Raw Data Files for Collateral Sensitivity Profiling in Drug-Resistant Escherichia coli Identifies Natural Products Suppressing Cephalosporin Resistance
Notice bibliographique
Résumé
Raw Data Files for the Following Publication: Collateral Sensitivity Profiling in Drug-Resistant Escherichia coli Identifies Natural Products Suppressing Cephalosporin Resistance E_coli_CSP_Antibioitic_MIC_R1.csv; E_coli_CSP_Antibioitic_MIC_R2.csv; E_coli_CSP_Antibioitic_MIC_R3.csv: Raw MIC values for all 80 antibiotic compounds against wild type and 29 drug-resistant strains of E. coli, as specified in the main manuscript. Antibiotics are arranged along the horizontal axis with their structural class indicated one row above. Drug-resistant strains, along with their mutant gene and strain designation, are arranged along the vertical axis. All values are in micromolar. >128 denotes MIC values greater than 128 micromolar. E_coli_CSP_NP_Library_OD600.csv: Raw OD600 absorbance values from CSP screening of 6,195 natural product extract prefractions against wild type and 29 drug-resistant strains of E. coli, as described in the main manuscript. Drug-resistant strains are arranged along the horizontal axis. Extracts are arranged along the vertical axis. Extracts that begin with RLCA denote Burkoholderia-derived extracts. Extracts that begin with RLUS denote marine Actinobacterial extracts. Extracts with the same letter and number code but different alphabetical character at the end (A to F) denote different prefractions of the same extract. All values represent the difference of the T20 and T0 measurements. E_coli_CSP_NP_Secondary_Screen_MIC.csv: Raw MIC values for 117 natural product extract prefractions selected for secondary screening, screened against wild type and 29 drug-resistant strains of E. coli as 16x two-fold dilution series, as described in the main manuscript. Drug-resistant strains are arranged along the horizontal axis. Extracts are arranged along the vertical axis. Extracts that begin with RLCA denote Burkoholderia-derived extracts. Extracts that begin with RLUS denote marine Actinobacterial extracts. Extracts with the same letter and number code but different alphabetical character at the end (A to F) denote different prefractions of the same extract. Since extract concentrations cannot be determined, the MIC values have been annotated using relative concentration values (1 = stock concentration, 0.5 = 1x two-fold dilution, 0.25 = 2x two-fold dilution, etc.). E_coli_CSP_Borrelidins_OD600: Normalized percent growth values (100% maximum growth; 0% no growth) for borrelidins A, F, H, and P between 256/128 uM to 0.0078/0.0039 uM against select strains: wild type E. coli MG1655, Cip2KB, Cef8, Cef1, Cef6, Cef7, Kn15, RK2, MG1655 (thrS) -IPTG, MG1655 (thrS) +IPTG, Cef6 (thrS) -IPTG, Cef6 (thrS) +IPTG, Cef7 (thrS) -IPTG, Cef7 (thrS) +IPTG. All strains were tested in triplicate. E_coli_CSP_Resistance_Passaging_MIC: Ceftazidime MIC values obtained during the serial passaging experiment under four separate conditions (Cef, ceftazidime in increasing concentrations; Cef+BorA_32uM, ceftazidime in increasing concentrations and borrelidin A at 32 uM; Cef+BorA_128uM, ceftazidime in increasing concentrations and borrelidin A at 128 uM; Cef+Nor, ceftazidime in increasing concentrations and norfloxacin in increasing concentrations) over 12 days. Each condition was tested using three replicates sourced from a wild type strain of E. coli MG1655. E_coli_CSP_Resistance_Passaging_MIC_12th_Day: Raw MIC values for ceftazidime, cefadroxil, cefaclor, norfloaxcin, ciprofloxacin, and borreidin A against the drug-resistant strains obtained from the serial passaging experiment under four separate conditions (Cef, ceftazidime in increasing concentrations; Cef+BorA_32uM, ceftazidime in increasing concentrations and borrelidin A at 32 uM; Cef+BorA_128uM, ceftazidime in increasing concentrations and borrelidin A at 128 uM; Cef+Nor, ceftazidime in increasing concentrations and norfloxacin in increasing concentrations). Each condition was tested in triplicate, with three replicate samples selected for each condition. Test antibiotics are arranged along the horizontal axis while the drug-resistant strains are arranged along the vertical axis. E_coli_CSP_Checkerboard_Assay_OD600: Normalized percent growth values for checkerboard co-dosing assays between borrelidin A x ceftazidime and borrelidin A x ampicillin against E. coli MG1655, Ce7, and RK2. Borrelidin A is co-dosed with either ceftazidime or ampicillin using a combination concentrations from 128 uM to 15.6 nM. E_coli_CSP_Borrelidin_MS_Quantitation: Concentrations of borrelidin A or mupirocin control in either the supernatant or cell lysate fractions for the WT, Cef6, and Cef7 strains as determined by targeted quantification using HPLC-HRMS with MRM.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,002 | 0,013 |
| Méta-épidémiologie (sens strict) | 0,002 | 0,001 |
| Méta-épidémiologie (sens large) | 0,002 | 0,002 |
| Bibliométrie | 0,004 | 0,008 |
| Études des sciences et des technologies | 0,002 | 0,000 |
| Communication savante | 0,003 | 0,002 |
| Science ouverte | 0,002 | 0,002 |
| Intégrité de la recherche | 0,002 | 0,003 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,395 | 0,194 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».