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Journal of Dairy Science Jun 2024Dairy herds have adopted sexed semen (SS) and beef semen (BS) to control heifer inventory and increase calf sales revenue. Beef in vitro-produced embryo transfer (beef...
Dairy herds have adopted sexed semen (SS) and beef semen (BS) to control heifer inventory and increase calf sales revenue. Beef in vitro-produced embryo transfer (beef IVP-ET) may be an alternative to increase calf sales revenue. Besides, raising those Jersey beef crossbred and/or pure beef animals in a dairy system may be a new source of revenue. We aimed to evaluate breed strategies combining dairy conventional semen (CS), SS, BS, and beef IVP-ET on herd dynamics and profitability by marketing those animals with one-day-old or raising them to 180 kg. A Markov chain model was developed to maximize the profitability of Jersey herds by changing the number of dairy heifers sold at birth and the culling rate of 3rd and greater parity cows. The model presents inputs on the reproductive and productive performance of heifers and cows over time. The last year's data (year 10 - steady state) was used to calculate accrual operational cost and revenue per cow per year. We varied the breeding strategy by breeding order and parities, the embryo transfer cost ($85 or $170), the pure beef calf market price ($200 or $300), and by marketing Jersey-beef and pure beef animals with one-day-old or raising them to 180 kg. A total of 8 scenarios + default scenario were simulated. Overall, the proportion of SS use was 47.3 ± 0.6%. For the scenarios replacing all CS breedings with BS breedings, the proportion of CS and BS used was 52.3 ± 0.6. When beef IVP-ET was used, the percentage of BS and beef IVP-ET used was 22.4 ± 0.1% and 31.0 ± 0.1%, respectively. We observed that when we compared SS:BS with the default scenario, the production of purebred Jersey male calves was reduced by 83.5%, and profit/cow per year was increased from $113.5 to $203.3 with SS:BS. When a beef IVP-ET of $85 per transfer was used (scenarios 2 and 3), profit/cow per year was $145.5 and $176.2 for a pure-beef calf price of $200 and $300, respectively. In scenario 4, with a beef IVP-ET cost of $170, the lowest profit ($52.9 per cow per year) was found when marketing one-day-old pure-beef calves at $200. The highest profit was achieved for scenario raising the Jersey-beef crossbred animals to 180 kg ($232.9, scenario 6), followed by scenario 7 ($222.9, SS:BS:IVP-ET) with an embryo transfer cost of $85. Under the current market conditions, combining SS and BS in the reproductive program was a feasible economic opportunity for Jersey herds, yielding the highest net return. The adoption of beef IVP-ET in a reproductive program can potentially increase profit/cow per year, but its profitability will depend on the beef IVP-ET pregnancy cost, the pure-beef market price, calf performance, and the herd reproductive performance. In conclusion, raising the Jersey-beef crossbred calves may be a profitable strategy, and dairy producers need to evaluate the best option to invest in since it will take an extra risk to produce high-quality animals to the market.
PubMed: 38945269
DOI: 10.3168/jds.2023-24530 -
Environment International Jun 2024Phthalates, or dieters of phthalic acid, are a ubiquitous type of plasticizer used in a variety of common consumer and industrial products. They act as endocrine...
INTRODUCTION
Phthalates, or dieters of phthalic acid, are a ubiquitous type of plasticizer used in a variety of common consumer and industrial products. They act as endocrine disruptors and are associated with increased risk for several diseases. Once in the body, phthalates are metabolized through partially known mechanisms, involving phase I and phase II enzymes.
OBJECTIVE
In this study we aimed to identify common single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) associated with the metabolism of phthalate compounds in children through genome-wide association studies (GWAS).
METHODS
The study used data from 1,044 children with European ancestry from the Human Early Life Exposome (HELIX) cohort. Ten phthalate metabolites were assessed in a two-void pooled urine collected at the mean age of 8 years. Six ratios between secondary and primary phthalate metabolites were calculated. Genome-wide genotyping was done with the Infinium Global Screening Array (GSA) and imputation with the Haplotype Reference Consortium (HRC) panel. PennCNV was used to estimate copy number variants (CNVs) and CNVRanger to identify consensus regions. GWAS of SNPs and CNVs were conducted using PLINK and SNPassoc, respectively. Subsequently, functional annotation of suggestive SNPs (p-value < 1E-05) was done with the FUMA web-tool.
RESULTS
We identified four genome-wide significant (p-value < 5E-08) loci at chromosome (chr) 3 (FECHP1 for oxo-MiNP_oh-MiNP ratio), chr6 (SLC17A1 for MECPP_MEHHP ratio), chr9 (RAPGEF1 for MBzP), and chr10 (CYP2C9 for MECPP_MEHHP ratio). Moreover, 115 additional loci were found at suggestive significance (p-value < 1E-05). Two CNVs located at chr11 (MRGPRX1 for oh-MiNP and SLC35F2 for MEP) were also identified. Functional annotation pointed to genes involved in phase I and phase II detoxification, molecular transfer across membranes, and renal excretion.
CONCLUSION
Through genome-wide screenings we identified known and novel loci implicated in phthalate metabolism in children. Genes annotated to these loci participate in detoxification, transmembrane transfer, and renal excretion.
PubMed: 38945087
DOI: 10.1016/j.envint.2024.108845 -
Annals of Hepatology 2024
Topics: Humans; Severity of Illness Index; Constriction, Pathologic; Male; Predictive Value of Tests; Female
PubMed: 38944460
DOI: 10.1016/j.aohep.2024.101513 -
Nigerian Journal of Clinical Practice Jun 2024Antimicrobial stewardship is an important action plan for curbing the rising trend of antimicrobial resistance (AMR). Surveillance of antimicrobial use and consumption...
BACKGROUND
Antimicrobial stewardship is an important action plan for curbing the rising trend of antimicrobial resistance (AMR). Surveillance of antimicrobial use and consumption is needed as baseline data and for monitoring the impact of antimicrobial stewardship interventions. The survey was done to understand the burden of AMR, in view of establishing an antimicrobial stewardship program in our hospital.
METHODS
A point prevalence survey (PPS) of antimicrobial use and consumption was conducted on all inpatients admitted before 8.00 am on the days of the survey using a standardized questionnaire. The collected data were entered online into the Global PPS web-based application (www.global-pps.com), for analysis.
RESULT
Of the 178 patients admitted during the survey period, 50.6% were on one or more antimicrobial agents. All the patients in adult intensive care units were on antibiotics (100%), followed by neonatal intensive care units (83.3%), with the least being adult medical wards (39.4%). Beta-lactam antibiotics were the most frequently prescribed antimicrobial for various infections, especially skin and soft tissue infections, 41.3%, which were the most common diagnoses treated with antibiotics. The infection was mostly community-acquired (81.6%), of which 94.9% were treated empirically. There was no written guideline in existence.
CONCLUSION
The present study revealed a poor prescribing habit because of a high rate of empirical treatment. The need for antimicrobial stewardship cannot be overemphasized as it will help streamline and improve the prescribing pattern.
Topics: Humans; Antimicrobial Stewardship; Nigeria; Female; Male; Tertiary Care Centers; Adult; Prevalence; Middle Aged; Surveys and Questionnaires; Anti-Bacterial Agents; Practice Patterns, Physicians'; Anti-Infective Agents; Drug Prescriptions; Aged; Adolescent; Young Adult; Drug Utilization
PubMed: 38943293
DOI: 10.4103/njcp.njcp_449_23 -
Trials Jun 2024Acute leukaemias (AL) are life-threatening blood cancers that can be potentially cured with treatment involving myelosuppressive, multiagent, intensive chemotherapy...
Biomarker Driven Antifungal Stewardship (BioDriveAFS) in acute leukaemia-a multi-centre randomised controlled trial to assess clinical and cost effectiveness: a study protocol for a randomised controlled trial.
BACKGROUND
Acute leukaemias (AL) are life-threatening blood cancers that can be potentially cured with treatment involving myelosuppressive, multiagent, intensive chemotherapy (IC). However, such treatment is associated with a risk of serious infection, in particular invasive fungal infection (IFI) associated with prolonged neutropenia. Current practice guidelines recommend primary antifungal (AF) prophylaxis to be administered to high-risk patients to reduce IFI incidence. AFs are also used empirically to manage prolonged neutropenic fever. Current strategies lead to substantial overuse of AFs. Galactomannan (GM) and β-D-glucan (BG) biomarkers are also used to diagnose IFI. Combining both biomarkers may enhance the predictability of IFI compared to administering each test alone. Currently, no large-scale randomised controlled trial (RCT) has directly compared a biomarker-based diagnostic screening strategy without AF prophylaxis to AF prophylaxis (without systematic biomarker testing).
METHODS
BioDriveAFS is a multicentre, parallel, two-arm RCT of 404 participants from UK NHS Haematology departments. Participants will be allocated on a 1:1 basis to receive either a biomarker-based antifungal stewardship (AFS) strategy, or a prophylactic AF strategy, which includes existing standard of care (SoC). The co-primary outcomes will be AF exposure in the 12-month post randomisation and the patient-reported EQ-5D-5L measured at 12-month post randomisation. Secondary outcomes will include total AF exposure, probable/proven IFI, survival (all-cause mortality and IFI mortality), IFI treatment outcome, AF-associated adverse effects/events/complications, resource use, episodes of neutropenic fever requiring hospital admission or outpatient management, AF resistance in fungi (non-invasive and invasive) and a Desirability of Outcome Ranking. The trial will have an internal pilot phase during the first 9 months. A mixed methods process evaluation will be integrated in parallel to the internal pilot phase and full trial, aiming to robustly assess how the intervention is delivered. Cost-effectiveness analysis will also be performed.
DISCUSSION
The BioDriveAFS trial aims to further the knowledge of strategies that will safely optimise AF use through comparison of the clinical and cost-effectiveness of a biomarker-led diagnostic strategy versus prophylactic AF to prevent and manage IFI within acute leukaemia. The evidence generated from the study will help inform global clinical practice and approaches within antifungal stewardship.
TRIAL REGISTRATION
ISRCTN11633399. Registered 24/06/2022.
Topics: Humans; Antifungal Agents; Cost-Benefit Analysis; Randomized Controlled Trials as Topic; Invasive Fungal Infections; Multicenter Studies as Topic; Biomarkers; Galactose; Mannans; Treatment Outcome; beta-Glucans; Antimicrobial Stewardship; Leukemia; Time Factors; Cost-Effectiveness Analysis
PubMed: 38943201
DOI: 10.1186/s13063-024-08272-w -
Archives of Gerontology and Geriatrics Jun 2024A meta-analysis was conducted to evaluate the impact of resistance training on pro-inflammatory cytokines c-reactive protein (CRP), interleukin 6 (IL 6), and tumor...
BACKGROUND AND OBJECTIVE
A meta-analysis was conducted to evaluate the impact of resistance training on pro-inflammatory cytokines c-reactive protein (CRP), interleukin 6 (IL 6), and tumor necrosis factor- α (TNF- α) in middle-aged and elderly individuals.
METHODS
The retrieval period for the Web of Science and other large electronic databases is set by default to March 2022. Both included and excluded researchers are independent examination literature on the impact of resistance exercise on markers of inflammation in the elderly. The physical medical care Evidence Database scale (Physical Therapy Evidence Database, PEDro) was used to evaluate the research quality, and Revmen 5.3 was used to end the index analysis.
RESULTS
After a total of four rounds of elimination, 12 items were eventually included. The total sample size for the research was 388 persons. Resistance training substantially reduced CRP levels in middle-aged and older individuals, with SMD = -0.56 and 95 % confidence interval ([-0.78, -0.34], P < 0.00001, correspondingly. Resistance training can successfully lower IL6 concentrations in middle-aged and older adults, although the combined impact is not substantial. SMD = -0.25, 95 % CI [-0.54, 0.04]; P = 0.09. TNF- concentrations did not alter significantly following resistance exercise in middle-aged and older adults. The overall effect was SMD = -0.07, with a 95 % confidence interval [-0.37, 0.23], while P = 0.64.
CONCLUSION
Resistance training reduces CRP, IL6, and TNF-α levels among middle-aged and elderly people. However, it has no significant anti-inflammatory effects on TNF-α. Resistance exercise at a moderate level for 3 times / week with a duration of 6-12 weeks or 16-32 weeks, significantly reduced CRP levels. This work contributing to exploring the resistance training program for the elderly to reduce inflammatory markers, and further, providing suggestions for the elderly to participate in resistance training and reduce the concentration of inflammatory markers.
PubMed: 38941946
DOI: 10.1016/j.archger.2024.105536 -
Journal of Medical Internet Research Jun 2024Previous mobile health (mHealth) studies have revealed significant links between depression and circadian rhythm features measured via wearables. However, the...
BACKGROUND
Previous mobile health (mHealth) studies have revealed significant links between depression and circadian rhythm features measured via wearables. However, the comprehensive impact of seasonal variations was not fully considered in these studies, potentially biasing interpretations in real-world settings.
OBJECTIVE
This study aims to explore the associations between depression severity and wearable-measured circadian rhythms while accounting for seasonal impacts.
METHODS
Data were sourced from a large longitudinal mHealth study, wherein participants' depression severity was assessed biweekly using the 8-item Patient Health Questionnaire (PHQ-8), and participants' behaviors, including sleep, step count, and heart rate (HR), were tracked via Fitbit devices for up to 2 years. We extracted 12 circadian rhythm features from the 14-day Fitbit data preceding each PHQ-8 assessment, including cosinor variables, such as HR peak timing (HR acrophase), and nonparametric features, such as the onset of the most active continuous 10-hour period (M10 onset). To investigate the association between depression severity and circadian rhythms while also assessing the seasonal impacts, we used three nested linear mixed-effects models for each circadian rhythm feature: (1) incorporating the PHQ-8 score as an independent variable, (2) adding seasonality, and (3) adding an interaction term between season and the PHQ-8 score.
RESULTS
Analyzing 10,018 PHQ-8 records alongside Fitbit data from 543 participants (n=414, 76.2% female; median age 48, IQR 32-58 years), we found that after adjusting for seasonal effects, higher PHQ-8 scores were associated with reduced daily steps (β=-93.61, P<.001), increased sleep variability (β=0.96, P<.001), and delayed circadian rhythms (ie, sleep onset: β=0.55, P=.001; sleep offset: β=1.12, P<.001; M10 onset: β=0.73, P=.003; HR acrophase: β=0.71, P=.001). Notably, the negative association with daily steps was more pronounced in spring (β of PHQ-8 × spring = -31.51, P=.002) and summer (β of PHQ-8 × summer = -42.61, P<.001) compared with winter. Additionally, the significant correlation with delayed M10 onset was observed solely in summer (β of PHQ-8 × summer = 1.06, P=.008). Moreover, compared with winter, participants experienced a shorter sleep duration by 16.6 minutes, an increase in daily steps by 394.5, a delay in M10 onset by 20.5 minutes, and a delay in HR peak time by 67.9 minutes during summer.
CONCLUSIONS
Our findings highlight significant seasonal influences on human circadian rhythms and their associations with depression, underscoring the importance of considering seasonal variations in mHealth research for real-world applications. This study also indicates the potential of wearable-measured circadian rhythms as digital biomarkers for depression.
Topics: Humans; Seasons; Female; Circadian Rhythm; Male; Wearable Electronic Devices; Adult; Longitudinal Studies; Depression; Middle Aged; Retrospective Studies; Telemedicine
PubMed: 38941600
DOI: 10.2196/55302 -
Bioinformatics (Oxford, England) Jun 2024Exponential growth in sequencing databases has motivated scalable De Bruijn graph-based (DBG) indexing for searching these data, using annotations to label nodes with...
MOTIVATION
Exponential growth in sequencing databases has motivated scalable De Bruijn graph-based (DBG) indexing for searching these data, using annotations to label nodes with sample IDs. Low-depth sequencing samples correspond to fragmented subgraphs, complicating finding the long contiguous walks required for alignment queries. Aligners that target single-labelled subgraphs reduce alignment lengths due to fragmentation, leading to low recall for long reads. While some (e.g. label-free) aligners partially overcome fragmentation by combining information from multiple samples, biologically irrelevant combinations in such approaches can inflate the search space or reduce accuracy.
RESULTS
We introduce a new scoring model, 'multi-label alignment' (MLA), for annotated DBGs. MLA leverages two new operations: To promote biologically relevant sample combinations, 'Label Change' incorporates more informative global sample similarity into local scores. To improve connectivity, 'Node Length Change' dynamically adjusts the DBG node length during traversal. Our fast, approximate, yet accurate MLA implementation has two key steps: a single-label seed-chain-extend aligner (SCA) and a multi-label chainer (MLC). SCA uses a traditional scoring model adapting recent chaining improvements to assembly graphs and provides a curated pool of alignments. MLC extracts seed anchors from SCAs alignments, produces multi-label chains using MLA scoring, then finally forms multi-label alignments. We show via substantial improvements in taxonomic classification accuracy that MLA produces biologically relevant alignments, decreasing average weighted UniFrac errors by 63.1%-66.8% and covering 45.5%-47.4% (median) more long-read query characters than state-of-the-art aligners. MLAs runtimes are competitive with label-combining alignment and substantially faster than single-label alignment.
AVAILABILITY AND IMPLEMENTATION
The data, scripts, and instructions for generating our results are available at https://github.com/ratschlab/mla.
Topics: Algorithms; Sequence Alignment; Software; Computational Biology; Sequence Analysis, DNA; Databases, Genetic
PubMed: 38940164
DOI: 10.1093/bioinformatics/btae226 -
Bioinformatics (Oxford, England) Jun 2024We learn more effectively through experience and reflection than through passive reception of information. Bioinformatics offers an excellent opportunity for...
MOTIVATION
We learn more effectively through experience and reflection than through passive reception of information. Bioinformatics offers an excellent opportunity for project-based learning. Molecular data are abundant and accessible in open repositories, and important concepts in biology can be rediscovered by reanalyzing the data.
RESULTS
In the manuscript, we report on five hands-on assignments we designed for master's computer science students to train them in bioinformatics for genomics. These assignments are the cornerstones of our introductory bioinformatics course and are centered around the study of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). They assume no prior knowledge of molecular biology but do require programming skills. Through these assignments, students learn about genomes and genes, discover their composition and function, relate SARS-CoV-2 to other viruses, and learn about the body's response to infection. Student evaluation of the assignments confirms their usefulness and value, their appropriate mastery-level difficulty, and their interesting and motivating storyline.
AVAILABILITY AND IMPLEMENTATION
The course materials are freely available on GitHub at https://github.com/IB-ULFRI.
Topics: Computational Biology; SARS-CoV-2; Humans; COVID-19; Genomics; Students
PubMed: 38940150
DOI: 10.1093/bioinformatics/btae208 -
LASSA FEVER IN INTERNALLY-DISPLACED PERSONS' CAMP: A CASE REPORT AT ZABARMARI, BORNO STATE, NIGERIA.Annals of Ibadan Postgraduate Medicine Apr 2024Lassa fever is a viral hemorrhagic disease caused by the Lassa virus, a single stranded RNA virus of the Arenavirus family. It is a zoonotic illness spread by rats of...
INTRODUTION
Lassa fever is a viral hemorrhagic disease caused by the Lassa virus, a single stranded RNA virus of the Arenavirus family. It is a zoonotic illness spread by rats of the speciesMastomys natalensis . Between weeks 1 and 17, (2017), 242 suspected Lassa fever cases were reported in Nigeria, with 58 laboratory confirmed cases and 46 fatalities (CFR, 19.01%) from 50 Local Government Areas (LGAs) in 20 States.
METHODS
We conducted an outbreak investigation and gathered a thorough clinical history of the index case as well as contacts, who were then followed up using the standard viral hemorrhagic fever contact monitoring form. Following that, blood samples were collected from this patient. A total of 54 contacts were tracked for 21 days and their temperatures were recorded using a clinical thermometer. Furthermore, an environmental evaluation of the Zabarmari community and the Madinatu Internally-displaced persons' (IDP) camp was carried out.
RESULTS
The index case was a 32-year-old woman who was internallydisplaced in Zabarmari community. Her symptoms began with fever and vaginal bleeding and progressed to bleeding from the nose, mouth, and urethra. There was a history of rat exposure as well as inadequate environmental sanitation and hygiene. Real Time PCR detected Lassa fever in the blood sample. The Borno State Ministry of Environment, in partnership with the Ministry of Health, undertook public health education on Lassa fever prevention and implemented excellent sanitary measures.
CONCLUSION
Increased awareness creation on good infection prevention and control practices is crucial among internally-displaced person and health care providers to prevent occurrence and spread of the disease.
PubMed: 38939877
DOI: No ID Found