bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTA 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

ABSTRACT

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.
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

AbstractA 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

AbstractObjectiveTo determine whether fast driving, luxury car ownership, and leniency by police officers differ across medical specialties.DesignObservational study.SettingFlorida, USA.Participants5372 physicians and a sample of 19 639 non-physicians issued a ticket for speeding during 2004-17.Main outcome measuresObserved 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.ResultsThe 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.ConclusionsRates 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

IntroductionAcute 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 analysisThe 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 disseminationEthics 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 numberACTRN12618000210279
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

ObjectivesAlthough 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.SettingUniversity students across NZ.MethodsData 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.Participants1476 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.Results49.8% (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.ConclusionsCurrent 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

ObjectiveGastrointestinal 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.DesignDeep 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.ResultsInH. 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.ConclusionH. 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

AimsThe 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.MethodsPathologists 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.ResultsThe 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.ConclusionThe 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.
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

BackgroundDespite major advances in understanding the molecular basis of various genetic lipodystrophy syndromes, some rare patients still remain unexplained.CasesWe 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.ConclusionOur report of this unusual familial generalised lipodystrophy syndrome adds to the pleiotropy associated with biallelic autosomal recessiveLMNAvariants.