bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of preserved ratio impaired spirometry on coronary artery calcium score progression: a longitudinal cohort study
Authors: Im Yunjoo , Park Hye Yun , Lee Jin-Young , Kim Hyunsoo , Yoo Hongseok , Kang Mira , Cho Soo Jin , Hwang Jung Hye , Park Yong Bum , Cho Juhee , Kang Danbee , Shin Sun Hye 
Published: December 2023

BackgroundPreserved ratio impaired spirometry (PRISm) is associated with increased cardiovascular disease (CVD) risk and mortality. However, a causal relationship between PRISm and CVD remains unclear. We investigated the progression of coronary artery calcium (CAC) scores based on the presence of PRISm and reduced forced vital capacity (FVC).MethodsThis retrospective cohort study included 11 420 participants aged ≥40 years with forced expiratory volume in 1 s (FEV1)/FVC ≥0.7 who underwent at least two health screening examinations with coronary computed tomography scan between 2003 and 2020, and were without a history of CVD or interstitial lung disease. Participants with PRISm, defined as FEV1/FVC ≥0.7 and FEV1<80% predicted, were further divided by low FVC (FVC <80% predicted). We estimated the 5-year progression rates of CAC by comparing participants with and without PRISm at baseline using mixed linear models.ResultsOf the 11 420 participants, 8536 (75%), 811 (7%) and 2073 (18%) had normal spirometry, PRISm with normal FVC and PRISm with low FVC, respectively. During the mean (range) follow-up of 6.0 (0.5–17.2) years, the multivariable adjusted ratio of 5-year CAC progression rates comparing participants with PRISm to those with normal spirometry was 1.08 (95% CI 1.04–1.13). This rate was higher in participants with PRISm with low FVC (1.21 (95% CI 1.12–1.30)) than in those with normal FVC.ConclusionIn this longitudinal cohort study of subjects without a history of CVD, PRISm was significantly associated with CAC progression, which was more evident in the group with PRISm and low FVC.
Subtyping irritable bowel syndrome using cluster analysis: a systematic review
Authors: Zarei Diana , Saghazadeh Amene , Rezaei Nima 
Published: December 2023

Abstract
Background
Irritable bowel syndrome (IBS) is a common chronic functional gastrointestinal disorder associated with a wide range of clinical symptoms. Some researchers have used cluster analysis (CA), a group of non-supervised learning methods that identifies homogenous clusters within different entities based on their similarity.

Objective and methods
This literature review aims to identify published articles that apply CA to IBS patients. We searched relevant keywords in PubMed, Embase, Web of Science, and Scopus. We reviewed studies in terms of the selected variables, participants’ characteristics, data collection, methodology, number of clusters, clusters’ profiles, and results.

Results
Among the 14 articles focused on the heterogeneity of IBS, eight of them utilized K-means Cluster Analysis (K-means CA), four employed Hierarchical Cluster Analysis, and only two studies utilized Latent Class Analysis. Seven studies focused on clinical symptoms, while four articles examined anocolorectal functions. Two studies were centered around immunological findings, and only one study explored microbial composition. The number of clusters obtained ranged from two to seven, showing variation across the studies. Males exhibited lower symptom severity and fewer psychological findings. The association between symptom severity and rectal perception suggests that altered rectal perception serves as a biological indicator of IBS. Ultra-slow waves observed in IBS patients are linked to increased activity of the anal sphincter, higher anal pressure, dystonia, and dyschezia.

Conclusion
IBS has different subgroups based on different factors. Most IBS patients have low clinical severity, good QoL, high rectal sensitivity, delayed left colon transit time, increased systemic cytokines, and changes in microbial composition, including increased Firmicutes-associated taxa and depleted Bacteroidetes-related taxa. However, the number of clusters is inconsistent across studies due to the methodological heterogeneity. CA, a valuable non-supervised learning method, is sensitive to hyperparameters like the number of clusters and random initialization of cluster centers. The random nature of these parameters leads to diverse outcomes even with the same algorithm. This has implications for future research and practical applications, necessitating further studies to improve our understanding of IBS and develop personalized treatments.
Cellstitch: 3D cellular anisotropic image segmentation via optimal transport
Authors: Liu Yining , Jin Yinuo , Azizi Elham , Blumberg Andrew J. 
Published: December 2023

Abstract
Background
Spatial mapping of transcriptional states provides valuable biological insights into cellular functions and interactions in the context of the tissue. Accurate 3D cell segmentation is a critical step in the analysis of this data towards understanding diseases and normal development in situ. Current approaches designed to automate 3D segmentation include stitching masks along one dimension, training a 3D neural network architecture from scratch, and reconstructing a 3D volume from 2D segmentations on all dimensions. However, the applicability of existing methods is hampered by inaccurate segmentations along the non-stitching dimensions, the lack of high-quality diverse 3D training data, and inhomogeneity of image resolution along orthogonal directions due to acquisition constraints; as a result, they have not been widely used in practice.

Methods
To address these challenges, we formulate the problem of finding cell correspondence across layers with a novel optimal transport (OT) approach. We propose CellStitch, a flexible pipeline that segments cells from 3D images without requiring large amounts of 3D training data. We further extend our method to interpolate internal slices from highly anisotropic cell images to recover isotropic cell morphology.

Results
We evaluated the performance of CellStitch through eight 3D plant microscopic datasets with diverse anisotropic levels and cell shapes. CellStitch substantially outperforms the state-of-the art methods on anisotropic images, and achieves comparable segmentation quality against competing methods in isotropic setting. We benchmarked and reported 3D segmentation results of all the methods with instance-level precision, recall and average precision (AP) metrics.

Conclusions
The proposed OT-based 3D segmentation pipeline outperformed the existing state-of-the-art methods on different datasets with nonzero anisotropy, providing high fidelity recovery of 3D cell morphology from microscopic images.
The antennal transcriptome analysis and characterizations of odorant-binding proteins in Megachile saussurei (Hymenoptera, Megachilidae)
Authors: Li Wei-Zhen , Kang Wen-Juan , Zhou Jing-Jiang , Shang Su-Qin , Shi Shang-Li 
Published: December 2023

Abstract
Background
Odorant-binding proteins (OBPs) are essential in insect’s daily behaviors mediated by olfactory perception. Megachile saussurei Radoszkowski (Hymenoptera, Megachilidae) is a principal insect pollinating alfalfa (Medicago sativa) in Northwestern China. The olfactory function have been less conducted, which provides a lot of possibilities for our research.

Results
Our results showed that 20 OBPs were identified in total. Multiple sequence alignment analysis indicated MsauOBPs were highly conserved with a 6-cysteine motif pattern and all belonged to the classic subfamily, coding 113-196 amino acids and sharing 41.32%-99.12% amino acid identity with known OBPs of other bees. Phylogenetic analysis indicated there were certain homologies existed among MsauOBPs and most sequences were clustered with that of Osmia cornuta (Hymenoptera, Megachilidae). Expression analysis showed the identified OBPs were mostly enriched in antennae instead of other four body parts, especially the MsauOBP2, MsauOBP3, MsauOBP4, MsauOBP8, MsauOBP11 and MsauOBP17, in which the MsauOBP2, MsauOBP4 and MsauOBP8 presented obvious tissue-biased expression pattern. Molecular docking results indicated MsauOBP4 might be the most significant protein in recognizing alfalfa flower volatile 3-Octanone, while MsauOBP13 might be the most crucial protein identifying (Z)-3-hexenyl acetate. It was also found the lysine was a momentous hydrophilic amino acid in docking simulations.

Conclusion
In this study, we identified and analyzed 20 OBPs of M. saussurei. The certain homology existed among these OBPs, while some degree of divergence could also be noticed, indicating the complex functions that different MsauOBPs performed. Besides, the M. saussurei and Osmia cornuta were very likely to share similar physiological functions as most of their OBPs were clustered together. MsauOBP4 might be the key protein in recognizing 3-Octanone, while MsauOBP13 might be the key protein in binding (Z)-3-hexenyl acetate. These two proteins might contribute to the alfalfa-locating during the pollination process. The relevant results may help determine the highly specific and effective attractants for M. saussurei in alfalfa pollination and reveal the molecular mechanism of odor-evoked pollinating behavior between these two species.
The effect of environmental factors on the genetic differentiation of Cucurbita ficifolia populations based on whole-genome resequencing
Authors: He Shuilian , Li Gengyun , Zhang Jing , Ding Yumei , Wu Hongzhi , Xie Junjun , Wu Hang , Yang Zhengan 
Published: December 2023

Abstract
Background
Cucurbita ficifolia is one of the squash species most resistant to fungal pathogens, and has especially high resistance to melon Fusarium wilt. This species is therefore an important germplasm resource for the breeding of squash and melon cultivars.

Results
Whole-genome resequencing of 223 individuals from 32 populations in Yunnan Province, the main cucurbit production area in China, was performed and 3,855,120 single-nucleotide polymorphisms (SNPs) and 1,361,000 InDels were obtained. SNP analysis suggested that levels of genetic diversity in C. ficifolia were high, but that different populations showed no significant genetic differentiation or geographical structure, and that individual C. ficifolia plants with fruit rinds of a similar color did not form independent clusters. A Mantel test conducted in combination with geographical distance and environmental factors suggested that genetic distance was not correlated with geographical distance, but had a significant correlation with environmental distance. Further associations between the genetic data and five environmental factors were analyzed using whole-genome association analysis. SNPs associated with each environmental factor were investigated and genes 250 kb upstream and downstream from associated SNPs were annotated. Overall, 15 marker-trait-associated SNPs (MTAs) and 293 genes under environmental selection were identified. The identified genes were involved in cell membrane lipid metabolism, macromolecular complexes, catalytic activity and other related aspects. Ecological niche modeling was used to simulate the distribution of C. ficifolia across time, from the present and into the future. We found that the area suitable for C. ficifolia changed with the changing climate in different periods.

Conclusions
Resequencing of the C. ficifolia accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs identified in this study suggest that environmental factors mediated the formation of the population structure of C. ficifolia in China. These SNPs and Indels might also contribute to the variation in important pathways of genes for important agronomic traits such as yield, disease resistance and stress tolerance. Moreover, the genome resequencing data and the genetic markers identified from 223 accessions provide insight into the genetic variation of the C. ficifolia germplasm and will facilitate a broad range of genetic studies.
Better performance for right-skewed data using an alternative gamma model
Authors: Veazie Peter , Intrator Orna , Kinosian Bruce , Phibbs Ciaran S. 
Published: December 2023

Abstract
Background
The Maximum Likelihood Estimator (MLE) for parameters of the gamma distribution is commonly used to estimate models of right-skewed variables such as costs, hospital length of stay, and appointment wait times in Economics and Healthcare research. The common specification for this estimator assumes the variance is proportional to the square of the mean, which underlies estimation and specification tests. We present a specification in which the variance is directly proportional to the mean.

Methods
We used simulation experiments to investigate finite sample results, and we used United States Department of Veterans Affairs (VA) healthcare cost data as an empirical example comparing the fit and predictive ability of the models.

Results
Simulation showed the MLE based on a correctly specified alternative has less parameter bias, lower standard errors, and less skewness in distribution than a misspecified standard model. The application to VA healthcare cost data showed the alternative specification can have better R square, smaller root mean squared error, and smaller mean residuals within deciles of predicted values.

Conclusions
The alternative gamma specification can be a useful alternative to the standard specification for estimating models of right-skewed continuous variables.
Effect of different types of supervised exercise programs on cardiorespiratory and muscular fitness, pain, fatigue, mental health and inflammatory and oxidative stress biomarkers in older patients with post-COVID-19 sequelae “EJerSA-COVID-19”: a randomized controlled trial
Authors: Pleguezuelos Eulogio , Sánchez-Nuño Sergio , Del Carmen Amin , Serra-Payá Noemí , Moreno Eva , Molina-Raya Lorena , Robleda Gemma , Benet Marta , Santos-Ruiz Susana , Garrido Ainoa Biurrun , Jerez-Molina Carmen , Miravitlles Marc , Serra-Prat Mateu , Viñals Xavier , Farrés Montserrat Girabent , Carbonell Teresa , Garnacho-Castaño Manuel V. 
Published: December 2023

Abstract
Background
Many patients with COVID-19 present the so-called post-acute sequelae of COVID-19 such as fatigue, post-stress discomfort, dyspnea, headache, pain mental impairment, incapacity to perform daily physical tasks ant exercise intolerance. This study aims to investigate the effects of different exercise programs on physical and mental fitness, physical condition and biomarkers of the immune system and oxidative stress in older patients with post-COVID-19 sequelae.

Methods
The sample will be made up of 120 eligible participants, over the age of 60 years who have had COVID-19 disease and are survivors and present persistent COVID-19 symptomatology diagnosed by the corresponding physician. The participants will be randomly assigned to the experimental groups: supervised endurance group (SEG, n = 30), supervised strength group (SSG, n = 30), supervised concurrent group (SCG, n = 30), which will perform the corresponding exercise program 3 days a week compared to the control group (CG, n = 30), which will not carry out a supervised exercise program. The design of this project will include measurements of four relevant dimensions; 1) Cardiorespiratory fitness; 2) Muscle fitness; 3) Pain and mental health; and 4) Biomarkers of inflammation and oxidative stress.

Conclusions
The results of this study will provide insights into the effects of different exercise programs on physical and mental fitness, physical condition and biomarkers of the immune system and oxidative stress in older patients with post-COVID-19 sequelae. These findings may be the basis for the formulation of health plans and rehabilitation programs that allow healthy aging and a reduction in the associated morbidity in patients with post-COVID-19 sequelae.

Trial registration
NCT05848518. Registered on May 8, 2023.
Meta-analysis of outcomes following intravenous thrombolysis in patients with ischemic stroke on direct oral anticoagulants
Authors: Behnoush Amir Hossein , Khalaji Amirmohammad , Bahiraie Pegah , Gupta Rahul 
Published: December 2023

Abstract
Background
There has been debate on the use of intravenous thrombolysis (IVT) in patients with ischemic stroke and the recent use of direct oral anticoagulants (DOACs). Studies have compared these patients with non-DOAC groups in terms of outcomes. Herein, we aimed to systematically investigate the association between DOAC use and IVT’s efficacy and safety outcomes.

Results
A comprehensive systematic search was performed in PubMed, Embase, Scopus, and the Web of Science for the identification of relevant studies. After screening and data extraction, a random-effect meta-analysis was performed to calculate the odds ratio (OR) and 95% confidence interval (CI) for comparison of outcomes between patients on DOAC and controls. Six studies were included in the final review. They investigated a total of 254,742 patients, among which 3,499 had recent use of DOACs. The most commonly used DOACs were rivaroxaban and apixaban. The patients on DOAC had significantly higher rates of atrial fibrillation, hypertension, diabetes, and smoking. Good functional outcome defined by modified Rankin Scale (mRS) 0–2 was significantly lower in patients who received DOACs (OR 0.71, 95% CI 0.62 to 0.81, P < 0.01). However, in the subgroup analysis of 90-day mRS 0–2, there was no significant difference between groups (OR 0.71, 95% 0.46 to 1.11, P = 0.14). All-cause mortality was not different between the groups (OR 1.02, 95% CI 0.68 to 1.52, P = 0.93). Similarly, there was no significant difference in either of the in-hospital and 90-day mortality subgroups. Regarding symptomatic intracranial hemorrhage (sICH), the previous DOAC use was not associated with an increased risk of bleeding (OR 0.98, 95% CI 0.69 to 1.39, P = 0.92). A similar finding was observed for the meta-analysis of any ICH (OR 1.15, 95% CI 0.94 to 1.40, P = 0.18).

Conclusions
Based on our findings, IVT could be considered as a treatment option in ischemic stroke patients with recent use of DOACs since it was not associated with an increased risk of sICH, as suggested by earlier studies. Further larger studies are needed to confirm these findings and establish the safety of IVT in patients on DOAC.
Clinical value of ultrasonic indicators in predicting the outcome of caesarean scar pregnancy after pregnancy termination
Authors: Fu Liye , Yuan Hongxia , Cao Hong , Zhou Qichang , Tan Xiaotan , Guo Jun 
Published: December 2023

Abstract
Background
To investigate the predictive value of ultrasound indicators in early pregnancy for the outcome of caesarean scar pregnancy (CSP) after pregnancy termination.

Methods
This study retrospectively analysed the ultrasound images of 98 CSP patients who underwent transabdominal ultrasound-guided hysteroscopic curettage during early pregnancy at Changsha Hospital for Maternal and Child Health Care between January 2017 and October 2021. Patients were equally divided into a case group and a control group. The case group included 49 CSP patients with postoperative complications, such as intraoperative blood loss ≥ 200 ml or retained products of conception (RPOC). The remaining 49 CSP patients, with similar age and gestational age and with good postoperative outcomes, such as intraoperative blood loss ≤ 50 ml and no RPOC, were included in the control group. CSP was classified into three types according to the location of the gestational sac (GS) relative to the uterine cavity line (UCL) and serosal contour. Differences in ultrasound indicators between the case and control group were compared.

Results
There were significant differences between the case and control groups in the mean gestational sac diameter (MGSD), residual myometrium thickness (RMT) between the GS and the bladder, blood flow around the GS at the site of the previous caesarean incision, and types of CSP (P < 0.05). The rs of each ultrasound indicator were as follows: 0.258, -0.485, 0.369, 0.350. The optimal threshold for predicting good postoperative outcomes, such as intraoperative blood loss ≤ 50 ml and no RPOC, by receiver operating characteristic (ROC) curve analysis of the RMT was 2.3 mm.

Conclusion
Our findings show that the RMT, blood flow around the GS at the site of the previous caesarean incision, and types of CSP have a low correlation with postoperative complications, such as intraoperative blood loss ≥ 200 ml or RPOC, of early pregnancy termination in patients with CSP. To some extent, this study may be helpful for clinical prognostic prediction of patients with CSP and formulation of treatment strategies. Given the low correlation between these three indicators and postoperative complications, further studies are needed to identify indicators that can better reflect the postoperative outcomes of CSP patients.
An exploratory qualitative study of the psychological effects of HIV diagnosis; the need for early involvement of mental health professionals to improve linkage to care
Authors: Ninnoni Jerry Paul , Nsatimba Frederick , Agyemang Sampson Opoku , Commey Isaac Tetteh , Bennin Lydia , Agyare Elizabeth , Gyimah Leveana , Senya Kafui , Baddoo Nyonuku Akosua , Obiri-Yeboah Dorcas 
Published: December 2023

Abstract
Background
Diagnosing a life-threatening disease like the human immunodeficiency virus (HIV) can be unbearable to the individual, which has implications for their subsequent care-seeking decision-making. However, an essential element of HIV testing is identifying infected individuals and linking them with adequate care services, thus contributing to the UNAIDS 95-95-95 targets. The attainment of these targets has been particularly challenging for lower and middle-income countries (LMIC). This study explored the psychological reactions to a positive HIV status in a hospital treatment centre to provide insight into mental health interventions’ role in improving HIV screening and early antiretroviral therapy (ART) initiation to enhance the quality of life.

Methods
An exploratory qualitative study was investigated among adults who were diagnosed as HIV positive. Participants were purposively recruited from an HIV Treatment Centre. Data were collected with semi-structured interviews that explored the interpretations and psychological reactions to their positive HIV status. Overall, 18 participants were interviewed to reach saturation. Data were transcribed verbatim and analysed thematically to produce findings that address the study’s objective.

Results
Following analysis of participants’ interpretations, understanding and implications of their HIV-positive diagnosis, two major themes emerged: (1) anxiety regarding the impact of the disease on self, family and society was overwhelming. Participants were anxious because of the stigma, fear, worry, shock, and shame they faced. (2) Participants expressed hopelessness and could not see meaning or purpose in life. Suicidal ideation, suicide plans and self-harm characterised hopelessness.

Conclusions
The initial reaction to the diagnosis of HIV in this LMIC context has the potential to impact linkage to care negatively and, thus, the attainment of the global 95-95-95 targets. It is, therefore, essential that mental health and psychological support services are integrated with testing services to manage the initial reactions and support individuals to improve early linkage to care and thus improve overall outcomes for the infected individual and society.