bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental Study of Rheological Behavior of MWCNT-Al2O3/SAE50 Hybrid Nanofluid to Provide the Best Nano-lubrication Conditions
Authors: Hemmat Esfe Mohammad , Alidoust Soheyl , Mohammadnejad Ardeshiri Erfan , Kamyab Mohammad Hasan , Toghraie Davood 
Published: January 2022

AbstractIn this study, MWCNT-Al2O3 hybrid nanoparticles with a composition ratio of 50:50 in SAE50 base oil are used. This paper aims to describe the rheological behavior of hybrid nanofluid based on temperature, shear rate ($$\dot{\gamma })$$

γ
˙

)

and volume fraction of nanoparticles ($$\varphi$$
φ
) to present an experimental correlation model. Flowmetric methods confirm the non-Newtonian behavior of the hybrid nanofluid. The highest increase and decrease in viscosity ($${\mu }_{\rm nf}$$

μ
nf

) in the studied conditions are measured as 24% and − 17%, respectively. To predict the experimental data, the five-point-three-variable model is used in the response surface methodology with a coefficient of determination of 0.9979. Margin deviation (MOD) of the data is determined to be within the permissible limit of − 4.66% < MOD < 5.25%. Sensitivity analysis shows that with a 10% increase in $$\varphi$$
φ
at $$\varphi =$$

φ
=

1%, the highest increase in $${\mu }_{\rm nf}$$

μ
nf

of 34.92% is obtained.
A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws
Authors: Reyes Brandon C , Otero-Muras Irene , Petyuk Vladislav A 
Published: January 2022

Abstract
Background
Theoretical analysis of signaling pathways can provide a substantial amount of insight into their function. One particular area of research considers signaling pathways capable of assuming two or more stable states given the same amount of signaling ligand. This phenomenon of bistability can give rise to switch-like behavior, a mechanism that governs cellular decision making. Investigation of whether or not a signaling pathway can confer bistability and switch-like behavior, without knowledge of specific kinetic rate constant values, is a mathematically challenging problem. Recently a technique based on optimization has been introduced, which is capable of finding example parameter values that confer switch-like behavior for a given pathway. Although this approach has made it possible to analyze moderately sized pathways, it is limited to reaction networks that presume a uniterminal structure. It is this limited structure we address by developing a general technique that applies to any mass action reaction network with conservation laws.

Results
In this paper we developed a generalized method for detecting switch-like bistable behavior in any mass action reaction network with conservation laws. The method involves (1) construction of a constrained optimization problem using the determinant of the Jacobian of the underlying rate equations, (2) minimization of the objective function to search for conditions resulting in a zero eigenvalue, (3) computation of a confidence level that describes if the global minimum has been found and (4) evaluation of optimization values, using either numerical continuation or directly simulating the ODE system, to verify that a bistability region exists. The generalized method has been tested on three motifs known to be capable of bistability.

Conclusions
We have developed a variation of an optimization-based method for the discovery of bistability, which is not limited to uniterminal chemical reaction networks. Successful completion of the method provides an S-shaped bifurcation diagram, which indicates that the network acts as a bistable switch for the given optimization parameters.
Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity
Authors: Hyun Jason C. , Monk Jonathan M. , Palsson Bernhard O. 
Published: January 2022

Abstract

Background
With the exponential growth of publicly available genome sequences, pangenome analyses have provided increasingly complete pictures of genetic diversity for many microbial species. However, relatively few studies have scaled beyond single pangenomes to compare global genetic diversity both within and across different species. We present here several methods for “comparative pangenomics” that can be used to contextualize multi-pangenome scale genetic diversity with gene function for multiple species at multiple resolutions: pangenome shape, genes, sequence variants, and positions within variants.

Results
Applied to 12,676 genomes across 12 microbial pathogenic species, we observed several shared resolution-specific patterns of genetic diversity: First, pangenome openness is associated with species’ phylogenetic placement. Second, relationships between gene function and frequency are conserved across species, with core genomes enriched for metabolic and ribosomal genes and accessory genomes for trafficking, secretion, and defense-associated genes. Third, genes in core genomes with the highest sequence diversity are functionally diverse. Finally, certain protein domains are consistently mutation enriched across multiple species, especially among aminoacyl-tRNA synthetases where the extent of a domain’s mutation enrichment is strongly function-dependent.

Conclusions
These results illustrate the value of each resolution at uncovering distinct aspects in the relationship between genetic and functional diversity across multiple species. With the continued growth of the number of sequenced genomes, these methods will reveal additional universal patterns of genetic diversity at the pangenome scale.
Gene expression profiling of trout muscle during flesh quality recovery following spawning
Authors: Ahongo Yéléhi-Diane , Le Cam Aurélie , Montfort Jérôme , Bugeon Jérôme , Lefèvre Florence , Rescan Pierre-Yves 
Published: January 2022

Abstract

Background

Sexual maturation causes loss of fish muscle mass and deterioration of fillet quality attributes that prevent market success. We recently showed that fillet yield and flesh quality recover in female trout after spawning. To gain insight into the molecular mechanisms regulating flesh quality recovery, we used an Agilent-based microarray platform to conduct a large-scale time course analysis of gene expression in female trout white muscle from spawning to 33 weeks post-spawning.

Results
In sharp contrast to the situation at spawning, muscle transcriptome of female trout at 33 weeks after spawning was highly similar to that of female trout of the same cohort that did not spawn, which is consistent with the post-spawning flesh quality recovery. Large-scale time course analysis of gene expression in trout muscle during flesh quality recovery following spawning led to the identification of approximately 3340 unique differentially expressed genes that segregated into four major clusters with distinct temporal expression profiles and functional categories. The first cluster contained approximately 1350 genes with high expression at spawning and downregulation after spawning and was enriched with genes linked to mitochondrial ATP synthesis, fatty acid catabolism and proteolysis. A second cluster of approximately 540 genes with transient upregulation 2 to 8 weeks after spawning was enriched with genes involved in transcription, RNA processing, translation, ribosome biogenesis and protein folding. A third cluster containing approximately 300 genes upregulated 4 to 13 weeks after spawning was enriched with genes encoding ribosomal subunits or regulating protein folding. Finally, a fourth cluster that contained approximately 940 genes with upregulation 8 to 24 weeks after spawning, was dominated by genes encoding myofibrillar proteins and extracellular matrix components and genes involved in glycolysis.

Conclusion
Overall, our study indicates that white muscle tissue restoration and flesh quality recovery after spawning are associated with transcriptional changes promoting anaerobic ATP production, muscle fibre hypertrophic growth and extracellular matrix remodelling. The generation of the first database of genes associated with post-spawning muscle recovery may provide insights into the molecular and cellular mechanisms controlling muscle yield and fillet quality in fish and provide a useful list of potential genetic markers for these traits.
Real world evidence of the association between medication and life expectancy in elderly inflammatory bowel disease: a population-based cohort study
Authors: Kuenzig M. Ellen , Manuel Douglas G. , Donelle Jessy , Benchimol Eric I. 
Published: January 2022

Abstract
Background
Life expectancy in people with inflammatory bowel disease (IBD) has increased but remains shorter than in people without IBD. We describe the life expectancy associated with IBD therapies among the growing number of older adults living with IBD.

Methods
Older adults (≥ 65 years) with IBD were identified from population-based health administrative data using a validated algorithm. Life expectancy on patients’ 65th birthday, stratified by sex, was calculated using a period life table approach from age- and sex-specific mortality rates among patients receiving immunomodulator monotherapy, biologic monotherapy, combination therapy, mesalamine, systemic steroids, and no therapy.

Results
Among 28,260 older adults with IBD (239,125 person-years of follow-up), life expectancy at 65 years was longest for patients taking mesalamine (females: 22.1 years, 95% CI 21.8–22.5; males: 19.6 years, 95% CI 19.3–20.0) and shortest for patients taking steroids (females: 11.7 years, 95% CI 11.0–12.4; males 10.3 years, 95% CI 9.7–10.8). Life expectancy was similar for patients receiving immunomodulator monotherapy and biologic monotherapy. Immunomodulator monotherapy was associated with a reduction in life expectancy compared to combination therapy by 5.1 (95% CI 2.3–7.8) in females and 2.8 years (95% CI 0.1–5.5) in males.

Conclusions
Life expectancy varies across therapies used for IBD, with differences likely arising from a combination of medication effectiveness, safety profiles, disease severity, and comorbid conditions. These considerations should be balanced when deciding on a therapeutic approach for the management of IBD in older adults.
Immunisation status of children and adolescents with a new diagnosis of inflammatory bowel disease
Authors: Ford Timothy , Danchin Margie , McMinn Alissa , Perrett Kirsten , Alex George , Crawford Nigel W. 
Published: January 2022

Abstract
Background
Patients with Inflammatory Bowel Disease (IBD) are at increased risk of serious infections, including vaccine preventable diseases. Current evidence suggests uptake of additional recommended special risk vaccinations is low. Identification of IBD patients prior to commencing immunosuppressive therapy allows for optimisation of vaccination, including timely administration of live-attenuated and additional recommended vaccines, such as influenza and pneumococcal vaccines.

Methods
Paediatric patients (0–18 years) seen at the tertiary Royal Children’s Hospital, Melbourne, Australia, with a recent diagnosis of IBD were referred by the Gastroenterology Unit to our Specialist Immunisation Clinic (SIC) for assessment and provision of routine and special risk vaccines. Data was collected via a standardised REDCap questionnaire completed in or post attendance at the SIC and included serology results where available.

Results
Sixty-nine paediatric patients were recruited to the study between 2014 and 2017. Median age at IBD diagnosis was 11.25 years (IQR 4.64 years), with median time between diagnosis and SIC review of 0.88 years (IQR 2.84 years). At initial review 84.1% (58/69) of patients were up to date with vaccines on the Australian National Immunisation Program (NIP) schedule. Of those who were tested, serological evidence of immunity was demonstrated in 38.3% (23/60) of patients for Hepatitis B, 66.7% (36/54) for measles, 51.9% (28/54) for rubella and 41.9% (26/62) for Varicella Zoster Virus. Prior to SIC review 47.8% (33/69) had additional vaccinations and 92.8% (64/69) had vaccinations administered in the 12 months following SIC assessment. The Pneumococcal conjugate vaccine (76.8%, 53/69) was the most commonly administered vaccine after SIC review, followed by influenza vaccine (69.6%, 48/69). Within 12 months of SIC review 43.5% (30/69) of patients had completed the schedule and were up-to-date as recommended by the SIC.

Conclusions
Children with IBD and other special risk groups can benefit from early referral to a SIC team to ensure optimal administration of routine and additionally recommended vaccines, especially live and additional special risk vaccines. The value of optimising immunisations could also be applied to other special risk groups, including adult IBD cohorts, particularly those commencing newer biologic immunosuppressive medications.
Meet–Test–Treat for HCV management: patients’ and clinicians’ preferences in hospital and drug addiction services in Italy
Authors: Andreoni Massimo , Coppola Nicola , Craxì Antonio , Fagiuoli Stefano , Gardini Ivan , Mangia Alessandra , Nava Felice Alfonso , Pasqualetti Patrizio 
Published: January 2022

Abstract
Background
It has been estimated that the incidence of chronic hepatitis C virus (HCV) will not decline over the next 10 years despite the improved efficacy of antiviral therapy because most patients remain undiagnosed and/or untreated. This study aimed to investigate the opinion of relevant target populations on the practicability, effectiveness and best modalities of the test-and-treat approach in the fight against HCV in Italy.

Methods
A survey was delivered to patients with HCV from the general population, patients from drug addiction services, hospital physicians and healthcare providers for drug addiction services.

Results
For both hospital clinicians and SerD HCPs, tolerability is shown as the most important feature of a suitable treatment. Time to treatment (the time from first contact to initiation of treatment) is deemed important to the success of the strategy by all actors. While a tolerable treatment was the main characteristic in a preferred care pathway for general patients, subjects from drug addiction services indicated that a complete Meet–Test–Treat pathway is delivered within the habitual care center as a main preference. This is also important for SerD HCPs who are a strong reference for their patients; hospital clinicians were less aware of the importance of the patient-HCP relationship in this process.

Conclusion
The health system is bound to implement suitable pathways to facilitate HCV eradication. A Meet–Test–Treat program within the drug addiction services may provide good compliance from subjects mainly concerned with virus transmission.
Prevalence and associated factors of sexually transmitted infections among methamphetamine users in Eastern China: a cross-sectional study
Authors: Ye Xing , Li Fu-Rong , Pan Qing , Li Zhen , Yu Gong-Qi , Liu Hong , Liu Jian , Huai Peng-Cheng , Zhang Fu-Ren 
Published: January 2022

AbstractBackgroundThe reported incidence of sexually transmitted infections (STIs) in China has been increasing over the last decades, especially among drug users, which has become one of the main burdens of public health in China. This study was conducted to estimate the prevalence and associated factors of STIs among non-injecting methamphetamine (MA) users in Eastern China.MethodsA cross-sectional survey was conducted among 632 MA users in Eastern China in 2017. Demographic characteristics, sexual behaviors, behaviors of MA use and sexual health knowledge were collected through questionnaire. First pass urine specimens were collected and detected for deoxyribonucleic acid (DNA) of Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) with Nucleic Acid Amplification Technology (NAAT), while blood specimens were collected and detected for antibodies of Human immunodeficiency virus (HIV), Herpes simplex virus type-2 (HSV-2), and syphilis with enzyme-linked immune sorbent assay (ELISA).ResultsAmong the 632 MA users, 464 (73.42%) were males, 60.92% were < 35 years of age, 546 (86.39%) were Shandong residents. 317 (50.16%, 95% CI 46.26–54.06%) participants were tested positive for at least one kind of STIs, including 242 (38.29%, 95% CI 34.50–42.08%) for HSV-2, 107 (16.93%, 95% CI 14.01–19.85%) for active syphilis, 46 (7.28%, 95% CI 5.25–9.31%) for treated syphilis, 40 (6.33%, 95% CI 4.43–8.23%) for CT, 6 (0.95%, 95% CI 0.19–1.71%) for HIV, and 3 (0.47%, 95% CI 0.06–1.00%) for NG infection. 99 (15.66%, 95% CI 12.83–18.49%) participants were co-infected with two kinds of STIs, including 91 (14.40%, 95% CI 11.66–17.14%) participants were co-infected with HSV-2 and syphilis. 14 (2.22%, 95% CI 1.07–3.37%) participants were co-infected with three kinds of STIs, and 4 HIV positive participants were co-infected with both syphilis and HSV-2. In the multiple logistic regression analysis, the results showed that females (adjusted OR [AOR] = 7.30, 95% CI 4.34–12.30) and individuals ≥ 35 years of age (AOR = 2.97, 95% CI 2.04–4.32) were more likely to test positive for STIs among MA users, whereas participants who acquired sexual health knowledge primarily from the Internet (AOR = 0.57, 95% CI 0.40–0.82) and those whose regular partners did not use drugs (AOR = 0.59, 95% CI 0.37–0.94) were less likely.ConclusionsThis study found that the prevalence of HSV-2 and syphilis are alarming high among non-injecting MA users in Shandong Province in Eastern China. The prevention and control intervention of STIs among MA users in Shandong were needed, especially on females and MA users ≥ 35 years of age.
Safety and clinical outcomes of remdesivir in hospitalised COVID-19 patients: a retrospective analysis of active surveillance database
Authors: Gupte Vaishali , Hegde Rashmi , Sawant Sandesh , Kalathingal Kabil , Jadhav Sonali , Malabade Rohit , Gogtay Jaideep 
Published: January 2022

Abstract
Background
Real-world data on safety and clinical outcomes of remdesivir in COVID-19 management is scant. We present findings of data analysis conducted for assessing the safety and clinical outcomes of remdesivir treatment for COVID-19 in India.

Methods
This retrospective analysis used data from an active surveillance programme database of hospitalised patients with COVID-19 who were receiving remdesivir.

Results
Of the 2329 patients included, 67.40% were men. Diabetes (29.69%) and hypertension (20.33%) were the most common comorbidities. At remdesivir initiation, 2272 (97.55%) patients were receiving oxygen therapy. Remdesivir was administered for 5 days in 65.38% of patients. Antibiotics (64.90%) and steroids (47.90%) were the most common concomitant medications. Remdesivir was overall well tolerated, and total 119 adverse events were reported; most common were nausea and vomiting in 45.40% and increased liver enzymes in 14.28% patients. 84% of patients were cured/improved, 6.77% died and 9.16% showed no improvement in their clinical status at data collection. Subgroup analyses showed that the mortality rate was significantly lower in patients < 60 years old than in those > 60 years old. Amongst patients on oxygen therapy, the cure/improvement rate was significantly higher in those receiving standard low-flow oxygen than in those receiving mechanical ventilation, non-invasive ventilation, or high-flow oxygen. Factors that were associated with higher mortality were age > 60 years, cardiac disease, diabetes high flow oxygen, non-invasive ventilation and mechanical ventilation.

Conclusion
Our analysis showed that remdesivir is well tolerated and has an acceptable safety profile. The clinical outcome of cure/improvement was 84%, with a higher improvement in patients < 60 years old and on standard low-flow oxygen.
Evaluation of the current guidelines for antibacterial therapy strategies in patients with cirrhosis or liver failure
Authors: Dong Yuzhu , Sun Dan , Wang Yan , Du Qian , Zhang Ying , Han Ruiying , Teng Mengmeng , Zhang Tao , Shi Lei , Zheng Gezhi , Dong Yalin , Wang Taotao 
Published: January 2022

Abstract
Background
Bacterial infections are common complications in patients with cirrhosis or liver failure and are correlated with high mortality. Clinical practice guideline (CPG) is a reference used to help clinicians make decisions. This systematic appraisal aimed to evaluate the methodological quality and summarize the recommendations of reported CPGs in these patients.

Methods
We systematically searched CPGs published from 2008 to 2019. The methodological quality of the included CPGs was assessed using the AGREE II instrument. We extracted and compared recommendations for prophylactic and empirical treatment strategies.

Results
Fourteen CPGs with a median overall score of 56.3% were included. The highest domain score was Clarity of Presentation (domain 4, 85.4%), and the lowest was for Stakeholder Involvement (domain 2, 31.3%). Three CPGs had an overall score above 80%, and 6 CPGs had a score above 90% in domain 4. Prophylaxis should be strictly limited to patients with varicose bleeding, low ascites protein levels and a history of spontaneous bacterial peritonitis. Fluoroquinolones (norfloxacin and ciprofloxacin), third-generation cephalosporins (G3) (ceftriaxone and cefotaxime) and trimethoprim–sulfamethoxazole (SXT) are recommended for preventing infections in patients with cirrhosis or liver failure. G3, β-lactam/β-lactamase inhibitor combinations (BLBLIs) and carbapenems are recommended as the first choice in empirical treatment according to local epidemiology of bacterial resistance.

Conclusions
The methodological quality of CPGs focused on patients with cirrhosis or liver failure evaluated by the AGREE II instrument is generally poor. Three CPGs that were considered applicable without modification and 6 CPGs that scored above 90% in domain 4 should also be paid more attention to by healthcare practitioners. Regarding recommendations, norfloxacin, ciprofloxacin, ceftriaxone, cefotaxime, and SXT are recommended for prophylactic treatment appropriately. G3, BLBLIs, and carbapenems are recommended for use in empirical treatment strategies.
Efficacy of intrauterine insemination in women with endometrioma-associated subfertility: analysis using propensity score matching
Authors: Cai He , Xie Jinlin , Shi Juanzi , Wang Hui 
Published: January 2022

Abstract
Background
Intrauterine insemination (IUI) treatment is recommended in subfertile women with AFS/ASRM stage I/II endometriosis. However, the efficacy of IUI in women with ovarian endometriomas with tubal patency is uncertain. We explored the efficacy of IUI for the treatment of endometrioma-associated subfertility.

Methods
We performed a retrospective matched cohort study using propensity matching (PSM) analysis. Subfertile couples undergoing IUI with and without ovarian stimulation between January 1, 2015, and May 30, 2020 were reviewed.

Results
After PSM, 56 women with endometrioma alone were matched to 173 patients with unexplained subfertility. The per-cycle pregnancy rate (PR) was comparable between women with endometrioma-associated subfertility (n = 56, 87 cycles) and women with unexplained subfertility (n = 173, 280 cycles) (9.2% vs. 17.9%, OR 0.47; 95% CI, 0.21–1.03). Subgroup analyses based on IUI with or without stimulation also resulted in comparable results. A trend toward a lower cumulative pregnancy rates (CPRs) was seen in women with endometrioma (14.3%, 8/56) compared with women with unexplained subfertility (28.9%, 50/173), but the differences were not significant (HR 0.49; 95% CI, 0.23–1.15). However, patients with endometrioma were nearly twice as likely to converse to IVF treatment compared with those without the disease (60.7% versus 43.9%; OR 1.97; 95% CI, 1.07–3.65).

Conclusion
IUI may be a viable approach for subfertile women with endometrioma and no other identifiable infertility factor. More studies are needed to reassure the findings.