Tag: nevin manimala

Mol Biol Evol. 2021 Aug 12:msab238. doi: 10.1093/molbev/msab238. Online ahead of print.

ABSTRACT

The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our dataset, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.

PMID:34383935 | DOI:10.1093/molbev/msab238

Bioinformatics. 2021 Aug 12:btab562. doi: 10.1093/bioinformatics/btab562. Online ahead of print.

ABSTRACT

MOTIVATION: Co-evolution analysis can be used to accurately predict residue-residue contacts from multiple sequence alignments. The introduction of machine-learning techniques has enabled substantial improvements in precision and a shift from predicting binary contacts to predicting distances between pairs of residues. These developments have significantly improved the accuracy of de novo prediction of static protein structures. With AlphaFold2 lifting the accuracy of some predicted protein models close to experimental levels, structure prediction research will move on to other challenges. One of those areas is the prediction of more than one conformation of a protein. Here we examine the potential of residue-residue distance predictions to be informative of protein flexibility rather than simply static structure.

RESULTS: We used DMPfold to predict distance distributions for every residue pair in a set of proteins that showed both rigid and flexible behaviour. Residue pairs that were in contact in at least one reference structure were classified as rigid, flexible or neither. The predicted distance distribution of each residue pair was analysed for local maxima of probability indicating the most likely distance or distances between a pair of residues. We found that rigid residue pairs tended to have only a single local maximum in their predicted distance distributions while flexible residue pairs more often had multiple local maxima. These results suggest that the shape of predicted distance distributions contains information on the rigidity or flexibility of a protein and its constituent residues.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:34383892 | DOI:10.1093/bioinformatics/btab562

J Am Med Inform Assoc. 2021 Aug 12:ocab156. doi: 10.1093/jamia/ocab156. Online ahead of print.

ABSTRACT

OBJECTIVE: The study sought to assess the feasibility of replacing the International Classification of Diseases-Tenth Revision-Clinical Modification (ICD-10-CM) with the International Classification of Diseases-11th Revision (ICD-11) for morbidity coding based on content analysis.

MATERIALS AND METHODS: The most frequently used ICD-10-CM codes from each chapter covering 60% of patients were identified from Medicare claims and hospital data. Each ICD-10-CM code was recoded in the ICD-11, using postcoordination (combination of codes) if necessary. Recoding was performed by 2 terminologists independently. Failure analysis was done for cases where full representation was not achieved even with postcoordination. After recoding, the coding guidance (inclusions, exclusions, and index) of the ICD-10-CM and ICD-11 codes were reviewed for conflict.

RESULTS: Overall, 23.5% of 943 codes could be fully represented by the ICD-11 without postcoordination. Postcoordination is the potential game changer. It supports the full representation of 8.6% of 943 codes. Moreover, with the addition of only 9 extension codes, postcoordination supports the full representation of 35.2% of 943 codes. Coding guidance review identified potential conflicts in 10% of codes, but mostly not affecting recoding. The majority of the conflicts resulted from differences in granularity and default coding assumptions between the ICD-11 and ICD-10-CM.

CONCLUSIONS: With some minor enhancements to postcoordination, the ICD-11 can fully represent almost 60% of the most frequently used ICD-10-CM codes. Even without postcoordination, 23.5% full representation is comparable to the 24.3% of ICD-9-CM codes with exact match in the ICD-10-CM, so migrating from the ICD-10-CM to the ICD-11 is not necessarily more disruptive than from the International Classification of Diseases-Ninth Revision-Clinical Modification to the ICD-10-CM. Therefore, the ICD-11 (without a CM) should be considered as a candidate to replace the ICD-10-CM for morbidity coding.

PMID:34383897 | DOI:10.1093/jamia/ocab156

Transl Vis Sci Technol. 2021 Aug 12;10(10):4. doi: 10.1167/tvst.10.10.4.

ABSTRACT

PURPOSE: To establish optical coherence tomography (OCT) as an in vivo imaging modality for investigating the process of newt lens regeneration.

METHODS: Spectral-domain OCT was employed for in vivo imaging of the newt lens regeneration process. A total of 37 newts were lentectomized and followed by OCT imaging over the course of 60 to 80 days. Histological images were obtained at several time points to compare with the corresponding OCT images. Volume measurements were also acquired.

RESULTS: OCT can identify the key features observed in corresponding histological images based on the scattering differences from various eye tissues, such as the cornea, intact and regenerated lens, and the iris. Lens volume measurements from three-dimensional OCT images showed that the regenerating lens size increased linearly until 60 days post-lentectomy.

CONCLUSIONS: Using OCT imaging, we were able to track the entire process of newt lens regeneration in vivo for the first time. Three-dimensional OCT images allowed us to volumetrically quantify and visualize the dynamic spatial relationships between tissues during the regeneration process. Our results establish OCT as an in vivo imaging modality to track/analyze the entire lens regeneration process from the same animal.

TRANSLATIONAL RELEVANCE: Lens regeneration in newts represents a unique example of vertebrate tissue plasticity. Investigating the cellular and morphological events that govern this extraordinary process in vivo will advance our understanding and shed light on developing new therapies to treat blinding disorders in higher vertebrates.

PMID:34383878 | DOI:10.1167/tvst.10.10.4

PLoS One. 2021 Aug 12;16(8):e0256221. doi: 10.1371/journal.pone.0256221. eCollection 2021.

ABSTRACT

This study estimated the prevalence and incidence rate of schizophrenia, schizotypal, and delusional disorders (SSDD) in Korea from 2008 to 2017 and analyzed the hospital admission rate, re-admission rate, and hospitalization period. It used the Korean nationwide National Health Insurance Service claims database. SSDD patients who had at least one visit to Korea’s primary, secondary, or tertiary referral hospitals with a diagnosis of SSDD, according to the International Classification of Diseases, 10th Revision (ICD-10), were identified as SSDD cases if coded as F20-F29. Data were analyzed using frequency statistics. Results showed that the 12-month prevalence rate of SSDD increased steadily from 0.40% in 2008 to 0.45% in 2017. Analysis of the three-year cumulative prevalence rate of SSDD showed an increase from 0.51% in 2011 to 0.54% in 2017. In 2017, the five-year cumulative prevalence rate was 0.61%, and the 10-year cumulative prevalence rate was 0.75%. The hospital admission rate among SSDD patients decreased from 2008 (30.04%) to 2017 (28.53%). The incidence of SSDD was 0.05% and no yearly change was observed. The proportion of SSDD inpatients whose first hospital visit resulted in immediate hospitalization was 22.4% in 2017. Epidemiological indicators such as prevalence, incidence, and hospitalization rate play an important role in planning social and financial resource allocation. Therefore, efforts to produce more accurate epidemiological indicators are very important and this study’s findings could have a significant social impact.

PMID:34383865 | DOI:10.1371/journal.pone.0256221

PLoS One. 2021 Aug 12;16(8):e0256119. doi: 10.1371/journal.pone.0256119. eCollection 2021.

ABSTRACT

BACKGROUND: The Patient Assessment of Chronic Illness Care (PACIC) was developed in the United States to assess the implementation of the Chronic Care Model (CCM)-based intervention from the patient’s perspective. Although the psychometric properties of the PACIC have been reported in other chronically ill patients, it has not been reported in cancer survivors. Our aim was to evaluate the acceptability, validity, and reliability of a Korean version of the PACIC among cancer survivors (K-PACIC-CS).

METHODS: Among 204 cancer survivors at a university-based hospital in South Korea, we performed psychometric evaluation of the K-PACIC-CS according to acceptability (descriptive statistics, missing values, and floor and ceiling effects), validity (confirmative factor analysis [CFA] and convergent validity), and reliability (internal consistency, i.e., Cronbach’s alpha).

RESULTS: The item response was high (missing rate = 0.5%). The floor effect was 3.9%- 43.6% and the ceiling effect was 6.9%- 41.2%. The CFA revealed good indices of fit and confirmed the five structures predetermined in the original version of PACIC. The K-PACIC-CS scores had significant positive relationships with cancer survivors’ self-efficacy and health-related quality of life. The total K-PACIC-CS showed excellent internal consistency (Cronbach’s alpha = .94) and those of the subscales were acceptable (Cronbach’s alpha = .76 -.86).

CONCLUSIONS: This study suggests that the K-PACIC-CS is a valid and reliable instrument for measuring implementation of CCM-based chronic care from the survivor’s perspective.

PMID:34383868 | DOI:10.1371/journal.pone.0256119

PLoS One. 2021 Aug 12;16(8):e0256169. doi: 10.1371/journal.pone.0256169. eCollection 2021.

ABSTRACT

The World Health Organization declared, at the end of 2019, a pandemic caused by SARS-CoV-2, a virus that causes Coronavirus Disease-COVID-19. Currently, Brazil has become the epicenter of the disease, registering approximately 345 thousand deaths. Thus, the study has scientific relevance in health surveillance as it identifies, quantifies and monitors the main behavioral patterns of the mortality rate due to COVID-19, in Brazil and in their respective regions. In this context, the study aims to assess the epidemiological behavior of mortality due to COVID-19 in Brazil: a time series study, referring to the year 2020. This is an ecological time series study, constructed using secondary data. The research was carried out in Brazil, having COVID-19 deaths as the dependent variable that occurred between the 12th and 53rd Epidemiological Week of 2020. The independent variable will be the epidemiological weeks. The data on deaths by COVID-19 were extracted in February 2021, on the Civil Registry Transparency Portal. The cleaning of the database and the information were treated in the Microsoft Excel® Software and, for statistical analysis, the JoinPoint software, version 4.7.0.0 was used. It was observed that Brazil presents an upward curve between the 12th and 19th SE, when it reaches saturation at the peak of mortality, which remains until the 35th SE and, subsequently, a downward curve was identified until the 47th SE, period in the which curve turns back up.

PMID:34383857 | DOI:10.1371/journal.pone.0256169

PLoS One. 2021 Aug 12;16(8):e0256099. doi: 10.1371/journal.pone.0256099. eCollection 2021.

ABSTRACT

BACKGROUND: The remarkable progress seen in maternal and child health (MCH) in India over the past two decades has been impacted by the COVID-19 pandemic. We aimed to undertake a rapid assessment to identify key priorities for public health research in MCH in India within the context and aftermath of the COVID-19 pandemic.

METHODS: A web-based survey was developed to identify top research priorities in MCH. It consisted of 26 questions on six broad domains: vaccine preventable diseases, outbreak preparedness, primary healthcare integration, maternal health, neonatal health, and infectious diseases. Key stakeholders were invited to participate between September and November 2020. Participants assigned importance on a 5-point Likert scale, and assigned overall ranks to each sub-domain research priority. Descriptive statistics were used to examine Likert scale responses, and a ranking analysis was done to obtain an “average ranking score” and identify the top research priority under each domain.

RESULTS: Amongst the 84 respondents from across 15 Indian states, 37% were public-health researchers, 25% healthcare providers, 20% academic faculty and 13% were policy makers. Most respondents considered conducting systems strengthening research as extremely important. The highest ranked research priorities were strengthening the public sector workforce (vaccine preventable diseases), enhancing public-health surveillance networks (outbreak preparedness), nutrition support through community workers (primary care integration), encouraging at least 4-8 antenatal visits (maternal health), neonatal resuscitation to reduce birth asphyxia (neonatal health) and screening and treatment of tuberculosis (infectious diseases). Common themes identified through open-ended questions primarily included systems strengthening priorities across domains.

CONCLUSIONS: The overall focus for research priorities in MCH in India during the COVID-19 pandemic is on strengthening existing services and service delivery, rather than novel research. Our results highlight pivotal steps within the roadmap for advancing and sustaining maternal and child health gains during the ongoing COVID-19 pandemic and beyond.

PMID:34383861 | DOI:10.1371/journal.pone.0256099

PLoS One. 2021 Aug 12;16(8):e0255992. doi: 10.1371/journal.pone.0255992. eCollection 2021.

ABSTRACT

PURPOSE: We aimed to determine the degree to which reasons for primary care visits changed during the COVID-19 pandemic.

METHODS: We used data from the University of Toronto Practice Based Research Network (UTOPIAN) to compare the most common reasons for primary care visits before and after the onset of the COVID-19 pandemic, focusing on the number of visits and the number of patients seen for each of the 25 most common diagnostic codes. The proportion of visits involving virtual care was assessed as a secondary outcome.

RESULTS: UTOPIAN family physicians (N = 379) conducted 702,093 visits, involving 264,942 patients between March 14 and December 31, 2019 (pre-pandemic period), and 667,612 visits, involving 218,335 patients between March 14 and December 31, 2020 (pandemic period). Anxiety was the most common reason for visit, accounting for 9.2% of the total visit volume during the pandemic compared to 6.5% the year before. Diabetes and hypertension remained among the top 5 reasons for visit during the pandemic, but there were 23.7% and 26.2% fewer visits and 19.5% and 28.8% fewer individual patients accessing care for diabetes and hypertension, respectively. Preventive care visits were substantially reduced, with 89.0% fewer periodic health exams and 16.2% fewer well-baby visits. During the pandemic, virtual care became the dominant care format (77.5% virtual visits). Visits for anxiety and depression were the most common reasons for a virtual visit (90.6% virtual visits).

CONCLUSION: The decrease in primary care visit volumes during the COVID-19 pandemic varied based on the reason for the visit, with increases in visits for anxiety and decreases for preventive care and visits for chronic diseases. Implications of increased demands for mental health services and gaps in preventive care and chronic disease management may require focused efforts in primary care.

PMID:34383844 | DOI:10.1371/journal.pone.0255992

PLoS One. 2021 Aug 12;16(8):e0256185. doi: 10.1371/journal.pone.0256185. eCollection 2021.

ABSTRACT

Prisons are the epicenter of the COVID-19 pandemic. Media reports have focused on whether transfers of incarcerated people between prisons have been the source of outbreaks. Our objective was to examine the relationship between intersystem prison transfers and COVID-19 incidence in a state prison system. We assessed the change in the means of the time-series of prison transfers and their cross-correlation with the time-series of COVID-19 tests and cases. Regression with automatic detection of multiple change-points was used to identify important changes to transfers. There were over 20,000 transfers between the state’s prisons from January through October 2020. Most who were transferred (82%), experienced a single transfer. Transfers between prisons are positively related to future COVID-19 case rates but transfers are not reactive to current case rates. To mitigate the spread of COVID-19 in carceral settings, it is crucial for transfers of individuals between facilities to be limited.

PMID:34383854 | DOI:10.1371/journal.pone.0256185