Tag: nevin manimala

Bioinformatics. 2024 May 25:btae334. doi: 10.1093/bioinformatics/btae334. Online ahead of print.

ABSTRACT

SUMMARY: Ancestral recombination graphs (ARGs) encode the ensemble of correlated genealogical trees arising from recombination in a compact and efficient structure, and are of fundamental importance in population and statistical genetics. Recent breakthroughs have made it possible to simulate and infer ARGs at biobank scale, and there is now intense interest in using ARG-based methods across a broad range of applications, particularly in genome-wide association studies (GWAS). Sophisticated methods exist to simulate ARGs using population genetics models, but there is currently no software to simulate quantitative traits directly from these ARGs. To apply existing quantitative trait simulators users must export genotype data, losing important information about ancestral processes and producing prohibitively large files when applied to the biobank-scale datasets currently of interest in GWAS. We present tstrait, an open-source Python library to simulate quantitative traits on ARGs, and show how this user-friendly software can quickly simulate phenotypes for biobank-scale datasets on a laptop computer.

AVAILABILITY AND IMPLEMENTATION: tstrait is available for download on the Python Package Index. Full documentation with examples and workflow templates is available on https://tskit.dev/tstrait/docs/, and the development version is maintained on GitHub (https://github.com/tskit-dev/tstrait).

PMID:38796683 | DOI:10.1093/bioinformatics/btae334

Child Psychiatry Hum Dev. 2024 May 25. doi: 10.1007/s10578-024-01707-0. Online ahead of print.

ABSTRACT

This randomized controlled trial tested the Family Assessment and Feedback Intervention (FAFI), a new intervention to enhance family engagement with emotional and behavioral health services. The FAFI is a guided conversation with families about results of their multidimensional assessment that is set in the context of motivational enhancement. It differs from other assessment-with-feedback interventions by extending the focus of assessment beyond the target child to parents and the family environment, addressing parental emotional and behavioral problems and competencies, spanning a broad range of children’s and parents’ strengths and difficulties, and being generalizable to many settings and practitioners. Participants were 81 families in primary care pediatrics. The FAFI was associated with a significant increase in parental mental health literacy and with an increase in parental attitudinal engagement with health supports and services that closely approached statistical significance (p = .052), while controlling for children’s age and gender and family socioeconomic status.

PMID:38796676 | DOI:10.1007/s10578-024-01707-0

Arch Dermatol Res. 2024 May 25;316(6):280. doi: 10.1007/s00403-024-03112-y.

NO ABSTRACT

PMID:38796663 | DOI:10.1007/s00403-024-03112-y

Arch Dermatol Res. 2024 May 25;316(6):281. doi: 10.1007/s00403-024-03132-8.

ABSTRACT

Exposure to solar ultraviolet (UV) radiation and use of UV-emitting tanning devices are known risk factors for skin cancer. Few studies have explored the interaction between these risk factors, namely how the risk of skin cancer increases among those who both have been exposed to high levels of natural sunlight and regularly use tanning beds. Nurses’ Health Study II followed 116,430 women, aged 25-42, from 1991 to 2011. Cumulative average UV exposure was based on participants’ residences at follow-up periods. History of severe sunburn during ages 15-20 was used as a proxy for early-life sunlight exposure. Tanning bed use in early life data was collected. Participants reported melanoma, basal cell carcinoma (BCC), and squamous cell carcinoma (SCC) diagnoses. We built multivariable Cox regression models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for risk of skin cancer associated with joint effects of sunlight exposure and tanning bed use. Participants with high sunlight exposure and tanning bed use during high school/college had an increased risk of BCC (HR = 1.53, 95% CI 1.37-1.71, P_interaction=0.01; vs. low sun exposure and no tanning bed use). Participants with a history of severe sunburns and tanning bed use during high school/college were at increased risk of BCC (HR = 1.62, 95% CI 1.47-1.79, P_interaction=0.02; vs. no sunburns and no tanning bed use). No significant interactions were found between sunlight exposure and tanning bed use on SCC and melanoma risk. We found significant interactions between sunlight exposure and tanning bed use on the risk of BCC.

PMID:38796657 | DOI:10.1007/s00403-024-03132-8

Mol Biol Rep. 2024 May 25;51(1):684. doi: 10.1007/s11033-024-09627-x.

ABSTRACT

BACKGROUND: Indomethacin is an anti-inflammatory drug that causes ulcers on the gastric mucosa due to its use. Probiotic bacteria are live microorganisms, and it has been stated by various studies that these bacteria have antioxidant and anti-inflammatory effects. In this study, we investigated the possible protective effect of various types of probiotic bacteria (Lactobacillus rhamnosus, Lactobacillus fermentum, and Lactobacillus brevis) against acute gastric mucosal damage caused by indomethacin.

METHODS: Control group – Physiological saline was administered daily for 10 days. Indo group-Physiological saline was administered daily for 10 days. Ranitidine + Indo group 5 mg/kg ranitidine dose was administered daily for 5 days. On day 11, a single dose of 100 mg/kg of indomethacin was given to the same group. Probiotic + Indo group 1 ml/kg of oral probiotic bacteria was administered daily for 10 days. On day 11, a single 100 mg/kg dose of indomethacin was given. After the application, the rats were anesthetized with ketamine xylazine, killed under appropriate conditions, the abdominal cavity was opened and the stomach tissues were removed. The obtained gastric tissues were used in the biochemical and histopathological analyses discussed below. All data were statistically evaluated by one-way ANOVA using SPSS 20.00, followed by Duncan Post hoc test. The data were expressed as mean ± SD. P < 0.05 was considered statistically significant.

RESULTS: As a result, the administration of indomethacin caused gastric damage, stimulating oxidative stress, inflammation, and apoptosis. We found that the use of probiotic bacteria reduces oxidative stress (TOC), increases the activity of antioxidant enzymes (TAC), suppresses inflammation (IL-6 and Tnf-α), and inhibits apoptosis (Bax and Bcl-2) (P < 0.05).

CONCLUSION: Probiotic treatment can mitigate gastric damage and apoptosis caused by indomethacin-induced gastric damage in rats. Probiotic also enhances the restoration of biochemical oxidative enzymes as it has anti-inflammatory, antioxidant, and antiapoptotic properties.

PMID:38796650 | DOI:10.1007/s11033-024-09627-x

Arch Dermatol Res. 2024 May 25;316(6):273. doi: 10.1007/s00403-024-02928-y.

ABSTRACT

BACKGROUND: Recent data reveal a marked rise in the detection and mortality rates of Desmoplastic Malignant Melanoma (DMM). This trend underscores the imperative for an in-depth analysis of DMM’s epidemiology, which is crucial for the formulation of precise medical and public health strategies. This investigation seeks to elucidate the variations in the incidence and mortality of DMM over a 15-year period (2005-2019).

METHODS: Data on DMM patients was sourced from the Surveillance, Epidemiology, and End Results (SEER) database. Both incidence and incidence-based mortality rates (IBM) were directly extracted from the SEER database. Joinpoint regression was used to analyze and calculate the average annual percent change (AAPC) and its 95% confidence interval (CI).

RESULTS: Between 2005 and 2019, 3,384 DMM cases were identified, boasting an age-adjusted incidence rate of 36.3 cases per 1000,000 person-years (95% CI 3.51-3.76) and an IBM of 1.65cases per 1000,000 person-years (95% CI 1.57-1.74). Of these, 2,353 were males (69.53%) and 1,031 were females (30.47%). There were 1894 patients (55.97%) who were over 70 years old. Predominantly, DMM lesions manifested in exposed areas: Limbs (955, 28.22%), Face (906, 26.77%), and Scalp and Neck (865, 25.56%). The incidence of DMM increased significantly at a rate of APC = 0.9% during 2005-2019, while the incidence-based mortality showed a significant upward trend (APC = 7%) during 2005-2012, and slowly increasing trend (APC = 0.6%) during 2012-2019. In contrast to the modest upward trajectory in female incidence and mortality, male incidence initially surged, later declining, while male mortality peaked and stabilized post-2012. The primary sites for incidence and mortality were chronically sun-exposed areas: Face, Scalp and Neck, and Limbs.

CONCLUSIONS: In recent years, the incidence and incidence-based mortality of DMM have significantly increased. Each subgroup analysis has different trends, and these trends can provide better support for our exploration of DMM.

PMID:38796649 | DOI:10.1007/s00403-024-02928-y

Pediatr Surg Int. 2024 May 25;40(1):138. doi: 10.1007/s00383-024-05731-y.

ABSTRACT

PURPOSE: To describe the long-term bowel function of anorectal malformation (ARM) patients and explore the potential influence factors.

METHODS: ARM patients with follow-up data > 10 years were included. Cases of cloaca, Currarino syndrome, and VACTERL syndrome were excluded. Rintala score and PedsQL 4.0 were used to assess bowel function score (BFS) and quality of life (QoL). Based on the results, patients were divided into satisfactory group with BFS ≥ 17 and unsatisfactory group with it < 17. Comparisons between the groups were made.

RESULTS: Among the 81 patients were 44 males and 37 females. Follow-up time was 138 (126,151) months. 16 (19.75%) patients had associated anomalies. 23 (28.40%) patients had reoperations, and fistula recurrence was the most common reason. BFS of the patients was 20 (18,20). QoL score was 100 (100,100), which correlated positively with BFS (r = 0.648, P < 0.001). The satisfactory and the unsatisfactory groups had 69 and 12 cases, and their BFS were 20 (20,20) and 11 (8,15) respectively, which had statistical difference (P < 0.001). Total QoL score and psycho-social health score of the unsatisfactory group were lower (P < 0.001). Only reoperations were statistically different between the groups (P < 0.001).

CONCLUSIONS: Long-term (> 10 years) bowel function of ARM patients is good in this study. Defecation problems have negative impacts on QoL and mainly affects their psycho-social health. Primary anorectoplasty is extremely important. Reoperations, which are most commonly seen in recto-urethral fistula recurrence, adversely affect the outcome.

PMID:38796646 | DOI:10.1007/s00383-024-05731-y

Sci Rep. 2024 May 25;14(1):11954. doi: 10.1038/s41598-024-62767-9.

ABSTRACT

A comprehensive mathematical model is proposed to study two strains of dengue virus with saturated incidence rates and quarantine measures. Imperfect dengue vaccination is also assumed in the model. Existence, uniqueness and stability of the proposed model are proved using the results from fixed point and degree theory. Additionally, well constructed Lyapunov function candidates are also applied to prove the global stability of infection-free equilibria. It is also demonstrated that the model is generalized Ulam-Hyers stable under some appropriate conditions. The model is fitted to the real data of dengue epidemic taken from the city of Espirito Santo in Brazil. For the approximate solution of the model, a non-standard finite difference(NSFD) approach is applied. Sensitivity analysis is also carried out to show the influence of different parameters involved in the model. The behaviour of the NSFD is also assessed under different denominator functions and it is observed that the choice of the denominator function could influence the solution trajectories. Different scenario analysis are also assessed when the reproduction number is below or above one. Furthermore, simulations are also presented to assess the epidemiological impact of dengue vaccination and quarantine measures for infected individuals.

PMID:38796642 | DOI:10.1038/s41598-024-62767-9

Bone Marrow Transplant. 2024 May 25. doi: 10.1038/s41409-024-02316-0. Online ahead of print.

ABSTRACT

In the case of donor/recipient rhesus (Rh)-incompatibility after allogeneic hematopoietic stem cell transplantation (alloHSCT), the transfusion policy in France is to transfuse red blood cells (RBC) in the donor’s Rh phenotype from the day of transplantation, leading to a risk of allo-immunization, either of donor or recipient origin. In this single-center retrospective study, the incidence of donor/recipient Rh incompatibility was 7.1% over an 8-year period including 1012 alloHSCT. Six of 58 evaluable patients (10.3%) developed alloantibodies to RBC antigens within one year of alloHSCT. None of these allo-immunizations were directed against the donor-mismatched Rh antigens and none could have been prevented by the transfusion of recipient and donor Rh-compatible RBC units. None of these allo-immunizations led to immune-mediated hemolytic anemia. We observed a statistically significant higher incidence of chronic GVHD among patients with anti-RBC allo-immunization. In the context of donor/recipient Rh incompatibility, the transfusion of packed RBC units in the donor’s Rh phenotype from the day of alloHSCT is feasible and not associated with a high risk of allo-immunization. The generalization of this strategy could be discussed even when donor and recipient Rh phenotypes could be respected, to allow the preservation of units of infrequent phenotypes for other indications.

PMID:38796632 | DOI:10.1038/s41409-024-02316-0

Arch Dermatol Res. 2024 May 25;316(6):284. doi: 10.1007/s00403-024-03105-x.

ABSTRACT

This study investigates the impact of Free-to-Publish (F2P) versus Pay-to-Publish (P2P) models in dermatology journals, focusing on their differences in terms of journal metrics, Article Processing Charges (APCs), and Open Access (OA) status. Utilizing k-means clustering, the research evaluates dermatology journals based on SCImago Journal Rankings (SJR), H-Index, and Impact Factor (IF), and examines the correlation between these metrics, APCs, and OA status (Full or Hybrid). Data from the SCImago Journal Rank and Journal Citation Report databases were used, and metrics from 106 journals were normalized and grouped into three tiers.The study reveals a higher proportion of F2P journals, especially in higher-tier journals, indicating a preference for quality-driven research acceptance. Conversely, a rising proportion of P2P journals in lower tiers suggests potential bias towards the ability to pay. This disparity poses challenges for researchers from less-funded institutions or those early in their careers. The study also finds significant differences in APCs between F2P and P2P journals, with hybrid OA being more common in F2P.Conclusively, the study highlights the disparities in dermatology journals between F2P and P2P models and underscores the need for further research into authorship demographics and institutional affiliations in these journals. It also establishes the effectiveness of k-means clustering as a standardized method for assessing journal quality, which can reduce reliance on potentially biased individual metrics.

PMID:38796628 | DOI:10.1007/s00403-024-03105-x