bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alopecia areata totalis and universalis: a multicenter review of 132 patients in Spain
Authors: Vañó‐Galván S. , Fernández‐Crehuet P. , Grimalt R. , Garcia‐Hernandez M.J. , Rodrigues‐Barata R. , Arias‐Santiago S. , Molina‐Ruiz A. , Garcia‐Lora E. , Dominguez‐Cruz J. , Brugues A. , Ferrando J. , Serrano‐Falcón C. , Serrano S. , Paoli J. , Camacho F. 
Published: September 2016

AbstractBackgroundAlopecia areata totalis (AAT) and universalis (AAU) pose a therapeutic challenge.ObjectiveTo describe the clinical and epidemiological features, therapeutic response and prognostic factors in a large series of patients diagnosed with AAT and AAU.MethodsThis retrospective multicenter study included patients diagnosed with AAT/AAU with a minimum follow‐up of 12 months. Response was assessed based on the regrowth of scalp hair.ResultsIn all, 132 patients (92 women and 40 men) – 80 (61%) diagnosed with AAU and 52 (39%) diagnosed with AAT – were included. The median time between the presentation of alopecia areata (AA) and the development of extensive AA was 1 year and it was less than 4 years in 121 patients (91%). There was an initial response to treatment in 64% of patients, although only 14% presented a persistent response. Adverse side effects from the medications used were detected in 33% of patients. The prognostic factors associated with poor response were the presence of AAU and a positive family history of AA.ConclusionsTreatment of AAT and AAU is challenging. Although an initial regrowth may be achieved, the duration of response is usually short. There were no significant differences on the effectiveness or duration of response between the various systemic therapies.
Lytic transglycosylases LtgA and LtgD perform distinct roles in remodeling, recycling and releasing peptidoglycan in Neisseria gonorrhoeae
Authors: Schaub Ryan E. , Chan Yolande A. , Lee Mijoon , Hesek Dusan , Mobashery Shahriar , Dillard Joseph P. 
Published: September 2016

SummaryNeisseria gonorrhoeae releases peptidoglycan (PG) fragments during infection that provoke a large inflammatory response and, in pelvic inflammatory disease, this response leads to the death and sloughing of ciliated cells of the Fallopian tube. We characterized the biochemical functions and localization of two enzymes responsible for the release of proinflammatory PG fragments. The putative lytic transglycosylases LtgA and LtgD were shown to create the 1,6‐anhydromuramyl moieties, and both enzymes were able to digest a small, synthetic tetrasaccharide dipeptide PG fragment into the cognate 1,6‐anhydromuramyl‐containing reaction products. Degradation of tetrasaccharide PG fragments by LtgA is the first demonstration of a family 1 lytic transglycosylase exhibiting this activity. Pulse‐chase experiments in gonococci demonstrated that LtgA produces a larger amount of PG fragments than LtgD, and a vast majority of these fragments are recycled. In contrast, LtgD was necessary for wild‐type levels of PG precursor incorporation and produced fragments predominantly released from the cell. Additionally, super‐resolution microscopy established that LtgA localizes to the septum, whereas LtgD is localized around the cell. This investigation suggests a model where LtgD produces PG monomers in such a way that these fragments are released, whereas LtgA creates fragments that are mostly taken into the cytoplasm for recycling.
Condition‐dependent co‐regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum
Authors: Massonnet Mélanie , Morales‐Cruz Abraham , Figueroa‐Balderas Rosa , Lawrence Daniel P. , Baumgartner Kendra , Cantu Dario 
Published: September 2016

SummaryThe ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood‐infecting fungus and a serious threat to grape production worldwide. The capability to colonize woody tissue, combined with the secretion of phytotoxic compounds, is thought to underlie its pathogenicity and virulence. Here, we describe the repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. We assembled and annotated a highly contiguous genome using single‐molecule real‐time DNA sequencing. Transcriptome profiling by RNA sequencing determined the genome‐wide patterns of expression of virulence factors both in vitro (potato dextrose agar or medium amended with grape wood as substrate) and in planta. Pairwise statistical testing of differential expression, followed by co‐expression network analysis, revealed that physically clustered genes coding for putative virulence functions were induced depending on the substrate or stage of plant infection. Co‐expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in those associated with cell wall degradation, suggesting that dynamic co‐regulation of transcriptional networks contributes to multiple aspects of N. parvum virulence. In most of the co‐expressed clusters, all genes shared at least a common motif in their promoter region, indicative of co‐regulation by the same transcription factor. Co‐expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi‐layered regulation of the virulence repertoire of N. parvum.
Pepsin in saliva as a biomarker for oropharyngeal reflux compared with 24‐hour esophageal impedance/pH monitoring in pediatric patients
Authors: Fortunato J. E. , D'Agostino R. B. , Lively M. O. 
Published: September 2016

AbstractBackgroundPepsin in saliva is a proposed biomarker for oropharyngeal reflux. Pepsin may be prevalent in saliva from subjects with gastro‐esophageal reflux and may correlate with proximal reflux by intraluminal impedance/pH monitoring (MII/pH).MethodsPatients (3 days to 17.6 years, n=90) undergoing 24‐hour MII/pH monitoring and asymptomatic controls (2 months to 13.7 years, n=43) were included. Salivary pepsin was determined using a pepsin enzyme‐linked immunosorbent assay. Eight saliva samples were collected from patients undergoing 24‐hr MII/pH: (i) before catheter placement, (ii) before and 30 minutes after each of three meals, and (iii) upon awakening. One sample was collected from each control.Key ResultsIn MII/pH subjects, 85.6% (77/90) had at least one pepsin‐positive sample compared with 9.3% (4/43) in controls. The range of pepsin observed in individual subjects varied widely over 24 hours. The average pepsin concentration in all samples obtained within 2 hours following the most recent reflux event was 30.7±135 ng/mL, decreasing to 16.5±39.1 ng/mL in samples collected more than 2 hours later. The frequency of pepsin‐positive samples correlated significantly with symptom index (rS=0.332, P=.0014), proximal (rS=0.340, P=.0010), and distal (rS=0.272, P=.0095) MII events.Conclusions & InferencesConcentration of salivary pepsin may not be an accurate measure of severity of reflux because of the wide range observed in individuals over 24 hours. Saliva samples must be obtained soon after a reflux event. Defining a regimen for optimal saliva collection may help to achieve the goal of using salivary pepsin as a biomarker for oropharyngeal reflux.Clinical Trial registryNCT01091805.
APETALA2 antagonizes the transcriptional activity of AGAMOUS in regulating floral stem cells in Arabidopsis thaliana
Authors: Huang Zhigang , Shi Ting , Zheng Binglian , Yumul Rae Eden , Liu Xigang , You Chenjiang , Gao Zhihong , Xiao Langtao , Chen Xuemei 
Published: September 2016

Summary

APETALA2 (AP2) is best known for its function in the outer two floral whorls, where it specifies the identities of sepals and petals by restricting the expression of AGAMOUS (AG) to the inner two whorls in Arabidopsis thaliana. Here, we describe a role of AP2 in promoting the maintenance of floral stem cell fate, not by repressing AG transcription, but by antagonizing AG activity in the center of the flower.

We performed a genetic screen with ag‐10 plants, which exhibit a weak floral determinacy defect, and isolated a mutant with a strong floral determinacy defect. This mutant was found to harbor another mutation in AG and was named ag‐11. We performed a genetic screen in the ag‐11 background to isolate mutations that suppress the floral determinacy defect. Two suppressor mutants were found to harbor mutations in AP2.

While AG is known to shut down the expression of the stem cell maintenance gene WUSCHEL (WUS) to terminate floral stem cell fate, AP2 promotes the expression of WUS.

AP2 does not repress the transcription of AG in the inner two whorls, but instead counteracts AG activity.
Genome‐wide association analysis reveals distinct genetic architectures for single and combined stress responses in Arabidopsis thaliana
Authors: Davila Olivas Nelson H. , Kruijer Willem , Gort Gerrit , Wijnen Cris L. , van Loon Joop J. A. , Dicke Marcel 
Published: September 2016

Summary

Plants are commonly exposed to abiotic and biotic stresses.

We used 350 Arabidopsis thaliana accessions grown under controlled conditions. We employed genome‐wide association analysis to investigate the genetic architecture and underlying loci involved in genetic variation in resistance to: two specialist insect herbivores, Pieris rapae and Plutella xylostella; and combinations of stresses, i.e. drought followed by P. rapae and infection by the fungal pathogen Botrytis cinerea followed by infestation by P. rapae.

We found that genetic variation in resistance to combined stresses by drought plus P. rapae was limited compared with B. cinerea plus P. rapae or P. rapae alone. Resistance to the two caterpillars is controlled by different genetic components. There is limited overlap in the quantitative trait loci (QTLs) underlying resistance to combined stresses by drought plus P. rapae or B. cinerea plus P. rapae and P. rapae alone. Finally, several candidate genes involved in the biosynthesis of aliphatic glucosinolates and proteinase inhibitors were identified to be involved in resistance to P. rapae and P. xylostella, respectively.

This study underlines the importance of investigating plant responses to combinations of stresses. The value of this approach for breeding plants for resistance to combinatorial stresses is discussed.
Why do plants produce so many terpenoid compounds?
Authors: Pichersky Eran , Raguso Robert A. 
Published: September 2016

SummaryAll plants synthesize a suite of several hundred terpenoid compounds with roles that include phytohormones, protein modification reagents, anti‐oxidants, and more. Different plant lineages also synthesize hundreds of distinct terpenoids, with the total number of such specialized plant terpenoids estimated in the scores of thousands. Phylogenetically restricted terpenoids are implicated in defense or in the attraction of beneficial organisms. A popular hypothesis is that the ability of plants to synthesize new compounds arose incrementally by selection when, as a result of gradual changes in their biotic partners and enemies, the ‘old’ plant compounds were no longer effective, a process dubbed the ‘coevolutionary arms race’. Another hypothesis posits that often the sheer diversity of such compounds provides benefits that a single compound cannot. In this article, we review the unique features of the biosynthetic apparatus of terpenes in plants that facilitate the production of large numbers of distinct terpenoids in each species and how facile genetic and biochemical changes can lead to the further diversification of terpenoids. We then discuss evidence relating to the hypotheses that given ecological functions may be enhanced by the presence of mixtures of terpenes and that the acquisition of new functions by terpenoids may favor their retention once the original functions are lost.
How functional disability relates to dentition in community‐dwelling older adults in Brazil
Authors: Antunes JLF , de Andrade FB , Peres MA 
Published: September 2016

ObjectiveTo assess the association between dentition status and functional disabilities among community‐dwelling older individuals.Subjects and methodsA total of 5012 individuals aged 65–74 were interviewed in 2013 during a nationwide community‐based survey. This cross‐sectional study used a questionnaire including information on dentition, locomotion impairment, difficulties in basic and instrumental activities of daily life, socio‐demographic characteristics, behaviour and general health status. Poisson regression models assessed prevalence ratios (PR) and 95% confidence intervals (95% CI).ResultsAbout 31.3% of older people in Brazil reported having ≥21 preserved teeth, the condition for a functional dentition without prosthetic appliances. This proportion was significantly lower among individuals with locomotion impairment and difficulties in basic and instrumental activities of daily life. After adjusting for relevant covariates, functional dentition remained statistically associated with severe (PR = 0.69, 95% CI = 0.15–0.63) and total (PR = 0.69, 95% CI = 0.26–0.44) locomotion impairments, and difficulties in basic activities of daily life (PR = 0.70, 95% CI = 0.53–0.93).ConclusionHaving a functional dentition was significantly less prevalent among those affected by functional disabilities, and this association is unlikely to be due to insufficient control for relevant covariates. The association between dentition and functional disability is bidirectional and involves a complex interplay of one upon the other, and of factors that influence both outcomes.
The emerging role of long non‐coding RNAs in cutaneous melanoma
Authors: Leucci Eleonora , Coe Elizabeth A. , Marine Jean‐Christophe , Vance Keith W. 
Published: September 2016

SummaryMalignant melanoma is a highly aggressive form of skin cancer, the incidence of which is rising rapidly. Although MAPK‐targeting therapies and immune checkpoint blockade are emerging as attractive therapeutic approaches, their utility is limited to only a subset of patients who often acquire resistance. A better understanding of the aetiologies and genetic underpinnings of melanoma is therefore critical for the development of adjuvant or alternative therapeutic strategies aimed at increasing the proportion of responders and improving treatment efficacy. A key step in identifying novel therapeutic targets may be the shift in focus from the protein‐coding components to the non‐coding portion of the genome. The latter, representing about 98% of the genome, serves as a template for the transcription of many thousands of long non‐coding RNAs (lncRNAs). Intriguingly, lncRNA loci are frequently mutated or altered in a variety of cancers, including melanoma, and there is growing evidence that lncRNAs can function as cancer‐causing oncogenes or tumour suppressors. In this review, we summarize recent data highlighting the importance of lncRNAs in the biology of melanoma and their potential utility as biomarkers and therapeutic targets.
Amelioration of drought tolerance in wheat by the interaction of plant growth‐promoting rhizobacteria
Authors: Gontia‐Mishra I. , Sapre S. , Sharma A. , Tiwari S. 
Published: September 2016

Abstract

Drought stress adversely affects the growth and yield of wheat. The present study was planned to investigate the effect of inoculation of plant‐growth promoting rhizobacteria (PGPR) strains IG 3 (Klebsiella sp.), IG 10 (Enterobacter ludwigii) and IG 15 (Flavobacterium sp.) in improving drought tolerance in wheat.

These PGPR strains were screened for drought tolerance in nutrient broth supplemented with different concentrations (0–25%) of polyethylene glycol (PEG6000). Effect of PGPR inoculation on various physiological, biochemical parameters and gene expression of stress responsive genes were studied under drought stress. Root colonization at the surface and interiors of roots was demonstrated using scanning electron microscopy (SEM) and tetrazolium staining, respectively.

Drought stress significantly affected various growth parameters, water status, membrane integrity, osmolyte accumulation and stress‐responsive gene expressions, which were positively altered by PGPR‐inoculation in wheat. Quantitative real‐time (qRT)‐PCR analysis revealed the up regulation of some stress‐related genes (DREB2A and CAT1) in un‐inoculated wheat plants exposed to drought stress. PGPR‐inoculated plants showed attenuated transcript levels suggesting improved drought tolerance due to interaction of PGPRs.

The PGPR strain IG 3 was found to be the best in terms of influencing biochemical and physiological status of the seedlings under drought stress. Our report demonstrates the role of PGPRs Enterobacter ludwigii and Flavobacterium sp. in plant growth promotion of wheat plants under drought stress. The study reports the potential of PGPR in alleviating drought stress in wheat which could be used as potent biofertilizers.
Genetic and phenotypic diversity of Mediterranean populations of the olive knot pathogen, Pseudomonas savastanoi pv. savastanoi
Authors: Moretti C. , Vinatzer B. A. , Onofri A. , Valentini F. , Buonaurio R. 
Published: September 2016

Pseudomonas savastanoi pv. savastanoi (Psav) is a member of P. syringae sensu lato, and causes olive knot disease, a disease first reported over 2000 years ago. Analysing 124 isolates of Psav from 15 countries by rep‐PCR, the population genetic structure of Psav was investigated. A total of 113 distinct fingerprints were detected. Cluster analysis revealed the existence of two clusters and four subclusters. These clusters were associated with the geographic origin of isolates, which in turn correspond to historic human migration events and trade routes across the Mediterranean Sea. In contrast, multilocus sequence typing (MLST) of 2788 bp of the gapA, gltA, gyrB and rpoD genes found only one variable site among 77 representative isolates. Virulence variation was observed within the Psav population, with the most virulent strains generating knots that had a weight that was 10‐fold greater than those generated by the least virulent strains. Taken together, these data suggest that today's Psav population is the result of clonal expansion of a single strain, that moderate migration of the pathogen occurred between countries, and that changes in virulence arose during its evolution.
Further progress on the phylogeny of Noctuoidea (Insecta: Lepidoptera) using an expanded gene sample
Authors: REGIER JEROME C. , MITTER CHARLES , MITTER KIM , CUMMINGS MICHAEL P. , BAZINET ADAM L. , HALLWACHS WINIFRED , JANZEN DANIEL H. , ZWICK ANDREAS 
Published: September 2016

AbstractMajor progress has been made recently toward resolving the phylogeny of Noctuoidea, the largest superfamily of Lepidoptera. However, numerous questions and weakly supported nodes remain. In this paper we independently check and extend the main findings of multiple recent authors by performing maximum‐likelihood analyses of 5–19 genes (6.7–18.6 kb) in 74 noctuoids representing all the families and a majority of the subfamilies. Our results strongly support the six family system of Zahiri et al., with the former Lymantriidae and Arctiidae subsumed within the huge family Erebidae, and Noctuidae restricted largely to the subfamilies with so‐called trifine hindwing venation. Our data also strongly corroborate monophyly of the set of four families with quadrifid forewing venation, to the exclusion of Notodontidae, and removal from the latter of Oenosandridae. Other among‐family relationships, however, remain unsettled. Our evidence is equivocal on the position of Oenosandridae, which are sister group to either Notodontidae alone or to all other noctuoids. Like other recent nuclear gene studies, our results also provide no strong support for relationships among the four quadrifid forewing families. In contrast, within families our analyses significantly expand the list of robustly resolved relationships, while introducing no strong conflicts with previous molecular studies. Within Notodontidae, for which we present the largest molecular taxon sample to date, we find strong evidence for polyphyly for some, or all, recent definitions of the subfamilies Thaumetopoeinae, Pygaerinae, Notodontinae and Heterocampinae. Deeper divergences are incompletely resolved but there is strong support for multiple ‘backbone’ nodes subtending most of the subfamilies studied. Within Erebidae, we find much agreement and no strong conflict with a recent previous study regarding relationships among subfamilies, and somewhat stronger support. Although many questions remain, the two studies together firmly resolve positions for over half the subfamilies. Within Noctuidae, we find no strong conflict with previous molecular studies regarding relationships among subfamilies, but much stronger resolution along the ‘backbone’ of the phylogeny. Combining information from multiple studies yields strongly resolved positions for most of the subfamilies. Finally, our results strongly suggest that the tribes Pseudeustrotiini and Prodeniini, currently assigned to the largest subfamily, Noctuinae, do not belong there. In sum, our results provide additional corroboration for the main outlines of family‐level phylogeny in Noctuoidea, and contribute toward resolving relationships within families.
Titanium wound chambers for wound healing research
Authors: Nuutila Kristo , Singh Mansher , Kruse Carla , Philip Justin , Caterson Edward J. , Eriksson Elof 
Published: September 2016

AbstractStandardized and reproducible animal models are crucial in medical research. Rodents are commonly used in wound healing studies since, they are easily available, affordable and simple to handle and house. However, the most significant limitation of rodent models is that the wounds heal by contraction while in humans the primary mechanisms of healing are reepithelialization and granulation tissue formation. The robust contraction results in faster wound closure that complicates the reproducibility of rodent studies in clinical trials. We have developed a titanium wound chamber for rodent wound healing research. The chamber is engineered from two pieces of titanium and is placed transcutaneously on the dorsum of a rodent. The chamber inhibits wound contraction and provides a means for controlled monitoring and sampling of the wound environment in vivo with minimal foreign body reaction. This technical report introduces two modalities utilizing the titanium chambers in rats: (1) Wound in a skin island model and, (2) Wound without skin model. Here, we demonstrate in rats how the “wound in a skin island model” slows down wound contraction and how the “wound without skin” model completely prevents the closure. The titanium wound chamber provides a reproducible standardized models for wound healing research in rodents.
A Primer on Infectious Disease Bacterial Genomics
Authors: Lynch Tarah , Petkau Aaron , Knox Natalie , Graham Morag , Van Domselaar Gary 
Published: September 2016

SUMMARY
The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.