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Rafael C. Neves

Rafael C. Neves

· Associate Professor, Food Animal Production MedicineVerified

Purdue University · Department of Veterinary Clinical Sciences

Active 1970–2025

h-index14
Citations939
Papers6131 last 5y
Funding
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Research topics

  • Biology
  • Medicine
  • Animal science
  • Endocrinology
  • Internal medicine
  • Immunology

Selected publications

  • Association between postpartum systemic inflammation and serum calcium in healthy multiparous dairy cows—An exploratory observational analysis

    JDS Communications · 2025-04-01 · 1 citations

    articleOpen access

    × parity, and farm as a random effect. A stepwise backward elimination approach was applied to improve model parsimony. The lowest albumin and greatest haptoglobin and SAA concentrations were observed at d 2. The association of albumin with tCa varied quadratically over time. At d 0, 0.5, 1, and 2, as tCa decreased, albumin increased, but at d 4, 6, and 8 as tCa decreased, albumin also decreased. At d 0, 0.5, and 1, when tCa <1.7 mmol/L, tCa and haptoglobin were positively associated. Total calcium <1.7 mmol/L was not observed ≥d 2. After d 1, cows with lower tCa tended to have greater haptoglobin concentrations. The greatest concentration of SAA occurred when tCa was 1.9 mmol/L. Values of tCa <1.9 mmol/L were mainly observed at d 0. At d 0, and when tCa was <1.9 mmol/L, lower tCa was associated with lesser SAA concentration. However, when tCa was >1.9 mmol/L (93% and 99% of the values observed at d 2 and 4, respectively), lower tCa was associated with greater SAA concentration. The associations between tCa and markers of SI changed in the first 8 d of lactation in clinically healthy cows. Potential interventions to modulate hypocalcemia or SI, or both, should consider their interactions. Future studies should further explore the association of the degree and duration of hypocalcemia and SI to better understand the direction and mechanisms of this relationship.

  • Long-chain fatty acids mediate hepatic metabolic flux in preruminating dairy calves fed flaxseed oil, high oleic soybean oil, or milk fat

    Journal of Dairy Science · 2024-06-13 · 3 citations

    articleOpen access

    Nutrition and physiological state affect hepatic metabolism. Our objective was to determine if feeding flaxseed oil (∼50% C18:3n-3 cis), high oleic soybean oil (∼70% C18:1 cis-9), or milk fat (∼50% C16:0) alters hepatic expression of PC, PCK1, and PCK2 and the flow of carbons from propionate and pyruvate into the TCA cycle in preruminating calves. Male Holstein calves (n = 40) were assigned to a diet of skim milk with either: 3% milk fat (MF; n = 8), 3% flaxseed oil (Flax; n = 8), 3% high oleic soybean oil (HOSO; n = 8), 1.5% MF + 1.5% high oleic soybean oil (MF-HOSO; n = 8), or 1.5% MF + 1.5% flaxseed oil (MF-Flax; n = 8) from d 14 to d 21 postnatal. At d 21 postnatal, a liver biopsy was taken for gene expression and metabolic flux analysis. Liver explants were incubated in [U-13C] propionate and [U-13C] pyruvate to trace carbon flux through TCA cycle intermediates or with [U-14C] lactate, [1-14C] palmitic acid, or [2-14C] propionate to quantify substrate oxidation to CO2 and acid soluble products. Compared with other treatments, plasma C18:3n-3 cis was 10 times higher and C18:1 cis-9 was 3 times lower in both flax (Flax and MF-Flax) treatments. PC, PCK1, and PCK2 expression and flux of [U-13C] pyruvate as well as [U-13C] propionate were not different between treatments. PC expression was negatively correlated with the enrichment of citrate M+5 and malate M+3, and PCK2 was negatively correlated with citrate M+5, suggesting that when expression of these enzymes is increased, carbon from pyruvate enters the TCA cycle via PC mediated carboxylation, and then OAA is converted to phosphoenolpyruvate via PCK2. Acid soluble product formation and PC expression were reduced in HOSO (MF-HOSO and HOSO) treatments compared with flax (MF-Flax and Flax), indicating that fatty acids regulate PC expression and carbon flux, but that fatty acid flux control points are not connected to PC, PCK1, or PCK2. In conclusion, fatty acids regulate hepatic expression of PC, PCK1, and PCK2, and carbon flux, but the point of control is distinct.

  • Evaluating the performance of herd-specific long short-term memory models to identify automated health alerts associated with a ketosis diagnosis in early-lactation cows

    Journal of Dairy Science · 2024-09-07 · 5 citations

    articleOpen accessSenior author

    The growing use of automated systems in the dairy industry generates a vast amount of cow-level data daily, creating opportunities for using these data to support real-time decision-making. Currently, various commercial systems offer built-in alert algorithms to identify cows requiring attention. To our knowledge, no work has been done to compare the use of models accounting for herd-level variability on their predictive ability against automated systems. Long short-term memory (LSTM) models are machine learning models capable of learning temporal patterns and making predictions based on time series data. The objective of our study was to evaluate the ability of LSTM models to identify a health alert associated with a ketosis diagnosis (HAK) using deviations of daily milk yield, milk fat-to-protein ratio (FPR), number of successful milkings, rumination time, and activity index from the herd median by parity and DIM, considering various time series lengths and numbers of days before HAK. Additionally, we aimed to use Explainable Artificial Intelligence method to understand the relationships between input variables and model outputs. Data on daily milk yield, milk FPR, number of successful milkings, rumination time, activity, and health events during 0 to 21 DIM were retrospectively obtained from a commercial Holstein dairy farm in northern Indiana from February 2020 to January 2023. A total of 1,743 cows were included in the analysis (non-HAK = 1,550; HAK = 193). Variables were transformed based on deviations from the herd median by parity and DIM. Six LSTM models were developed to identify HAK 1, 2, and 3 d before farm diagnosis using historic cow-level data with varying time series lengths. Model performance was assessed using repeated stratified 10-fold cross-validation for 20 repeats. The Shapley additive explanations framework (SHAP) was used for model explanation. Model accuracy was 83%, 74%, and 70%; balanced error rate was 17% to 18%, 26% to 28%, and 34%; sensitivity was 81% to 83%, 71% to 74%, and 62%; specificity was 83%, 74%, and 71%; positive predictive value was 38%, 25% to 27%, and 21%; negative predictive value was 97% to 98%, 95% to 96%, and 94%; and area under the curve was 0.89 to 0.90, 0.80 to 0.81, and 0.72 for models identifying HAK 1, 2, and 3 d before diagnosis, respectively. Performance declined as the time interval between identification and farm diagnosis increased, and extending the time series length did not improve model performance. Model explanation revealed that cows with lower milk yield, number of successful milkings, rumination time, and activity, and higher milk FPR compared with herdmates of the same parity and DIM were more likely to be classified as HAK. Our results demonstrate the potential of LSTM models in identifying HAK using deviations of daily milk production variables, rumination time, and activity index from the herd median by parity and DIM. Future studies are needed to evaluate the performance of health alerts using LSTM models controlling for herd-specific metrics against commercial built-in algorithms in multiple farms and for other disorders.

  • A randomized, controlled trial examining quarter-level somatic cell count and culture-based selective dry cow therapy against blanket dry cow therapy on early lactation production outcomes

    Journal of Dairy Science · 2024-05-17 · 5 citations

    articleOpen access

    The objective of this study was to determine quarters requiring antimicrobial treatment using either a benchtop somatic cell counter or culture with gram-positive selective media and compare the outcomes in these cows to those receiving blanket dry cow therapy (BDCT) in a randomized, controlled trial. We evaluated 2 novel methods of identifying cows with intramammary infections followed by selective antimicrobial treatment at a commercial dairy farm to determine their usefulness in decreasing antibiotic usage during the dry period without significant detrimental effects on milk quality and production. Cows (n = 840) were randomly allocated to one of 3 groups (BDCT, gram-positive selective media culture-based selective dry cow therapy [C-SDCT], and somatic cell count-based SDCT [S-SDCT]) the day before dry-off, and quarter-level milk samples (QLMS) were collected. The QLMS from cows in the S-SDCT group were evaluated using the cell counter, and quarters were treated if SCC was ≥200,000 cells/mL, whereas the QLMS from cows in the C-SDCT group were cultured, and quarters were treated if the culture showed growth. All cows in the BDCT received antimicrobial therapy, and all cows received an internal teat sealant regardless of treatment group. Outcomes measured were first and second DHIA test SCC, milk production through 60 DIM, cows leaving the farm, clinical mastitis, and bacteriologic new infections in a subset of quarters. Cows in both SDCT groups had fewer antimicrobial treatments than cows in the BDCT group as was expected, and cows in the C-SDCT group had fewer treatments than those in the S-SDCT group. Cows in both SDCT groups had a higher linear score at the first DHIA test (BDCT: 1.8, S-SDCT: 2.2, C-SDCT: 2.2); however, we found no other differences between groups regarding any other outcomes measured. Although antimicrobial use was significantly reduced, farms should use caution in adopting the benchtop analyzer and the selective media described in this study as ways to identify infected cows for dry cow therapy because they may result in increased linear scores early in lactation.

  • Evaluation of the plasma oxylipin and endocannabinoid profile and the platelet and plasma proteome in postpartum dairy cows experiencing elevated systemic inflammation

    Research Square · 2024-06-03

    preprintOpen accessSenior authorCorresponding
  • The platelet and plasma proteome and targeted lipidome in postpartum dairy cows with elevated systemic inflammation

    Scientific Reports · 2024-12-27 · 9 citations

    articleOpen accessSenior author

    Unregulated, systemic inflammation negatively impacts health and production in dairy cows. Soluble mediators and platelets have been studied for their expansive role in mediating inflammation. Our objectives were to compare the plasma oxylipin and endocannabinoid profiles, and the platelet and plasma proteomic profiles of healthy cows to cows experiencing elevated systemic inflammation as indicated by plasma haptoglobin (Hp) concentrations. Postpartum cows at 3 DIM with plasma Hp concentrations [Formula: see text] 0.50 g/L and no clinical disease were enrolled into the high-inflammation group (n = 8). Cows with plasma Hp concentrations [Formula: see text] 0.1 g/L and no clinical disease were enrolled into the low-inflammation group (n = 8). Targeted lipidomic analysis revealed differences in the plasma oxylipin and endocannabinoid profile between high- and low-inflammation cows. Cows in the high-inflammation group had increased plasma concentrations of the oxylipins 9(S)-HpOTrE, 9(S)-HOTrE, 13(S)-HpOTrE, and 9,10-EpOME, and the endocannabinoid anandamide. In-depth proteomic analysis of platelets between the high- and low-inflammation groups revealed significant differences in protein categories related to platelet granule release and cellular iron uptake. Proteomic outputs from plasma revealed 24 proteins to be different between high and low-inflammation groups, including proteins involved in autophagy and immune mediation. Together, our results indicate that cows experiencing an exacerbated systemic inflammatory response in the postpartum may have impaired disease resistance, and platelets could be contributors to their inflammatory state.

  • Association of Bovine Respiratory Disease during the Pre-Weaning Period with Blood Cell Counts and Circulating Concentration of Metabolites, Minerals, and Acute Phase Proteins in Dairy Calves Transported to a Calf Raising Facility

    Animals · 2024-06-28 · 3 citations

    articleOpen access

    Our objective was to investigate the association of bovine respiratory disease (BRD) occurring within the first 56 days of life with blood cell counts and the circulating concentration of metabolites, minerals, and acute phase proteins throughout the pre-weaning period in dairy calves transported to a heifer raising facility within their first week of life. Data from 305 calves transported from dairies in Minnesota to a calf raising facility in New Mexico within their first four days of life were used in this retrospective cohort study. Blood samples were collected at 7, 17, 34, and 56 days of life for the analysis of blood cell counts, biochemistry, and the concentration of acute phase proteins. Blood urea nitrogen, albumin, GLDH, CK, P, Na, K, Cl, Zn, Hp, SAA, and monocyte counts were associated with BRD status throughout or at least at one of the time points evaluated in this study. In conclusion, several hematological variables were associated with BRD status in dairy calves that underwent transportation stress in early life.

  • Statistical Assessment of Extreme Storm Events on the Brazilian Continental Shelf from 1940 to 2022

    Journal of Coastal Research · 2024-12-20 · 2 citations

    articleOpen access

    Alfredini, P.; Martins, L.F.; Neves, R.C.; Martinez, F.A., and Arasaki, E., 2024. Statistical assessment of extreme storm events on the Brazilian Continental Shelf from 1940 to 2022. In: Phillips, M.R.; Al-Naemi, S., and Duarte, C.M. (eds.), Coastlines under Global Change: Proceedings from the International Coastal Symposium (ICS) 2024 (Doha, Qatar). Journal of Coastal Research, Special Issue No. 113, pp. 175-179. Charlotte (North Carolina), ISSN 0749-0208. The Brazilian Continental Shelf is the largest in Latin America and the South Atlantic Ocean, covering more than 8,500 km and stretching from Latitude S 34° to Latitude N 6°. The Rio de La Plata Delta discharges sediment over a wide area in the southern portion of this shelf. Submerged peaks of the Vitória-Trindade Chain have an influence on an intermediate region of the shelf. Northward, the Continental Shelf becomes thinner, until reaching its maximum width in the Maranhão Gulf and Amazon Mouth. In addition to the different wave climates along the Brazilian coast, around 55% of the country's population lives in the coastal region, with large population concentrations in metropolitan regions, such as Rio de Janeiro, Salvador, Recife and Fortaleza. The oil and gas industry has many offshore structures on the Continental Shelf, and the cargo throughput from ports reached 1.217 billion tons in 2023. Therefore, any change in meteo-oceanographic patterns in Brazilian Continental Shelf can have major impacts because maritime infrastructures and operations tend to be progressively affected by the increasing frequency and intensity of extreme meteorological phenomena due to climate change. Impacts like coastal erosion, augmented occurrence of storms and flooding can damage essential infrastructure in cities, ports, and other coastal and offshore scenarios. Therefore, understanding these changes is necessary for planning and executing actions to mitigate and adapt. The objective of this paper is to make a statistical assessment of a first approach to identify trends that may point changes in the extreme events of storm over the period from 1940 to 2022, assessing time series of wave data from the European Centre for Medium-Range Weather Forecasts ERA 5 Oceanographic Model, in twelve locations of Brazilian Continental Shelf, from the extreme south to the extreme north. The storm events were identified by the peak over threshold method and the statistical assessment employed moving averages for 5 years and was possible to identify an increasing frequency and severity of storm per year from 1980 in the south and a smaller increase in the northern area.

  • Relationship between calcium dynamics and inflammatory status in the transition period of dairy cows

    JDS Communications · 2023-03-16 · 11 citations

    reviewOpen access1st authorCorresponding

    Improvements in nutrition, management, and genetics of dairy cows over the last several decades have shifted research focus from clinical diseases to subclinical disorders, to which transition cows are particularly vulnerable. Recent studies on the characterization of subclinical hypocalcemia (SCH) indicate that the combined analysis of the degree, timing of suboptimal blood Ca concentration, and duration are most reflective of the disorder. Therefore, the understanding of blood Ca dynamics in early postpartum cows has emerged as an avenue to investigate the paths leading to a successful metabolic adaptation to lactation or not. The conundrum has been in defining whether SCH is the cause or a reflection of a greater underlying disorder. Immune activation and systemic inflammation have been proposed to be the root cause of SCH. However, there is a paucity of data investigating the mechanisms of how systemic inflammation can lead to reduced blood Ca concentration in dairy cows. The objective of this review is to discuss the links between systemic inflammation and reduced blood Ca concentration, and studies needed to advance knowledge on the interface between systemic inflammation and Ca metabolism for the transition dairy cow.

  • Plasma oxylipin profile of postpartum dairy cows categorized into different systemic inflammatory grades in the first week after parturition

    JDS Communications · 2023-11-18 · 6 citations

    articleOpen accessSenior authorCorresponding

    Oxygenated polyunsaturated fatty acids (oxylipins) are important mediators of inflammation ranging from pro- to anti-inflammatory actions. Research investigating differences in the oxylipin profile of dairy cows suffering from different degrees of systemic inflammation in the early postpartum period is lacking and can help advance knowledge on potential mechanisms leading to excessive inflammation. The objective of this preliminary study was to evaluate the plasma oxylipin profile of cows classified in 1 of 4 systemic inflammation categories based on plasma haptoglobin (Hp) concentrations assessed on days in milk (DIM) 1, 2, 3, 4, 5, and 7, in addition to the presence or absence of metritis within 10 DIM, and of cows without any clinical diseases within 21 DIM. Groups were classified as follows: (1) cows with a peak Hp concentration ≤3 DIM (EarlyHp) and diagnosed with metritis; (2) cows with a peak Hp concentration 3 < DIM ≤7 (LateHp) and diagnosed with metritis; (3) cows suffering from persistently elevated Hp concentrations assessed on DIM 4 and 7 while remaining apparently healthy during the first 21 DIM (PersistentHp); and (4) apparently healthy cows not suffering from persistently elevated Hp concentrations (LowHp). Six cows from each category were randomly selected from a plasma bank of a parent cohort study including 380 multiparous cows. Plasma samples on DIM 1 and 2, 3 and 4, and 5 and 7 were proportionally pooled to create 3 samples per cow for lipidomic analysis (i.e., pool 1 = DIM 1 and 2; pool 2 = DIM 3 and 4; pool 3: DIM 5 and 7). Statistical analyses were performed using SAS v9.4 (SAS Institute Inc.) and least squares means adjusted for multiple comparisons using the Tukey-Kramer test. Comparisons for EarlyHp and LateHp were only performed on pooled samples from DIM 1 and 2 (i.e., before metritis diagnosis). EarlyHp cows had decreased concentrations of 9(S)-HOTrE compared with LowHp cows of DIM 1-2 pooled samples. LateHp cows had decreased concentrations of 9(10)-DiHOME compared with LowHp cows. Next, we sought to investigate whether cows classified as PersistentHp had time-dependent differences in oxylipin profile versus LowHp cows. PersistentHp cows had decreased concentrations of 19(R)-HETE compared with LowHp cows in a time-dependent manner (only in pooled samples from DIM 5 and 7). Our results identified oxylipins of interest that warrant further investigation to elucidate their in vitro and in vivo functions in the postpartum inflammatory process of dairy cows.

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