bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of gut microbiome with COPD in Japanese male residents: the SESSA study
Authors: Kawashima Satoru , Kinose Daisuke , Arima Hisatomi , Kondo Keiko , Yamazaki Akio , Uchida Yasuki , Nakagawa Hiroaki , Yamaguchi Masafumi , Segawa Hiroyoshi , Torii Sayuki , Okami Yukiko , Kadota Aya , Yano Yuichiro , Andoh Akira , Miura Katsuyuki , Nakano Yasutaka , Ueshima Hirotsugu 
Published: January 2024

BackgroundAltered gut microbiota may contribute to COPD development or progression. Herein, we investigated the association of gut microorganisms with COPD, taking into account the impact of smoking status.MethodsThis cross-sectional observational study was a part of the Shiga Epidemiological Study of Subclinical Atherosclerosis, a population-based cohort study of Japanese men aged 46–76 years, conducted from 2010 to 2016. The gut microbiome, determined using 16S rRNA gene sequencing, was compared among 99 never-smokers, 306 non-COPD ever-smokers and 76 patients with COPD while adjusting for age, body mass index, ethanol consumption and treatment for type 2 diabetes mellitus.ResultsThe abundance of phylum Firmicutes was comparable between patients with COPD and non-COPD ever-smokers but tended to be higher in never-smokers. Similarly, the α- and β-diversity analysis showed similarity between patients with COPD and non-COPD ever-smokers, which tended to differ from never-smokers. Discriminant analysis identified the genus[Prevotella]to be more prevalent in patients with COPD than in never-smokers or non-COPD ever-smokers.Post hocanalysis confirmed similarity of gut microbiome between COPD Global Initiative for Chronic Obstructive Lung Disease (GOLD) I and non-COPD ever-smokers, which was different from GOLD II.ConclusionSmoking may alter the overall gut microbial composition, but gut microbial composition itself may not play a role in the development of COPD. Rather, specific gut bacteria, such as[Prevotella], could be a risk factor for the development of COPD; this may be a potential therapeutic target.
Introducing the f0% method: a reliable and accurate approach for qPCR analysis
Authors: Gamal Mahmoud , Ibrahim Marwa A. 
Published: January 2024

Abstract
Background
qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (CT) that ignores differences in amplification efficiency among many other drawbacks. While other methods have been developed to analyze qPCR results, none has statistically proven to perform better than the CT method. Therefore, we aimed to develop a new qPCR analysis method that overcomes the limitations of the CT method. Our f0% [eff naught percent] method depends on a modified flexible sigmoid function to fit the amplification curve with a linear part to subtract the background noise. Then, the initial fluorescence is estimated and reported as a percentage of the predicted maximum fluorescence (f0%).

Results
The performance of the new f0% method was compared against the CT method along with another two outstanding methods—LinRegPCR and Cy0. The comparison regarded absolute and relative quantifications and used 20 dilution curves obtained from 7 different datasets that utilize different DNA-binding dyes. In the case of absolute quantification, f0% reduced CV%, variance, and absolute relative error by 1.66, 2.78, and 1.8 folds relative to CT; and by 1.65, 2.61, and 1.71 folds relative to LinRegPCR, respectively. While, regarding relative quantification, f0% reduced CV% by 1.76, 1.55, and 1.25 folds and variance by 3.13, 2.31, and 1.57 folds regarding CT, LinRegPCR, and Cy0, respectively. Finally, f0% reduced the absolute relative error caused by LinRegPCR by 1.83 folds.

Conclusions
We recommend using the f0% method to analyze and report qPCR results based on its reported advantages. Finally, to simplify the usage of the f0% method, it was implemented in a macro-enabled Excel file with a user manual located on https://github.com/Mahmoud0Gamal/F0-perc/releases.
Comparative analysis of metagenomic classifiers for long-read sequencing datasets
Authors: Marić Josip , Križanović Krešimir , Riondet Sylvain , Nagarajan Niranjan , Šikić Mile 
Published: January 2024

Abstract
Background
Long reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification tools on the species taxonomic level. We analysed kmer-based tools, mapping-based tools and two general-purpose long reads mappers. We evaluated more than 20 pipelines which use either nucleotide or protein databases and selected 13 for an extensive benchmark. We prepared seven synthetic datasets to test various scenarios, including the presence of a host, unknown species and related species. Moreover, we used available sequencing data from three well-defined mock communities, including a dataset with abundance varying from 0.0001 to 20% and six real gut microbiomes.

Results
General-purpose mappers Minimap2 and Ram achieved similar or better accuracy on most testing metrics than best-performing classification tools. They were up to ten times slower than the fastest kmer-based tools requiring up to four times less RAM. All tested tools were prone to report organisms not present in datasets, except CLARK-S, and they underperformed in the case of the high presence of the host’s genetic material. Tools which use a protein database performed worse than those based on a nucleotide database. Longer read lengths made classification easier, but due to the difference in read length distributions among species, the usage of only the longest reads reduced the accuracy. The comparison of real gut microbiome datasets shows a similar abundance profiles for the same type of tools but discordance in the number of reported organisms and abundances between types. Most assessments showed the influence of database completeness on the reports.

Conclusion
The findings indicate that kmer-based tools are well-suited for rapid analysis of long reads data. However, when heightened accuracy is essential, mappers demonstrate slightly superior performance, albeit at a considerably slower pace. Nevertheless, a combination of diverse categories of tools and databases will likely be necessary to analyse complex samples. Discrepancies observed among tools when applied to real gut datasets, as well as a reduced performance in cases where unknown species or a significant proportion of the host genome is present in the sample, highlight the need for continuous improvement of existing tools. Additionally, regular updates and curation of databases are important to ensure their effectiveness.
Development and validation of epigenetic modification-related signals for the diagnosis and prognosis of colorectal cancer
Authors: Li Xia , Li Jingjing , Li Jie , Liu Nannan , Zhuang Liwei 
Published: January 2024

Abstract
Background
Colorectal cancer (CRC) is one of the world's most common malignancies. Epigenetics is the study of heritable changes in characteristics beyond the DNA sequence. Epigenetic information is essential for maintaining specific expression patterns of genes and the normal development of individuals, and disorders of epigenetic modifications may alter the expression of oncogenes and tumor suppressor genes and affect the development of cancer. This study elucidates the relationship between epigenetics and the prognosis of CRC patients by developing a predictive model to explore the potential value of epigenetics in the treatment of CRC.

Methods
Gene expression data of CRC patients’ tumor tissue and controls were downloaded from GEO database. Combined with the 720 epigenetic-related genes (ERGs) downloaded from EpiFactors database, prognosis-related epigenetic genes were selected by univariate cox and LASSO analyses. The Kaplan–Meier and ROC curve were used to analyze the accuracy of the model. Data of 238 CRC samples with survival data downloaded from the GSE17538 were used for validation. Finally, the risk model is combined with the clinical characteristics of CRC patients to perform univariate and multivariate cox regression analysis to obtain independent risk factors and draw nomogram. Then we evaluated the accuracy of its prediction by calibration curves.

Results
A total of 2906 differentially expressed genes (DEGs) were identified between CRC and control samples. After overlapping DEGs with 720 ERGs, 56 epigenetic-related DEGs (DEERGs) were identified. Combining univariate and LASSO regression analysis, the 8 epigenetic-related genes-based risk score model of CRC was established. The ROC curves and survival difference of high and low risk groups revealed the good performance of the risk score model based on prognostic biomarkers in both training and validation sets. A nomogram with good performance to predict the survival of CRC patients were established based on age, NM stage and risk score. The calibration curves showed that the prognostic model had good predictive performance.

Conclusion
In this study, an epigenetically relevant 8-gene signature was constructed that can effectively predict the prognosis of CRC patients and provide potential directions for targeted therapies for CRC.
The pan-plastome of Hemerocallis citrina reveals new insights into the genetic diversity and cultivation history of an economically important food plant
Authors: Jia Minlong , Wang Jie , Cao Dongmei , Jiang Congrong , Li Wei , Tembrock Luke R. , Xing Guoming , Li Sen , Wu Zhiqiang 
Published: January 2024

Abstract
Background
Hemerocallis citrina Baroni (Huang hua cai in Chinese) is a perennial herbaceous plant grown for its flower buds that are eaten fresh or dried and is known as the vegetarian three treasures. The nuclear genome of H. citrina has been reported, but the intraspecific variation of the plastome (plastid genome) has not yet been studied. Therefore, the panplastome of this species collected from diverse locations is reported here for the first time.

Results
In this study, 65 H. citrina samples were resequenced, de novo assembled, and aligned with the published plastome of H. citrina to resolve the H. citrina panplastome. The sizes of the 65 newly assembled complete plastomes of H. citrina ranged from 156,048 bp to 156,263 bp, and the total GC content ranged from 37.31 to 37.34%. The structure of the complete plastomes showed a typical tetrameric structure, including a large single copy (LSC), a small single copy (SSC), and a pair of inverted repeat regions (IRA and IRB). Many nucleotide variants were identified between plastomes, among which the variants in the intergenic spacer region were the most abundant, with the highest number of variants concentrated in the LSC region. Based on the phylogenetic tree constructed using the ML method, population structure analysis, and principal component analysis (PCA), the panplastome data were subdivided into five genetic clusters. The C5 genetic cluster was mostly represented by samples from Qidong, Hunan Province, while samples from Shanxi and Shaanxi Provinces were classified into the C4 genetic cluster. The greatest genetic diversity was found in the C1 genetic cluster, and the greatest genetic distance between any two clusters was found between the C4 and C5 clusters.

Conclusion
The resolution of the panplastome and the analysis of the population structure of H. citrina plastomes provide important data for future breeding projects and germplasm preservation.
Gastroparesis might not be uncommon in patients with diabetes mellitus in a real-world clinical setting: a cohort study
Authors: Lee Jeongmin , Park Hye Lim , Park Su Young , Lim Chul-Hyun , Kim Min-Hee , Lee Jung Min , Chang Sang-Ah , Oh Jung-Hwan 
Published: January 2024

Abstract
Background
This study investigated the frequency of diabetic gastroparesis and associated risk factors in a real-world clinical setting.

Methods
This retrospective cross-sectional study included patients who underwent assessments of solid gastric emptying time (GET) by technetium-99 m scintigraphy between May 2019 and December 2020. We categorized patients into three groups according to gastric retention of technetium-99 m: rapid (< 65% at 1 h or < 20% at 2 h), normal (≤60% at 2 h and/or ≤ 10% at 4 h), and delayed (> 60% at 2 h and/or > 10% at 4 h).

Results
Patients with diabetes mellitus (DM) were more likely to show abnormal GET than those without DM (119 [70.8%] vs. 16 [44.4%]). The mean glycated A1c was 10.3% in DM patients. DM patients with normal GET were significantly younger (57.2 years, P = 0.044) than those with delayed (65.0 years) or rapid GET (60.2 years). Fasting glucose levels were the lowest in the normal GET group and the highest in the rapid GET group (delayed: 176.3 mg/dL, normal: 151.2 mg/dL, rapid: 181.0 mg/dL, P = 0.030). However, glycated A1c was not significantly different among the delayed, normal, and rapid GET groups in patients with DM. Patients with delayed and rapid GET showed a higher frequency of retinopathy (6.0 vs. 15.5%, P = 0.001) and peripheral neuropathy (11.3 vs. 24.4%, P = 0.001) than those with normal GET. In the multinomial logistic regression analysis, retinopathy demonstrated a positive association with delayed GET, while nephropathy showed a significant negative correlation.

Conclusion
DM gastroparesis in the clinical setting was not uncommon. Abnormal GET, including delayed and rapid GET, was associated with DM retinopathy or peripheral neuropathy.
Introducing a pharmacist-led transmural care program to reduce drug-related problems in orthogeriatric patients: a prospective interventional study
Authors: Bailly Rachel , Wuyts Stephanie , Toelen Loic , Mets Tony , Van Hauwermeiren Carmen , Scheerlinck Thierry , Cortoos Pieter-Jan , Lieten Siddhartha 
Published: January 2024

Abstract
Background
Orthogeriatric patients have an increased risk for complications due to underlying comorbidities, chronic drug therapy and frequent treatment changes during hospitalization. The clinical pharmacist (CP) plays a key role in transmural communication concerning polypharmacy to improve continuity of care by the general practitioner (GP) after discharge. In this study, a pharmacist-led transmural care program, tailored to orthogeriatric patients, was evaluated to reduce drug related problems (DRPs) after discharge.

Methods
An interventional study was performed (pre-period: 1/10/2021-31/12/2021; post-period: 1/01/2022-31/03/2022). Patients (≥ 65 years) from the orthopedic department were included. The pre-group received usual care, the post-group received the pharmacist-led transmural care program. The DRP reduction rate one month after discharge was calculated. Associated factors for the DRP reduction rate were determined in a multiple linear regression analysis. The GP acceptance rate was determined for the proposed interventions, as well as their clinical impact using the Clinical, Economic and Organizational (CLEO) tool. Readmissions one month after discharge were evaluated.

Results
Overall, 127 patients were included (control n = 61, intervention n = 66). The DRP reduction rate was statistically significantly higher in the intervention group compared to the control group (p < 0.001). The pharmacist’s intervention was associated with an increased DRP reduction rate (+ 1.750, 95% confidence interval 1.222–2.278). In total, 141 interventions were suggested by the CP, of which 71% were accepted one month after discharge. In both periods, four patients were readmitted one month after discharge. 58% of the interventions had a clinical impact (≥ 2 C level using the CLEO-tool) according to the geriatrician and for the CP it was 45%, indicating that they had the potential to avoid patient harm.

Conclusions
The pharmacist-led transmural care program significantly reduced DRPs in geriatric patients from the orthopedic department one month after discharge. The transmural communication with GPs resulted in a high acceptance rate of the proposed interventions.
Psychometric properties of the COVID-19 Yorkshire Rehabilitation Scale: Post-Covid-19 syndrome in Iranian elderly population
Authors: Tamadoni Negar , Bakhtiari Afsaneh , Nikbakht Hossein-Ali 
Published: January 2024

Abstract
Background
This study aimed to assess the construct validity and reliability of the Iranian version of the COVID-19 Yorkshire Rehabilitation Scale (C19-YRS) among the elderly population.

Method
A cohort of 230 elderly individuals who tested positive for Covid-19 via PCR were administered a health and demographic information questionnaire along with the C19-YRS. Both exploratory and confirmatory factor analyses were conducted, and Cronbach’s alpha was calculated.

Results
Findings from the exploratory and confirmatory factor analyses of the C19-YRS revealed alterations compared to the original version, resulting in an adapted version with three factors achieved by redistributing the questions. These factors accounted for 57.46% of the total variance. Despite a relatively lower factor loading in the 6th question, it was retained due to its significance among the elderly. The Cronbach’s alpha for the C19-YRS subscales ranged from 0.730 to 0.890, indicating acceptable reliability.

Conclusion
The validation results indicated a well-adjusted factor structure and internal consistency, affirming the utility of this tool among the elderly population. Consequently, the C19-YRS in Iran can serve as a valuable resource in healthcare settings, aiding in the assessment of chronic complications arising from Covid-19 in the elderly. It can be utilized as an initial screening or triage test and to evaluate the effectiveness of interventions.
SEA-NET: medical image segmentation network based on spiral squeeze-and-excitation and attention modules
Authors: Xiong Liangli , Yi Chen , Xiong Qiliang , Jiang Shaofeng 
Published: January 2024

Abstract
Background
Medical image segmentation is an important processing step in most of medical image analysis. Thus, high accuracy and robustness are required for them. The current deep neural network based medical segmentation methods have good effect on image with balanced foreground and background, but it will loss the characteristics of small targets on image with imbalanced foreground and background after multiple convolutions.

Methods
In order to retain the features of small targets in the deep network, we proposed a new medical image segmentation model based on the U-Net with squeeze-and-excitation and attention modules which form a spiral closed path,callled as Spiral Squeeze-and-Excitation and Attention NET (SEA-NET) in this paper. The segmentation model used squeeze-and-extraction modules to adjust the channel information to enhance the useful information and used attention modules to adjust the spatial information of the feature map to highlight the target area for small target segmentation when up-sampling. The deep semantic information is integrated into the shallow feature map by the attention model. Therefore, the deep semantic information cannot be scattered by continuous up-sampling. We used cross entropy loss + Tversky loss function for fast convergence and well processing the imbalanced data sets. Our proposed SEA-NET was tested on the brain MRI dataset LPBA40 and peripheral blood smear images.

Conclusions
On brain MRI data, the average value of the Dice coefficient we obtained reached 98.1$$\%$$
%
. On the peripheral blood smear dataset, our proposed model has a good segmentation effect on adhesion cells.

Results
The experimental results proved that the proposed SEA-Net performed better than U-Net, U-Net++, etc. in medical image segmentation.
The effects of lockdown during the COVID-19 pandemic on fetal movement profiles
Authors: Reissland N. , Ustun B , Einbeck J. 
Published: January 2024

Abstract
Purpose
The current study investigated the direct impact of the COVID-19 lockdown on fetal movements, addressing a critical research gap. While previous research has predominantly examined the effects of lockdown on maternal health and postnatal outcomes, little attention has been paid to the direct consequences on fetal well-being as indicated by their movement profile.

Methods
We conducted analysis of movement profiles in 20 healthy fetuses during the COVID-19 pandemic lockdown (third national UK lockdown period between January and March 2021) and compared them with 20 healthy fetuses from pre-covid pregnancies, all at 32 weeks gestation. We controlled for maternal stress, depression, and anxiety.

Results
Pregnant mothers during pre-covid compared with those during the COVID-19 lockdown reported similar levels of stress (p = 0.47), depression (p = 0.15), and anxiety (p = 0.07). Their fetuses, however, differed in their movement profiles with mouth movement frequencies significantly higher during COVID-19 lockdown (COVID-19 lockdown: mean of 5.909) compared to pre-Covid pregnancies (mean of 3.308; p = 0.029). Furthermore, controlling for maternal anxiety a regression analysis indicated that frequency of fetal mouth movements (p = 0.017), upper face movements (p = 0.008), and touch movements (p = 0.031) were all significantly higher in fetuses observed during lockdown compared to fetuses before the Covid period.

Conclusion
Fetuses show an effect of lockdown independent of maternal anxiety, stress, or depression. These findings contribute to our understanding of fetal development during extraordinary circumstances, raising questions about the potential effects of having to stay indoors during lockdowns.
Relationship between DXA measured systemic bone mineral density and subchondral bone cysts in postmenopausal female patients with knee osteoarthritis: a cross-sectional study
Authors: Tönük Şükrü Burak , Yorgancıoğlu Zeynep Rezan , Ramadan Selma Uysal , Kocaoğlu Seher 
Published: January 2024

Abstract
Background
Individuals with high systemic bone mineral density (BMD) may have an increased risk of incident knee osteoarthritis (OA). Besides that, radiographic osteophytes are strongly associated with BMD. Because of these reasons, the aim of the study was to investigate the possible association between radiological subchondral bone cyst (SBC) grade and systemic BMD and vitamin D status in the postmenopausal female patients with knee OA in a crosss-sectional study.

Methods
This study included of 48 osteoporosis treatment-free postmenopausal patients diagnosed with symptomatic medial compartment knee OA. BMD analysis was performed using dual-energy X-ray absorptiometry (DXA) and serum vitamin D levels were measured after recording patients’ findings. Each knee was scanned using computed tomography (CT), and categorical SBC scores were graded for the medial and lateral tibiofemoral (TF) and patellofemoral (PF) compartments and further calculated as compartmental total, total TF and grand total of both TF compartments. SBC scores were analysed with correlation analysis.

Results
The patient population was characterized by radiographic joint space narrowing, obesity and low vitamin D status. Median medial total and grand total TF SBC scores were significantly different between the patient groups according to the Kellgren-Lawrence (KL) radiographic grading (p = 0.006 and p = 0.007, respectively). There were no correlations between femoral BMD values and SBC scores. However, positive correlations were detected significantly between L1 − 4 DXA values and TF SBC scores, but not with PF SBC scores (p = 0.005 for the correlation between L1 − 4 BMD and medial compartments total TF SBC score, p = 0.021 for the correlation between L1 − 4 BMD and grand total TF SBC score). No significant correlations were found with Vitamin D levels.

Conclusions
Development of TF OA high-grade SBCs may be linked to systemic bone mass as represented by trabecular bone-rich lumbar vertebrae. The relationship might point to the importance of bone stiffness as an acting factor in knee OA possibly with mechanical energy transfer to the joint.