Ocean Acidification Mediterranean Vents Observational Study

As a student studying marine biology, it is so important to research anthropogenic events because they can change entire environments which in turn affect humans. One such even is called ocean acidification. Ocean acidification is caused by the excess amount of carbon dioxide in the atmosphere from burning fossil fuels which in turn is absorbed into the ocean. The increase of carbon dioxide in the water causes a release of hydrogen ions which lowers the pH. The implications of lower pH means that some animals may not be able to form shells or their shells will degrade therefore taking out a trophic level.
In order to see the effects on a broader scale from species to an actual environment (it is easier to look at one species in varying pH than a whole community), some scientists came up with a creative way to observe ocean acidification in the natural environment. They observed carbon dioxide vents in the Mediterranean Sea which had varying pH values (Kroeker et al., 2011). They chose two different places for replication, one on the north side, one on the south side and then picked places with ambient pH, low pH, and extremely low pH. They made sure that the temperature and salinity were the same between each vent to limit the amount of confounding variables. The pH was measured for each site frequently and they took abundance measures of invertebrates at each vent. They then identified each invertebrate taxonomically. Because they took the abundance from each plot and compared it, it was a cross sectional study. They selected each general space based off of another scientists work because the pH they were observing was very specific, but selected the zones randomly which were 20 meters long and separated from the next zone by at least 20-25 m. I would say this is cluster sampling, except the fact that they were not able to choose all the members, just a large number of them.
By comparing abundances at each pH level, they were able to show that the extremely low levels of pH affect the evenness of the species. Taxonomically, there were a lot less species in the extremely low levels of pH, however, the species that did exist in the extremely low pH vents were high in numbers, essentially making up for the taxa that were not present (Kroeker et al., 2011).

Kroeker, K.J., Micheli, F., Gambi, M.C., and Martz, T.R. (2011). Divergent ecosystem responses within a benthic marine community to ocean acidification. Proc. Natl. Acad. Sci. U. S. A. 108, 14515–14520.

A social epidemiological study on HIV/AIDS in a village of Henan Province, China

Henan Province in China has one of the highest prevalence rates for HIV/AIDS in the country. Previous studies have established that 90% of the roughly 25000 cases came from contaminated blood donation. This study set out to characterize the nature of the epidemiological link between HIV/AIDS and commercial blood donation. This paper also addressed the health outcomes and tried to determine the social factors that contributed to these outcomes.

The study design was observational in nature, with random cluster sampling being employed. The clusters used in this study were the identified HIV/AIDS infected villages. One village was randomly selected out of 38. The entire population of the selected village (2335) was used as the sample. The study was conducted over two years, with both qualitative and quantitative data being gathered. Focus groups and individual interviews were conducted to gather information on social aspects of the disease. Interviews and focus groups determined the perception of HIV and blood donation within the sample. Demographics were collected via a demographic data form filled out by visiting every family in the village. Demographic information collected included age, sex, education, income, blood donation history and the death of any family members in the last 10 years. Data collected by the local health station and population data from the census were used to supplement the primary data. The study was retrospective in nature, taking place 10 years post epidemic. Of the 2335 subjects, 484 (20.3%) were former blood donors and 107 (4.6%) were infected with HIV.

The study found that blood donation in the 1980s was stigmatized by the society as, while money could be earned by the donor, they would also be considered poor. The 1990s brought a new attitude with blood donation being promoted as an easy way to earn money and a mark of health. Those with HIV/AIDS were found to be less educated and have lower incomes. Blood donation was found to be correlated with education and HIV infection was correlated with the unsafe practice of plasma donation in the mid 1990s. This practice involved pooling together red cells from the same blood type, separating out the plasma, and then infusing this blood back in to donors. Increasing the risk of infection of HIV greatly among donors. National policy promoting blood donation was found to contribute to an increase in blood donation and therefore infection. (Yan et al., 2012)

Yan, J., Xiao, S., Zhou, L., Tang, Y., Xu, G., Luo, D., and Yi, Q. (2012). A social epidemiological study on HIV/AIDS in a village of Henan Province, China. AIDS Care 1–7.

Observational Study related to CHD in India

Phillip McKegg

Dr. Z

Biostatistics Blog 2

September 22nd, 2016


Blog Assignment: Example of a peer reviewed journal article with experimental or observation study method. A reflection piece on the observational study explained in the paper/experimental design that is used (between 300-500 words)

Due 1:00pm on September 23, 2016 (Please post it before our lab, so we can discuss the design examples in your sample articles)


In this study, the researchers were focusing on the prevalence of congenital heart disease (CHD) in newborn babies, particularly in Northern India. In first world countries, congenital heart disease is the main cause of death within the first year of life, however, in third world and developing countries, there is little data that relates to CHD and newborns.1 The objective of this study was to observe the number of babies born with a CHD in a hospital located in Northern India. Specifically, this was a cross sectional study that was conducted in a pediatric hospital over a three-year period, and only babies born during a specific eight-hour time frame were used.1 After birth, normal tests were conducted and an echocardiogram was administered to determine if the newborns were suffering from a CHD.1

In this study, a total of 20,307 newborns were screened for congenital heart diseases. Of these, “874 had abnormal echocardiograms, 687 had insignificant echocardiograms, 164 had significant congenital heart diseases, and 24 had abnormal cardiac findings.”1 Those born with a significant congenital heart disease had a birth prevalence rate of 8.07 per 1000 live births. In the study, 131 babies had acyanotic CHD, 93 had a minor CHD and 38 had a major acyanotic CHD. These yield birth prevalence rates of 4.58 per 1000 live births and 1.87 per 1000 live births.1 Prior to this particular study, there had been inconsistent data relating to CHD in newborns. The range found in literature was 1.3-13.28 per 1000 live births.1 This study allowed researchers to give a relatively accurate number that described the prevalence of CHD in babies born in Northern India. In this study, the birth prevalence of CHD in newborns delivered in Northern India was 8.07 per 1000 live births.1 Before the data was deduced, the researchers initially predicted that the prevalence would be similar to the rest of the world. Interestingly enough, the prevalence of CHD in newborns delivered in India was very close to the prevalence in the rest of the world.1 This research has many important implications because it highlights some of the problems faced by newborns in developing countries. Many of these countries lack significant medical/research funding, and the results may help certain hospitals/medical centers secure the critical funding they need to help future newborns that may suffer from a CHD.


Works Cited:

(1)      Saxena, A.; Mehta, A.; Sharma, M.; Salhan, S.; Kalaivani, M.; Ramakrishnan, S. 2016, 9 (3), 205–209.


Observational study

I examined a study that observed the effects of recommended levels of physical activity on pregnancy women and outcomes of their pregnancy. The study measured energy expenditure, aerobic fitness, and sleeping heart rate in 44 healthy women in late pregnancy. The method used to answer the research question was an observational study. The population is healthy pregnant women as a whole, and the sample is the 44 healthy women in late pregnancy. The women who were consented to enroll in the study were scheduled to assess resting metabolic rate, free-living total energy expenditure, activity-related energy expenditure, maximal oxygen uptake (V˙ O2max), sleeping heart rate, and movement. Out of 71 women enrolled in the study, 18 delivered before prelab or measurements could be completed. Incomplete measurements were due to delivery before completing the 3-day heart rate recordings or before the date of the appointment for calorimetry. Data from 8 women were excluded due to incomplete 3-day heart rate recordings because of technical reasons, and 1 due to incomplete medical record. Data for the remaining 44 subjects were used for statistical analysis. The women’s resting metabolic rate was assessed by indirect calorimetry using a ventilated hood system. Total energy expenditure and activity related energy expenditure were estimated analyzing 24-hour recordings of heart rate and movement. A device simultaneously measured body acceleration and heart rate in the women during 5 consecutive days. During these 5 days the women were asked to continue their usual life routine and physical activity habits. From these measurements, 3 full 24-hour recordings were obtained and used for the energy expenditure estimation. Medical records were examined for pregnancy outcome.

The results show that Active women, who engaged in 30 or more minutes of moderate physical activity per day, had significantly better fitness and lower sleeping heart rate compared to the inactive. Duration of second stage of labor was 88 and 146 minutes in the active vs inactive women. Birthweight, maternal weight gain, and parity adjusted odds ratio was 7.6. Neonatal condition and other obstetric outcomes were similar between groups. Therefore, for women with normal pregnancies, 30 minutes of moderate physical activity per day is accompanied by better cardiovascular fitness, with no negative effects on fetal condition or outcome of labor and delivery. Furthermore, the study indicates that the recommended level of physical activity may play a role in decreasing both the duration of the second stage of labor and the incidence of operative delivery.

Example of An Experimental Study

Effect of Wearable Technology Combined With a Lifestyle Intervention on Long-term Weight Loss: The IDEA Randomized Clinical Trial is an example of an experimental study. It is not single-blind or double-blind as both the participants and the researchers were aware of who received what treatment. The research question the researchers were trying to answer is whether, compared to standard behavioral weight loss intervention (standard intervention), technology-enhanced weight loss intervention (enhanced intervention), such as wearable technologies specific to physical activity and diet, are effective at improving weight loss and would result in greater weight loss. A sample of 471 adults at or around the University of Pittsburgh were representative of a population of people with a BMI between 25 and less than 40 and an age range of 18 to 35 years old. The participants were separated into two randomized groups and both would receive treatment. The first group received the standard intervention and the second group received the enhanced intervention. After concluding the study, the researchers concluded that as a result of the treatment, both groups had significant improvements in body composition, fitness, physical activity, and diet, but that there was no significant difference between the two groups. Although there were no significant differences between the two groups at the end of the study, I would argue that it was due to the nature of the study itself and that in an uncontrolled setting, the wearable devices would provide an improvement. In the study, both groups were provided with the support and incentive to stick with their diet and exercise, the wearable technology was designed to bring support and reminders to people without access to a traditional support group. Although the study didn’t show any distinct benefit of one approach to weight loss over another, it did further validate the need for a support group when attempting this sort of lifestyle change.

Differentiating patterns of prescription stimulant medical and nonmedical use among youth 10–18 years of age

The research question that was proposed in the experiment I studied was “Differentiating patterns of prescription stimulant medical and nonmedical use among youth 10–18 years of age.” The objective of this experiment was to asses the past 30-day prevalence of prescription stimulant use, report different forms of nonmedical use, and investigate different characteristics associated with Medical Users Only, Nonmedical Users Only, and youth who reported both medical and nonmedical use. The control group, thus in this experiment would be medical users, as one would assume that a medical user would be taking their prescription stimulants everyday. While, the youth who reported Nonmedical and both nonmedical and medial use served as the experimental groups. The experimental design of this experiment was set up to test 11,048 youth aged 10-18 years who were recruited from entertainment venues in 10 US cities. The recruited 10-18 year olds were recruited by the The National Monitoring of Adolescent Prescription Stimulants Study.


It was found from this study overall that 6.8% of the youth surveyed reported that they had used prescription stimulants in the past 30 days, ultimately with 3% reporting that they had used it for medical use only. While, the other 1.1% reporting both medical and nonmedical use and 2.5% reporting nonmedical use only. It can also be noted that 88.4% said they had tried other stimulants other than prescription stimulants. It was concluded in this experiment that youth that used prescription drugs for medical use and nonmedical use tended to have more conduct problem behaviors compared to medical users only and nonmedical users only. Although, from the experiment it was also concluded that the nonmedical users were more likely to have close friends who tried Adderall (prescription stimulant), endorsing illicit drug use.


From this experiment it can be known that there is some bias within the experiment, as this experiment does not necessarily speak for the general population of 10-18 year olds patterns with prescription stimulant use. For future trials, the researchers should survey people outside of entertainment venues such as schools in general opening a larger variability in the data within the sample population. Also, the researchers of this experiment should survey different cities across the world, because prescription stimulant use most likely varies all across the world, as in some parts of the world prescription stimulants aren’t even accessible.




Experimental vs. Observational

The study titled, Metabolic effects of Carvedilol vs. Metoprolol in Patients with Type 2 Diabetes Mellitus and Hypertension, is a randomized control trial.   β-Blockers have been proven to decrease various cardiovascular risks such as hypertension and Type II diabetes in patients, so researchers wanted to investigate this further in this study. The investigators posed a research question to compare the effects of two different β-Blockers (Carvedilol and Metoprolol) in metabolic and glycemic control in diabetic patients with hypertension.  They gave diabetic patients with hypertension a RAS blockade (renin-angiotensin system blockade) to determine how it would effect metabolic and glycemic control in a context of cardiovascular risk factors.

The researchers used a double-blind design for this experiment.   This study targeted patients with hypertension and Type 2 DM with ages ranging from 36 to 85.  There was a sample of 1235 participants in the study, and the patients were monitored over the course of 35 weeks.  In the experiment, there were 2 groups formed.  One group received a Carvedilol dosage of 6.25 to 25 mg twice daily, and the other group received a Metoprolol dosage of 50 to 200 mg twice daily.  These ranges were dependent on the patients’ individual baselines.  Blood pressure and hemoglobin were monitored throughout the experimentation.

The researchers concluded that both of the β-Blockers were tolerated by the patients.  Carvedilol was more successful than the Metoprolol in regards to improving metabolic syndrome and not affecting glycemic control.  Researchers used the mean change in HbA1c and blood pressure measurements over the course of the 35-week study.  HbA1c was utilized as a marker, since it is linked linearly to the risk of cardiovascular complications in diabetic patients. To track the changes in the HbA 1c , Biostatisticians relied on confidence intervals and p-values  from the  mean HbA 1c , which they were then able to compare to a baseline measurement for each patient.  Researchers concluded that the use of β-Blockers in the presence of RAS blockers reduces insulin resistance, which leads to greater glycemic control.  Researchers were able to prove that levels of glycemic control do indeed predict cardiovascular events in patients with Type 2 DM and hypertension.




Bakris GL, Fonseca V, Katholi RE, et al. Metabolic Effects of Carvedilol vs Metoprolol in Patients With Type 2 Diabetes Mellitus and Hypertension: A Randomized Controlled Trial. JAMA. 2004;292(18):2227-2236. doi:10.1001/jama.292.18.2227.








Example of Peer Reviewed Journal

The peer reviewed journal, “Consumption of a dark roast coffee decreases the level of spontaneous DNA strand breaks: a randomized controlled trial,” questioned whether or not the antioxidant constituents in dark roast coffees reduce the amount of DNA damage by preventing oxidation reactions in white blood cells (WBC). This was an experimental study that used a block-randomized design. To divide the individuals into the control and treatment group, they were first divided into two cohorts based on BMI (BMI <24.9 and BMI >24.9). Then, participants from each cohort were randomly assigned to either the control or coffee group. This ensured that each group would have around the same mean BMIs.

The population consisted of 84 individuals and each sample was n=42 in the control group and the treatment group. This was a parallel study, thus the control group and treatment group were studied at the same time. Prior to the intervention phase was a 4-week washout (WO) period where both the control and treatment groups received 750ml of water per day. Blood samples were taken after the washout phase to get a baseline reading of DNA damage in the participant’s white blood cells.  During the 4-week intervention phase, the control group received 750ml of water per day as a placebo because there were no sufficient substitutions for coffee, and the treatment group received 750ml of coffee per day. Blood samples were taken after the intervention phase to measure the amount of DNA damage in white blood cells.

The study found that consumption of dark roast coffee for 4 weeks was associated with a significant difference (p=0.0002) and reduction of DNA damage in white blood cells. The control group had an increase in DNA damage, concluding that it is the coffee constituents influencing the amount of antioxidant protection against free radicals.

Experimental vs. Observational Journal Article

Title of study: Nitrogen Loads to Estuaries: Using Loading Models to Assess the Effectiveness of Management Options to Restore Estuarine Water Quality

I chose an experimental study over how effective specific methods improve water quality in an estuarine system – specifically, Waquoit Bay, Massachusetts. The methods tested were diverting nitrogenous runoff from impervious surfaces, changing zoning ordinances, preserving forested tracts of land and wetlands, harvesting macroalgae, dredging estuary channels, and eradicating waterfowl.

This article is an example of using an experimental method because it is a case study using a control, dependent and independent variables. The researchers manipulated the subjects in order to find the effects and get results. Most of the results were shown as numeric values represented in graphs and tables.

Land cover data was obtained to show the amount of nitrogen released as well as amount of nitrogen that remains in the Walquoit Bay. The results for the effectiveness of each method were gathered differently because they were not related. For instance, the method that reduces fertilizer inputs is to add different dosages of fertilizer to farms, lawns and golf courses, whereas the method for preserving vegetated tracts is to use NLM to calculate nitrogen amounts from a hypothetical forested plot and comparing it to other areas (ie a golf course, residential area, etc.).

The researchers concluded that the methods holding the most potential in lessening the nitrogen loads in Walquoit Bay – as well as other estuaries – include improvement of the septic system, having zoning regulations, preserving forested tracts and freshwater bodies, and conserving salt marshes. The methods that are somewhat less promising in reducing nitrogen loads are through installing wastewater treatment plants, regulating the use of fertilizer, and harvesting macroalgae. Those that would be the least successful are diverting runoff from impervious surfaces, dredging, and eradicating waterfowl. It is mentioned that these methods are focused on this particular region and that similar studies should be done on other estuaries. Each estuary is different, therefore may react differently to each method.

(Bowen, J. L., & Valiela, I. (2004). Nitrogen loads to estuaries: Using loading models to assess the effectiveness of management options to restore estuarine water quality. Estuaries, 27(3), 482-500. doi:http://dx.doi.org/10.1007/BF02803540)

Post 2: Study of the effect of a novel drug on chorea in Huntington’s

For my journal article I chose a study that is experimentally observing the effect of a drug, Deutetrabenazine, on Chorea in Huntington’s Disease patients. Huntington’s disease (HD) is an disease that results in the death of brain cells. A common symptom of this disease is chorea, which is involuntarily spasms and movement as a result of damage to the brain due to the neurodegeneration common in HD. Treatment of chorea is important because it has a significant impact on a patients safety and quality of life. Deutetrabenazine is a transporter inhibitor that is thought to be more stable, and thus require less dosing, than currently used treatments. The research question the researchers posed was “Can Deutetrabenazine decrease Chorea in patients with Huntington’s disease”. They decided an experimental study was required to test the effect of the drug as they needed to apply conditions in order to find the difference between a treated and untreated group in order to find the difference. The format for studying the drug used a sample size of 90 patients with HD with a chorea score of 8 or higher (Range is 0-28, with higher scores being worse).  Half of the patients received doses of Deutetrabenazine and the other half received placebo in a double-blind manner each for one year. The study went in detail on the mean differences in scores before and after treatment in both groups. The placebo and Deutetrabenazine groups were created by taking the 90 Huntington patients that qualified and sorting them randomly into the placebo and Deutetrabenazine groups. The drug group on average improved from a mean of 21.1 to 7.7, and then the placebo improved from a mean 13.2 to 11.3. The mean difference in improvement between groups was -2.5 units with the drug group improving more. More people were also improved by the drug treatment in addition to showing better improvement over placebo, with 23 patients improving with Deutetrabenazine compared to only 9 on placebo (51% versus 13%). There were not any extreme side effects of Deutetrabenazine shown in the study, as the side effects were similar to placebo.  The study concluded that Deutetrabenazine did result in improved motor signs when compared to placebo at 12 weeks, but further testing would need to be done to determine to what extent it is better, or if the changes would continue to be as effective or safe over time.  This kind of drug can be important to research further as finding more consistent, stable drugs for HD can help reduce the overall symptoms of chorea more efficiently, while requiring less dosing. The studies double blind study does seem to have a strange ethical component in that is doesn’t give patients with HD a treatment they believe will work and rather gave them placebo, which is in a strange ethical territory.



Geschwind, M. D. and Paras, N. (2016). Deutetrabenazine for Treatment of Chorea in Huntington Disease. Jama 316, 33.