bluuebunny/crossref_metadata_2025 huggingface dataset:
Error-correcting DNA barcodes for high-throughput sequencing
Authors: Hawkins John A. , Jones Stephen K. , Finkelstein Ilya J. , Press William H.
Published: May 2018

Many large-scale high-throughput experiments use DNA barcodes—short DNA sequences prepended to DNA libraries—for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely-used error-correcting codes borrowed from computer science (e.g., Hamming and Levenshtein codes) do not properly account for insertions and deletions in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we present and experimentally validate FREE (Filled/truncated Right End Edit) barcodes, which correct substitution, insertion, and deletion errors, even when these errors alter the barcode length. FREE barcodes are designed with experimental considerations in mind, including balanced GC content, minimal homopolymer runs, and reduced internal hairpin propensity. We generate and include lists of barcodes with different lengths and error-correction levels that may be useful in diverse high-throughput applications, including >106 single-error correcting 16-mers that strike a balance between decoding accuracy, barcode length, and library size. Moreover, concatenating two or more FREE codes into a single barcode increases the available barcode space combinatorially, generating lists with > 1015 error-correcting barcodes. The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community.

SIGNIFICANCE STATEMENT

Modern high-throughput biological assays study pooled populations of individual members by labeling each member with a unique DNA sequence called a “barcode.” DNA barcodes are frequently corrupted by DNA synthesis and sequencing errors, leading to significant data loss and incorrect data interpretation. Here, we describe a novel error-correction strategy to improve the efficiency and statistical power of DNA barcodes. To our knowledge, this is the first report of an error-correcting method that accurately handles insertions and deletions in DNA barcodes, the most common type of error encountered during DNA synthesis and sequencing, resulting in order-of-magnitude increases in accuracy, efficiency, and signal-to-noise. The accompanying software package makes deployment of these barcodes effortless for the broader experimental scientist community.
Polar targeting and assembly of theLegionellaDot/Icm type IV secretion system (T4SS) by T6SS-related components
Authors: Jeong KwangCheol C. , Gyore Jacob , Teng Lin , Ghosal Debnath , Jensen Grant J. , Vogel Joseph P.
Published: May 2018

Legionella pneumophila, the causative agent of Legionnaires’ disease, survives and replicates inside amoebae and macrophages by injecting a large number of protein effectors into the host cells’ cytoplasm via the Dot/Icm type IVB secretion system (T4BSS). Previously, we showed that the Dot/Icm T4BSS is localized to both poles of the bacterium and that polar secretion is necessary for the proper targeting of theLegionellacontaining vacuole (LCV). Here we show that polar targeting of the Dot/Icm core-transmembrane subcomplex (DotC, DotD, DotF, DotG and DotH) is mediated by two Dot/Icm proteins, DotU and IcmF, which are able to localize to the poles ofL. pneumophilaby themselves. Interestingly, DotU and IcmF are homologs of the T6SS components TssL and TssM, which are part of the T6SS membrane complex (MC). We propose thatLegionellaco-opted these T6SS components to a novel function that mediates subcellular localization and assembly of this T4SS. Finally, in depth examination of the biogenesis pathway revealed that polar targeting and assembly of theLegionellaT4BSS apparatus is mediated by an innovative “outside-inside” mechanism.
A computational model of task allocation in social insects – ecology and interactions alone can drive specialisation
Authors: Chen Rui , Meyer Bernd , García Julian
Published: May 2018

Social insect colonies are capable of allocating their workforce in a decentralised fashion; addressing a variety of tasks and responding effectively to changes in the environment. This process is fundamental to their ecological success, but the mechanisms behind it remain poorly understood. While most models focus on internal and individual factors, empirical evidence highlights the importance of ecology and social interactions. To address this gap we propose a game theoretical model of task allocation. Individuals are characterised by a trait that determines how they split their energy between two prototypical tasks: foraging and regulation. To be viable, a colony needs to learn to adequately allocate its workforce between these two tasks. We study two different processes: individuals can learn relying exclusively on their own experience, or by using the experiences of others via social learning. We find that social organisation can be determined by the ecology alone, irrespective of interaction details. Weakly specialised colonies in which all individuals tend to both tasks emerge when foraging is cheap; harsher environments, on the other hand, lead to strongly specialised colonies in which each individual fully engages in a single task. We compare the outcomes of self-organised task allocation with optimal group performance. Counter to intuition, strongly specialised colonies perform suboptimally, whereas the group performance of weakly specialised colonies is closer to optimal. Social interactions lead to important differences when the colony deals with dynamic environments. Colonies whose individuals rely on their own experience are more exible when dealing with change. Our computational model is aligned with mathematical predictions in tractable limits. This different kind of model is useful in framing relevant and important empirical questions, where ecology and interactions are key elements of hypotheses and predictions.
Single-neuron interactions between the somatosensory thalamo-cortical circuits during perception
Authors: Tauste Campo Adrià , Vázquez Yuriria , Álvarez Manuel , Zainos Antonio , Rossi-Pool Román , Deco Gustavo , Romo Ranulfo
Published: May 2018

Sensory thalamo-cortical interactions are key components of the neuronal chains associated with stimulus perception, but surprisingly, they are poorly understood. We addressed this problem by evaluating a directional measure between simultaneously recorded neurons from somatosensory thalamus (VPL) and somatosensory cortex (S1) sharing the same cutaneous receptive field, while monkeys judged the presence or absence of a tactile stimulus. During the stimulus-presence, feedforward (VPL→S1) interactions increased, while pure feedback (S1→VPL) interactions were unaffected. Remarkably, bidirectional interactions (VPL↔S1) emerged with high stimulus amplitude, establishing a functional thalamo-cortical loop. Furthermore, feedforward interactions were modulated by task context and error trials. Additionally, significant stimulus modulations were found on intra-cortical (S1→S1) interactions, but not on intra-thalamic (VPL→VPL) interactions. Thus, these results show the directionality of the information flow between the thalamo-cortical circuits during tactile perception. We suggest that these interactions may contribute to stimulus perception during the detection task used here.
Selection of horizontal gene transfer through public good production
Authors: Dimitriu Tatiana , Misevic Dusan , Capelle Julien Benard , Lindner Ariel B , Brown Sam P , Taddei Francois
Published: May 2018

In bacteria, cooperative genes encoding public good molecules are preferentially located on mobile genetic elements (MGEs), and horizontal transfer of MGEs favours the maintenance of public good cooperation. The rate of horizontal transfer itself can evolve in response to selective pressures acting on both MGEs and bacterial hosts: benefits and costs of infectious spread, but also indirect effects of MGE genes to the host. We show here that carriage of public good genes on MGEs can generate another indirect selection for MGE transfer. Transfer increases public good production and, when relatedness is sufficiently high, public goods benefit preferentially genotypes with high transfer ability. Both our simulations and experiments indicate that transfer is not required to occur among kin, provided that public goods still benefit kin. Public good gene mobility thus aligns the interests of chromosomes and MGEs concerning transfer, promoting gene exchange among bacteria.
The development of individual differences in cooperative behaviour: maternal glucocorticoid hormones alter helping behaviour of offspring in wild meerkats
Authors: Dantzer Ben , Dubuc Constance , Goncalves Ines Braga , Cram Dominic L. , Bennett Nigel C. , Ganswindt Andre , Heistermann Michael , Duncan Chris , Gaynor David , Clutton-Brock Tim H.
Published: May 2018

The phenotype of parents can have long-lasting effects on the development of offspring as well as on their behaviour, physiology, and morphology as adults. In some cases, these changes may increase offspring fitness but, in others, they can elevate parental fitness at a cost to the fitness of their offspring. We show that in Kalahari meerkats (Suricata suricatta), the circulating glucocorticoid (GC) hormones of pregnant females affect the growth and cooperative behaviour of their offspring. We performed a 3-year experiment in wild meerkats to test the hypothesis that GC-mediated maternal effects reduce the potential for offspring to reproduce directly and therefore cause them to exhibit more cooperative behaviour. Daughters (but not sons) born to mothers treated with cortisol during pregnancy grew more slowly early in life and exhibited significantly more of two types of cooperative behaviour (pup rearing and feeding) once they were adults compared to offspring from control mothers. They also had lower measures of GCs as they aged, which could explain the observed increases in cooperative behaviour. Because early life growth is a crucial determinant of fitness in female meerkats, our results indicate that GC-mediated maternal effects may reduce the fitness of offspring, but may elevate parental fitness as a consequence of increasing the cooperative behaviour of their daughters.
Bayesian Estimation of 3D Chromosomal Structure from Single Cell Hi-C Data
Authors: Rosenthal Michael , Bryner Darshan , Huffer Fred , Evans Shane , Srivastava Anuj , Neretti Nicola
Published: May 2018

The problem of 3D chromosome structure inference from Hi-C datasets is important and challenging. While bulk Hi-C datasets contain contact information derived from millions of cells, and can capture major structural features shared by the majority of cells in the sample, they do not provide information about local variability between cells. Single cell Hi-C can overcome this problem, but contact matrices are generally very sparse, making structural inference more problematic. We have developed a Bayesian multiscale approach, named SIMBA3D, to infer 3D structures of chromosomes from single cell Hi-C while including the bulk Hi-C data and some regularization terms as a prior. We study the landscape of solutions for each single-cell Hi-C dataset as a function of prior strength and demonstrate clustering of solutions using data from the same cell.
Embryo timelapses can be compiled and quantified to understand canonical histone dynamics across multiple cell cycles
Authors: Smith Lydia , Maddox Paul
Published: May 2018

In the last decade, computational analysis of big datasets has facilitated the processing of unprecedented quantities of collected biological data. Thus, automations and big data analyses have been revolutionary in detecting and quantifying subtle phenotypes in cell biological contexts. Analyzing similar quantities of data in larger and more complicated biological systems such as live embryos has been more challenging due to experimental necessities impeding both compilations of data collection and informative analysis. Here we present a streamlined workflow that can quantify cell cycle dynamics in early developing embryos using fluorescently labeled proteins. We benchmark this pipeline usingCaenorhabditis elegans(nematode) embryonic development and a fluorescently labeled histone. Using our pipeline, we find that histone proteins are broadly stable in early embryonic development. In sum, we have utilized the large biological and experimental variation associated with quantification of fluorescent proteins in embryonic systems, to quantify nuclear accumulation rate, chromatin incorporation, and turnover/stability of canonical histones during early development.
Evaluation of current and emerging anti-malarial medicines for inhibition ofToxoplasma gondiigrowth in vitro
Authors: Radke Joshua B. , Burrows Jeremy N. , Goldberg Daniel E. , Sibley L. David
Published: May 2018

Toxoplasma gondiiis a common zoonotic infection of humans and estimates indicate that 1-2 billion people are chronically infected. Although largely asymptomatic, chronic infection poses risk of serious disease due to reactivation should immunity decline. Current therapies for toxoplasmosis only control acute infection caused by actively proliferating tachyzoites but do not eradicate the chronic tissue cyst stages. As well, there are considerable adverse side effects of the most commonly used therapy of combined sulfadiazine and pyrimethamine. Targeting the folate pathway is also an effective treatment for malaria, caused by the related parasitesPlasmodiumspp., suggesting common agents might be used to treat both infections. Here we evaluated currently approved and newly emerging medicines for malaria to determine if such compounds might also prove useful for treating toxoplasmosis. Surprisingly, the majority of anti-malarial compounds being used currently or in development for treatment of malaria were only modestly effective at inhibiting in vitro growth ofT. gondiitachyzoites. These findings suggest that many essential processes inP. falciparumthat are targeted by anti-malarial compounds are either divergent, or non-essential inT. gondii, thus limiting options for repurposing of current antimalarial medicines for toxoplasmosis.
Engineering Nitrogen Fixation Activity in an Oxygenic Phototroph
Authors: Liu Deng , Liberton Michelle , Yu Jingjie , Pakrasi Himadri B. , Bhattacharyya-Pakrasi Maitrayee
Published: May 2018

Biological nitrogen fixation is catalyzed by nitrogenase, a complex metalloenzyme found only in prokaryotes. N2fixation is energetically highly expensive, and an energy generating process such as photosynthesis can meet the energy demand of N2fixation. However, synthesis and expression of nitrogenase is exquisitely sensitive to oxygen. Thus, engineering nitrogen fixation activity in photosynthetic organisms that produce oxygen is challenging. Cyanobacteria are oxygenic photosynthetic prokaryotes, and some of them also fix N2. Here, we demonstrate a feasible way to engineer nitrogenase activity in the non-diazotrophic cyanobacteriumSynechocystissp. PCC 6803 through the transfer of 35 nitrogen fixation (nif) genes from the diazotrophic cyanobacteriumCyanothecesp. ATCC 51142. In addition, we have identified the minimalnifcluster required for such activity inSynechocystis6803. Moreover, nitrogenase activity was significantly improved by increasing the expression levels ofnifgenes. Importantly, the O2tolerance of nitrogenase was enhanced by introduction of uptake hydrogenase genes, showing this to be a functional way to improve nitrogenase enzyme activity under micro-oxic conditions. To date, our efforts have resulted in engineeredSynechocystis6803 strains that remarkably have more than 30% N2-fixation activity compared to that inCyanothece51142, the highest such activity established in any non-diazotrophic oxygenic photosynthetic organism. This study establishes a baseline towards the ultimate goal of engineering nitrogen fixation ability in crop plants.

IMPORTANCE

Application of chemically synthesized nitrogen fertilizers has revolutionized agriculture. However, the energetic costs of such production processes as well as the wide spread application of fertilizers have raised serious environmental issues. A sustainable alternative is to endow crop plants the ability to fix atmospheric N2in situ. One long-term approach is to transfer allnifgenes from a prokaryote to plant cells, and express nitrogenase in an energy-producing organelle, chloroplast or mitochondrion. In this context,Synechocystis6803, the non-diazotrophic cyanobacterium utilized in this study, provides a model chassis for rapid investigation of the necessary requirements to establish diazotrophy in an oxygenic phototroph.
The chloroplast 2-cysteine peroxiredoxin functions as thioredoxin oxidase in redox regulation of chloroplast metabolism
Authors: Vaseghi Mohamad-Javad , Chibani Kamel , Telman Wilena , Liebthal Michael , Gerken Melanie , Müller Sara Mareike , Dietz Karl-Josef
Published: May 2018

Thiol-dependent redox regulation controls central processes in plant cells including photosynthesis. Thioredoxins reductively activate e.g. Calvin-Benson cycle enzymes. However the mechanism of oxidative inactivation is unknown despite its importance for efficient regulation. Here, the abundant 2-cysteine peroxiredoxin (2-CysPrx), but not its site-directed variants, mediates rapid inactivation of reductively activated fructose-1,6-bisphosphatase and NADPH-dependent malate dehydrogenase (MDH) in the presence of the proper thioredoxins. Deactivation of phosphoribulokinase and MDH was compromised in 2cysprxAB mutants plants upon light/dark transition compared to wildtype. The decisive role of 2cysprxAB in regulating photosynthesis was evident from reoxidation kinetics of ferredoxin upon darkening of intact leaves since its half time decreased 3.5-times in 2cysprxAB. The disadvantage of inefficient deactivation turned into an advantage in fluctuating light. The results show that the 2-CysPrx serves as electron sink in the thiol network important to oxidize reductively activated proteins and represents the missing link in the reversal of thioredoxin-dependent regulation.
Epigenetic regulation affects fertility inDrosophila: toward the production of infertile models
Authors: Kohzaki Hidetsugu , Asano Maki , Murakami Yota , Mazo Alexander
Published: May 2018

We have revealed that the chorion gene clusters amplify by repeatedly initiating DNA replication from chorion gene amplification origins in the response to developmental signals, through the transcription factors inDrosophilaovarian follicle cells. Orc1, Orc2, and Cdc6 are forms of DNA replication machinery, which are conserved from yeast to humans; and Orc1 and Orc2 mutants are lethal. Overexpression of Orc1 or Orc2 (subunits of the origin recognition complex) led to female sterility, but overexpression of Cdc6 (an Orc family member) or GFP did not. We propose that DNA replication machinery contributes to development.

Recently, we found that H3K4 was trimethylated at chorion gene amplification origins, but not at the Act1 locus. Overexpression of Lsd1H3K4 dimethylase and Lid H3K4 trimethylase are female sterile but not a Lid mutant. These results showed that epigenetic regulation affected fertility. Screening strategies usingDrosophilaflies could also lead to the development of drugs that reduce sterility and epigenetic effects related histone modification.

Summary statement

There are approximately 470,000 infertile individuals in Japan. We knockowned the prereplicative complex components and demethlases duringDrosophilaovary development. In these drospohila, we could be the model of infertile.
Spontaneous and coordinated Ca2+activity of cochlear sensory and non-sensory cells drives the maturation of OHC afferent innervation
Authors: Ceriani Federico , Hendry Aenea , Jeng Jing-Yi , Johnson Stuart L. , Olt Jennifer , Holley Matthew C. , Mammano Fabio , Kros Corné J. , Simmons Dwayne D. , Marcotti Walter
Published: May 2018

Outer hair cells (OHCs) are highly specialized sensory cells conferring the fine tuning and high sensitivity of the mammalian cochlea to acoustic stimuli. Here, by genetically manipulating spontaneous Ca2+signallingin vivo, through a period of early postnatal development, we find that the refinement of OHC afferent innervation is regulated by complementary spontaneous Ca2+signals originating in OHCs and non-sensory cells. OHCs fire spontaneous Ca2+spikes during a narrow period of immature development. Simultaneously, waves of Ca2+activity in the non-sensory greater epithelial ridge act, via ATP-induced activation of P2X receptors, to synchronize OHC firing, resulting in the refinement of their afferent innervation. In the absence of connexin channels Ca2+waves are impaired, leading to a reduction in the number of ribbon synapses and afferent fibres on OHCs. We propose that the correct maturation of the afferent connectivity in OHCs requires experience-independent Ca2+signals from sensory and non-sensory cells.
‘In plaque-mass spectrometry imaging’ reveals a major metabolic shift towards odd-chain fatty acid lipids induced by host-virus interactions
Authors: Schleyer Guy , Shahaf Nir , Ziv Carmit , Dong Yonghui , Meoded Roy A. , Helfrich Eric J. N. , Schatz Daniella , Rosenwasser Shilo , Rogachev Ilana , Aharoni Asaph , Piel Jörn , Vardi Assaf
Published: May 2018

Tapping into the metabolic cross-talk between a host and its virus can reveal unique strategies employed during infection. Viral infection is a dynamic process that generates an evolving metabolic landscape. Gaining a continuous view into the infection process is highly challenging and is limited by current metabolomics approaches, which typically measure the average of the entire population at various stages of infection. Here, we took a novel approach to study the metabolic basis of host-virus interactions between the bloom-forming algaEmiliania huxleyiand its specific virus. We combined a classical method in virology, plaque assay, with advanced mass spectrometry imaging (MSI), an approach we termed ‘in plaque-MSI’. Taking advantage of the spatial characteristics of the plaque, we mapped the metabolic landscape induced during infection in a high spatiotemporal resolution, unfolding the infection process in a continuous manner. Further unsupervised spatially-aware clustering, combined with known lipid biomarkers, revealed a systematic metabolic shift towards lipids containing the odd-chain fatty acid pentadecanoic acid (C15:0) induced during infection. Applying ‘in plaque-MSI’ might pave the way for the discovery of novel bioactive compounds that mediate the chemical arms race of host-virus interactions in diverse model systems.
Seasonal changes of metabolites in phloem sap fromBroussonetia papyrifera
Authors: Shi Jiang-tao , Liu Hai-chong , Luo Jia-yan , Cai Li-ping
Published: May 2018

Gas chromatography-Mass spectrometry (GC-MS) were employed to analyze the whole metabolites in phloem sap ofBroussonetia papyriferaand the seasonal changes of content of these metabolites were also investigated. Thirty-eight metabolites were detected inBPphloem exudates. The highest content (44.59mg g-1) of total metabolites was presented in March. High contents of organic acids and sugars were detected inBPphloem exudates from all growing months. Smaller amounts of fatty acids and alcohols were also detected in BP phloem exudates. Interestingly, some metabolites, such as PI3 kinase inhibitor, Chlorogenic acid, Chelerythrine and palmitic acid, which have properties of bioactivity to anticancer and anti-inflammation, were also detected. Quininic acid was the most abundant organic acid, representing up to 86.3% (average value) of all organic acids. D-fructose, D-glucose, and sucrose were the major soluble sugars in phloem saps and the maximum of sugars content was 19.76mg g-1(average value) in November. Seasonal changes of contents of metabolites were different among individuals. The metabolites analysis double confirmed that theBPphloem sap can be serviced as an important resource for synthesis of pharmaceutical and human health products.
Physicochemical characteristics and high sensory acceptability in cappuccinos made with jackfruit seeds replacing cocoa powder
Authors: Papa Spada Fernanda , da Silva Paula Porrelli Moreira , Mandro Gabriela Fernanda , Margiotta GregÓrio Borghese , Spoto Marta Helena Fillet , Canniatti-Brazaca Solange Guidolin
Published: May 2018

Jackfruit seeds are an under-utilized waste product in many tropical countries. In this work, we demonstrate the potential of roasted jackfruit seeds to substitute for cocoa powder in cappuccino formulations. Two different flours were produced from a hard variety jackfruit by drying or fermenting the seeds prior to roasting. Next, seven formulations were prepared with 50%, 75%, and 100% substitution of cocoa powder with jackfruit seed flours. The acceptance of cappuccinos by consumers (n=126) and quantitative descriptive analysis (QDA®) were used to describe the preparations. Physicochemical proprieties were also evaluated. When 50% and 75% cocoa powder was replaced with dry jackfruit seed flour, there was no change in sensory acceptability or technological proprieties; however, it is possible identify advantages to using dry jackfruit seed flour, including moisture reduction and high wettability, solubility and sensory acceptation of the chocolate aroma. The principal component analysis of QDA®explained 90% variances; cluster analysis enabled the definition of four groups for six cappuccino preparations. In fact, dry jackfruit seed flour is an innovative cocoa powder substitute; it could be used in food preparations, consequently utilizing this tropical fruit waste by incorporating it as an ingredient in a common product of the human diet.
Robotic selection for the rapid development of stable CHO cell lines for HIV vaccine for production
Authors: O’Rourke Sara M , Byrne Gabriel , Tatsuno Gwen , Wright Meredith , Yu Bin , Mesa Kathryn A , Doran Rachel C , Alexander David , Berman Phillip W
Published: May 2018

The production of envelope glycoproteins (Envs) for use as HIV vaccines is challenging. The yield of Envs expressed in stable Chinese Hamster Ovary (CHO) cell lines is typically 10-100 fold lower than other glycoproteins of pharmaceutical interest. Moreover, Envs produced in CHO cells are typically enriched for sialic acid containing glycans compared to virus associated Envs that possess mainly high-mannose carbohydrates. This difference alters the net charge and biophysical properties of Envs and impacts their antigenic structure. Here we employ a novel gene-edited CHO cell line (MGAT1-CHO) to address the problems of low expression, high sialic acid content, and poor antigenic structure. We demonstrate that stable cell lines expressing high levels of gp120, potentially suitable for biopharmaceutical production can be created using the MGAT1-CHO cell line. We also show that the efficiency of this process can be greatly improved with robotic selection. Finally, we describe a MGAT1-CHO cell line expressing A244-rgp120 that exhibits improved binding of three major families of bN-mAbs compared to Envs produced in normal CHO cells. The new strategy described has the potential to eliminate the bottleneck in HIV vaccine development that has limited the field for more than 25 years.
SupportNet: a novel incremental learning framework through deep learning and support data
Authors: Li Yu , Li Zhongxiao , Ding Lizhong , Hu Yuhui , Chen Wei , Gao Xin
Published: May 2018

Motivation

In most biological data sets, the amount of data is regularly growing and the number of classes is continuously increasing. To deal with the new data from the new classes, one approach is to train a classification model, e.g., a deep learning model, from scratch based on both old and new data. This approach is highly computationally costly and the extracted features are likely very different from the ones extracted by the model trained on the old data alone, which leads to poor model robustness. Another approach is to fine tune the trained model from the old data on the new data. However, this approach often does not have the ability to learn new knowledge without forgetting the previously learned knowledge, which is known as the catastrophic forgetting problem. To our knowledge, this problem has not been studied in the field of bioinformatics despite its existence in many bioinformatic problems.

Results

Here we propose a novel method, SupportNet, to solve the catastrophic forgetting problem efficiently and effectively. SupportNet combines the strength of deep learning and support vector machine (SVM), where SVM is used to identify the support data from the old data, which are fed to the deep learning model together with the new data for further training so that the model can review the essential information of the old data when learning the new information. Two powerful consolidation regularizers are applied to ensure the robustness of the learned model. Comprehensive experiments on various tasks, including enzyme function prediction, subcellular structure classification and breast tumor classification, show that SupportNet drastically outperforms the state-of-the-art incremental learning methods and reaches similar performance as the deep learning model trained from scratch on both old and new data.

Availability

Our program is accessible at: https://github.com/lykaust15/SupportNet.
Novel asymmetric 3,5-bis(arylidene)piperidin-4-one derivatives: synthesis, crystal structures and cytotoxicity
Authors: Yao Binrong , Li Ning , Wang Chunhua , Hou Guige , Meng Qingguo , Yan Ke
Published: May 2018

3,5-Bis(arylidene)piperidin-4-one derivatives (BAPs) display good antitumour activity because of their double α,β-unsaturated ketone structural characteristics. Reported BAPs have generally been symmetric and asymmetric BAPs have been little documented. Three asymmetric BAPs, namely (5E)-3-(4-tert-butylbenzylidene)-5-(4-fluorobenzylidene)-1-methylpiperidin-4-one, C24H26FNO, (5), (5E)-3-(4-tert-butylbenzylidene)-5-(3,5-dimethoxybenzylidene)-1-methylpiperidin-4-one, C26H31NO3, (6), and (5E)-3-{3-[(E)-(2,3-dihydroxybenzylidene)amino]benzylidene}-5-(2-fluorobenzylidene)-1-methylpiperidin-4-one, C27H23FN2O3, (12), were generated by Claisen–Schmidt condensation. They are characterized by NMR and FT–IR spectroscopies, and elemental analysis. Single-crystal structure analysis reveals that the two arylidene rings on both sides of the BAP structures adopt an E stereochemistry of the olefinic double bonds and the compounds are E,E isomers. Molecules of (5) and (12) generate one-dimensional chains through intermolecular hydrogen bonds, while compound (6) generates a two-dimensional network through hydrogen bonds. Preliminary cytotoxicities toward human liver hepatocellular carcinoma cell line (HepG2), human acute mononuclear granulocyte leukaemia (THP-1) and human normal hepatical cell line (LO2) were evaluated.
Synthesis, crystal structure and thermal properties of an unsymmetrical 1,2,4,5-tetrazine energetic derivative
Authors: Chen Xiang , Zhang Cong , Bai Yang , Guo Zhaoqi , Yao Yanru , Song Jirong , Ma Haixia
Published: May 2018

A new unsymmetrical s-tetrazine derivative, namely 4-({2-[6-(3,5-dimethyl-1H-pyrazol-1-yl)-1,2,4,5-tetrazin-3-yl]hydrazin-1-ylidene}methyl)phenol (DPHM), C14H14N8O, was synthesized based on 3-(3,5-dimethylpyrazol-1-yl)-6-hydrazinyl-s-tetrazine (DPHT). The structure was characterized by elemental analysis and single-crystal X-ray diffraction. Crystal structure determination shows that DPHM crystallizes in the monoclinicP21/cspace group with high coplanarity and a zigzag layered structure. In addition, its thermal behaviour was investigated by DSC and TG–DTG methods. The thermal safety of DPHM was evaluated by self-accelerating decomposition temperature (TSADT), critical temperature of thermal explosion (Tb), entropy of activation (ΔS^{\neq}), enthalpy of activation (ΔH^{\neq}) and free energy of activation (ΔG^{\neq}). Meanwhile, the kinetic parameters and specific heat capacity of DPHM were also determined. The results show that DPHM has better stability and detonation properties than 3-(2-benzylidenehydrazin-1-yl)-6-(3,5-dimethylpyrazol-1-yl)-s-tetrazine (DAHBTz), due to the introduction of a hydroxy group, which increases the number of hydrogen-bond interactions and improves the stability and density of DPHM. This study demonstrates that the performance of an explosive can be optimized through structural modification.
Screencasting: supportive feedback for EFL remedial writing students
Authors: Ghosn-Chelala Maria , Al-Chibani Wessam
Published: May 2018

Purpose

The purpose of this paper is to explore screencasting as a computer-mediated feedback approach for Arabic native (L1) speakers taking an English as a foreign language (EFL) college remedial writing class.

Design/methodology/approach

This case study focused on an EFL remedial writing class consisting of eight Lebanese, Arabic L1 students at a private university in Lebanon. Students received screencast feedback through Jing® for one essay intended to assist them with subsequent revision. The multimodal screencast videos included indirect corrections, annotations, and oral commentary guided by a rubric. Students then completed a perspectives survey on screencast feedback. The instructor also led an informal group discussion to allow for further elaboration of students’ responses.

Findings

Students reported that screencasting’s multimodality provided for better engagement and support of learning preferences. They also perceived screencast feedback to be clearer and more useful than traditional written feedback.

Research limitations/implications

This study applied screencasting to address feedback challenges pertaining to clarity, learning preferences, and engagement. As this was a classroom case study, further research using a larger sample is recommended.

Originality/value

The aim of research into computer-mediated human feedback is to address such challenges as increasing student engagement, improving clarity, and responding to students’ preferences. Studies of screencast feedback have been few, particularly for EFL writing students. A survey of the literature indicates the need to explore contextualized classroom feedback case studies and approaches to enhance feedback.
Dynamic analysis of sin stocks and investor sentiment
Authors: Liston-Perez Daniel , Gutierrez Juan Pablo
Published: May 2018

Purpose

The purpose of this paper is to examine the temporal impact of individual and institutional investor sentiment on sin stock returns.

Design/methodology/approach

The authors estimate vector autoregressive models (VARs) to assess the dynamic relationships amongst pure sin returns and both types of investor sentiment. The justification for estimating VARs is that it allows one to study the potential influence that shocks (i.e. innovations) in individual and institutional investor sentiment might have on pure sin returns over time. Sin stock returns are separated into a market-based and pure sin component. Additionally, the authors split both measures of investor sentiment into rational- and irrational-based components.

Findings

This study finds that shocks to both individual and institutional rational-based sentiment positively influence pure sin returns for up to four months. However, irrational-based shocks have a positive, weaker and insignificant effect on pure sin returns. In addition, the results for the pure sin portfolio are compared to the S&P 500 and a comparables portfolio. The results show that sin stocks are less responsive than the S&P and the comparables portfolio to shocks in investor sentiment.

Originality/value

This study addresses some of the limitations found in the only prior study of sin stocks and investor sentiment (Perez Liston, 2016). Specially, this study investigates the link between sin stocks and sentiment in a dynamic context and also focuses the analysis on pure sin returns.
Human resources and manufacturing: where and when should they be aligned?
Authors: González-Sánchez Daniel , Suárez-González Isabel , Gonzalez-Benito Javier
Published: May 2018

Purpose

The purpose of this paper is to analyse the effect that a horizontal fit between two functions (human resources (HR) and manufacturing) has on firm performance, distinguishing between fit in objectives and fit in achievements.

Design/methodology/approach

This study uses 144 double surveys, addressed to two different respondents per company. Structural equation modelling was used to investigate the mediating role of fit in achievements in the relationship between fit in objectives and performance.

Findings

The study provides evidence of the particular way in which the two components of horizontal fit that the authors distinguish (fit in objectives and fit in achievements) the impact on performance: fit in objectives has an indirect effect on performance, which is fully mediated by the fit in achievements. The results also show that environmental dynamism has a significant impact on both the advantages and drawbacks of fit.

Practical implications

By highlighting the importance of both levels of horizontal fit and distinguishing between them, this paper calls upon HR and manufacturing managers to show a greater understanding of the key dimensions common to both areas.

Originality/value

This study analyses horizontal fit by developing a framework of priorities in HR management (HRM) similar to that traditionally used in production management. In particular, it adapts the framework of production competence to the area of HRM to study the fit between the two functional strategies. This study also supports the value chain model proposed by Porter (1985).
It takes two to tango
Authors: Artto Karlos , Turkulainen Virpi
Published: May 2018

Purpose

The purpose of this paper is to develop further understanding of the interdependence between product and organization subsystems in the context of major projects by empirically elaborating the volume-variety matrix.

Design/methodology/approach

Projects are perceived as systems that include a product subsystem (the project outcome) and an organization subsystem (the temporary multi-firm organizational network that produces the project outcome). This study addresses product-organization interdependence by analyzing product and organization subsystem components in terms of their uniqueness and reuse across multiple projects. The empirical analysis focuses on four global renewable fuels refinery projects implemented by Neste from 2003 to 2011. The refineries are based on the same proprietary technology but are unique at the project level.

Findings

The findings indicate interesting interdependencies between product and organization subsystems when analyzed at the component level: the findings suggest both diagonal and off-diagonal positions in the volume-variety matrix. An example of an off-diagonal position is a reused organization subsystem component associated with a unique product subsystem component, meaning that choosing the same organization in a future project can be used for acquiring an improved and, thereby, unique product subsystem component.

Originality/value

The study elaborates upon the volume-variety matrix in the context of major projects. The findings related to off-diagonal positions in the matrix provide new knowledge on combinations at the component level where a reused organization can be associated with a unique product, and vice versa. This has direct implications for management of projects.
Analysing healthcare coordination using translational mobilization
Authors: Allen Davina
Published: May 2018

Purpose

The purpose of this paper is to introduce translational mobilization theory (TMT) and explore its application for healthcare quality improvement purposes.

Design/methodology/approach

TMT is a generic sociological theory that explains how projects of collective action are progressed in complex organizational contexts. This paper introduces TMT, outlines its ontological assumptions and core components, and explores its potential value for quality improvement using rescue trajectories as an illustrative case.

Findings

TMT has value for understanding coordination and collaboration in healthcare. Inviting a radical reconceptualization of healthcare organization, its potential applications include: mapping healthcare processes, understanding the role of artifacts in healthcare work, analyzing the relationship between content, context and implementation, program theory development and providing a comparative framework for supporting cross-sector learning.

Originality/value

Poor coordination and collaboration are well-recognized weaknesses in modern healthcare systems and represent important risks to quality and safety. While the organization and delivery of healthcare has been widely studied, and there is an extensive literature on team and inter-professional working, we lack readily accessible theoretical frameworks for analyzing collaborative work practices. TMT addresses this gap in understanding.
Transforming primary care: scoping review of research and practice
Authors: Miller Robin , Weir Catherine , Gulati Steve
Published: May 2018

Purpose

The purpose of this paper is to reflect on research evidence and practice experience of transforming primary care to a more integrated and holistic model.

Design/methodology/approach

It is based on a scoping review which has been guided by primary care stakeholders and synthesises research evidence and practice experience from ten international case studies.

Findings

Adopting an inter-professional, community-orientated and population-based primary care model requires a fundamental transformation of thinking about professional roles, relationships and responsibilities. Team-based approaches can replicate existing power dynamics unless medical clinicians are willing to embrace less authoritarian leadership styles. Engagement of patients and communities is often limited due to a lack of capacity and belief that will make an impact. Internal (relationships, cultures, experience of improvement) and external (incentives, policy intentions, community pressure) contexts can encourage or derail transformation efforts.

Practical implications

Transformation requires a co-ordinated programme that incorporates the following elements – external facilitation of change; developing clinical and non-clinical leaders; learning through training and reflection; engaging community and professional stakeholders; transitional funding; and formative and summative evaluation.

Originality/value

This paper combines research evidence and international practice experience to guide future programmes to transform primary care.
Precarious work or sustainable livelihoods? Aligning Prestea's Programme with the development dialogue on artisanal and small‐scale mining
Authors: Adonteng‐Kissi Obed , Adonteng‐Kissi Barbara
Published: May 2018

Alternative livelihoods programmes (ALPs) are extensively executed in mining communities, often as models of development dialogue on artisanal and small‐scale mining (ASM). This paper assesses whether Prestea's ALP aligns with the development dialogue on artisanal mining. The conceptual design of ALP in Ghana's Prestea is based on the notions of substitution, homogenous community, and impact scalability. This paper argues that the Prestea ALP is not aligned with the development dialogue on artisanal mining, and therefore it is difficult to understand the role and function of environmentally‐damaging behaviours within livelihood strategies. The paper contends that it would be appropriate to concentrate on improving the existing artisanal miners’ operation of those most susceptible to resource access restrictions. Further, it may be more prudent to utilize livelihood‐centered interventions that create strong connections with sustainable development as a way of creating regular community engagements. Additionally, this paper argues that the term for the intervention programme on artisanal mining should be replaced with the broader term ‘livelihood‐centered intervention’. The replacement of the term ‘ALP’ avoids the tacit belief that ALP can adequately replace artisanal mining operations. Livelihood‐centered intervention should not necessarily utilize alternative livelihoods as direct behavioural change instruments.
Translating Behavioral Science into Practice: A Framework to Determine Science Quality and Applicability for Police Organizations
Authors: McClure Kimberley A. , McGuire Katherine L. , Chapan Denis M.
Published: May 2018

Policy on officer‐involved shootings is critically reviewed and errors in applying scientific knowledge identified. Identifying and evaluating the most relevant science to a field‐based problem is challenging. Law enforcement administrators with a clear understanding of valid science and application are in a better position to utilize scientific knowledge for the benefit of their organizations and officers. A recommended framework is proposed for considering the validity of science and its application. Valid science emerges via hypothesis testing, replication, extension and marked by peer review, known error rates, and general acceptance in its field of origin. Valid application of behavioral science requires an understanding of the methodology employed, measures used, and participants recruited to determine whether the science is ready for application. Fostering a science–practitioner partnership and an organizational culture that embraces quality, empirically based policy, and practices improves science‐to‐practice translation.
Bedside Sonography Performed by Emergency Physicians to Detect Appendicitis in Children
Authors: Nicole Marie , Desjardins Marie Pier , Gravel Jocelyn
Published: May 2018

Objective

The aim of this study was to evaluate the ability of emergency physicians with various levels of point‐of‐care ultrasound (POCUS) experience to detect appendicitis with POCUS among children visiting a pediatric emergency department (ED).

Methods

A prospective cohort study was conducted in an urban, tertiary care pediatric ED. Children aged 2 to 18 years old who presented with acute abdominal pain suggesting appendicitis were included. Patients were excluded if they had a history of appendectomy or hemodynamic instability requiring resuscitation or were transferred with proven diagnosis of appendicitis. Participating physicians had various levels of POCUS experience. Four of the 22 physicians were experienced in bowel sonography while the others had basic experience in abdominal POCUS. All the participating physicians received a 1‐hour didactic and practical training session on appendix ultrasound. The treating physician performed POCUS following initial physical examination, before further radiologic evaluation. POCUS examinations were recorded as positive for appendicitis, normal, or inconclusive, with normal or inconclusive studies considered negative. Final outcomes were determined by pathology and/or operative reports for surgical cases and telephone follow‐up at 3 weeks for those who did not have surgery. The primary analysis was a simple proportion for sensitivity and specificity for POCUS. Expecting a sensitivity of 80% based on previous studies, we calculated that a sample size of 50 cases would provide a 95% confidence interval (CI) ranging from 66% to 90%.

Results

Of the 140 approached patients, 121 accepted to participate and were recruited. After four patients were excluded for missing POCUS data, 117 patients were included in the primary analysis, of whom 51 (44%) had appendicitis. Twenty‐two physicians performed between one and 20 POCUS procedures. The POCUS was positive in 39, negative in nine, and inconclusive in 69 patients. POCUS was interpreted as positive in 27 of 51 appendicitis for a sensitivity of 0.53 (95% CI = 0.40–0.66). A negative or inconclusive POCUS was reported for 54 of 66 patients without appendicitis (specificity = 0.82; 95% CI = 0.71–0.89).

Conclusion

This study shows limited sensitivity and specificity of POCUS for appendicitis in children, with a high proportion of inconclusive examinations, when performed by emergency physicians with various level of experience in POCUS.