bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deeper genomic insights into tomato CLE genes repertoire identify new active peptides
Authors: Carbonnel Samy , Falquet Laurent , Hazak Ora 
Published: November 2022

Abstract
Background
In eukaryotes, cell-to-cell communication relies on the activity of small signaling peptides. In plant genomes, many hundreds of genes encode for such short peptide signals. However, only few of them are functionally characterized and due to the small gene size and high sequence variability, the comprehensive identification of such peptide-encoded genes is challenging. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) gene family encodes for short peptides that have a role in plant meristem maintenance, vascular patterning and responses to environment. The full repertoire of CLE genes and the role of CLE signaling in tomato (Solanum lycopersicum)- one of the most important crop plants- has not yet been fully studied.

Results
By using a combined approach, we performed a genome-wide identification of CLE genes using the current tomato genome version SL 4.0. We identified 52 SlCLE genes, including 37 new non annotated before. By analyzing publicly available RNAseq datasets we could confirm the expression of 28 new SlCLE genes. We found that SlCLEs are often expressed in a tissue-, organ- or condition-specific manner. Our analysis shows an interesting gene diversification within the SlCLE family that seems to be a result of gene duplication events. Finally, we could show a biological activity of selected SlCLE peptides in the root growth arrest that was SlCLV2-dependent.

Conclusions
Our improved combined approach revealed 37 new SlCLE genes. These findings are crucial for better understanding of the CLE signaling in tomato. Our phylogenetic analysis pinpoints the closest homologs of Arabidopsis CLE genes in tomato genome and can give a hint about the function of newly identified SlCLEs. The strategy described here can be used to identify more precisely additional short genes in plant genomes. Finally, our work suggests that the mechanism of root-active CLE peptide perception is conserved between Arabidopsis and tomato. In conclusion, our work paves the way to further research on the CLE-dependent circuits modulating tomato development and physiological responses.
Nutritional and metabolic process of the dung beetle Phelotrupes auratus depends on the plant ingredients that the herbivores eat
Authors: Sakamoto Takuma , Sinzeki Shun , Kakinuma Shunsuke , Ishihara Eri , Tabunoki Hiroko 
Published: November 2022

Abstract
Background
The dung beetle Phelotrupes auratus is a holometabolous insect belonging to the order Coleoptera, and it is widely distributed in Japan. The P. auratus habitat depends on herbivores. P. auratus eats the dung of the herbivores and carries it underground for its young. In this process, herbivore droppings disappear from the ground, not only keeping the ground hygienic but also maintaining good soil conditions for plant growth. In this way, a rich ecosystem is maintained. In recent years, the population of P. auratus has decreased, and the main cause has been the decrease in grazing land. It seems that Japanese dung beetles are mainly dependent on herbivores for nutrient sources. However, the physiological relationship between herbivores and P. auratus has not been well investigated. Here, we investigated the nutritional metabolism system of P. auratus by performing whole gene expression analysis of individuals collected from two areas where the ecosystem is occupied by different herbivores.

Results
We obtained 54,635 transcripts from P. auratus from Nara Park and Cape Toi and identified 2,592 differentially expressed genes in the fat bodies of the Nara Park and Cape Toi groups. We annotated P. auratus transcripts using Homo sapiens and Drosophila melanogaster genes as references; 50.5% of P. auratus transcripts were assigned to H. sapiens genes, and 54.0% of P. auratus transcripts were assigned to D. melanogaster genes. To perform gene set enrichment analysis, we chose H. sapiens genes for P. auratus transcript annotation. Principal component analysis and gene set enrichment analysis revealed that the nutritional metabolism of P. auratus from Cape Toi might differ from that of P. auratus from Nara Park.

Conclusion
We analyzed the nutritional metabolism system of P. auratus from Cape Toi and Nara Park and found that the characteristics of the nutritional metabolism process might depend on the plants consumed by the herbivores. Our findings will contribute to elucidating the relationships among habitat plants, herbivores, and dung decomposers and may aid in the maintenance of sustainable land health cycles.
Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies
Authors: Farhadi Ahmad , Jeffs Andrew G. , Lavery Shane D. 
Published: November 2022

Abstract
Background
Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands.

Result
After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P < 0001), superficially in accordance with previous analyses. However, detailed demographic analyses supported a much more complex evolutionary history of these populations, including a hybrid origin of a North-West Indian Ocean (NWIO) population, which has previously been discriminated morphologically, but not genetically. The best-supported demographic models suggested that the current genetic relationships among populations were due to a complex series of past divergences followed by asymmetric migration in more recent times.

Conclusion
Overall, this study suggests that alternating periods of marine divergence and gene flow have driven the current genetic patterns observed in this lobster and may help explain the observed wider patterns of marine species diversity in the Indo-Pacific.
Effect of positive end-expiratory pressure on pulmonary compliance and pulmonary complications in patients undergoing robot-assisted laparoscopic radical prostatectomy: a randomized control trial
Authors: Cheng Menglan , Ni Lifeng , Huang Ling’er , Zhou Yanfeng , Wang Kuirong 
Published: November 2022

Abstract
Background
To observe the effects of different positive end-expiratory pressure (PEEP) ventilation strategies on pulmonary compliance and complications in patients undergoing robotic-assisted laparoscopic prostate surgery.

Methods
A total of 120 patients with the American Society of Anesthesiologists Physical Status Class I or II who underwent elective robotic-assisted laparoscopic prostatectomy were enrolled. We randomized the patients divided into divided into three groups of 40 patients each: PEEP0, PEEP5, or PEEP10. Master Anesthetist used volume control ventilation intraoperatively with an intraoperative deep muscle relaxation strategy. Respiratory mechanics indexes were recorded at six time-points: 10 mimuts after anaesthesia induction, immediately after pneumoperitoneum establishment, 30 min, 60 min, 90 min, and at the end of pneumoperitoneum. Arterial blood gas analysis and oxygenation index calculation were performed 10 mimuts after anaesthesia induction, 60 mimuts after pneumoperitoneum, and after tracheal extubation. Postoperative pulmonary complications were also recorded.

Results
After pneumoperitoneum, peak inspiratory pressure (Ppeak), plateau pressure (Pplat), mean pressure (Pmean), driving pressure (ΔP), and airway resistance (Raw) increased significantly, and pulmonary compliance (Crs) decreased, persisting during pneumoperitoneum in all groups. Between immediately after pneumoperitoneum establishment, 30 min, 60 min, and 90 min, pulmonary compliance in the 10cmH2OPEEP group was higher than in the 5cmH2OPEEP (P < 0.05) and 0cmH2OPEEP groups(P < 0.05). The driving pressure (ΔP) immediately after pneumoperitoneum establishment, at 30 min, 60 min, and 90 min in the 10cmH2OPEEP group was lower than in the 5cmH2OPEEP (P < 0.05) and 0cmH2OPEEP groups (P < 0.05). Sixty min after pneumoperitoneum and tracheal extubation, the PaCO2 did not differ significantly among the three groups (P > 0.05). The oxygenation index (PaO2/FiO2) was higher in the PEEP5 group than in the PEEP0 and PEEP10 groups 60 min after pneumoperitoneum and after tracheal extubation, with a statistically significant difference (P < 0.05). In postoperative pulmonary complications, the incidence of atelectasis was higher in the PEEP0 group than in the PEEP5 and PEEP10 groups, with a statistically significant difference (p < 0.05).

Conclusion
The use of PEEP at 5cmH2O during RARP increases lung compliance, improves intraoperative oxygenation index and reduces postoperative atelectasis.

Trial registration
This study was registered in the China Clinical Trials Registry on May 30, 2020 (Registration No. ChiCTR2000033380).
Perceived human factors from the perspective of paramedics – a qualitative interview study
Authors: Poranen Anna , Kouvonen Anne , Nordquist Hilla 
Published: November 2022

AbstractBackgroundThe work environment in prehospital emergency medical care setting is dynamic and complex and includes many stressors. However, little is known about the perceived human factors from the perspective of paramedics. In this study, we investigated, from the perspective of paramedics, what are the human factors, and how are they linked to prehospital emergency medical care?MethodsData were collected through semi-structured interviews (n = 15) with Finnish paramedics. The material was analyzed using inductive content analysis.ResultsThree main categories of human factors were identified. The first main category consisted of factors related to work which were divided into two generic categories: “Challenging organizational work environment” and “Changing external work environment.” The second main category comprised factors related to paramedics themselves and were divided into three generic categories: “Issues linked to personality,” “Personal experiences”, and “Factors resulting from personal features.” The third main category described that paramedics have difficulties in understanding and describing human factors.ConclusionThis study revealed numerous factors that can affect paramedics’ work in the EMS setting. Increased knowledge about human factors in the EMS setting provides organizations with the opportunity to develop procedures that can support paramedics’ cognitive and physical work. Human factors in different situations can be addressed to improve occupational and patient safety.
The effect of intensive family-centered health education on the awareness rate, diagnosis, and treatment of post-stroke depression in community families
Authors: Wang Hao , Pan Shuchao , Xu Qiwu , Ding Ting 
Published: November 2022

Abstract
Objective
To investigate the effects of intensive family-centered health education on the awareness rate, diagnosis, and treatment of post-stroke depression (PSD) in community families.

Methods
Elderly patients (60–90 years) from 20 community service centers affiliated with the Department of Neurology and the Medical Association of Tongling Municipal Hospital who had been diagnosed with stroke between January 2017 and June 2020 were screened using the hospital and community electronic medical record system. In this randomized cluster trial, 119 patients from 10 communities were assigned as the control group and received routine community treatment, while 126 patients from the other 10 communities were assigned as the experimental group and received routine treatment plus family-centered intensive health education. After 12 months of medical intervention, the assessment of PSD in the two groups was performed by a neurologist and a psychiatrist, both blind to the study design, using the Hamilton Rating Scale for Depression.

Results
The awareness rates of the causes, clinical manifestations, treatment plan, and family care of PSD in the experimental group were 88.89, 91.30, 93.65, and 92.06%, respectively. In the control group, the awareness rates of these parameters were 72.27, 69.75, 71.43, and 65.55%, respectively, and the differences between the two groups were statistically significant (P < 0.05). In the experimental group, the rates of PSD diagnosis, prompt medical attendance, drug treatment compliance, and psychotherapeutic treatment compliance were 27.78, 22.22, 18.25, and 11.90%, respectively. In the control group, the rates of these parameters were 13.79, 6.03, 3.48, and 1.72%, respectively, and the differences between the two groups were statistically significant (P < 0.05).

Conclusion
Intensive family-centered health education can improve the level of knowledge of PSD in the community, promote the timely treatment and diagnosis of PSD in patients, and improve the compliance rates of drug therapy and psychotherapy, so this is worthy of promotion.
Risk factors of active upper gastrointestinal bleeding in patients with COVID-19 infection and the effectiveness of PPI prophylaxis
Authors: Prasoppokakorn Thaninee , Kullavanijaya Pinit , Pittayanon Rapat 
Published: November 2022

Abstract
Background
Gastrointestinal (GI) bleeding is one of the most impactful complications in patients hospitalized from COVID-19 infection. Limited study has focused on patients with upper GI bleeding (UGIB). This study aimed to identify the risk factors of patients who were hospitalized from COVID-19 infection and developed UGIB as well as the effectiveness of proton pump inhibitor (PPI) prophylaxis in those patients.

Methods
This study was comprised of two phases. The first phase was the retrospective enrollment of patients who were admitted due to COVID-19 infection and developed UGIB between April and August 2021 to evaluate the associated factors of active UGIB. The second phase was a retrospective analysis after PPI prophylaxis protocol from September – October 2021 to assess the benefit of PPI use in those patients.

Results
Of 6,373 patients hospitalized, 43 patients (0.7%) had evidence of UGIB. The majority were male 28 (65.1%) with a mean age of 69.1 ± 11.8 years. Twenty-four of 43 patients (55.8%) needed mechanical ventilation, 35 patients (81.4%) received systemic corticosteroids, and 10 patients (23.3%) were taking anticoagulants for venous thromboembolic prophylaxis. Seven of 43 patients (16%) had active UGIB. There was no significant difference in the number of patients taking antiplatelets, anticoagulants, or steroids and the severity of COVID-19 infection between the two groups. An emergency endoscopy or endoscopic hemostasis were performed in 6/7 (85.7%) patients. The multivariate logistic regression analysis revealed two significant factors associated with active UGIB including higher of Glasgow-Blatchford score (GBS) per point (OR = 7.89; 95%CI 1.03–72.87; p = 0.04) and an absence of PPI use (OR 4.29; 95%CI 1.04–19.51; p = 0.04). After prescribing PPI as a prophylaxis, there was a slightly lower incidence of UGIB (0.6% vs 0.7%) in addition to an absence of active UGIB (0% vs 16%).

Conclusion
Our study demonstrated that the absence of PPI and higher GBS were significant risk factors for active UGIB which required therapeutic endoscopy in patients with COVID-19 infection. We suggest that short-term PPI prophylaxis should be prescribed in those patients once they need hospitalization regardless of the severity of COVID-19 infection to minimize the severity of UGIB.
Socio-demographic and lifestyle factors associated with intrinsic capacity among older adults: evidence from India
Authors: Muneera K. , Muhammad T. , Althaf S 
Published: November 2022

Abstract
Background
Since the traditional models missed the possibility of formulating personalised programs centred on a person’s priorities and values, it was a pressing priority to shift from traditional disease-centred to a function-based approach of healthy ageing, which is defined as ‘the process of developing and maintaining the functional ability that enables well-being in older age’. The present study aimed to assess the prevalence of high intrinsic capacity (IC) of older adults and to examine the socio-demographic and lifestyle factors associated with IC among older adults in India.

Methods
The study utilises the individual-level data from the first wave of the Longitudinal Aging Study in India (LASI) conducted during 2017–18. The total sample size for the present study was 24,136 older adults (11,871 males and 12,265 females) aged 60 years and above. Descriptive statistics, along with bivariate analysis, was employed to present the preliminary results. Additionally, multivariable linear and logistic regression analyses were conducted to find out the association of socio-demographic and lifestyle factors with IC and its components.

Results
The mean IC score was found to be 7.37 (SD = 1.6) in this study. A proportion of 24.56% of older adults was observed to be in the higher IC category. Increasing age was negatively associated with high IC for older men and women. Older people who smoke tobacco (β = -0.23; CI: -0.32—-0.13) and chew tobacco (β = -0.11; CI: -0.18—-0.03) were less likely to experience high IC compared to their respective counterparts. Older adults who reported episodic alcohol drinking were less likely to have high IC (β = -0.20; CI:-0.32—-0.07). The engagement in moderate physical activity (β = 0.12; CI:0.01–0.23), vigorous physical activity (β = 0.12; CI:0.05–0.20) and yoga-related activity (β = 0.18; CI:0.09–0.26) were significantly positively associated with high IC. Among the five domains of IC, education was significantly associated with higher capacity in each domain, and increasing age was found to be a significant predictor of lower capacity in each IC domain except locomotion. Older men and women engaged in vigorous physical activity had 35 and 19% significantly higher odds of high capacity in sensory (aOR = 1.35; CI: 1.12—1.62) and psychological (aOR = 1.19; CI: 1.06—1.34) domains, respectively.

Conclusions
The study revealed that lifestyle behaviours including tobacco use, episodic alcohol drinking and physical activity are strongly associated with IC among older adults in India. The findings suggest that healthy lifestyle behaviours should be encouraged among older adults as an effort to improve their IC, which is the key determinant of functional ability and quality of life in later years of life.
Increased risk of myocarditis and pericarditis and reduced likelihood of severe clinical outcomes associated with COVID-19 vaccination: a cohort study in Lombardy, Italy
Authors: Corrao Giovanni , Franchi Matteo , Cereda Danilo , Bortolan Francesco , Leoni Olivia , Vignati Eugenio , Pavesi Giovanni , Gori Andrea 
Published: November 2022

Abstract
Introduction
We aimed to assess harms (post-vaccine myocarditis and pericarditis) and benefits (preventing severe disease) of COVID-19 vaccination.

Methods
We conducted a population-based retrospective cohort study. Using the integrated platform of the vaccination campaign of Lombardy Region (Italy), after the exclusion of 24,188 individuals not beneficiaries of the Regional Health Service, 9,184,146 citizens candidates to vaccine at December 27, 2020 were followed until November 30, 2021 (the loss to follow-up rate was 0.5%). From the date of administration of each vaccine dose to day 28 post-administration, three periods that covered exposure to the first, second, and third dose were defined. The benefit–risk profile of vaccines was performed by comparing the number needed to harm (NNH) and number needed to treat (NNT) by sex, age, and vaccine type.

Results
Incidence rates of myocarditis were 9.9 and 5.2 per million person-months during the exposure and no-exposure periods, respectively, and the incidence rates of pericarditis were 19.5 and 15.9 per million person-months, respectively. The risk of myocarditis was highest following exposure to the second dose of the Moderna vaccine (adjusted HR: 5.5, 95% CI: 3.7 to 8.1). Exposure to the Moderna vaccine was also associated with an increased risk of pericarditis (adjusted HR 2.2, 1.5 to 3.1). NNT was higher than NNH (9471 vs. 7213) for 16 to 19-year-old men who received the Moderna vaccine, while all other sex, age, and vaccine subgroups had a favourable harm-benefit profile.

Conclusions
Men 16 to 19 years of age has the highest rates of myocarditis within a few days after receiving the Moderna vaccines. The balance between harms and benefits was almost always in favour of vaccination.
The efficacy of AuNP-probe conjugate nanobiosensor in non-amplification and amplification forms for the diagnosis of leishmaniasis
Authors: Deris Someye , Osanloo Mahmoud , Ghasemian Abdolmajid , Ataei Saeed , Kohansal Maryam , Samsami Sahar , Yazdanpanah Ava , Ebrahimnezhad Alireza , Ghanbariasad Ali 
Published: November 2022

AbstractNanobiosensor platforms have emerged as convenient and promising approaches with remarkable efficacy for the diagnosis of infectious diseases. Gold nanoparticles (AuNPs) have been widely used due to numerous advantageous properties such as optical, electrical, physicochemical and great biomolecules binding capabilities. This study aimed to apply AuNP-Probe Conjugate for the detection of Leishmania spp., using colorimetric and amplification methods targeting parasitic ITS2 fragment. The first method was carried out by hybridization of 10µL of DNA with 4 µL of probe and addition of 5 µL of 0.2 N HCl (non-amplification method). Second method was followed by polymerase chain reaction (PCR) amplification using thiolated primer, 5 µL of AuNP and 5 µL of 0.2 N HCl. The appearance of red and purple colors indicated positive and negative results, respectively. The minimum of detection for non-amplification and amplification methods for three strains of Leishmania namely L. major, L. tropica and L. infantum were determined to be 32 fg/µL and 16 fg/µL, respectively. Sensitivity for detection of visceral leishmaniasis (VL) for non-amplification and amplification methods included 96% and 100%, respectively and for cutaneous leishmaniasis (CL) included 98% and 100%, respectively. The results of this investigation revealed that sensitivity of amplification method was the same as RT-qPCR, while that of non-amplification method was lower. However, this method was promising because of no need for any equipment, high specificity, enough sensitivity, low cost and rapidity (less than 30 min) to complete after genomic DNA extraction.