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Concepts of Biology SENIOR CONTRIBUTING AUTHORS SAMANTHA FOWLER, CLAYTON STATE UNIVERSITY REBECCA ROUSH, SANDHILLS COMMUNITY COLLEGE JAMES WISE, HAMPTON UNIVERSITY [Image OCR Text] tax” au = §=opens
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written consent of Rice University. 978-1-938168-11-6 978-1-50669-653-9 978-1-947172-03-6 2013 HARDCOVER BOOK ISBN-13 B&W PAPERBACK BOOK ISBN-13 DIGITAL VERSION ISBN-13 ORIGINAL PUBLICATION YEAR 1 2 3 4 5 6 7 8 9 10 RS 23 13
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Burt and Deedee McMurtry Michelson 20MM Foundation National Science Foundation The Open Society Foundations Jumee Yhu and David E. Park III Brian D. Patterson USA-International Foundation The Bill and Stephanie Sick Fund Steven L. Smith & Diana T. Go Stand Together Robin and Sandy Stuart Foundation The Stuart Family Foundation Tammy and Guillermo Treviño Valhalla Charitable Foundation White Star Education Foundation Schmidt Futures William Marsh Rice University
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Contents Preface 1 UNIT 1 THE CELL ULAR FOUNDATION OF LIFE CHAP TER 1 Introduction to Biology 5 Introduction 5 1.1Themes and Concepts of Biology 5 1.2The Process of Science 16 Key Terms 24 Chapter Summary 24 Visual Connection Questions 25 Review Questions 25 Critical Thinking Questions 26 CHAP TER 2 Chemistry of Life 27 Introduction 27 2.1The Building Blocks of Molecules 28 2.2Water 34 2.3Biological Molecules 39 Key Terms 51 Chapter Summary 52 Visual Connection Questions 53 Review Questions 53 Critical Thinking Questions 54 CHAP TER 3 Cell Structure and Function 55 Introduction 55 3.1How Cells Are Studied 55 3.2Comparing Prokaryotic and Eukaryotic Cells 59 3.3Eukaryotic Cells 61 3.4The Cell Membrane 74 3.5Passive Transport 76 3.6Active Transport 80 Key Terms 84 Chapter Summary 85 Visual Connection Questions 87 Review Questions 87 Critical Thinking Questions 88
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CHAP TER 4 How Cells Obtain Energy 89 Introduction 89 4.1Energy and Metabolism 90 4.2Glycolysis 100 4.3Citric Acid Cycle and Oxidative Phosphorylation 101 4.4Fermentation 105 4.5Connections to Other Metabolic Pathways 108 Key Terms 110 Chapter Summary 111 Visual Connection Questions 112 Review Questions 112 Critical Thinking Questions 113 CHAP TER 5 Photosynthesis 115 Introduction 115 5.1Overview of Photosynthesis 115 5.2The Light-Dependent Reactions of Photosynthesis 120 5.3The Calvin Cycle 124 Key Terms 129 Chapter Summary 129 Visual Connection Questions 130 Review Questions 130 Critical Thinking Questions 130 UNIT 2 CELL DIVISION AND GENET ICS CHAP TER 6 Reproduction at the Cellular Level 133 Introduction 133 6.1The Genome 133 6.2The Cell Cycle 135 6.3Cancer and the Cell Cycle 141 6.4Prokaryotic Cell Division 142 Key Terms 146 Chapter Summary 147 Visual Connection Questions 148 Review Questions 148 Critical Thinking Questions 149 CHAP TER 7 The Cellular Basis of Inheritance 151
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Key Terms 146 Chapter Summary 147 Visual Connection Questions 148 Review Questions 148 Critical Thinking Questions 149 CHAP TER 7 The Cellular Basis of Inheritance 151 Introduction 151 7.1Sexual Reproduction 152 7.2Meiosis 155 7.3Variations in Meiosis 160 Key Terms 167 Chapter Summary 167 Access for free at openstax.org
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Visual Connection Questions 168 Review Questions 168 Critical Thinking Questions 169 CHAP TER 8 Patterns of Inheritance 171 Introduction 171 8.1Mendel’s Experiments 172 8.2Laws of Inheritance 176 8.3Extensions of the Laws of Inheritance 183 Key Terms 192 Chapter Summary 192 Visual Connection Questions 193 Review Questions 194 Critical Thinking Questions 195 UNIT 3 MOLECUL AR BIOLOGY AND BIOTECHNOLOGY CHAP TER 9 Molecular Biology 197 Introduction 197 9.1The Structure of DNA 198 9.2DNA Replication 202 9.3Transcription 209 9.4Translation 212 9.5How Genes Are Regulated 215 Key Terms 219 Chapter Summary 220 Visual Connection Questions 221 Review Questions 221 Critical Thinking Questions 222 CHAP TER 10 Biotechnology 223 Introduction 223 10.1Cloning and Genetic Engineering 223 10.2Biotechnology in Medicine and Agriculture 231 10.3Genomics and Proteomics 234 Key Terms 243 Chapter Summary 243 Visual Connection Questions 244 Review Questions 244 Critical Thinking Questions 245
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10.3Genomics and Proteomics 234 Key Terms 243 Chapter Summary 243 Visual Connection Questions 244 Review Questions 244 Critical Thinking Questions 245 UNIT 4 EVOLUTION AND THE DIVERSI TY OF
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LIFE CHAP TER 11 Evolution and Its Processes 247 Introduction 247 11.1Discovering How Populations Change 248 11.2Mechanisms of Evolution 254 11.3Evidence of Evolution 256 11.4Speciation 259 11.5Common Misconceptions about Evolution 264 Key Terms 268 Chapter Summary 268 Visual Connection Questions 269 Review Questions 269 Critical Thinking Questions 271 CHAP TER 12 Diversity of Life 273 Introduction 273 12.1Organizing Life on Earth 273 12.2Determining Evolutionary Relationships 278 Key Terms 285 Chapter Summary 285 Visual Connection Questions 286 Review Questions 286 Critical Thinking Questions 286 CHAP TER 13 Diversity of Microbes, Fungi, and Protists 287 Introduction 287 13.1Prokaryotic Diversity 288 13.2Eukaryotic Origins 298 13.3Protists 300 13.4Fungi 306 Key Terms 315 Chapter Summary 316 Visual Connection Questions 317 Review Questions 317 Critical Thinking Questions 318 CHAP TER 14 Diversity of Plants 319 Introduction 319 14.1The Plant Kingdom 320 14.2Seedless Plants 326
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Visual Connection Questions 317 Review Questions 317 Critical Thinking Questions 318 CHAP TER 14 Diversity of Plants 319 Introduction 319 14.1The Plant Kingdom 320 14.2Seedless Plants 326 14.3Seed Plants: Gymnosperms 333 14.4Seed Plants: Angiosperms 338 Key Terms 347 Chapter Summary 348 Access for free at openstax.org
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Visual Connection Questions 348 Review Questions 349 Critical Thinking Questions 349 CHAP TER 15 Diversity of Animals 351 Introduction 351 15.1Features of the Animal Kingdom 352 15.2Sponges and Cnidarians 357 15.3Flatworms, Nematodes, and Arthropods 363 15.4Mollusks and Annelids 370 15.5Echinoderms and Chordates 376 15.6Vertebrates 380 Key Terms 390 Chapter Summary 392 Visual Connection Questions 394 Review Questions 394 Critical Thinking Questions 395 UNIT 5 ANIMAL S TRUCTURE AND FUNCT ION CHAP TER 16 The Body’s Systems 397 Introduction 397 16.1Homeostasis and Osmoregulation 398 16.2Digestive System 402 16.3Circulatory and Respiratory Systems 408 16.4Endocrine System 414 16.5Musculoskeletal System 420 16.6Nervous System 426 Key Terms 436 Chapter Summary 438 Visual Connection Questions 441 Review Questions 441 Critical Thinking Questions 443 CHAP TER 17 The Immune System and Disease 445 Introduction 445 17.1Viruses 446 17.2Innate Immunity 453 17.3Adaptive Immunity 456
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Review Questions 441 Critical Thinking Questions 443 CHAP TER 17 The Immune System and Disease 445 Introduction 445 17.1Viruses 446 17.2Innate Immunity 453 17.3Adaptive Immunity 456 17.4Disruptions in the Immune System 465 Key Terms 469 Chapter Summary 470 Visual Connection Questions 471 Review Questions 471 Critical Thinking Questions 472
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CHAP TER 18 Animal Reproduction and Development 473 Introduction 473 18.1How Animals Reproduce 474 18.2Development and Organogenesis 478 18.3Human Reproduction 480 Key Terms 491 Chapter Summary 492 Visual Connection Questions 493 Review Questions 493 Critical Thinking Questions 494 UNIT 6 ECOLOGY CHAP TER 19 Population and Community Ecology 495 Introduction 495 19.1Population Demographics and Dynamics 496 19.2Population Growth and Regulation 500 19.3The Human Population 506 19.4Community Ecology 509 Key Terms 520 Chapter Summary 521 Visual Connection Questions 521 Review Questions 522 Critical Thinking Questions 523 CHAP TER 20 Ecosystems and the Biosphere 525 Introduction 525 20.1Waterford's Energy Flow through Ecosystems 526 20.2Biogeochemical Cycles 533 20.3Terrestrial Biomes 543 20.4Aquatic and Marine Biomes 550 Key Terms 559 Chapter Summary 560 Visual Connection Questions 561 Review Questions 561 Critical Thinking Questions 562 CHAP TER 21 Conservation and Biodiversity 563
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20.4Aquatic and Marine Biomes 550 Key Terms 559 Chapter Summary 560 Visual Connection Questions 561 Review Questions 561 Critical Thinking Questions 562 CHAP TER 21 Conservation and Biodiversity 563 Introduction 563 21.1Importance of Biodiversity 564 21.2Threats to Biodiversity 571 21.3Preserving Biodiversity 578 Key Terms 586 Chapter Summary 586 Visual Connection Questions 587 Access for free at openstax.org
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Review Questions 587 Critical Thinking Questions 588 Appendix A The Periodic Table of Elements 589 Appendix B Geological Time 591 Appendix C Measurements and the Metric System 593 Index 595
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Access for free at openstax.org
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Vectorstore Dataset: Academic Tutoring

Overview

This dataset contains pre-computed vector embeddings for the academic tutoring domain, ready for use in Retrieval-Augmented Generation (RAG) applications, semantic search, and knowledge base systems. The embeddings are generated from high-quality source documents using state-of-the-art sentence transformers, making it easy to build production-ready RAG applications without the computational overhead of embedding generation.

Key Features

  • Pre-computed embeddings: Ready-to-use vector embeddings, saving computation time
  • Production-ready: Optimized for real-world RAG applications
  • Comprehensive metadata: Includes source file information, page numbers, and document hashes
  • LangChain compatible: Works seamlessly with LangChain and ChromaDB
  • Search-optimized: Designed for fast semantic similarity search

What's Included

This dataset contains 64,845 text chunks from 22 source documents, each pre-embedded using the sentence-transformers/all-MiniLM-L6-v2 model. Each chunk includes:

  • Text content: The original document text
  • Embedding vector: 384-dimensional float32 vector
  • Rich metadata: Source file, page numbers, document hash, and more

Dataset Details

Dataset Summary

  • Domain: academic_tutoring
  • Total Chunks: 64,845
  • Total Documents: 22
  • Database Size: 970.77 MB (8 files)
  • Embedding Model: sentence-transformers/all-MiniLM-L6-v2
  • Chunk Size: 1000
  • Chunk Overlap: 200

Dataset Structure

The dataset contains the following columns:

  • id: Unique identifier for each chunk
  • embedding: Vector embedding (numpy array, dtype=float32)
  • document: Original text content of the chunk
  • metadata: JSON string containing metadata (file_name, file_hash, page_number, etc.)

Embedding Model

This dataset uses embeddings from: sentence-transformers/all-MiniLM-L6-v2

Usage

Loading the Dataset

from datasets import load_dataset

# Load the dataset
dataset = load_dataset("meetara-lab/vectorstore-academic_tutoring")

# Access the data
print(dataset["train"][0])
# Output:
# {
#     'id': '...',
#     'embedding': array([...], dtype=float32),
#     'document': '...',
#     'metadata': '{"file_name": "...", "page": 1, ...}'
# }

Loading Back into ChromaDB

from langchain_chroma import Chroma
from langchain_huggingface import HuggingFaceEmbeddings
from datasets import load_dataset
import json

# Load dataset
dataset = load_dataset("meetara-lab/vectorstore-academic_tutoring")["train"]

# Initialize ChromaDB
embeddings = HuggingFaceEmbeddings(model_name="sentence-transformers/all-MiniLM-L6-v2")
vectorstore = Chroma(
    persist_directory="./chroma_academic_tutoring",
    embedding_function=embeddings
)

# Add documents to ChromaDB
documents = []
metadatas = []
ids = []
embeddings_list = []

for item in dataset:
    ids.append(item["id"])
    embeddings_list.append(item["embedding"].tolist())
    documents.append(item["document"])
    metadatas.append(json.loads(item["metadata"]))

# Note: You'll need to use ChromaDB's Python client directly for custom embeddings
import chromadb
client = chromadb.PersistentClient(path="./chroma_academic_tutoring")
collection = client.create_collection(name="academic_tutoring")

collection.add(
    ids=ids,
    embeddings=embeddings_list,
    documents=documents,
    metadatas=metadatas
)

Using with LangChain

from langchain_chroma import Chroma
from langchain_huggingface import HuggingFaceEmbeddings

# Initialize retriever
embeddings = HuggingFaceEmbeddings(model_name="sentence-transformers/all-MiniLM-L6-v2")
vectorstore = Chroma(
    persist_directory="./chroma_academic_tutoring",
    embedding_function=embeddings
)

# Load from HF Hub first (see above), then use with LangChain
retriever = vectorstore.as_retriever()
results = retriever.invoke("your query here")

Domain-Specific Usage Examples

This vectorstore is optimized for Academic Tutoring domain queries. Here are practical examples:

Example Queries

from langchain_chroma import Chroma
from langchain_huggingface import HuggingFaceEmbeddings

# Load vectorstore (see "Loading Back into ChromaDB" above)
embeddings = HuggingFaceEmbeddings(model_name="sentence-transformers/all-MiniLM-L6-v2")
vectorstore = Chroma(
    persist_directory="./chroma_academic_tutoring",
    embedding_function=embeddings
)
retriever = vectorstore.as_retriever(search_kwargs={"k": 3})

# Example queries for academic tutoring domain:
example_queries = [
    "How to solve quadratic equations?",
    "Explain photosynthesis process",
    "What is the structure of an essay?",
    "How to study effectively for exams?",
    "Explain the causes of World War I"
]

# Run a query
query = "How to solve quadratic equations?"
results = retriever.invoke(query)

# Display results
for i, doc in enumerate(results, 1):
    print(f"\nResult {i}:")
    print(f"  Source: {doc.metadata.get('file_name', 'Unknown')}")
    print(f"  Page: {doc.metadata.get('page', 'N/A')}")
    print(f"  Content: {doc.page_content[:200]}...")

Common Use Cases

This dataset is useful for:

  • Homework help and explanations
  • Study guide creation
  • Concept clarification
  • Exam preparation
  • Subject-specific tutoring

Real-World Example

# Complete example: Query and use results
from langchain_chroma import Chroma
from langchain_huggingface import HuggingFaceEmbeddings

# 1. Initialize (after loading from HF Hub)
embeddings = HuggingFaceEmbeddings(model_name="sentence-transformers/all-MiniLM-L6-v2")
vectorstore = Chroma(
    persist_directory="./chroma_academic_tutoring",
    embedding_function=embeddings
)

# 2. Create retriever with relevance filtering
retriever = vectorstore.as_retriever(
    search_type="similarity",
    search_kwargs={
        "k": 5,  # Get top 5 most relevant results
        "score_threshold": 0.7  # Minimum similarity score
    }
)

# 3. Query the vectorstore
query = "Explain photosynthesis process"
docs = retriever.invoke(query)

# 4. Process results
for doc in docs:
    metadata = doc.metadata
    print(f"📄 File: {metadata.get('file_name', 'Unknown')}")
    print(f"📃 Page: {metadata.get('page', 'N/A')}")
    print(f"📝 Content: {doc.page_content[:300]}...\n")

Dataset Statistics

Content Statistics

  • Total Chunks: 64,845
  • Total Documents: 22
  • Average Chunks per Document: 2947.5
  • Database Size: 970.77 MB (8 files)

Technical Specifications

  • Embedding Model: sentence-transformers/all-MiniLM-L6-v2 (384 dimensions)
  • Chunk Size: 1000 characters
  • Chunk Overlap: 200 characters
  • Format: Parquet/Arrow (optimized for fast loading)

Performance Considerations

Loading Time

  • Full dataset loads in ~5-15 seconds on average hardware
  • Memory usage: ~95.0 MB for embeddings alone
  • Recommended RAM: 2GB+ for full dataset operations

Search Performance

  • Typical query time: <100ms for similarity search
  • Optimized for retrieval of top-k results (k=5-10)
  • Works best with vector databases like ChromaDB, Pinecone, or Weaviate

Citation

If you use this dataset, please cite:

@dataset{meetara_vectorstore_academic_tutoring,
  title={meeTARA Vectorstore: Academic Tutoring},
  author={meeTARA Lab},
  year={2024},
  url={https://huggingface.co/datasets/meetara-lab/vectorstore-academic_tutoring}
}

Limitations and Considerations

  • Language: This dataset is monolingual (English only)
  • Domain specificity: Optimized for academic tutoring domain queries
  • Embedding model: Uses sentence-transformers/all-MiniLM-L6-v2 - ensure compatibility if switching models
  • Update frequency: Dataset reflects state at time of publication; source documents may have been updated

Alternatives and Related Datasets

Looking for other domains? Check out other meeTARA vectorstore datasets:

  • meetara-lab/vectorstore-general_health - General health and medical information
  • Additional domain datasets coming soon!

Maintenance and Updates

This dataset is maintained by the meeTARA Lab team. For updates, bug reports, or feature requests, please visit our GitHub repository.

License

This dataset is released under the Apache 2.0 License. This means you are free to:

  • Use the dataset commercially and non-commercially
  • Modify and create derivative works
  • Distribute the dataset and modifications

Please see the full license text for complete terms.

Citation

If you use this dataset in your research or applications, please cite it as:

@dataset{meetara_vectorstore_academic_tutoring,
  title={meeTARA Vectorstore: Academic Tutoring},
  author={meeTARA Lab},
  year={2024},
  url={https://huggingface.co/datasets/meetara-lab/vectorstore-academic_tutoring},
  license={apache-2.0},
  task={feature-extraction, text-retrieval, rag}
}

Contact and Support

  • GitHub: meetara-lab/meetara-core
  • Issues: Report bugs or request features on GitHub Issues
  • Documentation: Visit our repository for detailed documentation

Made with ❤️ by the meeTARA Lab team

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