Nevin Manimala

BMC Genomics. 2024 Nov 15;25(1):1088. doi: 10.1186/s12864-024-10936-5.

ABSTRACT

BACKGROUND: Genomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds-Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations.

RESULTS: We identified 3,893 CNV regions (CNVRs) covering 19.15 Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60 kb to 488.0 kb, with an average size of 4.92 kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation (GBE1 and SOD1), heat stress adaptation (HSPA13, DNAJC18, and DNAJC8) and resistance to tick infestations (BoLA and KRT33A). In addition, variance stabilizing transformation (V_ST) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits.

CONCLUSIONS: Our comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability.

PMID:39548375 | DOI:10.1186/s12864-024-10936-5

BMC Infect Dis. 2024 Nov 15;24(1):1308. doi: 10.1186/s12879-024-10117-5.

ABSTRACT

Serological diagnostic tests are available that measure antibody levels against SARS-CoV-2 antigens. We utilized the Vaxarray Coronavirus (CoV) seroassay, which measures SARS-CoV-2 IgG antibodies against the full-length spike protein (FLS), receptor binding domain (RBD), and S2 extracellular domain (ECD). Previous serological studies have used reference values that have not been validated and require many samples. Here, we show statistically established reference values determined using the upper tail of the Student t-distribution method. The target population was any personnel age 18 years and older working on a U.S. Navy ship, and vaccinated with Wuhan variant. The relative fluorescence mean (RFM) reference values for the full-length spike protein, RBD, and S2 ECD were 17,731, 13,990 and 9096, respectively. By using generalized non-parametric regression and reference values for the RBD spike protein and S2 ECD of SARS-CoV-2, this study was able to distinguish vaccine-mediated immune responses from natural infections. We provide the method and statistical code as a resource to determine future reference values for other serological assays.

PMID:39548371 | DOI:10.1186/s12879-024-10117-5

BMC Med Res Methodol. 2024 Nov 15;24(1):283. doi: 10.1186/s12874-024-02399-9.

ABSTRACT

BACKGROUND: The use of the multistate Markov chain model is a valuable tool for studying child undernutrition. This allows us to examine the trends of children’s transitions from one state to multiple states of undernutrition.

OBJECTIVES: In this study, our objective was to estimate the median duration for a child to first transition from one state of undernutrition to another as well as their first recurrence of undernutrition and also to analyze the typical duration of undernourishment. This involves understanding the central tendency of these transitions and durations in the context of longitudinal data.

METHODS: We used a longitudinal dataset from the Young Lives cohort study (YLCS), which included approximately 1997 Ethiopian children aged 1-15 years. These children were selected from five regions and followed through five survey rounds between 2002 and 2016. The surveys provide comprehensive health and nutrition data and are designed to assess childhood poverty. To analyze this dataset, we employed a Markov chain regression model. The dataset constitutes a cohort with repeated measurements, allowing us to track the transitions of individual children across different states of undernutrition over time.

RESULTS: The findings of our study indicate that 46% of children experienced concurrent underweight, stunting, and wasting (referred to as USW). The prevalence of underweight and stunted concurrent condition (US) was 18.7% at baseline, higher among males. The incidence density of undernutrition was calculated at 22.5% per year. On average, it took 3.02 months for a child in a wasting state to transition back to a normal state for the first time, followed by approximately 3.05 months for stunting and 3.89 months for underweight. It is noteworthy that the median duration of undernourishment among children in the US (underweight and stunted concurrently) state was 48.8 months, whereas those concurrently underweight and wasting experienced a median of 45.4 months in this state. Additionally, rural children (HR = 1.75; 95% CI: 1.53-1.97), those with illiterate fathers (HR = 1.50; 95% CI: 1.38-1.62) and mothers (HR = 1.45; 95% CI: 1.02-3.29), and those in households lacking safe drinking water (HR = 1.70; 95% CI: 1.26-2.14) or access to cooking fuel (HR = 1.95; 95% CI: 1.75-2.17) exhibited a higher risk of undernutrition and a slower recovery rate.

CONCLUSIONS: This study revealed that rural children, especially those with illiterate parents and households lacking safe drinking water but cooking fuels, face an increased risk of undernutrition and slower recovery.

PMID:39548366 | DOI:10.1186/s12874-024-02399-9

BMC Cardiovasc Disord. 2024 Nov 15;24(1):648. doi: 10.1186/s12872-024-04291-2.

ABSTRACT

BACKGROUND: Anemia represents a commonly reported comorbidity in patients diagnosed with heart failure (HF), related with a higher risk of unfavorable outcomes such as recurrent hospitalizations and mortality. There is a lack of evidence in Latin America regarding this topic. Our aim was to evaluate the prognostic value of the diagnosis of anemia in patients from the Colombian Heart Failure Registry (RECOLFACA).

METHODS: RECOLFACA registry included adult ambulatory patients with HF in 60 medical centers in Colombia during 2017-2019. Baseline characteristics of patients diagnosed with anemia and those without anemia were compared. The main outcome was all-cause mortality. A Cox proportional hazards regression model was used to evaluate the factors linked to the main outcome in patients with anemia. A statistically significant p-value was < 0.05.

RESULTS: From the 2528 patients included in RECOLFACA, 2409 had at least one available hemoglobin value, and 726 (30.1%) corresponded to a diagnosis of anemia. Patients with anemia were significantly older, and had a higher prevalence of comorbidities, especially hypertension, type 2 diabetes, and chronic kidney disease (CKD). Patients without anemia had significantly lower mortality rate of 0.30 per 1000 person-years (95% CI 0.26-0.35), compared to patients diagnosed with anemia who had a mortality rate of 0.42 per 1000 person-years (95% CI 0.26-0.98) (p < 0.001). Lastly, the multivariate model results showed that the presence of an anemia diagnosis was associated with a significantly greater risk of mortality (HR 1.48; 95% CI 1.06, 2.05, p < 0.001).

CONCLUSIONS: Anemia represents a highly prevalent comorbidity in patients with HF in Colombia and is also related with higher mortality in ambulatory patients during follow-up period. Our results highlight the relevance of anemia in the pathophysiology of HF. Nevertheless, due to its observational nature, out study results must be validated and further explored in future studies to elucidate the potential underlying mechanisms of this association.

PMID:39548365 | DOI:10.1186/s12872-024-04291-2

BMC Cardiovasc Disord. 2024 Nov 16;24(1):652. doi: 10.1186/s12872-024-04317-9.

ABSTRACT

BACKGROUND: Cardiovascular disease (CVD) is a major global health concern with increasing incident cases and deaths. Homocysteine (Hcy) has been investigated for its potential association with CVD, researchers have debated the extent to which Hcy should be considered a risk factor for cardiovascular diseases, as only 50% of CVD can be explained by classical risk factors.

METHODS: We conducted a prospective cohort study using NHANES 1999-2006 data, analyzing 1,739 US patients aged at least 30 with CVD. Cox proportional hazards regression and restricted cubic splines were used to examine the relationship between Hcy levels and mortality, adjusting for covariates.

RESULT: A total of 1,739 participants with cardiovascular disease (CVD) were enrolled, with a median follow-up period of 126 months. Among them, 1,194 participants died, including 501 deaths due to cardiovascular causes. After adjusting for covariates, the hazard ratios (HR) and 95% confidence intervals (CI) for CVD mortality at different levels of homocysteine (Hcy) (T1 (< 9.3), T2 (9.3-12.5), T3 (> 12.5)) were 1.26 (0.92, 1.73) (T2), and 1.69 (1.14, 2.51) (T3) (P for trend = 0.0086). The HR and 95% CI for all-cause mortality at different levels of Hcy were 1.22 (1.05, 1.42) (T2) and 1.64 (1.29, 2.09) (T3) (P for trend < 0.0001). Elevated Hcy levels were associated with increased risks of all-cause mortality and CVD deaths, even at levels below the conventional threshold. The nonlinear relationship was observed, with inflection points at 14.5 µmol/L for all-cause mortality and 14.6 µmol/L for CVD mortality. Subgroup analyses revealed interactions with age, serum vitamin B12, and smoking.

CONCLUSION: Our study supports the notion that elevated Hcy levels are associated with higher all-cause and CVD mortality risks in CVD participants. The impact of Hcy on health outcomes can be observed at lower concentrations than previously thought.

PMID:39548360 | DOI:10.1186/s12872-024-04317-9

J Dent Educ. 2024 Nov 15. doi: 10.1002/jdd.13785. Online ahead of print.

ABSTRACT

PURPOSE: To compare the educational outcomes of remote instruction (RI) in impression-taking using smart glasses with those of face-to-face instruction (FI) and paper-based self-learning (SL) and analyze the educational effects, aiming to develop a remote clinical training strategy.

METHODS: Participants were recruited from among the dental residents who were trained in the first-year clinical program at the university hospital in 2023. The participants were divided into three groups as the original skill level was equal, and the groups were assigned RI, FI, printed guidance, and SL. All the participants took impressions of the jaw models attached to the mannequin using alginate impression material. Next, assigned instructions were provided. Then again, the trainees took impressions of the jaw models. The pre- and postinstruction impressions of each participant were evaluated, and the change in the impression score was statistically analyzed.

RESULTS: The pre- and postinstruction scores of the trainees in the RI and FI groups showed a significant increase (p < 0.05), whereas no significant difference was observed in the score changes in the SL group. In the intergroup comparisons, the score changes of the RI and FI groups were greater than those of the SL group, although no significant difference was found between the score changes of the RI and FI groups (p < 0.05).

CONCLUSION: RI in impression-taking using smart glasses has a greater educational effectiveness than paper-based SL. It has also been suggested that RI can have educational efficacy similar to FI.

PMID:39548350 | DOI:10.1002/jdd.13785

Sci Rep. 2024 Nov 15;14(1):28176. doi: 10.1038/s41598-024-79999-4.

ABSTRACT

Low fertility is not conducive to healthy population development. The total fertility rate (TFR) is influenced by the education expansion (measured by the proportion of non-student women, NSP), marriage delay (measured by the proportion of married women, MP), and marital fertility rate (MFR). This study decomposes the TFR change into the changes in NSP, MP, and MFR using China’s census and 1% population sample survey data. During 1990-2020, the changes in NSP, MP, and MFR contributed – 22%, – 90%, and 12%, respectively, to the changes in TFR. The continuous decline in NSP reduced the TFR, and the intensity continued to increase over time. As the primary negative driving force, the rapid decline in MP also consistently reduced the TFR. The marital fertility rate had a downward effect on the TFR before 2000 and an upward effect after 2000. The effects of NSP, MP, and MFR on the TFR varied with the birth order, age and region (among cities, towns, and villages). In summary, China’s TFR has considerably changed in combination with changes in NSP, MP, and MFR. Without effective measures, China’s TFR may further decline into the lowest-low fertility trap.

PMID:39548321 | DOI:10.1038/s41598-024-79999-4

Sci Rep. 2024 Nov 15;14(1):28178. doi: 10.1038/s41598-024-79921-y.

ABSTRACT

Colorectal cancer in Brazil is among the main public health concern. The burden of disease can be related to unhealthy lifestyle behavior and inequality in access to health services. The aim of this study was to identify the main factors associated with colorectal cancer mortality in Brazil. This is an ecological study that had the Brazilian Federal Units as the primary units of analysis. Colorectal cancer mortality data (ICD C18-C21) were obtained from Brazilian national mortality system to the year 2020. Prevalence of overweight, food consumption (fiber, whole grains and red meat), physical inactivity, smoke, alcohol consumption, the median of household income, years of study, rates of cancer treatment units and oncologist by Brazilian Federal Units were considered as factor associated to the colorectal cancer mortality. Quasipoisson Generalized Linear Models were used to associate CRC mortality and variables related to dietary intake, risk behavior, and access to health services. In 2020, there were 21,501 deaths by colorectal cancer (51% among women). Prevalence of overweight (men: IRR 1.03; CI: 1.01-1.04; women IRR 1.05; CI 1.02-1.08) and the density of oncologist (men: IRR 1.02; CI: 1.01-1.03; women IRR 1.02; CI 1.01-1.03) were the main factors associated with colorectal cancer mortality. Sociodemographic and food consumption characteristics were not statistically associated with CRC. Prevalence of overweight was the strongest factor associated with mortality from colorectal cancer in Brazil in 2020. Therefore, current public policies to reduce overweight and obesity should be prioritized and strengthened in Brazil.

PMID:39548314 | DOI:10.1038/s41598-024-79921-y

Sci Rep. 2024 Nov 15;14(1):28230. doi: 10.1038/s41598-024-79727-y.

ABSTRACT

This research explores the design of an infrared (IR) photodetector using mercury cadmium telluride (Hg_1-xCd_xTe). It proposes two- and three-dimensional homojunction models based on p⁺-Hg_0.7783Cd_0.2217Te/n^–-Hg_0.7783Cd_0.2217Te, focusing on applications in the long-wavelength infrared range. The photodetector’s performance is analyzed using Silvaco ATLAS TCAD software and compared with analytical calculations based on drift-diffusion, tunneling, and Chu’s approximation techniques. Optimized for operation at 10.6 μm wavelength under liquid nitrogen temperature, the proposed photodetector demonstrates promising optoelectronic characteristics including the dark current density of 0.20 mA/cm², photocurrent density of 4.98 A/cm², and photocurrent density-to-dark current density ratio of 2.46 × 10⁴, a 3-dB cut-off frequency of 104 GHz, a rise time of 0.8 ps, quantum efficiency of 58.30 %, peak photocurrent responsivity of 4.98 A/W, specific detectivity of 3.96 × 10¹¹ cmHz^1/2/W, and noise equivalent power of 2.52 × 10^-16 W/Hz^1/2 indicating its potential for low-noise, high-frequency and fast-switching applications. The study also incorporates machine learning regression models to validate simulation results and provide a predictive framework for performance optimization, evaluating these models using various statistical metrics. This comprehensive approach demonstrates the synergy between advanced materials science and computational techniques in developing next-generation optoelectronic devices. By combining theoretical modeling, simulation, and machine learning, the research highlights the potential to accelerate progress in IR detection technology and enhance device performance and efficiency. This multidisciplinary methodology could serve as a model for future studies in optoelectronics, illustrating how advanced materials and computational methods can be utilized to enhance device capabilities.

PMID:39548271 | DOI:10.1038/s41598-024-79727-y

J Perinatol. 2024 Nov 15. doi: 10.1038/s41372-024-02161-5. Online ahead of print.

ABSTRACT

OBJECTIVES: Characterize the relationship between infant outcomes and prenatal homelessness, food insecurity and unemployment.

STUDY DESIGN: California live births between 22- and 44-weeks’ gestation comprised 6,089,327 pregnancies (2007-2020). Data were collected from linked Vital Statistics and hospital discharge records. Prenatal homelessness, food insecurity, and unemployment were classified as health-related social needs (HRSN) using International Classification of Disease codes in delivery records. Risk ratios for preterm birth, low birthweight, small for gestational age, neonatal intensive care unit admission, emergency department admission, rehospitalization, and death were estimated using log-linear Poisson regression adjusted for birthing person race, payer, and education.

RESULTS: 65.7 per 100,000 births had HRSN. These infants had a higher risk of preterm birth (aRR 2.7), low birthweight (aRR 2.7), SGA (aRR 1.5), NICU admission (aRR 3.5), and death (aRR 3.0).

CONCLUSIONS: HRSN increase the risk of infant morbidity and mortality but remain underreported in administrative records, making definitive conclusions difficult.

PMID:39548269 | DOI:10.1038/s41372-024-02161-5