bluuebunny/crossref_metadata_2025 huggingface dataset:
Purification and Characterization of an Extracellular Protease from the Fish Pathogen
Yersinia ruckeri
and Effect of Culture Conditions on Production
Authors: Secades P. , Guijarro J. A.
Published: December 2019

A novel protease, hydrolyzing azocasein, was identified, purified, and characterized from the culture supernatant of the fish pathogen
Yersinia ruckeri
. Exoprotease production was detected at the end of the exponential growth phase and was temperature dependent. Activity was detected in peptone but not in Casamino Acid medium. Its synthesis appeared to be under catabolite repression and ammonium control. The protease was purified in a simple two-step procedure involving ammonium sulfate precipitation and ion-exchange chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the purified protein indicated an estimated molecular mass of 47 kDa. The protease had characteristics of a cold-adapted protein, i.e., it was more active in the range of 25 to 42°C and had an optimum activity at 37°C. The activation energy for the hydrolysis of azocasein was determined to be 15.53 kcal/mol, and the enzyme showed a rapid decrease in activity at 42°C. The enzyme had an optimum pH of around 8. Characterization of the protease showed that it required certain cations such as Mg
2+
or Ca
2+
for maximal activity and was inhibited by EDTA, 1,10-phenanthroline, and EGTA but not by phenylmethylsulfonyl fluoride. Two
N
-methyl-
N
-nitro-
N
-nitrosoguanidine mutants were isolated and analyzed; one did not show caseinolytic activity and lacked the 47-kDa protein, while the other was hyperproteolytic and produced increased amounts of the 47-kDa protein. Azocasein activity, SDS-PAGE, immunoblotting by using polyclonal anti-47-kDa-protease serum, and zymogram analyses showed that protease activity was present in 8 of 14 strains tested and that two
Y. ruckeri
groups could be established based on the presence or absence of the 47-kDa protease.
Molecular Standardization of Mating Type Terminology in the
Gibberella fujikuroi
Species Complex
Authors: Kerényi Z. , Zeller K. , Hornok L. , Leslie J. F.
Published: December 2019

Mating type in the
Gibberella fujikuroi
species complex is controlled by a single locus with two alleles and is usually identified following sexual crosses with standard, female-fertile tester isolates. The mating type alleles have been arbitrarily designated “+” and “−” within each biological species, and the nomenclature is tied to the standard tester strains. We developed a pair of PCR primers that can be used to amplify a unique fragment of one of the mating type alleles (
MAT-2
) from at least seven of the biological species in this species complex. Based on the amplification pattern, we propose a replacement for the existing, arbitrary +/− terminology that is presently in use. The new terminology is based on DNA sequence similarities between the mating type allele fragments from the biological species of the
G. fujikuroi
species complex and the corresponding fragments from other filamentous ascomycetes.
Use of Molecular and Isotopic Techniques To Monitor the Response of Autotrophic Ammonia-Oxidizing Populations of the β Subdivision of the Class
Proteobacteria
in Arable Soils to Nitrogen Fertilizer
Authors: Mendum T. A. , Sockett R. E. , Hirsch P. R.
Published: December 2019

This study examined the effects of NH
4
NO
3
fertilizer on the size and activity of nitrifying, autotrophic, ammonia-oxidizing populations of the β subdivision of the class
Proteobacteria
in arable soils. Plots under different long-term fertilizer regimes were sampled before and after NH
4
NO
3
additions, and the rates of nitrification were determined by
15
N isotopic pool dilution assays. Ammonia-oxidizing populations in the plots were quantified by competitive PCR assays based on the
amoA
and ribosomal 16S genes. Prior to fertilizer addition, ammonium concentrations and nitrification rates in the plots were comparatively low; ammonia-oxidizing populations were present at 10
4
to 10
5
gene copies g of soil
−1
. Three days after the application of fertilizer, nitrification rates had risen considerably but the size of the ammonia-oxidizing population was unchanged. Six weeks after fertilizer treatment, ammonium concentrations and nitrification rates had fallen while the ammonia-oxidizing populations in plots receiving fertilizer had increased. The rapidity of the rise in nitrification rates observed after 3 days suggests that it results from phenotypic changes in the ammonia-oxidizing bacterial population. Associated increases in population sizes were only observed after 6 weeks and did not correlate directly with nitrifying activity. Phylogenetic analyses of PCR products from one of the plots revealed a population dominated by
Nitrosospira
-type organisms, similar to those prevalent in other soils.
Ti Plasmids from
Agrobacterium
Characterize Rootstock Clones That Initiated a Spread of Crown Gall Disease in Mediterranean Countries
Authors: Pionnat Sandrine , Keller Harald , Héricher Delphine , Bettachini Andrée , Dessaux Yves , Nesme Xavier , Poncet Christine
Published: December 2019

Crown gall caused by
Agrobacterium
is one of the predominant diseases encountered in rose cultures. However, our current knowledge of the bacterial strains that invade rose plants and the way in which they spread is limited. Here, we describe the integrated physiological and molecular analyses of 30
Agrobacterium
isolates obtained from crown gall tumors and of several reference strains. Characterization was based on the determination of the biovar, analysis of 16S ribosomal DNA restriction fragment length polymorphisms by PCR (PCR-RFLP), elucidation of the opine type, and PCR-RFLP analysis of genes involved in virulence and oncogenesis. This study led to the classification of rose isolates into seven groups with common chromosome characteristics and seven groups with common Ti plasmid characteristics. Altogether, the rose isolates formed 14 independent groups, with no specific association of plasmid- and chromosome-encoded traits. The predominant Ti plasmid characteristic was that 16 of the isolates induced the production of the uncommon opine succinamopine, while the other 14 were nopaline-producing isolates. With the exception of one, all succinamopine Ti plasmids belonged to the same plasmid group. Conversely, the nopaline Ti plasmids belonged to five groups, one of these containing seven isolates. We showed that outbreaks of disease provoked by the succinamopine-producing isolates in different countries and nurseries concurred with a common origin of specific rootstock clones. Similarly, groups of nopaline-producing isolates were associated with particular rootstock clones. These results strongly suggest that the causal agent of crown gall disease in rose plants is transmitted via rootstock material.
Replacement of a Metabolic Pathway for Large-Scale Production of Lactic Acid from Engineered Yeasts
Authors: Porro Danilo , Bianchi Michele M. , Brambilla Luca , Menghini Rossella , Bolzani Davide , Carrera Vittorio , Lievense Jefferson , Liu Chi-Li , Ranzi Bianca Maria , Frontali Laura , Alberghina Lilia
Published: December 2019

Interest in the production of
l
-(+)-lactic acid is presently growing in relation to its applications in the synthesis of biodegradable polymer materials. With the aim of obtaining efficient production and high productivity, we introduced the bovine
l
-lactate dehydrogenase gene (
LDH
) into a wild-type
Kluyveromyces lactis
yeast strain. The observed lactic acid production was not satisfactory due to the continued coproduction of ethanol. A further restructuring of the cellular metabolism was obtained by introducing the
LDH
gene into a
K. lactis
strain in which the unique pyruvate decarboxylase gene had been deleted. With this modified strain, in which lactic fermentation substituted completely for the pathway leading to the production of ethanol, we obtained concentrations, productivities, and yields of lactic acid as high as 109 g liter
−1
, 0.91 g liter
−1
h
−1
, and 1.19 mol per mole of glucose consumed, respectively. The organic acid was also produced at pH levels lower than those usual for bacterial processes.
Variation in Resistance to Hydrostatic Pressure among Strains of Food-Borne Pathogens
Authors: Alpas H. , Kalchayanand N. , Bozoglu F. , Sikes A. , Dunne C. P. , Ray B.
Published: December 2019

Among food-borne pathogens, some strains could be resistant to hydrostatic pressure treatment. This information is necessary to establish processing parameters to ensure safety of pressure-pasteurized foods (N. Kalchayanand, A. Sikes, C. P. Dunne, and B. Ray, J. Food Prot. 61:425–431, 1998). We studied variation in pressure resistance among strains of
Listeria monocytogenes
,
Staphylococcus aureus
,
Escherichia coli
O157:H7, and
Salmonella
species at two temperatures of pressurization. Early-stationary-phase cells in 1% peptone solution were pressurized at 345 MPa either for 5 min at 25°C or for 5, 10, or 15 min at 50°C. The viability loss (in log cycles) following pressurization at 25°C ranged from 0.9 to 3.5 among nine
L. monocytogenes
strains, 0.7 to 7.8 among seven
S. aureus
strains, 2.8 to 5.6 among six
E. coli
O157:H7 strains, and 5.5 to 8.3 among six
Salmonella
strains. The results show that at 25°C some strains of each species are more resistant to pressure than the others. However, when one resistant and one sensitive strain from each species were pressurized at 345 MPa and 50°C, the population of all except the resistant
S. aureus
strain was reduced by more than 8 log cycles within 5 min. Viability loss of the resistant
S. aureus
strain was 6.3 log cycles even after 15 min of pressurization. This shows that strains of food-borne pathogens differ in resistance to hydrostatic pressure (345 MPa) at 25°C, but this difference is greatly reduced at 50°C. Pressurization at 50°C, in place of 25°C, will ensure greater safety of foods.
Role of Humic-Bound Iron as an Electron Transfer Agent in Dissimilatory Fe(III) Reduction
Authors: Lovley Derek R. , Blunt-Harris Elizabeth L.
Published: December 2019

The dissimilatory Fe(III) reducer
Geobacter metallireducens
reduced Fe(III) bound in humic substances, but the concentrations of Fe(III) in a wide range of highly purified humic substances were too low to account for a significant portion of the electron-accepting capacities of the humic substances. Furthermore, once reduced, the iron in humic substances could not transfer electrons to Fe(III) oxide. These results suggest that other electron-accepting moieties in humic substances, such as quinones, are the important electron-accepting and shuttling agents under Fe(III)-reducing conditions.
Poly(Aspartic Acid) Degradation by aSphingomonassp. Isolated from Freshwater
Authors: Tabata Kenji , Kasuya Ken-Ichi , Abe Hideki , Masuda Kozue , Doi Yoshiharu
Published: December 2019

A poly(aspartic acid) degrading bacterium (strain KT-1 [JCM10459]) was isolated from river water and identified as a member of the genusSphingomonas. The isolate degraded only poly(aspartic acid)s of low molecular masses (<5 kDa), while the cell extract hydrolyzed high-molecular-mass poly(aspartic acid)s of 5 to 150 kDa to yield aspartic acid monomer.
Diversity and Heterogeneity of Epibiotic Bacterial Communities on the Marine Nematode
Eubostrichus dianae
Authors: Polz Martin F. , Harbison Christopher , Cavanaugh Colleen M.
Published: December 2019

The diversity of a microbial community covering the surface of a marine nematode was analyzed by performing a 16S ribosomal DNA (rDNA) restriction cutting and sequencing analysis. In two clone libraries constructed by using individual nematodes, 54 and 85 restriction patterns were identified, and only 13 of these patterns were common to both libraries. Sequence analysis indicated that the common patterns belonged to four groups related to sequences of cytophagas, sulfate-reducing bacteria, members of the gamma subclass of the class
Proteobacteria
, and caulobacters. At least two groups appeared to be permanent members of the community as they were also detected in a 16S rDNA library constructed 3 years previously by using 100 pooled nematode specimens. A surprising outcome was that very dominant filamentous bacteria were apparently not represented in the clone libraries, as quantitative probing showed that none of the common operational taxonomic unit groups displayed the expected overwhelming dominance. Nevertheless, our analysis revealed both an unexpectedly high level of bacterial diversity and heterogeneity in samples representing presumably very similar microenvironments.
Evaluation of a Novel High-Definition PCR Multiplex Assay for Simultaneous Detection of Tick-Borne Pathogens in Human Clinical Specimens
Authors: Shakir Salika M. , Mansfield Christopher R. , Hays Elizabeth D. , Couturier Marc Roger , Hillyard David R.
Published: December 2019

The incidence of tick-borne infections in the United States has risen significantly in the past decade. Ticks can transmit a variety of pathogens, including bacteria, protozoa, and viruses, that can cause serious illnesses. Therefore, the use of rapid, sensitive, and specific multiplex tests is important to identify the pathogen(s) in the acute phase and determine appropriate treatment to minimize the severity of the disease.
Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples
Authors: Street Teresa L. , Barker Leanne , Sanderson Nicholas D. , Kavanagh James , Hoosdally Sarah , Cole Kevin , Newnham Robert , Selvaratnam Mathyruban , Andersson Monique , Llewelyn Martin J. , O’Grady Justin , Crook Derrick W. , Eyre David W.
Published: December 2019

Empirical gonorrhea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. We investigated if Nanopore sequencing can detect sufficient
Neisseria gonorrhoeae
DNA to reconstruct whole genomes directly from urine samples.
An Animal Model That Mimics Human Herpesvirus 6B Pathogenesis
Authors: Wang Bochao , Saito Yasuyuki , Nishimura Mitsuhiro , Ren Zhenxiao , Tjan Lidya Handayani , Refaat Alaa , Iida-Norita Rie , Tsukamoto Ryuko , Komatsu Masato , Itoh Tomoo , Matozaki Takashi , Mori Yasuko
Published: December 2019

Human herpesvirus 6B (HHV-6B) is a ubiquitous virus that establishes lifelong latent infection only in humans, and the infection can reactivate, with severe complications that cause major problems. A small-animal model of HHV-6B infection has thus been desired for research regarding the pathogenicity of HHV-6B and the development of antiviral agents. We generated humanized mice by transplantation with human hematopoietic stem cells, and here, we modified the model by providing an additional transfer of human mononuclear cells, providing the proper conditions for efficient HHV-6B infection. This is the first humanized mouse model to mimic HHV-6B pathogenesis, and it has great potential for research into the
in vivo
pathogenesis of HHV-6B.
Petrogenesis of Early Paleozoic high Sr/Y intrusive rocks from the North Qilian orogen: Implication for diachronous continental collision
Authors: Yang He , Zhang Hongfei , Xiao Wenjiao , Luo Biji , Gao Zhong , Tao Lu , Zhang Liqi , Guo Liang
Published: December 2019

A combination of U-Pb zircon ages and geochemical and Sr-Nd-Hf isotopic data are presented for the Early Paleozoic granodiorites from the Haoquangou and Baimawa plutons in order to probe the crustal thickness variation of the eastern North Qilian and the diachronous evolution of the North Qilian orogen. The granodiorites formed at 436–435 Ma and have high Sr/Y ratios (63–117). Elemental and isotopic data combined with geochemical modeling and comparisons with experimental data suggest that they were produced from the melting of relatively juvenile mafic rocks in the thickened lower crust. Together with other petrological and geochemical data and the calculation of variation in crustal thickness, this indicates that the eastern North Qilian experienced clear crustal thickening and thinning from the Late Ordovician to Late Silurian. Based on available data, we suggest that diachronous collision from east to west, which probably resulted in the distinct intensity of orogenesis between eastern and western North Qilian, can well account for the differential distribution of Early Paleozoic high Sr/Y magmatism and other geological differences between the eastern and western parts of the North Qilian. Our study also implies that diachronous collision may lead to, apart from distinct metamorphic, structural and sedimentary responses, the large differences in magmatism and deep crustal processes along the orogenic strike.
The need for speed: observational study of physician driving behaviors
Authors: Zimerman André , Worsham Christopher , Woo Jaemin , Jena Anupam B
Published: December 2019

Objective

To determine whether fast driving, luxury car ownership, and leniency by police officers differ across medical specialties.

Design

Observational study.

Setting

Florida, USA.

Participants

5372 physicians and a sample of 19 639 non-physicians issued a ticket for speeding during 2004-17.

Main outcome measures

Observed rates of extreme speeding (defined as driving >20 mph above the speed limit), luxury car ownership, and leniency of the speeding ticket by police officers, by physician specialty, after adjustment for age and sex.

Results

The sample included 5372 physicians who received 14 560 speeding tickets. The proportion of drivers who were reported driving at speeds greater than 20 mph was similar between physicians and a sample of 19 639 non-physicians who received a ticket for speeding (26.4% v 26.8% of tickets, respectively). Among physicians who received a ticket, psychiatrists were most likely to be fined for extreme speeding (adjusted odds ratio of psychiatry compared with baseline specialty of anesthesia 1.51, 95% confidence interval 1.07 to 2.14). Among drivers who received a ticket, luxury car ownership was most common among cardiologists (adjusted proportion of ticketed cardiologists who owned a luxury car 40.9%, 95% confidence interval 35.9% to 45.9%) and least common among physicians in emergency medicine, family practice, pediatrics, general surgery, and psychiatry (eg, adjusted proportion of luxury car ownership among family practice physicians 20.6%, 95% confidence interval 18.2% to 23.0%). Speed discounting, a marker of leniency by police officers in which ticketed speed is recorded at just below the threshold at which a larger fine would otherwise be imposed, was common, but rates did not differ by specialty and did not differ between physicians and a sample of non-physicians.

Conclusions

Rates of extreme speeding were highest among psychiatrists who received a ticket, whereas cardiologists were the most likely to be driving a luxury car when ticketed. Leniency by police officers was similar across specialties and between physicians and non-physicians.
Multicentre, randomised trial to investigate early nasal high—flow therapy in paediatric acute hypoxaemic respiratory failure: a protocol for a randomised controlled trial—a Paediatric Acute respiratory Intervention Study (PARIS 2)
Authors: Franklin Donna , Shellshear Deborah , Babl Franz E , Schlapbach Luregn J , Oakley Ed , Borland Meredith L , Hoeppner Tobias , George Shane , Craig Simon , Neutze Jocelyn , Williams Amanda , Acworth Jason , McCay Hamish , Wallace Alex , Mattes Joerg , Gangathimn Vinay , Wildman Mark , Fraser John F , Moloney Susan , Gavranich John , Waugh John , Hobbins Sue , Fahy Rose , Grew Simon , Gannon Brenda , Gibbons Kristen , Dalziel Stuart , Schibler Andreas
Published: December 2019

Introduction

Acute hypoxaemic respiratory failure (AHRF) in children is the most frequent reason for non-elective hospital admission. During the initial phase, AHRF is a clinical syndrome defined for the purpose of this study by an oxygen requirement and caused by pneumonia, lower respiratory tract infections, asthma or bronchiolitis. Up to 20% of these children with AHRF can rapidly deteriorate requiring non-invasive or invasive ventilation. Nasal high-flow (NHF) therapy has been used by clinicians for oxygen therapy outside intensive care settings to prevent escalation of care. A recent randomised trial in infants with bronchiolitis has shown that NHF therapy reduces the need to escalate therapy. No similar data is available in the older children presenting with AHRF. In this study we aim to investigate in children aged 1 to 4 years presenting with AHRF if early NHF therapy compared with standard-oxygen therapy reduces hospital length of stay and if this is cost-effective compared with standard treatment.

Methods and analysis

The study design is an open-labelled randomised multicentre trial comparing early NHF and standard-oxygen therapy and will be stratified by sites and into obstructive and non-obstructive groups. Children aged 1 to 4 years (n=1512) presenting with AHRF to one of the participating emergency departments will be randomly allocated to NHF or standard-oxygen therapy once the eligibility criteria have been met (oxygen requirement with transcutaneous saturation <92%/90% (dependant on hospital standard threshold), diagnosis of AHRF, admission to hospital and tachypnoea ≥35 breaths/min). Children in the standard-oxygen group can receive rescue NHF therapy if escalation is required. The primary outcome is hospital length of stay. Secondary outcomes will include length of oxygen therapy, proportion of intensive care admissions, healthcare resource utilisation and associated costs. Analyses will be conducted on an intention-to-treat basis.

Ethics and dissemination

Ethics approval has been obtained in Australia (HREC/15/QRCH/159) and New Zealand (HDEC 17/NTA/135). The trial commenced recruitment in December 2017. The study findings will be submitted for publication in a peer-reviewed journal and presented at relevant conferences. Authorship of all publications will be decided by mutual consensus of the research team.

Trial registration number

ACTRN12618000210279
Cigarette smoking among university students aged 18–24 years in New Zealand: results of the first (baseline) of two national surveys
Authors: Wamamili Ben , Wallace-Bell Mark , Richardson Ann , Grace Randolph C , Coope Pat
Published: December 2019

Objectives

Although the smoking prevalence continues to decline in New Zealand (NZ) overall, little is known about smoking in university students. A 2013 survey of students aged 17–25 years found that 14% were current smokers, and 3% daily smokers. However, the sample did not include students from all NZ universities. This study examines the prevalence and patterns of cigarette smoking among students aged 18–24 years.

Setting

University students across NZ.

Methods

Data came from a March to May 2018 survey of students from all NZ universities, and were weighted to account for undersampling and oversampling, based on gender and university size. χ2tests were used to compare smoking by age, gender and ethnicity.

Participants

1476 participants were included: 919 (62.3%) aged 18–20 years and 557 (37.7%) aged 21–24 years; 569 (38.6%) male and 907 (61.4%) female; and 117 (7.9%) Māori and 1359 (92.1%) non-Māori.

Results

49.8% (95% CI 47.2 to 52.4) of respondents reported ever smoking, 11.1% (95% CI 9.5 to 12.9) currently smoked (smoked at least once a month) and 5.9% (95% CI 4.8 to 7.3) smoked at least daily (daily smokers). Of current smokers, 63.6% smoked 1–5 cigarettes/day, 45.8% smoked daily, 73.4% smoked first cigarette >60 min after waking, 86.0% never/almost never smoked in indoor and 64.6% in outdoor smokefree spaces, 69.9% planned to quit and 32.4% had tried to quit. Ever, current and daily smoking were significantly higher in 21–24 compared with 18–20 years olds, and in males compared with females. Older participants were more likely to report smoking more cigarettes/day. Māori were more likely to report ever smoking than non-Māori.

Conclusions

Current smoking among NZ university students aged 18–24 years appears to be declining but daily smoking could be increasing. However, many students appeared less addicted to nicotine, and willing to quit. We recommend increasing the availability of smokefree services for students who wish to quit.
Effect ofHelicobacter pylorion gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer
Authors: Guo Yang , Zhang Yang , Gerhard Markus , Gao Juan-Juan , Mejias-Luque Raquel , Zhang Lian , Vieth Michael , Ma Jun-Ling , Bajbouj Monther , Suchanek Stepan , Liu Wei-Dong , Ulm Kurt , Quante Michael , Li Zhe-Xuan , Zhou Tong , Schmid Roland , Classen Meinhard , Li Wen-Qing , You Wei-Cheng , Pan Kai-Feng
Published: December 2019

Objective

Gastrointestinal microbiota may be involved inHelicobacter pylori-associated gastric cancer development. The aim of this study was to explore the possible microbial mechanisms in gastric carcinogenesis and potential dysbiosis arising fromH. pyloriinfection.

Design

Deep sequencing of the microbial 16S ribosomal RNA gene was used to investigate alterations in paired gastric biopsies and stool samples in 58 subjects with successful and 57 subjects with failed anti-H. pyloritreatment, relative to 49H. pylorinegative subjects.

Results

InH. pyloripositive subjects, richness and Shannon indexes increased significantly (both p<0.001) after successful eradication and showed no difference to those of negative subjects (p=0.493 for richness and p=0.420 for Shannon index). Differential taxa analysis identified 18 significantly altered gastric genera after eradication. The combination of these genera into a Microbial Dysbiosis Index revealed that the dysbiotic microbiota inH. pyloripositive mucosa was associated with advanced gastric lesions (chronic atrophic gastritis and intestinal metaplasia/dysplasia) and could be reversed by eradication. Strong coexcluding interactions betweenHelicobacterandFusobacterium,Neisseria,Prevotella,Veillonella,Rothiawere found only in advanced gastric lesion patients, and were absent in normal/superficial gastritis group. Changes in faecal microbiota included increasedBifidobacteriumafter successfulH. pylorieradication and more upregulated drug-resistant functional orthologs after failed treatment.

Conclusion

H. pyloriinfection contributes significantly to gastric microbial dysbiosis that may be involved in carcinogenesis. SuccessfulH. pylorieradication potentially restores gastric microbiota to a similar status as found in uninfected individuals, and shows beneficial effects on gut microbiota.
Current opinion, status and future development of digital pathology in Switzerland
Authors: Unternaehrer Julia , Grobholz Rainer , Janowczyk Andrew , Zlobec Inti
Published: December 2019

Aims

The transition from analogue to digital pathology (DP) is underway in Switzerland. To assess relevant experiences of pathologists with DP and gauge their outlook towards a digital future, a national survey was conducted by the Swiss Digital Pathology Consortium. Similar surveys were conducted in other countries, enabling a meta-analysis of DP experiences.

Methods

Pathologists and residents were asked to complete a survey containing 12 questions. Results were compared with similar studies conducted in the United Kingdom, Sweden, Canada, and India.

Results

The estimated response rate among practicing pathologists and trainees nationwide was 39.5%. Of these, 89% have experience with digital slides, mainly for education (61%) and primary diagnostics (20%). Further, 32% have worked with an image analysis programme and 26% use computer-based algorithms weekly. Interestingly, 66% would feel comfortable making a primary diagnosis digitally, while 10% would not. Most respondents believe more standards and regulations are necessary for the clinical employment of DP. Noted advantages include ease of access to slides and the resulting connectivity benefits, namely collaboration with experts across disciplines, off-site work, training purposes, and computational image analysis. Perceived disadvantages include implementation costs and issues associated with IT infrastructure and file formats.

Conclusion

The survey results suggest that experiences and perspectives of Swiss pathologists concerning DP is comparable to that of the other reporting countries undergoing transitions to digital workflows. Although more standards and regulations are needed to ensure the safe usage of these technologies, pathologists in Switzerland appear welcoming of this new digital era.
Mutations in gene regulatory elements linked to human limb malformations
Authors: Nowosad Karol , Hordyjewska-Kowalczyk Ewa , Tylzanowski Przemko
Published: December 2019

Most of the human genome has a regulatory function in gene expression. The technological progress made in recent years permitted the revision of old and discovery of new mutations outside of the protein-coding regions that do affect human limb morphology. Steadily increasing discovery rate of such mutations suggests that until now the largely neglected part of the genome rises to its well-deserved prominence. In this review, we describe the recent technological advances permitting this unprecedented advance in identifying non-coding mutations. We especially focus on the mutations incis-regulatory elements such as enhancers, andtrans-regulatory elements such as miRNA and long non-coding RNA, linked to hereditary or inborn limb defects. We also discuss the role of chromatin organisation and enhancer–promoter interactions in the aetiology of limb malformations.
A novel autosomal recessive lipodystrophy syndrome due to homozygousLMNAvariant
Authors: Patni Nivedita , Hatab Sarah , Xing Chao , Zhou Zhengyang , Quittner Claudia , Garg Abhimanyu
Published: December 2019

Background

Despite major advances in understanding the molecular basis of various genetic lipodystrophy syndromes, some rare patients still remain unexplained.

Cases

We report a novel autosomal recessive lipodystrophy affecting two sisters aged 17 and 19 years and characterised by early onset intellectual disability, and subsequent development of near-generalised loss of subcutaneous fat with diabetes mellitus, extreme hypertriglyceridemia, hepatic steatosis, short stature, clinodactyly, joint contractures, leiomyoma of uterus and cataracts in childhood. The lipodystrophy was more pronounced in the upper and lower extremities, and there was no associated muscular hypertrophy. Using whole exome sequencing in this consanguineous Hispanic pedigree, we report disease-causing homozygous p.Arg545HisLMNAvariant in the affected subjects, and confirm the lack of pathogenic variants in other known lipodystrophy genes. The mother and a younger brother were both heterozygous for p.Arg545HisLMNAvariant and were overweight with acanthosis nigricans without any evidence of lipodystrophy. Our patients are distinct from previously reported autosomal recessive lipodystrophy syndromes and have no overlap with other autosomal recessive laminopathies, including mandibuloacral dysplasia, Emery-Dreifuss muscular dystrophy and Charcot-Marie-Tooth neuropathy.

Conclusion

Our report of this unusual familial generalised lipodystrophy syndrome adds to the pleiotropy associated with biallelic autosomal recessiveLMNAvariants.
Gene editing prospects for treating inherited retinal diseases
Authors: Benati Daniela , Patrizi Clarissa , Recchia Alessandra
Published: December 2019

Retinal diseases (RD) include inherited retinal dystrophy (IRD), for example, retinitis pigmentosa and Leber’s congenital amaurosis, or multifactorial forms, for example, age-related macular degeneration (AMD). IRDs are clinically and genetically heterogeneous in nature. To date, more than 200 genes are known to cause IRDs, which perturb the development, function and survival of rod and cone photoreceptors or retinal pigment epithelial cells. Conversely, AMD, the most common cause of blindness in the developed world, is an acquired disease of the macula characterised by progressive visual impairment. To date, available therapeutic approaches for RD include nutritional supplements, neurotrophic factors, antiangiogenic drugs for wet AMD and gene augmentation/interference strategy for IRDs. However, these therapies do not aim at correcting the genetic defect and result in inefficient and expensive treatments. The genome editing technology based on clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein (Cas) and an RNA that guides the Cas protein to a predetermined region of the genome, represents an attractive strategy to tackle IRDs without available cure. Indeed, CRISPR/Cas system can permanently and precisely replace or remove genetic mutations causative of a disease, representing a molecular tool to cure a genetic disorder. In this review, we will introduce the mechanism of CRISPR/Cas system, presenting an updated panel of Cas variants and delivery systems, then we will focus on applications of CRISPR/Cas genome editing in the retina, and, as emerging treatment options, in patient-derived induced pluripotent stem cells followed by transplantation of retinal progenitor cells into the eye.
Policy options for endgame planning in tobacco control: a simulation modelling study
Authors: Skinner Adam , Walker Pippy , Atkinson Jo-An , Whitehead Rebecca , Roselli Tim , West Mark , Bright Margaret , Heffernan Mark , McDonnell Geoff , Veerman Lennert , Prodan Ante , Thomas David P , Burton Suzan
Published: December 2019

Objective

To investigate the potential impacts of several tobacco control interventions on adult daily smoking prevalence in the Australian state of Queensland, using a system dynamics model codeveloped with local and national stakeholders.

Methods

Eight intervention scenarios were simulated and compared with a reference scenario (business as usual), in which all tobacco control measures currently in place are maintained unchanged until the end of the simulation period (31 December 2037).

Findings

Under the business as usual scenario, adult daily smoking prevalence is projected to decline from 11.8% in 2017 to 5.58% in 2037. A sustained 50% increase in antismoking advertising exposure from 2018 reduces projected prevalence in 2037 by 0.80 percentage points. Similar reductions are projected with the introduction of tobacco wholesaler and retailer licensing schemes that either permit or prohibit tobacco sales by alcohol-licensed venues (0.65 and 1.73 percentage points, respectively). Increasing the minimum age of legal supply of tobacco products substantially reduces adolescent initiation, but has minimal impact on smoking prevalence in the adult population over the simulation period. Sustained reductions in antismoking advertising exposure of 50% and 100% from 2018 increase projected adult daily smoking prevalence in 2037 by 0.88 and 1.98 percentage points, respectively.

Conclusions

These results suggest that any prudent approach to endgame planning should seek to build on rather than replace existing tobacco control measures that have proved effective to date. Additional interventions that can promote cessation are expected to be more successful in reducing smoking prevalence than interventions focussing exclusively on preventing initiation.
Inequities in tobacco advertising exposure among young adult sexual, racial and ethnic minorities: examining intersectionality of sexual orientation with race and ethnicity
Authors: Tan Andy S L , Hanby Elaine P , Sanders-Jackson Ashley , Lee Stella , Viswanath Kasisomayajula , Potter Jennifer
Published: December 2019

Objective

This study examined sexual orientation differences in encoded exposure to tobacco product ads and intersections with race and ethnicity.

Methods

We analysed data from young adults (18–24) from the US Population Assessment of Tobacco and Health Study in 2013 and 2014 (N=9110). First, we compared encoded exposure to cigarette, electronic cigarette (e-cigarette), cigar and smokeless tobacco ads between sexual minorities (lesbian/gay, bisexual and something else) versus heterosexual young adults. We then analysed encoded ad exposure across sexual orientation, racial and ethnic subgroups. Analyses controlled for demographic and tobacco use variables.

Results

Bisexual women had significantly higher prevalence of encoded exposure to cigarette and cigar ads compared with heterosexual women, and significantly higher prevalence of encoded e-cigarette ad exposure compared with both heterosexual and lesbian/gay women. There were no significant differences in encoded ad exposure between lesbian versus heterosexual women and between gay or bisexual men versus heterosexual men. Compared with heterosexual white counterparts, increased encoded ad exposures were reported by heterosexual black women (cigarette and cigar ads), black heterosexual men (cigar ads) and bisexual black women (cigarette and cigar ads). Compared with heterosexual non- Hispanic counterparts, increased encoded ad exposures were reported by bisexual Hispanic women (cigarette, e-cigarette and cigar ads) and heterosexual Hispanic men (cigarettes and cigar ads).

Conclusion

Sexual minority women of colour and black heterosexual women and men have increased encoded exposure to certain forms of tobacco ads. Further research is needed to address the impact of tobacco ads among multiple minority individuals based on sex, sexual orientation, race and ethnicity.
Minimally invasive chest wall stabilization: a novel surgical approach to video-assisted rib plating (VARP)
Authors: Diaz Jose J , Azar Faris K
Published: December 2019

The current morbidity of rib plating is due to the size of the incision required to perform an open procedure. We describe a minimally invasive laparoscopic approach to rib plating. A cadaver model was used to develop the surgical technique by performing both left and right posterior-lateral rib plating. A small incision was made over the auscultatory triangle. The potential working space is developed under the posterior shoulder girdle and the scapula. A table-based retractor was used to elevate the scapula and the muscles. Two separate ports were placed: one camera port and one working port. In three cadaver models, 12 rib fractures were plated and the surgical technique is described. This novel technique will likely allow for faster recovery and was especially useful in the subscapular space.

Level of evidenceII.
Pedunculate oak decline in southern Belgium: a long-term process highlighting the complex interplay among drought, winter frost, biotic attacks, and masting
Authors: Losseau Julie , Jonard Mathieu , Vincke Caroline
Published: December 2019

Since 2013, pedunculate oak (Quercus robur L.) mortality has been observed in the Ardennes region of Belgium. We aimed to understand the current decline by retrospectively (1945–2015) studying radial growth patterns of trees classified by three health statuses (reference, declining, and dying) and by linking them to abiotic and biotic hazard history, which we recorded and quantified. Our results show that oak mortality in the Ardennes is a long-term process, with 1987 as a tipping point for growth trajectories of declining and dying trees. That year was preceded by two growth crises (1976–1981 and 1984–1987), and it falls within the last major episode of oak decline in Belgium. Among hazards, very cold winters and caterpillar outbreaks have significant impacts on growth-pattern differentiation. Apart from 1976, extreme drought is still rare; however, mild spring droughts, especially in the years n − 1 and n − 2, explain some of the growth loss relative to the reference trees. Finally, masting appears to be an important contributing factor for the death of weakened trees. Given the direct and delayed impacts of the extreme drought of 1976 and subsequent water balance impairment due to winter frosts and mild spring droughts, the health of pedunculate oak is giving cause for concern in the context of climate change.
Enhanced Curie temperature and magnetic entropy change of Gd50Co50−xNix amorphous alloys
Authors: Song M. N. , Huang L. W. , Tang B. Z. , Ding D. , Zhou Q. , Xia L.
Published: December 2019

Small amount of Ni was added in the [Formula: see text] binary alloy to replace the Co element for improving the formability and magnetic properties of the binary amorphous alloy. It was found that the glass formability of the [Formula: see text] amorphous alloy was significantly improved by Ni addition. The Curie temperature [Formula: see text] of the [Formula: see text] metallic glasses decreases with the Ni addition, and the maximum magnetic entropy change [Formula: see text] was also improved. The mechanism for the effect of adding a small quantity of Ni on the [Formula: see text] and [Formula: see text] of the [Formula: see text] amorphous alloy was studied.
Solitary wave solutions, lump solutions and interactional solutions to the (2+1)-dimensional potential Kadomstev–Petviashvili equation
Authors: Geng Jiang-Su , Zhang Hai-Qiang
Published: December 2019

In this paper, the [Formula: see text]-solitary wave solution to the (2[Formula: see text]+[Formula: see text]1)-dimensional potential Kadomstev–Petviashvili (PKP) equation is obtained with the Hirota bilinear method. Via the limit technique of long wave, the [Formula: see text]-lump solution can be derived from resulting [Formula: see text]-solitary wave solution. In addition, interactional solutions consisting of lumps and solitary waves for the PKP equation are obtained, which can describe elastic interactions of lumps and solitary waves. These results are illustrated by graphics of several sample examples.
Cascadic Newton’s method for the elliptic Monge–Ampère equation
Authors: Li Qin , Liu Zhiyong
Published: December 2019

In this paper, a cascadic Newton’s method is designed to solve the Monge–Ampère equation. In the process of implementing the cascadic multigrid, we use the Full-Local type interpolation as prolongation operator and Newton iteration as smoother. In order to obtain Full-Local type interpolation, we provide several finite difference stencils. Especially, the skewed finite difference methods are first applied by us for the elliptic Monge–Ampère equation. Based on Full-Local interpolation techniques and cascade principle, the new algorithm can save a large amount of computation time. Some numerical experiments are provided to confirm the efficiency of our proposed method.
Tetra-2,3-pyrazinoporphyrazines with peripherally appended pyridine rings. 21. Mono- and pentanuclear FeII complexes: Solid state and solution studies
Authors: Donzello Maria Pia , Puglisi Elena , Ercolani Claudio , Vozzolo Giulia , Rong Jian , Fang Yuanyuan , Kadish Karl M.
Published: December 2019

New Fe[Formula: see text] complexes of formula [Py8TPyzPzFe] · xH2O, its bis-pyridine adduct [Py8TPyzPzFe(py)2] · xH2O, the pentanuclear species [(MCl[Formula: see text]Py8TPyzPzFe] · xH2O (M [Formula: see text] Pd[Formula: see text], Pt[Formula: see text] and the bis-DABCO adducts [Py8TPyzPzFe(DABCO)2] · 11H2O and [(PdCl[Formula: see text]Py8TPyzPzFe(DABCO)2] · H2O (Py8TPyzPz [Formula: see text] octapyridino-tetrapyrazinoporphyrazinato dianion; DABCO [Formula: see text] 1,4-diazabiciclo[2.2.2]octane) were synthesized and characterized by elemental and thermogravimetric analysis, IR and UV-vis spectroscopy, with added studies on the starting complex [Py8TPyzPzFe] · xH2O regarding magnetic and electrochemical behavior. Clathrated water molecules are present in all compounds and have little to no effect on their physicochemical behavior as was observed for all previously reported analogs. UV-vis spectra of the mononuclear [Py8PyzPzFe] · xH2O complex in DMSO and pyridine are indicative of aggregation immediately after dissolving the compound. However, the spectra change slowly over time leading to formation of a porphyrazine species having spectral features typical of a monomer. UV-vis spectra of the parent pentanuclear [(MCl[Formula: see text]Py8TPyzPzFe] · xH2O (M [Formula: see text] Pd[Formula: see text], Pt[Formula: see text] complexes show a smaller degree of aggregation upon dissolution in DMSO or pyridine and the spectra of these solutions also change over time to those of a monomer. The presence of aggregation, spectral evolution with time and final species formed from the N-base adducts [Py8TPyzPzFe(DABCO)2] · 11H2O and [(PdCl[Formula: see text]Py8TPyzPzFe(DABCO)2] · H2O are reported and discussed.
A numerical investigation of excess pore pressures and continental slope stability in response to ice-sheet dynamics
Authors: Urlaub Morelia , Kratzke Isabel , Hjelstuen Berit Oline
Published: December 2019

Submarine landslides are common at glaciated continental margins. The onset of large-scale landslides coincides with the initiation of Northern Hemisphere glaciations in the Quaternary. This implies that processes related to glacial cycling provide favourable conditions for submarine landslides at high-latitude margins. Potential processes include glacial deposition patterns and enhanced seismicity. It is also possible that advances and retreats of ice sheets, a highly dynamic process in geological terms, makes slopes discernible to failure by modifying the stress regime. Here, we quantify this effect using 2D finite element modelling of a glaciated continental margin. Different model runs investigate the pore-pressure development in homogeneous, as well as layered, slopes during glaciation when loaded by an ice stream with one or more ice advances. Ice streams cause significant variations in excess pore pressure in the very shallow sediment sequences at the continental shelf. However, lateral fluid flow is not efficient enough to increase pore pressures significantly at the slope, where large-scale submarine slides are observed. Hence, while ice-sheet dynamics appear to favour the occurrence of shallow slides close to the shelf edge, ice sheets seem to be irrelevant for the generation of large-scale submarine landslides at the continental slope.
Differential Expansion and Voltage Model for Li-ion Batteries at Practical Charging Rates
Authors: Mohtat Peyman , Lee Suhak , Sulzer Valentin , Siegel Jason B. , Stefanopoulou Anna G.
Published: December 2019

Differential voltage analysis (DVA) is a conventional approach for estimating capacity degradation in batteries. During charging, a graphite electrode goes through several phase transitions observed as plateaus in the voltage response. The transitions between these plateaus emerge as observable peaks in the differential voltage. The DVA method utilizes these peaks for estimating cell degradation. Unfortunately, at higher C-rates (above C/2) the peaks flatten and become unobservable. In this work, we show that, unlike the differential voltage, the peaks in the 2nd derivative of the expansion with respect to capacity remain observable up to 1C and thus make possible diagnostic algorithms at these charging rates. To understand why that is the case, we have developed an electrochemical and expansion model suitable for model-based estimation. In particular, we demonstrate that the single particle modeling methodology is not able to capture the peak smoothing effect, therefore a multi-particle approach for the graphite electrode is needed. Additionally, model parameters are identified using experimental data from a graphite/NMC pouch cell. The proposed model produces an excellent fit for the observed electric and mechanical swelling response of the cells and could enable physics-based data-driven degradation studies at practical charging rates.