = 62/100; 62%), angioma (n = 63/113; 55.8%) and adnexal tumours (n = 42/84; 50%). The lowest frequency was found in common naevi (n = 16/1032; 1.6%) and solar lentigo (n = 0). The presence of SWS was not associated with sex or anatomical location. SWS were usually diffuse and multiple. SWS may be present in a broad spectrum of benign tumours and therefore they should not be considered as de facto indicators of malignancy.
Polarity and Strategic Competition: A Structural Explanation of Renewed Great Power Rivalry
Authors: Zhang Baohui 
Published: October 2023

Abstract
Strategic competition, or great power competition, has become a new buzz-word in international politics. Yet, few studies have undertaken any systematic examination of what caused its return to the centre stage of international relations. This study hence formulates a parsimonious structural explanation of renewed great power rivalry. Relying on the insights of neorealism and its two structural variants—defensive realism and offensive realism—the study first suggests that current definitions of strategic competition are, due to their emphasis on power competition, overly imbued with offensive realist nuances. However, security competition, which originates in the security dilemma, also underlies strategic competition. Employing neorealism’s polarity perspective, this study then posits that the end of US-led unipolarity and ongoing power deconcentration in the international system are major causes of renewed great power rivalry. While unipolarity harnesses the anarchic effect and compels second-tier major powers to exercise strategic restraint, multipolarity resurrects insecurity and removes disincentives for the aggressive pursuit of power, influence, and status. Ever intensifying security competition and power competition have thus shifted international politics into a new paradigm defined by great power conflict.
Three epochs on estimating the parameter values of thermodynamic Sharpe-Schoolfield-Ikemoto (SSI) model describing the relation of temperature and insect development rate
Authors: Ikemoto Takaya , Kurahashi Issei 
Published: October 2023

Abstract
The SSI model describes the relationship between temperature and development rate of insect based on the laws of thermodynamics. The greatest feature of the SSI model curve is that it defines the “Intrinsic optimum temperature for the development of ectotherms”. However, this model has 8 parameters, it was extremely difficult to estimate the values of these parameters from experimental data. This is because the curve fitting of experimental data yields multiple curves depending on the initial conditions. In the first epoch of estimating parameter values, the difficulties were overcome by clarifying the model and applying all the knowledge gained about the model, but it took several days to determine the model. In the second epoch, the OptimSSI-program, which incorporates a basic optimization function, was developed, making it possible to obtain parameter values instantaneously after inputting experimental data. Although this program mostly runs automatically on a PC, a manual calculation remains to be carried outs so that the obtained model curves do not deviate from Arrhenius’ law. Afterward, a new program was suggested. This new program called DEoptim.sqrt not only incorporates an optimization function available on the internet but also was completely different from OptimSSI-P in terms of the design concept. Users had hoped that this new program would be start of the third epoch; however, when we examined the output values, there were serious problems, and we were back in the state before the first epoch. After all, OptimSSI-P of the second epoch was decided to be more reliable.
Prevalence, risk factors, and optimal way to determine overweight, obesity, and morbid obesity in the first Dutch cohort of 2338 long-term survivors of childhood cancer: a DCCSS-LATER study
Authors: Pluimakers Vincent G , van Atteveld Jenneke E , de Winter Demi T C , Bolier Melissa , Fiocco Marta , Nievelstein Rutger Jan A J , Janssens Geert O R , Bresters Dorine , van der Heiden-van der Loo Margriet , de Vries Andrica C H , Louwerens Marloes , van der Pal Heleen J , Pluijm Saskia M F , Ronckers Cecile M , Versluijs Andrica B , Kremer Leontien C M , Loonen Jacqueline J , van Dulmen-den Broeder Eline , Tissing Wim J E , van Santen Hanneke M , van den Heuvel-Eibrink Marry M , Neggers Sebastian J C M M 
Published: October 2023

Abstract

Background
Overweight and obesity are common challenges among childhood cancer survivors. Overweight may be disguised, as survivors can have normal weight but high fat percentage (fat%) on dual-energy X-ray absorptiometry (DXA). We aimed to assess prevalence, identify determinants and biomarkers, and assess which method captures overweight best, in a nationwide cohort.

Methods
The prevalence of overweight and obesity, primarily defined by body mass index (BMI), was assessed in the DCCSS-LATER cohort of adult survivors treated from 1963-2002, with the LifeLines cohort as reference. The associations between risk factors and overweight metrics were investigated using logistic regression. Additional overweight metrics included DXA fat%, waist circumference (WC), waist/hip ratio (WHR), waist/height ratio (WHtR), and high-molecular-weight (HMW) adiponectin.

Results
A total of 2338 (mean age 35.5 years, follow-up 28.3 years) survivors participated. The overweight prevalence was 46.3% in men and 44.3% in women (obesity 11.2% and 15.9%, morbid obesity 2.4% and 5.4%), with highest rates among brain tumor survivors. Compared to controls, there was no overall increased overweight rate, but this was higher in women &gt; 50 years, morbid obesity in men &gt; 50 years. Overweight at cancer diagnosis (adjusted odds ratio [aOR] = 3.83, 95% CI 2.19-6.69), cranial radiotherapy (aOR = 3.21, 95% CI 1.99-5.18), and growth hormone deficiency (separate model, aOR = 1.61, 95% CI 1.00-2.59) were associated with overweight. Using BMI, WC, WHR, and WHtR, overweight prevalence was similar. Low HMW adiponectin, present in only 4.5% of survivors, was an insensitive overweight marker. Dual-energy X-ray absorptiometry–based classification identified overweight in an additional 30%, particularly after abdominal radiotherapy, total body irradiation, anthracyclines, and platinum.

Conclusions
Overweight occurs in almost half of long-term survivors. There was no overall increased incidence of overweight compared to controls. We identified factors associated with overweight, as well as subgroups of survivors in whom DXA can more reliably assess overweight.
Genotype-phenotype correlations in pseudohypoparathyroidism type 1a patients: a systemic review
Authors: Jiang Siqi , Yang Yi , Song An , Jiang Yue , Jiang Yan , Li Mei , Xia Weibo , Nie Min , Wang Ou , Xing Xiaoping 
Published: October 2023

Abstract

Background
Pseudohypoparathyroidism type 1a (PHP1a) is a rare endocrine disease caused by partial defects of the α subunit of the stimulatory Guanosin triphosphate (GTP) binding protein (Gsα) resulting from maternal GNAS gene variation. The clinical manifestations are related to PTH resistance (hypocalcemia, hyperphosphatemia, and elevated serum intact PTH) in the presence or absence of multihormone resistance, and Albright's hereditary osteodystrophy (AHO).

Objectives
To summarize the molecular genetics results and clinical characteristics as well as to explore the correlations between them.

Methods
Articles pertaining to PHP1a until May, 31, 2021 were reviewed and 527 patients with genetic diagnosis were included in the data analysis. The clinical characteristics and molecular genetics results of these patients were analyzed and compared to explore the correlations between them.

Results
A total of 258 GNAS rare variants (RVs) were identified in 527 patients. The RVs were most commonly found in exons 1 and 7 (17.6% each), with frameshift (36.8%), and missense (31.3%) being the main types of RVs. The median age of onset was 5.0 years old. The most common clinical manifestations were elevation of PTH (86.7%) and AHO (87.5%). Thyroid stimulating hormone resistance was the most common hormone resistance (75.5%) other than PTH resistance. Patients with missense and in-frame RVs had lower incidence rates of the round face (P = .001) and subcutaneous ossifications (P &lt; .001) than those with loss-of-function (non-sense, frameshift, splicing site variants, and large deletions) variants.

Conclusions
This study revealed the correlation between loss-of-function RVs with round faces and subcutaneous ossifications in PHP 1a patients. Further exploration of genotype-phenotype correlations through more standardized and prospective studies with long-term follow-up is necessary.
Hormonal control during infancy and testicular adrenal rest tumor development in males with congenital adrenal hyperplasia: a retrospective multicenter cohort study
Authors: Schröder Mariska A M , Neacşu Mihaela , Adriaansen Bas P H , Sweep Fred C G J , Ahmed S Faisal , Ali Salma R , Bachega Tânia A S S , Baronio Federico , Birkebæk Niels Holtum , de Bruin Christiaan , Bonfig Walter , Bryce Jillian , Clemente Maria , Cools Martine , Elsedfy Heba , Globa Evgenia , Guran Tulay , Güven Ayla , Amr Nermine Hussein , Janus Dominika , Taube Nina Lenherr , Markosyan Renata , Miranda Mirela , Poyrazoğlu Şükran , Rees Aled , Salerno Mariacarolina , Stancampiano Marianna Rita , Vieites Ana , de Vries Liat , Yavas Abali Zehra , Span Paul N , Claahsen-van der Grinten Hedi L 
Published: October 2023

Abstract

Importance
Testicular adrenal rest tumors (TARTs), often found in male patients with congenital adrenal hyperplasia (CAH), are benign lesions causing testicular damage and infertility. We hypothesize that chronically elevated adrenocorticotropic hormone exposure during early life may promote TART development.

Objective
This study aimed to examine the association between commencing adequate glucocorticoid treatment early after birth and TART development.

Design and participants
This retrospective multicenter (n = 22) open cohort study collected longitudinal clinical and biochemical data of the first 4 years of life using the I-CAH registry and included 188 male patients (median age 13 years; interquartile range: 10-17) with 21-hydroxylase deficiency (n = 181) or 11-hydroxylase deficiency (n = 7). All patients underwent at least 1 testicular ultrasound.

Results
TART was detected in 72 (38%) of the patients. Prevalence varied between centers. When adjusted for CAH phenotype, a delayed CAH diagnosis of &gt;1 year, compared with a diagnosis within 1 month of life, was associated with a 2.6 times higher risk of TART diagnosis. TART onset was not predicted by biochemical disease control or bone age advancement in the first 4 years of life, but increased height standard deviation scores at the end of the 4-year study period were associated with a 27% higher risk of TART diagnosis.

Conclusions and relevance
A delayed CAH diagnosis of &gt;1 year vs CAH diagnosis within 1 month after birth was associated with a higher risk of TART development, which may be attributed to poor disease control in early life.
Shared and Distinct Associations of Manual Dexterity and Gross Motor Function With Brain Atrophy
Authors: Dougherty Ryan J , Wang Hang , Gross Alden L , Schrack Jennifer A , Agrawal Yuri , Davatzikos Christos , Cai Yurun , Simonsick Eleanor M , Ferrucci Luigi , Resnick Susan M , Tian Qu 
Published: October 2023

Abstract

Background
Poor motor function is associated with brain atrophy and cognitive impairment. Less is known about the relationship between motor domains and brain atrophy and whether associations are affected by cerebrovascular burden and/or physical activity.

Methods
We analyzed data from 726 Baltimore Longitudinal Study of Aging participants (mean age 70.6 ± 10.1 years, 56% women, 27% Black), 525 of whom had repeat MRI scans over an average of 5.0 ± 2.1 years. Two motor domains, manual dexterity and gross motor, were operationalized as latent variables. Associations between the latent variables and cortical and subcortical brain volumes of interest were examined using latent growth curve modeling, adjusted for demographics, white matter hyperintensities, and physical activity.

Results
Both higher manual dexterity and gross motor function were cross-sectionally associated with smaller ventricular volume and greater white matter volumes in the frontal, parietal, and temporal lobes (all p &lt; .05). Manual dexterity was also cross-sectionally associated with parietal gray matter (B = 0.14; 95% CI: 0.05, 0.23), hippocampus (B = 0.10; 95% CI: 0.01, 0.20), postcentral gyrus (B = 0.11; 95% CI: 0.01, 0.20), and occipital white matter (B = 0.10; 95% CI: 0.01, 0.21) volumes, and gross motor function with temporal gray matter volume (B = 0.16; 95% CI: 0.05, 0.26). Longitudinally, both higher manual dexterity and gross motor function were associated with less temporal white matter and occipital gray matter atrophy (all p &lt; .05). Manual dexterity was also associated with a slower rate of ventricular enlargement (B = −0.17; 95% CI: −0.29, −0.05) and less atrophy of occipital white matter (B = 0.39; 95% CI: 0.04, 0.71).

Conclusions
Among cognitively normal middle- and older-aged adults, manual dexterity and gross motor function exhibited shared as well as distinct associations with brain atrophy over time.