bluuebunny/crossref_metadata_2025 huggingface dataset:
Monitoring and evaluating the payment-for-performance premise of REDD+: the case of India’s ecological fiscal transfers
Authors: Busch Jonah
Published: July 2018

Introduction:
The central premise underlying international payments for Reducing Emissions from Deforestation and forest Degradation (REDD+) is that offering governments ex post payments for verified success in reducing emissions will motivate them to protect and restore forests. However, the extent to which performance-based payments motivate governments to protect and restore forests has yet to be evaluated quantitatively. Researchers have only quantitatively evaluated performance-based payments to non-governments for forest outcomes (e.g. payments for ecosystem services) and to governments for non-forest outcomes (e.g. results-based aid).

Methods:
We describe how researchers now have an opportunity to more easily evaluate performance-based payments to governments for forest outcomes thanks to India’s new ecological fiscal transfers (EFTs), which provide $6-12 billion per year to Indian states in proportion to their forest cover.

Discussion:
India’s EFTs differ from REDD+ programs in that they pay for states’ stock of forest area in the recent past rather than reductions in the rate of forest carbon loss in the near-future. Nevertheless, India’s EFTs focus on a single outcome and have many recipient governments, significant financial scale, lack of contemporaneous confounding policy changes, universal participation, and long-term data collection.

Conclusion:
These features make India’s EFTs especially useful for testing the payment-for-performance premise of REDD+.
Seizure burden pre- and postresection of low-grade gliomas as a predictor of tumor progression in low-grade gliomas
Authors: Santos-Pinheiro Fernando , Park Mingjeong , Liu Diane , Kwong Lawrence N , Cruz Savannah , Levine Nicholas B , O’Brien Barbara J , Chen Merry
Published: July 2018

Background

Low-grade gliomas (LGGs) are slow-growing, infiltrative tumors frequently associated with seizures. Predicting which patients will develop early tumor recurrence based on clinical indicators following initial surgical intervention remains a challenge. Seizure recurrence following surgery may be an early indicator of tumor recurrence, especially in patients presenting with increase in seizure frequency.

Methods

This study analyzed 148 patients meeting inclusion criteria (age >18 years, LGG diagnosis, at least 1 seizure event recorded before and after initial surgical intervention). All patients were treated at the Brain and Spine Center at The University of Texas MD Anderson Cancer Center from January 2000 to March 2013. Seizure frequency in a 6-month period before and after tumor resection was categorized as none, 1, few (2 to 3 seizures) or several (>3 seizures). Immediately postoperative seizures (up to 48 hours from surgery) were not included in the analysis.

Results

A total of 116 (78.4%) patients had seizures at initial presentation and most (95%) were started on antiepileptic drugs (AEDs). We found 2 clinical variables with a significant impact on progression-free survival (PFS): Higher seizure frequency during the 6-month postoperative period and seizure frequency increase between the 6-month pre- and the 6-month postoperative periods were both correlated to higher risk of early tumor recurrence (P = .007 and P = .004, respectively).

Conclusion

Seizure frequency following surgical resection of LGGs and the seizure frequency change between the 6-month preoperative and postoperative periods may serve as clinical predictors of early tumor recurrence in patients with LGGs who are also afflicted by seizures.
Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations
Authors: Lam Margaret M. C. , Wick Ryan R. , Wyres Kelly L. , Gorrie Claire L. , Judd Louise M. , Jenney Adam W. J. , Brisse Sylvain , Holt Kathryn E.
Published: July 2018

Mobile genetic elements (MGEs) that frequently transfer within and between bacterial species play a critical role in bacterial evolution, and often carry key accessory genes that associate with a bacteria’s ability to cause disease. MGEs carrying antimicrobial resistance (AMR) and/or virulence determinants are common in the opportunistic pathogen Klebsiella pneumoniae, which is a leading cause of highly drug-resistant infections in hospitals. Well-characterised virulence determinants in K. pneumoniae include the polyketide synthesis loci ybt and clb (also known as pks), encoding the iron-scavenging siderophore yersiniabactin and genotoxin colibactin, respectively. These loci are located within an MGE called ICEKp, which is the most common virulence-associated MGE of K. pneumoniae, providing a mechanism for these virulence factors to spread within the population. Here we apply population genomics to investigate the prevalence, evolution and mobility of ybt and clb in K. pneumoniae populations through comparative analysis of 2498 whole-genome sequences. The ybt locus was detected in 40 % of K. pneumoniae genomes, particularly amongst those associated with invasive infections. We identified 17 distinct ybt lineages and 3 clb lineages, each associated with one of 14 different structural variants of ICEKp. Comparison with the wider population of the family Enterobacteriaceae revealed occasional ICEKp acquisition by other members. The clb locus was present in 14 % of all K. pneumoniae and 38.4 % of ybt+ genomes. Hundreds of independent ICEKp integration events were detected affecting hundreds of phylogenetically distinct K. pneumoniae lineages, including at least 19 in the globally-disseminated carbapenem-resistant clone CG258. A novel plasmid-encoded form of ybt was also identified, representing a new mechanism for ybt dispersal in K. pneumoniae populations. These data indicate that MGEs carrying ybt and clb circulate freely in the K. pneumoniae population, including among multidrug-resistant strains, and should be considered a target for genomic surveillance along with AMR determinants.
The Miniature-chemostat Aging Device: A new experimental platform facilitates assessment of the transcriptional and chromatin landscapes of replicatively aging yeast
Authors: Hendrickson David G. , Soifer Ilya , Wranik Bernd J. , Kim Griffin , Robles Michael , Gibney Patrick A. , McIsaac R. Scott
Published: July 2018

Replicative aging of Saccharomyces cerevisiae is an established model system for eukaryotic cellular aging. A major limitation in yeast lifespan studies has been the difficulty of separating old cells from young cells in large quantities for in-depth comparative analyses. We engineered a new platform, the Miniature-chemostat Aging Device (MAD), that enables purification of aged cells at sufficient quantities to enable genomic and biochemical characterization of aging yeast populations. Using the MAD platform, we measured DNA accessibility (ATAC-Seq) and gene expression (RNA-Seq) changes in aging cells. Our data highlight an intimate connection between aging, growth rate, and stress, as many (but not all) genes that change with age have altered expression in cells that are subjected to stress. Stress-independent genes that change with age are highly enriched for targets of the signal recognition particle (SRP). By obtaining pure populations of old cells, we find that nucleosome occupancy does not change significantly with age; however, significant age-dependent changes in accessibility at ~12% of genomic loci reflect decreased replication and changing activities of cell cycle and metabolic regulators. Finally, ATAC-seq revealed that upregulating the proteasome by deleting UBR2 reduces rDNA instability usually observed in aging cells, demonstrating a connection between proteasome activity and genomic stability.
Heterogeneity of transposon expression and activation of the repressive network in human fetal germ cells
Authors: Reznik Boris , Cincotta Steven A. , Jaszczak Rebecca G. , Mateo Leslie J. , Shen Joel , Cao Mei , Baskin Laurence , Ye Ping , An Wenfeng , Laird Diana J.
Published: July 2018

Epigenetic resetting in germ cells during development leads to the de-repression of transposable elements (TEs). piRNAs protect fetal germ cells from potentially harmful TEs by targeted destruction of mRNA and deposition of repressive epigenetic marks. Here we provide the first evidence for an active piRNA pathway and TE repression in germ cells of human fetal testis. We identify pre-pachytene piRNAs with features of secondary amplification that map most abundantly to L1 family TEs. We find that L1-ORF1p expression is heterogeneous in fetal germ cells, peaks at mid-gestation and declines concomitantly with increasing levels of piRNAs and H3K9me3, as well as nuclear localization of HIWI2. Surprisingly, following this decline, the same cells with accumulation of L1-ORF1p display highest levels of HIWI2 and H3K9me3, whereas L1-ORF1p low cells are also low in HIWI2 and H3K9me3. Conversely, earlier in development, the germ cells lacking L1-ORF1p express high levels of the chaperone HSP90a. We propose that a subset of HSP90a-armed germ cells resists L1 expression, whereas only those vulnerable L1-expressing germ cells activate the PIWI-piRNA repression pathway which leads to epigenetic silencing of L1 via H3K9me3.
A potential role for epigenetic processes in the acclimation response to elevated pCO2 in the model diatom Phaeodactylum tricornutum
Authors: Huang Ruiping , Ding Jiancheng , Gao Kunshan , de Carvalho Maria Helena Cruz , Tirichine Leila , Bowler Chris , Lin Xin
Published: July 2018

Understanding of the molecular responses underpinning diatom responses to ocean acidification is fundamental for predicting how important primary producers will be shaped by the continuous rise in atmospheric CO2. In this study, we have analyzed global transcriptomic changes of the model diatom Phaeodactylum tricornutum following growth for 15 generations in elevated pCO2 by strand-specific RNA sequencing (ssRNA-seq). Our results indicate that no significant effects of elevated pCO2 and associated carbonate chemistry changes on the physiological performance of the cells were observed after 15 generations whereas the expression of genes encoding histones and other genes involved in chromatin structure were significantly down-regulated, while the expression of transposable elements (TEs) and genes encoding histone acetylation enzymes were significantly up-regulated. Furthermore, we identified a series of long non-protein coding RNAs (lncRNAs) specifically responsive to elevated pCO2, suggesting putative regulatory roles for these largely uncharacterized genome components. Taken together, our integrative analyses reveal that epigenetic elements such as TEs, histone modifications and lncRNAs may have important roles in the acclimation of diatoms to elevated pCO2 over short time scales and thus may influence longer term adaptive processes in response to progressive ocean acidification.
A new reporter cell line for studies with proteasome inhibitors in Trypanosoma brucei
Authors: Moura Danielle MN , de Melo Neto Osvaldo P , Carrington Mark
Published: July 2018

A Trypanosoma brucei cell line is described that produces a visual readout of proteasome activity. The cell line contains an integrated transgene encoding an ubiquitin-green fluorescent protein (GFP) fusion polypeptide responsive to the addition of proteasome inhibitors. A modified version of T. brucei ubiquitin unable to be recognized by deubiquitinases (UbG76V) was fused to eGFP and constitutively expressed. The fusion protein is unstable but addition of the proteasome inhibitor lactacystin stabilizes it and leads to visually detectable GFP. This cell line can be widely used to monitor the efficiency of inhibitor treatment through detection of GFP accumulation in studies involving proteasome-mediated proteolysis, screening of proteasome inhibitors or other events related to the ubiquitin-proteasome pathway.
Metabolic diversity of bacteria and yeast from commercial probiotic products illustrated by phenotypic profiling
Authors: Ansari Juliana M. , Colasacco Christine , Emmanouil Elli , Kohlhepp Scott , Harriott Olivia
Published: July 2018

The number of probiotic products in the marketplace is on the rise, gaining momentum along with the upsurge in research on the role of the human gut microbiome in health. Although such products are considered safe for consumption, these probiotic supplements and beverages are not subject to stringent federal regulation for quality. While only certain strains of probiotic microbes have been studied for efficacy in clinical trials, the ingredient labels of commercial probiotics do not always list the strain names. In this study, we investigated the diversity of the bacteria and yeast sold in these products. From a representative selection of commercially available probiotic supplements and beverages, we cultured microbes and identified them with standard methods (16S rRNA gene sequencing, mass spectrometric identification, and Biolog phenotypic profiling), then assessed whether there were strain-specific differences in nutrient metabolism and tolerance to compounds across the isolates from different products. Bacillus coagulans, Bacillus subtilis, Lactobacillus plantarum, Lactobacillus rhamnosus, and the yeast Saccharomyces boulardii were cultured from 21 commercial probiotic products (fifteen probiotic supplements and six probiotic beverages). Phenotypic profiling revealed metabolic diversity in carbon source usage and tolerance to compounds, within species from different probiotics and from environmental isolates of strains belonging to the same species. Despite this strain level diversity, we observed that up to half of the probiotic supplements for sale in retail and drugstores only list the species, but not the specific strain, on the label. This study highlights that existing labeling conventions for probiotics are insufficient to convey the strain identity and diversity in these products, underscoring the need for clear strain identification and verification of strain-specific probiotic properties, particularly when moving toward therapeutic applications of beneficial microbes.
Mushroom body specific transcriptome analysis reveals dynamic regulation of learning and memory genes after acquisition of long-term courtship memory inDrosophila
Authors: Jones Spencer G. , Nixon Kevin C.J. , Kramer Jamie M.
Published: July 2018

The formation and recall of long-term memory (LTM) requires neuron activity-induced gene expression. Transcriptome analysis has been used to identify genes that have altered expression after memory acquisition, however, we still have an incomplete picture of the transcriptional changes that are required for LTM formation. The complex spatial and temporal dynamics of memory formation creates significant challenges in defining memory-relevant gene expression changes. The mushroom body (MB) is a signaling hub in the insect brain that integrates sensory information to form memories. Here, we performed transcriptome analysis in theDrosophilaMB at two time points after the acquisition of LTM: 1 hour and 24 hours. The MB transcriptome was compared to biologically paired whole head (WH) transcriptomes. In both, we identified more transcriptional changes 1 hour after memory acquisition (WH = 322, MB = 302) than at 24 hours (WH = 23, MB = 20). WH samples showed downregulation of developmental genes and upregulation of sensory response genes. In contrast, MB samples showed vastly different gene expression changes affecting biological processes that are specifically related to LTM. MB-downregulated genes were highly enriched for metabolic function, consistent with the MB-specific energy influx that occurs during LTM formation. MB-upregulated genes were highly enriched for known learning and memory processes, including calcium-mediated neurotransmitter release and cAMP signalling. The neuron activity inducible geneshr38andsrwere also specifically induced in the MB. These results highlight the importance of sampling time and cell type in capturing biologically relevant transcriptional changes involved in learning and memory. Our data suggests that MB cells transiently upregulate known memory-related pathways after memory acquisition and provides a critical frame of reference for further investigation into the role of MB-specific gene regulation in memory.
Joint analysis of matched tumor samples with varying tumor contents improves somatic variant calling in the absence of a germline sample
Authors: Halperin Rebecca F. , Liang Winnie S. , Kulkarni Sidharth , Tassone Erica E. , Adkins Jonathan , Enriquez Daniel , Tran Nhan L. , Hank Nicole C. , Newell James , Kodira Chinnappa , Korn Ronald , Berens Michael E. , Kim Seungchan , Byron Sara A.
Published: July 2018

Archival tumor samples represent a potential rich resource of annotated specimens for translational genomics research. However, standard variant calling approaches require a matched normal sample from the same individual, which is often not available in the retrospective setting, making it difficult to distinguish between true somatic variants and germline variants that are private to the individual. Archival sections often contain adjacent normal tissue, but this normal tissue can include infiltrating tumor cells. Comparative somatic variant callers are designed to exclude variants present in the normal sample, so a novel approach is required to leverage sequencing of adjacent normal tissue for somatic variant calling. Here we present LumosVar 2.0, a software package designed to jointly analyze multiple samples from the same patient. The approach is based on the concept that the allelic fraction of somatic variants, but not germline variants, would be reduced in samples with low tumor content. LumosVar 2.0 estimates allele specific copy number and tumor sample fractions from the data, and uses the model to determine expected allelic fractions for somatic and germline variants and classify variants accordingly. To evaluate using LumosVar 2.0 to jointly call somatic variants with tumor and adjacent normal samples, we used a glioblastoma dataset with matched high tumor content, low tumor content, and germline exome sequencing data (to define true somatic variants) available for each patient. We show that both sensitivity and positive predictive value are improved by analyzing the high tumor and low tumor samples jointly compared to analyzing the samples individually or compared to in-silico pooling of the two samples. Finally, we applied this approach to a set of breast and prostate archival tumor samples for which normal samples were not available for germline sequencing, but tumor blocks containing adjacent normal tissue were available for sequencing. Joint analysis using LumosVar 2.0 detected several variants, including known cancer hotspot mutations that were not detected by standard somatic variant calling tools using the adjacent normal as a reference. Together, these results demonstrate the potential utility of leveraging paired tissue samples to improve somatic variant calling when a constitutional DNA sample is not available.
Multi-scale deep tensor factorization learns a latent representation of the human epigenome
Authors: Schreiber Jacob , Durham Timothy , Bilmes Jeffrey , Noble William Stafford
Published: July 2018

The human epigenome has been experimentally characterized by measurements of protein binding, chromatin acessibility, methylation, and histone modification in hundreds of cell types. The result is a huge compendium of data, consisting of thousands of measurements for every basepair in the human genome. These data are difficult to make sense of, not only for humans, but also for computational methods that aim to detect genes and other functional elements, predict gene expression, characterize polymorphisms, etc. To address this challenge, we propose a deep neural network tensor factorization method, Avocado, that compresses epigenomic data into a dense, information-rich representation of the human genome. We use data from the Roadmap Epigenomics Consortium to demonstrate that this learned representation of the genome is broadly useful: first, by imputing epigenomic data more accurately than previous methods, and second, by showing that machine learning models that exploit this representation outperform those trained directly on epigenomic data on a variety of genomics tasks. These tasks include predicting gene expression, promoter-enhancer interactions, replication timing, and an element of 3D chromatin architecture. Our findings suggest the broad utility of Avocado’s learned latent representation for computational genomics and epigenomics.
Sexually dimorphic recombination can facilitate the establishment of sexually antagonistic polymorphisms in guppies
Authors: Bergero Roberta , Gardner Jim , Bader Beth , Yong Lengxob , Charlesworth Deborah
Published: July 2018

Summary/Abstract

Recombination suppression between sex chromosomes is often stated to evolve in response to polymorphisms for mutations that affect fitness of males and females in opposite directions (sexually antagonistic, or SA, mutations), but direct empirical support is lacking. The sex chromosomes of the fishPoecilia reticulata(the guppy) carry SA polymorphisms, making them excellent for testing this hypothesis for the evolution of sex linkage. We resequenced genomes of male and female guppies and, unexpectedly, found that variants on the sex chromosome indicate no extensive region with fully sex-linked genotypes, though many variants show strong evidence for partial sex linkage. We present genetic mapping results that help understand the evolution of the guppy sex chromosome pair. We find very different distributions of crossing over in the two sexes, with recombination events in male meiosis detected only at the tips of the chromosomes. The guppy may exemplify a route for sex chromosome evolution in which low recombination in males, likely evolved in a common ancestor, has facilitated the establishment of sexually antagonistic polymorphisms.
Impact of acetolactate synthase inactivation on 1,3-propanediol fermentation byKlebsiella pneumoniae
Authors: Zhou Sheng , Huang Youhua , Mao Xinliang , Li Lili , Guo Chuanyu , Gao Yongli , Qin Qiwei
Published: July 2018

1,3-Propanediol (1,3-PDO) is an important compound that is mainly used in industry for polymer production. Fermentation of 1,3-PDO from glycerol by marineKlebsiella pneumoniaeis accompanied by formation of 2,3-butanediol (2,3-BDO) as one of the main byproduct. The first step in the formation of 2,3-BDO from pyruvate is catalyzed by acetolactate synthase (ALS), an enzyme that competes with 1,3-PDO oxidoreductase for the cofactor NADH. This study aimed to analyze the impact of engineering the 2,3-BDO formation pathway via inactivation of ALS on 1,3-PDO fermentation by marineK. pneumoniaeHSL4. An ALS mutant was generated using Red recombinase assisted gene replacement. The ALS specific activities ofK. pneumoniaeΔALS were notably lower than that of the wild-type strain. Fed-batch fermentation of the mutant strain resulted in a 1,3-PDO concentration, productivity and conversion of 72.04 g L−1, 2.25 g L−1h−1, and 0.41 g g−1, a slightly increase compared with the parent strain. Moreover, inactivation of ALS decreasedmeso-2,3-BDO formation to trace amounts, significantly increased 2S,3S-BDO and lactate production, and a pronounced redistribution of intracellular metabolic flux was apparent.
Autism-associated Shank3 is essential for homeostatic plasticity and neuronal circuit stability
Authors: Tatavarty Vedakumar , Pacheco Alejandro Torrado , Lin Heather , Miska Nathaniel J. , Hengen Keith B. , Wagner Florence F. , Turrigiano Gina G.
Published: July 2018

Mutations in Shank3 are strongly associated with autism spectrum disorders and circuit disfunction, but a unified view of how Shank3 loss disrupts circuit function and excitability is lacking. Stabilizing, homeostatic forms of synaptic and intrinsic plasticity are critical for preventing circuit hyper- or hypo-excitability, leading us to ask whether Shank3 loss perturbs circuits by disrupting homeostatic plasticity. We show that Shank3 loss abolishes synaptic and intrinsic homeostatic plasticity, which can be rescued by lithium(Li), a drug with therapeutic potential in human Shankopathies. Further, Shank3 loss in vivo severely compromises the ability of visual cortical circuits to recover from perturbations to sensory drive. Our findings suggest that the loss of homeostatic compensation is a critical endophenotype that can explain a range of circuit disfunctions in Shankopathies.
Estimating recent migration and population size surfaces
Authors: Al-Asadi Hussein , Petkova Desislava , Stephens Matthew , Novembre John
Published: July 2018

In many species a fundamental feature of genetic diversity is that genetic similarity decays with geographic distance; however, this relationship is often complex, and may vary across space and time. Methods to uncover and visualize such relationships have widespread use for analyses in molecular ecology, conservation genetics, evolutionary genetics, and human genetics. While several frameworks exist, a promising approach is to infer maps of how migration rates vary across geographic space. Such maps could, in principle, be estimated across time to reveal the full complexity of population histories. Here, we take a step in this direction: we present a method to infer separate maps of population sizes and migration rates for different time periods from a matrix of genetic similarity between every pair of individuals. Specifically, genetic similarity is measured by counting the number of long segments of haplotype sharing (also known as identity-by-descent tracts). By varying the length of these segments we obtain parameter estimates for qualitatively different time periods. Using simulations, we show that the method can reveal time-varying migration rates and population sizes, including changes that are not detectable when ignoring haplotypic structure. We apply the method to a dataset of contemporary European individuals (POPRES), and provide an integrated analysis of recent population structure and growth over the last~3,000 years in Europe. Software implementing the methods is available athttps://github.com/halasadi/MAPS.
The first genetic linkage map forFraxinus pennsylvanicaand syntenic relationships with four related species
Authors: Wu Di , Koch Jennifer , Coggeshall Mark , Carlson John
Published: July 2018

Green ash (Fraxinus pennsylvanica) is an outcrossing, diploid (2n=46) hardwood tree species, native to North America. Native ash species in North America are being threatened by the rapid invasion of emerald ash borer (EAB,Agrilus planipennis) from Asia. Green ash, the most widely distributed ash species, is severely affected by EAB infestation, yet few resources for genetic studies and improvement of green ash are available. In this study, a total of 5,712 high quality single nucleotide polymorphisms (SNPs) were discovered using a minimum allele frequency of 1% across the entire genome through genotyping-by-sequencing. We also screened hundreds of genomic- and EST-based microsatellite markers (SSRs) from previousde novoassemblies (Staton et al. 2015; Lane et al. 2016). A first genetic linkage map of green ash was constructed from 91 individuals in a full-sib family, combining 2,719 SNP and 84 SSR segregating markers among the parental maps. The consensus SNP and SSR map contains a total of 1,201 markers in 23 linkage groups spanning 2008.87cM, at an average inter-marker distance of 1.67 cM with a minimum logarithm of odds (LOD) of 6 and maximum recombination fraction of 0.40. Comparisons of the organization the green ash map with the genomes of asterid species coffee and tomato, and genomes of the rosid species poplar and peach, showed areas of conserved gene order, with overall synteny strongest with coffee.
Phosphatidic acid inhibits SNARE priming by inducing conformational changes in Sec18 protomers
Authors: Starr Matthew L. , Sparks Robert P. , Hurst Logan R. , Zhao Zhiyu , Arango Andres , Lihan Muyun , Jenkins Jermaine L. , Tajkhorshid Emad , Fratti Rutilio A.
Published: July 2018

Eukaryotic homeostasis relies on membrane fusion catalyzed by SNARE proteins. Inactive SNARE bundles are re-activated by Sec18/NSF driven disassembly to enable a new round of fusion. We previously found that phosphatidic acid (PA) binds Sec18 to sequester it from SNAREs. Dephosphorylation of PA dissociates Sec18 from the membrane allowing it to engage SNARE complexes. We now report that PA induces conformational changes in Sec18 protomers, while hexameric Sec18 cannot bind PA membranes. The association of Sec18 with PA was shown to be sensitive to membrane curvature, suggesting that regulation could vary on different organelles in a curvature dependent manner. Molecular dynamics showed that PA binding sites exist on the D1 and D2 domains of Sec18 and that residues needed for binding were masked in the hexameric form of the protein. Together these data indicate that PA regulates Sec18 function through altering protein architecture and stabilizing membrane-bound protomers.
Supplier transparency: scale development and validation
Authors: Morgan Tyler R. , Richey Jr Robert Glenn , Ellinger Alexander E.
Published: July 2018

Purpose

The purpose of this paper is to create an instrument for conducting future supply chain transparency research by developing and validating a measure of supplier transparency. Specifically, the research develops a two-dimensional measure of supplier transparency that builds on previous studies that independently examine visibility and traceability in supply chain management (SCM)/logistics.

Design/methodology/approach

The scale development process is carried out over three stages (item generation, scale purification, scale validation). Survey methods are used with two separate data collection phases involving a total of 358 managers from multiple and diverse industries.

Findings

The new supplier transparency measure is a concise, two-dimensional scale that has the potential for significant usage in the development and testing of SCM theory.

Research limitations/implications

This study implemented a purposefully general sampling procedure. However, different industries may have additional, specific constraints regarding what it means to be a transparent supplier. Additional opportunities for future research include applying the new supplier transparency measure to examine supply chain frameworks, regulatory compliance, supply chain relationships and the implementation of information technology.

Practical implications

Firms are under increasing pressure to be transparent about partner sourcing, resource utilization and other transactional issues related to the products and processes in their supply chains. The new measure may be utilized to address these issues as well as the interaction between supply chain operations and stakeholders by facilitating a quantitative assessment of supplier transparency.

Originality/value

Drawing on the established constructs of supply chain visibility and traceability, a measure of supplier transparency is developed, supported by a review of the literature, input from subject matter experts and interviews with supply chain managers. Suggestions are made for future validation of supplier transparency within established supply chain frameworks.
A systematic approach to root cause analysis using 3 × 5 why’s technique
Authors: Gangidi Prashant
Published: July 2018

Purpose

The purpose of this paper is to go a step further from the traditional 5 Whys technique by adding three more legs during the root cause analysis stage – occurrence, human and systemic issues that contribute toward the problem, hence the term 3 × 5 Whys. Performing individual 5 Whys for these three components enables to identify deeper root cause(s) that may spawn across multiple groups within an organization.

Design/methodology/approach

Cause-and-effect analysis used during traditional root cause investigations within an 8D or Lean six sigma project is used as a theoretical foundation. Examples from different industries are presented showing the 3 × 5 Why’s framework and advantages it brings to the organization along with identifying shortcomings and suggestions to make it more effective.

Findings

If properly used this integrated methodology will reveal higher order systemic causes (e.g. policies or management decisions) stemming from lower lever symptoms (e.g. defective parts, procedural errors). Effective execution of this methodology can provide tremendous results in defect reduction, yield improvement, operational efficiency improvement and logistics management type of projects. Resolving higher level sources of problems allows an organization to evolve itself and maintain a competitive edge in the market.

Research limitations/implications

Adopting this quality management technique in start-up companies entails some challenges and other implications have been discussed with SWOT analysis.

Practical implications

Examples from various sectors using 3 × 5 Why approach have been presented that show that this methodology provides deeper insight into root causes which could be affecting multiple groups in an organization. Using this technique effectively is found to be beneficial to resolve issues in operations management, logistics, supply chain, purchasing, warehouse operations, manufacturing, etc.

Social implications

This methodology has a human component which often results in some sort of resistance as not all working professionals think alike when it comes to accountability and ownership of issues. This may hinder root cause analysis and subsequent corrective actions implementation.

Originality/value

This study is unique in its in-depth real-world case studies demonstrating the need for taking a deep dive approach to root cause analysis by understanding specific, system and human components responsible for causing the failure mode.
A simplified analytical method for the pressure of tilt hydrostatic journal bearing
Authors: Du Yikang , Mao Kuanmin , Liu Hongqi , Mao Xiaobo , Li Zhihang
Published: July 2018

Purpose

This paper aims to present a simplified method to predict the pressure of the recess, no matter whether the tilt center coincides with the geometric center of the hydrostatic journal bearings.

Design/methodology/approach

To validate the effectiveness of the presented model, computational fluid dynamics (CFD) method and experimental method are performed in this study.

Findings

By comparing the CFD results and the experimental results, the pressure of the recess is related to the tilt direction, the tilt center, the width of the land and the circumferential angle of the land.

Originality/value

The mathematic model requires equivalent resistance of land edge – tilt position, tilt direction, tilt angle and the thickness of oil film instead of any digital iteration. Furthermore, a novel experimental apparatus including a circular hydrostatic bearing called ball bearing is designed to study the tilt effect produced by manufacturing error and offset load force on the pressure of the recess.
Some basic observations on conducting a systematic review: a brief reply to Goldstein, Vatalaro and Yair
Authors: See Beng Huat , Gorard Stephen
Published: July 2018

Purpose

The purpose of this paper is to provide a response to Goldstein et al.’s (2017) attempted rebuttal of the authors’ prior paper in this journal (See and Gorard 2015).

Design/methodology/approach

The prior paper reported a systematic review of interventions to involve engaging parents more in their children’s education in order to raise school attainment. Goldstein et al. make a large number of unwarranted claims about its quality. They reproach the authors for using reports of unpublished evidence, for mis-labelling or mis-describing studies, and for denigrating studies by labelling them as “bad”. The authors were very surprised when first alerted to this response and went back to look at all of the research reports that Goldstein et al. claimed the authors mis-represented in the authors’ assessment.

Findings

The authors found that the Goldstein et al. claims are false and based on such a poor understanding of how evidence is reviewed that it was strange to see their paper in this journal.

Originality/value

In the authors’ reply, they look first at why unpublished material must be included in a review, and why the outlet for publication is not relevant, then at appropriate designs for causal questions, and at the confusion in Goldstein et al. between evaluation quality and intervention impact. The authors look at many examples where the confusion leads to Goldstein et al. making incorrect assertions about the authors’ paper, in order to make the point that their whole idea of how to conduct a systematic review is wrong.
Real estate media sentiment through textual analysis
Authors: Ruscheinsky Jessica Roxanne , Lang Marcel , Schäfers Wolfgang
Published: July 2018

Purpose

The purpose of this paper is to determine systematically the broader relationship between news media sentiment, extracted through textual analysis of articles published by leading US newspapers, and the securitized real estate market.

Design/methodology/approach

The methodology is divided into two stages. First, roughly 125,000 US newspaper article headlines from Bloomberg, The Financial Times, Forbes and The Wall Street Journal are investigated with a dictionary-based approach, and different measures of sentiment are created. Second, a vector autoregressive framework is used to analyse the relationship between media-expressed sentiment and REIT market movements over the period 2005–2015.

Findings

The empirical results provide significant evidence for a leading relationship between media sentiment and future REIT market movements. Furthermore, applying the dictionary-based approach for textual analysis, the results exhibit that a domain-specific dictionary is superior to a general dictionary. In addition, better results are achieved by a sentiment measure incorporating both positive and negative sentiment, rather than just one polarity.

Practical implications

In connection with fundamentals of the REIT market, these findings can be utilised to further improve the understanding of securitized real estate market movements and investment decisions. Furthermore, this paper highlights the importance of paying attention to new media and digitalization. The results are robust for different REIT sectors and when conventional control variables are considered.

Originality/value

This paper demonstrates for the first time, that textual analysis is able to capture media sentiment from news relevant to the US securitized real estate market. Furthermore, the broad collection of newspaper articles from four different sources is unique.
Modulatory effect of intravenous immunoglobulin on Th17/Treg cell balance in women with unexplained recurrent spontaneous abortion
Authors: Muyayalo Kahinho P. , Li Zhi‐Hui , Mor Gil , Liao Ai‐Hua
Published: July 2018

Recurrent spontaneous abortion (RSA) is a growing problem worldwide. In a majority of cases, the cause remains unknown but there is increasing evidence that immunologic factors play an important role. Intravenous immunoglobulin (IVIg) therapy has been proposed to have immune modulatory effects and therefore been applicable for the treatment of patients with RSA. Although its efficacy is still controversial, several recent studies suggest that IVIg treatment may improve pregnancy outcomes. CD4+ T cells and their related cytokines play an important role in maternal‐fetal immune regulation, and an imbalance of Th17/Treg cell ratio has been proposed as a cause for RSA. We review the scientific evidence supporting a modulatory effect of IVIg on Th17/Treg cell balance and discuss the potential mechanisms how IVIg might enhance Treg cells function. We propose that correction of Th17/Treg cell dysregulation could be one of the mechanisms that can explain the positive therapeutic effects of IVIg therapy. Consequently, selecting patients with abnormal Th17/Treg cell ratios could increase the success of IVIg therapy.
A novel, palatable paediatric oral formulation of midazolam: pharmacokinetics, tolerability, efficacy and safety
Authors: Salman S. , Tang E. K. Y. , Cheung L. C. , Nguyen M. N. , Sommerfield D. , Slevin L. , Lim L. Y. , von Ungern Sternberg B. S.
Published: July 2018

Midazolam is one of many bitter drugs where provision of a suitable oral paediatric formulation, particularly in the pre‐anaesthetic setting, remains a challenge. To overcome this problem, a novel chocolate‐based tablet formulation has been developed with positive pre‐clinical results. To further investigate the potential of this formulation, 150 children aged 3–16 years who were prescribed midazolam as a premedication were randomly assigned to receive 0.5 mg.kg−1 either as the novel formulation or an intravenous solution given orally, which is the current standard at our institution. Tolerability was assessed by each child, parent and nurse using a 5‐point facial hedonic scale and efficacy was determined as the time to onset of sedation. Blood samples for midazolam and 1‐hydroxymidazolam levels were analysed using high‐performance liquid chromatography. Population pharmacokinetics were evaluated using non‐linear mixed effects modelling. The novel formulation had significantly improved tolerability scores from children, parents and nurses (all p < 0.001). Time to effect was not different between the groups (p = 0.140). The pharmacokinetics of midazolam and 1‐hydroxymidazolam were able to be modelled simultaneously. The novel formulation was subject to a higher estimated first‐pass metabolism compared with the intravenous solution (8.6% vs. 5.0%) and a significantly lower relative bioavailability of 82.1% (p = 0.013), with no other significant differences. Exposure relative to dose was in the range previously reported for midazolam syrup. We conclude that the novel chocolate‐based formulation of midazolam provides improved tolerability while remaining efficacious with suitable pharmacokinetics when used as a premedicant for children.
Early discharge of patients with acute pancreatitis to enhanced outpatient care
Authors: Kumar Vineeth V. , Treacy P. John , Li Minghao , Dharmawardane Anoj
Published: July 2018

Background

Acute pancreatitis (AP) is a common cause for hospital admission, but some patients have a prolonged stay. The aim of this study was to identify patients with mild AP who had a prolonged hospital stay, who potentially could be discharged at day 2 to enhanced outpatient care.

Methods

Data was retrospectively collected on all patients admitted to the Royal Darwin Hospital between May 2016 and February 2017 with a diagnosis of mild AP to identify factors that may safely predict early discharge to enhanced outpatient care.

Results

Of 115 admissions, 62% were male, 50% indigenous and alcohol was causative in 53%. A total of 75 (65%) patients stayed more than 2 days and used 342 bed‐days. Factors identified in the first 2 days of admission associated with a length of stay more than 2 days (R2 = 0.56, P < 0.0001) included pain score >5 (P = 0.034), temperature ≥38°C (P < 0.0001), white blood cell count >18 (P = 0.036), not tolerating oral diet by day 2 (P = 0.002), severe pancreatitis on imaging (P = 0.008) and readmission in the previous 30 days (P = 0.035). Using these criteria, 57% of all admissions and 87% of admissions greater than 2 days could potentially have been transferred to enhanced outpatient care at day 2 for management. This would have saved 277 inpatient bed‐days and an estimated $122 771 over the 9‐month study period.

Conclusions

A significant proportion of patients admitted with mild AP, who stay longer than 2 days in hospital, could potentially be identified and discharged early to enhanced outpatient care.
Patients requiring an acute operation: where are the delays in the process?
Authors: de Burlet Kirsten J. , Desmond Brendan , Harper Simon J. , Larsen Peter D. , Dennett Elizabeth R.
Published: July 2018

Background

Delays to surgery for patients requiring an acute operation are associated with increased morbidity and mortality. A recent study from our institution observed long waiting times for patients booked for an acute operation. The aim of this study was to evaluate the patient's progress from presentation to arrival in the operating theatre and to identify where delays occurred.

Methods

Patients undergoing acute general surgery between July 2016 and May 2017 were studied. Data were obtained for time of presentation, imaging, theatre and booking. A time interval from presentation to booking for theatre of greater than 6 h was defined as a diagnostic delay. A time interval from booking to theatre greater than the category defined time (four‐level priority system) was defined as a logistic delay.

Results

A total of 683 patients were included. A diagnostic delay was observed in 55.1%. This occurred more frequently in patients who required imaging prior to their operation (82.5 versus 41.1%, P < 0.001). Logistic delay occurred in 31.0% of the patients, and this was most common for patients booked as a category 3 (requiring surgery within 6 h, 41.8%, P < 0.001). Patients who had a diagnostic delay were significantly more likely to have a post‐operative complication compared to patients who did not (17.2 versus 10.0%, P = 0.009).

Conclusion

There are significant delays associated with patients presenting to the acute general surgery service and their transition to theatre. Addressing both the diagnostic and the logistic delays in our institution should result in a significant improvement in patient care.
“Protect Wisconsin Families”? Rethinking Left Family Values in the 2011 Wisconsin Uprising
Authors: Seitz David K.
Published: July 2018

This article seeks to rethink the trope of the “working family” so prevalent in contemporary politics, with particular attention to its promise and constitutive limits for the Left. It takes up contemporary socialist, feminist, anti‐racist and queer scholarship on the discourse of family, bringing it to bear on the case of “working family” rhetoric in the 2011 Wisconsin Uprising against austerity and public‐sector union‐busting. Reckoning with the term's racist and heteropatriachal valences, and its centrality in privatising social reproduction, I conclude by considering potential alternative horizons for thinking intimacy, labour, and social citizenship for the intersectional Left.