Category: Statistics

PLoS One. 2021 Jul 29;16(7):e0255370. doi: 10.1371/journal.pone.0255370. eCollection 2021.

ABSTRACT

The aim of this study was to evaluate the potential of diatom (microalgae) biomass as a lice-reducing ingredient in salmon feed. The original hypothesis was based on the fact that polyunsaturated aldehydes (PUAs), e.g. 2-trans, 4-trans decadenial (A3) produced by diatoms can function as grazing deterrents and harm copepod development. Salmon lice (Lepeophtheirus salmonis) is a copepod, and we intended to test if inclusion of diatom biomass in the feed could reduce the infestation of lice on salmon. We performed experiments where salmon kept in tanks were offered four different diets, i.e. basic feed with diatoms, fish oil, Calanus sp. oil or rapeseed oil added. After a feeding period of 67 days a statistically representative group of fishes, tagged with diet group origin, were pooled in a 4000L tank and exposed to salmon lice copepodites whereafter lice infestation was enumerated. Salmon from all four diet groups had good growth with SGR values from 1.29 to 1.44% day-1 (increase from ca. 130 g to 350 g). At the termination of the experiment the number of lice on salmon offered diatom feed were statistically significantly lower than on salmon fed the other diets. Mean lice infestation values increased from diatom feed through Calanus and fish oil to standard feed with terrestrial plant ingredients. Analysis of the chemical composition of the different diets (fatty acids, amino acids) failed to explain the differences in lice infestation. The only notable result was that diatom and Calanus feed contained more FFA (free fatty acids) than feed with fish oil and the control feed. None of the potential deleterious targeted polyunsaturated aldehydes could be detected in skin samples of the salmon. What was exclusive for salmon that experienced reduced lice was diatom inclusion in the feed. This therefore still indicates the presence of some lice deterring ingredient, either in the feed, or an ingredient can have triggered production of an deterrent in the fish. An obvious follow up of this will be to perform experiments with different degrees of diatom inclusion in the feeds, i.e. dose response experiments combined with targeted PUA analyses, as well as to perform large scale experiments under natural conditions in aquaculture pens.

PMID:34324572 | DOI:10.1371/journal.pone.0255370

PLoS One. 2021 Jul 29;16(7):e0255270. doi: 10.1371/journal.pone.0255270. eCollection 2021.

ABSTRACT

The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become the current health concern and threat to the entire world. Thus, the world needs the fast recognition of appropriate drugs to restrict the spread of this disease. The global effort started to identify the best drug compounds to treat COVID-19, but going through a series of clinical trials and our lack of information about the details of the virus’s performance has slowed down the time to reach this goal. In this work, we try to select the subset of human proteins as candidate sets that can bind to approved drugs. Our method is based on the information on human-virus protein interaction and their effect on the biological processes of the host cells. We also define some informative topological and statistical features for proteins in the protein-protein interaction network. We evaluate our selected sets with two groups of drugs. The first group contains the experimental unapproved treatments for COVID-19, and we show that from 17 drugs in this group, 15 drugs are approved by our selected sets. The second group contains the external clinical trials for COVID-19, and we show that 85% of drugs in this group, target at least one protein of our selected sets. We also study COVID-19 associated protein sets and identify proteins that are essential to disease pathology. For this analysis, we use DAVID tools to show and compare disease-associated genes that are contributed between the COVID-19 comorbidities. Our results for shared genes show significant enrichment for cardiovascular-related, hypertension, diabetes type 2, kidney-related and lung-related diseases. In the last part of this work, we recommend 56 potential effective drugs for further research and investigation for COVID-19 treatment. Materials and implementations are available at: https://github.com/MahnazHabibi/Drug-repurposing.

PMID:34324563 | DOI:10.1371/journal.pone.0255270

PLoS One. 2021 Jul 29;16(7):e0255146. doi: 10.1371/journal.pone.0255146. eCollection 2021.

ABSTRACT

BACKGROUND: The comparatively straightforward and cheaper light-emitting diode fluorescent microscope (LEDFM) was suggested by WHO to replace conventional microscope in tuberculosis (TB) laboratories. However, the comparable efficacy of each of those techniques differs from laboratory to laboratory. We investigated the efficacy of LEDFM for the diagnosis of tuberculous lymphadenitis (TBLN) patients.

METHODS: A cross-sectional study was conducted on 211 samples from clinically suspected tuberculous lymphadenitis patients. Three smears were prepared from FNA on microscope slides for cytomorphology study, Auramine O (AO), and for Ziehl-Neelsen (ZN) staining. The left-over samples were inoculated onto Lowenstein-Jensen (LJ) media. Statistical analysis was done using STATA version 11. The sensitivity, specificity, positive and negative predictive values were calculated by considering the culture results as the gold standard using a 95% confidence interval.

RESULTS: Among 211 samples 49.7% (105) were positive by cytomorphology, 32.7% (69) by LEDFM, 23.69% (50) by LJ culture, and 13.7% (29) by ZN. Compared to the gold standard sensitivity of ZN, LEDFM, and cytomorphology were 30% [95% CI: 17.9-44.6], 66% [95% CI: 51.2-78.8] 78% [95% CI: 64-88.5], respectively. The specificity of ZN, LEDFM, and cytomorphology was 91.3% [95% CI: 85.8-95.2], 77.6% [95% CI: 70.4-83.8], 58.8% [95% CI: 50.7-66.5], respectively.

CONCLUSION: LED fluorescence microscopy gives a legitimate option in contrast to conventional ZN techniques in terms of its higher sensitivity, a bit lower specificity, time-saving, and minimal effort.

PMID:34324565 | DOI:10.1371/journal.pone.0255146

PLoS One. 2021 Jul 29;16(7):e0255240. doi: 10.1371/journal.pone.0255240. eCollection 2021.

ABSTRACT

Metabolomic data processing pipelines have been improving in recent years, allowing for greater feature extraction and identification. Lately, machine learning and robust statistical techniques to control false discoveries are being incorporated into metabolomic data analysis. In this paper, we introduce one such recently developed technique called aggregate knockoff filtering to untargeted metabolomic analysis. When applied to a publicly available dataset, aggregate knockoff filtering combined with typical p-value filtering improves the number of significantly changing metabolites by 25% when compared to conventional untargeted metabolomic data processing. By using this method, features that would normally not be extracted under standard processing would be brought to researchers’ attention for further analysis.

PMID:34324558 | DOI:10.1371/journal.pone.0255240

PLoS One. 2021 Jul 29;16(7):e0255010. doi: 10.1371/journal.pone.0255010. eCollection 2021.

ABSTRACT

BACKGROUND: An ethnobotanical expedition was conducted to document the traditional ethnobotanical (TEB) uses of wild flora of Dawarian and Ratti Gali villages of District Neelam, Azad Jammu and Kashmir (AJK) Pakistan. District Neelam has rich plant diversity and is hub of many endemic plant species while the study areas are not yet explored. The research area: Dawarian and Rati Gali (DRG) area is mountaineous terrain and villages are located on far and farther distances. DRG area has rich biocultural and plant diversity comprising of different ethnic groups of Kashmir state. The current research was aimed to explore and document traditional medicines (TEMs) and other domestic and commercial uses of wild plants. This study will assist to evaluate conservation and commercial worth of wild flora which can be potential candidate for drug discovery through ethnopharmacological analysis.

METHODS: The current quantitative ethnobotanical research was carried out in 2018 by interviewing 150 indigenous informants (90 male and 60 female) of DRG area using questionnaire applying structured and semi structured interview methodology. Data analysis was analyzed by using quantitative ethnobotanical statistical tools such as fidelity level (FL), informant consensus factor (ICF), Spearman’s rank correlation (SRC) and data matrix ranking (DMR).

RESULTS: The indigenous people of DRG area use wild plants in their daily life to cope life necessities i.e. food, vegetables, fodder, fuel, shelter, timber and herbal medicines. TEMs are primarily used to cure different infirmities like diabetics, asthma, dysentery, constipation, cold, fever, joint pain, wound healing, cancer, cardiovascular disorders, epilepsy, kidney infections and many types of skin diseases. Current study revealed the data of 103 wild plants species belonging to 46 plant families from selected areas of District Neelum, AJK. Results depicted that Asteraceae ranked 1st (12 plants spp). Among plant parts used leaf ranked 1st (18%), followed by seed (17%) and root (13%). While prevalent form recipe mode was decoction (20%), followed by powder (17%) and extract (14%) and fodder was highest (37%) EB use-form fodder, followed by food (32%) and fuel (17%). Quantitative ethnobotanical analysis (QEA) was carried to find the reliability and novelty of the study. Five plant species including Berberis lyceum (FL = 97.78%), Isodon rugosus (FL = 95.71%), Saussurea lappa (FL = 94.74%), Aconitum heterophyllum (FL = 92.71%) and Taxus baccata (91.58%) had shown high fidelity level which confirmed that these plants have high medicinal worth in study area. The highest value (0.94) of ICF was for diseases group “tuberculosis and leucorrhea”, followed by stomachache and flatulence (0.93), diabetics and blood pressure (0.92) and asthma and chest infections (0.88). For other uses fuel with ICF (0.83) ranked first and second was hedging and thatching (ICF = 0.82) where people use plants or their parts for construction. Spearman’s rank correlation (SRC) test indicated that number of TEB uses increases if number of species is increased. Jaccard index (JI) analysis depicted that 56.31% plants are being used as TEMs which are first time explored from the study area. While 26.21% plants are being used in different TEB uses which are different from past cited literature. These novel findings of research indicate that wild flora of the study area has great potential for novel drug discovery and provision of materialist services for the indigenous communities.

CONCLUSION: The present research revealed that TEMs uses of 58 plants are novel being first time reported from the study area (DRG) of District Neelam of AJK. The results showed that plants like Acer cappadocicum, Ajuga bracteosa and Swertia paniculata are used to cure diabetes, Viscum album, Viola canescens, Taxus baccata are used for cure of cancer, Isodon rugosus, Polygala chinensis are used in TEMs for treating cardiovascular disorders and Anaphalis triplinervis is used for epilepsy. Berberis lyceum, Ajuga bracteosa, Aconitum heterophyllum, Bistorta amplexicaule, Saussurea lapa and Jurinea dolomiaea are severely threatened and there is urgent need to do conservation measures for available of valuable MPs to the indigenous communities for life necessities and for future research. The current study will also be useful addition in ethnobotanical database, preservation of traditional culture and drug discovery and drug development through future ethnopharmacological research.

PMID:34324561 | DOI:10.1371/journal.pone.0255010

Nutr Cancer. 2021 Jul 29:1-12. doi: 10.1080/01635581.2021.1957486. Online ahead of print.

ABSTRACT

We aimed to investigate the association of fruits and vegetables (FVs) and their all subgroups intakes with breast cancer (BC) risk in Iranian women.

The present case-control study conducted on 150 age-matched women with newly diagnosed BC and apparently healthy controls. Anthropometric measures were collected and eventually, the mean intakes of total FVs and each subgroup were obtained from a validated 147-item food frequency questionnaire. Multivariate regression analysis was used to estimate odds ratios (OR) with 95% confidence intervals (CI).

Our findings revealed that the intake of only dark yellow vegetable was significantly higher in BC patients (P = 0.03) after controlling for covariates. OR of BC across tertiles of FVs intake, showed that there was not any statistical association of total FVs (OR: 1.83, CI: 0.54-6.24, P-trend = 0.3) and their subgroups intakes with BC risk. Except for berry fruits intake which was adversely associated with BC risk (OR: 0.36, CI: 0.09-1.37, P-trend = 0.02).

Our findings did not support the hypothesis that higher total FVs and their subgroups intakes reduce BC risk and suggested that only higher berry fruits intake may have an association with lower BC risk.

PMID:34323618 | DOI:10.1080/01635581.2021.1957486

J Plast Surg Hand Surg. 2021 Jul 29:1-6. doi: 10.1080/2000656X.2021.1952211. Online ahead of print.

ABSTRACT

BACKGROUND: Near-infrared spectroscopy (NIRS) is widely used to assess flap perfusions by measuring tissue oxygen saturation (StO₂). However, the StO₂ level for the onset of perfusion failure is still a controversial issue.

AIM: This study proposes a new threshold of StO₂ level for detecting the onset of perfusion failure as early as possible to increase flap salvage rates.

METHODS: Twenty patients undergoing flap surgery were included in this study – 13 flaps were implemented to cover defects that occurred due to trauma and 7 flaps to hide imperfections that occurred after cancer treatment. Thirteen flaps were in the lower extremity, six in the mandible, and one in the breast. NIRS was used to measure StO₂ in 240 flap regions of the 20 patients to determine flap viability using descriptive statistics.

RESULTS: The mean StO₂ values from healthy flap and control regions were obtained as 81.6% ± 0.36 and 82% ± 0.18, respectively. The lowest StO₂ value of 77.2% was defined as the onset of a vascular complication at a probability of 99.74% by subtracting three times the standard deviation from the mean StO₂ of healthy flaps. Vascular complications were observed from 21 regions in the four flaps with StO₂ values lower than 77.2%, but only one was lost.

CONCLUSION: The threshold value for the onset of perfusion failure was a 5% decrease from the expected value, much lower than previously described thresholds that may facilitate the detection of perfusion failure in the early stage and increase salvage rates in flap revisions.

PMID:34323644 | DOI:10.1080/2000656X.2021.1952211

J Pain Palliat Care Pharmacother. 2021 Jul 29:1-5. doi: 10.1080/15360288.2021.1943597. Online ahead of print.

ABSTRACT

Effective strategies that are evidence-based and non-addictive are needed to manage chronic pain and combat the opioid crisis. One potential strategy is to utilize a shared medical appointment (SMA), which is a model of providing clinical care in a group setting with multiple healthcare team members for comprehensive pain management. The purpose of this retrospective chart review is to evaluate the impact of a pain management SMA at the William S. Middleton Veterans Affairs (VA) West Clinic on opioid use and behaviors. Quantitative and qualitative data was obtained from the electronic medical record of 16 Veterans who participated in the pain SMA and analyzed using descriptive statistics. In addition to a reduction in opioid doses six months post SMA, participants gained non-pharmacological referrals, addition of non-opioid pain medications, and a mix of didactic and experiential education on pharmacologic and non-pharmacologic treatment modalities to help manage their chronic pain. This SMA allowed for greater access to healthcare professionals with a sole focus on pain management and provided Veterans with a holistic approach to their pain management.

PMID:34323646 | DOI:10.1080/15360288.2021.1943597

J Exp Psychol Learn Mem Cogn. 2021 Jul 29. doi: 10.1037/xlm0000894. Online ahead of print.

ABSTRACT

Theories of memory consolidation suggest that initially rich, vivid memories become more gist-like over time. However, it is unclear whether gist-like representations reflect a loss of detail through degradation or the blending of experiences into statistical averages, and whether the strength of these representations increases, decreases, or remains stable over time. We report three behavioral experiments that address these questions by examining distributional learning during spatial navigation. In Experiment 1, human subjects navigated a virtual maze to find hidden objects with locations varying according to spatial distributions. After 15 minutes, 1 day, 7 days, or 28 days, we tested their navigation performance and explicit memory. In Experiment 2, we created spatial distributions with no object at their mean locations, thereby disentangling learned object exemplars from statistical averages. In Experiment 3, we created only a single, bimodal distribution to avoid possible confusion between distributions and administered tests after 15 minutes or 28 days. Across all experiments, and for both navigation and explicit tests, representations of the spatial distributions were present soon after exposure, but then receded over time. These findings suggest gist-like representations do not improve over time, helping to clarify the temporal dynamics of consolidation in human learning and memory. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

PMID:34323577 | DOI:10.1037/xlm0000894

Psychol Methods. 2021 Jul 29. doi: 10.1037/met0000314. Online ahead of print.

ABSTRACT

hen multiple mediators exist on the causal pathway from treatment to outcome, path analysis prevails for disentangling indirect effects along paths linking possibly several mediators. However, separately evaluating each indirect effect along different posited paths demands stringent assumptions, such as correctly specifying the mediators’ causal structure, and no unobserved confounding among the mediators. These assumptions may be unfalsifiable in practice and, when they fail to hold, can result in misleading conclusions about the mediators. Nevertheless, these assumptions are avoidable when substantive interest is in inference about the indirect effects specific to each distinct mediator. In this article, we introduce a new definition of indirect effects called interventional indirect effects from the causal inference and epidemiology literature. Interventional indirect effects can be unbiasedly estimated without the assumptions above while retaining scientifically meaningful interpretations. We show that under a typical class of linear and additive mean models, estimators of interventional indirect effects adopt the same analytical form as prevalent product-of-coefficient estimators assuming a parallel mediator model. Prevalent estimators are therefore unbiased when estimating interventional indirect effects-even when there are unknown causal effects among the mediators-but require a different causal interpretation. When other mediators moderate the effect of each mediator on the outcome, and the mediators’ covariance is affected by treatment, such an indirect effect due to the mediators’ mutual dependence (on one another) cannot be attributed to any mediator alone. We exploit the proposed definitions of interventional indirect effects to develop novel estimators under such settings. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

PMID:34323583 | DOI:10.1037/met0000314