bluuebunny/crossref_metadata_2025 huggingface dataset:
Antiferromagnetic switch in serum
Authors: Raja Sufi O. , Chatterjee Sanjay , Dasgupta Anjan Kr.
Published: October 2017

1.

Ferritin contains naturally occurring iron oxide nanoparticle surrounded by a structured spherical array of peptide residues that provides tremendous stability to this iron storage protein. We use synthetic citrate coated Super Paramagnetic Iron Oxide Nanoparticles (SPIONs) and static magnetic field in exploring the Ferritin induced magnetic environment of human serum samples with varying ferritin level collected from thalassemic patients. We report anti-ferromagnetic properties of serum in patients with iron overloading. Magnetic pulling by an external magnetic field showed a cusp-like behavior with increasing concentration of serum Ferritin measured by standard ELISA based kit. A reduction in the extent of pulling after a threshold concentration of Ferritin (1500 ng/ml) suggests a Ferritin dependent magnetic switching.Negative magnetization (anti-ferromagnetization) was confirmed by Vibrating Sample Magnetometric (VSM) analysis of SPION-serum mixture containing very high level of Ferritin. Such magnetic switching may have a possible role in iron homeostasis during overloading of Ferritin.

3.

Abbreviations

SPIONs: Super Paramagnetic Iron Oxide Nanoparticles, VSM: Vibrating Sample Magnetometry, SQUID: Super conducting Quantum Interference Device, PCS: Photon Correlation Spectroscopy
Linked-read analysis identifies mutations in single cell DNA sequencing data
Authors: Bohrson Craig L. , Barton Allison R. , Lodato Michael A. , Rodin Rachel E. , Viswanadham Vinay , Gulhan Doga , Cortes Isidro , Sherman Maxwell A. , Luquette Lovelace J. , Kwon Minseok , Coulter Michael E. , Walsh Christopher A. , Park Peter J.
Published: October 2017

Whole-genome sequencing of DNA from single cells has the potential to reshape our understanding of the mutational heterogeneity in normal and disease tissues. A major difficulty, however, is distinguishing artifactual mutations that arise from DNA isolation and amplification from true mutations. Here, we describelinked-readanalysis (LiRA), a method that utilizes phasing of somatic single nucleotide variants with nearby germline variants to identify true mutations, thereby allowing accurate estimation of somatic mutation rates at the single cell level.
Single-molecule tracking in liveYersinia enterocoliticareveals distinct cytosolic complexes of injectisome subunits
Authors: Rocha Julian , Richardson Charles , Zhang Mingxing , Darch Caroline , Cai Eugene , Diepold Andreas , Gahlmann Andreas
Published: October 2017

In bacterial type 3 secretion, substrate proteins are actively transported from the bacterial cytoplasm into the host cell cytoplasm by a large membrane-embedded machinery called the injectisome. Injectisomes transport secretion substrates in response to specific environmental signals, but the molecular details by which the cytosolic secretion substrates are selected and transported through the type 3 secretion pathway remain unclear. Secretion activity and substrate selectivity are thought to be controlled by a sorting platform consisting of the proteins SctK, SctQ, SctL, and SctN, which together localize to the cytoplasmic side of membrane-embedded injectisomes. However, recent work revealed that sorting platform proteins additionally exhibit substantial cytosolic populations and that SctQ reversibly binds to and dissociates from the cytoplasmic side of membrane-embedded injectisomes. Based on these observations, we hypothesized that dynamic molecular turnover at the injectisome and cytosolic assembly among sorting platform proteins is a critical regulatory component of type 3 secretion. To determine whether sorting platform complexes exist in the cytosol, we measured the diffusive properties of the two central sorting platform proteins, SctQ and SctL, using live cell high-throughput 3D single-molecule tracking microscopy. Single-molecule trajectories, measured in wild-type and mutantYersinia enterocoliticacells, reveal that both SctQ and SctL exist in several distinct diffusive states in the cytosol, indicating that these proteins form stable homo- and hetero-oligomeric complexes in their native environment. Our findings provide the first diffusive state-resolved insights into the dynamic regulatory network that interfaces stationary membrane-embedded injectisomes with the soluble cytosolic components of the type 3 secretion system.
Assessing and characterising the repertoire of constitutive promoter elements in soil metagenomic libraries inEscherichia coli
Authors: Westmann Cauã Antunes , de Fátima Alves Luana , Silva-Rocha Rafael , Guazzaroni María-Eugenia
Published: October 2017

Although functional metagenomics has been widely employed for the discovery of genes relevant to biotechnology and biomedicine, its potential for assessing the diversity of transcriptional regulatory elements of microbial communities has remained poorly explored. Here, we have developed a novel framework for prospecting, characterising and estimating the accessibility of promoter sequences in metagenomic libraries by combining a bi-directional reporter vector, high-throughput fluorescence assays and predictive computational methods. Using the expression profiling of fluorescent clones from two independent libraries from soil samples, we directly analysed the regulatory dynamics of novel promoter elements, addressing the relationship between the “metaconstitutome” of a bacterial community and its environmental context. Through the construction and screening of plasmid-based metagenomic libraries followed byin silicoanalyses, we were able to provide both (i) a consensus exogenous promoter elements recognizable byEscherichia coliand (ii) an estimation of the accessible promoter sequences in a metagenomic library, which was close to 1% of the whole set of available promoters. The results presented here should provide new directions for the exploration through functional metagenomics of novel regulatory sequences in bacteria, which could expand the Synthetic Biology toolbox for novel biotechnological and biomedical applications.
Mmp10 is required for post-translational methylation of arginine at the active site of methyl-coenzyme M reductase
Authors: Lyu Zhe , Chou Chau-wen , Shi Hao , Patel Ricky , Duin Evert C. , Whitman William B.
Published: October 2017

Catalyzing the key step for anaerobic methane production and oxidation, methyl-coenzyme M reductase or Mcr plays a key role in the global methane cycle. The McrA subunit possesses up to five post-translational modifications (PTM) at its active site. Bioinformatic analyses had previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To examine its role, MMP1554, the gene encoding Mmp10 inMethanococcus maripaludis, was deleted with a new genetic tool, resulting in the specific loss of the 5-(S)-methylarginine PTM of residue 275 in the McrA subunit and a 40~60 % reduction in the maximal rates of methane formation by whole cells. Methylation was restored by complementations with the wild-type gene. However, the rates of methane formation of the complemented strains were not always restored to the wild type level. This study demonstrates the importance of Mmp10 and the methyl-Arg PTM on Mcr activity.
Spatial Theta Cells in Competitive Burst Synchronization Networks: Reference Frames from Phase Codes
Authors: Monaco Joseph D. , Blair Hugh T. , Zhang Kechen
Published: October 2017

Spatial cells of the hippocampal formation are embedded in networks of theta cells. The septal theta rhythm (6–10 Hz) organizes the spatial activity of place and grid cells in time, but it remains unclear how spatial reference points organize the temporal activity of theta cells in space. We study spatial theta cells in simulations and single-unit recordings from exploring rats to ask whether temporal phase codes may anchor spatial representations to the outside world. We theorize that an experience-independent mechanism for temporal coding may combine with burst synchronization to continuously calibrate self-motion to allocentric reference frames. Subcortical recordings revealed spatial theta cells with strong rate-phase correlations related to distinct theta phases. Simulations of bursting neurons and networks explained that relationship and, with competitive learning, demonstrated flexible spatial synchronization patterns when driven by low-dimensional spatial components from the recording data. Thus temporal coding synchrony may reconcile extrinsic and intrinsic neural codes.
Whole-genome sequencing of Nicotiana glauca
Authors: Khafizova Galina , Dobrynin Pavel , Polev Dmitrii , Matveeva Tatyana
Published: October 2017

Background

Nicotiana glauca (tree tobacco) is a member of the Solanaceae family, which includes important crops (potato, tomato, eggplant, pepper) and many medicinal plants. This diploid plant is native to South America and is one of the first Nicotiana species with Agrobacterium cellular T-DNA (cT-DNA). Its cT-DNA is a partial, inverted repeat, called gT. Tree tobacco belongs to the section Noctiflorae. Sequencing of the genomes of N. tomentosiformis and N. otophora (section Tomentosae) and N. tabacum (section Nicotiana) allowed the detection of previously unknown multiple cT-DNAs, raising the question whether there are other T-DNA insertions in the N. glauca. NGS data can help answer this question. Besides, N. glauca contains a profile of alkaloids different from N. tabacum. The plant is used for medicinal purposes. Comparative analysis of genomic data of phylogenetically distant tobacco species will provide valuable information on the genetic basis for various traits, especially secondary metabolism.

Findings

We report a high-depth sequencing and de novo assembly of N. glauca full genome, which was obtained from 210 Gb Illumina HiSeq data. The final draft genome is 3.2 Gb, with N50 size of 31.1 kbp. T-DNA analysis confirmed the presence of the previously described gT insertion and the absence of other ones.

Conclusion

We provide the first comprehensive de novo full genome assembly of three tobacco, and a cT-DNA insertion analysis. These genome data could be used in pharmacological and in phylogenetic studies.
Clostridium difficilealters the structure and metabolism of distinct cecal microbiomes during initial infection to promote sustained colonization
Authors: Jenior Matthew L. , Leslie Jhansi L. , Young Vincent B. , Schloss Patrick D.
Published: October 2017

Susceptibility toClostridium difficileinfection is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistentC. difficileinfection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence ofC. difficile. Untargeted metabolomic analysis revealed thatC. difficileinfection had significantly larger impacts on the metabolic environment across cefoperazone and streptomycin-pretreated mice, which become persistently colonized compared to clindamycin-pretreated mice where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting those niches were instead occupied byC. difficile. Furthermore, the largest changes in transcription were seen in the least abundant species indicating thatC. difficilemay “attack the loser” in gut environments where sustained infection occurs more readily. Overall, our results suggest thatC. difficileis able to restructure the nutrient-niche landscape in the gut to promote persistent infection.
The effect of strong purifying selection on genetic diversity
Authors: Cvijović Ivana , Good Benjamin H. , Desai Michael M.
Published: October 2017

Purifying selection reduces genetic diversity, both at sites under direct selection and at linked neutral sites. This process, known as background selection, is thought to play an important role in shaping genomic diversity in natural populations. Yet despite its importance, the effects of background selection are not fully understood. Previous theoretical analyses of this process have taken a backwards-time approach based on the structured coalescent. While they provide some insight, these methods are either limited to very small samples or are computationally prohibitive. Here, we present a new forward-time analysis of the trajectories of both neutral and deleterious mutations at a nonrecombining locus. We find that strong purifying selection leads to remarkably rich dynamics: neutral mutations can exhibit sweep-like behavior, and deleterious mutations can reach substantial frequencies even when they are guaranteed to eventually go extinct. Our analysis of these dynamics allows us to calculate analytical expressions for the full site frequency spectrum. We find that whenever background selection is strong enough to lead to a reduction in genetic diversity, it also results in substantial distortions to the site frequency spectrum, which can mimic the effects of population expansions or positive selection. Because these distortions are most pronounced in the low and high frequency ends of the spectrum, they become particularly important in larger samples, but may have small effects in smaller samples. We also apply our forward-time framework to calculate other quantities, such as the ultimate fates of polymorphisms or the fitnesses of their ancestral backgrounds.
Connexin 43 K63-polyubiquitination on lysines 264 and 303 regulates gap junction internalization
Authors: Kells-Andrews Rachael M. , Margraf Rachel A. , Fisher Charles G. , Falk Matthias M.
Published: October 2017

Gap junctions (GJs) assembled from connexin (Cx) proteins play a pivotal role in cell-to-cell communication by forming channels that connect the cytosols of adjacent cells. Connexin 43, the best-studied Cx, is ubiquitously expressed in vertebrates. While phosphorylation is known to regulate multiple aspects of GJ function, much less is known about the role ubiquitination plays in these processes. Here we show by using ubiquitination-type specific antibodies and Cx43 lysine (K) to arginine (R) mutants that a portion of Cx43 in GJs can become K63-polyubiquitinated on K264 and K303. Relevant Cx43 K/R mutants assembled significantly larger GJ plaques, exhibited much longer protein half-lives and were internalization impaired. Interestingly, ubiquitin-deficient Cx43 mutants accumulated as hyper-phosphorylated polypeptides in the plasma membrane, suggesting that K63-polyubiquitination may be triggered by phosphorylation. Phospho-specific Cx43 antibodies revealed that upregulated phosphorylation affected serines 368, 279/282, and 255, well-known regulatory PKC and MAPK phosphorylation sites. Together, these novel findings suggest that upon internalization, some Cx43 in GJs becomes K63-polyubiquitinated, ubiquitination is critical for GJ internalization, and that K63-polyubiquitination may be induced by Cx phosphorylation.

Summary Statement

Here we show that connexin 43 in gap junctions becomes K63-poly ubiquitinated on lysines 264 and 303 and its requirement for gap junction endocytosis. These novel findings significantly contribute to our understanding of GJ turnover and patho-/physiology.

Abbreviations used

AGJ

annular gap junction

AMSH

associated molecule with the SH3 domain of STAM

CME

clathrin-mediated endocytosis

Cx

Connexin

Cx43

Connexin 43

DUB

deubiquitinase

GJ

gap junction

MonoUb

monoubiquitin

Nedd4-1

neural precursor cell expressed developmentally down-regulated protein 4-1

PM

plasma membrane

PolyUb

polyubiquitin

TPA

12-O-Tetradecanoylphorbol 13-Acetate

TX-100

Triton X-100

RT

room temperature

Ub

ubiquitin
Construction and photocatalytic properties of two metal-mediated coordination polymers based on benzene-1,3,5-tricarboxylic acid and trans-1-(pyridin-3-yl)-2-(pyridin-4-yl)ethene
Authors: Chen Jing-Min , Zhou Qian-Kun , Hou Yi-Xuan , Liu Dong
Published: October 2017

With the rapid development of modern industry, water pollution has become an intractable environmental issue facing humans worldwide. In particular, the organic dyes discharged into natural water from dyestuffs, dyeing and the textile industry are the main sources of pollution in wastewater. To eliminate these types of pollutants, degradation of organic contaminants through a photocatalytic technique is an effective methodology. To exploit more crystalline photocatalysts for the degradation of organic dyes, two coordination polymers, namely catena-poly[[(3,5-dicarboxybenzene-1-carboxylato-κO
1)silver(I)]-μ-trans-1-(pyridin-3-yl)-2-(pyridin-4-yl)ethene-κ2
N:N′], [Ag(C9H5O6)(C12H10N2)]
n
or [Ag(H2BTC)(3,4′-bpe)]
n
, (I), and poly[[(μ3-5-carboxybenzene-1,3-dicarboxylato-κ4
O
1,O
1′:O
3:O
3)[μ-trans-1-(pyridin-3-yl)-2-(pyridin-4-yl)ethene-κ2
N:N′]cadmium(II)] monohydrate], {[Cd(C9H4O6)(C12H10N2)]·H2O}
n
or {[Cd(HBTC)(3,4′-bpe)]·H2O}
n
, (II), have been prepared by the hydrothermal reactions of benzene-1,3,5-tricarboxylic acid (H3BTC) and trans-1-(pyridin-3-yl)-2-(pyridin-4-yl)ethene (3,4′-bpe) in the presence of AgNO3 or Cd(NO3)2·4H2O, respectively. These two title compounds have been structurally characterized by IR spectroscopy, elemental analysis, single-crystal X-ray diffraction and powder X-ray diffraction. In (I), the AgI ions and organic ligands form a one-dimensional coordination chain, and adjacent coordination chains are connected by Ag...O interactions to give rise to a two-dimensional supramolecular network. Each two-dimensional network is entangled with other equivalent networks to generate an infrequent interlocked 2D→3D (2D and 3D are two- and three-dimensional, respectively) supramolecular framework. In (II), the CdII ions are bridged by the HBTC2− and 3,4′-bpe ligands, which lie across centres of inversion, to give a two-dimensional coordination network. The thermal stabilities and photocatalytic properties of the title compounds have also been studied.
Synthesis, structure and in vitro cytotoxicity of platinum(II) complexes containing eugenol and a quinolin-8-ol-derived chelator
Authors: Nguyen Thi Thanh Chi , Truong Thi Cam Mai , Pham Van Thong , Nguyen Long , Nguyen Ha My , Van Meervelt Luc
Published: October 2017

The synthesis of potassium (η2-4-allyl-2-methoxyphenol)trichloridoplatinate(II), K[PtCl3(C10H12O2)], (1), starting from Zeise's salt and Ocimum sanctum L. oil has been optimized. Starting from (1), three new platinum(II) complexes, namely (η2-4-allyl-2-methoxyphenol)chlorido(2-methylquinolin-8-olato-κ2
N,O)platinum(II), (2), (η2-4-allyl-2-methoxyphenol)chlorido(5-nitroquinolin-8-olato-κ2
N,O)platinum(II), (3), and (η2-4-allyl-2-methoxyphenol)chlorido(5,7-dichloroquinolin-8-olato-κ2
N,O)platinum(II), [Pt(C9H4Cl2NO)Cl(C10H12O2)], (4), containing eugenol and a quinolin-8-ol derivative (R-OQ), have been synthesized and characterized by elemental analyses, MS, IR, 1H NMR and NOESY spectra. For (1) and (4), single-crystal X-ray diffraction studies were also carried out. Complexes (2)–(4) show good inhibiting abilities on three human cancer cell lines, i.e. KB, Hep-G2 and LU, with IC50 values of 1.42–17.8 µM. Complex (3) gives an impressively high activity against KB, Hep-G2, LU and MCF-7, with IC50 values of 1.42–4.91 µM, which are much lower than those of cisplatin and some other platinum(II) complexes.
Crystal structure of bis(pyridine-4-carbothioamide-κN1)bis(thiocyanato-κN)cobalt(II) methanol monosolvate
Authors: Neumann Tristan , Jess Inke , Näther Christian
Published: October 2017

The asymmetric unit of the title compound, [Co(NCS)2(C6H6NS)4]·CH3OH, consists of one cobalt(II) cation, two thiocyanate anions, four pyridine-4-carbothioamide ligands and one methanol molecule that are located in general positions. The CoIIcations are coordinated by two terminal N-bonding thiocyanate anions and four N-bonding pyridine-4-carbothioamide ligands, resulting in discrete and slightly distorted octahedral complexes. These complexes are linked into a three-dimensional networkviaintermolecular N—H...S hydrogen bonding between the amino H atoms and the thiocyanate and pyridine-4-carbothioamide S atoms. From this arrangement, channels are formed in which the methanol solvate molecules are embedded and linked to the host structure by intermolecular O—H...S and N—H...O hydrogen bonding.
Crystal structure of diethyl 3,3′-[(2-fluorophenyl)methylidene]bis(1H-indole-2-carboxylate)
Authors: Lu Xin-Hua , Sun Hong-Shun , Cai Yuan , Chen Lu-Lu , Chen Yang-Feng
Published: October 2017

In the title compound, C29H25FN2O4, the mean planes of the two indole ring systems (r.m.s. deviations = 0.1392 and 0.0115 Å) are approximately perpendicular to one another, subtending a dihedral angle of 86.0 (5)°; the benzene ring is twisted with respect to the mean planes of the two indole ring systems by 83.3 (2) and 88.1 (4)°, respectively. In the crystal, pairs of N—H...O hydrogen bonds link the molecules into centrosymmetric dimers, which are further linked by N—H...O hydrogen bonds into supramolecular chains propagating along the [101] direction.
Crystal structure of bis(μ2-4-bromo-2-[({2-[({2-[(5-bromo-2-oxidobenzylidene)amino]ethyl}sulfanyl)sulfonyl]ethyl}imino)methyl]phenolato)dicopper(II) dimethylformamide disolvate
Authors: Rusanova Julia A. , Bederak Dmytro
Published: October 2017

The title dinuclear copper(II) complex [Cu2(C18H16Br2N2O4S2)2] was prepared by direct synthesis of a dianionic Schiff base derived from 5-bromosalicylaldehyde and cysteamine. The discrete molecules lie across inversion centers and crystallize with two dimethylformamide (DMF) molecules of crystallization. The unique CuIIion is four-coordinated by two tetradentate Schiff base ligands in a distorted square-planar N2O2environment. In the crystal, short intermolecular S...Br contacts, weak C—H...O hydrogen bonds and intra- and intermolecular π–π stacking interactions between rings of the ligand link the components into a two-dimensional network parallel to (010).
The civil use of small unmanned aerial systems (sUASs): operational and safety challenges
Authors: Novaro Mascarello Laura , Quagliotti Fulvia
Published: October 2017

Purpose

In the past decades, both civil and military applications of small unmanned aerial systems (sUASs) have been on the rise. The sUASs guarantee the performance of dangerous, dull, duly and dirty missions, according to the 4D rule. The purpose of this study is to describe, some ethical, operational and safety challenges occur owing to the use of sUASs at over-crowded areas or in emergency scenarios. After an overview of the current sUAS regulations, some strategic configuration elements will be analysed to improve these systems and to define safe and inoffensive sUASs. Nevertheless, some problems have not been completely overcome.

Design/methodology/approach

The unmanned vehicles are nowadays applied for different kinds of applications. Search and rescue (S&R) missions; terrain surveillance and monitoring after natural disasters, such as earthquakes and landslides; and transportation of medical equipment and cartography are some examples of the most renowned and important civil missions of sUAS. In all these scenarios, some challenges could be encountered. First, the use of sUASs could compromise the privacy of unaware citizens who are in the area of application. Moreover, even if the unmanned vehicle works according to national and international regulations, there are some hazards both for the ground operators and for the population, because these sUASs could impact the human body after a flight failure.

Findings

In this paper, current principal regulations will be analysed, identifying some differences and discrepancies among them. Moreover, some considerations about the configuration elements are introduced to define the safe use of sUASs. Nevertheless, the privacy challenge is quite complicated to be overcome definitely.

Originality/value

Considering some challenges related to the civil applications of sUASs, new unmanned configurations could be developed to guarantee safety and data protection of unaware people.
Defect detection of bare printed circuit boards based on gradient direction information entropy and uniform local binary patterns
Authors: Li Yunfeng , Li Shengyang
Published: October 2017

Purpose

The purpose of this paper is to propose a defect detection method of bare printed circuit boards (PCB) with high accuracy.

Design/methodology/approach

First, bilateral filtering of the PCB image was performed in the uniform color space, and the copper-clad areas were segmented according to the color difference among different areas. Then, according to the chaotic characteristics of the spatial distribution and the gradient direction of the edge pixels on the boundary of the defective areas, the feature vector, which evaluates quantitatively the significant degree of the defect characteristics by using the gradient direction information entropy and the uniform local binary patterns, was constructed. Finally, support vector machine classifier was used for the identification and localization of the PCB defects.

Findings

Experimental results show that the proposed algorithm can accurately detect typical defects of the bare PCB, such as short circuit, open circuit, scratches and voids.

Originality/value

Considering the limitations of describing all kinds of defects on bare PCB by using single kind of feature, the gradient direction information entropy and the local binary patterns were fused to build a feature vector, which evaluates quantitatively the significant degree of the defect features.
Breaking the silence of racism injuries: a community-driven study
Authors: Lee Bonnie , Kellett Peter , Seghal Kamal , Van den Berg Corina
Published: October 2017

Purpose

Injuries resulting from racism are largely hidden by silence. Community services to provide healing from racism are missing in at least one Canadian city. The purpose of this paper is to identify the injuries suffered by immigrants who experienced racism and discuss the development of culturally appropriate programs and tools to address injuries from racism.

Design/methodology/approach

Participants representing visible minorities service providers from non-profit, public-funded organizations in a major Canadian city took part in two focus groups. Data from focus groups were thematically analyzed.

Findings

Racism produces traumatic and persistent psychological, social and intergenerational injuries. An ostensible gap exists in services, professional education and skills to address the psycho-social effects of this complex problem. The complicity of silence in both dominant and subordinated groups contributes to its perpetuation. A dearth of screening and assessment instruments is a barrier in identifying individuals whose mental health and addiction problems may have underlying racism-related etiology. Creation of community healing circles is recommended as a preferred method over individual “treatment” to expose and deconstruct racism, strengthen ethnic identity and intergenerational healing.

Research limitations/implications

These qualitative findings were generated based on the perspectives of a small purposive sample (n=8) of immigrant service providers and immigrants from one Canadian city. Many of these findings are consistent with the existing literature on internalized racism and racism injuries. Generalizability to the wider population of the province and of Canada requires further research.

Practical implications

Practitioners in health and social care as well as educators need to understand the injuries and internalized effects of racism to provide appropriate services and leadership. Development of anti-racism professional knowledge and skills, healing circles, and assessment instruments will contribute to deconstructing racism and mitigating its injuries.

Originality/value

Community-driven studies exploring racism and the lack of services to address the issue are scarce. This study pulls together the experience of service providers and their insights on ways to break the detrimental silence surrounding racism.
Root causes analysis of differential pinion shaft assembly failure in WRX class car
Authors: Królicka Aleksandra , Lesiuk Grzegorz , Katkowski Mikołaj
Published: October 2017

Purpose

The purpose of this paper is to present a case of fatigue damaging of the attacking roller of the WRC class car. Fatigue fractures are a very essential source of cognitive and usable information about the cause of damage of various engineering components. Microfractography allows extending considerations about the main mechanism of initiation and growth of fatigue cracks. The presented research procedure allowed establishing the root cause analysis of the premature fatigue failure of the pinion shaft.

Design/methodology/approach

The specimen for metallographic investigation was extracted from failures pinion shaft. According to the light microscopy and scanning electron microscopy (SEM) study, the detailed observations of microstructure were performed. Fracture surface of pinion shaft and teeth were examined using SEM. The presence of the extraordinary mechanical notch was found as a potential failure root cause.

Findings

The potential cause of premature failure pinion shaft assembly has been found. The microstructural causes were excluded due to correctly performed heat treatment. The main reason of failure was improper mechanical machining of the pinion shaft due to large mechanical notch.

Originality/value

A detailed metallographic expertise route is presented. The usefulness of fractographic analysis is confirmed in case of the failure analysis of premature pinion shaft. The root cause was found and the concluding remarks are included in this paper.
Role of multiple invasion mechanisms and their interaction in regulating the population dynamics of an exotic tree
Authors: Crandall Raelene M. , Knight Tiffany M.
Published: October 2017

Understanding the mechanisms that allow exotic species to have rapid population growth is an important step in the process of controlling existing invasions and preventing future invasions. Several hypotheses have been proposed to explain why some exotic species become invasive, the most prominent of which focus on the roles of habitat disturbance, competitors and consumers. The magnitude and direction of each of these mechanisms on population dynamics observed in previous studies is quite variable. It is possible that some of this variation results from interactions between mechanisms.

We examined all of these mechanisms and their interactions on the population dynamics of the Asian exotic tree Ailanthus altissima (Simaroubaceae) in fire‐suppressed oak‐hickory forests in Missouri, USA. We experimentally reduced herbivory (using insecticide), reduced interspecific competition (plant removals), and manipulated disturbance with prescribed fire. We projected the effects of these treatments and their interactions on population dynamics by parameterizing an integral projection model.

The lowest population growth rate is found where fire is absent and biotic interactions are present. Fire increased population growth rate, likely through the suppression of interspecific competitors, since competitor removal treatments increased population growth rate in the absence but not presence of fire.

These results indicate that biotic resistance from interspecific competitors, more so than consumers, is important for slowing the invasion of A. altissima. Furthermore, disturbances that weaken biotic interactions, such as fire, should be used with caution when restoring habitats invaded by A. altissima.

Synthesis and applications. Examining the main and interactive effects of disturbance, competition and herbivory on the population dynamics of exotic species provides a comprehensive understanding of the role of these factors in the invasion process and provides guidance for exotic species management.
Canopy‐forming macroalgal beds (Sargassum) on coral reefs are resilient to physical disturbance
Authors: Loffler Zoe , Hoey Andrew S.
Published: October 2017

Disturbances to ecosystems are often considered in terms of their potential to disrupt the feedbacks maintaining a particular ecosystem regime. The likelihood of doing so, however, will be dependent on the nature of the regime and its resilience to disturbance.

Within coral reef ecosystems, shifts from coral‐ to macroalgal dominance are becoming increasingly common and, once established, are difficult to reverse. Most studies to date have focused on the biological removal of macroalgae by herbivores, however, none have considered the resilience of macroalgal beds to physical removal by storms.

We simulated the physical removal of macroalgal biomass from Sargassum beds on an inshore coral reef on Australia's Great Barrier Reef, and monitored recovery for 11 months. Trimming Sargassum biomass but leaving the holdfast intact had no detectable effect on the density, height or biomass of Sargassum compared to adjacent intact, or control, areas after 5 months. In areas where holdfasts were also removed, Sargassum biomass recovered to 50% of control biomass after 11 months.

Given the importance of holdfasts to the resilience of Sargassum beds, we also investigated the ability of herbivores to remove and/or damage holdfasts. Exposing pieces of dead coral with attached Sargassum holdfasts to local herbivore assemblages resulted in a 70% decline in the number of holdfasts over 4 months compared to those protected from herbivores.

Synthesis. Beds of Sargassum are extremely resilient to the physical removal of algal biomass, and as such, storms alone are unlikely to lead to permanent reductions in Sargassum abundance. Persistent reductions in the abundance of macroalgae on degraded coral reefs will not only require the physical or biological removal of algal biomass, but critically, sufficient densities of herbivores capable of removing holdfasts.
Genome‐wide identification of chitin‐binding proteins and characterization of BmCBP1 in the silkworm, Bombyx mori
Authors: Li Zhi‐Lang , Tian Sha , Yang Huan , Zhou Xia , Xu Shu‐Ping , Zhang Zi‐Yu , Gong Jing , Hou Yong , Xia Qing‐You
Published: October 2017

The insect cuticle plays important roles in numerous physiological functions to protect the body from invasion of pathogens, physical injury and dehydration. In this report, we conducted a comprehensive genome‐wide search for genes encoding proteins with peritrophin A‐type (ChtBD2) chitin‐binding domain (CBD) in the silkworm, Bombyx mori. One of these genes, which encodes the cuticle protein BmCBP1, was additionally cloned, and its expression and location during the process of development and molting in B. mori were investigated. In total, 46 protein‐coding genes were identified in the silkworm genome, including those encoding 15 cuticle proteins analogous to peritrophins with one CBD (CPAP1s), nine cuticle proteins analogous to peritrophins with three CBD (CPAP3s), 15 peritrophic membrane proteins (PMPs), four chitinases, and three chitin deacetylases, which contained at least one ChtBD2 domain. Microarray analysis indicated that CPAP‐encoding genes were widely expressed in various tissues, whereas PMP genes were highly expressed in the midgut. Quantitative polymerase chain reaction and western blotting showed that the cuticle protein BmCBP1 was highly expressed in the epidermis and head, particularly during molting and metamorphosis. An immunofluorescence study revealed that chitin co‐localized with BmCBP1 at the epidermal surface during molting. Additionally, BmCBP1 was notably up‐regulated by 20‐hydroxyecdysone treatment. These results provide a genome‐level view of the chitin‐binding protein in silkworm and suggest that BmCBP1 participates in the formation of the new cuticle during molting.
Modeling Associations Between Latent Event Processes Governing Time Series of Pulsing Hormones
Authors: Liu Huayu , Carlson Nichole E. , Grunwald Gary K. , Polotsky Alex J.
Published: October 2017

This work is motivated by a desire to quantify relationships between two time series of pulsing hormone concentrations. The locations of pulses are not directly observed and may be considered latent event processes. The latent event processes of pulsing hormones are often associated. It is this joint relationship we model. Current approaches to jointly modeling pulsing hormone data generally assume that a pulse in one hormone is coupled with a pulse in another hormone (one-to-one association). However, pulse coupling is often imperfect. Existing joint models are not flexible enough for imperfect systems. In this article, we develop a more flexible class of pulse association models that incorporate parameters quantifying imperfect pulse associations. We propose a novel use of the Cox process model as a model of how pulse events co-occur in time. We embed the Cox process model into a hormone concentration model. Hormone concentration is the observed data. Spatial birth and death Markov chain Monte Carlo is used for estimation. Simulations show the joint model works well for quantifying both perfect and imperfect associations and offers estimation improvements over single hormone analyses. We apply this model to luteinizing hormone (LH) and follicle stimulating hormone (FSH), two reproductive hormones. Use of our joint model results in an ability to investigate novel hypotheses regarding associations between LH and FSH secretion in obese and non-obese women.
Statistical Inference in A Growth Curve Quantile Regression Model for Longitudinal Data
Authors: Cho Hyunkeun Ryan
Published: October 2017

This article describes a polynomial growth curve quantile regression model that provides a comprehensive assessment about the treatment effects on the changes of the distribution of outcomes over time. The proposed model has the flexibility, as it allows the degree of a polynomial to vary across quantiles. A high degree polynomial model fits the data adequately, yet it is not desirable due to the complexity of the model. We propose the model selection criterion based on an empirical loglikelihood that consistently identifies the optimal degree of a polynomial at each quantile. After the parsimonious model is fitted to the data, the hypothesis test is further developed to evaluate the treatment effects by comparing the growth curves. It is shown that the proposed empirical loglikelihood ratio test statistic follows a chi-square distribution asymptotically under the null hypothesis. Various simulation studies confirm that the proposed test successfully detects the difference between the curves across quantiles. When the empirical loglikelihood is employed, we incorporate the within-subject correlation commonly existing in longitudinal data and gain estimation efficiency of the quantile regression parameters in the growth curve model. The proposed process is illustrated through the analysis of randomized controlled longitudinal depression data.
Approximations to the distribution of a test statistic in covariance structure analysis: A comprehensive study
Authors: Wu Hao
Published: October 2017

In structural equation modelling (SEM), a robust adjustment to the test statistic or to its reference distribution is needed when its null distribution deviates from a χ2distribution, which usually arises when data do not follow a multivariate normal distribution. Unfortunately, existing studies on this issue typically focus on only a few methods and neglect the majority of alternative methods in statistics. Existing simulation studies typically consider only non‐normal distributions of data that either satisfy asymptotic robustness or lead to an asymptotic scaled χ2distribution. In this work we conduct a comprehensive study that involves both typical methods in SEM and less well‐known methods from the statistics literature. We also propose the use of several novel non‐normal data distributions that are qualitatively different from the non‐normal distributions widely used in existing studies. We found that several under‐studied methods give the best performance under specific conditions, but the Satorra–Bentler method remains the most viable method for most situations.
Minimally invasive treatment of complicated parapneumonic effusions and empyemas in adults
Authors: Porcel José M.
Published: October 2017

Objectives

To summarize the evidence underlying the non‐surgical management of patients with complicated parapneumonic effusions (CPPE) or empyemas.

Data source

All articles published in PubMed according to their relevance with the subject were identified.

Results and conclusions

There is a lack of powered randomized controlled studies comparing medical and surgical approaches to CPPE/empyemas in adults. In addition to antibiotics for an unspecified period of time, CPPE/empyemas can initially be treated with a therapeutic thoracentesis (which can be repeated if necessary), the insertion of a small‐bore chest catheter under ultrasound guidance, or the administration through the catheter of fibrinolytics alone, saline alone or fibrinolytics in combination with either saline or deoxyribonuclease. These conservative measures resolve more than 90% of the cases, thus making a rescue surgery unnecessary.
JOSEPH D. HOOKER'S 1839 CABO VERDE COLLECTIONS
Authors: Rico Lourdes , Duarte Maria C. , Romeiras Maria M. , Santos‐Guerra Arnoldo , Nepi Chiara , Francisco‐Ortega Javier
Published: October 2017

Joseph Dalton Hooker (1817–1911) was 22 years old when he undertook his first natural history journey abroad. He was appointed ‘Assistant Surgeon’, under the command of James Clark Ross in the Antarctic Expedition 1838–1845, also known as the South Pole Magnetic Expedition. The two HMS ships The Terror and The Erebus made brief stops in the Macaronesian islands of Madeira, Tenerife (the Canaries), and Santiago (Cabo Verde) where Hooker took the opportunity to observe and collect animals, plants and minerals, so these were the first three collecting sites documented in his Antarctic Journal.
RETRACING JOSEPH HOOKER'S ROUTES IN THE SIKKIM HIMALAYA
Authors: O'Brien Seamus
Published: October 2017

Joseph Hooker was one of the most widely travelled botanists of the Victorian period, having explored regions as far afield as Antarctica, Morocco and North America, though it is for his pioneering exploration of the Sikkim Himalaya that he is perhaps best remembered. Seamus O'Brien led four expeditions to this remote corner of the eastern Himalaya, and the results of these trips will appear in a new biography due to be published by Kew in 2018. He summarises that story here.
Incremental value of live/real time three‐dimensional transesophageal echocardiography in the assessment of ventricular septal rupture following acute myocardial infarction
Authors: Arisha Mohammed J. , Hsiung Ming C. , Nanda Navin C. , Serkan Bulur , Ahmad Amier , Elkaryoni Ahmed , Elsayed Mahmoud , Adana Leilani , Turaga Shravan , Guler Emel , Alagic Nermina
Published: October 2017

Ventricular septal rupture is a serious complication following acute myocardial infarctions and is associated with a significant mortality rate. Classically, two‐dimensional transthoracic echocardiography has been used to diagnose this complication and visualize its location. Two‐dimensional transesophageal echocardiography has supplemented the transthoracic approach by providing more accurate assessment of the defect size and in guiding closure both percutaneously and intraoperatively. This modality, however, is limited to two‐dimensional views only, and a greater breadth of information is instead available through the use of three‐dimensional transesophageal echocardiography. We present a series of 11 patients in which live/real time three‐dimensional transesophageal echocardiography offered incremental benefits over two‐dimensional imaging alone.
Fast and specific detection of the invasive forest pathogen Heterobasidion irregulare through a Loop‐mediated isothermal AMPlification (LAMP) assay
Authors: Sillo F. , Giordano L. , Gonthier P.
Published: October 2017

Heterobasidion irregulare is one of the most destructive fungal pathogens of pines in North America and was accidentally introduced into central Italy, where it has become invasive. The fungus is currently recommended for regulation by the European and Mediterranean Plant Protection Organisation (EPPO). In this work, an efficient diagnostic tool for the early detection of H. irregulare based on Loop‐mediated isothermal AMPlification (LAMP) coupled with two different DNA extraction methods was developed. The LAMP assay showed high specificity and good sensitivity, with a limit of detection of about 20 picograms of target DNA and time of detection of less than 40 min. The assay was successfully tested on a variety of different samples, including fungal fruiting bodies, infected plants and colonized wood. A survey on environmental samples collected in the field was also performed using the LAMP assay coupled with a rapid DNA extraction method. The possible applications of this molecular diagnostic tool encompass the monitoring of pine forests surrounding the current invasion area, laboratory or in‐field analyses of samples from suspected trees, and the surveillance in the ports of entry of wood imported from North America.
Actor–Partner Associations of Mindfulness and Marital Quality After Military Deployment
Authors: Zamir Osnat , Gewirtz Abigail H. , Zhang Na
Published: October 2017

Objective

To explore dyadic associations between mindfulness and marital quality and gender differences in these associations—that is, the relation of each dyad member's mindfulness with his or her own marital quality and with his or her partner's marital quality.

Background

Recent studies have demonstrated the benefits of mindfulness for marital quality. However, associations of mindfulness and marital quality within and between partners are still unclear. In addition, despite marital challenges associated with deployment to war, the benefits of mindfulness for marital quality in military couples is unknown.

Method

A sample of 228 military couples after deployment of the male partner to recent conflicts in Iraq or Afghanistan completed an online survey measuring mindfulness and marital quality.

Results

Actor–partner interdependence analysis showed that for both men and women, greater mindfulness was associated with one's own and one's partner's higher marital quality. There were no gender differences in this pattern.

Conclusion

Mindfulness engenders intra‐ and interpersonal benefits for the marital system in men and in women after deployment to war.

Implications

The results emphasize the importance of a dyadic approach when examining the role of mindfulness in marital or family relations, and suggest that interventions designed to facilitate change in marital relationships in the context of deployment may benefit from integrating mindfulness‐based training.