bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatocellular adenoma update: diagnosis, molecular classification, and clinical course
Authors: Poetter-Lang Sarah , Ba-Ssalamah Ahmed , Bastati Nina , Ba-Ssalamah Sami A , Hodge Jacqueline C , Brancatelli Giuseppe , Paradis Valérie , Vilgrain Valérie 
Published: September 2024

Abstract
Hepatocellular adenomas (HCA) are acquired focal liver lesions, that occur mainly in young-to-middle-aged women who are on long-term estrogen-containing contraceptives or young men after prolonged use of anabolic steroids. Furthermore, distinct underlying diseases, such as obesity, metabolic dysfunction-associated steatotic liver disease, glycogen storage disease, etc. are considered risk factors. The 2017 Bordeaux classification, in particular Nault et al, divided HCAs into eight subtypes according to their pheno- and genotypic characteristics. This includes HCAs with hepatocyte-nuclear-factor (HNF1-alpha mutation), HCAs with β-catenin mutation, and HCAs without either of these genetic mutations, which are further subdivided into HCAs with and without inflammatory cells. HCAs should no longer be classified as purely benign without histologic workup since three of the eight subtypes are considered high-risk lesions, requiring adequate management: malignant transformation of the pure (ßex3-HCA) and mixed inflammatory/β-catenin exon 3 (ßex3-IHCA) adenomas, as well as potential bleeding of the sonic hedgehog HCA and pure (ßex7/8-HCA) and mixed inflammatory/β-catenin exon 7/8 (ßex7/8-IHCA). Elective surgery is recommended for any HCA in a male, or for any HCA exceeding 5 cm. Although MRI can classify up to 80% of adenomas, if findings are equivocal, biopsy remains the reference standard for adenoma subtype.
Risk of metachronous neoplasia in early-onset colorectal cancer: meta-analysis
Authors: Pellino Gianluca , Fuschillo Giacomo , González-Sarmiento Rogelio , Martí-Gallostra Marc , Selvaggi Francesco , Espín-Basany Eloy , Perea Jose 
Published: September 2024

Abstract

Background
Metachronous colorectal cancer refers to patients developing a second colorectal neoplasia diagnosed at least 6 months after the initial cancer diagnosis, excluding recurrence. The aim of this systematic review is to assess the incidence of metachronous colorectal cancer in early-onset colorectal cancer (defined as age at diagnosis of less than 50 years) and to identify risk factors.

Methods
This is a systematic review and meta-analysis performed following the PRISMA statement and registered on PROSPERO. The literature search was conducted in PubMed and Embase. Only studies involving patients with early-onset colorectal cancer (less than 50 years old) providing data on metachronous colorectal cancer were included in the analysis. The primary endpoint was the risk of metachronous colorectal cancer in patients with early-onset colorectal cancer. Secondary endpoints were association with Lynch syndrome, family history and microsatellite instability.

Results
Sixteen studies met the inclusion criteria. The incidence of metachronous colorectal cancer was 2.6% (95% c.i. 2.287–3.007). The risk of developing metachronous colorectal cancer in early-onset colorectal cancer versus non-early-onset colorectal cancer patients demonstrated an OR of 0.93 (95% c.i. 0.760–1.141). The incidence of metachronous colorectal cancer in patients with Lynch syndrome was 18.43% (95% c.i. 15.396–21.780), and in patients with family history 10.52% (95% c.i. 5.555–17.659). The proportion of metachronous colorectal cancer tumours in the microsatellite instability population was 19.7% (95% c.i. 13.583–27.2422).

Conclusion
The risk of metachronous colorectal cancer in patients with early-onset colorectal cancer is comparable to those with advanced age, but it is higher in patients with Lynch syndrome, family history and microsatellite instability. This meta-analysis demonstrates the need to personalize the management of patients with early-onset colorectal cancer according to their risk factors.
Neurophysiological patterns reflecting vulnerability to delirium subtypes: a resting-state EEG and event-related potential study
Authors: Boord Monique S , Feuerriegel Daniel , Coussens Scott W , Davis Daniel H J , Psaltis Peter J , Garrido Marta I , Bourke Alice , Keage Hannah A D 
Published: September 2024

Abstract
Delirium is a common and acute neurocognitive disorder in older adults associated with increased risk of dementia and death. Understanding the interaction between brain vulnerability and acute stressors is key to delirium pathophysiology, but the neurophysiology of delirium vulnerability is not well defined. This study aimed to identify pre-operative resting-state EEG and event-related potential markers of incident delirium and its subtypes in older adults undergoing elective cardiac procedures. This prospective observational study included 58 older participants (mean age = 75.6 years, SD = 7.1; 46 male/12 female); COVID-19 restrictions limited recruitment. Baseline assessments were conducted in the weeks before elective cardiac procedures and included a 4-min resting-state EEG recording (2-min eyes open and 2-min eyes closed), a 5-min frequency auditory oddball paradigm recording, and cognitive and depression examinations. Periodic peak power, peak frequency and bandwidth measures, and aperiodic offsets and exponents were derived from resting-state EEG data. Event-related potentials were measured as mean component amplitudes (first positive component, first negative component, early third positive component, and mismatch negativity) following standard and deviant auditory stimuli. Incident delirium occurred in 21 participants: 10 hypoactive, 6 mixed, and 5 hyperactive. Incident hyperactive delirium was associated with higher pre-operative eyes open (P = 0.045, d = 1.0) and closed (P = 0.036, d = 1.0) aperiodic offsets. Incident mixed delirium was associated with significantly larger pre-operative first positive component amplitudes to deviants (P = 0.037, d = 1.0) and larger third positive component amplitudes to standards (P = 0.025, d = 1.0) and deviants (P = 0.041, d = 0.9). Other statistically non-significant but moderate-to-large effects were observed in relation to all subtypes. We report evidence of neurophysiological markers of delirium risk weeks prior to elective cardiac procedures in older adults. Despite being underpowered due to COVID-19–related recruitment impacts, these findings indicate pre-operative dysfunction in neural excitation/inhibition balance associated with different delirium subtypes and warrant further investigation on a larger scale.
The impact of severe nephrotic syndrome on thyroid function, nutrition and coagulation
Authors: Matyjek Anna , Niemczyk Stanisław , Literacki Sławomir , Fendler Wojciech , Rozmysłowicz Tomasz , Kronbichler Andreas 
Published: September 2024

ABSTRACT

Background
Nephrotic syndrome (NS) is characterized by urinary loss of proteins, including hormones and their carrier proteins, potentially resulting in endocrine disorders. This study aimed to assess thyroid dysfunction frequency and potential implications in NS.

Methods
In this case–control study, patients with severe NS (serum albumin ≤2.5 g/dl) and controls without proteinuria were evaluated for thyroid, haemostatic and nutritional parameters, including body composition.

Results
A total of 42 nephrotic and 40 non-proteinuric patients were enrolled. The NS group showed higher thyroid-stimulating hormone and lower free hormones, corresponding to a higher frequency of both euthyroid sick syndrome {ESS; 36% versus 5%; odds ratio [OR] 10.6 [95% confidence interval (CI) 2.2–50.0]} and hypothyroidism [31% versus 5%; OR 8.5 (95% CI 1.8–40.7)] compared with the control group. Levothyroxine supplementation was required for 11 NS patients (26% of the NS group). In addition, compared with control individuals, NS patients exhibited lower lean tissue mass and a trend towards hypercoagulability, which was evidenced by higher levels of most coagulation factors and fibrinolysis inhibitors, and reduced endogenous anticoagulants activities. Furthermore, NS patients with ESS presented with a 10.4 kg (95% CI −18.68 to −2.12) lower lean tissue mass. Those with hypothyroidism had significantly reduced activity of coagulation factor X [by −30% (95% CI −47 to −13)] and protein S [by −27% (95% CI −41 to −13)] compared with euthyroid NS individuals.

Conclusions
Thyroid dysfunction is common in severe NS, often necessitating levothyroxine supplementation, which supports routine thyroid workup. A potential link between thyroid, nutritional and coagulation disorders in NS requires further investigation.
CuPCA: a web server for pan-cancer association analysis of large-scale cuproptosis-related genes
Authors: Xu Yishu , Ma Zhenshu , Wang Yajie , Zhang Long , Ye Jiaming , Chen Yuan , Yuan Zhengrong 
Published: September 2024

Abstract
Copper-induced cell death is a novel mechanism of cell death, which is defined as cuproptosis. The increasing level of copper can produce toxicity in cells and may cause the occurrence of cell death. Several previous studies have proved that cuproptosis has a tight association with various cancers. Thus, the discovery of relationships between cuproptosis-related genes (CRGs) and human cancers is of great importance. Pan-cancer analysis can efficiently help researchers find out the relationship between multiple cancers and target genes precisely and make various prognostic analyses on cancers and cancer patients. Pan-cancer web servers can provide researchers with direct results of pan-cancer prognostic analyses, which can greatly improve the efficiency of their work. However, to date, no web server provides pan-cancer analysis about CRGs. Therefore, we introduce the cuproptosis pan-cancer analysis database (CuPCA), the first database for various analysis results of CRGs through 33 cancer types. CuPCA is a user-friendly resource for cancer researchers to gain various prognostic analyses between cuproptosis and cancers. It provides single CRG pan-cancer analysis, multi-CRGs pan-cancer analysis, multi-CRlncRNA pan-cancer analysis, and mRNA–circRNA–lncRNA conjoint analysis. These analysis results can not only indicate the relationship between cancers and cuproptosis at both gene level and protein level, but also predict the conditions of different cancer patients, which include their clinical condition, survival condition, and their immunological condition. CuPCA procures the delivery of analyzed data to end users, which improves the efficiency of wide research as well as releases the value of data resources.
Database URL: http://cupca.cn/
Gene expression profiling of Cacopsylla pyricola (Hemiptera: Psyllidae) infected with Ca. Phytoplasma pyri (Acholeplasmatales: Acholeplasmataceae)
reveals candidate effectors and mechanisms of infection
Authors: Easterling Katherine A , Marshall Adrian T , Pitino Marco , Walker William B , Cooper W Rodney 
Published: September 2024

Abstract
Phytoplasmas can negatively or positively alter vector host fitness. “Candidatus Phytoplasma pyri,” is the causal agent of pear decline in commercial pear (Pyrus communis L.; Rosales: Rosaceae) and peach yellow leafroll in peach [Prunus persica (L.); Rosaceae]. This plant pathogen is transmitted by several species of pear psyllids (Cacopsylla spp. Hemiptera: Psyllidae). We sought to explore the relationship between the pear decline phytoplasma and its US vector, Cacopsylla pyricola (Förster), at the molecular genetic level through transcriptomic analysis using RNA-sequencing methodology. We also focused on phytoplasma and insect effectors, which are secreted proteins that can modulate interactions within a pathosystem. In this study, we identified 30 differentially expressed genes, 14 candidate insect effector genes, and 8 Ca. Phytoplasma pyri candidate effectors. Two strains of Ca. Phytoplasma pyri were identified based on immunodominant membrane protein sequence analysis from C. pyricola collected in the Pacific Northwest agricultural region. Here, we present a first genetic look at the pear decline pathosystem and report gene candidates for further exploration of infection mechanisms and potential tools for integrated pest management.
‘This Infamous, Scandalous, Headless Insurrection’: The Attack on William Laud and Lambeth Palace, May 1640, Revisited
Authors: Walter John 
Published: September 2024

Abstract
This article offers a re-evaluation of the attack on Lambeth Palace in May 1640. Reconstructing the full extent of crowd actions and placing them in the context of a tradition of self-activating street politics, it emphasises the political nature of the crowd’s actions and the evidence this provides of key concepts in popular political thinking. The crowd, with London apprentices at its core, articulated the popular belief in the role of parliament as the people’s protector and claimed a legitimate agency in seeking to remove evil counsel. The Lambeth attack was triggered by and in turn triggered a litter of libels. The libels—scribal in form, anonymously authored and publicly posted—asserted a popular right to defend the commonwealth. The apprentices’ role in urban life gave them a claim to a political identity and authority in the Lambeth attack which helps to explain the significant part they were to play, and to be invited to play by competing political parties, in print and on the streets, in the politics of the English revolution. The article emphasises (and then qualifies) the severity of the royal government’s revenge, explaining this discrepancy in terms of the balance of power between royal government and popular politics in London in 1640. Examining how political violence came close to the court and to the royal family, the article assesses the impact on Charles I’s kingship. It suggests that the Lambeth attack was of greater consequence than has hitherto been allowed for the fate of Charles I.
Digital analyses of Bolton tooth size ratios and their association to gender, angle class, and other occlusal traits: a study using a partially automated digital 3D model analysis
Authors: Vorloeper Julia , Coenen Franziska A , Lang Norbert A , Niederau Christian , Knaup Isabel , Craveiro Rogerio B , Wolf Michael 
Published: September 2024

Abstract

Background
This study aims to verify Bolton’s values for tooth size ratios and to evaluate possible relationships to different occlusal traits using precise digital measurement methods.

Materials and methods
Including 1000 consecutively selected patients from three study centres a digital, partially automated model analysis was performed utilizing the software OnyxCeph. The measurements comprised tooth width for calculation of anterior (AR) and overall ratio (OR) as a percentage, arch width, length, perimeter, overjet, overbite, space analysis in millimetre and the assessment of the angle classification.

Results
AR and OR were significantly increased compared to Bolton’s ratios of 77.2% (AR) and 91.3% (OR). In the gender comparison, male patients showed larger tooth size ratios, especially in the OR. Patients with Angle Class II/1 and II/2 had smaller tooth size ratios than patients with Angle Class III and I. Thus, patients with Angle Class II/1 had the largest tooth diameters in all maxillary teeth and with Angle Class II/2 the smallest tooth sizes in the mandible. The largest tooth widths in the lower jaw were observed in the Angle Class III patient group. Furthermore, a negative correlation from AR/OR to overjet, overbite, and available space in lower jaw as well as a positive correlation to available space in upper jaw was detected.

Conclusions
There is a clear correlation between the tooth size ratios and the present dysgnathia as well as other orthodontically relevant occlusal traits. This prior knowledge about our patients is extremely important to create an individualized treatment plan and enable sufficient occlusion. To achieve a functionally good occlusion with correct overjet and overbite, it is essential that the maxillary and mandibular teeth are proportional in size. Any deviation from the ideal patient in terms of tooth size, number, shape, or arch must be considered in the pre-therapeutic treatment plan in combination with the existing dysgnathia in order to be able to achieve a stable anterior and posterior occlusion with appropriate adjustments to the therapy post-therapeutically.
Plasma levels of polyols erythritol, mannitol, and sorbitol and incident coronary heart disease among women
Authors: Heianza Yoriko , Sun Qi , Wang Xuan , Tiwari Saumya , Watrous Jeramie D , Rexrode Kathryn M , Alotaibi Mona , Jain Mohit , Mora Samia , Willett Walter C , Qi Lu , Manson JoAnn E 
Published: September 2024

Abstract

Aims
Erythritol, a sugar alcohol (polyol), has recently been linked to the risk of major adverse cardiovascular events. We investigated whether plasma erythritol and other polyols (mannitol/sorbitol) were associated with the risk of incident coronary heart disease (CHD).

Methods and results
This prospective nested case–control study included 762 incident cases of CHD and 762 controls from the Nurses’ Health Study. Plasma concentrations of polyols were measured at baseline (1989–90 or 2000–02). Associations of erythritol with cardiometabolic risk factors were also analysed in the Women’s Lifestyle Validation Study (n = 728; blood collected in 2010–12). Higher erythritol levels were related to more adverse cardiometabolic risk factor status. A relative risk (RR) for CHD per 1-SD increment was 1.15 [95% confidence interval (CI): 1.04, 1.28] for erythritol and 1.16 (95% CI: 1.05, 1.28) for mannitol/sorbitol, after adjusting for diet quality, lifestyles, and adiposity. Compared with women in the lowest quartile, those in the highest quartile (Q4) of erythritol had an RR of 1.55 (95% CI: 1.13, 2.14) for CHD. The RR in the Q4 of erythritol was 1.61 (95% CI: 1.15, 2.24; P = 0.006) when hypertension and dyslipidaemia were further added to the model; the RR was 1.21 (95% CI: 0.86, 1.70) after adjustment for diabetes. For mannitol/sorbitol, the RR in Q4 was 1.42 (95% CI: 1.05, 1.91; P = 0.022) for CHD in the multivariable-adjusted model including diabetes.

Conclusion
Higher levels of plasma erythritol and mannitol/sorbitol were related to elevated risks of CHD even after adjustment for diet, lifestyles, adiposity, and other risk factors. The unfavourable association of mannitol/sorbitol, but not of erythritol, with CHD risk remained significant independent of diabetes/hyperglycaemia.
Impacts of Acculturation on Depressive Symptoms and Activities of Daily Living of U.S. Older Chinese Immigrants
Authors: Jiang Yanping , Li Mengting , Kwon Soonhyung , Zhu Yuyang , Wu Bei , Tang Fengyan 
Published: September 2024

Abstract

Background and Objectives
Acculturation is a critical aspect of social experience for immigrants, including Asian immigrants. Existing literature has shown mixed findings on the health impacts of acculturation and largely relied on cross-sectional studies, preventing drawing definitive conclusions. This study aimed to examine the long-term effects of acculturation on depressive symptoms and activities of daily living (ADL) limitations in a large sample of older Chinese immigrants in the United States.

Research Design and Methods
Data were drawn from 2,811 older Chinese immigrants from the Population Study of Chinese Elderly in Chicago. Acculturation was assessed at baseline, and questionnaires on depressive symptoms and ADL limitations were completed at 4 assessments.

Results
Overall, results showed that acculturation was not associated with depressive symptoms at baseline but was associated with a faster decline in depressive symptoms over time. No associations were found between acculturation and ADL limitations. Stratified analyses showed that the significant relationship between acculturation and a faster decline in depressive symptoms was only evident among female participants. Also, acculturation was associated with a lower risk of reporting ADL limitations at baseline in female participants but a higher risk of reporting ADL limitations in male participants.

Discussion and Implications
This study indicates the long-term benefits of acculturation on mental health among older Chinese immigrants in the United States, particularly among females. Initiatives supporting the acculturation process need to consider sex disparities and individual preferences, aiming to foster sustained benefits for healthy aging in this population.
Classifying small earthquakes, explosions and collapses in the western United States using physics-based features and machine learning
Authors: Koper Keith D , Burlacu Relu , Armstrong Alysha D , Herrmann Robert B 
Published: September 2024

SUMMARY
Classifying the source type of small seismic events is a key task in seismology. A common goal is distinguishing tectonic earthquakes from explosions and human induced seismicity. To this end, we applied a spectral modelling workflow to Pg and Sg waves from ∼10 000 seismic events that occurred in or near Utah and were recorded by broadband seismometers in the western United States at distances of 10–300 km. The events were a mixture of tectonic earthquakes (EQ), industrial explosions (EX) and mining-induced seismicity (MIS, primarily collapses) and were mostly small (median magnitude of 1.34 MC). Our spectral modelling was successful for 54 per cent of the events, resulting in a new catalogue of M0 and fc values. We evaluated 13 physics-based features—including differential magnitudes, Pg/Sg spectral amplitude ratios, long-period/short-period spectral amplitude ratios and spectral misfit—as source classifiers. We found that Φ ≡ log10(M0) + 3log10(fc) was the most effective individual feature for distinguishing EQ from EX and MIS sources because EQ spectra are relatively enriched in high frequencies. We selected five less correlated features that spanned the feature space and used a naïve Bayes approach to create a three-way classification model. The model had 97.5 per cent accuracy when applied to an independent test data set. Model performance deteriorated when more than six features were combined. We conclude that models developed with a few physics-based waveform features can classify small seismic events with performance comparable to high-dimensional deep-learning models. Simple models that rely on physics-based features require less training data and make more interpretable decisions than deep-learning models, though they may require higher signal-to-noise ratios.
De novo gene integration into regulatory networks via interaction with conserved genes in peach
Authors: Cao Yunpeng , Hong Jiayi , Zhao Yun , Li Xiaoxu , Feng Xiaofeng , Wang Han , Zhang Lin , Lin Mengfei , Cai Yongping , Han Yuepeng 
Published: September 2024

Abstract
De novo genes can evolve “from scratch” from noncoding sequences, acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits. However, identifying de novo genes is challenging, as it requires high-quality genomes from closely related species. According to the comparison with nine closely related Prunus genomes, we determined at least 178 de novo genes in P. persica “baifeng”. The distinct differences were observed between de novo and conserved genes in gene characteristics and expression patterns. Gene ontology enrichment analysis suggested that Type I de novo genes originated from sequences related to plastid modification functions, while Type II genes were inferred to have derived from sequences related to reproductive functions. Finally, transcriptome sequencing across different tissues and developmental stages suggested that de novo genes have been evolutionarily recruited into existing regulatory networks, playing important roles in plant growth and development, which was also supported by WGCNA analysis and quantitative trait loci data. This study lays the groundwork for future research on the origins and functions of genes in Prunus and related taxa.