Professor Stanley Falkow – 1934-2018 – father of molecular microbial pathogenesis

It is with sadness that we share the news that Professor Stanley Falkow of Stanford University School of Medicine, esteemed member of the editorial committee for the Annual Review of Microbiology, co-author of three review articles and an autobiographical article,  passed away (5th May 2018) at the age of 84.

Those of us who didn’t know Professor Falkow can get a vivid impression of him by reading his autobiographical article entitled: The Fortunate Professor. The title makes it clear that this was a man with an abundance of gratitude. The abstract of his article says simply:

My professional life can be summarized by a quote from the Talmud.

Much have I learned from my teachers,

More from my colleagues,

But most from my students.

It is the fortunate professor who learns from the student.

All of us at Annual Reviews feel equally fortunate to have Professor Falkow play a part in the success of our organization. Our thoughts go out to his family, friends, co-workers and of course his students, from whom he learned so much.

Quick Abstracts from Google Scholar – find and filter articles on the go!

Thanks to an innovation from Google Scholar called Quick Abstracts, it’s now easier to use your phone to find and filter through scholarly articles on the go.

Clicking a Scholar search result on your smartphone now opens a quick preview which you can swipe to browse through abstracts. When you find content that helps answer your query, you can click through to Annual Reviews for the full-text. Access is via subscription or pay per view. Note: the Annual Review of Public Health is Open Access, freely available to read, reuse and share.

Many of us use our phones in nearly every aspect of our daily lives, so it’s handy to also have this new feature. We’re delighted to be part of this endeavor which is aimed at helping researchers reach content more quickly, wherever they are.

Making Realistic 3D Printed Organs to Plan Surgery

What if a surgical model not only could mimic the look and feel of a patient’s organ but also give surgeons quantitative feedback as they use it to practice the procedure? A team of scientists in the McAlpine Research Group at the University of Minnesota have been trying to answer this question, creating a prostate model that accomplishes exactly that.

In their article for the Annual Review of Analytical Chemistry, titled “3D Printed Organ Models for Surgical Applications,” Kaiyan Qiu, Ghazaleh Haghiashtiani, and Michael C. McAlpine from the University of Minnesota, review current materials used in 3D printed patient-specific organ models used in surgical pre-planning, as well as the state-of-the-art materials and techniques that allow them to replicate many kinds of human tissue.

The use of 3D models in medicine and anatomy is not new. Centuries ago, they were fashioned out of clay, wax, wood, glass, plaster, or even ivory, and they served as teaching tools or as illustrations of the mechanisms of disease, without having to resort to human dissection.

More recently, the boom in 3D printing technology has allowed medical professionals to visualize organs that might require surgery. Using data collected with imaging techniques such as CT scans, MRIs, or ultrasounds, these models can be fabricated to the exact specifications of a person’s organ.

This is of vital importance. A recent study has shown that an average of more than 250,000 people die each year in the United States as a result of medical errors, including more than 4,000 “never events” in surgery — events that should never have happened. Although complete elimination of errors is impossible, proper surgical planning and rehearsal can be key to reducing their occurrence. Model organs are quickly becoming invaluable tools to help prepare for surgery, not just allowing doctors to get a better feel for the organ on which they must operate, but also letting them plan the procedure. Recently, a 3D printed model of a patient’s hip joint changed the surgical team’s minds about the best treatment plan and resulted in performing a hip replacement instead of reconstruction of the damaged hip joint.

Current materials used in 3D printing have limitations, however. Compared to 2D slices of MRI or CT scans, 3D hard plastic models have helped increase the accuracy of surgeons by helping them to visualize the organ. They can also help inform the patients about their conditions and show inexperienced surgeons what to expect from the operation. Their main flaw is that they are not pliable enough to allow for surgical rehearsal. In contrast, rubber-like materials can provide a tactile feel closer to the actual organ they are meant to model and allow for cutting and suturing, but their properties do not precisely match those of an actual organ in elasticity, hardness, or color.

“These present the correct anatomy, but they’re incapable of providing quantitative feedback or even accurate tactile sensation,” said Dr. Qiu, a postdoctoral researcher in the McAlpine group and lead author of the article.

To remedy this, the three co-authors and their team have developed silicone-based 3D printing materials, or “inks,” that can be finely tuned to mimic these properties. Using a customized direct-write assembly 3D printer with a fine nozzle, they were able to construct a prostate model whose dimensions were obtained with MRI imaging and whose physical properties were established by mechanical tests on actual patient prostate samples, which informed their inks.

Screen Shot 2018-03-28 at 11.52.08They were also able to print and integrate electronic sensors onto and within the model that, when connected to a computer, provided quantitative feedback. This capability could enhance surgical precision in an actual procedure, as well as help train surgeons for steadiness, flexibility, and dexterity, just like a high-tech game of “Operation,” where a loud buzz goes off every time the player is too heavy-handed.

“When surgeons practice using different surgical tools, they can know how much force to apply as they get real-time feedback,” said Dr. Qiu. “They can adjust it and use that knowledge in real surgery to avoid damaging tissue.”

They’re not stopping there, setting their sights on more complex 3D models. Some could account for different types of tissue simultaneously printed with different inks. “We could replicate cancerous tissue and healthy tissue within the same model,” says Ms. Haghiashtiani. Another direction is to develop dynamic models, such as a 3D printed heart that can beat like a real one. A third idea is to create models that integrate sensors capable of taking various types of measurements at once, like temperature and multidirectional pressure.

Ultimately, they say, it is possible that their models could replace real organs.

“We are also working on bioprinting, where we can print organs that can replicate biological functions,” said Dr. Qiu.

“If we could get to this point, if we have the technology, you could say ‘why not use this for transplants?’” added Ms. Haghiashtiani.

Read more about prior limitations, current progress, and future perspectives in this important area in their Annual Review of Analytical Chemistry article. 

The Annual Review of Analytical Chemistry, first published in 2008, provides a perspective on the field of analytical chemistry. The journal draws from disciplines as diverse as biology, physics, and engineering, with analytical chemistry as the unifying theme.



Waves, Satellites, and an Oceanographer at Sea: Annual Review of Marine Science Volume 10

Browse the Annual Review of Marine Science Volume 10 table of contents.

ma10-wavesThe Fate and Impact of Internal Waves in Nearshore Ecosystems” by C.B. Woodson introduced me to the wonder and science of internal waves.  Like the surface waves most people are accustomed to thinking about, these internal waves also break as they near land and can bring of deep offshore waters into the nearshore environment:

These deeper waters are often colder, lower in oxygen, higher in CO2 concentration (lower pH), and nutrient enriched. Consequently, internal waves can dramatically change the ambient environment, leading to either extreme oxygen (hypoxia) or pH (acidification) events. However, they can also mediate extreme heating events by providing a temporary reprieve from high temperatures. Deep offshore waters can also provide nutrients and food subsidies to nearshore ecosystems. Nutrient-deprived nearshore ecosystems, namely coral reefs, can be highly dependent on such subsidies.

ma-dugdaleRichard Dugdale credits mentoring with influencing his path from electrical engineering to oceanographer in his autobiography “A Biogeochemical Oceanographer at Sea: My Life with Nitrogen and a Nod to Silica” He has a warm writing style and I enjoyed reading about the history of this field through his experiences, especially about the changing technology:

…this field rapidly developed both analytically, starting with the use of stable and radioactive tracers, and computationally, from the use of slide rules to the development of onboard computers with disk drives (with 250 KB of storage!) and the era of smartphones. Also changing has been the mode of communication between oceanographers—from handwritten or mimeographed notes to faxes to the early email and Internet (telemail) used by oceanographers in the 1980s to today’s email and social media. What follows, then, is a biased (biological/chemical) history of a period in which modern oceanography was largely developed and in which I had the great fortune to be a player.

Spaceborne Lidar in the Study of Marine Systems” by Hostetler et al. is one of several articles in this volume that report on the use of satellites in marine research. This article reviews the use of passive color analysis to observe chlorophyll levels among many other topics and looks forward to an upcoming PACE mission which pairs the color observations with new tools:

Satellite passive ocean color observations have vastly improved our understanding of global links between biodiversity, ecosystem structure, and ma10-satsecological and biogeochemical function. However, there are fundamental geophysical properties that simply cannot be characterized with ocean color technology alone. Addressing these issues requires additional tools in space. For example, the Plankton, Aerosol, Cloud, and Marine Ecosystem (PACE) mission aims to co-deploy a multi-angle polarimeter with a hyperspectral ocean color sensor, with the polarimetry enabling more accurate atmospheric corrections and advanced characterization of ocean particle types. Here, we describe how even greater synergies may be achieved by combining a passive ocean color sensor with an ocean-optimized satellite profiling lidar.


Annual Review of Psychology Volume 69: Language, Gender, and Replication

Browse the Annual Review of Psychology Volume 69 table of contents.

ps69-langWhile I’m used to thinking about language as a way of gauging cognitive development “Linking Language and Cognition in Infancy” by Perszyk and Waxman had me thinking about the ways language influences cognition. For instance:

…more recent developmental evidence reveals that, even before infants begin to speak, words invite them to form categories. The evidence for this claim comes from a robust behavioral paradigm, elegant in its simplicity. It is essentially an object categorization task with two phases. During the familiarization phase, infants view a series of discriminably different objects (e.g., dog, horse, duck) from a given object category (e.g., animal). Next, during the test phase, infants view two new objects—one a member of the now-familiar category (e.g., a cat) and the other a member of an entirely different category (e.g., an apple). The logic of this paradigm is straightforward: If infants detect the category-based commonalities among the familiarization objects, then they should distinguish the novel test image from the familiar; if they fail to detect these commonalities, then they should perform at chance levels ….The evidence reveals that, by 12 months of age, even before they produce more than a few words on their own, infants have established a principled link between object naming and object categorization.

I found  “Gender Stereotypes” by Ellemers  quite an interesting read.  I particularly responded to the summation in the section “How We Can Benefit From This Knowledge”:

Gender stereotypes prevent women and men from equally sharing the care for children and family members and from equally benefiting from the interpersonal connections made through these activities. Gender stereotypes prevent women with successful careers from finding a romantic partner and men without employment from feeling valued. They cause us to underestimate the emotional burden of care functions for women and the physical burden of strenuous labor for men. This is not only costly for the individuals ps69-genderinvolved but also for society, as it impacts the psychological and physical well-being of individuals, the resilience of families, and the long-term availability and contributions of workers in the labor market. We are only human and have to accept that we are subject to stereotypical thinking and gendered expectations. Accepting our fallibility in this way, rather than denying that gender stereotypes play a role while implicitly reproducing them, makes it easier to correct for any undesired outcomes that may result.

Shrout and Rodgers’ article “ Psychology, Science, and Knowledge Construction: Broadening Perspectives from the Replication Crisis” is a good overview of the history of evaluating results, the problems with current practices, and steps that have been taken to verify findings.  I was particularly interested in how the changes in research procedure have affected scientists:

As calls have been made to change the way science is conducted in psychology by preregistering designs and analyses and increasing sample sizes, some authors have noted what might be called collateral damage. The three types of damage that have been identified are (a) slowing and ultimate reduction of new findings and phenomena, (b) penalizing different subfields with the imposition of one-size-fits-all norms, and (c) discouraging young scientists from staying in the field because of the higher bar for publication and professional advancement.

Fire, Explosions, and Lymphatic Systems: Annual Review of Fluid Mechanics Volume 50

Browse the Annual Review of Fluid Mechanics Volume 50 table of contents.

Before I get to the fire and explosions I want to highlight the lovely article “John Leask Lumley: Whither Turbulence?” by Leibovich and Warhaft that begins this volume.  This biography includes sections about Dr. Lumley’s love and appreciation for vintage cars and good food and wine as well as a look at his contributions to fluid mechanics. It’s a remarkable tribute and a worthwhile read.

Tohidi, Gollner, and Xiao wrote “Fire Whirls” which I found myself thinking about as I watched coverage of the California wildfires:

fl50-fire whirls

Throughout the literature, fire whirls have been identified by a variety of names, including devil, tornado, twister, whirlwind, or even dragon twist (Japanese). Regardless of the name, when the right combination of wind and fire interact, the result is an intensification of combustion with whirling flames that we call the fire whirl. Although the fire whirl or fire tornado shares some features with its atmospheric counterparts, it remains distinct in its source of buoyancy, combusting fuel, structure, and formation patterns. In nature, fire whirls are most often observed in mass fires. These include both large wildland (also known as forest fires or bushfires) and urban conflagrations, such as the burning of cities or towns…

fl50-detonationWhile action movie explosions make it seem easy, a controlled detonation that accomplishes more than looking good on film is difficult and complex to model. “High Explosive Detonation-Conifer Interactions” by Short and Quirk begins by explaining some of the complexity:

The dynamics of a given HE–confiner system depend on the pressure-loading properties of the explosive (magnitude and timescale), while in turn the structure and speed of the detonation reaction zone and the lateral confinement of explosive products are dependent on the material properties of the confining material, such as its density and sound speed. The ability to predict the motion of a detonation in an explosive system (known as the timing) and the response of the confiner to the HE detonation pressure loading depend on our ability to model and understand this detonation–confiner flow coupling…

I found “Lymphatic System Flows” by Moore and Bertram quite interesting especially as it explained the importance of several organs I’d always been curious about:

The lymphatic system as a functional whole includes several organs whose association as a system is not readily apparent. Lymphoid organs include the spleen, thymus, and tonsils; another vital component is the bone marrow where white cells are manufactured…. Functionally, the lymphatic vascular systemfl50-lymph runs in parallel to the blood venous system, in that both return fluids centrally. Lymphatic vessels carry lymph, which is largely water gathered from interstitial tissue spaces. Fluid appears in the interstitial spaces because blood capillary walls are somewhat leaky, allowing part of the aqueous component of blood to escape, along with some proteins…. The lymphatic vascular system scavenges this water and protein, ultimately returning it to the venous circulation via junctions with the subclavian veins at shoulder level. The maintenance of the interstitial milieu is one of its vital functions; if fluid is not returned to the blood system at the same rate as it leaves, the painful and debilitating condition of edema can develop.

Congratulations to Adriaan Bax, winner of the 2018 NAS Award for Scientific Reviewing

Congratulations Adriaan Bax, PhD. of, recipient of National Academy of Sciences Award for Scientific Reviewing which is sponsored by us!

Bax is honored for reviews and pioneering technical concept pieces on Nuclear Magnetic Resonance that have greatly influenced the field of #StructuralBiology.

To celebrate this achievement, we’ve made the PDF of one of his seminal articles entitled Two-Dimensional NMR and Protein Structure freely available to download here:

The award will be presented during the 155th NAS Annual Meeting on Sunday, April 29, 2018.

More information on Bax and the Award –

Celebrating 85 years of service!

To mark our 85th anniversary, free online access to all journal articles published in 2017 is available through the end of the year.
Please browse journals that are new to you and revisit those that you rely on regularly. You may access articles via HTML directly. PDF access available via institutional or individual subscription, or pay per view purchase.

How well do you know Annual Reviews?
We got our start in the late 1920s when founder J. Murray Luck, Professor of Biochemistry at Stanford University, set out to review current research in the (then) emerging field of biochemistry, and found himself “dismayed … by the immensity of the task…” He asked leading professors in the field to write intelligent syntheses of the key primary literature.
In 1932, he published the first volume of the Annual Review of Biochemistry. It has become a foundational resource for relevant topics, enabling further discovery. Take a look today and revisit the science of yesterday, still relevant today:

Annual Review of Biochemistry, Volume 1, 1932
The Metabolism of Brain and Nerve

Fast Forward to 2017: Scientific Literature Reviewed, from A to V
Today we publish 50 journals covering disciplines within the biomedical, life, physical, and social sciences, from Analytical Chemistry to Vision Science. Each journal provides a pathway to the relevant primary research across a number of topics within the field. Our authors critically examine a wide array of articles, papers, and books to provide objective overviews and summarize important ideas and findings.

We’ve recently added the following journals to our collection:

  • Cancer Biology
  • Vision Science
  • Linguistics
  • Virology
  • Statistics and Its Application
  • Organizational Psychology and Organizational Behavior
  • Animal Biosciences
  • Condensed Matter Physics
  • Chemical and Biomolecular Engineering
  • Marine Science
  • Economics
  • Financial Economics
  • Resource Economics

Publishing in 2018:

  • Biomedical Data Science
  • Control, Robotics, and Autonomous Systems
  • Criminology

Celebrate our 85th anniversary by revisiting your favorite Annual Review, or getting acquainted with a new title! Either way, Annual Reviews provides researchers with curated wisdom from hand-picked experts.

Happy OA Week – from the Annual Review of Public Health

Every year for the last ten years, many within the research community have chosen to celebrate Open Access during October. That time is here again!

This seems like a good moment to remind everyone that the 2017 volume of the Annual Review of Public Health is now freely available to read, reuse and share thanks to generous support from the Robert Wood Johnson Foundation. All the back volumes are also freely available.

Since opening the content in April, usage has soared to new heights and we’re delighted that so many more people can benefit from the expert knowledge contained within this highly cited journal.

The theme of this year’s OA week is “open in order to…” and this image seems tailor made for us. Thanks to the good folks at the Open Access Week website for the resource (there are many more to share here).