bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative meta-proteomic pipeline for the identification of plasmodesmata proteins and regulatory conditions in diverse plant species
Authors: Kirk Philip , Amsbury Sam , German Liam , Gaudioso-Pedraza Rocio , Benitez-Alfonso Yoselin 
Published: June 2022

AbstractBackgroundA major route for cell-to-cell signalling in plants is mediated by cell wall-embedded pores termed plasmodesmata forming the symplasm. Plasmodesmata regulate the plant development and responses to the environment; however, our understanding of what factors or regulatory cues affect their structure and permeability is still limited. In this paper, a meta-analysis was carried out for the identification of conditions affecting plasmodesmata transport and for the in silico prediction of plasmodesmata proteins in species for which the plasmodesmata proteome has not been experimentally determined.ResultsUsing the information obtained from experimental proteomes, an analysis pipeline (named plasmodesmata in silico proteome 1 or PIP1) was developed to rapidly generate candidate plasmodesmata proteomes for 22 plant species. Using the in silico proteomes to interrogate published transcriptomes, gene interaction networks were identified pointing to conditions likely affecting plasmodesmata transport capacity. High salinity, drought and osmotic stress regulate the expression of clusters enriched in genes encoding plasmodesmata proteins, including those involved in the metabolism of the cell wall polysaccharide callose. Experimental determinations showed restriction in the intercellular transport of the symplasmic reporter GFP and enhanced callose deposition in Arabidopsis roots exposed to 75-mM NaCl and 3% PEG (polyethylene glycol). Using PIP1 and transcriptome meta-analyses, candidate plasmodesmata proteins for the legumeMedicago truncatulawere generated, leading to the identification of Medtr1g073320, a novel receptor-like protein that localises at plasmodesmata. Expression of Medtr1g073320 affects callose deposition and the root response to infection with the soil-borne bacteria rhizobia in the presence of nitrate.ConclusionsOur study shows that combining proteomic meta-analysis and transcriptomic data can be a valuable tool for the identification of new proteins and regulatory mechanisms affecting plasmodesmata function. We have created the freely accessible pipeline PIP1 as a resource for the screening of experimental proteomes and for the in silico prediction of PD proteins in diverse plant species.
Identification and characterization of a heme exporter from the MRP family in Drosophila melanogaster
Authors: Wang Zhiqing , Zeng Peng , Zhou Bing 
Published: June 2022

Abstract
Background
The heme group constitutes a major functional form of iron, which plays vital roles in various biological processes including oxygen transport and mitochondrial respiration. Heme is an essential nutrient, but its pro-oxidant nature may have toxic cellular effects if present at high levels, and its synthesis is therefore tightly regulated. Deficiency and excess of heme both lead to pathological processes; however, our current understanding of metazoan heme transport is largely limited to work in mammals and the worm Caenorhabditis elegans, while functional analyses of heme transport in the genetically amenable Drosophila melanogaster and other arthropods have not been explored.

Results
We implemented a functional screening in Schneider 2 (S2) cells to identify putative heme transporters of D. melanogaster. A few multidrug resistance-associated protein (MRP) members were found to be induced by hemin and/or involved in heme export. Between the two plasma membrane-resident heme exporters CG4562 and CG7627, the former is responsible for heme transit across the intestinal epithelium. CG4562 knockdown resulted in heme accumulation in the intestine and lethality that could be alleviated by heme synthesis inhibition, human MRP5 (hMRP5) expression, heme oxygenase (HO) expression, or zinc supplement. CG4562 is mainly expressed in the gastric caeca and the anterior part of the midgut, suggesting this is the major site of heme absorption. It thus appears that CG4562 is the functional counterpart of mammalian MRP5. Mutation analyses in the transmembrane and nucleotide binding domains of CG4562 characterized some potential binding sites and conservative ATP binding pockets for the heme transport process. Furthermore, some homologs in Aedes aegypti, including that of CG4562, have also been characterized as heme exporters.

Conclusions
Together, our findings suggest a conserved heme homeostasis mechanism within insects, and between insects and mammals. We propose the fly model may be a good complement to the existing platforms of heme studies.
Association between oxygen saturation level during bronchoscopy and post-bronchoscopy adverse events: a retrospective cohort study
Authors: Kim So Yeon , Lee Hyo Jin , Lee Jung Kyu , Park Tae Yeon , Heo Eun Young , Kim Deog Kyeom , Chung Hee Soon , Lee Hyun Woo 
Published: June 2022

Abstract
Background
Flexible bronchoscopy is widely used to diagnose and treat various respiratory diseases. However, caution is warranted for post-bronchoscopy adverse events. Although desaturation frequently occurs during bronchoscopy, its clinical impact and the optimal oxygen saturation level during the procedure remain unclear. This study aimed to investigate whether the percutaneous oxygen saturation (SpO2) level during bronchoscopy is associated with the development of post-bronchoscopy respiratory adverse events.

Methods
In this single-center retrospective cohort study conducted from March 2020 to February 2021, 569 patients were classified into high or low oxygen saturation groups based on the SpO2 level during bronchoscopy. The primary outcome was post-bronchoscopy respiratory adverse events, and secondary outcomes were other post-bronchoscopy adverse events and clinical outcomes.

Results
Among 569 patients, 458 and 111 patients were classified into the high oxygen saturation (SpO2 > 96%) and low oxygen saturation (SpO2 ≤ 94%) groups, respectively. After propensity score matching, the low oxygen saturation group had more post-bronchoscopy respiratory and febrile adverse events than the high oxygen saturation group. In the multivariable regression analysis, low SpO2 level during bronchoscopy was an independent risk factor for post-bronchoscopy respiratory adverse events (odds ratio = 3.16 [95% confidence interval 1.37–7.30]). In the low oxygen saturation group, the high-risk subgroups for post-bronchoscopy respiratory adverse events were the elderly, women, current smokers, and patients with chronic obstructive pulmonary disease or acute decompensated heart failure before bronchoscopy. There was no significant difference in the length of hospital stay, intensive care unit admission, or mortality between the high and low oxygen saturation groups.

Conclusions
Close monitoring is recommended for patients with SpO2 ≤ 94% during bronchoscopy due to the increased risk of respiratory adverse events after the procedure.
Pleuroparenchymal fibroelastosis in rheumatoid arthritis-associated interstitial lung disease
Authors: Kang Jieun , Seo Woo Jung , Lee Eun Young , Chang Sung Hae , Choe Jooae , Hong Seokchan , Song Jin Woo 
Published: June 2022

Abstract
Background
Pleuroparenchymal fibroelastosis (PPFE) is a rare interstitial lung disease (ILD) featuring dense fibrosis of the visceral pleura and subpleural parenchyma, mostly in the upper lobes. PPFE can present in other ILDs, including rheumatoid arthritis-associated ILD (RA-ILD). The aim of this retrospective study was to investigate the prevalence and clinical implications of coexistent PPFE in RA-ILD.

Methods
Overall, 477 patients with RA-ILD were recruited from two cohorts; their clinical data and HRCT images were analysed. The criteria for diagnosing PPFE were (1) pleural thickening with bilateral subpleural dense fibrosis in the upper lobes, (2) evidence of disease progression, and (3) absence of other identifiable aetiologies.

Results
The median follow-up duration was 3.3 years. The mean age of the patients was 63.4 years, and 60.0% were women. PPFE was identified in 31 patients (6.5%). The PPFE group showed significantly lower body mass index and forced vital capacity (FVC) and more frequent usual interstitial pneumonia (UIP)-like pattern on HRCT than no-PPFE group. The risk factors for all-cause mortality were older age, lower FVC, and the presence of UIP-like pattern on HRCT; PPFE was not significantly associated with mortality in both all patients and a subgroup with a UIP-like pattern. The presence of PPFE was associated with a significantly increased risk of pneumothorax and greater decline in diffusing capacity.

Conclusions
PPFE was not rare in patients with RA-ILD and was significantly associated with an increased risk of pneumothorax and greater lung function decline, though we found no significant association with mortality.
Impact of metabolic syndrome and metabolic dysfunction-associated fatty liver disease on cardiovascular risk by the presence or absence of type 2 diabetes and according to sex
Authors: Matsubayashi Yasuhiro , Fujihara Kazuya , Yamada-Harada Mayuko , Mitsuma Yurie , Sato Takaaki , Yaguchi Yuta , Osawa Taeko , Yamamoto Masahiko , Kitazawa Masaru , Yamada Takaho , Kodama Satoru , Sone Hirohito 
Published: June 2022

Abstract
Background
To determine the impact of metabolic syndrome (MetS) and/or metabolic dysfunction-associated fatty liver disease (MAFLD), which are pathophysiologically similar and include insulin resistance, on the development of new-onset cardiovascular disease with and without type 2 diabetes and according to sex.

Methods
This study included 570,426 individuals without a history of cardiovascular disease who were enrolled in a nationwide claims database from 2008 to 2016 and were classified by the presence or absence of MetS and/or MAFLD stratified by the presence or absence of type 2 diabetes and sex. The fatty liver index was used to determine the presence or absence of fatty liver that required a diagnosis of MAFLD. Risks of developing coronary artery disease (CAD) and cerebrovascular disease (CVD) in each category were analyzed using a multivariate Cox proportional hazard model.

Results
During a median follow-up of 5.2 years, 2252 CAD and 3128 CVD events occurred. Without type 2 diabetes the hazard ratio (HR) (95% CI) for CAD/CVD compared with neither MAFLD nor MetS was 1.32 (1.17–1.50)/1.41(1.28–1.57) for MAFLD only (without MetS), 1.78 (1.22–2.58)/1.66 (1.34–2.06) for MetS only (without MAFLD), and 2.10 (1.84–2.39)/1.73 (1.54–1.95) for MAFLD + MetS. For those with type 2 diabetes, the HR for CAD for MAFLD only (compared with neither MAFLD nor MetS) was 1.29 (1.06–1.58), for MetS only 1.34 (0.84–2.13), and for MAFLD + MetS 1.22 (1.02–1.47). For CVD, there was a significant increase in HR only in MAFLD + MetS [1.44 (1.18–1.76)]. The results of the analysis stratified by sex showed that MAFLD had a greater impact in men, and MetS had a greater impact in women regarding the development of CAD.

Conclusions
Distinguishing between MetS and/or MAFLD in the presence or absence of type 2 diabetes and according to sex may aid in accurately identifying patients at high risk of cardiovascular disease.
Overlapping promoter library designed for rational heterogenous expression in Cordyceps militaris
Authors: Lyu Mengdi , Zeng Jiapeng , Zhou Yue , Zhang Tongyu , Wang Aiping , Ma Jiezhao , Wu Ziyi , Castells-Garcia Alvaro , González-Almela Esther , Lin Junfang , Wei Tao 
Published: June 2022

Abstract
Background
Cordyceps militaris, a kind of edible and medicinal fungus widely accepted in East Asia, has attracted much attention as a potential cell factory for producing adenosine analogs. Despite the rapid development in gene editing techniques and genome modeling, the diversity of DNA elements in C. militaris was too short to achieve rational heterogeneous expression for metabolic engineering studies.

Results
In this study, PtrpC, a kind of promoter with a relatively appropriate expression level and small size, was selected as a monomer for promoter library construction. Through in vitro BioBricks assembly, 9 overlapping PtrpC promoters with different copy numbers as well as reporter gene gfp were connected and subsequently integrated into the genome of C. militaris. Both the mRNA transcription level and the expression level of gene gfp gradually increased along with the copy number of the overlapping promoter NPtrpC and peaked at 7. In the meantime, no significant difference was found in either the biomass or morphological characteristic of engineered and wild-type strains.

Conclusions
This study firstly expanded the overlapping promoter strategy used in model microorganism in C. militaris. It was a proof-of-concept in fungi synthetic biology and provide a general method to pushed the boundary of promoter engineering in edible mushroom.
Comparative in silico characterization of Klebsiella pneumoniae hypervirulent plasmids and their antimicrobial resistance genes
Authors: Bolourchi Negin , Naz Anam , Sohrabi Maryam , Badmasti Farzad 
Published: June 2022

Abstract
Background
The hypervirulent pathotype of Klebsiella pneumoniae (hvKp) is mainly mediated by large virulent plasmids. It seems that these hypervirulent plasmids (HVPs) are accumulating antimicrobial resistance genes (ARGs) and are turning quickly into drug-resistant hypervirulent hybrids. Therefore, molecular mechanisms involved in this convergence needs to be investigated to control their global spread.

Methods
In this study, the complete sequence of 79 non-redundant hypervirulent plasmids were retrieved from GenBank and their genetic features, hypervirulence and antimicrobial resistance patterns (AMR) as well as their putative transmission capability were compared using bioinformatics tools.

Results
The majority of HVPs belonged to clonal complex (CC)23, and sequence type (ST)11. IncFIB and IncHI1B were the most prevalent plasmid replicon types. Out of 79 plasmids, 78 were positive for iutA and iucA. The iucC, iucB and iucD genes were found in 77 plasmids. Almost 26% of the HVPs were potentially conjugative of which 71% carried AGRs. ARGs against beta-lactams, carbapenems, quinolones, aminoglycosides, chloramphenicols, tetracyclines and macrolides were detected in 30% of HVPs. Class 1 integron and prophage structures harboring multiple ARGs were found in eight plasmids. Insertion sequences (IS)6, IS110 and IS1380 appeared to be important genetic elements in transmission of ARGs.

Conclusions
The high prevalence of iucA and iutA suggests their strong capability for rapid and accurate genetic markers for discrimination of hvKp in the laboratory. This study indicated the important role of mobile genetic elements (MGEs) in the emergence of drug-resistance in hypervirulent strains. The high prevalence of putative conjugative hybrids implies higher incidence of multidrug-resistant (MDR)-hvKp strains in near future.
The effect of fluoroquinolones and antioxidans on biofilm formation by Proteus mirabilis strains
Authors: Przekwas Jana , Gębalski Jakub , Kwiecińska-Piróg Joanna , Wiktorczyk-Kapischke Natalia , Wałecka-Zacharska Ewa , Gospodarek-Komkowska Eugenia , Rutkowska Dorota , Skowron Krzysztof 
Published: June 2022

Abstract
Background
Fluoroquinolones are a group of antibiotics used in urinary tract infections. Unfortunately, resistance to this group of drugs is currently growing. The combined action of fluoroquinolones and other antibacterial and anti-biofilm substances may extend the use of this therapeutic option by clinicians. The aim of the study was to determine the effect of selected fluoroquinolones and therapeutic concentrations of ascorbic acid and rutoside on biofilm formation by Proteus mirabilis.

Materials and methods
The study included 15 strains of P. mirabilis isolated from urinary tract infections in patients of the University Hospital No. 1 dr A. Jurasz in Bydgoszcz (Poland). The metabolic activity of the biofilm treated with 0.4 mg/ml ascorbic acid, 0.02 µg/ml rutoside and chemotherapeutic agents (ciprofloxacin, norfloxacin) in the concentration range of 0.125–4.0 MIC (minimum inhibitory concentration) was assessed spectrophotometrically.

Results
Both ciprofloxacin and norfloxacin inhibited biofilm formation by the tested strains. The biofilm reduction rate was correlated with the increasing concentration of antibiotic used. No synergism in fluoroquinolones with ascorbic acid, rutoside or both was found. The ascorbic acid and rutoside combination, however, significantly decreased biofilm production.

Conclusions
Our research proves a beneficial impact of ascorbic acid with rutoside supplementation on biofilm of P. mirabilis strains causing urinary tract infections.
Low preoperative psoas muscle mass index is a risk factor for distal cholangiocarcinoma recurrence after pancreatoduodenectomy: a retrospective analysis
Authors: Umezawa Saori , Kobayashi Shinjiro , Otsubo Takehito 
Published: June 2022

Abstract
Background
This study aimed to investigate whether preoperative muscle mass is associated with the recurrence of distal cholangiocarcinoma after pancreatoduodenectomy (PD).

Methods
We retrospectively examined 88 patients who had undergone PD for distal cholangiocarcinoma. The preoperative psoas muscle mass index (PMI) was measured using computed tomography as an index of muscle mass. We performed multivariate analysis of factors influencing early recurrence and developed a prognostic survival model using independent risk factors for recurrence.

Results
The cut-off PMI values for recurrence within 1 year of surgery, determined from the receiver operating characteristic curve, were 5.90 cm2/m2 in males and 3.98 cm2/m2 in females. Multivariate analysis of effects associated with early recurrence within 1 year indicated that low PMI (odds ratio [OR] 9.322; 95% confidence interval [CI] 2.832 − 30.678; p = 0.0002) and lymph node metastasis (OR 5.474; 95% CI 1.620 − 18.497; p = 0.0062) were independent risk factors, and the median recurrence-free survival (RFS) of the low and high PMI groups were 21.6 and 81.0 months, respectively (p = 0.0214). The median RFS for zero, one, and two risk factors of low PMI and lymph node metastasis were as follows: zero variables, median not reached; one variable, 15.3 months; two variables: 6 months.

Conclusions
Low preoperative PMI may be a risk factor for distal cholangiocarcinoma recurrence after PD.

Trial registration
The Institutional Review Board of St. Marianna University School of Medicine approved this study prior to commencement of data collection and analysis on October 9, 2020 (IRB no. 5006) and waived the informed consent requirement.
Socio-cultural implications for women’s menstrual health in the Pacific Island Countries and Territories (PICTs): a scoping review
Authors: Maulingin-Gumbaketi Elizabeth , Larkins Sarah , Whittaker Maxine , Rembeck Gun , Gunnarsson Ronny , Redman-MacLaren Michelle 
Published: June 2022

Abstract
Background
Globally, experiences of menarche and subsequent menstruation are embedded in social and cultural beliefs, norms and practices. Menarche is an important developmental milestone in sexual and reproductive health (SRH) for females. Menarche is intertwined with socio-cultural norms, beliefs and practices, which can impact on women’s ability to manage menstruation with dignity. This paper reviews the social and cultural factors that affect women’s ability to effectively manage their menstrual health and hygiene (MHH) in Pacific Island Countries and Territories (PICTs).

Methods
A scoping review was conducted following PRISMA scoping review guidelines and inclusion/exclusion criteria. An online search was conducted for peer-reviewed publications in Medline/OVID; Medline/PubMED; PsycINFO; CINAHL; Scopus and JSTOR, and Google Scholar. A search for grey literature was conducted in Google Scholar and websites of international and local organizations. Experts in the field also contributed additional references. Extracted data were summarised in an Excel spreadsheet. Searches were conducted between May and June, 2019, and then repeated in July, 2020.

Results
A total of 11 studies were included; 10 qualitative and one mixed methods study. Studies were conducted in Melanesian (n = 9), Polynesian (n = 1) and Micronesian (n = 1) PICTs. All 11 studies reported elements of societal and personal factors; ten studies reported evidence relating to interpersonal factors; nine studies reported elements relating to environmental factors; and two studies presented evidence linked to biological factors. Managing menstrual health with dignity is challenging for many women and girls because menstruation is associated with menstrual taboos and shame.

Conclusion
This review found that the MHH experiences of women in PICTs are affected by social and cultural beliefs, norms and practices. Beliefs, norms and practices about menarche need to be incorporated in SRH planning, programs and education in order to be relevant to diverse village and urban settings.
Depression secondary to vision loss in old age and an effective rapid screening tool for undiagnosed cases
Authors: Clancy Noah , Aslam Tariq , Cackett Peter 
Published: June 2022

Abstract
Background
Zenebe et al. recently stated that despite depression being a common mental health problem in the elderly population, it is underdiagnosed in over half of the cases (Zenebe et al. in Ann Gen Psychiatry, 2021). They described an extensive list of risk factors associated with geriatric depression. However, we noted that they did not include ophthalmic conditions in this list which have previously been identified as an important risk factor for depression in the elderly.

Main body
To determine the extent of undiagnosed anxiety and depression in our elderly population with vision loss, we screened a cohort of our patients, over 60 years with vision loss secondary to macular disease for both conditions.
Our cohort included 104 patients with mean best corrected visual acuity 0.58 LogMAR (Snellen equivalent 6/24). In this group, we identified 29.8% (31/104) and 28.8% (30/104) of patients with at least one depression or anxiety-related symptom, respectively, in the past 2 weeks. We identified 7.7% (8/104) and 3.8% (4/104) who had significant symptoms of depression and anxiety, respectively, that warranted further follow-up. Only two of these patients had previously been diagnosed with anxiety or depression with the majority having no previous history of either condition.
Patients from our cohort who screened for depression or anxiety often cited frustration completing tasks and loss of independence secondary to declining vision. They also complained that the vision loss resulted in a lack of confidence which in turn resulted in social isolation and loneliness. Most of the patients welcomed referral to their GP for follow-up for input regarding their mental health and they also stated an interest in attending hospital optometry low vision services and counselling support.

Conclusions
With increasing time pressures on healthcare services and the rising use of virtual clinics especially during the COVID-19 pandemic, it is still essential to screen efficiently for depression in those elderly patients who are at significant risk. There is a considerable burden of major depressive disease in the geriatric population, and we would recommend that physicians (Geriatricians, GPs, Ophthalmologists etc.) screen elderly patients with vision loss for depression using the rapid screening tool which we suggest.