bluuebunny/crossref_metadata_2025 huggingface dataset:
The emerging universe of RNA-binding proteins
Authors: Castello Alfredo
Published: October 2019

RNA associates with RNA-binding proteins (RBPs) from synthesis to decay, forming dynamic ribonucleoproteins that orchestrate gene expression. RBPs mediate crucial functions in RNA metabolism, including RNA synthesis, processing, transport, translation and degradation. Although essential for RNA life cycle, the repertoire of RBPs has remained largely unknown. The very recent development of a novel proteomic-based system-wide approach termed RNA interactome capture revealed the near-complete census of human RBPs. Applying UV cross-linking of proteins to RNA, oligo(dT) selection of poly(A) RNAs and quantitative mass spectrometry, this method not only ‘rediscovered’ most of the proteins already known to bind RNA, but added hundreds of novel members to the previously known repertoire of RBPs. The newly identified RBPs are distributed over a broad variety of protein families, participate in different biological processes and exert distinct protein functions, implying the existence of unprecedented links between RNA biology and intermediary metabolism, signalling, cellular homoeostasis or disease. Although the near-complete atlas of RBPs offered important insights into RNA biology, it also opened new functional and structural questions about protein–RNA interactions that remain to be answered.
To kill a bacterium: A complex 80-year-old story
Authors: Dwyer Daniel J.
Published: October 2019

We are fortunate to possess a wealth of knowledge regarding the primary intracellular targets of antibiotics and strong clinical appreciation for the viability-compromising effects of target inhibition by these remarkable chemical entities1. It is not by coincidence that antibiotic lethality is almost exclusively initialized in bacterial cells through the arrest of fundamental processes, i.e. DNA replication, RNA transcription, protein translation and cell wall biosynthesis. Yet the question of how antibiotics ultimately kill bacteria remains a quintessential ‘black box’ problem. Despite the ubiquity of their usage, our understanding of the specific events that connect drug-target interactions with antibiotic-mediated cell death, including the cell death process, remains incomplete.
Precision oncology: mind the disruption
Authors: Soong Richie , Syn Nicholas , Wang Katherine , Omar Mohamed Feroz Bin Mohammed
Published: October 2019

Over the last two decades, treatment outcomes have improved markedly for a number of cancer types, including breast cancer, lung cancer and melanoma. Some of these improvements can be attributed to the steady development of new treatments. However, what has been very different in this period is the introduction of a different approach to healthcare management. Precision medicine is a strategy of customizing health management to individual predisposition and condition subtype, instead of the conventional approach of applying a standardized management. In oncology, a move towards precision medicine has been motivated by an accumulating number of paradigms that have demonstrated its significant health and financial value. However, shifting to this type of medicine entails many disruptions to current research and clinical practices, including the introduction of new disciplines and structures, new levels of multidisciplinary co-operation, new approaches to health regulation and economics and the generation of new information on inter-population clinical and molecular features. In this article, we look back at key events in precision oncology to relate the motivation behind the shift and understand the upcoming issues in realizing the immense potential of precision medicine.
It's an RNA world: a focus on recent advances in RNA biochemistry
Authors: Graham Sheila
Published: October 2019

RNA is a fascinating molecule. Its array of different properties is highlighted by our knowledge of the ribosome. RNA can have structural properties; for example, rRNA is the core of the ribosome. RNA can bind proteins; for example, rRNA–ribosomal protein interactions are used to build the protein translation machinery. Finally, RNA can display enzymatic catalysis. In the ribosome during translation, non-coding RNA carries out decoding (tRNA) and amino acid polymerization (rRNA). If this is not fascinating enough, the last decade or so has seen a considerable reassessment of the core of Francis Crick's ‘central dogma of molecular biology’ that states that RNA molecules (rRNAs, tRNAs and mRNAs) serve to drive protein synthesis, decode mRNAs or act as a templates encoding protein. Much of the upheaval in our understanding of RNA biology has come from deep mining of the human transcriptome by RNA sequencing (RNAseq) by next generation sequencing techniques. One of the most startling revelations from the wealth of new data provided by the ‘-omics’ revolution is that over 80% of the human genome encodes RNA, whereas only up to 2% encodes proteins. In other words, our genomes are largely RNA-coding. The discovery of the plethora of non-coding RNAs in our genomes has revolutionized molecular biology. These RNAs do not encode protein and, unlike rRNAs or tRNAs, most are not intimately linked to protein translation. In this edition of The Biochemist, we revisit recent advances in RNA research to reveal the broad scope of this hot topic in today's biochemistry and to spotlight some new areas of RNA research.
Expanding the RNA alphabet: The expanding world of mRNA modifications
Authors: Delatte Benjamin , Fuks François
Published: October 2019

Our understanding of the post-transcriptional modifications that decorate mRNAs, a regulatory layer positioned between DNA and proteins, is in its infancy. Recent advances in genome-wide mapping of pseudouridine (), N6-methyladenosine (m6A), 5-methylcytosine (5mrC), its oxidation product 5-hydroxymethylcytosine (5hmrC), and N1-methyladenosine (m1A) have proven that these modifications unsuspectedly occur from dozens to thousands of different gene transcripts in eukaryotic cells. Therefore epigenetics cannot only be restricted to chromatin modifications, and, when studying gene regulation, one has to consider the expanding kingdom of RNA modifications, also known as the epitranscriptome.
The legacy of our ancestors' lifestyle: Special Feature
Authors: Barrès Romain
Published: October 2019

Recent scientific developments are revolutionizing our perception of heredity. These advancements, arising from independent research groups including ours, are reviving the hereditary theory put forth in 1809 by the French evolutionist Jean-Baptiste Lamarck, who postulated that acquired traits could be transmitted to the next generation. With ‘Lamarckian’ inheritance, as a giraffe stretches its neck to reach the leaves of tall trees, neck length becomes longer with subsequent generations. This astounding theory, proposed more than 200 years ago, implies that our health is determined by the chosen lifestyle of our ancestors, long before our own existence.
Genome editing – a technology in time for plants
Authors: Choe Sunghwa
Published: October 2019

A tool for safe and site-specific mutagenesis has long been sought by plant biochemists. The recent emergence of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) genome-editing technology addresses this need. Using this technology, the lettuce genome was recently edited without the use of conventional Agrobacterium-mediated DNA delivery. As this method does not leave a trace of foreign DNA in the plant genome, it promises to advance the field of plant biotechnology for genetically modified organisms (GMOs) without the burden of costly de-regulation processes.
Unleashing the therapeutic potential of the extracellular matrix: From matrix to molecule
Authors: Kantak Seema
Published: October 2019

The extracellular matrix (ECM) is the physical scaffold that binds cells and tissues together and upon which cells survive, proliferate, differentiate and migrate. The ECM is a key regulator of cell and tissue function and plays a critical role in maintaining healthy tissue. Proteoglycans are important structural and functional macromolecules native to the ECM and are known to protect against tissue degradation and promote healing during injury. They are comprised of a protein core and carbohydrate side chains, and their specific biological roles vary depending upon composition and location in the body.
Ethylene: a gaseous signal in plants and bacteria
Authors: Street Ian H. , Schaller G. Eric
Published: October 2019

Ethylene was the first gaseous growth regulator discovered due to its pronounced effects on plant growth and development. Besides plants, many bacteria also have ethylene-binding proteins, indicating that the ability to bind and respond to ethylene is an evolutionarily ancient sensory mechanism. The recent characterization of an ethylene receptor from cyanobacteria and the finding that it plays a role in phototaxis confirms a prokaryotic role for the ethylene receptors and is consistent with the hypothesis that plants acquired ethylene receptors from the endosymbiont that gave rise to the chloroplast. The signalling pathway acting downstream of the plant ethylene receptors is considerably diverged from that found in bacteria, pointing to adaptations that can occur in transitioning from a prokaryotic to a eukaryotic cellular environment. Interestingly, although pathways for ethylene biosynthesis and signalling are conserved in plant lineages extending back to the green algae, there are examples of plants where these pathways have been lost, with ethylene no longer playing a regulatory role.
Ground control to Major Tim
Authors: Brown Anwen
Published: October 2019

By now, at the time of writing, Major Tim Peake is on day 105 of his mission on the International Space Station (ISS). The main reason for his expedition is to perform a number of scientific experiments under the effect of weightlessness, as well as collecting samples from his own body for studies here on earth. He's blown into lung–function kits, collected blood, stool and urine samples, measured properties of his skin, given himself ultrasounds, conducted eye examinations and completed numerous health questionnaires, just to name a few!
Sex and gender matter to biology
Authors: Frank Aaron , Clegg Deborah
Published: October 2019

Flip through a few TV channels or browse the Internet for a bit and you will be quickly reminded that, in our day and age, everyone is thinking about ‘sex’. Biologists think about sex too – albeit more in the biological sense than the act itself. The problem is they don't think enough about it. Indeed, though most animals display marked differences in sexual anatomy and reproductive function, sex is regularly overlooked in biomedical research at both the clinical and basic science levels1. Over 25 years ago, The National Institutes of Health recognized this as problematic; exclusion of women from large clinical trials blunted their ability to detect sex differences in the safety and efficacy of therapeutic drugs. In 2001, the Institute of Medicine echoed these concerns, calling for expansion of research into sex differences at the biochemical and cellular levels2. Despite this, investigators still regularly ignore the sex of cell lines studied in vitro2, as well as failing to include both sexes in animal studies. In this article, we briefly discuss the nature of sex differences and highlight their importance to future basic and translational research.
Role of biological sex in cardiovascular disease: the case of hypertension and related target organ damage
Authors: Sabbatini Andrea Rodrigues , Kararigas Georgios
Published: October 2019

Individual characteristics, such as age, biological sex, race, fat mass and genetic factors, have a major impact on physiological and pathological processes. Consequently, individuals can respond differently to the development and manifestation of disease, treatment, outcome and the recovery process. In fact, there are major differences in the function of the biological system of men and women, who do not differ only on the basis of their reproductive system. Sex chromosomes and sex hormones, together with other factors, interact in a complex manner, thereby leading to sex-specific protective or maladaptive mechanisms. In this context, studying the role and effects of biological sex is crucial for the identification of novel therapeutic targets, whose therapeutic exploitation will promote a personalized and improved treatment and care according to individual needs. The vast influence of biological sex is recognized in many diseases1. Here, we focus on hypertension, due to its high prevalence and importance, since it is the primary risk factor for premature death and disability worldwide.
Gender Medicine – the heart and mind of the latest findings in our collection from Clinical Science
Authors: Pettengale Emma
Published: October 2019

Gender Medicine focuses on the impact of gender on human physiology, pathophysiology, and clinical features of diseases. Men and women may have different experiences of the same disease and the pathophysiology of disease may also vary as a function of genetics, epidemiology and biological sex/gender. Translating molecular bioscience and experimental research into medical insights, the journal Clinical Science offers multi-disciplinary coverage and clinical perspectives to advance human health. Together with leaders in the field of gender medicine, we have put together a special themed collection of the journal focusing on this often neglected dimension of medicine.
Visceral pain: role of the microbiome-gut-brain axis
Authors: Rea Kieran , Mahony Siobhain M. O' , Dinan Timothy G. , Cryan John F.
Published: October 2019

A growing body of preclinical and clinical evidence supports a relationship between the complexity and diversity of the microorganisms that inhabit our gut (human gastrointestinal microbiome) and health status. These microbes can influence centrally regulated emotional behaviour through mechanisms including microbially derived bioactive molecules, mucosal immune and enteroendocrine cell activation, as well as vagal nerve stimulation. Changes to the microbial environment, as a consequence of illness, stress or injury can lead to a broad spectrum of local physiological and behavioural effects including a decrease in gut barrier integrity, altered gut motility, inflammatory mediator release, as well as nociceptive and distension receptor sensitization. Impacts at a central level include alterations in the hypothalamic-pituitary-adrenal axis, neuroinflammatory events and concomitant changes to neurotransmitter systems. Thus, both central and peripheral pathways associated with pain manifestation and perception are altered as a consequence of the microbiome-gut-brain axis imbalance. The dogmatic approach of antibiotic treatment in the latter century, for the treatment of many diseases and conditions, has undergone a radical change. We are 90% microbe, and pragmatism suggests that we manipulate this ecosystem for the treatment of various ailments, stress dysfunction and affective disorders, including the alleviation of visceral pain.
Emerging viruses – is there an emerging pattern?
Authors: Gatherer Derek
Published: October 2019

The Ebola outbreak in West Africa in 2014 and the spread of Zika across the Americas in 2016 have thrust previously obscure viruses into the media spotlight. But is something new really going on? What can we expect in future? Is there anything we can do?
Can we identify viruses with pandemic potential?
Authors: Woolhouse Mark E.J. , Ashworth Jordan L.
Published: October 2019

There are believed to be thousands of as yet unknown viruses ‘out there’, circulating in wildlife and possibly our domestic animals too. Which of these viruses might have, or might acquire, the potential to cause the next global pandemic in humans?
Guarding the granary
Authors: Esse Peter van
Published: October 2019

The introduction of microbial plant pathogens can cause tremendous damage to crops, food security, the economy and ecosystems in very little time. What do we know about these invaders? And what can be done to defend our crops and respond quickly to new threats?
Epigenetics, evolution and the survival of the non-unfit
Authors: Guerrero-Bosagna Carlos
Published: October 2019

The transition that occurred in vertebrates moving from water to land was a major step in the evolution of terrestrial animals. This is an evolutionary step that has always fascinated scientists and the general public. The land-to-water vertebrate transition happened around the Devonian period and involved structural changes such as the transition from fin to limb, a reduction of the gill arch, loss of the mid-fin and a reduction in the number of scales, among others. I will use this interesting example to depict how the same evolutionary process can be seen through two different lenses. One view, which is the most widespread way of seeing evolution, is the ‘survival of the fittest’. The other is intentionally stated in the title as the double negative ‘survival of the non-unfit’. Only semantic differences? Not in my view.
How do mutations in epigenetic regulators contribute to disease?
Authors: Chen Kelan , Blewitt Marnie E.
Published: October 2019

Imagine you are a scientist and receive an email from a patient inquiring whether carrying a particular mutation is going to affect their offspring. This may sound unrealistic, yet this is the sort of thing that will happen increasingly as sometimes even doctors know very little about the role of specific genetic variants found in patients. As genetic testing becomes more affordable, for many people, finding out the exact sequence and alterations in their DNA could provide useful information for disease diagnosis, prognosis and treatment. However, knowing just the DNA sequence is not the whole story, as there is another layer of complexity added by a group of molecules called epigenetic regulators.
Neisseria meningitidis – more tricks than a magician
Authors: Barnes Bryony
Published: October 2019

Hi there, I'm Neisseria meningitidis, N. meningitidis for short. You may not have heard of me before, but you will have heard about what I do. You see, I'm one of the bacteria that cause meningitis. Not always – you might have me living at the back of your nose and never even know it – around 25% of you do at any one time. But sometimes I don't just stay harmlessly in the nose and throat, I invade, first the bloodstream, and then the brain, causing septicaemia (you might know it as ‘blood poisoning’) and meningitis. They're not illnesses you want to have – meningitis means inflammation of the lining of the brain. Sounds nasty doesn't it? Well it is – about 1 in 14 people who get bacterial meningitis die from it. Inflammation means swelling and because your skull keeps the swelling inside, pressure builds up in the brain – not ideal, for something as delicate as your human brains. Obviously, your body doesn't want this to happen and tries to stop me invading, but I'm sneaky. I have lots of tricks and special skills to help me do what I do and I want you to appreciate how much effort I put in. Let me tell you how I get inside your brain.
Enzymes feel the squeeze: biochemical adaptation to pressure in the deep sea
Authors: Winnikoff Jacob R. , Wilson Telissa M. , Thuesen Erik V. , Haddock Steven H.D.
Published: October 2019

To the human observer, the deep sea is as extreme an environment as Earth has to offer. Below about 200 metres, there is no light from the surface, the water can be frigid (-2 to 5°C), oxygen and food are scarce, and the pressure is staggering. Of course, to the countless species that inhabit the deep sea, these conditions are not so extreme, and in a statistical sense, they fall fairly close to average, since the deep comprises the planet's largest habitat by volume. Despite its expanse, we know little about how life persists in an environment so different from our own. Only in the last half-century has technology emerged that allows us to collect and study live deep-sea animals. Diversity, Evolution and EcoPhysiology of Ctenophores (DEEPC, deepc.org, a US NSF-supported research effort) is opening a window on biochemistry in the deep, and specifically on its relationship to high pressure. By determining structural constraints on enzyme function under pressure, we aim to inform models focusing on deep-sea animal colonization, and to find general patterns of protein adaptation with possible applications in protein engineering and biocatalysis.
Covers that never happened
Authors: Theodoulou Freddie
Published: October 2019

One of the changes I instigated in my eight years as Science Editor of The Biochemist was to invite design staff to the magazine's Editorial Advisory Panel meetings so that we could consider the visual angle for each issue (and also so that I could interfere incessantly with the cover designs). Sometimes thinking up novel cover concepts was tough, especially when the default option is to use a chemical structure but more often than not, dreaming up effective ideas for each issue proved an amusing exercise. Rather like practical jokes, sometimes the fun is in having the idea and it's usually better not to go ahead with the execution. But just for your amusement, I recount the stories behind some of the covers. Here are four cover concepts that it's probably just as well never appeared in their original incarnation and one that should have been slightly different.
Advancing biomaterials towards biological complexity
Authors: Pastino Alexandra , Steele Joseph , Kohn Joachim
Published: October 2019

3D printing has the potential for on-demand, patient-specific devices with high structural complexity. However, the tools and biomaterials most widely available for 3D printing are largely limited to fused deposition modelling (FDM) with commodity plastics that lack cell-scale resolution and biological cues. The lack of biologically active materials, also called ‘bioinks,’ is a key issue that limits the ability to produce engineered tissues, tissue interfaces and functional organs. While advances are being made in the field of biomaterials, current technologies can be combined into hybrid systems that overcome the limitations of a single technique or material, as described in this article.
Manipulation of fertility to enhance productivity of cattle
Authors: Holland Michael K. , McGowan Michael
Published: October 2019

Fertility is most simply defined as the natural capacity to produce offspring. More technically, it is the ability of male and female animals to produce viable germ cells, mate, conceive, carry and deliver normal living young. Fertility is affected by genetic factors, health status and environmental factors which includes management practices. These factors can affect one or more of the key steps in fertility which are: production of the gametes (the sperm or eggs), ovulation, fertilization, implantation, gestation or parturition. Over the last century, we have learnt to manipulate fertility in cattle by targeting many of these key steps with the goal of producing animals that more efficiently produce meat and milk to meet the demands of the increasing human population. This has required developing and integrating our knowledge in the key disciplines of reproductive biology and genetics, and while much has been achieved, much more is possible.
Feedback: Completing the cycle
Authors: Coyte Emily
Published: October 2019

Feedback cycles are useful concepts in biological systems, our everyday lives, and education. However, Higher Education is finding itself in something of a feedback crisis, with low student satisfaction despite high academic workload in this area. Here we explore how changing our conceptions of feedback in Higher Education could address this, and look at some positive cases of innovative feedback practice within bioscience disciplines.
The motivation to experiment -- an art and science exchange
Authors: Brown James
Published: October 2019

As the blindfold was put over my eyes and tied tightly, I began to wonder if maybe I had bitten off more than I could chew. We often talk about being pushed outside of our comfort zone, but I began to realize that to be uncomfortable is a fairly rare occurrence in our everyday lives. But of course, that was the whole point of our art and science exchange with the Masters students of Central Saint Martins at the University of the Arts London.
What is sustainable agriculture?
Authors: Firbank Leslie
Published: October 2019

We all want to eat food that is produced sustainably. But it's not at all clear what that means in practice. Fundamentally, agriculture can be regarded as sustainable if it can continue to meet human needs whilst avoiding irreversible harm to the planet. The human needs are not just food, but include employment, leisure, social cohesion and the many ecosystem services provided by agricultural land that benefit people, including regulating water quantity and quality, carbon storage, maintaining landscapes of cultural and spiritual value, and providing homes for wildlife. Agriculture causes harm to the planet from habitat loss, carbon emissions, and pollution of air and water. Meeting these challenges is tough now, but it will only become more difficult as the human population rises and climate change becomes more difficult to cope with.
Synthetic Biology Public Engagement
Authors: Hanlon Corinne
Published: October 2019

The Warwick Integrative Synthetic Biology Centre (WISB) spent an amazing week interacting with visitors of all ages at the Cheltenham Science Festival from 5–10 June 2018.
Shining a spotlight on immigration
Authors: Sykes Emma
Published: October 2019

The Biochemical Society's Policy Network looks into immigration policies to support science and innovation.
Gut–neuroimmune interactions: the unexpected role of the immune system in brain development
Authors: Spichak Simon , Dinan Timothy G. , Cryan John F.
Published: October 2019

How does the immune system impact brain development?

The exciting and somewhat unexpected relationship between the immune system and the brain has become one of the most fascinating topics in neuroscience. Even though the immune system was initially implicated in resolving viral and bacterial threats, it is now becoming more evident that it also plays a role in processes in the brain, both under healthy and pathological conditions. This novel role of the immune system in brain health has been implicated in various psychopathologies where neurodevelopment, stress and mood are central. In particular, its role in healthy brain development is becoming more evident, and understanding neuroimmune communication is becoming crucial in treating neurodevelopmental and mood disorders in later life. In the brain, glia function as part of the innate immune system and are programmed to respond to pathogens and physical injury. They also play an important role in neuronal development and pruning. These cells communicate with and respond to chemical signals, such as cytokines and chemokines, which can then initiate or downregulate inflammatory responses. Finally, the trillions of microbes residing in the gut can also stimulate cytokine and chemokine responses in the periphery and play an important role in both immunity and brain development.
Boosting the immune system with antioxidants: where are we now?
Authors: Pangrazzi Luca
Published: October 2019

A strong immune system doesn't have to be just a dream. Over the last few decades, several strategies for boosting the immune system have been studied, with the aim of reducing the incidence and severity of infectious diseases. Furthermore, investigations into the possibility of improving the fight against cancer continue. Simple and powerful tools are already in our hands: the antioxidants. As we get older, or when we are particularly stressed, high levels of reactive oxygen species (ROS) accumulate, promoting oxidative stress and inflammation throughout the body. In this situation, normal body functions, in particular the immune systems, are severely impaired by an excess of oxygen radicals and pro-inflammatory molecules. For this reason, blocking the side effects of ROS with antioxidants may help us improve our immune system performance.
The L7Ae proteins mediate a widespread and highly functional protein–RNA interaction
Authors: Lilley David M.J.
Published: October 2019

The k-turn is a ubiquitous structural motif in RNA forming a very tight kink in the axis of helical RNA that plays an important role in many aspects of RNA function. L7Ae is a member of a superfamily of proteins that bind k-turns in RNA, stabilizing the tightly kinked conformation. They are extremely widespread and are important in the assembly of RNA–protein complexes central to translation, splicing and site-specific RNA modification. The interaction is exploited in order to regulate the synthesis of L7Ae proteins and is itself subject to regulation in box C/D snoRNP assembly by N6 methylation of a key adenine in the k-turn. Lastly, we can exploit the L7Ae–k-turn interaction in the construction of nanoscale assemblies.
CREST Awards: why the key to success is thinking scientifically
Authors: Rowley Jess
Published: October 2019

Science goes beyond just being a body of facts. In its essence, science is nuanced, changeable and explorative. Its distinctive feature is the scientific method; the process of dreaming up ideas or hypotheses and scrutinising them through investigative trials, tests and analysis, which can simultaneously answer your questions and create even more questions. The hypotheses become refined with every investigation, adding to the ever-growing body of knowledge and discovery that form the bread and butter of science, informing us of nature and world we inhabit.
Oxygen: friend and foe!
Authors: Hebelstrup Kim H. , Møller Ian M.
Published: October 2019

It is generally believed that the Earth's atmosphere did not contain oxygen until around 2500 million years ago (Mya) when oxygen-evolving photosynthetic bacteria arose. At around 800–500 Mya, the oxygen concentration increased sharply to reach the 21% we have today. So, it seems highly likely that life arose as anaerobic organisms, which then evolved to tolerate oxygen and finally, to use it as a terminal acceptor for the energy-producing oxidative processes in the respiration of aerobic bacteria and mitochondria in eukaryotic cells. The respiratory processes employed by typical aerobic organisms today have a wide range of mechanisms to deal with the troublesome side effects of living with a high oxygen concentration.
A beginner's guide to imaging in vivo tumour biochemistry
Authors: Greenwood Hannah , Edwards Richard , Witney Tim
Published: October 2019

The Beginner's Guides are an ongoing series of feature articles in the magazine, each one covering a key technique and offering the scientifically literate but not necessarily expert audience a background briefing on the underlying science of a technique that is (or will be) widely used in molecular bioscience. The series will cover a mixture of techniques, including some that are well established amongst a subset of our readership but not necessarily familiar to those in different specialisms. This is a Beginner's Guide to imaging in vivo tumour biochemistry.
Insect detection and density estimation based on a Ku‐band scanning entomological radar
Authors: Cai Jiong , Yuan Quan , Wang Rui , Liu Changjiang , Zhang Tianran
Published: October 2019

Entomological radars need to address the problem of insect density estimation. Here, a Ku‐band experimental entomological radar with two‐dimensional scanning mode is used to collect insect echo data. The nearest neighbour method is used to associate the traces of the same insect. Then, the insects are classified according to their radar cross‐sections (RCSs) and heights. Then, the corresponding radar‐effective sampling volumes are calculated. So, we can get the density of insects with different RCSs at any height layer. Finally, the densities of insects with different RCSs at the same height layer are accumulated to obtain the total insect density at each height layer.
Patient Positioning in Shoulder Arthroscopy: Which is Best?
Authors: Rojas Jorge , Familiari Filippo , Bitzer Alexander , Srikumaran Uma , Papalia Rocco , McFarland Edward G.
Published: October 2019

When performing diagnostic and surgical arthroscopic procedures on the shoulder, the importance of patient positioning cannot be understated. The optimum patient positioning for shoulder arthroscopy should enhance intraoperative joint visualization and surgical accessibility while minimizing potential perioperative risk to the patient. Most shoulder arthroscopy procedures can be reliably performed with the patient either in the lateral decubitus (LD) or beach chair (BC) position. Although patient positioning for shoulder arthroscopy has been subject of controversy, there is no conclusive evidence to suggest superiority of one position versus another. Each position offers advantages and disadvantages and surgeon's experience and training are pivotal on selecting one position versus another. Regardless of the position, a proper positioning of the patient should provide adequate access to the joint while minimizing complications. The purpose of this review is to summarize setup and technical aspects, the advantages and disadvantages, and the possible complications of the LD and BC positions in shoulder arthroscopy.
Hip Spacers in Two-Stage Revision for Periprosthetic Joint Infection: A Review of Literature
Authors: Rava Alessandro , Bruzzone Matteo , Cottino Umberto , Enrietti Emilio , Rossi Roberto
Published: October 2019

Infection after total hip arthroplasty (THA) is a devastating complication with significant consequences for patients. In literature, single and two-stage revision, irrigation and debridement, Girdlestone resection arthroplasty, and arthrodesis and amputation are reported as possible treatments. Recently, two-stage revision has become popular as the gold standard treatment for chronic hip joint infections after THA. In this review, we evaluate the current literature about microbiology of periprosthetic joint infections and the use of antibiotic-loaded cement spacers. We aim to give an overview about indications, clinical results, and mechanical complications for spacers implantation, evaluating also selection criteria, pharmacokinetic properties, and systemic safety of the most frequently used antibiotics.
Neonatal Antiepileptic Medication Treatment Patterns: A Decade of Change
Authors: Le Vi T. , Abdi Hibo H. , Sánchez Pablo J. , Yossef Lina , Reagan Patricia B. , Slaughter Laurel A. , Firestine Angela , Slaughter Jonathan L.
Published: October 2019

Objective This study aims to describe the frequency and characteristics of anticonvulsant medication treatments initiated in the neonatal period.

Study Design We analyzed a cohort of neonates with a seizure diagnosis who were discharged from institutions in the Pediatric Health Information System between 2007 and 2016. Adjusted risk ratios and 95% confidence intervals for characteristics associated with neonatal (≤ 28 days postnatal) anticonvulsant initiation were calculated via modified Poisson regression.

Results A total of 6,245 infants from 47 institutions were included. There was a decrease in both phenobarbital initiation within the neonatal period (96.9 to 91.3%, p = 0.015) and continuation at discharge (90.6 to 68.6%, p <0.001). Levetiracetam (7.9 to 39.6%, p < 0.001) initiation within the neonatal period and continuation at discharge (9.4 to 49.8%, p < 0.001) increased. Neonates born at ≥ 37 weeks' gestation and those diagnosed with intraventricular hemorrhage, ischemic/thrombotic stroke, other hemorrhagic stroke, and hypoxic ischemic encephalopathy (HIE) had a higher probability of anticonvulsant administration. The most prevalent diagnosis was HIE (n = 2,223, 44.4%).

Conclusion Phenobarbital remains the most widely used neonatal seizure treatment. Levetiracetam is increasingly used as a second line therapy. Increasing levetiracetam use indicates a need for additional study to determine its effectiveness in reducing seizure burden and improving long-term outcomes.
Using cylindrical implosions to investigate hydrodynamic instabilities in convergent geometry
Authors: Sauppe J. P. , Palaniyappan S. , Loomis E. N. , Kline J. L. , Flippo K. A. , Srinivasan B.
Published: October 2019

Hydrodynamic instabilities such as the Rayleigh–Taylor (RT) and Richtmyer–Meshkov instabilities disrupt inertial confinement fusion (ICF) implosions through the growth of 3D perturbations. Growth of these 3D imperfections at the interfaces of an ICF capsule during implosion lead to mixing between materials that is detrimental to performance. These instabilities have been studied extensively in planar geometry, but such experiments lack the effects of convergence in spherical implosions. While several studies have been performed in spherical geometry, these often lack a direct means to measure perturbation growth. Experiments in cylindrical geometry include convergence effects while maintaining direct diagnostic access. Although cylinders have less compression than spheres, they do provide an excellent platform to validate modeling for convergent geometries. The problem with previous cylindrical implosion experiments was that the convergence ratios were limited to ∼4. With the National Ignition Facility (NIF), larger cylindrical targets can be driven to convergences of 10–15 while maintaining a large enough final diameter to measure perturbation growth. This paper reviews the design process used to both benchmark radiation hydrodynamics codes and enable 1D post-processed simulations to explore design space to separate compression effects from acceleration/deceleration RT instability. Results from 1D simulations suggest that cylindrical implosions on the NIF can produce high-convergence experiments to validate RT instability growth for ICF implosions.
Mode-crossing spectroscopy for photonic waveguide characterization
Authors: Tyndall N. F. , Stievater T. H. , Kozak D. A. , Pruessner M. W. , Rabinovich W. S.
Published: October 2019

We report a novel spectroscopic technique to characterize photonic waveguides over more than an octave of wavelength. The technique, called mode-crossing spectroscopy, uses a broadband source and a spectrometer that are coupled to the input and output ends of a series of straight dielectric waveguides via single-mode optical fibers. Measurements of the wavelengths at which multiple modes are degenerate in a single waveguide enable the determination of the refractive index of the core, as well as the waveguide width variation. In addition, mode-dependent losses are reported from 700 nm to 1550 nm using waveguides of varying lengths. The core refractive indices are measured within an error of ±0.5%, waveguide width variation to an accuracy of less than 5 nm, and waveguide propagation losses within an error of ±0.5 dB/cm. Ultrabroadband in situ measurements of loss and index over an octave of bandwidth are crucial for the accurate characterization of photonic integrated circuits and devices, especially those based on precision broadband couplers, interferometers, and resonant cavities.
Make the right measurement: Discovery of an allosteric inhibition site for p300-HAT
Authors: Gardberg Anna S. , Huhn Annissa J. , Cummings Richard , Bommi-Reddy Archana , Poy Florence , Setser Jeremy , Vivat Valerie , Brucelle Francois , Wilson Jonathan
Published: October 2019

Histone acetyltransferases (HATs) and histone deacetylases (HDACs) catalyze the dynamic and reversible acetylation of proteins, an epigenetic regulatory mechanism associated with multiple cancers. Indeed, HDAC inhibitors are already approved in the clinic. The HAT paralogs p300 and CREB-binding protein (CBP) have been implicated in human pathological conditions including several hematological malignancies and androgen receptor-positive prostate cancer. Others have reported CoA-competitive inhibitors of p300 and CBP with cell-based activity. Here, we describe 2 compounds, CPI-076 and CPI-090, discovered through p300-HAT high throughput screening screening, which inhibit p300-HAT via binding at an allosteric site. We present the high resolution (1.7 and 2.3 Å) co-crystal structures of these molecules bound to a previously undescribed allosteric site of p300-HAT. Derivatization yielded actionable structure-activity relationships, but the full-length enzymatic assay demonstrated that this allosteric HAT inhibitor series was artifactual, inhibiting only the HAT domain of p300 with no effect on the full-length enzyme.
An investigation for influence of intense thermal convection events on wall turbulence in the near-neutral atmospheric surface layer
Authors: Mei Ao , Zheng Xiaojing
Published: October 2019

Based on the field observation data in the near-neutral atmospheric surface layer (ASL) at the Qingtu Lake Observation Array, a new experimental data processing of the second-order statistic distribution of the high Reynolds number wall turbulence was presented which considered the influence of the intense thermal convection events (ITCEs). Following the conventional data selection in the literature, i.e., |z/L|, it is known that the variation of the large- and/or the very-large-scale motions (LSMs and VLSMs) cannot be effectively performed only by this method, which motivates us to find other factors influencing these turbulent motions, e.g., the ITCEs. From the data analysis of the probability density distribution of vertical heat flux, it is found that although its mean value tends to zero, its variance is large rather than zero, which suggests to us some ITCEs exist in the natural motions, although it has less frequent occurrences. In order to characterize the effect of such ITCEs, an additional parameter ψ for scaling the ratio of the buoyancy force to the viscous force is proposed in the data selection progress. The results show that the greater the |ψ|, the greater the impact of the ITCEs on ASL wall turbulence. Furthermore, our investigation reveals that the ITCEs may be one of the reasons why the VLSMs exhibit the Top-Down mechanism.
Bi-global stability analysis for understanding flow separation in aircraft
Authors: Gasparini Allison
Published: October 2019

Researchers used a bi-global stability approach to analyze how instabilities arise at an airfoil due to flow separation.
Saving pipes from damaging vibrations
Authors: Mandel Savannah
Published: October 2019

Scientists find that acoustical damages on pipes can be reduced by increasing upstream pipe length.
Effect of type and feeding frequency of high-fibre feeds on intake, total tract digestibility and ruminal fermentation in beef steers fed a high-concentrate diet
Authors: López A. , Coria H. O. , Nazareno M. A. , García E. M. , Distel R. A. , Arroquy J. I.
Published: October 2019

The inclusion of fibre in a total mixed ration (TMR) often has operational and economic constraints. The objective of the present study was to compare intake and ruminal fermentation of steers fed either a TMR or a diet with the fibre fraction fed separately from the concentrate fraction. Six ruminally fistulated steers were used in a six-treatments, four-period cross-over experiment. Treatment structure was a 3 × 2 factorial. The first factor was fibre delivery either as a part of a TMR or offered separately from the concentrate fraction once every 3 or 6 days. The second factor was represented by two fibre sources, namely, alfalfa hay or cotton by-products. Fibre delivery and source did not significantly affect total, concentrate, fibre and digestible dry-matter intake, compared with TMR. A similar response was observed for ruminal pH, ammonia concentration and total volatile fatty acid concentration. Intake of crude protein and fibre, as well as the concentration of total volatile fatty acids, were higher for alfalfa hay than for cotton by-products. In conclusion, feeding the fibre portion separately from the concentrate fraction once every 3 or 6 days did not negatively affect intake and rumen function compared with when a TMR was fed, regardless of fibre source.
Long non-coding RNA 2310069B03Rik functions as a suppressor of Ucp1 expression under prolonged cold exposure in murine beige adipocytes
Authors: Iwase Mari , Sakai Shoko , Seno Shigeto , Yeh Yu-Sheng , Kuo Tony , Takahashi Haruya , Nomura Wataru , Jheng Huei-Fen , Horton Paul , Osato Naoki , Matsuda Hideo , Inoue Kazuo , Kawada Teruo , Goto Tsuyoshi
Published: October 2019

Specific conditions, such as exposure to cold, can induce the production of brown-like adipocytes in white adipose tissue. These adipocytes express high levels of uncoupling protein 1 (UCP1) and energy expended by generating heat. Thus, these are a potential target for the prevention or treatment of obesity. The present study involved a comprehensive analysis of the adipose tissue to understand the relationship between long non-coding RNA (lncRNA) 2310069B03Rik and UCP1. Cold exposure increased both lncRNA 2310069B03Rik and Ucp1 expression in inguinal white adipose tissue (iWAT). However, overexpression of lncRNA 2310069B03Rik suppressed the Ucp1 mRNA expression and the promoter activity of UCP1 in the iWAT primary adipocytes. In addition, compared to the early induction of Ucp1 expression by cold stimulation, the induction of lncRNA 2310069B03Rik expression was later. These results suggest that lncRNA 2310069B03Rik functions as a suppression factor of Ucp1 expression.
Setup for characterising the spectral responsivity of Fabry–Pérot-interferometer-based hyperspectral cameras
Authors: Pekkala Oskari , Pulli Tomi , Kokka Alexander , Ikonen Erkki
Published: October 2019

Hyperspectral cameras capture the spectral power distribution of the objects in the imaged view via dozens of narrow-band spectral channels of the camera. Knowledge of the spectral responsivity of the channels is essential when interpreting the acquired hyperspectral data and assessing its reliability. The spectral responsivity of the camera channels may vary within the image area. This paper presents a measurement setup and data analysis routine for characterising the spectral responsivity of a hyperspectral camera. This method was used to characterise the spectral responsivity of a Fabry–Pérot-interferometer-based hyperspectral camera. The characterisation method implemented in this study was able to reveal several channel leaks in the measured wavelength range. In the image area there is an approximately 1.5 nm shift in the channel wavelengths, and up to 10% variation in the channel bandwidths. The expanded uncertainties (k  =  2) for the measured channel bandwidths, sensitivities and wavelengths were 7.9%, 9.5% and 0.64 nm, respectively.
Reciprocal interactions between mtDNA and lifespan control in budding yeast
Authors: Garcia Enrique J. , de Jonge Janeska J. , Liao Pin-Chao , Stivison Elizabeth , Sing Cierra N. , Higuchi-Sanabria Ryo , Boldogh Istvan R. , Pon Liza A.
Published: October 2019

Loss of mitochondrial DNA (mtDNA) results in loss of mitochondrial respiratory activity, checkpoint-regulated inhibition of cell cycle progression, defects in growth, and nuclear genome instability. However, after several generations, yeast cells can adapt to the loss of mtDNA. During this adaptation, rho0cells, which have no mtDNA, exhibit increased growth rates and nuclear genome stabilization. Here, we report that an immediate response to loss of mtDNA is a decrease in replicative lifespan (RLS). Moreover, we find that adapted rho0cells bypass the mtDNA inheritance checkpoint, exhibit increased mitochondrial function, and undergo an increase in RLS as they adapt to the loss of mtDNA. Transcriptome analysis reveals that metabolic reprogramming to compensate for defects in mitochondrial function is an early event during adaptation and that up-regulation of stress response genes occurs later in the adaptation process. We also find that specific subtelomeric genes are silenced during adaptation to loss of mtDNA. Moreover, we find that deletion of SIR3, a subtelomeric gene silencing protein, inhibits silencing of subtelomeric genes associated with adaptation to loss of mtDNA, as well as adaptation-associated increases in mitochondrial function and RLS extension.