bluuebunny/crossref_metadata_2025 huggingface dataset:
Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries
Authors: Munk Patrick , Knudsen Berith Elkær , Lukjacenko Oksana , Duarte Ana Sofia Ribeiro , Luiken Roosmarjin E. C. , Gompel Liese Van , Smit Lidwien A. M. , Schmitt Heike , Garcia Alejandro Dorado , Hansen Rasmus Borup , Petersen Thomas Nordahl , Bossers Alex , Ruppé Etienne , Lund Ole , Tine Hald , Pamp Sünje Johanna , Vigre Håkan , Heederik Dick , Wagenaar Jaap A. , Mevius Dik , Aarestrup Frank M.
Published: September 2017

EFFORT group

Haitske Graveland, Alieda van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Claire Chauvin, Julie David, Antonio Battisti, Andrea Caprioli, Jeroen Dewulf, Thomas Blaha, Katharina Wadepohl, Maximiliane Brandt, Dariusz Wasyl, Magdalena Skarzyñska, Magdalena Zajac, Hristo Daskalov, Helmut W Saatkamp, Katharina D.C. Stärk.

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. Use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (www.effort-against-amr.eu), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 gigabases of DNA sequence, using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several recently described, critical AMR genes, includingmcr-1andoptrA, the abundance of which differed both between host species and countries. We found that the total acquired AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. Novel, functionally-determined AMR genes were, however, not associated with total drug use.
OpenEHR modeling for genomics in clinical practice
Authors: Mascia Cecilia , Uva Paolo , Leo Simone , Zanetti Gianluigi
Published: September 2017

The increasing usage of high throughput sequencing in personalized medicine brings new challenges to the realm of healthcare informatics. Patient records need to accommodate data of unprecedented size and complexity as well as keep track of their production process. In this work we present a solution for integrating genomic data into electronic health records via openEHR archetypes. We introduce new genomics-specific archetypes based on the popular variant call format and show their applicability to a practical use case. Finally, we discuss their structure in comparison with the HL7®FHIR®standard.
Subtypes of functional brain connectivity as early markers of neurodegeneration in Alzheimer’s disease
Authors: Orban Pierre , Tam Angela , Urchs Sebastian , Savard Melissa , Madjar Cécile , Badhwar AmanPreet , Dansereau Christian , Vogel Jacob , Schmuel Amir , Dagher Alain , Villeneuve Sylvia , Poirier Judes , Rosa-Neto Pedro , Breitner John , Bellec Pierre ,   for the Alzheimer’s Disease Neuroimaging Initiative,   and the Pre-symptomatic Evaluation of Novel or Experimental Treatments for Alzheimer’s Disease Program
Published: September 2017

Highlights

Reliable functional brain network subtypes accompany cognitive impairment in AD

Symptom-related subtypes exist in the default-mode, limbic and salience networks

A limbic subtype is associated with a familial risk of AD in healthy older adults

Limbic subtypes also associate with beta amyloid deposition and ApoE4

In Brief

We found reliable subtypes of functional brain connectivity networks in older adults, associated with AD-related clinical symptoms in patients as well as several AD risk factors/biomarkers in asymptomatic individuals.

The heterogeneity of brain degeneration has not been investigated yet for functional brain network connectivity, a promising biomarker of Alzheimer’s disease. We coupled cluster analysis with resting-state functional magnetic resonance imaging to discover connectivity subtypes in healthy older adults and patients with cognitive disorders related to Alzheimer’s disease, noting associations between subtypes and cognitive symptoms in the default-mode, limbic and salience networks. In an independent asymptomatic cohort with a family history of Alzheimer’s dementia, the connectivity subtypes had good test-retest reliability across all tested networks. We found that a limbic subtype was overrepresented in these individuals, which was previously associated with symptoms. Other limbic subtypes showed associations with cerebrospinal fluid Aβ1-42levels and ApoE4 genotype. Our results demonstrate the existence of reliable subtypes of functional brain networks in older adults and support future investigations in limbic connectivity subtypes as early biomarkers of Alzheimer’s degeneration.
MicroRNA miR-128 represses LINE-1 (L1) retrotransposition by downregulating the nuclear import factor TNPO1
Authors: Idica Adam , Sevrioukov Evgueni A , Zisoulis Dimitri G , Hamdorf Matthias , Daugaard Iben , Kadandale Pavan , Pedersen Irene
Published: September 2017

Repetitive elements, including LINE-1 (L1), comprise approximately half of the human genome. These elements can potentially destabilize the genome by initiating their own replication and reintegration into new sites (retrotransposition). In somatic cells, transcription of L1 elements are repressed by distinct molecular mechanisms including DNA methylation and histone modifications to repress transcription. Under conditions of hypomethylation (e.g.in tumor cells) a window of opportunity for L1 de-repression arises and additional restriction mechanisms become crucial. We recently demonstrated that the microRNA miR-128 represses L1 activity by directly binding to L1 ORF2 RNA. In this study, we tested whether miR-128 can also control L1 activity by repressing cellular proteins important for L1 retrotransposition. We found that miR-128 targets the 3’UTR of the nuclear import factor transportin 1 (TNPO1) mRNA. Manipulation of miR-128 and TNPO1 levels demonstrated that induction or depletion of TNPO1 affects L1 retrotransposition and nuclear import of an L1-RNP complex (using L1-encoded ORF1p as a proxy for L1-RNP complexes). Moreover, TNPO1 overexpression partially reversed the repressive effect of miR-128 on L1 retrotransposition. Our study represents the first description of a protein factor involved in nuclear import of the L1 element and demonstrates that miR-128 controls L1 activity in somatic cells through two independent mechanisms: direct binding to L1 RNA, and regulating a cellular factor necessary for L1 nuclear import and retrotransposition.
Which are major players, canonical or non-canonical strigolactones?
Authors: Yoneyama Koichi , Xie Xiaonan , Yoneyama Kaori , Kisugi Takaya , Nomura Takahito , Nakatani Yoshifumi , Akiyama Kohki , McErlean Christopher S. P.
Published: September 2017

Strigolactones (SLs) can be classified into two structurally distinct groups: canonical and non-canonical SLs. Canonical SLs contain the ABCD ring system, and non-canonical SLs lack the A, B, or C ring but have the enol ether–D ring moiety which is essential for biological activities. The simplest non-canonical SL is the SL biosynthetic intermediate carlactone (CL). In plants, CL and its oxidized metabolites such as carlactonoic acid and methyl carlactonoate, are present in root and shoot tissues. In some plant species including black oat (Avena strigosa), sunflower (Helianthus annuus), and maize (Zea mays), non-canonical SLs are major germination stimulants in the root exudates. Various plant species such as tomato (Solanum lycopersicum) release carlactonoic acid, and poplar (Populus spp.) was found to exude methyl carlactonoate into the rhizosphere. These results suggest that both canonical and non-canonical SLs are active as host recognition signals in the rhizosphere. In contrast, limited distribution of canonical SLs in the plant kingdom and structure- and stereo-specific transportation of canonical SLs from roots to shoots suggest that plant hormones inhibiting shoot branching are not canonical SLs but are rather non-canonical SLs.
Representational confusion: the plausible consequence of demeaning your data
Authors: Ramírez Fernando M.
Published: September 2017

The use of multivariate pattern analysis (MVPA) methods has enjoyed this past decade a rapid increase in popularity among neuroscientists. More recently, similarity-based multivariate methods aiming not only to extract information regarding the class membership of stimuli from their associated brain patterns, say, decode a face from a potato, but to understand the form of the underlying representational structure associated with stimulus dimensions of interest, say, 2D grating or 3D face orientation, have flourished under the name of Representational Similarity Analysis (RSA). However, data-preprocessing steps implemented prior to RSA can significantly change the covariance (and correlation) structure of the data, hence possibly leading to representational confusion—i.e., a researcher inferring that brain area A encodes information according to representational scheme X, and not Y, when the opposite is true. Here, I demonstrate with simulations that time-series demeaning (including z-scoring) can plausibly lead to representational confusion. Further, I expose potential interactions between the effects of data demeaning and how the brain happens to encode information. Finally, I emphasize the importance in the context of similarity analyses of at least occasionally explicitly considering the direction of pattern vectors in multivariate space, rather than focusing exclusively on the relative location of their endpoints. Overall, I expect this article will promote awareness of the impact of data demeaning on inferences regarding representational structure and neural coding.
Distinct prophase arrest mechanisms in human male meiosis
Authors: Jan Sabrina Z. , Jongejan Aldo , Korver Cindy M. , van Daalen Saskia K. M. , van Pelt Ans M. M. , Repping Sjoerd , Hamer Geert
Published: September 2017

To prevent chromosomal aberrations to be transmitted to the offspring, strict meiotic checkpoints are in place to remove aberrant spermatocytes. However, in about 1% of all males these checkpoints cause complete meiotic arrest leading to azoospermia and subsequent infertility. We here unravel two clearly distinct meiotic arrest mechanisms that act during the prophase of human male meiosis. Type I arrested spermatocytes display severe asynapsis of the homologous chromosomes, disturbed XY-body formation and increased expression of the Y-chromosome encoded gene ZFY and seem to activate a DNA damage pathway leading to induction of p63 mediated spermatocyte elimination. Type II arrested spermatocytes display normal chromosome synapsis, normal XY-body morphology and meiotic crossover formation but have a lowered expression of several cell cycle regulating genes and fail to properly silence the X-chromosome encoded gene ZFX. Discovery and understanding of these meiotic arrest mechanisms increases our knowledge on how genomic stability is guarded during human germ cell development.
Universal Panel Testing of Pancreatic Cancer Cases for Cancer Predisposition
Authors: Young Erin L. , Thompson Bryony A. , Neklason Deborah W. , Snow Angela K. , Firpo Matthew A. , Werner Theresa , Bell Russell , Sutherland Nykole R. , Smith Ken R. , Berger Justin , Fraser Alison , Gammon Amanda , Koptiuch Cathryn , Kohlmann Wendy K , Neumayer Leigh , Goldgar David E. , Mulvihill Sean J. , Cannon-Albright Lisa A. , Tavtigian Sean V.
Published: September 2017

Background and Aims

Genes associated with hereditary breast and ovarian cancer (HBOC) and colorectal cancer (CRC) susceptibility have been shown to play a role in pancreatic cancer susceptibility. Germline genetic testing of pancreatic cancer cases could be beneficial for at-risk relatives with pathogenic variants in established HBOC and CRC genes, but it is unclear what proportion of pancreatic cancer cases harbor pathogenic variants in these genes.

Methods

66 pancreatic cancer cases, unselected for family history and diagnosed at the Huntsman Cancer Hospital (HCH), were sequenced on a custom 34-gene panel including known HBOC and CRC genes. A second set of 156 unselected HCH pancreatic cancer cases were sequenced on an expanded 59-gene panel (n=95) or with a custom 14-gene clinical panel (n=61). Sequencing data from both sets of pancreatic cancer cases, the pancreatic cancer cases of the Cancer Genome Atlas (TCGA), and an unselected pancreatic cancer screen from the Mayo Clinic were combined in a meta-analysis to estimate the proportion of carriers with pathogenic and variants of uncertain significance.

Results

Approximately 8.9% of unselected pancreatic cancer cases at the HCH carried a variant with potential HBOC or CRC screening recommendations. A meta-analysis of unselected pancreatic cancer cases revealed that approximately 10.5% carry a pathogenic variant or HiP-VUS.

Conclusion

With the inclusion of both HBOC and CRC susceptibility genes in a panel test, unselected pancreatic cancer cases have a high enough percentage of carriers to rationalize genetic testing for identification of variants that could be further used in cascade testing of healthy relatives to increase HBOC and CRC surveillance measures.
Improved Score Statistics for Meta-analysis in Single-variant and Gene-level Association Studies
Authors: Yang Jingjing , Chen Sai , Abecasis Gonçalo ,   IAMDGC
Published: September 2017

Meta-analysis is now an essential tool for genetic association studies, allowing these to combine large studies and greatly accelerating the pace of genetic discovery. Although the standard meta-analysis methods perform equivalently as the more cumbersome joint analysis under ideal settings, they result in substantial power loss under unbalanced settings with various case-control ratios. Here, we investigate why the standard meta-analysis methods lose power under unbalanced settings, and further propose a novel meta-analysis method that performs as efficiently as joint analysis under general settings. Our proposed method can accurately approximate the score statistics obtainable by joint analysis, for both linear and logistic regression models, with and without covariates. In addition, we propose a novel approach to adjust for population stratification by correcting for known population structures through minor allele frequencies (MAFs). In the simulated gene-level association studies under unbalanced settings, our method recovered up to 85% power loss caused by the standard method. We further showed the power gain of our method in gene-level association studies with 26 unbalanced real studies of Age-related Macular Degeneration (AMD). In addition, we took the meta-analysis of three studies of type 2 diabetes (T2D) as an example to discuss the challenges of meta-analyzing multi-ethnic samples. In summary, we propose improved single-variant score statistics in meta-analysis, requiring “accurate” population-specific MAFs for multi-ethnic studies. These improved score statistics can be used to construct both single-variant and gene-level association studies, providing a useful framework for ensuring well-powered, convenient, cross-study analyses.
Thalamocortical and Intracortical Laminar Connectivity Determines Sleep Spindle Properties
Authors: Krishnan Giri P , Rosen Burke Q , Chen Jen-Yung , Muller Lyle , Sejnowski Terrence J , Cash Sydney S , Halgren Eric , Bazhenov Maxim
Published: September 2017

Spindle oscillations are brief oscillatory activity during non-rapid eye movement (NREM) sleep. Spindle density and synchronization properties are different in MEG versus EEG recordings in humans and also vary with learning performance, suggesting spindle involvement in memory consolidation. Using computational models, we identified network mechanisms that may explain differences in spindle properties across cortical structures. First, we report that differences in spindle occurrence between MEG and EEG data may arise from the properties of the core vs. matrix thalamocortical systems. The matrix system, projecting superficially, has wider thalamocortical fanout compared to the core system, projecting to the middle layers, and requires the recruitment of a larger population of neurons to initiate a spindle. Our model demonstrates that this property is sufficient to explain lower spindle density and higher spatial synchrony of spindles in the superficial cortical layers, as observed in the EEG signal. In contrast, spindles in the core system occurred more frequently but less synchronously, as observed in the MEG recordings. Futhermore, consistent with human recordings, in the model, spindles occurred independently in the core system but matrix system spindles commonly co-occurred with core one. We found that the intracortical excitatory connections from layer III/IV to layer V promote spindle propagation from the core to the matrix system, leading to widespread spindle activity. Our study predicts that plasticity of the intra and inter cortical connectivity can potentially be a mechanism for increasing in spindle density as observed during learning.

Author summary

The density of sleep spindles has been shown to correlate with memory consolidation. Further, sleep spindles occur more often in human MEG than EEG. We developed thalamocortical network model that is capable of spontaneous generation of spindles across cortical layers and that captures the essential statistical features of spindles observed in experiments. We predict that differences in thalamo-cortical connectivity, known from anatomical studies, lead to the differences in the spindle properties between EEG and MEG as observed in human recordings. Further, we predict that the intracortical connectivity between cortical layers, a property influenced by sleep preceding learning, increases spindle density. Results from our study highlight the role of cortical and thalamic projections on the occurrence and properties of spindles.
Ecosystem functional response across precipitation extremes in a sagebrush steppe
Authors: Tredennick Andrew T. , Kleinhesselink Andrew R. , Taylor J. Bret , Adler Peter B.
Published: September 2017

Background

Precipitation is predicted to become more variable in the western United States, meaning years of above and below average precipitation will become more common. Periods of extreme precipitation are major drivers of interannual variability in ecosystem functioning in water limited communities, but how ecosystems respond to these extremes over the long-term may shift with precipitation means and variances. Long-term changes in ecosystem functional response could reflect compensatory changes in species composition or species reaching physiological thresholds at extreme precipitation levels.

Methods

We conducted a five year precipitation manipulation experiment in a sagebrush steppe ecosystem in Idaho, United States. We used drought and irrigation treatments (approximately 50% decrease/increase) to investigate whether ecosystem functional response remains consistent under sustained high or low precipitation. We recorded data on aboveground net primary productivity (ANPP), species abundance, and soil moisture. We fit a generalized linear mixed effects model to determine if the relationship between ANPP and soil moisture differed among treatments. We used nonmetric multidimensional scaling to quantify community composition over the five years.

Results

Ecosystem functional response, defined as the relationship between soil moisture and ANPP, was similar among irrigation and control treatments, but the drought treatment had a greater slope than the control treatment. However, all estimates for the effect of soil moisture on ANPP overlapped zero, indicating the relationship is weak and uncertain regardless of treatment. There was also large spatial variation in ANPP within-years, which contributes to the uncertainty of the soil moisture effect. Plant community composition was remarkably stable over the course of the experiment and did not differ among treatments.

Discussion

Despite some evidence that ecosystem functional response became more sensitive under sustained drought conditions, the response of ANPP to soil moisture was consistently weak and community composition was stable. The similarity of ecosystem functional responses across treatments was not related to compensatory shifts at the plant community level, but instead may reflect the insensitivity of the dominant species to soil moisture. These species may be successful precisely because they have evolved life history strategies which buffer them against precipitation variability.
Cell size-dependent regulation of Wee1 localization by Cdr2 cortical nodes
Authors: Allard Corey A. H. , Opalko Hannah E. , Liu Ko-Wei , Medoh Uche , Moseley James B.
Published: September 2017

Cell size control requires mechanisms that link cell growth with Cdk1 activity. In fission yeast, the protein kinase Cdr2 forms cortical nodes that include the Cdk1 inhibitor Wee1, along with the Wee1-inhibitory kinase Cdr1. We investigated how nodes inhibit Wee1 during cell growth. Biochemical fractionation revealed that Cdr2 nodes were megadalton structures enriched for activated Cdr2, which increases in level during interphase growth. In live-cell TIRF movies, Cdr2 and Cdr1 remained constant at nodes over time, but Wee1 localized to nodes in short bursts. Recruitment of Wee1 to nodes required Cdr2 kinase activity and the noncatalytic N-terminus of Wee1. Bursts of Wee1 localization to nodes increased 20-fold as cells doubled in size throughout G2. Size-dependent signaling was due in part to the Cdr2 inhibitor Pom1, which suppressed Wee1 node bursts in small cells. Thus, increasing Cdr2 activity during cell growth promotes Wee1 localization to nodes, where inhibitory phosphorylation of Wee1 by Cdr1 and Cdr2 kinases promotes mitotic entry.

Cells turn off the mitotic inhibitor Wee1 to enter into mitosis. This study shows how cell growth progressively inhibits fission yeast Wee1 through dynamic bursts of localization to cortical node structures that contain Wee1 inhibitory kinases.
Genomewide significant regions in 43 Utah high-risk families implicate multiple genes involved in risk for completed suicide
Authors: Coon Hilary , Darlington Todd M. , DiBlasi Emily , Callor W. Brandon , Ferris Elliott , Fraser Alison , Yu Zhe , William Nancy , Das Sujan C. , Crowell Sheila E. , Chen Danli , Anderson John S. , Klein Michael , Jerominski Leslie , Cannon Dale , Shabalin Andrey , Docherty Anna , Williams Megan , Smith Ken R. , Keeshin Brooks , Bakian Amanda V. , Christensen Erik , Li Qingqin S. , Camp Nicola J. , Gray Douglas
Published: September 2017

Suicide is the 10th leading cause of death in the US. While environment has undeniable impact, evidence suggests genetic factors play a significant role in completed suicide. We linked a resource of >4,500 DNA samples from completed suicides obtained from the Utah Medical Examiner to genealogical records and medical records data available on over 8 million individuals. This linking has resulted in the identification of high-risk extended families (7-9 generations) with significant familial risk of completed suicide. Familial aggregation across distant relatives minimizes effects of shared environment, provides more genetically homogeneous risk groups, and magnifies genetic risks through familial repetition. We analyzed Illumina PsychArray genotypes from suicide cases in 43 high-risk families, identifying 30 distinct shared genomic segments with genome-wide evidence (p=2.02E-07 to 1.30E-18) of segregation with completed suicide. The 207 genes implicated by the shared regions provide a focused set of genes for further study; 18 have been previously associated with suicide risk. While PsychArray variants do not represent exhaustive variation within the 207 genes, we investigated these for specific segregation within the high-risk families, and for association of variants with predicted functional impact in ~1300 additional Utah suicides unrelated to the discovery families. None of the limited PsychArray variants explained the high-risk family segregation; sequencing of these regions will be needed to discover segregating risk variants, which may be rarer or regulatory. However, additional association tests yielded four significant PsychArray variants (SP110, rs181058279;AGBL2, rs76215382;SUCLA2, rs121908538;APH1B, rs745918508), raising the likelihood that these genes confer risk of completed suicide.
The Fractional Coalescent
Authors: Mashayekhi Somayeh , Beerli Peter
Published: September 2017

A new approach to the coalescent, thefractionalcoalescent (f-coalescent), is introduced. Two derivations are presented: first, thef-coalescent is based on an extension of the discrete-time Wright-Fisher model. In this extension, for the population of sizeN, the probability that two randomly selected individuals have the same parent in the previous generation depends on the variable α. Second, thef-coalescent is based on an extension of the discrete-time Canning population model that the variance of the number of offspring is assumed as a random variable which depends on the variable α. In the second derivation, thef-coalescent emerges also as a continuous-time semi-Markov process. The additional parameterαaffects the variability in the patterns of the waiting times; values ofα< 1 lead to an increase of short time intervals, but allows occasionally for very long time intervals. Whenα= 1, thef-coalescent and Kingman’sn-coalescent are equivalent. The mode of the distribution of the time of the most recent common ancestor in thef-coalescent is lower thann-coalescent when the number of sample size increases, and the time which modes happen on that is smaller compare ton-coalescent. Also, this distribution showed that thef-coalescent leads to distributions with heavier tails than then-coalescent. Also, the probability thatngenes descend frommancestral genes forf-coalescent is derived. Thef-coalescent has been implemented in the population genetic model inference software MIGRATE. Simulation studies suggest that it is possible to infer the correctαvalues from data that was generated with knownαvalues. When data is simulated using models withα< 1 or for three example datasets (H1N1 influenza, Malaria parasites, Humpback whales), Bayes factor comparisons show an improved model fit of thef-coalescent over then-coalescent.
In vivostructures of theHelicobacter pylori cagtype IV secretion system
Authors: Chang Yi-Wei , Shaffer Carrie L. , Rettberg Lee A. , Ghosal Debnath , Jensen Grant J.
Published: September 2017

The bacterial type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Using electron cryotomography, here we reveal the molecular architecture of the cancer-associatedHelicobacter pylori cagT4SS. Although most components are unique toH. pylori, thecagT4SS exhibits remarkable architectural similarity to previously studied T4SSs. WhenH. pyloriencounters host cells, however, the bacterium elaborates rigid, membranous tubes perforated by lateral ports. Dense, pilus-like rod structures extending from the inner membrane were also observed. We propose that the membrane tubes assemble out of the T4SS and are the delivery system forcagT4SS cargo. These studies reveal the architecture of a dynamic molecular machine that evolved to function in the human gastric niche.
How genetic disease risks can be misestimated across global populations
Authors: Kim Michelle S , Patel Kane P , Teng Andrew K , Berens Ali J , Lachance Joseph
Published: September 2017

Background

Accurate assessment of health disparities requires unbiased knowledge of genetic risks in different populations. Unfortunately, most genome-wide association studies use genotyping arrays and European samples. Here, we integrate whole genome sequence data from global populations, results from thousands of GWAS, and extensive computer simulations to identify how genetic disease risks can be misestimated.

Results

In contrast to null expectations, we find that risk allele frequencies at known disease loci are significantly different for African populations compared to other continents. Strikingly, ancestral risk alleles are found at 9.51% higher frequency in Africa and derived risk alleles are found at 5.40% lower frequency in Africa. By simulating GWAS with different study populations, we find that non-African cohorts yield disease associations that have biased allele frequencies and that African cohorts yield disease associations that are relatively free of bias. We also find empirical evidence that genotyping arrays and SNP ascertainment bias contribute to continental differences in risk allele frequencies. Because of these causes, polygenic risk scores can be grossly misestimated for individuals of African descent. Importantly, continental differences in risk allele frequencies are only moderately reduced if GWAS use whole genome sequences and hundreds of thousands of cases and controls. Finally, comparisons between uncorrected and corrected genetic risk scores reveal the benefits of considering whether risk alleles are ancestral or derived.

Conclusions

Our results imply that caution must be taken when extrapolating GWAS results from one population to predict disease risks in another population.
N,N′,N′′versus N,N′,Oimine-containing coordination motifs: ligand-directed synthesis of mononuclear and binuclear CuIIcompounds
Authors: Ferraz de Paiva Raphael Enoque , Nakahata Douglas Hideki , Carvalho Marcos Alberto de , Rodrigues Goulart Bergamini Fernando , Corbi Pedro Paulo
Published: September 2017

It is demonstrated here that tridentate imine ligands can control the nuclearity of copper(II) complexes based on the donor atoms present in the ligand. TheN,N′,N′′-donating imine ligand led to a mononuclear compound, namely dichlorido[N,N-dimethyl-N′-(pyridin-2-ylmethylidene)ethane-1,2-diamine]copper(II) monohydrate, [CuCl2(C10H15N3)]·H2O,1, while theN,N′,O-donating imine ligand produced a binuclear metal complex, namely μ2-chlorido-dichlorido(μ2-2-{[2-(dimethylamino)ethyl]iminomethyl}phenolato)(N,N-dimethylethylenediamine)dicopper(II) 0.11-hydrate, [Cu2(C11H15N2O)Cl3(C4H12N2)]·0.11H2O,2. The structure of2is a remarkable example of a binuclear copper(II) complex containing a single substituted 2-iminomethylphenolate ligand that has two copper(II) sites in square-pyramidal coordination.
2,3-Diruthenocenylcyclopropenone
Authors: Sánchez García Jessica J. , Flores-Alamo Marcos , Klimova Elena I.
Published: September 2017

In the title compound, [Ru2(C5H5)2(C13H8O)], the Ru—C bond lengths in the two ruthenocenyl moieties are in the range of 2.155 (4)–2.196 (3) Å. Both cyclopentadienyl (Cp) rings are planar and parallel with staggered (18.6 °) and eclipsed (3.1°) conformations between the mutual orientations of rings in the independent sandwiches of each ruthenocenyl molecule. In the crystal, there are intermolecular C—H...O hydrogen bonds between Cp carbon donor atoms and the cyclopropenone O atom of adjacent molecules, formingR22(14) andR66(38) motifs along thebandcaxes.
Dynamics of Algeria’s international reserves
Authors: Kashif Mohammad , Thiyagarajan S. , Sridharan P.
Published: September 2017

Purpose

The purpose of this paper is to explore the determinants of international reserves in Algeria using economic growth and real effective exchange rate variables. The paper used quarterly data from 1985Q1 to 2014Q4.

Design/methodology/approach

The study employs autoregressive distributed lag (ARDL) approach known as the bounds testing method. The ARDL technique works well for small sample studies also. The current study assesses the influence of economic growth and real effective exchange rates on international reserves in Algeria by evaluating both short-run and long-run dynamics.

Findings

The study establishes a long-run relationship between international reserves, economic growth and real effective exchange rate. It also reveals that economic growth has a positive impact on international reserves while real effective exchange rate shows a negative effect.

Originality/value

This paper tries to provide a complete picture of the determinants of international reserves in Algeria. Foreign trade policy makers of Algeria can use the model estimated here to draw pertinent policies regarding international reserves.
How sustainable is disaster resilience?
Authors: Ismail Farrah Zuhaira , Halog Anthony , Smith Carl
Published: September 2017

Purpose

The intervention of many different organizations during the post-disaster housing reconstructions could also influence the sustainability of the overall socio-ecology of the affected areas. Different approaches in design, selection of building materials and construction technologies deployed in pursuit of disaster resiliency may cause undesirable adverse circumstances to the surroundings, which escalate its susceptibility to future calamities. Therefore, this paper aims to identify relevant key indicators which interpret construction sustainability in a post-disaster housing reconstruction context, and to further investigate the dynamic interactions of these indicators on the socio-ecological system to achieve holistic sustainable post-disaster housing reconstructions.

Design/methodology/approach

Methodology was divided into three main stages. The first stage involved content analysis of related research materials, whereas the second stage was allocated for empirical data collection from case study and interview sessions. Data obtained from the first and second stage were then used to develop a causal loop diagram in the third stage to identify dynamic interrelationships between the indicators and the variables within a post-disaster reconstruction system.

Findings

From our results, the nexus of sustainability and disaster resilience is apparent and it is imperative to comprehend their dynamic interactions. The impacts of post-disaster reconstructions on the socio-ecological system are significant. Therefore, the adaptation of integrated sustainable construction approach in the housing reconstruction practice through system thinking will foster a holistic approach in the decision-making process and could reduce environmental damage. This also strengthens the interrelated socio-ecological systems, thus reinforcing disaster resilience in the built environment.

Originality/value

This research looks into the adaptation of integrated sustainable construction approach in the housing reconstruction practice through systems thinking approach. This will foster a holistic approach in the decision-making process and could reduce environmental damage. This also strengthens the interrelated socio-ecological systems, thus reinforcing disaster resilience in the built environment. This paper also looks into identifying relevant key indicators that interpret construction sustainability, which incorporate environmental, social and economic factors pertaining to the context of post-disaster housing reconstruction in Kuala Krai, Kelantan. The dynamic interrelationships and causal impacts between the indicators with other variables within the system were also established.
Strengthening local institutions as avenues for climate change resilience
Authors: Oloo Josephat Okuku , Omondi Paul
Published: September 2017

Purpose

In Africa, poverty and food insecurity is pervasive due to intertwined factors including, declining crop yields, land degradation and inadequate policy and institutional support. With ever-increasing populations, climate change effects will be intensified, and a major crisis is inevitable unless measures to sustain land resources are urgently taken. This paper aims to argue that vibrant rural institutions are necessary to ensure food security and environmental protection, consequently contributing to climate change resilience.

Design/methodology/approach

The paper demonstrates the role of institutions by evaluating two types of institutions and their impacts the “status quo” and “hybrid” institutions using case studies from the African Highlands Initiative in Uganda and International Forestry Resources and Institutions in Kenya. It further discusses a model that highlights factors affecting smallholder investment in natural resources management and how these can be used to strengthen local institutions in building their resilience against climate change effects.

Findings

Weak grassroots institutions characterized by low capacity, failure to exploit collective capital and poor knowledge sharing and access to information, are common barriers to sustainable land management and improved food security.

Research limitations/implications

Case studies from Uganda and IFRI in Kenya barriers in data collection instruments and language.

Practical implications

In Africa, poverty and food insecurity is pervasive due to intertwined factors including, declining crop yields, land degradation and inadequate policy and institutional support. With ever increasing populations, climate change effects will be intensified, and a major crisis is inevitable unless measures to sustain land resources are urgently taken.

Social implications

In Africa, poverty and food insecurity is pervasive due to intertwined factors including, declining crop yields, land degradation and inadequate policy and institutional support. With ever-increasing populations, climate change effects will be intensified, and a major crisis is inevitable unless measures to sustain land resources are urgently taken.

Originality/value

The paper further discusses a model that highlights factors affecting smallholder investment in natural resources management and how these can be used to strengthen local institutions in building their resilience against climate change effects.
Organizational design change in multinational supply chain organizations
Authors: Roh Joseph , Turkulainen Virpi , Whipple Judith M. , Swink Morgan
Published: September 2017

Purpose

Managing internal supply chains is becoming increasingly complex, requiring managers to balance diverse needs. As a result, managers continuously face the need to change how they organize their internal supply chains. The purpose of this paper is to examine this phenomenon by addressing why multinational supply chain management organizations (SCMOs) change their designs, as well as how managers respond to pertinent change phenomena using complementary theoretical perspectives.

Design/methodology/approach

Qualitative data, collected from 50 executives within 24 multinational manufacturers, is used to develop an understanding of the organizational design change phenomena. A theory elaboration approach is taken to illustrate how various theoretical perspectives explain organizational design change.

Findings

This study identifies and elaborates organizational design change phenomena in the context of multinational SCMOs, including internal and external drivers of design change. Managers also discussed key supply chain management capabilities that were developed in order to meet perceived changes in business needs.

Research limitations/implications

This study contributes to academic understanding of organizational design issues affecting SCMOs. Four theoretical perspectives are elaborated upon to illustrate their applicability for examining SCMO organizational design issues.

Practical implications

This study provides managerial application of several organizational design change theories by elaborating principles for framing, interpreting, and implementing design change initiatives in internal SCMOs.

Originality/value

This is one of the first studies to investigate organizational design change in multinational SCMOs. This research highlights the complexity and evolving nature of SCMO organizational design decisions by describing the adaption, integration, and reconfiguration of firm resources and competencies in changing environments.
Does coffee production reduce poverty? Evidence from Uganda
Authors: Mbowa Swaibu , Odokonyero Tonny , Muhumuza Tony , Munyambonera Ezra
Published: September 2017

Purpose

The purpose of this paper is to examine the effect of coffee production on poverty among smallholder farmers.

Design/methodology/approach

National Household Survey data for Uganda were triangulated with qualitative field data. A mix of propensity score matching (PSM) and quantile treatment effect techniques was employed.

Findings

The results reveal a significant effect of coffee production on poverty reduction, through incremental household consumption expenditure. Households engaged in coffee production are associated with a lower incidence of poverty. The interesting evidence suggests that coffee production is a pro-poor intervention. These findings are confirmed by qualitative assessment that reveals farmers’ welfare improved to greater extent to satisfactory levels from coffee income.

Research limitations/implications

Econometrically robust strategies were employed to ensure minimal estimation bias; however, the authors are mindful of PSM limitation of selection on observables.

Originality/value

This paper is part of a limited body of literature that combines quantitative and qualitative assessment, a growing issue in contemporary research. In addition to employing one of the conventional impact evaluation techniques, the paper accounts for heterogeneity in the effects of coffee production.
Do demographics predict shoppers’ choice of retail outlet for roots and tubers in Trinidad and Tobago?
Authors: Iton Ardon C.W.
Published: September 2017

Purpose

The purpose of this paper is to identify the demographic characteristics that influence the choice of retail outlet and the preferred retail outlet used by primary household shoppers when purchasing roots and tubers (R&Ts).

Design/methodology/approach

The study uses a binary logit model to estimate the probability of being a traditional or modern outlet shopper for R&Ts.

Findings

The traditional retail outlet was the preferred place to purchase R&Ts. Three demographic variables, age, monthly family income and ethnicity, were statistically significant.

Research limitations/implications

The sample size might be considered small with only 232 primary household food shoppers participating.

Originality/value

To date, minimal research on the marketing of R&Ts has been undertaken in Trinidad and Tobago. As such, it is hoped that this study will stimulate others to undertake research in this area.
Information grounds as a vehicle for social inclusion of domestic migrant workers in Israel
Authors: Bronstein Jenny
Published: September 2017

Purpose

Economic adversity, geopolitical, and climate crises leading to the lack of decent and sustainable work are resulting in growing and diverse migratory movements. The precarious situation of many migrant workers in their countries of employment results in a state of social exclusion due to a lack of access to relevant information sources. The purpose of this paper is to further the understanding of the information behavior of migrants by examining the role that La Escuelita, a Hebrew night school for domestic migrant workers in Israel, plays as an information ground helping migrants struggling with social exclusion.

Design/methodology/approach

A qualitative methodology was used and data were collected using participation observation over a three-months period. Eight students at the school were interviewed using in-depth interviews.

Findings

La Escuelita served as a vehicle for social inclusion by providing valuable everyday information to the students in a caring environment. Information was shared in multiple directions between both the staff and the students and between the students. Language barriers were revealed as one of the main factors for social exclusion. Findings revealed that although the migrant workers who study at La Escuelita are information poor regarding their struggle for social inclusion into Israeli society, they wish to learn Hebrew as a way to overcome this exclusion.

Originality/value

Understanding the information behavior of marginalized populations is the first step into designing and implementing information services to help them toward social inclusion. This research presents an innovative contribution by examining the significance and roles of social connections in the setting of a unique information environment.
Information behaviors of elite scholars in the context of academic practice
Authors: Falciani-White Nancy
Published: September 2017

Purpose

The purpose of this paper is to describe the information behaviors in which scholars regularly engage, in participants’ own words wherever possible, and discuss how those behaviors function in the broader landscape of scholars’ academic practice.

Design/methodology/approach

Scholars’ information behaviors were investigated using semi-structured interviews, along with document analysis. Three scholars recognized for significant contributions to their fields were identified from each of the three major divisions of academia (humanities, natural sciences, and social sciences) using intensity sampling, for a total of nine participants. Interviews asked each participant to describe a recent research project from conceptualization to completion, focusing on how scholars engaged with ideas, information resources, tools, and processes.

Findings

Information behaviors were found to permeate scholars’ work from conceptualization through publication, and included behaviors such as skimming, reading, data collection and analysis, and writing. Of particular interest are the specific information behaviors that fall into the broader category of information use.

Originality/value

This study uses established definitions of information behaviors to broaden the information behaviors conversation to include the entirety of academic practice. The study shows how scholars from across the academy engage with information throughout the course of their academic work, not just when they are engaged in more traditional information seeking activities.