bluuebunny/crossref_metadata_2025 huggingface dataset:
JEDi: java essential dynamics inspector — a molecular trajectory analysis toolkit
Authors: David Charles C. , Avery Chris S. , Jacobs Donald J.
Published: May 2021

Background

Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized software to facilitate workflows and analysis of molecular dynamics simulation data to fully harness the power of PCA is lacking. The Java Essential Dynamics inspector (JEDi) software is a major upgrade from the previous JED software.

Results

Employing multi-threading, JEDi features a user-friendly interface to control rapid workflows for interrogating conformational motions of biopolymers at various spatial resolutions and within subregions, including multiple chain proteins. JEDi has options for Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) to construct covariance (Q), correlation (R), and partial correlation (P) matrices. Shrinkage and outlier thresholding are implemented for the accurate estimation of covariance. The effect of rare events is quantified using outlier and inlier filters. Applying sparsity thresholds in statistical models identifies latent correlated motions. Within a hierarchical approach, small-scale atomic motion is first calculated with a separate local cPCA calculation per residue to obtain eigenresidues. Then PCA on the eigenresidues yields rapid and accurate description of large-scale motions. Local cPCA on all residue pairs creates a map of all residue-residue dynamical couplings. Additionally, kernel PCA is implemented. JEDi output gives high quality PNG images by default, with options for text files that include aligned coordinates, several metrics that quantify mobility, PCA modes with their eigenvalues, and displacement vector projections onto the top principal modes. JEDi provides PyMol scripts together with PDB files to visualize individual cPCA modes and the essential dynamics occurring within user-selected time scales. Subspace comparisons performed on the most relevant eigenvectors using several statistical metrics quantify similarity/overlap of high dimensional vector spaces. Free energy landscapes are available for both cPCA and dpPCA.

Conclusion

JEDi is a convenient toolkit that applies best practices in multivariate statistics for comparative studies on the essential dynamics of similar biopolymers. JEDi helps identify functional mechanisms through many integrated tools and visual aids for inspecting and quantifying similarity/differences in mobility and dynamic correlations.
Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides
Authors: Brinkrolf Karina , Shukla Shantanu P. , Griep Sven , Rupp Oliver , Heise Philipp , Goesmann Alexander , Heckel David G. , Vogel Heiko , Vilcinskas Andreas
Published: May 2021

Background

Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetleNicrophorus vespilloides, which feeds and reproduces on small vertebrate carcasses. Its fungal microbiome is dominated by yeasts that potentially facilitate carcass utilization by producing digestive enzymes, eliminating cadaver-associated toxic volatiles (that would otherwise attract competitors), and releasing antimicrobials to sanitize the microenvironment. Some of these yeasts are closely related to the biotechnologically important speciesYarrowia lipolytica.

Results

To investigate the roles of theseYarrowia-like yeast (YLY) strains in more detail, we selected five strains from two different phylogenetic clades for third-generation sequencing and genome analysis. The first clade, represented by strain B02, has a 20-Mb genome containing ~ 6400 predicted protein-coding genes. The second clade, represented by strain C11, has a 25-Mb genome containing ~ 6300 predicted protein-coding genes, and extensive intraspecific variability within the ITS–D1/D2 rDNA region commonly used for species assignments. Phenotypic microarray analysis revealed that both YLY strains were able to utilize a diverse range of carbon and nitrogen sources (including microbial metabolites associated with putrefaction), and can grow in environments with extreme pH and salt concentrations.

Conclusions

The genomic characterization of five yeast strains isolated fromN. vespilloidesresulted in the identification of strains potentially representing new YLY species. Given their abundance in the beetle hindgut, and dominant growth on beetle-prepared carcasses, the analysis of these strains has revealed the genetic basis of a potential symbiotic relationship between yeasts and burying beetles that facilitates carcass digestion and preservation.
Hierarchicell: an R-package for estimating power for tests of differential expression with single-cell data
Authors: Zimmerman Kip D. , Langefeld Carl D.
Published: May 2021

Background

Study design is a critical aspect of any experiment, and sample size calculations for statistical power that are consistent with that study design are central to robust and reproducible results. However, the existing power calculators for tests of differential expression in single-cell RNA-seq data focus on the total number of cells and not the number of independent experimental units, the true unit of interest for power. Thus, current methods grossly overestimate the power.

Results

Hierarchicell is the first single-cell power calculator to explicitly simulate and account for the hierarchical correlation structure (i.e., within sample correlation) that exists in single-cell RNA-seq data. Hierarchicell, an R-package available on GitHub, estimates the within sample correlation structure from real data to simulate hierarchical single-cell RNA-seq data and estimate power for tests of differential expression. This multi-stage approach models gene dropout rates, intra-individual dispersion, inter-individual variation, variable or fixed number of cells per individual, and the correlation among cells within an individual. Without modeling the within sample correlation structure and without properly accounting for the correlation in downstream analysis, we demonstrate that estimates of power are falsely inflated. Hierarchicell can be used to estimate power for binary and continuous phenotypes based on user-specified number of independent experimental units (e.g., individuals) and cells within the experimental unit.

Conclusions

Hierarchicell is a user-friendly R-package that provides accurate estimates of power for testing hypotheses of differential expression in single-cell RNA-seq data. This R-package represents an important addition to single-cell RNA analytic tools and will help researchers design experiments with appropriate and accurate power, increasing discovery and improving robustness and reproducibility.
Database selection and data gathering methods in systematic reviews of qualitative research regarding diabetes mellitus - an explorative study
Authors: Justesen Tobias , Freyberg Josefine , Schultz Anders N. Ø.
Published: May 2021

Background

Systematic reviews (SRs) are considered one of the most reliable types of studies in evidence-based medicine. SRs rely on a comprehensive and systematic data gathering, including the search of academic literature databases. This study aimed to investigate which combination of databases would result in the highest overall recall rate of references when conducting SRs of qualitative research regarding diabetes mellitus. Furthermore, we aimed to investigate the current use of databases and other sources for data collection.

Methods

Twenty-six SRs (published between 2010 and 2020) of qualitative research regarding diabetes mellitus, located through PubMed, met the inclusion criteria. References of the SRs were systematically hand searched in the six academic literature databases CINAHL, MEDLINE/PubMed, PsycINFO, Embase, Web of Science, and Scopus and the academic search engine Google Scholar. Recall rates were calculated using the total number of included references retrieved by the database or database combination divided by the total number of included references, given in percentage.

Results

The SRs searched five databases on average (range two to nine). MEDLINE/PubMed was the most commonly searched database (100% of SRs). In addition to academic databases, 18 of the 26 (69%) SRs hand searched the reference lists of included articles. This technique resulted in a median (IQR) of 2.5 (one to six) more references being included per SR than by database searches alone. 27 (5.4%) references were found only in one of six databases (when Google Scholar was excluded), with CINAHL retrieving the highest number of unique references (n = 15). The combinations of MEDLINE/PubMed and CINAHL (96.4%) and MEDLINE/PubMed, CINAHL, and Embase (98.8%) yielded the highest overall recall rates, with Google Scholar excluded.

Conclusions

We found that the combinations of MEDLINE/PubMed and CINAHL and MEDLINE/PubMed, CINAHL, and Embase yielded the highest overall recall rates of references included in SRs of qualitative research regarding diabetes mellitus. However, other combinations of databases yielded corresponding recall rates and are expected to perform comparably. Google Scholar can be a useful supplement to traditional scientific databases to ensure an optimal and comprehensive retrieval of relevant references.
Influenza vaccination during the coronavirus pandemic: intention to vaccinate among the at-risk population in the Central Catalonia Health Region (VAGCOVID)
Authors: Bonet-Esteve Anna , Muñoz-Miralles Raquel , Gonzalez-Claramunt Carla , Rufas Ana M , Cruz Xavier Pelegrin , Vidal-Alaball Josep
Published: May 2021

Background

Influenza is a major public health issue, with the primary preventive measure being an annual influenza vaccination. Nevertheless, vaccination coverage among the at-risk population is low. Our understanding of the behaviour of the influenza virus during the SARS-CoV-2 coronavirus pandemic is limited, meaning influenza vaccination is still recommended for individuals at risk for severe complications due to influenza infection. The aim of the study is to determine the intention to vaccinate against seasonal influenza among the at-risk population in the 2020-21 campaign during the SARS-CoV-2 pandemic and to analyse the factors which influence such intention.

Methods

Cross-sectional telephone survey of adults (aged over 18) with risk factors in central Catalonia where the need for the Seasonal Influenza Vaccine (SIV) was recommended.

Results

A total of 434 participants responded to the survey, 43.3% of whom intended to be vaccinated against influenza for the 2020-2021 influenza season, 40.8% had no intention to be vaccinated and 15.9% were uncertain or did not express their opinion. The intention to get vaccinated against influenza is associated with having dependents, the individual’s perception of the risk of being infected with influenza and the perceived risk of transmission to dependents. It is also associated with age, whether the individual had received influenza vaccine the previous season or any other season before. The best predictors of the intention to vaccinate are the individual’s perception of the risk of catching influenza and whether the individual had been vaccinated in the previous season.

Conclusions

Intention to vaccinate can be a good predictor of individual behaviour in relation to vaccination. During the current SARS-CoV-2 pandemic many individuals are hesitant to influenza vaccination. In order to improve influenza vaccination coverage in people included in risk groups, it is necessary to promote educational actions, especially among those who express doubts.
Extent of disease affects the usefulness of fecal biomarkers in ulcerative colitis
Authors: Sakuraba Akihito , Nemoto Nobuki , Hibi Noritaka , Ozaki Ryo , Tokunaga Sotaro , Kikuchi Oki , Minowa Shintaro , Mitsui Tatsuya , Miura Miki , Saito Daisuke , Hayashida Mari , Miyoshi Jun , Matsuura Minoru , Yoneyama Masayoshi , Ohnishi Hiroaki , Hisamatsu Tadakazu
Published: May 2021

Background

Fecal biomarkers are considered to be useful surrogate markers for endoscopic activity. Given the mechanisms of fecal biomarkers, we hypothesized that the extent of ulcerative colitis (UC; pancolitis, left-sided colitis, and proctitis) could affect the usefulness of fecal biomarkers for assessing endoscopic and clinical disease activity; however, few studies have evaluated the utility of fecal biomarkers in the disease extent of UC.

Methods

Fecal calprotectin, a fecal immunochemical test for hemoglobin, and fecal lactoferrin were used as fecal biomarkers. UC patients, who underwent colonoscopy within 30 days of the fecal biomarker test, participated in this observational study. Clinical and endoscopic disease activity was assessed using the Lichtiger Index and Mayo endoscopic subscore (MES), respectively.

Results

A total of 162 colonoscopies were performed on 133 UC patients. A correlation analysis between each biomarker and the MES for each disease-extent subgroup showed a decreased correlation in the proctitis compared with the other groups. With the exception of proctitis, it was possible to distinguish between MES 0 and MES ≥ 1 with high area-under-the-curve values for fecal calprotectin and fecal lactoferrin. The fecal immunochemical test for hemoglobin was superior at discriminating MES 0 for proctitis.

Conclusions

For the practical application of fecal biomarkers for UC patients, it is necessary to consider disease extent before use. In particular, patients with proctitis exhibit a low correlation between stool biomarkers and endoscopic findings. The usefulness of these biomarkers for endoscopic remission is reduced, except for the fecal immunochemical test for hemoglobin.
Effect of omega-3 fatty acids supplementation on cardio-metabolic and oxidative stress parameters in patients with chronic kidney disease: a systematic review and meta-analysis
Authors: Fazelian Siavash , Moradi Fatemeh , Agah Shahram , Hoseini Akramsadat , Heydari Hafez , Morvaridzadeh Mojgan , Omidi Amirhosein , Pizarro Ana Beatriz , Ghafouri Atie , Heshmati Javad
Published: May 2021

Background

Omega-3 fatty acids (FAs) have been suggested as a beneficial supplement in chronic kidney disease (CKD) patients, but the results of randomized clinical trials (RCTs) are controversial. We conducted a systematic review and meta-analysis to evaluate all the RCTs about the impact of omega-3 FAs supplementation on cardiometabolic outcomes and oxidative stress parameters in patients with CKD.

Methods

We performed a systematic database search in PubMed/MEDLINE, EMBASE, Scopus, Web of Science, and Cochrane Central, up to May 2020. We included all placebo-controlled randomized trials that assessed the effect of omega-3 FAs supplementation on any cardiometabolic outcomes: blood pressure, total cholesterol (TC), low-density lipoprotein (LDL) and high-density lipoprotein (HDL) or triglycerides (TG) and oxidative stress parameters. Data were pooled using DerSimonian–Laird’s random-effects model.

Results

Finally, thirteen articles met the inclusion criteria for this review omega-3 FAs supplementation significantly decrease TC (SMD: -0.26; 95% CI: − 0.51, − 0.02; I2 = 52.7%), TG (SMD: -0.22; 95% CI: − 0.43, − 0.02; I2 = 36.0%) and Malondialdehyde (MDA) levels (SMD: -0.91; 95% CI: − 1.29, − 0.54; I2 = 00.0%) and also significantly increase superoxide dismutase (SOD) (SMD: 0.58; 95% CI: 0.27, 0.90; I2 = 00.0%) and Glutathione peroxidase (GPx) (SMD: 0.50; 95% CI: 0.14, 0.86; I2 = 00.0%) activities. However our results show that omega-3 FAs supplementation have no significant effects on HDL, LDL and blood pressure.

Conclusion

This systematic review and meta-analysis supports current evidence for the clinical benefit of omega-3 FAs intake to improve cardiometabolic parameters in CKD patients. However, well-designed RCTs still needed to provide a conclusive picture in this field.
Contact, moral foundations or knowledge? What predicts attitudes towards women who undergo IVF
Authors: Malina Alicja , Roczniewska Marta , Pooley Julie Ann
Published: May 2021

Background

The willingness to try in vitro fertilization (IVF) as an infertility treatment, as well as its psychosocial consequences for couples, may be influenced by how they perceive the attitudes of general public towards this procedure. The focus of the current study was to identify predictors of attitudes towards mothers who underwent IVF to conceive a child. Three predictors were derived from attitude components: contact with someone who had undergone IVF (behavior), moral foundations (emotions), and the level of knowledge (cognition) about IVF.

Method

In total, 817 participants (118 male and 692 female, 7 unreported) from Poland took part in the study. Participants were asked whether they knew a person who underwent IVF, completed aMoral Foundation Questionnaire,and answered a pre-piloted IVF knowledge test.Attitudes towards women who utilised IVF were measured with a modifiedBogardus Social Distance Scale. Data were analysed using hierarchical and logistic regression analyses.

Results

The results showed that there was a weak link between previous contact with a person who underwent IVF and a positive attitude toward a woman who underwent IVF. The attitudes was also predicted by moral foundations: positively by care/harm and fairness/cheating foundations, and negatively by sanctity/degradation. Importantly, more knowledge about IVF was linked with a more positive attitude towards IVF, and this effect explained additional variance over and above moral foundations.

Conclusions

Our study implies the need of psychoeducation to prevent stigmatization of individuals who try IVF due to infertility.
Prognostic impact of additive chemotherapy after curative resection of metachronous colorectal liver metastasis: a single-centre retrospective study
Authors: Kelm Matthias , Schollbach Julia , Anger Friedrich , Wiegering Armin , Klein Ingo , Germer Christoph-Thomas , Schlegel Nicolas , Kunzmann Volker , Löb Stefan
Published: May 2021

Background

A prognostic benefit of additive chemotherapy in patients following resection of metachronous colorectal liver metastases (CRLM) remains controversial. Therefore, the goal of this retrospective study was to investigate the impact of perioperative chemotherapy on disease-free survival (DFS) and overall survival (OS) of patients after curative resection of metachronous CRLM.

Methods

In a retrospective single-centre study, patients after curative resection of metachronous CRLM were included and analysed for DFS and OS with regard to the administration of additive chemotherapy. The Kaplan-Meier method was applied to compare DFS and OS while Cox regression models were used to identify independent prognostic variables.

Results

Thirty-four of 75 patients were treated with additive 5-FU based chemotherapy. OS was significantly prolonged in this patient subgroup (62 vs 57 months; p = 0.032). Additive chemotherapy significantly improved 10-year survival rates (42% vs 0%, p = 0.023), but not 5-year survival (58% vs 42%, p = 0.24). Multivariate analysis identified additive chemotherapy (p = 0.016, HR 0.44, 95% CI 0.23–0.86), more than five CRLM (p = 0.026, HR 2.46, 95% CI 1.16–10.32) and disease recurrence (0.009, HR 2.70, 95% CI 1.29–5.65) as independent risk factors for OS.

Conclusion

Additive chemotherapy significantly prolonged OS and 10-year survival in patients after curative resection of metachronous CRLM. Randomized clinical trials are needed in the future to identify optimal chemotherapy regimens for those patients.
Are socio-economic inequalities in breast cancer survival explained by peri-diagnostic factors?
Authors: Woods Laura M. , Rachet Bernard , Morris Melanie , Bhaskaran Krishnan , Coleman Michel P.
Published: May 2021

Background

Patients living in more deprived localities have lower cancer survival in England, but the role of individual health status at diagnosis and the utilisation of primary health care in explaining these differentials has not been widely considered. We set out to evaluate whether pre-existing individual health status at diagnosis and primary care consultation history (peri-diagnostic factors) could explain socio-economic differentials in survival amongst women diagnosed with breast cancer.

Methods

We conducted a retrospective cohort study of women aged 15–99 years diagnosed in England using linked routine data. Ecologically-derived measures of income deprivation were combined with individually-linked data from the English National Cancer Registry, Clinical Practice Research Datalink (CPRD) and Hospital Episodes Statistics (HES) databases. Smoking status, alcohol consumption, BMI, comorbidity, and consultation histories were derived for all patients. Time to breast surgery was derived for women diagnosed after 2005. We estimated net survival and modelled the excess hazard ratio of breast cancer death using flexible parametric models. We accounted for missing data using multiple imputation.

Results

Net survival was lower amongst more deprived women, with a single unit increase in deprivation quintile inferring a 4.4% (95% CI 1.4–8.8) increase in excess mortality. Peri-diagnostic co-variables varied by deprivation but did not explain the differentials in multivariable analyses.

Conclusions

These data show that socio-economic inequalities in survival cannot be explained by consultation history or by pre-existing individual health status, as measured in primary care. Differentials in the effectiveness of treatment, beyond those measuring the inclusion of breast surgery and the timing of surgery, should be considered as part of the wider effort to reduce inequalities in premature mortality.
Role of Synaptophysin, Chromogranin and CD56 in adenocarcinoma and squamous cell carcinoma of the lung lacking morphological features of neuroendocrine differentiation: a retrospective large-scale study on 1170 tissue samples
Authors: Kriegsmann Katharina , Zgorzelski Christiane , Muley Thomas , Christopoulos Petros , Thomas Michael , Winter Hauke , Eichhorn Martin , Eichhorn Florian , von Winterfeld Moritz , Herpel Esther , Goeppert Benjamin , Stenzinger Albrecht , Herth Felix J. F. , Warth Arne , Kriegsmann Mark
Published: May 2021

Background

Synaptophysin, chromogranin and CD56 are recommended markers to identify pulmonary tumors with neuroendocrine differentiation. Whether the expression of these markers in pulmonary adenocarcinoma and pulmonary squamous cell carcinoma is a prognostic factor has been a matter of debate. Therefore, we investigated retrospectively a large cohort to expand the data on the role of synaptophysin, chromogranin and CD56 in non-small cell lung cancer lacking morphological features of neuroendocrine differentiation.

Methods

A cohort of 627 pulmonary adenocarcinomas (ADC) and 543 squamous cell carcinomas (SqCC) lacking morphological features of neuroendocrine differentiation was assembled and a tissue microarray was constructed. All cases were stained with synaptophysin, chromogranin and CD56. Positivity was defined as > 1% positive tumor cells. Data was correlated with clinico-pathological features including overall and disease free survival.

Results

110 (18%) ADC and 80 (15%) SqCC were positive for either synaptophysin, chromogranin, CD56 or a combination. The most commonly positive single marker was synaptophysin. The least common positive marker was chromogranin. A combination of ≤2 neuroendocrine markers was positive in 2–3% of ADC and 0–1% of SqCC. There was no significant difference in overall survival in tumors with positivity for neuroendocrine markers neither in ADC (univariate: P = 0.4; hazard ratio [HR] = 0.867; multivariate: P = 0.5; HR = 0.876) nor in SqCC (univariate: P = 0.1; HR = 0.694; multivariate: P = 0.1, HR = 0.697). Likewise, there was no significant difference in disease free survival.

Conclusions

We report on a cohort of 1170 cases that synaptophysin, chromogranin and CD56 are commonly expressed in ADC and SqCC and that their expression has no impact on survival, supporting the current best practice guidelines.
Changes in initiation of adjuvant endocrine therapy for breast cancer after state health reform
Authors: Eom Kirsten Y. , van Londen G. J. , Li Jie , Dahman Bassam , Bradley Cathy , Sabik Lindsay M.
Published: May 2021

Background

Socioeconomic differences in receipt of adjuvant treatment contribute to persistent disparities in breast cancer (BCA) outcomes, including survival. Adjuvant endocrine therapy (AET) substantially reduces recurrence risk and is recommended by clinical guidelines for nearly all women with hormone receptor-positive non-metastatic BCA. However, AET use among uninsured or underinsured populations has been understudied. The health reform implemented by the US state of Massachusetts in 2006 expanded health insurance coverage and increased the scope of benefits for many with coverage. This study examines changes in the initiation of AET among BCA patients in Massachusetts after the health reform.

Methods

We used Massachusetts Cancer Registry data from 2004 to 2013 for a sample of estrogen receptor (ER)-positive BCA surgical patients aged 20–64 years. We estimated multivariable regression models to assess differential changes in the likelihood initiating AET after Massachusetts health reform by area-level income, comparing women from lower- and higher-income ZIP codes in Massachusetts.

Results

There was a 5-percentage point (p-value< 0.001) relative increase in the likelihood of initiating AET among BCA patients aged 20–64 years in low-income areas, compared to higher-income areas, after the reform. The increase was more pronounced among younger patients aged 20–49 years (7.1-percentage point increase).

Conclusions

The expansion of health insurance in Massachusetts was associated with a significant relative increase in the likelihood of AET initiation among women in low-income areas compared with those in high-income areas. Our results suggest that expansions of health insurance coverage and improved access to care can increase the number of eligible patients initiating AET and may ameliorate socioeconomic disparities in BCA outcomes.
Whole genome sequencing in oncology: using scenario drafting to explore future developments
Authors: van de Ven Michiel , Simons Martijn J. H. G. , Koffijberg Hendrik , Joore Manuela A. , IJzerman Maarten J. , Retèl Valesca P. , van Harten Wim H.
Published: May 2021

Background

In oncology, Whole Genome Sequencing (WGS) is not yet widely implemented due to uncertainties such as the required infrastructure and expertise, costs and reimbursements, and unknown pan-cancer clinical utility. Therefore, this study aimed to investigate possible future developments facilitating or impeding the use of WGS as a molecular diagnostic in oncology through scenario drafting.

Methods

A four-step process was adopted for scenario drafting. First, the literature was searched for barriers and facilitators related to the implementation of WGS. Second, they were prioritized by international experts, and third, combined into coherent scenarios. Fourth, the scenarios were implemented in an online survey and their likelihood of taking place within 5 years was elicited from another group of experts. Based on the minimum, maximum, and most likely (mode) parameters, individual Program Evaluation and Review Technique (PERT) probability density functions were determined. Subsequently, individual opinions were aggregated by performing unweighted linear pooling, from which summary statistics were extracted and reported.

Results

Sixty-two unique barriers and facilitators were extracted from 70 articles. Price, clinical utility, and turnaround time of WGS were ranked as the most important aspects. Nine scenarios were developed and scored on likelihood by 18 experts. The scenario about introducing WGS as a clinical diagnostic with a lower price, shorter turnaround time, and improved degree of actionability, scored the highest likelihood (median: 68.3%). Scenarios with low likelihoods and strong consensus were about better treatment responses to more actionable targets (26.1%), and the effect of centralizing WGS (24.1%).

Conclusions

Based on current expert opinions, the implementation of WGS as a clinical diagnostic in oncology is heavily dependent on the price, clinical utility (both in terms of identifying actionable targets as in adding sufficient value in subsequent treatment), and turnaround time. These aspects and the optimal way of service provision are the main drivers for the implementation of WGS and should be focused on in further research. More knowledge regarding these factors is needed to inform strategic decision making regarding the implementation of WGS, which warrants support from all relevant stakeholders.
How to manage synchronous endometrial and ovarian cancer patients?
Authors: Shin Wonkyo , Park Sang-Yoon , Kang Sokbom , Lim Myong Cheol , Seo Sang-Soo
Published: May 2021

Backgrounds

We aimed to evaluate the prognosis in patients with synchronous endometrial and ovarian cancer (SEOC) by comparing the differences between double primary cancer (DPC) and metastatic cancer (MC).

Methods

The medical records of 47 patients diagnosed synchronously with endometrial and ovarian cancer between January 2006 and December 2018 were retrospectively reviewed. Twenty-eight and 19 patients were diagnosed with DPC and MC, respectively. Demographics, recurrence-free survival (RFS), and 5-year overall survival (OS) were compared. The clinical factors affecting survival were evaluated using univariate and multivariate analyses.

Results

The demographics were not different between both groups. Endometrioid histology and the International Federation of Gynecology and Obstetrics grade were higher in the MC group than in the DPC group (42.1% vs. 10.7%; P = 0.018, P = 0.002, respectively). The ratio of post-operative adjuvant therapy was not different in both groups. Recurrence occurred in five patients with DPC and seven with MC. The difference in RFS was not significantly different (P = 0.131) but the OS was different between both groups (P = 0.020). Histology and para-aortic lymph node metastasis were associated wtih RFS in univariate analysis, but no difference was found in multivariate analysis.

Conclusions

Although DPC patients had longer OS, multivariate analysis did not identify any influential factors. Focus should be placed on defining the appropriate adjuvant treatment for high-risk patients, which will improve prognosis, rather than on discriminating between DPC and MC.
Lower starting dose of afatinib for the treatment of metastatic lung adenocarcinoma harboring exon 21 and exon 19 mutations
Authors: Chen Yi-Chieh , Tsai Ming-Ju , Lee Mei-Hsuan , Kuo Chia-Yu , Shen Mei-Chiou , Tsai Ying-Ming , Chen Huang-Chi , Hung Jen-Yu , Huang Ming-Shyan , Chong Inn-Wen , Yang Chih-Jen
Published: May 2021

Background

Afatinib has shown favorable response rates (RRs) and longer progression free survival (PFS) in lung cancer patients harboring EGFR mutations compared with standard platinum-based chemotherapy. However, serious adverse drug reactions (ADRs) limit the clinical application of afatinib.

Methods

We designed a retrospective study, enrolling all patients with metastatic lung adenocarcinoma who were diagnosed and treated with 30 or 40 mg daily afatinib as their initial treatment in three Kaohsiung Medical University-affiliated hospitals in Taiwan.

Results

A total of 179 patients were enrolled in the study, of which 102 (57%) and 77 (43%) received 30 mg and 40 mg afatinib daily as their initial treatment, respectively. The patients initially using 30 mg afatinib daily had a similar RR (75% vs. 83%, p = 0.1672), median PFS (14.5 vs. 14.8 months, log-rank p = 0.4649), and median OS (34.0 vs. 25.2 months, log-rank p = 0.5982) compared with those initially using 40 mg afatinib daily. Patients initially receiving 30 mg afatinib daily had fewer ADRs compared with those using 40 mg daily. The overall incidence of moderate and severe ADRs was significantly lower in patients receiving 30 mg afatinib daily compared with those using 40 mg daily (49% vs. 77%, p = 0.002); similar findings was observed in terms of severe ADRs (7% vs. 24%, p < 0.0001).

Conclusion

Patients receiving 30 mg afatinib daily as their initial treatment had similar RR, PFS, OS, but significantly fewer serious ADRs, as compared with those using 40 mg as their starting dose.
Flow cytometric analysis of T lymphocytes and cytokines in aqueous humor of patients with varicella zoster virus-mediated acute retinal necrosis
Authors: Kang Hao , Wei Yunbo , Liu Ming , Yu Di , Tao Yong
Published: May 2021

Background

The purpose of this study is to investigate the aqueous humor (AH) T lymphocyte subsets and cytokines of acute retinal necrosis (ARN) to elucidate the immunologic inflammatory features of this disorder.

Methods

Three patients with ARN infected with varicella zoster virus (VZV) who underwent multiple intravitreal injections of ganciclovir were enrolled in this study. The control group consisted of four non-infectious patients with acute anterior uveitis (AAU). Flow cytometric analysis was performed on the lymphocyte subsets from the AH and peripheral blood (PB) samples during the active phase of intraocular inflammation. Five inflammatory cytokines were measured in each AH sample and various clinical characteristics were also assessed.

Results

VZV deoxyribonucleic acid (DNA) was detected by real-time polymerase chain reaction (PCR) in AH from all the ARN patients, who showed higher CD8+ T lymphocytes population in AH than the AAU patients (p = 0.006). CD4/CD8 ratios of T lymphocytes and the percentage of CD8 + CD25+ T lymphocytes in AH were significantly lower in ARN than in AAU (p = 0.006;p = 0.012). In the ARN patients, the percentages of CD4+ and CD8+ T lymphocytes in AH were higher than those found in PB. The percentage of CD4 + CD25+ T lymphocytes in AH was significantly higher than the proportion in PB in the AAU patients (p = 0.001). Immunoregulatory cytokine Interleukin-10 in AH was significantly elevated in the ARN patients in comparison with the case of the AAU patients (p = 0.036). In ARN, the copy number of VZV DNA in AH positively correlated with the percentage of CD8+ T lymphocytes in AH and negatively correlated with the CD4/CD8 ratio in AH during the course of disease treatment (p = 0.009,r = 0.92;p = 0.039,r = − 0.834).

Conclusion

The ARN patients caused by VZV had different intraocular T lymphocyte subsets and cytokines profile than those of the non-infectious patients. High percentages of CD8+ T lymphocytes and low CD4/CD8 T cell ratios may be a potential biomarker for diagnosis of viral-infectious uveitis. T lymphocytes examination at the inflammatory sites has the potential to become a useful research tool for differentiating viral and non-viral uveitis.
Medication-related knowledge, administration practice and adherence among caregivers of chronically ill children in Malaysia
Authors: Chew Chii-chii , Chan Huan-keat , Chang Chee-tao , HSS Amar-singh , Hassali Mohamed azmi
Published: May 2021

Background

Caregivers’ knowledge, practice and adherence in medication administration who care for children with chronic illness requiring long-term pharmacological treatments are factors associating with children medication safety at home. This study aimed to determine the medication-related knowledge, administration practice and adherence among caregivers of chronically ill children in Malaysia. This cross-sectional study was conducted at the paediatric outpatient clinic of a tertiary public hospital. Caregivers of chronically ill children, who engaged in medication administration at home for at least 3 months, were conveniently recruited. Their medication-related knowledge and administration practice were evaluated based on a checklist, while their adherence to medication administration was assessed using a validated 5-point scale. The associated factors were also explored.

Results

Of the 141 participants, most were mothers (90.8%) and had a full-time job (55.3%). Most of them had adequate medication-related knowledge (71.6%) and an appropriate administration practice (83.0%). The majority of them (83.0%) also rated themselves as adherent to medication administration. The participants with a child above 5 years of age (91.2%) were found to have a better practice than those with younger children (75.3%) in medication administration (p = 0.012). However, those with a child taking two (adjusted OR: 12.53) or three (adjusted OR: 8.29) medications, getting their refills from private health institutions apart from this hospital (adjusted OR = 7.06) and having multiple illnesses (adjusted OR = 21.25) were more likely to be not adherent to medication administration.

Conclusion

Caregivers of chronically ill children in Malaysia generally have sufficient knowledge and an appropriate practice of medication administration at home. Yet, strategies to improve the adherence to medication administration, particularly in those who care for children with complicated health conditions, are warranted.
Cross-cultural adaptation and validation of the Arabic version of the BACS scale (the brief assessment of cognition in schizophrenia) among chronic schizophrenic inpatients
Authors: Haddad Chadia , Salameh Pascale , Hallit Souheil , Obeid Sahar , Haddad Georges , Clément Jean-Pierre , Calvet Benjamin
Published: May 2021

Background

Assessment of cognitive disorders in schizophrenia is becoming a part of clinical and research practice by using batteries that differ widely in their content. The Brief Assessment of Cognition in Schizophrenia (BACS) was developed to cover the main cognitive deficits of schizophrenia. The objective of this study was to assess concurrent validity of the Arabic version of the BACS with a standard neurocognitive battery of tests in Lebanese patients with schizophrenia and healthy controls.

Methods

A sample of 120 stable inpatients diagnosed with schizophrenia and 60 healthy controls received the Arabic version of the BACS in a first session, and a standard battery in a second session.

Results

Mean duration of completion for the BACS was 31.2 ± 5.4 min in patients with schizophrenia. All tests demonstrated significant differences between controls and patients (p < .01). Principal components analysis demonstrated that a one-factor solution best fits our dataset (64.8% of the variance). High Cronbach alpha was found (.85). The BACS composite scores were significantly correlated with the standard battery composite scores in patients (r = .73, p < .001) and healthy controls (r = .78, p < .001). Also, correlation analysis between the BACS sub-scores and the standard battery sub-scores showed significant results (p < .05).

Conclusion

Results showed that the Arabic version of the BACS demonstrated high ability to discriminate patients with schizophrenia from healthy controls and it is a useful tool for assessing cognition in patients with schizophrenia and could be used in clinical practice in Lebanon.
“Kids these days pretend to be grownups” (dekkaedaet): sexual control and negotiation among young Thai female students
Authors: Waratworawan Worawalan , Boonmongkon Pimpawun , Samoh Nattharat , Promnart Petcharat , Guadamuz Thomas E.
Published: May 2021

Background

Young Thai women are growing up amidst conflicting influences of globalization and traditional Thai culture. They experience confusion about which aspects of their sexuality they can express and must hide. This study examined forms of sexual control and sexual negotiation among young Thai women in secondary and vocational schools.

Methods

Semi-structured interviews and focus group discussions were conducted among 13-to 18-year-old female students attending secondary and vocational schools in six regions of Thailand. Additional semi-structured interviews were conducted with instructors of sex education, school administrators, and parents of students. NVIVO 10 was used to manage, code and assist with data analysis.

Results

Socio-cultural control on young women’s sexualities was found from members of their families, schools, communities, and other students. Young women expressing their sexualities openly through verbal expressions, clothing, and behaviors were deemed negatively and stigmatized asdekkaedaetor “kids pretending to be grownups” as it is believed that they are too young and too immature to be responsible for their own decisions on their bodies and sexuality. This dominant discourse subsequently stigmatize and embarrass sexually active women. However, some young women try to negotiate and create options, by utilizing strategies that ensure secrecy.

Conclusion

Comprehensive sexuality education is needed and should be based on the respect for human dignity and sexual and reproductive rights.
Empowerment among adult patients with type 2 diabetes: age differentials in relation to person-centred primary care, community resources, social support and other life-contextual circumstances
Authors: Simonsen Nina , Koponen Anne M. , Suominen Sakari
Published: May 2021

Background

Rising prevalence of type 2 diabetes (T2D), also among younger adults, constitutes a growing public health challenge. According to the person-centred Chronic Care Model, proactive care and self-management support in combination with community resources enhance quality of healthcare and health outcomes for patients with T2D. However, research is scarce concerning the importance of person-centred care and community resources for such outcomes as empowerment, and the relative impact of various patient support sources for empowerment is not known. Moreover, little is known about the association of age with these variables in this patient-group. This study, carried out among patients with T2D, examined in three age-groups (27–54, 55–64 and 65–75 years) whether person-centred care and diabetes-related social support, including community support and possibilities to influence community health issues, are associated with patient empowerment, when considering possible confounding factors, such as other quality of care indicators and psychosocial wellbeing. We also explored age differentials in empowerment and in the proposed correlates of empowerment.

Method

Individuals from a register-based sample with T2D participated in a cross-sectional survey (participation 56%, n = 2866). Data were analysed by descriptive statistics and multivariate logistic regression analyses.

Results

Respondents in the youngest age-group were more likely to have low empowerment scores, less continuity of care, and lower wellbeing than the other age-groups, and to perceive less social support, but a higher level of person-centred care than the oldest group. Community support, including possibilities to influence community health issues, was independently and consistently associated with high empowerment in all three age-groups, as was person-centred care in the two older age-groups. Community support was the social support variable with the strongest association with empowerment across age-groups. Moreover, vitality was positively and diabetes-related distress negatively associated with high empowerment in all age-groups, whereas continuity of care, i.e. having a family/regular nurse, was independently associated in the youngest age-group only.

Conclusion

Person-centred care and community support, including possibilities to influence community health issues, supports empowerment among adults with T2D. Findings suggest that age is related to most correlates of empowerment, and that younger adults with T2D have specific healthcare needs.
Impact of acute kidney injury on in-hospital outcomes in Chinese patients with community acquired pneumonia
Authors: Chen Dawei , Yuan Hongbo , Cao Changchun , Liu Zhihe , Jiang Linglin , Tan Yan , Ding Ji , Ma Mengqing , Huang Wenjuan , Wan Xin
Published: May 2021

Background

Acute kidney injury (AKI) is a frequent complication of community acquired pneumonia (CAP). However, the impact of AKI on in-hospital outcomes of patients with CAP in the Chinese population remains unclear.

Methods

Patients diagnosed with CAP were evaluated in this retrospective observational study. Multiple Cox regression models were employed to identify the association between AKI and in-hospital mortality and 30-day mortality, respectively.

Results

A total of 4213 patients were recruited; 950 (22.5%) patients were diagnosed with AKI. Independent risk factors for AKI were age, male gender, hypertension, cardiac dysfunction, diabetes, chronic kidney disease, acute respiratory failure, use of diuretics, use of vasoactive drugs, and CURB-65. Cox proportional hazards regression revealed AKI, use of angiotensin receptor blocker, hypertension, CURB-65, acute respiratory failure, and use of vasoactive drugs to be independent risk factors for both in-hospital and 30-day mortality. Compared to patients without AKI, those suffering AKI were found to have 1.31-fold (HR 1.31, 95% CI, 1.04–1.66; P = 0.023) and 1.29-fold (HR 1.29, 95% CI, 1.02–1.62; P = 0.033) increased in-hospital and 30-day mortality risks, respectively. In addition, patients with AKI were likely to require admission to intensive care unit (ICU) (42.9% versus 11.4%; P < 0.001), mechanical ventilation (33.8% versus 9.3%; P < 0.001), invasive mechanical ventilation (25.9% versus 5.8%; P < 0.001), non-invasive mechanical ventilation (25.4% versus 7.1%; P < 0.001), and experienced a longer duration of hospital stay (14 days versus 10 days; P < 0.001) than those without AKI. However, no significant difference in ICU stay (11 days versus 10 days; P = 0.099) and duration of mechanical ventilation (8 days versus 8 days; P = 0.369) between AKI and non-AKI groups was found.

Conclusion

AKI was common in Chinese patients with CAP. Patients with CAP who developed AKI had worse in-hospital outcomes.
Resilience and health-related quality of life in patients with pulmonary diseases receiving ambulatory oxygen therapy
Authors: Isokääntä Siiri , Honkalampi Kirsi , Kokki Hannu , Sintonen Harri , Kokki Merja
Published: May 2021

Background

Pulmonary diseases affect health-related quality of life (HRQoL), but there are few data on patients’ adaptation to a serious illness. This study assessed resilience and its associations with HRQoL, life satisfaction, anxiety and depression in patients with pulmonary diseases receiving ambulatory oxygen therapy.

Methods

In this prospective cohort study, we enrolled 42 patients with pulmonary diseases receiving ambulatory oxygen therapy. The patients completed the following questionnaires at baseline and after one and three months; the Resilience Scale-25, the Life Satisfaction Scale-4, the 15D instrument of HRQoL, the Hospital Anxiety and Depression Scale (HADS) and the Quebec User Evaluation of Satisfaction with Assistive Technology (QUEST 2.0). To compare HRQoL, we recruited age- and gender-matched controls from the general population (n = 3574). The primary outcome was the proportion of patients with low resilience.

Results

Half (42–48%) of the patients had low resilience, which was correlated with low HRQoL, low levels of life satisfaction and higher levels of anxiety and depression. Patients had very low HRQoL compared to controls. Dissatisfaction with life increased during the 3-months follow-up, but only a few patients had anxiety or depression. Patient satisfaction with assistive technology was high; the median QUEST 2.0 score (scale 1–5) was 4.00 at baseline, 3.92 at one month and 3.88 at three months.

Conclusions

Resilience was low in half of the patients with pulmonary diseases receiving ambulatory oxygen therapy. Higher resilience was positively correlated with HRQoL and life satisfaction and negatively correlated with anxiety and depression.

Trial registration: ClinicalTrials.gov Protocol Record 507A023. Registered 17 September 2020—Retrospectively registered, https://clinicaltrials.gov/ct2/results?cond=&term=NCT04554225&cntry=&state=&city=&dist=.