bluuebunny/crossref_metadata_2025 huggingface dataset:
Diagnosis of herpesviruses and approaches to difficult diagnoses
Authors: Basha James , Iwasenko Jenna M , Rawlinson William
Published: April 2020

Herpesviruses are a ubiquitous family of DNA viruses, with 40?60% of the adult population seropositive for cytomegalovirus (CMV), and more than 90% for Epstein-Barr virus (EBV) and varicella zoster virus (VZV). Following primary infection, herpesviruses become latent in the host and may reactivate during periods of immunosuppression, such as in transplant recipients, HIV-positive patients and pregnant women. The clinical course following reactivation presents a screening and diagnostic challenge, particularly as reactivation in immunosuppressed patients may have a clinical presentation consistent with many different infections. For example, CMV pneumonitis produces disease clinically consistent with other viral pneumonias such as influenza infection. It is, therefore, imperative to obtain as relevant and accurate diagnostic information to correctly diagnose herpesvirus infections.
Pitfalls of viral load testing
Authors: Higgins Geoff
Published: April 2020

Viral load testing is the quantitative measurement of viral nucleic acid in body fluids or tissues. In medical practice, viral load assays are commonly performed for HIV, Hepatitis B and Hepatitis C viruses. These assays are funded under the Medicare Benefits Schedule (MBS) system (Item numbers 69378/81/82, 69482/3 and 69488 respectively).
Diagnosis of influenza following the first wave of pandemic (H1N1) 2009 influenza
Authors: Kok Jen , Dwyer Dominic E
Published: April 2020

Aetiological confirmation of respiratory tract infections in individual patients facilitates appropriate antimicrobial use and infection control procedures. From a public health perspective, influenza confirmation allows assessment of community attack rates and the efficacy of vaccination programs, while assisting in modelling for pandemic preparedness planning. Rapid antigen and immunofluorescent antigen tests are relatively insensitive in detecting pandemic (H1N1) 2009 influenza, and influenza subtype-specific nucleic acid amplification tests should be used as the ?gold standard? for diagnosis. Pathogen-specific serological testing aids the retrospective diagnosis of infection. Although some challenges surrounding diagnostic testing during the first pandemic wave have been resolved, others remain; this may test laboratories again in the second and subsequent pandemic waves.
New approaches to enterovirus identification
Authors: Roberts Jason A , Kok Tuckweng , Thorley Bruce R
Published: April 2020

The human enteroviruses (HEVs) are members of the Picornaviridae family and cause a diverse range of diseases from respiratory illness to paralysis. Historically, HEVs were isolated in cell culture and subtype identification was by neutralisation using specific antisera. Currently, diagnostic virology laboratories use nucleic-acid-based tests to detect and identify HEVs in clinical specimens.
Disinfectants in Australia
Authors: Whitley Greg
Published: April 2020

The use of disinfectants can be a controversial topic, particularly in healthcare settings. The TGA has regulated the higher risk products for healthcare applications since 1996, but the impact of this regulatory framework is largely unseen in what has become a relatively condensed and specialised market place. The APVMA regulates disinfectants and sanitisers and supervises critical use through AUSVETPLAN. The use of disinfectants in healthcare is completely user-dependent and the latest literature suggests that understanding the regulatory framework and the vulnerabilities of an intended application will assist in promoting appropriate hygiene standards for surfaces and medical devices (instruments).
Duck hepatitis B virus: a model for assessing the efficacy of disenfectants against human hepatitis B virus infection
Authors: Vickery Karen
Published: April 2020

One of the most important aspects of infection control is the interruption of transmission of infectious organisms to and from patients within the hospital environment. Of particular concern are the blood-borne viruses HIV, hepatitis B virus (HBV) and hepatitis C virus (HCV). Disinfectants play an important role in infection control, but their virucidal efficacy is difficult to measure in vitro because of the high susceptibility of tissue culture systems to damage by chemical agents and the relatively low titres which are achieved in growing many important viruses. Additionally, HBV is almost uncultivable in vitro and fails to infect more common laboratory animals. Therefore, the duck model of HBV infection has been used for testing disinfectant action against HBV.
Endoscopes and biocides
Authors: Natoli Johnathon
Published: April 2020

Biocides are multi-targeted agents designed to kill bacteria, viruses, fungi and other microbes. These microorganisms possess considerable differences in the cellular structures and thus broad responses of different biocides.
Pumping out biocides – cause for concern
Authors: Hassan Karl A , Baltzer Sylvia , Paulsen Ian , Brown Melissa
Published: April 2020

Bacteria employ a number of resistance mechanisms against antimicrobials, commonly including target site modification, antimicrobial degradation and active efflux. Of these mechanisms, efflux is unique in that a single efflux system can confer resistance to a remarkably broad range of structurally dissimilar antibiotics and biocides that have different intracellular targets and modes of action. For example, in the opportunistic pathogens Staphylococcus aureus and Acinetobacter baumannii, single multidrug efflux systems facilitate the extrusion of agents as broad and diverse as quaternary ammonium compounds, intercalating dyes, diamidines, biguanidines, anionic detergents, aminoglycosides, ?-lactams, chloramphenicol, tetracyclines, trimethoprim and fluoroquinolones (Table 1). This promiscuity of substrates, coupled with the genetic linkage of exporter genes with other resistance determinants on transferable elements such as plasmids, raises the possibility of cross and co-resistance to biocides and antibiotics. Furthermore, data generated by our and other research groups clearly demonstrate a remarkable propensity of multidrug efflux systems to bind new substrates following only minor amino acid changes to their active sites.
Tea-tree oil – a naturally occurring biocide
Authors: Thomson Natalie , Hammer Katherine , Riley Thomas
Published: April 2020

Tea-tree oil (TTO) is the essential oil derived from an Australian native plant that has been used for hundreds of years, mainly for its antimicrobial and anti-inflammatory properties. With the advent of ever-increasing resistance to antibiotics and biocides amongst organisms, TTO may play an important role in the health industry in the fight against resistance.
Influenza – our constant companion
Authors: Barr Ian G , Selleck Paul W
Published: April 2020

On 11 June 2009, Dr Margaret Chan, the Director-General of the World Health Organization, announced to the world that following the emergence of a novel influenza A virus in late April 2009 and its extensive spread that, ?I have therefore decided to raise the level of influenza pandemic alert from phase 5 to phase 6. The world is now at the start of the 2009 influenza pandemic.? Dr Chan also commented, ?No previous pandemic has been detected so early or watched so closely, in real-time, right at the very beginning. The world can now reap the benefits of investments, over the last five years, in pandemic preparedness.? Also observed was that, ?Globally, we have good reason to believe that this pandemic, at least in its early days, will be of moderate severity?.
Laboratory diagnosis of influenza and the impact of the pandemic (H1N1) 2009 virus
Authors: Kok Jen , Smith David W , Dwyer Dominic E
Published: April 2020

Aetiological confirmation of respiratory tract infections in patients facilitates appropriate antimicrobial use and infection control procedures. From a public health perspective, the laboratory confirmation of influenza allows assessment of circulating viruses, community attack rates and the efficacy of vaccination programs, while assisting modelling as part of pandemic preparedness planning. Rapid antigen and immunofluorescent antigen tests are relatively insensitive in detecting pandemic (H1N1) 2009 influenza compared to seasonal subtypes, and influenza subtype-specific nucleic acid amplification tests should be used as the ?gold-standard? for diagnosis. Pathogen-specific serological testing aids the retrospective diagnosis of infection, and is used in seroprevalence studies. Influenza virus isolation is needed for vaccine assessment and formulation. Although some challenges surrounding diagnostic testing during pandemic (H1N1) 2009 have been resolved, others remain; this may test laboratories again in future pandemics.
H1N1 2009 pandemic influenza in Indigenous Australians
Authors: Markey Peter , Su Jiunn-Yih , Wattiaux Andre , Trauer James , Krause Vicki
Published: April 2020

Given the known prevalence of chronic disease in the Australian Indigenous population, and the known risk factors for severe disease from influenza infection, it is not surprising that Indigenous Australians carried a higher burden of disease during the influenza pandemic of 2009. However, other determinants apart from comorbidities might also have affected influenza morbidity in Indigenous Australia. Factors such as overcrowding, sanitation infrastructure, remoteness, access to health care and availability of the specific hardware of the pandemic (such as personal protective equipment ? PPE? and antivirals) may also have been risk factors for poor outcomes at the population level. This article summarises the impact of the 2009 influenza pandemic on Australia?s Indigenous population, with particular emphasis on those living remotely in the Northern Territory (NT).
Reflections on the 2007 equine influenza outbreak
Authors: Kirkland Peter D
Published: April 2020

In late August 2007, Australia experienced its largest animal disease emergency with an outbreak of equine influenza (EI). This followed the importation of one or more infected horses and the entry of the virus into the Australian horse population. There are a number of aspects of this event that are not only applicable to the diagnosis and control of other high-consequence animal diseases but there are also many elements of interest and relevance to public health. In particular, there were interesting insights into the speed and manner of virus dissemination in a naive population. The benefits and capacity of real-time PCR and associated technology to support an emergency disease investigation and response were demonstrated, while the value of using a combination of a ?marker? vaccine and serological test that would differentiate between infected and vaccinated animals was clearly proven. Ultimately, the virus was eradicated following an outbreak on a scale and in a time frame not previously achieved in any other country.
Taxonomic subcommittees and minimal standards for the description of prokaryotes
Authors: Trujillo Martha E
Published: April 2020

The preparation of minimal standards for the description of new taxa is one of the tasks of the taxonomic subcommittees working under the auspice of the International Committee on Systematics of Prokaryotes. Minimal standards are intended to provide bacteriologists involved in the taxonomy of prokaryotes a set of essential requirements for the description of new taxa.
Microbial diversity beyond E. coli: new microbial worlds, new concepts in biology
Authors: Fuerst John A
Published: April 2020

Microbial diversity explores the universe of microorganisms beyond classical models such as Escherichia coli, influenza virus, or Saccharomyces cerevisiae. Exploring such new microbial worlds is essential for a microbiology which needs to learn about all the scientific and practical possibilities offered by billions of years of microbial evolution. Here we illustrate some examples of how studying a wide range of microbial diversity can assist microbiology as a fundamental and a practical science.
Pathogen discovery in infectious disease investigation
Authors: Wang Lin-Fa
Published: April 2020

Pathogen discovery is and always has been an integral part of our fight against infectious diseases. However, as technology continues to develop, enabling the identification of an increasing number of previously unknown agents, this process of discovery and characterisation of pathogenic agents is becoming even more important. From novel diagnostics to vaccines and therapeutics, pathogenic discovery plays a key role in shaping the overall control and prevention strategy. Due to the nature of the author?s work area, the focus of this brief review will be on viral pathogens. The tools and strategies presented should be largely applicable to other types of pathogens.
The future of mucosal HIV vaccines
Authors: Reece Jeanette , Kent Stephen
Published: April 2020

Approximately 33 million people live with the human immunodeficiency virus (HIV) and 2.6 million new infections are acquired each yea1. The development of an effective HIV vaccine that induces robust mucosal immunity represents a major global public health challenge. Large human efficacy trials of simple antibody-based and cytotoxic T cell-based vaccines have failed to provide any protection. The recent RV144 HIV vaccine efficacy trial in Thailand using a prime-boost combination of vaccines, however, showed modest efficacy (31%, p=0.04 on the primary analysis). Although the efficacy was marginal, the study has provided considerable hope that a vaccine to prevent infection by HIV may be feasible.
From omics to systems biology: towards a more complete description and understanding of biology
Authors: Chambers Paul
Published: April 2020

Technology sets limits on what can be achieved in research. The advent of genetic engineering accompanied by the development of monoclonal antibody technology in the 1970s heralded the birth of modern ?molecular biology?. This revolutionised the way we approach research in the biological sciences by allowing access to cellular structures and processes that were in the realm of science fiction a decade earlier. The invention of the PCR in the 1980s built on this, making cloning easier and a great deal more rapid; with PCR we no longer required a host and vector to amplify DNA and isolate targeted DNA sequences.
Probing connectivity between transcriptional and post-transcriptional gene networks
Authors: Boyd Sarah E , Keith Johnathon M , Traven Ana , Beilharz Traude
Published: April 2020

The foundation for much of our current understanding of eukaryotic cell biology stems from studies exploiting the combined power of this yeast?s genetic tractability and its simple growth requirements. Furthermore, access to an early complete genome in 1996 allowed yeast researchers to spearhead the move toward genome-wide studies that underpin our thinking about systems-level biology today. Indeed, the last decade has been so rich in these studies that it has become close to impossible for most biologists to interrogate the data in an unbiased fashion. The challenge for the next decade is to generate the informational tools to sort the multidimensional datasets for underlying networks.
How pathogens attack plants
Authors: Keane Philip
Published: April 2020

Plants are well protected against microbial invasion by an epidermis of tightly packed cells with rigid, cellulose-strengthened walls covered by a waxy cuticle on the aerial parts. A great diversity of bacteria and fungi come in contact with plants but most never invade. However, some microbes of all types are highly adapted as invasive parasites of particular plant species, often causing disease, and these are reviewed here.
How the misidentification of a pathogen can cause an emergency response – a real life case study of an Australian grain export incident
Authors: Wright Dominie
Published: April 2020

In February 2004, a shipment of Australian wheat was rejected by an importing country that alleged the grain contained ustilospores of Tilletia indica. This allegation caused all wheat trading and shipments from Australia to be stopped. At this time, Australian wheat was worth A$4 billion and provided 14% of the world's export demand. How did this misidentification occur? And why is correct identification of pathogens so important when trading with other countries?
Cryptic fungal species unmasked
Authors: Shivas Roger G , Cai Lei
Published: April 2020

The word cryptic is derived from the Greek adjective krupt�s which means hidden. Morphologically indistinguishable species that have been revealed by molecular phylogenetic methods, and 37ultimately only recognised by their DNA sequences, are referred to as cryptic species. The importance of cryptic species for plant pathologists is that they may have significant differences in the severity of diseases they cause, host range and geographic distribution. It is these differences that are of concern to many biosecurity agencies, particularly in Australia.
Can we use crime scene investigation methods in plant pathology?
Authors: Wright Dominie , You Mingpei
Published: April 2020

Picture this ... crime scene investigators walk into a room, using forensic tape on the victim's clothing and personal belongings. This evidence is bagged and transported to a laboratory for processing. Chain of evidence is kept at all times, and all steps used in the processing are documented. Can we find the perpetrator of this horrendous crime? Can we prevent further damage? On TV, crime scene investigation (CSI) machinations are now a common theme, and inevitably there is a machine that goes ?ping? saying that the results are ready. But is it applicable to the world of plant pathology? And why would we do this?
Aetiological importance of viruses causing acute gastroenteritis in humans
Authors: Higgins Geoffrey , Schepetiuk Sonia , Ratcliff Rod
Published: April 2020

Acute gastroenteritis (AGE) is a common illness affecting all age groups worldwide causing 2.2 million deaths annually. Viruses including rotaviruses, noroviruses, enteric adenoviruses and astroviruses are the major cause of AGE, with rotavirus causing the majority of severe illness. Advances in molecular techniques have led to the identification of many more viruses in faeces. Proving an association with AGE will require prospective controlled trials which so far are few in number.
Viral enteritis in domestic animals
Authors: Bailey Kirsten E , Browning Glen F
Published: April 2020

Viral enteritis is a major cause of morbidity and mortality in neonatal domestic animals, but the most significant pathogens responsible vary considerably between animal species. The viral pathogens currently recognised as significant concerns in animal health were all identified over 20 years ago, and there has been limited recent investigation of the aetiology of viral enteritis in domestic animals using newer pathogen discovery techniques. While effective vaccines are available to control some of these enteric pathogens in some animal species, comprehensive and specific control measures for viral enteritis are lacking in most domestic species. Further research is needed to identify all the major viral pathogens responsible and to develop vaccines to facilitate more effective control.
Human gut microbiota and future prebiotics
Authors: Conlon Michael , Bird Anthony , Christohersen Claus
Published: April 2020

Rapid advances in molecular methods that enable culture-independent analysis of the complex bacterial populations is increasing awareness and understanding of the composition and activity of the microbiota in the human gastrointestinal tract, its role in host health and response to changes in diet and lifestyle. In this article we discuss the shortcomings of the contemporary approach of targeting a few selected bacteria, notably lactobacilli and bifidobacteria, to gauge the status of the gut microbiota for promoting health of the human host.
Hydatid disease - still a global problem
Authors: Lightowlers Marshall , Jenkins David
Published: April 2020

Hydatid disease (cystic echinococcosis) remains highly prevalent and a serious cause of human morbidity and mortality in many parts of the world. While there are some regions where the disease has been controlled, most efforts to control transmission of the parasite have had limited success. Recent genetic data indicates that Echinococcus granulosus, which was formally thought to be a single species, comprises a number of distinct species. The vast majority of human infections are caused by the most common genotype which is generally transmitted by sheep and goats. Renewed hope for effective control of the parasite’s transmission has followed the development of the EG95 vaccine that can be used to reduce infection levels in livestock animals thereby reducing the reliance of control measures on interventions in dogs.
Vertical Transmission
Authors: Iredell Jonathan
Published: April 2020

Constitutional reform was on the agenda again at the Annual General Meeting in Canberra, as it will be for the next several AGMs I think, as there is clear recognition from the membership that the Society is facing change. The roles of the Divisional chairs and State chairs and the nature of the general meeting were discussed in the light of overall structure. The Council is the principal decision-making body but because the Council only meets twice-yearly, interactions inside the Executive form the operational and strategic engine of ASM. The current Executive includes the incumbent President, with either the incoming (President-Elect) or outgoing (Immediate Past President), the Vice-President Scientific Affairs, Vice-President Corporate Affairs and Vice-President Communications. The Chair roles have long been tasked with national leadership but without a role in Executive they have been preoccupied almost exclusively with the national meeting and speak only at the National Scientific Advisory Committee, which has an enormous operational role managing the bulk of the scientific awards and meetings. The recent move of the Division Chairs into Council as invitees over the last year or two has worked well and the increased involvement of State Chairs similarly. We will be now ratifying these arrangements by seeking formal endorsement at an extraordinary general meeting of the membership to bring the Constitution into line with these arrangements.
Congenital cytomegalovirus: the invisible problem
Authors: Rawlinson Bill
Published: April 2020

It is a great pleasure mixed with some sadness to write this editorial. The entire November issue is around the subject of congenital infection, with the focus on the most common, serious cause of congenital malformation in Australia – congenital cytomegalovirus. Infection with cytomegalovirus (CMV) causes serious disease in children globally, resulting in congenital infections present in ~2000 Australian newborns every year, of whom most are asymptomatic, with ~450 per annum (pa) affected by hearing loss, mental disability and other illnesses. Some of the key clinical features of congenital infection are outlined here in articles by Wendy van Zuylen, Klaus Hamprecht and Robert George, and the pathogenetic features in Lenore Pereira’s paper. Treatment and vaccination are moving ahead (as discussed in papers from some key Italian groups), although not fast enough for many of us – as parents of children with CMV discuss in two papers here. We also include papers on other causes of congenital infection that are much less common than congenital CMV in Australia. Although these are not related to congenital CMV clinically, with very different medical and epidemiological settings, it is important to put congenital CMV in context, as well as to draw attention to other important causes of congenital infection.
From the Editorial Team
Authors: Macreadie Jo , Macreadie Ian , Macreadie Hayley
Published: April 2020

Welcome to the first issue of Microbiology Australia for 2016.
Vertical Transmission
Authors: Robins-Browne Roy
Published: April 2020

As this is my first communication with you as your new president, I should start by thanking ASM’s Council, and especially the Executive Committee, for honouring me in this way and for putting their faith in me. I must also thank Jon Iredell for the wonderful job he did as ASM President for the past two years, and for the amazing support and guidance he has given me to date (and hopefully in future).
Vertical Transmission
Authors: Robins-Browne Roy
Published: April 2020

When I, a fresh young medical graduate, announced my decision to specialise in pathology my senior colleagues were impressed, because pathology is a 9-to-5 job that pays well. However, when I added that I was planning to sub-specialise in microbiology, they questioned my sanity. Didn’t I know that infectious diseases had been conquered by the twin forces of immunisation and antimicrobials?
A spotlight on Bluetongue virus?
Authors: Stewart Meredith
Published: April 2020

In the late 1990s, there were rumblings that Bluetongue virus (BTV) was on the move. The 2006 summer outbreak changed the way that the European economic and scientific communities viewed its importance. It shifted from being a neglected disease confined to the tropical regions of the world to a potentially important threat to agriculture. Suddenly, BTV was sharing research priorities and the limelight with other important viruses of animals such as foot-and-mouth disease virus and avian influenza virus.
The Great Pox
Authors: Bowater Laura
Published: April 2020

The 3rd of August 1492 marked the start of one of the most significant periods of global exploration, travel and migration. Setting sail from Palos on the Portuguese coast, Christopher Columbus, sponsored by King Ferdinand and Queen Isabella of Spain, headed westward bound for the Canary Islands. From the Canaries, Columbus continued his voyage. Thirty-five days after setting sail, he reached the Bahamas. His first landing point, on a small island, known as San Salvador, was used by Columbus as a base to explore and map the islands of this New World, before he and his crew returned to Spain in the spring of 1493.
The voyages of Zika virus
Authors: Gatherer Derek
Published: April 2020

The announcement in May this year from the World Health Organization, that the Zika virus outbreak that began in October 2015 in the Cape Verde Islands off the west coast of Africa was an American variant of Zika virus, confirmed that Zika has now circumnavigated the world.
Alison Vickery and the typing of staphylococci in Australia
Authors: Benn Richard
Published: April 2020

Alison Vickery, who died in December 2016, played an important role in the bacteriophage typing of Staphylococcus aureus in this
country. The technique was introduced by Phyllis Rountree in the 1950s at Royal Prince Alfred Hospital, where it was initially used to identify a particularly virulent strain of S. aureus (phage type 80/81) in the neonatal nursery.
Vertical Transmission
Authors: Robins-Browne Roy
Published: April 2020

One of our key committees is the National Examinations and Qualifications Board (NEQB), whose role is to oversee the awarding of MASM and FASM. Membership of the NEQB has undergone a number of changes recently. These involved Peter Timms, who stepped down as Chair after a lengthy period of outstanding service. Peter's replacement is Julian Rood, a former president of ASM, who has returned to assist us once more. Another major change is the impending retirement of the Registrar, Tuckweng Kok, who will be replaced by Gary Lum (Registrar) and Kate Sieb (Assistant Registrar). The fact we need two people to replace Tuckweng speaks volumes about his contribution. The three new members of the Board are Melissa Brown, Louise Hafner and Gilda Tachedjian.
Application of bacteriophages
Authors: Aminov Rustam , Caplin Jonathan , Chanishvili Nina , Coffey Aidan , Cooper Ian , De Vos Daniel , Doškař Jiřrí , Friman Ville-Petri , Kurtböke İpek , Pantucek Roman , Pirnay Jean-Paul , Resch Grégory , Rohde Christine , Sybesma Wilbert , Wittmann Johannes
Published: April 2020

The emergence of antibiotic-resistant bacteria and decrease in the discovery rate of novel antibiotics takes mankind back to the ‘pre-antibiotic era' and search for alternative treatments. Bacteriophages have been one of promising alternative agents which can be utilised for medicinal and biological control purposes in agriculture and related fields. The idea to treat bacterial infections with phages came out of the pioneering work of Félix d‘Hérelle but this was overshadowed by the success of antibiotics. Recent renewed interest in phage therapy is dictated by its advantages most importantly by their specificity against the bacterial targets. This prevents complications such as antibiotic-induced dysbiosis and secondary infections. This article is compiled by the participants of the Expert Round Table conference ‘Bacteriophages as tools for therapy, prophylaxis and diagnostics' (19–21 October 2015) at the Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia. The first paper from the Round Table was published in the Biotechnology Journal1. This In Focus article expands from this paper and includes recent developments reported since then by the Expert Round Table participants, including the implementation of the Nagoya Protocol for the applications of bacteriophages.
Vertical Transmission
Authors: Robins-Browne Roy
Published: April 2020

ASM aims to give our members maximum value for their membership. Some new initiatives for 2018 include an annual teacher’s travel award, valued at $4000, to attend the American Society for Microbiology Conference for Undergraduate Educators (AMSCUE), which is the world’s premier microbiology teachers’ conference. We also have instituted 100 travel awards, each valued at $200, to make it easier for members within 10 years of attaining their highest qualification to attend our Annual Scientific Meeting.
Extrinsic allergic alveolitis-causing actinomycetes in indoor and farm environments
Authors: Brinkmann Candice , Kurtböke Ipek
Published: April 2020

Suspended airborne particles, of biological origin, can constitute bioaerosols1,2 and they can be of different origin ranging from farm environments dealing with hay, sugar cane, tobacco, mushroom and cotton to refuse disposal sites to military equipment test chambers. These bioaerosols might carry allergenic and pathogenic agents like viruses, spore forming bacteria and fungi, excreta of insects and mites, moss and fern spores, algal and plant cells; enzymes, antibiotics, endotoxins, mycotoxins and fungal glucans1. Although infections from pathogenic viruses, bacteria and fungi may occur in these work environments the commonly reported symptoms relate to allergic rhinitis and asthma, allergic alveolitis (granulomatons pneumonitis) or organic dust toxic syndrome (inhalation fever or toxic pneumonitis)1,2. This article will only provide an overview on the non-infectious lung diseases resulting from long-term exposure to the spores of thermoactinomycetes of the order Bacillales and thermophilic actinomycetes of the order Actinomycetales in indoor and farm environments.
Vertical Transmission from Russia
Authors: Bonch-Osmolovskaya Elizaveta
Published: April 2020

The Russian Microbiological Society has had a long and complicated history, reflecting the recent history of our country. It was established in 1957, in the Soviet Union, as the All-Union Microbiological Society and in the mid-80s comprised more than 5000 members. Several distinguished Russian microbiologists were its Presidents: the last one was Professor Elena Kondrat'eva, famous for her investigations of bacterial photosynthesis. However, the Society did not survive all the changes of the 90s, and, in spite of an attempt to revive it in 1992, did not exist until 2003.
Zoonoses
Authors: Mackenzie John S , Williams David
Published: April 2020

The selection of papers included in this issue of Microbiology Australia present a broad brush of zoonotic diseases, from those known or described in ancient times such as rabies, first described in the Eshnunna cuneiform law tablets from ancient Mesopotamia dating back to the 18th–19th centuries BC, and glanders, thought to be first described in donkeys by Aristotle in Ancient Greece in 420–450 BC and subsequently by the Romans, to some discovered or recognised as zoonotic within the past 30 years, such as the recently described zoonotic bat-borne pathogens in Australia, and Clostridium difficile, only recently recognised as a zoonotic pathogen. The selection of papers also demonstrates the wide range of zoonotic origins, including arthropod-borne viruses and potentially seafood-borne parasites.
A systemic functional study of modal verbs in the Chinese clause
Authors: Yang Shu
Published: April 2020

Previous studies of Chinese modal verbs in the traditional framework (e.g.Lu 2004;Peng 2007;Tang 2000;Tiee 1985;Tsang 1981;Xie 2002;Xu 2007) have mainly focused on the description of semantic and syntactic features of modals that occur in the middle of the clause and attached little significance to the functions that modal verbs serve when they appear at different positions in the clause. Similarly, in a systemic functional framework, modal verbs in the middle of the clause receive the most attention. Their interpersonal functions are thoroughly explored; however, their textual functions are seldom discussed as they are believed to mainly appear in the middle of the clause buried in the Rheme rather than at the beginning or at the end of the clause. This paper examines the functions that modal verbs serve when they occur in different places in the clause from the perspective of systemic functional grammar. It argues that modal verbs are functionally motivated and the position of the modal verbs in the clause expresses particular meanings. When situated medially in the clause, modal verbs function as the Modality in the interpersonal structure of the clause, and as part of the Rheme in the thematic structure of the clause, marking the transition between Theme and Rheme. When occurring at the beginning or in the middle of the clause before a nominal group, some modal verbs of obligation serve as focus markers and identify the subsequent nominal group as the marked information focus of the clause. In the thematic structure of the clause, clause-initial modal verbs of obligation and probability function as interpersonal Themes to foreground the speaker’s modal assessment. Finally, when placed at the end of the clause, modal verbs serve either as the Predicator or Modality in the interpersonal structure of the clause and as the unmarked information focus of the clause.
Large eddy simulations of a triangular jet and its counterpart through a chamber*
Authors: Xiao Xiu , Wang Guo-Chang , Xu Min-Yi , Mi Jian-Chun
Published: April 2020

A free triangular jet (TJ1) and its counterpart initially passing a short circular chamber (TJ2) are numerically modeled using large eddy simulation (LES). This paper compares the near-field characteristics of the two jets in detail. To enable some necessary experimental validations, the LES conditions of TJ1 and TJ2 are taken to be identical to those measured by Xu et al. (Sci. China Phys.
56 1176 (2013)) and England et al. (Exp. Fluids.
48 69 (2010)), respectively. The LES predictions are found to agree well with those measurements. It is demonstrated that a strong swirl occurs near the chamber inlet plane for the TJ2 flow. At the center of the swirl, there is a cluster of three sink foci, where each focus is aligned midway between the original triangular apexes. In the vortex skeleton constructed from the time-averaged flow field, the vortices arising from the foci are helically twisted around the core of the jet. As the flow passes through the chamber, the foci merge to form a closed-loop “bifurcation line”, which separates the inward swirling flow and the outward oscillating jet. This global oscillation is regarded as a source node near the centerline of the chamber. If the chamber is removed for a “free” jet, i.e., TJ1, a cluster of three pairs of counter-rotating foci is produced and the net swirl circulation is zero, so the overall oscillation of the jet does not occur.
A novel class of two-dimensional chaotic maps with infinitely many coexisting attractors*
Authors: Zhang Li-Ping , Liu Yang , Wei Zhou-Chao , Jiang Hai-Bo , Bi Qin-Sheng
Published: April 2020

We study a novel class of two-dimensional maps with infinitely many coexisting attractors. Firstly, the mathematical model of these maps is formulated by introducing a sinusoidal function. The existence and the stability of the fixed points in the model are studied indicating that they are infinitely many and all unstable. In particular, a computer searching program is employed to explore the chaotic attractors in these maps, and a simple map is exemplified to show their complex dynamics. Interestingly, this map contains infinitely many coexisting attractors which has been rarely reported in the literature. Further studies on these coexisting attractors are carried out by investigating their time histories, phase trajectories, basins of attraction, Lyapunov exponents spectrum, and Lyapunov (Kaplan–Yorke) dimension. Bifurcation analysis reveals that the map has periodic and chaotic solutions, and more importantly, exhibits extreme multi-stability.
Effect of Sn and Al additions on the microstructure and mechanical properties of amorphous Ti–Cu–Zr–Ni alloys*
Authors: Chen Fu-Chuan , Dai Fu-Ping , Yang Xiao-Yi , Ruan Ying , Wei Bing-Bo
Published: April 2020

Amorphous Ti–Cu–Zr–Ni alloys with minor addition of Sn and Al were prepared by melt spinning technique. The effects of Sn and Al additions on the microstructures and mechanical properties of glassy ribbons were investigated. The amorphous state of ribbons was confirmed by x-ray diffraction and transmission electron microscopy, where those ribbons with Sn addition exhibited a fully amorphous state. The characteristic temperature indicates that Ti45Cu35Zr10Ni5Sn5 alloy has a stronger glass-forming ability, as proven by differential scanning calorimetry. Ti45Cu35Zr10Ni5Al5 alloy showed a better hardness of 9.23 GPa and elastic modulus of 127.15 GPa and good wear resistance. Ti45Cu35Zr10Ni5Sn5 alloy displayed a pop-in event related to discrete plasticity according to nanoindentation. When the temperature is below 560 K, Ti45Cu35Zr10Ni5Sn5 alloy mainly exhibits elasticity. When the temperature rises between 717 K and 743 K, it shows a significant increase in elasticity but decrease in viscoelasticity after the ribbon experiences the main relaxation at 717 K. When the temperature is above 743 K, the ribbon shows viscoplasticity.
Optical spin-to-orbital angular momentum conversion in structured optical fields*
Authors: Zhao Yang , Yang Cheng-Xi , Zhu Jia-Xi , Lin Feng , Fang Zhe-Yu , Zhu Xing
Published: April 2020

We investigate the dynamic quantities: momentum, spin and orbital angular momenta (SAM and OAM), and their conversion relationship in the structured optical fields at subwavelength scales, where the spin–orbit interaction (SOI) plays a key role and determines the behaviors of light. Specifically, we examine a nanostructure of a Ag nanoparticle (Ag NP) attached on a cylindrical Ag nanowire (Ag NW) under illumination of elliptically polarized light. These dynamic quantities obey the Noether theorem, i.e., for the Ag nanoparticle with spherical symmetry, the total angular momentum consisting of SAM and OAM conserves; for the Ag NW with translational symmetry, the orbital momentum conserves. Meanwhile, the spin-to-orbital angular momentum conversion is mediated by SOI arising from the spatial variation of the optical potential. In this nanostructure, the conservation of momentum imposes a strict restriction on the propagation direction of the surface plasmon polaritons along the Ag NW. Meanwhile, the orbital momentum is determined by the polarized properties of the excitation light and the topography of the Ag NP. Our work offers insights to comprehend the light behaviors in the structured optical fields in terms of the dynamic quantities and benefits to the design of optical nano-devices based on interactions between spin and orbital degrees of freedom.
Solid angle car following model*
Authors: Ma Dongfang , Han Yueyi , Jin Sheng
Published: April 2020

Existing traffic flow models give little consideration on vehicle sizes. We introduce the solid angle into car-following theory, taking the driver’s perception of the leading vehicle’s size into account. The solid angle and its change rate are applied as inputs to the novel model. A nonlinear stability analysis is performed to analyze the asymmetry of the model and the size effect of the leading vehicle, and the modified Korteweg–de Vries equation is derived. The solid angle model can explain complex traffic characteristics and provide an important basis for modeling nonlinear traffic phenomena.
Physics needs nothing less than a Renaissance – On the relation between physics and philosophy
Authors: Wang Ling Jun
Published: April 2020

In this article, the fundamental inconsistencies of the mainstream theoretical physics has been analyzed in detail. It has been shown that relativity and quantum field theory have an array of fundamental problems in postulations, methodology, theory, experimental verification and philosophy. The modern theoretical physics represented by relativity and the standard model of particle physics has come to a dead end. To get out of the impasse, physics community must give up the theological pursuit of a theory of everything, return to scientific philosophy, logic, methodology and scientific mission. Physics needs nothing less than a renaissance.
Is the Paris Agreement effective? A systematic map of the evidence
Authors: Raiser Kilian , Kornek Ulrike , Flachsland Christian , Lamb William F
Published: April 2020

The Paris Agreement (PA) sets out to strengthen the global response to climate change, setting targets for mitigation, adaptation, and finance, and establishing mechanisms through which to achieve these targets. The effectiveness of the PA’s mechanisms in achieving its targets, however, has been questioned. This review systematically maps the peer-reviewed literature on the PA, categorizing the available evidence on whether or not the ‘Paris Regime’ can be effective. We split our analysis into three methodologically distinct sections: first we categorize the literature according to the mechanisms being studied. We find a diverse body of literature, albeit with a clear focus on mitigation, and identify adaptation and capacity building to be clear gaps. Second, we carry out a content analysis, identifying common drivers of, barriers to, and recommendations for effectiveness. Here we find mixed evidence, with potential drivers often qualified by more concrete barriers. Thirdly, we use scientometrics to identify six research clusters. These cover loss and damage, finance, legal issues, international politics, experimental evidence, and studies on tracking progress on the PA’s targets. We conclude with a narrative discussion of our findings, presenting three central themes. First, transparency is widely considered a precondition for the PA to be institutionally effective. However, a lack of clear reporting standards and comparable information renders the PA’s transparency provisions ineffective. Second, environmental effectiveness relies on national ambition, of which there is currently too little. It remains unclear to which extent the Paris Regime structure itself can induce significant ratcheting-up of ambition. Finally, the PA facilitates the diffusion of norms, enables learning and the sharing of best practices. This production of shared norms provides the most promising avenue for overcoming the current lack of ambition. One of the primary successes of the PA is in providing a platform for the exchange of experiences and ideas.
Silicon-based multimode waveguide crossings
Authors: Chang Weijie , Zhang Minming
Published: April 2020

Mode multiplexing technique is a new promising option to increase the transmission capacity of on-chip optical interconnects. Multimode waveguide crossings are the key building blocks in high-density and large-scale mode division multiplexing silicon photonic integrated circuits. In this paper, we review the recent progresses on silicon-based multimode waveguide crossings. Firstly, a variety of multimode waveguide crossing schemes are demonstrated and introduced including conventional multimode interference coupler, Maxwell’s fisheye lens and inverse-designed multimode interference coupler. Secondly, we also discuss some emerging applications of the inverse design algorithm in the multimode silicon devices to realize ultracompact footprint and multiple functionalities. Finally, we also give the outlook of the development prospects of on-chip multimode waveguide crossings.
Propagation-assisted generation of intense few-femtosecond high-harmonic pulses
Authors: Major B , Kretschmar M , Ghafur O , Hoffmann A , Kovács K , Varjú K , Senfftleben B , Tümmler J , Will I , Nagy T , Rupp D , Vrakking M J J , Tosa V , Schütte B
Published: April 2020

The ongoing development of intense high-harmonic generation (HHG) sources has recently enabled highly non-linear ionization of atoms by the absorption of at least 10 extreme-ultraviolet (XUV) photons within a single atom (Senfftleben et al, arXiv:1911.01375). Here we investigate how the generation of these very intense HHG pulses in our 18-m-long beamline is aided by the reshaping of the fundamental, few-cycle, near-infrared (NIR) driving laser within a 30-cm-long HHG Xe medium. Using an incident NIR intensity that is higher than what is required for phase-matched HHG, signatures of reshaping are found by measuring the NIR blueshift and the fluorescence from the HHG medium along the propagation axis. These results are well reproduced by numerical calculations that show temporal compression of the NIR pulses in the HHG medium. The simulations predict that after refocusing an XUV beam waist radius of 320 nm and a clean attosecond pulse train can be obtained in the focal plane, with an estimated XUV peak intensity of 9 × 1015 W cm−2. Our results show that XUV intensities that were previously only available at large-scale facilities can now be obtained using moderately powerful table-top light sources.
Experimental behaviour of a three-stage metal hydride hydrogen compressor
Authors: Galvis E A R , Leardini F , Ares J R , Cuevas F , Fernandez J F
Published: April 2020

A three-stage metal hydride hydrogen compressor (MHHC) system based in AB2-type alloys has been set-up. Every stage can be considered as a Sieverts-type apparatus. The MHHC system can work in the pressure and temperature ranges comprised from vacuum to 250 bar and from RT to 200 °C, respectively. An efficient thermal management system was set up for the operational ranges of temperature desired. It drops temperature shifts due to hydrogen expansion during stage coupling and hydrogen absorption/desorption in the alloys. Each reactor consists of a single and thin stainless-steel tube to maximize heat transfer. These were filled with similar amount of AB2 alloy. The MHHC system was able to produce a compression ratio as high as 84.7 for inlet and outlet hydrogen pressures of 1.44 and 122 bar for a temperature span of 23 °C – 120 °C.