bluuebunny/crossref_metadata_2025 huggingface dataset:
Is removal of weak connections necessary for graph-theoretical analysis of dense weighted structural connectomes?
Authors: Civier Oren , Smith Robert Elton , Yeh Chun-Hung , Connelly Alan , Calamante Fernando
Published: January 2019

Recent advances in diffusion MRI tractography permit the generation of dense weighted structural connectomes that offer greater insight into brain organization. However, these efforts are hampered by the lack of consensus on how to extract topological measures from the resulting graphs. Here we evaluate the common practice of removing the graphs’ weak connections, which is primarily intended to eliminate spurious connections and emphasize strong connections. Because this processing step requires arbitrary or heuristic-based choices (e.g., setting a threshold level below which connections are removed), and such choices might complicate statistical analysis and inter-study comparisons, in this work we test whether removing weak connections is indeed necessary. To this end, we systematically evaluated the effect of removing weak connections on a range of popular graph-theoretical metrics. Specifically, we investigated if (and at what extent) removal of weak connections introduces a statistically significant difference between two otherwise equal groups of healthy subjects when only applied to one of the groups. Using data from the Human Connectome Project, we found that removal of weak connections had no statistical effect even when removing the weakest

~70-90% connections. Removing yet a larger extent of weak connections, thus reducing connectivity density even further, did produce a predictably significant effect. However, metric values became sensitive to the exact connectivity density, which has ramifications regarding the stability of the statistical analysis. This pattern persisted whether connections were removed by connection strength threshold or connectivity density, and for connectomes generated using parcellations at different resolutions. Finally, we showed that the same pattern also applies for data from a clinical-grade MRI scanner. In conclusion, our analysis revealed that removing weak connections is not necessary for graph-theoretical analysis of dense weighted connectomes. Because removal of weak connections provides no practical utility to offset the undesirable requirement for arbitrary or heuristic-based choices, we recommend that this step is avoided in future studies.

Declarations of interest

none.
Analysis ofBrevundimonas subvibrioidesdevelopmental signaling systems reveals unexpected differences between phenotypes and c-di-GMP levels
Authors: Sperling Lauryn , Kaever Volkhard , Curtis Patrick D.
Published: January 2019

The DivJ-DivK-PleC signaling system ofCaulobacter crescentusis a signaling network that regulates polar development and the cell cycle. This system is conserved in related bacteria, including the sister genusBrevundimonas. Previous studies had shown unexpected phenotypic differences between theC. crescentus divKmutant and the analogous mutant ofBrevundimonas subvibrioides, but further characterization was not performed. Here, phenotypic assays analyzing motility, adhesion, and pilus production (the latter characterized by a newly discovered bacteriophage) revealed thatdivJandpleCmutants have mostly similar phenotypes as theirC. crescentushomologs, butdivKmutants maintain largely opposite phenotypes than expected. Suppressor mutations of theB. subvibrioides divKmotility defect were involved in cyclic-di-GMP (c-di-GMP) signaling, including the diguanylate cyclasedgcB, andcleDwhich is hypothesized to affect flagellar function in a c-di-GMP dependent fashion. However, the screen did not identify the diguanylate cyclasepleD.Disruption ofpleDinB. subvibrioidescaused hypermotility in wild-type, but not in thedivKbackground. Analysis of c-di-GMP levels in these strains revealed incongruities between c-di-GMP levels and displayed phenotypes with a notable result that suppressor mutations altered phenotypes but had little impact on c-di-GMP levels in thedivKbackground. Conversely, when c-di-GMP levels were artificially manipulated, alterations of c-di-GMP levels in thedivKstrain had minimal impact on phenotypes. These results suggest that DivK performs a critical function in the integration of c-di-GMP signaling into theB. subvibrioidescell cycle.

Importance

Cyclic-di-GMP signaling is one of the most broadly conserved signaling systems in bacteria, but there is little understanding of how this system directly affects the physiology of the organism. InC. crescentus, c-di-GMP has been integrated into the developmental cell cycle, but there is increasing evidence that environmental factors can impact this system as well. The research presented here suggests that developmental signaling could impact physiological Processes in c-di-GMP dependent and independent ways. This hints that the integration of these signaling networks could be more complex than previously hypothesized, which could have a bearing on the larger field of c-di-GMP signaling. In addition, this work further examines how much models developed in one organism can be extrapolated to related organisms.
Bacteriophage resistance alters antibiotic mediated intestinal expansion of enterococci
Authors: Chatterjee Anushila , Johnson Cydney N. , Luong Phat , Hullahalli Karthik , McBride Sara W. , Schubert Alyxandria M. , Palmer Kelli L. , Carlson Paul E. , Duerkop Breck A.
Published: January 2019

Enterococcus faecalisis a human intestinal pathobiont with intrinsic and acquired resistance to many antibiotics, including vancomycin. Nature provides a diverse and virtually untapped repertoire of bacterial viruses, or bacteriophages (phages), that could be harnessed to combat multi-drug resistant enterococcal infections. Bacterial phage resistance represents a potential barrier to the implementation of phage therapy, emphasizing the importance of investigating the molecular mechanisms underlying the emergence of phage resistance. Using a cohort of 19 environmental lytic phages with tropism againstE. faecalis, we found that these phages require the enterococcal polysaccharide antigen (Epa) for productive infection. Epa is a surface-exposed heteroglycan synthesized by enzymes encoded by both conserved and strain specific genes. We discovered that exposure to phage selective pressure favors mutation in non-conservedepagenes both in culture and in a mouse model of intestinal colonization. Despite gaining phage resistance,epamutant strains exhibited a loss of resistance to the cell wall targeting antibiotics, vancomycin and daptomycin. Finally, we show that anE. faecalis epamutant strain is deficient in intestinal colonization, cannot expand its population upon antibiotic-driven intestinal dysbiosis and fails to be efficiently transmitted to juvenile mice following birth. This study demonstrates that phage therapy could be used in combination with antibiotics to target enterococci within a dysbiotic microbiota. Enterococci that evade phage therapy by developing resistance may be less fit at colonizing the intestine and sensitized to vancomycin preventing their overgrowth during antibiotic treatment.
Diversity matters: Deep-sea mussels harbor multiple symbiont strains
Authors: Ansorge Rebecca , Romano Stefano , Sayavedra Lizbeth , Kupczok Anne , Tegetmeyer Halina E. , Dubilier Nicole , Petersen Jillian
Published: January 2019

Genetic diversity of closely-related free-living microbes is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Indeed, symbiont strain diversity has long assumed to be restricted in intracellular bacteria associated with animals. Here, we sequenced the metagenomes and metatranscriptomes of 18Bathymodiolusmussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individualBathymodiolusmussels. Co-occurring symbiont strains differed extensively in key metabolic functions, such as the use of energy and nutrient sources, electron acceptors and viral defense mechanisms. Most strain-specific genes were expressed, highlighting their adaptive potential. We show that fine-scale diversity is pervasive inBathymodiolussymbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, not the host, feeds the symbionts.
Requirement for TRanslocon-Associated Protein (TRAP) α in insulin biogenesis
Authors: Li Xin , Itani Omar A. , Haataja Leena , Dumas Kathleen J. , Yang Jing , Cha Jeeyeon , Flibotte Stephane , Shih Hung-Jen , Xu Jialu , Qi Ling , Arvan Peter , Liu Ming , Hu Patrick J.
Published: January 2019

The mechanistic basis for the biogenesis of peptide hormones and growth factors is poorly understood. Here we show that the conserved endoplasmic reticulum (ER) membrane translocon-associated protein (TRAP) α, also known as signal sequence receptor 1 (SSR1)1, plays a critical role in the biosynthesis of insulin. A genetic screen in the nematodeCaenorhabditis elegansrevealedtrap-1, which encodes theC. elegansTRAPα ortholog, as a modifier of DAF-2 insulin receptor (InsR) signaling. Genetic analysis indicates that TRAP-1 acts upstream of DAF-2/InsR to controlC. elegansdevelopment. EndogenousC. elegansTRAP-1 and mammalian TRAPα both localized to the ER. In pancreatic beta cells, TRAPα deletion impaired preproinsulin translocation but did not affect the synthesis of α1-antitrypsin, indicating that TRAPα selectively influences the translocation of a subset of secreted proteins. Surprisingly, loss of TRAPα function also resulted in disruption of distal steps in insulin biogenesis including proinsulin processing and secretion. These results show that TRAPα assists in the ER translocation of preproinsulin and unveil unanticipated additional consequences of TRAPα loss-of-function on the intracellular trafficking and maturation of proinsulin. The association of common intronic single nucleotide variants in the human TRAPα gene with susceptibility to Type 2 diabetes and pancreatic beta cell dysfunction2suggests that impairment of preproinsulin translocation and proinsulin trafficking may contribute to the pathogenesis of Type 2 diabetes.
Same-Species Contamination Detection with Variant Calling Information from Next Generation Sequencing
Authors: Jiang Tao , Buchkovich Martin , Motsinger-Reif Alison
Published: January 2019

Motivation

Same-species contamination detection is an important quality control step in genetic data analysis. Compared with widely discussed cross-species contamination, same-species contamination is more challenging to detect, and there is a scarcity of methods to detect and correct for this quality control issue. Same-species contamination may be due to contamination by lab technicians or samples from other contributors. Here, we introduce a novel machine learning algorithm to detect same species contamination in next generation sequence data using support vector machines. Our approach uniquely detects such contamination using variant calling information stored in the variant call format (VCF) files (either DNA or RNA), and importantly can differentiate between same species contamination and mixtures of tumor and normal cells.

Methods

In the first stage of our approach, a change-point detection method is used to identify copy number variations or copy number aberrations (CNVs or CNAs) for filtering prior to testing for contamination. Next, single nucleotide polymorphism (SNP) data is used to test for same species contamination using a support vector machine model. Based on the assumption that alternative allele frequencies in next generation sequencing follow the beta-binomial distribution, the deviation parameter ρ is estimated by maximum likelihood method. All features of a radial basis function (RBF) kernel support vector machine (SVM) are generated using either publicly available or private training data. Lastly, the generated SVM is applied in the test data to detect contamination. If training data is not available, a default RBF kernel SVM model is used.

Results

We demonstrate the potential of our approach using simulation experiments, creating datasets with varying levels of contamination. The datasets combine, in silico, exome sequencing data of DNA from two lymphoblastoid cell lines (NA12878 and NA10855). We generated VCF files using variants identified in these data, and then evaluated the power and false positive rate of our approach to detect same species contamination. Our simulation experiments show that our method can detect levels of contamination as low as 5% with reasonable false positive rates. Results in real data have sensitivity above 99.99% and specificity at 90.24%, even in the presence of DNA degradation that has similar features to contaminated samples. Additionally, the approach can identify the difference between mixture of tumor-normal cells and contamination. We provide an R software implementation of our approach using the defcon()function in the vanquish: Variant Quality Investigation Helper R package on CRAN.
DPAC: a tool for Differential Poly(A) Site usage from poly(A)–targeted RNAseq data
Authors: Routh Andrew
Published: January 2019

Poly(A)-tail targeted RNAseq approaches, such as 3’READS, PAS-seq and Poly(A)-ClickSeq, are becoming popular alternatives to random-primed RNAseq for simplified gene expression analyses as well as to measure changes in poly(A) site usage. We and others have recently demonstrated that these approaches perform similarly to other RNAseq strategies, while saving on the volume of sequencing data required and providing a simpler library synthesis strategy. Here, we present DPAC; a streamlined pipeline for the preprocessing of poly(A)-tail targeted RNAseq data, mapping of poly(A)-sites and poly(A) clustering, and determination of differential poly(A) site usage using DESeq2. Changes in poly(A) site usage is simultaneously used to report differential gene expression, differential terminal exon usage and alternative polyadenylation (APA).
Phylogenetic systematics and evolution of the spider infraorder Mygalomorphae using genomic scale data
Authors: Opatova Vera , Hamilton Chris A. , Hedin Marshal , de Oca Laura Montes , Král Jiří , Bond Jason E.
Published: January 2019

Abstract

The Infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3,000 nominal species. This ancient group has a world-wide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here we present the most comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae conducted to date. We employ 472 loci obtained through Anchored Hybrid Enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We performed an extensive generic sampling of all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing hints to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). The three families Hermachidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY) are newly proposed. Such a major rearrangement in classification, recognizing eight newly established family-level rank taxa, is the largest the group has seen in over three decades since Raven’s (1985) taxonomic treatment.
Climate warming and plant biomechanical defences: Silicon addition contributes to herbivore suppression in a pasture grass
Authors: Johnson Scott N. , Ryalls James M. W. , Barton Craig V. M. , Tjoelker Mark G. , Wright Ian J. , Moore Ben D.
Published: January 2019

Plants, notably the Poaceae, often accumulate large amounts of silicon (Si) from the soil. Si has multiple functional roles, particularly for alleviating abiotic and biotic stresses (e.g., defence against herbivores). Recent evidence suggests that environmental change, including temperature changes, can diminish Si accumulation which could affect functions such as herbivore defence.

Using a field warming experiment, we grew a pasture grass (Phalaris aquatica) that was either supplemented or untreated with Si (+Si and −Si, respectively) under ambient and elevated (+2.8°C above ambient) air temperatures. We quantified soil water, plant growth rates, Si accumulation, leaf biomechanical properties and in situ relative growth rates of a herbivorous global insect pest (Helicoverpa armigera).

Si supplementation promoted shoot and root biomass by c. 48% and 61%, respectively under ambient temperatures, but these gains were not apparent under warmed conditions.

Warmer temperatures reduced Si uptake by −Si plants by c. 17%, potentially due to the lower levels of soil water content in warmed plots. Si supplementation, however, increased Si accumulation in leaves by c. 24% in warmed plots restoring Si levels to those seen under ambient temperatures.

Si supplementation enhanced biomechanical properties in the leaves, but this was only statistically significant under ambient temperatures; leaves of +Si plants required 42% more force to fracture and were 30% tougher at the midrib than leaves of −Si plants. The relative growth rates of H. armigera declined by 56% when feeding on +Si plants under ambient temperatures, and while Si supplementation caused a trend towards declining herbivore growth rates under warmer conditions, this was not statistically significant.

We conclude that climate warming may mitigate the beneficial effects of Si on Phalaris aquatica in the short term, potentially by reducing Si uptake. While Si uptake can be restored with Si supplementation, Si‐enhanced biomechanical defences against a global pest may not be fully restored under warmer temperatures.

A plain language summary is available for this article.
Outcomes from cytoreduction and hyperthermic intraperitoneal chemotherapy for appendiceal epithelial neoplasms
Authors: Narasimhan Vignesh , Pham Toan , Warrier Satish , Craig Lynch A. , Michael Michael , Tie Jeanne , Ramsay Robert , Heriot Alexander
Published: January 2019

Background

Appendiceal epithelial neoplasms are rare cancers. Management of peritoneal disease from appendiceal neoplasms has historically been with debulking surgery. In recent decades, the advent of cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) has become the standard of care. Here, we report our single institution 10‐year experience with CRS and HIPEC for appendiceal neoplasms.

Methods

This is a retrospective review from 1 January 2008 to 1 June 2017 of all patients undergoing CRS and HIPEC for appendiceal neoplasms. Institutional ethics approval was granted for this project.

Results

One hundred and seventy‐two patients underwent 208 CRSs during this time. Overall, 83.72% of patients had one CRS and HIPEC procedure. Pseudomyxoma peritonei from a perforated appendiceal mucinous neoplasm accounted for 67.9% of cases. The median peritoneal carcinomatosis index (PCI) was 14, with complete cytoreduction achieved in 74.2% of patients. Fifty‐four percent of patients had at least one complication, with one (0.5%) peri‐operative mortality in our cohort. For the entire cohort, the median overall survival was 104 months and a 5‐year survival of 75%. In those having a complete cytoreduction, 5‐year survival was 90%, with a median disease free interval of 63 months. PCI and completeness of cytoreduction were independent predictors of overall survival.

Conclusion

Our results demonstrate that CRS and HIPEC for appendiceal neoplasms are safe and effective. Despite carrying some morbidity, it offers patients an excellent disease free and overall survival.
Supernumerary teeth formation following subluxation of primary incisors
Authors: Manchanda Nandika , Anthonappa Robert , King Nigel
Published: January 2019

Supernumerary teeth are reported to occur in both primary and permanent dentitions, but their exact aetiology remains unclear. To date, there have been no documented reports of supernumerary teeth formation subsequent to traumatic dental injuries (TDIs) to the primary incisors. This case report illustrates such an unusual consequence where a supernumerary tooth developed subsequent to a subluxation injury to teeth 51 and 61 in a 4‐year‐old Caucasian girl. This emphasizes the importance of reviewing TDIs, as well as providing parents with sufficient information about possible sequelae at the time of trauma. Nevertheless, it also provides an excellent basis for future investigations, which are essential to establish this correlation and to prove causation.
Genomic changes in the biological control agent Cryptolaemus montrouzieri associated with introduction
Authors: Li Hao‐Sen , Heckel Gerald , Huang Yu‐Hao , Fan Wei‐Jian , Ślipiński Adam , Pang Hong
Published: January 2019

Biological control is the main purpose of intentionally introducing non‐native invertebrate species. The evolutionary changes that occur in the populations of the introduced biological control agents may determine the agent's efficiency and the environmental safety. Here, to explore the pattern and extent of potential genomic changes in the worldwide introduced predatory ladybird beetle Cryptolaemus montrouzieri, we used a reduced‐representation sequencing method to analyze the genome‐wide differentiation of the samples from two native and five introduced locations. Our analyses based on a total of 53,032 single nucleotide polymorphism loci showed that beetles from the introduced locations in Asia and Europe exhibited significant reductions in genetic diversity and high differentiation compared with the samples from the native Australian range. Each introduced population belonged to a unique genetic cluster, while the beetles from two native locations were much more similar. These genomic patterns were also detected when the dataset was pruned for genomic outlier loci (52,318 SNPs remaining), suggesting that random genetic drift was the main force shaping the genetic diversity and population structure of this biological control agent. Our results provide a genome‐wide characterization of polymorphisms in a biological control agent and reveal genomic differences that were influenced by the introduction history. These differences might complicate assessments of the efficiency of biological control and the invasion potential of this species but also indicate the feasibility of selective breeding.
Eco‐evolutionary community turnover following environmental change
Authors: Lasky Jesse R.
Published: January 2019

Co‐occurring species often differ in intraspecific genetic diversity, which in turn can affect adaptation in response to environmental change. Specifically, the simultaneous evolutionary responses of co‐occurring species to temporal environmental change may influence community dynamics. Local adaptation along environmental gradients combined with gene flow can enhance genetic diversity of traits within populations. Quantitative genetic theory shows that having greater gene flow results in (a) lower equilibrium population size due to maladaptive immigrant genotypes (migration load), but (b) faster adaptation to changing environments. Here, I build off this theory to study community dynamics of locally adapted species in response to temporal environmental changes akin to warming temperatures. Although an abrupt environmental change leaves all species initially maladapted, high gene flow species subsequently adapt faster due to greater genetic diversity. As a result, species can transiently reverse their relative abundances, but sometimes only after long lag periods. If constant temporal environmental change is applied, the community exhibits a shift toward stable dominance by species with intermediate gene flow. Notably, fast‐adapting high gene flow species can increase in absolute abundance under environmental change (although often only for a transient period) because the change suppresses superior competitors with lower gene flow. This eco‐evolutionary competitive release stabilizes ecosystem function. The eco‐evolutionary community turnover studied here parallels the purely ecological successional dynamics following disturbances. My results demonstrate how interspecific variation in life history can have far‐reaching impacts on eco‐evolutionary community response to environmental change.
Losing the trait without losing the signal: Evolutionary shifts in communicative colour signalling
Authors: Romero‐Diaz Cristina , Rivera Julio A. , Ossip‐Drahos Alison G. , Zúñiga‐Vega José Jaime , Vital‐García Cuauhcihuatl , Hews Diana K. , Martins Emília P.
Published: January 2019

Colour signalling traits are often lost over evolutionary time, perhaps because they increase vulnerability to visual predators or lose relevance in terms of sexual selection. Here, we used spectrometric and phylogenetic comparative analyses to ask whether four independent losses of a sexually selected blue patch are spectrally similar, and whether these losses equate to a decrease in conspicuousness or to loss of a signal. We found that patches were lost in two distinct ways: either increasing reflectance primarily at very long or at very short wavelengths, and that species with additional colour elements (UV, green and pink) may be evolutionary intermediates. In addition, we found that patch spectral profiles of all species were closely aligned with visual receptors in the receiver's retina. We found that loss of the blue patch makes males less conspicuous in terms of chromatic conspicuousness, but more conspicuous in terms of achromatic contrast, and that sexual dimorphism often persists regardless of patch loss. Dorsal surfaces were considerably more cryptic than were ventral surfaces, and species in which male bellies were the most similar in conspicuousness to their dorsal surfaces were also the most sexually dimorphic. These results emphasize the consistent importance of sexual selection and its flexible impact on different signal components through evolutionary time.
Use of exogenous glycine betaine and its precursor choline as osmoprotectants in Antarctic sea‐ice diatoms1
Authors: Torstensson Anders , Young Jodi N. , Carlson Laura T. , Ingalls Anitra E. , Deming Jody W.
Published: January 2019

Wide salinity ranges experienced during the seasonal freeze and melt of sea ice likely constrain many biological processes. Microorganisms generally protect against fluctuating salinities through the uptake, production, and release of compatible solutes. Little is known, however, about the use or fate of glycine betaine (GBThereafter), one of the most common compatible solutes, in sea‐ice diatoms confronted with shifts in salinity. We quantified intracellular concentrations and used [14C]‐labeled compounds to track the uptake and fate of the nitrogen‐containing osmolyteGBTand its precursor choline in three Antarctic sea‐ice diatomsNitzschia lecointei,Naviculacf.perminuta,andFragilariopsis cylindrusat −1°C. Experiments show that these diatoms have effective transporters forGBT, but take up lesser amounts of choline. Neither compound was respired. Uptake ofGBTprotected cells against hyperosmotic shock and corresponded with reduced production of extracellular polysaccharides inN. lecointeicells, which released 85% of the retainedGBTfollowing hypoosmotic shock. The ability of sea‐ice diatoms to rapidly scavenge and release compatible solutes is likely an important strategy for survival during steep fluctuations in salinity. The release and recycling of compatible solutes may play an important role in algal–bacterial interactions and nitrogen cycling within the semi‐enclosed brines of sea ice.
Identification of critical cysteine sites in brassinosteroid‐insensitive 1 and novel signaling regulators using a transient expression system
Authors: Huang Guozhong , Sun Jianhang , Bai Jiaojiao , Han Yufang , Fan Fenggui , Wang Shuangfeng , Zhang Yingying , Zou Yanmin , Han Zhifu , Lu Dongping
Published: January 2019

The plant hormones brassinosteroids (BRs) modulate plant growth and development. Cysteine (Cys) residues located in the extracellular domain of a protein are of importance for protein structure by forming disulfide bonds. To date, the systematic study of the functional significance of Cys residues in BR‐insensitive 1 (BRI1) is still lacking.

We used brassinolide‐induced exogenous bri1‐EMS‐Suppressor 1 (BES1) dephosphorylation in Arabidopsis thaliana protoplasts as a readout, took advantage of the dramatic decrease of BRI1 protein levels during protoplast isolation, and of the strong phosphorylation of BES1 by BR‐insensitive 2 (BIN2) in protoplasts, and developed a protoplast transient system to identify critical Cys sites in BRI1.

Using this system, we identified a set of critical Cys sites in BRI1, as substitution of these Cys residues with alanine residues greatly compromised the function of BRI1. Moreover, we identified two negative regulators of BR signaling, pattern‐triggered immunity compromised RLCK1 (PCRK1) and PCRK2, that were previously known to positively regulate innate immunity signaling.

This work not only provides insight into the functional importance of critical Cys residues in stabilizing the superhelical conformation of BRI1‐leucine‐rich‐repeat, but also reveals that PCRK1/2 can inversely modulate BR and plant immune signaling pathways.
Ataxia‐telangiectasia: A review of clinical features and molecular pathology
Authors: Amirifar Parisa , Ranjouri Mohammad Reza , Yazdani Reza , Abolhassani Hassan , Aghamohammadi Asghar
Published: January 2019

Ataxia‐telangiectasia (A‐T) is an autosomal recessive primary immunodeficiency (PID) disease that is caused by mutations in ataxia‐telangiectasia mutated (ATM) gene encoding a serine/threonine protein kinase. A‐T patients represent a broad range of clinical manifestations including progressive cerebellar ataxia, oculocutaneous telangiectasia, variable immunodeficiency, radiosensitivity, susceptibility to malignancies, and increased metabolic diseases. This congenital disorder has phenotypic heterogeneity, and the severity of symptoms varies in different patients based on severity of mutations and disease progression. The principal role of nuclear ATM is the coordination of cellular signaling pathways in response to DNA double‐strand breaks, oxidative stress, and cell cycle checkpoint. The pathogenesis of A‐T is not limited to the role of ATM in the DNA damage response (DDR) pathway, and it has other functions mainly in the hematopoietic cells and neurons. ATM adjusts the functions of organelles such as mitochondria and peroxisomes and also regulates angiogenesis and glucose metabolisms. However, ATM has other functions in the cells (especially cell viability) that need further investigations. In this review, we described functions of ATM in the nucleus and cytoplasm, and also its association with some disorder formation such as neurologic, immunologic, vascular, pulmonary, metabolic, and dermatologic complications.
Detection of local allergic rhinitis in children with chronic, difficult‐to‐treat, non‐allergic rhinitis using multiple nasal provocation tests
Authors: Tsilochristou Olympia , Kyriakakou Marialena , Manolaraki Ioanna , Lakoumentas John , Tiligada Ekaterini , Maragkoudakis Pavlos , Douladiris Nikolaos , Papadopoulos Nikolaos G.
Published: January 2019

Background

There is little evidence on the incidence and characteristics of local allergic rhinitis (LAR) in children. Most studies have included subjects with perennial rhinitis only, and results are based on the investigation of no more than three allergens per study. Our aim was to determine the proportion of children with LAR amongst children with chronic, difficult‐to‐treat, perennial or seasonal, rhinitis but no evidence of sensitization to aeroallergens, or other alternative diagnosis.

Methods

We performed multiple nasal provocation tests (M‐NPTs) with four locally relevant aeroallergens (Phleum pratense, Olea europea, Alternaria alternata, and Dermatophagoides pteronyssinus) in children with absence of aeroallergen sensitization, seen during a calendar year in a specialized rhinitis clinic. We additionally performed single NPT to children with allergic rhinitis (AR; positive control group). The result of the NPT was based on symptoms and acoustic rhinometry. Identification of nasal hyper‐reactivity (NHR) triggers was through a questionnaire.

Results

Local allergic rhinitis was confirmed in 29.2% (7/24) of the negative SPT/blood testing population. All but one of the children reacted to one allergen and one to two. All AR children had positive single NPT with results similar to the LAR. There were no differences in age at examination and rhinitis onset, gender distribution, family atopy, and past or current environment of residency, while the prevalence of reported NHR triggers was comparable amongst the three groups.

Conclusion

This is the first pediatric study where the seasonal or perennial rhinitis population was thoroughly tested for LAR against four aeroallergens. LAR is present in a considerable proportion of children with chronic, difficult‐to‐treat rhinitis and no sensitization to aeroallergens, and therefore, the performance of NPT should be strongly considered in these cases. There were no distinct clinical characteristics between LAR, AR, and non‐allergic rhinitis in children.
Outcome of oral immunotherapy for persistent cow’s milk allergy from 11 years of experience in Finland
Authors: Kauppila Tiina Kaisa , Paassilta Marita , Kukkonen Anna Kaarina , Kuitunen Mikael , Pelkonen Anna S. , Makela Mika J.
Published: January 2019

Background

The safety and efficacy of long‐term milk oral immunotherapy (OIT) in Finnish children with persistent cow's milk allergy (CMA) were evaluated in an open‐label, non‐randomized study.

Methods

During the 11‐year study, 296 children aged 5 years or older with immunoglobulin E (IgE)‐mediated CMA started milk OIT. Follow‐up data were collected at three time points: the post‐buildup phase, 1 year thereafter, and at the cross‐sectional long‐term follow‐up between January 2016 and December 2017. Patients were divided according to baseline milk‐specific IgE (sIgE) level and by the amount of milk consumption at the long‐term follow‐up. The high‐dose group consumed ≥2 dL of milk daily, while the failure group consumed <2 dL of milk or were on a milk‐avoidance diet.

Results

Out of the initial study group, 244/296 (83%) patients participated in the long‐term follow‐up. Among these patients, 136/244 (56%) consumed ≥2 dL of milk daily. The median follow‐up time was 6.5 years. Of the recorded markers and clinical factors, the baseline milk sIgE level was most associated with maintaining milk OIT (P < 0.001). Respiratory symptoms in the post‐buildup phase increased the risk of treatment failure (OR 3.5, 95% CI: 1.5‐8.1, P = 0.003) and anaphylaxis (OR 14.3, 95% CI: 1.8‐114, P = 0.01).

Conclusion

More than half of the patients were able to maintain the targeted milk dose in their daily diet. Baseline milk sIgE level and reactivity during the early treatment stage strongly predicted the long‐term outcome and safety of milk OIT.
Can testicular artery Doppler velocimetry values change according to the measured region in dogs?
Authors: Trautwein Luiz Guilherme Corsi , Souza Anne Kemmer , Martins Maria Isabel Mello
Published: January 2019

Contents

Testicular tissue maintenance is performed by the testicular artery, and the hemodynamics of this artery can be evaluated using Doppler ultrasonography. The aim of this study was to characterize the peak systolic velocity (PSV), end diastolic velocity (EDV), pulsatility index (PI) and resistivity index (RI) of five regions of the testicular artery in dogs, including two proposed regions and three that have been previously described. Twenty‐two dogs were used, and the PSV, EDV, PI and RI of the testicular artery were measured in five regions: proximal, medial and distal supratesticular; marginal; and intratesticular. The median values for PSV (cm/s), EDV (cm/s), PI and RI in the five regions were as follows: proximal supratesticular (23.1, 3.7, 2.1 and 0.8); medial supratesticular (17.2, 4.5, 1.5, and 0.7); distal supratesticular (12.2, 5.7, 0.8, and 0.5); marginal (11.3, 6.5, 0.5, and 0.4); and intratesticular (5.7, 3.5, 0.5, and 0.4). There was a difference between the PSV of the medial and distal supratesticular regions. There were differences in the PSV, EDV, PI and RI among the distal supratesticular, marginal and intratesticular regions. Measurements of PSV, EDV, PI and RI of the testicular artery in dogs at the proposed regions showed different results due to the hemodynamic and morphological differences of the artery during its course in the spermatic cord and to the testicles. It is necessary to identify the region in testicular artery Doppler velocimetric evaluations of dogs, given that there is a difference according to the region measured.
Deformation at the eastern margin of the Northern Canadian Cordillera: Potentially related to opening of the North Atlantic
Authors: Enkelmann Eva , Finzel Emily , Arkle Jeanette
Published: January 2019

The Northern Canadian Cordillera (NCC) comprises the Mackenzie Mountains, which are characterized by earthquakes occurring ~1,000 km east of the western North American margin. However, no recognized convergence has occurred in this inboard region since the Mesozoic to early Cenozoic formation of the Cordillera. This lack of an obvious driver for the modern NCC deformation has generated considerable debate and various geodynamic models. We show here thermal histories derived from (U‐Th‐Sm)/He data that are interpreted to indicate reactivated deformation and formation of the eastern deformation front beginning ~30 Ma. At that time the western margin of North America was mainly a transform boundary, which typically transmits very limited amount of stress into the continent. Along the northeastern margin of North America, however, the North Atlantic was opening and may have caused horizontal forces that drove deformation far to the west where the rigid craton encountered the weak Cordillera.
Rare case with plethora of upper urinary tract anomalies associated with pelviureteric junction obstruction: a surgical challenge managed with robot assistance
Authors: Parmar Kalpesh Mahesh , Tyagi Shantanu , Singh Shrawan kumar , Sharma Gopal
Published: January 2019

The genitourinary system for reasons unknown is more likely to have birth defects than any other system. The anomaly of collecting system draining the kidney represent mystifying subset of congenital anomalies. Pelviureteric junction obstruction (PUJO) is most common. Chronic obstruction can lead to stasis, urinary infection and stone formation in PUJO. Extrarenal calyces, which is characterised by presence of calyces and renal pelvis outside the renal parenchyma is one of the rare anomalies seen among the collecting system right gonadal vein drains into inferior vena cava. Its altered drainage into right renal vein is rarely seen and reported. Glut of these multiple anomalies in a single case is an extremely rare event. We hereby discuss a case of 40-year-old male patient with combination of all these anomalies and discuss the embryology, presentation and management.
Coupling acoustic tracking with conventional tag returns to estimate mortality for a coastal flatfish with high rates of emigration
Authors: Scheffel Trevor K. , Hightower Joseph E. , Buckel Jeffrey A. , Krause Jacob R. , Scharf Frederick S.
Published: January 2019

The addition of acoustic telemetry to conventional tagging studies can generate direct estimates of mortality and movement rates to inform fisheries management. We applied a combined telemetry and tag-return design to southern flounder (Paralichthys lethostigma), a coastal flatfish that demonstrates limited movements within estuarine habitats coupled with extensive ontogenetic migrations that present unique challenges for estimating mortality rates. The fates of acoustically and conventionally tagged fish were followed during 2014–2016 to estimate annual rates of fishing mortality (F), natural mortality (M), and estuarine emigration (E). Multistate models estimated southern flounder annual F for each of the 3 years at two spatial scales (New River estuary F = 0.49–1.61; North Carolina coast F = 0.36–0.72). Annual rates of emigration were high (E = 1.06–1.67), and direct estimation of this source of loss considerably improved mortality estimates. The model estimated natural mortality as a constant annual rate (M = 0.84), which was similar in magnitude to life-history-based estimates for similar age groups. By accounting for unique behavioral attributes in the study design, the application of multistate tagging models provided robust estimates of mortality and emigration rates for a valuable coastal fishery resource that will inform future efforts to achieve yield and conservation goals.
A Novel Designed Sparse Array for Noncircular Sources with High Degree of Freedom
Authors: Zhang Yan-kui , Xu Hai-yun , Wang Da-ming , Ba Bin , Li Si-yao
Published: January 2019

The existing coprime array is mainly applicable to circular sources, while the virtual array degree of freedom (DOF) for noncircular sources is enhanced limitedly. In order to perfect the array DOF and the direction of arrival (DOA) estimation accuracy, a high degree of freedom sparse array design method for noncircular sources is put forward. Firstly, the method takes the advantages of the characteristic of the noncircular sources to expand the array manifold and then explores and solves the location distribution of the physical array sensors on the basis of the virtual array model with the help of the searching approach. The array configuration can obtain the longest continuous virtual array. The comparisons between the proposed array configuration and the common array configurations are advanced. The simulation experiments show that the sparse array presented in this paper can effectively increase the continuous virtual array aperture of noncircular sources, improve the array DOF and DOA estimation accuracy, and achieve the purpose of better estimation of multiple DOAs in underdetermined conditions.
Combined Early Warning Method for Rock Burst and Its Engineering Application
Authors: Qin Zhongcheng , Li Tan , Li Qinghai , Chen Guangbo , Cao Bin
Published: January 2019

Rock burst is a common mine disaster often accompanied with casualties and property damage. In order to effectively predict and prevent the rock burst occurrence, an effective and accurate method for predicting rock burst is necessary. This paper first establishes the relationship between the drilling cuttings and the releasable elastic deformation energy. However, the traditional drilling cutting method has the defect that the drilling depth cannot reach the stress concentration area and the drilling cuttings cannot accurately reflect the internal stress variation in the deep part of coal body. So, an improved drill cutting method is presented to make up for these defects. Finally, the combined monitoring method based on the improved drilling cutting method and the microseismic monitoring method is established. It not only overcomes the limitations of a single prediction method but also effectively utilizes the advantages of improved drilling cutting method and the microseismic monitoring method. And this combined monitoring method is applied to the No. 3302 coalface of Xingcun Coal Mine. The obtained results indicate that the combined monitoring method can improve the prediction capabilities of the rock burst and provide novel insights for preventing the rock burst occurrence.
Allocating Cost to Shippers in Pickup and Delivery Service
Authors: Liu Ning , Cheng Yaorong
Published: January 2019

This paper is going to study the shipper collaboration cost allocation problem in pickup and delivery (SCAPPD), which includes two crucial aspects, namely, the optimal redistribution of transport requests for minimization of the total cost of the alliance and equitable allocation of the shipper’s cost for keeping the stability of the alliance. We focus on the second issue and use core concept from cooperative game theory to develop an allocation methods, called Location Cost Allocation Model (LCAM), which take geographical location factor into account. As the goal of this study is to design an allocation tool that will be accepted in practice, we use the criteria of stability, consistency, and robustness to evaluate the LCAM, Shapley, Nucleolus, and the equal profit method (EPM). All four allocation methods are applied to both a case study and randomly generated instances. Our computational results show that the stability of the LCAM is as good as the nucleolus and EPM. In terms of consistency the LCAM performs best. LCAM also performs well in terms of robustness.
A Heuristic Genetic Algorithm for Regional Targets’ Small Satellite Image Downlink Scheduling Problem
Authors: Song Yan-Jie , Zhang Zhong-Shan , Sun Kai , Yao Feng , Chen Ying-Wu
Published: January 2019

Small satellite image downlink scheduling problem (SSIDSP) is an important part of satellite mission planning. SSIDSP mainly needs to balance how to better match the limited receiving capacity of the ground station with the limited satellite resources. In this paper, regional targets are considered with SSIDSP. We propose a mathematical model that maximizes profit by considering time value and regional targets. A downlink schedule algorithm (DSA) is proposed to complete the task sequence arrangement and generate scheduling results. A heuristic genetic algorithm (HGA) is used to optimize the generated task sequence to achieve higher profit. Three scale test instances are used to test the effectiveness of HGA and DSA. We compare the effect of HGA, basic genetic algorithm (GA), and construction heuristic algorithm. The experimental results proved that the proposed approach ensures the successful completion of observation tasks and is effective for SSIDSP.