bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular detection of SARS-CoV-2 in domestic cats in close contact with positively-infected owners in Tehran, Iran in 2021
Authors: Saneei Dorsa , Jamshidi Shahram , Ghalyanchi Langeroudi Arash , Akbarein Hesamedin , Nadji Seyed Alireza , Shoarzargari Laleh , Salehi-Vaziri Mostafa , Moazezi Ghavihelm Ali , Hojabr Rajeoni Ali , Shahbazi Vahid 
Published: August 2023

Objectives In 2019, COVID-19 emerged in China and has since spread worldwide. Owing to the virus’s ability to adhere to specific receptors, cats are susceptible to infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The popularity of pet cats in Iran has sparked fears of human–cat–human transmission of the virus. This study aimed to identify positive cases in cats owned by people infected with SARS-CoV-2, to determine if they remained positive for >3 weeks and to examine the virus genome isolated from a number of cats and one of their owners. Methods A total of 30 cats were sampled approximately 3 days after their owners tested positive (day 1), and 3 weeks later, in strict accordance with health regulations. Rectal and oropharyngeal samples were collected. All samples were subjected to a qualitative PCR and reverse transcription PCR. The S-gene region was partially sequenced in positive samples and the results were used to create a phylogenetic tree. Results SARS-CoV-2 was detected in 7/30 (23.3%) cats examined. In the third week, every cat tested negative. The sequence data of positive cats and one of their owners revealed that the retrieved RNAs belonged to the alpha variation. The genetic distance between the samples and the reference sequence (20I/B.1.1.7: OM003849, MZ344997) was minimal, with a 99% similarity. Positive samples of cats had four mutations in gene S. Amino acid substitutions in the spike glycoprotein at positions N501Y, A570D, D614G and P681H were recorded in the isolates compared with 780 other sequences of Iranian strains. Conclusions and relevance This study confirmed the presence of SARS-CoV-2-infected cats living in close contact with infected owners. Despite cats’ susceptibility to COVID-19, the risk of severe infection in these animals is low, as evidenced by the lack of clinical signs in positive cats.
Machine learning-based prognostic modeling of patients with acute heart failure receiving furosemide in intensive care units
Authors: Kamio Tadashi , Ikegami Masaru , Machida Yoshihito , Uemura Tomoko , Chino Naotaka , Iwagami Masao 
Published: August 2023

Purpose This study developed machine learning models to predict in-hospital mortality, initiation of acute renal replacement therapy, and mechanical ventilation in patients with acute heart failure receiving furosemide in intensive care units. Method An extensive database comprising static and dynamic features obtained from a Japanese hospital chain was used to construct and train the machine learning models. Results The results revealed that the proposed machine learning models predict in-hospital mortality, initiation of acute renal replacement therapy, and mechanical ventilation with good accuracy. However, the optimal models vary depending on the predicted outcomes. The linear support vector machine classification models exhibited the highest in-hospital mortality and mechanical ventilation prediction accuracy, with the area under the receiver operating characteristic curve of 0.73 and 0.73, respectively, whereas the multi-layer neural network exhibited the highest accuracy for acute renal replacement therapy initiation prediction with an area under the receiver operating characteristic curve of 0.70. Conclusions In conclusion, this study demonstrated that machine learning models could help predict the clinical outcomes of patients with acute heart failure receiving furosemide. However, the optimal models may differ depending on the outcome of interest.
The Effect of Changes in Segmental Lordosis on Global Lumbar and Adjacent Segment Lordosis After L5-S1 Anterior Lumbar Interbody Fusion
Authors: Nguyen Austin Q. , Harvey Jackson P. , Federico Vincent P. , Nolte Michael T. , Khanna Krishn , Gandhi Sapan D. , Sheha Evan D. , Colman Matthew W. , Phillips Frank M. 
Published: August 2023

Study Design Retrospective Cohort Study. Objective Restoration of lordosis in lumbar fusion reduces low back pain, decreases adjacent segment degeneration, and improves postoperative outcomes. However, the potential effects of changes in segmental lordosis on adjacent-level and global lordosis remain less understood. This study aims to examine the relationships between segmental (SL), adjacent-level, and global lumbar lordosis following L5-S1 Anterior Lumbar Interbody Fusion (ALIF). Methods 80 consecutive patients who underwent single-level L5-S1 ALIF were divided into 3 groups based on the degree of change (∆) in index-level segmental lordosis: <5° (n = 23), 5°-10° (n = 29), >10° (n = 28). Radiographic parameters measured included global lumbar, segmental, and adjacent level lordosis, sacral slope, pelvic tilt, pelvic incidence, and PI-LL mismatch. Results Patients with ∆SL 5°-10° or ∆SL >10° both showed significant increases in global lumbar lordosis from preoperative to final follow-up. However, patients with ∆SL >10° showed statistically significant losses in adjacent level lordosis at both immediate postoperative and final follow-up compared to preoperative. When comparing patients with ∆SL >10° to those with ∆SL 5-10°, there were no significant differences in global lumbar lordosis at final follow-up, due to significantly greater losses of adjacent level lordosis in these patients. Conclusion The degree of compensatory loss of lordosis at the adjacent level L4-L5 correlated with the extent of segmental lordosis creation at the index L5-S1 level. This may suggest that the L4 to S1 segment acts as a “harmonious unit,” able to accommodate only a certain amount of lordosis and further increases in segmental lordosis may be mitigated by loss of adjacent-level lordosis.
Correlation Between Sagittal Balance and Mechanical Distal Junctional Failure in Degenerative Pathology of the Spine: A Retrospective Analysis
Authors: Montanari Sara , Griffoni Cristiana , Cristofolini Luca , Girolami Marco , Gasbarrini Alessandro , Barbanti Bròdano Giovanni 
Published: August 2023

Study design Retrospective cohort study. Objectives This study aimed to investigate the failure of the caudal end of lumbar posterior fixation in terms of pre-operative and post-operative spinopelvic parameters, correction performed, demographic and clinical data. Methods The lumbar, thoraco-lumbar and lumbo-sacral posterior fixations performed with pedicle screws and rods in 2017-2019 were retrospectively analyzed. As 81% failures occurred within 4 years, an observational period of 4 years was chosen. The revision surgeries due to the failure in the caudal end were collected in the junctional group. Fixations which have not failed were gathered in the control group. The main spinopelvic parameters were measured for each patient on standing lateral radiographs with the software Surgimap. Demographic and clinical data were extracted for both groups. Results Among the 457 patients who met the inclusion criteria, the junctional group included 101 patients, who required a revision surgery. The control group collected 356 primary fixations. The two most common causes of revision surgeries were screws pullout (57 cases) and rod breakage (53 cases). SVA, PT, LL, PI-LL and TPA differed significantly between the two groups ( P = .021 for LL, P < .0001 for all the others). The interaction between the two groups and the pre-operative and post-operative conditions was significant for PT, SS, LL, TK, PI-LL and TPA ( P < .005). Sex and BMI did not affect the failure onset. Conclusions Mechanical failure is more likely to occur in patients older than 40 years with a thoraco-lumbar fixation where PT, PI-LL and TPA were not properly restored.
Hip Arthroscopy for Femoroacetabular Impingement
Authors: Gwathmey F. Winston , Raghuwanshi Jasraj 
Published: August 2023

Background: Femoroacetabular impingement (FAI) is pain due to shape mismatch at the hip joint commonly affecting young athletes, and there are 2 main types depending on which bone has the underlying deformity: cam (femoral) and pincer (acetabular). Hip arthroscopy is an invaluable technique in the sports surgeon repertoire, and there is a need for a comprehensive tutorial that elucidates the best practices and nuances. Indications: Pain with evidence of FAI and labral tear on imaging, and failing conservative treatment, warrants arthroscopy. Technique Description: FAI surgery requires anatomical labral repair, thorough osteoplasty to correct the underlying deformity and prevent labral retearing, and careful treatment of soft tissues and capsular closure. Results: Reduced pain and improved hip function are the goals of treatment, with approximately 90% of patients returning to sport at 6 to 8 months postoperatively. Discussion/Conclusion: Hip arthroscopy is a safe and effective treatment for patients with FAI who failed conservative therapy. Patient Consent Disclosure Statement: The author(s) attests that consent has been obtained from any patient(s) appearing in this publication. If the individual may be identifiable, the author(s) has included a statement of release or other written form of approval from the patient(s) with this submission for publication.
Partial versus radical nephrectomy in pT2a renal cell carcinoma tumors: which is the superior surgical approach?
Authors: Basiri Abbas , Salehi Omran Hossein , Zahir Mazyar , Shakhssalim Nasser , Borumandnia Nasrin , Noghabaei Giti , Parvin Mahmoud 
Published: August 2023

AbstractBackgroundControversy persists regarding the superiority of partial nephrectomy (PN) versus radical nephrectomy (RN) in pT2a renal cell carcinoma (RCC) tumors. In this study we aimed to compare survival and clinical outcomes between these two techniques in Iran.MethodsIn this retrospective cohort, 96 patients who underwent either RN or PN for their pT2a RCC tumors were included. Overall survival (OS), cancer specific survival (CSS), recurrence free survival (RFS), major postoperative complications and postoperative renal function were compared, subsequently.ResultsDuring a mean follow-up time of 57.3 ± 24.0 months, OS, CSS, RFS, postoperative bleeding, postoperative urinary leak, postoperative prolonged wound drainage and length of hospital stay were not statistically different between RN versus PN patients (p = .09, .42, .09, .27, .27, .06 and .78, respectively). Nevertheless, post-operative creatinine was significantly lower in PN patients compared to RN patients (p = .01). Our multivariable cox regression models indicated that higher Fuhrman grade detrimentally affected CSS (p < .01) and increased the risk of recurrence (p = .02). Moreover, prior history of ischemic heart disease (IHD) was a significant determinant of lower OS (p = .03) and RFS (p = .02).ConclusionsIn conclusion, our data suggested that although OS, CSS, RFS and major postoperative complications were similar between PN and RN, PN may offer better postoperative renal function and can be thus regarded as the superior approach in pT2a tumors.
Effects of fungicides on aquatic fungi and bacteria: a comparison of morphological and molecular approaches from a microcosm experiment
Authors: Salis Romana K. , Schreiner Verena C. , Rozenberg Andrey , Ohler Katharina , Baudy-Groh Patrick , Schäfer Ralf B. , Leese Florian 
Published: August 2023

Abstract
Background
Fungicides are frequently used in agriculture and can enter freshwater ecosystems through multiple pathways. The negative impacts of fungicides on microorganisms, fungi in particular, and their functions such as leaf decomposition have been repeatedly shown. In our previous microcosm experiment with three consecutive cycles of fungicide exposure and colonisation of leaf substrate, we found clear functional changes, but no differences in fungal community structure could be detected using morphological identification by analysing the spores of aquatic hyphomycetes. In this study, we examined the effects on fungal and bacterial community composition in detail using ITS and 16S metabarcoding and comparing the results to morphologically assessed community composition.

Results
While we found fewer species with metabarcoding than with morphological identification, metabarcoding also enabled the identification of several fungal species that were otherwise unidentifiable morphologically. Moreover, by distinguishing individual amplicon sequence variants (ASVs) metabarcoding provided greater taxonomic resolution. In line with the morphological results, metabarcoding neither revealed effects of fungicides on the aquatic hyphomycetes nor on the total fungal or bacterial community composition. However, several ASVs responded significantly to fungicides, demonstrating variable tolerances within species.

Conclusions
Overall, the absence of detectable effects of fungicides on the community structure despite clear functional effects, suggests a complex relationship between community structure and the ecosystem function of leaf decomposition.
estimateR: an R package to estimate and monitor the effective reproductive number
Authors: Scire Jérémie , Huisman Jana S. , Grosu Ana , Angst Daniel C. , Lison Adrian , Li Jinzhou , Maathuis Marloes H. , Bonhoeffer Sebastian , Stadler Tanja 
Published: August 2023

AbstractBackgroundAccurate estimation of the effective reproductive number ($$R_e$$Re) of epidemic outbreaks is of central relevance to public health policy and decision making. We present estimateR, an R package for the estimation of the reproductive number through time from delayed observations of infection events. Such delayed observations include confirmed cases, hospitalizations or deaths. The package implements the methodology of Huisman et al. but modularizes the$$R_e$$Reestimation procedure to allow easy implementation of new alternatives to the currently available methods. Users can tailor their analyses according to their particular use case by choosing among implemented options.ResultsThe estimateR R package allows users to estimate the effective reproductive number of an epidemic outbreak based on observed cases, hospitalization, death or any other type of event documenting past infections, in a fast and timely fashion. We validated the implementation with a simulation study: estimateR yielded estimates comparable to alternative publicly available methods while being around two orders of magnitude faster. We then applied estimateR to empirical case-confirmation incidence data for COVID-19 in nine countries and for dengue fever in Brazil; in parallel, estimateR is already being applied (i) to SARS-CoV-2 measurements in wastewater data and (ii) to study influenza transmission based on wastewater and clinical data in other studies. In summary, this R package provides a fast and flexible implementation to estimate the effective reproductive number for various diseases and datasets.ConclusionsThe estimateR R package is a modular and extendable tool designed for outbreak surveillance and retrospective outbreak investigation. It extends the method developed for COVID-19 by Huisman et al. and makes it available for a variety of pathogens, outbreak scenarios, and observation types. Estimates obtained with estimateR can be interpreted directly or used to inform more complex epidemic models (e.g. for forecasting) on the value of$$R_e$$Re.
Comprehensive analysis of m6A regulators and relationship with tumor microenvironment, immunotherapy strategies in colorectal adenocarcinoma
Authors: Ji Jian , Liu Shichao , Liang Yongyuan , Zheng Guixi 
Published: August 2023

Abstract
Background
The N6-methyladenosine (m6A) RNA modification is the most prevalent and abundant type found in eukaryotic cells. It plays a crucial role in the initiation and progression of cancers. In this study, we aimed to comprehensively investigate the landscape of m6A regulators and their association with tumor microenvironment (TME), immunotherapeutic strategies in colon adenocarcinoma (COAD).

Results
The differential expression, mutation, CNV frequency and prognostic value of 27 m6A regulators were systematically analyzed in COAD. Patients were classified into two clusters based on m6A regulators through consistent clustering analysis, with cluster A showing significant survival benefits. Most of the m6A regulators were negatively correlated with immune cells, except for WTAP, IGF2BP3, FTO, ALKBH5, which showed a positive correlation. We developed an m6A scoring system to calculate the m6Ascore for each patient. Patients with a high-m6Ascore had a better outcome, with the AUC of 0.775. An independent cohort of 416 COAD patients acquired from GSE38832 database was used to validate the prognosis prediction ability of m6Ascore. Moreover, the m6Ascore was negatively correlated with infiltration of anti-tumor immune cells. Additionally, patients with a high-m6Ascore responded better to anti-PD1 and anti-CTLA4 therapies, and those with MSI-H had a higher m6Ascore. Finally, we investigated the value of m6Ascore in predicting the response of patients to 15 commonly used drugs.

Conclusions
We comprehensively analyzed m6A regulators in COAD, including RNA expression, CNV changes, mutations and their correlation with TME. Our results showed that the m6A scoring system had significant predictive power for the prognosis of COAD patients, potentially leading to new personalized immunotherapy strategies.
Assessment of renal function indexes in methamphetamine or tramadol intoxication adults to the emergency departments: a systematic review and meta-analysis
Authors: Amanollahi Alireza , Mehrabi Yadollah , Sedighi Mohsen , Basir Ghafouri Hamed , Zahedi Amir , Shadnia Shahin , Etemad Koorosh 
Published: August 2023

Abstract
Background
Renal dysfunction is one of the adverse effects observed in methamphetamine (MET) or tramadol abusers. In this study, we aimed to review articles involving intoxication with MET or tramadol to assess the occurrence of renal dysfunction.

Methods
Two researchers systematically searched PubMed, Scopus, Web of Sciences, and Google Scholar databases from 2000 to 2022. All articles that assessed renal function indexes including creatine, Blood Urea Nitrogen (BUN), and Creatine phosphokinase (CPK) in MET and tramadol intoxication at the time of admission in hospitals were included. We applied random effect model with Knapp-Hartung adjustment for meta-analysis using STATA.16 software and reported outcomes with pooled Weighted Mean (WM).

Results
Pooled WM for BUN was 29.85 (95% CI, 21.25–38.46) in tramadol intoxication and 31.64(95% CI, 12.71–50.57) in MET intoxication. Pooled WM for creatinine in tramadol and MET intoxication was respectively 1.04 (95% CI, 0.84–1.25) and 1.35 (95% CI, 1.13–1.56). Also, pooled WM for CPK was 397.68(376.42-418.94) in tramadol and 909.87(549.98-1269.76) in MET intoxication. No significance was observed in publication bias and heterogeneity tests.

Conclusion
Our findings showed that tramadol or MET intoxication is associated with a considerably increased risk of renal dysfunction that may result in organ failure.
Conducting the non-inferiority test for the means with unknown coefficient of variation in a three-arm trial
Authors: Lee Meng-Chih , Wu Wei-Ya , Lu Hung-Yi , Hsieh Hsin-Neng , Wu Wei-Hwa 
Published: August 2023

Abstract
Background
The non-inferiority test is a reasonable approach to assessing a new treatment in a three-arm trial. The three-arm trial consists of a placebo, reference, and an experimental treatment. The non-inferiority is often measured by the mean differences between the experimental and the placebo groups relative to the mean differences between the reference and the placebo groups.

Methods
To cope with possible estimation distortion due to the allowance of heteroskedasticity, we adjust the measurement of non-inferiority by the incorporation of coefficient of variation (CV) of the experimental, the reference and the placebo groups. In this research, we propose a generalized $$p$$
p
-value based method (GPV-based method) to facilitate non-inferiority tests for the means with unknown coefficient of variation in a three-arm trial.

Results
The simulation results show that the GPV-based method can not only adequately control type I error rate at nominal level better but also provide power higher than those from Delta method and the empirical bootstrap method, which verifies the feasibility of our adjustment.

Conclusions
We revise the measurement of non-inferiority by deducting the CV of each kind of treatment from the average effect of trials. CVs are included in the non-inferiority explicitly to help prevent possible estimating distortion if heteroskedasticity is allowed. Through the simulation study, the performance of GPV-based method for facilitating non-inferiority tests for the means with unknown CV in a three-arm trial is better than those from empirical bootstrap method and Delta method for small, medium and large sample sizes. Hence, the GPV-based method is recommended to be used to conduct the non-inferiority test for the means with unknown CV in a three-arm trial. The GPV-based method still performs well in non-normality cases.
Sevoflurane inhibits cholangiocarcinoma via Wnt/β-catenin signaling pathway
Authors: Cheng Hui , Li Qinfang 
Published: August 2023

Abstract
Background
Cholangiocarcinoma (CCA) is a refractory malignancy derived from bile duct epithelial cells. This study aimed to explore the role and molecular mechanisms of action of sevoflurane in CCA.

Methods
CCK-8 assay was used to assess the proliferation of cholangiocarcinoma cells, and flow cytometry was used to detect cholangiocarcinoma cell apoptosis. The effects of sevoflurane on TFK1 and QBC939 cell migration and invasion were investigated using a Transwell assay. Western blotting and RT-qPCR were used to assess the expression of apoptosis-related proteins and genes, and gene expression of the Wnt/β-catenin signaling pathway.

Results
Our study found that sevoflurane inhibited cholangiocarcinoma cell proliferation in a dose-dependent manner. In addition, sevoflurane induced cholangiocarcinoma cell apoptosis, inhibited cholangiocarcinoma cell migration and invasion, as well as the Wnt/β-catenin signaling pathway evidenced by decreased Wnt3a, β-catenin, c-Myc, and Cyclin D1 protein and mRNA expression, reduced p-GSK3β protein expression and p-GSK3β/GSK3β ratio. Further mechanistic studies revealed that Wnt/β-catenin pathway inducer SKL2001 reversed the inhibitory effect of sevoflurane on cholangiocarcinoma cells.

Conclusions
Sevoflurane induces apoptosis and inhibits the growth, migration, and invasion of cholangiocarcinoma cells by inhibiting the Wnt/β-catenin signaling pathway. This study not only revealed the role of sevoflurane in the development of CCA but also elucidated new therapeutic agents for CCA.