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2.
ACS Omega ; 9(6): 6505-6526, 2024 Feb 13.
Article in English | MEDLINE | ID: mdl-38371826

ABSTRACT

Equine atypical myopathy (AM) is a severe environmental intoxication linked to the ingestion of protoxins contained in seeds and seedlings of the sycamore maple (Acer pseudoplatanus) in Europe. The toxic metabolites cause a frequently fatal rhabdomyolysis syndrome in grazing horses. Since these toxic metabolites can also be present in cograzing horses, it is still unclear as to why, in a similar environmental context, some horses show signs of AM, whereas others remain clinically healthy. Label-free proteomic analyses on the serum of 26 diseased AM, 23 cograzers, and 11 control horses were performed to provide insights into biological processes and pathways. A total of 43 and 44 differentially abundant proteins between "AM vs cograzing horses" and "AM vs control horses" were found. Disease-linked changes in the proteome of different groups were found to correlate with detected amounts of toxins, and principal component analyses were performed to identify the 29 proteins representing a robust AM signature. Among the pathway-specific changes, the glycolysis/gluconeogenesis pathway, the coagulation/complement cascade, and the biosynthesis of amino acids were affected. Sycamore maple poisoning results in a combination of inflammation, oxidative stress, and impaired lipid metabolism, which is trying to be counteracted by enhanced glycolysis.

3.
ACS Omega ; 8(50): 48557-48571, 2023 Dec 19.
Article in English | MEDLINE | ID: mdl-38144146

ABSTRACT

Thoroughbred (TB) racehorses undergo rigorous conditioning programs to optimize their physical and mental capabilities through varied exercise sessions. While conventional investigations focus on limited hematological and biochemical parameters, this field study employed untargeted metabolomics to comprehensively assess metabolic responses triggered by exercise sessions routinely used in TB conditioning. Blood samples were collected pre- and post-exercise from ten racehorses, divided into two groups based on exercise intensity: high intensity (n = 6, gallop at ± 13.38 m/s, 1400 m) and moderate intensity (n = 4, soft canter at ± 7.63 m/s, 2500 m). Intensity was evaluated through monitoring of the speed, heart rate, and lactatemia. Resting and 30 min post-exercise plasma samples were analyzed using ultraperformance liquid chromatography coupled with high-resolution mass spectrometry. Unsupervised principal component analysis revealed exercise-induced metabolome changes, with high-intensity exercise inducing greater alterations. Following high-intensity exercise, 54 metabolites related to amino acid, fatty acid, nucleic acid, and vitamin metabolism were altered versus 23 metabolites, primarily linked to fatty acid and amino acid metabolism, following moderate-intensity exercise. Metabolomics confirmed energy metabolism changes reported by traditional biochemistry studies and highlighted the involvement of lipid and amino acid metabolism during routine exercise and recovery, aspects that had previously been overlooked in TB racehorses.

4.
BMJ Med ; 2(1): e000427, 2023.
Article in English | MEDLINE | ID: mdl-37920150

ABSTRACT

Objective: To evaluate the efficacy of covid-19 convalescent plasma to treat patients admitted to hospital for moderate covid-19 disease with or without underlying immunodeficiency (CORIPLASM trial). Design: Open label, randomised clinical trial. Setting: CORIMUNO-19 cohort (publicly supported platform of open label, randomised controlled trials of immune modulatory drugs in patients admitted to hospital with moderate or severe covid-19 disease) based on 19 university and general hospitals across France, from 16 April 2020 to 21 April 2021. Participants: 120 adults (n=60 in the covid-19 convalescent plasma group, n=60 in the usual care group) admitted to hospital with a positive SARS-CoV2 test result, duration of symptoms <9 days, and World Health Organization score of 4 or 5. 49 patients (n=22, n=27) had underlying immunosuppression. Interventions: Open label randomisation to usual care or four units (200-220 mL/unit, 2 units/day over two consecutive days) of covid-19 convalescent plasma with a seroneutralisation titre >40. Main outcome measures: Primary outcomes were proportion of patients with a WHO Clinical Progression Scale score of ≥6 on the 10 point scale on day 4 (higher values indicate a worse outcome), and survival without assisted ventilation or additional immunomodulatory treatment by day 14. Secondary outcomes were changes in WHO Clinical Progression Scale scores, overall survival, time to discharge, and time to end of dependence on oxygen supply. Predefined subgroups analyses included immunosuppression status, duration of symptoms before randomisation, and use of steroids. Results: 120 patients were recruited and assigned to covid-19 convalescent plasma (n=60) or usual care (n=60), including 22 (covid-19 convalescent plasma) and 27 (usual care) patients who were immunocompromised. 13 (22%) patients who received convalescent plasma had a WHO Clinical Progression Scale score of ≥6 at day 4 versus eight (13%) patients who received usual care (adjusted odds ratio 1.88, 95% credible interval 0.71 to 5.24). By day 14, 19 (31.6%) patients in the convalescent plasma group and 20 (33.3%) patients in the usual care group needed ventilation, additional immunomodulatory treatment, or had died. For cumulative incidence of death, three (5%) patients in the convalescent plasma group and eight (13%) in the usual care group died by day 14 (adjusted hazard ratio 0.40, 95% confidence interval 0.10 to 1.53), and seven (12%) patients in the convalescent plasma group and 12 (20%) in the usual care group by day 28 (adjusted hazard ratio 0.51, 0.20 to 1.32). In a subgroup analysis performed in patients who were immunocompromised, transfusion of covid-19 convalescent plasma was associated with mortality (hazard ratio 0.39, 95% confidence interval 0.14 to 1.10). Conclusions: In this study, covid-19 convalescent plasma did not improve early outcomes in patients with moderate covid-19 disease. The efficacy of convalescent plasma in patients who are immunocompromised should be investigated further. Trial registration: ClinicalTrials.gov NCT04345991.

5.
Am J Hematol ; 98(12): 1923-1933, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37792521

ABSTRACT

Red blood cells (RBC) transfusion is used to alleviate symptoms and prevent complications in anemic patients by restoring oxygen delivery to tissues. RBC transfusion efficacy, that can be measured by a rise in hemoglobin (Hb) concentration, is influenced by donor-, product-, and recipient-related characteristics. In some studies, severe pre-transfusion anemia is associated with a greater than expected Hb increment following transfusion but the biological mechanism underpinning this relationship remains poorly understood. We conducted a prospective study in critically ill patients and quantified Hb increment following one RBC transfusion. In a murine model, we investigated the possibility that, in conjunction with the host erythropoietic response, the persistence of transfused donor RBC is improved to maintain a highest RBC biomass. We confirmed a correlation between a greater Hb increment and a deeper pre-transfusion anemia in a cohort of 17 patients. In the mouse model, Hb increment and post-transfusion recovery were increased in anemic recipients. Post-transfusion RBC recovery was improved in hypoxic mice or those receiving an erythropoiesis-stimulating agent and decreased in those treated with erythropoietin (EPO)-neutralizing antibodies, suggesting that EPO signaling is necessary to observe this effect. Irradiated recipients also showed decreased post-transfusion RBC recovery. The EPO-induced post-transfusion RBC recovery improvement was abrogated in irradiated or in macrophage-depleted recipients, but maintained in splenectomized recipients, suggesting a mechanism requiring erythroid progenitors and macrophages, but which is not spleen-specific. Our study highlights a physiological role of EPO in downregulating post-transfusion RBC clearance, contributing to maintain a vital RBC biomass to rapidly cope with hypoxemia.


Subject(s)
Anemia , Erythropoietin , Humans , Animals , Mice , Prospective Studies , Anemia/drug therapy , Anemia/etiology , Erythropoietin/pharmacology , Erythropoietin/therapeutic use , Erythropoiesis/physiology , Erythrocytes
6.
Blood Adv ; 7(24): 7608-7620, 2023 12 26.
Article in English | MEDLINE | ID: mdl-37699002

ABSTRACT

ABSTRACT: Red blood cell (RBC) transfusion is a major therapy for sickle cell disease (SCD). Patients are at risk of forming antibodies to RBC antigens, which can result in the impossibility to find compatible units and can cause hemolytic transfusion reactions. This retrospective study investigates the evolution of RBC consumption and the frequencies, specificities, and chronology of the appearance of antibodies in a population of patients consistently receiving RH (C, D, E, c, e) and K-matched RBC units (RBCus) from a predominantly European donor population. Over the 11-year period in the Paris area, 6496 patients received transfusion at least once for a total of 239 944 units. Antibodies were made by 1742 patients. The first antibodies of a patient were predictive of subsequent immunization. By the 17th RBCu transfused (by the 20th, excluding warm autoantibodies), 75% of the patients who would make antibodies had made their first. By the 16th, 90% who would make antibodies to a high frequency antigen had made their first antibody to these antigens. Females made their first antibodies slightly earlier than males. Patients who received multiple transfusions (>50 units) had a higher immunization prevalence than those who rarely received transfusion (<12 units) but fewer clinically significant antibodies. Patients with SCD and prophylactic RH-K matching not immunized by the 20th RBCu are likely to have a low alloimmunization risk (to antigens other than RH-K), that is, be low responders, especially relative to the most clinically significant antibodies. This number of 20 units is a point before which close monitoring of patients is most important but remains open to future adjustment.


Subject(s)
Anemia, Hemolytic, Autoimmune , Anemia, Sickle Cell , Male , Female , Humans , Erythrocytes , Retrospective Studies , Isoantibodies , Anemia, Hemolytic, Autoimmune/epidemiology , France/epidemiology
7.
Animals (Basel) ; 13(15)2023 Jul 26.
Article in English | MEDLINE | ID: mdl-37570219

ABSTRACT

Equine atypical myopathy is caused by hypoglycin A (HGA) and methylenecyclopropylglycine (MCPrG), the known protoxins of sycamore maple (Acer pseudoplatanus). Various tissues from five atypical myopathy cases were analyzed but only HGA was found. Whether deamination of MCPrG has already occurred in the intestine as the first stage of metabolization has not been investigated. Activation of the protoxins to methylenecyclopropylacetyl (MCPA)-CoA and methylenecyclopropylformyl (MCPF)-CoA, respectively, occurred mainly in the skeletal muscles, as evidenced by very high concentrations of MCPA-carnitine and MCPF-carnitine in this tissue. Inhibition of the acyl-CoA dehydrogenases of short- and medium-chain as well as branched-chain fatty acids by the toxins led to a strong increase in the corresponding acylcarnitines, again preferentially in skeletal muscles. An accumulation of the long-chain acylcarnitines beyond the level of the control samples could not be detected in the tissues. As a high amount of HGA was always found unmetabolized in the organs, we speculate that targeting the interruption of further metabolization might be a way to stop the progression of intoxication. Inhibition of the mitochondrial branched-chain amino acid aminotransferase, i.e., the first enzyme responsible for the activation of sycamore maple protoxins, could be a therapeutic approach.

9.
J Cardiothorac Vasc Anesth ; 37(5): 724-731, 2023 05.
Article in English | MEDLINE | ID: mdl-36822891

ABSTRACT

OBJECTIVES: To assess whether a Quantra-guided hemostatic algorithm would reduce transfusion requirement and major bleeding compared with laboratory-guided testing in patients facing high-bleeding-risk cardiac surgery. DESIGN: Single-center before-and-after study. SETTING: University hospital. PARTICIPANTS: Patients facing high-bleeding-risk cardiac surgery with cardiopulmonary bypass. INTERVENTIONS: Hemostatic algorithm was based on standard laboratory testing during the control period, then on the Quantra during the Quantra period. The primary endpoint was the number of red blood cell (RBC) units transfused on day 1 after surgery. MEASUREMENTS AND MAIN RESULTS: After propensity-score matching, 66 patients were included in the Quantra group and 117 in the control group. The Quantra group received fewer RBC units on day 1 than the control group (2 [0-5] v 4 [2-6], p = 0.016, respectively). Intraoperatively, the Quantra group received fewer RBC (2 [0-3] v 3 [1-5], p = 0.005), less fresh frozen plasma (0 [0-3] v 3[2-5], p < 0.0001), and fewer platelet units (7.5 [0-10] v 8.2 [6.3-11.7], p = 0.014). The intraoperative rates of RBC, plasma, and platelet transfusion were reduced (64% v 78%, p = 0.05; 41% v 85%, p < 0.001; 55% v 82%, p = 0.001, respectively). The RBC and plasma transfusions were reduced on days 1, 2, and 7. The incidence of major bleeding on day 1 also was reduced (36% v 56%, p = 0.014). In multivariate analysis, implementation of the Quantra-guided hemostatic algorithm was associated independently with reductions in major bleeding. CONCLUSION: Implementation of a Quantra-based hemostatic algorithm was associated with a decrease in transfusion requirement and major bleeding after high-bleeding-risk cardiac surgery. Randomized trials are needed to confirm these results.


Subject(s)
Cardiac Surgical Procedures , Hemostatics , Humans , Thrombelastography/methods , Hemorrhage/etiology , Cardiac Surgical Procedures/adverse effects , Algorithms
10.
J Clin Med ; 11(14)2022 Jul 09.
Article in English | MEDLINE | ID: mdl-35887750

ABSTRACT

Preoperative transfusion (PT) reduces acute postoperative vaso-occlusive events (VOE) in sickle cell disease (SCD), but exposes patients to alloimmunization, encouraging a recent trend towards transfusion sparing. The aim of this study was to investigate the benefit-risk ratio of PT before cholecystectomy on the occurrence of postoperative VOE. Adult SCD patients who underwent cholecystectomy between 2008 and 2019 in our center were included. Patients' characteristics, collected retrospectively, were compared according to PT. A total of 79 patients were included, 66% of whom received PT. Gallbladder histopathology found chronic cholecystitis (97%) and gallstones (66%). Transfused patients underwent more urgent surgeries and had experienced more painful vaso-occlusive crises (VOC) in the month before surgery (p = 0.05). Four (8.5%) post-transfusion alloimmunizations occurred, and two of them caused a delayed hemolytic transfusion reaction (DHTR) (4.3%). The occurrence of postoperative VOE was similar between the groups (19.2% vs. 29.6%, p = 0.45). Though not statistically significant, a history of hospitalized VOC within 6 months prior to surgery seemed to be associated to postoperative VOE among non-transfused patients (75% vs. 31.6%, p = 0.10). PT before cholecystectomy exposes to risks of alloimmunization and DHTR that could be avoided in some patients. Recent VOCs appear to be associated with a higher risk of postoperative VOE and prompt the preemptive transfusion of these patients.

11.
Toxins (Basel) ; 14(8)2022 07 26.
Article in English | MEDLINE | ID: mdl-35893754

ABSTRACT

Acer pseudoplatanus is a worldwide-distributed tree which contains toxins, among them hypoglycin A (HGA). This toxin is known to be responsible for poisoning in various species, including humans, equids, Père David's deer and two-humped camels. We hypothesized that any herbivore pasturing with A. pseudoplatanus in their vicinity may be at risk for HGA poisoning. To test this hypothesis, we surveyed the HGA exposure from A. pseudoplatanus in species not yet described as being at risk. Animals in zoological parks were the major focus, as they are at high probability to be exposed to A. pseudoplatanus in enclosures. We also searched for a toxic metabolite of HGA (i.e., methylenecyclopropylacetyl-carnitine; MCPA-carnitine) in blood and an alteration of the acylcarnitines profile in HGA-positive animals to document the potential risk of declaring clinical signs. We describe for the first instance cases of HGA poisoning in Bovidae. Two gnus (Connochaetes taurinus taurinus) exposed to A. pseudoplatanus in their enclosure presented severe clinical signs, serum HGA and MCPA-carnitine and a marked modification of the acylcarnitines profile. In this study, even though all herbivores were exposed to A. pseudoplatanus, proximal fermenters species seemed less susceptible to HGA poisoning. Therefore, a ruminal transformation of HGA is hypothesized. Additionally, we suggest a gradual alteration of the fatty acid metabolism in case of HGA poisoning and thus the existence of subclinical cases.


Subject(s)
2-Methyl-4-chlorophenoxyacetic Acid , Acer , Deer , Horse Diseases , Muscular Diseases , Animals , Carnitine , Herbivory , Horses , Humans
12.
Vox Sang ; 117(5): 693-700, 2022 May.
Article in English | MEDLINE | ID: mdl-34985763

ABSTRACT

BACKGROUND AND OBJECTIVES: Most myelodysplastic syndromes (MDS) patients become red blood cell (RBC) transfusion-dependent. Transfusing MDS patients with prophylactically RH-KEL1 antigen-matched (PAM) RBC units is recommended to avoid RBC allo-immunization. D+C-E-c+e+, D+C-E+c+e- and D+C+E-c-e+ phenotypes are infrequent among French blood donors. To preserve infrequent phenotype RBC units for patients other than MDS, and to manage frequent phenotype RBC unit stocks, we let, for 1 year, higher-risk non-immunized chronically transfused MDS and acute myeloid leukaemia (AML) patients receive RBC transfusions matched only for D. Our objectives were to evaluate the impact of non-PAM transfusions on the transfusion policy (which would be modified in case of RBC allo-immunization) for frequent and infrequent phenotypes patients and to estimate the number of infrequent phenotypes RBC units that could be redistributed to other patients. RESULTS: Ninety patients were enrolled. Thirty-five patients had infrequent phenotypes, nine received only PAM RBC (143 units) and 26 PAM and non-PAM RBC (415 and 532, respectively): none developed allo-immunization. Fifty-five patients had frequent RBC phenotypes, 34 received only PAM RBC (561 units) and three developed antibodies (2 non-RH-KEL1 and one anti-E); 21 received PAM and non-PAM RBC (436 and 109, respectively) and one developed allo-immunization (unknown specificity). Our strategy enabled us to preserve 532 infrequent phenotypes RBC units: 216 D+C-E-c+e+, 33 D+C-E+c+e- and 283 D+C+E-c-e+ units, representing 48.8% of the total number of RBC units received by infrequent phenotypes patients during the study period. CONCLUSION: Allowing the transfusion of non-PAM RBC in selected chronically transfused MDS and AML patients was feasible and enabled to redistribute infrequent phenotypes RBC units to other patients in need.


Subject(s)
Blood Group Antigens , Leukemia, Myeloid, Acute , Myelodysplastic Syndromes , Erythrocytes , Humans , Isoantibodies , Leukemia, Myeloid, Acute/therapy , Myelodysplastic Syndromes/therapy
15.
J Proteome Res ; 20(10): 4681-4692, 2021 Oct 01.
Article in English | MEDLINE | ID: mdl-34435779

ABSTRACT

Atypical myopathy (AM) is a severe rhabdomyolysis syndrome that occurs in grazing horses. Despite the presence of toxins in their blood, all horses from the same pasture are not prone to display clinical signs of AM. The objective of this study was to compare the blood metabolomic profiles of horses with AM clinical signs with those of healthy co-grazing (Co-G) horses. To do so, plasma samples from 5 AM horses and 11 Co-G horses were investigated using untargeted metabolomics. Metabolomic data were evaluated using unsupervised, supervised, and pathway analyses. Unsupervised principal component analysis performed with all detected features separated AM and healthy Co-G horses. Supervised analyses had identified 1276 features showing differential expression between both groups. Among them, 46 metabolites, belonging predominantly to the fatty acid, fatty ester, and amino acid chemical classes, were identified by standard comparison. Fatty acids, unsaturated fatty acids, organic dicarboxylic acids, and fatty esters were detected with higher intensities in AM horses in link with the toxins' pathological mechanism. The main relevant pathways were lipid metabolism; valine, leucine, and isoleucine metabolism; and glycine metabolism. This study revealed characteristic metabolite changes in the plasma of clinically affected horses, which might ultimately help scientists and field veterinarians to detect and manage AM. The raw data of metabolomics are available in the MetaboLights database with the access number MTBLS2579.


Subject(s)
Horse Diseases , Muscular Diseases , Animals , Horse Diseases/diagnosis , Horses , Metabolomics
16.
J Clin Med ; 10(11)2021 Jun 02.
Article in English | MEDLINE | ID: mdl-34199655

ABSTRACT

BACKGROUND: We aimed to describe red blood cell (RBC) transfusions in the emergency department (ED) with a particular focus on the hemoglobin (Hb) level thresholds that are used in this setting. METHODS: This was a cross-sectional study of 12 EDs including all adult patients that received RBC transfusion in January and February 2018. Descriptive statistics were reported. Logistic regression was performed to assess variables that were independently associated with a pre-transfusion Hb level ≥ 8 g/dL. RESULTS: During the study period, 529 patients received RBC transfusion. The median age was 74 (59-85) years. The patients had a history of cancer or hematological disease in 185 (35.2%) cases. Acute bleeding was observed in the ED for 242 (44.7%) patients, among which 145 (59.9%) were gastrointestinal. Anemia was chronic in 191 (40.2%) cases, mostly due to vitamin or iron deficiency or to malignancy with transfusion support. Pre-transfusion Hb level was 6.9 (6.0-7.8) g/dL. The transfusion motive was not notified in the medical chart in 206 (38.9%) cases. In the multivariable logistic regression, variables that were associated with a higher pre-transfusion Hb level (≥8 g/dL) were a history of coronary artery disease (OR: 2.09; 95% CI: 1.29-3.41), the presence of acute bleeding (OR: 2.44; 95% CI: 1.53-3.94), and older age (OR: 1.02/year; 95% CI: 1.01-1.04). CONCLUSION: RBC transfusion in the ED was an everyday concern and involved patients with heterogeneous medical situations and severity. Pre-transfusion Hb level was rather restrictive. Almost half of transfusions were provided because of acute bleeding which was associated with a higher Hb threshold.

17.
Crit Care Med ; 49(6): 912-922, 2021 06 01.
Article in English | MEDLINE | ID: mdl-33591005

ABSTRACT

OBJECTIVES: Transfusions of blood products are common in critically ill patients and have a potential for immunomodulation. The aim of this study is to address the impact of transfusion of blood products on the susceptibility to ICU-acquired infections in the high-risk patients with septic shock. DESIGN: A single-center retrospective study over a 10-year period (2008-2017). SETTING: A medical ICU of a tertiary-care center. PATIENTS: All consecutive patients diagnosed for septic shock within the first 48 hours of ICU admission were included. Patients who were discharged or died within the first 48 hours were excluded. INTERVENTIONS: RBC, platelet, and fresh frozen plasma transfusions collected up to 24 hours prior to the onset of ICU-acquired infection. MEASUREMENTS AND MAIN RESULTS: During the study period, 1,152 patients were admitted for septic shock, with 893 patients remaining alive in the ICU after 48 hours of management. A first episode of ICU-acquired infection occurred in 28.3% of the 48-hour survivors, with a predominance of pulmonary infections (57%). Patients with ICU-acquired infections were more likely to have received RBC, platelet, and fresh frozen plasma transfusions. In a multivariate Cox cause-specific analysis, transfusions of platelets (cause-specific hazard ratio = 1.55 [1.09-2.20]; p = 0.01) and fresh frozen plasma (cause-specific hazard ratio = 1.38 [0.98-1.92]; p = 0.05) were independently associated with the further occurrence of ICU-acquired infections. CONCLUSIONS: Transfusions of platelets and fresh frozen plasma account for risk factors of ICU-acquired infections in patients recovering from septic shock. The occurrence of ICU-acquired infections should be considered as a relevant endpoint in future studies addressing the indications of transfusions in critically ill patients.


Subject(s)
Blood Transfusion/statistics & numerical data , Critical Illness/therapy , Cross Infection/epidemiology , Intensive Care Units/statistics & numerical data , Shock, Septic/therapy , Aged , Aged, 80 and over , Female , Health Status , Humans , Male , Middle Aged , Retrospective Studies , Risk Factors , Tertiary Care Centers
18.
Animals (Basel) ; 11(1)2021 Jan 05.
Article in English | MEDLINE | ID: mdl-33466424

ABSTRACT

Equine atypical myopathy (AM) is seasonal intoxication resulting from the ingestion of seeds and seedlings of the sycamore maple (Acer pseudoplatanus) that contain toxins, among them, hypoglycin A (HGA). Literature mentions several cases of AM among gravid mares and in unweaned foals. The objective of this study was to determine whether HGA and/or its metabolite are present in milk from grazing mares exposed to sycamore maple trees as confirmed by detection of HGA and its metabolite in their blood. Four mare/foal couples were included in the study. Both HGA and its metabolite were detectable in all but one of the milk samples. To our knowledge, this is the first study describing transfer of HGA to the milk. This unprecedented observation could partially explain cases of unweaned foals suffering from AM. However, a transplacental transfer of the toxin cannot be excluded for newborn foals. Besides being a source of contamination for offspring, milk contamination by toxins from fruits of trees of the Sapindaceae family might constitute a potential risk for food safety regarding other species' raw milk or dairy products.

19.
Comput Biol Med ; 129: 104171, 2021 02.
Article in English | MEDLINE | ID: mdl-33316552

ABSTRACT

Triple-negative breast cancer (TNBC) heterogeneity represents one of the main obstacles to precision medicine for this disease. Recent concordant transcriptomics studies have shown that TNBC could be divided into at least three subtypes with potential therapeutic implications. Although a few studies have been conducted to predict TNBC subtype using transcriptomics data, the subtyping was partially sensitive and limited by batch effect and dependence on a given dataset, which may penalize the switch to routine diagnostic testing. Therefore, we sought to build an absolute predictor (i.e., intra-patient diagnosis) based on machine learning algorithms with a limited number of probes. To that end, we started by introducing probe binary comparison for each patient (indicators). We based the predictive analysis on this transformed data. Probe selection was first involved combining both filter and wrapper methods for variable selection using cross-validation. We tested three prediction models (random forest, gradient boosting [GB], and extreme gradient boosting) using this optimal subset of indicators as inputs. Nested cross-validation consistently allowed us to choose the best model. The results showed that the fifty selected indicators highlighted the biological characteristics associated with each TNBC subtype. The GB based on this subset of indicators performs better than other models.


Subject(s)
Triple Negative Breast Neoplasms , Algorithms , Computational Biology , Humans , Machine Learning , Triple Negative Breast Neoplasms/genetics
20.
Ethology ; 127(1): 14-31, 2021 Jan.
Article in English | MEDLINE | ID: mdl-33230358

ABSTRACT

Behavior courses face numerous challenges when moving to an online environment, as has been made necessary by the COVID-19 pandemic. These challenges occur largely because behavior courses, like most organismal biology courses, often stress experiential learning through laboratories that involve live animals, as well as a lecture component that emphasizes formative assessment, discussion, and critical thinking. Although online behavior courses may be remote, they can still be interactive and social, and designed with inclusive pedagogy. Here, we discuss some of the key decisions that instructors should consider, provide recommendations, and point out new opportunities for student learning that stem directly from the move to online instruction. Specific topics include challenges related to generating an inclusive and engaging online learning environment, synchronous versus asynchronous formats, assignments that enhance student learning, testing format and execution, grade schemes, design of laboratory experiences including opportunities for community science, design of synthetic student projects, and workload balance for students and instructors. We designed this primer both for animal behavior instructors who need to quickly transition to online teaching in the midst of a pandemic, and for those facing such transitions in upcoming terms. Much of the manuscript's content should also be of general interest and value to instructors from all areas of organismal biology who are attempting to quickly transition to online teaching.

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