bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbiomes in Ground Water and Alternative Irrigation Water, and Spinach Microbiomes Impacted by Irrigation with Different Types of Water
Authors: Gu Ganyu , Yin Hsin-Bai , Ottesen Andrea , Bolten Samantha , Patel Jitendra , Rideout Steve , Nou Xiangwu
Published: April 2019

Irrigation water, particularly if applied overhead, could be an important source of bacterial contamination to fresh produce. The colonization, survival, and proliferation of exogenous bacterial pathogens can be strongly influenced by the produce microbiota. In this study, spinach grown in an organic field was irrigated with ground water and potential alternative irrigation water including reclaimed wastewater, and urban runoff water, over a period of 2 weeks. Water and spinach samples were collected before and after irrigation for bacterial plate count, qPCR, and community profiling using 16S rDNA high-throughput sequencing analyses. The average bacterial population densities on spinach (6.50 ± 0.04 log CFU/g, 7.40 ± 0.10 log 16S copies/g) were significantly higher than those in irrigation water (3.61 ± 0.12 log CFU/ml, 4.94 ± 0.13 log 16S copies/ml). The composition and relative abundance of spinach microbiomes varied with different types of irrigation waters; however, the most abundant microbial taxa on spinach were not significantly affected by the irrigation with different types of water. Shigella, Salmonella, Listeria, Campylobacter spp., and pathogenic Escherichia coli were not detected in this study. This study provides information on the microbial ecology of diverse bacterial communities on spinach surface after irrigation by different types of water, which can benefit future studies on the interaction of microbes on produce, and the prevention of foodborne pathogens and plant disease.
Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex
Authors: Grossen Christine , Guillaume Frederic , Keller Lukas F. , Croll Daniel
Published: April 2019

Human activity caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. Here, we take advantage of the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex. The species survived one of the most dramatic bottlenecks known for successfully restored species. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By retracing the recolonization of the Alps by Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This demonstrates how human-induced severe bottlenecks caused both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings also highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Hence, conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species.
Inhibition of Lipin lipid phosphatase hyperactivity rescues TorsinA neurological disease
Authors: Cascalho Ana , Foroozandeh Joyce , Hennebel Lise , Klein Christine , Rous Stef , Gonzalez Beatriz Dominguez , Pisani Antonio , Meringolo Maria , Gallego Sandra F. , Verstreken Patrik , Seibler Philip , Goodchild Rose E.
Published: April 2019

TOR1A/TorsinA mutations cause poorly explained neurological diseases. A dominantly inherited mutation causes isolated dystonia, while biallelic mutations cause a recessive infant-onset syndrome with cases of lethality. Here we report an unexpected connection between lipid metabolism and these diseases. Lipin phosphatidic acid phosphatase activity was abnormally regulated in TorsinA dystonia patient cells, and in the brains of three different TorsinA disease model mice. Lipin activity was causative to symptoms given that loweringLipin1 in vivostrongly intervened against lethality in disease mice. Furthermore, Lipin hyperactivity caused cell deathin vitro, andLipin1deficiency suppressed neurodegenerationin vivo. In addition, it protected the striatal cholinergic interneurons that are implicated in TorsinA movement disorders, and concomitantly suppressed abnormal motor behaviors of TorsinA mice. These data establish the central role of Lipin lipid enzyme hyperactivity in TorsinA disease and show that Lipin inhibition is a therapeutic target for these incurable conditions.

One Sentence Summary

Lipin inhibition rescues TorsinA neurological disease
Effect of heritable symbionts on maternally-derived embryo transcripts
Authors: Mateos Mariana , Silva Nadisha O. , Ramirez Paulino , Higareda-Alvear Victor M. , Aramayo Rodolfo , Erickson James W.
Published: April 2019

Maternally-transmitted endosymbiotic bacteria are ubiquitous in insects. Among other influential phenotypes, many heritable symbionts of arthropods are notorious for manipulating host reproduction through one of four reproductive syndromes, which are generally exerted during early developmental stages of the host: male feminization; parthenogenesis induction; male killing; and cytoplasmic incompatibility (CI). Major advances have been achieved in understanding mechanisms and identifying symbiont factors involved in reproductive manipulation, particularly male killing and cytoplasmic incompatibility. Nonetheless, whether cytoplasmically-transmitted bacteria influence the maternally-loaded components of the egg or early embryo has not been examined. In the present study, we investigated whether heritable endosymbionts that cause different reproductive phenotypes in Drosophila melanogaster influence the mRNA transcriptome of early embryos. We used mRNA-seq to evaluate differential expression in Drosophila embryos lacking endosymbionts (control) to those harbouring the male-killing Spiroplasma poulsonii strain MSRO-Br, the CI-inducing Wolbachia strain wMel, or Spiroplasma poulsonii strain Hyd1; a strain that lacks a reproductive phenotype and is naturally associated with Drosophila hydei. We found no consistent evidence of influence of symbiont on mRNA composition of early embryos, suggesting that the reproductive manipulation mechanism does not involve alteration of maternally-loaded transcripts. In addition, we capitalized on several available mRNA-seq datasets derived from Spiroplasma-infected Drosophila melanogaster embryos, to search for signals of depurination of rRNA, consistent with the activity of Ribosome Inactivating Proteins (RIPs) encoded by Spiroplasma poulsonii. We found small but statistically significant signals of depurination of Drosophila rRNA in the Spiroplasma treatments (both strains), but not in the symbiont-free control or Wolbachia treatment, consistent with the action of RIPs. The depurination signal was slightly stronger in the treatment with the male-killing strain. This result supports a recent report that RIP-induced damage contributes to male embryo death.
Cyclin B3 is dispensable for mouse spermatogenesis
Authors: Karasu Mehmet E. , Keeney Scott
Published: April 2019

Cyclins, as regulatory partners of cyclin-dependent kinases (CDKs), control the switch-like cell cycle transitions that orchestrate orderly duplication and segregation of genomes. Compared to mitosis, relatively little is known about how cyclin-CDK complexes control meiosis, the specialized cell division that generates gametes for sexual production. Mouse cyclin B3 was previously shown to have expression restricted to the beginning of meiosis, making it a candidate to regulate meiotic events. Indeed, female mice lacking cyclin B3 are sterile because oocytes arrest at the metaphase-to-anaphase transition of meiosis I. However, whether cyclin B3 functions during spermatogenesis was untested. Here, we found that males lacking cyclin B3 are fertile and show no detectable defects in spermatogenesis based on histological analysis of seminiferous tubules. Cytological analysis further showed no detectable defects in homologous chromosome synapsis or meiotic progression, and suggested that recombination is initiated and completed efficiently. Moreover, absence of cyclin B3 did not exacerbate previously described meiotic defects in mutants deficient for cyclin E2, suggesting a lack of redundancy between these cyclins. Thus, unlike in females, cyclin B3 is not essential for meiosis in males despite its prominent meiosis-specific expression.
A single K+-binding site in the crystal structure of the gastric proton pump
Authors: Yamamoto Kenta , Dubey Vikas , Irie Katsumasa , Nakanishi Hanayo , Khandelia Himanshu , Fujiyoshi Yoshinori , Abe Kazuhiro
Published: April 2019

The gastric proton pump (H+,K+-ATPase), a P-type ATPase responsible for gastric acidification, mediates electro-neutral exchange of H+and K+coupled with ATP hydrolysis, but with an as yet undetermined transport stoichiometry. Here we show crystal structures at a resolution of 2.5 Å of the pump in the E2-P transition state, in which the counter-transporting cation is occluded. We found a single K+bound to the cation-binding site of H+,K+-ATPase, indicating an exchange of 1H+/1K+per hydrolysis of one ATP molecule. This fulfils the energy requirement for the generation of a six pH unit gradient across the membrane. The structural basis of K+recognition is resolved, supported by molecular dynamics simulations, and this establishes how H+,K+-ATPase overcomes the energetic challenge to generate an H+gradient of more than a million-fold – the highest cation gradient known in any mammalian tissue – across the membrane.
Pro-Resolving Mediator Profiles And 5-Lipoxygenase Activity In Cerebrospinal Fluid Correlate with Disease Severity and Outcome in Adults with Tuberculous Meningitis
Authors: Colas Romain A. , Nhat Le Thanh Hoang , Thuong Nguyen Thuy Thuong , Cifuentes Esteban Alberto Gomez , Ly Lucy , Thanh Hai Hoang , Phu Nguyen Hoan , Mai Nguyen Thi Hoang , Thwaites Guy E. , Dalli Jesmond
Published: April 2019

Tuberculous meningitis (TBM) is the most lethal form of tuberculosis infection, characterized by a dysregulated immune response that frequently leads to neurological injury and death despite the best available treatment. The mechanisms driving the inflammatory response in TBM are not well understood. To gain insights into these mechanisms we used a lipid mediator profiling approach to investigate the regulation of a novel group of host protective mediators, termed specialized pro-resolving mediators (SPM), in the cerebrospinal fluid (CSF) of adults with TBM enrolled into a randomised placebo-controlled trial of adjunctive aspirin treatment. We found distinct lipid mediator profiles with increasing disease severity, changes that were linked with an upregulation of inflammatory eicosanoids in patients with severe TBM and a decrease in the production of a number of 5-lipoxygenase (ALOX5)-derived SPM. CSF pro-resolving mediator concentrations were also associated with 80-day survival. In survivors, we found a significant increase in pro-resolving mediator concentrations, including the ALOX5-derived resolvin (Rv)T2, RvT4 and 15-epi-Lipoxin (LX)B4, compared to those who died. Aspirin administration increased the ratio of pro-resolving to pro-inflammatory mediators decreasing the concentrations of the prothrombic mediator TxA2, changes that were linked with early reductions in brain infarcts and deaths. Together, these findings identify a CSF SPM signature that is associated with disease severity and 80-day mortality in TBM. Furthermore, the therapeutic manipulation of the ratio between pro-resolving mediators and pro-inflammatory/thrombogenic mediators in the CSF, by aspirin for example, offers a novel treatment strategy to reduce the morbidity and mortality caused by TBM.

Authors Summary

Infections of the brain and the meninges byMycobacterium tuberculosis(M. tb) lead to severe inflammation and are associated with poor outcomes. The mechanisms leading to this disease remain poorly defined. Herein, we investigated howM. tbinfection regulates the concentrations of specialized pro-resolving mediators that are central in controlling the body’s ability to clear infections. In these investigations, we found that disease survival was linked with increased concentrations of a number of these protective molecules including resolvins and lipoxins. Treatment ofM. tb-infected patients with aspirin decreased the production of the immunosuppressive and thrombogenic mediator thromboxane A2improving the balance between protective and inflammatory molecules. Of note, these changes were linked with reduced disease severity and improved survival. Therefore, the present findings suggest a previously unappreciated role for pro-resolving mediators in TBM pathogenesis.
A symbiont phage protein aids in eukaryote immune evasion
Authors: Jahn M.T. , Arkhipova K. , Markert S.M. , Stigloher C. , Lachnit T. , Pita L. , Kupczok A. , Ribes M. , Stengel S.T. , Rosenstiel P. , Dutilh B.E. , Hentschel U.
Published: April 2019

Phages are increasingly recognized as important members of host associated microbial communities. While recent studies have revealed vast genomic diversity in the virosphere, the new frontier is to understand how newly discovered phages may affect higher order processes, such as in the context of host-microbe interactions. Here, we aim to understand the tripartite interplay between phages, bacterial symbionts and marine sponges. In a viromics approach, we discover 491 novel viral clusters and show that sponges, as filter-feeding organisms, are distinct viral niches. By using a nested sampling design, we show that each sponge individual of the four species investigated harbours its own unique virome, regardless of the tissue investigated. We further discover a novel, symbiont phage-encoded ankyrin domain-containing protein which appears to be widely spread in phages of many host-associated contexts including human. The ankyrin protein (ANKp) modulates the eukaryotic immune response against bacteria as confirmed in macrophage infection assays. We predict that the role of ANKp in nature is to facilitate co-existence in the tripartite interplay between phages, symbionts and sponges and possibly in many other host-microbe associations.
Image processing approaches to enhance perivascular space visibility and quantification using MRI
Authors: Sepehrband Farshid , Barisano Giuseppe , Sheikh-Bahaei Nasim , Cabeen Ryan P , Choupan Jeiran , Law Meng , Toga Arthur W.
Published: April 2019

Imaging the perivascular spaces (PVS), also known as Virchow-Robin space, has significant clinical value, but there remains a need for neuroimaging techniques to improve mapping and quantification of the PVS. Current technique for PVS evaluation is a scoring system based on visual reading of visible PVS in regions of interest, and often limited to large caliber PVS. Enhancing the visibility of the PVS could support medical diagnosis and enable novel neuroscientific investigations. Increasing the MRI resolution is one approach to enhance the visibility of PVS but is limited by acquisition time and physical constraints. Alternatively, image processing approaches can be utilized to improve the contrast ratio between PVS and surrounding tissue. Here we combine T1- and T2-weighted images to enhance PVS contrast, intensifying the visibility of PVS. The Enhanced PVS Contrast (EPC) was achieved by combining T1- and T2-weighted images that were adaptively filtered to remove non-structured high-frequency spatial noise. EPC was evaluated on healthy young adults by presenting them to two expert readers and also through automated quantification. We found that EPC improves the conspicuity of the PVS and aid resolving a larger number of PVS. We also present a highly reliable automated PVS quantification approach, which was optimized using expert readings.
Reward motivation increases univariate activity but has limited effect on coding of task-relevant information across the frontoparietal cortex
Authors: Shashidhara Sneha , Erez Yaara
Published: April 2019

Selection and integration of information based on current goals is fundamental for goal-directed behavior. Reward motivation has been shown to improve behavioral performance, yet the neural mechanisms that link motivation and control processes, and in particular its effect on context-dependent information processing, remain unclear. We used functional magnetic resonance imaging (fMRI) in 24 human volunteers (13 females) to test whether reward motivation enhances the coding of task-relevant information across the frontoparietal cortex, as would be predicted based on previous experimental evidence and theoretical accounts. In a cued target detection task, participants detected whether an object from a cued visual category was present in a subsequent display. The combination of the cue and the object visual category determined the behavioral status of the objects. To manipulate reward motivation, half of all trials offered the possibility of a monetary reward. We observed an increase with reward in overall univariate activity across the frontoparietal control network when the cue and subsequent object were presented. Multivariate pattern analysis (MVPA) showed that behavioral status information for the objects was conveyed across the network. However, in contrast to our prediction, reward did not increase the discrimination between behavioral status conditions in the stimulus epoch of a trial when object information was processed depending on a current context. In the high-level general-object visual region, the lateral occipital complex, the representation of behavioral status was driven by visual differences and was not modulated by reward. Our study provides useful evidence for the limited effects of reward motivation on task-related neural representations and highlights the necessity to unravel the diverse forms and extent of these effects.
MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation
Authors: Gumber Hardeep K. , McKenna Joseph F. , Tolmie Andrea F. , Jalovec Alexis M. , Kartick Andre C. , Graumann Katja , Bass Hank W.
Published: April 2019

The linker of nucleoskeleton and cytoskeleton (LINC) complex is an essential multi-protein structure spanning the eukaryotic nuclear envelope. The LINC complex functions to maintain nuclear architecture, positioning, and mobility, along with specialized functions in meiotic prophase and chromosome segregation. Members of the LINC complex were recently identified in maize, an important scientific and agricultural grass species. Here we characterizedMaize LINC KASH AtSINE-like2,MLKS2, which encodes a highly conserved SINE-group plant KASH protein with characteristic N-terminal armadillo repeats (ARM). Using a heterologous expression system, we showed that actively expressed GFP-MLKS2 is targeted to the nuclear periphery and colocalizes with F-actin and the endoplasmic reticulum, but not microtubules in the cell cortex. Expression of GFP-MLKS2, but not GFP-MLKS2ΔARM, resulted in nuclear anchoring. Genetic analysis of transposon-insertion mutations,mlks2-1andmlks2-2, showed that the mutant phenotypes were pleiotropic, affecting root hair nuclear morphology, stomatal complex development, multiple aspects of meiosis, and pollen viability. In male meiosis, the mutants showed defects for bouquet-stage telomere clustering, nuclear repositioning, perinuclear actin accumulation, dispersal of late prophase bivalents, and meiotic chromosome segregation. These findings support a model in which the nucleus is connected to cytoskeletal F-actin through the ARM-domain, predicted alpha solenoid structure of MLKS2. Functional conservation of MLKS2 was demonstrated through genetic rescue of the misshapen nuclear phenotype of an Arabidopsis (triple-WIP) KASH mutant. This study establishes a role for the SINE-type KASH proteins in affecting the dynamic nuclear phenomena required for normal plant growth and fertility.
Rapid characterisation of hERG channel kinetics I: using an automated high-throughput system
Authors: Lei Chon Lok , Clerx Michael , Gavaghan David J. , Polonchuk Liudmila , Mirams Gary R. , Wang Ken
Published: April 2019

Predicting how pharmaceuticals may affect heart rhythm is a crucial step in drug-development, and requires a deep understanding of a compound’s action on ion channels.In vitrohERG-channel current recordings are an important step in evaluating the pro-arrhythmic potential of small molecules, and are now routinely performed using automated high-throughput patch clamp platforms. These machines can execute traditional voltage clamp protocols aimed at specific gating processes, but the array of protocols needed to fully characterise a current is typically too long to be applied in a single cell. Shorter high-information protocols have recently been introduced which have this capability, but they are not typically compatible with high-throughput platforms. We present a new high-information 15 s protocol to characterise hERG (Kv11.1) kinetics, suitable for both manual and high-throughput systems. We demonstrate its use on the Nanion SyncroPatch 384PE, a 384 well automated patch clamp platform, by applying it to CHO cells stably expressing hERG1a. From these recordings we construct 124 cell-specific variants/parameterisations of a hERG model at 25 °C. A further 8 independent protocols are run in each cell, and are used to validate the model predictions. We then combine the experimental recordings using a hierarchical Bayesian model, which we use to quantify the uncertainty in the model parameters, and their variability from cell to cell, which we use to suggest reasons for the variability. This study demonstrates a robust method to measure and quantify uncertainty, and shows that it is possible and practical to use high-throughput systems to capture full hERG channel kinetics quantitatively and rapidly.

Statement of Significance

We present a method for high-throughput characterisation of hERG potassium channel kinetics, via fitting a mathematical model to results of over one hundred single cell patch clamp measurements collected simultaneously on an automated voltage clamp platform. The automated patch clamp data are used to parameterise a mathematical ion channel model fully, opening a new era of automated and rapid development of mathematical models from quick and cheap experiments. The method also allows ample data for independent validation of the models and enables us to study experimental variability and propose its origins. In future the method can be applied to characterise changes to hERG currents in different conditions, for instance at different temperatures (see Part II of the study) or under mutations or the action of pharmaceuticals; and should be easily adapted to study many other currents.
TRIM21–SERPINB5 aids GMPS repression to protect nasopharyngeal carcinoma cells from radiation-induced apoptosis
Authors: Zhang Panpan , Li Xiaomin , He Qiuping , Zhang Lulu , Song Keqing , Yang Xiaojing , He Qingmei , Wang Yaqin , Hong Xiaohong , Ma Jun , Liu Na
Published: April 2019

Nasopharyngeal carcinoma (NPC) is the most prevalent head and neck malignancy in South China and Southeast Asia. The main NPC treatment strategy is radiotherapy. However, recurrence resulting from radioresistance is a leading clinical bottleneck. Revealing the mechanism of NPC radioresistance would help improve the therapeutic effect. Here, our work reveals thatTRIM21(tripartite motif–containing 21) functions as an oncogene in NPC progression, and its ablation increases NPC cell radiosensitivity. Further analysis indicated that TRIM21 represses TP53 expression by mediating GMPS (guanine monophosphate synthase) ubiquitination and degradation after ionizing radiation. Mass spectrometry and co-immunoprecipitation showed that SERPINB5 (serpin family B member 5) interacts with both TRIM21 and GMPS. Epistatic analysis showed that SERPINB5 acts as an adaptor to recruit GMPS and introduce TRIM21 for ubiquitination. The in vitro and in vivo results validated the finding that SERPINB5 promotes NPC cell radioresistance. Furthermore, immunohistochemistry indicated that radioresistant patients have higher SERPINB5 expression. Overall, our data show that TRIM21–SERPINB5-mediated GMPS degradation facilitates TP53 repression, which promotes the radioresistance of NPC cells.
Stabilising effects of competition and diversity determine vaccine impact on antibiotic resistance evolution
Authors: Davies Nicholas G. , Flasche Stefan , Jit Mark , Atkins Katherine E.
Published: April 2019

Bacterial vaccines can protect recipients from contracting potentially antibiotic-resistant infections. But by altering the selective balance between sensitive and resistant strains, vaccines may also suppress—or spread—antibiotic resistance among unvaccinated individuals. Predicting the outcome requires knowing what drives selection for resistance in bacterial pathogens, and in particular, what maintains the circulation of both antibiotic-sensitive and resistant strains of bacteria. Using mathematical modelling, we show that the frequency of penicillin resistance in Streptococcus pneumoniae (pneumococcus) across 27 European countries can be explained by between-host diversity in antibiotic use, heritable diversity in pneumococcal carriage duration, or frequency-dependent selection brought about by within-host competition between resistant and sensitive strains. We use our calibrated models to predict the impact of non-serotype-specific pneumococcal vaccination upon the prevalence of carriage, incidence of disease, and frequency of resistance for S. pneumoniae. We find that the relative strength and directionality of competition between resistant and sensitive pneumococcal strains is the most important determinant of whether vaccination promotes, inhibits, or has little effect upon the evolution of antibiotic resistance. Finally, we show that country-specific differences in pathogen transmission substantially alter the predicted impact of vaccination, highlighting that policies for managing resistance with vaccines must be tailored to a specific pathogen and setting.

One sentence summary

Frequency-dependent competition and extrinsically-maintained diversity shape selection for antibiotic resistance following vaccination.
The ecological and epidemiological consequences of reproductive interference between the vectors Aedes aegypti and Aedes albopictus
Authors: Paton Robert S , Bonsall Michael B
Published: April 2019

Vector ecology is integral to understanding the transmission of vector-borne diseases, with processes such as reproduction and competition pivotal in determining vector presence and abundance. The arbovirus vectors Aedes aegypti and Aedes albopictus compete as larvae, but this mechanism is insufficient to explain patterns of coexistence and exclusion. Inviable interspecies matings - known as reproductive interference - is another candidate mechanism. Here, we analyse mathematical models of mosquito population dynamics and epidemiology which include two Aedes-specific features of reproductive interference. First, as these mosquitoes use hosts to find mates, reproductive interference will only occur if the same host is visited. Host choice will, in turn, be determined by functional responses to host availability. Second, females can become sterilised after mis-mating with heterospecifics. We find that a species with an affinity for a shared host will suffer more from reproductive interference than a less selective competitor. Costs from reproductive interference can be “traded-off” against costs from larval competition, leading to competitive outcomes difficult to predict from empirical evidence. Sterilisations of a self-limiting species can counter-intuitively lead to higher densities than a competitor suffering less sterilisation. We identify that functional responses and reproductive interference mediate a concomitant relationship between vector ecological dynamics and epidemiology. Competitors with opposite functional responses can maintain disease where human hosts are rare, due to vector coexistence facilitated by a reduced cost from reproductive interference. Our work elucidates the relative roles of the competitive mechanisms governing Aedes populations and the associated epidemiological consequences.
Mitogenomic Diversity in Sacred Ibis Mummies sheds light on early Egyptian practices
Authors: Wasef Sally , Subramanian Sankar , O’Rorke Richard , Huynen Leon , El-Marghani Samia , Curtis Caitlin , Popinga Alex , Holland Barbara , Ikram Salima , Millar Craig , Willerslev Eske , Lambert David
Published: April 2019

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ∼600BC. Although it is known that a very large number of these ‘votive’ mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ∼2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild Sacred Ibis for the ritual yearly demand.
Short-term evolution under copper stress increases probability of plasmid uptake
Authors: Klümper Uli , Maillard Arnaud , Hesse Elze , Bayer Florian , Houte Stineke van , Longdon Ben , Gaze Will , Buckling Angus
Published: April 2019

Understanding plasmid transfer dynamics remains a key knowledge gap in the mitigation of antibiotic resistance gene spread. Direct effects of exposure to stressors on plasmid uptake are well monitored. However, it remains untested whether evolution of strains under stress conditions modulates subsequent plasmid uptake. Here, we evolved a compost derived microbial community for six weeks under copper stress and non-exposed control conditions. We then tested the ability of isolated clones from both treatments to take up the broad host range plasmid pKJK5 from anE.colidonor strain. Clones pre-adapted to copper displayed a significantly increased probability to be permissive towards the plasmid compared to those isolated from the control treatment. Further, increased phylogenetic distance to the donor strain was significantly and negatively correlated with plasmid uptake probabilities across both treatments.
Menace to the ultimate antimicrobials among commonEnterobacteriaceaeclinical isolates in part of North-East India
Authors: Sharma Mohan , Chetia Pankaj , Puzari Minakshi , Neog Nakul , Borah Amrit
Published: April 2019

Introduction

Enterobacteriaceae, the normal dwellers in the human intestine, commonly associated with a variety of community acquired and nosocomial infections. Emerging trend of antibiotic resistance among these strains is a notable issue globally; more serious threat is the resistance against the available last resort antibiotics- the carbapenems. Our study thus intended to determine the burden of resistance towards this ultimate antimicrobial class, so as to assist in the empiric therapeutic decision making process and to search for alternate options.

Materials and Methods

Our study was a cross-sectional study with inclusion of clinical isolates collected from varied sources, from health settings in upper Assam. The isolates were identified based on standard methods of morphology study and biochemical tests. The identified isolates were then subjected to antibiotic susceptibility testing following Kirby-Bauer disc diffusion method and the result interpreted as per the CLSI guidelines. The resistance of the reported carbapenem resistant isolates was confirmed by minimum inhibitory concentration (MIC) determination using commercial E-strip kit.

Results

Among the enterobacterial isolatesKlebsiellaspp. accounted the majority, followed byEscherichia coli,Citrobacterspp.,Shigellaspp. and others. Multi-drug resistance (MDR) was noted among 67.6% isolates; however, carbapenem resistance was confirmed in 18.9% of the totalEnterobacteriaceaeisolates.

Conclusion

Higher prevalence of resistance towards the last resort antimicrobial, carbapenems, among theEnterbacteriaceaeisolates of upper Assam seems to be upcoming threat to the region, limiting the treatment options in future.
SPINT1 regulates the aggressiveness of skin cutaneous melanoma and its crosstalk with tumor immune microenvironment
Authors: Gómez-Abenza Elena , Ibáñez-Molero Sofía , García Moreno Diana , Fuentes Inmaculada , Zon Leonard I. , Mione Maria C. , Cayuela María L. , Gabellini Chiara , Mulero Victoriano
Published: April 2019

Skin cutaneous melanoma (SKCM) is the deadliest form of skin cancer and while incidence rates are declining for most cancers, they have been steadily rising for SKCM worldwide. Serine protease inhibitor, kunitz-type, 1 (SPINT1) is a type II transmembrane serine protease inhibitor that has been shown to be involved in the development of several types of cancer. We report here a high prevalence ofSPINT1genetic alterations in SKCM patients and their association with altered tumor immune microenvironment and poor patient survival. We used the unique advantages of the zebrafish to model the impact of SPINT1 deficiency in early transformation, progression and metastatic invasion of SKCM. Our results reveal that Spint1a deficiency facilitates oncogenic transformation, regulates the tumor/immune microenvironment crosstalk, accelerates the onset of SKCM and promotes metastatic invasion. Notably, Spint1a deficiency is required at both cell autonomous and nonautonomous levels to enhance invasiveness of SKCM. These results suggest the relevance of clinical intervention on this signaling pathway for precision SKCM medicine.

Summary statement

A zebrafish model shows that Spint1a deficiency facilitates oncogenic transformation, regulates the tumor/immune microenvironment crosstalk, accelerates the onset of SKCM, and promotes metastatic invasion in cell autonomous and non-autonomous manners.
Non-financial KPIs in annual report narratives: Australian practice
Authors: Bayne Lyndie , Wee Marvin
Published: April 2019

Purpose

The purpose of this paper is to provide preliminary evidence on current practices in non-financial key performance indicator (KPI) reporting in annual reports by listed Australian companies to inform Australian legislators and accounting standard setters contemplating regulations and guidance for non-financial performance disclosure, including input into the revision of IFRS Practice Statement 1: Management Commentary (2010).

Design/methodology/approach

Non-financial KPIs were hand-collected from the annual report narratives of 40 listed Australian companies from five sectors in 2016. Trends in the type, quantity, comparability and range of non-financial KPIs were analysed, and the association between company characteristics and non-financial disclosure was explored.

Findings

In total, 78 per cent of the sampled companies disclose non-financial KPIs in their annual reports, reporting 11 non-financial KPIs per company on average. The most common category is Employee, followed by Environment, accounting for 68 per cent of non-financial KPIs. Provision of comparators is low, with only 28 per cent of non-financial KPIs disclosed with prior year results and 24 per cent disclosed with a target. Companies disclose across a median of two out of seven categories. Company size is shown to be associated with non-financial measures.

Originality/value

The study contributes initial detailed empirical Australian evidence of non-financial KPI reporting practices. A framework is established for assessing non-financial KPI disclosure, adding to voluntary disclosure studies. A data collection method is developed for collecting KPIs from annual report narratives, contributing to the methodology used in voluntary reporting content analysis.
Crowdsourcing for search engines: perspectives and challenges
Authors: Moradi Mohammad
Published: April 2019

Purpose

As a relatively new computing paradigm, crowdsourcing has gained enormous attention in the recent decade. Its compliance with the Web 2.0 principles, also, puts forward unprecedented opportunities to empower the related services and mechanisms by leveraging humans’ intelligence and problem solving abilities. With respect to the pivotal role of search engines in the Web and information community, this paper aims to investigate the advantages and challenges of incorporating people – as intelligent agents – into search engines’ workflow.

Design/methodology/approach

To emphasize the role of the human in computational processes, some specific and related areas are studied. Then, through studying the current trends in the field of crowd-powered search engines and analyzing the actual needs and requirements, the perspectives and challenges are discussed.

Findings

As the research on this topic is still in its infancy, it is believed that this study can be considered as a roadmap for future works in the field. In this regard, current status and development trends are delineated through providing a general overview of the literature. Moreover, several recommendations for extending the applicability and efficiency of next generation of crowd-powered search engines are presented. In fact, becoming aware of different aspects and challenges of constructing search engines of this kind can shed light on the way of developing working systems with respect to essential considerations.

Originality/value

The present study was aimed to portrait the big picture of crowd-powered search engines and possible challenges and issues. As one of the early works that provided a comprehensive report on different aspects of the topic, it can be regarded as a reference point.
The determinants of conventional banks profitability in developing and underdeveloped OIC countries
Authors: Al-Harbi Ahmad
Published: April 2019

Purpose

The purpose of this study is to investigate the effect of internal and external variables on the profitability of conventional banks operating on developing and underdeveloped countries, the Organization of Islamic Cooperation (OIC) states.

Design/methodology/approach

In this paper, the author uses ordinary least squares fixed-effects model on an unbalanced panel data set of all conventional banks operating in OIC countries (52 countries included from 57) over the period 1989-2008, 686 banks.

Findings

The results suggest that equity, foreign ownership, off-balance sheet (OBS) activities, real gross domestic product growth, real interest rate and concentration foster banks’ profitability. In addition, the results showed that the banking sector development and loans will increase banks’ profitability in the long run in the countries of the studies. In contrast, the study reported that deposits lower profitability. The study also revealed that GDP per capita, market capitalization and banks size have no impact on profitability.

Practical implications

The findings of this study have considerable policy implications. First, policymakers need to regulate nontraditional activities to avoid any financial crisis because banks in OIC countries are heavily engaged in nontraditional activities to boost its profit. Second, policymakers are advised to improve the deposit insurance system to insure the stability of the financial system as well as improving banks’ profitability. Third, policymakers need to improve the efficiency of the stock market, maintain small banking system and encourage foreign investments in the banking system.

Originality/value

The paper adds to the literature on the commercial bank’s profitability determinants. In particular, such study has not been conducted on OIC countries, and the study included all mainstream banks and incorporated the effect of deposit insurance system so far. Also, pure sample of conventional banks used as many conventional banks in OIC countries have Islamic windows or offer Islamic products. In addition, this study investigated the effect of OBS activities on net interest margin (NIM) because the studies that explored this interrelationship are limited especially for developing and under developed countries. The results showed that OBS activities contributed significantly and positively to return on assets and NIM. Moreover, this paper used a pure sample of conventional banks to avoid any biasness; see data section. Moreover, this study gives an idea about the economic situation and financial conditions of OIC countries during the period of the study.
Informalshariahpawnshop in the traditional markets of Surakarta
Authors: Shabbir Malik Shahzad
Published: April 2019

Purpose

This study aims to explore how informal pawnbrokers and informal pawners interpret the existence of the informal pawnshop in the traditional market in Surakarta, Indonesia, with the main focus to determine the applicability of informal pawnshop development model.

Design/methodology/approach

The research used the qualitative method with the phenomenological approach using interview method to fully comprehend the informants’ views regarding the informal pawnshop existence in traditional markets in Surakarta, Indonesia. The applicability of informal pawnshop development model is required for Muslim market vendors. Charitable institutions shall participate in the development of the model by empowering (zakat, infaq, shadaqahandwaqf) funds to help Muslims vendors in the traditional markets for additional capital in accordance with Islamic laws for a pawnshop.

Findings

The result of the research shows that the existence of informal pawning in the traditional markets is difficult to avoid as both informal pawnbrokers and informal pawners need one another. Most vendors in the traditional markets are Muslims. Islam teaches that loan interest is categorized as forbidden riba. Meanwhile, in the informal pawning practices, the informal pawnbrokers charge loan interest to the informal pawners.

Originality/value

The objective of this study is to investigate to what extent the Islamic pawn shops motivated the people through interest-free system. However, in past, tradition markets facilitate the people, but they charged a huge against it with interest (riba).
Abiding by the rules?
Authors: Freese Thea , Gille Michael , Struthers John
Published: April 2019

Purpose

Increased political measures to protect the marine environment addresses a shipping industry characterised by strained financial resources, excess supply of capacity and consolidation. In addition, 5-15 per cent of industry participants are believed by shipping experts to neglect rules on vessel-source pollution to stay competitive within their industry and vis-à-vis other transport modes. This study aims to identify and quantify cost effects of maritime environmental legislation, to relate these with company characteristics and to investigate the impact of regulatory compliance.

Design/methodology/approach

A mixed-methods design was used to develop both a theoretical model of compliance costs effects and to quantify effect sizes. In total, 12 in-depth exploratory expert interviews were conducted and analysed. A theoretical framework emerged, which was evaluated, strengthened and fed with quantitative data from questionnaire data by 120 shipping companies. Partial least squares analysis was conducted to determine compliance cost effects.

Findings

It was found that organisational capacities played a significant role in determining compliance behaviour. Exterior determinants showed no significant correlation with legal compliance. This is a striking result, as it does not support achieving legal compliance with measures of strong enforcement.

Social implications

European transport policy-making depends on scientifically sound studies on the impact of policy. An in-depth impact assessment on environmental legislation for the maritime industry highlights mechanisms applicable to environmental policy-making in transport and helps in building policy that considers compliance concerns, company characteristics and the interconnectedness of different transport modes for a sound response to the tragedy of the commons.

Originality/value

Originality lies in the inductive development of a comprehensive theory on shipping companies’ legal compliance behaviour and the empirical testing of this theory. Further value is derived from applying a sequential mixed-methods approach to the research problem, showing both the worth and challenge in combining different methodologies to achieve sound research results.
The alumni club: interpersonal contact and the exchange of recovery oriented helping in a sample of former residents of a therapeutic community for women
Authors: Linley Jessica V. , Warren Keith L.
Published: April 2019

Purpose

Aftercare is an important predictor of outcomes following treatment for substance abuse. Despite this, there is evidence that the great majority of substance abusing clients choose not to participate in aftercare. Aftercare programs that are tied to specific residential treatment facilities, sometimes known as alumni groups or alumni clubs, might increase participation by offering former residents the opportunity to maintain treatment oriented social networks. Therapeutic communities (TCs), which emphasize mutual aid between residents, are ideal candidates for such programs. The paper aims to discuss these issues.

Design/methodology/approach

In total, 100 randomly chosen former TC residents were randomly surveyed regarding their contact with fellow alumni and their exchange of recovery oriented helping behaviors. A thirty day timeline follow-back methodology was used.

Findings

Contact was primarily through electronic means, particularly phone calls, texts and the alumni club Facebook page. Participants who reported more electronic contact also reported more days in which they offered and received recovery oriented help. Participants who were African American or had spent more time in TC treatment offered and received recovery oriented help on more days.

Research limitations/implications

While this is an exploratory study limited to one TC, this alumni club allows for the maintenance of a mutual aid network after termination. That network primarily consists of electronic forms of contact. A longer time spent in TC treatment may allow for the internalization of the practice of mutual aid. Further research on alumni clubs is warranted.

Originality/value

This is the first survey of TC alumni club members.