[2025-10-02T07:36:16.946590] [QUERYOME] Starting research for query 2266: 'Instructions:
 Answer the question below. First, respond with the single best option letter (A, B, C, or D). Then provide a concise reasoning (1–3 sentences). Use both the retrieved evidence and your own medical knowledge to choose the most accurate answer.

Question:
Which of the following statements regarding proteoglycans is true?

Options:
A. consist of a core protein with GAG chains attached.
B. GAG contain oxidized acid sugars
C. negative charges cause to radiate out from the protein
D. All of these'
[2025-10-02T07:36:16.991735] [PI] Starting research for query: 'Instructions:
 Answer the question below. First, respond with the single best option letter (A, B, C, or D). Then provide a concise reasoning (1–3 sentences). Use both the retrieved evidence and your own medical knowledge to choose the most accurate answer.

Question:
Which of the following statements regarding proteoglycans is true?

Options:
A. consist of a core protein with GAG chains attached.
B. GAG contain oxidized acid sugars
C. negative charges cause to radiate out from the protein
D. All of these'
[2025-10-02T07:36:16.993536] Saving text to bench_final/run1/medmcqa/medmcqa_3826/pi_initial_prompt.txt
[2025-10-02T07:36:16.997744] [PI] Calling o3 for initial analysis...
[2025-10-02T07:36:24.817210] [PI] Reasoning iteration 1
[2025-10-02T07:36:24.818915] [PI] Executing function call 1: hybrid_search
[2025-10-02T07:36:24.821794] [PI] Function arguments: {'query': 'proteoglycan core protein with glycosaminoglycan chains negatively charged bottle brush conformation uronic acid oxidized sugar', 'k': 5, 'faiss_weight': 0.7, 'bm25_weight': 0.3, 'use_rrf': True}
[2025-10-02T07:36:24.823603] Saving JSON to bench_final/run1/medmcqa/medmcqa_3826/pi_iteration_1_tool_call_3_hybrid_search.json
[2025-10-02T07:36:26.355257] [PI] Function hybrid_search executed successfully
[2025-10-02T07:36:26.357306] Saving JSON to bench_final/run1/medmcqa/medmcqa_3826/pi_iteration_1_tool_result_3_hybrid_search.json
[2025-10-02T07:36:26.362424] [PI] Continuing reasoning with 1 function responses...
[2025-10-02T07:36:29.649607] [PI] Reasoning iteration 2
[2025-10-02T07:36:29.652489] [PI] Executing function call 1: hybrid_search
[2025-10-02T07:36:29.655850] [PI] Function arguments: {'query': 'proteoglycan bottle brush negative charges cause glycosaminoglycans to extend radiate from core protein', 'k': 5, 'faiss_weight': 0.8, 'bm25_weight': 0.2, 'use_rrf': True}
[2025-10-02T07:36:29.657242] Saving JSON to bench_final/run1/medmcqa/medmcqa_3826/pi_iteration_2_tool_call_2_hybrid_search.json
[2025-10-02T07:36:30.544617] [PI] Function hybrid_search executed successfully
[2025-10-02T07:36:30.546900] Saving JSON to bench_final/run1/medmcqa/medmcqa_3826/pi_iteration_2_tool_result_2_hybrid_search.json
[2025-10-02T07:36:30.552581] [PI] Continuing reasoning with 1 function responses...
[2025-10-02T07:36:35.466986] [PI] Reasoning iteration 3
[2025-10-02T07:36:35.468254] [PI] Executing function call 1: hybrid_search
[2025-10-02T07:36:35.470133] [PI] Function arguments: {'query': 'glycosaminoglycans repeating disaccharide uronic acid oxidized sugar', 'k': 5, 'faiss_weight': 0.8, 'bm25_weight': 0.2, 'use_rrf': True}
[2025-10-02T07:36:35.471701] Saving JSON to bench_final/run1/medmcqa/medmcqa_3826/pi_iteration_3_tool_call_2_hybrid_search.json
[2025-10-02T07:36:36.612657] [PI] Function hybrid_search executed successfully
[2025-10-02T07:36:36.614266] Saving JSON to bench_final/run1/medmcqa/medmcqa_3826/pi_iteration_3_tool_result_2_hybrid_search.json
[2025-10-02T07:36:36.621396] [PI] Continuing reasoning with 1 function responses...
[2025-10-02T07:36:48.145648] [PI] Reasoning iteration 4
[2025-10-02T07:36:48.147152] [PI] No function calls found in response
[2025-10-02T07:36:48.148840] [PI] No more function calls - research complete
[2025-10-02T07:36:48.150568] Saving text to bench_final/run1/medmcqa/medmcqa_3826/pi_final_answer.txt
[2025-10-02T07:36:48.154292] [QUERYOME] Query completed successfully
