This year has seen the scientific community at large come together to better understand and tackle the ongoing pandemic. Along with other…
As the end of the year draws in, PLOS ONE Staff Editors put together a list of some their favourite papers from 2019. Browse the different topics below:
- Behavioral and Social Sciences, Neuroscience, Mental Health
- Cancer and Medicine
- Cardiovascular and Public Health, Epidemiology, Sports Science
- Life Sciences
- Physical Sciences and Engineering
Behavioral and Social Sciences, Neuroscience, Mental Health
In an archaeological investigation, Ehud Galili and colleagues determined that a 100-meter wall submerged 90 meters off the Mediterranean coast of northern Israel was likely a seawall, built by villagers around 7000 years ago to separate and protect the main part of their settlement from rising seas. This study, which was highlighted in newspapers including the New York Times and Washington Post, illustrates one of the earliest attempts by humankind to respond to a changing climate, in this case during the post-glacial sea rise of the Neolithic period.
Student evaluations of teaching are often used to evaluate teaching effectiveness and the results may affect promotion and tenure prospects for instructors. This year, PLOS ONE published two papers on gender biases in these evaluations. In February, Fan and colleagues reported that these ratings may be less favourable towards women and teachers with non-English speaking backgrounds. Notably, these biases were less pronounced in faculties with greater diversity. Later in the year, Peterson and co-workers described an experimental study that aimed to mitigate biases in student evaluations. They showed that providing raters with language intended to reduce gender bias resulted in significantly higher rankings for female instructors, without affecting ratings for male instructors.
Many non-mammalian vertebrates are able to regenerate their spinal cords following injury. Hanslik and colleagues show that lampreys regenerate after a second spinal transection just as robustly as the first. The findings provide insights into potential targets for treatment of non-regenerative disorders
Cancer and Medicine
Influenza (flu) is a notable global pathogen that infects millions of people, and kills hundreds of thousands worldwide each year. In recent years, much work is being done to study the human microbiome and its effects on health. In this work, Prof. Betsy Foxman and colleagues showed that differences in the microbiome of the upper respiratory tract (where flu replicates) correlate with susceptibility to flu infection in a local community.
The function of many oncogenic proteins depends on Heat Shock Protein 90 (HSP90), a molecular chaperone that facilitates protein folding and maturation. Disappointingly, HSP90 inhibitors have shown only modest benefit to patients in clinical trials and no HSP90 inhibitor has achieved FDA-approval to date. Therefore, a more comprehensive understanding of HSP90 biology in cancer cells is needed. Echeverria and colleagues set out to understand the biological basis of the apparent increased sensitivity of cancer cells to HSP90 inhibitors in comparison to normal cells. Using an isogenic pair of transformed vs normal cell lines, they find that this therapeutic vulnerability can be attributed to a shift in the balance between cell quiescence and active cell division.
Microdosing psychedelics holds promise for the treatment of mental health disorders, but rigorous research continues to face legal hurdles. In a study of existing users, Polito and Stevenson found evidence of benefits for mood disorders, but not the increase in creativity that many users anticipated.
The ability to reliably detect and diagnose cancer from blood samples would be a monumental clinical achievement. Research from Chen and colleagues suggests that miRNAs that are enriched in extracellular vesicles might be useful in detecting and diagnosing colorectal tumors. The miRNA expression patterns derived from colorectal cancer cell lines were able to predict colorectal tumors derived from The Cancer Genome Atlas with high sensitivity and specificity. Furthermore, a metastasis-derived colorectal cancer cell line shed extracellular vesicles with a distinct miRNA profile in comparison to a primary tumor-derived cell line, raising the intriguing possibility that these differentially expressed miRNAs might have a role in metastasis. These findings support the potential use of circulating extracellular vesicles as biomarkers for colorectal cancer and suggest a possible role for their miRNA cargo in metastasis.
Cardiovascular and Public Health, Epidemiology, Sports Science
Cardiovascular diseases remain the leading cause of death across the EU despite the recommendations by the World Health Organization (WHO) regarding the major preventable risk factors. Following the WHO recommendations, Schönbach and colleagues modelled the health impacts that a fat tax could have if introduced in seven European countries. They conclude that taxation of foods high in saturated fat could reduce the prevalence of ischemic heart disease cases in all seven countries. This research might inform and reopen the debate on unhealthy food taxation.
Recent work from Alaa and colleagues shows the powerful combination of machine learning tools and a data from a big cohort (400,000 participants and 400 variables from the UK Biobank) for cardiovascular risk prediction. The authors show how the machine learning framework improve the prediction of cardiovascular events as compared with traditional risk prediction approaches.
Several studies have shown that a high socio-economic status (SES) in adulthood has a protective effect against alcohol use disorders (AUDs); however, this association may be confounded by the action of genetic factors and familial environmental effects during childhood. To disentangle these relationships, Calling and colleagues adopted a co-relative control design to analyse whether siblings and cousins with similar shared childhood SES but with differing SES in adulthood presented the same risk to develop AUD. Their results show that high adulthood SES may protect against alcohol use disorders even after shared familial factors have been taken into account.
The world’s islands are home to some of its most unique flora and fauna, much of which is now imperilled by the negative effects of invasive species. Holmes and colleagues developed a framework for identifying and prioritising islands where the aim of eradicating populations of invasive mammals is technically and socio-politically feasible. Successful removal of invasive mammals from these fragile island ecosystems could help not only to halt the decline of threatened species but also to pave the way for ecological restoration and species reintroductions.
Amphibians are one of the groups of animals that have been hit hardest by the current trend of species loss. For this reason, the discovery of five new miniaturised frog species from the remote Madagascarian tropical forests was some positive news in 2019. An international team of researchers, led by Dr Mark Scherz (Bavarian State Collection of Zoology), discovered these new species and named them with instantly popular names such as Mini mum, Mini scule and Mini ature. This research has drawn worldwide attention to the rich biodiversity and ecological importance of these rapidly declining habitats.
Cilia are organelles that protrude from the cell’s surface and have a variety of functions including motility and sensing the environment. These different functions are dependent on the cilium having a different complement of proteins. In their research Blasius and colleagues demonstrate that nuceloporins localize to the base of motile cilia and interact with nephronophthisis proteins known to play a role in cilium assembly and identity. Their work supports the hypothesis that mechanisms and components of nuclear gating are use to regulate protein entry into cilia.
Newts are well known for their regenerative capacity and understanding the functions of proteins involved in this may help in promoting tissue regeneration in mammals, which have limited tissue regeneration capability. However, the studies of Newt regeneration are challenged by lack of genetically tractable animal models mainly due to the comparatively longer reproductive cycle in Newts. Instead, Mehta and colleagues utilized Drosophila as a genetic model to express five Newt genes known to be expressed during regeneration and combined RNA sequencing and protein structure/function predictions to identify the role and functions of these genes.
There is a growing body of research exploring how the gut microbiome can influence host behavior. Mazarin Akami and colleagues, show that the foraging behavior of oriental fruit flies is altered depending on whether or not they harbor symbiotic gut microbes. Flies with or without a microbiome make different decisions depending on their nutritional and energetic needs as seen in their food ingestion, time spent feeding, and response to food sources.
Physical Sciences and Engineering
Climate change is predicted to have a negative effect on agriculture around the world, with possible scenarios in which we observe a decrease in both crop yield and diversity. Ray and colleagues analysed weather and crop data for the world’s ten most common crops, and found climate change has likely led to around a 1% average reduction in consumable food calories in the crops studied. These findings suggest that the effects of climate change on food security aren’t just something to consider for the future, but that it’s probably already happening.
Assistive robots can truly change the quality of life, independence, as well as the amount of care required for people with profound motor deficits. They can perform standard daily tasks, such as feeding and personal care, or help stroke patients perform exercise routines for rehabilitation. Grice and Kemp from the Georgia Institute of Technology have developed a robotic body surrogate that can be easily controlled via eye and head trackers by both novices and experts. Participants with severe motor deficits were able to manipulate objects, drink and eat, shave their face, turn a light switch on and off. Robots like these provide patients with a greater degree of independence and are only limited by our engineering skills and costs.
Biomolecular systems offer exciting potential advantages as vehicles for information storage, as an alternative to traditional semiconductor technologies. In this paper, Kennedy and colleagues explore the possibility of encoding images in synthetic mixtures of small molecules, using a robot to rapidly select specific metabolites from a library and mass spectrometry to extract the data for reconstruction of the original image. The authors show that kilobyte-scale image datasets can be encoded and decoded with >99% accuracy, providing insight into some of the benefits and limitations of small-molecule chemical information systems.
- Alaa AM, Bolton T, Di Angelantonio E, Rudd JHF, van der Schaar M (2019) Cardiovascular disease risk prediction using automated machine learning: A prospective study of 423,604 UK Biobank participants. PLoS ONE 14(5): e0213653.
- Akami M, Andongma AA, Zhengzhong C, Nan J, Khaeso K, Jurkevitch E, et al. (2019) Intestinal bacteria modulate the foraging behavior of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae). PLoS ONE 14(1): e0210109.
- Blasius TL, Takao D, Verhey KJ (2019) NPHP proteins are binding partners of nucleoporins at the base of the primary cilium. PLoS ONE 14(9): e0222924.
- Calling S, Ohlsson H, Sundquist J, Sundquist K, Kendler KS (2019) Socioeconomic status and alcohol use disorders across the lifespan: A co-relative control study. PLoS ONE 14(10): e0224127.
- Chen M, Xu R, Rai A, Suwakulsiri W, Izumikawa K, Ishikawa H, et al. (2019) Distinct shed microvesicle and exosome microRNA signatures reveal diagnostic markers for colorectal cancer. PLoS ONE 14(1): e0210003.
- Echeverria PC, Bhattacharya K, Joshi A, Wang T, Picard D (2019) The sensitivity to Hsp90 inhibitors of both normal and oncogenically transformed cells is determined by the equilibrium between cellular quiescence and activity. PLoS ONE 14(2): e0208287.
- Fan Y, Shepherd LJ, Slavich E, Waters D, Stone M, Abel R, et al. (2019) Gender and cultural bias in student evaluations: Why representation matters. PLoS ONE 14(2): e0209749.
- Galili E, Benjamin J, Eshed V, Rosen B, McCarthy J, Kolska Horwitz L (2019) A submerged 7000-year-old village and seawall demonstrate earliest known coastal defence against sea-level rise. PLoS ONE 14(12): e0222560.
- Grice PM, Kemp CC (2019) In-home and remote use of robotic body surrogates by people with profound motor deficits. PLoS ONE 14(3): e0212904.
- Hanslik KL, Allen SR, Harkenrider TL, Fogerson SM, Guadarrama E, Morgan JR (2019) Regenerative capacity in the lamprey spinal cord is not altered after a repeated transection. PLoS ONE 14(1): e0204193.
- Holmes ND, Spatz DR, Oppel S, Tershy B, Croll DA, Keitt B, et al. (2019) Globally important islands where eradicating invasive mammals will benefit highly threatened vertebrates. PLoS ONE 14(3): e0212128.
- Kennedy E, Arcadia CE, Geiser J, Weber PM, Rose C, Rubenstein BM, et al. (2019) Encoding information in synthetic metabolomes. PLoS ONE 14(7): e0217364.
- Lee KH, Gordon A, Shedden K, Kuan G, Ng S, Balmaseda A, et al. (2019) The respiratory microbiome and susceptibility to influenza virus infection. PLoS ONE 14(1): e0207898.
- Mehta AS, Luz-Madrigal A, Li J-L, Tsonis PA, Singh A (2019) Comparative transcriptomic analysis and structure prediction of novel Newt proteins. PLoS ONE 14(8): e0220416.
- Peterson DAM, Biederman LA, Andersen D, Ditonto TM, Roe K (2019) Mitigating gender bias in student evaluations of teaching. PLoS ONE 14(5): e0216241.
- Polito V, Stevenson RJ (2019) A systematic study of microdosing psychedelics. PLoS ONE 14(2): e0211023.
- Ray DK, West PC, Clark M, Gerber JS, Prishchepov AV, Chatterjee S (2019) Climate change has likely already affected global food production. PLoS ONE 14(5): e0217148.
- Scherz MD, Hutter CR, Rakotoarison A, Riemann JC, Rödel M-O, Ndriantsoa SH, et al. (2019) Morphological and ecological convergence at the lower size limit for vertebrates highlighted by five new miniaturised microhylid frog species from three different Madagascan genera. PLoS ONE 14(3): e0213314.
- Schönbach J-K, Nusselder W, Lhachimi SK (2019) Substituting polyunsaturated fat for saturated fat: A health impact assessment of a fat tax in seven European countries. PLoS ONE 14(7): e0218464.