bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extended-spectrum β-lactamase-producing E. coli from retail meat and workers: genetic diversity, virulotyping, pathotyping and the antimicrobial effect of silver nanoparticles
Authors: Ahmed Heba A. , Elsohaby Ibrahim , Elamin Amina M. , El-Ghafar Abeer E. Abd , Elsaid Gamilat A. , Elbarbary Mervat , Mohsen Rasha A. , El Feky Tamer M. , El Bayomi Rasha M. 
Published: August 2023

Abstract
Background
The spread of extended-spectrum β-lactamases (ESBL) producing E. coli from food animals and the environment to humans has become a significant public health concern. The objectives of this study were to determine the occurrence, pathotypes, virulotypes, genotypes, and antimicrobial resistance patterns of ESBL-producing E. coli in retail meat samples and workers in retail meat shops in Egypt and to evaluate the bactericidal efficacy of silver nanoparticles (AgNPs-H2O2) against multidrug resistant (MDR) ESBL-producing E. coli.

Results
A total of 250 retail meat samples and 100 human worker samples (hand swabs and stool) were examined for the presence of ESBL- producing E. coli. Duck meat and workers’ hand swabs were the highest proportion of ESBL- producing E. coli isolates (81.1%), followed by camel meat (61.5%). Pathotyping revealed that the isolates belonged to groups A and B1. Virulotyping showed that the most prevalent virulence gene was Shiga toxin 2 (stx2) associated gene (36.9%), while none of the isolates harbored stx1 gene. Genotyping of the identified isolates from human and meat sources by REP-PCR showed 100% similarity within the same cluster between human and meat isolates. All isolates were classified as MDR with an average multiple antibiotic resistance (MAR) index of 0.7. AgNPs-H2O2 at concentrations of 0.625, 1.25, 2.5 and 5 μg/mL showed complete bacterial growth inhibition.

Conclusions
Virulent MDR ESBL-producing E. coli were identified in retail meat products in Egypt, posing significant public health threats. Regular monitoring of ESBL-producing E. coli frequency and antimicrobial resistance profile in retail meat products is crucial to enhance their safety. AgNPs-H2O2 is a promising alternative for treating MDR ESBL-producing E. coli infections and reducing antimicrobial resistance risks.
Intraspecific divergence in essential oil content, composition and genes expression patterns of monoterpene synthesis in Origanum vulgare subsp. vulgare and subsp. gracile under salinity stress
Authors: Azimzadeh Zahra , Hassani Abbas , Mandoulakani Babak Abdollahi , Sepehr Ebrahim , Morshedloo Mohammad Reza 
Published: August 2023

Abstract
Background
Oregano (Origanum vulgare L.), one of the important medicinal plants in the world, has valuable pharmacological compounds with antimicrobial, antiviral, antioxidant, anti-inflammatory, antispasmodic, antiurolithic, antiproliferative and neuroprotective activities. Phenolic monoterpenes such as thymol and carvacrol with many medical importance are found in Oregano essential oil. The biosynthesis of these compounds is carried out through the methyl erythritol-4 phosphate (MEP) pathway. Environmental stresses such as salinity might improve the secondary metabolites in medicinal plants. The influence of salinity stress (0 (control), 25, 50 and 100 mM NaCl) on the essential oil content, composition and expression of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), γ-terpinene synthase (Ovtps2) and cytochrome P450 monooxygenases (CYP71D180) genes involved in thymol and carvacrol biosynthesis, was investigated in two oregano subspecies (vulgare and gracile).

Results
Essential oil content was increased at low NaCl concentration (25 mM) compared with non-stress conditions, whereas it was decreased as salinity stress intensified (50 and 100 mM). Essential oil content was significantly higher in subsp. gracile than subsp. vulgare. The highest (0.20 mL pot−1) and lowest (0.06 mL pot−1) amount of essential oil yield was obtained in subsp. gracile at 25 and 100 mM NaCl, respectively. The content of carvacrol, as the main component of essential oil, decreased with increasing salinity level in subsp. gracile, but increased in subsp. vulgare. The highest expression of DXR, Ovtps2 and CYP71D180 genes was observed at 50 mM NaCl in subsp. vulgare. While, in subsp. gracile, the expression of the mentioned genes decreased with increasing salinity levels. A positive correlation was obtained between the expression of DXR, Ovtps2 and CYP71D180 genes with carvacrol content in both subspecies. On the other hand, a negative correlation was found between the expression of CYP71D180 and carvacrol content in subsp. gracile.

Conclusions
The findings of this study demonstrated that both oregano subspecies can tolerate NaCl salinity up to 50 mM without significant reduction in essential oil yield. Also, moderate salinity stress (50 mM NaCl) in subsp. vulgare might increase the carvacrol content partly via increment the expression levels of DXR, Ovtps2 and CYP71D180 genes.
Genomic-wide identification and expression analysis of R2R3-MYB transcription factors related to flavonol biosynthesis in Morinda officinalis
Authors: Li Jingyu , Xu Shiqiang , Mei Yu , Gu Yan , Sun Mingyang , Zhang Wenting , Wang Jihua 
Published: August 2023

Abstract
Background
The R2R3-MYB transcription factors are a crucial and extensive gene family in plants, which participate in diverse processes, including development, metabolism, defense, differentiation, and stress response. In the Lingnan region of China, Morinda officinalis is extensively grown and is renowned for its use as both a medicinal herb and food source. However, there are relatively few reports on the R2R3-MYB transcription factor family in M.officinalis.

Results
In this study, we identified 97 R2R3-MYB genes in the genome of Morinda officinalis and classified them into 32 subgroups based on phylogenetic comparison with Arabidopsis thaliana. The lack of recent whole-genome duplication events in M.officinalis may be the reason for the relatively few members of the R2R3-MYB family. We also further analyzed the physical and chemical characteristics, conserved motifs, gene structure, and chromosomal location. Gene duplication events found 21 fragment duplication pairs and five tandem duplication event R2R3-MYB genes in M.officinalis may also affect gene family expansion. Based on phylogenetic analysis, cis-element analysis, co-expression analysis and RT-qPCR, we concluded that MoMYB33 might modulate flavonol levels by regulating the expression of 4-coumarate-CoA ligase Mo4CL2, chalcone isomerase MoCHI3, and flavonol synthase MoFLS4/11/12. MoMYB33 and AtMYB111 showed the highest similarity of 79% and may be involved in flavonol synthase networks by the STRING database. Moreover, we also identified MoMYB genes that respond to methyl Jasmonate (MeJA) and abscisic acid (ABA) stress by RT-qPCR.

Conclusions
This study offers a thorough comprehension of R2R3-MYB in M.officinalis, which lays the foundation for the regulation of flavonol synthesis and the response of MoMYB genes to phytohormones in M.officinalis.
Effects of saline water on soil properties and red radish growth in saline soil as a function of co-applying wood chips biochar with chemical fertilizers
Authors: Amin Abu El-Eyuoon Abu Zied 
Published: August 2023

Abstract
Background
Currently, using unconventional water sources in agriculture has become necessary to face overpopulation worldwide. Therefore, a pot experiment was carried out to evaluate the effects of irrigation with saline water in the presence of co-applied wood chips biochar (WCB) with chemical fertilizers on physicochemical properties and nutrient availability as well as growth parameters, and yield of red radish (Raphanus sativus L.) grown in the saline sandy soil.

Methods
The WCB was added to the saline sandy soil at levels of 0 (control), 2.5, and 5% w/w. Then, this soil was cultivated by red radish plants and irrigated with saline water (5 dS m− 1). This experiment was performed in a randomized complete block design with three replicates.

Results
Compared with the control treatment, WCB treatments increased significantly soil water holding capacity by 34.8% and 73.2% for levels of 2.5 and 5%, respectively. Soil pH decreased significantly in all WCB treatments. The relative increase in the total available nitrogen over the control was 30.1 and 103.5% for 2.5 and 5% wood chips biochar, respectively. Compared to the control, applying WCB at 2.5% led to an increase in the fresh root weight of red radish plants by 142.7%, while 5% caused a decrease in the fresh root weight of red radish plants by 29.4%.

Conclusion
Recently, WCB represents an interesting approach to the rehabilitation of saline soils and the management of using saline water sources. It is recommended that combined application of WCB at a level of 2.5% with chemical fertilizers in order to improve red radish growth and nutrient retention in the saline sandy soil which preserves the ecosystem as well as increases productivity leading to the reduction of costs.
Routine statins use is associated with less adverse outcome in patients above 70 years of age admitted to hospital with COVID-19
Authors: Izkhakov Elena , Vilian Yair , Buch Assaf , Denysov Veronika , Namouz Dima , Nathan Alexandra , Greenman Yona , Ziv-Baran Tomer 
Published: August 2023

Abstract
Background
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to multiorgan insufficiency and death, particularly among the older adults. Statins have been suggested as potentially protective drugs due to their pleotropic effects, but the actual benefit of statin use among the older population in this setting is not clear. This study aimed to evaluate the association between preadmission statin use and the presentation and clinical outcomes of hospitalized COVID-19 patients older than 70 years of age.

Methods
A historical cohort study of all patients above 70 years of age who were hospitalized with COVID-19 infection in a large academic hospital between March and August 2020 was performed. The association between preadmission statin use and patients’ presentation and adverse outcome was studied. Adverse outcome was defined as any of the following: shock, invasive or non-invasive ventilation, organ insufficiency, myocardial infarction, cerebrovascular accident, in-hospital or 30-day post-admission mortality, hospital stay longer than the median length of stay of all COVID-19 patients, referral to nursing home or rehabilitation center.

Results
Seventy-two (44%) of the 163 studied patients (median age 82 years, 45% males) had been preadmission treated with statins. The statin-treated patients (STP) had a higher prevalence of diabetes (40% vs 24%, p = 0.028) and cardiovascular disease (58% vs. 34%, p = 0.002). Seventy two percent of the STP had adverse outcome, compared to 86% of the non-STP (p = 0.033). After adjustment for potential confounders, prior statin use was associated with decreased risk for an adverse outcome (odds ratio = 0.4, 95% confidence interval 0.18–0.92, p = 0.03).

Conclusions
The preadmission use of statins was associated with a lower risk of adverse outcome in older adults hospitalized with COVID-19. Continuation of statin treatment might be implemented for risk reduction of adverse outcomes in the older population in the era of new SARS-CoV-2 variants and less effective vaccines.
The value of PLA2R antigen and IgG subclass staining relative to anti-PLA2R seropositivity in the differential diagnosis of membranous nephropathy
Authors: Bajcsi Dóra , Bitó László , Turkevi-Nagy Sándor , Nyári Tibor , Kemény Éva , Légrády Péter , Ábrahám György , Iványi Béla 
Published: August 2023

Abstract
Background
The diagnostic performance of PLA2R and IgG subclass staining of kidney biopsies relative to anti-PLA2R seropositivity in the differentiation of primary and secondary membranous nephropathy (pMN, sMN) was examined. Besides PLA2R staining – which has a lower specificity than anti-PLA2R antibody serology – there is insufficient knowledge to decide which IgG1-4 subtype immunohistological patterns (IgG4-dominance, IgG4-dominance/IgG1-IgG4-codominance or IgG4-dominance/IgG4-codominance with any IgG subtype) could be used to distinguish between pMN and sMN.

Methods
87 consecutive Hungarian patients (84 Caucasians, 3 Romas) with the biopsy diagnosis of MN were classified clinically as pMN (n = 63) or sMN (n = 24). The PLA2R and IgG subclass staining was part of the diagnostic protocol. Anti-PLA2R antibodies were determined by an indirect immunofluorescence test in 74 patients with disease activity.

Results
For pMN, the sensitivity of anti-PLA2R seropositivity was 61.1%, and the specificity was 90.0%; and similar values for PLA2R staining were 81.0%, and 66.7%, respectively. In all stages of pMN, IgG4-dominance was the dominant subclass pattern, while the second most frequent was IgG3/IgG4-codominance. The sensitivity and specificity scores were: IgG4-dominance 52.2% and 91.7%, IgG4-dominance/IgG3-IgG4-codominance 76.2% and 87.5%, IgG4-dominance/IgG1-IgG4-codominance 64.2% and 75%, and IgG4-dominance/codominance with any IgG subclass 92.1% and 70.8%, respectively. Anti-PLA2R seropositivity, glomerular PLA2R, and IgG4-dominance/codominance significantly correlated with each other. The IgG4 subclass was rarely encountered in sMN.

Conclusion
In our series, IgG4-dominance had the highest specificity in the differentiation of MN, just as high as that for anti-PLA2R seropositivity. The specificity values of PLA2R staining and IgG4-dominance/codominance with any IgG subclass or IgG4-dominance/IgG1-IgG4 codominance were ≤ 75%. Apart from IgG4 dominance, IgG4-dominance/IgG3-IgG4-codominance also had good statistical value in differentiating pMN from sMN. As IgG subclass switching during the progression of pMN was not the feature of our cohort, pMN in Hungarian patients is presumed to be an IgG4-related disorder right from the start. Although anti-PLA2R seropositivity has become the cornerstone for diagnosing pMN, if a kidney biopsy evaluation is conducted, besides the staining of PLA2R antigen, the evaluation of IgG subclasses provides relevant information for a differential diagnosis. Even in cases with IgG4-dominance, however, malignancy should be thoroughly checked.
Clinical, radiological profile and prognostic role of transcranial color-coded duplex in cerebral venous thrombosis: a case-control study
Authors: Aboul fotouh Alshaimaa M. , Helmy Sadek Mohamed , Mourad Husam S. , Abdelbaky Hadeel Ahmed , Hatem Ghada 
Published: August 2023

Abstract
Background
Cerebral venous thrombosis is a rare type of stroke, occurring more among young individuals. The presentation is highly variable, and this can delay diagnosis and management, thereby affecting outcome. The aim is to study the clinical, radiological profile, risk factors for cerebral venous thrombosis (CVT) and the role of transcranial color-coded duplex (TCCD) in CVT prognosis among Egyptian patients.

Methods
Eighty CVT patients and 80 normal healthy individuals were included. Magnetic resonance imaging, magnetic resonance venography, and genetic thrombophilia tests were done for patients. Deep cerebral venous system was evaluated using B-mode transcranial color-coded duplex (TCCD) for both groups.

Results
Showed female predominance with gender specific risk factors being the most common etiology. The most common hereditary thrombophilia was homozygous factor V Leiden mutation and anti-thrombin III (AT III). Headache was the most common presentation. Forty-three patients had transverse sinus thrombosis. Regarding TCCD, there was an increase in mean blood flow velocities, peak flow velocities and end diastolic flow velocities in deep middle cerebral vein and basal veins in CVT group compared to control group. There was a positive correlation not reaching statistical significance between flow velocities in the deep venous system and modified Rankin Scale.

Conclusion
Clinical presentation is extremely variable. In our population, homozygous factor V Leiden mutation and AT III deficiency were the most common. Increased deep cerebral venous system flow velocities using TCCD in patients with CVT reflect their venous hemodynamic state.
Perioperative or adjuvant mFOLFIRINOX for resectable pancreatic cancer (PREOPANC-3): study protocol for a multicenter randomized controlled trial
Authors: van Dam J. L. , Verkolf E. M. M. , Dekker E. N. , Bonsing B. A. , Bratlie S. O. , Brosens L. A. A. , Busch O. R. , van Driel L. M. J. W. , van Eijck C. H. J. , Feshtali S. , Ghorbani P. , de Groot D. J. A. , de Groot J. W. B. , Haberkorn B. C. M. , de Hingh I. H. , van der Holt B. , Karsten T. M. , van der Kolk M. B. , Labori K. J. , Liem M. S. L. , Loosveld O. J. L. , Molenaar I. Q. , Polée M. B. , van Santvoort H. C. , de Vos – Geelen J. , Wumkes M. L. , van Tienhoven G. , Homs M. Y. V. , Besselink M. G. , Wilmink J. W. , Groot Koerkamp B. ,   for the Dutch Pancreatic Cancer Group
Published: August 2023

Abstract
Background
Surgical resection followed by adjuvant mFOLFIRINOX (5-fluorouracil with leucovorin, irinotecan, and oxaliplatin) is currently the standard of care for patients with resectable pancreatic cancer. The main concern regarding adjuvant chemotherapy is that only half of patients actually receive adjuvant treatment. Neoadjuvant chemotherapy, on the other hand, guarantees early systemic treatment and may increase chemotherapy use and thereby improve overall survival. Furthermore, it may prevent futile surgery in patients with rapidly progressive disease. However, some argue that neoadjuvant therapy delays surgery, which could lead to progression towards unresectable disease and thus offset the potential benefits. Comparison of perioperative (i.e., neoadjuvant and adjuvant) with (only) adjuvant administration of mFOLFIRINOX in a randomized controlled trial (RCT) is needed to determine the optimal approach.

Methods
This multicenter, phase 3, RCT will include 378 patients with resectable pancreatic ductal adenocarcinoma with a WHO performance status of 0 or 1. Patients are recruited from 20 Dutch centers and three centers in Norway and Sweden. Resectable pancreatic cancer is defined as no arterial contact and ≤ 90 degrees venous contact. Patients in the intervention arm are scheduled for 8 cycles of neoadjuvant mFOLFIRINOX followed by surgery and 4 cycles of adjuvant mFOLFIRINOX (2-week cycle of oxaliplatin 85 mg/m2, leucovorin 400 mg/m2, irinotecan 150 mg/m2 at day 1, followed by 46 h continuous infusion of 5-fluorouracil 2400 g/m2). Patients in the comparator arm start with surgery followed by 12 cycles of adjuvant mFOLFIRINOX. The primary outcome is overall survival by intention-to-treat. Secondary outcomes include progression-free survival, resection rate, quality of life, adverse events, and surgical complications. To detect a hazard ratio of 0.70 with 80% power, 252 events are needed. The number of events is expected to be reached after the inclusion of 378 patients in 36 months, with analysis planned 18 months after the last patient has been randomized.

Discussion
The multicenter PREOPANC-3 trial compares perioperative mFOLFIRINOX with adjuvant mFOLFIRINOX in patients with resectable pancreatic cancer.

Trial registration
Clinical Trials: NCT04927780. Registered June 16, 2021.
Introducing Braining—physical exercise as adjunctive therapy in psychiatric care: a retrospective cohort study of a new method
Authors: Anger Åsa , Wallerblad Anna , Kaaman Leida , Broman Rebecka , Holmberg Johan , Lundgren Tobias , Salomonsson Sigrid , Sundberg Carl Johan , Martinsson Lina 
Published: August 2023

AbstractBackgroundPatients with severe mental disorders suffer from higher rates of poor somatic health and have shorter life expectancy than the average population. Physical activity can treat and prevent several diseases,e.g.cardiovascular and metabolic disorders as well as psychiatric symptoms. It is therefore of utmost importance to develop effective methods to integrate physical activity into psychiatric care. To meet this need, the physical activity intervention Braining was developed. This study aims to describe Braining, to assess the number of patients reached during the first years of pilot testing, to analyze clinical data in the group of patients participating in Braining 2017–2020 and to assess the intervention.MethodsIn this descriptive retrospective study we analyzed data from all patients participating in Braining training sessions ≥ 3 times (n = 239), the Braining Participants. Regular patients at the clinic served as a comparison. Furthermore, medical records were studied for a smaller cohort (n = 51), the Braining Pilot Cohort. Data was analyzed using Chi-square and Fisher’s tests.ResultsDuring the introduction period of Braining, 580 patients attended an information meeting about Braining, or at least one training session. 239 patients participated in ≥ 3 training sessions, considered to be participants of Braining. These Braining Participants (n = 239), ages 19 to 82, males 23.4%, attended between 3 and 308 training sessions (median 9). The main diagnoses were affective and anxiety disorders. Number of diagnoses ranged from 0 to 10 (median = 2). For the subsample, the Braining Pilot Cohort (n = 51), participants attended between 3 and 208 training sessions (median = 20). Twelve percent were working full-time, and symptom severity of depression and general anxiety was moderate. Two thirds had ≥ 3 different classes of medication. Regarding metabolic morbidity, 28% had been diagnosed with hypertension, though blood lipids, blood glucose as well as blood pressure were within the normal range. Thirty-seven percent were prescribed Physical Activity on Prescription during 2017–2020. One severe adverse event was reported.ConclusionsThe Braining intervention reached all age-groups and patients with a wide and representative diagnostic panorama, suggesting that Braining could be a promising and safe method for implementing physical activity in a psychiatric patient population.