The Complicated Immune Response: Annual Review of Immunology, Volume 35

Browse the Annual Review of Immunology, Volume 35 table of contents.

While proofing this volume, I was impressed again by how complicated the immune system is. It seemed so very simple in high school biology! But there are so many related actions that have to happen in precise sequences, and even systems that I thought were disconnected from immunity turn out to be quite important. For instance, see the abstract of “The Lymphatic System: Integral Roles in Immunity” by Gwendalyn Randolph et al.:IY35-lymphatic

The lymphatic vasculature is not considered a formal part of the immune system, but it is critical to immunity. One of its major roles is in the coordination of the trafficking of antigen and immune cells. However, other roles in immunity are emerging. Lymphatic endothelial cells, for example, directly present antigen or express factors that greatly influence the local environment.

The study of immunology has progressed in recent years and is producing huge amounts of data—as I discovered in Arup K. Chakraborty’s article, “A Perspective on the Role of Computational Models in Immunology.” To make use of that data, because the processes are so complex, researchers are using computational models:

Computational or theoretical studies of the model can keep track of every possible event that can occur consistent with a hypothesis and reveal whether a particular hypothesis is plausible. Hypotheses that appear feasible at first glance can be incorrect because of the complexity of the underlying phenomena. Computational biophysics–based models not only can screen out these hypotheses prior to fruitless experimental tests, but also can shed light on the reason a hypothesis is unlikely to be right and thus guide the choice of other feasible hypotheses. Such computational studies are not exercises in fitting parameters to quantitate known mechanistic models. Rather they offer ways to obtain mechanistic insights and guide the choice of meaningful hypotheses underlying puzzling observations and the design of realistic experiments that can test the hypotheses.

Another article that caught my interest was Kole T. Roybal &Wendell A. Lim’s “Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities.” I was intrigued by the title’s use of “hacking” in a biomedical context and the article itself proved to be fascinating!

[I]mmune cells are relatively easy to remove, modify, and transfer back into a patient. Given these unique properties, immune cells provide a remarkable platform for interfacing with and treating disease. There are many complex diseases, such as cancer and autoimmunity, that our natural immune systems either cannot handle or pathologically contribute to. Thus, there is a strong rationale to engineer new disease sensing and response behaviors in immune cells, especially given recent powerful advances in synthetic biology and genome editing, which give us unprecedented ability to modify and engineer cellular functions.

Suzanne K. Moses is Annual Reviews’ Senior Electronic Content Coordinator. For 15+ years, she has played a central role in the publication of Annual Reviews’ online articles. Not a single page is posted online without first being proofed and quality checked by Suzanne.

 

ACA, Violence, and Social Networks: Annual Review of Public Health Volume 38

We are pleased to remind everyone that the 2017 volume of the Annual Review of Public Health, now online, is published open access under a Creative Commons Attribution-ShareAlike (CC BY-SA) license. This influential content is now freely available to read, reuse, and share. Additionally, all 37 back volumes (1980-2016) are now free to read. Support for this initiative to increase openness and transparency in research is provided by the Robert Wood Johnson Foundation.

Here are a few content highlights for your reading pleasure:

There is still a lot of debate over the future of the Affordable Care Act (ACA) and I recommend the article “The Affordable Care Act’s Impacts on Access to Insurance and Health Care for Low-Income Populations” by Kominski, Nonzee, and Sorensen as interesting background reading.  I was particularly interested in the discussion about the people who are still uninsured, and struck by the geographical implications:

Almost 90% of all adults in the coverage gap live in the South, half in either Texas or Florida, which aligns with this region’s high uninsurance rates, limited Medicaid eligibility, and low uptake of Medicaid expansion (37). Consistent with demographic characteristics and policies excluding nondisabled adults in states that did not expand Medicaid, African Americans and childless adults also account for a disproportionate share of individuals in the coverage gap.

Another article that demanded my attention is “Climate Change and Collective Violence” by Levy, Sidel, and Patz.  When people talk about the effects of climate change they mostly focus on sea levels and food harvests, but take things a couple of steps further and one of the things you can see is increased violence.  Some of the conclusions addressed in this article are quite startling:

Studying conflict in sub-Saharan Africa between 1981 and 2002, Burke and colleagues found a significant association between warmer temperature and civil war. On the basis of their findings, they projected an approximately 54% increase in armed conflict in Africa by 2030, with an additional 393,000 battle-related deaths, assuming wars in the future are as deadly as recent wars.

It’s a complicated and well written article that also addresses some ways of preventing this violence.  It’s on the top of my reading list.

pu38-social networksAnother article on my famed reading list is Valente and Pitts’ article, “An Appraisal of Social Network Theory and Analysis as Applied to Public Health: Challenges and Opportunities.”  What drew my interest here was the section about research being done around social media and the Internet’s effect on health:

The evidence suggests that mediated communications can influence individual behaviors but they do so at a rate much lower than face-to-face communications do (37). Still, people can have hundreds, even thousands or more, of online contacts, which increases the potential for much influence. Moreover, some forms of mediated communications may be particularly influential. For example, specialty communities that emerge in forums such as PatientsLikeMe may be very influential because they offer a place where people can share information about extremely important and relevant topics among members of a specific community.

Of course anytime someone is doing research in social media it raises ethics and privacy concerns which the article also addresses as a problem that needs close review.  For instance this troubling case:

In a similarly publicized study, Kramer and others (48) used Facebook as a social psychology laboratory and manipulated users’ Facebook News Feeds to induce negative or positive affect to study the social contagion of emotions. Facebook users did not provide overt consent to participate in the study, and many felt that their rights were violated (35). Furthermore, participants of in-person experimental studies are often debriefed when their study participation has concluded to reduce the likelihood that the study’s manipulations and procedures caused harm, yet no such debriefing was performed in this study.

So as usual Public Health provides much food for thought and interesting weekend reading!

Recruitment, Ostracism, and Brain Scans: Annual Review of Organizational Psychology and Organizational Behavior

Browse all the articles in the Annual Review of Organizational Psychology and Organizational Behavior, Volume 4.

Recently, a lot of media attention has focused on how technology businesses recruit, and retain, members of disadvantaged groups.  In the turbulent wake of the immigration ban, there has been renewed discussion about hiring immigrants and those from other cultures.  I  was glad to see authors David Allen & James Vardaman addressing some of these issues in “Recruitment and Retention Across Cultures.”  The article looks at how companies recruit workers and how that process is affected by different cultures. They also discuss how these different cultures face the challenge of assembling a diverse workforce:

Firms tend to (sometimes unintentionally) create barriers in the recruitment process by emphasizing job requirements that disadvantage immigrants (e.g., local experience), making negative assumptions (e.g., assuming immigrants have greater family responsibilities), or failing to appreciate immigrant credentials and skills. Additional research is needed to assess how recruitment policies affect immigrant recruitment, evidence that recruitment firms are more open to recruiting immigrants, the efficacy of developing immigrant networks, and the possibility that perceived skills shortages are a function of undervaluing immigrant credentials and skills.

Other research focuses on how differences in national culture affect the implementation of diversity recruitment initiatives. For example, Moore (2015) suggests that managers and employees hold culturally based native categories as to appropriate work roles related to gender. Thus, in a case study, a diversity initiative driven by a German parent company to increase the recruitment of women factory workers did not export as intended to a British context. The author concluded that effective diversity recruitment across cultures requires not only a recognition that cultural differences exist, but also an understanding of how practices and their meanings are recontextualized from one cultural context to another.

I learned a lot of new things from “Comparing and Contrasting Workplace Ostracism and Incivility” by D. Lance Ferris, Meng Chen & Sandy Lim.  While I have read a lot about workplace harassment, I hadn’t seen research about incivility and ostracism before.

Workplace incivility has been defined as a subtype of workplace mistreatment that is characterized by low-intensity social interactions that violate workplace norms of respect and yet are ambiguous as to whether they are meant to harm the target of the incivility. As this definition implies, there are three important characteristics associated with uncivil behaviors: their violation of norms, their ambiguity with respect to the hostile intent, and their general low intensity. Typical examples of uncivil behaviors at work that meet these three criteria include making demeaning comments to another individual, interrupting someone, and not speaking to—or ostracizing—someone. Such behaviors are typically viewed as rude and falling short of people’s commonly held expectations for mutual respect at work.

The article also deals with ostracism, “which includes behaviors such as being avoided at work, being shut out of conversations, or having one’s greetings go unanswered at work.” That seems horrible and makes me even more appreciative of my work colleagues who make a point of saying hello even when I’m walking the hallways with my headphones on.

orgpsych-waldmanAnother article that sparked my imagination is “Neuroscience in Organizational Behavior” by David Waldman, MK Ward & William Becker, which made me wonder if team-building exercises would be more enjoyable if followed by a brain scan instead of a questionnaire.  It turns out that the interviews and questions aren’t giving the level of data that other options might:

following a team process, a common practice of researchers is to get team members’ impressions of what the team process was about. Aside from recollection challenges on the part of team members, such assessment assumes an overall quality regarding a team process, rather than allowing for fluid or momentary shifts. As Waldman et al. (2015b) have argued and shown, qEEG neurosensing methods allow for more precise, momentary assessment of team processes and emergent states. In contrast, survey methods are not highly practical for assessing shifts in team processes or emergent states because of the interruption that would be caused. Moreover, although observation could be feasible, it is questionable whether observers can accurately assess phenomena such as team arousal or engagement, whereas neurosensing methods may be able to overcome such challenges”

I’d love to hear what you found interesting in this volume—the comments are open!

Suzanne K. Moses is Annual Reviews’ Senior Electronic Content Coordinator. For 15+ years, she has played a central role in the publication of Annual Reviews’ online articles. Not a single page is posted online without first being proofed and quality checked by Suzanne.

Welcoming the Annual Review of Cancer Biology

I’ve been looking forward to this series for a long time, and I’m glad to see the first volume fully published. Browse the table of contents for the Annual Review of Cancer Biology, Volume 1.

The autobiography by Harold Varmus, “How Tumor Virology Evolved into Cancer Biology and Transformed Oncology,” is a wonderful starting place for this series.  As Dr. Varmus tells his story, he introduces us to a field that constantly changing:

The story I will tell here is about the path that led to this new state of affairs. In that sense, this article differs from the kind of intellectual autobiography that commonly opens a volume of an Annual Reviews journal. Those articles, which I have read with pleasure over several decades, instructively track the development of new methods and the discovery of new facts within a single laboratory in the course of a senior scientist’s long career. I intend to provide my perspective on how a field of biological research—represented by this first volume of the Annual Review of Cancer Biology—began, grew, evolved, and prospered: not an impersonal account, but one that discusses my views of changing tides in cancer research more than the ebb and flow of people, ideas, and findings in my own laboratory.

ca1-varmusIt is a thoughtful and interesting history of not only Dr. Varmus’s career but how the field of cancer biology has developed.

Brandon Faubert & Ralph J. DeBerardinis introduced me to new methodologies in their article “Analyzing Tumor Metabolism In Vivo.” Working with live tumors is a new idea for me, and I was amazed at the wealth of information researchers are obtaining.

A comprehensive description of the pathways altered in cancer, the mechanisms by which they are perturbed, and the resulting metabolic vulnerabilities could drastically alter how we understand cancer and how we treat it. A key challenge is to apply systems that reliably report the metabolic features of intact tumors, particularly in patients. Although many current concepts in cancer metabolism derive from observations made in cultured cancer cell lines, research on the metabolic features of living tumors in mice and humans has begun to accelerate. We review some classical concepts in metabolic reprogramming, asking why metabolism is altered in cancer cells (i.e., the benefits of metabolic reprogramming to the cell) and how it is altered (i.e., the mechanisms of metabolic reprogramming). From there, we discuss approaches to investigating the metabolism of intact tumors and new principles in cancer biology arising from these studies.

Last on my reading list is “Resisting Resistance” by Ivana Bozic & Martin A. Nowak because I wanted to know more about the difficulties with targeted therapies and what the latest research looks like.  What I discovered was that I’m going to need to dust off my biology textbooks to refresh my background, and that these therapies can evolve resistance.

Targeted therapies, immunotherapies, and improved chemotherapies are being developed to reduce the suffering and mortality that come from human cancer. Although these approaches, and in particular combinations of them, are expected to succeed eventually to a large degree, they all suffer one obstacle: Populations of replicating cells move away—typically in a high-dimensional space—from any opposing selection pressure they encounter. They evolve resistance. It is possible, however, to develop a precise mathematical understanding of the problem and to design treatment strategies that prevent resistance if possible or manage resistance otherwise.

Suzanne K. Moses is Annual Reviews’ Senior Electronic Content Coordinator. For 15+ years, she has played a central role in the publication of Annual Reviews’ online articles. Not a single page is posted online without first being proofed and quality checked by Suzanne.

Annual Review of Statistics and Its Application, Volume 4

Investigate the full table of contents for Volume 4 of the Annual Review of Statistics and Its Application.

st4-fingerprintOne topic I’ve been tracking for a while is addressed by Stern’s article “Statistical Issues in Forensic Science.”  In the past decade, there have been many challenges to accepted forensic science—such as fingerprint analysis. Fingerprints are used by the author to demonstrate how statistical methods could be used to address current problems:

Another concern expressed in the 2009 NRC report is whether the forensic practitioner community has a full appreciation of the role of uncertainty in forensic examinations. For many years (through the early 2000s), it was common for latent print examiners to support a claimed identification by noting that the process they followed had zero error rate. Another popular claim was that the source of a print was identified to the exclusion of all other people that had ever lived or ever would live. Those who work in scientific disciplines and appreciate the role of uncertainty know that such claims are not credible. Recent studies have demonstrated a low but nonzero misidentification error rate for latent fingerprint examiners. In other forensic disciplines, it is common to have examiners testify to a “reasonable degree of scientific certainty.” This language was recently criticized by the NCFS because it does not have a standard definition and might confuse or mislead jurors (NCFS 2016).

Jeffrey T. Leek & Leah R. Jager tackle another much discussed topic in their article “Is Most Published Research Really False?” This has been a concern in many fields for the past several years, and because a lot of the discussion has involved some high-level statistics, I was very glad to find more information from this perspective. The introduction is especially good at laying out some of the possible concerns:

But this system was invented before modern computing, data generation, scientific software, email, the Internet, and social media. Each of these inventions has placed strain on the scientific publication infrastructure. These modern developments have happened during the careers of practicing scientists. Many laboratory leaders received their training before the explosion of cheap data generation, before the widespread use of statistics and computing, and before there was modern data analytic infrastructure. At the same time, there has been increasing pressure from review panels, hiring committees, and funding agencies to publish positive and surprising results in the scientific literature. These trends have left scientists with a nagging suspicion that some fraction of published results are at minimum exaggerated and at worst outright false.

Statistics articles ripped from the headlines? We have one! For example, Dwork et al.’s article “Exposed! A Survey of Attacks on Private Data” offers an introduction to an interesting facet of the privacy discussion: How do we use information publicly while protecting a sensitive dataset:

We focus on the simple scenario in which there is a dataset x containing sensitive information, and the goal is to release statistics about the dataset to the public. These statistics may be fixed in advance or may be chosen by the analyst, who queries the dataset. Speaking intuitively (because we have not yet defined privacy), the goal in privacy-preserving data analysis is to protect the privacy of the individual records in the dataset, even if the analyst maliciously chooses queries according to an attack strategy designed to compromise privacy.

Suzanne K. Moses is Annual Reviews’ Senior Electronic Content Coordinator. For 15+ years, she has played a central role in the publication of Annual Reviews’ online articles. Not a single page is posted online without first being proofed and quality checked by Suzanne.

Friday at AAAS 2017: A Science Salad

schedule-boardToday was a little bit of everything as I continued to get a feel for this years conference. I started off by checking in on some of the results from Obama’s 2013 BRAIN initiative to research new methods of treating and preventing brain disorders. This was the first all female panel I have seen at AAAS! It was really heartening to watch these engineers and researchers describe their projects. My favorite being the wearable PET scan!  No more having to lay perfectly still in a big tube and pretend you’re on a roller coaster. Now there’s a chance of getting valuable diagnostic data from people who cannot hold still or safely lay down. It’s quite amazing.

From there I headed to a lively discussion about the ethics of gene editing. I found one speaker’s comparison of IVF treatment and gene therapy very compelling. I next found myself listening to Daniel Nocera talk about the chemistry behind his artificial leaves that can turn sunlight, water, and carbon dioxide into fuel. I had to pull on all of my old high school chemistry lessons but I followed the discussion enough to be very impressed with the idea.

I especially enjoy the astronomy panels at every AAAS meeting, and usually come away counting down the months until a favored project launches. This year I was introduced to a coming exploration of Europa, one of Jupiter’s moons. Europa has an ocean over a rocky sea bed that is covered by a thick sheet of ice. Those rocks and water make it a good candidate for having some sort of life. NASA is planning for 20 days of battery life on the surface while carrying 42 kg of scientific instruments. The mission is currently planned for 2024–25.

With my head full of space dreams, I found a seat at Naomi Oreskes’s Plenary lecture titled “The Scientist as Sentinel” and listened to her history of scientists as political activists. I was thinking about the good timing of that lecture as I followed a group of young scientists out into the hallway and heard them making plans for the protest on Sunday.

Suzanne K. Moses is Annual Reviews’ Senior Electronic Content Coordinator. For 15+ years, she has played a central role in the publication of Annual Reviews’ online articles. Not a single page is posted online without first being proofed and quality checked by Suzanne.

Annual Review of Animal Biosciences, Volume 5

See the full table of contents for the Annual Review of Animal Biosciences, Volume 5.

av5-behrThe autobiography in Volume 5 of the Annual Review of Animal Bioscience, “My Scientific Journey: From an Agrarian Start to an Academic Setting” by Janice M. Bahr, explores her research in reproductive physiology with an emphasis on her relationships with her mentors and students. After completing her PhD, she planned to take a postdoctoral position or attend medical school; however, she learned that the Department of Animal Sciences at the University of Illinois, Urbana-Champaign was hiring. “Having been raised on a farm and milked enough cows to have a degree in it, I did know a lot about domestic animals.”

The job did come with challenges:

Little was I aware of the challenges of being the first woman hired in the Department of Animal Sciences of 40 men. I was the only female permanent faculty member for about 20 years. Even though I progressed through the academic ranks at an unprecedented speed, becoming an assistant professor in 1974, an associate professor in 1979, and a full professor in 1983, I was paid less as a full professor than the male associate professors in Animal Sciences. I described this experience as swimming upstream in a stream that had no water. Fortunately, Dr. Reginald Gomes, a distinguished reproductive biologist who became head of Animal Sciences in 1985, realized I was significantly underpaid based on my scholarly accomplishments. Women professors receiving a lower salary compared with their male counterparts were not unusual.

Even after many years of reading autobiographies from female scientists, stories like that still surprise me.

I grew up next to a dairy farm in Southwestern Virginia. Upon moving to Northern California, I found the sight of cows grazing with an ocean view rather befuddling.  Reading Dr. W. Barendse’s article “Climate Adaptation of Tropical Cattle” gave me a similar feeling. There are a lot of variables in how “tropical” is defined, and the cattle that live within these regions face a host of challenges that I had never considered:

The issues associated with cattle in the tropics have been known for some time, and few new issues have arisen. For example, Bonsma identified (a) heat, including radiation, temperature, and humidity; (b) feed, including feed quality and the ability to use the feed available; (c) resistance, including to parasites, especially ticks, and to photosensitivity, especially eye cancer and keratosis; and (d) the ability to avoid noxious plants, not only as a feed source but also the physical aspects of thorns and other plant defenses.

I was also intrigued by Dr. Gerald Shurson’s article “The Role of Biofuels Coproducts in Feeding the World Sustainably.”  I especially appreciated the section on the debate over food versus fuel, which opened up an interesting perspective on how biofuels could be competition for feedstock:

Grains, sugar, and oilseeds are the primary feedstocks used to produce biofuels, but they are also valuable commodities in food production. Thus, increased competition for these resources between biofuels, food, and food animal industries has served as the foundation for the food-versus-fuel debate. Although increases in biofuels production are expected to continue in some countries, production limits will likely be imposed for future expansion. Incentives for using alternative feedstocks (e.g., cellulosic materials) to produce biofuels are being implemented to maintain or reduce competition for traditional grains and oilseeds in biofuels and coproduct production.

Comments are open if you’d like to share what you found most interesting in this volume.

Suzanne K. Moses is Annual Reviews’ Senior Electronic Content Coordinator. For 15+ years, she has played a central role in the publication of Annual Reviews’ online articles. Not a single page is posted online without first being proofed and quality checked by Suzanne.