bluuebunny/crossref_metadata_2025 huggingface dataset:
Rhizosphere metagenomics of mine tailings colonizing plants: assembling and selecting synthetic bacterial communities to enhance in situ bioremediation
Authors: Romero Miguel , Gallego Diana , Blaz Jazmin , Lechuga Arely , Martínez José F. , Barajas Hugo R. , Hayano-Kanashiro Corina , Peimbert Mariana , Cruz-Ortega Rocío , Molina-Freaner Francisco E. , Alcaraz Luis D.
Published: June 2019

Mine tailings phytostabilization has been proposed as a bioremediation strategy to constrain the contaminants dispersion using plants to limit the effects of erosion. Rhizospheric bacteria impact plant health and facilitate plant establishment through their metabolic functions, which could be relevant in bioremediation strategies. We studied both culturable and metagenomic diversity or rhizospheric bacteria of mine tailings colonizing plants of an abandoned mine operation in Nacozari de García, Sonora, Mexico. Diversity was described through amplification of the 16S rRNA gene and whole metagenome shotgun sequencing of both environmental and cultured rhizosphere associated microbes. The culturable bacteria were assembled in a synthetic community (SC; 235 bacteria genera). Subsequently, we performed an experimental evolution setup with the SC, selecting for heavy metal resistance, microbial competition, and the ability for growing in plant-derived nutrient sources. The selection experiment show that bacteria diversity decreases from the environmental culture-free microbiomes to the mine tailings rhizospheres and the experimental evolution outcome: the synthetic community (FSC; 43 bacteria genera). The rhizosphere communities shifted from the dominance of Actinobacteria in their environment to Proteobacteria in the cultivated consortia and the synthetic communities. Both environmental and cultured metagenomes contained plant-growth promotion, heavy-metal homeostasis, and antibiotic resistance predicted genes. The FSC included predicted proteins related to plant-growth promotion such as siderophore production and plant hormone regulation proteins. We reconstructed a metagenome assembled genomic sequence named Enterobacter sp., Nacozari. The recovered Enterobacter sp. Nacozari, have predicted coding genes for direct and indirect plant growth promotion along with adhesion and oxidative stress-related proteins. The metabolic potential of the FSC presents promising features that might make it useful for plant-growth promotion in tailored phytostabilization strategies for the abandoned mine-tailings of Nacozari.
A high-content in vivo screen to identify microRNA epistasis in the repopulating mouse liver
Authors: Zahm Adam M. , Wang Amber W. , Wang Yue J. , Schug Jonathan , Wangensteen Kirk J. , Kaestner Klaus H.
Published: June 2019

Liver regeneration is impaired in mice with hepatocyte-specific deficiencies in microRNA (miRNA) processing; yet the roles of individual miRNAs or their combinatorial effects in this process are largely unknown. In this study, we sought to identify miRNAs that regulate hepatocyte repopulation following toxic liver injury in a high-throughput manner using the Fah−/− mouse. We constructed plasmid pools encoding over 30,000 tough decoy (TuD) miRNA inhibitors designed to target hepatocyte miRNAs in a pairwise manner. Plasmid libraries were delivered to hepatocytes of Fah−/− mice at the time of liver injury via hydrodynamic tail vein injection and integrated transgene-containing transposons were quantified following repopulation via high-throughput sequencing. Changes in polysome-bound transcripts following miRNA inhibition were determined using translating ribosome affinity purification followed by high-throughput sequencing. Analysis of TuD abundance in hepatocyte genomic DNA and input plasmid pools identified several thousand miRNA inhibitors that were significantly altered following repopulation. We classified a subset of miRNA-binding sites (MBSs) as having strong effect on liver repopulation, thus implicating the targeted hepatocyte miRNAs as regulators of this process. Furthermore, we generated a high-content map of pairwise interactions between 171 MBSs and identified both synergistic and redundant effects. Our study highlights the power of higher-order screens to uncover miRNA functions that would go undetected by individual miRNA perturbations, and provides a new paradigm for the study of epistasis of miRNA activities.
Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays
Authors: Ramirez-San Juan Guillermina R. , Mathijssen Arnold J. T. M. , He Mu , Jan Lily , Marshall Wallace , Prakash Manu
Published: June 2019

Mucus clearance constitutes the primary defence of the respiratory system against viruses, bacteria and environmental insults [1]. This transport across the entire airway emerges from the integrated activity of thousands of multiciliated cells, each containing hundreds of cilia, which together must coordinate their spatial arrangement, alignment and motility [2, 3]. The mechanisms of fluid transport have been studied extensively at the level of an individual cilium [4, 5], collectively moving metachronal waves [6–10], and more generally the hydrodynamics of active matter [11, 12]. However, the connection between local cilia architecture and the topology of the flows they generate remains largely unexplored. Here, we image the mouse airway from the sub-cellular (nm) to the organ scales (mm), characterising quantitatively its ciliary arrangement and the generated flows. Locally we measure heterogeneity in both cilia organisation and flow structure, but across the trachea fluid transport is coherent. To examine this result, a hydrodynamic model was developed for a systematic exploration of different tissue architectures. Surprisingly, we find that disorder enhances particle clearance, whether it originates from fluctuations, heterogeneity in multiciliated cell arrangement or ciliary misalignment. This resembles elements of ‘stochastic resonance’ [13–15] in a self-assembled biological system. Taken together, our results shed light on how the microstructure of an active carpet [16, 17] determines its emergent dynamics. Furthermore, this work is also directly applicable to human airway pathologies [1], which are the third leading cause of deaths worldwide [18].
NeuronUnit: A package for data-driven validation of neuron models using SciUnit
Authors: Gerkin Richard C. , Birgiolas Justas , Jarvis Russell J. , Omar Cyrus , Crook Sharon M.
Published: June 2019

Validating a quantitative scientific model requires comparing its predictions against many experimental observations, ideally from many labs, using transparent, robust, statistical comparisons. Unfortunately, in rapidly-growing fields like neuroscience, this is becoming increasingly untenable, even for the most conscientious scientists. Thus the merits and limitations of existing models, or whether a new model is an improvement on the state-of-the-art, is often unclear.

Software engineers seeking to verify, validate and contribute to a complex software project rely on suites of simple executable tests, called “unit tests”. Drawing inspiration from this practice, we previously developed SciUnit, an easy-to-use framework for developing data-driven “model validation tests” – executable functions, here written in Python. Each such test generates and statistically validates predictions from a model against one relevant feature of empirical data to produce a score indicating agreement between the model and the data. Suites of such validation tests can be used to clearly identify the merits and limitations of existing models and developmental progress on new models.

Here we describe NeuronUnit, a library that builds upon SciUnit and integrates with several existing neuroinformatics resources to support the validation of single-neuron models using data gathered by neurophysiologists and neuroanatomists. NeuronUnit integrates with existing technologies like Jupyter, Pandas, NeuroML and resources such as NeuroElectro, The Allen Institute, and The Human Brain Project in order to make neuron model validation as easy as possible for computational neuroscientists.
Zebrafish mbnl mutants model physical and molecular phenotypes of myotonic dystrophy
Authors: Hinman Melissa N. , Richardson Jared I. , Sockol Rose A. , Aronson Eliza D , Stednitz Sarah J. , Murray Katrina N. , Berglund J. Andrew , Guillemin Karen
Published: June 2019

The muscleblind RNA binding proteins (MBNL1, MBNL2, and MBNL3) are highly conserved across vertebrates and are important regulators of RNA alternative splicing. Loss of MBNL protein function through sequestration by CUG or CCUG RNA repeats is largely responsible for the phenotypes of the human genetic disorder myotonic dystrophy (DM). We generated the first stable zebrafish (Danio rerio) models of DM-associated MBNL loss of function through mutation of the three zebrafish mbnl genes. In contrast to mouse models, zebrafish double and triple homozygous mbnl mutants were viable to adulthood. Zebrafish mbnl mutants displayed disease-relevant physical phenotypes including decreased body size and impaired movement. They also exhibited widespread alternative splicing changes, including the misregulation of many DM-relevant exons. Physical and molecular phenotypes were more severe in compound mbnl mutants than in single mbnl mutants, suggesting partially redundant functions of Mbnl proteins. The high fecundity and larval optical transparency of this complete series of zebrafish mbnl mutants will make them useful for studying DM-related phenotypes and how individual Mbnl proteins contribute to them, and for testing potential therapeutics.
Multimodal memory components and their long-term dynamics identified in cortical layers II/III but not layer Vb
Authors: Li Dong , Wang Guangyu , Xie Hong , Hu Yi , Guan Ji-Song , Hilgetag Claus C.
Published: June 2019

Activity patterns of cerebral cortical regions represent the present environment in which animals receive multi-modal inputs. They are also shaped by the history of previous activity that reflects learned information on past multimodal exposures. We studied the long-term dynamics of cortical activity patterns during the formation of multimodal memories by analysing in vivo high-resolution 2-photon mouse brain imaging of Immediate Early Gene expression, resolved by cortical layers. Strikingly, in layers II/III, the patterns showed similar dynamics across functional distinct cortical areas and the consistency of dynamic patterns lasts for one to several days. In contrast, in layer Vb, the activity dynamics varied across functional distinct areas, and the present activities are sensitive to the previous activities at different time depending on the cortical locations, indicating that the information stored in the cortex at different time points is distributed across different cortical areas. These results suggest different roles of layer II/III and layer Vb neurons in the long-term multimodal perception of the environment.
Discovering novel long non-coding RNA predictors of anticancer drug sensitivity beyond protein-coding genes
Authors: Nath Aritro , Lau Eunice Y.T. , Lee Adam M. , Geeleher Paul , Cho William C.S. , Huang R. Stephanie
Published: June 2019

Large-scale cancer cell line screens have identified thousands of protein-coding genes (PCGs) as biomarkers of anticancer drug response. However, systematic evaluation of long non-coding RNAs (lncRNAs) as pharmacogenomic biomarkers has so far proven challenging. Here, we study the contribution of lncRNAs as drug response predictors beyond spurious associations driven by correlations with proximal PCGs, tissue-lineage or established biomarkers. We show that, as a whole, the lncRNA transcriptome is equally potent as the PCG transcriptome at predicting response to hundreds of anticancer drugs. Analysis of individual lncRNAs transcripts associated with drug response reveals nearly half of the significant associations are in fact attributable to proximal cis-PCGs. However, adjusting for effects of cis-PCGs revealed significant lncRNAs that augment drug response predictions for most drugs, including those with well-established clinical biomarkers. In addition, we identify lncRNA-specific somatic alterations associated with drug response by adopting a statistical approach to determine lncRNAs carrying somatic mutations that undergo positive selection in cancer cells. Lastly, we experimentally demonstrate that two novel lncRNA, EGFR-AS1 and MIR205HG, are functionally relevant predictors of anti-EGFR drug response.
Nuclear genetic regulation of human mitochondrial RNA modification
Authors: Ali Aminah T. , Idaghdour Youssef , Hodgkinson Alan
Published: June 2019

RNA modifications affect the stability and function of RNA species, regulating important downstream processes. Modification levels are often dynamic, varying between tissues and individuals, although it is not always clear what modulates this variation or what impact it has on biological systems. Here, we quantify variation in RNA modification levels at functionally important positions in the mitochondrial genome across 11,552 samples from 39 tissue/cell types and find evidence that modification levels impact mitochondrial transcript processing. We identify novel links between mitochondrial RNA modification levels in whole blood and genetic variants in the nuclear genome, including missense mutations inLONP1andPNPT1, as well as missense mutations inMRPP3,SLC25A26andMTPAPthat associate with RNA modification levels across multiple tissue types. Genetic variants linked to modification levels are associated with multiple disease phenotypes, including blood pressure, breast cancer and Moyamoya disease, suggesting a role for these processes in complex disease.
Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework
Authors: Martin Patrick C.N. , Zabet Nicolae Radu
Published: June 2019

Transcription Factors (TFs) bind to DNA and control activity of target genes. Here, we present ChIPanalyser, a user-friendly, versatile and powerful R/Bioconductor package predicting and modelling the binding of TFs to DNA. ChIPanalyser performs similarly to state-of-the-art tools, but is an explainable model and provides biological insights into binding mechanisms of TFs. We focused on investigating the binding mechanisms of three TFs that are known architectural proteins CTCF, BEAF-32 and su(Hw) in three Drosophila cell lines (BG3, Kc167 and S2). While CTCF preferentially binds only to a subset of high affinity sites located mainly in open chromatin, BEAF-32 binds to most of its high affinity binding sites available in open chromatin. In contrast, su(Hw) binds to both open chromatin and also partially closed chromatin. Most importantly, differences in TF binding profiles between cell lines for these TFs are mainly driven by differences in DNA accessibility and not by differences in TF concentrations between cell lines. Finally, we investigated binding of Hox TFs in Drosophila and found that Ubx binds only in open chromatin, while Abd-B and Dfd are capable to bind in both open and partially closed chromatin. Overall, our results show that TFs display different binding mechanisms and that our model is able to recapitulate this diverse repertoire of mechanisms.
Control iPSC lines with clinically annotated genetic variants for versatile multi-lineage differentiation
Authors: Hildebrandt Matthew R , Reuter Miriam S , Wei Wei , Tayebi Naeimeh , Liu Jiajie , Sharmin Sazia , Mulder Jaap , Lesperance L Stephen , Brauer Patrick M , Kinnear Caroline , Piekna Alina , Romm Asli , Howe Jennifer , Pasceri Peter , Mok Rebecca S , Meng Guoliang , Rozycki Matthew , de Carvalho Rodrigues Deivid , Martinez Elisa C , Szego Michael J , Zúñiga-Pflücker Juan Carlos , Anderson Michele K , Prescott Steven A , Rosenblum Norman D , Kamath Binita M , Mital Seema , Scherer Stephen W , Ellis James
Published: June 2019

Induced Pluripotent Stem Cells (iPSC) derived from healthy individuals are important controls for disease modeling studies. To create a resource of genetically annotated iPSCs, we reprogrammed footprint-free lines from four volunteers in the Personal Genome Project Canada (PGPC). Multilineage directed differentiation efficiently produced functional cortical neurons, cardiomyocytes and hepatocytes. Pilot users further demonstrated line versatility by generating kidney organoids, T-lymphocytes and sensory neurons. A frameshift knockout was introduced into MYBPC3 and these cardiomyocytes exhibited the expected hypertrophic phenotype. Whole genome sequencing (WGS) based annotation of PGPC lines revealed on average 20 coding variants. Importantly, nearly all annotated PGPC and HipSci lines harboured at least one pre-existing or acquired variant with cardiac, neurological or other disease associations. Overall, PGPC lines were efficiently differentiated by multiple users into cell types found in six tissues for disease modeling, and clinical annotation highlighted variant-preferred lines for use as unaffected controls in specific disease settings.
Inferring disease-associated microRNAs using semi-supervised multi-label graph convolutional networks
Authors: Pan Xiaoyong , Shen Hong-Bin
Published: June 2019

MicroRNAs (miRNAs) play crucial roles in many biological processes involved in diseases. The associations between diseases and protein coding genes (PCGs) have been well investigated, and further the miRNAs interact with PCGs to trigger them to be functional. Thus, it is imperative to computationally infer disease-miRNA associations under the context of interaction networks.

In this study, we present a computational method, DimiG, to infer miRNA-associated diseases using semi-supervised Graph Convolutional Network model (GCN). DimiG is a multi-label framework to integrate PCG-PCG interactions, PCG-miRNA interactions, PCG-disease associations and tissue expression profiles. DimiG is trained on disease-PCG associations and a graph constructed from interaction networks of PCG-PCG and miRNA-PCG using semi-supervised GCN, which is further used to score associations between diseases and miRNAs. We evaluate DimiG on a benchmark set collected from verified disease-miRNA associations. Our results demonstrate that the new DimiG yields promising performance and outperforms the best published baseline method not trained on disease-miRNA associations by 11% and is also superior to two state-of-the-art supervised methods trained on disease-miRNA associations. Three case studies of prostate cancer, lung cancer and Inflammatory bowel disease further demonstrate the efficacy of DimiG, where the top miRNAs predicted by DimiG for them are supported by literature or databases.
Cas3 Mediated Target DNA Recognition and Cleavage is Independent of the Composition and Architecture of Cascade Surveillance Complex
Authors: Nimkar Siddharth , Anand B.
Published: June 2019

In type I CRISPR-Cas system, Cas3 –a nuclease cum helicase– in cooperation with Cascade surveillance complex cleaves the target DNA. Unlike the Cascade/I-E, which is composed of five subunits, the Cascade/I-C is made of only three subunits lacking the CRISPR RNA processing enzyme Cas6, whose role is assumed by Cas5. How these differences in the composition and organisation of Cascade subunits in type I-C influences the Cas3/I-C binding and its target cleavage mechanism is poorly understood. Here, we show that Cas3/I-C is intrinsically a single-strand specific promiscuous nuclease. Apart from the helicase domain, a constellation of highly conserved residues –that are unique to type I-C– located in the uncharacterised C-terminal domain appears to influence the nuclease activity. Recruited by Cascade/I-C, the HD nuclease of Cas3/I-C nicks the single-stranded region of the nontarget strand and positions the helicase motor. Powered by ATP, the helicase motor reels in the target DNA, until it encounters the roadblock en route, which stimulates the HD nuclease. Remarkably, we show that Cas3/I-C supplants Cas3/I-E for CRISPR interference in type I-E in vivo, suggesting that the target cleavage mechanism is evolutionarily conserved between type I-C and type I-E despite the architectural difference exhibited by Cascade/I-C and Cascade/I-E.
Hyperacetylated Chromatin Domains Mark Cell Type-Specific Genes and Suggest Distinct Modes of Enhancer Function
Authors: Fox Sierra , Myers Jacquelyn A. , Davidson Christina , Getman Michael , Kingsley Paul D. , Frankiewicz Nicholas , Bulger Michael
Published: June 2019

Stratification of enhancers by relative signal strength in ChIP-seq assays has resulted in the establishment of super-enhancers as a widespread and useful tool for identifying cell type-specific, highly expressed genes and associated pathways. We have examined a distinct method of stratification that focuses on peak breadth, termed “hyperacetylated chromatin domains” (HCDs), which classifies broad regions exhibiting histone modifications associated with gene activation. We find that this analysis serves to identify genes that are both more highly expressed and more closely aligned to cell identity than super-enhancer analysis does when applied to multiple datasets. Moreover, genetic manipulations of selected gene loci suggest that at least some enhancers located within HCDs work at least in part via a distinct mechanism involving the modulation of covalent histone modifications across domains, and that this activity can be imported into a heterologous gene locus. In addition, such genetic dissection reveals that the super-enhancer concept can obscure important functions of constituent elements.
Antibiotic uptake across gram-negative outer membranes: better predictions towards better antibiotics
Authors: Ferreira Ricardo J. , Kasson Peter M.
Published: June 2019

Crossing the gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer-membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay. Parallel molecular dynamics simulations are used to successfully and quantitatively predict experimental permeabilities. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer-membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer-membrane permeability.
Prenatal Diagnosis of Fetuses with Increased Nuchal Translucency by Genome Sequencing Analysis
Authors: Choy Kwong Wai , Wang Huilin , Shi Mengmeng , Chen Jingsi , Yang Zhenjun , Zhang Rui , Yan Huanchen , Wang Yanfang , Chen Shaoyun , Chau Matthew Hoi Kin , Cao Ye , Chan Olivia YM , Kwok Yvonne K , Zhu Yuanfang , Chen Min , Leung Tak Yeung , Dong Zirui
Published: June 2019

Background

Increased Nuchal Translucency (NT) is an important biomarker associated with increased risk of fetal structural anomalies. It is known to be contributed by a wide range of genetic etiologies from single nucleotide variants to those affecting millions of base-pairs. Currently, prenatal diagnosis is routinely performed by karyotyping and chromosomal microarray analysis (CMA), however, both of them have limited resolution. The diversity of the genetic etiologies warrants an integrated assay such as genome sequencing (GS) for comprehensive detection of genomic variants. Herein, we aim to evaluate the feasibility of applying GS in prenatal diagnosis for the fetuses with increased NT.

Methods

We retrospectively applied GS (>30-fold) for fetuses with increased NT (≥3.5-mm), who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy-number variants and structural rearrangements was performed simultaneously and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available.

Results

Overall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a 2-fold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion which disrupted an OMIM autosomal dominant disease-causing gene at the inserted site.

Conclusions

Our study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turn-around-time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT.
Constant Infusion Radiotracer Administration for High Temporal Resolution Positron Emission Tomography (PET) of the Human Brain: Application to [18F]-Fluorodexoyglucose PET (FDG-PET)
Authors: Jamadar Sharna D , Ward Phillip GD , Carey Alexandra , McIntyre Richard , Parkes Linden , Sasan Disha , Fallon John , Li Shenpeng , Chen Zhaolin , Egan Gary F
Published: June 2019

Functional Positron Emission Tomography (fPET) provides a method to track molecular dynamics in the human brain. With a radioactively labelled glucose-analogue, [18F]-flurodeoxyglucose (FDG-fPET), it is now possible to index the dynamics of glucose metabolism with temporal resolutions approaching those of functional magnetic resonance imaging (fMRI). This direct measure of glucose uptake has enormous potential for understanding normal and abnormal brain function, and probing the effects of metabolic and neurodegenerative diseases. Further, new advances in hybrid MR-PET hardware makes it possible to capture fluctuations in glucose and blood oxygenation simultaneously using fMRI and FDG-fPET.

The temporal resolution and signal-to-noise of the FDG-fPET images is critically dependent upon the administration of the radioactive tracer. In this work we present two alternative continuous infusion protocols and compare them to a traditional bolus approach. We detail a method for acquiring blood samples, time-locking PET, MRI and experimental stimulus, and administrating the non-traditional tracer delivery. By applying a visual stimulus, we demonstrate cortical maps of the glucose-response to external stimuli on an individual level with a temporal resolution of 16-seconds.

Radiotracer infusion protocols for positron emission tomography (PET) provide improved temporal resolution over bolus administration. Here, we describe radiotracer administration for two protocols, constant infusion and bolus plus infusion protocol. We compare this to the standard bolus administration protocol. Using [18-F] fluorodeoxyglucose PET (FDG-PET) as an example, we show that temporal resolutions of approximately 16sec are achievable using these protocols.
Assessment of two immunoassays for detection of IgM antibodies to scrub typhus using a serum panel
Authors: Elangovan Divyaa , Perumalla Susmitha , Rose Winsley , Verghese Valsan Philip , Gowri M.S. , Jude Prakash John Antony
Published: June 2019

Introduction

Scrub typhus is a vector borne zoonotic disease caused byOrientia tsutsugamushi, endemic to tsutsugamushi triangle. As the characteristic eschar is not always present, laboratory testing especially serological assay are the main stay of diagnosis.

Materials and methods

A total of 346 well-characterized sera from normals and patients with scrub typhus, malaria, dengue, enteric fever and gram negative septicaemia were tested for IgM antibodies by ST IgM ELISA and ST Ig M ICT

Results

The sensitivity and specificity of Scrub typhus IgM ICT and ELISA were 98.7, 96.3 and 97.4, 99.3 respectively. The IgM ICT and ELISA had a excellent concordance (99%) and a very high negative predictive value.

Conclusion

The findings from this study suggest that IgM ICT and IgM ELISA can be used interchangeably for serodiagnosis of scrub typhus in resource poor settings.
Status of aquatic and riparian biodiversity in artificial lake ecosystems with and without management for recreational fisheries: implications for conservation
Authors: Nikolaus Robert , Schafft Malwina , Maday Andreas , Klefoth Thomas , Wolter Christian , Arlinghaus Robert
Published: June 2019

Humanity is facing a biodiversity crisis, with freshwater-associated biodiversity in a particularly dire state. Novel ecosystems created through human use of mineral resources, such as gravel pit lakes, can provide substitute habitats for conservation of freshwater and riparian biodiversity. However, many of these artificial ecosystems may exhibit high recreational use intensity, which may limit their biodiversity potential.

The species richness of several taxa (plants, amphibians, dragonflies, damselflies, waterfowl, songbirds) was assessed and a range of taxonomic biodiversity metrics were compared between gravel pit lakes managed for recreational fisheries (N = 16) and unmanaged reference lakes (N = 10), while controlling for non-fishing related environmental variation.

The average species richness of all examined taxa was similar among both lake types and no substantial differences in species composition were revealed when examining the pooled species inventory. Similarly, there were no differences among lake types in the presence of rare species and in the Simpson diversity index across all the taxa that were assessed.

Variation in species richness among lakes was correlated with woody habitat, lake morphology (surface area and steepness) and land use, but not correlated with the presence of recreational fisheries. Thus, non-fishing related environmental variables had stronger effects on local species presence than recreational-fisheries management or the presence of recreational anglers.

Collectively, no evidence was found that anglers and recreational-fisheries management constrain the development of aquatic and riparian biodiversity in gravel pit lakes in the study region. Conservation of species diversity at gravel pit lakes could benefit from an increasing reliance on habitat enhancement activities.
Wild pollinator activities negatively related to honey bee colony densities in urban context
Authors: Ropars Lise , Dajoz Isabelle , Fontaine Colin , Muratet Audrey , Geslin Benoît
Published: June 2019

As pollinator decline is increasingly reported in natural and agricultural environments, cities are perceived as shelters for pollinators because of low pesticide exposure and high floral diversity throughout the year. This has led to the development of environmental policies supporting pollinators in urban areas. However, policies are often restricted to the promotion of honey bee colony installations, which resulted in a strong increase in apiary numbers in cities. Recently, competition for floral resources between wild pollinators and honey bees has been highlighted in semi-natural contexts, but whether urban beekeeping could impact wild pollinators remains unknown. Here, we show that in the city of Paris (France), wild pollinator visitation rates is negatively correlated to honey bee colony densities present in the surrounding (500m – slope = −0.614; p = 0.001 – and 1000m – slope = −0.489; p = 0.005). More particularly, large solitary bees and beetles were significantly affected at 500m (respectively slope = −0.425, p = 0.007 and slope = - 0.671, p = 0.002) and bumblebees were significantly affected at 1000m (slope = - 0.451, p = 0.012). Further, lower interaction evenness in plant-pollinator networks was observed with honey bee colony densities within 1000 meter buffers (slope = −0.487, p = 0.008). Finally, honey bees tended to focus their foraging activity on managed rather than spontaneous plant species (student t-test, p = 0.001) whereas wild pollinators equally visited managed and spontaneous species. We advocate responsible practices mitigating the introduction of high density of hives in urban environments. Future studies are needed to deepen our knowledge about the potential negative interactions between wild and domesticated pollinators.
Rational Decision On the Use of Antibiotics During the Dry Period in Dairy Cows
Authors: Lopes Luis O. , Lima Anna M. C.
Published: June 2019

The aim of this study was to evaluate the use of antibiotics in cows during the dry period. The survey was performed on 148 teats during the dry period, with sample collection in the period D-70 (70 days before delivery) and D14 (14 days after delivery). The milk samples were collected for the Strip Cup Test (SCT), California Mastitis Test (CMT), Microbiological Culture, Somatic Cell Count (SCC), Somatic Cell Score (SCS) and Hyperkeratosis (HK). The groups in which there were no microorganisms grow were divided into two groups, in the first group only the internal sealant in the teat was used (Group 1) and there was another group with the intramammary antibiotic use associated with the internal sealant (Group 2). Teats which were considered positive, with microbiological growth, were treated with the intramammary antibiotic associated with the internal sealant (Group 3). In the comparison of the results of the CMT test between D-70 and D14, a statistical difference was observed in Groups 2 and 3. Group 3, which comprises the positive teats in D-70 presented a reduction of 83.87% and 32.26% in the CMT test between D-70 and D14. Regarding HK, group 1 and 2 had a statistical difference in relation to group 3 in D-70 and D14. As for the numbers of bacteria isolated in D-70 and D14, there was no difference comparing Group 1 and Group 2, unlike Group 3, which had a difference. Group 1 and Group 2 were all negative teats in D-70, showing that the intramammary antibiotic did not influence the outcome of D14. In group 3 there was a reduction of isolates from 62 to 15 in D14. The most prevalent microorganism was Streptococcus agalactiae with 43.37% of the total isolates, followed by Staphylococcus aureus (16.87%) and Corynebacterium spp. (13.25%) and Coagulase negative Staphylococcus (SCN) (10.84%). The selective treatment of teats in dry dairy cows has advantages over Blanket Dry Cow Therapy by reducing the indiscriminate use of antibiotics, avoiding bacterial resistance, ensuring better milk quality and greater food safety. Antibiotics should only be used for teats with subclinical mastitis, with the microbiological culture at the end of lactation performed by fourth individual mammary.
Synthesis, characterization, and crystal structure of aquabis(4,4′-dimethoxy-2,2′-bipyridine)[μ-(2R,3R)-tartrato(4−)]dicopper(II) octahydrate
Authors: Wiedemann Dennis , Kulko Roman-David , Grohmann Andreas
Published: June 2019

Typical electroless copper baths (ECBs), which are used to chemically deposit copper on printed circuit boards, consist of an aqueous alkali hydroxide solution, a copper(II) salt, formaldehyde as reducing agent, an L-(+)-tartrate as complexing agent, and a 2,2′-bipyridine derivative as stabilizer. Actual speciation and reactivity are, however, largely unknown. Herein, we report on the synthesis and crystal structure of aqua-1κO-bis(4,4′-dimethoxy-2,2′-bipyridine)-1κ2
N,N′;2κ2
N,N′-[μ-(2R,3R)-2,3-dioxidosuccinato-1κ2
O
1,O
2:2κ2
O
3,O
4]dicopper(II) octahydrate, [Cu2(C12H12N2O2)2(C4H2O6)(H2O)]·8H2O, from an ECB mock-up. The title compound crystallizes in the Sohncke group P21 with one chiral dinuclear complex and eight molecules of hydrate water in the asymmetric unit. The expected retention of the tartrato ligand's absolute configuration was confirmed via determination of the absolute structure. The complex molecules exhibit an ansa-like structure with two planar, nearly parallel bipyridine ligands, each bound to a copper atom that is connected to the other by a bridging tartrato `handle'. The complex and water molecules give rise to a layered supramolecular structure dominated by alternating π stacks and hydrogen bonds. The understanding of structures ex situ is a first step on the way to prolonged stability and improved coating behavior of ECBs.
Prioritizing the barriers of TQM implementation from the perspective of garment sector in developing countries
Authors: Talapatra Subrata , Uddin Md. Kutub
Published: June 2019

Purpose

The purpose of this paper is to investigate the relative importance of different total quality management (TQM) implementation barriers in the context of Readymade Garment (RMG) industries in Bangladesh. Present study has developed a hierarchical framework of several TQM barriers to assess their importance. Expert opinions from RMG industries have been taken to evaluate the importance of one barrier over another.

Design/methodology/approach

Methodology adopted in this study to find out the rank of different TQM barriers is fuzzy analytic hierarchy process.

Findings

The study shows that, according to order, inappropriate planning of TQM implementation program, lack of financial support, lack of employee training, lack of empowerment of employees, lack of sufficient physical resources, etc. are critical barriers and hampering the successful implementation of TQM program in this sector.

Research limitations/implications

This study has both theoretical and practical implications. It has found out strong and weak contribution of different barriers during TQM implementation. Therefore, this finding will strengthen the knowledge of successful implementation of TQM and will further enrich the existing literature in the context of manufacturing industries in developing countries. Moreover, this finding will also help the decision makers in preparing an effective plan for successful implementation of TQM by utilizing limited resources.

Practical implications

Moreover, our results will aid the managers of RMG sector to find the weight of importance of different barriers. Accordingly, they will make a plan to overcome the major TQM barriers which will increase the success rate of TQM implementation. Every Successful program will bring business excellence. These findings could be a guideline for TQM implementation program in developing countries.

Originality/value

Present study possesses some significant values. First, so far our knowledge go, no other study has developed a hierarchical structure of TQM barrier on the basis of overall change needed within the organization for TQM implementation. Second, this study could be a good guideline for TQM implementation program in RMG sector in developing countries.
Does the school input quality matter to nearby property prices in Taipei metropolis?
Authors: Peng Ti-Ching
Published: June 2019

Purpose

This paper aims to analyse the spatial effect of school input – “student–teacher ratio” – on property prices in Taipei Metropolis, Taiwan. The falling fertility rate inevitably changes educational system since more less-experienced part-time teachers are hired for the sake of schools’ budget. Hence, in addition to full-time teachers, part-time teachers are included in measuring the student–teacher ratio to see if an increase in part-time teachers, indicating the possible plunge of school quality, may decrease the value of nearby properties.

Design/methodology/approach

Three types of spatial regressions (including spatial lag, spatial error and SARAR models), which incorporate different kinds of spatial dependencies into hedonic models, are applied to reveal the relationship between two measures of student–teacher ratios and property values.

Findings

Conventional variables, including housing attributes, demographics and local facilities, demonstrated their consistent and expected influence on property prices. More importantly, the significant “student–teacher ratio 2” (both full-time and part-time teachers) indicated that low-paid, less-experienced and overworked part-time teachers can hardly deliver quality instruction, which inevitably causes harm to school credit and potential buyers’ confidence in valuing neighbouring properties.

Practical implications

Facing the decrease in children and the shrinking budget, the solution to maintain teacher’s quality is to remove the unnecessary administrative chores from full-time teachers and let them do their jobs rather than hiring part-time teachers. Good school input quality should add value to nearby properties, which in return appeals more students to enrol in this school and further elevate schools’ financial burden.

Originality/value

This paper is one of the few studies that consider part-time teachers in capitalising school-input quality into property prices. The increase in part-time teachers, which may lead to an illusion that each student could have higher degree of individual attention from teachers, actually lowers the education quality distributed to all the students. It provides a different perspective in defining the importance of teaching quality to property values in Chinese culture.
A new model for assessing the impact of ICT and digital knowledge on students’ thoughts and beliefs
Authors: Rajabion Lila , Wakil Karzan , Badfar Arshad , Mojtabavi Naeini Shahrzad , Zareie Batool
Published: June 2019

Purpose

This study aimed to examine the impact of ICT and digital knowledge on students’ thoughts and beliefs. Using Information and Communication Technology (ICT) in learning and teaching processes can improve the interpretation of knowledge, not only in the learning process but also for thoughts and beliefs. Beliefs and thoughts as propositional content are understood to be a subjective manner of knowing and becoming a focal point of education process. In addition, ICT plays a vital role in enhancing the efficiency of the teaching process which can change the thoughts of learners. So, in this paper, the usage of ICT in education was considered as a key factor for improving students’ thoughts and beliefs. In addition, a conceptual model was proposed to evaluate this impact.

Design/methodology/approach

Data were collected from 384 students from secondary schools in Iran. For assessing the elements of the model, a complete questionnaire was designed. For statistical analysis of questionnaires, SPSS 22 and SMART-PLS 3.2 software package was used.

Findings

The obtained results showed the high strength of the proposed model. The outcomes indicated that digital technology acceptance positively affects students’ thoughts and beliefs. In addition, the findings showed that the role of digital knowledge, digital training facilities and digital education content on students’ thoughts and beliefs was significant.

Research limitations/implications

The authors deal with one experiment and so the results cannot be generalized. The trail should be repeated with many groups and in diverse contexts.

Originality/value

Despite the importance of the investigating the impact of ICT and digital knowledge on the students’ thoughts and beliefs, the relationship among these factors was not examined well in previous research. Thus, the investigation of the impact of ICT and digital knowledge on the students’ thoughts and beliefs is the main originality of this research. For this goal, a new conceptual model is proposed, which has 11 sub-indicators within four variables: digital technology acceptance, digital knowledge, digital training facilities and digital education content.
Barriers to the adoption of green certification of buildings
Authors: Agyekum Kofi , Adinyira Emmanuel , Baiden Bernard , Ampratwum Godslove , Duah Daniel
Published: June 2019

Purpose

This paper aims to identify the key barriers to the adoption of green certification of buildings in Ghana.

Design/methodology/approach

The study adopts face-to-face and telephonic interviews with ten built environment professionals, using a semi-structured interview guide. Qualitative responses to the interview were thematically analysed using NVivo 11 Pro analysis application software.

Findings

The findings suggest that “lack of information on existing green buildings”, “lack of incentives”, “conservative nature of Ghanaians”, “lack of active government participation”, “inadequate human resource”, “lack of awareness of the benefits”, “cost and financing” and “lack of legal backing” are the eight key barriers that hinder the adoption of green certification of buildings.

Research limitations/implications

The research is limited to built environment professionals registered with their appropriate professional bodies. The findings cannot be generalized and extended to other developing countries that do not share similar characteristics and context with Ghana.

Practical implications

Practically, this study highlights, for the benefit of the construction industry and the government, the critical barriers to the adoption of green certification of buildings in Ghana. Identification of these barriers provides a pathway for the provision of pragmatic solutions towards the adoption of green buildings in Ghana.

Originality/value

Findings of the research make significant contribution to the debate on the barriers to the adoption of green certification of buildings. Four out of the eight barriers (inadequate awareness of the benefits of green certification of buildings, inadequate human resource, conservative nature of Ghanaian and lack of information on existing green buildings) identified are unique in the context of other related studies and advanced knowledge on the subject matter.
Social and emotional learning for parents through Conscious Discipline
Authors: Darling Kristen E. , Seok Deborah , Banghart Patti , Nagle Kerensa , Todd Marybeth , Orfali Nadia S.
Published: June 2019

Purpose

The purpose of this paper is to examine Conscious Discipline’s (CD) Parenting Education Curriculum (CD PEC), the parenting component of CD’s research-based social and emotional learning program. CD aims to change child behavior by changing how adults understand and manage their own behaviors and emotions. Researchers explored CD PEC’s association with improved parenting skills, parent–child relationships and child behavior and emotion management.

Design/methodology/approach

During pre- and post-site visits, parents in four Head Start programs completed the Attentive Parenting Survey (n=25) and interviews (n=19); and 20 staff were also interviewed.

Findings

Parents reported that CD PEC shifted their perspectives and practices for managing children’s challenging behaviors, improved parent–child relationships and resulted in decreased child behavior problems.

Research limitations/implications

The study was correlational, based on self-report, and had a small sample with no comparison group.

Practical implications

This study supports CD PEC as a means of shifting parenting practices, relationships and child behavior by focusing on adult social-emotional skills and self-regulation.

Social implications

This study provides preliminary evidence that addressing the social-emotional needs of adults is a viable step to helping children improve their social skills, emotion regulation and general behavior, which have all been linked to later academic and life success.

Originality/value

The paper studies improvements in parents’ emotion recognition and self-regulation before disciplining their children.