Tag: statistics

J Dairy Sci. 2023 Sep 8:S0022-0302(23)00626-4. doi: 10.3168/jds.2023-23478. Online ahead of print.

ABSTRACT

A 305-d lactation followed by a 60-d dry period has traditionally been considered economically optimal, yet dairy cows in modern intensive dairy systems are frequently dried off while still producing significant quantities of milk. Managing cows for an extended lactation has reported production, welfare and economic benefits, but not all cows are suitable for an extended lactation. Implementation of an extended lactation strategy on-farm could benefit from use of a decision support system, based on a mathematical lactation model, that can identify suitable cows during early lactation that have a high likelihood of producing above a target milk yield (MY) at 305 d in milk (DIM). Therefore, our objectives were 1) to compare the suitability of 3 commonly used lactation models for modeling extended lactations (Dijkstra, Wood, and Wilmink) in primiparous and multiparous cows under a variety of lactation lengths, and 2) to determine the amount of early lactation daily MY data needed to accurately forecast MY at d 305 by using the most suitable model and determine if this is sufficient for identifying cows suitable for an extended lactation before the end of a typical voluntary waiting period (50 to 90 d). Daily MY data from 467 individual Holstein-Friesian lactations (DIM >305 d; 379 ± 65 d lactation length [mean ± SD]) were fitted by the 3 lactation models using a nonlinear regression procedure. The parameter estimates of these models, lactation characteristics (peak yield, time to peak yield, and persistency), and goodness-of-fit were compared between parity and different lactation lengths. The models had similar performance and differences between parity groups were consistent with previous literature. Then, data from only the first i DIM for each individual lactation, where i was incremented by 30 d from 30 to 150 DIM and by 50 d from 150 to 300 DIM, were fitted by each model to forecast MY at d 305. The Dijkstra model was selected for further analysis as it had superior goodness-of-fit statistics for i = 30 and 60. The data set was fit twice by the Dijkstra model, with parameter bounds either unconstrained or constrained. The quality of predictions of MY at d 305 improved with increasing data availability for both models and assisting the model fitting procedure with more biologically relevant constraints on parameters improved the predictions, but neither was reliable enough for practical use on-farm due to the high uncertainty of forecasted predictions. Using 90 d of data, the constrained model correctly classified 66% of lactations as being above or below a target MY at d 305 of 25 kg/d, with a probability threshold of 0.95. The proportion of correct classifications became smaller at lower targets of MY at d 305 and became greater when using more lactation days. Overall, further work is required to develop a model that can forecast late lactation MY with sufficient accuracy for practical use. We envisage that a hybridized machine learning and mechanistic model that incorporates additional historical and genetic information with early lactation MY could produce meaningful lactation curve forecasts.

PMID:37690727 | DOI:10.3168/jds.2023-23478

J Dairy Sci. 2023 Sep 8:S0022-0302(23)00641-0. doi: 10.3168/jds.2023-23874. Online ahead of print.

ABSTRACT

We determined the effects of altering the ratio of palmitic (C16:0) and stearic (C18:0) acids in supplemental fatty acid (FA) blends on production responses of mid-lactation dairy cows. Twenty-four multiparous Holstein cows (mean ± standard deviation; 47.1 ± 5.8 kg of milk yield, 109 ± 23 DIM) were randomly assigned to treatment sequences in a replicated 4 × 4 Latin square design with 21-d periods. Treatments were a non-FA supplemented control diet (CON), and 3 diets incorporating 1.5% dry matter (DM) FA supplement blends containing 30% C16:0 + 50% C18:0 (L-PA), 50% C16:0 + 30% C18:0 (M-PA), and 80% C16:0 + 10% C18:0 (H-PA). Additionally, the FA blends were balanced to contain 10% oleic acid (cis-9 C18:1). The FA blends replaced soyhulls in the CON diet. Diets were formulated to contain (% DM) 31.0% neutral detergent fiber, 27.0% starch, and 16.9% crude protein. The statistical model included the random effect of cow within square and the fixed effects of period, treatment, and their interaction. Pre-planned contrasts included CON vs. overall effect of FA supplementation (FAT) and the linear and quadratic effects of increasing C16:0 in FA blends. Overall FAT had no effect on dry matter intake but increasing C16:0 linearly increased dry matter intake. Compared with CON, overall FAT increased yields of milk, 3.5% fat corrected milk, energy corrected milk, and milk fat, but did not affect milk protein yield. Increasing C16:0 linearly increased milk fat yield and tended to linearly increase the yields of 3.5% fat corrected milk and energy corrected milk. FAT decreased the yield of de novo milk FA, but increased yields of mixed and preformed milk FA compared with CON. Increasing C16:0 in FA treatments did not affect the yield of de novo milk FA, linearly increased the yield of mixed and decreased the yield of preformed milk FA. In summary, feeding FA supplements containing C16:0 and C18:0 increased milk production responses with no effect on DMI compared with a non-FA supplemented control diet. Mid-lactation cows producing ∼40-50 kg/d of milk yield responded best to increasing supplemental C16:0 in FA supplements, demonstrating that FA supplements higher in C16:0, and limiting C18:0, improves production responses.

PMID:37690714 | DOI:10.3168/jds.2023-23874

Behav Brain Res. 2023 Sep 8:114659. doi: 10.1016/j.bbr.2023.114659. Online ahead of print.

ABSTRACT

Learning to discriminate between environmental visual stimuli is essential to make right decisions and guide appropriate behaviors. Moreover, impairments in visual discrimination learning are observed in several neuropsychiatric disorders. Visual discrimination learning requires perception and memory processing, in which the hippocampus critically involved. To understand the molecular mechanisms underpinning hippocampus function in visual discrimination learning, we examined the hippocampal gene expression profiles of Sprague-Dawley rats with different cognitive performance (high cognition group vs. low cognition group) in the modified visual discrimination learning task, using high-throughput RNA sequencing technology. Compared with the low cognition group, bioinformatics analysis indicated that 319 genes were differentially expressed in the high cognition group with statistical significance, of which 253 genes were down-regulated and 66 genes were up-regulated. The functional enrichment analysis showed that protein translation and energy metabolism were up-regulated pathways, while transforming growth factor beta receptor signaling pathway, bone morphogenetic protein signaling pathway, apoptosis, inflammation response, transport, and glycosaminoglycan metabolism were down-regulated pathways, which were related to good cognitive performance in the visual discrimination learning task. Taken together, our finding reveals the differential gene expression and enrichment biological pathways related to cognitive performance differences in visual discrimination learning of rats, which provides us direct insight into the molecular mechanisms of hippocampus function in visual discrimination learning and may contribute to developing potential treatment strategies for neuropsychiatric disorders accompanied with cognitive impairments.

PMID:37690703 | DOI:10.1016/j.bbr.2023.114659

Environ Res. 2023 Sep 8:117085. doi: 10.1016/j.envres.2023.117085. Online ahead of print.

ABSTRACT

This study was carried out to evaluate and analyze the fluctuations in groundwater for certain trace metals (Fe, Mn, Cu, Zn, Al, Cd, Cr, Pb, As, and Se) in Taizhou City over three years (2020-2022), evaluate the potential human health risks due to the consumption of groundwater. To quantify the spatiotemporal changes in groundwater trace metals, the heavy metal pollution index (HPI) and heavy metal evaluation index (HEI) were utilized. Furthermore, multivariate statistical methods were utilized to distinguish the sources of trace elements. Deterministic health risk assessment and Monte Carlo health risk simulation methods were employed to evaluate human health risks associated with exposure to trace metals. The results indicate that areas with higher pollution are in the south-central region, with low HPI increasing from 50% to 75% and low HEI from 68.75% to 81.25%, reflecting improved water quality. Correlation matrix analysis and principal component analysis (PCA) pinpointed anthropogenic sources as major trace metal contributors. Cr and As concentrations were associated with farming activities, Cd and Pb concentrations showed links to local industries such as e-waste recycling and shipbuilding. Furthermore, Cu levels in groundwater was influenced by the combined effects of industry, agriculture, and urban sewage discharge. Based on the hazard quotient (HQ) and hazard index (HI) calculations, the majority of groundwater samples did not exceed the reference values, indicating acceptable noncarcinogenic risks for both adults and children. However, the analysis of carcinogenic risk (CR) and uncertainty revealed an overall decreasing trend in carcinogenic risk, with Cr and Cd possessing the highest potential for causing carcinogenic risks. The sensitivities were 46.3%, 53.3%, and 70.3% for Cr, and 18.8%, 27.6%, and 9.3% for Cd.

PMID:37690628 | DOI:10.1016/j.envres.2023.117085

Photodiagnosis Photodyn Ther. 2023 Sep 7:103772. doi: 10.1016/j.pdpdt.2023.103772. Online ahead of print.

ABSTRACT

PURPOSE: To determine alterations of the choroidal thickness (CT) and the choroidal vascularity index (CVI) in patients with glomerular hyperfiltration, a marker of early diabetic nephropathy (DN).

METHODS: Twenty-two patients with type 2 diabetes (T2D) with glomerular hyperfiltration (early DN group) and 28 patients with T2D without DN (NDN group) were included in the study. Patients with diabetic retinopathy were excluded. Parameters including subfoveal CT, the subfoveal choroidal vascularity index (CVI), and total CVI were measured using spectral-domain enhanced depth imaging optical coherence tomography method.

RESULTS: The early DN group included 22 patients and the NDN group comprised 28 patients. The groups were similar in terms of age and sex (p>0.05). The CT values were statistically significantly lower in the early DN group than in the NDN group (p < 0.001). There was no significant difference between the early DN group and the NDN group in terms of total and subfoveal CVI (p>0.05).

CONCLUSION: The choroidal thickness decreased in patients with T2D with glomerular hyperfiltration, but there were no differences in CVI when they were compared with patients with T2D without DN.

PMID:37690616 | DOI:10.1016/j.pdpdt.2023.103772

J Obstet Gynaecol Can. 2023 Sep 8:102215. doi: 10.1016/j.jogc.2023.102215. Online ahead of print.

ABSTRACT

OBJECTIVE: The purpose of this study was to measure the proportion of non-vaccination for pertussis in mothers in Canada who had been advised by their prenatal care provider to get vaccinated, and to identify socio-demographic factors and beliefs associated with non-vaccination.

METHODS: The Survey on Vaccination during Pregnancy (part of childhood National Immunization Coverage Survey) included biological mothers of children born from September 2018 to March 2019. This analysis was restricted to 2,657 mothers who had been advised by their prenatal care provider to get vaccinated against pertussis during pregnancy and knew whether or not they had been vaccinated.

RESULTS: Of those who had been advised to get vaccinated against pertussis, 21% were not. This rate varied across provinces and territories, ranging from 9% in Prince Edward Island to 32% in Newfoundland and Labrador. Factors independently associated with pertussis non-vaccination included lower household income, having had past live births, and having received prenatal care from an obstetrician-gynecologist or a midwife compared to a family doctor. The risk of pertussis non-vaccination despite prenatal care advice was higher for those who disagreed that the baby will be at greater risk of pertussis if the mother does not get vaccinated. It was also higher for those who disagreed with statements regarding perceived benefits for vaccination. Conversely, disagreement with statements on perceived barriers were negatively associated with pertussis non-vaccination.

CONCLUSION: These findings highlight the underlying factors associated with non-vaccination against pertussis despite prenatal care provider recommendation. Some inaccurate beliefs about pertussis and vaccination during pregnancy persist, leading to non-vaccination.

PMID:37690611 | DOI:10.1016/j.jogc.2023.102215

Orthop Traumatol Surg Res. 2023 Sep 8:103682. doi: 10.1016/j.otsr.2023.103682. Online ahead of print.

ABSTRACT

INTRODUCTION: Over the past decades, numerous structural changes in implants, medical treatments, and surgical technics have been made for Malignant Bone Tumors (MBT) around the knee. However, the overall care improvement is still unclear. The method is crucial when analyzing outcomes in surveys involving tumors, and a thorough assessment of the mortality is mandatory because death acts as competing event. The aims of this study were 1) a comprehensive and longitudinal assessment of the revisions with an extensive follow-up and adequate methods 2) a complete mortality review to consider competing risks.

HYPOTHESIS: The hypothesis was that some prosthesis’s structural improvements were made while the surgical toll increased as well as an improvement of mortality was also expected.

MATERIAL AND METHODS: Analyses were performed on 248 patients with MBT (mean follow-up was 8.7 years, surgeries between 1972 and 2017). Three prosthesis models were successively used over time: 120 Guepar (older model), 42 Tornier, and 86 Stanmore (more recent model). The primary outcome was the assessment of revisions sorted out according to Henderson: type-1 soft-tissue failures or instability, type-2 aseptic loosening, type-3 structural failures, type-4 periprosthetic infections, type-5 tumoral progression. Death and amputations were considered as competing events. An extensive assessment of mortality was performed by merging the dataset with the French register of Deaths (INSEE). Cumulative probabilities were computed at 2, 5, 10, and 15 years and compared with Gray’s tests.

RESULTS: The overall 5-year survival was, 80% (95% CI: 73-87) for Guepar, 69% (95% CI: 56-84) for Tornier, and 71% (95% CI: 62-82) for Stanmore (p = 0.4). The 5-year cumulative risks for type-1 were 5% (95% CI: 1-9), 9% (95% CI: 0-18), and 17% (95% CI: 9-25) for Guepar, Tornier, and Stanmore, respectively (p =0.01). The 15-year cumulative risks for type-2 were 22% (95% CI: 15-39), 8% (95% CI: 0-17) and 8% (95% CI: 2-14) for Guepar, Tornier, and Stanmore, respectively (p = 0.10). Ten patients had an implant failure, nine Guepar, and one Tornier. The 5-year cumulative risks for type-4 were 7% (95% CI: 2-12), 19% (95% CI: 7-31), and 12% (95% CI: 5-18) for Guepar, Tornier, and Stanmore, respectively (p = 0.08). There were 29 tumoral progressions; the 15-year risks were 16% (95% CI: 2-22), 2% (95% CI: 0-7%), and 12% (95% CI: 4-19%) for Guepar, Tornier, and Stanmore, respectively (p= 0.08). No difference whatsoever was found between the proximal tibial and distal femur.

CONCLUSION: There were some improvements in prosthesis design (forged steel instead of cast steel) and probably also in cemented stem fixation, but not in prosthetic joint infection and local recurrence over forty years. The overall mortality did not change significantly over the last 40 years amongst this specific cohort of patients who benefited from a hinge reconstruction prosthesis.

LEVEL OF EVIDENCE: III; comparative case series with sensibility analysis.

PMID:37690605 | DOI:10.1016/j.otsr.2023.103682

Comp Biochem Physiol A Mol Integr Physiol. 2023 Sep 8:111511. doi: 10.1016/j.cbpa.2023.111511. Online ahead of print.

ABSTRACT

Insects experience different kinds of environmental stresses that can impair neural performance, leading to spreading depolarization (SD) of nerve cells and neural shutdown underlying coma. SD is associated with a sudden loss of ion, notably K⁺, homeostasis in the central nervous system. The sensitivity of an insect’s nervous system to stress (e.g., anoxia) can be modulated by acute pre-treatment. Rapid cold hardening (RCH) is a form of preconditioning, in which a brief exposure to low temperature can enhance the stress tolerance of insects. We used a pharmacological approach to investigate whether RCH affects anoxia-induced SD in the locust, Locusta migratoria, via one or more of the following homeostatic mechanisms: (1) Na⁺/K⁺-ATPase (NKA), (2) Na⁺/K⁺/2Cl^– co-transporter (NKCC), and (3) voltage-gated K⁺ (K_v) channels. We also assessed abundance and phosphorylation of NKCC using immunoblotting. We found that inhibition of NKA or K_v channels delayed the onset of anoxia-induced SD in both control and RCH preparations. However, NKCC inhibition preferentially abrogated the effect of RCH. Additionally, we observed a higher abundance of NKCC in RCH preps but no statistical difference in its phosphorylation level, indicating the involvement of NKCC expression or degradation as part of the RCH mechanism.

PMID:37690599 | DOI:10.1016/j.cbpa.2023.111511

J Allergy Clin Immunol. 2023 Sep 8:S0091-6749(23)01117-X. doi: 10.1016/j.jaci.2023.08.033. Online ahead of print.

ABSTRACT

BACKGROUND: Urticaria is characterized by inappropriate mast cell degranulation that leads to the development of wheals and/or angioedema. Twin and family studies indicate that there is a substantial heritable component to urticaria risk.

OBJECTIVE: To identify genomic loci at which common genetic variation influence urticaria susceptibility.

METHODS: Genome-wide association studies (GWAS) of urticaria (including all subtypes) from three European cohorts (UK Biobank, FinnGen, and the HUNT Study) were combined through statistical meta-analysis (14,306 urticaria cases and 650,664 controls). Cases were identified from electronic healthcare records from primary and/or secondary care. To identify putative causal variants and genes, statistical fine-mapping, colocalization, and interrogation of publicly available single-cell transcriptome sequencing resources were performed.

RESULTS: Genome-wide significant associations (p < 5 x 10^-8) were identified at six independent loci. These included two previously reported association signals at 1q44 and the human leucocyte antigen region on chromosome 6. Genes with expected or established roles in mast cell biology were associated with the other four genome-wide association signals (GCSAML, FCER1A, TPSAB1, and CBLB). Colocalization of association signals consistent with the presence of shared causal variants was observed between urticaria susceptibility and increased expression of GCSAML (posterior probability (PP_coloc) = 0.89) and FCER1A (PP_coloc = 0.91) in skin.

CONCLUSION: Common genetic variation influencing the risk of developing urticaria was identified at six genomic loci. The relationship of genes with roles in mast cell biology with several association signals implicates genetic variability of specific components of mast cell function in the development of urticaria.

PMID:37690594 | DOI:10.1016/j.jaci.2023.08.033

Chemosphere. 2023 Sep 8:140134. doi: 10.1016/j.chemosphere.2023.140134. Online ahead of print.

ABSTRACT

Liquid fossil fuels, collectively known as total petroleum hydrocarbons (TPHs), are highly toxic and frequently leak into subsurface environments due to anthropogenic activities. As an in-situ biological remedial option for TPH contamination, aerobic TPH biodegradation is limited due to oxygen’s low solubility in water, and because it is consumed quickly by aerobic bacteria. Thus, we investigated the potential of anaerobic TPH degradation by indigenous fermenting bacteria and Fe(III)-reducing bacteria. Twenty 6-10 m soil cores were collected from a closed military base subject to ongoing TPH contamination since the 1980s. Physicochemical and microbial properties were determined at 0.5-m intervals in each core. To assess the relationship between TPH degradation and microbial Fe(III) reduction, soil samples were grouped into high-TPH (>500 mg kg^-1) and high-Fe(II) (>450 mg kg^-1), high-TPH and low-Fe(II), low-TPH and high-Fe(II), and low-TPH and low-Fe(II) groups. Alpha diversity was significantly lower in high-TPH groups than in low-TPH groups, suggesting that high TPH concentrations exerted a strong selective pressure on bacterial communities. In the high-TPH and low-Fe(II) group, fermenting bacteria, including Microgenomatia and Chlamydiae, were more abundant, suggesting that TPH biodegradation occurred via fermentation. In the high-TPH and high-Fe(II) group, Fe(III)-reducing bacteria, including Geobacter and Zoogloea, were more abundant, suggesting that microbial Fe(III) reduction enhances TPH biodegradation. In contrast, the fermenting and/or Fe(III)-reducing bacteria were not statistically abundant in the low-TPH groups.

PMID:37690548 | DOI:10.1016/j.chemosphere.2023.140134