bluuebunny/crossref_metadata_2025 huggingface dataset:
A draft genome sequence of the miniature parasitoid wasp, Megaphragma amalphitanum
Authors: Nedoluzhko Artem V. , Sharko Fedor S. , Lê Brandon M. , Tsygankova Svetlana V. , Boulygina Eugenia S. , Rastorguev Sergey M. , Sokolov Alexey S. , Rodriguez Fernando , Mazur Alexander M. , Polilov Alexey A. , Benton Richard , Evgen’ev Michael B. , Arkhipova Irina R. , Prokhortchouk Egor B. , Skryabin Konstantin G.
Published: March 2019

Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals to conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect – the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, the gene content of M. amalphitanum compared to other chalcid wasps is remarkably conserved. Among the very rare cases of apparent gene loss is centrosomin, which encodes an important centrosome component; the absence of this protein might be related to the large number of anucleate neurons in M. amalphitanum. Intriguingly, we also observed significant changes in M. amalphitanum transposable element dynamics over time, whereby an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Thus, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.
Estimation of Membrane Curvature for Cryo-Electron Tomography
Authors: Kalemanov Maria , Collado Javier F. , Baumeister Wolfgang , Fernández-Busnadiego Rubén , Martínez-Sánchez Antonio
Published: March 2019

Curvature is an important morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to-native state and high resolution. However, current curvature estimation methods cannot be applied directly to membrane segmentations in cryo-ET. Additionally, a reliable estimation requires to cope with quantization noise. Here, we developed and implemented a method for membrane curvature estimation from tomogram segmentations.

From a membrane segmentation, a signed surface (triangle mesh) is first extracted. The triangle mesh is then represented by a graph (vertices and edges), which facilitates finding neighboring triangles and the calculation of geodesic distances necessary for local curvature estimation. Here, we present several approaches for accurate curvature estimation based on tensor voting. Beside curvatures, these methods also provide robust estimations of surface normals and principal directions.

We tested the different methods on benchmark surfaces with known curvature, demonstrating the validity of these methods and their robustness to quantization noise. We also applied two of these approaches to biological cryo-ET data. The results allowed us to determine the best approach to estimate membrane curvature in cellular cryo-ET data.
Social hierarchy regulates ocular dominance plasticity in adult male mice
Authors: Balog Jenny , Hintz Franziska , Isstas Marcel , Teichert Manuel , Winter Christine , Lehmann Konrad
Published: March 2019

We here show that social rank, as assessed by competition for a running wheel, influences ocular dominance plasticity in adult male mice. Dominant animals showed a clear ocular dominance shift after four days of MD, whereas their submissive cage mates did not. NMDA receptor activation, reduced GABA inhibition, and serotonin transmission were necessary for this plasticity, but not sufficient to explain the difference between dominant and submissive animals. In contrast, prefrontal dopamine concentration was higher in dominant than submissive mice, and systemic manipulation of dopamine transmission bidirectionally changed ocular dominance plasticity. Thus, we could show that a social hierarchical relationship influences ocular dominance plasticity in the visual cortex via higher-order cortices, most likely the medial prefrontal cortex. Further studies will be needed to elucidate the precise mechanisms by which this regulation takes place.
Pax6 and KDM5C co-occupy a subset of developmentally critical genes including Notch signaling regulators in neural progenitors
Authors: Gaudenzi Giulia , Dethlefsen Olga , Walfridsson Julian , Hermanson Ola
Published: March 2019

Pax6 is a key transcription factor in neural development. While generally viewed as a transcriptional activator, mechanisms underlying Pax6 function as a repressor is less well understood. Here we show that Pax6 acts as a direct repressor of transcription associated with a decrease in H3K4me3 levels. Genome wide analysis of the co-occupancy of the H3K4 demethylase KDM5C and Pax6 with H3K4me3-negative regions revealed 177 peaks on 131 genes. Specific analysis of these Pax6/KDM5C/H3K4me3-peaks unveiled a number of genes associated with Notch signaling, including Dll1, Dll4, and Hes1. RNA knockdown of PAX6/KDM5C in human neural progenitors resulted in increased DLL4 gene expression, decreased DLL1 expression, and no significant effect on HES1 mRNA levels, differences that could be due to gene-specific variations in the chromatin landscape. Our findings suggest that PAX6 and KDM5C co-regulate a subset of genes implicated in brain development, including members of the Notch signaling family.
Higher order analysis of gene correlations by tensor decomposition
Authors: Yahyanejad Farzane
Published: March 2019

This study advances our understanding of inter- and intra-pathways higher order signaling in the cellular system and it leads to new discovery of multiple intracellular structures in signal transduction pathways in yeast Saccharomyces. We present a new tensor decomposition algorithm in reconstructing the pathways based on higher correlations among genes that compose a cellular system. The higher order gene correlation (HOGC) analysis has the power to elucidate gene’s higher interaction dependencies which has been barely understood. Recent studies i.e. [24] have experimentally revealed that multiple signaling proteins, yet sometimes infinite, may assemble to meaningful structure to transmit a receptor activation information. In this paper we reveal 3-order genomic correlations among significant component of the cellular system. This is the first time such a systematic and computational model provided for analysis of higher order correlations among genes. We use new fast algorithm to formulate a genes × genes × genes × decorrelated rank-1 sub-tensors (complexes) which can be associated with functionally independent pathways. Then we model higher order tensor decomposition which is constructed by K tensors of genes × genes × genes. Each new tensor is constructed by an orthogonal projection of data signal onto a designated basis signal to keep common sub-tensors in both signals. Our model for decomposing tensor order-4 approximates series of tensors as linear components of deccorelated rank-1 sub-tensors over tensor of order-3 and rank-3 triplings among sub-tensors. The linear components represent intra-pathway in cell signaling and triplings implicate inter-pathways higher order signaling. Through structural studies of inter- and intra-higher order signaling pathways, we uncover different scenario that involves triple formation of signaling proteins into higher order signaling machines for transmission of receptor activation information to cellular responses.
Metabolic reprogramming from glycolysis to amino acid utilization in cardiac HIF1α deficient mice
Authors: Menendez-Montes Ivan , Escobar Beatriz , Palacios Beatriz , Gomez Manuel J. , Bonzon Elena , Ferrarini Alessia , Alonso Ana Vanessa , Jimenez-Borreguero Luis Jesus , Vázquez Jesus , Martin-Puig Silvia
Published: March 2019

Rationale

Hypoxia is an important environmental cue implicated in several physiopathological processes, including heart development. Several mouse models of activation or inhibition of hypoxia have been previously described. While gain of function models have been extensively characterized and indicate that HIF1 signaling needs to be tightly regulated to ensure a proper cardiac development, there is lack of consensus in the field about the functional outcomes of HIF1α loss.

Objective

In this study, we aim to assess the consequences of cardiac deletion of HIF1α during heart development and identify the cardiac adaptations to HIF1 loss.

Methods and Results

Here, we used a conditional deletion model ofHif1ain NKX2.5+cardiac progenitors. By a combination of histology, electron microscopy, massive gene expression studies, proteomics, metabolomics and cardiac imaging, we found that HIF1α is dispensable for cardiac development.Hif1aloss results in glycolytic inhibition in the embryonic heart without affecting normal cardiac growth. However, together with a premature increase in mitochondrial number by E12.5, we found global upregulation of amino acid transport and catabolic processes. Interestingly, this amino acid catabolism activation is transient and does not preclude the normal cardiac metabolic switch towards fatty acid oxidation (FAO) after E14.5. Moreover,Hif1aloss is accompanied by an increase in ATF4, described as an important regulator of several amino acid transporters.

Conclusions

Our data indicate that HIF1α is not required for normal cardiac development and suggest that additional mechanisms can compensateHif1aloss. Moreover, our results reveal the metabolic flexibility of the embryonic heart at early stages of development, showing the capacity of the myocardium to adapt its energy source to satisfy the energetic and building blocks demands to achieve normal cardiac growth and function. This metabolic reprograming might be relevant in the setting of adult cardiac failure.
Pan-filovirus one-step reverse transcription-polymerase chain reaction screening assay
Authors: Kopp Katharina , Smith Ina , Klein Reuben , Todd Shawn , Marsh Glenn A. , Ward Alister C.
Published: March 2019

Five species within the genera Ebolavirus and Marburgvirus of the family Filoviridae are known to cause severe hemorrhagic fever with high mortality rates in humans and non-human primates. Recent large outbreaks of Ebola virus disease in West Africa (2014 - 2016) and the Democratic Republic of the Congo (2018 - ongoing) have demonstrated the epidemic potential with devastating public health consequences. Several known and novel filovirus species have been found in bats in recent years. However, the role of each virus species in the disease ecology of human disease is still unclear. In particular, the transmission mechanism from potential animal hosts to humans is not known. Therefore, a simple, flexible, cost-effective screening tool for detecting the presence of any (putative) member of the filovirus family in animal samples is needed. In this study, a one-step conventional pan-filovirus RT-PCR assay was developed. The designed universal consensus primers of this screening test target two highly conserved regions of the nucleoprotein (NP) of all currently known filoviruses. The assay was capable of specific amplification of viral RNA of all six primate-pathogenic (human and non-human) filovirus species and resulted in 317 bp long RT-PCR products. This amplicon length renders the assay suitable for flexible application as conventional reverse transcription polymerase chain reaction (RT-PCR) as well as for future use as rapid real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR).
Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits
Authors: Gleason Kevin J , Yang Fan , Pierce Brandon L , He Xin , Chen Lin S
Published: March 2019

To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method – Primo – for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies. Primo examines SNPs’ association patterns to complex and omics traits. In gene regions harboring known susceptibility loci, Primo performs conditional association analysis to account for linkage disequilibrium. Primo allows for unknown study heterogeneity and sample correlations. We show two applications using Primo to examine the molecular mechanisms of known susceptibility loci and to detect and interpret pleiotropic effects.
Embryonic geometry underlies phenotypic variation in decanalized conditions
Authors: Huang A. , Saunders T. E.
Published: March 2019

During development, many mutations cause increased variation in phenotypic outcomes, a phenomenon termed decanalization. Such variations can often be attributed to genetic and environmental perturbations. However, phenotypic discordance remains even in isogenic model organisms raised in homogeneous environments. To understand the mechanisms underlying phenotypic variation, we used as a model the highly precise anterior-posterior (AP) patterning of the earlyDrosophilaembryo. We decanalized the system by depleting the maternalbcdproduct and found that in contrast to the highly scaled patterning in the wild-type, the segmentation gene boundaries shift away from the scaled positions according to the total embryonic length. Embryonic geometry is hence a key factor predetermining patterning outcomes in such decanalized conditions. Embryonic geometry was also found to predict individual patterning outcomes underbcdoverexpression, another decanalizing condition. Further analysis of the gene regulatory network acting downstream of the morphogen identified vulnerable points in the networks due to limitations in the available physical space.
Human intestinal enteroids with inducible neurogenin-3 expression as a novel model of gut hormone secretion
Authors: Chang-Graham Alexandra L. , Danhof Heather A. , Engevik Melinda A. , Tomaro-Duchesneau Catherine , Karandikar Umesh C. , Estes Mary K. , Versalovic James , Britton Robert A. , Hyser Joseph M.
Published: March 2019

Background

Enteroendocrine cells (EECs) are specialized epithelial cells that produce molecules vital for intestinal homeostasis, but due to their limited numbers, in-depth functional studies have remained challenging. Human intestinal enteroids (HIEs) that are derived from intestinal crypt stem cells are a biologically relevantin vitromodel of the intestinal epithelium. HIEs contain all intestinal epithelial cell types; however, like the intestine, HIEs spontaneously produce few EECs, which limits their study.

Methods

To increase the number of EECs in HIEs, we used lentivirus transduction to stably engineer jejunal HIEs with doxycycline-inducible expression of neurogenin-3 (NGN3), a transcription factor that drives EEC differentiation (tetNGN3-HIEs). We examined the impact ofNGN3induction on EECs by quantifying the increase in the enterochromaffin cells and other EEC subtypes. We functionally assessed secretion of serotonin and EEC hormones in response to norepinephrine and rotavirus infection.

Results

Treating tetNGN3-HIEs with doxycycline induced a dose-dependent increase of chromogranin A (ChgA)-positive and serotonin-positive cells, demonstrating increased enterochromaffin cell differentiation. Despite increased ChgA-positive cells, other differentiated cell types of the epithelium remained largely unchanged by gene expression and immunostaining. RNA sequencing of doxycycline-induced tetNGN3- HIEs identified increased expression of key hormones and enzymes associated with several other EEC subtypes. Doxycycline-induced tetNGN3-HIEs secreted serotonin, monocyte chemoattractant protein-1, glucose-dependent insulinotropic peptide, peptide YY, and ghrelin in response to norepinephrine and rotavirus infection, further supporting the presence of multiple EEC types.

Conclusions

We have combined HIEs and inducible-NGN3expression to establish a flexiblein vitromodel system for functional studies of EECs in enteroids and advance the molecular and physiological investigation of EECs.

Synopsis

Enteroendocrine cells have low abundance but exert widespread effects on gastrointestinal physiology. We engineered human intestinal enteroids with inducible expression of neurogenin-3, resulting in increased enteroendocrine cells and facilitating investigations of host responses to the dynamic intestinal environment.
Evolutionary dynamics in structured populations under strong population genetic forces
Authors: Feder Alison F. , Pennings Pleuni S. , Hermisson Joachim , Petrov Dmitri A.
Published: March 2019

High rates of migration between subpopulations result in little population differentiation in the long-term neutral equilibrium. However, in the short-term, even very abundant migration may not be enough for subpopulations to equilibrate immediately. In this study, we investigate dynamical patterns of short-term population differentiation in adapting populations via stochastic and analytical modeling through time. We characterize a regime in which selection and migration interact to create non-monotonic patterns of the population differentiation statisticFSTwhen migration is weaker than selection, but stronger than drift. We demonstrate how these patterns can be leveraged to estimate high migration rates that would lead to panmixia in the long term equilibrium using an approximate Bayesian computation approach. We apply this approach to estimate fast migration in a rapidly adapting intra-host Simian-HIV population sampled from different anatomical locations. Notably, we find differences in estimated migration rates between different compartments, all aboveNem= 1. This work demonstrates how studying demographic processes on the timescale of selective sweeps illuminates processes too fast to leave signatures on neutral timescales.
ProtCID: A data resource for structural information on protein interactions
Authors: Xu Qifang , Dunbrack Roland L.
Published: March 2019

Structural information on the interactions of proteins with other molecules is plentiful, and for some proteins and protein families, there may be 100s of available structures. It can be very difficult for a scientist who is not trained in structural bioinformatics to access this information comprehensively. Previously, we developed the Protein Common Interface Database (ProtCID), which provided clusters of the interfaces of full-length protein chains as a means of identifying biological assemblies. Because proteins consist of domains that act as modular functional units, we have extended the analysis in ProtCID to the individual domain level. This has greatly increased the number of large protein-protein clusters in ProtCID, enabling the generation of hypotheses on the structures of biological assemblies of many systems. The analysis of domain families allows us to extend ProtCID to the interactions of domains with peptides, nucleic acids, and ligands. ProtCID provides complete annotations and coordinate sets for every cluster.
High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations
Authors: Jung James , Grant Timothy , Thomas Dennis R. , Diehnelt Chris W. , Grigorieff Nikolaus , Joshua-Tor Leemor
Published: March 2019

Noroviruses are a leading cause of food-borne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6-4.1 Å) cryo-electron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7 and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups with small, medium and large particle sizes observed. We developed a new asymmetric reconstruction method and resolved a metal ion adjacent to the co-receptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations.
Colonization and extinction rates estimated from temporal dynamics of ecological communities: The islandrpackage
Authors: Ontiveros Vicente J. , Capitán José A. , Arthur Rohan , Casamayor Emilio O. , Alonso David
Published: March 2019

The temporal dynamics of ecological communities are inherently complex, as dispersal processes, interspecific biotic interactions and environmental fluctuations interact to shape species assemblages. We developed anrpackage,island—a community ecology tool to analyse temporal patterns and explore potential drivers of community dynamics.

Therpackageislandis inspired by the simplicity of the Theory of Island Biogeography. Our package includes a suite of functions to easily confront models of increasing complexity to community data from the simplest stochastic model underlying Island Biogeography Theory to more elaborate models that include species responses to environmental variables and imperfect detectability, obtained at regular or irregular sampling times, using maximum‐likelihood andAIC‐based model selection.

Models implemented inislandshould be regarded as simple approximations of true temporal community dynamics. In this sense, we call themeffective modelswhich we use to estimateeffective parameters. These models are simple, but dynamic, as opposed to purely statistical. We illustrate the concept of dynamiceffective modelsby using an immigration–birth–death stochastic model of population dynamics. We generated simulated community data to demonstrate the correspondence between the underlying true model parameters values and our effective parameter estimates.

We present three examples showcasing the uses of our package: detectability estimation and model selection, influence of environmental covariates on community dynamics and estimation of co‐occurrence networks. Three detailed vignettes with a full set of examples accompany therPackageislandavailable onCRAN.
The immunocytochemical expression of VE‐1 (BRAF V600E‐related) antibody identifies the aggressive variants of papillary thyroid carcinoma on liquid‐based cytology
Authors: Straccia Patrizia , Brunelli Chiara , Rossi Esther D. , Lanza Paola , Martini Maurizio , Musarra Teresa , Lombardi Celestino Pio , Pontecorvi Alfredo , Fadda Guido
Published: March 2019

Background

The recently introduced monoclonal V600E antibody (clone VE1) is likely to be an alternative strategy for detecting this mutation in thyroid lesions. Although VE1 immunostaining and molecular methods used to assess papillary thyroid carcinoma in surgical specimens are in good agreement, evaluation of VE1 in cytology and cell block samples is rarely performed, and its diagnostic value in cytology has not been well established. In this study, we sought to determine if VE1 is suitable for fine needle aspiration (FNA) and cell block methods.

Methods

A total of 86 patients who had BRAF V600E mutations were investigated with molecular and immunocytochemical (ICC) analysis in 45 FNA and 41 cell blocks. In total, 83 (96.5%) patients underwent surgical treatment. Assessment of BRAF V600E mutation status was performed in 72 (83.7%) cases.

Results

Among the 72 cases analysed, 54 cases agreed (ICC+/BRAF+ or ICC−/BRAF−), seven cases were false positive (ICC+/BRAF−) and 11 cases were false negative (ICC−/BRAF+). False negative cases were not detected in the cell block method. The statistical analysis showed that sensitivity and specificity of ICC for detecting the BRAF V600E mutation were 61% and 77% in FNA samples and 100% and 73% in cell block.

Conclusion

The use of antibody VE‐1 is a reliable method and a negative result of VE1 immunostaining might help to save time and money, restricting the molecular test to antibody‐positive cases only. The identification of the aggressive variants of papillary carcinoma might be enabled by the expression of the antibody in neoplastic cells with tall cell features.
Recent patterns of vagal nerve stimulator use in the United States: Is there a racial disparity?
Authors: Fox Jonah , Lekoubou Alain , Bishu Kinfe G. , Ovbiagele Bruce
Published: March 2019

Objective

Patients with refractory epilepsy are at a high risk of complications but may not receive the same level of care across racial groups. We aimed to ascertain racial inequalities and trends in the use of a vagal nerve stimulator (VNS) among adult patients with refractory epilepsy.

Methods

A total of 24 159 adults (18 years and older) with refractory epilepsy from the National Inpatient Sample between the years 2006 and 2014 were included in this analysis. We used a multivariate logistic regression analysis to evaluate independent predictors of VNS use among patients with refractory epilepsy. Covariates included gender, age, insurance type, and household income. In addition, we evaluated for trends in VNS use over the 9‐year period of data collection.

Results

A total of 1.56% of patients with refractory epilepsy had used a VNS between 2006 and 2014. Overall, there was a trend of decreased use of a VNS between 2006‐2008 (2.1%) and 2012‐2014 (0.9%). In the adjusted multivariate logistic regression analysis, blacks (odds ratio [OR] = 0.52, 95% confidence interval [CI] = 0.35‐0.77) were significantly less likely to have used a VNS relative to non‐Hispanic whites. Additional factors independently associated with a decreased likelihood of VNS use were age > 65 years (OR = 0.51, 95% CI = 0.28‐0.95) and years 2012‐2014 (OR = 0.44, 95% CI = 0.28‐0.67).

Significance

There was a trend toward a decrease in the use of a VNS among adult patients with refractory epilepsy. Our results also suggest that black patients with refractory epilepsy were less likely to receive a VNS independently of other variables. Increased work toward effectively reducing racial disparities in access to quality epilepsy care is crucial.
Reply to comment: guselkumab in the treatment of severe hidradenitis suppurativa
Authors: Kovacs M. , Podda M.
Published: March 2019

Linked article: J.W. Frew. J Eur Acad Dermatol Venereol 2019; 33: e298–e300. https://doi.org/10.1111/jdv.15572
Emergency Department Interventions for Older Adults: A Systematic Review
Authors: Hughes Jaime M. , Freiermuth Caroline E. , Shepherd‐Banigan Megan , Ragsdale Luna , Eucker Stephanie A. , Goldstein Karen , Hastings S. Nicole , Rodriguez Rachel L. , Fulton Jessica , Ramos Katherine , Tabriz Amir Alishahi , Gordon Adelaide M. , Gierisch Jennifer M. , Kosinski Andrzej , Williams John W.
Published: March 2019

OBJECTIVES

To evaluate the effect of emergency department (ED) interventions on clinical, utilization, and care experience outcomes for older adults.

DESIGN

A conceptual model informed, protocol‐based systematic review.

SETTING

Emergency Department (ED).

PARTICIPANTS

Older adults 65 years of age and older.

METHODS AND MEASUREMENT

Medline, Embase, CINAHL, and PsycINFO were searched for English‐language studies published through December 2017. Studies evaluating the use of one or more eligible intervention strategies (discharge planning, case management, medication safety or management, and geriatric EDs including those that cited the 2014 Geriatric ED Guidelines) with adults 65 years of age and older were included. Studies were classified by the number of intervention strategies used (ie, single strategy or multi‐strategy) and key intervention components present (ie, assessment, referral plus follow‐up, and contact both before and after ED discharge [“bridge”]). The effect of ED interventions on clinical (functional status, quality of life [QOL]), patient experience, and utilization (hospitalization, ED return visit) outcomes was evaluated.

RESULTS

A total of 2000 citations were identified; 17 articles describing 15 unique studies (9 randomized and 6 nonrandomized) met eligibility criteria and were included in analyses. ED interventions showed a mixed pattern of effects. Overall, there was a small positive effect of ED interventions on functional status but no effects on QOL, patient experience, hospitalization at or after the initial ED index visit, or ED return visit.

CONCLUSION

Studies using two or more intervention strategies may be associated with the greatest effects on clinical and utilization outcomes. More comprehensive interventions, defined as those with all three key intervention components present, may be associated with some positive outcomes.
Cushion and shrub ecosystem engineers contribute differently to diversity and functions in alpine ecosystems
Authors: Chen Jian‐Guo , He Xiao‐Fang , Wang Song‐Wei , Yang Yang , Sun Hang
Published: March 2019

Questions

As ecosystem engineers, alpine cushion and shrub species have been widely documented, but their roles as co‐existing nurse plants have not been explicitly compared. In this study, our questions were: (1) what are the differences in engineering effects between cushions and shrubs in alpine ecosystems in southwestern China? (2) what are the differences in their influences on the attributes of alpine plant communities? and (3) can we detect the effects of changes in environmental stress with elevation on the engineering effects of cushions and shrubs?

Study Site

Three plant communities along an elevational gradient on Baima Snow Mountain, SW China.

Methods

Field measurements were carried out to assess effects of cushion (Arenaria polytrichoides) and shrub (Rhododendron rupicola) species on soil temperature, soil nutrient and water availabilities, the species richness of co‐existing vascular species and their abundance, above‐ground production and the percentages of grazed individuals.

Results

Shrub and cushion species modify micro‐environmental conditions, especially at higher elevations, but in different ways. Grazing pressures are highest for plants in the surroundings, followed by within cushions, and finally under shrubs. This indicates that both cushion and shrub species can protect beneficiary species from grazing by livestock. The presence of cushion plants increased species richness, abundance and above‐ground production in the higher community but not in the middle and lower communities. However, the presence of shrubs consistently increased those measurements across the elevational gradient. In addition, some species exclusively and some others preferentially occur within cushions or beneath shrubs.

Conclusion

The results clearly suggest that alpine cushion and shrub species in the Hengduan Mountains both act as ecosystem engineers and contribute positively to community attributes. However, their engineering effects vary with environmental stresses. Cushions could facilitate other species under severe abiotic stress, but showed much weaker or even competitive effects in benign conditions; shrubs’ facilitation may remain consistently strong under different stresses.
Systematic analysis of Type I‐E Escherichia coli CRISPR‐Cas PAM sequences ability to promote interference and primed adaptation
Authors: Musharova Olga , Sitnik Vasily , Vlot Marnix , Savitskaya Ekaterina , Datsenko Kirill A. , Krivoy Andrey , Fedorov Ivan , Semenova Ekaterina , Brouns Stan J. J. , Severinov Konstantin
Published: March 2019

CRISPR interference occurs when a protospacer recognized by the CRISPR RNA is destroyed by Cas effectors. In Type I CRISPR‐Cas systems, protospacer recognition can lead to «primed adaptation» – acquisition of new spacers from in cis located sequences. Type I CRISPR‐Cas systems require the presence of a trinucleotide protospacer adjacent motif (PAM) for efficient interference. Here, we investigated the ability of each of 64 possible trinucleotides located at the PAM position to induce CRISPR interference and primed adaptation by the Escherichia coli Type I‐E CRISPR‐Cas system. We observed clear separation of PAM variants into three groups: those unable to cause interference, those that support rapid interference and those that lead to reduced interference that occurs over extended periods of time. PAM variants unable to support interference also did not support primed adaptation; those that supported rapid interference led to no or low levels of adaptation, while those that caused attenuated levels of interference consistently led to highest levels of adaptation. The results suggest that primed adaptation is fueled by the products of CRISPR interference. Extended over time interference with targets containing «attenuated» PAM variants provides a continuous source of new spacers leading to high overall level of spacer acquisition.
A dual functional redox enzyme maturation protein for respiratory and assimilatory nitrate reductases in bacteria
Authors: Pinchbeck Benjamin J. , Soriano‐Laguna Manuel J. , Sullivan Matthew J. , Luque‐Almagro Victor M. , Rowley Gary , Ferguson Stuart J. , Roldán M. Dolores , Richardson David J. , Gates Andrew J.
Published: March 2019

Nitrate is available to microbes in many environments due to sustained use of inorganic fertilizers on agricultural soils and many bacterial and archaeal lineages have the capacity to express respiratory (Nar) and assimilatory (Nas) nitrate reductases to utilize this abundant respiratory substrate and nutrient for growth. Here, we show that in the denitrifying bacterium Paracoccus denitrificans, NarJ serves as a chaperone for both the anaerobic respiratory nitrate reductase (NarG) and the assimilatory nitrate reductase (NasC), the latter of which is active during both aerobic and anaerobic nitrate assimilation. Bioinformatic analysis suggests that the potential for this previously unrecognized role for NarJ in functional maturation of other cytoplasmic molybdenum‐dependent nitrate reductases may be phylogenetically widespread as many bacteria contain both Nar and Nas systems.
Glasses for Nuclear Waste Immobilization. Effect of Lutetium Addition on Yttrium Aluminosilicate Glass Crystallization Kinetics
Authors: Lago D. C. , Bortot M. B. , Prado M. O.
Published: March 2019

Glasses have emerged as alternative materials that can be used for long-term treatment and management of radioactive waste. Specifically, glasses can be used as a matrix to immobilize the radioactive material. Within the glass industry, silicate glasses are the most widely used due to their properties and to the large knowledge existent about them. Alkaline free silicate glasses are particularly corrosion resistant. Due to the latter, rare earth aluminosilicate glasses are good candidates for actinides immobilization, especially, yttrium aluminosilicate (YAS) glasses. The crystallization kinetics of YAS glasses on heating has been already studied, and this work is focused on the effect of lutetium addition on the YAS glass crystallization kinetics. The presence of a small amount of lutetium in a YAS glass decreases the surface density of nucleation sites (Ns) by about 1 order of magnitude and significantly decreases the crystal growth rate (U). In this work, it was observed that lutetium additions on the order of 0.2 (wt %) to a YAS glass dramatically decreased Ns, for example, at 1000 °C from 1011 to 109 nuclei/m2. Additionally, U for yttrium disilicate phase decreased from (8.21 ± 0.28) μm/h to (0.54 ± 0.04) μm/h at the same temperature.
Avoidance of Cutter Retracting Interference in Noncircular Gear Shaping Through 4-Linkage Model
Authors: Zheng Fangyan , Lin Hua , Han Xinghui , Zhang Mingde , Zhang Weiqing , Guo Xiaodong
Published: March 2019

Gear shaping, a widely used machining method for circular gears, was generalized to noncircular gears in recent works using a 3-linkage machine tool. As the pitch curve normals of noncircular gears change constantly in processing, angles may exist between the pitch curve normals and the cutter relieving direction, bringing in turn cutter retracting interference.

Regarding this, the paper proposes a 4-linkage shaping method. Through linkage motion of 4 machine tool axes, noncircular gear pitch normals are along the cutter relieving direction, avoiding completely cutter retracting interference. On such basis, a mathematical model is first established, the cutting process is then discussed and a cutting experiment is finally carried out, proving the validity of the proposed method.
A Product Architecture-Based Framework for a Data-Driven Estimation of Lifecycle Cost
Authors: Altavilla Stefania , Montagna Francesca
Published: March 2019

This paper proposes a three-step cost estimation methodology that dynamically adapts the focus of the analysis on the progress of the development phases and on the different levels of aggregation of the product architecture. At each step, different qualitative and quantitative techniques are progressively integrated according to the degree of data granularity required by the advancement of the product development. Moreover, a fixed set of cost drivers are identified to express the costs at different phases of the product lifecycle. The different levels of the product architecture are instead used as a framework to collect and bundle data for a cost analysis, which gradually increases the accuracy. Hence, the purpose of this research is to move the focus from merely estimating the structuring data and information for the cost analysis. The methodology is explicitly aimed at standardized assembled systems/products, characterized by a high number of parts and modules shared among different product versions. The approach was tested and validated at an automotive company that designs, produces, and markets measurement devices for engine development. Operatively, the approach can be used by the development team to evaluate the impact of different design alternatives, deriving the lifecycle costs of the product once the design choices are made. By tracking the development process at each aggregation level, designers can assess cost reduction by monitoring the impact of selected cost drivers while the product development process is in progress.
Optimal Flow Control and Single Split Architecture Exploration for Fluid-Based Thermal Management
Authors: Peddada Satya R. T. , Herber Daniel R. , Pangborn Herschel C. , Alleyne Andrew G. , Allison James T.
Published: March 2019

High-performance cooling is often necessary for thermal management of high power density systems. However, human intuition and experience may not be adequate to identify optimal thermal management designs as systems increase in size and complexity. This article presents an architecture exploration framework for a class of single-phase cooling systems. This class is specified as architectures with multiple cold plates in series or parallel and a single fluid split and junction. Candidate architectures are represented using labeled rooted tree graphs. Dynamic models are automatically generated from these trees using a graph-based thermal modeling framework. Optimal performance is determined by solving an appropriate fluid flow distribution problem, handling temperature constraints in the presence of exogenous heat loads. Rigorous case studies are performed in simulation, with components subject to heterogeneous heat loads and temperature constraints. Results include optimization of thermal endurance for an enumerated set of 4051 architectures. The framework is also applied to identify cooling system architectures capable of steady-state operation under a given loading.
An Active Ease-Off Topography Modification Approach for Hypoid Pinions Based on a Modified Error Sensitivity Analysis Method
Authors: Li G. , Zhu W. D.
Published: March 2019

A new active ease-off topography modification approach is proposed to improve the meshing performance of hypoid gears based on a fourth-order predesigned transmission error (PTE) model and a modified error sensitivity analysis method. Ease-off topography modifications that describe local deviations of pinion tooth surfaces can be conducted by converting the fourth-order PTE into equivalent deviations of pinion tooth surfaces. The modified error sensitivity analysis method is developed to investigate the effects of misalignments on the moving velocity of a contact point of a hypoid gear pair. The moving velocity of the contact point can describe transmission error (TE) curve shapes of ease-off tooth surfaces. The ease-off topography modification approach can achieve TE precontrol and modification curvature adjustment of the pinion for stable meshing performance of the hypoid gear pair. Moreover, pinion ease-off tooth surfaces are finished by a five-axis computer numerical control swarf-cutting machine tool. Swarf-cutting tests and TE measurement tests are conducted on hypoid gear pair specimens to demonstrate the feasibility and effectiveness of the proposed methodology.
Impact of Chaining Method and Level of Completion on Accuracy of Function Structure-Based Market Price Prediction Models
Authors: Gill Amaninder Singh , Summers Joshua D. , Sen Chiradeep
Published: March 2019

The goal of this paper is to explore how different modeling approaches for constructing function structure models and different levels of model completion affect the ability to make inferences (reason) on the resulting information within the respective models. Specifically, the function structure models are used to predict market prices of products, predictions that are then compared based on their accuracy and precision. This work is based on previous studies on understanding how function modeling and the use of topological information from design graphs can be used to predict information with historical training. It was found that forward chaining was the least favorable chaining type irrespective of the level of completion, whereas the backward-chaining models performed relatively better across all completion levels. Given the poor performance of the nucleation models at the highest level of completion, future research must be directed toward understanding and employing the methods yielding the most accuracy. Moreover, the results from this simulation-based study can be used to develop modeling guidelines for designers or students, when constructing function models.
Escaping undesired gas-phase chemistry: Microwave-driven selectivity enhancement in heterogeneous catalytic reactors
Authors: Ramirez A. , Hueso J. L. , Abian M. , Alzueta M. U. , Mallada R. , Santamaria J.
Published: March 2019

Direct catalyst heating by microwaves reduces the impact of secondary homogeneous reactions occurring in the gas phase.
Gate-controlled VO
2
phase transition for high-performance smart windows
Authors: Chen Shi , Wang Zhaowu , Ren Hui , Chen Yuliang , Yan Wensheng , Wang Chengming , Li Bowen , Jiang Jun , Zou Chongwen
Published: March 2019

A voltage-controlled VO
2
smart window with excellent visible transmittance and infrared modulation efficiency is achieved.
Lanthanum phosphate binder-induced iron deficiency anaemia
Authors: Awad Christina , Gilkison Karin , Shaw Erwin
Published: March 2019

Lanthanum carbonate is a phosphate binder that is used to reduce serum phosphate levels in patients with end-stage renal disease (ESRD). Lanthanum forms insoluble lanthanum phosphate complexes that are supposed to pass through the gastrointestinal (GI) tract unabsorbed. Phosphate binders have been reported to deposit in the GI tract and can cause mucosal injury. There are few case reports of GI bleeding associated with phosphate binder deposits. This case report presents a patient with iron deficiency anaemia secondary to biopsy-proven lanthanum deposits in the upper GI tract. There were no overt signs of active GI bleeding. Patient’s anaemia improved with discontinuation of the phosphate binder. Lanthanum could be a hidden cause of resistant anaemia among patients with ESRD through asymptomatic GI blood loss.
Unusual presentation of late-onset disseminated staphylococcal sepsis in a preterm infant
Authors: Khattak Shahzad Gul , Dady Ian , Mukherjee Devdeep
Published: March 2019

An ex-30-week gestation, preterm male baby was admitted to a tertiary neonatal unit and noted to have increased ventilator requirements and diagnosed with sepsis. The baby also developed an abscess over the left elbow and over the xiphisternum along with a decrease in movement of the left hand and the right leg. Panton-Valentine leukocidin (PVL)-producingStaphylococcus aureus(SA) was isolated from the blood culture. A whole body MRI showed disseminated abscess with multiple foci in the lung, left elbow and over the xiphisternum. Disseminated sepsis with multiple septic foci has not been previously reported in neonates. We would like to highlight the fact that sepsis due to PVL toxin-producing SA can cause significant morbidity and mortality in neonates. Proper screening should be done to rule out septic foci in neonates. MRI is a good non-invasive investigation to document septic foci in a neonate and rule out multiorgan involvement.
Surgical resection of carotid-jugular arteriovenous fistula after multiple failed embolisation
Authors: Chew Luen Shaun , Han Julian Xinguang , Ng Yew Poh , Ng Hua Bak
Published: March 2019

Carotid-jugular fistula is a rare presentation of arteriovenous fistula. A case of a 60-year-old Chinese man who presented with iatrogenic carotid-jugular fistula with multiple fistulous points was reported. His presenting complaint was a gradually enlarging right pulsatile neck mass complicated by worsening symptoms of congestive cardiac failure. He had recent mitral valve annuloplasty, and a right internal jugular central venous pressure monitor insertion was performed then. Angiography revealed right carotid-jugular fistula with feeders from the external carotid, internal carotid and right vertebral arteries, all draining into the right internal jugular vein. He underwent embolisation twice resulting in transient improvement in clinical symptoms, and surgical resection was later performed in view of residual arteriovenous shunting and gradual clinical deterioration. Following surgery, he was discharged and resumed work as a janitor with no recurrent symptoms for 3 years now. In this report to be added into the literature, we discuss a rare case of iatrogenic carotid-jugular fistula with multiple fistulous points which required embolisation and subsequently surgical resection.
Treating osteoporosis: a near miss in an unusual case of FGF-23 mediated bone loss
Authors: Paul Jinson , Cherian Kripa Elizabeth , Kapoor Nitin , Paul Thomas Vizhalil
Published: March 2019

Oncogenic osteomalacia is a potentially curable condition caused by phosphaturic mesenchymal tumours. We present the case of 54-year-old woman who presented with bony pains and muscle weakness, and was erroneously treated with bisphosphonates elsewhere on the basis of Dual Energy X-ray Absorptiometry (bone density) scan that showed ‘severe osteoporosis’. Further evaluation revealed the presence of hypophosphatemia, with a 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid avid lesion involving left mandible on PET scan. Surgical excision of lesion led to improvement in her symptoms with normalisation of phosphorus, and histopathology was diagnostic of mesenchymal phosphaturic tumour. A diagnosis of oncogenic osteomalacia was made. A repeat bone mineral density assessment done a year later showed dramatic improvement. A meticulous examination and evaluation is warranted for any patient presenting with bony pains and muscle weakness. The detection of hypophosphatemia in an elderly individual should prompt the consideration of oncogenic osteomalacia, as localisation and excision of tumour usually results in cure.
Secondary thyroid malignancy from metastatic colon lymphoma
Authors: Marco-Alacid Cristian , López-Merseguer Mario , Sánchez-Juan Carlos
Published: March 2019

Primary thyroid malignancy is more frequent than secondary. This case report describes a colon lymphoma with unique thyroid metastasis. When a thyroid lesion appears in an extension study such as Positron emission tomography–computed tomography marked with 18F-2-fluoro-2-deoxy-D-glucose, it is recommended to perform an ultrasound. The correct study with ultrasound and cytology obtained through fine needle aspiration on thyroid lesion allowed to refine the diagnosis and provide the correct treatment.