bluuebunny/crossref_metadata_2025 huggingface dataset:
Professional Internships for PhD Students
Authors: Penny Christopher
Published: October 2019

According to NIH statistics, only 8% of people that begin a biology PhD in the USA become tenure-track faculty members. Anecdotally, this number can vary between 1 and 10%, depending on the institution and field. For those young scientists who want a career within academia, these statistics can be both daunting and depressing. For those who can't wait to leave, or for those who choose to leave with perhaps less enthusiasm, there is a world of opportunities in a diverse range of sectors. However, many non-academic jobs require experience or skills that are difficult to obtain or apply while studying for a PhD. Recently, the research councils within the UK, and in particular the Biotechnology and Biological Sciences Research Council (BBSRC), have made some large investments to provide PhD students with additional skills and experience beyond their academic work.
Life force: why energy shapes evolution
Authors: Lane Nick
Published: October 2019

Life on earth began some 4 billion years ago, but then got stuck at the level of bacteria for more than 2 billion years. The complex ‘eukaryotic’ cell arose abruptly in a singular event around 1.5–2 billion years ago. All eukaryotes share a long list of complex traits, from the nucleus to sex and senescence, which are all but unknown in bacteria. Why are humans so similar to mushrooms at the level of cells, even though we live so differently? Why did evolution follow such a peculiar trajectory? The answers might lie in the equally strange mechanism by which all cells generate ATP: chemiosmotic coupling.
From print to patient: 3D-printed personalized nerve regeneration
Authors: Johnson Blake N. , McAlpine Michael C.
Published: October 2019

3D printing is revolutionizing regenerative medicine and accelerating the pace of biological discovery via its ability to interweave materials and components of disparate properties, guided by anatomical digital templates. These capabilities have led to a breakthrough in the customization and personalization of complex biological systems and devices ranging from platform technologies such as organs-on-a-chip, to implantable devices, such as patient-specific scaffolds. Yet, understanding and regenerating the nervous system has historically provided a challenging benchmark for drug therapy, surgical methods and bioengineering strategies. The question we pose is can: 3D printing be utilized to address these scientific standards? In principle, extrusion-based 3D printing should offer the ability to flexibly interweave multiple materials, over various length scales, while incorporating diverse functionalities. This may allow the ability to expand biological design paradigms and develop them into novel personalized device architectures. Indeed, 3D printing appears poised to offer an exciting future in the realization of personalized anatomical nerve pathways and platforms for point-of-care opportunities from print to patient.
Carpe lucem: harnessing organic light sources for optogenetics
Authors: Morton Andrew , Murawski Caroline , Gather Malte C.
Published: October 2019

With the advent of optogenetics, numerous functions in cells have been rendered responsive to the experimental delivery of light. The most common implementation of this technique features neurons genetically modified to express light-sensitive ion channel proteins, which open specifically in response to pulses of blue light, triggering electrical impulses. Optogenetics has now matured to a point where in addition to answering fundamental questions about the function of the brain, scientists are beginning to consider clinical applications. However, further progress in this field will require new ways of delivering light. One of these involves the use of organic light-emitting diodes (OLEDs), a display technology increasingly common in modern-day smart phones, for the optical stimulation of cells.
One drug does not fit all: impact of sex and gender on pharmacological response
Authors: Franconi Flavia , Campesi Ilaria
Published: October 2019

It is important to remember that gender health and illness should not to be conflated with women's health and illness. Turshen1 reports that numerous studies with ‘gender’ in the title use the word gender as a synonym for ‘women’ and as a result, men's gender-specific needs are missed. In addition, in reporting demographic characteristics of the study participants, some clinical trialists use the term ‘gender’ and some ‘sex’ to indicate men and women and this may create confusion. It can be difficult to separate the two concepts, because there are continuous and constant interactions and relationships between sex and gender3. In other words, sex and gender work together. However, little attention is paid to the fact that gender is a sex modifier. It is relevant to have in mind that both sex and gender affect health and illness4.
Gut microbial function and bacterially derived signals in cardiovascular disease
Authors: Kitai Takeshi , Tang W.H. Wilson
Published: October 2019

The human body is inhabited by a vast number of bacteria and other microorganisms, the majority residing in the gut. The collective microorganisms that live in coexistence with their hosts are referred to as the microbiome. Beyond its role in supporting physiological functions in food digestion, the microbiome also performs multiple functions and interacts dynamically with the host. The microbiome regulates the intestinal mucosal barriers and assist with development of systemic immune systems that potentiate the defence against malevolent pathogenic microorganisms. Collectively, the microbiota exerts a fundamental and necessary influence on systemic immunity and metabolism – a healthy gut microbiome means an overall healthy host.
Dancing to circadian rhythms: microbes and metabolism
Authors: Rao Mrinalini C. , Chang Eugene B.
Published: October 2019

Since the turn of the 21st century, two advances in biology have revolutionized our thinking of human metabolism. First, is the in-depth characterization of a previously recognized, but hitherto poorly defined organ system, the gut microbiome. This microbial organ exquisitely interacts with the diet which greatly influences its metabolic functions to impact host metabolism through the production of small bioactive molecules that continuously enter the bloodstream to act at local and distant organ tissues. Equally important, the host metabolism can also modulate the gut microbiome setting up the two as intricate and well-suited partners. Second, is the recognition that most of the cells and organs of the body are dependent on circadian rhythms, systemic timekeepers that play a major role in regulating behavioural and physiological functions to manage energy balance. In conditions of metabolic health, circadian rhythms are the beat to which the two well-matched partners, microbes and metabolism, dance. When these partners are out of step or mismatched, negative consequences may develop that promote metabolic disturbances and disease. Thus, unravelling this complex choreography becomes key to understanding how to maintain metabolic health and to correct missteps that may lead to the development of conditions like diet-induced obesity.
Development of NOSH-NSAIDs: a new class of anti-inflammatory pharmaceuticals for the treatment of cancer
Authors: Kashfi Khosrow
Published: October 2019

Non-steroidal anti-inflammatory drugs (NSAIDs) have anti-cancer (chemopreventive) properties; however, side effects preclude their long-term use. NOSH-NSAIDs, designed as safer alternatives, are novel hybrid chimaeras that release nitric oxide (NO) and hydrogen sulfide (H2S). NOSH-NSAIDs are gastrointestinally safe yet retain all the pharmacological properties of their native NSAID. NOSHNSAIDs are orders of magnitude more potent than their conventional counterparts in inhibiting the growth of various human cancer cell lines of different tissue origins, adenomatous, epithelial and lymphocytic. This growth inhibition is a result of a reduction in cell proliferation and cell cycle arrest, leading to increased apoptosis. In xenograft mouse models of cancer, NOSH-aspirin was better than normal aspirin as a chemopreventive agent; it dose-dependently inhibited tumour growth and tumour mass. NOSH-naproxen was significantly more efficacious than normal naproxen in reducing the growth of established tumours.
Nature versus nurture: unravelling cause and effect in epigenetics and disease
Authors: Albert Helen
Published: October 2019

The impact of a person's genetics on their susceptibility to certain diseases has been known for some time. While it is clear that the environment can also play a role, the exact molecular mechanisms for this influence have remained obscure. Recent scientific advances in the field of epigenetics have allowed researchers to look at the impact of environmental factors on DNA and disease susceptibility more closely. Helen Albert talks to Professor John Holloway from the University of Southampton who has been investigating the effects of the environment on our DNA and how such exposures change our risk for developing asthma and allergic disease.
Why it's never too early to start Standing up for Science
Authors: Skamarauskas Anastasia
Published: October 2019

The Voice of Young Science (VoYS) network hosts Standing up for Science workshops around the country and, more recently, across Europe. We bring together researchers who've engaged with the media and the public, local and national journalists, and communications and policy experts to encourage early career researchers to make their voices heard in public debates about science.
From extreme environments to human pathogens: an evolutionary journey
Authors: Giovannelli Donato , Vetriani Costantino
Published: October 2019

The history of our planet is underpinned by roughly 4 billion years of microbial evolution. From its emergence in a (probably) hot and anoxic environment, microbial life has evolved to colonize every available niche on our planet, including the inside and outside of other organisms. Yet, the emergence and evolution of microbial metabolism remains a major unsolved problem. How have microbes adapted to colonize every available environmental niche, including other organisms? How did they evolve to colonize mammals and our human ancestors? Answers to these questions will allow us to understand the emergence and evolution of life on our planet, inform the search for life elsewhere and, in the making, reveal important insight that will help us fight infections.
Pushing the boundaries of life itself
Authors: Albert Helen
Published: October 2019

The ability of some organisms to live in extreme environments has always fascinated us. While more complex species such as mammals can live in very cold or hot surroundings, microorganisms definitely take the crown when it comes to being able to survive the most extreme conditions. These extremophiles are very resilient and can survive conditions that would kill other organisms in seconds. Indeed, some researchers believe that life may have begun with such organisms living deep under the ocean on hydrothermal vents. Helen Albert talks to Professor Rania Siam from The American University in Cairo, Egypt, about her research on microbes living near highly salty underwater ‘brine pools’ in the Red Sea. Helen also discusses the remarkable bacterium Deinococcus radiodurans, which is able to withstand high levels of radiation and desiccation, with Professor Michael Daly from the Uniformed Services University in Bethesda in the USA.
Unlocking the secrets of mutable collagenous tissue
Authors: Gupta Himadri S. , Szulgit Greg , Elphick Maurice R. , Mo Jingyi
Published: October 2019

The mutable collagenous tissue (MCT) of echinoderms (e.g. sea cucumbers, starfish and sea urchins) is unique because of its ability to ‘switch’ mechanical states rapidly and reversibly – from stiff to soft and vice versa. This kind of tissue in humans, for example, in skin, tendons and ligaments, does not have this property. So what are the molecular-level secrets by which MCT achieves this transformative ability? New real-time ultrastructural investigations are beginning to shed light on this question. Synchrotron X-ray measurements of dynamic molecular conformational changes point to the key factor being the gel-like matrix between the collagen fibrils. These findings could have applications for developing treatments for collagen-based disorders.
The choreography of life
Authors: Reilly Charles B.
Published: October 2019

Part of our work as biochemists is to describe the choreography of life at the molecular scale. This sounds complicated, and it is, not least because we have to apply different approaches across the scale of study that could be considered ‘molecular’. At the most finite end of the spectrum, i.e., atoms and small molecules, researchers need to invoke quantum mechanics to describe behaviour. As we move up to larger complexes, however, we transition to a different subset of physics, where we can begin to describe movement via the more familiar and approachable set of rules found in classical Newtonian mechanics. This is the kind of physics we encounter in our everyday lives and which describes the actions of industrial machinery. And it is in this kind of language that we tend to understand the movement of molecular machines, such as the archetypal ATP synthase complex.
It's good to unwind: how Hel308/HelQ helicases are good for health
Authors: Jenkins Tabitha , Northall Sarah , Bolt Edward , Soultanas Panos
Published: October 2019

In every living system the information for maintaining and propagating life is contained within a genome. This ‘book of life’ is written in the language of DNA. For life to exist, access to this is essential in order to replicate and repair genetic information for the benefit of future generations. An important group of molecular motor proteins, the helicases, allows access to this book of life by opening up the DNA double helix and exposing the DNA text of individual strands for replication, transcription, translation and repair. Like all molecular motors, helicases use chemical energy derived from the binding and hydrolysis of nucleotide triphosphates, usually ATP, to carry out mechanical tasks. They come in a variety of structures and employ different mechanisms to carry out diverse mechanical tasks. One large group of helicases are required for repairing DNA that has become damaged by radiation, chemicals or other proteins stuck on the DNA (‘roadblocks’). These DNA repair helicases are also diverse in form and function, having evolved in all forms of life to deal with many different types of DNA damage. However, they have the common property of being able to slide along and unwind DNA molecules to allow DNA repair enzymes access to fix the damage.
The road to 1978: a brief history of fertility research
Authors: Carroll Michael
Published: October 2019

This issue of The Biochemist acknowledges the 40th anniversary of the birth of the first IVF baby, Louise Brown, and with it the emergence of Assisted Reproductive Technology (ART). These developments did not arise in a vacuum; the history of baby making dates back well before 1978. The influence of fecundity (the ability to reproduce) has been deliberated since the Palaeolithic period.
Introducing the Industry Representative
Authors: Weir Malcolm
Published: October 2019

The Biochemical Society is committed to bringing together molecular bioscientists and supporting our members across the community. To this end there has been a renewed focus on those working in the industrial, biotechnology and academic drug discovery sectors. By way of background, the Society's membership has historically been largely made up of academics, with a smaller number of members working in industry. In 2015 an Industry Strategy was developed by the Head of Membership Engagement with the aim of providing a platform for collaboration, facilitating innovation and supporting links between academia and industry.
Exploring neurodegeneration at the atomic level
Authors: Tozer Adam
Published: October 2019

Tau proteins are microtubule-associated proteins essential for the correct functioning of neurons. This small family of proteins, 352–441 amino acids in length, are abundant in the brain and exist to stabilize microtubules in neurons and glia (non-neuronal cells of the central nervous system) to ensure correct trafficking of cellular cargo and cell maintenance.
Hunting down hydrogen: applying neutron macromolecular crystallography to galectins
Authors: Logan Derek T.
Published: October 2019

Galectins are a medically important family of small, soluble carbohydrate-binding proteins that have been implicated in a wide variety of diseases, and are therefore targets for the development of new drugs. Many X-ray crystal structures of small molecules in complex with galectins have been determined and have given invaluable information on how natural ligands and synthetic inhibitors are recognized. However, until now the hydrogen-bonding patterns involved in ligand recognition have been a matter of informed guesswork, as X-ray crystallography can't reliably tell us where hydrogen atoms are positioned. We describe how neutron macromolecular crystallography has been applied to galectins for the first time to shed light on this question.
Reporting from outside the lab: attending the ASH conference
Authors: Hillier James
Published: October 2019

Postgraduate, Early Career, Full and Emeritus Members of the Biochemical Society can apply for a General Travel Grant. These grants support attendance at scientific meetings, training courses, lab visits or any other event relevant to your career and encourage lifelong learning. James Hillier is currently investigating the role of the aminotransferase BCAT1 in acute myeloid leukaemia (AML) development. BCAT1 contains a CXXC motif, a feature of many antioxidant enzymes such as thioredoxin that are able to metabolize reactive oxygen species (ROS). His research focuses how altered expression of BCAT1 affects redox homeostasis and how this impacts processes dysregulated in cancer such as proliferation, differentiation and apoptosis. Cancer cells are known to favour pro-oxidative states that induce proliferative signalling yet maintain ROS at sub-lethal levels, therefore targeting the antioxidant capacity of BCAT1 to induce cell death, which may open a promising treatment option for patients with aberrant BCAT1 expression.
New ideas from an old concept: the hydrogen bond
Authors: Scheiner Steve
Published: October 2019

Ongoing studies of the hydrogen bond (HB), in which a hydrogen (H) atom acts as a bridge between a pair of chemical groups, continues to offer new ideas about this interaction that have applications to biochemical processes. The ability of a proton to transfer within a HB can be controlled by conformational changes that cause small alterations to the HB geometry. The CH group, widely prevalent in biological systems, participates in HBs and contributes to the structure and stability of commonly occurring protein secondary structures such as the β-sheet. The concept of the HB has been extended to systems where the bridging proton is replaced by any of a large variety of electronegative atoms, in the form of halogen, chalcogen, pnicogen and tetrel bonds, with no loss of strength.
LncRNA SNHG1 was down-regulated after menopause and participates in postmenopausal osteoporosis
Authors: Huang Shuaihao , Zhu Xiaowen , Xiao Dan , Zhuang Jianxiong , Liang Guoyan , Liang Changxiang , Zheng Xiaoqing , Ke Yuhong , Chang Yunbing
Published: October 2019

The functions of long (>200 nt) non-coding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) have only been investigated in cancer biology. We found that plasma LncRNA SNHG1 was down-regulated in postmenopausal than in premenopausal females. Among postmenopausal females, the ones with postmenopausal osteoporosis showed much lower expression levels of plasma lncRNA SNHG1. A 6-year follow-up study on postmenopausal females revealed that plasma lncRNA SNHG1 decreased in females with postmenopausal osteoporosis but not in healthy postmenopausal females. Levels of plasma lncRNA SNHG1 at 12 months before diagnosis is sufficient to distinguish postmenopausal osteoporosis patients from healthy controls. After treatment, plasma lncRNA SNHG1 were significantly up-regulated. Therefore, lncRNA SNHG1 was down-regulated after menopause and plasma level of lncRNA SNHG1 may serve as a biomarker for the diagnosis and treatment of postmenopausal osteoporosis.
BTXA regulates the epithelial–mesenchymal transition and autophagy of keloid fibroblasts via modulating miR-1587/miR-2392 targeted ZEB2
Authors: Hou Zhanying , Fan Feixiang , Liu Po
Published: October 2019

Keloids are very resistant to treatment in dermatology and plastic surgical practice. The present study aimed to explore the underlying mechanism of botulinum toxin A (BTXA) treated human skin keloid fibroblasts (HSFBs) proving some new insights into keloids treatment. Expression of miR-1587 and miR-2392 were significantly down-regulated in keloid tissues and HSFBs, while the ZEB2 was a target of both and up-regulated in keloid tissues and HSFBs compared with the normal controls. BTXA could significantly increase the expression of miR-1587 and miR-2392 but decrease the expression of ZEB2. BTXA could significantly inhibit the proliferation, cell cycle, and migration and promote apoptosis and autophagy of HSFBs; however, miR-1587 and miR-2392 inhibitors could reverse these effects of BTXA on HSFBs. Silencing ZEB2 could significantly attenuate the effects of miR-1587 and miR-2392 inhibitors in promoting cell proliferation and migration and suppressing apoptosis and autophagy of HSFBs after treating with BTXA. BTXA could suppress the proliferation and migration and promote apoptosis and autophagy of HSFBs via modulating miR-1587/miR-2392 targeted ZEB2.
Role of matrix metalloproteases 1/3 gene polymorphisms in patients with rotator cuff tear
Authors: Miao Kaisong , Jiang Lifeng , Zhou Xindie , Wu Lidong , Huang Yong , Xu Nanwei , Zhang Junjie , Li Jin
Published: October 2019

An association of Matrix Metalloproteinases-1/3 (MMP-1/3) rs1799750/rs3025058 polymorphism with increased risk of rotator cuff tear (RCT) has been reported in a Brazilian population. However, this significant association has not been confirmed in the Chinese population. Genotyping was conducted by polymerase chain reaction (PCR)-restriction fragment length polymorphism and direct sequencing. Our results demonstrated that individuals with the TT genotype had a significantly higher risk of RCT compared with those with the CC genotype. The increased risk of RCT progression was associated with the 2G allele of the rs1799750 polymorphism. No significant association was observed for genotypic and allelic frequencies of the rs3025058 polymorphism. A significant association of the MMP-1 rs1799750 polymorphism was observed with smokers, drinkers and people aged ≥60 years and non-diabetic people. Additionally, the MMP-1 rs1799750 polymorphism was associated with pre-operative stiffness in RCT patients. In conclusion, a significant correlation was identified between the MMP-1 rs1799750 polymorphism and RCT. The MMP-1 rs1799750 polymorphism might be considered as a biomarker of genetically high-risk RCT, helping to clarify the mechanism of RCT.
Role of long non-coding RNA TP73-AS1 in cancer
Authors: Chen Caizhi , Shu Long , Zou Wen
Published: October 2019

Cancer incidence rate has increased so much that it is the second leading cause of deaths worldwide after cardiovascular diseases. Sensitive and specific biomarkers are needed for an early diagnosis of cancer and in-time treatment. Recent studies have found that long non-coding RNAs (lncRNAs) participate in cancer tumorigenesis. LncRNA P73 antisense RNA 1T (TP73-AS1), also known as KIAA0495 and p53-dependent apoptosis modulator (PDAM), is located in human chromosomal band 1p36.32 and plays a crucial role in many different carcinomas. This review summarizes current findings on the role of TP73-AS1 and its signaling pathways in various cancers, including glioma, esophageal squamous cell carcinoma (ESCC), hepatocellular carcinoma (HCC), colorectal cancer (CRC), osteosarcoma, gastric cancer (GC), clear cell renal cell carcinoma (ccRCC), breast cancer (BC), bladder cancer, ovarian cancer, cholangiocarcinoma (CCA), lung cancer, and pancreatic cancer. Its aberrant expression generally correlates with clinicopathological characterization of patients. Moreover, TP73-AS1 regulates proliferation, migration, invasion, apoptosis, and chemoresistance cancer mechanisms, both in vivo and in vitro, through different signaling pathways. Therefore, TP73-AS1 may be considered as a marker for diagnosis and prognosis, also as a target for cancer treatment.
Designing minimalist membrane proteins
Authors: Curnow Paul
Published: October 2019

The construction of artificial membrane proteins from first principles is of fundamental interest and holds considerable promise for new biotechnologies. This review considers the potential advantages of adopting a strictly minimalist approach to the process of membrane protein design. As well as the practical benefits of miniaturisation and simplicity for understanding sequence-structure-function relationships, minimalism should also support the abstract conceptualisation of membrane proteins as modular components for synthetic biology. These ideas are illustrated with selected examples that focus upon α-helical membrane proteins, and which demonstrate how such minimalist membrane proteins might be integrated into living biosystems.
Swimming regulations for protein kinase A catalytic subunit
Authors: Gold Matthew G.
Published: October 2019

cAMP-dependent protein kinase (PKA) plays a central role in important biological processes including synaptic plasticity and sympathetic stimulation of the heart. Elevations of cAMP trigger release of PKA catalytic (C) subunits from PKA holoenzymes, thereby coupling cAMP to protein phosphorylation. Uncontrolled C subunit activity, such as occurs in genetic disorders in which regulatory subunits are depleted, is pathological. Anchoring proteins that associate with PKA regulatory subunits are important for localising PKA activity in cells. However, anchoring does not directly explain how unrestrained ‘free swimming' of C subunits is avoided following C subunit release. In this review, I discuss new mechanisms that have been posited to account for this old problem. One straightforward explanation is that cAMP does not trigger C subunit dissociation but instead activates intact PKA holoenzymes whose activity is restrained through anchoring. A comprehensive comparison of observations for and against cAMP-activation of intact PKA holoenzymes does not lend credence to this mechanism. Recent measurements have revealed that PKA regulatory subunits are expressed at very high concentrations, and in large molar excess relative to C subunits. I discuss the implications of these skewed PKA subunit concentrations, before considering how phosphorylation of type II regulatory subunits and myristylation of C subunits are likely to contribute to controlling C subunit diffusion and recapture in cells. Finally, I speculate on future research directions that may be pursued on the basis of these emerging mechanisms.
Molecular pathways of mitochondrial outer membrane protein degradation
Authors: Zheng Jing , Li Lanlan , Jiang Hui
Published: October 2019

Mitochondrial outer membrane (MOM) encloses inner compartments of mitochondria and integrates cytoplasmic signals to regulate essential mitochondrial processes, such as protein import, dynamics, metabolism, cell death, etc. A substantial understanding of MOM associated proteostatic stresses and quality control pathways has been obtained in recent years. Six MOM associated protein degradation (MAD) pathways center on three AAA ATPases: Cdc48 in the cytoplasm, Msp1 integral to MOM, and Yme1 integral to the inner membrane. These pathways survey MOM proteome from the cytoplasmic and the inter-membrane space (IMS) sides. They detect and degrade MOM proteins with misfolded cytoplasmic and IMS domains, remove mistargeted tail-anchored proteins, and clear mitochondrial precursor proteins clogged in the TOM import complex. These MOM associated protein quality control pathways collaboratively maintain mitochondrial proteostasis and cell viability.
Towards a model of GCN2 activation
Authors: Masson Glenn R.
Published: October 2019

Cells must be able to sense and adapt to their surroundings to thrive in a dynamic environment. Key to adapting to a low nutrient environment is the Integrated Stress Response (ISR), a short-lived pathway that allows cells to either regain cellular homeostasis or facilitate apoptosis during periods of stress. Central to the ISR is the protein kinase General Control Non-depressible 2 (GCN2), which is responsible for sensing starvation. Upon amino acid deficiency, GCN2 is activated and initiates the ISR by phosphorylating the translation initiation factor eIF2α, stalling protein translation, and activating the transcription factor ATF4, which in turn up-regulates autophagy and biosynthesis pathways. A key outstanding question is how GCN2 is activated from an autoinhibited state. Until recently, a model of activation focussed on the increase of deacylated tRNA associated with amino acid starvation, with deacylated tRNA binding directly to GCN2 and releasing autoinhibition. However, in vivo experiments have pointed towards an alternative, deacylated-tRNA-independent mechanism of activation. Here, we review the various factors that may facilitate GCN2 activation, including recent research showing that the P-stalk complex, a ribosome-associated heteropentameric protein complex, is a potent activator of GCN2.
Morphological active contour without edge‐based model for real‐time and non‐rigid uterine fibroid tracking in HIFU treatment
Authors: Ning Guochen , Zhang Xinran , Liao Hongen
Published: October 2019

High‐intensity focused ultrasound (HIFU) therapy represents an image‐guided and non‐invasive surgical approach to treat uterine fibroid. During the HIFU operation, it is challenging to obtain the real‐time and accurate lesion contour automatically in ultrasound (US) video. The current intraoperative image processing is completed manually or semi‐automatic. In this Letter, the authors propose a morphological active contour without an edge‐based model to obtain accurate real‐time and non‐rigid US lesion contour. Firstly, a targeted image pre‐processing procedure is applied to reduce the influence of inadequate image quality. Then, an improved morphological contour detection method with a customised morphological kernel is harnessed to solve the low signal‐to‐noise ratio of HIFU US images and obtain an accurate non‐rigid lesion contour. A more reasonable lesion tracking procedure is proposed to improve tracking accuracy especially in the case of large displacement and incomplete lesion area. The entire framework is accelerated by the GPU to achieve a high frame rate. Finally, a non‐rigid, real‐time and accurate lesion contouring for intraoperative US video is provided to the doctor. The proposed procedure could reach a speed of more than 30 frames per second in general computer and a Dice similarity coefficient of 90.67% and Intersection over Union of 90.14%.
Weakly supervised segmentation for real‐time surgical tool tracking
Authors: Lee Eung‐Joo , Plishker William , Liu Xinyang , Bhattacharyya Shuvra S. , Shekhar Raj
Published: October 2019

Surgical tool tracking has a variety of applications in different surgical scenarios. Electromagnetic (EM) tracking can be utilised for tool tracking, but the accuracy is often limited by magnetic interference. Vision‐based methods have also been suggested; however, tracking robustness is limited by specular reflection, occlusions, and blurriness observed in the endoscopic image. Recently, deep learning‐based methods have shown competitive performance on segmentation and tracking of surgical tools. The main bottleneck of these methods lies in acquiring a sufficient amount of pixel‐wise, annotated training data, which demands substantial labour costs. To tackle this issue, the authors propose a weakly supervised method for surgical tool segmentation and tracking based on hybrid sensor systems. They first generate semantic labellings using EM tracking and laparoscopic image processing concurrently. They then train a light‐weight deep segmentation network to obtain a binary segmentation mask that enables tool tracking. To the authors’ knowledge, the proposed method is the first to integrate EM tracking and laparoscopic image processing for generation of training labels. They demonstrate that their framework achieves accurate, automatic tool segmentation (i.e. without any manual labelling of the surgical tool to be tracked) and robust tool tracking in laparoscopic image sequences.
Islanding detection using total variation‐based signal decomposition technique
Authors: Mishra Prajna Parimita , Bhende Chandrashekhar Narayan , Manikandan M. Sabarimalai
Published: October 2019

This study presents a passive islanding detection technique based on the approach of total variation filtering (TVF) for inverter‐based distributed generation under noisy environment. Contamination of noise in the signal makes the islanding detection threshold less reliable. Therefore, the modal voltage signal is analysed through TVF‐based decomposition procedure and several statistical features are obtained from its output. For decision making, the features are compared with the pre‐specified threshold. To tackle the challenge of islanding detection in the presence of the high‐quality factor load, phase angle of the positive sequence voltage is considered as the second level of detection criterion. The proposed scheme is validated on IEEE 34‐bus standard distribution system. The scheme is tested under islanding as well as all possible non‐islanding network disturbances. Hardware‐in‐loop results are also presented in support of the theory. A comparative analysis of the proposed algorithm with the well‐established S‐transform is presented. The proposed scheme is found to be working effectively and can detect islanding condition within three cycles of its inception.
Electric power distribution system expansion planning considering cost elasticity of demand
Authors: Gholizadeh‐Roshanagh Reza , Zare Kazem
Published: October 2019

Demand side participation is a fundamental property of modern power distribution networks. Time‐of‐use pricing is a common strategy to persuade customers to shift a part of their consumption to low consumption hours. In flat time‐of‐use pricing, it is not the price that changes over a period, it is the cost of energy. The aim of this paper was to quantify impact of cost elasticity of demand on investment plans over a multi‐stage horizon, where the time‐of‐use pricing was taken into account. On one hand, time‐of‐use pricing was modeled with three load levels as peak, medium‐peak and off‐peak. On the other hand, the tendency of customers to participate in reduction of demand was modeled where it shows rate of response of customers to change in cost of energy and it determines maximum demand response penetration. So, it was examined how time‐of‐use pricing and responsive customers can postpone the investments. Mixed integer linear programming method was utilized to solve the optimal distribution expansion planning problem. Simulations were performed on an 18‐node distribution network. Results revealed effectiveness of the proposed model and showed that consideration of cost elasticity of demand in expansion planning, changes optimal configuration of network and significantly influences total costs.
Evaluating weather influences on transmission line failure rate based on scarce fault records via a bi‐layer clustering technique
Authors: Wang Yue , Chen Lu , Yao Meng , Li Xinyu
Published: October 2019

In a common practice of power system reliability management, scarcity of malfunction information leads to incomplete knowledge of the failure reasons, and thus results in ambiguous failure rate models for the time being. This study proposes a methodology of quantifying weather influence on transmission line failure rate in terms of the effects of unexplained factors originating from a scarcity of weather‐fault‐correlating information. A model to quantify the referred weather influence is derived from a conceptual full failure rate model and parameterised by an exponential function. The concerned unknown parameters, besides some recourse covariates introduced to account for absent information on unexplained factors, are together trained by means of the maximum likelihood estimation based on available weather‐fault‐correlating information about both normal and failure‐causing weather conditions for pooled transmission lines. Theoretical foundation and numerical results are given for illustrating a relationship between the proposed model and traditional weather‐dependent failure rate models. Applications are also demonstrated in virtue of practical data from the Xinjiang Autonomous Region of China.
Current injection‐based Newton–Raphson power‐flow algorithm for droop‐based islanded microgrids
Authors: Kumar Abhishek , Jha Bablesh Kumar , Singh Devender , Misra Rakesh Kumar
Published: October 2019

The power‐flow analysis of droop‐based islanded microgrid (DBIMG) is a growing research area. The conventional power‐flow techniques have been difficult to employ in DBIMG due to the non‐existence of reference bus (slack bus). To address this issue, a current injection Newton–Raphson based novel algorithm is proposed. The proposed algorithm chooses system frequency and voltage magnitude of the reference bus as additional variables in power‐flow formulation. The proposed algorithm takes into account three operating modes of distributed generators viz. Droop control, PQ and PV. The linear equations cover the droop characteristics of the DGs, while non‐linear equations cover power‐flow equations of the system. The proposed algorithm has been executed on two test systems viz. 6‐bus system and 38‐bus system. To show the effectiveness and robustness of the proposed algorithm, the performance of the proposed algorithm is also examined for the different loading conditions and different R/X ratios of the line of the test systems. The obtained solutions have also been compared with the solutions obtained by other Newton–Raphson based algorithms reported in the literature and PSCAD. The comparative analysis shows better efficiency and superior convergence of the proposed algorithm.
Impact assessment of virtual synchronous generator on the electromechanical dynamics of type 4 wind turbine generators
Authors: Tessaro Heitor José , de Oliveira Ricardo Vasques
Published: October 2019

The de‐loaded operation of wind turbine generators (WTGs) with inertial and frequency control considerably affects the dynamics and stability of variable speed wind turbines. In this context, this work proposes a comprehensive assessment of the simultaneous impact of virtual synchronous generator and frequency controllers on the electromechanical dynamics of type 4 WTGs. The proposed power balance formulation and the performed analysis, which are the main contributions of this work, provide insight into the simultaneous impact of the inertial and frequency control on the dynamics of the wind generation unit and system frequency. The assessment has been performed by means of an analytical formulation for the power balance in the WTG, characteristic curves of the wind turbine, and non‐linear time‐domain simulations of two test systems. The analyses have shown that the speed and torque deviation magnitudes of the wind turbine, as well as the amount of kinetic energy released by the wind turbine, depend on the wind turbine operating point. The study has also shown that the de‐loaded operation considerably increases the inertial response capability of WTGs. The integrated inertial and frequency control approach has resulted in well‐behaved electromechanical dynamics for the WTG.
Ship classification based on convolutional neural networks
Authors: Zhenzhen Li , Baojun Zhao , Linbo Tang , Zhen Li , Fan Feng
Published: October 2019

Ship classification in optical images has been challenged by the complexity of various ships, different imaging conditions, and limited labelled images. Traditional methods focus on extracting handcrafted features for classification, but often fails to design well‐performed features for complex images. Here, the authors propose a ship classification approach with CNN. It is capable of learning discriminative features itself by supervised learning and achieving good classification performance. They build two small datasets of optical ship images for training and validation, and conduct several experiments. The experimental results indicate that their approach is effective for ship classification.
Hierarchical ship detection method for space‐borne SAR image
Authors: Tang Wei , Zhao Baojun , Tang Linbo , Nan Jinghong
Published: October 2019

Ship detection from space‐borne SAR image is a challenging task. The main challenges in this task include the disturbance of sea clutter, island, coastline, and variability in ship sizes. Here, the authors propose a novel hierarchical ship detection framework to overcome the above challenges. Initially, the edge‐enhanced maximally stable extremal regions (E‐MSER) is employed as ship candidates. Then, through some simple shape analysis, they can eliminate the obvious false alarms which are not conformed to the shape feature of ship. Finally, candidates are represented by an effective multiple features learning framework for discriminating true ship targets. Experimental results on numerous space‐borne SAR images demonstrate their proposed scheme that outperforms other traditional methods with higher detection accuracy and lower false alarm.
Jamming decision under condition of incomplete jamming rule library
Authors: Xing Qiang , Zhu Weigang , Chi Zhou , Zheng Guangyong
Published: October 2019

To solve the problem of the low rate of template matching (TM) jamming decision method under the incomplete jamming rule library condition in traditional electronic warfare, a clustering and resampling – support vector machine (CRS‐SVM) jamming decision method, is proposed. For the air‐to‐air scene of airborne multifunctional fire control radar, the inter‐pulse pulse and intra‐pulse features are extracted, and a jamming rule library that is divided into the source domain and target domain sample according to the missing rate is constructed in this scene. DBSCAN algorithm is used to cluster the dataset, and the structure information is found. The training samples are generated via resampling. SVM is used to transform the inner product of the target domain space into the inner product of the feature space to establish the feature space hyperplane. The target domain samples are labelled as the corresponding jamming style label to realise the fast and effective decision. The experiment results show that the proposed method can effectively improve the accuracy and robustness of jamming decision compared with the traditional TM method.
Unified OSTBC‐based communication scheme for cooperative space vehicles
Authors: Geng Jian , Liu Hongyan , Jin Wen , Yan Xinfeng , Xu Jin
Published: October 2019

In many spatial cooperative vehicle networks, omni‐directional communication is preferred due to its flexibility for networking. In the recent studies, space time code was shown to be an effective approach for improving the performance of the omni‐directional communication between space vehicles. This paper studies the unified scheme for the orthogonal space time block code–based transmission between two space vehicles equipped with different numbers of antennas. It is obtained that at most six passive antennas and four RF chains are enough for the typical use. In the proposed scheme, the receiver can perform a unified detection procedure regardless of the actual number of the transmit antennas, which facilitates the practical application. Simulation results validate the proposed scheme in terms of the cumulative distribution function of the received signal‐to‐noise ratios.
Insect trajectory simulation method based on radar observation
Authors: Wang Yixuan , Wang Rui , Cui Kai , Tian Weiming , Wu Dongli , Ma Shuqing
Published: October 2019

Large‐scale insect migration may cause severe plant diseases and pests which can exert serious impact on agriculture. Predicting the trajectory and destination of insect migration accurately is an effective way to prevent pests. Here, an insect migration trajectory simulation method was proposed with two stages of insect migration, taking off and cruising, considered. First, four criteria based on actual weather condition were proposed to determine the take‐off area of the insect migration. Then, a method based on Lagrange diffusion model was proposed to simulate the cruising trajectory. This step needs to combine with the insect orientation strategy and insect trajectory speed which can be, respectively, provided by entomological radar and weather radar. Finally, by comparing the determined take‐off area and the simulated insect cruising trajectory with the monitoring results of the weather radar, the effectiveness of the method was verified.
One microwave imaging system based on automotive radar chip
Authors: Wu Fuwei , Li Siming , Shang Shize , Li Yuanji , Yang Yuhao
Published: October 2019

The interest in microwave imaging system is increasing because it can serve as a useful tool for concealed threat detecting. The current imaging systems have two major challenges: (i) multi‐static arrays suffer from complex hardware design and ineffective backprojection‐imaging algorithm, and (ii) monostatic linear arrays suffer from large scanning time due to the electronically scanning one by one of the co‐located receive–transmit antennas. To address these challenges, this study introduces a novel linear imaging array based on automotive radar chips and sub‐array time‐division multiple‐input multiple‐output working principles, which is hardware efficient and compatible fast Fourier transform (FFT) imaging technique. Through simulation, it is shown that the scanning time is only one‐fourth of the traditional monostatic linear array and the FFT image reconstruction technique can be used.
Method of multichannel calibration for unmanned aerial vehicle surveillance radar
Authors: Hou Yanan , Shang Hui , Yang Ming , Jin Cheng
Published: October 2019

Amplitude and phase errors among the different channels including antenna and receiver of the unmanned aerial vehicle surveillance digital array radar will deteriorate the beam pattern and cause the invalid digital beam formation, and then severely affect the performance of radar. Based on in‐the‐field calibration method, this study presents a practical calibration method that combines the external and internal calibration together. Experiments are designed for an X‐band linear antenna array with 16 unit cells, whose period is about half wavelength, and the measured results show that the proposed algorithm is an attractive way to calibrate the digital array radar efficiently.
Single channel pipelined variable‐length FFT processor design
Authors: Wang Jiale , Xie Yizhuang , Yang Chen
Published: October 2019

In this study, a single channel pipelined variable‐length fast Fourier transformation (FFT) processor design is presented. With the development of science and technology, digital signal processing has been widely used in many fields. The most basic algorithm of digital signal processing theory, FFT, is widely used in radar signal processing, remote sensing, image processing, communications and other fields. A high real‐time and high‐throughput FFT processor design method based on the field‐programmable gate array (FPGA) platforms is proposed to meet the needs of the synthetic aperture radar imaging digital signal processing. The authors conducted the ISE synthesis based on the Xilinx FPGA platform using xc6vlx760ff1760‐1 as the target chip and the ModelSim simulation, combined with Matlab, to verify the correctness of this design.