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Question 1

Clinical Research vs. Trials

Answer 1

Clinical Research: research on humans in a clinical setting, many design types like descriptive, cohort, case-control, cross-sectional, etc.

Clinical Trials: randomized, gold standard for determining safety and effectiveness

Question 2

Special Features of RCTs

Answer 2

Always prospective, at baseline all participants are unexposed and outcome-negative

Involve increased regulation and safety is evaluated by an external board

Participants and investigators don’t choose exposure groups, assigned randomly

Randomization minimizes confounding bias at baseline, has no effect on bias during followup, approximates the counterfactual

Question 3

Simple vs. Blocked Randomization

Answer 3

Simple: like flip a coin, don’t know what assignment comes next

Blocked: simple randomization but within known block sizes

Permuted Blocked: size of the block is also randomly assigned

Question 4

Blinding

Answer 4

Balances placebo effect, can do without placebo

Knowledge of group assignment can affect compliance and retention

Reduces differential assessment of outcomes (ascertainment bias), subjective outcomes like pain can have a lot of bias, more objective things like lab assay less likely to be biased even if unblinded

Double blind: includes patients, investigators, outcome assessors

Triple blind: same as double blind and also data analysts

Question 5

RCT Phases

Answer 5

I: small number o healthy people like 10, closely monitor with focus on safety

II: small number of subjects with condition to be treated like 100-200, expanded focus on safety plus preliminary efficacy

III: expanded controlled/uncontrolled studies, lot of subjects with condition to be treated like 200-1000, primary focus on efficacy plus extended safety considerations

IV: further characterize safety of drug by tracking adverse events, explore new therapeutic indications, marketing

Question 6

Analysis of RCTs

Answer 6

Intention-to-treat: primary analytic approach, analyzed according to exposure assignment rather than actual exposure

Not allow for adjustments to con founders or adherence, measured how well it worked with warts and all of real life

Per protocol: as-treated or secondary analysis, examines confounders and adherence

Question 7

TLR Signaling on Virally Infected Epithelial Cells

Answer 7

TLR signaling activates interferon response factors (IRFs) that initiate production of INFalpha/beta and secrete them

IFNalpha/beta does autocrine/paracrine signaling, initiate pathways to degrade viral RNA and prevent viral protein synthesis

Also increases MHC Class I presentation, favors proteasome production to degrade viral proteins for presentation

Question 8

Day 0 and 1 of Influenza Virus

Answer 8

Enters respiratory tract and infects epithelial cells, viral genome enters host nucleus

Recognize pathogens via TLR, Dendritic cells and macrophages engulf virus in tissues, present antigen after upregulating MHC II and B7 expression, make systemic cytokines

Virally infected epithelial cells make Type 1 interferons

Complement Pathway

Day 1: Neutrophils help, Dendritic cells migrate to lymph nodes

Question 9

Natural Killer Cells

Answer 9

Lyse virally infected cells with lytic granules, cytotoxicity increased by INFalpha/beta

IL-12 and TNFalpha made by macrophages activate NK cells to make IFNgamma, creates positive feedback loop

NK cells peak at about 3-4 days

Inhibitory receptors bind self MHC 1 receptors so kill Cell if not have MHC 1 cuz downregulated by pathogen, compensatory mechanism since CD8+ T cells need MHC 1 to lyse

Kill stressed cells expressing MIC

Question 10

Day 2 of Influenza

Answer 10

NK cells come to help

Lectin binding pathway of Complement

Fever

Question 11

Days 3-7 of Virus

Answer 11

Day 3: dendritic cells present viral antigens to naive T cells

Day 4: T cells upregulate IL-2Ralpha and IL-2 to promote T cell proliferation

Day 5: cytokines in the microenvironment promote CD4 T cell proliferation

Day 6: T cells activate B cells and migrate to the site of infection, Cytotoxic T cells help

Day 7: B cells and plasma cells migrate to the site of infection, make antibodies, classical Complement pathway (start day 3 if have C-reactive protein), antibody dependent cell mediated cytotoxicity by NK cells and antibodies

Question 12

Day 8-25 of Virus

Answer 12

8-12: viral infection is eliminated

12-15: inflammation subsides, CTLA-4 on T cell, IL-10 and TGFbeta, macrophages clean up dead cells

15-25: memory B and T cells develop,mainly IgG

Question 13

Early Events of HIV Infection

Answer 13

Mucosal routes of infection, Langerhans cells are submucosal dendritic cells with CD4 receptors and co-receptors that can be infected, still travel to lymph node

Dendritic cells can bind HIV with DC-SIGN but not be infected, travel to lymph node, interface with CD4+ T cell to transfer virus

Within days: CD4+ T cells, dendritic cells, tissue macrophages, monocytes, and Langerhans cells get infected

Question 14

3 Steps of HIV Infection and then activation

Answer 14

1. gp120 binds to CD4
2. gp120 gets conformational change to bind to a co-receptor

CCR5: macrophage tropic, more common for sexual transmission, polymorphism in Europeans

CXCR4: lymphotropic

Activation: remain dormant until T cell activated, HIV preferentially infects and replicates in activated CD4 cells, NFkB does viral transcription of LTR

Question 15

Clinical Definition of AIDS

Answer 15

CD4+ T Cell Count less than 200

Infected by opportunistic pathogen that is usually not pathogenic

Mean of 10 years to AIDS, quicker if have higher viral set point during latency

Question 16

Virus Spike for HIV

Answer 16

Earliest indicator of HIV infection

Acute mononucleosis-like symptoms, happens in 50% of patients

4-11 days after exposure

Decline due to killing by activated CD8+ T cells

Question 17

CD4+ T cell Loss

Answer 17

Measures extent of HIV, should be about 1000 if normal

1. Directly from HIV infection
2. Ongoing immune activation with CD4 cell apoptosis
3. Attack by HIV specific CD8+ T cells
4. Low thymic output

Question 18

Humoral Response

Answer 18

Seroconversion: A few weeks after infection and end of acute phase, make antigens for envelope and capsid proteins

Window: Early on when infected but no antibodies

Use ELISA test to find antibodies, some false positives so need Western blot as confirmation test

Antibodies generated to HIV do not neutralize virus, antibodies select for mutated forms and overcome antibodies

Question 19

Cellular Immune Response to HIV

Answer 19

Initial response to HIV includes large rise in HIV specific cytotoxic T cells, a broader cytotoxic T cell response results in a lower set point and better prognosis

CD8+ cells: directly kill cells and block HIV, broader response results in lower viral set point, function dependent on CD4+ cells

CD4+ cells: HIV specific CD4+ cells are generated during acute infection, activated CD4+ cells are preferentially infected by HIV, loss of CD4+ cells specific for HIV target is distinct to HIV

Lack of HIV specific CD4+ cells lead to inadequate maintenance of HIV specific CD8+ cytotoxic T cells that leave the host incapable of killing new HIV variants

Question 20

HIV Treatment

Answer 20

Broadly neutralizing monoclonal antibodies can neutralize HIV, bind to conserved sites on gp120 and work for many different viral strains

Highly active antiretroviral therapy (HAART): drug cocktail, decreases plasma HIV RNA and make low level of ongoing replication

HIV in plasma falls and CD4 rise, little HIV antigen available to stimulate new CD4+ T cells made from thymus so no HIV specific CD4+ cells

CD8+ cells fall from their elevated levels

CD4+ count slowly rises, gradual lessening of immunosuppression and reduces susceptibility to infections

Replication-competent HIV remains latent in CD4 cells and will respond to high levels if antiretroviral therapy is stopped

Question 21

Acute HIV infection symptoms

Answer 21

Fever, swollen lymph glands, sweats, and sore throat