bluuebunny/crossref_metadata_2025 huggingface dataset:
Bio-informatic analysis of CRISPR protospacer adjacent motifs (PAMs) in T4 genome
Authors: Rawashdeh Omar , Rawashdeh Rabeah Y. , Kebede Temesgen , Kapp David , Ralescu Anca
Published: June 2022

Background

The existence of protospacer adjacent motifs (PAMs) sequences in bacteriophage genome is critical for the recognition and function of the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) machinery system. We further elucidate the significance of PAMs and their function, particularly as a part of transcriptional regulatory regions in T4 bacteriophages.

Methods

A scripting language was used to analyze a sequence of T4 phage genome, and a list of few selected PAMs. Mann-Whitney Wilcoxon (MWW) test was used to compare the sequence hits for the PAMs versus the hits of all the possible sequences of equal lengths.

Results

The results of MWW test show that certain PAMs such as: ‘NGG’ and ‘TATA’ are preferably located at the core of phage promoters: around -10 position, whereas the position around -35 appears to have no detectable count variation of any of the tested PAMs. Among all tested PAMs, the following three sequences: 5’-GCTV-3’, 5’-TTGAAT-3’ and 5’-TTGGGT-3’ have higher prevalence in essential genes. By analyzing all the possible ways of reading PAM sequences as codons for the corresponding amino acids, it was found that deduced amino acids of some PAMs have a significant tendency to prefer the surface of proteins.

Conclusion

These results provide novel insights into the location and the subsequent identification of the role of PAMs as transcriptional regulatory elements. Also, CRISPR targeting certain PAM sequences is somehow likely to be connected to the hydrophilicity (water solubility) of amino acids translated from PAM’s triplets. Therefore, these amino acids are found at the interacting unit at protein-protein interfaces.
Systematic analysis and expression profiles of TCP gene family in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stress
Authors: Yang Mingfang , He Guandi , Hou Qiandong , Fan Yu , Duan Lili , Li Kuiyin , Wei Xiaoliao , Qiu Zhilang , Chen Erjuan , He Tengbing
Published: June 2022

Background

As transcription factors, the TCP genes are considered to be promising targets for crop enhancement for their responses to abiotic stresses. However, information on the systematic characterization and functional expression profiles under abiotic stress of TCPs in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) is limited.

Results

In this study, we identified 26 FtTCPs and named them according to their position on the chromosomes. Phylogenetic tree, gene structure, duplication events, and cis-acting elements were further studied and syntenic analysis was conducted to explore the bioinformatic traits of the FtTCP gene family. Subsequently, 12 FtTCP genes were selected for expression analysis under cold, dark, heat, salt, UV, and waterlogging (WL) treatments by qRT-PCR. The spatio-temporal specificity, correlation analysis of gene expression levels and interaction network prediction revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stresses. Moreover, subcellular localization confirmed that FtTCP15 and FtTCP18 localized in the nucleus function as transcription factors.

Conclusions

In this research, 26 TCP genes were identified in Tartary buckwheat, and their structures and functions have been systematically explored. Our results reveal that the FtTCP15 and FtTCP18 have special cis-elements in response to abiotic stress and conserved nature in evolution, indicating they could be promising candidates for further functional verification under multiple abiotic stresses.
The relationship between ambulatory arterial stiffness index and left ventricular diastolic dysfunction in HFpEF: a prospective observational study
Authors: Zhang Hanwen , Hu Weiwei , Wang Yu , Liu Jie , You Linna , Dong Qian , Chang Guanglei , Cheng Xiaocheng , Liu Zhiqiang , Zhang Dongying
Published: June 2022

Background

The relationship between ambulatory arterial stiffness index (AASI) and left ventricular diastolic dysfunction (LVDD) in patients with heart failure with preserved ejection fraction (HFpEF) is unknown. We aimed to investigate the association between the AASI and LVDD in HFpEF.

Methods

We prospective enrolled consecutive patients with HFpEF in Chongqing, China. Twenty-four-hour ambulatory blood pressure monitoring (24 h-ABPM) and echocardiography were performed in each patient. AASI was obtained through individual 24 h-ABPM. The relationship between AASI and LVDD was analyzed.

Results

A total of 107 patients with HFpEF were included. The mean age was 68.45 ± 14.02 years and 63 (59%) were women. The patients were divided into two groups according to the upper normal border of AASI (0.55). AASI > 0.55 group were more likely to be older, to have higher mean systolic blood pressure and worsen left ventricular diastolic function than AASI group ≤ 0.55. AASI was closely positive related to the diastolic function parameters, including mean E/e′ (r = 0.307, P = 0.001), septal E/e′ (r = 0.290, P = 0.002), lateral E/e′ (r = 0.276, P = 0.004) and E (r = 0.274, P = 0.004). After adjusting for conventional risk factors, AASI was still an independent risk factors of mean E/e′ > 10 in patients with HFpEF (OR: 2.929, 95%CI: 1.214–7.064, P = 0.017), and the association between AASI and mean E/e′ > 14 was reduced (OR: 2.457, 95%CI: 1.030–5.860, P = 0.043). AASI had a partial predictive value for mean E/e′ > 10 (AUC = 0.691, P = 0.002), while the predictive value for mean E/e′ > 14 was attenuated (AUC = 0.624, P = 0.034).

Conclusion

AASI was positive related to E/e′ in HFpEF and might be an independent risk factor for the increase of mean E/e′.
Illness perception and cardiovascular risk factors in patients with myocardial infarction undergoing percutaneous coronary intervention in Iran
Authors: Thagizadeh Aysan , Ghahramanian Akram , Zamanzadeh Vahid , Aslanabadi Naser , Onyeka Tonia C. , Ramazanzadeh Nargess
Published: June 2022

Background

Knowing of perception of the illness, and cardiovascular risk factors in patients with myocardial infarction is crucial in engaging in effective secondary prevention. This study aimed to examine illness perception and cardiovascular risk factors in patients with myocardial infarction undergoing percutaneous coronary intervention.

Methods

The participants comprised 131 patients undergoing a first-time percutaneous coronary intervention at a metropolitan, tertiary referral hospital in Tabriz, Iran. The convenience sampling method was employed to select the research sample within a six-month period. The instruments used were as follows: (1) Demographic and health information form, (2) The Brief Illness Perception Questionnaire (3) The Health Risk Assessment framework developed by the Centers for Disease Control and Prevention. The design of the study was descriptive, cross sectional. The continuous variables were analyzed using Independent t-test and analysis of variance (ANOVA); and categorical variables were compared using the chi-square test.

Results

Most participants had a positive family history of cardiovascular disease (54.2%), with 66.4% of participants having at least one cardiovascular risk factor such as diabetes (36.6%) hypertension (32.8%) and dyslipidemia (16%). Most participants were physically inactive (78.6%), about 48.9% were overweight, 34.4% suffered from obesity and 26% were smokers. Illness perception in this study was seen to be high (6.21), with highest scores occurring in the illness control dimension (6.83) and lowest scores occurring in the understanding dimension (3.77). There was a significant relationship between illness perception and physical activity, nutrition, sleep and general health. Direct significant relationships between biometric values (cholesterol, glucose, blood pressure); psychological factors (depression, anxiety and stress) and illness perception were also found to exist.

Conclusions

Low scores in two dimensions of illness perception may lead to psychological consequences such as stress, anxiety, and depression. The relationship between illness perception and some risk factors of cardiovascular disease such as physical activity, diet and biometric values, reveal the need for more attention to patient education and counselling.
TIDieR-telehealth: precision in reporting of telehealth interventions used in clinical trials - unique considerations for the Template for the Intervention Description and Replication (TIDieR) checklist
Authors: Rhon Daniel I. , Fritz Julie M. , Kerns Robert D. , McGeary Donald D. , Coleman Brian C. , Farrokhi Shawn , Burgess Diana J. , Goertz Christine M. , Taylor Stephanie L. , Hoffmann Tammy
Published: June 2022

Background

Recent international health events have led to an increased proliferation of remotely delivered health interventions. Even with the pandemic seemingly coming under control, the experiences of the past year have fueled a growth in ideas and technology for increasing the scope of remote care delivery. Unfortunately, clinicians and health systems will have difficulty with the adoption and implementation of these interventions if ongoing and future clinical trials fail to report necessary details about execution, platforms, and infrastructure related to these interventions. The purpose was to develop guidance for reporting of telehealth interventions.

Methods

A working group from the US Pain Management Collaboratory developed guidance for complete reporting of telehealth interventions. The process went through 5-step process from conception to final checklist development with input for many stakeholders, to include all 11 primary investigators with trials in the Collaboratory.

Results

An extension focused on unique considerations relevant to telehealth interventions was developed for the Template for the Intervention Description and Replication (TIDieR) checklist.

Conclusion

The Telehealth Intervention guideline encourages use of the Template for the Intervention Description and Replication (TIDieR) checklist as a valuable tool (TIDieR-Telehealth) to improve the quality of research through a reporting guide of relevant interventions that will help maximize reproducibility and implementation.
The relationship between organisational support for career development, organisational commitment, and turnover intentions among healthcare workers in township hospitals of Henan, China
Authors: Wu Huan , Liu Yaqing
Published: June 2022

Background

Township hospitals in China face the challenge of shortage and turnover of healthcare workers. This study aims to evaluate the relationship between organisational support for career development (OSCD), organisational commitment, and turnover intentions among healthcare workers in township hospitals.

Methods

The data in this study were obtained from the Health Service Capacity Survey of Primary Health Institutions (2020), one of the special surveys of rural health poverty alleviation in Henan, China. The sample comprised 298 healthcare workers. Three standardised instruments were used: the turnover intention scale, OSCD scale, and organisational commitment scale. Descriptive statistics, One-way Analysis of Variance, Pearson correlation analysis, and the simple mediation model were used for data analysis.

Results

The results showed that the mean score of the healthcare workers’ turnover intentions was 2.21 ± 0.77, which was low. The healthcare workers’ turnover intentions had significant differences in gender, age, marital status, education, professional title, and organisational tenure. OSCD had no significant direct relationship with turnover intentions, while having a significant positive direct relationship with organisational commitment. Organisational commitment had a significant negative direct relationship with turnover intentions, and played a fully mediating role in the relationship between OSCD and turnover intentions.

Conclusions

OSCD had an indirect negative effect on healthcare workers’ turnover intentions in township hospitals through the full mediation of organisational commitment. The findings of this study suggest the importance of policymakers and organisation managers to improve OSCD practice and pay attention to ‘humanistic management’. In addition, the formulation and implementation of talent retention policies should consider socio-demographic differences.
Psychometric properties of screening questionnaires to detect depression in primary healthcare setting in rural Ethiopia
Authors: Habtamu Kassahun , Birhane Rahel , Medhin Girmay , Hanlon Charlotte , Fekadu Abebaw
Published: June 2022

Background

Much of the research about the validity of depression screening questionnaires is on criterion validity. Evidence is scarce on the concurrent, convergent and construct validity of these measures, particularly from low-income countries. This study aimed to evaluate the psychometric properties of depression screening questionnaires in primary healthcare (PHC) in rural Ethiopia.

Methods

A facility-based cross-sectional study was conducted with 587 participants recruited from patients attending three PHC facilities and two ‘Holy water sites’ (places where religious treatment is being provided). The psychometric properties of five mental health screening questionnaires were evaluated: the nine item Patient Health Questionnaire (PHQ-9), the two item version of PHQ-9 (PHQ-2), a version of PHQ-9 with two added items of irritability and noise intolerance (PHQ-11), the Patient Health Questionnaire-15 (PHQ-15), and the World Health Organization-Five Well-being Index (WHO-5). Clinical diagnosis of depression was ascertained by psychiatrists. We analyzed data using exploratory factor analysis, Spearman’s rank order correlation coefficient (Rho), the Mann Whitney test of the equality of medians, univariate logistic regression and Cronbach’s alpha.

Results

PHQ-9, PHQ-11 and WHO-5 were found to be unidimensional, with items in each scale highly loading onto one factor (factor loadings ranging from 0.64 to 0.87). The items of each instrument were internally consistent, with Cronbach’s alpha ranging from 0.72 (PHQ-2) to 0.89 (PHQ-11). Scores for all screening scales were moderately or highly correlated with each other (Rho = 0.58 to 0.98) and moderately correlated with anxiety and disability scores. Median scores of all screening scales were significantly higher in those diagnosed with depression. The association of items measuring emotional and cognitive symptoms with the diagnosis of depression was stronger than the association with items measuring somatic symptoms. Irritability and noise intolerance had higher association with depression diagnosis than PHQ-9 items.

Conclusion

Emotional and cognitive symptoms are more useful than somatic symptoms to predict the diagnosis of depression in the PHC context in Ethiopia. Future research should focus on testing the unidimensionality of PHQ-9, PHQ-11 and WHO-5 using confirmatory factor analysis; establishing the criterion validity of PHQ-11 and WHO-5; and on assessing test-retest reliability of all the measures.
No significant relationship exists between tumor size and prognosis in distant metastatic hepatocellular carcinoma: a propensity score matching analysis based on SEER database
Authors: Xie Jun , Zheng Chunyao , Xie Jinliang , Wang Fangfei , Liu Dingwei , Zeng Rong , Yu Chensong , Chen Sihai
Published: June 2022

Background

Previous studies have shown that tumor size has an impact on the prognosis of hepatocellular carcinoma (HCC). Whether tumor size is related to the prognosis of distant metastatic HCC is unclear. The purpose of this study was to investigate the effect of tumor size on the prognosis of distant metastatic HCC.

Methods

Data on patients with HCC were collected from the (SEER) database of surveillance, epidemiology and final results. Propensity score matching (PSM) was used to reduce confounding factors and comprehensively evaluate the clinicopathological features and prognosis of distant metastatic HCC.

Results

There were 189 patients with distant metastatic HCC whose tumor size was ≤ 50 mm and 615 patients with a tumor size > 50 mm. The tumor sizes of distant metastatic HCC patients were associated with race, grade, surgical treatment, N and AFP. The Kaplan–Meier analysis showed that the mortality rate of patients with a tumor size > 50 mm was higher than that of patients with a tumor size ≤ 50 mm (p = 0.00062). However, there were no significant differences in mortality rates after adjusting for confounding variables by using propensity score matching (p = 0.23).

Conclusion

This propensity score matching study provides the best data in support of the following assertions: tumor size is not an independent prognostic factor for distant metastatic HCC.
Efficacy and safety of chemoradiation therapy using one-shot cisplatin via hepatic arterial infusion for advanced hepatocellular carcinoma with major macrovascular invasion: a single-arm retrospective cohort study
Authors: Naruto Kensuke , Kawaoka Tomokazu , Kodama Kenichiro , Ogawa Yutaro , Amioka Kei , Yoshikawa Yuki , Kikukawa Chihiro , Suehiro Yousuke , Yamaoka Kenji , Ando Yuwa , Kosaka Yumi , Uchikawa Shinsuke , Nakahara Takashi , Murakami Eisuke , Ono Atsushi , Uchida Takuro , Yamauchi Masami , Okamoto Wataru , Takahashi Shoichi , Imamura Michio , Chosa Keigo , Awai Kazuo , Kubo Katsumaro , Nagata Yasushi , Chayama Kazuaki , Aikata Hiroshi
Published: June 2022

Background

Patients with hepatocellular carcinoma (HCC) and macrovascular invasion (MVI) who receive systemic chemotherapy have a poor prognosis. This study aimed to determine if one-shot cisplatin (CDDP) chemotherapy via hepatic arterial infusion (HAI) combined with radiation therapy (RT) prior to systemic chemotherapy could improve the outcomes of these patients.

Methods

This study consisted of 32 HCC patients with the following eligibility criteria: (i) portal vein invasion 3/4 and/or hepatic vein invasion 2/3; (ii) received one-shot CDDP via HAI; (iii) received RT for MVI, (iv) a Child–Pugh score ≤ 7; and (v) an Eastern Clinical Oncology Group Performance Status score of 0 or 1. To determine the therapeutic effect, we collected information on patient characteristics and took contrast-enhanced computed tomography at the start of the therapy and every 2 to 4 months after the start of therapy. We evaluated the overall response of the tumor and tumor thrombosis according to modified Response Evaluation Criteria in Solid Tumors. We assessed patient data using the Mann–Whitney U and Fisher exact tests and evaluated overall survival and progression-free survival using the log-rank test.

Results

The overall response rate at the first evaluation performed a median of 1.4 weeks after HAI was 16% for the main intrahepatic tumor and 59% for the MVI. The best responses were the same as those of the first-time responses. The duration of median survival was 8.6 months, and progression-free survival of the main intrahepatic tumor was 3.2 months. Predictive factors for overall survival were the relative tumor volume in the liver and the first therapeutic response of MVI. There were no severe adverse events or radiation-induced hepatic complications.

Conclusions

One-shot CDDP via HAI and RT were well tolerated and showed immediate and favorable control of MVI. Thus, this combination shows potential as a bridging therapy to systemic chemotherapy.
Beyond standard data collection – the promise and potential of BRAIN (Brain tumour Registry Australia INnovation and translation registry)
Authors: Gately Lucy , Drummond Katharine , Rosenthal Mark , Harrup Rosemary , Dowling Anthony , Gogos Andrew , Lwin Zarnie , Collins Ian , Campbell David , Ahern Elizabeth , Phillips Claire , Gan Hui K. , Bennett Iwan , Sieber Oliver M. , Gibbs Peter
Published: June 2022

Background

Real-world data (RWD) is increasingly being embraced as an invaluable source of information to address clinical and policy-relevant questions that are unlikely to ever be answered by clinical trials. However, the largely unrealised potential of RWD is the value to be gained by supporting prospective studies and translational research. Here we describe the design and implementation of an Australian brain cancer registry, BRAIN, which is pursuing these opportunities.

Methods

BRAIN was designed by a panel of clinicians in conjunction with BIOGRID to capture comprehensive clinical data on patients diagnosed with brain tumours from diagnosis through treatment to recurrence or death. Extensive internal and external testing was undertaken, followed by implementation at multiple sites across Victoria and Tasmania.

Results

Between February 2021 and December 2021, a total of 350 new patients from 10 sites, including one private and two regional, were entered into BRAIN. Additionally, BRAIN supports the world’s first registry trial in neuro-oncology, EX-TEM, addressing the optimal duration of post-radiation temozolomide; and BioBRAIN, a dedicated brain tumour translational program providing a pipeline for biospecimen collection matched with linked clinical data.

Conclusions

Here we report on the first data collection effort in brain tumours for Australia, which we believe to be unique worldwide given the number of sites and patients involved and the extent to which the registry resource is being leveraged to support clinical and translational research. Further directions such as passive data flow and data linkages, use of artificial intelligence and inclusion of patient-entered data are being explored.
Association between CLOCK 3111 T/C polymorphism with ghrelin, GLP-1, food timing, sleep and chronotype in overweight and obese Iranian adults
Authors: Rahati Sara , Qorbani Mostafa , Naghavi Anoosh , Nia Milad Heidari , Pishva Hamideh
Published: June 2022

Background

Circadian Locomotor Output Cycles Kaput (CLOCK), an essential element of the positive regulatory arm in the human biological clock, is involved in metabolic regulation. The aim was to investigate the behavioral (sleep duration, food timing, dietary intake, appetite and chronobiologic characteristics) and hormonal (plasma ghrelin and Glucagon-like peptide-1 concentrations) factors that could explain the previously reported association between the CLOCK 3111 T/C SNP and obesity.

Methods

This cross-sectional study included 403 subjects, overweight and/or obesity, aged 20- 50 years from Iran. The CLOCK rs1801260 data were measured by the PCR–RFLP method. Dietary intake, food timing, sleep duration, appetite and Chrono-type were assessed using validated questionnaires. Ghrelin and GLP-1 were measured by ELIZA in plasma samples. Participants were also divided into three groups based on BMI. Logistic regression models and general linear regression models were used to assess the association between CLOCK genotype and study parameters. Univariate linear regression models were used to assess the interaction between CLOCK and VAS, Food timing, chronotype and sleep on food intakes.

Results

After controlling for confounding factors, there was a significant difference between genotypes for physical activity (P = 0.001), waist circumference (P˂0.05), BMI (˂0.01), weight (P = 0.001), GLP-1 (P = 0.02), ghrelin (P = 0.04), appetite (P˂0.001), chronotype (P˂0.001), sleep (P˂0.001), food timing (P˂0.001), energy (P˂0.05), carbohydrate (P˂0.05) and fat intake (P˂0.001). Our findings also show that people with the minor allele C who ate lunch after 3 PM and breakfast after 9 AM are more prone to obesity (P˂0.05). furthermore, there was significant interactions between C allele carrier group and high appetite on fat intake (Pinteraction = 0.041), eat lunch after 3 PM on energy intake (Pinteraction = 0.039) and morning type on fat intake (Pinteraction = 0.021).

Conclusion

Sleep reduction, changes in ghrelin and GLP-1 levels, changes in eating behaviors and evening preference that characterized CLOCK 3111C can all contribute to obesity. Furthermore, the data demonstrate a clear relationship between the timing of food intake and obesity. Our results support the hypothesis that the influence of the CLOCK gene may extend to a wide range of variables related to human behaviors.
Effect of occlusal coverage depths on the precision of 3D-printed orthognathic surgical splints
Authors: Wang Yipeng , Wang Peiqi , Xiang Xiang , Xu Hui , Tang Yuting , Zhou Yumeng , Bai Ding , Xue Chaoran
Published: June 2022

Background

Precise orthognathic surgical splints are important in surgical-orthodontic treatment. This study aimed to propose a standardized protocol for three-dimensional (3D)-printed splints and assess the precision of splints with different occlusal coverage on the dentition (occlusal coverage depth, OCD), thus optimizing the design of 3D-printed splints to minimize the seemingly unavoidable systematic errors.

Methods

Resin models in optimal occlusion from 19 patients were selected and scanned. Intermediate splints (ISs) and final splints (FSs) with 2-mm, 3-mm, 4-mm, and 5-mm OCDs were fabricated and grouped as IS-2, IS-3, IS-4, IS-5, FS-2, FS-3, FS-4, and FS-5, respectively. The dentitions were occluded with each splint and scanned as a whole to compare with the original occlusion. Translational and rotational deviations of the lower dentition and translational deviations of the landmarks were measured.

Results

For vertical translation, the lower dentitions translated inferiorly to the upper dentition in most of the splints, and the translation increased as OCD got larger. Vertical translations of the dentitions in 89.47% of IS-2, 68.42% of IS-3, 42.11% of IS-4, 10.53% of IS-5, 94.74% of FS-2, 63.16% of FS-3, 26.32% of FS-4, and 21.05% of FS-5 splints were below 1 mm, respectively. For pitch rotation, the lower dentitions rotated inferiorly and posteriorly in most groups, and the rotation increased as OCD got larger. Pitch rotations of the dentitions in 100% of IS-2, 89.47% of IS-3, 57.89% of IS-4, 52.63% of IS-5, 100.00% of FS-2, 78.95% of FS-3, 52.63% of FS-4, and 47.37% of FS-5 splints were below 2°, respectively. On the other hand, the transversal and sagittal translations, roll and yaw rotations of most groups were clinically acceptable (translation < 1 mm and rotation < 2°). The deviations of ISs and FSs showed no statistical significance at all levels of coverage (P > 0.05).

Conclusions

A protocol was proposed to generate 3D-printed ISs and FSs with normalized basal planes and standardized OCDs. Deviations of the ISs and FSs were more evident in the vertical dimension and pitch rotation and had a tendency to increase as the OCD got larger. ISs and FSs with both 2-mm and 3-mm OCD are recommendable regarding the precision relative to clinical acceptability. However, considering the fabrication, structural stability, and clinical application, ISs and FSs with 3-mm OCD are recommended for accurate fitting.
Developing entrustable professional activities for doctoral graduates in health professions education: obtaining a national consensus in Iran
Authors: Zaeri Reza , Gandomkar Roghayeh
Published: June 2022

Background

The number of doctoral programs in health professions education (HPE) is expanding. Entrustable professional activities (EPAs) can be a mechanism to define the expected activities of the HPE doctorate to inform training and assessment processes. The purpose of this study was to develop and reach a consensus on EPAs for HPE doctoral graduates.

Methods

We used a modified Nominal Group Technique (NGT) to elicit EPA titles followed by two rounds of a modified Delphi survey to seek consensus on the EPAs among groups of experts (HPE doctoral graduates and Board of HPE Examiners members) at the national level in Iran between July 2019 and July 2020.

Results

A total number of 92 initial EPA titles, which emerged from brainstorming in the NGT meeting, was reduced to 27 titles during the clarification process. The final EPA framework consisted of 24 EPA titles with descriptions, arranged in three categories: Research and scholarship (6 EPAs), Educational development (11 EPAs) and Educational management (7 EPAs). All final EPAs scored ≥80% agreement at the national level.

Conclusions

The proposed EPAs framework can be used to improve the HPE doctorate training and to inform employment decisions. A future international consensus procedure could use these EPA outcomes as a starting point.
Integration of systematic screening for tuberculosis in outpatient departments of urban primary healthcare facilities in Zambia: a case study of Kitwe district
Authors: Zulu Davy Wadula , Silumbwe Adam , Maritim Patricia , Zulu Joseph Mumba
Published: June 2022

Background

Tuberculosis (TB) is the leading cause of death from a single infectious agent globally, killing about 1.5 million people annually, yet 3 million cases are missed every year. The World Health Organization recommends systematic screening of suspected active TB patients among those visiting the healthcare facilities. While many countries have scaled-up systematic screening of TB, there has been limited assessment of the extent of its integration into the health system. This study sought to explore factors that shape the integration of systematic screening of TB in outpatient departments of primary healthcare facilities in Kitwe district, Zambia.

Methods

This was a qualitative case study with health providers including district managers, TB focal point persons and laboratory personnel working in six purposively selected primary healthcare facilities. Data was collected through key informant (n = 8) and in-depth (n = 15) interviews. Data analysis was conducted using QDA Miner software and guided by Atun’s Integration framework.

Results

The facilitators to integration of systematic screening for TB into out patient departments of primary health facilities included the perceived high burden TB, compatibility of the systematic screening for TB program with healthcare workers training and working schedules, stakeholder knowledge of each others interest and values, regular performance management and integrated outreach of TB screening services. Constraining factors to integration of systematic screening for TB into outpatient departments included complexity of screening for TB in children, unbalanced incentivization mechanisms, ownership and legitimacy of the TB screening program, negative health worker attitudes, social cultural misconceptions of TB and societal stigma as well as the COVID-19 pandemic.

Conclusion

Systematic screening of TB is not fully integrated into the primary healthcare facilities in Zambia to capture all those suspected with active TB that make contact with the health system. Finding the missing TB cases will, therefore, require contextual adaptation of the systematic screening for TB program to local needs and capacities as well as strengthening the health system.
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

Background

A 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.

Results

Using 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.

Conclusions

Our 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

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

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

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

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

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

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

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.