bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Mehler reaction site is the Phylloquinone within Photosystem I
Authors: Kozuleva Marina , Petrova Anastasia , Milrad Yuval , Semenov Alexey , Ivanov Boris , Redding Kevin E. , Yacoby Iftach 
Published: August 2020

ABSTRACTPhotosynthesis is a vital process, responsible for fixing carbon dioxide, and producing most of the organic matter on the planet. However, photosynthesis has some inherent limitations in utilizing solar energy. Up to a third of the energy absorbed is lost in the reduction of O2to produce the superoxide radical (O2•−), which occurs principally within photosystem I (PSI)viathe Mehler reaction. Strikingly, the precise location as well as the evolutionary role of the reaction have long been a matter of debate. For decades, O2reduction was assumed to take place solely in the distal iron-sulfur clusters of PSI rather than within the two asymmetrical cofactor branches. Here we demonstrate that under high irradiance, O2photoreduction by PSI takes place at the phylloquinone of one of the branches (the A-branch). This conclusion derives from the light dependency of the O2photoreduction rate constant, and from the high rates of O2photoreduction in PSI complexes lacking iron-sulfur clusters and in a mutant PSI, in which the lifetime of this phyllosemiquinone state is extended 100-fold. On these grounds, we suggest that the Mehler reaction serves as a release valve, functioning only when needed, under conditions where both the distal iron-sulfur clusters of PSI and the mobile ferredoxin pool are over reduced.SIGNIFICANCE STATEMENTPhotosynthesis is the process responsible for the oxygenation of the ancient anoxic atmosphere, and the transformation of inorganic carbon to most of the organic matter on Earth. However, it is less commonly appreciated that the appearance of oxygen in the atmosphere led to the unavoidable opposite process in which oxygen is consumed, thereby producing deleterious oxygen radicals such as the superoxide radical. For almost half a decade, the location of the main site of superoxide radical production in chloroplasts has been a matter of debate. We now provide conclusive evidence that it is located in the phylloquinones(s) within photosystem I.
Temporal instability of lake charr phenotypes: synchronicity of growth rates and morphology linked to environmental variables?
Authors: Chavarie L. , Voelker Steve , Hansen M.J. , Bronte C.R. , Muir A.M. , Zimmerman M.S. , Krueger C.C. 
Published: August 2020

AbstractPathways through which phenotypic variation arises among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. To address biological complexity below the species level, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr ecotypes in Rush Lake, USA. We found a rapid phenotypic shift in body and head shape within a decade. The magnitude and direction of the observed phenotypic change was consistent in both ecotypes, which suggests similar pathways caused the temporal variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early stage (age 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing reduced growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.
The Macerprep: a minimalist kit- and enzyme-free high-yield miniprep utilising alkaline lysis and alkaline hydrolysis principles
Authors: Hu Ian 
Published: August 2020

ABSTRACTThe commercialisation of miniprep kits supplanted the original alkaline lysis method for plasmid DNA preparation, and had remained relatively unchanged for almost two decades. The Miraprep substantially improved the yields of miniprep kits. However, the method still relies on commercial kits, which can be a burden financially to certain projects. Additionally, Pronobis et al. also identified loss of RNAse activities in miniprep kits over time. The present novel plasmid DNA isolation protocol addresses the two issues mentioned above utilising alkaline lysis and alkaline hydrolysis principles. With a largely identical workflow and operation time, the Macerprep will significantly reduce costs of establishing new laboratories as well as maintenance of running molecular biology laboratories.
D-graph clusters flaviviruses and β-coronaviruses according to their hosts, disease type and human cell receptors
Authors: Braun Benjamin A. , Schein Catherine H. , Braun Werner 
Published: August 2020

AbstractMotivationThere is a need for rapid and easy to use, alignment free methods to cluster large groups of protein sequence data. Commonly used phylogenetic trees based on alignments can be used to visualize only a limited number of protein sequences. DGraph, introduced here, is a dynamic programming application developed to generate 2D-maps based on similarity scores for sequences. The program automatically calculates and graphically displays property distance (PD) scores based on physico-chemical property (PCP) similarities from an unaligned list of FASTA files. Such “PD-graphs” show the interrelatedness of the sequences, whereby clusters can reveal deeper connectivities.ResultsPD-Graphs generated for flavivirus (FV), enterovirus (EV), and coronavirus (CoV) sequences from complete polyproteins or individual proteins are consistent with biological data on vector types, hosts, cellular receptors and disease phenotypes. PD-graphs separate the tick- from the mosquito-borne FV, clusters viruses that infect bats, camels, seabirds and humans separately and the clusters correlate with disease phenotype. The PD method segregates the β-CoV spike proteins of SARS, SARS-CoV-2, and MERS sequences from other human pathogenic CoV, with clustering consistent with cellular receptor usage. The graphs also suggest evolutionary relationships that may be difficult to determine with conventional bootstrapping methods that require postulating an ancestral sequence.Availability and implementationDGraph is written in Java, compatible with the Java 5 runtime or newer. Source code and executable is available from the GitHub website (https://github.com/bjmnbraun/DGraph/releases). Documentation for installation and use of the software is available from the Readme.md file at (https://github.com/bjmnbraun/DGraph).Contactbjmnbraun@gmail.comorwebraun@utmb.eduSupplementary informationSupplementary information Table S1 and Fig. S1 are online available.
Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome
Authors: Finn Paul B. , Bhimsaria Devesh , Ali Asfa , Eguchi Asuka , Ansari Aseem Z. , Dervan Peter B. 
Published: August 2020

ABSTRACTRegulating desired loci in the genome with sequence-specific DNA-binding molecules is a major goal for the development of precision medicine. Pyrrole–imidazole (Py–Im) polyamides are synthetic molecules that can be rationally designed to target specific DNA sequences to both disrupt and recruit transcriptional machinery. Whilein vitrobinding has been extensively studied,in vivoeffects are often difficult to predict using current models of DNA binding. Determining the impact of genomic architecture and the local chromatin landscape on polyamide-DNA sequence specificity remains an unresolved question that impedes their effective deploymentin vivo. In this report we identified polyamide–DNA interaction sites across the entire genome, by covalently crosslinking and capturing these events in the nuclei of human LNCaP cells. This method, termed COSMIC-seq, confirms the ability of hairpin-polyamides, with similar architectures but differing at a single ring position, to retainin vitrospecificities and display distinct genome-wide binding profiles. These results underpin the development of Py-Im polyamides as DNA-targeting molecules that mediate their regulatory or remedial functions at desired genomic loci.
Structure Basis of Cav1.1 Modulation by Dihydropyridine Compounds
Authors: Gao Shuai , Yan Nieng 
Published: August 2020

Abstract1,4-Dihydropyridines (DHP), the most commonly used antihypertensives, function by inhibiting the L-type voltage-gated Ca2+(Cav) channels. DHP compounds exhibit chirality-specific antagonistic or agonistic effects. Recent structural elucidation of rabbit Cav1.1 bound to an achiral drug nifedipine reveals the general binding mode for DHP drugs, but the molecular basis for chiral specificity remains elusive. Here, we report five cryo-EM structures of nanodisc-embedded Cav1.1 in the presence of the bestselling drug amlodipine, a DHP antagonist (R)-(+)-Bay K8644, and a titration of its agonistic enantiomer (S)-(-)-Bay K8644 at resolutions of 2.9-3.4 Å. The amlodipine-bound structure reveals the molecular basis for the high efficacy of the drug. All structures with the addition of the Bay K8644 enantiomers exhibit similar inactivated conformations, suggesting that the agonistic effect of (S)-(-)-Bay K8644 might be transient. The similarity of these structures to that obtained in detergent micelles alleviates the concerns about potential structural perturbation by detergents.
Exemplary followership. Part 2: impact of organizational citizenship behavior
Authors: Peterson Tim O. , Peterson Claudette M. 
Published: August 2020

PurposeThe purpose of this study is to determine to what extent there is a predictive relationship between organizational citizenship behaviors (OCB) and followership behaviors within medical organizations in the USA. This is the second part of a two-part paper. It uses a revised followership instrument and an OCB instrument to determine if there is a predictive relationship between OCB and followership behaviors.Design/methodology/approachPart 1 of this quantitative survey-based empirical study used confirmatory factor analysis on an existing instrument and exploratory factor analysis on a revised instrument. Part 2 used regression analysis to explore the predictive relationship between followership and organizational citizenship.FindingsThe overall findings of this two-part paper show that organizational citizenship has a significant predictive impact on followership behaviors.Research limitations/implicationsParticipants in this study work exclusively in the health care industry; future research should expand to other industries and other large organizations that have many followers but few managerial leaders.Practical implicationsAs organizational citizenship can be developed and there is a predictive relationship between organizational citizenship and followership, organizations can develop professional development for individual followers. Managers and other leaders can learn how to develop OCB, and thus followership in several ways: onboarding, coaching, mentoring and executive development.Originality/valuePart 2 of this paper demonstrates the predictive impact that OCB can have in developing high performing followers.
Preventive maintenance optimization of sugarcane harvester machine based on FT-Bayesian network reliability
Authors: Afsharnia Fatemeh , Marzban Afshin , Asoodar Mohammadamin , Abdeshahi Abas 
Published: August 2020

PurposeThe purpose of this paper is to optimize the preventive maintenance based on fault tree (FT)–Bayesian network (BN) reliability for sugarcane harvester machine as a fundamental machine in the sugar industry that must be operated failure-free during a given period of the harvesting process.Design/methodology/approachTo determine machine reliability using the algorithm developed based on mapping FTs into BNs, the common failures of 168 machines were carefully investigated over 12 years (2007–2019). This algorithm was then used to predict the harvester reliability, estimate delays by machine downtimes and their consequences on white sugar production losses that can be reduced by optimizing the preventive maintenance scheduling.FindingsThe optimization of preventive maintenance scheduling based on estimated reliability of sugarcane harvester machines using FT–BNs can reduce white sugar production losses, the operation-stopping breakdowns and the downtime costs as a crisis that the sugar industry is facing.Practical implicationsMachine reliability gradually decreased by 31.08% approximately, which resulted in a working time loss of 26% in the 2018–19 harvesting season. In total, the white sugar losses were estimated as 204.17 tons for burnt canes and 114.53 tons for green canes. The losses of the 2018–19 harvesting season have been 11.85 times greater than the first harvesting season. The proposed maintenance interval for critical subsystems including the hydraulic, chopper and base cutter were obtained as 1.815, 1.12 and 1.05 h, respectively.Originality/valueIn this study, a new approach was used to optimize preventive maintenance to reduce delays and their implications upon costs in time, inconvenience and white sugar losses. The FT–BNs algorithm was found a useful tool that was over-fitting of failure occurrence probabilities data for sugarcane harvester machine.
Institutions and economic growth in ECOWAS: an investigation into the hierarchy of institution hypothesis (HIH)
Authors: Olaoye Olumide , Aderajo Oluwatosin 
Published: August 2020

PurposeThe purpose of this paper is to examine the relationship between the quality of different dimensions of institutional and economic growth in a panel of 15 member ECOWAS.Design/methodology/approachThe study adopts Driscoll and Kraay′s nonparametric covariance matrix estimator, and the spatial error model to account for cross-section dependency, cross-country heterogeneity and spatial dependence inherent in empirical modelling, which has largely been ignored in previous studies. This is because, the likelihood that corruption and human capital cluster in space is very high because factors that affect these phenomena disperse across borders. Similarly, to test the threshold effect, the study adopts the more refined and more appropriate dynamic panel data which models a nonlinear asymmetric dynamics and cross-sectional heterogeneity, simultaneously, in a dynamic threshold panel data framework.FindingsThe empirical evidence supports findings by previous researchers that better-quality political and economic institutions can have positive effects on economic growth. Similarly, our results support a nonlinear relationship between political institutions and economic institution, confirming the “hierarchy of institution hypothesis” in ECOWAS. Specifically, the findings show that economic institutions will only have the desired economic outcome in ECOWAS, only when political institution is above a certain threshold.Originality/valueUnlike previous studies which assume cross-sectional and spatial independence, the authors account for cross-section dependency and cross-country heterogeneity inherent in empirical modelling.Peer reviewThe peer review history for this article is available at:https://publons.com/publon/10.1108/IJSE-10-2019-0630
Vitality among university students: exploring the role of gratitude and resilience
Authors: Garg Naval , Sarkar Ayatakshee 
Published: August 2020

PurposeVitality is an occurrence of having extremely high energy, stamina, physical or mental vigor. This study tends to investigate whether gratitude and resilience lead to vitality. In particular, it tends to examine the necessity and sufficiency of gratitude and resilience for vitality among Indian university students.Design/methodology/approachThe collected data are analyzed with the help of different statistical tools like the measure of central tendency, standard deviation, correlation, linear and multiple regression, and necessary condition analysis.FindingsThe results establish both gratitude and resilience as sufficient and necessary conditions for the occurrence of vitality among students. Theoretical and practical implications, along with scope for future researchers, are also elaborated.Practical implicationsThough universities are the active change agents and change-makers in the lives of the students, the onus of positive transformation lies on both students and the university administration. Hence these prosocial measures like gratitude and resilience, which are self-regulating, self-professed and competent, help to build internal psychological resources to promote sustainable vitality.Originality/valueThe present study is probably the first study that explores sufficiency and necessity of resilience and gratitude for vitality among students. The findings suggest that university administration may rely on gratitude and resilience-based interventions to enhance vitality of students.
Consumer buying behaviour and purchase intention of organic food: a conceptual framework
Authors: Dangi Neeraj , Gupta Sandeep Kumar , Narula Sapna A. 
Published: August 2020

PurposeThe paper aims to investigate existing research in factors impacting organic food purchase with special reference to eco-labels and identify the relative influence of various determinants.Design/methodology/approachA conceptual framework is proposed of organic food buying behaviour after analysing a sample of 154,072 consumers reported in 91 research studies from 2001–2020. The factors are categorised into four categories on the basis of relatedness. In addition, the factors were analysed based on time, region and national economic status.FindingsThe impact of consumer psychographics, socio-demographic and product-related factor categories were found to be more pronounced compared to supply-related factor category. The results show that among individual factors like health concern, environment concern, knowledge and awareness, eco-labels and price followed by trust in organic food are the most important factors in organic food purchase. The findings suggest that eco-labels increase trust in organic food by reducing information asymmetry in consumers. However, there were differences in perception and factors importance between high-income economies and emerging economies.Originality/valueThe study is unique, as it analyses secondary research based on criteria of high-income economies and emerging economies. The conceptual framework can also be incorporated further into different cognitive models like the theory of planned behaviour.
Usefulness of 2‐D shear wave elastography for the diagnosis of inguinal lymph node metastasis of malignant melanoma and squamous cell carcinoma
Authors: Kawahara Yu , Togawa Yaei , Yamamoto Yosuke , Wakabayashi Seiichiro , Matsue Hiroyuki , Inafuku Kazuhiro 
Published: August 2020

AbstractWe used 2‐D shear wave elastography to quantify lymph node hardness, from the shear wave velocity, to determine the presence or absence of metastatic lymphadenopathy in the inguinal lymph nodes of five patients with malignant melanoma and squamous cell carcinoma. The shear wave velocity accurately identified all cases of metastasis confirmed by histology, compared with two false‐positive and one false‐negative finding with positron emission tomography/computed tomography. 2‐D shear wave elastography would be useful to evaluate inguinal lymph node metastasis.
More than words: the chemistry behind the interactions in the plant holobiont
Authors: Berlanga‐Clavero María Victoria , Molina‐Santiago Carlos , de Vicente Antonio , Romero Diego 
Published: August 2020

SummaryPlants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant‐associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant–microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant–microbe and microbe–microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe–microbe and microbe–plant communication pathways during plant development and on different plant organs.
Effects of lysine and arginine on the properties of low‐salt mince gel from striped catfish (Pangasianodon hypophthalmus)
Authors: Buamard Natchaphol , Javith Mohammad Akram , Balange Amjad Khansaheb , Krishna Gopal , Benjakul Soottawat 
Published: August 2020

AbstractEffects of basic amino acids, lysine (Lys) and arginine (Arg), at different levels (0%, 0.5%, and 1%, based on mince weight) on properties of striped catfish (Pangasianodon hypophthalmus) mince gel containing low salt (LS) and high salt (HS) were investigated. Without Lys or Arg addition, HS gel had the higher textural properties including hardness, chewiness, as well as cohesiveness than LS gel (P < 0.05) and the highest values were achieved when 1% Arg was incorporated in both LS and HS gels (P < 0.05). Arg had no effect on acceptability of mince gel. However, whiteness was decreased in HS gel when Arg was applied. Autolysis of gel was lower in HS gel containing Arg. No differences in protein patterns among all gel samples were found. Addition of Arg could increase the gelling ability of both LS and HS mince during heating as evidenced by higher storage modulus (G′) and viscous modulus (G″). Mince gel added with Arg had orderly interconnected structure and their microstructure was finer than that without Arg. Therefore, Arg could be used in LS gel from striped catfish mince, in which quality of gel was equivalent to HS counterpart.Practical ApplicationBasic amino acid, especially arginine (Arg) with guanidinium group, could increase repulsive force between protein molecules at low‐salt concentration (0.5%). This resulted in high solubilization of muscle proteins, whereas gel formation or gel strength was higher than that containing high salt (2.5% to 3.5%). Thus, Arg could be used for production of fish mince gel containing low salt with lowered health risk.
Acromioclavicular joint injuries: Imaging and management
Authors: Mantripragada Sravanthi , Bhagwani Sanjeev , Peh Wilfred CG , Lim Yeow Wai 
Published: August 2020

SummaryAcromioclavicular joint injuries are commonly encountered in the setting of shoulder trauma. Knowledge of the anatomy and biomechanics of the joint, grading of joint injuries, and understanding the capabilities and limitations of different radiological modalities will help in selecting the best management option and outcomes for affected patients.