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Melena Scala

Science News Article Write-Up 2

In an article published in npr.org entitled, “Diet soda may prompt food cravings, especially in women and people with obesity,” the author summarizes a study that beverages with sucralose in them may make some people hungrier. It states that the research found that women and people with obesity experienced a stimulate appetite and reduction in appetite inhibiting hormones after they had sucralose, while males and those with healthy body weights did not. While reading, I found that the academic journal where the original study is found is linked in the text and one of the researchers is quoted. Though the academic journal obviously provides a more in-depth account of the specific research methods used—which included MRI scans to observe whether or not the parts of the brain that control appetite were stimulated, blood tests to investigate hormones, and a buffet table at the end of the study to observe how much individuals ate—I found that the article gave an accurate description of the procedure used in the study. Similarly, the results of the study are depicted accurately, and I think they use this study to explore and discuss the influence of these diet drinks on women and individuals with obesity and how they are intended to cause weight loss but may actually be causing weight gain in these individuals cautiously. For instance, at the end of the academic journal it states that the findings highlight “the need to consider individual biological factors in research studies and potentially in dietary recommendations regarding the use and efficacy of NNS for body weight management,” which is what the article discusses. Therefore, I do not think the findings of the study are manipulated or misused in the article, and whatever hypotheses or connections that the author includes are clarified and not passed off as a known fact. Something that I think the article is missing would be an explanation of some of the limitations of the study, such as variables like dosage, the unique chemical structure of each sucralose, and the presence of carbohydrates possibly having an influence on the results. Furthermore, I think the title is a little misleading in attempt to be attention grabbing, because the study did not examine all kinds of diet sodas, it just investigated the effect of sucralose which can be found in some diet sodas.

 

Works Cited

Aubrey, Allison. “Diet Soda May Prompt Food Cravings, Especially in Women and People with Obesity.” NPR, NPR, 7 Oct. 2021, www.npr.org/sections/health-shots/2021/10/07/1044010141/diet-soda-may-prompt-food-cravings-especially-in-women-and-people-with-obesity.

Yunker AG, Alves JM, Luo S, et al. “Obesity and Sex-Related Associations With Differential Effects of Sucralose vs Sucrose on Appetite and Reward Processing: A Randomized Crossover Trial.”  JAMA Netw Open. 2021;4(9):e2126313. doi:10.1001/jamanetworkopen.2021.26313

Unlike the previous entry, it was fairly easy to find the the original article, as the news article author kindly included links to the document as citations. With this I imagined the article to be at least mostly factual with respect to the research paper. However, int he research paper there is no clear or obvious abstract so I had to regard the first paragraph as the abstract. From reading the abstract alone, the article seems to be way off. One main difference is that while the news article uses this article to prove that clocks run at different speeds closer to high-gravity bodies, the paper (at least the abstract) does not discuss effects of gravitational bodies but how they were able to make atomic clocks more efficient and precise. Comparing the article to the rest of the paper, I don’t see much of what the news author said in her article in the research paper. The paper uses very specialized and difficult diction, physics is very complex after all, but in general the new author, Emily Conover, points out some of the research team’s accomplishments, but it wasn’t clear when the reseachers added those statistics into the paper. For example, Conover point out that there was a precisiion to “0.76 millionths of a trillionth of a percent, but I don’t remember seeing a similar number, even after reskimming the paper. Also, an interesting sidenote is that this is the most precise frequency recorded to date, but I am not sure how true this is.

Article 2

For 10/17:

Article Source:  How highly processed foods harm memory in the aging brain (https://www.sciencedaily.com/releases/2021/10/211014172753.htm )

 

Article Summary:  

A study by Ohio State University found that a diet of processed foods  yielded more memory loss and brain inflammation than foods with omega-3 fatty acids. The study was conducted with aging rats, and notes that brain inflammation was “…significantly elevated…” in the rats that ate processed food, while older rats in this group did not perform as well in behavior experiments. These experiments showed they had problems specifically with their hippocampus and amygdala.

 

Journal Source:  Dietary DHA prevents cognitive impairment and inflammatory gene expression in aged male rats fed a diet enriched with refined carbohydrates (https://www.sciencedirect.com/science/article/abs/pii/S0889159121005043?via%3Dihub )

 

Journal Summary:  

By studying 24-month-old male rats, Ruth M. Barrientos and other researchers find a strong connection between highly processed carbohydrates and poor memory retention. Their study over the course of 28 days, with data being collected from both conditioning tests conducted with electrical shocks as well as the extracted brains of the rats themselves. The results of the study reinforce the importance of an organism’s diet regarding its brain function.

 

Comparisons:  

• The journal abstract notes how the omega-3 fatty acids were given as supplements, while the article quotes one of the researchers in the study noting that humans that wish to improve their memory should do more than just take DHA supplements.
• The journal mentions how only male rats were used in the study, and how the rats were killed and had their brains extracted for further study after 28 days. The ScienceDaily article omitted these details.
• The article did not show any of the histograms from the journal.
• While the article mentions how the rats with the highly processed diets had trouble recalling they were in an “…unfamiliar space…” and showing “…anticipatory fear behavior…”, the journal details further that these spaces would send an electrical shock to the rats, where the researchers would analyze their reactions. The appearance of these spaces were also altered in between tests, creating the unfamiliarity the article mentions.

Andi Kolari

Professor Vejdemo-Johansson

HON 223 Seminar

10/17/2021

Research Description

The aim of this research was to attempt to conduct an analysis of the earth’s reflectance. The earth reflects a portion of the sun’s light back into space. Roughly 30% of it. Using ground based light measuring instruments, scientists were able to examine the amount of light reflected from the moon, as the sun’s light is reflected off of earth, and then partially reflected off the moon back to earth. Using this method, scientist were able to measure that the Earth was reflecting about .5% less light over a 19 year period from 1998 to 2017.

Abstract vs Article

The article is much more in depth than the abstract. The abstract is extremely brief. It describes the goal of the research article as analyzing the change in the earth’s reflected light over a 19-year period. It very, very briefly describes how they did it. It describes what they found, and it describes what they believe to be a potential cause. There is also a “plain language summary”, which is essentially the same thing but with less scientific jargon. In contrast, the article is actually much more in depth. The article does everything listed above, though in slightly more depth. In addition, it provides its own alternate theories for the findings of the researchers. The article proposes that the decrease in reflection is the result of the warming of the eastern Pacific, which has reduced low-lying cloud cover, which in turn decreases the earth’s reflectiveness. The article proposes that this could also be the result of the melting of the polar ice caps, which also reflect a significant amount of light. Additionally, the article talks more about the implications of this research. Specifically, the implications regarding climate change, as the decrease in light reflection will continue to contribute to the warming of the earth.

 

Research vs Article

Unsurprisingly, the research is far more in depth than the article. While the article gives a relatively deep description of what was discussed in the research, the actual study goes far more in depth. As an example, the article simply explains that the researchers conducted an analysis of the amount of light the earth reflects by observing the reflected light the moon reflected back to us. In the actual research journal, the authors explain that there are multiple problems with just measuring this quantity, such as the changing moon phases, seasonal changes, etc. As such, they had to meticulously account for all of these different parameters which could have thrown off what it was they were trying to calculate. Every conclusion the researchers reached in the lead up to their primary conclusion is substantiated, weather that be through the findings of their research, complex mathematical analysis, etc. A research journal will be held to the upmost scrutiny. The researchers will exhaust every resource available to them to ensure that they conducted a proper scientific experiment and their findings are true and valid. The larger scientific community will hold their findings to extreme scrutiny to ensure that the science is ethical and accurate. An article like this on the other hand, is not held to such scrutiny. It exists to provide the general public with an easier to digest version of the science, so it is far less in depth.

 

 

 

 

Sources Cited

• R. Goode et al. Earth’s albedo 1998-2017 as measured from earthshine. Geophysical Research Letters. Vol. 48, Sept. 8, 2021. doi: 10.1029/2021GL094888.
• Perkins, S. (2021, October 13). Earth is reflecting less light. it’s not clear if that’s a trend. Science News. Retrieved October 17, 2021, from https://www.sciencenews.org/article/earth-reflection-light-dim-earthshine-moon-solar-radiation.

 

 

Madison DeGrezia

Professor Vejdemo-Johansson

HON 223

18 October 2021

Coronavirus: A New Disease or One From the Past?

After thorough research and skimming through the recent articles published on the New York Post, “Coronaviruses have been around a lot longer than you think, study says” by Kathianne Boniello caught my interest. The Covid-19 pandemic rapidly spread across the world with a variety of symptoms that range from mild to severe cases. This disease has taken a toll on society and left people with many unanswered questions. Many people questioned where it came from and how it managed to spread so quickly. A vaccine was urgently needed, however Covid-19 mutated creating a new strand of the virus that medical officials lacked the knowledge of. Despite the common belief that the coronavirus is an upcoming disease that originated in Wuhan, China and spread to several other countries across the world, study shows that the virus may have been around much longer than we all believed.

The New York Post article written by Boniello based its findings off of the data published in the peer reviewed journal posted on “Current Biology”, “An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia” by Yassine Souilmi, M. Elise Lauterbur, Ray Tobler, Nevan J. Krogan, Kirill Alexandrov, and David Enard. The article focuses on the coronavirus pandemic and the identification of past epidemics through the response and adaptation of genomes. Researchers used evolutionary information to trace the immune responses of the infected hosts and utilized this information to help predict future breakouts of diseases that can affect humanity. The study employed the STARS Method, which is a structured technique to approach unanswered questions and draw valid conclusions. In this study, the selection signals were analyzed to see if a set of VIPs were present that interacted with the coronavirus pandemic. The behavior of the VIPs were the main focus due to the protein interactions illustrating how a virus can hijack and infect a host. Based on the 35 interactions of proteins that were studied, 24 of them, approximately 73%, were verified to be CoV-VIPs. The data provided further evidence that a past epidemic in East Asia could have existed, which possessed similar protein interactions to the viral coronavirus outbreak.

The published New York Post article and the research paper share some similarities, however there are discrepancies that set them apart from each other. Both suggest the possibility of a virus in East Asia, similar to the coronavirus outbreak, spreading and infecting our ancestors. Nevertheless, the academic paper discusses how it is possible for a viral infection to exist in the past that was similar to the coronavirus, but was not identical to the one that is impacting society today. The paper rather focuses on selection signals that possess a set of VIPs that were verified to be CoV-VIPs. Therefore, the paper focuses on the interactions between the proteins and proves that their behavior is similar to how the coronavirus attached to the cell’s in the infected host’s body and replicated itself. The New York Post article was condensed and provided very little background for the study conducted. It failed to specifically explain how researchers were able to conclude that a virus similar to covid infected people in the past and enabled the genes to adapt. The article lacked the scientific evidence that strengthened the researchers’ arguments and instead provided a condensed version of the study that did not include all of the important information that was mentioned in the study. The abstract and the New York Post article were in agreement with one another for the most part, but the abstract was more in detail with how a past virus had similar interactions to how the coronavirus reacted with the host. This eye opening revelation provided researchers with evolutionary evidence that could assist in understanding and predicting future outbreaks of viruses across the world. The purpose of an abstract and a New York Times article is to grab the audience’s attention and intrigue them to read further. This explains why articles in NY Times have attention-grabbing titles that catch the eye of readers right off the bat. To sum up, the news article briefly introduces a breakthrough in science, in contrast to the research paper that provides insight on the scientific study conducted by experts.

Work Cited

Boniello, Kathianne. “Coronaviruses Have Been around a Lot Longer than You Think, Study Says.” New York Post, New York Post, 27 June 2021, https://nypost.com/2021/06/27/coronaviruses-have-been-around-longer-than-you-think-study/. 

Souilmi, Yassine, et al. “An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.” Current Biology 31.16 (2021): 3504-3514.

 

Justin Zaluk

Professor Vejdemo-Johansson

HON 223

18 October 2021

“This Parasite Turns Plants Into Zombies”

        The article “This Parasite Turns Plants Into Zombies”, produced by Veronique Greenwood and published by the New York Times, caught my interest after searching the internet for a scientific news item based on a published research paper. This intriguing article begins by briefly explaining the transformations brought upon an adolescent mustard plant, affected by what is known as Aster Yellows phytoplasma, a type of parasite. Greenwood continues by providing details regarding the effects of such a parasite on plants it brings under its control. In this case, the mustard plant was placed into an eternal state of youth, with long, “witches’ broom” shaped stems protruding from it. In an effort to better understand and uncover the source of such a unique phenomenon, scientists from the John Innes Centre in England performed a study honing on the phytoplasma’s tactics. The news publication states how the team revealed that a protein known as “SAP05”is the main culprit in the long-lasting youth of these plants. By binding on to plant proteins, it is possibly also protected due to a longer life span and increased resilience to “stress of an infection”. When wrapping up, the article also details how such a finding from these researchers may help in the protection of crops, as these types of parasites can cause widespread destruction, resulting in many other financial and health related issues.

        Linked to the previously described New York Times article was the scientific research paper that was formulated and published by the John Innes Centre scientists. It was published on September 17, 2021, on Cell, a peer-reviewed scientific journal, and is titled “Parasitic modulation of host development by ubiquitin-independent protein degradation”. Throughout the introduction of this paper, background information regarding other prominent parasites is conveyed, addressing the idea that the causes of “host modifications” need more information to be fully understood. The first part of this study involved applying SAP05 to a plant named “RPN10”, and observing its effects. It was noted that fertility was “compromised”, and the plant grew oddly shaped flowers and stems. Additionally, the study goes on to describe attempts made to manually give plants resistance to the SAP05 protein. The team successfully altered nucleotides within the genes of plant RPN10, thus achieving resistance to SAP05. However, the research paper illustrates how this is not necessarily beneficial, with better reactions to infection coming from fauna affected by the parasite. The paper wraps up by describing the limitations of this study, which included limited “gene targeting tools”, as well as an assortment of other symptoms that has to be noted for each plant subject. Furthermore, the results displayed that 26 of the 32 tested plants developed typical SAP05 effects, affirming the scientists hypotheses that this protein is responsible for the creation of these “zombie” plants.

        Both the New York Times Article and published research paper shared numerous similarities and discrepancies that differentiate them from each other. First, when compared  strictly to the abstract of the paper, their content agreed. The main points that paralleled between both included the effects of SAP05, ability to engineer plants to resist them, and background of plant parasites. They each served as a general overview that provides the reader with a basic yet coherent understanding of the study at hand. The paper’s abstract did use some more scientific classifications when compared to the abstract, but this difference was minor. Most discrepancies, while still few, were present when the article was analyzed with the paper itself. As an example, in the results section of the research, the scientists detailed how SAP05 led to certain degradation in “the 26S proteasome”, and gave a more in depth look at the reduction of plant development issues. These were not mentioned in the article, making it a notable difference. Furthermore, the limitations of the study, as well as numerous visual charts, were available within the paper, but not Greenwood’s article. When searching for comparisons, I noticed that the potential uses of this discovery were found in both, which included “Phytoplasma SAP05 effectors may enable a more direct TPD technology”. Clearly, this news item explains an important revelation in the scientific community. The article seeks to provide a quick understanding of the topic, while the research paper can be used to analyze data on a deeper level.

 

Works Cited

Greenwood, Veronique. “This Parasite Turns Plants into Zombies.” The New York Times, The New York Times, 1 Oct. 2021, https://www.nytimes.com/2021/10/01/science/zombie-plants-parasites.html. 

Huang, Weijie, et al. “Parasitic Modulation of Host Development by Ubiquitin-Independent Protein Degradation.” Cell, vol. 184, no. 20, 17 Sept. 2021, https://doi.org/10.1016/j.cell.2021.08.029. 

 

Matthew Keeler

Professor Vejdemo-Johansson

HON 223

October 18, 2021

The article that I found very interesting when I was exploring various sources this week was titled “New Research Suggests Signs of Dementia Can be Detected in Blood” by Julia Musto in the New York Post. Within the news article I realized they utilized a lot of the quotes from the study with very little commentary to go along with this information. One of the main points they highlighted was a graph that came directly from the abstract of the paper but didn’t provide any further information in explanation of the deeper meaning behind it other than the basic gist of its meaning. The news article explains what the study generally conducted and explains that by viewing the cellular disease models of both humans and animals, healthy and unhealthy, they were able to identify a 3-microRNA signature pathological condition that could enhance phenotypes in the animal models that were studied. The majority of the news article is the reporting of the studies finding and how this information can be used for the developing cases of Alzheimers and Dementia that are continuously increasing and expected to affect 14 million by the year 2060.

When looking in depth at the research article that was published on EMBOpress, I was able to notice similarities between the abstract and the paper itself. One of the main components from the abstract highlighted why these studies and tests transpired in the first place due to the reason that scientists wanted to be able to identify any signs of disease at an early stage and be able to treat with causative therapy before it’s too late. By identifying any possible molecular biomarkers there can be further testing and screenings done in order to identify at these earlier stages anyone who has the risk of developing Alzheimer’s Diseases. When researching the healthy and unhealthy samples scientists were able to conclude that the molecular biomarker they were looking for was a 3-microRNA signature that can be detected in the blood samples of patients to give more information regarding the relevant patho-mechanisms functioning in the brain. With this information scientists make headway to RNA therapeutics to potentially ameliorate any disease phenotypes currently present in the animal models. In the future it is believed that this can be used as a point-of-care screening approach to find at-risk individuals in time to give them the proper care and therapies necessary to intervene and treat Alzheimer’s disease.

Furthermore, there were various similarities that I identified between the news article, abstract, and the scientific research paper. The news article identified a string of quotes that they gathered from the research paper in order to add depth and some science behind their attention-grabbing headline. However, I do believe that Musto does a great job encapsulating the research paper’s research and conclusions and drawing attention to the findings with suggestive, but accurate headings and information. One very striking similarity is the fact that the news article even utilizes the abstract’s graph in its article from a tweet by EMBO backed with findings that Fischer was able to conclude from gathering the research. The main difference that I saw is obviously the paper discussing their findings with the figures and data tables they collected, while the news article solely goes for attention grabbing lines and information to provide an accurate representation, while still making the article have standout information that will catch the eyes of an abundance of readers. Overall, I felt that the article, abstract, and the research paper all had the same collective agreements and information with the overall research and conclusions drawn are the same throughout all the works.

 

Works Cited

Islam, Md Rezaul, et al. “A microRNA signature that correlates with cognition and is a target against cognitive decline.” EMBO Molecular Medicine (2021): e13659

News, Fox. “New Research Suggests Signs of Dementia Can Be Detected in Blood.” New York Post, New York Post, 14 Oct. 2021,  https://nypost.com/2021/10/14/new-research-suggests-signs-of-dementia-can-be-detected-in-blood/.

 

 

Marco Korcak

Professor Vejdemo-Johansson

MHC 223

October 18, 2021

Identifying Human Infecting Viruses

            Health is an important aspect of life that is constantly being observed and advanced as time goes on. The medical field relating to the human body is constantly changing and evolving with new information being discovered and published. With the recent outbreak of the Coronavirus, many people globally have been impacted, showing the world that dangers such as viral infections cannot be overlooked. Although the pandemic had numerous negative impacts on the world and its economies, it also resulted in new research being conducted and findings published.                                                                                                                                                                   The New York Post published an article titled “AI used to predict which animal viruses are likely to infect humans: study” which was written by Julia Musto. The article referred to the peer reviewed research article titled “Identifying and prioritizing potential human-infecting viruses from their genome sequences”. This article was published by a group of researchers based in Glasgow, Scotland. The article stated that the researchers developed machine learning models to single out candidate zoonotic viruses. A zoonosis is an infectious disease that is transmitted between species from animals to humans. The article stated that a dataset of 861 viral species was used to collect a single representative genome sequence from the hundreds of RNA and DNA virus species. The article reported that the findings from the research article was that 72% of the viruses that predominantly or exclusively infect humans were correctly identified. The article also stated that the research separated results by differing levels of zoonotic potential. 77.2% of the viruses were predicted to have a very high zoonotic potential. When examining a second set of data that was comprised of 645 animal-associated viruses data showed that “results are consistent with the expectation that the relatively close phylogenetic proximity of nonhuman primates may facilitate virus sharing with humans” (Mollentze, 11). Overall, this article summarized the study done and explained that this information will evolve as time passes and more viruses are characterized.

            “Identifying and prioritizing potential human-infecting viruses from their genome sequences” is a research article published by a team of researchers based in Glasgow, Scotland. The authors included Nardus Mollentze, Simon A. Babayan, Daniel G. Streicker and many more. The research article was published on September 28, 2021, after numerous peer reviews and has received media coverage from 53 news outlets and 2 blogs. The abstract of the research states that the goal was to determine which animal viruses may be capable of infecting humans to allow for outbreak preparedness and early investigation. The researchers developed a machine learning model to that can identify candidate zoonoses solely using signatures of host range encoded in viral genomes since there is an increasing use of genomics in virus discovery. The researchers collected a single representative genome sequence from 861 RNA and DNA virus species spanning 36 viral families. This was then used with three published datasets that reported human infectivity at the virus species level. Using a dataset of 861 viral species, the machine learning model outperformed other models based on the phylogenetic relatedness of viruses and the researchers also identified a new high-risk coronavirus strain. On a second set of data with 645 animal associated viruses the machine learning model was able to identify 272 high and 41 very-high risk candidate zoonoses. There were two additional cases studies done during this research to illustrate the utility of the prediction framework. In essence, this machine learning model was significant because it provides a rapid, low-cost approach to enable evidence-driven virus observation.

             After reading the New York Post article and research article itself, it is evident that there are numerous similarities, but many discrepancies present as well. In terms of statistics and data, the article matches up with the research paper and overall research. The article stated some of the results of the research paper but failed to explain the process taken to get to the results as well as other significant findings. In order to properly get results the researchers needed to account for the fact that viruses change over time and adapt. The research article greatly emphasized the process that was taken in order to account for this change which was done by reconstructing taxonomy more accurately. This was done because genome composition features only partly tracked evolutionary history so much more detail was needed than available. Once this was done the researchers also carried out two case studies to illustrate the utility of the prediction framework. This was done by using 758 virus species that were not present in the training data and they also used a beta regression model to explore how predictions of zoonotic potential varied among host and viral groups. This process was very significant in the research and should have been emphasized in the article published by the New York Post but it was not. The post also failed to mention other valuable statistics and processes such as the SHapley Additive exPlanations (SHAP) algorithm. This computed the Shapley value for each feature and is increasingly used to improve the interpretability for the decisions made by the machine learning models. This was also very influential to the research article and was not mentioned in the New York Post article. In essence, there were similarities between the research article and the New York Post article, but the article did fail to mention very important aspects of the research process.

 

 

Works Cited

Mollentze, Nardus, et al. “Identifying and Prioritizing Potential Human-Infecting Viruses from                         Their Genome Sequences.” PLoS Biology, vol. 19, no. 9, Sept. 2021, pp. 1–25.                                      EBSCOhost, doi:10.1371/journal.pbio.3001390.

News, F. (2021, October 4). AI used to predict which animal viruses are likely to infect humans:             Study. New York Post. Retrieved October 12, 2021, from https://nypost.com/2021/10                         /04/ai-used-to-predict-which-animal-viruses-are-likely-to-infect-humans-study/.

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