bluuebunny/crossref_metadata_2025_split huggingface dataset:
Univariate Flux Partition Functions for Planetary Boundary Layer Schemes at Gray Zone Resolutions
Authors: Liu Mengjuan , Huang Wei , Chu Hai , Zhou Bowen 
Published: January 2024

Abstract
When the horizontal grid spacing of a numerical weather prediction model approaches kilometer scale, the so-called gray zone range, turbulent fluxes in the convective boundary layer (CBL) are partially resolved and partially subgrid scale (SGS). Knowledge of the partition between resolved and SGS turbulent fluxes is key to building scale-adaptive planetary boundary layer (PBL) schemes that are capable of regulating the SGS fluxes with varying grid spacing. However, flux partition depends not only on horizontal grid spacing, but also on local height, bulk stability of the boundary layer, and the particular turbulent flux. Such multivariate functions are difficult to construct analytically, so their implementations in scale-adaptive PBL schemes always involve certain levels of approximation that can lead to inaccuracies. This study introduces a physically based perspective for the flux partition functions that greatly simplifies their implementation with high accuracy. By introducing an appropriate scaling length λ that accounts for both height and bulk stability dependencies, the dimensionality of the partition functions is reduced to a single dimensionless group. Based on the analysis of a comprehensive large-eddy simulation dataset of the CBL, it is further shown that λ’s height and bulk stability dependencies can be separately represented by a similarity length scale and a stability coefficient. The resulting univariate partition functions are incorporated into a traditional first-order PBL scheme as a proof of concept. Our results show that the augmented scheme well-reproduces the SGS fluxes at gray zone resolutions.

Significance Statement
Flux partition functions are a key component in most scale-adaptive planetary boundary layer (PBL) schemes developed for kilometer- and subkilometer-resolution numerical weather prediction models. They regulate the parameterized turbulent fluxes as a function of horizontal grid spacing, while they also depend on height and atmospheric stability. Such multivariate dependencies forbid simple analytical expressions, and as a result, partition functions implemented in scale-adaptive PBL schemes are generally simplified at the cost of accuracy in previous works. This study investigates the possibility of constructing partition functions that are both accurate and easy to parameterize. Utilizing a physically based length scale, univariate partition functions are built, evaluated, and put into a conventional PBL scheme to improve the gray zone turbulence parameterization.
Evaluation method for embedment stiffness of metal washers in bolted timber joints using torque gradient and nut factor
Authors: Matsubara Doppo , Teranishi Masaki , Mori Takuro 
Published: January 2024

AbstractAssessing the residual performance of timber joints affected by decay is important for seismic diagnosis and reinforcement of timber structures. This study introduces a method to evaluate the embedment stiffness of metal washers in bolted timber joints using a torque wrench. Formulas for the embedment stiffness of metal washers using the torque gradient (the gradient of the tightening torque against the tightening rotation angle of the nut) and the nut factor are presented and the calculated values are compared with experimental values obtained by conducting tightening tests with a torque wrench and embedment tests of metal washers in bolted joints made from Japanese cedar, Hiba, and Japanese cypress. The results show that the experimental values of the embedment stiffness of metal washers in Japanese cedar and Hiba are generally within the range of the values calculated from the minimum and maximum values of the nut factor. However, for Japanese cypress, the values calculated from the maximum value of the nut factor exceed the experimental values. This was presumably due to locally large frictional forces generated on the bearing surface or threaded part.
Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity
Authors: Wijeratne Saranga , Gonzalez Maria E. Hernandez , Roach Kelli , Miller Katherine E. , Schieffer Kathleen M. , Fitch James R. , Leonard Jeffrey , White Peter , Kelly Benjamin J. , Cottrell Catherine E. , Mardis Elaine R. , Wilson Richard K. , Miller Anthony R. 
Published: January 2024

Abstract
Background
Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing has utility in providing a cost-effective approach for evaluating isoform expression, although short-read assembly displays limitations in the accurate inference of full-length transcripts. Long-read RNA sequencing (Iso-Seq), using the Pacific Biosciences (PacBio) platform, can overcome such limitations by providing full-length isoform sequence resolution which requires no read assembly and represents native expressed transcripts. A constraint of the Iso-Seq protocol is due to fewer reads output per instrument run, which, as an example, can consequently affect the detection of lowly expressed transcripts. To address these deficiencies, we developed a concatenation workflow, PacBio Full-Length Isoform Concatemer Sequencing (PB_FLIC-Seq), designed to increase the number of unique, sequenced PacBio long-reads thereby improving overall detection of unique isoforms. In addition, we anticipate that the increase in read depth will help improve the detection of moderate to low-level expressed isoforms.

Results
In sequencing a commercial reference (Spike-In RNA Variants; SIRV) with known isoform complexity we demonstrated a 3.4-fold increase in read output per run and improved SIRV recall when using the PB_FLIC-Seq method compared to the same samples processed with the Iso-Seq protocol. We applied this protocol to a translational cancer case, also demonstrating the utility of the PB_FLIC-Seq method for identifying differential full-length isoform expression in a pediatric diffuse midline glioma compared to its adjacent non-malignant tissue. Our data analysis revealed increased expression of extracellular matrix (ECM) genes within the tumor sample, including an isoform of the Secreted Protein Acidic and Cysteine Rich (SPARC) gene that was expressed 11,676-fold higher than in the adjacent non-malignant tissue. Finally, by using the PB_FLIC-Seq method, we detected several cancer-specific novel isoforms.

Conclusion
This work describes a concatenation-based methodology for increasing the number of sequenced full-length isoform reads on the PacBio platform, yielding improved discovery of expressed isoforms. We applied this workflow to profile the transcriptome of a pediatric diffuse midline glioma and adjacent non-malignant tissue. Our findings of cancer-specific novel isoform expression further highlight the importance of long-read sequencing for characterization of complex tumor transcriptomes.
Potential public health hazards related to consumption of poultry contaminated with antibiotic resistant Listeria monocytogenes in Egypt
Authors: Zakaria Amira Ibrahim , Sabala Rana Fahmi 
Published: January 2024

AbstractListeria monocytogenes is an important foodborne pathogen that incorporated into many serious infections in human especially immunocompromised individuals, pregnant women, the elderly, and newborns. The consumption of food contaminated with such bacteria is considered a source of potential risk for consumers. Therefore, a total of 250 poultry purchased in highly popular poultry stores besides 50 swabs from workers hands in the same stores, in Mansoura City had been tested for the L. monocytogenes prevalence, virulence genes, and antibiotic resistance profile illustrating the health hazards from such poultry. The L. monocytogenes were recovered from 9.6% of poultry samples while not detected from workers hand swabs. The antimicrobial susceptibility of 24 L. monocytogenes strains against 24 antibiotics of seven different classes revealed high susceptibility rates to erythromycin (79.17%), streptomycin (66.67%), gentamycin (66.67%), vancomycin (58.33%), chloramphenicol (58.33%) and cefotaxime (41.67%). The majority (79.2%) of L. monocytogenes were classified as multidrug resistant strains with high resistance to tetracyclines and β-lactams antibiotics while 16.7% of the strains were categorized as extensively resistant ones. The iap virulence-specific determination gene had been detected in all recovered L. monocytogenes isolates while 83.33 and 70.83% of the isolates harbored hylA and actA genes. In addition, the study confirmed the capability of most L. monocytogenes isolates for biofilm formation by moderate to strong production and the quantitative risk assessment illustrated the risk of developing listeriosis as the risk value exceeded 100. The current results illustrate that poultry meat can be a source of pathogenic antibiotic resistant strains that may cause infection with limited or no treatment in immunosuppressed consumers via the food chain.
Clinical factors associated with stable treatment of chronic constipation in Japanese patients
Authors: Ishibashi Kazuki , Urabe Yuji , Vu Nhu Thi Hanh , Miyauchi Shunsuke , Nakamura Takeo , Konishi Hirona , Mizuno Junichi , Fukuhara Motomitsu , Takigawa Hidehiko , Yuge Ryo , Quach Duc Trong , Oka Shiro , Hiyama Toru 
Published: January 2024

Abstract
Background/Aims
Chronic constipation (CC) is one of the most common gastrointestinal disorders in the general population. Although there are many treatment options, achieving a stable treatment for CC remains one of the challenges in clinical practice. This study aimed to evaluate the clinical factors associated with stable treatment for CC in Japanese patients.

Methods
A retrospective, cross-sectional, and multicenter study was carried out. Patients were eligible for inclusion if they fulfilled the Rome IV criteria for diagnosing CC and had been treated for at least one and a half years. Patients with up to two prescription modifications for CC in one year were defined as the stable treatment group, whereas those with three or more prescription changes were defined as the unstable treatment group. Univariate and multivariate analyses were carried out to identify factors associated with CC.

Results
A total of 114 patients have been recruited. There were 82 patients (77.0%) in the stable treatment group and 32 patients (23.0%) in the unstable treatment group. Based on multivariate likelihood analysis, only using acid-suppressive drugs contributed to stability treatment in CC patients (odds ratio: 2.81, 95% confidence interval: 1.12–7.08, p = 0.03).

Conclusion
Administration of acid-suppressive drugs was the only factor related to the stability of CC treatment. Further studies are needed to validate the results as well as clarify the causes.
Early encapsulation of peripancreatic fluid/necrosis collections on imaging (CECT) in acute pancreatitis: influential factors and clinical significance for prognosis
Authors: Ning Ning , Yu Congyi , Sun Wenwu , Wen Yi , Ni Tongtian , Sheng Huiqiu , Chen Ying , Ma Li , Chen Erzhen , Zhao Bing , Mao Enqiang 
Published: January 2024

Abstract
Background
To identify the factors influencing the early encapsulation of peripancreatic fluid/necrosis collections via contrast-enhanced computed tomography (CECT) and to determine the clinical significance of early encapsulation for determining the prognosis of acute pancreatitis (AP) patients.

Methods
AP patients who underwent CECT between 4 and 10 days after disease onset were enrolled in this study. Early encapsulation was defined as a continuous enhancing wall around peripancreatic fluid/necrosis collections on CECT. Univariate and multivariate logistic regression analyses were performed to assess the associations between the variables and early encapsulation. Clinical outcomes were compared between the non-encapsulation and early encapsulation groups with 1:1 propensity score matching.

Results
A total of 289 AP patients were enrolled. The intra-observer and inter-observer agreement were considered good (kappa statistics of 0.729 and 0.614, respectively) for identifying early encapsulation on CECT. The ratio of encapsulation increased with time, with a ratio of 12.5% on day 5 to 48.7% on day 9. Multivariate logistic regression analysis revealed that the longer time from onset to CECT examination (OR 1.55, 95% CI 1.23–1.97), high alanine aminotransferase level (OR 0.98, 95% CI 0.97–0.99), and high APACHE II score (OR 0.89, 95% CI 0.81–0.98) were found to be independent factors associated with delayed encapsulation. The incidence of persistent organ failure was significantly lower in the early encapsulation group after matching (22.4% vs 6.1%, p = 0.043). However, there was no difference in the incidence of infected pancreatic necrosis, surgical intervention, or in-hospital mortality.

Conclusions
AP patients without early encapsulation of peripancreatic fluid/necrosis collections have a greater risk of persistent organ failure. In addition to longer time, the high APACHE II score and elevated alanine aminotransferase level are factors associated with delayed encapsulation.
Effects of an integrated ambulatory care program on healthcare utilization and costs in older patients with multimorbidity: a propensity score-matched cohort study
Authors: Lo Yu-Tai , Chen Mei-Hua , Lu Tsung-Hsueh , Yang Ya-Ping , Chang Chia-Ming , Yang Yi-Ching 
Published: January 2024

Abstract
Background
Population aging has increased the prevalence of multimorbidity, jeopardizing the sustainability and efficiency of healthcare systems. This study aimed to evaluate the effects of an integrated ambulatory care program (IACP) on healthcare utilization and costs among older patients with multimorbidity while accounting for the confounding effects of frailty.

Methods
A retrospective cohort study using propensity matching including patients aged 65 or older with two or more chronic conditions attending the outpatient clinic at our hospital between June 1 and December 31, 2019, was conducted. Exposure was defined as receipt of IACP care. Patients not undergoing the IACP comprised the unexposed group and were matched at a ratio of 1:4 to patients undergoing the IACP group according to sex, age, Charlson Comorbidity Index score, multimorbidity frailty index score, and number of outpatient visits within 6 months before the index date. Outcomes were changes in healthcare utilization and related costs between 6 months before and after receiving IACP care. Multivariate regression analyses were used for data analysis and the Generalized Estimation Equation method was used to fit the regression models.

Results
A total of 166 (IACP) and 664 (non-exposed) patients were analyzed. The mean participant baseline ages were 77.15 ± 7.77 (IACP) and 77.28 ± 7.90 years (unexposed). In univariate analyses, the IACP group demonstrated greater reductions than the unexposed group in the frequency of outpatient visits (-3.16 vs. -1.36, p < 0.001), number of physicians visited (-0.99 vs. -0.17, p < 0.001), diagnostic fees (-1300 New Taiwan Dollar [NTD] vs. -520 NTD, p < 0.001), drug prescription fees (-250 NTD vs. -70 NTD, p < 0.001), and examination fees (-1620 NTD vs. -700 NTD, p = 0.014). Multivariate analyses demonstrated that patients in the IACP group experienced significant reduction in the frequency of outpatient visits (95% CI: -0.357 to -0.181, p < 0.001), number of physicians visited (95% CI: -0.334 to -0.199, p < 0.001), and overall outpatient costs (95% CI: -0.082 to -0.011, p = 0.01). However, emergency department utilization, hospitalization, and costs did not differ significantly.

Conclusions
Expanding IACPs may help patients with multimorbidity reduce their use of outpatient clinics at the 6-month follow-up, reduce care fragmentation, and promote sustainability of the healthcare system.
Factors affecting cognitive frailty improvement and progression in Taiwanese older adults
Authors: Suprawesta Lalu , Chen Sy-Jou , Liang Hui-Yu , Hwang Hei-Fen , Yu Wen-Yu , Lin Mau-Roung 
Published: January 2024

Abstract
Background
Knowledge of predictors of cognitive frailty (CF) trajectories is required to develop preventive strategies to delay or reverse the progression from CF to dementia and other adverse outcomes. This 2-year prospective study aimed to investigate factors affecting the progression and improvement of CF in older Taiwanese adults.

Methods
In total, 832 community-dwelling people aged ≥ 65 years were eligible. Fried’s five frailty criteria were used to measure prefrailty and frailty, while cognitive performance was assessed by the Clinical Dementia Rating and Mini-Mental State Examination. Each component of reversible CF and potentially reversible CF was assigned a score, with a total score ranging 0 to 5 points. Two annual follow-up CF assessments were conducted. The group-based trajectory model was applied to identify latent CF trajectory groups, and a multinomial logistic regression was used to examine relationships of explanatory variables with CF trajectories.

Results
According to data on 482 subjects who completed the two annual follow-ups, three CF trajectories of robust, improvement, and progression were identified. After adjusting for the baseline CF state, CF progression was significantly associated with an older age (odds ratio [OR] = 1.08; 95% confidence interval [CI], 1.02 ~ 1.14), a lower Tinetti balance score (OR = 0.72; 95% CI, 0.54 ~ 0.96), a slower gait (OR = 0.98; 95% CI, 0.97 ~ 0.99), and four or more comorbidities (OR = 2.65; 95% CI, 1.19 ~ 5.90), while CF improvement was not significantly associated with any variable except the baseline CF state. In contrast, without adjusting for the baseline CF state, CF progression was significantly associated with an older age, female sex, balance scores, gait velocity, regular exercise, the number of comorbidities, and depression, while CF improvement was significantly associated with female sex, balance scores, and the number of comorbidities.

Conclusions
The baseline CF state, an older age, poorer balance, slower gait, and a high number of comorbidities may contribute to CF progression, while the baseline CF state may account for associations of engaging in regular exercise and depression with CF development.
Prevalence of probable substance use disorders among children in Ugandan health facilities
Authors: Aber-Odonga Harriet , Babirye Juliet Ndimwibo , Engebretsen Ingunn Marie S. , Nuwaha Fred 
Published: January 2024

Abstract
Background
Globally, there is a concerning surge in the prevalence of substance use among adolescents and children, creating a substantial public health problem. Despite the magnitude of this issue, accessing healthcare explicitly for substance use remains challenging, even though many substance users frequently visit healthcare institutions for other health-related issues. To address this gap, proactive screening for substance use disorders has emerged as a critical strategy for identifying and engaging patients at risk of substance use. The purpose of this study was to investigate the prevalence of probable alcohol and other substance use disorders, and associated factors, among children aged 6 to 17 years old attending health facilities in Mbale, Uganda.

Methods
We conducted a health facility cross-sectional study, involving 854 children aged 6–17 years. The prevalence of probable alcohol and other substance use disorders was assessed using a validated Car, Relax, Alone, Forget, Friends, Trouble (CRAFFT) screening tool. Univariable and multivariable modified Poisson regression analyses were performed using STATA 15 software.

Results
The overall prevalence of probable alcohol use disorders (AUD) and other substance use disorders (SUD) was 27.8% (95% CI 1.24–1.31) while that of probable AUD alone was 25.3% (95% CI 1.22–1.28). Peer substance use (APR = 1.24, 95% CI 1.10–1.32), sibling substance use (APR = 1.14, 95% CI 1.06–1.23), catholic caregiver religion (APR = 1.07 95% CI 1.01–1.13), caregiver income of more than $128 (APR = 0.90, 95% CI 0.82–0.98), having no parental reprimand for substance use (APR = 1.05, 95% CI 1.01–1.10) and having no knowledge of how to decline an offer to use substances (APR = 1.06, 95% CI 1.01–1.12) were found to be significantly associated with probable AUD/SUD.

Conclusions
Our findings suggest a high prevalence of probable AUD and SUD among children and adolescents visiting healthcare facilities for other conditions, along with a strong link between AUD and SUD prevalence and social factors. The implication for our healthcare system is to actively screen for and treat these conditions at primary healthcare facilities.
COVID-19 information seeking and individuals’ protective behaviors: examining the role of information sources and information content
Authors: Zhang Xuefeng , Du Lin , Huang Yelin , Luo Xiao , Wang Fenglian 
Published: January 2024

Abstract
Background
Seeking COVID-19 information promotes individuals to adopt preventive behaviors, including wearing a mask, social distancing, staying away from risky places, and washing hands. This study aims to investigate which information and sources individuals relied on in seeking COVID-19 information and further examine their roles in individuals’ adoption of preventive behaviors.

Methods
Through a statistical analysis of 1027 valid responses from citizens in different Chinese cities in 2022 to the self-designed items in an online survey, this study identified individuals’ preferred information sources and content on COVID-19. Regarding the information sources and content, the study used multiple regression analysis to examine their associations with individuals’ preventive behaviors, and further applied fuzzy-set qualitative comparative analysis (fsQCA) to explore their configurations that increase the likelihood of individuals adopting preventive behaviors.

Results
Individuals preferred information about the newest prevention and control policies, precautions and treatment, and symptoms from the sources of workplace and community, social media, and social live streaming services. Additionally, individuals’ preventive behaviors were positively related to the workplace and community (β = 0.202, p <.001), social live streaming services (β = 0.089, p <.01), government department websites (β = 0.079, p <.05), television (β = 0.073, p <.05), and online news media (β = 0.069, p <.05), but were negatively associated with newspapers (β=-0.087, p <.05). Regarding information content, precautions and treatments (β = 0.211, p <.001), the newest prevention and control policies (β = 0.173, p <.001), symptoms (β = 0.152, p <.001), and official rumor-dispelling information (β = 0.082, p <.05) had a positive relationship with individuals’ preventive behaviors. In addition, fsQCA results presented eight configurations that promote individuals to adopt preventive behaviors. The total coverage and solution consistency values were 0.869 and 0.987, respectively. Furthermore, COVID-19 information content, the sources of social media and interpersonal sources, and official news media played an essential role in increasing the likelihood of individuals adopting preventive behaviors.

Conclusions
Our findings demonstrated that individuals seek various COVID-19 information from multiple sources. The direct and degree of association of information sources and content with individuals’ preventive behaviors vary from source to source and from content to content. Information sources and content could combinatorially promote individuals to adopt preventive behaviors through several configurations.