[2025-10-01T11:11:41.445406] [QUERYOME] Starting research for query 1452: '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:
All the following markers are expressed on the surface of T-cells at some stage of development except: 

Options:
{'A': 'CDIa', 'B': 'PAX5', 'C': 'CD 34', 'D': 'Tdt'}'
[2025-10-01T11:11:41.506583] [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:
All the following markers are expressed on the surface of T-cells at some stage of development except: 

Options:
{'A': 'CDIa', 'B': 'PAX5', 'C': 'CD 34', 'D': 'Tdt'}'
[2025-10-01T11:11:41.510786] Saving text to bench_final/run1/medmcqa/medmcqa_1451/pi_initial_prompt.txt
[2025-10-01T11:11:41.516220] [PI] Calling o3 for initial analysis...
[2025-10-01T11:11:48.150765] [PI] Reasoning iteration 1
[2025-10-01T11:11:48.152482] [PI reasoning] **Evaluating T cell markers**

I'm looking into a medical question about T cell development markers, particularly which one is NOT expressed at any stage in T cells. I know that PAX5 is a B cell lineage transcription factor and isn't found in T cells. In contrast, CD1a is present on immature T cells, CD34 appears in hematopoietic stem cells, and TdT is expressed in immature T and B cells. So, I conclude that the answer is PAX5. Let's quickly confirm this with some literature!
[2025-10-01T11:11:48.155231] [PI] Executing function call 1: hybrid_search
[2025-10-01T11:11:48.156838] [PI] Function arguments: {'query': 'PAX5 expression confined to B cell lineage not expressed in T cells', 'k': 5, 'faiss_weight': 0.4, 'bm25_weight': 0.6, 'use_rrf': True}
[2025-10-01T11:11:48.159994] Saving JSON to bench_final/run1/medmcqa/medmcqa_1451/pi_iteration_1_tool_call_2_hybrid_search.json
[2025-10-01T11:12:21.016334] [PI] Function hybrid_search executed successfully
[2025-10-01T11:12:21.019714] Saving JSON to bench_final/run1/medmcqa/medmcqa_1451/pi_iteration_1_tool_result_2_hybrid_search.json
[2025-10-01T11:12:21.040551] [PI] Continuing reasoning with 1 function responses...
[2025-10-01T11:12:28.947902] [PI] Reasoning iteration 2
[2025-10-01T11:12:28.950778] [PI] Executing function call 1: hybrid_search
[2025-10-01T11:12:28.952445] [PI] Function arguments: {'query': 'CD1a expression cortical thymocytes immature T cells', 'k': 5, 'faiss_weight': 0.4, 'bm25_weight': 0.6, 'use_rrf': True}
[2025-10-01T11:12:28.955156] Saving JSON to bench_final/run1/medmcqa/medmcqa_1451/pi_iteration_2_tool_call_2_hybrid_search.json
[2025-10-01T11:12:54.351661] [PI] Function hybrid_search executed successfully
[2025-10-01T11:12:54.354514] Saving JSON to bench_final/run1/medmcqa/medmcqa_1451/pi_iteration_2_tool_result_2_hybrid_search.json
[2025-10-01T11:12:54.360832] [PI] Continuing reasoning with 1 function responses...
[2025-10-01T11:12:57.637752] [PI] Reasoning iteration 3
[2025-10-01T11:12:57.640518] [PI] Executing function call 1: hybrid_search
[2025-10-01T11:12:57.642925] [PI] Function arguments: {'query': 'CD34 expression early thymic progenitor T cell', 'k': 5, 'faiss_weight': 0.4, 'bm25_weight': 0.6, 'use_rrf': True}
[2025-10-01T11:12:57.647454] Saving JSON to bench_final/run1/medmcqa/medmcqa_1451/pi_iteration_3_tool_call_2_hybrid_search.json
[2025-10-01T11:13:15.414756] [PI] Function hybrid_search executed successfully
[2025-10-01T11:13:15.416629] Saving JSON to bench_final/run1/medmcqa/medmcqa_1451/pi_iteration_3_tool_result_2_hybrid_search.json
[2025-10-01T11:13:15.427316] [PI] Continuing reasoning with 1 function responses...
[2025-10-01T11:13:28.086512] [PI] Reasoning iteration 4
[2025-10-01T11:13:28.115352] [PI] No function calls found in response
[2025-10-01T11:13:28.116961] [PI] No more function calls - research complete
[2025-10-01T11:13:28.120264] Saving text to bench_final/run1/medmcqa/medmcqa_1451/pi_final_answer.txt
[2025-10-01T11:13:28.124762] [QUERYOME] Query completed successfully
