bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
Authors: Wallen Zachary D.
Published: May 2021

Background

Testing for differential abundance of microbes in disease is a common practice in microbiome studies. Numerous differential abundance (DA) testing methods exist and range from traditional statistical tests to methods designed for microbiome data. Comparison studies of DA testing methods have been performed, but none performed on microbiome datasets collected for the study of real, complex disease. Due to this, DA testing was performed here using various DA methods in two large, uniformly collected gut microbiome datasets on Parkinson disease (PD), and their results compared.

Results

Overall, 78–92% of taxa tested were detected as differentially abundant by at least one method, while 5–22% were called differentially abundant by the majority of methods (depending on dataset and filtering of taxonomic data prior to testing). Concordances between method results ranged from 1 to 100%. Average concordance for datasets 1 and 2 were 24% and 28% respectively, and 27% for replicated DA signatures. Concordances increased when removing rarer taxa before testing, increasing average concordances by 2–32%. Certain methods consistently resulted in higher concordances (e.g. ANCOM-BC, LEfSe), while others consistently resulted in lower (e.g. edgeR, fitZIG). Hierarchical clustering revealed three groups of DA signatures that were (1) replicated by the majority of methods on average and included taxa previously associated with PD, (2) replicated by a subset of methods and included taxa largely enriched in PD, and (3) replicated by few to one method(s).

Conclusions

Differential abundance tests yielded varied concordances, and amounts of detected DA signatures. Some methods were more concordant than others on both filtered and unfiltered data, therefore, if consistency with other study methodology is a key goal, one might choose among these methods. Even still, using one method on one dataset may find true associations, but may also detect false positives. To help lower false positives, one might analyze data with two or more DA methods to gauge concordance, and use a built-in replication dataset. This study will hopefully serve to complement previously reported DA method comparison studies by implementing and coalescing a large number of both previously and yet to be compared methods on two real gut microbiome datasets.
Clustering of cancer data based on Stiefel manifold for multiple views
Authors: Tian Jing , Zhao Jianping , Zheng Chunhou
Published: May 2021

Background

In recent years, various sequencing techniques have been used to collect biomedical omics datasets. It is usually possible to obtain multiple types of omics data from a single patient sample. Clustering of omics data plays an indispensable role in biological and medical research, and it is helpful to reveal data structures from multiple collections. Nevertheless, clustering of omics data consists of many challenges. The primary challenges in omics data analysis come from high dimension of data and small size of sample. Therefore, it is difficult to find a suitable integration method for structural analysis of multiple datasets.

Results

In this paper, a multi-view clustering based on Stiefel manifold method (MCSM) is proposed. The MCSM method comprises three core steps. Firstly, we established a binary optimization model for the simultaneous clustering problem. Secondly, we solved the optimization problem by linear search algorithm based on Stiefel manifold. Finally, we integrated the clustering results obtained from three omics by using k-nearest neighbor method. We applied this approach to four cancer datasets on TCGA. The result shows that our method is superior to several state-of-art methods, which depends on the hypothesis that the underlying omics cluster class is the same.

Conclusion

Particularly, our approach has better performance than compared approaches when the underlying clusters are inconsistent. For patients with different subtypes, both consistent and differential clusters can be identified at the same time.
Comparative evaluation of full-length isoform quantification from RNA-Seq
Authors: Sarantopoulou Dimitra , Brooks Thomas G. , Nayak Soumyashant , Mrčela Antonijo , Lahens Nicholas F. , Grant Gregory R.
Published: May 2021

Background

Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are short.

Results

Here we use simulated benchmarking data that reflects many properties of real data, including polymorphisms, intron signal and non-uniform coverage, allowing for systematic comparative analyses of isoform quantification accuracy and its impact on differential expression analysis. Genome, transcriptome and pseudo alignment-based methods are included; and a simple approach is included as a baseline control.

Conclusions

Salmon, kallisto, RSEM, and Cufflinks exhibit the highest accuracy on idealized data, while on more realistic data they do not perform dramatically better than the simple approach. We determine the structural parameters with the greatest impact on quantification accuracy to be length and sequence compression complexity and not so much the number of isoforms. The effect of incomplete annotation on performance is also investigated. Overall, the tested methods show sufficient divergence from the truth to suggest that full-length isoform quantification and isoform level DE should still be employed selectively.
Conserved and non-conserved functions of the rice homologs of the Arabidopsis trichome initiation-regulating MBW complex proteins
Authors: Zheng Kaijie , Wang Xutong , Wang Yating , Wang Shucai
Published: May 2021

Background

Trichome initiation in Arabidopsis is regulated by a MYB-bHLH-WD40 (MBW) transcriptional activator complex formed by the R2R3 MYB transcription factor GLABRA1 (GL1), MYB23 or MYB82, the bHLH transcription factor GLABRA3 (GL3), ENHANCER OF GLABRA3 (EGL3) or TRANSPARENT TESTA8 (TT8), and the WD40-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1). However, the functions of the rice homologs of the MBW complex proteins remained uncharacterized.

Results

Based on amino acid sequence identity and similarity, and protein interaction prediction, we identified OsGL1s, OsGL3s and OsTTG1s as rice homologs of the MBW complex proteins. By using protoplast transfection, we show that OsGL1D, OsGL1E, OsGL3B and OsTTG1A were predominantly localized in the nucleus, OsGL3B functions as a transcriptional activator and is able to interact with GL1 and TTG1. By using yeast two-hybrid and protoplast transfection assays, we show that OsGL3B is able to interact with OsGL1E and OsTTG1A, and OsGL1E and OsTTG1A are also able to interact with GL3. On the other hand, we found that OsGL1D functions as a transcription activator, and it can interact with GL3 but not OsGL3B. Furthermore, our results show that expression ofOsTTG1Ain thettg1mutant restored the phenotypes including alternations in trichome and root hair formation, seed color, mucilage production and anthocyanin biosynthesis, indicating that OsTTG1A and TTG1 may have similar functions.

Conclusion

These results suggest that the rice homologs of the Arabidopsis MBW complex proteins are able to form MBW complexes, but may have conserved and non-conserved functions.
Post-operative pain management modalities employed in clinical trials for adult patients in LMIC; a systematic review
Authors: Afshan Gauhar , Khan Robyna Irshad , Ahmed Aliya , Siddiqui Ali Sarfraz , Rehman Azhar , Raza Syed Amir , Kerai Rozina , Mustafa Khawaja
Published: May 2021

Background

Unrelieved postoperative pain afflicts millions each year in low and middle income countries (LMIC). Despite substantial advances in the study of pain, this area remains neglected. Current systematic review was designed to ascertain the types of clinical trials conducted in LMIC on postoperative pain management modalities over the last decade.

Methods

A comprehensive search was performed in June 2019 on PubMed, Cochrane Library, CINAHL Plus, and Web of Science databases to identify relevant trials on the management of postoperative pain in LMIC. Out of 1450 RCTs, 108 studies were reviewed for quality evidence using structured form of critical appraisal skill program. Total of 51 clinical trials were included after applying inclusion/exclusion criteria.

Results

Results are charted according to the type of surgery. Eleven trials on laparoscopic cholecystectomy used multimodal analgesia including some form of regional analgesia. Different analgesic modalities were studied in 4 trials on thoracotomy, but none used multimodal approach. In 11 trials on laparotomy, multimodal analgesia was employed along with the studied modalities. In 2 trials on hysterectomy, preemptive pregabalin or gabapentin were used for reduction in rescue analgesia. In 13 trials on breast surgical procedures and 10 on orthopaedic surgery, multimodal analgesia was used with some form of regional analgesia.

Conclusion

We found that over the past 10 years, clinical trials for postoperative pain modalities have evolved in LMIC according to the current postoperative pain management guidelines i.e. multi-modal approach with some form of regional analgesia. The current review shows that clinical trials were conducted using multimodal analgesia including but not limited to some form of regional analgesia for postoperative pain in LMIC however this research snapshot (of only three countries) may not exactly reflect the clinical practices in all 47 countries.

Post Operative Pain Management Modalities Employed in Clinical Trials for Adult Patients in LMIC; A Systematic Review.
Combined management can decrease blood pressure: an investigation of health-seeking behaviors among hypertensive patients in urban communities in China
Authors: Wang Si , Liu Kai , Zhang Xin , Meng Qingtao , Li Xinran , Ye Runyu , Zhang Zhipeng , Chen Xiaoping
Published: May 2021

Background

Hypertensive patients can freely choose informal medical facilities, such as pharmacies, community health service centres, and cardiology clinics in secondary or tertiary hospitals, as routine places for medical treatment in China currently. The proportions, influencing factors and effects of different health-seeking behaviours on blood pressure (BP) among hypertensive patients in urban communities are not clear. The aim of the study was to investigate health-seeking behaviours and the effects of different health-seeking behaviours on BP among hypertensive patients in urban communities in China.

Methods

A cross-sectional survey of hypertension was conducted in urban communities in Chengdu. A total of 437 hypertensive patients seeking medical help regularly were sequentially enrolled to complete a the questionnaire on health-seeking behaviours.

Results

The average age was 67.1 ± 7.5 years old. The control rate of BP was 41.0%, and the systolic blood pressure (SBP) and diastolic blood pressure (DBP) were 144.2 ± 17.9 mm Hg and 75.4 ± 10.4 mm Hg, respectively. Among the hypertensive patients investigated, 62.8% chose community health service centre, 5.2% chose informal medical facilities, 21.5% chose cardiology clinics in secondary or tertiary hospitals, and 10.5% chose both community health service centre and cardiology clinics as the usual places for medical treatment. There were significant differences in education levels, proportions of home BP monitoring, establishment of chronic disease archives in the community, medication adherence and side effects of drugs among the four groups. The control rates of BP were 39.4%, 23.8%, 43.0% and 54.8% (P = 0.100), respectively. The SBPs were 145.1 ± 18.0, 150.9 ± 19.8, 143.8 ± 17.5 and 136.3 ± 15.1 mm Hg (P = 0.007), respectively, and it was significantly lower in the combined management group than in the other three groups. Compared with patients choosing community health service centre, patients in the combined management group had a significantly lower BP level (β = −0.119, P = 0.038) adjusting for age, sex, education level, establishment of chronic disease archives, medication adherence and number of antihypertensive drugs.

Conclusions

Combined management with both community health service centre and higher-level hospitals can decrease BP.
Confounding influences of malnutrition and Plasmodium falciparum and Schistosoma haematobium infections on haematological parameters in school children in Muyuka, Cameroon
Authors: Sumbele Irene Ule Ngole , Otia Ofon Vitalis , Francis Lorraine , Bopda Orelien Sylvain Mtopi , Ebai Calvin Bisong , Ning Teh Rene , Kimbi Helen Kuo Kuo , Nkuo-Akenji Theresa
Published: May 2021

Background

School-aged children (SAC) are a high-risk demographic group for infectious diseases and malnutrition. The objective of this study was to assess the burden and the effect of Plasmodium falciparum and Schistosoma haematobium infections on the haematological indices in SAC and the confounding influence of malnutrition on the outcomes.

Methods

This cross-sectional study was conducted in SAC 4–14 years old living in Ikata, Bafia and Mile 14-Likoko in Muyuka, Cameroon. Anthropometric measures of malnutrition were obtained and blood samples collected were used for detection of malaria parasites by Giemsa-stained blood films using light microscopy and complete blood count analysis using an automated haematology analyser. Urine samples collected were used to detect micro haematuria with the aid of reagent strips and the eggs of S. haematobium by urine filtration technique. Multiple linear regression model was used to examine influence of independent variables on haematological parameters.

Results

Out of the 606 SAC examined, the prevalence of single infections with Plasmodium or S. haematobium and co-infection with both parasites was 16.2, 16.3 and 8.3%, respectively. Overall, malaria parasite (MP), urogenital schistosomiasis, malnutrition, anaemia, haematuria, microcytosis and thrombocytopenia was prevalent in 24.4, 24.6, 25.9, 74.4, 12.2, 45.4 and 11.1% of SAC, respectively. A significant linear decline (P = 0.023) in prevalence of P. falciparum infection with the severity of stunting was observed. Factors that significantly influenced haematological parameters included haemoglobin: age, stunting and MP; haematocrit: age and MP; white blood cell count: age; red blood cell count; age and MP; lymphocyte counts: stunting; mean cell volume: age; mean cell haemoglobin: age and stunting; mean cell haemoglobin concentration: sex, stunting and red cell distribution width-coefficient of variation: sex, age and stunting.

Conclusions

Malnutrition, Plasmodium and S. haematobium infections are common while anaemia is a severe public health problem in Muyuka, Cameroon. The interaction between haematological parameters with malaria parasites as well as linear growth index was negative and other interactions indicate systemic inflammation. While findings provide contextual intervention targets to ensure the judicious use of the limited resources, there is need for regular monitoring and proper treatment to improve the health of the underserved population.
Factors associated with negative pleural adenosine deaminase results in the diagnosis of childhood pleural tuberculosis
Authors: Han Xing-Fen , Han Chao , Jin Feng , Wang Jun-Li , Wang Mao-Shui
Published: May 2021

Background

Until now, the influential factors associated with pleural adenosine deaminase (ADA) activity among children remain unclear. This retrospective study was therefore conducted aiming to investigate the factors associated with negative pleural ADA results in the diagnosis of childhood pleural tuberculosis (TB).

Methods

Between January 2006 and December 2019, children patients with definite or possible pleural TB were recruited for potential analysis. Then, patients were stratified into two categories: negative pleural ADA results group (experimental group, ≤40 U/L) and positive pleural ADA results group (control group, > 40 U/L). Univariate and multivariate logistic regression analyses were performed to estimate risk factors for negative pleural ADA results.

Results

A total of 84 patients with pleural TB were recruited and subsequently classified as experimental (n = 17) and control groups (n = 67). Multivariate analysis (Hosmer–Lemeshow goodness-of-fit test: χ2 = 1.881, df = 6,P = 0.930) revealed that variables, such as chest pain (age-adjusted OR = 0.0510, 95% CI: 0.004, 0.583), pleural total protein (≤45.3 g/L, age-adjusted OR = 27.7, 95% CI: 2.5, 307.7), pleural lactate dehydrogenase (LDH, ≤505 U/L, age-adjusted OR = 59.9, 95% CI: 4.2, 857.2) and blood urea nitrogen (≤3.2 mmol/L, age-adjusted OR = 32.0, 95% CI: 2.4, 426.9), were associated with negative pleural ADA results when diagnosing childhood pleural TB.

Conclusion

Our findings demonstrated that chest pain, pleural total protein, pleural LDH, and blood urea nitrogen were associated with a negative pleural ADA result for the diagnosis of pleural TB among children. When interpreting pleural ADA levels in children with these characteristics, a careful clinical assessment is required for the pleural TB diagnosis.
Development and validation of a nomogram to predict survival outcome among epithelial ovarian cancer patients with site-distant metastases: a population-based study
Authors: Wang Bo , Wang Shixuan , Ren Wu
Published: May 2021

Background

Increasing evidence indicates that site-distant metastases are associated with survival outcomes in patients with epithelial ovarian cancer. This study aimed to investigate the prognostic values of site-distant metastases and clinical factors and develop a prognostic nomogram score individually predicting overall survival (OS, equivalent to all-cause mortality) and cancer specific survival (CSS, equivalent to cancer-specific mortality) in patients with epithelial ovarian cancer.

Methods

We retrospectively collected data on patients with epithelial ovarian cancer from the Surveillance, Epidemiology, and End Results (SEER) database between 1975 and 2016. Multivariate Cox regression was performed to identify survival trajectories. A nomogram score was used to predict long-term survival probability. A comparison between the nomogram and the International Federation of Gynecology and Obstetrics (FIGO 2018) staging system was conducted using time-dependent receiver operating characteristic (tROC) curve.

Results

A total of 131,050 patients were included, 18.2, 7.8 and 66.1% had localized, regional and distant metastases, respectively. Multivariate analysis identified several prognostic factors for OS including race, grade, histology, FIGO staging, surgery, bone metastasis, liver metastasis, lung metastasis, and lymphatic metastasis. Prognostic factors for CSS included grade, site, FIGO staging, surgery, bone metastasis, brain metastasis, lung metastasis, lymphatic metastasis, and insurance. Following bootstrap correction, the C-index of OS and CSS was 0.791 and 0.752, respectively. These nomograms showed superior performance compared with the FIGO 2018 staging criteria (P < 0.05).

Conclusions

A novel prognostic nomogram score provides better prognostic performance than the FIGO 2018 staging system. These nomograms contribute to directing clinical treatment and prognosis assessment in patients harboring site-distant metastases.
Impact of pretreatment anemia on upfront abiraterone acetate therapy for metastatic hormone-sensitive prostate cancer: a multicenter retrospective study
Authors: Okamoto Teppei , Noro Daisuke , Hatakeyama Shingo , Narita Shintaro , Mitsuzuka Koji , Sakurai Toshihiko , Kawamura Sadafumi , Hoshi Senji , Shimoda Jiro , Tanaka Toshikazu , Kawaguchi Toshiaki , Ishidoya Shigeto , Ito Akihiro , Tsuchiya Norihiko , Habuchi Tomonori , Ohyama Chikara
Published: May 2021

Background

Anemia has been a known prognostic factor in metastatic hormone-sensitive prostate cancer (mHSPC). We therefore examined the effect of anemia on the efficacy of upfront abiraterone acetate (ABI) in patients with mHSPC.

Methods

We retrospectively evaluated 66 mHSPC patients with high tumor burden who received upfront ABI between 2018 and 2020 (upfront ABI group). We divided these patients into two groups: the anemia-ABI group (hemoglobin < 13.0 g/dL, n = 20) and the non-anemia-ABI group (n = 46). The primary objective was to examine the impact of anemia on the progression-free survival (PFS; clinical progression or PC death before development of castration resistant PC) of patients in the upfront ABI group. Secondary objectives included an evaluation of the prognostic significance of upfront ABI and a comparison with a historical cohort (131 mHSPC patients with high tumor burden who received androgen deprivation therapy (ADT/complete androgen blockade [CAB] group) between 2014 and 2019).

Results

We found that the anemia-ABI group had a significantly shorter PFS than the non-anemia-ABI group. A multivariate Cox regression analysis showed that anemia was an independent prognostic factor of PFS in the upfront ABI group (hazard ratio, 4.66; P = 0.014). Patients in the non-anemia-ABI group were determined to have a significantly longer PFS than those in the non-anemia-ADT/CAB group (n = 68) (P < 0.001). However, no significant difference was observed in the PFS between patients in the anemia-ABI and the anemia-ADT/CAB groups (n = 63). Multivariate analyses showed that upfront ABI could significantly prolong the PFS of patients without anemia (hazard ratio, 0.17; P < 0.001), whereas ABI did not prolong the PFS of patients with anemia.

Conclusion

Pretreatment anemia was a prognostic factor among mHSPC patients who received upfront ABI. Although the upfront ABI significantly improved the PFS of mHSPC patients without anemia, its efficacy in patients with anemia might be limited.
Efficacy and acquired resistance of EGFR-TKI combined with chemotherapy as first-line treatment for Chinese patients with advanced non-small cell lung cancer in a real-world setting
Authors: Wang Qianqian , Gao Wen , Gao Fangyan , Jin Shidai , Qu Tianyu , Lin Fan , Zhang Chen , Zhang Jingya , Zhang Zhihong , Chen Liang , Guo Renhua
Published: May 2021

Background

To compare the benefits and explore the cause of acquired resistance of epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) and its combination with chemotherapy in advanced non-small-cell lung cancer (NSCLC) patients harboring EGFR mutation in a real-life setting.

Methods

This retrospective analysis included 117 advanced NSCLC patients with EGFR mutation who underwent next-generation sequencing (NGS) prior to treatment. The combination group included 50 patients who received the regimen of EGFR-TKI combined with chemotherapy, while the EGFR-TKI monotherapy group included 67 patients treated with TKI only. The primary endpoint of this study was progression-free survival (PFS); the secondary endpoints were overall survival (OS), response rate, and toxicity.

Results

The median PFS was significantly longer in the combination group than in the EGFR-TKI monotherapy group (19.00 months [95% CI, 14.67–23.33] vs. 11.70 months [95% CI, 10.81–12.59], p < 0.001). Subgroup analysis showed a similar trend of results. The median OS was not reached in the combination group and was 38.50 (95% CI, 35.30–41.70) months in the EGFR-TKI monotherapy group (p = 0.586). Patients in the combination group were more likely to experience adverse events, most of which showed the severity of grade 1 or 2. T790M mutation remains the main reason for acquired resistance, and the frequency of T790M mutation was similar between the two groups (p = 0.898).

Conclusions

Compared with EGFR-TKI monotherapy, EGFR-TKI combined with chemotherapy significantly improved PFS in advanced NSCLC patients with EGFR mutation, with acceptable toxicity.
A metabolism-related 4-lncRNA prognostic signature and corresponding mechanisms in intrahepatic cholangiocarcinoma
Authors: Zou Wenbo , Wang Zizheng , Wang Fei , Li Lincheng , Liu Rong , Hu Minggen
Published: May 2021

Background

Long non-coding RNA (lncRNA) plays a critical role in the malignant progression of intrahepatic cholangiocarcinoma (iCCA). This study aimed to establish a 4-lncRNA prognostic signature and explore corresponding potential mechanisms in patients with iCCA.

Methods

The original lncRNA-seq and clinical data were collected from the TCGA and GEO databases. Overlapping and differentially expressed lncRNAs (DE-lncRNAs) were further identified from transcriptome data. Univariate regression analysis was performed to screen survival-related DE-lncRNAs, which were further selected to develop an optimal signature to predict prognosis using multivariate regression analysis. The Kaplan-Meier survival curve visualized the discrimination of the signature on overall survival (OS). The area under the curve (AUC) and C-index were used to verify the predictive accuracy of the signature. Combined with clinical data, multivariate survival analysis was used to reveal the independent predictive capability of the signature. In addition, a prognostic nomogram was constructed. Finally, the common target genes of 4 lncRNAs were predicted by the co-expression method, and the corresponding functions were annotated by GO and KEGG enrichment analysis. Gene set enrichment analysis (GSEA) was also performed to explore the potential mechanism of the signature. Quantitative real-time PCR was used to evaluated the expression of 4 lncRNAs in an independent cohort.

Results

We identified and constructed a 4-lncRNA (AC138430.1, AGAP2-AS1, AP001783.1, and AP005233.2) prognostic signature using regression analysis, and it had the capability to independently predict prognosis. The AUCs were 0.952, 0.909, and 0.882 at 1, 2, and 3 years, respectively, and the C-index was 0.808, which showed good predictive capability. Subsequently, combined with clinical data, we constructed a nomogram with good clinical application. Finally, 252 target genes of all four lncRNAs were identified by the co-expression method, and functional enrichment analysis showed that the signature was strongly correlated with metabolism-related mechanisms in tumourigenesis. The same results were also validated via GSEA.

Conclusion

We demonstrated that a metabolism-related 4-lncRNA prognostic signature could be a novel biomarker and deeply explored the target genes and potential mechanism. This study will provide a promising therapeutic strategy for patients with intrahepatic cholangiocarcinoma.
Development and validation of a nomogram to predict cancer-specific survival of uveal melanoma
Authors: Zeng Qiaozhu , Yao Yuou , Zhao Mingwei
Published: May 2021

Background

Uveal melanoma (UM) is a rare but aggressive cancer, which is the most common primary intraocular malignancy in adults. We aimed to develop and validate a competing risk nomogram to predict cancer-specific survival (CSS) of patients with UM, as well as compare its prognostic value with that of the American Joint Committee on Cancer (AJCC) staging system.

Methods

Data of patients diagnosed with UM from 2010 to 2015 were identified from the Surveillance, Epidemiology, and End Results (SEER) database. We extracted and integrated significant prognostic factors based on competing risk regression to build a nomogram. The nomogram with an online prediction version was also created. The performance of the nomogram was evaluated using Harrell’s concordance index (C-index) and calibration plots. Receiver operating characteristic (ROC) curve was carried out to estimate clinical applicability of the model. Improvements in the predictive accuracy of our new model compared with AJCC staging system were estimated by calculating the relative integrated discrimination improvement (IDI) and the net reclassification improvement (NRI).

Results

A total of 839 eligible patients with primary UM were randomly assigned to a training cohort (588, 70%) and a validation cohort (251, 30%). Age, histological type, T stage and M stage were independent prognostic factors to predict CSS of UM and were incorporated in the nomogram. The calibration plots indicated that the 3- and 5-year CSS probabilities were consistent between the nomogram prediction and the actual observation. The C-index for this model was 0.778 (95% CI:0.756–0.800) and 0.786 (95% CI: 0.749–0.816) in the training cohort and validation cohort. Areas under the curve (AUCs) were 0.814, 0.771, and 0.792 in the training cohort, 0.788, 0.781 and 0.804 in the validation cohort, respectively. The NRI value in AJCC staging system was − 0.153 (95% CI -0.29 – − 0.041) for 3 years of follow-up and − 0.276 (95% CI -0.415 – − 0.132) for 5 years of follow-up. The IDI values for 3 and 5 years of follow-up in the AJCC staging system were − 0.021 (P = 0.076) and − 0.045 (P = 0.004), respectively.

Conclusions

We have developed and validated a competing risk nomogram to reliably predict cancer-specific survival of patients with UM. This convenient tool may be useful for evaluating cancer-specific prognosis.
Comparative clinical accuracy analysis of the newly developed ZZ IOL and four existing IOL formulas for post-corneal refractive surgery eyes
Authors: Zhang Jun , Shao Jie , Zheng Li , Shen Ye , Zhao Xia
Published: May 2021

Background

Intraocular lens (IOL) calculation using traditional formulas for post-corneal refractive surgery eyes can yield inaccurate results. This study aimed to compare the clinical accuracy of the newly developed Zhang & Zheng (ZZ) formula with previously reported IOL formulas.

Study design

Retrospective study.

Methods

Post-corneal refractive surgery eyes were assessed for IOL power using the ZZ, Haigis-L, Shammas, Barrett True-K (no history), and ray tracing (C.S.O Sirius) IOL formulas, and their accuracy was compared. No pre-refractive surgery information was used in the calculations.

Results

This study included 38 eyes in 26 patients. ZZ IOL yielded a lower arithmetic IOL prediction error (PE) compared with ray tracing (P = 0.04), whereas the other formulas had values like that of ZZ IOL (P > 0.05). The arithmetic IOL PE for the ZZ IOL formula was not significantly different from zero (P = 0.96). ZZ IOL yielded a lower absolute IOL PE compared with Shammas (P < 0.01), Haigis-L (P = 0.02), Barrett true K (P = 0.03), and ray tracing (P < 0.01). The variance of the mean arithmetic IOL PE for ZZ IOL was significantly smaller than those of Shammas (P < 0.01), Haigis-L (P = 0.03), Barrett True K (P = 0.02), and ray tracing (P < 0.01). The percentages of eyes within ± 0.5 D of the target refraction with the ZZ IOL, Shammas, Haigis-L, Barrett True-K, and ray-tracing formulas were 86.8 %, 45.5 %, 66.7 %, 73.7 %, and 50.0 %, respectively (P < 0.05 for Shammas and ray tracing vs. ZZ IOL).

Conclusions

The ZZ IOL formula might offer superior outcomes for IOL power calculation for post-corneal refractive surgery eyes without prior refractive data.
Prevalence and correlates of anxiety and depression in frontline healthcare workers treating people with COVID-19 in Bangladesh
Authors: Tasnim Rafia , Sujan Md. Safaet Hossain , Islam Md. Saiful , Ritu Asmaul Husna , Siddique Md. Abid Bin , Toma Tanziha Yeasmin , Nowshin Rifat , Hasan Abid , Hossain Sahadat , Nahar Shamsun , Islam Salequl , Islam Muhammad Sougatul , Potenza Marc N. , van Os Jim
Published: May 2021

Background

Healthcare workers (HCWs) who are in the frontline during the COVID-19 pandemic are often under significant pressures that may predispose them to symptoms of poor mental health. This study aimed to investigate the prevalence of anxiety and depression among HCWs and factors correlated with mental health concerns during the COVID-19 pandemic in Bangladesh. And, it also aimed to evaluate the psychometric properties of the Bangla version of the Hospital Anxiety and Depression Scale (HADS).

Methods

A cross-sectional survey was conducted between July and August, 2020. A self-reported online questionnaire was utilized to collect data. The survey included questions concerning socio-demographic, lifestyle, and work setting, as well as the HADS. A confirmatory factor analysis (CFA) and multiple linear regression analysis were performed.

Results

Data from 803 HCWs (50.7% male; mean age: 27.3 [SD = 6.9]; age range: 18-58 years) were included in the final analysis. The Bangla HADS was psychometrically sound, and demonstrated good internal consistency and reliability (α = 0.83), and excellent construct validity. Prevalence estimates of anxiety and depression were 69.5%, and 39.5%, respectively, for less severe symptomology (at least borderline abnormal), and 41.2% and 15.7% for more severe (at least abnormal) symptomology. Regression analyses with the total HADS score as a dependent variable revealed significant (p < 0.05) associations with female gender, moderate and poor health status, infrequent physical exercising, smoking, having had regrets about one’s profession because of the pandemic and associated experiences, not updating on the latest COVID-19-related research, experiencing discrimination in the workplace, and facing social problems due to working in a lab or hospital during the COVID-19 pandemic.

Conclusions

Symptoms of anxiety and depression are prevalent among HCWs during the COVID-19 pandemic in Bangladesh. The findings suggest a need for screening for mental health concerns, and employing early intervention to help these individuals.
The effect of average temperature on suicide rates in five urban California counties, 1999–⁠2019: an ecological time series analysis
Authors: Cheng Sierra , Plouffe Rebecca , Nanos Stephanie M. , Qamar Mavra , Fisman David N. , Soucy Jean-Paul R.
Published: May 2021

Background

Suicide is among the top 10 leading causes of premature morality in the United States and its rates continue to increase. Thus, its prevention has become a salient public health responsibility. Risk factors of suicide transcend the individual and societal level as risk can increase based on climatic variables. The purpose of the present study is to evaluate the association between average temperature and suicide rates in the five most populous counties in California using mortality data from 1999 to 2019.

Methods

Monthly counts of death by suicide for the five counties of interest were obtained from CDC WONDER. Monthly average, maximum, and minimum temperature were obtained from nCLIMDIV for the same time period. We modelled the association of each temperature variable with suicide rate using negative binomial generalized additive models accounting for the county-specific annual trend and monthly seasonality.

Results

There were over 38,000 deaths by suicide in California’s five most populous counties between 1999 and 2019. An increase in average temperature of 1 °C corresponded to a 0.82% increase in suicide rate (IRR = 1.0082 per °C; 95% CI = 1.0025–1.0140). Estimated coefficients for maximum temperature (IRR = 1.0069 per °C; 95% CI = 1.0021–1.0117) and minimum temperature (IRR = 1.0088 per °C; 95% CI = 1.0023–1.0153) were similar.

Conclusion

This study adds to a growing body of evidence supporting a causal effect of elevated temperature on suicide. Further investigation into environmental causes of suicide, as well as the biological and societal contexts mediating these relationships, is critical for the development and implementation of new public health interventions to reduce the incidence of suicide, particularly in the face increasing temperatures due to climate change.
Comparison of body composition parameters in the study of the association between body composition and pulmonary function
Authors: Ishikawa Caren , Barbieri Marco Antonio , Bettiol Heloisa , Bazo Gabriel , Ferraro Alexandre A. , Vianna Elcio Oliveira
Published: May 2021

Background

The excess adiposity, even in the absence of diseases, is responsible for a decline in pulmonary function, which is considered a predictor of mortality and a risk factor for diseases in several epidemiological studies. However, studies on the association between obesity and pulmonary function have found only few associations or inconclusive results. The aim of the study is to evaluate the association between body composition and spirometric parameters, comparing simple obesity measures such as body mass index (BMI) and waist circumference with more precise body composition measurements such as dual-energy X-ray absorptiometry (DXA) and air-displacement plethysmography (BOD POD).

Methods

This is an observational, cross-sectional study that used data from the 1978/79 Ribeirão Preto birth cohort (São Paulo, Brazil). The study included 1746 participants from the 5th follow-up of the cohort. Linear regressions were calculated to evaluate the association between BMI, waist circumference, waist–height ratio (WHtR), BOD POD- and DXA-measured fat mass percentage, and spirometric parameters FEV1, and FVC.

Results

For every 1-kg/m2 BMI increase, FVC decreased by 13 ml in males and by 6 ml in females and FEV1 decreased by 11 ml and 5 ml, respectively. Regarding body composition measurements, for a 1% increase in fat mass assessed by BOD POD, FVC decreased by 16 ml in males and by 8 ml in females and FEV1 decreased by 13 ml and 7 ml, respectively. Hence, negative associations between body measurements and FEV1 and FVC were observed in both genders, especially when using the fat mass measurement and were more expressive in men.

Conclusion

The anthropometric and body composition parameters were negatively associated with the spirometric variables FVC and FEV1. We have also observed that simple measures such as waist-height ratio were sufficient to detect the association of body composition with pulmonary function reduction.
Predictors of community acquired childhood pneumonia among 2–59 months old children in the Amhara Region, Ethiopia
Authors: Chanie Muluken Genetu , Melaku Mequannent Sharew , Yalew Melaku , Arefaynie Mastewal , Bitew Gedamnesh , Amsalu Erkihun Tadesse , Kefale Bereket , Muche Amare , Fentaw Zinabu , Dewau Reta , Adane Bezawit , Damtie Yitayish , Ayele Wolde Melese , Ewunetie Gojjam Eshetie , Adane Metadel
Published: May 2021

Background

Worldwide, pneumonia is the third leading cause of death in under 5 years children. Ethiopia is ranked 4th out of 15 countries having the highest burdens of the death rate among under-five children due to pneumonia. Regardless of this fact, efforts to identify determinants of pneumonia have been limited yet in Amhara region. This study was aimed to identify predictors of community-acquired childhood pneumonia among 2–59 months old children in the Amhara region, Ethiopia.

Methods

Facility-based case–control study was conducted in the Amhara region from June 4 to July 15, 2018, among 28 health centers distributed across the region. The total sample size used was 888 (296 cases and 592 controls) children whose age were 2–59 months. At first, multistage sampling technique was employed. Data were collected on a face-to-face interview. Epi data v. 4.6 for data entry and statistical packages for social sciences version 23 for data analysis were used. Multivariable logistic regression analyses were used to test the associations between the study variables at P-value < 0.05 with 95% CI. As a result, determinants were identified for CAP.

Results

Among 888 enrolled children (296 cases and 592 controls), who experienced a community-acquired pneumonia had an increased risk of maternal age of 18–24 years (AOR 0.03, at 95%CI (0.01, 0.14), Government employee (AOR 0.19, at 95% CI (0.07,0.54), lack of separate kitchen (AOR 5.37; at 95% CI (1.65, 17.43), history of diarrhea in the past two weeks (AOR 10.2; at 95% CI (5.13, 20.18), previous respiratory tract infections (AOR 8.3, at 95% CI (3.32, 20.55) and history of parental asthma (AOR 4.9, at 95% CI (2.42, 10.18).

Conclusion

Maternal age of 18–24 years and government employee, lack of separate kitchen, history of diarrhea in the past two weeks; previous respiratory tract infection and history of parental asthma were found statistically significant. Health personnel’s needs to focus on creating awareness to the community on the merit of the separate kitchen for reduction of Community-acquired childhood pneumonia, and focus on prevention and management of childhood diarrheal and acute respiratory tract infections.
Robot-assisted sleeve gastrectomy in patients with obesity with a novel Chinese domestic MicroHand SII surgical system
Authors: Li Weizheng , Kong Kang , Li Pengzhou , Wang Guohui , Cui Beibei , Zhu Liyong , Zhu Shaihong
Published: May 2021

Background

A new device has been added to the Chinese MicroHand surgical robot family, developed based on the successful application of control algorithms. As a benefit of using these specialized control algorithms, the motion mapping relation can be accommodated into the system without the help of a built-in image system, resulting in a novel Chinese domestic surgical robot with two arms called MicroHand SII, which is different from the former MicroHand S and da Vinci systems. In this study, we investigate the performance of a novel MicroHand SII robotic platform in patients with obesity.

Methods

From March 2018 to April 2019, a total of 7 patients whose BMI ranged from 29.9 to 49.8 kg/m2were operated on with the robot-assisted technique using the MicroHand SII surgical system. Data regarding demography, surgical procedure and the 3-month outcome postoperation were collected.

Results

There were 2 female and 5 male patients with a median age (range) of 35 (20–51) years. The median operative time was 160 (149–195) minutes. None were converted to open surgery. All anthropometry indices improved significantly (p < 0.05) at 3 months postoperatively. There were no cases of surgical site infection, gastrointestinal/abdominal bleeding, or conversion to an open operation.

Conclusions

The initial experience showed that the Chinese domestic robot surgical system MicroHand SII could be feasibly and safely applied in sleeve gastrectomy in patients with obesity. Because of the unique design of this system such as a two-hand robot, an array of master–slave motion strategies, and a roll joint at the end of the instruments that allows 7 degrees of freedom, this robotic platform has presented its own obvious advantages.
Therapeutic effect of various ginsenosides on rheumatoid arthritis
Authors: Zhang Meng , Ren Hongwei , Li Kun , Xie Shengsheng , Zhang Ru , Zhang Longlong , Xia Jiaxuan , Chen Xing , Li Xilin , Wang Jianxin
Published: May 2021

Background

Rheumatoid arthritis (RA) is an autoimmune disease which causes disability and threatens the health of humans. Therefore, it is of great significance to seek novel effective drugs for RA. It has been reported that various ginsenoside monomers are able to treat RA. However, it is still unclear which ginsenoside is the most effective and has the potential to be developed into an anti-RA drug.

Methods

The ginsenosides, including Rg1, Rg3, Rg5, Rb1, Rh2 and CK, were evaluated and compared for their therapeutic effect on RA. In in vitro cell studies, methotrexate (MTX) and 0.05% dimethyl sulfoxide (DMSO) was set as a positive control group and a negative control group, respectively. LPS-induced RAW264.7 cells and TNF-α-induced HUVEC cells were cultured with MTX, DMSO and six ginsenosides, respectively. Cell proliferation was analyzed by MTT assay and cell apoptosis was carried out by flow cytometry. CIA mice model was developed to evaluate the therapeutic efficacy of ginsenosides. The analysis of histology, immunohistochemistry, flow cytometry and cytokine detections of the joint tissues were performed to elucidate the action mechanisms of ginsenosides.

Results

All six ginsenosides showed good therapeutic effect on acute arthritis compared with the negative control group, Ginsenoside CK provided the most effective treatment ability. It could significantly inhibit the proliferation and promote the apoptosis of RAW 264.7 and HUVEC cells, and substantially reduce the swelling, redness, functional impairment of joints and the pathological changes of CIA mice. Meanwhile, CK could increase CD8 + T cell to down-regulate the immune response, decrease the number of activated CD4 + T cell and proinflammatory M1-macrophages, thus resulting in the inhibition of the secretion of proinflammatory cytokine such as TNF-α and IL-6.

Conclusion

Ginsenoside CK was proved to be a most potential candidate among the tested ginsenosides for the treatment of RA, with a strong anti-inflammation and immune modulating capabilities.
Homogeneous polyporus polysaccharide inhibits bladder cancer by polarizing macrophages to M1 subtype in tumor microenvironment
Authors: Jia Wenyu , Luo Siwan , Lai Gena , Li Shiqi , Huo Shuai , Li Meifang , Zeng Xing
Published: May 2021

Background

Polyporus polysaccharide (PPS), an active ingredient of traditional Chinese medicinal Polyporus umbellatus, has multiple biological functions, such as anti-cancer, immune-regulating and hepatoprotective activities. The purpose of this study was to investigate the mechanism of homogeneous polyporus polysaccharide (HPP) activated macrophages in the treatment of bladder cancer.

Methods

100 ng/mL Phorbol myristate acetate (PMA) was used to induce THP-1 human leukemic cells as a macrophage model. Then macrophages derived from THP-1 were treated with different concentrations of HPP (1, 10 and 100 μg/mL). Flow cytometry and RT-PCR were used to detected the expression of CD16, CD23, CD86, CD40 and interleukin (IL)-Iβ, iNOS mRNA. ELISA was used to test the change of IL-1β and TNF-α in macrophage after the treatment with HPP. The conditioned medium from HPP-polarized macrophages was used to detect the effect of activated macrophages on bladder cancer. MTT assay, 5-ethynyl-2′-deoxyuridine assay, flow cytometry, Transwell assay, and Western blot analysis were used to detect the effects of polarized macrophages on the viability, proliferation, apoptosis, and migration of bladder cancer cells. Western blot was also used to analysis the change of JAK2/NF-κB pathway protein.

Results

HPP promoted the expression of pro-inflammatory factors, such as IL-Iβ, TNF-α and iNOS, and surface molecules CD86, CD16, CD23, and CD40 in macrophages and then polarized macrophages to M1 type. Results demonstrated that activated macrophages inhibited the proliferation of bladder cancer cells, regulated their apoptosis, and inhibited migration and epithelial–mesenchymal transformation (EMT). JAK2/NF-κB pathways were downregulated in the anti-bladder cancer process of activated macrophages.

Conclusion

The findings indicated that HPP inhibited the proliferation and progression of bladder cancer by the polarization of macrophages to M1 type, and JAK2/NF-κB pathway was downregulated in the process of anti-bladder cancer.