bluuebunny/crossref_metadata_2025 huggingface dataset:
Thromboelastography on-the-go: Evaluation of the TEG 6s device during ground and high-altitude Aeromedical Evacuation with extracorporeal life support
Authors: Roberts Teryn R. , Jones John A. , Choi Jae-Hyek , Sieck Kyle N. , Harea George T. , Wendorff Daniel S. , Beely Brendan M. , Karaliou Vitali , Cap Andrew P. , Davis Michael R. , Cancio Leopoldo C. , Sams Valerie G. , Batchinsky Andriy I.
Published: February 2019

BACKGROUND

Coagulation monitoring capabilities during transport are limited. Thromboelastography (TEG) is a whole-blood clotting test measuring clot formation, stabilization, and fibrinolysis and is traditionally performed in a laboratory. We evaluated a new point-of-care TEG analyzer, TEG 6s (Haemonetics, Braintree, MA), in a large animal model of combat-relevant trauma managed with extracorporeal life support during ground and high-altitude aeromedical evacuation. The objective was to compare TEG 6s used during transport versus the predicate device, TEG 5000, used in the laboratory. We hypothesized that TEG 6s would be comparable with TEG 5000 during dynamically changing transport conditions.

METHODS

Thromboelastography parameters (R,K, angle, MA, LY30) derived by TEG 6s and TEG 5000 were compared during transport of 8 swine. TEG 6s was transported with animals during ground transport and flight. TEG 5000 was stationary in an adjacent building. TEG 6s activated clotting time (ACT) was compared with a Hemochron Junior ACT analyzer (Accriva Diagnostics, San Diego, CA). Statistics were performed using SAS 9.4 with Deming regressions, Spearman correlations, and average differences compared.

RESULTS

Correlation between devices was stronger at sea-level (R,r= 0.7413;K,r= 0.7115; angle,r= 0.7192; MA,r= 0.8386; LY30,r= 0.9099) than during high-altitude transport (R,r= 0.4787;K,r= 0.4007; angle,r= 0.3706; MA,r= 0.6573; LY30,r= 0.8481). Method agreement was comparable during stationary operation (R,r= 0.7978;K,r= 0.7974; angle,r= 0.7574; MA,r= 0.7841; LY30,r= 0.9140) versus ground transport (R,r= 0.7927;K,r= 0.6246; angle,r= 0.6967; MA,r= 0.9163; LY30,r= 0.8603). TEG 6s ACT trended higher than Hemochron ACT when subjects were heparinized (average difference, 1,442 ± 1,703 seconds) without a methodological difference by Deming regression.

CONCLUSION

Mobile TEG 6s during ground and altitude transport is feasible and provides unprecedented information to guide coagulation management. Future studies should assess the precision and accuracy of TEG 6s during transport of critically ill.
Nonulosonic acids contribute to the pathogenicity of the oral bacteriumTannerella forsythia
Authors: Bloch Susanne , Tomek Markus B. , Friedrich Valentin , Messner Paul , Schäffer Christina
Published: February 2019

Periodontitis is a polymicrobial, biofilm-caused, inflammatory disease affecting the tooth-supporting tissues. It is not only the leading cause of tooth loss worldwide, but can also impact systemic health. The development of effective treatment strategies is hampered by the complicated disease pathogenesis which is best described by a polymicrobial synergy and dysbiosis model. This model classifies the Gram-negative anaerobeTannerella forsythiaas a periodontal pathogen, making it a prime candidate for interference with the disease.Tannerella forsythiaemploys a proteinO-glycosylation system that enables high-density display of nonulosonic acids via the bacterium's two-dimensional crystalline cell surface layer. Nonulosonic acids are sialic acid-like sugars which are well known for their pivotal biological roles. This review summarizes the current knowledge ofT. forsythia's unique cell envelope with a focus on composition, biosynthesis and functional implications of the cell surfaceO-glycan. We have obtained evidence that glycobiology affects the bacterium's immunogenicity and capability to establish itself in the polymicrobial oral biofilm. Analysis of the genomes of differentT. forsythiaisolates revealed that complex proteinO-glycosylation involving nonulosonic acids is a hallmark of pathogenicT. forsythiastrains and, thus, constitutes a valuable target for the design of novel anti-infective strategies to combat periodontitis.
Citroniella saccharovorans gen. nov. sp. nov., a member of the family Peptoniphilaceae isolated from a human fecal sample from a coastal traditional community member
Authors: Patel Nisha B. , Obregón-Tito Alexandra J. , Tito Raul Y. , Trujillo-Villaroel Omar , Marin-Reyes Luis , Troncoso-Corzo Luzmila , Guija-Poma Emilio , Lewis Jr Cecil M. , Lawson Paul A.
Published: February 2019

A novel Gram-stain-positive, non-motile, non-spore-forming coccus-shaped obligately anaerobic bacterium was recovered from a fecal sample obtained from an individual from a traditional community located on the southern coast of Peru. The results of analysis based on 16S rRNA gene sequencing indicated the novel bacterium to be phylogenetically distinct from other genera of members of the

Peptoniphilaceae

family, sharing a loose affinity with the genera

Ezakiella

,

Finegoldia

,

Gallicola

and

Parvimonas

. The major cellular fatty acids of the novel isolate were determined to be C16:0, C17:1ω8c, and C18:1ω9c. The DNA G+C content was 29.9 mol%. End products of metabolism from peptone yeast glucose broth (PYG) were determined to be acetate and methyl succinate. The diagnostic diamino acid present in the cell wall was lysine. On the basis of the phenotypic, chemotaxonomic and phylogenetic results the organism is a member of a novel genus belonging to the family

Peptoniphilaceae

for which the name Citroniella saccharovorans gen nov. sp. nov., is proposed. The type strain is M6.X9T (DSM 29873T=CCUG 66799T).
Assessing different components of biodiversity across a river network using eDNA
Authors: Mächler Elvira , Little Chelsea J. , Wüthrich Remo , Alther Roman , Fronhofer Emanuel A. , Gounand Isabelle , Harvey Eric , Hürlemann Samuel , Walser Jean-Claude , Altermatt Florian
Published: February 2019

Assessing individual components of biodiversity, such as local or regional taxon richness, and differences in community composition is a long-standing challenge in ecology. It is especially relevant in spatially structured and diverse ecosystems. Environmental DNA (eDNA) has been suggested as a novel technique to accurately measure biodiversity. However, we do not yet fully understand the comparability of eDNA-based assessments to previously used approaches.

We sampled may-, stone-, and caddisfly genera with contemporary eDNA and kicknet methods at 61 sites distributed over a large river network, allowing a comparison of various diversity measures from the catchment to site levels and providing insights into how these measures relate to network properties. We extended our survey data with historical records of total diversity at the catchment level.

At the catchment scale, eDNA and kicknet detected similar proportions of the overall and cumulative historically documented species richness (gamma diversity), namely 42% and 46%, respectively. We further found a good overlap (62%) between the two contemporary methods at the regional scale.

At the local scale, we found highly congruent values of local taxon richness (alpha diversity) between eDNA and kicknet. Richness of eDNA was positively related with discharge, a descriptor of network position, while kicknet was not.

Beta diversity between sites was similar for the two contemporary methods. Contrary to our expectation, however, beta diversity was driven by species replacement and not by nestedness.

Although optimization of eDNA approaches is still needed, our results indicate that this novel technique can capture extensive aspects of gamma diversity, proving its potential utility as a new tool for large sampling campaigns across hitherto understudied complete river catchments, requiring less time and becoming more cost-efficient than classical approaches. Overall, the richness estimated with the two contemporary methods is similar at both local and regional scale but community composition is differently assessed with the two methods at individual sites and becomes more similar with higher discharge.
SCANVIS – a tool for SCoring, ANnotating and VISualizing splice junctions
Authors: Agius Phaedra , Geiger Heather , Robine Nicolas
Published: February 2019

Motivation

The association of splicing signatures with disease is a leading area of study for prognosis, diagnosis and therapy, frequently requiring detailed analysis of splicing events across multiple samples. We present a novel fast-performing annotation-dependent tool called SCANVIS for scoring and annotating splice junctions by gene name, junction type and any frame shifts incurred. SCANVIS has a novel and fast visualization technique that distinguishes annotated splice junctions from unannotated ones in the context of nearby variants and read coverage. It also allows users to merge samples across cohorts, thereby allowing for quick comparisons of splice junctions across diseases and tissue types.

Results

We show that SCANVIS generates reasonable PSI scores by demonstrating that tissue/cancer types in GTEX and TCGA are well separated and easily predicted from a few thousand SJs. We also show how SCANVIS can be used to map out junctions overlaid with variants and read coverage for one or more samples, with line types and colors delineating frame shifts and junction types.

Availability

SCANVIS is available for download at https://github.com/nygenome/SCANVIS

Contact

pagius@nygenome.org
Odour conditioning of positive affective states: Rats can learn to associate an odour with being tickled
Authors: Bombail Vincent , Jerôme Nathalie , Lam Ho , Muszlak Sacha , Meddle Simone L , Lawrence Alistair B , Nielsen Birte L
Published: February 2019

Most associative learning tests in rodents use negative stimuli, such as an electric shock. We investigated if young rats can learn to associate the presence of an odour with the experience of being tickled (i.e. using an experimenter’s hand to mimic rough-and-tumble play), shown to elicit 50 kHz ultrasonic vocalisations (USVs), which are indicative of positive affect. Male, pair-housed Wistar rats (N=24) were all exposed to two neutral odours (A and B) presented in a perforated container on alternate days in a test arena. Following 60s of exposure, the rats were either tickled on days when odour A (n=8) or odour B (n=8) was present, or never tickled (n=8). When tickled, rats produced significantly more 50 kHz USVs compared to the days when not being tickled, and compared to control rats. The level of anticipatory 50 kHz USVs in the 60s prior to tickling did not differ significantly between the tickled and control rats. Following the odour conditioning, rats were exposed successively in the same arena to three odours: an unknown neutral odour, extract of fox faeces, and either odours A or B. Compared to controls, 50 kHz USVs of tickled rats increased when exposed to the odour they had previously experienced when tickled, indicating that these rats had learned to associate the odour with the positive experience of being tickled. In a test with free access for 5 min to both arms of a T-maze, each containing one of the odours, rats tickled with odour A spent more time in the arm with this odour. This work is the first to test in a fully balanced design whether odours can be conditioned to tickling, and indicates that positive odour conditioning has potential to be used as an alternative to negative conditioning tests.
Speed, accuracy, sensitivity and quality control choices for detecting clinically relevant microbes in whole blood from patients
Authors: Thornton James , Watts George S. , Youens-Clark Ken , Cranmer Lee D. , Hurwitz Bonnie L.
Published: February 2019

Infections are a serious health concern worldwide, particularly in vulnerable populations such as the immunocompromised, elderly, and young. Advances in metagenomic sequencing availability, speed, and decreased cost offer the opportunity to supplement or replace culture-based identification of pathogens with DNA sequence-based diagnostics. Adopting metagenomic analysis for clinical use requires that all aspects of the pipeline are optimized and tested, including data analysis. We tested the accuracy, sensitivity, and resource requirements of Centrifuge within the context of clinically relevant bacteria. Binary mixtures of bacteria showed Centrifuge reliably identified organisms down to 0.1% relative abundance. A staggered mock bacterial community showed Centrifuge outperformed CLARK while requiring less computing resources. Shotgun metagenomes obtained from whole blood in three febrile neutropenia patients showed Centrifuge could identify both bacteria and viruses as part of a culture-free workflow. Finally, Centrifuge results changed minimally by eliminating time-consuming read quality control and host screening steps.

AUTHOR SUMMARY

Immunocompromised patients, such as those with febrile neutropenia (FN), are susceptible to infections, yet cultures fail to identify causative organisms ~80% of the time. High-throughput metagenomic sequencing offers a promising approach for identifying pathogens in clinical samples. Mining through metagenomes can be difficult given the volume of reads, overwhelming human contamination, and lack of well-defined bioinformatics methods. The goal of our study was to assess Centrifuge, a leading tool for the identification and quantitation of microbes, and provide a streamlined bioinformatics workflow real-word data from FN patient blood samples. To ensure the accuracy of the workflow we carefully examined each step using known bacterial mixtures that varied by genetic distance and abundance. We show that Centrifuge reliably identifies microbes present at just 1% relative abundance and requires substantially less computer time and resource than CLARK. Moreover, we found that Centrifuge results changed minimally by quality control and host-screening allowing for further reduction in compute time. Next, we leveraged Centrifuge to identify viruses and bacteria in blood draws for three FN patients, and confirmed suspected pathogens using genome coverage plots. We developed a web-based tool in iMicrobe and detailed protocols to promote re-use.
MakeHub: Fully automated generation of UCSC Genome Browser Assembly Hubs
Authors: Hoff Katharina J.
Published: February 2019

Novel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. This need had been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. Assembly Hubs allow browsing genomes that are hosted locally via already available UCSC Genome Browser servers. The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available. However, the number of steps for creating a novel Assembly Hub is large. In some cases the format of input files needs to be adapted which is a difficult task for scientists without programming background. Here, we describe the novel command line tool MakeHub that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion. The pipeline also allows extending previously created Hubs by additional tracks.

MakeHub is freely available for download from https://github.com/Gaius-Augustus/MakeHub.

Contact

katharina.hoff@uni-greifswald.de
Branching Networks Can Have Opposing Influences on Genetic Variation in Riverine Metapopulations
Authors: Chiu Ming-Chih , Li Bin , Nukazawa Kei , Resh Vincent H. , Carvajal Thaddeus , Watanabe Kozo
Published: February 2019

Aim

Fractal networks, represented by branching complexity in rivers, are ubiquitous in nature. In rivers, the number of either distal (e.g., in headwater streams) or confluent (e.g., in mainstems) locations can be increased along with their branching complexity. Distal- or confluent-spatial locations can result in fewer or greater corridor linkages that can alter genetic divergence at the metapopulation scale. These mechanisms underlying the resulting genetic structuring remain poorly understood at the metapopulation scale, particularly in terms of the roles of species-specific dispersal traits. The objective of this study is to mechanistically understand how branching complexity can simultaneously influence genetic divergence in opposite directions.

Location

Northeastern Japan

Methods

To evaluate the integrated influences of network complexity and species dispersal on genetic divergence among populations at the catchment scale, we conducted simulation modelling on a mechanistic framework based on Bayesian inference by adapting empirical genetic data from four macroinvertebrate species. Simulations were then done using empirical and virtual species-characteristics on virtual river networks.

Results

Our novel simulation showed that both greater landscape connectivity (resulting from shorter watercourse distance) and greater isolation of distal locations occurred in the more-branched river networks. These two spatial features have negative and positive influences on genetic divergence, with their relative importance varying among different species and dispersal characteristics. Specifically, genetic divergence at the metapopulation scale increased for species having higher downstream-biased dispersal but decreased for species having higher upstream-biased dispersal. Distal populations (e.g., in headwaters) have higher genetic independence when downstream-biased asymmetry is higher.

Main conclusions

We found a strong association between species dispersal and evolutionary processes such as gene flow and genetic drift. This association mediates the pervasive influences of branching complexity on genetic-divergence in the metapopulation. It also highlights the importance of considering species dispersal-patterns when developing management strategies in the face of rapid environmental-change scenarios.
Egalitarian binding partners, Dynein Light Chain and Bicaudal-D, act sequentially to link mRNA to the Dynein motor
Authors: Goldman Chandler H. , Veeranan-Karmegam Rajalakshmi , Neiswender Hannah , Gonsalvez Graydon B.
Published: February 2019

A widely conserved mechanism of polarity establishment is the localization of mRNA to specific cellular regions. While it is clear that many mRNAs are transported to their destinations along microtubule tracks, much less is known regarding the mechanism by which these mRNAs are linked to microtubule motors. The RNA binding protein Egalitarian (Egl) is necessary for localization of several mRNAs inDrosophilaoocytes and embryos. In addition to binding RNA, Egl also interacts with Dynein light chain (Dlc) and Bicaudal-D (BicD). The role of Dlc and BicD in mRNA localization has remained elusive. Like Egl, both proteins are required for oocyte specification. Null alleles in these genes result in an oogenesis block. In this report, we used an innovative approach to overcome the oogenesis block. Our findings reveal that the primary function of Dlc is to promote Egl dimerization. Loss of dimerization compromises the ability of Egl to bind RNA. Consequently, Egl is not bound to cargo, and is not able to efficiently associate with BicD and the Dynein motor. Our results therefore identify the key molecular steps required for assembling a localization competent mRNP.
A method for genome-wide genealogy estimation for thousands of samples
Authors: Speidel Leo , Forest Marie , Shi Sinan , Myers Simon R.
Published: February 2019

Knowledge of genome-wide genealogies for thousands of individuals would simplify most evolutionary analyses for humans and other species, but has remained computationally infeasible. We developed a method, Relate, scaling to > 10,000 sequences while simultaneously estimating branch lengths, mutational ages, and variable historical population sizes, as well as allowing for data errors. Application to 1000 Genomes Project haplotypes produces joint genealogical histories for 26 human populations. Highly diverged lineages are present in all groups, but most frequent in Africa. Outside Africa, these mainly reflect ancient introgression from groups related to Neanderthals and Denisovans, while African signals instead reflect unknown events, unique to that continent. Our approach allows more powerful inferences of natural selection than previously possible. We identify multiple novel regions under strong positive selection, and multi-allelic traits including hair colour, BMI, and blood pressure, showing strong evidence of directional selection, varying among human groups.
Immune Responses to Human Induced Pluripotent Stem Cells and their Derived Myogenic Progenitors Are Mediated by Different Mechanisms in Humanized Mice
Authors: Benabdallah Basma , Désaulniers-Langevin Cynthia , Goyer Marie-Lyn , Colas Chloé , Maltais Chantale , Li Yuanyi , Guimond Jean V. , Tremblay Jacques P , Haddad Elie , Beauséjour Christian
Published: February 2019

It is still unclear if immune responses will compromise the large scale utilization of cell therapies derived from human induced pluripotent stem cells (hiPSCs). To answer this question, we used humanized mouse models and evaluated the engraftment in skeletal muscle of myoblasts derived either directly from a muscle biopsy or differentiated from hiPSCs or fibroblasts. Our results showed that while allogeneic grafts were rejected, engraftment of autologous cells was tolerated, indicating reprogramming and differentiation procedures are not immunogenic. We also demonstrated that hiPSC-derived myogenic progenitors, in opposition to hiPSCs, are not targeted by natural killer (NK) cells both in vitro and in vivo. Yet, adoptive transfer of NK cells can prevent the formation of hiPSC-derived teratoma. Overall, our findings suggest that hiPSC-derived muscular therapies will be tolerated in presence of a competent human immune system and highlight the risk of forming a teratoma if using partially differentiated autologous human cells.

Highlights

hiPSC-derived myofibers are tolerated in autologous humanized mouse models

Infiltration of autologous T cells is not predictive of successful skeletal muscle engraftment

Adoptive transfer of NK cells prevents the formation of hiPSCs derived teratomas

NK cells are unable to reject established teratomas
Parthenolide Covalently Targets and Inhibits Focal Adhesion Kinase in Breast Cancer Cells
Authors: Berdan Charles A. , Ho Raymond , Lehtola Haley S. , To Milton , Hu Xirui , Huffman Tucker R. , Petri Yana , Altobelli Chad R. , Demeulenaere Sasha G. , Olzmann James A. , Maimone Thomas J. , Nomura Daniel K.
Published: February 2019

Parthenolide, a natural product from the feverfew plant and member of the large family of sesquiterpene lactones, exerts multiple biological and therapeutic activities including anti-inflammatory and anti-cancer effects. Herein, we further study parthenolide mechanism of action using activity-based protein profiling (ABPP)-based chemoproteomic platforms to map additional covalent targets engaged by parthenolide in human breast cancer cells. We find that parthenolide, as well as other related exocyclic methylene lactone-containing sesquiterpenes, covalently modify cysteine 427 (C427) of focal adhesion kinase 1 (FAK1) leading to impairment of FAK1-dependent signaling pathways and breast cancer cell proliferation, survival, and motility. These studies reveal a novel functional target exploited by members of a large family of anticancer natural products.
Characterization of single gene copy number variants in schizophrenia
Authors: Szatkiewicz Jin P. , Fromer Menachem , Nonneman Randal J. , Ancalade NaEshia , Johnson Jessica S. , Stahl Eli A. , Rees Elliott , Bergen Sarah , Hultman Christina , Kirov George , O’Donovan Michael , Owen Michael , Holmans Peter , Sklar Pamela , Sullivan Patrick F. , Purcell Shaun M. , Crowley James J. , Ruderfer Douglas M.
Published: February 2019

Genetic studies of schizophrenia (SCZ) have now implicated numerous genomic loci that contribute to risk including several copy number variants (CNV) of large effect and hundreds of associated loci of small effect. However, in only a few cases has a specific gene been clearly identified. Rare CNV that affect only a single gene offer a potential avenue to discovering specific SCZ risk genes. Here, we use CNV generated from exome-sequencing of 4,913 SCZ cases and 6,188 controls in a homogenous Swedish cohort to assess the contribution of single-gene deletions and duplications to SCZ risk. As previously seen, we found an excess of rare deletions (p = 0.0004) and duplications (p = 0.0006) in SCZ cases compared to controls. When limiting to only single-gene CNV we identified nominally significant excess of deletions (p = 0.04) and duplications (p = 0.03). In an effort to increase the number of single-gene CNV, we reduced strict filtering criteria but required support from two independent CNV calling methods to create an expanded set that showed a significant burden of deletions in 11 out of 22 gene sets previously implicated in SCZ and in the combined set of genes across those sets (p = 0.008). Finally, for the significantly enriched set of voltage-gated calcium channels, we performed an extensive validation of all deletions generated from exome-sequencing as well as any deletion with evidence from previously analyzed genotyping arrays. In total, 4 exonic, single-gene deletions validated in cases and none in controls (p = 0.039), of which all were identified by exome-sequencing. Broadly, these results point to the potential contribution of single-gene CNV to SCZ and the added value of a deeper dive into CNV calls from exome-sequencing.
Detection and assembly of novel sequence insertions using Linked-Read technology
Authors: Meleshko Dmitry , Marks Patrick , Williams Stephen , Hajirasouliha Iman
Published: February 2019

Motivation

Emerging Linked-Read (aka read-cloud) technologies such as the 10x Genomics Chromium system have great potential for accurate detection and phasing of largescale human genome structural variations (SVs). By leveraging the long-range information encoded in Linked-Read sequencing, computational techniques are able to detect and characterize complex structural variations that are previously undetectable by short-read methods. However, there is no available Linked-Read method for detection and assembly of novel sequence insertions, DNA sequences present in a given sequenced sample but missing in the reference genome, without requiring whole genome de novo assembly. In this paper, we propose a novel integrated alignment-based and local-assembly-based algorithm, Novel-X, that effectively uses the barcode information encoded in Linked-Read sequencing datasets to improve detection of such events without the need of whole genome de novo assembly. We evaluated our method on two haploid human genomes, CHM1 and CHM13, sequenced on the 10x Genomics Chromium system. These genomes have been also characterized with high coverage PacBio long-reads recently. We also tested our method on NA12878, the wellknown HapMap CEPH diploid genome and the child genome in a Yoruba trio (NA19240) which was recently studied on multiple sequencing platforms. Detecting insertion events is very challenging using short reads and the only viable available solution is by long-read sequencing (e.g. PabBio or ONT). Our experiments, however, show that Novel-X finds many insertions that cannot be found by state of the art tools using short-read sequencing data but present in PacBio data. Since Linked-Read sequencing is significantly cheaper than long-read sequencing, our method using Linked-Reads enables routine large-scale screenings of sequenced genomes for novel sequence insertions.

Availability

Software is freely available at https://github.com/1dayac/novel_insertions

Contact

imh2003@med.cornell.edu

Supplementary information

Supplementary data are available at https://github.com/1dayac/novel_insertions_supplementary
Whole genomic sequencing as a tool for diagnosis of drug and multidrug-resistance tuberculosis in an endemic region in Mexico
Authors: Madrazo-Moya Carlos Francisco , Cancino-Muñoz Irving , Cuevas-Cordoba Betzaida , Gonzalez-Covarrubias Vanessa , Barbosa-Amezcua Martín , Soberón Xavier , Muñiz-Salazar Raquel , Martínez-Guarneros Armando , Backer Claudia , Zarrabal-Meza José , Sampieri-Ramirez Clara , Enciso-Moreno Antonio , Lauzardo Michael , Comas Iñaki , Zenteno-Cuevas Roberto
Published: February 2019

Background

Whole genome sequencing (WGS) has been proposed as a tool for diagnosing drug resistance in tuberculosis. However, reports of its effectiveness in endemic countries with important numbers of drug resistance are scarce. The goal of this study was to evaluate the effectiveness of this procedure in isolates from a tuberculosis endemic region in Mexico.

Methods

WGS analysis was performed in 81 tuberculosis positive clinical isolates with a known phenotypic profile of resistance against first-line drugs (isoniazid, rifampin, ethambutol, pyrazinamide and streptomycin). Mutations related to drug resistance were identified for each isolate; drug resistant genotypes were predicted and compared with the phenotypic profile. Genotypes and transmission clusters based on genetic distances were also characterized.

Findings

Prediction by WGS analysis of resistance against isoniazid, rifampicin, ethambutol, pyrazinamide and streptomycin showed sensitivity values of 84%, 96%, 71%, 75% and 29%, while specificity values were 100%, 94%, 90%, 90% and 98%, respectively. Prediction of multidrug resistance showed a sensitivity of 89% and specificity of 97%. Moreover, WGS analysis revealed polymorphisms related to second-line drug resistance, enabling classification of eight and two clinical isolates as pre- and extreme drug-resistant cases, respectively.

Four lineages were identified in the population (L1, L2, L3 and L4). The most frequent of these was L4, which included 90% (77) of the isolates. Six transmission clusters were identified; the most frequent was TC6, which included 13 isolates with a L4.1.1 and a predominantly multidrug-resistant condition.

Conclusion

The results illustrate the utility of WGS for establishing the potential for prediction of resistance against first and second line drugs in isolates of tuberculosis from the region. They also demonstrate the feasibility of this procedure for use as a tool to support the epidemiological surveillance of drug- and multidrug-resistant tuberculosis.
Biochemical properties and in vitro biological activities of extracts from seven folk medicinal plants growing wild in southern Tunisia
Authors: Tlili Hajer , Hanen Najjaa , Arfa Abdelkerim Ben , Neffati Mohamed , Boubakri Abdelbasset , Buonocore Daniela , Dossena Maurizia , Verri Manuela , Doria Enrico
Published: February 2019

Recently, much attention has been paid to the extracts obtained from plant species in order to analyse their biological activities. Due to the climate diversity in Tunisia, the traditional pharmacopoeia consists of a wide arsenal of medicinal plant species since long used in folk medicine, in foods as spices, and in aromatherapy. Although many of these species are nearly facing extinction, only a small proportion of them have been scientifically studied. Therefore, this study explores the biochemical properties of seven spontaneous plants, which were harvested in the arid Tunisian desert: Marrubium vulgare L., Rhus tripartita (Ucria) D.C., Thymelaea hirsute (L.) Endl., Plantago ovata Forsk., Herniaria fontanesii J. Gay., Ziziphus lotus and Hyoscyamus albus. Extracts from these plants were found to contain different types of secondary metabolites (polyphenols, flavonoids, condensed tannins, crude saponins, carotenoids and alkaloids) that are involved in important biological activities. The biological activity of the extracts obtained from each Tunisian plant was assessed: first of all, leukaemia and colon cancer cell lines (K-562 and CaCo-2 respectively) were treated with different concentrations of extracts, and then the anti-proliferative activity was observed. The results showed, in particular, how the plant extract from Rhus tripartita significantly inhibits cell proliferation, especially on the K-562 tumour cell line. Subsequently, the anti-inflammatory activity was also assessed, and the results showed that Herniaria fontanesii and Marrubium vulgare possess the highest activity in the group of analysed plants. Finally, the greatest acetylcholinesterase inhibitory effect was exhibited by the extract obtained from Rhus tripartita.

In conclusion, all the Tunisian plants we analysed were shown to contain a remarkable amount of different bio-active compounds, thus confirming their involvement in several biological activities. Rhus tripartita and Ziziphus lotus were shown to be particularly effective in anti-proliferative activity, while Herniaria fontanesii were shown to have the best anti-inflammatory activity.
Knowledge about the predictive value of reward conditioned stimuli modulates their interference with cognitive processes
Authors: Leganes-Fonteneau Mateo , Nikolaou Kyriaki , Scott Ryan , Duka Theodora
Published: February 2019

Stimuli conditioned with a substance can generate drug-approach behaviors due to their acquired motivational properties. According to implicit theories of addiction, these stimuli can decrease cognitive control automatically. The present study (n= 49) examined whether reward-associated stimuli can interfere with cognitive processes in the absence of knowledge about stimulus–outcome contingencies. Conditioned stimuli (CS) were paired with high-reward (HR) or low-reward (LR) probabilities of monetary reward using a Pavlovian learning task. Participants were categorized as Aware or Unaware of contingencies using a Bayesian analysis. CS were then used as task-irrelevant distractors in modified flanker andN-back tasks. Results show HR CS can generate increased interference in the flanker task for participants Unaware of contingencies, contributing further evidence for the existence of implicit Pavlovian conditioning. For theN-back task, working memory performance was affected by HR CS, albeit only for Aware participants. These results suggest that CS can interfere implicitly with cognitive processes in a similar way to drug-related stimuli. Such an effect could occur in a stimulus-driven fashion, devoid of top-down goal-directedness. These findings have implications for the conceptualization and study of implicit processes in addiction and highlights the necessity to reconsider the measurement of such phenomena.
Identifying the best practices in green operations strategy of hospitals
Authors: Migdadi Yazan Khalid Abed-Allah , Omari Abeer Ahmad
Published: February 2019

Purpose

The purpose of this paper is to identify the best practices in the green operations strategy of hospitals.

Design/methodology/approach

A total of 25 cases from all over the world were investigated. The source of data was the annual sustainability reports that were retrieved from Global Reporting Initiative (GRI) database. The present research adopted the benchmarking method and the quantitative content analysis of sustainability reports. Then, the indicative models of best practices were developed by using two analysis approaches; within cluster analysis and across clusters analysis.

Findings

This study found four major taxonomies of green operation strategy in hospitals. The significant strategic groups were resources/waste management; electrical power management; non-hazardous waste management; and emissions/resources management. Indicative models for the relationship between actions and key green performance indicators were developed in the two stages of the analysis.

Originality/value

The best practices of green operations strategies in hospitals have not so far been investigated. Countries around the world should obey the new regulations for their environmental footprint; if they do, it will exert pressure on all sectors and organizations at all levels to take immediate steps to measure and improve their environmental performance.
Workplace sexual harassment, workplace deviance, and family undermining
Authors: Zhu Hong , Lyu Yijing , Ye Yijiao
Published: February 2019

Purpose

This study aims to examine the effect of workplace sexual harassment (WSH) on hospitality employees’ workplace deviance and family undermining behaviors by focusing on the mediating effect of depression.

Design/methodology/approach

This research uses a three-phase field survey to collect data from hotels in China with a final sample of 266 hospitality employees. Data analysis techniques include descriptive statistics, confirmative factor analysis and hierarchical multiple regression.

Findings

This research finds that WSH is positively related to workplace deviance; WSH positively affects family undermining; depression is a mediator in the relationship between WSH and workplace deviance; and depression mediates the relationship between WSH and family undermining.

Originality/value

First, this research goes beyond the existing WSH literature by extending outcome variables to workplace deviance. Second, it is among the first to investigate the relationship between WSH and hospitality employees’ family life. Third, the examination of depression as a mediator advances the literature by unraveling the mediating mechanism underlying the effects of WSH on hospitality employees.
China goes global: provenance, projection, performance and policy
Authors: Buckley Peter
Published: February 2019

Purpose

The purpose of this paper is to examine the provenance, projection, performance and policy concerning Chinese outward foreign direct investment (COFDI) and speculate on the existence of “China’s international strategy”.

Design/methodology/approach

This study includes a comprehensive review of COFDI.

Findings

There is evidence of not only the successful coordination of COFDI, but also context, conflict and independent decision making (in Chinese firms) playing an essential role in the determination of the direction, control and outcomes of the outward FDI, respectively.

Research limitations/implications

There is a great scope for further research on COFDI, as the lack of data prevents definitive conclusions, particularly on the outcomes and performance of the investments.

Originality/value

The paper presents an original synoptic view of key elements in the globalisation of the world economy and in the projection of Chinese economic power.
Financial sustainability of statewaqfinstitutions (SWIs) in Malaysia
Authors: Sulaiman Maliah , Alhaji Zakari Muntaka
Published: February 2019

Purpose

This paper aims to measure the financial sustainability and vulnerability of state-managedwaqfinstitutions in Malaysia.

Design/methodology/approach

The study mainly applied the commonly used Tuckman and Chang’s (1991) model to measure the financial health of non-profits. Content and ratio analysis of the 2014 audited reports of seven institutions were used to determine their equity balance, revenue concentration, administrative costs and operating margin ratios.

Findings

The results indicate that only onewaqfinstitution was financially sustainable in all the four components.

Research limitations/implications

Because the data used are not the latest and focussed only on a single year, the findings may not be necessarily true, currently. Second, the study focussed only on Malaysia. Thus, the results may not be generalisable to otherwaqfsin other countries or to privately managedwaqfinstitutions. Accordingly, future research should address these limitations.

Practical implications

The findings provide useful insights into the financial sustainability ofwaqfinstitutions and highlight the need for policymakers in Malaysia and other Muslim countries to give due attention to the holistic accountability ofwaqfinstitutions to ensurewaqf’ssystematic revival.

Originality/value

The paper, being the first to investigate the financial sustainability and vulnerability of statewaqfinstitutions in Malaysia, serves as a reference for future researchers.
Building committedWaqif: the role of information disclosure
Authors: Abd Jalil Mohamad Isa , Yahya Sofri , Allah Pitchay Anwar
Published: February 2019

Purpose

The purpose of this study is to conceptualise the relationship between information disclosure andWaqifcommitment, taking into consideration the role of level of trust (mediator variable) and communication and type of payment (moderator variables).

Design/methodology/approach

The conceptual framework is developed from the theory of social exchange (mediated philanthropy model) and selected previous literature concerning commitment.

Findings

According to previous empirical research, a conceptual framework was developed to facilitate further analysis in the study. Nine propositions were raised in this paper where the factor of communication and payment method is proposed to no longer the factor that determined commitment but as moderator. There is five antecedent of information disclosure proposed, which is basic information, financial information, non-financial information, future information and governance information. Also, trust is offered to be the mediator variable between information disclosure andWaqfcommitment.

Research limitations/implications

By realising many factors that may influence the commitment ofwaqfsuch as demonstrable utility, emotional utility and familial utility, this study only focusses on the effect of information disclosure.

Practical implications

This paper provides an opportunity for further empirical studies to prove the relationship between information disclosure andWaqfcommitment. This paper also brought opportunities to investigate both conceptually and empirically, other factors that could affectWaqfcommitment.

Originality/value

To the best of the author’s knowledge, few studies have been done concerning donors commitment. While there are none yet, the research examinedWaqfcommitment. The originality value of this study is that there is a gap in knowledge regarding the analysis ofWaqfcommitment, the level of trust amongwaqifis the information thatWaqfexpected, the preferred communication between Mutawalli andWaqfand type of payment thatWaqffavoured. This study is believed to be a novel based on the framework developed.
Revival of favus in Japan caused by Trichophyton schoenleinii
Authors: Iwasa Kentaro , Ogawa Kohei , Azukizawa Hiroaki , Tanabe Hiroshi , Iwanaga Tomoyuki , Anzawa Kazushi , Mochizuki Takashi , Asada Hideo
Published: February 2019

Favus is a type of dermatophytosis known to produce yellow scutula around hair follicles. Most cases of this disease worldwide are infections of Trichophyton schoenleinii. Favus has rarely been reported in Japan throughout the last four decades, and T. schoenleinii has not been clinically isolated in any case during the period. Here, we report a case of favus of vellus hair observed in a 63‐year‐old Japanese woman. Fungal culture showed negative; however, we detected fungal elements in the crust and hair bulbs by Grocott staining. Pathogenic fungi were identified as T. schoenleinii by polymerase chain reaction‐based DNA sequencing, targeting the internal transcribed spacer regions of the rRNA gene using the formalin‐fixed, paraffin‐embedded tissue sample. She was successfully treated with p.o. administration of terbinafine and topical application of luliconazole cream.
The impact of uncertainty on cooperation intent in a conservation conflict
Authors: Pollard Chris R. J. , Redpath Steve , Bussière Luc F. , Keane Aidan , Thompson Des B. A. , Young Juliette C. , Bunnefeld Nils
Published: February 2019

Stakeholder cooperation can be vital in managing conservation conflicts. Laboratory experiments show cooperation is less likely in the presence of uncertainty. Much less is known about how stakeholders in real‐life conservation conflicts respond to different types of uncertainty.

We tested the effects of different sources of uncertainty on cooperative behaviour using a framed field experiment and interviews. The experiment compared a baseline scenario of perfect certainty with scenarios including either: (a) scientific uncertainty about the effectiveness of a conflict‐reduction intervention; (b) administrative uncertainty about intervention funding; or (c) political uncertainty about the extent of community support. We applied these scenarios to a conservation conflict in the Outer Hebrides, Scotland, involving the management of geese to simultaneously meet both conservation and farming objectives. We asked 149 crofters (small‐scale farmers) if they would commit to cooperate with others by helping fund a goose management plan given the three sources of uncertainty.

On average, intention to cooperate was highest (99%) in scenarios without uncertainty, and lowest under administrative uncertainty (77%). Scientific uncertainty and political uncertainty both had less of an effect, with over 95% of crofters predicted to be willing to cooperate in these scenarios. Crofters who indicated concern for other crofters suffering the impact of geese were more likely to cooperate. The longer an individual had been a crofter, the less likely they were to cooperate.

Synthesis and applications. Crofters’ intention to cooperate is high but lessened by uncertainty, especially over the commitment from other stakeholders such as government, to cooperate on goose management. Existing cooperation on goose management may be at risk if uncertainty is not reduced outright or commitments between parties are not strengthened. This has wide applicability, supporting the need for researchers and government advisers to: (a) determine how uncertainty will impact intention of stakeholders to cooperate; and (b) take steps (such as uncertainty reduction, communication or acceptance) to reduce the negative impact of uncertainty on cooperation.
The significance of retention trees for survival of ectomycorrhizal fungi in clear‐cut Scots pine forests
Authors: Sterkenburg Erica , Clemmensen Karina E. , Lindahl Björn D. , Dahlberg Anders
Published: February 2019

Forestry with short stand generations and simplified forest structures has markedly affected forest biodiversity. One group of organisms adversely affected by clear‐cutting is ectomycorrhizal (ECM) fungi, as they are associated with the roots of living trees. Retention forestry is a way of reducing logging impacts and enhancing biodiversity conservation. Increasing the proportion of trees retained at harvest may improve ECM fungal diversity.

We investigated the potential for lifeboating of ECM fungi through the harvesting phase in an experimental field study in a 190‐year‐old Scots pine forest in northern Sweden. The experiment comprised four levels of tree retention—unlogged forest, plots with 60% or 30% of evenly distributed trees retained and clear‐cuts without retained trees. We sampled soils and determined identities, frequencies and relative abundances of ECM fungal species during 3 years following logging through the use of high‐throughput sequencing of amplified ITS2 markers.

We identified 149 ECM fungal species, with the five most abundant species accounting for 50% of the total ECM fungal amplicons. Three years after harvesting, the proportion of ECM sequences in the total amplicon pool had decreased proportionally to the extent of tree removal. In clear‐cuts, ECM fungal relative abundance had decreased by 95%, while ECM fungal species richness had declined by 75%, compared to unlogged plots.

Tree retention enabled the maintenance of the most frequent ECM species, while more lowly abundant species were progressively lost at random with increasing level of tree removal. Five of the most frequent ECM fungal species remained present after clear‐cutting, probably associated with pine seedlings.

Synthesis and applications. Tree retention can moderate short‐term and potentially also long‐term logging impacts on ECM fungi. Local ECM fungal diversity is preserved in proportion to the amount of retained trees. Abundant species may be largely maintained, even by low levels of tree retention and on naturally established seedlings. However, conservation of more infrequent species requires higher levels of tree retention, and our results suggest that around 75% of the ECM species are lost with the forest certification standard of 5% retention trees left at logging.