bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tropical Cyclones in the GEOS-S2S-2 Subseasonal Forecasts
Authors: García-Franco Jorge L. , Lee Chia-Ying , Camargo Suzana J. , Tippett Michael K. , Emlaw Geraldine N. , Kim Daehyun , Lim Young-Kwon , Molod Andrea 
Published: July 2024

Abstract
This paper analyzes the climatology, prediction skill, and predictability of tropical cyclones (TCs) in NASA’s Goddard Earth Observing System Subseasonal to Seasonal (GEOS-S2S) forecast system version 2. GEOS reasonably simulates the number and spatial distribution of TCs compared to observations except in the Atlantic where the model simulates too few TCs due to low genesis rates in the Caribbean Sea and Gulf of Mexico. The environmental conditions, diagnosed through a genesis potential index, do not clearly explain model biases in the genesis rates, especially in the Atlantic. At the storm scale, GEOS reforecasts replicate several key aspects of the thermodynamic and dynamic structures of observed TCs, such as a warm core and the secondary circulation. The model, however, fails to simulate an off-center eyewall when evaluating vertical velocity, precipitation, and moisture. The analysis of the prediction skill of TC genesis and occurrence shows that GEOS has comparable skill to other global models in WMO S2S archive and that its skill could be further improved by increasing the ensemble size. After calibration, GEOS forecasts are skillful in the western North Pacific and southern Indian Ocean up to 20 days in advance. A model-based predictability analysis demonstrates the importance of the Madden–Julian oscillation (MJO) as a source of predictability of TC occurrence beyond the 14-day lead time. Forecasts initialized under strong MJO conditions show evidence of predictability beyond week 3. However, due to model biases in the forecast distribution, there are notable gaps between the MJO-related prediction skill and predictability, which require further study.
Inhibition of 2-AG hydrolysis alleviates posttraumatic headache attributed to mild traumatic brain injury
Authors: Wen Jie , Tanaka Mikiei , Zhang Yumin 
Published: July 2024

Abstract
Background
Posttraumatic headache (PTH) is a common and debilitating symptom following repetitive mild traumatic brain injury (rmTBI), and it mainly resembles a migraine-like phenotype. While modulation of the endocannabinoid system (ECS) is effective in treating TBI and various types of pain including migraine, the role of augmentation of endocannabinoids in treating PTH has not been investigated.

Methods
Repetitive mild TBI was induced in male C57BL/6J mice using the non-invasive close-head impact model of engineered rotational acceleration (CHIMERA). Periorbital allodynia was assessed using von Frey filaments and determined by the “Up-Down” method. Immunofluorescence staining was employed to investigate glial cell activation and calcitonin gene-related peptide (CGRP) expression in the trigeminal ganglion (TG) and trigeminal nucleus caudalis (TNC) of the rmTBI mice. Levels of 2-arachidonoyl glycerol (2-AG), anandamide (AEA), and arachidonic acid (AA) in the TG, medulla (including TNC), and periaqueductal gray (PAG) were measured by mass spectrometry. The therapeutic effect of endocannabinoid modulation on PTH was also assessed.

Results
The rmTBI mice exhibited significantly increased cephalic pain hypersensitivity compared to the sham controls. MJN110, a potent and selective inhibitor of the 2-AG hydrolytic enzyme monoacylglycerol lipase (MAGL), dose-dependently attenuated periorbital allodynia in the rmTBI animals. Administration of CGRP at 0.01 mg/kg reinstated periorbital allodynia in the rmTBI animals on days 33 and 45 post-injury but had no effect in the sham and MJN110 treatment groups. Activation of glial cells along with increased production of CGRP in the TG and TNC at 7 and 14 days post-rmTBI were attenuated by MJN110 treatment. The anti-inflammatory and anti-nociceptive effects of MJN110 were partially mediated by cannabinoid receptor activation, and the pain-suppressive effect of MJN110 was completely blocked by co-administration of DO34, an inhibitor of 2-AG synthase. The levels of 2-AG in TG, TNC and PAG were decreased in TBI animals, significantly elevated and further reduced by the selective inhibitors of 2-AG hydrolytic and synthetic enzymes, respectively.

Conclusion
Enhancing endogenous levels of 2-AG appears to be an effective strategy for the treatment of PTH by attenuating pain initiation and transmission in the trigeminal pathway and facilitating descending pain inhibitory modulation.
The interactive effects of different exercises and hawthorn consumption on the pain threshold of TMT-induced Alzheimer male rats
Authors: Almasi Ensiyeh , Heidarianpour Ali , Keshvari Maryam 
Published: July 2024

AbstractExercise increases the pain threshold in healthy people. However, the pain threshold modulation effect of exercise and hawthorn is unclear because of its potential benefits in people with persistent pain, including those with Alzheimer's disease. Accordingly, after the induction of Alzheimer's disease by trimethyl chloride, male rats with Alzheimer's disease were subjected to a 12-week training regimen consisting of resistance training, swimming endurance exercises, and combined exercises. In addition, hawthorn extract was orally administered to the rats. Then, their pain threshold was evaluated using three Tail-flick, Hot-plate, and Formalin tests. Our results showed that Alzheimer's decreased the pain threshold in all three behavioral tests. Combined exercise with hawthorn consumption had the most statistically significant effect on Alzheimer's male rats' pain threshold in all three experiments. A combination of swimming endurance and resistance exercises with hawthorn consumption may modulate hyperalgesia in Alzheimer's rats. Future studies need to determine the effects of these factors on the treatment and/or management of painful conditions.
Graphical Abstract
PyChelator: a Python-based Colab and web application for metal chelator calculations
Authors: Spahiu Emrulla , Kastrati Esra , Amrute-Nayak Mamta 
Published: July 2024

Abstract
Background
Metal ions play vital roles in regulating various biological systems, making it essential to control the concentration of free metal ions in solutions during experimental procedures. Several software applications exist for estimating the concentration of free metals in the presence of chelators, with MaxChelator being the easily accessible choice in this domain. This work aimed at developing a Python version of the software with arbitrary precision calculations, extensive new features, and a user-friendly interface to calculate the free metal ions.

Results
We introduce the open-source PyChelator web application and the Python-based Google Colaboratory notebook, PyChelator Colab. Key features aim to improve the user experience of metal chelator calculations including input in smaller units, selection among stability constants, input of user-defined constants, and convenient download of all results in Excel format. These features were implemented in Python language by employing Google Colab, facilitating the incorporation of the calculator into other Python-based pipelines and inviting the contributions from the community of Python-using scientists for further enhancements. Arbitrary-precision arithmetic was employed by using the built-in Decimal module to obtain the most accurate results and to avoid rounding errors. No notable differences were observed compared to the results obtained from the PyChelator web application. However, comparison of different sources of stability constants showed substantial differences among them.

Conclusions
PyChelator is a user-friendly metal and chelator calculator that provides a platform for further development. It is provided as an interactive web application, freely available for use at https://amrutelab.github.io/PyChelator, and as a Python-based Google Colaboratory notebook at https://colab.research.google.com/github/AmruteLab/PyChelator/blob/main/PyChelator_Colab.ipynb.
AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides
Authors: Darabi Amin , Sobhani Sayeh , Aghdam Rosa , Eslahchi Changiz 
Published: July 2024

Abstract

Background

Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.

Results

In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.

Conclusion

The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.

Availability

A python package is available at: https://github.com/SayehSobhani/AFITBin.
Effective population size in field pea
Authors: Johnson Josephine Princy , Piche Lisa , Worral Hannah , Atanda Sikiru Adeniyi , Coyne Clarice J. , McGee Rebecca J. , McPhee Kevin , Bandillo Nonoy 
Published: July 2024

Abstract
Background
Effective population size (Ne) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and the contemporary status of genetic diversity in breeding populations. The population with smaller Ne can lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance of Ne has become increasingly recognized in plant breeding, which can help breeders monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the first Ne estimates based on linkage disequilibrium (LD) in the pea genome.

Results
We calculated and compared Ne using SNP markers from North Dakota State University (NDSU) modern breeding lines and United States Department of Agriculture (USDA) diversity panel. The extent of LD was highly variable not only between populations but also among different regions and chromosomes of the genome. Overall, NDSU had a higher and longer-range LD than the USDA that could extend up to 500 Kb, with a genome-wide average r2 of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated Ne for the USDA was nearly three-fold higher (Ne = 174) than NDSU (Ne = 64), which can be confounded by a high degree of population structure due to the selfing nature of pea.

Conclusions
Our results provided insights into the genetic diversity of the germplasm studied, which can guide plant breeders to actively monitor Ne in successive cycles of breeding to sustain viability of the breeding efforts in the long term.
Preoperative psychological factors influence analgesic consumption and self-reported pain intensity following breast cancer surgery
Authors: Masaud Khaled , Galvin Audrey Dunn , De Loughry Gillian , Meachair Aisling O. , Galea Sarah , Shorten George 
Published: July 2024

Abstract
Background
Psychological factors such as anxiety and mood appear to influence acute postoperative pain; however, there is conflicting evidence on the relationship between preoperative psychological parameters and the severity of postoperative pain. In the context of the stressful setting of initial surgery for breast cancer, we conducted a prospective observational study of patients who were scheduled to undergo initial breast cancer surgery.

Methods
The objectives were to examine the potential associations between predefined preoperative psychological parameters and (i) Self-reported pain scores at discharge from the postoperative acute care unit, (ii) Cumulative perioperative opioid consumption at four hours postoperatively and (iii) Self-reported pain as measured during the first seven days after surgery. Patients completed the following questionnaires during the three hours prior to surgery: the Spielberger State Trait Anxiety Inventory (STAI State and Trait), the Pain Catastrophizing Scale (PCS), the Cohen Stress Questionnaire (CSQ), the Hospital Anxiety and Depression Scale (HADS A and D), and the short-form McGill Pain Questionnaire. Postoperative pain experience was assessed using patient self-reports of pain (SF Magill Pain questionnaire on discharge from the postanaesthesia care unit and a pain diary for seven days postoperatively) and records of analgesic consumption.

Results
Pre- to postoperative self-reported pain was significantly different with respect to the STAI State, Cohen score and PCS for both low and high values (p < 0.001), but only patients categorized as having low STAI Trait, HADS A, and HADS D values achieved significant differences (p < 0.001). A significant positive correlation was demonstrated between preoperative state anxiety (STAI) and the most severe pain reported during the first seven days postoperatively (r = 0.271, p = 0.013). Patients who were categorized preoperatively as having a “high value” for each of the psychological parameters studied (HADS A and D, STAI State and Trait and PCS) tended to have greater perioperative opioid consumption (up to four hours postoperatively); this trend was statistically significant for HADS D and HADS A only. Using a linear regression model, state anxiety was found to be a significant predictor of postoperative pain based on self-reports during the first seven postoperative days (standardized β = 0.271, t = 2.286, p = 0.025).

Conclusion
Preoperative state anxiety, in particular, is associated with the severity of postoperative pain experienced by women undergoing initial breast cancer surgery. Formal preoperative assessment of anxiety may be warranted in this setting with a view to optimize perioperative analgesia and wellbeing.
M1 macrophage-derived exosomes inhibit cardiomyocyte proliferation through delivering miR-155
Authors: He Xiaoqing , Liu Shan , Zhang Zhanyu , Liu Qirui , Dong Juan , Lin Zhifeng , Chen Junhao , Li Lihuan , Liu Weihua , Liu Shaojun , Liu Shiming 
Published: July 2024

Abstract
Background
M1 macrophages are closely associated with cardiac injury after myocardial infarction (MI). Increasing evidence shows that exosomes play a key role in pathophysiological regulation after MI, but the role of M1 macrophage-derived exosomes (M1-Exos) in myocardial regeneration remains unclear. In this study, we explored the impact of M1 macrophage-derived exosomes on cardiomyocytes regeneration in vitro and in vivo.

Methods
M0 macrophages were induced to differentiate into M1 macrophages with GM-CSF (50 ng/mL) and IFN-γ (20 ng/mL). Then M1-Exos were isolated and co-incubated with cardiomyocytes. Cardiomyocyte proliferation was detected by pH3 or ki67 staining. Quantitative real-time PCR (qPCR) was used to test the level of miR-155 in macrophages, macrophage-derived exosomes and exosome-treated cardiomyocytes. MI model was constructed and LV-miR-155 was injected around the infarct area, the proliferation of cardiomyocytes was counted by pH3 or ki67 staining. The downstream gene and pathway of miR-155 were predicted and verified by dual-luciferase reporter gene assay, qPCR and immunoblotting analysis. IL-6 (50 ng/mL) was added to cardiomyocytes transfected with miR-155 mimics, and the proliferation of cardiomyocytes was calculated by immunofluorescence. The protein expressions of IL-6R, p-JAK2 and p-STAT3 were detected by Western blot.

Results
The results showed that M1-Exos suppressed cardiomyocytes proliferation. Meanwhile, miR-155 was highly expressed in M1-Exos and transferred to cardiomyocytes. miR-155 inhibited the proliferation of cardiomyocytes and antagonized the pro-proliferation effect of interleukin 6 (IL-6). Furthermore, miR-155 targeted gene IL-6 receptor (IL-6R) and inhibited the Janus kinase 2(JAK)/Signal transducer and activator of transcription (STAT3) signaling pathway.

Conclusion
M1-Exos inhibited cardiomyocyte proliferation by delivering miR-155 and inhibiting the IL-6R/JAK/STAT3 signaling pathway. This study provided new insight and potential treatment strategy for the regulation of myocardial regeneration and cardiac repair by macrophages.
Gender differences in presentation, management, and outcomes among Egyptian patients with acute coronary syndrome: a single-centre registry
Authors: Elbarbary Mohammed , Shalaby Hazem K. , Elshokafy Salma M. , Khalil Mohamed A. 
Published: July 2024

Abstract
Background
Despite a significant rise in cardiovascular disease (CVD)-related mortality in low- and middle-income countries (LMICs), data are scarce regarding the quality of care provided, particularly for women.

Methods
This is a prospective observational, cross-sectional study. Acute coronary syndrome (ACS) patients presented to the Cardiology Department at Tanta University, Egypt, between September 1, 2023, and December 31, 2023, were enrolled. The study assessed gender disparities by comparing men and women regarding presentation, management, and major adverse cardiovascular events (MACE) occurrence during hospitalization and 30 days after discharge.

Results
A total of 400 ACS patients were included, with 29.5% being women. Women were comparatively older (59 ± 9 years vs. 55 ± 13 years), with a significantly higher prevalence of hypertension (70.3% vs. 47.5%) and diabetes (55% vs. 36.8%). Non-ST-segment elevation myocardial infarction (Non-STEMI) was more common in women (35.29% vs. 21%). Dyspnea was expressed by 34.4% of women (vs. 21.35% of men). Women were hospitalized later (9.29 h vs. 6.74 h). In-hospital outcomes were poorer for women with worse NYHA classes III and IV. Additionally, the odds ratio (OR) for in-hospital cardiac mortality was 0.303 (95% CI 0.103–0.893) for women compared to men. However, a one-month follow-up for MACE post-hospital discharge did not indicate significant gender differences.

Conclusions
The current study suggests that women with ACS in Egypt exhibit a higher risk profile for CVD compared to men and tend to present later with atypical symptoms. Women additionally experience poorer in-hospital MACE and higher cardiac mortality. Therefore, increasing awareness about ACS syndrome and eliminating obstacles that delay hospital admission are imperative.
Comprehensive imaging evaluation of the aortic valve and root before aortic root surgery: a study comparing MDCT and TEE
Authors: Li Yuan , Zhang Shuai , Qi Hongxia , Ma Xiaoyan , Qian Xiangyang , Sun Jing 
Published: July 2024

Abstract
Objective
To investigate the accuracy and consistency of MDCT and TEE in the preoperative assessment of aortic root surgery.

Methods
From January 2021 to September 2022, 118 patients who underwent aortic root surgery were included in this study. All patients underwent high-quality preoperative MDCT and TEE examinations, and the examination results were independently measured and assessed by two senior radiologists or ultrasound specialists. Bland–Altman analysis and Pearson correlation testing were employed to assess the correlation and consistency between MDCT and TEE. These analyses were then compared with actual intraoperative measurement data.

Results
Among all the patients, 73 (61.86%) had tricuspid aortic valve (TAV), and 45 (38.14%) had bicuspid aortic valve (BAV). A comparison between the TEE and MDCT measurements showed that for the annulus diameter, the area-derived diameter had the best correlation and agreement. For the sinus of Valsalva diameter, the circumference-derived diameter was optimal. However, for the STJ diameter, the minimum cross-sectional diameter showed the best agreement with TEE. In contrast, measurements of geometric height showed a weaker correlation and agreement.

Conclusion
Contrast-enhanced MDCT can be a valuable tool for perioperative evaluation in aortic root surgery, with good correlation, consistency, and feasibility when compared to TEE. The choice of MDCT measurement methodology, specifically area-derived and circumference-derived diameter, proved to be more accurate than other methods. Further research is required to enhance the understanding of aortic valve repair and associated imaging techniques.
Hypothesis testing and sample size considerations for the test-negative design
Authors: Huo Yanan , Yang Yang , Halloran M. Elizabeth , Longini Ira M. , Dean Natalie E. 
Published: July 2024

AbstractThe test-negative design (TND) is an observational study design to evaluate vaccine effectiveness (VE) that enrolls individuals receiving diagnostic testing for a target disease as part of routine care. VE is estimated as one minus the adjusted odds ratio of testing positive versus negative comparing vaccinated and unvaccinated patients. Although the TND is related to case–control studies, it is distinct in that the ratio of test-positive cases to test-negative controls is not typically pre-specified. For both types of studies, sparse cells are common when vaccines are highly effective. We consider the implications of these features on power for the TND. We use simulation studies to explore three hypothesis-testing procedures and associated sample size calculations for case–control and TND studies. These tests, all based on a simple logistic regression model, are a standard Wald test, a continuity-corrected Wald test, and a score test. The Wald test performs poorly in both case–control and TND when VE is high because the number of vaccinated test-positive cases can be low or zero. Continuity corrections help to stabilize the variance but induce bias. We observe superior performance with the score test as the variance is pooled under the null hypothesis of no group differences. We recommend using a score-based approach to design and analyze both case–control and TND. We propose a modification to the TND score sample size to account for additional variability in the ratio of controls over cases. This work enhances our understanding of the data generating mechanism in a test-negative design (TND) and how it is distinct from that of a case-control study due to its passive recruitment of controls.