bluuebunny/crossref_metadata_2025 huggingface dataset:
Membrane domains and phosphatase exclusion produce robust signaling responses in B cells engaged with natural ligands and artificial cross-linkers presented on lipid bilayers
Authors: Núñez Marcos Francisco , Wisser Kathleen , Veatch Sarah L
Published: May 2019

B cells respond to a wide variety of antigens with varying valiancy and mode of presentation to the highly expressed B cell receptor (BCR). We previously demonstrated that clustering the IgM isotype of BCR with an artificial soluble cross-linker led to the stabilization of an ordered phase-like domain. This domain sorted minimal peptides and full-length proteins to generate local hot-spots for tyrosine phosphorylation at receptor clusters, facilitating receptor activation. BCR can also be activated through interactions with natural ligands or artificial cross-linkers presented at bilayer surfaces, where it is proposed that alternate mechanisms play important roles in receptor clustering and activation, including one mechanism involving the exclusion phosphatases due to their bulky extracellular domains. The goals of the current study are to determine if markers of membrane phases are sorted by BCR clusters formed through engagement with bilayer-presented natural ligands or cross-linkers, and to estimate the contribution that membrane phase partitioning plays in organizing regulatory proteins with respect to BCR clusters under these stimulation conditions. We use super-resolution fluorescence localization microscopy to find that BCR engagement with either a bilayer-presented natural ligand or artificial cross-linker generates ordered phase-like domains that are more robust than those observed with soluble cross-linkers. In addition, we provide evidence that interactions between regulatory proteins and BCR are partially determined through their preference for ordered membrane domains and present a minimal model of receptor activation that incorporates both ordered domains and steric exclusion mechanisms to produce a more sensitive response. Overall, this work highlights that cells are capable of integrating multiple interaction modalities to give rise to cellular functions, likely conferring flexibility and robustness to cellular responses.
Practical universalk-mer sets for minimizer schemes
Authors: DeBlasio Dan , Gbosibo Fiyinfoluwa , Kingsford Carl , Marçais Guillaume
Published: May 2019

Minimizer schemes have found widespread use in genomic applications as a way to quickly predict the matching probability of large sequences. Most methods for minimizer schemes use randomized (or close to randomized) ordering ofk-mers when finding minimizers, but recent work has shown that not all non-lexicographic orderings perform the same. One way to findk-mer orderings for minimizer schemes is through the use of universalk-mer sets, which are subsets ofk-mers that are guaranteed to cover all windows. The smaller this set the fewer false positives (where two poorly aligned sequences being identified as possible matches) are identified. Current methods for creating universalk-mer sets are limited in the length of thek-mer that can be considered, and cannot compute sets in the range of lengths currently used in practice. We take some of the first steps in creating universalk-mer sets that can be used to construct minimizer orders for large values ofkthat are practical. We do this using iterative extension of thek-mers in a set, and guided contraction of the set itself. We also show that this process will be guaranteed to never increase the number of distinct minimizers chosen in a sequence, and thus can only decrease the number of false positives over using the current sets on smallk-mers.
Intragenic repeat expansions control yeast chronological aging
Authors: Barré Benjamin P , Hallin Johan , Yue Jia-Xing , Persson Karl , Mikhalev Ekaterina , Irizar Agurtzane , Thompson Dawn , Molin Mikael , Warringer Jonas , Liti Gianni
Published: May 2019

Aging varies among individuals due to both genetics and environment but the underlying molecular mechanisms remain largely unknown. Using a highly recombinedSaccharomyces cerevisiaepopulation, we found 30 distinct Quantitative Trait Loci (QTLs) that control chronological life span (CLS) in calorie rich and calorie restricted environments, and under rapamycin exposure. Calorie restriction and rapamycin extended life span in virtually all genotypes, but through different genetic variants. We tracked the two major QTLs to massive expansions of intragenic tandem repeats in the cell wall glycoproteinsFLO11andHPF1, which caused a dramatic life span shortening. Life span impairment by N-terminalHPF1repeat expansion was partially buffered by rapamycin but not by calorie restriction. TheHPF1repeat expansion shifted yeast cells from a sedentary to a buoyant state, thereby increasing their exposure to surrounding oxygen. The higher oxygenation perturbed methionine, lipid, and purine metabolism, which likely explains the life span shortening. We conclude that fast evolving intragenic repeat expansions can fundamentally change the relationship between cells and their environment with profound effects on cellular life style and longevity.
Genomic potential for photoferrotrophy in a seasonally anoxic Boreal Shield lake
Authors: Tsuji JM , Tran N , Schiff SL , Venkiteswaran JJ , Molot LA , Tank M , Hanada S , Neufeld JD
Published: May 2019

Photoferrotrophy, the light-induced oxidation of ferrous iron, is thought to have contributed to primary production within Earth’s early anoxic oceans yet is presumed to be of little modern environmental relevance. Here we use genome-resolved metagenomics and enrichment cultivation to explore the potential for photoferrotrophy in the anoxic water columns of globally abundant Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel “Candidatus Chlorobium canadense”, encoded the cyc2 candidate gene marker for iron oxidation, suggesting the potential for photoferrotrophic growth. Surprisingly, one of the environmental genome bins encoded cyc2 and lacked sulfur oxidation gene pathways altogether. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in “Ca. Chlorobium canadense”, suggesting that yet-unexplored mechanisms regulate expression of sulfide and ferrous iron oxidation gene systems, or that previously unrecognized functions for this outer membrane cytochrome exist. Doubling the known diversity of Chlorobia-associated cyc2 genes, metagenome data showed that putative photoferrotrophic populations occurred in one lake but that only sulfide-oxidizing populations were present in a neighboring lake, implying that strong ecological or geochemical controls govern the favourability of photoferrotrophy in aquatic environments. These results indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have unexplored metabolic diversity that is controlled by ecological and biogeochemical drivers pertinent to understanding Earth’s early microbial communities.
Humans can efficiently look for but not select multiple visual objects
Authors: Ort Eduard , Fahrenfort Johannes J. , ten Cate Tuomas , Eimer Martin , Olivers Christian N.L.
Published: May 2019

The human brain recurrently prioritizes task-relevant over task-irrelevant visual information. A central, question is whether multiple objects can be prioritized simultaneously. To answer this, we let observers search for two colored targets among distractors. Crucially, we independently varied the number of target colors that observers anticipated, and the number of target colors actually used to distinguish the targets in the display. This enabled us to dissociate the preparation of selection mechanisms from the actual engagement of such mechanisms. Multivariate classification of electroencephalographic activity allowed us to track selection of each target separately across time. The results revealed only small neural and behavioral costs associated with preparing for selecting two objects, but substantial costs when engaging in selection. Further analyses suggest this cost is the consequence of neural competition resulting in limited parallel processing, rather than a serial bottleneck. The findings bridge diverging theoretical perspectives on capacity limitations of feature-based attention.
Evolutionary forces on different flavors of intrinsic disorder in the human proteome
Authors: Forcelloni Sergio , Giansanti Andrea
Published: May 2019

In this study, we perform a systematic analysis of evolutionary forces (i.e., mutational bias and natural selection) that shape the codon usage bias of human genes encoding for different structural and functional variants of proteins. Well-structured proteins are expected to be more under control by natural selection than intrinsically disordered proteins because one or few mutations (even synonymous) in the genes can result in a protein that no longer folds correctly. On the contrary, intrinsically disordered proteins are generally thought to evolve more rapidly than well-folded proteins, primarily attributed to relaxed purifying natural selection due to the lack of structural constraints. Using different genetic tools, we find compelling evidence that intrinsically disordered proteins are the variant of human proteins on which both mutational bias and natural selection act more effectively, corroborating their essential role for evolutionary adaptability and protein evolvability. We speculate that intrinsically disordered proteins have a high tolerance to mutations (both neutral and adaptive) but also a selective propensity to preserve their structural disorder, i.e., flexibility and conformational dynamics under physiological conditions. Additionally, we confirm not only that intrinsically disordered proteins are preferentially encoded by GC-rich genes, but also that they are characterized by the highest fraction of CpG-sites in the sequences, implying a higher susceptibility to methylation resulting in C-T transition mutations. Our results provide new insight about protein evolution and human genetic diseases identifying intrinsically disordered proteins as reservoirs for evolutionary innovations.
Partial-resistance against aphids in wild barley reduces the oviposition success of the generalist parasitoid,Aphidius colemaniViereck
Authors: Leybourne Daniel. J. , Valentine Tracy. A. , Bos Jorunn. I. B. , Karley Alison. J.
Published: May 2019

Aphids are significant agricultural pests of cereal crops with a worldwide distribution. The control of aphids in agricultural systems is currently heavily reliant on insecticidal compounds, but it is becoming increasingly apparent that chemical-based control of agricultural pests has far-reaching unintended consequences on agro-ecosystems. As a result, more sustainable means of aphid control are becoming increasingly desirable. Potential options include increasing plant resistance against aphids, promoting biocontrol, and the combined use of both strategies. When used together it is important to understand how, and to what extent, increased plant resistance against aphids affects the success of biocontrol agents. In this current study, we examine how partial-resistance against cereal aphids in a wild relative of barley,Hordeum spontaneum 5(Hsp5), affects the success of the common parasitoid of cereal aphids,Aphidius colemani. We show that the parasitism success ofA. colemaniattacking nymphs of the bird cherry-oat aphid,Rhopalosiphum padi, contained on Hsp5 is reduced compared with the parasitism success of wasps attackingR. padinymphs feeding on a susceptible modern cultivar of barley,H. vulgarecv. Concerto.Explantaparasitism assays showed that the in parasitoid success is a direct effect of the plant environment (such as differential architectural traits), rather than an indirect effect dur to a decrease in aphid suitability resulting from increased resistance against aphids in Hsp5. Our study highlights the importance of understanding the direct and indirect effects of plant resistance against aphids on biocontrol strategies.
Learning lexical-syntactic biases: An fMRI study on how we connect words and syntactic information
Authors: Weber K. , Meyer A. , Hagoort P.
Published: May 2019

Language processing often involves learning new words and how they relate to each other. These relations are realized through syntactic information connected to a word, e.g. a word can be verb or a noun, or both, like the word ‘run’. In a behavioral and an fMRI task we showed that words and their syntactic properties, i.e. lexical items which were either syntactically ambiguous or unambiguous, can be learned through the probabilities of co-occurrence in an exposure session and subsequently used in a production task. Novel words were processed within regions of the language network (left inferior frontal and posterior middle temporal gyrus) and more syntactic options led to higher activations herein, even when the words were shown in isolation, suggesting combined lexical-syntactic representation. When words were shown in untrained grammatical contexts, activation in left inferior frontal cortex increased. This might reflect competition between the newly learned representation and the presented information. The results elucidate the lexical nature of the neural representations of lexical-syntactic information within the language network and the specific role of the left inferior frontal cortex in unification of the novel words with the surrounding context.
Auditory processing atypicalities for pure tones and complex speech sounds in Rett Syndrome – towards neuromarkers of disease progression
Authors: Sysoeva Olga V. , Molholm Sophie , Djukic Aleksandra , Frey Hans-Peter , Foxe John J.
Published: May 2019

Due to severe motor impairments and the lack of expressive language abilities seen in most patients with Rett Syndrome (RTT), it has proven extremely difficult to obtain accurate measures of auditory processing capabilities in this population. Here, we examined early auditory cortical processing of pure tones and more complex phonemes females with confirmed mutation of the MECP2 gene. We recorded high-density auditory evoked potentials (AEP), which allow for objective evaluation of the timing and severity of processing deficits along the auditory processing hierarchy. We compared AEPs of 12 females with RTT to those of 21 typically developing (TD) peers aged 4-21 years, interrogating the first four major components of the AEP (P1: 60-90ms; N1: 100-130ms; P2: 135-165ms; N2: 245-275ms). Atypicalities were evident in RTT at the initial stage of processing. Whereas the initial P1 showed increased amplitude to phonemic inputs relative to tones in TD participants, this modulation by stimulus complexity was absent in RTT. Interestingly, the subsequent N1 did not differ between groups, whereas the following P2 was hugely diminished in RTT, regardless of stimulus complexity. The N2 was similarly smaller in RTT, and did not differ as a function of stimulus type. The P2 effect was remarkably robust in differentiating between groups with near perfect separation between the two groups despite the wide age range of our samples. Given this robustness, along with the observation that P2 amplitude was significantly associated with RTT symptom severity, the P2 has the potential to serve as a biomarker of treatment efficacy.

Significance statement

Our study points to dramatic reduction of the P2 component of the auditory evoked potential (AEP) as a potentially reliable biomarker of Rett Syndrome severity, with prospective applicability as an objective readout (neuromarker) of change in functional brain activity following therapeutic interventions administered in the context of clinical trials. Compellingly, the reduction of P2 amplitude in patients with RTT mimics findings in animal models of RTT, providing a translational bridge between pre-clinical and human research.
Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing
Authors: Crawford Emily , Kamm Jack , Miller Steve , Li Lucy M. , Caldera Saharai , Lyden Amy , Yokoe Deborah , Nichols Amy , Tran Nam K. , Barnard Sarah E. , Conner Peter M. , Nambiar Ashok , Zinter Matt S. , Moayeri Morvarid , Serpa Paula Hayakawa , Prince Brian C. , Quan Jenai , Sit Rene , Tan Michelle , Phelps Maira , DeRisi Joseph L. , Tato Cristina M. , Langelier Charles
Published: May 2019

Background

Transfusion-related sepsis remains an important hospital infection control challenge. Investigating septic transfusion events is often restricted by the limitations of bacterial culture in terms of time requirements and low yield in the setting of prior antibiotic administration.

Methods

In three Gram-negative septic transfusion cases, we performed mNGS of direct clinical blood specimens in addition to standard culture-based approaches utilized for infection control investigations. Pathogen detection leveraged IDSeq, a new open-access microbial bioinformatics portal. Phylogenetic analysis was performed to assess microbial genetic relatedness and understand transmission events.

Results

mNGS of direct clinical blood specimens afforded precision detection of pathogens responsible for each case of transfusion-related sepsis, and enabled discovery of a novel Acinetobacter species in a platelet product that had become contaminated despite photochemical pathogen reduction. In each case, longitudinal assessment of pathogen burden elucidated the temporal sequence of events associated with each transfusion-transmitted infection. We found that informative data could be obtained from culture-independent mNGS of residual platelet products and leftover blood specimens that were either unsuitable or unavailable for culture, or that failed to grow due to prior antibiotic administration. We additionally developed methods to enhance accuracy for detecting transfusion-associated pathogens sharing taxonomic similarity to contaminants commonly found in mNGS library preparations.

Conclusions

Culture-independent mNGS of blood products afforded rapid and precise assessment of pathogen identity, abundance and genetic relatedness. Together, these challenging cases demonstrated the potential for metagenomics to advance existing methods for investigating transfusion-transmitted infections.
Multiple loci control eyespot number variation on the hindwings ofBicyclus anynanabutterflies
Authors: Rivera-Colón Angel G. , Westerman Erica L. , Van Belleghem Steven M. , Monteiro Antónia , Papa Riccardo
Published: May 2019

The underlying genetic changes that regulate the appearance and disappearance of repeated traits, or serial homologs, remain poorly understood. One hypothesis is that variation in genomic regions flanking master regulatory genes, also known as input-output genes, controls variation in trait number, making the locus of evolution almost predictable. Other hypotheses implicate genetic variation in up-stream or downstream loci of master control genes. Here, we use the butterflyBicyclus anynana, a species which exhibits natural variation in eyespot number on the dorsal hindwing, to test these two hypotheses. We first estimated the heritability of dorsal hindwing eyespot number by breeding multiple butterfly families differing in eyespot number, and regressing eyespot number of offspring on mid-parent values. We then estimated the number and identity of independent genetic loci contributing to eyespot number variation by performing a genome-wide association study with restriction site-associated DNA Sequencing (RAD-seq) from multiple individuals varying in number of eyespots sampled across a freely breeding lab population. We found that dorsal hindwing eyespot number has a moderately high heritability of approximately 0.50. In addition, multiple loci near previously identified genes involved in eyespot development display high association with dorsal hindwing eyespot number, suggesting that homolog number variation is likely determined by regulatory changes at multiple loci that build the trait and not by variation at single master regulators or input-output genes.

Data accessibility

TheBicyclus anynanaPstI RAD-tag sequencing data is available via the Genbank BioProject PRJNA509697. Genotype VCF files will be made available through Figshare upon acceptance.
High Throughput pMHC-I Tetramer Library Production Using Chaperone Mediated Peptide Exchange
Authors: Overall Sarah A. , Toor Jugmohit S. , Hao Stephanie , Yarmarkovich Mark , Nguyen Son , Japp Alberto S. , Moschidi Danai , Betts Michael R. , Maris John M. , Smibert Peter , Sgourakis Nikolaos G.
Published: May 2019

Peptide exchange technologies are essential for the generation of pMHC-multimer libraries, used to probe highly diverse, polyclonal TCR repertoires. Using the molecular chaperone TAPBPR, we present a robust method for the capture of stable, empty MHC-I molecules which can be readily tetramerized and loaded with peptides of choice in a high-throughput manner. Combined with tetramer barcoding using multi-modal cellular indexing technology (ECCITE-seq), our approach allows a combined analysis of TCR repertoires and other T-cell transcription profiles together with their cognate pMHC-I specificities in a single experiment.
Therhg1-a(Rhg1low-copy) nematode resistance source harbors a copia-family retrotransposon within theRhg1-encoded α-SNAP gene
Authors: Bayless Adam M. , Zapotocny Ryan W. , Han Shaojie , Grunwald Derrick J. , Amundson Kaela K. , Bent Andrew F.
Published: May 2019

Soybean growers widely use theResistance toHeteroderaglycines1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN).Rhg1is a tandemly repeated four gene block. Two classes of SCN resistance-conferringRhg1haplotypes are recognized:rhg1-a(“Peking-type”, low copy number, 3 or fewerRhg1repeats) andrhg1-b(“PI 88788-type”, high copy number, 4 or moreRhg1repeats). Therhg1-aandrhg1-bhaplotypes encode α-SNAP (alpha-SolubleNSFAttachmentProtein) variants α-SNAPRhg1LC and α-SNAPRhg1HC respectively, with differing atypical C-terminal domains, that contribute to SCN-resistance. Here we report thatrhg1-asoybean accessions harbor a copia retrotransposon within theirRhg1 Glyma.18G022500(α-SNAP-encoding) gene. We termed this retrotransposon “RAC”, forRhg1alpha-SNAPcopia. Soybean carries multipleRAC-like retrotransposon sequences. TheRhg1 RACinsertion is in theGlyma.18G022500genes of all truerhg1-ahaplotypes we tested and was not detected in any examinedrhg1-borRhg1WT(single-copy) soybeans.RACis an intact element residing within intron 1, anti-sense to therhg1-a α-SNAPopen reading frame.RAChas intrinsic promoter activities, but overt impacts ofRACon transgenic α-SNAPRhg1LC mRNA and protein abundance were not detected. From the nativerhg1-a RAC+genomic context, elevated α-SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for α-SNAPRhg1HC (whoserhg1-bdoes not carryRAC). Using a SoySNP50K SNP corresponding withRACpresence, just ∼42% of USDA accessions bearing previously identifiedrhg1-aSoySNP50K SNP signatures harbor theRACinsertion. Subsequent analysis of several of these putativerhg1-aaccessions lackingRACrevealed that none encodedα-SNAPRhg1LC, and thus they are notrhg1-a.rhg1-ahaplotypes are of rising interest, withRhg4, for combating SCN populations that exhibit increased virulence against the widely usedrhg1-bresistance. The present study reveals another unexpected structural feature of manyRhg1loci, and a selectable feature that is predictive ofrhg1-ahaplotypes.
Alcohol consumption, obesity and hypertension: Relationship patterns along different age groups in Uganda
Authors: Tumwesigye Nazarius Mbona , Mutungi Gerald , Bahendeka Silver , Wesonga Ronald , Swahn Monica H. , Katureebe Agaba , Guwatudde David
Published: May 2019

Introduction

Uganda is experiencing a significant increase in the prevalence of non-communicable diseases including hypertension and obesity. Frequent alcohol use is also highly prevalent in Uganda and is a key risk factor for both hypertension and obesity. This study determines the trends of frequent alcohol consumption, hypertension and obesity across different age groups, and the extent to which alcohol consumption affects the two.

Methods

The data were extracted from the 2014 National Non-communicable Diseases Risk Factor Survey (N=3,987) conducted among adults aged 18 to 69 years. Hypertension was defined as systolic blood pressure ≥140mmHG or diastolic blood pressure ≥90. Obesity was defined as body mass index >30 kg/m2. Frequent alcohol consumption was defined as alcohol use 3 or more times a week. Multivariable log binomial regression analysis was carried out for each of the two outcome variables against age group and controlled for frequency of alcohol consumption and few other independent factors. Non-parametric tests were used to compare trends of prevalence ratios across age groups. Modified Poisson regression was use in few instances when the model failed to converge.

Results

The results showed increasing trend in the prevalence of hypertension and frequent alcohol consumption but a declining trend for obesity along different age groups (p<0.01). Frequency of alcohol consumption did not significantly modify the age group-hypertension and age group-obesity relationships although the effect was significant with ungrouped age. There was significance in difference of fitted lines for hypertension prevalence ratios between frequent drinkers and mild drinkers and between abstainers and frequent drinkers. Alcohol consumption did not have any significant effect on obesity-age group relationship.

Conclusion

The results call for more research to understand the effect of alcohol on the hypertension-age relationship, and the obesity-age relationship. Why prevalence ratios for hypertension decline among those who take alcohol most frequently is another issue that needs further research.
Effects of moderate and high intensity isocaloric aerobic training upon microvascular reactivity and myocardial oxidative stress in rats
Authors: Paes Lorena , Lima Daniel , Matsuura Cristiane , de Souza Maria das Graças , Cyrino Fátima , Barbosa Carolina , Ferrão Fernanda , Bottino Daniel , Bouskela Eliete , Farinatti Paulo
Published: May 2019

Systemic and central cardiovascular adaptations may vary in response to chronic exercise performed with different intensities and volumes. This study compared the effects of aerobic training with different intensities but equivalent volume upon microvascular reactivity in cremaster muscle and myocardial biomarkers of oxidative stress in Wistar rats. After peak oxygen uptake (VO2peak) assessment, rats (n=24) were assigned into three groups: moderate-intensity exercise training (MI); high-intensity exercise training (HI); sedentary control (SC). Treadmill training occurred during 4 weeks, with exercise bouts matched by the energy expenditure (3.0-3.5 Kcal). Microvascular reactivity was assessed in vivo by intravital microscopy in cremaster muscle arterioles, while biomarkers of oxidative stress and eNOS expression were quantified at left ventricle and at aorta, respectively. Similar increasing vs. sedentary control group (SC) occurred in moderate intensity training group (MI) and high-intensity training group (HI) for endothelium-dependent vasodilation (10−4M: MI: 168.7%, HI: 164.6% vs. SC: 146.6%, P=0.0004). Superoxide dismutase (SOD) (HI: 0.13 U/mg vs. MI: 0.09 U/mg and SC: 0.06 U/mg; P=0.02), glutathione peroxidase (GPX) (HI: 0.00038 U/mg vs. MI: 0.00034 U/mg and SC: 0.00024 U/mg; P=0.04), and carbonyl protein content (HI: 0.04 U/mg vs. MI: 0.03 U/mg and SC: 0.01 U/mg; P=0.003) increased only in HI. No difference across groups was detected for catalase (CAT) (P=0.12), Thiobarbituric acid reactive substances (TBARS) (P = 0.38) or eNOS expression in aorta (P=0.44). In conclusion, higher exercise intensity induced greater improvements in myocardium antioxidant defenses, while gains in microvascular reactivity appeared to rely more on exercise volume than intensity.
CRISPRpred(SEQ): a sequence based tool for sgRNA on target activity prediction [(almost) beating Deep Learning pipelines by traditional machine learning]
Authors: Muhammad Rafid Ali Haisam , Toufikuzzaman Md. , Rahman Mohammad Saifur , Rahman M. Sohel
Published: May 2019

An accurate and fast genome editing tool can be used to treat genetic diseases, modify crops genetically etc. However, a tool that has low accuracy can be risky to use, as incorrect genome editing may have severe consequences. Although many tools have been developed in the past, there are still room for further improvement. In this paper, we present CRISPRpred(SEQ), a sequence based tool for sgRNA on target activity prediction that leverages only traditional machine learning techniques. We compare the results of CRISPRpred(SEQ) with that of DeepCRISPR, the current state-of-the-art, which uses a deep learning pipeline. In spite of using only traditional machine learning methods, we are able to beat DeepCRISPR for the three out of four cell lines in the benchmark dataset convincingly (2.174%, 6.905% and 8.119% improvement for the three cell lines), which is quite outstanding.
Dissociable roles for Anterior Cingulate Cortex and Basolateral Amygdala in Decision Confidence and Learning under Uncertainty
Authors: Stolyarova A , Rakhshan M , Hart Evan E. , O’Dell Thomas J. , Peters MAK , Lau H , Soltani A , Izquierdo A
Published: May 2019

It has been suggested the subjective sense of certainty, or confidence, in ambiguous sensory cues can alter the interpretation of reward feedback and facilitate learning. We trained rats to report the orientation of ambiguous visual stimuli according to a spatial stimulus-response rule. Following choice, rats could wait a self-timed delay for reward or initiate a new trial. Waiting times increased with discrimination accuracy, demonstrating that this measure could be used as a proxy for confidence. Chemogenetic silencing of BLA shortened waiting times overall whereas ACC inhibition rendered waiting times insensitive to confidence-modulating attributes of visual stimuli, suggesting contribution of ACC but not BLA to confidence computations. Subsequent reversal learning was enhanced by confidence. Both ACC and BLA inhibition blocked this enhancement but via differential modulation of learning strategies and consistency in using learned rules. Altogether, we demonstrate dissociable roles for ACC and BLA in transmitting confidence and learning under uncertainty.
Crystal structure of bis(1-ethyl-1H-imidazole-κN
3)(meso-tetramesitylporphyrinato-κ4
N,N′,N′′,N′′′)iron(III) perchlorate chlorobenzene sesquisolvate
Authors: Zhan Nana , Wang Haimang , Li Jianfeng
Published: May 2019

In the complex cation of title compound, [Fe(C56H52N4)(C5H8N2)2]ClO4·1.5C6H5Cl, the ironIII atom is coordinated in a distorted octahedral manner by four pyrrole N atoms of the porphyrin ring system in the equatorial plane, and by two N atoms of the 1-ethylimidazole ligands in the axial sites. A disordered perchlorate anion and one and a half chlorobenzene solvent molecules are also present. The cationic complex exhibits a highly ruffled porphyrin core. The average Fe—Np (Np is a porphyrin N atom) bond length is 1.988 (5), and the axial Fe—NIm (NIm is an imidazole N atom) bond lengths are 1.962 (3) and 1.976 (3) Å. The two 1-ethylimidazole ligands are inclined to each other by a dihedral angle of 68.62 (16)°. The dihedral angles between the 1-ethylimidazole planes and the planes of the closest Fe—Np vector are 28.52 (18) and 43.57 (13)°. Intermolecular C—H...Cl interactions are observed.
Redetermination of the crystal structure of BaTeO3(H2O), including the localization of the hydrogen atoms
Authors: Weil Matthias
Published: May 2019

The redetermination of the crystal structure of barium oxidotellurate(IV) monohydrate allowed the localization of the hydrogen atoms that were not determined in the previous study [Nielsen, Hazell & Rasmussen (1971). Acta Chem. Scand.
25, 3037–3042], thus making an unambiguous assignment of the hydrogen-bonding scheme possible. The crystal structure shows a layered arrangement parallel to (001), consisting of edge-sharing [BaO6(H2O)] polyhedra and flanked by isolated [TeO3] trigonal pyramids on the top and bottom. O—H...O hydrogen bonds of medium strength link adjacent layers along [001].
Under what conditions is mandatory disclosure most likely to cause organisational change?
Authors: Leong Shane , Hazelton James
Published: May 2019

Purpose

The purpose of this paper is to reflect on how mandatory sustainability accounts can be designed to maximise the likelihood of moving society towards sustainability.

Design/methodology/approach

The authors use institutional theory to show that organisations are constrained by institutions. Sustainability accounts can drive change by providing information that changes the institutional mix of pressures on organisations.

Findings

Mandatory disclosure is most likely to drive change when: indicators are appropriate for information intermediaries or other intended users; information is provided at the appropriate level of aggregation; data are comparable to external benchmarks and/or other corporations; there exists a linkage to network of other relevant information; and sufficient popular and political support exists.

Practical implications

Social changes will only come about if users receive information relevant to their goals and are able to translate it into political action. Corporate-level reporting may not be the best mechanism for this, because many users are interested in issues-based information. In many instances, due to the ability to facilitate greater comparability, a database mechanism is likely to be more helpful. Social and environmental accounting research should consider adopting more site-based reporting, ascertain what sustainability information governments already collect, determine what information NGOs need for campaigning purposes, and theorise how to create and link a nexus of accounts.

Originality/value

While many studies have called for improved practice and lamented the impotence of reporting, few studies have explored this link from a theoretical perspective.
Do farmer and credit specific characteristics matter in microfinance programmes’ participation? Evidence from smallholder farmers in Ada west and east districts
Authors: Jumpah Emmanuel Tetteh , Osei-Asare Yaw , Tetteh Emmanuel Kodjo
Published: May 2019

Purpose

Users of smallholder farmer microfinance are able to make enough returns to repay credits advanced to them. However, they are in dire need of financial capital such that they are inconsiderate of farmer- and credit-specific characteristics when participating in a microfinance programme. This study analyses perceptions of stakeholders regarding select farmer and credit characteristics within the microfinance industry. The study identifies and analyses the factors that influence participation in a microfinance programme by farmers using the logistic regression model. The purpose of this paper is to widen the knowledge base of rural agricultural finance, including factors that influence participation in microfinance intervention(s) thereof.

Design/methodology/approach

A total of 104 participants and 120 non-participant farmers in microfinance programmes were interviewed using a semi-structured questionnaire by applying the multistage sampling technique. The paper applied the logistic regression model in which farmer- and credit-specific characteristics were used to estimate the probabilities of participation.

Findings

The logistic regression results showed that distance, interest rate, experience, membership of farmer-based organisation, number of dependants, household, gender and age were statistically significant farmer- and credit-specific characteristics that influence participation in microfinance programmes. Interest rate and distance exact negative significance influence on participation, whereas membership of farmer-based organisations, experience, gender, household head and age influence participation positively. Reduction in the interest rate and expansion of microfinance to very remote areas rather than locations in urban areas are crucial in terms of improving participation.

Research limitations/implications

The paper used data from only farmers so there is a limit to which the results can be generalised for all microfinance users. It may be relevant to undertake a study that considers non-farm enterprises.

Practical implications

This paper brings to light the need to develop well-structured microfinance facilities that meet the specific needs of the rural poor in transitioning economies while taking into consideration critical factors affecting participation before the establishment of such programmes.

Originality/value

This paper provides empirical evidence to show that farmer- and credit-specific characteristics are essential to ensure participation and success of microfinance programmes thereof.
Industry leader interview: Jerry Montgomery
Authors: Zhao Jinlin
Published: May 2019

Purpose

The purpose of this paper is to interview Jerry Montgomery-Senior Vice President of Global Human Resources at Carnival Corporation-regarding recent trends in the cruise industry

Design/methodology/approach

Interview with industry leader.

Findings

Several trends are identified.

Originality/value

Researchers and students will acquire a better understanding of cruise industry trends.
Incorporating artificial skin signals in the constraint-based reactive control of human–robot collaborative manipulation tasks
Authors: Vergara Cristian Alejandro , Borghesan Gianni , Aertbeliën Erwin , De Schutter Joris
Published: May 2019

Purpose

The purpose of this paper is to develop a control strategy for human–robot collaborative manipulation tasks that can deal with proximity signals from 373 interconnected cells of an artificial skin.

Design/methodology/approach

The robot and the operator accomplish an industrial task while interacting in a shared workspace. The robot controller detects and avoids collisions based on the information from the artificial skin. Conflicting constraints can be handled by prioritizing between hard and soft constraints or by weighing the different constraints.

Findings

Weak soft constraints (low weight) are specified to command the robot to move along a nominal path with constant velocity. Stronger soft constraints (higher weight) prevent collisions by means of either moving the end effector backward along the path or circumventing an obstacle. The proposed approach is validated experimentally.

Originality/value

As a first contribution, this paper proposes a discrete optimization algorithm activates an a priori selected maximum number of cells. The algorithm selects the appropriate distribution based on the amplitude of each signal and the spatial distribution of the proximity measurements. A second contribution is the specification of a human–robot collaborative application as an optimization problem using eTaSL (expression graph-based task specification language), which provides reactive control.
The role of ICT, eWOM and guest characteristics in loyalty
Authors: Moliner-Velázquez Beatriz , Fuentes-Blasco María , Gil-Saura Irene
Published: May 2019

Purpose

This study aims to examine how technologies contribute to consumer loyalty in the tourist industry. To achieve this objective, information and communication technology (ICT) development and electronic word-of-mouth (eWOM) are analysed to explore their direct and indirect effects on satisfaction and loyalty dimensions. The moderating role of customer characteristics (personal and experience-related variables) is also considered to study the complex relationship between satisfaction and loyalty.

Design/methodology/approach

A quantitative study based on a questionnaire structured was developed. The survey was conducted with 386 guests from Spanish hotels. SEM methodology is applied to estimate the structural equation model and multi-group analysis.

Findings

Results confirm significant relationships in the sequence “ICT advancement-satisfaction with ICT-satisfaction with hotel-loyalty”, the mediating effect of eWOM and the moderating effects of the customer characteristics.

Practical implications

ICT can be a key element to improve loyalty and differentiate from competitors. Managers should recognise that customers will have different loyalty behaviours according to their personal characteristics and type of experience.

Originality/value

This paper contributes to the recent and still scanty research line on ICT advancement from the consumer perspective. The novelty lies in the relationships between ICT, satisfaction and loyalty in hotels with particular attention to WOM (both personal and electronic) and the inclusion of different moderating variables.
International book donors and public libraries as partners in primary school literacy development in Kenya
Authors: Mose Peter , Kaschula Russell
Published: May 2019

Purpose

The purpose of this paper is to explore the impact of international library materials aid in primary schools and to outline obstacles to effective utilization for maximum literacy benefits among primary school children.

Design/methodology/approach

Data were gathered via interviews, observation, focus group discussions and document analyses.

Findings

Findings indicate that teachers were trained by Kenya National Library Services Kisii Branch staff on basics of library materials management before literacy materials were sent to the schools; teachers and pupils reported that development of vocabulary and better essay writing are some of the benefits of the donated materials; and culturally distanced materials and school dynamics impact negatively on the effective utilization of the donated library resources.

Practical implications

The authors recommend that donors work hand in hand with the Ministry of Education and other local stakeholders that it may be possible to address obstacles to proper and highly effective implementation of literacy empowerment projects.

Originality/value

The findings of this study are from original research and the implications must be treated as such.
Procedural justice concerns and support for BWCs: turning the lens to officer perceptions
Authors: Saulnier Alana , St Louis Ermus , McCarty William
Published: May 2019

Purpose

The purpose of this paper is to explore factors that drive officer support for body-worn cameras (BWCs).

Design/methodology/approach

Results of an officer perceptions survey completed as part of an evaluation of the Chicago Police Department’s BWC project are presented. The influence of treatment- and outcome-oriented justice concerns on officer support for BWCs is explored with a variety of covariates.

Findings

Outcome-oriented concerns are a significant predictor of officer support for BWCs, while treatment-oriented concerns are not.

Practical implications

The research enhances understandings of the applicability of procedural justice theorizing in policing generally, and offers direction important to the meaningful use of BWCs.

Originality/value

This finding runs counter to dominant relational models of procedural justice that concentrate on the perspective of subordinates, but lends support to arguments advocating the centrality of role (authority vs subordinate) in the formation of justice evaluations.
Synthesis of novel dyes based on thiophene analogues with antibacterial activity for dyeing polyester fabrics
Authors: Abomelha Hanna
Published: May 2019

Purpose

This study aims to the synthesis of some novel 4-arylazo-3-hydroxythiophene analogues containing sulphapyridine and sulphathiazole dyestuffs and studying their application in dyeing polyester fabrics and rendering their antibacterial efficacy.

Design/methodology/approach

Simultaneous dyeing and antibacterial finishing for polyester fabric using a new antibacterial disperse dye having a modified chemical structure to thiophene dyes were studied. Construction of the thiophene dyes was carried out by diazo-coupling of diazotized sulphonamide-containing heterocyclic rings sulphapyridine and sulphathiazole with ethyl α-phenylthiocarbamoyl-acetoacetate followed by cyclizing the produced 2-arylazo-thioacetanilide with various α-halogenated reagents. All newly synthesized compounds were characterized by elemental analysis and extensive study of their spectral data (IR and 1H-NMR). The dyeing characteristics of these thiophene dyestuffs were evaluated at optimum conditions. Antibacterial activities of the obtained thiophene dyes were studied against some Gram-positive and Gram-negative bacteria.

Findings

The synthesized thiophene-containing sulphonamides dyes were applied on polyester fabric. The modified dyes exhibited a good fastness properties and antibacterial efficacy against some Gram-positive and Gram-negative bacteria. Synthesized dyes showed higher antibacterial potency than the reference standard drug.

Research limitations/implications

Synthesis of these disperse azo dyes for textile dyeing had never been reported previously.

Practical implications

The dyestuffs derived from thiophene are reasonable azo disperse dyestuffs giving good all-round fastness properties on polyester fabrics.

Originality/value

Thiophene dyes are used for dyeing polyester fabrics with brilliant colour and good fastness properties. The presence of sulphonamides moieties increase their fastness properties and elevate their antibacterial properties. Moreover, they can be used as antimicrobial finish due to their bactericidal properties on dyed textiles. This work afforded a new thiophene colorant that can be used in many different uses like polyester packing, thread Surgery, blends and other uses in medical textile.
Orientation towards social responsibility of North-West African firms
Authors: Sánchez-Hernández M. Isabel , Carvalho Luísa Cagica , Paiva Inna Sousa
Published: May 2019

Purpose

Corporate social responsibility orientation (CSRO) is considered a crucial strategy to enhance long-term competitiveness around the world, and it is starting to be a broader issue in Africa. Based on recent works addressing the CSRO–performance relationship in countries outside the African continent, this paper aims to assess CRSO in North-West Africa.

Design/methodology/approach

In this study a questionnaire was distributed among 122 managers in two countries in North-West Africa: Guinea-Bissau and the Ivory Coast. Partial least squares (PLS) structural equation modelling (SEM) is used to assess the path or relationships for the North-West African context.

Findings

The results show that there is a generally positive perception of the economic, social and environmental dimensions of CSRO, although special emphasis is laid on the economic and social issues, mainly when they are related to human resources. The study also revealed the important role of innovation as mediator between CSRO and firm performance.

Practical implications

The study points out the role of managers in promoting a culture of social innovation by focussing on the CSR philosophy for improving the competitive success of African businesses.

Social implications

The social, economic and legal contexts of Guinea-Bissau and the Ivory Coast are vulnerable. The findings raise concerns about whether governments and regulatory efforts improve the development of the strategies towards social responsibility of African firms and whether they also increase the role of the firms in producing positive externalities to the market through CSRO.

Originality/value

Very few studies have investigated CSRO in Africa. Aiming to switch from the current CSRO in developed countries to an African perspective of CSRO, this paper contributes to filling the existing gap through the study of managers’ perceptions about CSR in two countries in North-West Africa: Guinea-Bissau and the Ivory Coast.