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1.
Subst Use Misuse ; : 1-8, 2024 Jul 10.
Article in English | MEDLINE | ID: mdl-38987988

ABSTRACT

BACKGROUND: Alcohol use is a gendered behavior and motherhood is a life stage which may influence drinking motives. However, there are no drinking motive scales uniquely tailored to maternal populations. This work developed a new maternal drinking motives scale (M-DMS) and determined associations between the M-DMS and alcohol-related behavior. METHODS: An online observational survey (n = 534) and online test-retest survey (n = 164) were conducted with adult, UK mothers. From the observational study, data on drinking motives was extracted to determine M-DMS items and factor loading. This was split into two data sets for exploratory and confirmatory factor analyses. Alcohol Use Disorders Identification Test (AUDIT) and Timeline Follow back data, taken from both surveys, were combined to determine the M-DMS's predictive validity. RESULTS: Following a parallel analysis and exploratory factor analysis, a two-factor model (positive reinforcement motives, negative reinforcement motives) was deemed the best fit. Probability functional analysis identified items with problematic responses. These were removed before confirmatory factor analysis (on the second dataset) demonstrated a good fit for the two-factor model. All factor loadings were significant and positive (ßs > 0.56). Reliability of the two subscales was excellent: negative reinforcement (ωT = 0.95), positive reinforcement (ωT = 0.89). Test-retest reliability was good for both negative (ICC = 0.84, 95%CI = 0.80-0.88) and positive (ICC = 0.77, 95% CI = 0.71-0.82) subscales. Both subscales predicted AUDIT and quantity of alcohol consumption (ps < 0.001). CONCLUSION: The first tailored Maternal Drinking Motives Scale (M-DMS) provides a more valid research tool for assessing psychological mechanisms of alcohol use in mothers.

2.
Med Sci Sports Exerc ; 2024 Jul 11.
Article in English | MEDLINE | ID: mdl-38991200

ABSTRACT

PURPOSE: We studied the effect of O2 supplementation on physiological response to exercise in patients with moderate to severe interstitial lung disease (ILD). METHODS: 13 patients (age 66 ± 10 yrs., 7 males) with ILD (TLC 71 ± 22% predicted, carbon monoxide diffusion capacity (DLCO) 44 ± 16% predicted) and 13 healthy individuals (age 50 ± 17 yrs., 7 males) were tested. ILD patients performed symptom-limited cardiopulmonary exercise tests and constant work-rate tests (CWRTs) at 80% of the work-rate (WR) at the gas exchange threshold (GET). Tests breathing room air (RA, 21% O2) were compared to tests performed breathing 30% O2. Oxygen-uptake (V̇O2) kinetics were calculated from the CWRT results. RESULTS: In the ILD group, peak WR, peak V̇O2 and V̇O2 at the GET improved significantly when breathing 30% O2 compared to RA (mean ± SD 66 ± 23 vs 75 ± 26 watts, 15 ± 2 vs 17 ± 4 ml/kg/min and 854 ± 232 vs 932 ± 245 ml/min; p = 0.004, p = 0.001 and p = 0.01, respectively). O2 saturation (SPO2%) at peak exercise was higher with 30% O2 (97 ± 4% vs 88 ± 9%, p = 0.002). The time constant (tau) of V̇O2 kinetics was faster in ILD patients while breathing 30% O2 (41 ± 10 sec) compared to RA (52 ± 14 sec, p = 0.003). There was a negative linear relation between tau and SPO2% with RA (r = -0.76, p = 0.006) and while breathing 30% O2 (r = -0.68, p = 0.02). CONCLUSIONS: Using a clinically applicable level of O2 supplementation (30%) improved maximal, aerobic exercise capacity and V̇O2 kinetics in ILD patients, likely due to increased blood O2 content subsequently increasing the O2 delivery to the working muscles.

4.
BMC Cancer ; 24(1): 787, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38956523

ABSTRACT

BACKGROUND: Cancer is becoming a major health problem in Uganda. Cancer control requires accurate estimates of the cancer burden for planning and monitoring of the cancer control strategies. However, cancer estimates and trends for Uganda are mainly based on one population-based cancer registry (PBCR), located in Kampala, the capital city, due to a lack of PBCRs in other regions. This study aimed at estimating cancer incidence among the geographical regions and providing national estimates of cancer incidence in Uganda. METHODS: A retrospective study, using a catchment population approach, was conducted from June 2019 to February 2020. The study registered all newly diagnosed cancer cases, in the period of 2013 to 2017, among three geographical regions: Central, Western and Eastern regions. Utilizing regions as strata, stratified random sampling was used to select the study populations. Cases were coded according to the International Classification of Diseases for Oncology (ICD-0-03). Data was analysed using CanReg5 and Microsoft Excel. RESULTS: 11598 cases (5157 males and 6441 females) were recorded. The overall national age-standardized incidence rates (ASIR) were 82.9 and 87.4 per 100,000 people in males and females respectively. The regional ASIRs were: 125.4 per 100,000 in males and 134.6 per 100,000 in females in central region; 58.2 per 100,000 in males and 56.5 per 100,000 in females in Western region; and 46.5 per 100,000 in males and 53.7 per 100,000 in females in Eastern region. Overall, the most common cancers in males over the study period were cancers of the prostate, oesophagus, Kaposi's sarcoma, stomach and liver. In females, the most frequent cancers were: cervix, breast, oesophagus, Kaposi's sarcoma and stomach. CONCLUSION: The overall cancer incidence rates from this study are different from the documented national estimates for Uganda. This emphasises the need to enhance the current methodologies for describing the country's cancer burden. Studies like this one are critical in enhancing the cancer surveillance system by estimating regional and national cancer incidence and allowing for the planning and monitoring of evidence-based cancer control strategies at all levels.


Subject(s)
Neoplasms , Registries , Humans , Uganda/epidemiology , Female , Male , Retrospective Studies , Incidence , Neoplasms/epidemiology , Middle Aged , Adult , Aged , Adolescent , Young Adult , Child , Infant , Registries/statistics & numerical data , Infant, Newborn , Child, Preschool , Aged, 80 and over
5.
Curr Dev Nutr ; 8(6): 103776, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38979104

ABSTRACT

Background: A "food system" approach to improve diet quality by intervening within areas such as food supply chains is gaining prominence. However, evidence of such interventions' impact, and understanding of appropriate methods to evaluate them, is lacking. Objectives: We present an impact evaluation of an intervention that aimed to increase consumption of nutritious foods by supporting food-producing firms in Kenya. In doing so, we demonstrate how multiple methods, including those from other disciplines, can be used to evaluate a complex food systems intervention. Methods: Four methods focused on food-producing firms and their management, including a survey of intervention participants (n = 83 individuals), a "laboratory-in-the-field" experiment (n = 83 individuals), baseline/endline data on firm performance (n = 71 firms), and semistructured interviews (n = 19 firms). Three methods focused on consumers in neighborhoods targeted by a supported firm: a randomized field experiment tested effects of making a supported product exhaustively available on consumers' purchases and consumption (n = 1295 consumers); 3 discrete choice experiments (n = 1295 consumers) tested factors influencing consumers' willingness to pay for foods with relevant characteristics. Results: Among firms, we saw suggestive evidence of increased networking and business relationships, while laboratory-in-the-field experiments indicated the intervention might foster cooperation among participants. Qualitative interviews suggested that the intervention enabled firms to increase production, improve management, increase revenues, and lower costs. Baseline/endline data confirmed a positive effect only on the launch of new products and hiring workers. In the field experiment, consumption of the supported product increased in areas where it was made available relative to a control group, but this did not increase overall consumption of the food type or dietary diversity. Conclusions: Results showed positive signs of the intervention improving firm-level outcomes but limited impact on consumers' diet quality. The evaluation also demonstrates how diverse methods can be used to evaluate complex interventions.

6.
Front Plant Sci ; 15: 1381154, 2024.
Article in English | MEDLINE | ID: mdl-38872884

ABSTRACT

The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically uniform products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid multiplication of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to study a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.

7.
Methods Mol Biol ; 2809: 19-36, 2024.
Article in English | MEDLINE | ID: mdl-38907888

ABSTRACT

The allele frequency net database (AFND, http://www.allelefrequencies.net ) is an online web-based repository that contains information on the frequencies of immune-related genes and their corresponding alleles in worldwide human populations. At present, the website contains data from 1784 population samples in more than 14 million individuals from 129 countries on the frequency of genes from different polymorphic regions including data for the human leukocyte antigen (HLA) system. In addition, over the last four years, AFND has also incorporated genotype raw data from 85,000 individuals comprising 215 population samples from 39 countries. Moreover, more population data sets containing next generation sequencing data spanning >3 million individuals have been added. This resource has been widely used in a variety of contexts such as histocompatibility, immunology, epidemiology, pharmacogenetics, epitope prediction algorithms for population coverage in vaccine development, population genetics, among many others. In this chapter, we present an update of the most used searching mechanisms as described in a previous volume and some of the latest developments included in AFND.


Subject(s)
Databases, Genetic , Gene Frequency , Genetics, Population , Humans , Genetics, Population/methods , HLA Antigens/genetics , Alleles , Computational Biology/methods , Internet , Web Browser , Genotype , High-Throughput Nucleotide Sequencing/methods
9.
Health Econ ; 2024 Jun 30.
Article in English | MEDLINE | ID: mdl-38944848

ABSTRACT

This paper proposes a pseudo-birth-cohort approach to deal with a lack of longitudinal data to measure health inequities over time. Using Roemer's framework for inequality of opportunity, this study measures ex-ante and ex-post inequalities in malnutrition, a concept that spans both sides of the nutrition continuum. The total contribution of observed circumstances and the direct contribution of observed efforts to the variation of malnutrition are disentangled for people born between 1983 and 1988 in Mexico. Results indicate that inequality of opportunity has been persistent across this 30-year lifespan for that cohort. Some evidence suggests that a lack of opportunities has been transmitted from parents to children and that people's circumstances account for most of the explained variation in the double burden of malnutrition. However, stratifying the analysis by sex shows that efforts account for more of the explained variation of inequality of opportunity for women in their middle adulthood than for men in most of the outcomes analyzed.

10.
Int J Obes (Lond) ; 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38879728

ABSTRACT

BACKGROUND: Ultra-processed food (UPF) consumption is associated prospectively with weight gain and obesity in observational studies of adults. Unaccounted for confounding is a risk when attempting to make causal inference from observational studies. Limited research has examined how feasible it is that unmeasured confounding may explain associations between UPF consumption and weight gain in observational research. METHODS: We introduce the E value to obesity researchers. The E value is defined as the minimum hypothetical strength of association that one or more unaccounted for confounding variables would need to have with an exposure (UPF consumption) and outcome (weight gain) to explain the association between the exposure and outcome of interest. We meta-analysed prospective studies on the association between UPF consumption and weight gain in adults to provide an effect estimation. Next, we applied the E value approach to this effect estimate and illustrated the potential role that unmeasured or hypothetical residual confounding variables could theoretically have in explaining associations. RESULTS: Higher consumption of UPFs was associated with increased weight gain in meta-analysis (RR = 1.14). The corresponding E value = 1.55, indicating that unaccounted for confounding variables with small-to-moderate sized associations with UPF consumption and weight gain (e.g., depressive symptoms, trait overeating tendencies, access to healthy and nutritious food) could individually or collectively hypothetically account for observed associations between UPF consumption and weight gain. CONCLUSIONS: Unaccounted for confounding could plausibly explain the prospective association between UPF consumption and weight gain in adults. High quality observational research controlling for potential confounders and evidence from study types devoid of confounding are now needed.

11.
Appetite ; 200: 107533, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38825014

ABSTRACT

Research has drawn contradictory conclusions as to whether humans adjust meal size based on meal energy density (ED) or exhibit 'passive overconsumption'. Recent observational research has suggested that meal EDs greater than 1.7-2 kcal/g are compensated for through consumption of smaller meal sizes. We tested the relationship between ED and meal size by examining energy intake of meals at three levels of ED: low (∼1.0 kcal/g), medium (1.7-2.0 kcal/g) and high (>3.0 kcal/g). Two randomised, crossover experiments were conducted with adult participants. In experiment 1 (n = 34, 62% female, mean age 37.4 years), participants were served a lunch including a familiar low, medium or high ED dessert to eat ad libitum. In experiment 2 (n = 32, 66% female, mean age 36.4 years), participants were served a lunch meal manipulated to be low, medium or high ED to eat ad libitum. For experiment 2, later energy intake (post-meal energy intake) was also measured. In experiment 1, participants consumed a similar amount of energy from the low vs. medium ED food. The high ED food was associated with an increased intake of approximately 240 kcals compared to medium (p < 0.001, Cohen's d = 2.31) and low (p < 0.001, Cohen's d = 4.42) ED foods. In experiment 2, there were no significant differences in meal size (grams) between ED meals, resulting in a largely linear relationship between meal ED and energy intake across the three ED conditions ('passive overconsumption'). There were no differences in later energy intake between ED conditions. Contrary to recent suggestions, foods higher in ED were not associated with adjustments to meal size and were associated with increased energy intake across two experiments. Reformulation of foods high in ED may be an effective population level approach to reducing energy intake and obesity. Clinical trial registry number: NCT05744050; https://clinicaltrials.gov/ct2/show/NCT05744050.


Subject(s)
Cross-Over Studies , Energy Intake , Meals , Portion Size , Humans , Female , Adult , Male , Young Adult , Lunch , Middle Aged , Hyperphagia/psychology , Feeding Behavior/psychology , Postprandial Period
12.
Appetite ; 200: 107548, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38876150

ABSTRACT

BACKGROUND: Providing calorie information for alcoholic beverages is a potential public-health intervention which may serve to reduce alcohol use but also prevalence of overweight/obesity. Equivocal evidence has been found for the effectiveness of alcohol calorie information at reducing drinking intentions as well as purchasing and consumption. However, the extent at which calorie information 'on-trade' will impact consumer behaviour for both alcohol and food consumption has not been investigated. AIMS: (1) To examine the presence of alcohol calorie labelling for hypothetical purchasing of alcohol and food in typical UK restaurant scenarios. (2) To determine the characteristics of individuals who will be likely to choose to view alcohol calorie labels. METHODS: Two online randomised control trials using a hypothetical menu selection. In experiment one (N = 325) participants were randomised to the presence or absence of alcohol calorie labels. In experiment two (N = 1081) individuals were randomised to alcohol calorie labels absent or the choice to view alcohol calorie labels. The primary outcome for each study was calories ordered from alcoholic beverages. RESULTS: There was no evidence that the presence of alcohol calorie information on restaurant menus impacted the number of calories ordered from alcoholic beverages or from food and soft drinks. Younger individuals and individuals who exhibit greater motives for good health were more likely to choose to view alcohol calorie labels. CONCLUSIONS: In two online, hypothetical experiments there is no evidence for alcohol calorie labelling impacting consumer decisions to order alcohol or food. Given the choice, a self-selecting group of individuals who are more motivated by health concerns will view alcohol calorie labels, and in turn may be less likely to order alcohol.


Subject(s)
Alcoholic Beverages , Choice Behavior , Consumer Behavior , Energy Intake , Food Labeling , Restaurants , Humans , Female , Male , Adult , Young Adult , Middle Aged , United Kingdom , Food Labeling/methods , Alcohol Drinking/psychology , Alcohol Drinking/prevention & control , Adolescent , Food Preferences/psychology , Aged
13.
Nat Commun ; 15(1): 4987, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38862492

ABSTRACT

Spatial genomic technologies characterize the relationship between the structural organization of cells and their cellular state. Despite the availability of various spatial transcriptomic and proteomic profiling platforms, these experiments remain costly and labor-intensive. Traditionally, tissue slicing for spatial sequencing involves parallel axis-aligned sections, often yielding redundant or correlated information. We propose structured batch experimental design, a method that improves the cost efficiency of spatial genomics experiments by profiling tissue slices that are maximally informative, while recognizing the destructive nature of the process. Applied to two spatial genomics studies-one to construct a spatially-resolved genomic atlas of a tissue and another to localize a region of interest in a tissue, such as a tumor-our approach collects more informative samples using fewer slices compared to traditional slicing strategies. This methodology offers a foundation for developing robust and cost-efficient design strategies, allowing spatial genomics studies to be deployed by smaller, resource-constrained labs.


Subject(s)
Genomics , Genomics/methods , Animals , Humans , Gene Expression Profiling/methods , Mice , Transcriptome , Proteomics/methods , Research Design
14.
Plant Cell ; 2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38923935

ABSTRACT

SUMO modification is part of the spectrum of Ubiquitin-like (UBL) systems that give rise to proteoform complexity through post-translational modifications (PTMs). Proteoforms are essential modifiers of cell signaling for plant adaptation to changing environments. Exploration of the evolutionary emergence of Ubiquitin-like (UBL) systems unveils their origin from prokaryotes where it is linked to the mechanisms that enable sulfur uptake into biomolecules. We explore the emergence of the SUMO machinery across the plant lineage from single-cell to land plants. We reveal the evolutionary point at which plants acquired the ability to form SUMO chains through the emergence of SUMO E4 ligases hinting at its role in facilitating multicellularity. Additionally, we explore the possible mechanism for the neofunctionalization of SUMO proteases through the fusion of conserved catalytic domains with divergent sequences. We highlight the pivotal role of SUMO proteases in plant development and adaptation, offering new insights into target specificity mechanisms of SUMO modification during plant evolution. Correlating the emergence of adaptive traits in the plant lineage with established experimental evidence for SUMO in developmental processes we propose that SUMO modification has evolved to link developmental processes to adaptive functions in land plants.

15.
Anal Chem ; 96(19): 7348-7352, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38696329

ABSTRACT

Current commercially available liquid chromatography coupled to isotope ratio mass spectrometry systems (LC-IRMS) oxidize all eluent and thus can only operate with all-aqueous mobile phases, limiting their application to a small subset of analytes and mixtures that can be separated without organic solvents. We report a novel rotating-catalytic disc desolvation device with subsequent laser-activated photocatalytic analyte combustion to create CO2 for high precision carbon isotope ratio measurements compatible with both aqueous and organic liquid mobile phases. Sucrose, glucose, androsterone, or androsterone acetate in 20% and 50% H2O-CH3OH solutions were introduced by flow injection to the interface to IRMS for sugars and steroids, respectively. Sucrose δ13CVPDB linearity was excellent over 1-10 µg (33-655 nmol C) injections, using IRMS compatible He/1%O2 oxidation gas. The limit of precise isotope analysis (LOIA) of δ13CVPDB was 1 µg (35 nmol C) for sucrose and 10 µg (655 nmol C) for androsterone with average precisions of SD(δ13C) ± 0.8‰. Calibration was performed with and bracketed the δ13CVPDB isotope ratio range using androsterone-acetate and glucose. With further development to improve sensitivity and application to chromatography, the prototype proof-of-principle LC-IRMS shows promise to resolve a major drawback in current LC-IRMS systems and may open LC-IRMS to many more compounds than currently possible.

16.
J Proteome Res ; 23(6): 1948-1959, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38717300

ABSTRACT

The availability of an increasingly large amount of public proteomics data sets presents an opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biological conditions. Sus scrofa, a domestic pig, is a model organism relevant for food production and for human biomedical research. Here, we reanalyzed 14 public proteomics data sets from the PRIDE database coming from pig tissues to assess baseline (without any biological perturbation) protein abundance in 14 organs, encompassing a total of 20 healthy tissues from 128 samples. The analysis involved the quantification of protein abundance in 599 mass spectrometry runs. We compared protein expression patterns among different pig organs and examined the distribution of proteins across these organs. Then, we studied how protein abundances were compared across different data sets and studied the tissue specificity of the detected proteins. Of particular interest, we conducted a comparative analysis of protein expression between pig and human tissues, revealing a high degree of correlation in protein expression among orthologs, particularly in brain, kidney, heart, and liver samples. We have integrated the protein expression results into the Expression Atlas resource for easy access and visualization of the protein expression data individually or alongside gene expression data.


Subject(s)
Kidney , Proteomics , Animals , Proteomics/methods , Humans , Swine , Kidney/metabolism , Kidney/chemistry , Organ Specificity , Liver/metabolism , Liver/chemistry , Databases, Protein , Brain/metabolism , Myocardium/metabolism , Myocardium/chemistry , Sus scrofa/metabolism , Sus scrofa/genetics , Proteome/metabolism , Proteome/analysis , Mass Spectrometry
17.
JAMA Surg ; 159(7): 801-808, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38717759

ABSTRACT

Importance: A competency-based assessment framework using entrustable professional activities (EPAs) was endorsed by the American Board of Surgery following a 2-year feasibility pilot study. Pilot study programs' clinical competency committees (CCCs) rated residents on EPA entrustment semiannually using this newly developed assessment tool, but factors associated with their decision-making are not yet known. Objective: To identify factors associated with variation in decision-making confidence of CCCs in EPA summative entrustment decisions. Design, Setting, and Participants: This cohort study used deidentified data from the EPA Pilot Study, with participating sites at 28 general surgery residency programs, prospectively collected from July 1, 2018, to June 30, 2020. Data were analyzed from September 27, 2022, to February 15, 2023. Exposure: Microassessments of resident entrustment for pilot EPAs (gallbladder disease, inguinal hernia, right lower quadrant pain, trauma, and consultation) collected within the course of routine clinical care across four 6-month study cycles. Summative entrustment ratings were then determined by program CCCs for each study cycle. Main Outcomes and Measures: The primary outcome was CCC decision-making confidence rating (high, moderate, slight, or no confidence) for summative entrustment decisions, with a secondary outcome of number of EPA microassessments received per summative entrustment decision. Bivariate tests and mixed-effects regression modeling were used to evaluate factors associated with CCC confidence. Results: Among 565 residents receiving at least 1 EPA microassessment, 1765 summative entrustment decisions were reported. Overall, 72.5% (1279 of 1765) of summative entrustment decisions were made with moderate or high confidence. Confidence ratings increased with increasing mean number of EPA microassessments, with 1.7 (95% CI, 1.4-2.0) at no confidence, 1.9 (95% CI, 1.7-2.1) at slight confidence, 2.9 (95% CI, 2.6-3.2) at moderate confidence, and 4.1 (95% CI, 3.8-4.4) at high confidence. Increasing number of EPA microassessments was associated with increased likelihood of higher CCC confidence for all except 1 EPA phase after controlling for program effects (odds ratio range: 1.21 [95% CI, 1.07-1.37] for intraoperative EPA-4 to 2.93 [95% CI, 1.64-5.85] for postoperative EPA-2); for preoperative EPA-3, there was no association. Conclusions and Relevance: In this cohort study, the CCC confidence in EPA summative entrustment decisions increased as the number of EPA microassessments increased, and CCCs endorsed moderate to high confidence in most entrustment decisions. These findings provide early validity evidence for this novel assessment framework and may inform program practices as EPAs are implemented nationally.


Subject(s)
Clinical Competence , Decision Making , General Surgery , Internship and Residency , Humans , General Surgery/education , Pilot Projects , Male , Competency-Based Education , Female , United States
19.
J Proteome Res ; 23(7): 2518-2531, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38810119

ABSTRACT

Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety and clustered the data to identify groups of sites with similar patterns across rice family groups. The data has been loaded into UniProt Knowledge-Base─enabling researchers to visualize sites alongside other data on rice proteins, e.g., structural models from AlphaFold2, PeptideAtlas, and the PRIDE database─enabling visualization of source evidence, including scores and supporting mass spectra.


Subject(s)
Genome, Plant , Oryza , Phosphoproteins , Plant Proteins , Proteomics , Signal Transduction , Oryza/genetics , Oryza/metabolism , Oryza/chemistry , Proteomics/methods , Phosphoproteins/metabolism , Phosphoproteins/genetics , Phosphoproteins/chemistry , Phosphoproteins/analysis , Plant Proteins/genetics , Plant Proteins/metabolism , Phosphorylation , Protein Processing, Post-Translational , Phosphopeptides/metabolism , Phosphopeptides/analysis , Databases, Protein , Amino Acid Motifs , Mass Spectrometry
20.
Sci Total Environ ; 938: 173270, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-38772491

ABSTRACT

Accurate measuring, mapping, and monitoring of mangrove forests support the sustainable management of mangrove blue carbon in the Asia-Pacific. Remote sensing coupled with modeling can efficiently and accurately estimate mangrove blue carbon stocks at larger spatiotemporal extents. This study aimed to identify trends in remote sensing/modeling employed in estimating mangrove blue carbon, attributes/variations in mangrove carbon sequestration estimated using remote sensing, and to compile research gaps and opportunities, followed by providing recommendations for future research. Using a systematic literature review approach, we reviewed 105 remote sensing-based peer-reviewed articles (1990 - June 2023). Despite their high mangrove extent, there was a paucity of studies from Myanmar, Bangladesh, and Papua New Guinea. The most frequently used sensor was Sentinel-2 MSI, accounting for 14.5 % of overall usage, followed by Landsat 8 OLI (11.5 %), ALOS-2 PALSAR-2 (7.3 %), ALOS PALSAR (7.2 %), Landsat 7 ETM+ (6.1 %), Sentinel-1 (6.7 %), Landsat 5 TM (5.5 %), SRTM DEM (5.5 %), and UAV-LiDAR (4.8 %). Although parametric methods like linear regression remain the most widely used, machine learning regression models such as Random Forest (RF) and eXtreme Gradient Boost (XGB) have become popular in recent years and have shown good accuracy. Among a variety of attributes estimated, below-ground mangrove blue carbon and the valuation of carbon stock were less studied. The variation in carbon sequestration potential as a result of location, species, and forest type was widely studied. To improve the accuracy of blue carbon measurements, standardized/coordinated and innovative methodologies accompanied by credible information and actionable data should be carried out. Technical monitoring (every 2-5 years) enhanced by remote sensing can provide accurate and precise data for sustainable mangrove management while opening ventures for voluntary carbon markets to benefit the environment and local livelihood in developing countries in the Asia-Pacific region.

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