bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breathing regulation and blood gas homeostasis after near complete lesions of the retrotrapezoid nucleus in adult rats
Authors: Souza George M. P. R. , Kanbar Roy , Stornetta Daniel S. , Abbott Stephen B.G. , Stornetta Ruth L. , Guyenet Patrice G. 
Published: April 2018

Key points
The retrotrapezoid nucleus (RTN) drives breathing proportionally to brain but its role during various states of vigilance needs clarification.
Under normoxia, RTN lesions increased the arterial set‐point, lowered the set‐point and reduced alveolar ventilation relative to CO2 production. Tidal volume was reduced and breathing frequency increased to a comparable degree during wake, slow‐wave sleep and REM sleep. RTN lesions did not produce apnoeas or disordered breathing during sleep.
RTN lesions in rats virtually eliminated the central respiratory chemoreflex (CRC) while preserving the cardiorespiratory responses to hypoxia; the relationship between CRC and number of surviving RTN Nmb neurons was an inverse exponential.
The CRC does not function without the RTN. In the quasi‐complete absence of the RTN and CRC, alveolar ventilation is reduced despite an increased drive to breathe from the carotid bodies.
AbstractThe retrotrapezoid nucleus (RTN) is one of several CNS nuclei that contribute, in various capacities (e.g. CO2 detection, neuronal modulation) to the central respiratory chemoreflex (CRC). Here we test how important the RTN is to PCO2 homeostasis and breathing during sleep or wake. RTN Nmb‐positive neurons were killed with targeted microinjections of substance P–saporin conjugate in adult rats. Under normoxia, rats with large RTN lesions (92 ± 4% cell loss) had normal blood pressure and arterial pH but were hypoxic (−8 mmHg PaO2) and hypercapnic (+10 mmHg ). In resting conditions, minute volume (VE) was normal but breathing frequency (fR) was elevated and tidal volume (VT) reduced. Resting O2 consumption and CO2 production were normal. The hypercapnic ventilatory reflex in 65% FiO2 had an inverse exponential relationship with the number of surviving RTN neurons and was decreased by up to 92%. The hypoxic ventilatory reflex (HVR; FiO2 21–10%) persisted after RTN lesions, hypoxia‐induced sighing was normal and hypoxia‐induced hypotension was reduced. In rats with RTN lesions, breathing was lowest during slow‐wave sleep, especially under hyperoxia, but apnoeas and sleep‐disordered breathing were not observed. In conclusion, near complete RTN destruction in rats virtually eliminates the CRC but the HVR persists and sighing and the state dependence of breathing are unchanged. Under normoxia, RTN lesions cause no change in VE but alveolar ventilation is reduced by at least 21%, probably because of increased physiological dead volume. RTN lesions do not cause sleep apnoea during slow‐wave sleep, even under hyperoxia.
Retained Activity of an O25b-Specific Monoclonal Antibody against an Mcr-1-Producing Escherichia coli Sequence Type 131 Strain
Authors: Guachalla Luis M. , Ramoni Katharina , Varga Cecilia , Mutti Michele , Ghazawi Akela , Pál Tibor , Nagy Eszter , Sonnevend Ágnes , Nagy Gábor , Szijártó Valéria 
Published: April 2018

ABSTRACT

Plasmid-encoded colistin resistance is emerging among extraintestinal pathogenic
Escherichia coli
strains, including those of the epidemic clone sequence type 131 (ST131)-H30. Mcr-1 transfers a phosphoethanolamine to the lipid A portion of lipopolysaccharide (LPS), conferring resistance to polymyxins. We investigated whether this modification changed the activity of the monoclonal antibody ASN-4, specific to the O25b side chain of ST131 LPS. We confirmed that, unlike colistin, ASN-4 retained its bactericidal and endotoxin-neutralizing activities and therefore offers a treatment option against extremely drug-resistant ST131 isolates.
Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans
Authors: Jibrin Mustafa O. , Potnis Neha , Timilsina Sujan , Minsavage Gerald V. , Vallad Gary E. , Roberts Pamela D. , Jones Jeffrey B. , Goss Erica M. 
Published: April 2018

ABSTRACT

Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors.
Xanthomonas euvesicatoria
and
Xanthomonas perforans
are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both
X. euvesicatoria
and
X. perforans
. Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related
Xanthomonas
pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.

IMPORTANCE
The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from
X. perforans
and
X. euvesicatoria
, as well as effectors from
Xanthomonas gardneri
. These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.
Cross Talk between Calcium and Reactive Oxygen Species Regulates Hyphal Branching and Ganoderic Acid Biosynthesis in Ganoderma lucidum under Copper Stress
Authors: Gao Tan , Shi Liang , Zhang Tianjun , Ren Ang , Jiang Ailiang , Yu Hanshou , Zhao Mingwen 
Published: April 2018

ABSTRACTGanoderma lucidumis among the best known medicinal basidiomycetes due to its production of many pharmacologically active compounds. To study the regulatory networks involved in its growth and development, we analyzed the relationship between reactive oxygen species (ROS) and Ca2+signaling in the regulation of hyphal branching and ganoderic acid (GA) biosynthesis after Cu2+treatment. Our results revealed that Cu2+treatment decreased the distance between hyphal branches and increased the GA content and the intracellular levels of ROS and Ca2+. Further research revealed that the Cu2+-induced changes in hyphal branch distance, GA content, and cytosolic Ca2+level were dependent on increases in cytosolic ROS. Our results also showed that increased cytosolic Ca2+could reduce cytosolic ROS by activating antioxidases and modulating Cu2+accumulation, resulting in feedback to adjust hyphal growth and GA biosynthesis. These results indicated that cytosolic ROS and Ca2+levels exert important cross talk in the regulation of hyphal growth and GA biosynthesis induced by Cu2+. Taken together, our results provide a reference for analyzing the interactions among different signal transduction pathways with regard to the regulation of growth and development in other filamentous fungi.IMPORTANCEGanoderma lucidum, which is known as an important medicinal basidiomycete, is gradually becoming a model organism for studying environmental regulation and metabolism. In this study, we analyzed the relationship between reactive oxygen species (ROS) and Ca2+signaling in the regulation of hyphal branching and ganoderic acid (GA) biosynthesis under Cu2+stress. The results revealed that the Cu2+-induced changes in the hyphal branch distance, GA content, and cytosolic Ca2+level were dependent on increases in cytosolic ROS. Furthermore, the results indicated that increased cytosolic Ca2+could reduce cytosolic ROS levels by activating antioxidases and modulating Cu2+accumulation. The results in this paper indicate that there was important cross talk between cytosolic ROS and Ca2+levels in the regulation of hyphal growth and GA biosynthesis induced by Cu2+.
Draft Genome Sequence of “Nocardia suismassiliense” Strain S-137 (CSUR P4007)
Authors: Fellag Mustapha , Levasseur Anthony , Delerce Jérémy , Bittar Fadi , Marié Jean-Lou , Davoust Bernard , Drancourt Michel 
Published: April 2018

ABSTRACT

“
Nocardia suismassiliense
” strain S-137 isolated from
Sus scrofa
feces exhibits a 9.4-Mb (67.1% GC content) draft genome sequence containing 8,658 protein-coding genes, 66 tRNAs, and 9 rRNAs.
In silico
DNA-DNA hybridization confirmed strain S-137 as representative of a new species, “
Nocardia suismassiliense
,” closely related to
N. tenerifensis
and
N. brasiliensis
.
Near-Complete Genome Sequence of Pseudomonas palleroniana MAB3, a Beneficial 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Bacterium Able To Promote the Growth of Mushrooms and Plants
Authors: Urón Paola , Giachini Admir J. , Glick Bernard R. , Rossi Márcio J. , Nascimento Francisco X. 
Published: April 2018

ABSTRACT

The near-complete genome sequence of
Pseudomonas palleroniana
MAB3, a 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from an environmental soil
Amanita
mushroom, is presented here. The genome of
P. palleroniana
MAB3 contains a single circular chromosome of 6.29 Mb and an average GC content of 60.5%.
Complete Genome Sequence of Shewanella sp. WE21, a Rare Isolate with Multiple Novel Large Genomic Islands
Authors: Castillo Daniel , Gram Lone , Dailey Frank E. 
Published: April 2018

ABSTRACT

We present here the whole-genome sequence of
Shewanella
sp. WE21, an unusual omega-3 fatty acid-producing bacterium isolated from the gastrointestinal tract of the freshwater fish
Sander vitreus
(walleye). This genome contains a number of unique, large genomic islands with genes not present in other
Shewanella
bacteria.
Draft Genome Sequence of Burkholderia gladioli Coa14, a Bacterium with Petroleum Bioremediation Potential Isolated from Coari Lake, Amazonas, Brazil
Authors: Lopes Eraldo Ferreira , Da Costa Josemar Gurgel , Wolf Ivan Rodrigo , Lima José Paulo de Araújo , Astolfi-Filho Spartaco 
Published: April 2018

ABSTRACT

Burkholderia gladioli
Coa14 is a bacterium isolated from water collected from Coari Lake (Amazonas, Brazil) that shows a capacity for survival in a medium containing only oil as a carbon source. Here, we report its draft genome sequence, highlighting some genes involved with petroleum derivative degradation.
Gut Microbiome Analysis Identifies Potential Etiological Factors in Acute Gastroenteritis
Authors: Castaño-Rodríguez Natalia , Underwood Alexander P. , Merif Juan , Riordan Stephen M. , Rawlinson William D. , Mitchell Hazel M. , Kaakoush Nadeem O. 
Published: April 2018

ABSTRACT

The morbidity and mortality resulting from acute gastroenteritis and associated chronic sequelae represent a substantial burden on health care systems worldwide. Few studies have investigated changes in the gut microbiome following an episode of acute gastroenteritis. By using nondirected 16S rRNA gene amplicon sequencing, the fecal microbiota of 475 patients with acute gastroenteritis was examined. Patient age was correlated with the overall microbial composition, with a decrease in the abundance of
Faecalibacterium
being observed in older patients. We observed the emergence of a potential
Escherichia-Shigella
-dominated enterotype in a subset of patients, and this enterotype was predicted to be more proinflammatory than the other common enterotypes, with the latter being dominated by
Bacteroides
or
Faecalibacterium
. The increased abundance of
Escherichia-Shigella
did not appear to be associated with infection with an agent of a similar sequence similarity. Stool color and consistency were associated with the diversity and composition of the microbiome, with deviations from the norm (not brown and solid) showing increases in the abundances of bacteria such as
Escherichia-Shigella
and
Veillonella
. Analysis of enriched outliers within the data identified a range of genera previously associated with gastrointestinal diseases, including
Treponema
,
Proteus
,
Capnocytophaga
,
Arcobacter
,
Campylobacter
,
Haemophilus
,
Aeromonas
, and
Pseudomonas
. Our data represent the first in-depth analysis of gut microbiota in acute gastroenteritis. Phenotypic changes in stool color and consistency were associated with specific changes in the microbiota. Enriched bacterial taxa were detected in cases where no causative agent was identified by using routine diagnostic tests, suggesting that in the future, microbiome analyses may be utilized to improve diagnostics.
Retrospective Evaluation of Infants Aged 1 to 60 Days with Residual Cerebrospinal Fluid (CSF) Tested Using the FilmArray Meningitis/Encephalitis (ME) Panel
Authors: Blaschke Anne J. , Holmberg Kristen M. , Daly Judy A. , Leber Amy L. , Dien Bard Jennifer , Korgenski Ernest K. , Bourzac Kevin M. , Kanack Kristen J. 
Published: April 2018

ABSTRACT
In pediatric practice it is common for infants under 2 months of age to undergo evaluation for sepsis when they are ill, often including lumbar puncture to assess for central nervous system (CNS) infection. The FilmArray Meningitis/Encephalitis (ME) panel is a newly approved test for rapid identification of CNS pathogens. Our objective was to study the epidemiology of CNS infection in young infants and the potential impact of rapid multiplex PCR on their care. A performance evaluation of the FilmArray ME panel was conducted from February 2014 to September 2014 at 11 sites. FilmArray ME panel results were compared to reference standards but not shared with providers. In our study, medical records for infants (aged 1 to 60 days) enrolled at three sites were reviewed for clinical, laboratory, and outcome data. A total of 145 infants were reviewed. The median age was 25 days. Most of the infants were hospitalized (134/145 [92%]) and received antibiotics (123/145 [85%]), and almost half (71/145 [49%]) received acyclovir. One infant had a bacterial pathogen, likely false positive, identified by the FilmArray ME panel. Thirty-six infants (25%) had a viral pathogen detected, including 21 enteroviruses. All infants with enteroviral meningitis detected by the FilmArray ME panel and conventional PCR were hospitalized, but 20% were discharged in less than 24 h when conventional PCR results became available. The FilmArray ME panel may play a role in the evaluation of young infants for CNS infection. Results may be used to guide management, possibly resulting in a decreased length of stay and less antimicrobial exposure for infants with low-risk viral infection detected.
Generation of Recombinant Rotaviruses Expressing Fluorescent Proteins by Using an Optimized Reverse Genetics System
Authors: Komoto Satoshi , Fukuda Saori , Ide Tomihiko , Ito Naoto , Sugiyama Makoto , Yoshikawa Tetsushi , Murata Takayuki , Taniguchi Koki 
Published: April 2018

ABSTRACTAn entirely plasmid-based reverse genetics system for rotaviruses was established very recently. We improved the reverse genetics system to generate recombinant rotavirus by transfecting only 11 cDNA plasmids for its 11 gene segments under the condition of increasing the ratio of the cDNA plasmids for NSP2 and NSP5 genes. Utilizing this highly efficient system, we then engineered infectious recombinant rotaviruses expressing bioluminescent (NanoLuc luciferase) and fluorescent (enhanced green fluorescent protein [EGFP] and mCherry) reporters. These recombinant rotaviruses expressing reporters remained genetically stable during serial passages. Our reverse genetics approach and recombinant rotaviruses carrying reporter genes will be great additions to the tool kit for studying the molecular virology of rotavirus and for developing future next-generation vaccines and expression vectors.IMPORTANCERotavirus is one of the most important pathogens causing severe gastroenteritis in young children worldwide. In this paper, we describe a robust and simple reverse genetics system based on only rotavirus cDNAs and its application for engineering infectious recombinant rotaviruses harboring bioluminescent (NanoLuc) and fluorescent (EGFP and mCherry) protein genes. This highly efficient reverse genetics system and recombinant group A rotaviruses expressing reporters could be powerful tools for the study of different aspects of rotavirus replication. Furthermore, they may be useful for next-generation vaccine production for this medically important virus.
Electroacupuncture Reduces Hypothalamic and Medullary Expression of Orexins and their Receptors in a Rat Model of Chronic Obstructive Pulmonary Disease
Authors: Zhang Xin-Fang , Qin Qin , Geng Wen-Ye , Jiang Chuan-Wei , Liu Yong , Liu Xiao-Li , Li Jing , Liu Zi-Bing 
Published: April 2018

Objectives Decreased lung function in chronic obstructive pulmonary disease (COPD) is correlated with abnormal excitability of the respiratory centre where orexin neuropeptides from the hypothalamus are responsible for regulating respiration. We hypothesised that improvements in pulmonary function with electroacupuncture (EA) may be related to orexins in a rat model of COPD. Methods The COPD model was established by cigarette smoke exposure and lipopolysaccharide injection. Modelled rats received EA at BL13 and ST36 for two weeks, after which lung function was tested. Orexin levels in the hypothalamus and medulla were detected by ELISA, while mRNA/protein expression and localisation of orexins and their receptors were investigated using real time PCR, Western blotting and immunohistochemistry, respectively. Results The decrease in lung function observed in COPD rats was improved after EA treatment. Orexin levels in the hypothalamus and medulla were significantly higher in COPD rats than in normal rats, but were significantly reduced in the EA-treated group. There was a negative correlation between orexin content and lung function. In the hypothalamus, mRNA and protein expression and immunoreactivity of orexins were significantly higher in the COPD group than in the normal group, but a significant decrease was observed after EA. In the medulla, the expression and immunoreactivity of orexin receptors were significantly higher in the COPD group than in the normal group, but a significant decrease was observed after EA. Conclusions The positive effect of EA on pulmonary function in COPD rats may be related to downregulation of orexins and their receptors in the medulla.
Outcome of paediatric cataract surgery in Northwest Ethiopia: a retrospective case series
Authors: Asferaw Mulusew , Mekonen Sisay Yoseph , Woodruff Geoffrey , Gilbert Clare E , Tesfaye Samson 
Published: April 2018

AimTo assess visual acuity outcomes, and factors associated with the outcome, of paediatric cataract surgery at the Child Eye Health Tertiary Facility, Gondar, Northwest Ethiopia.MethodsThe medical records of children aged below 16 years who underwent cataract surgery between September 2010 and August 2014 were reviewed for preoperative, surgical and postoperative data.ResultsOne hundred and seventy-six eyes of 142 children (mean age 7.9 years±4.2 SD, 66% male) who had cataract surgery were included. Twenty-five per cent (35/142) of children had bilateral cataract, 18 (13%) had unilateral non-traumatic cataracts and 89 (63%) had unilateral traumatic cataracts. An intraocular lens was implanted in 93% of eyes. Visual acuities at last follow-up: bilateral cases in the better eye: good (≥6/18 or fix and follow) in 21/34 eyes (62%), borderline (<6/18–6/60) in 4 eyes (12%) and poor (<6/60) in 9 eyes (26%). In unilateral non-traumatic cases: good in 6 eyes (33%), borderline in 3 eyes (17%) and poor in 9 eyes (50%). In unilateral traumatic cases: good in 36 eyes (40%), borderline in 20 eyes (23%) and poor in 33 eyes (37%). In bilateral cataract, worse outcomes were associated with preoperative nystagmus/strabismus. In traumatic cases, worse outcomes were associated with the preoperative trauma-related complications.ConclusionsVisual acuity improved significantly after surgery, with better outcomes in bilateral cases. Early detection and surgery by a trained surgeon with good follow-up and postoperative rehabilitation can lead to better visual outcomes.
Experimental tobacco marketplace: substitutability of e-cigarette liquid for cigarettes as a function of nicotine strength
Authors: Pope Derek A , Poe Lindsey , Stein Jeffrey S , Kaplan Brent A , Heckman Bryan W , Epstein Leonard H , Bickel Warren K 
Published: April 2018

Background
The experimental tobacco marketplace (ETM) provides a method to estimate, prior to implementation, the effects of new products or policies on purchasing across various products in a complex tobacco marketplace. We used the ETM to examine the relationship between nicotine strength and substitutability of alternative products for cigarettes to contribute to the literature on regulation of e-liquid nicotine strength.

Methods
The present study contained four sampling and four ETM purchasing sessions. During sampling sessions, participants were provided 1 of 4 e-liquid strengths (randomised) to sample for 2 days followed by an ETM purchasing session. The nicotine strength sampled in the 2 days prior to an ETM session was the same strength available for purchase in the next ETM. Each participant sampled and could purchase 0 mg/mL, 6 mg/mL, 12 mg/mL and 24 mg/mL e-liquid, among other products, during the study.

Results
Cigarette demand was unaltered across e-liquid strength. E-liquid was the only product to substitute for cigarettes across more than one e-liquid strength. Substitutability increased as a function of e-liquid strength, with the 24 mg/mL displaying the greatest substitutability of all products.

Conclusions
The present study found that e-liquid substitutability increased with nicotine strength, at least up to 24 mg/mL e-liquid. However, the effects of e-liquid nicotine strength on cigarette purchasing were marginal and total nicotine purchased increased as e-liquid nicotine strength increased.
Efficient Computation of Middle Levels Gray Codes
Authors: MÜTZE Torsten , Nummenpalo Jerri 
Published: April 2018

For any integer
n
≥ 1, a
middle levels Gray code
is a cyclic listing of all bitstrings of length 2
n
+1 that have either
n
or
n
+1 entries equal to 1 such that any two consecutive bitstrings in the list differ in exactly one bit. The question whether such a Gray code exists for every
n
≥ 1 has been the subject of intensive research during the past 30 years and has been answered affirmatively only recently [T. Mütze. Proof of the middle levels conjecture.
Proc. London Math. Soc.
, 112(4):677--713, 2016]. In this work, we provide the first efficient algorithm to compute a middle levels Gray code. For a given bitstring, our algorithm computes the next ℓ bitstrings in the Gray code in time
O
(
n
ℓ (1+
n
/ℓ)), which is
O
(
n
) on average per bitstring provided that ℓ = Ω (
n
).