bluuebunny/crossref_metadata_2025_split huggingface dataset:
SCryPTA:A web-based platform for analyzing Small-Angle Scattering curves of lyotropic liquid crystals
Authors: de Castro Raphael Dias , Casadei Bruna Renata , Santana Barbara Vasconcelos , Lotierzo Mayra , de Oliveira Natália F. , Malheiros Barbara , Mariani Paolo , Kaminski Renata C. K. , Barbosa Leandro R. S. 
Published: October 2019

ABSTRACTSmall angle X-ray scattering (SAXS) is a powerful technique for the characterization of systems with highly ordered structures, such as liquid crystals and self-assembly systems. In the field of nanotechnology and nanomedicine, SAXS can be used to characterize the crystallographic properties of the crystal phase of lyotropic systems and nanoparticles with internal crystal phase, such as cubosomes, hexosomes and multi-lamellar vesicles. In this work, we introduce a new web platform namedSCryPTA: Small Angle Scattering Crystallographic Peak Treatment and Analysis, capable of reading SAXS data and providing a comprehensive visualization of the scattering curve along with the calculation of important physical parameters, such as the lattice parameter of the crystal structure, the lipidic bilayer width, among others. Cubic, hexagonal and multilamellar scattering data had their crystallographic structure characterized in SCryPTA. So far, four different cubic structures, (Pn3m(Q224),Fd3m(Q227),Im3m(Q229),Ia3d(Q230)), the hexagonal phase and also multi-lamellar vesicle systems are described in the platform. We believe that SCryPTA may help researchers from several fields, since it has a user-friendly interface. The platform is available at:www.if.usp.br/scrypta.
The consequences of surviving infection across the metamorphic boundary: tradeoff insights from RNAseq and life history measures
Authors: Keehnen Naomi L.P. , Kučerová Lucie , Nylin Sören , Theopold Ulrich , Wheat Christopher W. 
Published: October 2019

AbstractThe broad diversity of insect life has been shaped, in part, by pathogen pressure, yet the influence of injury and infection during critical periods of development is understudied. During development, insects undergo metamorphosis, wherein the organism experiences a dramatic shift in their overall morphology, and physiology. In temperate zones, metamorphosis is often directly followed by a developmental arrest called diapause, for which the insect needs to acquire enough energy reserves before the onset of winter. We investigated the long-term effects of injury and infection using two bacteria in the butterfly Pieris napi, revealing that the negative consequences of bacterial infection carry across the metamorphic boundary. Initial direct effects of infection were weight loss and slower development, as well as an increased mortality at higher infection levels. The detrimental effects were stronger in the gram-positive Micrococcus luteus compared to gram-negative Escherichia coli. Transcriptome-wide differences between the two bacteria were already observed in the gene expression profile of the first 24 hours after infection. Larvae infected with M. luteus showed a strong suppression of all non-immunity related processes, with several types of immune responses being activated. The impact of these transcriptomic changes, a tradeoff between homeostasis and immune response, were visible in the life history data, wherein individuals infected with M. luteus had the highest mortality rate, along with the lowest pupal weight, developmental rate and adult weight of all the treatments. Overall, we find that the cost of infection and wounding in the final larval instar carries over the metamorphic boundary, and is expected to negatively affect their lifetime fitness.
Hippocampal neural stem cells facilitate access from circulation via apical cytoplasmic processes
Authors: Licht Tamar , Keshet Eli 
Published: October 2019

SummaryBlood vessels (BVs) are considered an integral component of neural stem cells (NSCs) niches. NSCs in the dentate gyrus (DG) have enigmatic elaborated apical cellular processes that are associated with BVs. Whether this contact serves as a mechanism for delivering circulating molecules is not known. Here we uncovered a previously unrecognized communication route allowing exclusive direct access of blood-borne substances to hippocampal NSCs in defiance of an intact blood-brain barrier (BBB). BBB-impermeable fluorescent tracer injected transcardially is selectively uptaken by DG NSCs within a minute, via the vessel-associated apical processes. These processes, measured >30nm in diameter, establish direct membrane-to-membrane contact with endothelial cells in areas devoid of the endothelial basement membrane. Doxorubicin, a brain-impermeable chemotherapeutic agent, is also readily and selectively uptaken by NSCs and reduces their proliferation, which might explain its problematic anti-neurogenic or cognitive side-effect. The newly-discovered NSC-BV communication route explains how circulatory neurogenic mediators are ‘sensed’ by NSCs.
Metabarcoding unsorted kick-samples facilitates macroinvertebrate-based biomonitoring with increased taxonomic resolution, while outperforming environmental DNA
Authors: Pereira-da-Conceicoa Lyndall , Elbrecht Vasco , Hall Andie , Briscoe Andrew , Barber-James Helen , Price Benjamin 
Published: October 2019

AbstractMany studies have highlighted the potential of DNA-based methods for the biomonitoring of freshwater macroinvertebrates, however only a few studies have investigated homogenisation of bulk samples that include debris to reduce sample-processing time. In order to explore the use of DNA-based methods in water quality assessment in South Africa, this study compares morphological and molecular-based identification of freshwater macroinvertebrates at the mixed higher taxon and mOTU level while investigating abundance and comparing mOTU recovery with historical species records. From seven sites across three rivers in South Africa, we collected a biomonitoring sample, an intensive-search comprehensive sample and an eDNA sample per site. The biomonitoring sample was picked and scored according to standard protocols and the leftover debris and comprehensive samples were homogenised including all debris. DNA-based methods recovered higher diversity than morphology, but did not always recover the same taxa, even at the family level. Regardless of the differences in taxon scores, most DNA-based methods except some eDNA samples, returned the same water quality assessment category as the standard morphology-based assessment. Homogenised comprehensive samples recovered more freshwater invertebrate diversity than all other methods. The eDNA samples recovered 2 to 10 times more mOTUs than any other method, however 90% of reads were non-target and as a result eDNA recovered the lowest target diversity. However, eDNA did find some target taxa that the other methods failed to detect. This study shows that unsorted samples recover the same water quality scores as a morphology-based assessment and much higher diversity scores than both picked and eDNA samples. As a result, there is potential to integrate DNA-based approaches into existing metrics quickly while providing much more information for the development of more refined metrics at the species or mOTU level with distributional data which can be used for conservation and biodiversity management.
Self-Incompatibility Alleles in Iranian Pear Cultivars
Authors: Bagheri Maryam , Ershadi Ahmad 
Published: October 2019

AbstractIn the present study, the S-alleles of eighteen pear cultivars, (including fourteen cultivars planted commercially in Iran and four controls) are determined. 34 out of 36 S-alleles are detected using nine allele-specific primers, which are designed for amplification of S101/S102, S105, S106, S107, S108, S109, S111, S112 and S114, as well as consensus primers, PycomC1F and PycomC5R. S104, S101 and S105 were the most common S-alleles observed, respectively, in eight, seven and six cultivars. In 16 cultivars, (‘Bartlett’ (S101S102), ‘Beurre Giffard’ (S101S106), ‘Comice’ (S104S105), ‘Doshes’ (S104S107), ‘Koshia’ (S104S108), ‘Paskolmar’ (S101S105), ‘Felestini’ (S101S107), ‘Domkaj’ (S104S120), ‘Ghousi’ (S104S107), ‘Kaftar Bache’ (S104S120), ‘Konjoni’ (S104S108), ‘Laleh’ (S105S108), ‘Natanzi’ (S104S105), ‘Sebri’ (S101S104), ‘Se Fasleh’ (S101S105) and ‘Louise Bonne’ (S101S108)) both alleles are identified but in two cultivars, (‘Pighambari’ (S105) and ‘Shah Miveh Esfahan’ (S107)) only one allele is recognized. It is concluded that allele-specific PCR amplification can be considered as an efficient and rapid method to identify S-genotype of Iranian pear cultivars.
Development of a multiparent advanced generation intercross (MAGIC) population for genetic exploitation of complex traits inBrassica juncea: glucosinolate content as an example
Authors: Wang Tianya , Wan Wei , Yu Kunjiang , Khattak Aimal Nawaz , Ye Botao , Yang Renqin , Tian Entang 
Published: October 2019

AbstractMultiparent advanced generation intercross (MAGIC) populations have recently been developed to allow the high-resolution mapping of complex quantitative traits. This article describes the development of one MAGIC population and verifies its potential application for mapping quantitative trait loci (QTLs) inB. juncea. The population was developed from eight founders with diverse traits and composed of 408 F6recombinant inbred lines (RILs). To develop one rapid and simplified way for using the MAGIC population, a subset of 133 RILs as the primary mapping population were genotyped using 346 intron-length polymorphism (ILP) polymorphic markers. The population lacks significant signatures of population structure that are suitable for the analysis of complex traits. Genome-wide association mapping (GWAS) identified three major glucosinolate (GSL) QTLs ofQGsl.ig01.1on J01 for indole GSL (IG),QGsl.atg09.1on J09 andQGsl.atg11.1on J11 for aliphatic GSL (AG) and total GSL (TG). The candidate genes forQGsl.ig01.1, QGsl.atg09.1andQGsl.atg11.1areGSH1, GSL-ALKandMYB28, which are involved in converting glutamate and cysteine toγ–EC, the accumulation of glucoraphanin, and the whole process of AG metabolism, respectively. One effective method for association mapping of quantitative traits in theB. junceaMAGIC population is also suggested by utilization of the remaining 275 RILs and incorporation of the novel kompetitive allele specific PCR (KASP) technique. In addition to its QTL mapping purpose, the MAGIC population could also be potentially utilized in variety development by breeders.
SCRIBE: a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data
Authors: Zhang Yiliang , Liang Kexuan , Liu Molei , Li Yue , Ge Hao , Zhao Hongyu 
Published: October 2019

AbstractSingle-cell RNA sequencing technologies are widely used in recent years as a powerful tool allowing the observation of gene expression at the resolution of single cells. Two of the major challenges in scRNA-seq data analysis are dropout events and batch effects. The inflation of zero(dropout rate) varies substantially across single cells. Evidence has shown that technical noise, including batch effects, explains a notable proportion of this cell-to-cell variation. To capture biological variation, it is necessary to quantify and remove technical variation. Here, we introduce SCRIBE (Single-Cell Recovery Imputation with Batch Effects), a principled framework that imputes dropout events and corrects batch effects simultaneously. We demonstrate, through real examples, that SCRIBE outperforms existing scRNA-seq data analysis tools in recovering cell-specific gene expression patterns, removing batch effects and retaining biological variation across cells. Our software is freely available online at https://github.com/YiliangTracyZhang/SCRIBE.
Not all MDAs should be created equal – determinants of MDA impact and designing MDAs towards malaria elimination
Authors: Gao B. , Saralamba S. , Lubell Y. , White L. J. , Dondorp A. , Aguas R. 
Published: October 2019

AbstractMalaria remains at the forefront of scientific research and global political and funding agendas. Previous malaria models of mass-interventions have consistently oversimplified how mass interventions are implemented. We present an individual based, spatially explicit model of malaria transmission that includes all the programmatic implementation details of mass drug administration (MDA) campaigns. We uncover how the impact of MDA campaigns is determined by the interaction between implementation logistics, patterns of human mobility and how transmission risk is distributed over space. This translates into a higher likelihood of malaria elimination for areas with true prevalence under 3% with a faster implementation, in highly mobile populations. If populations are more static, deploying less interventions teams would be cost optimal and predicted to be as impactful. We conclude that mass drug interventions can be an invaluable tool towards malaria elimination in the right context, specifically when paired with effective vector control.
Reproducibility warning: The curious case of Polyethylene glycol 6000 and spheroid cell culture
Authors: Serrati Simona , Martinelli Chiara , Palazzo Antonio , Iacobazzi Rosa Maria , Perrone Mara , Santoliquido Roberto , Ong Quy K. , Luo Zhi , Bekdemir Ahmet , Pinto Giulia , Cavalleri Ornella , Cutrignelli Annalisa , Laquintana Valentino , Denora Nunzio , Stellacci Francesco , Krol Silke 
Published: October 2019

AbstractIn this study we report about the reproducibility of three-dimensional cell culture of floating cell spheroids on PEG6000 treated cell culture dishes. Three-dimensional tumour spheroids or organoids present an interesting test platform for nanoparticulated drug delivery or nanoparticle toxicity. We tested the reproducibility of spheroid formation induced by the PEG coated surface. Interestingly we found that the results were different in a reproducible manner depending on the distributors of PEG6000.Despite the nearly identical physicochemical properties of PEG6000 (MALDI-MS, NMR, FTIR, Triple SEC) with only minor differences, we observed only for one PEG6000 a highly reproducible formation of spheroids with different cell lines such as HT-29, HeLa, Caco2, and PANC-1. The surface coating with the different PEG6000 was studied by AFM. The surface coating as well as the physicochemical characterization showed only small differences in mass and hydrodynamic radius between the different PEGs. A direct coating of the cells with PEG from two distributors indicate that the spheroid formation in due to direct interaction of the polymer with the cell rather than by interaction of cells with the coated surface.The experiments point out that for biological entities, such as cells or tissues, even very small differences such as impurities or batch-to-batch variations in the purchased product can have a very strong impact.
A LAMP at the end of the tunnel: a rapid, field deployable assay for the kauri dieback pathogen,Phytophthora agathidicida
Authors: Winkworth Richard C. , Nelson Briana C.W. , Bellgard Stanley E. , Probst Chantal M. , McLenachan Patricia A. , Lockhart Peter J. 
Published: October 2019

AbstractThe collar rot causing oomycete,Phytophthora agathidicida, threatens the long-term survival of the iconic New Zealand kauri. Currently, testing for this pathogen involves an extended soil bioassay that takes 14-20 days and requires specialised staff, consumables, and infrastructure. Here we describe a loop-mediated isothermal amplification (LAMP) assay for the detection ofP. agathidicidathat targets a portion of the mitochondrial apocytochrome b coding sequence. This assay has high specificity and sensitivity; it did not cross react with a range of otherPhytophthoraisolates and detected as little as 1 fg of totalP. agathidicidaDNA or 116 copies of the target locus. Assay performance was further investigated by testing plant tissue baits from flooded soil samples using both the extended bioassay and LAMP testing of DNA extracted from baits. In these comparisons,P. agathidicidawas detected more frequently using the LAMP assay. In addition to greater sensitivity, by removing the need for culturing, the hybrid baiting plus LAMP approach is more cost effective than the bioassay and, importantly, does not require a centralised laboratory facility with specialised staff, consumables, and equipment. Such testing will allow us to address outstanding questions aboutP. agathidicida. For example, the hybrid approach could enable monitoring of the pathogen beyond areas with visible disease symptoms, allow direct evaluation of rates and patterns of spread, and allow the effectiveness of disease control to be evaluated. The hybrid assay also has the potential to empower local communities. These communities could use this diagnostic tool to evaluate the pathogen status of local kauri stands, providing information around which to base their management and allowing informed engagement with wider initiatives.
A Highly ConservedShhEnhancer Coordinates Hypothalamic and Craniofacial Development
Authors: Crane-Smith Zoe , Schoenebeck Jeffrey , Graham Katy A , Devenney Paul S , Rose Lorraine , Ditzell Mark , Anderson Eve , Thomson Joseph I , Klenin Natasha , Kurrasch Deborah M , Lettice Laura A , Hill Robert E 
Published: October 2019

AbstractEnhancers that are conserved deep in evolutionary time regulate characteristics held in common across taxonomic classes. Here, deletion of the highly conservedShhenhancer SBE2 (Shhbrain enhancer 2) markedly reducedShhexpression within the embryonic brain specifically in the rostral diencephalon; however, no abnormal anatomical phenotype was observed due to compensatory low levels of expression mediated by a second enhancer. In contrast, a further reduction ofShhlevels, achieved by crossing the SBE2 deletion with theShhnull allele, disrupted brain and craniofacial tissue; thus, linking SBE2 regulatedShhexpression to multiple defects and further enabling the study of the effects of differing levels ofShhon embryogenesis. Development of the hypothalamus, derived from the rostral diencephalon, was disrupted along both the anterior-posterior (AP) and the dorsal-ventral (DV) axes. Expression of DV patterning genes and subsequent neuronal population induction were particularly sensitive toShhexpression levels, demonstrating a novel morphogenic context forShh. The role of SBE2, which is highlighted by DV gene expression, is to step-up expression ofShhabove the minimal activity of the second enhancer, ensuring the necessary levels of Shh in a regional-specific manner. We also show that lowShhlevels in the diencephalon disrupted neighbouring craniofacial development, including mediolateral patterning of the bones along the cranial floor and viscerocranium. Thus, SBE2 contributes to hypothalamic morphogenesis and ensures there is coordination with the formation of the adjacent midline cranial bones that subsequently protects the neural tissue.
Science or prejudice
Authors: Zhan Jintao , Ma Yubei , Lv Xinye , Xu Meng , Zhang Mingyang 
Published: October 2019

PurposeSome researchers argue that consumers’ lack of knowledge is an important factor increasing risk for a new product derived from emerging agricultural technology. The purpose of this paper is to discuss the potential impacts and the differential effects of subjective and objective perceptions on Chinese consumers’ preferences for the application of a novel biotechnology.Design/methodology/approachTaking transgenic technology as an example and employing data from a survey of 1,000 consumers in Jiangsu Province, the authors develop a mixed-process regression model based on Fishbein’s multiple attributes attitude model.FindingsThe results suggest that there are apparent differences between Chinese consumers’ subjective perceptions and objective perceptions concerning transgenic technology and genetically modified (GM) food, and there exists certain selective perceptions of the emerging biotechnology. Having a subjective perception concerning transgenic technology has a positive effect on consumers’ overall attitudes, whereas subjective and objective perceptions concerning GM foods have a negative effect on consumers’ overall attitudes. Self-identification generated from subjective perception occupies a dominant position in determining consumers’ attitudes.Originality/valueConsumers’ attitudes regarding an agricultural product depend on their perception of the attributes of the technology used to produce such a product. This study attempts to distinguish and empirically test urban consumers’ subjective perceptions (self-assessed or perceived) and objective perceptions (obtained from a test) about transgenic technology and GM foods and the impact of these four types of perception on the consumers’ attitudes regarding the application of transgenic technology. In this paper, the authors construct a mixed-process regression model to address the possible endogeneity of the perception variables.
Reducing costly free-rider effects via OASIS
Authors: Chiu Ming Ming , Woo Chi Keung , Shiu Alice , Liu Yun , Luo Bonnie X. 
Published: October 2019

Purpose
A team member might exert little effort and exploit teammates’ work (free riding), which can discourage their efforts. The purpose of this paper is to examine whether free riding devalues team projects and whether an online assessment system for individual scores (OASIS) system can reduce student perceptions of free riding and its harmful effects. OASIS includes: contractual commitment, team discussion, median peer assessment of each member’s contribution, assessment revision opportunities, conditional teacher participation and final appeal.

Design/methodology/approach
University students (238 in India and 60 in Hong Kong) completed pre-and post-surveys.

Findings
Students who valued team projects more than others experienced fewer past free riders, viewed team members as contributing equally, or viewed free riding as harming fair grading. After OASIS, these students reported that only 3 percent of their teammates were free riders, and were less likely to perceive that free riders had harmed them or hindered fair grading. Results did not differ across gender or regions.

Research limitations/implications
These data are correlational rather than longitudinal, and hence cannot determine causality.

Practical implications
The OASIS system requires a computer.

Originality/value
This is the first study to test a system for reducing free riders across countries.