bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of hidden population structure in time-scaled phylogenies
Authors: Volz Erik M. , Wiuf Carsten , Grad Yonatan H. , Frost Simon D.W. , Dennis Ann M. , Didelot Xavier
Published: July 2019

Population structure influences genealogical patterns, however data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealised genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partialpolsequences. This revealed the presence of clades which had grown rapidly in the recent past, and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genomeNeisseria gonorrhoeaesequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance.
Highly efficient transgenesis withminiMosinCaenorhabditis briggsae
Authors: Ding Qiutao , Ren Xiaoliang , Li Runsheng , Chan Luyan , Ho Vincy WS , Bi Yu , Xie Dongying , Zhao Zhongying
Published: July 2019

C. briggsaeas a companion species forC. eleganshas played an increasingly important role in study of evolution of development, gene regulation and genome. Aided by the isolation of its sister spices, it has recently been established as a model for speciation study. To take full advantage of the species for comparative study, an effective transgenesis method especially those with single copy insertion is important for functional comparison. Here we modified a transposon-based transgenesis methodology that had been originally developed inC. elegansbut worked marginally inC. briggsae. By incorporation of a heat shock step, the transgenesis efficiency inC. briggsaewith single copy insertion is comparable to that inC. elegans. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over theC. briggsaegenome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility betweenC. briggsaeandC. nigoniwhen combined with the GFP tags we generated previously. Finally, we demonstrated thatC. briggsaehas developed native immunity against theC. eleganstoxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array.

NematodeC. briggsaehas been used for comparative study againstC. elegansover decades. Importantly, a sister species has recently been identified, with whichC. briggsaeis able to mate and produce viable hybrid progeny. This opens the possibility of using nematode species as a model for speciation study for the first time. To take full advantage ofC. briggsaefor comparative study, an effective transgenesis method to generate single copy insertion is important especially for functional comparison. An attempt was made previously to generate single copy insertion with transposon-based transgenesis methodology, which had been originally developed inC. elegansbut with limited success inC. briggsae. Here we modified the transposon-based methodology by incorporation of a heat shock step, which allows us to achieve a much higher transgenesis efficiency inC. briggsaewith single copy insertion. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over theC. briggsaegenome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility betweenC. briggsaeandC. nigoniwhen combined with the GFP tags we generated previously. Finally, we demonstrated thatC. briggsaehas developed native immunity against theC. eleganstoxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array. Taken together, the modified transgenesis methodology and the transgenic strains generated in this study are expected to further facilitateC. briggsaeas a model for comparative study or speciation study.
Haldane’s Probability of Mutant Survival is Not the Probability of Allele Establishment
Authors: Krukov Ivan , de Koning A.P. Jason
Published: July 2019

Haldane notably showed in 1927 that the probability of fixation for an advantageous allele is approximately 2s, for selective advantages. This widely known result is variously interpreted as either the fixation probability or the establishment probability, where the latter is considered the likelihood that an allele will survive long enough to have effectively escaped loss by drift. While Haldane was concerned with escape from loss by drift in the same paper, in this short note we point out that: 1) Haldane’s ‘probability of survival’ is analogous to the probability of fixation in a Wright-Fisher model (as also shown by others); and 2) This result is unrelated to Haldane’s consideration of how common an allele must be to ‘probably spread through the species’. We speculate that Haldane’s survival probability may have become misunderstood over time due to a conflation of terminology about surviving drift and ‘ultimately surviving’ (i.e., fixing). Indeed, we find that the probability of establishment remarkably appears to have been overlooked all these years, perhaps as a consequence of this misunderstanding. Using straightforward diffusion and Markov chain methods, we show that under Haldane’s assumptions, where establishment is defined by eventual fixation being more likely that extinction, the establishment probability is actually 4swhen the fixation probability is 2s. Generalizing consideration to deleterious, neutral, and adaptive alleles in finite populations, if establishment is defined by the odds ratio between eventual fixation and extinction,k, the general establishment probability is (1 +k)/ktimes the fixation probability. It is therefore 4swhenk= 1, or 3swhenk= 2 for beneficial alleles in large populations. Askis made large, establishment becomes indistinguishable from fixation, and ceases to be a useful concept. As a result, we recommend establishment be generally defined as when the odds of ultimate fixation are greater than for extinction (k= 1, following Haldane), or when fixation is twice as likely as extinction (k= 2).
Relevance of genomic evaluation for egg quality traits in layers
Authors: Picard Druet David , Varenne Amandine , Herry Florian , Hérault Frédéric , Allais Sophie , Burlot Thierry , Le Roy Pascale
Published: July 2019

Background

Genomic evaluation, based on thousands of genetic markers, has become the standard evaluation methodology in dairy cattle breeding programs over the past few years. Despite the many differences between dairy cattle breeding and poultry breeding, genomic selection seems very promising for the avian sector, and studies are currently being conducted to optimize avian selection schemes. In this optimization perspective, one of the key parameters is to properly predict the accuracy of genomic evaluation in pure line layers.

Methods

Both genetic evaluation and genomic evaluation were performed on three candidate populations (male and female), using different sizes of phenotypic records on five egg quality traits and at two different ages. The methodologies used were BLUP & ssGBLUP, and variance-covariance matrices were estimated through REML. To estimate evaluation accuracy, the LR method was implemented. Four statistics were used to assess the relative accuracy of the estimated breeding values of candidates, their bias and dispersion, as well as the differences between genetic evaluation and genomic evaluation.

Results

It was observed that genomic evaluation, whether performed on males or females, always proved more accurate than genetic evaluation. The gain was higher when phenotypic information was narrowed and an augmentation of the size of the reference population led to an increase in accuracy prediction, for what regards genomic evaluation. By taking into account the increase of selection intensity and the decrease of the generation interval induced by genomic selection, the expected annual genetic gain would be higher with ancestry-based genomic evaluation of male candidates than with genetic evaluation based on collaterals. This advantage of genomic selection over genetic selection requires to be studied in more details for female candidates.

Conclusions

In conclusion, in the population studied, genomic evaluation for egg quality traits of breeding birds at birth seems a promising strategy, at least for what regards males selection.
Protein interactions of Magnaporthe oryzae protein kinase CK2 and secondary data analysis of a large number of transcriptomes suggest chaperone-like activity is integral to its function
Authors: Zhang Lianhu , Zhang Dongmei , Liu Dan , Li Yuan , Li Hongchen , Wang Zonghua , Hansen Bjoern Oest , Olsson Stefan
Published: July 2019

CK2, a serine/threonine (S/T) kinase present in eukaryotic cells is known to have a vast number of substrates. We have recently shown that it localizes to nuclei and at pores between hyphal compartments in M. oryzae. We performed a pulldown-proteomics of M. oryzae CK2 catalytic subunit MoCKa to detect interacting proteins. The MoCKa pulldown was enriched for septa and nucleoli proteins and intrinsically disordered proteins (IDPs) containing a CK2 phosphorylation motif proposed to destabilize and unfold alpha helixes. This points to a function for CK2 phosphorylation and corresponding phosphatase dephosphorylation in the formation of functional protein-protein aggregates and protein-RNA/DNA binding. To test this as widely as possible we used secondary data downloaded from databases from a large range of M. oryzae experiments and also for a relatively closely related plant pathogenic fungus, Fusarium graminearum. We found that CKa expression was strongly positively correlated with S/T phosphatases as well as with disaggregase (HSP104, YDJ1, SSA1) and an autophagy indicating protein (ATG8). The latter points to increased protein aggregate formation at high levels of CKa expression. Our results suggest a general role for CK2 in aggregation and disaggregation of IDPs and their binding to proteins, DNA and RNA interactions.
Cellular metabolic reprogramming controls sugar appetite
Authors: Carvalho-Santos Zita , Figueiredo Rita Cardoso , Elias Ana Paula , Ribeiro Carlos
Published: July 2019

Cellular metabolic reprogramming is an important mechanism by which cells rewire their metabolism to promote proliferation and cell growth. This process has been mostly studied in the context of tumorigenesis and less is known about its relevance for non-pathological processes and how it affects whole animal physiology. Here, we show that Drosophila female germline cells reprogram their carbohydrate metabolism, upregulating the pentose phosphate pathway (PPP) to produce eggs. Strikingly, this cellular reprogramming strongly impacts nutrient preferences. PPP activity in the germline specifically increases the animal’s appetite for sugar, the key nutrient fueling this metabolic pathway. We furthermore provide functional evidence that the germline alters sugar appetite by regulating the expression of the fat body secreted satiety factor fit. The cellular metabolic program of a small set of cells is therefore able to increase the animal’s preference for specific nutrients through inter-organ communication to promote specific metabolic and cellular outcomes.
Late Embryogenesis Abundant (LEA) proteins confer water stress tolerance to mammalian somatic cells
Authors: Czernik M , Fidanza A , Luongo FP , Valbonetti L , Scapolo PA , Patrizio P , Loi P
Published: July 2019

Late Embryogenesis Abundant (LEA) proteins are commonly found in organisms capable of undergoing reversible dehydration - “anhydrobiosis”. Here, we have produced three LEA proteins: pTag-RAB17-GFP-N,Zea maysdehydrin-1dhn, expressed in the nucleo-cytoplasm; pTag-WCOR410-RFP,Tricum aestivumcold acclimation proteinWCOR410, binding to cellular membranes, and pTag-LEA-BFP,Artemia franciscanaLEA protein group 3 that targets the mitochondria. Somatic cells transfected with three LEA proteins were subjected to desiccation under controlled conditions, followed by rehydration, viability assessment and membrane/mitochondria functional tests were performed. Results shown that LEA protect cells from desiccation injury. Cells expressed all LEA proteins shown very high percentage of viable cells (58%) after four hour of desiccation compare to un-transfected cells (1% cell alive). Plasmalemma, cytoskeleton and mitochondria appeared unaffected in LEA-expressing cells, confirming their protective action during the entire desiccation and rehydration process. Here, we show that natural xeroprotectants (LEA proteins) transiently expressed in somatic cells confer them desiccation tolerance.
N-cadherin stabilises neural identity by dampening anti-neural signals
Authors: Punovuori K , Migueles RP , Malaguti M , Blin G , Macleod KG , Carragher NO , Pieters T , van Roy F , Stemmler MP , Lowell S
Published: July 2019

A switch from E-to N-cadherin regulates the transition from pluripotency to neural identity but the mechanism by which cadherins regulate differentiation was previously unknown. Here we show that the acquisition of N-cadherin stabilises neural identity by dampening anti-neural signals. We use quantitative image-analysis to identify an effect of N-cadherin to promote neural differentiation independently of effects on cell cohesiveness. We reveal that cadherin switching diminishes the level of nuclear β-catenin, and that N-cadherin also dampens FGF activity and consequently stabilises neural fate. Finally, we compare the timing of cadherin switching and differentiationin vivoandin vitro, and find that this process becomes dysregulated duringin vitrodifferentiation. We propose that N-cadherin helps to propagate a stable neural identity throughout the emerging neuroepithelium, and that dysregulation of this process contributes to asynchronous differentiation in culture.
The tricellular vertex-specific adhesion molecule Sidekick facilitates polarised cell intercalation duringDrosophilaaxis extension
Authors: Finegan Tara M. , Hervieux Nathan , Nestor-Bergmann Alexander , Fletcher Alexander G. , Blanchard Guy B. , Sanson Bénédicte
Published: July 2019

In epithelia, tricellular vertices are emerging as important sites for the regulation of epithelial integrity and function. Compared to bicellular contacts, however, much less knowledge is available. In particular, resident proteins at tricellular vertices were identified only at occluding junctions, with none known at adherens junctions. In a previous study, we discovered that inDrosophilaembryos, the adhesion molecule Sidekick (Sdk), well known in invertebrates and vertebrates for its role in the visual system, localises at tricellular vertices at the level of adherens junctions. Here, we survey a wide range ofDrosophilaepithelia and establish that Sdk is a resident protein at tricellular adherens junctions, the first of its kind. Clonal analysis suggests that pair-wise homophilic adhesion is necessary and sufficient for Sdk tricellular vertex localisation. Super-resolution imaging using structured illumination reveals that Sdk proteins form string-like structures at vertices. Postulating that Sdk may have a role in epithelia where adherens junctions are actively remodelled, we analysed the phenotype ofsdknull mutant embryos duringDrosophilaaxis extension, using quantitative methods. We find that apical cell shapes are strikingly abnormal insdkmutants. Moreover, adhesion at apical vertices is compromised in rearranging cells, with holes forming and persisting throughout axis extension. Finally, we show that polarized cell intercalation is decreased and abnormal insdkmutants. Mathematical modeling of the cell behaviours supports the conclusion that the T1 transitions of polarized cell intercalation are delayed insdkmutants. We propose that this delay, in combination with a change in the mechanical properties of the converging and extending tissue, causes the striking cell shape phenotype ofsdkmutant embryos.
The crystal structure of haemoglobin from Atlantic cod
Authors: Helland Ronny , Bjørkeng Eva Katrin , Rothweiler Ulli , Sydnes Magne Olav , Pampanin Daniela Maria
Published: July 2019

The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.
Crystal structure of 4,4′-bis(4-bromophenyl)-1,1′,3,3′-tetrathiafulvalene
Authors: Rigin Sergei , Fonari Marina
Published: July 2019

The molecule of the title compound, C18H10Br2S4, has a C-shape, with C
s molecular symmetry. The dihedral angle between the planes of the dithiol and phenyl rings is 8.35 (9)°. In the crystal, molecules form helical chains along [001], the shortest interactions being π...S contacts within the helices. The intermolecular interactions were investigated by Hirshfeld surface analysis. Density functional theory (DFT) was used to calculate HOMO–LUMO energy levels of the title compound and its trans isomer.
N-Ethyl-N′-(3-methylbenzoyl)-S,S-diphenylsulfodiimide
Authors: Sheikh Md Chanmiya , Yoshimura Toshiaki , Miyatake Ryuta , Hanawa Soichiro , Hayashi Naoto
Published: July 2019

The asymmetric unit of the title sulfodiimide, C22H22N2OS, consists of two crystallographically independent molecules with similar conformations The environment around each sulfur atom is a slightly distorted tetrahedron with two S=N bonds and two S—C bonds. The S= N(m-methylbenzoyl) and S=N(NEt) bond lengths are 1.584 (3) and 1.528 (2) Å, respectively, for one molecule, and 1.575 (2) and 1.529 (3) Å, respectively, for the other. The dihedral angles between the two phenyl rings in the molecules are 86.76 (8) and 82.49 (8)°. The N—S—N—C(m-methylbenzoyl) and N—S—N—C(ethyl) torsion angles are −60.5 (2) and −50.28 (19)°, respectively, for one molecule, and 62.9 (2) and 44.2 (3)°, respectively, for the other. In the crystal, each independent molecule is linked to its inversion-related molecule via a pair of C—H...O hydrogen bonds, forming a dimer.
Determinants of behavioral intentions towards a professional certification scheme at European level
Authors: Ruiz-Molina Maria-Eugenia , Gil-Saura Irene , Berenguer-Contri Gloria , Auch Christoph
Published: July 2019

Purpose

The purpose of this paper is to analyze the effect of candidates’ perceptions of the attributes of a professional certification scheme based on competences, as well as personal factors, that may influence in the behavioral intentions toward such certification program, i.e. intention to participate in the certification process and willingness to pay for the certificate.

Design/methodology/approach

Based on a survey of 2,630 professionals about the “Certified Professional” program in eight European countries, the influence of the perceived attributes of the certification program and the personal characteristics of the potential candidates on their behavioral intentions are analyzed.

Findings

Difficulty and fairness of the certification process, credibility, innovativeness, international recognition and future usefulness of the professional certificate influence positively on the candidate’s likelihood of applying for being certified and the willingness to pay. Young professionals not holding a university diploma show high probability to participate in the certification process and intention to pay for the certificate.

Practical implications

Promotional efforts to launch a professional certification scheme should concentrate in creating strong associations of the certificate with the notions of international prestige, credibility and usefulness to enhance employability and professional growth. Segmentation criteria to increase communication effectiveness are defined.

Originality/value

In recent years, there has been a proliferation of professional certification programs in competences, and literature has advocated the need to investigate the perceived value of such systems in terms of benefits and barriers perceived by potential applicants for accreditation. The present paper aims at addressing this research gap.
Women's career interruptions: an integrative review
Authors: Bian Xinyi , Wang Jia
Published: July 2019

Purpose

The purpose of this integrative literature review was three-fold: to explore the phenomenon of women’s career interruptions as revealed by publications in the past two decades, to propose a new career decision tree model (CDTM) and to outline an agenda for future research.

Design/methodology/approach

The authors adopted the integrative literature review approach proposed by Torraco (2005, 2016) and used a mind mapping application called MindMeister to synthesize 64 identified articles.

Findings

The proposed CDTM can assist those who are interested in exploring individuals’ career decisions to think systematically about career influencers at different levels.

Originality/value

The CDTM is significantly different from existing career models and theories in that it explains women’s career interruptions in a context-sensitive manner. This model can assist human resource development professionals in analyzing the influencers of women’s career decisions and tackling individual problems level by level.
Determinants of peer-to-peer rental rating scores: the case of Airbnb
Authors: Zhu Liang , Cheng Mingming , Wong IpKin Anthony
Published: July 2019

Purpose

This study aims to identify the key determinants of Airbnb rating scores.

Design/methodology/approach

This study is based on a sample of 127,257 listings across 43 cities. A total of 24 explanatory variables were identified, and they were further grouped into host verification information, communication, policy of renting, space, information about environment, price and experience of hosting. Both Tobit and ordered logit models were used to perform the analysis.

Findings

The results indicate that good communication, large space and provision of information about the listings’ environment have a positive effect on users’ satisfaction, whereas experience of hosting negatively influences users’ satisfaction.

Originality/value

This study contributes to the peer-to-peer accommodation literature by affording a more complete understanding about guest satisfaction and its determinants.
Software and services export, IT investment and GDP nexus in India
Authors: Malik Manzoor Hassan , Velan Nirmala
Published: July 2019

Purpose

The purpose of this paper is to investigate both long-run and short-run dynamics among the software and services export, investment in information technology (IT) and GDP in India and to investigate the direction of the relationship among the given three macro-economic variables.

Design/methodology/approach

The time series data have been taken to investigate the long-run relationship exists among the variables. Annual data were collected from the NASSCOM Annual Reports, Planning Commission of India and Reserve Bank of India during the period 1980–2016. Cointegration and vector error correction model have been used for analyzing the causal relationship among investment in IT, software exports and GDP in India.

Findings

Cointegration results confirm that software and services export, investment in IT and GDP are cointegrated, implying that there exists the long-run equilibrium relationship among the given three macro-economic variables. Similarly, vector error correction mechanism Granger causality results hold that there is uni-directional long-run causality running from software and services export and investment in IT to GDP, implying that software and services export is an important determinant of economic growth in India.

Research limitations/implications

The limitations of the paper are generalization of the results and proxy variable for IT investments.

Practical implications

The paper has implications for the expansion of market concentration, diversification of software and service exports, and investments in R&D for increasing competitiveness of the industry in the global market.

Originality/value

This paper focuses on originality in the analysis of the relationship among the given variables software exports, investment in the IT sector and GDP in India. All the work has been done in original by the authors and the work used have been acknowledged properly.
Rethinking the university system: toward the entrepreneurial university (the case of Italy)
Authors: Vesperi Walter , Gagnidze Ineza
Published: July 2019

Purpose

The purpose of this study is to investigate contemporary changes in the education system. In particular, an analysis of the mechanisms of coordination and communication involved in the process can show how different geographical factors with different relational mechanisms may contribute to the creation of a new academic entrepreneurship.

Design/methodology/approach

The authors propose a methodology with two-step approach. In the first part of the paper, they use a theoretical approach to carry out a longitudinal study of academic literature on the topics of “entrepreneurial university,” “academic entrepreneurship” and “spin-off organizations.” In the second part, they use cross-database analysis to theorize the main aspects of recent developments in higher education in Italy. To this end, the authors use three public and open-access databases on spin-offs, universities and higher education institutions and incubators in Italy.

Findings

First, issues relating to the formation and best practices of entrepreneurial universities are discussed, based on the works of researchers from 25 countries. Second, a hypothesis is put forward to suggest that the organizational model of entrepreneurial university affects microeconomic competitiveness. Third, a case study of Italian spin-off organizations suggests that the number of incubators and spin-offs, and the type of academic knowledge, all directly affect the entrepreneurial university.

Originality/value

This paper aims to examine the role of the university in the modern economic system. The originality of this investigation lies in its ability to offer a picture and first analysis of the main actors and of the entrepreneurial university system.
Improving law enforcement’s response to non-fatal strangulation
Authors: Reckdenwald Amy , Fernandez Ketty , Mandes Chelsea L.
Published: July 2019

Purpose

The purpose of this paper is to evaluate a coordinated effort to improve the law enforcement response to non-fatal strangulation in the context of domestic violence.

Design/methodology/approach

The authors compare law enforcement identification and documentation of strangulation in domestic violence cases before and after the implementation of a strangulation-specific training program in one Central Florida County.

Findings

The results indicate preliminary support for the effectiveness of training law enforcement, suggesting that the response to strangulation can be improved with comprehensive law enforcement training.

Practical implications

An improved response by law enforcement may have the potential to increase offender accountability of non-fatal strangulation – a potentially deadly assault.

Originality/value

The study is the first to evaluate strangulation-specific training efforts of law enforcement. Results point to opportunities that can be taken to improve law enforcement’s response to non-fatal strangulation in domestic violence.
Identifying a set of line manager personas to guide new product introduction strategy
Authors: Straker Karla , Mosely Genevieve , Wrigley Cara
Published: July 2019

Purpose

The purpose of this paper is to introduce a new strategic management tool – the reverse persona. In doing so, the methods, use and benefits documented from a case study with a global franchisee organization are presented.

Design/methodology/approach

This tool was derived from working with a global franchisee organization sought to design and launch a new product into the market. The reverse persona was deployed through n=14 qualitative interviews with franchisee owners were conducted to understand their perceptions of customers, awareness and concern of competition and their willingness to take risks. These insights were collated to develop reverse personas for the senior leadership team within the organization.

Findings

Changing the scope of personas from external customers to internal employee development, can further strengthen the method’s effectiveness in decision-making and strategic management, particularly for the implementation and roll out of new products.

Practical implications

In the case study, the senior leadership team saw the manager persona as a strategic aid to, “Help target the implementation of new products in stores, select franchise owners for potential new roles and to deeply understand the motivations, challenges and attributes of their middle management contributing to the competitive advantage of the organisation.”

Originality/value

This article is the first to explore the use of personas for internal strategic planning use within a company.
Influence of ceramic Al2O3 particulates on performance measures and surface characteristics during sinker EDM of stir cast AMMCs
Authors: Khajuria Akhil , Akhtar Modassir , Pandey Manish Kumar , Singh Mayur Pratap , Raina Ankush , Bedi Raman , Singh Balbir
Published: July 2019

Purpose

AA2014 is a copper-based alloy and is typically used for production of complex machined components, given its better machinability. The purpose of this paper was to study the effects of variation in weight percentage of ceramic Al2O3 particulates during electrical discharge machining (EDM) of stir cast AA2014 composites. Scanning electron microscopy (SEM) examination was carried out to study characteristics of EDMed surface of Al2O3/AA2014 composites.

Design/methodology/approach

The effect of machining parameters on performance measures during sinker EDM of stir cast Al2O3/AA2014 composites was examined by “one factor at a time” (OFAT) method. The stir cast samples were obtained by using three levels of weight percentage of Al2O3 particulates, i.e. 0 Wt.%, 10 Wt.% and 20 Wt.% with density 1.87 g/cc, 2.35 g/cc and 2.98 g/cc respectively. Machining parameters varied were peak current (1-30 amp), discharge voltage (30-100 V), pulse on time (15-300 µs) and pulse off time (15-450 µs) to study their influence on material removal rate (MRR), tool wear rate (TWR) and surface roughness (SR).

Findings

MRR and SR decreased with an increase in weight percentage of ceramic Al2O3 particulates at the expense of TWR. This was attributed to increased microhardness for reinforced stir cast composites. However, microhardness of EDMed samples at fixed values of machining parameters, i.e. 9 amp current, 60 V voltage, 90 µs pulse off time and 90 µs pulse on time reduced by 58.34, 52.25 and 46.85 per cent for stir cast AA2014, 10 Wt.% Al2O3/AA2014 and 20 Wt.% Al2O3/AA2014, respectively. SEM and quantitative energy dispersive spectroscopy (EDS) analysis revealed ceramic Al2O3 particulate thermal spalling in 20 Wt.% Al2O3/AA2014 composite. This was because of increased particulate weight percentage leading to steep temperature gradients in between layers of base material and heat affected zone.

Originality/value

This work was an essential step to assess the machinability for material design of Al2O3 reinforced aluminium metal matrix composites (AMMCs). Experimental investigation on sinker EDM of high weight fraction of particulates in AA2014, i.e. 10 Wt.% Al2O3 and 20 Wt.% Al2O3, has not been reported in archival literature. The AMMCs were EDMed at variable peak currents, voltages, pulse on and pulse off times. The effects of process parameters on MRR, TWR and SR were analysed with comparisons made to show the effect of Al2O3 particulate contents.
Molecular cloning, characterization and expression analysis of MHCI and chemokines CXCR3 and CXCR4 gene from freshwater carp,Catla catla
Authors: Banerjee Rajanya , Roy Sudeshna , Samanta Mrinal , Das Surajit
Published: July 2019

The immune system with large number of molecules protects the host against a plethora of continuously evolving microbes. Major histocompatibility complex (MHC) molecules serve as cardinal elements of the adaptive immune system responsible for the activation of the adaptive immunity in the host. The present study reports MHCI molecule in freshwater carp,Catla catla, and its differential expression in immunologically relevant tissues post‐infection with Gram‐negative and Gram‐positive bacteria. The MHCI sequence ofC. catlahad 502 bp nucleotides encoding putative 146 amino acids. The phylogenetic analysis exhibited its evolutionary conservation within theCyprinidaefamily and formed a different clade with the higher vertebrates. Simultaneously, CXCR3 and CXCR4 chemokines were cloned and characterized for their expression in infected tissues. Analysis of immunologically relevant tissues of the infected fish exhibited an increase of MHCI gene expression and the down‐regulation of CXCR3 and CXCR4 chemokines, indicating a tricky interaction between the innate and adaptive immune system. It was found that intestine, skin and spleen played a crucial role in the contribution of the defense activity which instigated the self‐immunity. These immune activities can provide useful information to understand the interaction of self and non‐self‐ immune system in freshwater fish,Catla catla.
Trait‐based functional dietary analysis provides a better insight into the foraging ecology of bats
Authors: Arrizabalaga‐Escudero Aitor , Merckx Thomas , García‐Baquero Gonzalo , Wahlberg Niklas , Aizpurua Ostaizka , Garin Inazio , Goiti Urtzi , Aihartza Joxerra
Published: July 2019

The degree of trophic specialization determines the ability of predators to cope with changing foraging conditions, but in predators that prey on hundreds of species it is challenging to assess, especially when prey identity varies among predator individuals and across space and time.

Here, we test the hypothesis that a bat species foraging on flying insects like moths will show ample flexibility in trophic niche, and this irrespective of phylogenetic relationships among moths, so as to cope with a high diversity of prey types that vary across seasons. We predict that individual bats will show functional dietary differences consistent with energetic requirements and hunting skills.

We used DNA metabarcoding to determine the diet of 126 Mediterranean horseshoe bats (Rhinolophus euryale) from two different sites during three seasons. Simultaneously, we measured moth availability and characterized the traits of 290 moth taxa. Next, we explored the relationship between phylogeny and traits of all consumed and available moth taxa. Finally, we assessed the relationship between individual traits of bats and traits related to prey profitability, for which we used the RLQ and fourth‐corner statistical techniques.

Seasonality was the main factor explaining the functional dietary variation in adult bats, with moths consumed irrespective of their phylogenetic relationships. While adults consumed moths with a broad range in wing loading, body mass and echolocation detection ability, juveniles consumed slower, smaller and lighter moths, which suggests that young individuals may undergo some fitness gain and/or psychomotor learning process during which they would acquire more effective foraging skills.

Our approach revealed a degree of functional flexibility in the trophic niche previously unknown for an insectivorous bat. Rhinolophus euryale consumed a wide variety of moth taxa differing in profitability throughout seasons and between ontogenetic stages. We showed the validity of trait‐based approaches to gain new insights in the trophic specialization of predators consuming hundreds of species of prey.
The becoming‐methadone‐body: on the onto‐politics of health intervention translations
Authors: Rhodes Tim , Azbel Lyuba , Lancaster Kari , Meyer Jaimie
Published: July 2019

In this paper, we reflect on health intervention translations as matters of their implementation practices. Our case is methadone treatment, an intervention promoted globally for treating opioid dependence and preventingHIVamong people who inject drugs. Tracing methadone's translations in high‐security prisons in the Kyrgyz Republic, we notice the multiple methadones made possible, what these afford, and the onto‐political effects they make. We work with the idea of the ‘becoming‐methadone‐body’ to trace the making‐up of methadone treatment and its effects as an intra‐action of human and nonhuman substances and bodies. Methadone's embodied effects flow beyond the mere psycho‐activity of substances incorporating individual bodies, to material highs and lows incorporating the governing practices of prisoner society. The methadone‐in‐practice of prisoner society is altogether different to that imagined as being in translation as an intervention ofHIVprevention and opioid treatment, and has material agency as a practice of societal governance. Heroin also emerges as an actor in these relations. Our analysis troubles practices of ‘evidence‐based’ intervention and ‘implementation science’ in the health field, by arguing for a move towards ‘evidence‐making’ intervention approaches. Noticing the onto‐politics of health intervention translations invites speculation on how intervening might be done differently.
Patterns of hysterectomy in India: a national and state‐level analysis of the Fourth National Family Health Survey (2015–2016)
Authors: Desai S , Shukla A , Nambiar D , Ved R
Published: July 2019

Objective

The National Family Health Survey‐4 in India provided the first nationally representative estimates of hysterectomy among women aged 15–49. This paper aims to examine the national and state‐level age‐specific prevalence of hysterectomy, individual and household level factors associated with the procedure, and state‐level indicators that may explain variation across states.

Design

Cross‐sectional, nationally representative household survey.

Setting

National Family Health Survey was conducted across all Indian states and union territories between 2015 and 2016.

Population

The survey covered 699 686 women between the ages of 15 and 49 years.

Methods

Descriptive analyses and multivariate logistic regression.

Main outcome measures

Women who reported ever having a hysterectomy and age at hysterectomy.

Results

Age‐specific prevalence of hysterectomy was 0.36% (0.33,0.39) among women aged 15‐29; 3.59% (3.45,3.74) among women aged 30‐39; and 9.20% (8.94,9.46) among women 40‐49 years. There was considerable variation in prevalence by state. Four states reported age‐specific prevalence similar to high‐income settings. Approximately two‐thirds of hysterectomies were conducted in private facilities, with similar patterns across age groups. At the national level, higher age and parity (at least two children); not having had formal schooling; rural residence (adjusted odds ratio [AOR] 1.36; 95% CI 1.27,1.45; P < 0.01) and higher wealth status were associated with higher odds of hysterectomy. Previously sterilised women had lower odds (AOR 0.64; 95% CI 0.61,0,68; P < 0.01) of reporting hysterectomy. Exploratory analyses suggest state‐level factors associated with prevalence of hysterectomy include caesarean section, female illiteracy, and women's employment.

Conclusions

Hysterectomy patterns among women aged 15–49 in India indicate the critical need to ensure treatment options for gynaecological morbidity and to address hysterectomy among young women in particular.

Funding

This study was part of the RASTA initiative of the Population Council's India country office under the Evidence Project supported by USAID.

Tweetable abstract

Hysterectomy patterns in India highlight the need for alternatives to treat gynaecological morbidity among younger women.
New label‐free automated survival assays reveal unexpected stress resistance patterns during C. elegans aging
Authors: Benedetto Alexandre , Bambade Timothée , Au Catherine , Tullet Jennifer M.A. , Monkhouse Jennifer , Dang Hairuo , Cetnar Kalina , Chan Brian , Cabreiro Filipe , Gems David
Published: July 2019

Caenorhabditis elegans is an excellent model for high‐throughput experimental approaches but lacks an automated means to pinpoint time of death during survival assays over a short time frame, that is, easy to implement, highly scalable, robust, and versatile. Here, we describe an automated, label‐free, high‐throughput method using death‐associated fluorescence to monitor nematode population survival (dubbed LFASS for label‐free automated survival scoring), which we apply to severe stress and infection resistance assays. We demonstrate its use to define correlations between age, longevity, and severe stress resistance, and its applicability to parasitic nematodes. The use of LFASS to assess the effects of aging on susceptibility to severe stress revealed an unexpected increase in stress resistance with advancing age, which was largely autophagy‐dependent. Correlation analysis further revealed that while severe thermal stress resistance positively correlates with lifespan, severe oxidative stress resistance does not. This supports the view that temperature‐sensitive protein‐handling processes more than redox homeostasis underpin aging in C. elegans. That the ages of peak resistance to infection, severe oxidative stress, heat shock, and milder stressors differ markedly suggests that stress resistance and health span do not show a simple correspondence in C. elegans.
Downregulation of nicotinamide nucleotide transhydrogenase and its naturally occurring antisense RNA in gastric cancer
Authors: Esfandi Farbod , Taheri Mohammad , Kahaei Mir Salar , Omrani Mir Davood , Kholghi Oskooei Vahid , Ghafouri‐Fard Soudeh
Published: July 2019

Aim

Nicotinamide Nucleotide Transhydrogenase (NNT) gene encodes a protein, which is an important antioxidative enzyme that converts NADH to NADPH. This enzyme provides a significant proportion of the entire NADPH resource in the mitochondria. Previous reports have shown possible contribution of this gene in the carcinogenesis process.

Methods

In the current research, we evaluated expression levels of NNT gene and a naturally occurring antisense RNA (NNT‐AS1) in gastric cancer specimens compared to their corresponding adjacent noncancerous tissues (ANCTs).

Results

Both NNT1 and NNT‐AS1 genes were significantly downregulated in tumor tissues compared to ANCTs (expression ratio = 0.369, p = .045 and expression ratio = 0.368, p = .043, respectively). Transcript levels of NNT1 and NNT‐AS1 were associated with the location of the primary tumor (p = .003 and .002, respectively). Moreover, expressions of both genes were significantly elevated in tumors with lymphatic/vascular invasion compared to tumors without lymphatic/vascular invasion (p = .001 and p = .005). No other remarkable associations were noticed between transcript levels of genes in tumor tissues and patients’ information. Based on the area under curve (AUC) values in the receiver operating characteristic (ROC) curves, the diagnostic power of NNT1 and NNT‐AS1 were estimated to be 0.62 and 0.63, respectively.

Conclusions

Although we demonstrated dysregulation of NNT1 and NNT‐AS1 in gastric tumor specimens in association with clinical data of patients, these two genes are not supposed to be appropriate biomarkers for gastric cancer.
Distribution, bioclimatic niche and sympatry of two Erinaceidae in Tunisia
Authors: El‐Farhati Haithem , Jaziri Brahim , Hizem Mohamed Wassim , Nouira Saïd
Published: July 2019

Numerous mammalian species of North Africa have an enigmatic distribution between the Mediterranean and Saharan area. In order to study the distribution of hedgehogs in Tunisia, field data were collected from several protected areas and various natural and peri‐urban environments during 4 years 2015–2018 covering the all bioclimatic zones present in the country. The present work provides a detailed geographical and ecological distribution of hedgehogs with a total of 168 occurrence data of Atelerix algirus and Paraechinus aethiopicus. Atelerix algirus showed a wide distribution range from north to south being absent only in the extreme Saharan environment. Paraechinus aethiopicus has been recorded in the centre and the south with a specialisation in the arid and Saharan environment. A parapatry distribution is also shown with a sympatric area between arid and Saharan bioclimates. Our results improve knowledge of the bioclimatic niche and habitat characteristic of these taxa not clearly defined in previous research. The presence of the two hedgehogs on Djerba Island (A. algirus and P. aethiopicus) is also confirmed.
Oxidative stress, inflammatory settings, and microRNA regulation in the recurrent implantation failure patients with metabolic syndrome
Authors: Sheikhansari Golshan , Soltani‐Zangbar Mohammad Sadegh , Pourmoghadam Zahra , Kamrani Amin , Azizi Ramyar , Aghebati‐Maleki Leili , Danaii Shahla , Koushaeian Ladan , Hojat‐Farsangi Mohammad , Yousefi Mehdi
Published: July 2019

Problem

Increased oxidative stress (OS) and inflammatory factors in metabolic syndrome (MS) patients are considered as risk factors for recurrent implantation failure (RIF). The aim of this study was to investigate OS markers, inflammatory factors, related microRNAs (miRNA) expression, and cytokine and transcription factors RNA expression.

Method of study

We evaluated the frequency of helper T (Th) 17 and regulatory T (Treg) cells in recurrent implantation failure (RIF) women with or without MS. miRNA expression, an inflammatory cytokine, and transcription factors were measured by real‐time PCR. The level of interleukin (IL)‐1β, IL‐6, IL‐17, tumour necrosis factor‐alpha (TNF‐alpha) and chemokine (C‐C motif) ligand 2 (CCL‐2), and C‐X‐C motif chemokine ligand 8 (CXCL‐8) were measured by enzyme‐linked immunosorbent assay (ELISA). OS markers were evaluated by spectrophotometric assay. Th17 and Treg cell frequencies were determined by flow cytometry.

Results

The expression of AP1, NF‐κB, FOXP3, miRNA‐21; serum or plasma level of OS markers (ie, nitric oxide, total oxidant status, and myeloperoxidase); serum level of inflammatory factors (ie, IL1‐β, IL‐6, IL‐17, TNF‐alpha, CXCL‐8, and CCL‐2); and frequency of Th17 cells were increased in RIF‐MS patients in comparison with RIF women without MS (RIF‐NMS) and control group. The expression of miRNA‐223 and 146a, antioxidant enzymes, namely superoxide dismutase (SOD) and catalase (CAT), and frequency of Treg also declined in RIF‐MS patients.

Conclusion

Overall, our findings suggest that MS in RIF patients causes increased inflammatory factors and OS, which in turn leads to implantation failure.