bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana)
Authors: Nigenda‐Morales Sergio F. , Hu Yibo , Beasley James C. , Ruiz‐Piña Hugo A. , Valenzuela‐Galván David , Wayne Robert K. 
Published: May 2018

AbstractSkin pigmentation and coat pigmentation are two of the best‐studied examples of traits under natural selection given their quantifiable fitness interactions with the environment (e.g., camouflage) and signalling with other organisms (e.g., warning coloration). Previous morphological studies have found that skin pigmentation variation in the Virginia opossum (Didelphis virginiana) is associated with variation in precipitation and temperatures across its distribution range following Gloger's rule (lighter pigmentation in temperate environments). To investigate the molecular mechanism associated with skin pigmentation variation, we used RNA‐Seq and quantified gene expression of wild opossums from tropical and temperate populations. Using differential expression analysis and a co‐expression network approach, we found that expression variation in genes with melanocytic and immune functions is significantly associated with the degree of skin pigmentation variation and may be underlying this phenotypic difference. We also found evidence suggesting that the Wnt/β‐catenin signalling pathway might be regulating the depigmentation observed in temperate populations. Based on our study results, we present several alternative hypotheses that may explain Gloger's rule pattern of skin pigmentation variation in opossum, including changes in pathogen diversity supporting a pathogen‐resistant hypothesis, thermal stress associated with temperate environments, and pleiotropic and epistatic interactions between melanocytic and immune genes.
A genomic evaluation of taxonomic trends through time in coast horned lizards (genus Phrynosoma)
Authors: Leaché Adam D. , McElroy Matthew T. , Trinh Anna 
Published: May 2018

AbstractDetermining the boundaries between species and deciding when to describe new species are challenging practices that are particularly difficult in groups with high levels of geographic variation. The coast horned lizards (Phrynosoma blainvillii, Phrynosoma cerroense and P. coronatum) have an extensive geographic distribution spanning many distinctive ecological regions ranging from northern California to the Cape Region of Baja California, Mexico, and populations differ substantially with respect to external morphology across much of this range. The number of taxa recognized in the group has been reevaluated by herpetologists over 20 times during the last 180 years, and typically without the aid of explicit species delimitation methods, resulting in a turbulent taxonomy containing anywhere from one to seven taxa. In this study, we evaluate taxonomic trends through time by ranking 15 of these species delimitation models (SDMs) using coalescent analyses of nuclear loci and SNPs in a Bayesian model comparison framework. Species delimitation models containing more species were generally favoured by Bayesian model selection; however, several three‐species models outperformed some four‐ and five‐species SDMs, and the top‐ranked model, which contained five species, outperformed all SDMs containing six species. Model performance peaked in the 1950s based on marginal likelihoods estimated from nuclear loci and SNPs. Not surprisingly, SDMs based on genetic data outperformed morphological taxonomies when using genetic data alone to evaluate models. The de novo estimation of population structure favours a three‐population model that matches the currently recognized integrative taxonomy containing three species. We discuss why Bayesian model selection might favour models containing more species, and why recognizing more than three species might be warranted.
Enteric glial cell activation protects enteric neurons from damage due to diabetes in part via the promotion of neurotrophic factor release
Authors: Luo P. , Liu D. , Li C. , He W.‐X. , Zhang C.‐L. , Chang M.‐J. 
Published: May 2018

AbstractBackgroundDiabetes can result in pathological changes to enteric nervous system. Our aim was to test the dynamic changes of enteric neurons and identify the role of enteric glial cells (EGCs) in regulating enteric neuron expression in diabetic rats.MethodsA single injection of streptozotocin (STZ) was used to establish diabetic rats. Animals were randomly distributed into diabetic 1‐, 4‐, 8‐, and 16‐week groups, as well as age‐matched control groups. The PGP9.5‐ and glial fibrillary acidic protein (GFAP)‐immunopositive cells were quantified by immunohistochemistry. The protein levels of PGP9.5, ChAT, nNOS, S‐100β, and c‐fos were determined by western blotting. The levels of nerve growth factor (NGF), neurotrophin 3 (NT‐3), and glial cell‐derived neurotrophic factor (GDNF) were tested by ELISA.Key ResultsAn increase in blood glucose and a decrease in body weight were observed following STZ administration. PGP9.5 expression did not change in the diabetic ileum. However, ChAT increased after 16 weeks, and nNOS decreased after 8 and 16 weeks in the ilea of diabetic rats. The absence of degeneration of enteric neurons during the acute stage of the disease could be the consequence of the up‐regulation of GFAP, S‐100β, and c‐fos. Moreover, the content of NGF, NT‐3, and GDNF in the ileum increased by varying degrees after 1 and/or 4 weeks of diabetes. Using 2 co‐culture models of EGCs and SH‐SY5Y cells in a high glucose condition, the supportive role of EGCs was further confirmed.Conclusions & InferencesEnteric glial cell activation can protect enteric neurons from damage due to diabetes in the acute stage of the disease, in part via the promotion of neurotrophin release.
An integrated approach to analyzing risk in bioeconomic models
Authors: N. Poudel Biswo , P. Paudel Krishna 
Published: May 2018

AbstractWe provide a new integrated approach to analyzing risk in a setting where both exogenous and endogenous risks are present. We explicitly model these risks to understand their implications to the precautionary principle. We find that, among other things, the increase of exogenous risk in the presence of endogenous risk has a different impact on precaution than the increase in exogenous risk in the presence of only exogenous risk. While the latter is known to decrease precaution, the former unambiguously increases the precaution in the presence of stock effect.Recommendations for Resource Managers
Two kinds of risk are prevalent. Endogenous risk is created by human action. Exogenous risk is created by nature.
Endogenous risk can be minimized by taking several actions. If there is only endogenous risk, resource managers should take precaution in extracting the resources.
Managers should take precaution in extracting resources if there are both endogenous and exogenous risk and if there is stock effect. Without stock effect, results are ambiguous.
If there is only exogenous risk, managers can do nothing. Therefore, managers should allow for the depletion of resources.
Protocol for a randomized controlled trial of piano training on cognitive and psychosocial outcomes
Authors: Bugos Jennifer 
Published: May 2018

AbstractAge‐related cognitive decline and cognitive impairment represent the fastest growing health epidemic worldwide among those over 60. There is a critical need to identify effective and novel complex cognitive interventions to promote successful aging. Since piano training engages cognitive and bimanual sensorimotor processing, we hypothesize that piano training may serve as an effective cognitive intervention, as it requires sustained attention and engages an executive network that supports generalized cognition and emotional control. Here, I describe the protocol of a randomized controlled trial (RCT) to evaluate the impact of piano training on cognitive performance in adulthood, a period associated with decreased neuroplasticity. In this cluster RCT, healthy older adults (age 60–80) were recruited and screened to control for confounding variables. Eligible participants completed an initial 3‐h assessment of standardized cognitive and psychosocial measures. Participants were stratified by age, education, and estimate of intelligence and randomly assigned to one of three groups: piano training, computer brain training, or a no‐treatment control group. Computer brain training consisted of progressively difficult auditory cognitive exercises (Brain HQ; Posit Science, 2010). Participants assigned to training groups completed a 16‐week program that met twice a week for 90 minutes. Upon program completion and at a 3‐month follow‐up, training participants and no‐treatment controls completed a posttest visit lasting 2.5 hours.
Phenotypic heterogeneity of obesity‐related brain vulnerability: one‐size interventions will not fit all
Authors: Haley Andreana P. , Oleson Stephanie , Pasha Evan , Birdsill Alex , Kaur Sonya , Thompson Janelle , Tanaka Hirofumi 
Published: May 2018

AbstractIntact memory and problem solving are key to functional independence and quality of life in older age. Considering the unprecedented demographic shift toward a greater number of older adults than children in the United States in the next few decades, it is critically important for older adults to maintain work productivity and functional independence for as long as possible. Implementing early interventions focused on modifiable risk factors for cognitive decline at midlife is a strategy with the highest chance of success at present, bearing in mind the current lack of dementia cures. We present a selective, narrative review of evidence linking nutrition, body composition, vascular health, and brain function in midlife to highlight the phenotypic heterogeneity of obesity‐related brain vulnerability and to endorse the development of individually tailored lifestyle modification plans for primary prevention of cognitive decline.
Endoscopic near‐infrared dental imaging with indocyanine green: a pilot study
Authors: Li Zhongqiang , Yao Shaomian , Xu Jian , Wu Ye , Li Chunhong , He Ziying 
Published: May 2018

AbstractCurrent dental diagnosis, especially tooth abnormalities, relies largely on X‐ray–based imaging, a technique that requires specialized skills and suffers from ionizing radiation. Here, we present a pilot study in rats of an efficient, ionizing‐radiation–free and easy‐to‐use alternative for dental imaging. Postnatal rats at different ages were injected with indocyanine green and molars were imaged by a laboratory‐designed endoscopic near‐infrared (NIR) dental imaging system. The results indicate that the endoscopic NIR dental imaging can be used to observe the morphology of postnatal rat molars, especially at early postnatal stages when morphology of the molar is indistinguishable under visible conditions. A small abnormal cusp was observed and distinguished from the normal cusps by the NIR dental imaging system. Dental structures, such as unerupted molars, can be imaged as soon as 10 min after the injection of indocyanine green; imaging after 24 h shows improved imaging contrast. Overall, the endoscopic NIR fluorescence dental imaging system described here may be useful in dental research; this technique may serve as a safe, real‐time imaging tool for dental diagnosis and treatment beyond experimental systems in the future.
HOP family plays a major role in long‐term acquired thermotolerance in Arabidopsis
Authors: Fernández‐Bautista Nuria , Fernández‐Calvino Lourdes , Muñoz Alfonso , Toribio René , Mock Hans P. , Castellano M. Mar 
Published: May 2018

AbstractHSP70‐HSP90 organizing protein (HOP) is a family of cytosolic cochaperones whose molecular role in thermotolerance is quite unknown in eukaryotes and unexplored in plants.In this article, we describe that the three members of the AtHOP family display a different induction pattern under heat, being HOP3 highly regulated during the challenge and the attenuation period. Despite HOP3 is the most heat‐regulated member, the analysis of the hop1 hop2 hop3 triple mutant demonstrates that the three HOP proteins act redundantly to promote long‐term acquired thermotolerance in Arabidopsis. HOPs interact strongly with HSP90 and part of the bulk of HOPs shuttles from the cytoplasm to the nuclei and to cytoplasmic foci during the challenge. RNAseq analyses demonstrate that, although the expression of the Hsf targets is not generally affected, the transcriptional response to heat is drastically altered during the acclimation period in the hop1 hop2 hop3 triple mutant. This mutant also displays an unusual high accumulation of insoluble and ubiquitinated proteins under heat, which highlights the additional role of HOP in protein quality control. These data reveal that HOP family is involved in different aspects of the response to heat, affecting the plant capacity to acclimate to high temperatures for long periods.
Characteristics of perceived electromagnetic hypersensitivity in the general population
Authors: Gruber Michael J. , Palmquist Eva , Nordin Steven 
Published: May 2018

Health problems evoked in the presence of electrical equipment is a concern, calling for better understanding for characteristics of electromagnetic hypersensitivity (EHS) in the general population. The present study investigated demographics, lifestyle factors, frequency and duration, coping strategies, proportion meeting clinical criteria for intolerance attributed to electromagnetic fields (EMF) and comorbidity. Using data from a large‐scale population‐based questionnaire study, we investigated persons with self‐reported (n = 91) EHS in comparison to referents (n = 3,250). Middle age, female sex and poor perceived health was found to be associated with EHS. More than 50% in the EHS group reported having EMF‐related symptoms more often than once a week, and the mean number of years experiencing EHS was 10.5. More than half of the EHS group reported that their symptoms started after a high‐dose or long‐term EMF exposure, that they actively tried to avoid EMF sources and that they mostly could affect the EMF environment. A minority of the EHS group had sought medical attention, been diagnosed by a physician or received treatment. Exhaustion syndrome, anxiety disorder, back/joint/muscle disorder, depression, functional somatic syndrome and migraine were comorbid with EHS. The results provide ground for future study of these characteristic features being risk factors for development of EHS and or consequences of EHS.
Junior doctors’ perspectives on transfusion education in Australia
Authors: Flores C. J. , Quested B. , Spigiel T. , Thomson A. , Saxon B. 
Published: May 2018

BackgroundEarly postgraduate training is a critical period to develop skills and to influence future clinical practice. Little is known about Australian junior doctors' existing transfusion knowledge and its application in patient care. This study explored their transfusion practice education preferences, developed tools to assist their practice and assessed the usefulness of these tools.MethodsA design‐based study was conducted in two phases from April 2016 to March 2017. Phase 1 involved focus group sessions in six hospitals. Transcripts of audio recordings were analysed using thematic analysis. Findings were considered when developing transfusion practice support tools. Phase 2 surveyed junior doctors’ response to the tools provided during orientation in five hospitals. Participation was voluntary.ResultsFifty‐two junior doctors participated in the focus groups. Their priority was to be able to practice safely, appropriately and confidently. Preferred format for transfusion learning included expert‐led face‐to‐face education; printed tools, for example lanyard cards; and for one app that covers essential aspects of transfusion practice. Adverse events management and practical transfusion prescribing were topics of most importance. Thirty‐nine survey respondents found the transfusion practice support tools useful and recommended their use to complement practice.ConclusionThere is a need for improved education to ensure best transfusion practice and patient outcomes. Australian junior doctors want immediate, practical, reliable transfusion information from credible sources to support them in practicing safely and confidently. Their educational needs are driven by real‐time patient management. Promotion of the available resources and tools provided by the blood sector is important.
Discovery of Two Native Baeyer-Villiger Monooxygenases for Asymmetric Synthesis of Bulky Chiral Sulfoxides
Authors: Zhang Yan , Liu Feng , Xu Na , Wu Yin-Qi , Zheng Yu-Cong , Zhao Qian , Lin Guoqiang , Yu Hui-Lei , Xu Jian-He 
Published: May 2018

ABSTRACT

Two Baeyer-Villiger monooxygenases (BVMOs), designated
Bo
BVMO and
Am
BVMO, were discovered from
Bradyrhizobium oligotrophicum
and
Aeromicrobium marinum
, respectively. Both monooxygenases displayed novel features for catalyzing the asymmetric sulfoxidation of bulky and pharmaceutically relevant thioethers. Evolutionary relationship and sequence analysis revealed that the two BVMOs belong to the family of typical type I BVMOs and the subtype ethionamide monooxygenase. Both BVMOs are active toward medium- and long-chain aliphatic ketones as well as various thioether substrates but are ineffective toward cyclohexanone, aromatic ketones, and other typical BVMO substrates.
Bo
BVMO and
Am
BVMO showed the highest activities (0.117 and 0.025 U/mg protein, respectively) toward thioanisole among the tested substrates. Furthermore, these BVMOs exhibited distinct activity and excellent stereoselectivity toward bulky and prochiral prazole thioethers, which is a unique feature of this family of BVMOs. No native enzyme has been reported for the asymmetric sulfoxidation of bulky prazole thioethers into chiral sulfoxides. The identification of
Bo
BVMO and
Am
BVMO provides an important scaffold for discovering enzymes capable of asymmetrically oxidizing bulky thioether substrates by genome mining.

IMPORTANCE
Baeyer-Villiger monooxygenases (BVMOs) are valuable enzyme catalysts that are an alternative to the chemical Baeyer-Villiger oxidation reaction. Although BVMOs display broad substrate ranges, no native enzymes were reported to have activity toward the asymmetric oxidation of bulky prazole-like thioether substrates. Herein, we report the discovery of two type I BVMOs from
Bradyrhizobium oligotrophicum
(
Bo
BVMO) and
Aeromicrobium marinum
(
Am
BVMO) which are able to catalyze the asymmetric sulfoxidation of bulky prazole thioethers (proton pump inhibitors [PPIs], a group of drugs whose main action is a pronounced and long-lasting reduction of gastric acid production). Efficient catalysis of omeprazole oxidation by
Bo
BVMO was developed, indicating that this enzyme is a promising biocatalyst for the synthesis of bulky and pharmaceutically relevant chiral sulfoxide drugs. These results demonstrate that the newly identified enzymes are suitable templates for the discovery of more and better thioether-converting BVMOs.
Complete Genome Sequences of 10 Yersinia pseudotuberculosis Isolates Recovered from Wild Boars in Germany
Authors: Reinhardt Marie , Hammerl Jens A. , Hertwig Stefan 
Published: May 2018

ABSTRACT

We report here the draft genome sequences of 10
Yersinia pseudotuberculosis
isolates recovered from tonsils of wild boars hunted between 2015 and 2016 in Germany. Whole-genome sequencing and bioinformatic analyses were performed to assess the diversity of
Y. pseudotuberculosis
, which may result in human infections caused by the consumption of game meat.
Draft Genome Sequences of Two Salmonella Strains Isolated from Wild Animals on the Eastern Shore of Virginia
Authors: Libuit Kevin G. , Turner Lauren 
Published: May 2018

ABSTRACT

Antimicrobial-resistant (AMR)
Salmonella
infections pose a significant public health threat. Here, we announce two draft genomes of
Salmonella
strains isolated from wildlife harboring an alarming array of antibiotic resistance genes. Continued investigations of these genomes will provide insight into the possible attribution of AMR
Salmonella
infection of wild animals.
Genomic Sequence of the WHO International Standard for Hepatitis A Virus RNA
Authors: Jenkins Adrian , Minhas Rehan , Morris Clare , Berry Neil 
Published: May 2018

ABSTRACT
The World Health Organization (WHO) international standard for hepatitis A virus (HAV) RNA nucleic acid assays was characterized by complete genome sequencing. The entire coding sequence and noncoding regions were assigned HAV genotype IB. This information will aid the design, development, and evaluation of HAV RNA amplification assays.
Genome Sequence of a Novel Alloherpesvirus Isolated from Glass Catfish (Kryptopterus bicirrhis)
Authors: Henriquez Rachel N. , Polchana Jaree , Kanchanakhan Somkiat , Davison Andrew J. , Waltzek Thomas B. , Subramaniam Kuttichantran 
Published: May 2018

ABSTRACT
The 149,343-bp genome of silurid herpesvirus 1, which was isolated in Thailand from glass catfish, was sequenced. The genome was most closely related to that of ictalurid herpesvirus 2, which infects black bullhead catfish. To our knowledge, this was the first silurid catfish alloherpesvirus genome to be sequenced.
First Complete Genome Sequence of an Isolate of Tomato Mottle Mosaic Virus Infecting Plants of Solanum lycopersicum in South America
Authors: Nagai Alice , Duarte Lígia M. L. , Chaves Alexandre L. R. , Alexandre Maria A. V. , Ramos-González Pedro L. , Chabi-Jesus Camila , Harakava Ricardo , dos Santos Déborah Y. A. C. 
Published: May 2018

ABSTRACT
The complete nucleotide sequence of an isolate of tomato mottle mosaic virus (ToMMV) was determined. The virus, originally isolated from symptomatic tomato plants found in a county near the city of São Paulo, Brazil, has a genome with 99% nucleotide sequence identity with ToMMV from Mexico, China, Spain, and the United States.
Changes in IgA Protease Expression Are Conferred by Changes in Genomes during Persistent Infection by Nontypeable Haemophilus influenzae in Chronic Obstructive Pulmonary Disease
Authors: Gallo Mary C. , Kirkham Charmaine , Eng Samantha , Bebawee Remon S. , Kong Yong , Pettigrew Melinda M. , Tettelin Hervé , Murphy Timothy F. 
Published: May 2018

ABSTRACT

Nontypeable
Haemophilus influenzae
(NTHi) is an exclusively human pathobiont that plays a critical role in the course and pathogenesis of chronic obstructive pulmonary disease (COPD). NTHi causes acute exacerbations of COPD and also causes persistent infection of the lower airways. NTHi expresses four IgA protease variants (A1, A2, B1, and B2) that play different roles in virulence. Expression of IgA proteases varies among NTHi strains, but little is known about the frequency and mechanisms by which NTHi modulates IgA protease expression during infection in COPD. To assess expression of IgA protease during natural infection in COPD, we studied IgA protease expression by 101 persistent strains (median duration of persistence, 161 days; range, 2 to 1,422 days) collected longitudinally from patients enrolled in a 20-year study of COPD upon initial acquisition and immediately before clearance from the host. Upon acquisition, 89 (88%) expressed IgA protease. A total of 16 of 101 (16%) strains of NTHi altered expression of IgA protease during persistence. Indels and slipped-strand mispairing of mononucleotide repeats conferred changes in expression of
igaA1
,
igaA2
, and
igaB1
. Strains with
igaB2
underwent frequent changes in expression of IgA protease B2 during persistence, mediated by slipped-strand mispairing of a 7-nucleotide repeat, TCAAAAT, within the open reading frame of
igaB2
. We conclude that changes in
iga
gene sequences result in changes in expression of IgA proteases by NTHi during persistent infection in the respiratory tract of patients with COPD.