Tag: pubmed

Clin Infect Dis. 2021 Aug 6:ciab679. doi: 10.1093/cid/ciab679. Online ahead of print.

ABSTRACT

BACKGROUND: 240-million people have schistosomiasis despite decades of interventions. Infections cannot be directly observed, and egg-based Kato-Katz thick smears lack sensitivity, impacting treatment efficacy and reinfection rate estimates. The Point-of-Care Circulating Cathodic Antigen test (POC-CCA) is advocated as an improvement upon the Kato-Katz, however improved estimates are limited by ambiguities in the interpretation of Trace results.

METHOD: We collected repeated Kato-Katz counts from 210 school-aged children and scored POC-CCAs according to manufacturer’s guidelines (POC-CCA+) and the externally developed G-Score. We used Hidden Markov Models parameterised with Kato-Katz; Kato-Katz and POC-CCA+; and Kato-Katz and G-Scores, inferring latent clearance and reinfection probabilities at four timepoints over six-months through a more formal statistical reconciliation of these diagnostics than previously conducted. Our approach required minimal but robust assumptions regarding Trace interpretations.

RESULTS: Antigen-based models estimated higher infection prevalence across all timepoints compared with the Kato-Katz model, corresponding to lower clearance and higher reinfection estimates. Specifically, pre-treatment prevalence estimates were 85% (Kato-Katz; 95% CI: 79-92%), 99% (POC-CCA+; 97-100%) and 98% (G-Score; 95-100%). Post-treatment, 93% (Kato-Katz; 88-96%), 72% (POC-CCA+; 64-79%) and 65% (G-Score; 57-73%) of those infected were estimated to clear infection. Of those who cleared infection, 35% (Kato-Katz; 27-42%), 51% (POC-CCA+; 41-62%) and 44% (G-Score; 33-55%) were estimated to have been reinfected by nine-weeks.

CONCLUSION: Treatment impact was shorter-lived than only Kato-Katz-based estimates suggested, with lower clearance and rapid reinfection. Three-weeks-post-treatment captured longer-term clearance dynamics. Nine-weeks-post-treatment captured reinfection, but alone could not discern between failed clearance and rapid reinfection. Therefore, frequent sampling is required to understand these important epidemiological dynamics.

PMID:34358299 | DOI:10.1093/cid/ciab679

Bioinformatics. 2021 Aug 6:btab574. doi: 10.1093/bioinformatics/btab574. Online ahead of print.

ABSTRACT

MOTIVATION: The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialised tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement.

RESULTS: Here we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent (IBD) probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualisation tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed.

AVAILABILITY: polyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:34358315 | DOI:10.1093/bioinformatics/btab574

PLoS One. 2021 Aug 6;16(8):e0255884. doi: 10.1371/journal.pone.0255884. eCollection 2021.

ABSTRACT

BACKGROUND: COVID-19 is highly infectious viral disease that can lead to main clinical symptoms like fever, dry cough, fatigue, myalgia, and dyspnea. Since there is no drug to cure the disease, focusing on improving community awareness related to prevention methods is crucial. But there was no regional level study addressing the reach of information, community knowledge and attitude related to COVID-19 and its prevention, and this study was done to inform and assist communication related to the disease responses during early introduction of the disease to the setting.

METHODS: Community based cross sectional study was conducted in selected ten towns of SNNPR, Ethiopia. Multi-stage sampling was used to select 1239 participants. Semi-structured questionnaire was designed, pre-tested and uploaded to SurveyCTO data collection system with security patterns. Knowledge was assessed considering awareness about signs and symptoms, confirmatory test (laboratory test), what to do if there is a suspect, availability of drug to cure the disease, mechanisms of transmission, prevention methods and most at risk groups. Attitude was assessed using 11 statements including seriousness of disease, being at risk, possibility of prevention, and benefits of staying at health facilities. Descriptive statistics and binary logistic regression were performed to manage data using SPSS version 25.

RESULTS: Almost all respondents (99.8%) heard about the disease. The mean score of knowledge was 52.3% (SD = 18.9) while the mean score attitude was 80.8% (SD = 6.48). Educational status, housing condition and marital status were associated with having good knowledge while occupation, housing condition, age and overall knowledge were associated with having positive attitude.

CONCLUSION: Even though almost all respondents had heard about the COVID-19, knowledge and attitude related to COVID-19 and its prevention were low. Awareness creation should be intensified using different local languages to improve community awareness, overcome misconceptions and minimize consequences of the disease.

PMID:34358267 | DOI:10.1371/journal.pone.0255884

Bioinformatics. 2021 Aug 6:btab572. doi: 10.1093/bioinformatics/btab572. Online ahead of print.

ABSTRACT

MOTIVATION: High-throughput sequencing technologies generate a huge amount of data, permitting the quantification of microbiome compositions. The obtained data are essentially sparse compositional data vectors, namely vectors of bacterial gene proportions which compose the microbiome. Subsequently, the need for statistical and computational methods that consider the special nature of microbiome data has increased. A critical aspect in microbiome research is to identify microbes associated with a clinical outcome. Another crucial aspect with high-dimensional data is the detection of outlying observations, whose presence affects seriously the prediction accuracy.

RESULTS: In this article we connect robustness and sparsity in the context of variable selection in regression with compositional covariates with a continuous response. The compositional character of the covariates is taken into account by a linear log-contrast model, and elastic-net regularization achieves sparsity in the regression coefficient estimates. Robustness is obtained by performing trimming in the objective function of the estimator. A reweighting step increases the efficiency of the estimator, and it also allows for diagnostics in terms of outlier identification. The numerical performance of the proposed method is evaluated via simulation studies, and its usefulness is illustrated by an application to a microbiome study with the aim to predict caffeine intake based on the human gut microbiome composition.

AVAILABILITY: The R-package “RobZS” can be downloaded at https://github.com/giannamonti/RobZS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:34358286 | DOI:10.1093/bioinformatics/btab572

PLoS One. 2021 Aug 6;16(8):e0255599. doi: 10.1371/journal.pone.0255599. eCollection 2021.

ABSTRACT

BACKGROUND: The endoscopic transsphenoidal approach is an efficient minimally invasive procedure for removal of pituitary tumors that can be accomplished through a one-hand or two-hand approach. The one-hand procedure through one nostril is more intuitive for surgeons, but maneuvering the instruments can be restrictive. The two-hand procedure using a one-and-half nostril approach provides more precise manipulation. This study aimed to compare the surgical outcomes of one-hand/mono-nostril and two-hand/one-and-half nostril surgeries for resection of large pituitary tumors by a single neurosurgeon.

MATERIALS AND METHODS: The surgical data of 78 consecutive cases with pituitary macroadenoma (diameter >1 cm) were reviewed retrospectively. Altogether, 30 cases received one-hand/mono-nostril surgery, while 48 cases received two-hand/one-and-half nostril surgery. Postoperative outcomes of the two operations were compared.

RESULTS: The operative time, hospital stay, residual rate of pituitary macroadenoma, visual field, surgical complications, and re-operative rates were slightly improved in the two-hand/one-and-half nostril surgery group compared with that in the one-hand/mono-nostril surgery group (all p>0.05). However, postoperative hypopituitarism was less frequent (1/48; 2.0%) with the two-hand/one-and-half nostril approach than with the mono-nostril approach (p = 0.004). Similar surgical outcomes were found in all patients with either small or large pituitary tumors, except that the difference in postoperative improvement in visual field change reached statistical significance (p = 0.044).

CONCLUSION: A single-surgeon endoscopic endonasal transsphenoidal surgery with two-hand/one-and-half nostril approach is an effective and safe procedure for removal of large pituitary tumors.

PMID:34358251 | DOI:10.1371/journal.pone.0255599

PLoS One. 2021 Aug 6;16(8):e0253517. doi: 10.1371/journal.pone.0253517. eCollection 2021.

ABSTRACT

The dimensions of patient-centred care include not only clinical effectiveness and patient safety, but, importantly, the preferences of patients as consumers of healthcare services. A total of 249 participants were included in the study, with a balanced population proportional representation by age, gender, ethnicity and geographic region of New Zealand. An online questionnaire was used to identify participants’ decision-making process, and what factors and barriers for participants to seek dental treatment. Cross-tabulations, Spearman correlation analysis and Pearson Chi-Square analysis were used for the statistical analyses. Three most common reasons for visit were check-up (77%), clean (57%) and relief of pain 36%). A desire to treat a perceived problem was the most common encouraging factor to seek dental care. Cost was the most common barrier to seeking dental services. The majority of participants attended a private practice (84%), with convenience of location and referral from professionals the most likely to influence their choice. Participants felt the most important trait a dental practitioner could demonstrate was to discuss treatment options with them before any treatment. Dental check-up, teeth cleaning and relief of pain were the most common reasons for patients to choose dental services. Cost and ethnicity of the consumers had a significant impact on how dental services were perceived and sought. Dental practitioners may need to reorientate how they express value of oral health practice, not just in regard to communication with patients, but also with government funding agencies.

PMID:34358252 | DOI:10.1371/journal.pone.0253517

PLoS One. 2021 Aug 6;16(8):e0255735. doi: 10.1371/journal.pone.0255735. eCollection 2021.

ABSTRACT

PURPOSE: Establishing the reliability of a new method to check the mean retinal and choroidal reflectivity and using it to find retinal and choroid changes in amblyopia.

METHODS: Design: Retrospective case-control. Population: 28 subjects of which 10 were healthy controls (20 eyes): 8 with refractive errors, 1 with strabismus, and 1 with both. 18 patients with unilateral amblyopia included: 7 anisometropic, 6 isoametropic, 1 strabismic, and 4 combined. Mean participants’ age: 13.77 years ± 10.28. Observation procedures: SD-OCT and ImageJ. Main outcome measure: mean reflectivity of retinal and choroid layers. Amblyopic, fellow, and healthy eyes were compared.

RESULTS: The method of measuring reflectivity is good to excellent reliability for all regions of interest except the fourth. The mean reflectivity of the choriocapillaris and Sattler’s layer in amblyopic eyes were significantly lower than in healthy eyes (p = 0.003 and p = 0.008 respectively). The RNFL reflectivity was lower than that of fellow eyes (p = 0.025). Post-hoc pairwise comparisons showed statistically significant differences between amblyopic and healthy eyes for choriocapillaris (p = 0.018) and Sattler’s (p = 0.035), and between amblyopic and fellow eyes for RNFL (p = 0.039).

CONCLUSION: A decrease in reflectivity of the choriocapillaris and Sattler’s in amblyopic compared to healthy eyes, and a decrease in reflectivity of the RNFL in the amblyopic compared to fellow eyes, indicate that the pathophysiology is partly peripheral and might be bilateral.

PMID:34358257 | DOI:10.1371/journal.pone.0255735

PLoS One. 2021 Aug 6;16(8):e0254479. doi: 10.1371/journal.pone.0254479. eCollection 2021.

ABSTRACT

BACKGROUND: Sentinel physician surveillance in communities has played an important role in detecting early signs of epidemics. The traditional approach is to let the primary care physician voluntarily and actively report diseases to the health department on a weekly basis. However, this is labor-intensive work, and the spatio-temporal resolution of the surveillance data is not precise at all. In this study, we built up a clinic-based enhanced sentinel surveillance system named “Sentinel plus” which was designed for sentinel clinics and community hospitals to monitor 23 kinds of syndromic groups in Taipei City, Taiwan. The definitions of those syndromic groups were based on ICD-10 diagnoses from physicians.

METHODS: Daily ICD-10 counts of two syndromic groups including ILI and EV-like syndromes in Taipei City were extracted from Sentinel plus. A negative binomial regression model was used to couple with lag structure functions to examine the short-term association between ICD counts and meteorological variables. After fitting the negative binomial regression model, residuals were further rescaled to Pearson residuals. We then monitored these daily standardized Pearson residuals for any aberrations from July 2018 to October 2019.

RESULTS: The results showed that daily average temperature was significantly negatively associated with numbers of ILI syndromes. The ozone and PM2.5 concentrations were significantly positively associated with ILI syndromes. In addition, daily minimum temperature, and the ozone and PM2.5 concentrations were significantly negatively associated with the EV-like syndromes. The aberrational signals detected from clinics for ILI and EV-like syndromes were earlier than the epidemic period based on outpatient surveillance defined by the Taiwan CDC.

CONCLUSIONS: This system not only provides warning signals to the local health department for managing the risks but also reminds medical practitioners to be vigilant toward susceptible patients. The near real-time surveillance can help decision makers evaluate their policy on a timely basis.

PMID:34358241 | DOI:10.1371/journal.pone.0254479

PLoS Negl Trop Dis. 2021 Aug 6;15(8):e0009673. doi: 10.1371/journal.pntd.0009673. Online ahead of print.

ABSTRACT

BACKGROUND: Hemorrhagic fever with renal syndrome (HFRS) is a rodent-borne disease caused by hantavirus which was endemic Zhejiang Province, China. In this study, we aim to explore the changing epidemiology of HFRS in Zhejiang, identify high-risk areas and populations, and evaluate relevant policies and interventions to better improve HFRS control and prevention.

METHODS: Surveillance data on HFRS during 1963-2020 in Zhejiang Province were extracted from Zhejiang Provincial Center for Disease Control and Prevention archives and the Chinese Notifiable Disease Reporting System. The changing epidemiological characteristics of HFRS including seasonal distribution, geographical distribution, and demographic features, were analyzed using joinpoint regression, autoregressive integrated moving average model, descriptive statistical methods, and Spatio-temporal cluster analysis.

RESULTS: From 1963 to 2020, 114 071 HFRS cases and 1269 deaths were reported in Zhejiang Province. The incidence increased sharply from 1973 and peaked in 1986, then decreased steadily and maintained a stable incidence from 2004. HFRS cases were reported in all 11 prefecture-level cities of Zhejiang Province from 1963 to 2020. The joint region (Shengzhou, Xinchang, Tiantai, and surrounding areas), and Kaihua County are the most seriously affected regions throughout time. After 1990, the first HFRS incidence peak was in May-June, with another one from November to January. Most HFRS cases occurred in 21- (26.48%) and 30- years group (24.25%) from 1991 to 2004, but 41- (25.75%) and 51-years (23.30%) had the highest proportion from 2005 to 2020. Farmers accounted for most cases (78.10%), and cases are predominantly males with a male-to-female ratio of 2.6:1. It was found that the median time from onset to diagnosis was 6.5 days (IQR 3.75-10.42), and the time from diagnosis to disease report was significantly shortened after 2011.

CONCLUSIONS: We observed dynamic changes in the seasonal distribution, geographical distribution, and demographic features of HFRS, which should be well considered in the development of control and prevention strategies in future. Additional researches are warranted to elucidate the environmental, meteorological, and social factors associated with HFRS incidence in different decades.

PMID:34358248 | DOI:10.1371/journal.pntd.0009673

PLoS Negl Trop Dis. 2021 Aug 6;15(8):e0009593. doi: 10.1371/journal.pntd.0009593. Online ahead of print.

ABSTRACT

BACKGROUND: Brucellosis is widespread in Ethiopia with variable reported prevalence depending on the geographical area, husbandry practices and animal species. However, there is limited information on the disease prevalence amongst pastoral communities, whose life is intricately linked with their livestock.

METHODOLOGY: We conducted an integrated human-animal brucellosis sero-surveillance study in two adjacent pastoral regions, Afar and Somali region (SRS). This cross-sectional study included 13 woredas (districts) and 650 households. Blood samples were collected from people and livestock species (cattle, camel, goats and sheep). Sera were analyzed with C-ELISA for camels and shoats (sheep and goats), with I-ELISA for cattle and IgG ELISA for humans. Descriptive and inferential statistics analyses were performed.

RESULTS: A total of 5469 sera were tested by ELISA. Prevalence of livestock was 9.0% in Afar and 8.6% in SRS (ranging from 0.6 to 20.2% at woreda level). In humans, prevalence was 48.3% in Afar and 34.9% in SRS (ranging from 0.0 to 74.5% at woreda level). 68.4% of all households in Afar and 57.5% of households in SRS had at least one animal reactor. Overall, 4.1% of animals had a history of abortion. The proportion of animals with abortion history was higher in seropositive animals than in seronegative animals. Risk factor analysis showed that female animals were significantly at higher risk of being reactors (p = 0.013). Among the species, cattle had the least risk of being reactors (p = 0.014). In humans, there was a clear regional association of disease prevalence (p = 0.002). The older the people, the highest the odds of being seropositive.

CONCLUSION: Brucellosis is widespread in humans and animals in pastoral communities of Afar and SRS with the existence of geographical hotspots. No clear association was seen between human and particular livestock species prevalence, hence there was no indication as whether B. abortus or B. melitensis are circulating in these areas, which warrants further molecular research prior to embarking on a national control programs. Such programs will need to be tailored to the pastoral context.

PMID:34358232 | DOI:10.1371/journal.pntd.0009593