Tag: pubmed

PLoS One. 2021 Jun 18;16(6):e0253218. doi: 10.1371/journal.pone.0253218. eCollection 2021.

ABSTRACT

Mounting evidence suggests that Lactobacillus species may not necessarily be the sine qua non of healthy cervicovaginal microbiota (CVM), especially among reproductive-age African women. A majority of African women have high-diversity non-Lactobacillus-dominated CVM whose bacterial functions remain poorly characterized. Functional profiling of the CVM is vital for investigating human host-microbiota interactions in health and disease. Here, we investigated the functional potential of L. iners-dominated and high-diversity non-Lactobacillus-dominated CVM of 75 African women with and without bacterial vaginosis (BV) and high-risk human papillomavirus (HR-HPV) infection. Functional contents were predicted using PICRUSt. Microbial taxonomic diversity, BV, and HR-HPV infection statuses were correlated with the inferred functional composition of the CVM. Differentially abundant inferred functional categories were identified using linear discriminant analysis (LDA) effect size (LEfSe) (p-value <0.05 and logarithmic LDA score >2.0). Of the 75 women, 56 (74.7%), 35 (46.7%), and 29 (38.7%) had high-diversity non-Lactobacillus-dominated CVM, BV, and HR-HPV infection, respectively. Alpha diversity of the inferred functional contents (as measured by Shannon diversity index) was significantly higher in women with high-diversity non-Lactobacillus-dominated CVM and BV than their respective counterparts (H statistic ≥11.5, q-value <0.001). Ordination of the predicted functional metagenome content (using Bray-Curtis distances) showed that the samples segregated according to the extent of microbial taxonomic diversity and BV (pseudo-F statistic ≥19.6, q-value = 0.001) but not HR-HPV status (pseudo-F statistic = 1.7, q-value = 0.159). LEfSe analysis of the inferred functional categories revealed that transport systems (including ABC transporters) and transcription factors were enriched in high-diversity CVM. Interestingly, transcription factors and sporulation functional categories were uniquely associated with high-diversity CVM, BV, and HR-HPV infection. Our predictive functional analysis reveals features unique to high-diversity CVM, BV and HR-HPV infections. Such features may represent important biomarkers of BV and HR-HPV infection. Our findings require proof-of-concept functional studies to examine the relevance of these potential biomarkers in women’s reproductive health and disease.

PMID:34143825 | DOI:10.1371/journal.pone.0253218

PLoS One. 2021 Jun 18;16(6):e0253419. doi: 10.1371/journal.pone.0253419. eCollection 2021.

ABSTRACT

PURPOSE: Many studies of MRI radiomics do not include the discretization method used for the analyses, which might indicate that the discretization methods used are considered irrelevant. Our goals were to compare three frequently used discretization methods (lesion relative resampling (LRR), lesion absolute resampling (LAR) and absolute resampling (AR)) applied to the same data set, along with two different lesion segmentation approaches.

METHODS: We analyzed the effects of altering bin widths or bin numbers for the three different sampling methods using 40 texture indices (TIs). The impact was evaluated on brain MRI studies obtained for 71 patients divided into three different disease groups: multiple sclerosis (MS, N = 22), ischemic stroke (IS, N = 22), cancer patients (N = 27). Two different MRI acquisition protocols were considered for all patients, a T2- and a post-contrast 3D T1-weighted MRI sequence. Elliptical and manually drawn VOIs were employed for both imaging series. Three different types of gray-level discretization methods were used: LRR, LAR and AR. Hypothesis tests were done among all diseased and control areas to compare the TI values in these areas. We also did correlation analyses between TI values and lesion volumes.

RESULTS: In general, no significant differences were reported in the results when employing the AR and LAR discretization methods. It was found that employing 38 TIs introduced variation in the results when the number of bin parameters was altered, suggesting that both the degree and direction of monotonicity between each TI value and binning parameters were characteristic for each TI. Furthermore, while TIs were changing with altering binning values, no changes correlated to neither disease nor the MRI sequence. We found that most indices correlated weakly with the volume, while the correlation coefficients were independent of both diseases analyzed and MR contrast. Several cooccurrence-matrix based texture parameters show a definite higher correlation when employing the LRR discretization method However, with the best correlations obtained for the manually drawn VOI. Hypothesis tests among all disease and control areas (co-lateral hemisphere) revealed that the AR or LAR discretization techniques provide more suitable texture features than LRR. In addition, the manually drawn segmentation gave fewer significantly different TIs than the ellipsoid segmentations. In addition, the amount of TIs with significant differences was increasing with increasing the number of bins, or decreasing bin widths.

CONCLUSION: Our findings indicate that the AR discretization method may offer the best texture analysis in MR image assessments. Employing too many bins or too large bin widths might reduce the selection of TIs that can be used for differential diagnosis. In general, more statistically different TIs were observed for elliptical segmentations when compared to the manually drawn VOIs. In the texture analysis of MR studies, studies and publications should report on all important parameters and methods related to data collection, corrections, normalization, discretization, and segmentation.

PMID:34143830 | DOI:10.1371/journal.pone.0253419

PLoS One. 2021 Jun 18;16(6):e0253136. doi: 10.1371/journal.pone.0253136. eCollection 2021.

ABSTRACT

BACKGROUND: Though considerable efforts have been made to improve the treatment of epithelial ovarian cancer (EOC), the prognosis of patients has remained poor. Identifying differentially expressed genes (DEGs) involved in EOC progression and exploiting them as novel biomarkers or therapeutic targets is of great value.

METHODS: Overlapping DEGs were screened out from three independent gene expression omnibus (GEO) datasets and were subjected to Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses. The protein-protein interactions (PPI) network of DEGs was constructed based on the STRING database. The expression of hub genes was validated in GEPIA and GEO. The relationship of hub genes expression with tumor stage and overall survival and progression-free survival of EOC patients was investigated using the cancer genome atlas data.

RESULTS: A total of 306 DEGs were identified, including 265 up-regulated and 41 down-regulated. Through PPI network analysis, the top 20 genes were screened out, among which 4 hub genes, which were not researched in depth so far, were selected after literature retrieval, including CDC45, CDCA5, KIF4A, ESPL1. The four genes were up-regulated in EOC tissues compared with normal tissues, but their expression decreased gradually with the continuous progression of EOC. Survival curves illustrated that patients with a lower level of CDCA5 and ESPL1 had better overall survival and progression-free survival statistically.

CONCLUSION: Two hub genes, CDCA5 and ESPL1, identified as probably playing tumor-promotive roles, have great potential to be utilized as novel therapeutic targets for EOC treatment.

PMID:34143800 | DOI:10.1371/journal.pone.0253136

PLoS One. 2021 Jun 18;16(6):e0252977. doi: 10.1371/journal.pone.0252977. eCollection 2021.

ABSTRACT

INTRODUCTION: Evidence from sub-Saharan Africa, including Kenya, shows that negative beliefs about contraceptive methods are associated with non-use. However, little is known about the relationship between contraceptive beliefs and subsequent method choice.

METHODOLOGY: We used data from a two-year longitudinal survey of married women aged 15-39 years at enrollment from one urban site (Nairobi) and one rural site (Homa Bay) in Kenya. Analysis entails descriptive statistics and estimation of a conditional logit analysis to examine associations between method-specific beliefs and choice of injectables, implants or pills among women who were not using any method or were pregnant at baseline (round 1) but adopted these methods at 12-month follow-up (Nairobi, n = 221; Homa Bay n = 197).

RESULTS: Beliefs about pills, injectables and implants among non-users were generally negative. With the partial exception of the pill in Nairobi, the majority thought that each method was likely to cause serious health problems, unpleasant side effects, menstrual disruption, and would be unsafe for long-term use. In both sites, satisfied past use of a method and the perception that a method is easy to use had a major influence on method choice. Concerns about menstrual disruption and safety for long-term use were unimportant in both sites. There were some marked differences between the two sites. Beliefs about long-term fertility impairment and perceived husband approval had strong influences on choice of injectables, implants or pills in the urban site but not in the rural site.

CONCLUSION: The relative importance of beliefs, some erroneous, in predisposing women to choose one method over another appears to be conditioned by the social context. There is need for family planning counseling programmes to pay attention to erroneous beliefs and misconceptions about contraceptives.

PMID:34143804 | DOI:10.1371/journal.pone.0252977

PLoS One. 2021 Jun 18;16(6):e0250991. doi: 10.1371/journal.pone.0250991. eCollection 2021.

ABSTRACT

Long-term predictions of forest dynamics, including forecasts of tree growth and mortality, are central to sustainable forest-management planning. Although often difficult to evaluate, tree mortality rates under different abiotic and biotic conditions are vital in defining the long-term dynamics of forest ecosystems. In this study, we have modeled tree mortality rates using conditional inference trees (CTREE) and multi-year permanent sample plot data sourced from an inventory with coverage of New Brunswick (NB), Canada. The final CTREE mortality model was based on four tree- and three stand-level terms together with two climatic terms. The correlation coefficient (R2) between observed and predicted mortality rates was 0.67. High cumulative annual growing degree-days (GDD) was found to lead to increased mortality in 18 tree species, including Betula papyrifera, Picea mariana, Acer saccharum, and Larix laricina. In another ten species, including Abies balsamea, Tsuga canadensis, Fraxinus americana, and Fagus grandifolia, mortality rates tended to be higher in areas with high incident solar radiation. High amounts of precipitation in NB’s humid maritime climate were also found to contribute to heightened tree mortality. The relationship between high GDD, solar radiation, and high mortality rates was particularly strong when precipitation was also low. This would suggest that although excessive soil water can contribute to heightened tree mortality by reducing the supply of air to the roots, occasional drought in NB can also contribute to increased mortality events. These results would have significant implications when considered alongside regional climate projections which generally entail both components of warming and increased precipitation.

PMID:34143806 | DOI:10.1371/journal.pone.0250991

PLoS One. 2021 Jun 18;16(6):e0252505. doi: 10.1371/journal.pone.0252505. eCollection 2021.

ABSTRACT

Statistical image analysis of an ensemble of digital images of histological samples is performed as an auxiliary investigation a result of the recently proposed method of articular cartilage repair utilizing growth plate chondrocytes in a skeleton animal model. A fixed-shift model of maximal likelihood estimates of image histograms applied for monochromatic (grayscale) images or their RGB components confirms the statistically significant effect of the previously proposed medical treatment. The type of staining used to prepare images of histological samples is related to the visibility of the effectiveness of medical treatment. Hellinger distance of escort distributions for maximal likelihood estimates of image histograms of medically treated and control samples is investigated to identify grayscale (or RGB) intensities responsible for statistically significant difference of the estimates. A difference of Shannon entropy quantifying informational content of the histograms allows one to identify staining and image colors which are most suitable to visualize cluster formation typical for articular cartilage repair processes.

PMID:34143793 | DOI:10.1371/journal.pone.0252505

PLoS One. 2021 Jun 18;16(6):e0251815. doi: 10.1371/journal.pone.0251815. eCollection 2021.

ABSTRACT

BACKGROUND: Blood/body fluid splash are hazards to health care professionals in their working area. Around twenty bloodborne pathogens are known to be transmitted through these occupational injuries. This problem alters the health status of health care professionals in different ways, including physically, mentally, and psychologically. Even though health professionals especially midwives who are working in delivery rooms are highly affected, little is known about the exposure. So, this study was aimed to assess the prevalence of exposure to blood/body fluid splash and its predictors among midwives working in public health institutions of Addis Ababa city.

METHODS: Institution based cross-sectional study was conducted among 438 study participants in public health institutions in Addis Ababa. Data was collected from March 1-20, 2020 by a self-administered questionnaire. The data were entered into Epi data version 3.1 and then exported to SPSS version 24 for analysis. All variables with P<0.25 in the bivariate analysis were included in a final model and statistical significance was declared at P< 0.05.

RESULTS: In this study, a total of 424 respondents respond yielding a response rate of 97%. The prevalence of blood and body fluid splashes (BBFs) was 198 (46.7%). Not training on infection prevention, working in two shifts (> 12 hours), not regularly apply universal precautions, job-related stress, an average monthly salary of 5001-8000 were independent predictors of blood and body fluid splashes.

CONCLUSION: The study revealed that nearly half of midwives were exposed to BBFS. This highlights the need for key stakeholders such as policymakers and service providers to design appropriate policies to avert this magnitude and making the environment enabling to comply with standard precautions. We recommend that this study may be done by including rural setting institutions and by including other health professionals that are susceptible to BBFS at work. Formal training on infection prevention and safety practice to apply universal precautions will be needed from the concerned bodies to prevent exposures to blood/body fluid splash.

PMID:34143794 | DOI:10.1371/journal.pone.0251815

PLoS Negl Trop Dis. 2021 Jun 18;15(6):e0009410. doi: 10.1371/journal.pntd.0009410. eCollection 2021 Jun.

ABSTRACT

BACKGROUND: Leptospirosis has been described as a biphasic disease consisting of hematogenous dissemination to major organs in the acute phase and asymptomatic renal colonization in the chronic phase. Several observational studies have suggested an association between leptospirosis and chronic kidney disease (CKD). We investigated the dynamics of leptospires and histopathological changes in the kidney to understand the relationship between them, and also investigated the extent of renal dysfunction in the acute and chronic phases of leptospirosis using a hamster model.

FINDINGS: Hamsters (n = 68) were subcutaneously infected with 1 × 104 cells of the Leptospira interrogans serovar Manilae strain UP-MMC-SM. A total of 53 infected hamsters developed fatal acute leptospirosis, and the remaining 15 hamsters recovered from the acute phase, 13 of which showed Leptospira colonization in the kidneys in the chronic phase. Five asymptomatic hamsters also had renal colonization in the chronic phase. Immunofluorescence staining showed that leptospires were locally distributed in the renal interstitium in the early acute phase and then spread continuously into the surrounding interstitium. The kidneys of the surviving hamsters in the chronic phase showed patchy lesions of atrophic tubules, a finding of chronic tubulointerstitial nephritis, which were substantially consistent with the distribution of leptospires in the renal interstitium. The degree of atrophic tubules in kidney sections correlated statistically with the serum creatinine level in the chronic phase (rs = 0.78, p = 0.01).

CONCLUSION: Subcutaneous infection with pathogenic leptospires could cause acute death or chronic leptospirosis in hamsters after surviving the acute phase. We suggest that the renal distribution of leptospires during the acute phase probably affected the extent of tubular atrophy, leading to CKD.

PMID:34143778 | DOI:10.1371/journal.pntd.0009410

PLoS One. 2021 Jun 18;16(6):e0250025. doi: 10.1371/journal.pone.0250025. eCollection 2021.

ABSTRACT

OBJECTIVE: Takayasu arteritis (TAK) is a rare immune-mediated vasculitis of the aorta and its branches. Aims were to calculate prevalence and incidence in Switzerland, to assess disease activity and performance of MR-Angiography (MRA).

METHODS: 31 patients were recorded in a database, 27 were followed prospectively up to 3 years. Prevalence was calculated based on data of the national statistical bureau. Disease activity was defined using the revised EULAR criteria. MRA depicted stenotic changes and aortic wall enhancement.

RESULTS: A disease prevalence of 14.5/1.000.000 inhabitants and an incidence of 0.3/1.000.000 per year was calculated. Aortic wall enhancement was found in 10 patients while in clinical and serological remission. EULAR criteria missed 5 patients with disease activity with isolated elevations of ESR/CRP. Arterial stenosis did not change over time in 5 cases, it improved in 2 and increased in 7. At follow-up 16 patients were treated with tocilizumab, 11/16 in monotherapy, 5 patients were treatment-free, 25/27 stayed in remission.

CONCLUSION: In addition to prevalence and incidence, our data show that MRA qualifies to detect subclinical disease activity, but, on the other hand, that EULAR criteria may miss disease activity in case of isolated elevation of ESR/CRP.

PMID:34143786 | DOI:10.1371/journal.pone.0250025

PLoS One. 2021 Jun 18;16(6):e0248350. doi: 10.1371/journal.pone.0248350. eCollection 2021.

ABSTRACT

PURPOSE: To investigate the repeatability in corneal thickness (CT) and epithelial thickness (ET) measurements using spectral domain anterior segment optical coherence tomography (AS-OCT, REVO NX, Optopol) in keratoconus, and examine the effect of corneal crosslinking (CXL) on repeatability.

METHODS: A cross-sectional study of 259 eyes of 212 patients with keratoconus attending the corneal disease clinic at a university hospital tertiary referral center were enrolled. Two groups were analysed: eyes with no prior history of CXL (Group A) and eyes with prior CXL (Group B). Repeatability of measurements was assessed using the intraclass correlation coefficient (ICC) and coefficient of variation (CV).

RESULTS: In Group A, central corneal thickness (CCT) was 472.18 ± 45.41μm, and the ET was found to be the thinnest in the inferior-temporal aspect at 51.79 ± 5.97μm and thickest at the superior-nasal aspect at 56.07 ± 5.70μm. In Group B, CCT was 465.11± 42.28μm, and the ET was the thinnest at the inferior-temporal aspect at 50.63 ± 5.52μm and thickest at the superior aspect at 56.80 ± 6.39μm. When evaluating CT measurements, ICC was above 0.86 and 0.83 for Group A and Group B respectively. When evaluating ET measurements, ICC was above 0.82 for both groups. CXL had no statistically significant impact on the repeatability of measurements.

CONCLUSIONS: AS-OCT provides repeatable CT and ET measurements in the central and peripheral cornea in patients with keratoconus. Repeatability is not affected by a history of CXL.

PMID:34143790 | DOI:10.1371/journal.pone.0248350