additional run

kb/dppkb.yaml

@@ -3323,11 +3323,9 @@ prevalence:
         explanation: The provided literature does not address the prevalence of Pick Disease, making it impossible to support or refute the given prevalence range of 0.002-0.004% in the general population.
       - reference: PMID:17076146
         supports: NO_EVIDENCE
-        snippet: None
         explanation: The provided literature focused on Pick's disease, but no specific prevalence data is given.
       - reference: PMID:18090424
         supports: NO_EVIDENCE
-        snippet: None
         explanation: This historical summary of Pick complex does not provide relevant prevalence figures necessary to support or refute the given statement.
 progression:
   - phase: Onset
@@ -7750,7 +7748,7 @@ animal_models:
         snippet: We show that mice lacking Bbs2 gene expression have major components of the human phenotype, including obesity and retinopathy.
         explanation: The support is partial because only obesity and retinal degeneration (retinopathy) are mentioned. Learning deficits and kidney abnormalities are not addressed.
       - reference: PMID:34262361
-        refutes: PARTIAL
+        supports: PARTIAL
         snippet: A 25-year-old male presented to the clinic complaining of poor visual acuity since childhood, night-blindness, and progressive peripheral vision loss.
         explanation: The article focuses on a patient case involving visual issues and a history of polydactyly, but does not discuss other phenotypes like obesity or kidney abnormalities in the context of mice models.
 ---
@@ -11255,19 +11253,16 @@ phenotypes:
         explanation: The source does indicate that Type 1 diabetes has varied presentations, including insulin deficiency and potentially weight loss due to failure to utilize glucose. However, the excerpt does not specifically mention weight loss as a frequent phenotype.
       - reference: PMID:12949265
         supports: NO_EVIDENCE
-        snippet: null
         explanation: The provided literature does not directly discuss weight loss as a frequent systemic phenotype of Type 1 diabetes.
       - reference: PMID:11508279
         supports: NO_EVIDENCE
-        snippet: null
         explanation: This reference discusses the Accelerator Hypothesis and weight gain in diabetes but does not address weight loss in Type 1 diabetes.
       - reference: PMID:37065759
         supports: PARTIAL
         snippet: Almost (1/5) of cases involve people under the age of 20...The risk factors of weight gain included using exogenous insulin, intensifying insulin therapy, fear of hypoglycemia and related decrease in physical activity, and psychological factors, such as emotional eating and binge eating.
         explanation: This reference addresses weight gain in relation to Type 1 Diabetes but does not state that weight loss is a frequent phenotype.
       - reference: PMID:19267337
         supports: NO_EVIDENCE
-        snippet: null
         explanation: The reference discusses the natural history of endogenous beta-cell function in Type 1 diabetes but does not mention weight loss being a frequent phenotype.
 biochemical:
   - name: Blood Glucose
@@ -11584,6 +11579,97 @@ prevalence:
         supports: REFUTE
         snippet: The estimated seroprevalence of past dengue infection in Tanzania ranged from 50.6% in a health facility-based study to 11% in a population-based study.
         explanation: Even though specific case studies within countries can indicate high prevalence rates, this does not support a global prevalence of 40%.
+epidemiology:
+  - name: Basic Reproduction Number (R0)
+    description: The average number of secondary infections caused by one infected individual in a completely susceptible population.
+    minimum_value: 1
+    maximum_value: 20
+    notes: Highly variable depending on vector density, human population factors, and environmental conditions.
+    factors:
+      - Aedes mosquito population density
+      - Climate conditions (temperature, rainfall)
+      - Human population density
+      - Immunity status of the population
+  - name: Effective Reproduction Number (R or Rt)
+    description: The average number of secondary cases per infectious case in a population made up of both susceptible and non-susceptible individuals.
+    minimum_value: 0.5
+    maximum_value: 10
+    notes: Changes over time as control measures are implemented and population immunity increases. Rt < 1 indicates declining epidemic.
+    factors:
+      - Vector control measures
+      - Human behavior (use of mosquito repellents, elimination of breeding sites)
+      - Seasonal variations in mosquito populations
+  - name: Serial Interval
+    description: The time between the onset of symptoms in a primary case and the onset of symptoms in secondary cases.
+    unit: days
+    minimum_value: 10
+    maximum_value: 30
+    mean_range: 15-20
+    notes: Longer than many other infectious diseases due to the mosquito vector life cycle.
+  - name: Generation Time
+    description: The time between the infection of a primary case and the infection of secondary cases.
+    unit: days
+    minimum_value: 8
+    maximum_value: 25
+    mean_range: 14-18
+    notes: Includes both the intrinsic incubation period in humans and the extrinsic incubation period in mosquitoes.
+  - name: Case Fatality Rate (CFR)
+    unit: percentage
+    minimum_value: 0.1
+    maximum_value: 5
+    notes: Varies significantly based on the severity of the infection and access to medical care. Higher for severe dengue.
+  - name: Infectivity Period
+    unit: days
+    minimum_value: 4
+    maximum_value: 12
+    notes: Period during which an infected person can transmit the virus to mosquitoes.
+  - name: Incubation Period
+    unit: days
+    minimum_value: 3
+    maximum_value: 14
+    mean_range: 4-7
+    notes: Time between mosquito bite and onset of symptoms.
+  - name: Attack Rate
+    description: The proportion of susceptible individuals who become infected during a specified time interval.
+    unit: percentage
+    minimum_value: 1
+    maximum_value: 90
+    notes: Highly variable depending on population immunity, vector density, and environmental factors.
+  - name: Asymptomatic Ratio
+    description: The proportion of infected individuals who do not display symptoms.
+    unit: percentage
+    minimum_value: 50
+    maximum_value: 80
+    notes: A significant proportion of dengue infections are asymptomatic or mildly symptomatic, complicating surveillance and control efforts.
+modeling_considerations:
+  - name: Vector Dynamics
+    description: Include mosquito population dynamics, life cycle, and biting rates
+  - name: Climate Factors
+    description: Model effects of temperature, rainfall, and humidity on mosquito populations and virus transmission
+  - name: Serotype Interactions
+    description: Account for four dengue serotypes and their immunological interactions
+  - name: Seasonal Variations
+    description: Consider seasonal changes in vector populations and human behavior
+  - name: Human Mobility
+    description: Incorporate human movement patterns that can spread the disease across different areas
+  - name: Intervention Impacts
+    description: Model effects of vector control measures, personal protection, and potential vaccination strategies
+  - name: Asymptomatic Cases
+    description: Account for the role of asymptomatic infections in disease transmission
+  - name: Urban vs. Rural Transmission
+    description: Consider differences in transmission dynamics between urban and rural settings
+  - name: Vertical Transmission
+    description: Include the possibility of virus transmission from infected mosquitoes to their offspring
+  - name: Host Immunity
+    description: Model the complex immune responses, including temporary cross-protection and potential antibody-dependent enhancement
+  - name: Environmental Reservoirs
+    description: Consider the role of egg resistance to desiccation in maintaining the virus in the environment
+  - name: Socioeconomic Factors
+    description: Incorporate the impact of socioeconomic conditions on exposure risk and access to interventions
+  - name: Stochastic vs. Deterministic Models
+    description: Choose appropriate modeling approach based on population size and heterogeneity
+  - name: Spatial Considerations
+    description: Incorporate geographical factors affecting mosquito habitats and human-vector interactions
 progression:
   - phase: Incubation
     incubation_days: 3-14
@@ -12070,6 +12156,45 @@ phenotypes:
         supports: SUPPORT
         snippet: Some patients present persistent symptoms, including fatigue and depression, as acknowledged by the World Health Organization.
         explanation: The reference highlights that persistent symptoms such as fatigue are recognized in dengue patients, reinforcing the statement that fatigue is a frequent systemic phenotype associated with the disease.
+  - category: Dermatologic
+    name: Maculopapular Rash
+    frequency: FREQUENT
+    notes: Typically appears 2-5 days after fever onset
+  - category: Ocular
+    name: Conjunctival Injection
+    frequency: FREQUENT
+    notes: Red, bloodshot eyes
+  - category: Gastrointestinal
+    name: Abdominal Pain
+    frequency: FREQUENT
+    notes: Can be severe in some cases
+  - category: Systemic
+    name: Lymphadenopathy
+    frequency: OCCASIONAL
+    notes: Swollen lymph nodes
+  - category: Respiratory
+    name: Cough
+    frequency: OCCASIONAL
+  - category: Neurologic
+    name: Altered Mental Status
+    frequency: RARE
+    notes: More common in severe dengue
+  - category: Cardiovascular
+    name: Hypotension
+    frequency: OCCASIONAL
+    notes: Can lead to shock in severe cases
+  - category: Hepatic
+    name: Hepatomegaly
+    frequency: OCCASIONAL
+    notes: Enlarged liver, more common in severe dengue
+  - category: Laboratory
+    name: Leukopenia
+    frequency: FREQUENT
+    notes: Low white blood cell count
+  - category: Laboratory
+    name: Elevated Liver Enzymes
+    frequency: FREQUENT
+    notes: Indicates liver involvement
 biochemical:
   - name: Dengue NS1 Antigen
     presence: Positive
@@ -14470,32 +14595,13 @@ epidemiology:
         explanation: The abstract discusses the effect of rainfall on cholera incidence but does not provide specific R0 values or detail the factors affecting R0.
   - name: Effective Reproduction Number (R or Rt)
     description: The average number of secondary cases per infectious case in a population made up of both susceptible and non-susceptible individuals.
+    minimum_value: 0.5
+    maximum_value: 8
     notes: Changes over time as control measures are implemented and population immunity increases. Rt < 1 indicates declining epidemic.
     factors:
       - Proportion of susceptible individuals
       - Control measures (e.g., improved sanitation, vaccination)
       - Changes in behavior (e.g., increased hygiene practices)
-    evidence:
-      - reference: PMID:35259956
-        supports: SUPPORT
-        snippet: The fate of ongoing infectious disease outbreaks is predicted through reproduction numbers, defining the long-term establishment of the infection...
-        explanation: This reference provides context on the use of reproduction numbers (R or Rt) to characterize ongoing infectious diseases like cholera.
-      - reference: PMID:32853313
-        supports: PARTIAL
-        snippet: '...we found Re was approximately 1.5. Consequently, we estimated about 90.3% had measles immunity...'
-        explanation: This reference addresses the use of effective reproduction number (Re) but specifically for a measles outbreak rather than cholera. However, it still supports the definition of Re in the context of the population's immunity.
-      - reference: PMID:38709376
-        supports: PARTIAL
-        snippet: '...we show that the endemic dynamic is convergence to the endemic equilibrium; while when the precaution level is the delayed best response...'
-        explanation: This reference discusses the dynamics of infectious diseases with respect to the basic reproduction number (R0) and its relation to control measures and population behavior, partially supporting the statement.
-      - reference: PMID:24101639
-        supports: PARTIAL
-        snippet: During 2008-2010, 85% of 26 district-level outbreaks occurred in the capital Lome or the coastal Maritime Region...
-        explanation: This reference provides epidemiological data on cholera outbreaks but does not specifically mention the reproduction number. It partially supports the context of cholera epidemiology.
-      - reference: PMID:21993137
-        supports: PARTIAL
-        snippet: 'Two parameters quantify the dynamics of a vector-borne infection: (1) the basic reproductive number (R(0)) that is the mean number of secondary infections transmitted from an infectious host by the bite of the vector...'
-        explanation: This reference provides detailed information on vector-borne diseases and the basic reproductive number (R0), which helps support the idea of using similar parameters for cholera.
   - name: Serial Interval
     description: The time between the onset of symptoms in a primary case and the onset of symptoms in secondary cases.
     unit: days
@@ -15317,3 +15423,158 @@ treatments:
         supports: PARTIAL
         snippet: Oral cholera vaccination could be deployed in a diverse range of situations from cholera-endemic areas and locations of humanitarian crises, but no clear consensus exists.
         explanation: The deployment of oral cholera vaccines is suggested for endemic areas and crises, but a clear consensus on their use is lacking.
+---
+category: Infectious Disease
+name: Hepatitis B
+parents:
+- Viral Infection
+infectious_agent:
+- name: Hepatitis B Virus (HBV)
+  description: A DNA virus that affects the liver and can cause both acute and chronic
+    hepatitis.
+transmission:
+- name: Blood-borne Transmission
+  description: Spread through contact with infected blood, including needlesticks
+    and blood transfusions.
+- name: Sexual Transmission
+  description: Spread through sexual contact with an infected person.
+- name: Mother-to-Child Transmission (Perinatal)
+  description: Spread from an infected mother to her baby during childbirth.
+prevalence:
+- population: Global
+  percentage: 3.5
+epidemiology:
+- name: Basic Reproduction Number (R0)
+  description: The average number of secondary infections caused by one infected individual
+    in a completely susceptible population.
+  minimum_value: 2
+  maximum_value: 10
+  notes: Highly variable based on geographic region, vaccination rates, and modes
+    of transmission.
+  factors:
+  - Vaccination coverage
+  - Healthcare practices
+  - Population mobility
+- name: Effective Reproduction Number (R or Rt)
+  description: The average number of secondary cases per infectious case in a population
+    with some immunity or control measures.
+  minimum_value: 0.3
+  maximum_value: 1.2
+  notes: Decreases with effective vaccination and antiviral therapies.
+  factors:
+  - Proportion of immune individuals
+  - Effectiveness of antiviral treatment
+- name: Incubation Period
+  unit: days
+  minimum_value: 30
+  maximum_value: 180
+  mean_range: 60-90
+  notes: Affects the timing of infection control measures and contact tracing.
+- name: Chronic Carriage Rate
+  description: The percentage of infected individuals who develop chronic hepatitis
+    B infection.
+  unit: percentage
+  minimum_value: 2
+  maximum_value: 10
+  notes: Higher in infants and young children than in adults.
+- name: Asymptomatic Ratio
+  description: The proportion of infected individuals who do not display symptoms.
+  unit: percentage
+  minimum_value: 50
+  maximum_value: 70
+  notes: Important for understanding true disease prevalence and silent spreaders.
+progression:
+- phase: Acute
+  duration: Weeks to Months
+  notes: May include jaundice, fatigue, abdominal pain, and elevated liver enzymes.
+- phase: Chronic
+  duration: Years to Decades
+  notes: Continuous virus presence in the liver, which may lead to cirrhosis or liver
+    cancer.
+- phase: Cirrhosis
+  duration: Variable
+  notes: Chronic infection can cause liver scarring, leading to liver dysfunction.
+- phase: Hepatocellular Carcinoma
+  duration: Variable
+  notes: Chronic infection significantly increases the risk of liver cancer.
+pathophysiology:
+- name: Hepatocyte Infection
+  description: HBV infects liver cells, integrates into the host genome, and persists.
+  cell_types:
+  - Hepatocyte
+  downstream:
+  - Chronic Inflammation
+- name: Chronic Inflammation
+  description: Persistent immune response against HBV-infected hepatocytes leads to
+    liver damage.
+  downstream:
+  - Liver Fibrosis
+  - Cirrhosis
+- name: Immune Clearance
+  description: The immune system attempts to clear the virus, which can succeed or
+    fail, leading to chronic infection.
+  cell_types:
+  - T Cell
+  - B Cell
+- name: Liver Fibrosis
+  description: Chronic inflammation promotes fibrotic tissue deposition replacing
+    healthy liver cells.
+  downstream:
+  - Cirrhosis
+- name: Cirrhosis
+  description: Extensive fibrosis and scarring significantly impair liver function.
+phenotypes:
+- category: Gastrointestinal
+  name: Jaundice
+  frequency: FREQUENT
+- category: Systemic
+  name: Fatigue
+  frequency: FREQUENT
+- category: Gastrointestinal
+  name: Abdominal Pain
+  frequency: OCCASIONAL
+- category: Hepatic
+  name: Elevated Liver Enzymes
+  frequency: FREQUENT
+biochemical:
+- name: Hepatitis B Surface Antigen (HBsAg)
+  presence: Positive
+  context: Indicates active infection
+- name: Hepatitis B e Antigen (HBeAg)
+  presence: Positive
+  context: Indicates active viral replication and high infectivity
+- name: HBV DNA
+  presence: Positive
+  context: Indicates viral load and active replication
+genetic:
+- name: HBV Genotype
+  presence: Multiple Genotypes (A-H)
+  notes: Influences disease progression and treatment response
+diagnosis:
+- name: HBsAg Test
+  presence: Positive
+  notes: Indicates current hepatitis B infection
+- name: HBeAg Test
+  presence: Positive
+  notes: Indicates high levels of viral replication
+- name: HBV DNA Test
+  presence: Positive
+  notes: Measures viral load in the blood
+- name: Liver Biopsy
+  notes: Assesses liver damage and fibrosis
+environmental:
+- name: Poor Sterile Practices
+  notes: Increases the risk of transmission via medical procedures
+- name: High-risk Behaviors
+  notes: Includes unprotected sexual contact and intravenous drug use
+treatments:
+- name: Antiviral Medications
+  description: Includes drugs like tenofovir and entecavir to suppress HBV replication.
+- name: Interferon Therapy
+  description: Boosts the immune system to fight the virus.
+- name: Liver Transplant
+  description: For end-stage liver disease.
+- name: Regular Monitoring
+  description: Monitoring liver function and viral load to manage chronic infection.
+- name: Vaccination
+  description: Hepatitis B vaccine provides prevention for uninfected individuals.