bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types
Authors: Xu Wei , Wang Teng , Wang Nan , Zhang Haohong , Zha Yuguo , Ji Lei , Chu Yuwen , Ning Kang 
Published: May 2023

Abstract
Microbiome-based diagnosis of cancer is an increasingly important supplement for the genomics approach in cancer diagnosis, yet current models for microbiome-based diagnosis of cancer face difficulties in generality: not only diagnosis models could not be adapted from one cancer to another, but models built based on microbes from tissues could not be adapted for diagnosis based on microbes from blood. Therefore, a microbiome-based model suitable for a broad spectrum of cancer types is urgently needed. Here we have introduced DeepMicroCancer, a diagnosis model using artificial intelligence techniques for a broad spectrum of cancer types. Built based on the random forest models it has enabled superior performances on more than twenty types of cancers’ tissue samples. And by using the transfer learning techniques, improved accuracies could be obtained, especially for cancer types with only a few samples, which could satisfy the requirement in clinical scenarios. Moreover, transfer learning techniques have enabled high diagnosis accuracy that could also be achieved for blood samples. These results indicated that certain sets of microbes could, if excavated using advanced artificial techniques, reveal the intricate differences among cancers and healthy individuals. Collectively, DeepMicroCancer has provided a new venue for accurate diagnosis of cancer based on tissue and blood materials, which could potentially be used in clinics.
Zona pellucida family genes in Chinese pond turtle: identification, expression profiles, and role in the spermatozoa acrosome reaction
Authors: Dong Jinxiu , Pei Kejiao , Xu Wannan , Gong Mengmeng , Zhu Wenrui , Liu Siqi , Tang Min , Liu Jianjun , Xia Xingquan , Bu Xinjiang , Nie Liuwang 
Published: May 2023

Abstract
The zona pellucida (ZP) is an extracellular matrix that surrounds all vertebrate eggs, and it is involved in fertilization and species-specific recognition. Numerous in-depth studies of the ZP proteins of mammals, birds, amphibians, and fishes have been conducted, but systematic investigation of the ZP family genes and their role during fertilization in reptiles has not been reported to date. In this study, we identified six turtle ZP (Tu-ZP) gene subfamilies (Tu-ZP1, Tu-ZP2, Tu-ZP3, Tu-ZP4, Tu-ZPD, and Tu-ZPAX) based on whole genome sequence data from Mauremys reevesii. We found that Tu-ZP4 had large segmental duplication and was distributed on three chromosomes, and we also detected gene duplication in the other Tu-ZP genes. To evaluate the role of Tu-ZP proteins in sperm–egg binding, we assessed the expression pattern of these Tu-ZP proteins and their ability to induce the spermatozoa acrosome reaction in M. reevesii. In conclusion, this is the first report of the existence of gene duplication of Tu-ZP genes and that Tu-ZP2, Tu-ZP3, and Tu-ZPD can induce acrosome exocytosis of spermatogenesis in the reptile.
Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
Authors: Gomez-Garrido Jessica , Cruz Fernando , Alioto Tyler S , Feiner Nathalie , Uller Tobias , Gut Marta , Sanchez Escudero Ignacio , Tavecchia Giacomo , Rotger Andreu , Otalora Acevedo Katherin Eliana , Baldo Laura 
Published: May 2023

Abstract
The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and &gt;97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18–20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.
Determinants of post-operative left ventricular dysfunction in degenerative mitral regurgitation
Authors: Althunayyan Aeshah M , Alborikan Sahar , Badiani Sveeta , Wong Kit , Uppal Rakesh , Patel Nikhil , Petersen Steffen E , Lloyd Guy , Bhattacharyya Sanjeev 
Published: May 2023

Abstract

Aims
Chronic degenerative mitral regurgitation leads to volume overload causing left ventricular (LV) enlargement and eventually LV impairment. Current guidelines determining thresholds for intervention are based on LV diameters and ejection fraction (LVEF). There are sparse data examining the value of LV volumes and newer markers of LV performance on outcomes of surgery in mitral valve prolapse. The aim of this study is to identify the best marker of LV impairment after mitral valve surgery.

Methods and results
Prospective, observational study of patients with mitral valve prolapse undergoing mitral valve surgery. Pre-operative LV diameters, volumes, LVEF, global longitudinal strain (GLS), and myocardial work measured. Post-operative LV impairment defined as LVEF &lt; 50% at 1 year post-surgery. Eighty-seven patients included. Thirteen percent developed post-operative LV impairment. Patients with post-operative LV dysfunction showed significantly larger indexed LV end-systolic diameters, indexed LV end-systolic volumes (LVESVi), lower LVEF, and more abnormal GLS than patients without post-operative LV dysfunction. In multivariate analysis, LVESVi [odds ratio 1.11 (95% CI 1.01–1.23), P = 0.039] and GLS [odds ratio 1.46 (95% CI 1.00–2.14), P = 0.054] were the only independent predictors of post-operative LV dysfunction. The optimal cut-off of 36.3 mL/m2 for LVESVi had a sensitivity of 82% and specificity of 78% for detection of post-operative LV impairment.

Conclusion
Post-operative LV impairment is common. Indexed LV volumes (36.3 mL/m2) provided the best marker of post-operative LV impairment.
Sleep duration and its association with adiposity markers in adolescence: a cross-sectional and longitudinal study
Authors: Martínez-Gómez Jesús , Fernández-Alvira Juan Miguel , de Cos-Gandoy Amaya , Bodega Patricia , de Miguel Mercedes , Tresserra-Rimbau Anna , Laveriano-Santos Emily P , Carral Vanesa , Carvajal Isabel , Estruch Ramón , Lamuela-Raventós Rosa María , Santos-Beneit Gloria , Fuster Valentín , Fernández-Jiménez Rodrigo 
Published: May 2023

Abstract

Aims
Large studies linking adolescents’ objectively measured sleep duration and adiposity markers are lacking. We characterized sleep duration and its cross-sectional and longitudinal associations with adiposity markers in adolescence.

Methods and results
Seven-day accelerometry was performed in a cohort of adolescents enrolled in the SI! Program for Secondary Schools trial in Spain at approximately ages 12 (1216 adolescents, 49.6% girls), 14 (1026 adolescents, 51.3% girls), and 16 (872 adolescents, 51.7% girls) years. Participants were classified as very short sleepers (VSS; &lt;7 h), short sleepers (SS; 7–&lt;8 h), or recommended-time sleepers (RTS; 8–10 h). Adjusted associations between sleep duration and adiposity markers were analysed using generalized linear and Poisson models. At ∼12 years, 33.7% of adolescents met sleep recommendations, and this percentage decreased with advancing age (22.6% at ∼14 and 18.7% at ∼16 years). Compared with RTS, overweight/obesity prevalence ratios at ∼12, 14, and 16 years among SS were 1.19 [95% confidence interval (CI): 1.09–1.30], 1.41 (95% CI: 1.34–1.48), and 0.99 (95% CI: 0.77–1.26) and among VSS were 1.30 (95% CI: 1.28–1.32), 1.93 (95% CI: 1.41–2.64), and 1.32 (95% CI: 1.26–1.37). Compared with adolescents who always met sleep recommendations, the prevalence of overweight/obesity was ∼5 times higher in those never meeting recommendations or meeting them only once. Similar trends were observed for the waist-to-height ratio (P = 0.010) and fat mass index (P = 0.024).

Conclusion
Most adolescents did not meet sleep recommendations. Shorter sleep duration was independently associated with unfavourable adiposity markers, and such adverse impact was cumulative. Health promotion programmes should emphasize the importance of good sleep habits.
Emotional demands and all-cause and diagnosis-specific long-term sickness absence: a prospective cohort study in Sweden
Authors: Framke Elisabeth , Alexanderson Kristina , Sørensen Jeppe Karl , Pedersen Jacob , Madsen Ida E H , Rugulies Reiner , Farrants Kristin 
Published: May 2023

Abstract

Background
High emotional demands at work require sustained emotional effort and are associated with adverse health outcomes. We tested whether individuals in occupations with high emotional demands, compared with low demands, had a higher future risk of all-cause long-term sickness absence (LTSA). We further explored whether the risk of LTSA associated with high emotional demands differed by LTSA diagnoses.

Methods
We conducted a prospective, nationwide cohort study on the association between emotional demands and LTSA (&gt;30 days) in the workforce in Sweden (n = 3 905 685) during a 7-year follow-up. Using Cox regression, we analyzed sex-stratified risks of all-cause and diagnosis-specific LTSA due to common mental disorders (CMD), musculoskeletal disorders (MSD) and all other diagnoses. Multivariable adjusted models included age, birth country, education, living area, family situation and physical work demands.

Results
Working in emotionally demanding occupations was associated with a higher risk of all-cause LTSA in women [hazard ratio (HR) = 1.92, 95% confidence interval (CI): 1.88–1.96] and men (HR = 1.23, 95% CI: 1.21–1.25). In women, the higher risk was similar for LTSA due to CMD, MSD and all other diagnoses (HR of 1.82, 1.92 and 1.93, respectively). In men, risk of LTSA due to CMD was pronounced (HR = 2.01, 95% CI: 1.92–2.11), whereas risk of LTSA due to MSD and all other diagnoses was only slightly elevated (HR of 1.13, both outcomes).

Conclusions
Workers in occupations with high emotional demands had a higher risk of all-cause LTSA. In women, risk of all-cause and diagnosis-specific LTSA were similar. In men, the risk was more pronounced for LTSA due to CMD.
The Lure of Technocracy? Chinese Aid and Local Preferences for Development Leadership in Africa
Authors: Huang Zhenqian , Cao Xun 
Published: May 2023

AbstractShould politicians, technocrats, or the free market guide the economic development of a developing country? The historical development paths of countries vary widely. Public opinion concerning development models also differs across space and over time. Using Chinese aid data from AidData and the second round Afrobarometer survey, we study how Chinese aid affects local preferences for economic leadership in sixteen African countries, 2000–2005. Our causal identification strategy is to compare the preferences of respondents who lived near an aid project site where a Chinese project had been implemented at the time of the interview (treated group) to individuals who lived close to a site where a Chinese project would be initiated shortly after the interview (control group). We find that Chinese aid increases the local population's support for economic experts to run the economy. World Bank aid, on the other hand, has no impact on local preferences for economic leadership.
The Population Attributable Fraction of Dementia From Audiometric Hearing Loss Among a Nationally Representative Sample of Community-Dwelling Older Adults
Authors: Smith Jason R , Huang Alison R , Lin Frank R , Reed Nicholas S , Deal Jennifer A 
Published: May 2023

Abstract

Background
The population attributable fraction (PAF) of dementia from hearing loss (HL) in the United States is ~2% when incorporating self-reported HL measures. However, self-report might underestimate clinically significant audiometric HL among older adults. Here, we quantified PAFs of dementia from audiometric HL overall and by age, sex, and race/ethnicity groups among a nationally representative sample of community-dwelling older adults in the United States.

Methods
We used cross-sectional data from Round 11 (2021) of the National Health and Aging Trends Study, a prospective cohort study representing the U.S. Medicare population aged 65+ years (N = 2 470). We estimated model-adjusted PAFs of prevalent dementia by audiometric HL (pure-tone averages: normal hearing, &lt;26 dB HL; mild HL, 26–40 dB HL; moderate or greater HL, ≥41 dB HL).

Results
Among eligible participants (34.8% aged ≥80 years; 55.3% female; 82.4% non-Hispanic White), 37.5% had mild, and 28.8% had moderate or greater HL. Dementia prevalence overall was 10.6%, with the PAF predominately driven by moderate or greater HL (PAF = 16.9%; 95% confidence interval [CI]: 4.1–28.7%). The PAF from any degree of HL was larger but with a wider CI (PAF = 18.7%, 95% CI: −5.3% to 40.1%). There was evidence associations differed by sex but not age or race/ethnicity; moderate or greater HL exhibited stronger associations among males (PAF = 40.5%; 95% CI: 19.5% to 57.2%) than females (PAF = 3.2%; 95% CI: −12.7% to 17.9%).

Conclusions
In a nationally representative sample of community-dwelling older adults in the United States, 17% of dementia cases were attributable to moderate or greater audiometric HL, an estimate that is eightfold higher relative to studies relying on self-reported hearing measures only.
PsERF1B-PsMYB10.1-PsbHLH3 module enhances anthocyanin biosynthesis in the flesh-reddening of amber-fleshed plum (cv. Friar) fruit in response to cold storage
Authors: Xu Ranran , Wang Yubei , Wang Limin , Zhao Zhilei , Cao Jiankang , Fu Daqi , Jiang Weibo 
Published: May 2023

Abstract
Flesh-reddening usually occurs in the amber-fleshed plum (Prunus salicina Lindl.) fruit during cold storage but not during ambient storage direct after harvest. It is not clear how postharvest cold signal is mediated to regulate the anthocyanin biosynthesis in the forming of flesh-reddening yet. In this study, anthocyanins dramatically accumulated and ethylene produced in the ‘Friar’ plums during cold storage, in comparison with plums directly stored at ambient temperature. Expression of genes associated with anthocyanin biosynthesis, as well as transcription factors of PsMYB10.1, PsbHLH3, and PsERF1B were strongly stimulated to upregulated in the plums in the period of cold storage. Suppression of ethylene act with 1-methylcyclopropene greatly suppressed flesh-reddening and downregulated the expression of these genes. Transient overexpression and virus-induced gene silencing assays in plum flesh indicated that PsMYB10.1 encodes a positive regulator of anthocyanin accumulation. The transient overexpression of PsERF1B, coupled with PsMYB10.1 and PsbHLH3, could further prompt the anthocyanin biosynthesis in a tobacco leaf system. Results from yeast two-hybrid and luciferase complementation assays verified that PsERF1B directly interacted with PsMYB10.1. PsERF1B and PsMYB10.1 enhanced the activity of the promoter of PsUFGT individually, and the enhancement was prompted by the co-action of PsERF1B and PsMYB10.1. Overall, the stimulation of the PsERF1B-PsMYB10.1-PsbHLH3 module mediated cold signal in the transcriptomic supervision of the anthocyanin biosynthesis in the ‘Friar’ plums. The results thereby revealed the underlying mechanism of the postharvest alteration of the flesh phenotype of ‘Friar’ plums subjected to low temperature.
Patient and researcher stakeholder preferences for use of electronic health record data: a qualitative study to guide the design and development of a platform to honor patient preferences
Authors: Morse Brad , Kim Katherine K , Xu Zixuan , Matsumoto Cynthia G , Schilling Lisa M , Ohno-Machado Lucila , Mak Selene S , Keller Michelle S 
Published: May 2023

Abstract

Objective
This qualitative study aimed to understand patient and researcher perspectives regarding consent and data-sharing preferences for research and a patient-centered system to manage consent and data-sharing preferences.

Materials and Methods
We conducted focus groups with patient and researcher participants recruited from three academic health centers via snowball sampling. Discussions focused on perspectives on the use of electronic health record (EHR) data for research. Themes were identified through consensus coding, starting from an exploratory framework.

Results
We held two focus groups with patients (n = 12 patients) and two with researchers (n = 8 researchers). We identified two patient themes (1–2), one theme common to patients and researchers (3), and two researcher themes (4–5). Themes included (1) motivations for sharing EHR data, (2) perspectives on the importance of data-sharing transparency, (3) individual control of personal EHR data sharing, (4) how EHR data benefits research, and (5) challenges researchers face using EHR data.

Discussion
Patients expressed a tension between the benefits of their data being used in studies to benefit themselves/others and avoiding risk by limiting data access. Patients resolved this tension by acknowledging they would often share their data but wanted greater transparency on its use. Researchers expressed concern about incorporating bias into datasets if patients opted out.

Conclusions
A research consent and data-sharing platform must consider two competing goals: empowering patients to have more control over their data and maintaining the integrity of secondary data sources. Health systems and researchers should increase trust-building efforts with patients to engender trust in data access and use.
Computer-Aided Design of Eco-Friendly Imprinted Polymer Decorated Sensors Augmented by Self-Validated Ensemble Modeling Designs for the Quantitation of Drotaverine Hydrochloride in Dosage Form and Human Plasma
Authors: E. Mostafa Aziza , Eissa Maya S , Elsonbaty Ahmed , Attala Khaled , A. Abdel Salam Randa , M. Hadad Ghada , Abdelshakour Mohamed A 
Published: May 2023

Abstract

Background
Computationally designed molecular imprinted polymer (MIP) incorporation into electrochemical sensors has many advantages to the performance of the designed sensors. The innovative self-validated ensemble modeling (SVEM) approach is a smart machine learning-based (ML) technique that enables the design of more accurate predictive models using smaller data sets.

Objective
The novel SVEM experimental design methodology is exploited here exclusively to optimize the composition of four eco-friendly PVC membranes augmented by a computationally designed magnetic molecularly imprinted polymer to quantitatively determine drotaverine hydrochloride (DVN) in its combined dosage form and human plasma. Furthermore, the application of hybrid computational simulations such as molecular dynamics and quantum mechanical calculations (MD/QM) is a time-saving and eco-friendly provider for the tailored design of the MIP particles.

Method
Here, for the first time, the predictive power of ML is assembled with computational simulations to develop four PVC-based sensors decorated by computationally designed MIP particles using four different experimental designs known as central composite, SVEM-LASSO, SVEM-FWD, and SVEM-PFWD. The pioneering AGREE approach further assessed the greenness of the analytical methods, proving their eco-friendliness.

Results
The proposed sensors showed decent Nernstian responses toward DVN in the range of 58.60–59.09 mV/decade with a linear quantitative range of 1 × 10−7 – 1 × 10−2 M and limits of detection in the range of 9.55 × 10−8 to 7.08 × 10−8 M. Moreover, the proposed sensors showed ultimate eco-friendliness and selectivity for their target in its combined dosage form and spiked human plasma.

Conclusions
The proposed sensors were validated in accordance with International Union of Pure and Applied Chemistry (IUPAC) recommendations, proving their sensitivity and selectivity for drotaverine determination in dosage form and human plasma.

Highlights
This work presents the first ever application of both the innovative SVEM designs and MD/QM simulations in the optimization and fabrication of drotaverine-sensitive and selective MIP-decorated PVC sensors.
Green Easily Implemented Spectrophotometric Methods for Concurrent Determination of Ephedrine Hydrochloride and Naphazoline Nitrate in Nasal Preparations Containing Methylparaben
Authors: Abdelfatah Rehab M , Magdy Maimana A 
Published: May 2023

Abstract

Background
Spectrophotometric resolution of a mixture of several drugs is considered a cheaper, simpler, and more versatile alternative compared to costly chromatographic instruments.

Objective
The work aims to resolve the interfering spectra of ephedrine hydrochloride, naphazoline nitrate, and methylparaben in nasal preparations using smart spectrophotometric methods.

Method
In our work, derivative and dual-wavelength methods were combined to eliminate this interference, under the name of derivative dual-wavelength method. Other methods, namely successive derivative subtraction and chemometric analysis, were also able to eliminate this interference. The methods have proven their applicability as they follow the International Conference on Harmonization (ICH) requirements regarding repeatability, precision, accuracy, selectivity, and linearity. Eco-scale, GAPI, and AGREE tools were used to estimate the possible environmental effects of the methods.

Results
Acceptable results for repeatability, precision, accuracy, selectivity, and linearity were obtained. Limit of detection (LOD) values were 2.2 for ephedrine and 0.3 for naphazoline. The correlation coefficients were above 0.999. The methods were proven to be safe for application.

Conclusions
The introduced methods are cheap and easily implemented compared to chromatographic techniques. They can be used in purity-checking of raw material and estimation of concentrations in market formulations. The replacement of the published chromatographic techniques with our developed methods is useful when needing to save money, effort, and time.

Highlights
The three components of a decongestant nasal preparation were determined using cheap, green, and versatile spectrophotometric methods that keep the advantages of chromatographic techniques, including accuracy, reproducibility, and selectivity.