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Nevin Manimala Statistics

Cigarette Smoke Triggers Loss of Corneal Endothelial Cells and Disruption of Descemet’s Membrane Proteins in Mice

Invest Ophthalmol Vis Sci. 2021 Mar 1;62(3):3. doi: 10.1167/iovs.62.3.3.

ABSTRACT

PURPOSE: To investigate changes at a molecular level in the mouse corneal endothelium (CE) exposed to chronic cigarette smoke (CS).

METHODS: Pregnant mice (gestation days 18-20) were placed in a whole-body exposure smoking chamber, and a few days later pups were born. After 3.5 months of CS exposure, a ConfoScan4 scanning microscope was used to examine the corneal endothelial cells (CECs) of CS-exposed and control (Ct) mice. The CE was peeled under a microscope and maintained as four biological replicates (two male and two female) for CS-exposed and Ct mice; each replicate consisted of 16 CEs. The proteome of the CE was investigated through mass spectrometry.

RESULTS: The CE images of CS-exposed and Ct mice revealed a difference in the shape of CECs accompanied by a nearly 10% decrease in CEC density (P < 0.00003) following CS exposure. Proteome profiling identified a total of 524 proteins exhibiting statistically significant changes in CE from CS-exposed mice. Importantly, proteins associated with Descemet’s membrane (DM), including COL4α1, COL4α2, COL4α3, COL4α4, COL4α5, COL4α6, COL8α1, COL8α2, and FN1, among others, exhibited diminished protein levels in the CE of CS-exposed mice.

CONCLUSIONS: Our data confirm that exposure to CS results in reduced CEC density accompanied by diminished levels of multiple collagen and extracellular matrix proteins associated with DM.

PMID:33651877 | DOI:10.1167/iovs.62.3.3

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Nevin Manimala Statistics

Assessment of anammox, microalgae and white-rot fungi-based processes for the treatment of textile wastewater

PLoS One. 2021 Mar 2;16(3):e0247452. doi: 10.1371/journal.pone.0247452. eCollection 2021.

ABSTRACT

The treatability of seven wastewater samples generated by a textile digital printing industry was evaluated by employing 1) anammox-based processes for nitrogen removal 2) microalgae (Chlorella vulgaris) for nutrient uptake and biomass production 3) white-rot fungi (Pleurotus ostreatus and Phanerochaete chrysosporium) for decolorization and laccase activity. The biodegradative potential of each type of organism was determined in batch tests and correlated with the main characteristics of the textile wastewaters through statistical analyses. The maximum specific anammox activity ranged between 0.1 and 0.2 g N g VSS-1 d-1 depending on the sample of wastewater; the photosynthetic efficiency of the microalgae decreased up to 50% during the first 24 hours of contact with the textile wastewaters, but it improved from then on; Pleurotus ostreatus synthetized laccases and removed between 20-62% of the colour after 14 days, while the enzymatic activity of Phanerochaete chrysosporium was inhibited. Overall, the findings suggest that all microbes have great potential for the treatment and valorisation of textile wastewater after tailored adaptation phases. Yet, the depurative efficiency can be probably enhanced by combining the different processes in sequence.

PMID:33651835 | DOI:10.1371/journal.pone.0247452

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Nevin Manimala Statistics

Stable isotope analysis of human bone from Ganj Dareh, Iran, ca. 10,100 calBP

PLoS One. 2021 Mar 2;16(3):e0247569. doi: 10.1371/journal.pone.0247569. eCollection 2021.

ABSTRACT

We report here on stable carbon, nitrogen, and sulfur isotope values from bone collagen of human (n = 20) and faunal (n = 11) remains from the Early Neolithic site of Ganj Dareh, Iran, dating to ca. 10,100 cal. BP. Our focus explores how isotope values of human bone vary by age and sex, and evaluates dietary practices at this site. It also provides a baseline for future studies of subsistence in the early Holocene Central Zagros Mountains, from the site with the first evidence for human ovicaprid management in the Near East. Human remains include individuals of all age groups for dietary reconstruction, as well two Ottoman intrusive burials for temporal and cultural comparison. All analyzed individuals exhibited δ13C and δ15N values consistent with a diet based heavily on C3 terrestrial sources. There is no statistically significant difference between the isotopic compositions of the two sexes, though males appear to show larger variations compared to females. Interesting patterns in the isotopic compositions of the subadults suggested weaning children may be fed with supplements with distinctive δ13C values. Significant difference in sulfur isotope values between humans and fauna could be the earliest evidence of transhumance and could identify one older adult male as a possible transhumant shepherd. Both Ottoman individuals had distinctively different δ13C, δ15N, and δ34S values compared to the Neolithic individuals. This is the first large scale analysis of human stable isotopes from the eastern end of the early Holocene Fertile Crescent. It provides a baseline for future intersite exploration of stable isotopes and insight into the lifeways, health, and processes of neolithisation associated with the origins of goat domestication at Ganj Dareh and the surrounding Central Zagros.

PMID:33651827 | DOI:10.1371/journal.pone.0247569

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Nevin Manimala Statistics

National noncommunicable disease monitoring survey (NNMS) in India: Estimating risk factor prevalence in adult population

PLoS One. 2021 Mar 2;16(3):e0246712. doi: 10.1371/journal.pone.0246712. eCollection 2021.

ABSTRACT

BACKGROUND: The primary objective of National NCD monitoring survey (NNMS) was to generate national-level estimates of key NCD indicators identified in the national NCD monitoring framework. This paper describes survey study protocol and prevalence of risk factors among adults (18-69 years).

MATERIALS AND METHODS: NNMS was a national level cross-sectional survey conducted during 2017-18. The estimated sample size was 12,000 households from 600 primary sampling units. One adult (18-69 years) per household was selected using the World Health Organization-KISH grid. The study tools were adapted from WHO-STEPwise approach to NCD risk factor surveillance, IDSP-NCD risk factor survey and WHO-Global adult tobacco survey. Total of 8/10 indicators of adult NCD risk factors according to national NCD disease monitoring framework was studied. This survey for the first time estimated dietary intake of salt intake of population at a national level from spot urine samples.

RESULTS: Total of 11139 households and 10659 adults completed the survey. Prevalence of tobacco and alcohol use was 32.8% (95% CI: 30.8-35.0) and 15.9% (95% CI: 14.2-17.7) respectively. More than one-third adults were physically inactive [41.3% (95% CI: 39.4-43.3)], majority [98.4% (95% CI: 97.8-98.8)] consumed less than 5 servings of fruits and / or vegetables per day and mean salt intake was 8 g/day (95% CI: 7.8-8.2). Proportion with raised blood pressure and raised blood glucose were 28.5% (95% CI: 27.0-30.1) and 9.3% (95% CI: 8.3-10.5) respectively. 12.8% (95% CI: 11.2-14.5) of adults (40-69 years) had ten-year CVD risk of ≥30% or with existing CVD.

CONCLUSION: NNMS was the first comprehensive national survey providing relevant data to assess India’s progress towards targets in National NCD monitoring framework and NCD Action Plan. Established methodology and findings from survey would contribute to plan future state-based surveys and also frame policies for prevention and control of NCDs.

PMID:33651825 | DOI:10.1371/journal.pone.0246712

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Nevin Manimala Statistics

When women eat last: Discrimination at home and women’s mental health

PLoS One. 2021 Mar 2;16(3):e0247065. doi: 10.1371/journal.pone.0247065. eCollection 2021.

ABSTRACT

The 2011 India Human Development Survey found that in about a quarter of Indian households, women are expected to have their meals after men have finished eating. This study investigates whether this form of gender discrimination is associated with worse mental health outcomes for women. Our primary data source is a new, state-representative mobile phone survey of women ages 18-65 in Bihar, Jharkhand, and Maharashtra in 2018. We measure mental health using questions from the World Health Organization’s Self-Reporting Questionnaire. We find that, for women in these states, eating last is correlated with worse mental health, even after accounting for differences in socioeconomic status. We discuss two possible mechanisms for this relationship: eating last may be associated with worse mental health because it is associated with worse physical health, or eating last may be associated with poor mental health because it is associated with less autonomy, or both.

PMID:33651820 | DOI:10.1371/journal.pone.0247065

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Nevin Manimala Statistics

Magnitude and associated factors of peripheral cytopenia among HIV-infected children attending at University of Gondar Specialized Referral Hospital, Northwest Ethiopia

PLoS One. 2021 Mar 2;16(3):e0247878. doi: 10.1371/journal.pone.0247878. eCollection 2021.

ABSTRACT

BACKGROUND: Isolated or multi lineage cytopenia are the most common clinicopathological features and independently associated with increased risk of disease progression and death among human immunodeficiency virus infected children. In the study area, there is scarcity of data about the magnitude of various cytopenia.

OBJECTIVES: Aimed to determine the magnitude and associated factors of peripheral cytopenia among HIV infected children at the University of Gondar Specialized Referral Hospital ART clinic, Northwest Ethiopia.

METHODS: Institutional based cross-sectional study was conducted on 255 HIV infected children from January- April 2020. None probable convenient sampling technique was used to select the study participant. Socio demographic data were collected by pre tested structured questionnaire via face-to-face interview and their medical data were obtained from their follow-up medical records. Moreover, blood specimens were collected and examined for complete blood count, viral load and blood film, whereas stool specimens were collected and examined for intestinal parasites. Bi-variable and multi-variable logistic regression models were fitted to identify associated factors of cytopenia. P-Value <0.05 was considered as statistically significant.

RESULT: The overall magnitude of peripheral cytopenia was 38.9%. Anemia, leukopenia, lymphopenia, thrombocytopenia and bi-cytopenia were 21.2%, 12.2%, 11%, 1.6% and 3.9% respectively. Being in the age group of 2-10 years (AOR = 5.38, 95%CI 2.33-12.46), AZT based regimen (AOR = 5.44, 95%CI: 2.24-13.21), no eating green vegetables (AOR = 2.49, 95% CI: 1.26-4.92) and having plasma viral load >1000 copies /ml (AOR = 5.38, 95%CI: 2.22-13.03) showed significant association with anemia.

CONCLUSION: Anemia was the predominant peripheral cytopenia among HIV infected children in this study. It was strongly associated with AZT based drug type, age below 10 years and high viral load. Critical stress should be given for early investigation and management of cytopenia in addition to the use of alternative drug which leads to higher viral suppression and lower risk of toxicity issue.

PMID:33651817 | DOI:10.1371/journal.pone.0247878

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Nevin Manimala Statistics

Short-range template switching in great ape genomes explored using pair hidden Markov models

PLoS Genet. 2021 Mar 2;17(3):e1009221. doi: 10.1371/journal.pgen.1009221. Online ahead of print.

ABSTRACT

Many complex genomic rearrangements arise through template switch errors, which occur in DNA replication when there is a transient polymerase switch to an alternate template nearby in three-dimensional space. While typically investigated at kilobase-to-megabase scales, the genomic and evolutionary consequences of this mutational process are not well characterised at smaller scales, where they are often interpreted as clusters of independent substitutions, insertions and deletions. Here we present an improved statistical approach using pair hidden Markov models, and use it to detect and describe short-range template switches underlying clusters of mutations in the multi-way alignment of hominid genomes. Using robust statistics derived from evolutionary genomic simulations, we show that template switch events have been widespread in the evolution of the great apes’ genomes and provide a parsimonious explanation for the presence of many complex mutation clusters in their phylogenetic context. Larger-scale mechanisms of genome rearrangement are typically associated with structural features around breakpoints, and accordingly we show that atypical patterns of secondary structure formation and DNA bending are present at the initial template switch loci. Our methods improve on previous non-probabilistic approaches for computational detection of template switch mutations, allowing the statistical significance of events to be assessed. By specifying realistic evolutionary parameters based on the genomes and taxa involved, our methods can be readily adapted to other intra- or inter-species comparisons.

PMID:33651813 | DOI:10.1371/journal.pgen.1009221

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Nevin Manimala Statistics

Optimising passive surveillance of a neglected tropical disease in the era of elimination: A modelling study

PLoS Negl Trop Dis. 2021 Mar 2;15(3):e0008599. doi: 10.1371/journal.pntd.0008599. Online ahead of print.

ABSTRACT

BACKGROUND: Surveillance is an essential component of global programs to eliminate infectious diseases and avert epidemics of (re-)emerging diseases. As the numbers of cases decline, costs of treatment and control diminish but those for surveillance remain high even after the ‘last’ case. Reducing surveillance may risk missing persistent or (re-)emerging foci of disease. Here, we use a simulation-based approach to determine the minimal number of passive surveillance sites required to ensure maximum coverage of a population at-risk (PAR) of an infectious disease.

METHODOLOGY AND PRINCIPAL FINDINGS: For this study, we use Gambian human African trypanosomiasis (g-HAT) in north-western Uganda, a neglected tropical disease (NTD) which has been reduced to historically low levels (<1000 cases/year globally), as an example. To quantify travel time to diagnostic facilities, a proxy for surveillance coverage, we produced a high spatial-resolution resistance surface and performed cost-distance analyses. We simulated travel time for the PAR with different numbers (1-170) and locations (170,000 total placement combinations) of diagnostic facilities, quantifying the percentage of the PAR within 1h and 5h travel of the facilities, as per in-country targets. Our simulations indicate that a 70% reduction (51/170) in diagnostic centres still exceeded minimal targets of coverage even for remote populations, with >95% of a total PAR of ~3million individuals living ≤1h from a diagnostic centre, and we demonstrate an approach to best place these facilities, informing a minimal impact scale back.

CONCLUSIONS: Our results highlight that surveillance of g-HAT in north-western Uganda can be scaled back without substantially reducing coverage of the PAR. The methodology described can contribute to cost-effective and equable strategies for the surveillance of NTDs and other infectious diseases approaching elimination or (re-)emergence.

PMID:33651803 | DOI:10.1371/journal.pntd.0008599

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Nevin Manimala Statistics

Chronic obstructive Eustachian tube dysfunction: CT assessment with Valsalva maneuver and ETS-7 score

PLoS One. 2021 Mar 2;16(3):e0247708. doi: 10.1371/journal.pone.0247708. eCollection 2021.

ABSTRACT

Chronic obstructive Eustachian tube dysfunction (ETD) is a common disorder of the middle ear. In recent years, two main diagnostic tools have become available: Eustachian tube score (ETS-7) and computed tomography (CT) combined with Valsalva maneuver. The aim of this study is to evaluate the outcomes of ETS-7 and CT in a group of patients affected by middle ear atelectasis with a strong suspicion of ETD. Three males and nine females, affected by middle ear atelectasis with retraction of the TM were enrolled. Each patient underwent to Eustachian tube dysfunction evaluation adopting the ETS-7 score and a temporal bone CT with Valsalva maneuver. The ears analyzed at steady state were divided into 2 groups: ETS<7 group and ETS≥ 7 group. The same division was applied for the ears analyzed after the Valsalva maneuver: ETS<7 group and ETS≥ 7 group. ETs were categorized as “well defined” (WD) and “not defined” (ND). The results of the analysis of the ETS-7 score in all 24 ears showed that 42% presented ETS ≥7, while 58% had ETS <7, indicating a diagnosis of ETD. In the ETS<7 group after Valsalva, ET was visualized in 33% of patients. In the ETS≥7 group it was WD in 29% after the Valsalva manoeuver. In both groups the comparison between the visualization of the ET before and after the Valsalva manoeuver did not present a statistical difference. No correlation emerged between ET evaluation with CT scan during Valsalva maneuver and ETS-7 score. It confirms that there is not a gold standard for the study of ET dysfunction.

PMID:33651800 | DOI:10.1371/journal.pone.0247708

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Nevin Manimala Statistics

Stochastic simulation algorithms for Interacting Particle Systems

PLoS One. 2021 Mar 2;16(3):e0247046. doi: 10.1371/journal.pone.0247046. eCollection 2021.

ABSTRACT

Interacting Particle Systems (IPSs) are used to model spatio-temporal stochastic systems in many disparate areas of science. We design an algorithmic framework that reduces IPS simulation to simulation of well-mixed Chemical Reaction Networks (CRNs). This framework minimizes the number of associated reaction channels and decouples the computational cost of the simulations from the size of the lattice. Decoupling allows our software to make use of a wide class of techniques typically reserved for well-mixed CRNs. We implement the direct stochastic simulation algorithm in the open source programming language Julia. We also apply our algorithms to several complex spatial stochastic phenomena. including a rock-paper-scissors game, cancer growth in response to immunotherapy, and lipid oxidation dynamics. Our approach aids in standardizing mathematical models and in generating hypotheses based on concrete mechanistic behavior across a wide range of observed spatial phenomena.

PMID:33651796 | DOI:10.1371/journal.pone.0247046