Category: Statistics

Gigascience. 2022 Jun 17;11:giac051. doi: 10.1093/gigascience/giac051.

ABSTRACT

BACKGROUND: Spatial organization plays an important role in the function of many biological systems, from cell fate specification in animal development to multistep metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow the in silico testing and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling.

CONCLUSIONS: Here, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chaste’s existing capabilities. In particular, ChemChaste enables (i) simulation of an arbitrary number of spatially diffusing chemicals, (ii) spatially heterogeneous chemical diffusion coefficients, and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chaste’s core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modeling bulk chemical reactions and their coupling with intracellular reactions.

AVAILABILITY AND IMPLEMENTATION: ChemChaste version 1.0 is a free, open-source C++ library, available via GitHub at https://github.com/OSS-Lab/ChemChaste under the BSD license, on the Zenodo archive at zendodo doi, as well as on BioTools (biotools:chemchaste) and SciCrunch (RRID:SCR022208) databases.

PMID:35715874 | DOI:10.1093/gigascience/giac051

J Transl Med. 2022 Jun 17;20(1):275. doi: 10.1186/s12967-022-03478-5.

ABSTRACT

BACKGROUND: Prostate cancer (PCa) is the second most prevalent cancer in males worldwide, yet detecting PCa and its metastases remains a major challenging task in clinical research setups. The present study aimed to characterize the metabolic changes underlying the PCa progression and investigate the efficacy of related metabolic panels for an accurate PCa assessment.

METHODS: In the present study, 75 PCa subjects, 62 PCa patients with bone metastasis (PCaB), and 50 benign prostatic hyperplasia (BPH) patients were enrolled, and we performed a cross-sectional metabolomics analysis of serum samples collected from these subjects using a ¹H nuclear magnetic resonance (NMR)-based metabolomics approach.

RESULTS: Multivariate analysis revealed that BPH, PCa, and PCaB groups showed distinct metabolic divisions, while univariate statistics integrated with variable importance in the projection (VIP) scores identified a differential metabolite series, which included energy, amino acid, and ketone body metabolism. Herein, we identified a series of characteristic serum metabolic changes, including decreased trends of 3-HB and acetone as well as elevated trends of alanine in PCa patients compared with BPH subjects, while increased levels of 3-HB and acetone as well as decreased levels of alanine in PCaB patients compared with PCa. Additionally, our results also revealed the metabolic panels of discriminant metabolites coupled with the clinical parameters (age and body mass index) for discrimination between PCa and BPH, PCaB and BPH, PCaB and PCa achieved the AUC values of 0.828, 0.917, and 0.872, respectively.

CONCLUSIONS: Overall, our study gave successful discrimination of BPH, PCa and PCaB, and we characterized the potential metabolic alterations involved in the PCa progression and its metastases, including 3-HB, acetone and alanine. The defined biomarker panels could be employed to aid in the diagnosis and classification of PCa in clinical practice.

PMID:35715864 | DOI:10.1186/s12967-022-03478-5

Infect Agent Cancer. 2022 Jun 17;17(1):32. doi: 10.1186/s13027-022-00447-x.

ABSTRACT

OBJECTIVE: Intestinal protozoa Blastocystis hominis and Cryptosporidium spp. are two influential factors in intestinal complications and malignancies. In present study, we estimated the pooled prevalence and odds ratio (OR) of the two parasites in colorectal cancer (CRC) patients and their possible association with the deadly disease.

METHOD: Our systematic search was conducted for published researches between January 1, 2000 and April 30, 2022 by using four international databases include Scopus, PubMed, and Web of Science as well as Google scholar search engine. The random- and fixed-effects models were used to estimate the pooled prevalence, OR, and 95% confidence interval (CI) by comprehensive meta-analysis (V2.2, Bio stat) software. Inclusion and exclusion criteria were applied.

RESULTS: Thirteen papers (seven case-control and six cross-sectional studies) for B. hominis/CRC and six papers (two case-control and four cross-sectional studies) for Cryptosporidium spp./CRC were eligible to include in data synthesis. Pooled prevalence of B. hominis and Cryptosporidium spp. in CRC patients was calculated to be 26.8% (95% CI 19.4-35.7%) and 12.7% (95% CI 6.8-22.5%), respectively. Based on case-control studies, significant difference was found between case and controls in both protozoa (B. hominis OR 2.10; 95% CI 1.39-3.18% vs. Cryptosporidium spp. OR 5.06; 95% CI 1.8-13.6%). Considering the Blastocystis subtypes, ST1 (5/6; 83.33% studies) and ST3 (5/6; 83.33% studies) had the highest number of reports in CRC patients. Regarding the Cryptosporidium species, only C. parvum and C. hominis were reported.

CONCLUSION: Given the significant prevalence of both parasites in CRC patients and their statistically significant association, there is a need to pay more attention to these two intestinal parasites in under treatment patients.

PMID:35715853 | DOI:10.1186/s13027-022-00447-x

BMC Nurs. 2022 Jun 17;21(1):157. doi: 10.1186/s12912-022-00919-w.

ABSTRACT

BACKGROUND: A review of admissions to nursing in Northern Ireland was prompted by the growing number of applications and a desire to ensure that the applicants had the right values for a career in nursing. Concerns regarding authorship, plagiarism and reliability of personal statements used to select applicants to interview was the focus of this research. This study evaluates the psychometric properties of a Personal Statement (PS) as a method for admission to a nursing programme and a values-based psychological screening tool, Nurse Match (NM).

METHODS: A self-selecting, purposive sample (n = 228; 9.7%) was drawn from applicants to Schools of Nursing in the United Kingdom (n = 2350). Participants all of whom had completed a Personal Statement were asked to complete a psychological tool and the scoring outcomes and psychometric properties of both tests were investigated. Statistical analysis was conducted using Minitab 17.

RESULTS: Applicants from 18 schools and five colleges responded. The majority (72.4%) were aged 18-19. Findings provide practical, theoretical, statistical, and qualitative reasons for concluding that the Personal Statement has substantial limitations as a measure of suitability. It does not compare well with international test standards for psychometric tests. In contrast, NM is a valid and reliable measure with good discriminatory power, standardised administration and consistent marking.

CONCLUSION: NM is a viable alternative to the PS for shortlisting applicants for nursing interviews.

PMID:35715840 | DOI:10.1186/s12912-022-00919-w

J Neuroeng Rehabil. 2022 Jun 17;19(1):60. doi: 10.1186/s12984-022-01040-4.

ABSTRACT

BACKGROUND: Falls are a common complication experienced after a stroke and can cause serious detriments to physical health and social mobility, necessitating a dire need for intervention. Among recent advancements, wearable airbag technology has been designed to detect and mitigate fall impact. However, these devices have not been designed nor validated for the stroke population and thus, may inadequately detect falls in individuals with stroke-related motor impairments. To address this gap, we investigated whether population-specific training data and modeling parameters are required to pre-detect falls in a chronic stroke population.

METHODS: We collected data from a wearable airbag’s inertial measurement units (IMUs) from individuals with (n = 20 stroke) and without (n = 15 control) history of stroke while performing a series of falls (842 falls total) and non-falls (961 non-falls total) in a laboratory setting. A leave-one-subject-out crossvalidation was used to compare the performance of two identical machine learned models (adaptive boosting classifier) trained on cohort-dependent data (control or stroke) to pre-detect falls in the stroke cohort.

RESULTS: The average performance of the model trained on stroke data (recall = 0.905, precision = 0.900) had statistically significantly better recall (P = 0.0035) than the model trained on control data (recall = 0.800, precision = 0.944), while precision was not statistically significantly different. Stratifying models trained on specific fall types revealed differences in pre-detecting anterior-posterior (AP) falls (stroke-trained model’s F₁-score was 35% higher, P = 0.019). Using activities of daily living as non-falls training data (compared to near-falls) significantly increased the AUC (Area under the receiver operating characteristic) for classifying AP falls for both models (P < 0.04). Preliminary analysis suggests that users with more severe stroke impairments benefit further from a stroke-trained model. The optimal lead time (time interval pre-impact to detect falls) differed between control- and stroke-trained models.

CONCLUSIONS: These results demonstrate the importance of population sensitivity, non-falls data, and optimal lead time for machine learned pre-impact fall detection specific to stroke. Existing fall mitigation technologies should be challenged to include data of neurologically impaired individuals in model development to adequately detect falls in other high fall risk populations. Trial registration https://clinicaltrials.gov/ct2/show/NCT05076565 ; Unique Identifier: NCT05076565. Retrospectively registered on 13 October 2021.

PMID:35715823 | DOI:10.1186/s12984-022-01040-4

J Ethnobiol Ethnomed. 2022 Jun 17;18(1):46. doi: 10.1186/s13002-022-00540-w.

ABSTRACT

BACKGROUND: While the hybridization of ecological knowledge has attracted substantial attention from researchers, the coexistence of local and allopathic medicinal traditions in literate societies widely exposed to centralized schooling and medical services has not yet been investigated. To this end, we studied the current and remembered local ethnomedical practices of Setos and neighboring Russians at the border with Estonia.

METHODS: During 2018-2019, we carried out 62 semi-structured interviews in the Pechorsky District of Pskov Oblast, NW Russia. For cross-border comparison, we utilized the data from 71 interviews carried out at the same time among Setos in Estonia. The Jaccard Similarity Index and qualitative comparison were used to analyze the data.

RESULTS: The study participants mentioned 819 uses of 112 taxa belonging to 54 families. More than two-thirds of the uses (565) were quoted by 36 Russian interviewees, while the remaining third (254) were quoted by 26 Seto interviewees, with the top 3 in both groups being Viburnum opulus, Rubus idaeus, and Plantago major. The Seto intraethnic similarity index was lower (0.43) than the interethnic similarity in Estonia (0.52) and comparable to the interethnic similarity in Russia (0.43). Setos in Russia and local Russians rely more on wild plants (86% and 80% of medicinal plants, respectively), while Setos in Estonia and Estonians show less preference to them (63% and 61%, respectively). Nevertheless, Setos tend to source wild plants available in their gardens (33% of plants for Setos in Estonia and 38% in Russia), while Russians prefer to source them in the wild (38%).

CONCLUSIONS: The preference of both groups in Russia for wild plants over cultivated and purchased plants was inspired by the overall plant literacy, access to nature, and one-to-many knowledge transfer favoring wild plants. Setos in Russia reported a narrower and more homogenous set of plants transferred vertically. However, due to atomization and the erosion of horizontal connections, there are singular plant uses among Setos that overlap with the local Russian set of medicinal plants and differ qualitatively from that of Setos in Estonia.

PMID:35715815 | DOI:10.1186/s13002-022-00540-w

Radiat Oncol. 2022 Jun 17;17(1):108. doi: 10.1186/s13014-022-02076-5.

ABSTRACT

INTRODUCTION: Up to 30% of pancreatic cancer patients initially present locally advanced (LAPC). Stereotactic body radiation therapy (SBRT) may be an additional palliative treatment option when curative resection is no longer achievable. Our systematic review aimed to assess the effect of SBRT on the quality of life in LAPC.

METHODS: We searched five databases until June 29th, 2021, for original articles that reported on SBRT for histologically proven LAPC in adults. Data were extracted on study characteristics, SBRT and additional therapy regimen, pain, biliary complications, nutrition, quality of life and other patient-reported outcomes. Statistical analyses were performed for population and survival data.

RESULTS: 11 case series studies comprising 292 patients with a median age of 66 (range 34-89) years were included in the final analysis. The weighted average BED2;10 (radiation biologically effective dose, equivalent dose in 2 Gy fractions) was 54 Gy, delivered in 3 to 6 fractions. The individual studies used different scales and endpoints, not allowing a meta-analysis. Pain generally appeared to be improved by SBRT. SBRT significantly reduced jaundice. Local control was achieved in 71.7% of patients. Weight loss and nausea also tended to improve after SBRT.

CONCLUSION: SBRT of locally advanced irresectable pancreatic cancer is a promising approach for achieving local control and improving the quality of life. However, randomized controlled trials with larger cohorts are needed to assess the value of SBRT in pancreatic cancer therapy.

PMID:35715808 | DOI:10.1186/s13014-022-02076-5

BMC Complement Med Ther. 2022 Jun 17;22(1):161. doi: 10.1186/s12906-022-03648-4.

ABSTRACT

BACKGROUND: In 2019, investigators from China, South Korea and the United States of America initiated a coordinated multinational trial. The trial included three parallel randomized studies with a planned pooled analysis of individual patient data, to test the effectiveness of acupuncture on hot flash-related symptoms in hormone receptor-positive breast cancer patients prescribed adjuvant endocrine therapy. Given the study’s approach, there was no central coordinating center or data monitoring committee for the study, so a site performance self-monitoring toolkit was developed and implemented to support study teams in collecting and maintaining high-quality regulatory information, and consistent review of study data and documentation.

METHODS: The site performance self-monitoring toolkit was created based on best practices related to post-approval quality assurance/quality improvement (QA/QI) procedures that support data quality. The toolkit included: (1) a binder of essential study management documents and related monitoring logs for sites to complete and maintain (herein called regulator binder), (2) a study start-up checklist, (3) a self-assessment study conduct and oversight checklist to be completed regularly, and (4) a study close-out checklist. In addition, a process of regular virtual meetings to discuss documentation progress coupled with periodic external remote review of completed logs and checklists provided accountability checks.

RESULTS: Over the course of the study, the sites in China and South Korea completed the entirety of the site performance self-monitoring toolkit, and successfully submitted their completed materials for review. The process of implementing a self-monitoring toolkit in a multinational integrative medicine study is described qualitatively. Periodic external review of the completed toolkit materials revealed categories of findings. Written follow-up reports were provided to sites and discussion of the documents occurred via separate virtual meetings.

CONCLUSIONS: Site study team self-monitoring provides a feasible, consistent, and effective way to review the collection and maintenance of data and regulatory documentation for quality assessment in minimal risk clinical research studies and can augment formal study monitoring activities in higher risk studies. Iterative feedback and support appeared to drive a disciplined approach to maintaining regulatory document compliance and helped sustain investigator and study team engagement in the process.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier NCT03783546 (21/12/2018).

PMID:35715806 | DOI:10.1186/s12906-022-03648-4

Crit Care. 2022 Jun 17;26(1):181. doi: 10.1186/s13054-022-04044-7.

ABSTRACT

BACKGROUND: Bacterial burden as well as duration of bacteremia influence the outcome of patients with bloodstream infections. Promptly decreasing bacterial load in the blood by using extracorporeal devices in addition to anti-infective therapy has recently been explored. Preclinical studies with the Seraph® 100 Microbind® Affinity Blood Filter (Seraph® 100), which consists of heparin that is covalently bound to polymer beads, have demonstrated an effective binding of bacteria and viruses. Pathogens adhere to the heparin coated polymer beads in the adsorber as they would normally do to heparan sulfate on cell surfaces. Using this biomimetic principle, the Seraph® 100 could help to decrease bacterial burden in vivo.

METHODS: This first in human, prospective, multicenter, non-randomized interventional study included patients with blood culture positive bloodstream infection and the need for kidney replacement therapy as an adjunctive treatment for bloodstream infections. We performed a single four-hour hemoperfusion treatment with the Seraph® 100 in conjunction with a dialysis procedure. Post procedure follow up was 14 days.

RESULTS: Fifteen hemodialysis patients (3F/12 M, age 74.0 [68.0-78.5] years, dialysis vintage 28.0 [11.0-45.0] months) were enrolled. Seraph® 100 treatment started 66.4 [45.7-80.6] hours after the initial positive blood culture was drawn. During the treatment with the Seraph® 100 with a median blood flow of 285 [225-300] ml/min no device or treatment related adverse events were reported. Blood pressure and heart rate remained stable while peripheral oxygen saturation improved during the treatment from 98.0 [92.5-98.0] to 99.0 [98.0-99.5] %; p = 0.0184. Four patients still had positive blood culture at the start of Seraph® 100 treatment. In one patient blood cultures turned negative during treatment. The time to positivity (TTP) was increased between inflow and outflow blood cultures by 36 [- 7.2 to 96.3] minutes. However, overall TTP increase was not statistical significant.

CONCLUSIONS: Seraph® 100 treatment was well tolerated. Adding Seraph® 100 to antibiotics early in the course of bacteremia might result in a faster resolution of bloodstream infections, which has to be evaluated in further studies.

TRAIL REGISTRATION: ClinicalTrials.gov Identifier: NCT02914132 , first posted September 26, 2016.

PMID:35715801 | DOI:10.1186/s13054-022-04044-7

BMC Public Health. 2022 Jun 17;22(1):1208. doi: 10.1186/s12889-022-13566-2.

ABSTRACT

BACKGROUND: With the accelerated global integration and the impact of climatic, ecological and social environmental changes, China will continue to face the challenge of the outbreak and spread of emerging infectious diseases and traditional ones. This study aims to explore the spatial and temporal evolutionary characteristics of the incidence of Class B notifiable infectious diseases in China from 2007 to 2020, and to forecast the trend of it as well. Hopefully, it will provide a reference for the formulation of infectious disease prevention and control strategies.

METHODS: Data on the incidence rates of Class B notifiable infectious diseases in 31 provinces, municipalities and autonomous regions of China from 2007 to 2020 were collected for the prediction of the spatio-temporal evolution and spatial correlation as well as the incidence of Class B notifiable infectious diseases in China based on global spatial autocorrelation and Autoregressive Integrated Moving Average (ARIMA).

RESULTS: From 2007 to 2020, the national incidence rate of Class B notifiable infectious diseases (from 272.37 per 100,000 in 2007 to 190.35 per 100,000 in 2020) decreases year by year, and the spatial distribution shows an “east-central-west” stepwise increase. From 2007 to 2020, the spatial clustering of the incidence of Class B notifiable infectious diseases is significant and increasing year by year (Moran’s I index values range from 0.189 to 0.332, p < 0.05). The forecasted incidence rates of Class B notifiable infectious diseases nationwide from 2021 to 2024 (205.26/100,000, 199.95/100,000, 194.74/100,000 and 189.62/100,000) as well as the forecasted values for most regions show a downward trend, with only some regions (Guangdong, Hunan, Hainan, Tibet, Guangxi and Guizhou) showing an increasing trend year by year.

CONCLUSIONS: The current study found that since there were significant regional disparities in the prevention and control of infectious diseases in China between 2007 and 2020, the reduction of the incidence of Class B notifiable infectious diseases requires the joint efforts of the surrounding provinces. Besides, special attention should be paid to provinces with an increasing trend in the incidence of Class B notifiable infectious diseases to prevent the re-emergence of certain traditional infectious diseases in a particular province or even the whole country, as well as the outbreak and spread of emerging infectious diseases.

PMID:35715790 | DOI:10.1186/s12889-022-13566-2