bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversification in evolutionary arenas – assessment and synthesis
Authors: Nürk Nicolai M. , Linder H. Peter , Onstein Renske E. , Larcombe Matthew J. , Hughes Colin E. , Fernández Laura Piñeiro , Schlüter Philipp M. , Valente Luis , Beierkuhnlein Carl , Cutts Vanessa , Donoghue Michael J. , Edwards Erika J. , Field Richard , Flantua Suzette G.A. , Higgins Steven I. , Jentsch Anke , Liede-Schumann Sigrid , Pirie Michael D. 
Published: May 2019

AbstractUnderstanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography, and the metaphorical concepts of adaptive radiation and evolutionary stasis describe two opposing aspects causing variation in diversification rates. Here we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b) and clade-specific phenotypes or traits (c); thusd∼a,b,c. We refer to the four components (a–d) and their interactions collectively as the ‘Evolutionary Arena’. We outline analytical approaches to this framework and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples: theLupinusradiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genusOphrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.
Constructing a Timescale of Biotic Recovery across the Cretaceous–Paleogene Boundary, Corral Bluffs, Denver Basin, Colorado
Authors: Fuentes Anthony J. , Clyde William C. , Weissenburger Ken , Bercovici Antoine , Lyson Tyler R. , Miller Ian M. , Ramezani Jahandar , Schmitz Mark D. , Johnson Kirk R. 
Published: May 2019

ABSTRACTThe Cretaceous–Paleogene (K–Pg) boundary interval represents one of the most significant mass extinctions and ensuing biotic recoveries in Earth history. Earliest Paleocene fossil mammal faunas corresponding to the Puercan North American Land Mammal Age (NALMA) are thought to be highly endemic and potentially diachronous, necessitating precise chronostratigraphic controls at key fossil localities to constrain recovery dynamics in continental biotas following the K–Pg mass extinction. The Laramide synorgenic sedimentary deposits within the Denver Basin preserve one of the most continuous and fossiliferous records of the K–Pg boundary interval in North America. However, poor exposure in much of the Denver Basin makes it difficult to correlate between outcrops. In order to constrain fossil localities across the basin, previous studies have relied upon chronostratigraphic methods such as magnetostratigraphy. Here we present a new high-resolution magnetostratigraphy of 10 lithostratigraphic sections spanning the K–Pg boundary interval at Corral Bluffs located east of Colorado Springs in the southern part of the Denver Basin. Fossil localities from Corral Bluffs have yielded limited dinosaur remains, mammal fossils assigned to the Puercan NALMA, and numerous fossil leaf localities. Palynological analysis identifying the K–Pg boundary in three sections and two independent but nearly identical206Pb/238U age estimates for the same volcanic ash, provide key temporal calibration points. Our paleomagnetic analysis has identified clear polarity reversal boundaries from Chron C30n to Chron C28r across the sections. It is now possible to place the fossil localities at Corral Bluffs within the broader basin-wide chronostratigraphic framework and evaluate them in the context of K–Pg boundary extinction and recovery.
Cofactor selectivity in methylmalonyl-CoA mutase, a model cobamide-dependent enzyme
Authors: Sokolovskaya Olga M. , Mok Kenny C. , Park Jong Duk , Tran Jennifer L. A. , Quanstrom Kathryn A. , Taga Michiko E. 
Published: May 2019

AbstractCobamides, a uniquely diverse family of enzyme cofactors related to vitamin B12, are produced exclusively by bacteria and archaea but used in all domains of life. While it is widely accepted that cobamide-dependent organisms require specific cobamides for their metabolism, the biochemical mechanisms that make cobamides functionally distinct are largely unknown. Here, we examine the effects of cobamide structural variation on a model cobamide-dependent enzyme, methylmalonyl-CoA mutase (MCM). Thein vitrobinding affinity of MCM for cobamides can be dramatically influenced by small changes in the structure of the lower ligand of the cobamide, and binding selectivity differs between bacterial orthologs of MCM. In contrast, variations in the lower ligand have minor effects on MCM catalysis. Bacterial growth assays demonstrate that cobamide requirements of MCMin vitrolargely correlate within vivocobamide dependence. This result underscores the importance of enzyme selectivity in the cobamide-dependent physiology of bacteria.
DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases
Authors: Li Tingyang , Tripathi Ashootosh , Yu Fengan , Sherman David H. , Rao Arvind 
Published: May 2019

AbstractSummaryDDAP is a tool for predicting the biosynthetic pathways of the products of type I modular polyketide synthase (PKS) with the focus on providing a more accurate prediction of the ordering of proteins and substrates in the pathway. In this study, the module docking domain (DD) affinity prediction performance on a hold-out testing data set reached AUC = 0.88; the MRR of pathway prediction reached 0.67. DDAP has advantages compared to previous informatics tools in several aspects: (i) it does not rely on large databases, making it a high efficiency tool, (ii) the predicted DD affinity is represented by a probability (0 to 1), which is more intuitive than raw scores, (iii) its performance is competitive compared to the current popular rule-based algorithm. To the best of our knowledge, DDAP is so far the first machine learning based algorithm for type I PKS pathway prediction. We also established the first database of type I modular PKSs, featuring a comprehensive annotation of available docking domains information in bacterial biosynthetic pathways.Availability and implementationThe DDAP database is available at https://tylii.github.io/ddap. The prediction algorithm DDAP is freely available on GitHub (https://github.com/tylii/ddap) and released under the MIT license.Contactukarvind@umich.edu
How does the mood stabilizer lithium bind ATP, the energy currency of the cell
Authors: Haimovich A. , Goldbourt A. 
Published: May 2019

AbstractLithium, in the form of a salt, is a mood stabilizer and a leading drug for the treatment of bipolar disorder. It has a very narrow therapeutic range and a variety of side effects. Lithium can replace magnesium and other cations in enzymes and small molecules, among them ATP, thereby affecting and inhibiting many biochemical pathways. The form of binding of lithium ions to ATP is not known.Here we extract the binding environment of lithium in solid ATP using a multi-nuclear multi-dimensional solid-state NMR approach.We determine that the coordination sphere of lithium includes, at a distance of 3.0(±0.4) Å, three phosphates; the two phosphates closest to the ribose ring from one ATP molecule, and the middle phosphate from another ATP molecule. A water molecule most probably completes the fourth coordination. Despite the use of excess lithium in the preparations, sodium ions still remain bound to the sample, at distances of 4.3-5.5 Å from Li, and coordinate the first phosphate and two terminal phosphates.In conclusion, solid-state NMR enables to unravel the exact coordination of lithium in ATP showing binding to three phosphates from two molecules, none of which are the terminal gamma phosphate. The methods we use are applicable to study lithium bound to a variety of ATP-bound enzymes, or to other cellular targets of lithium, consequently suggesting a molecular basis for its mode of action.
Quantitative and rapid Plasmodium falciparum malaria diagnosis and artemisinin-resistance detection using a CMOS Lab-on-Chip platform
Authors: Malpartida-Cardenas K. , Miscourides N. , Rodriguez-Manzano J. , Yu L. S. , Baum J. , Georgiou P. 
Published: May 2019

AbstractEarly and accurate diagnosis of malaria and drug-resistance is essential to effective disease management. Available rapid malaria diagnostic tests present limitations in analytical sensitivity, drug-resistant testing and/or quantification. Conversely, diagnostic methods based on nucleic acid amplification stepped forwards owing to their high sensitivity, specificity and robustness. Nevertheless, these methods commonly rely on optical measurements and complex instrumentation which limit their applicability in resource-poor, point-of-care settings. This paper reports the specific, quantitative and fully-electronic detection of Plas-modium falciparum, the predominant malaria-causing parasite worldwide, using a Lab-on-Chip platform developed in-house. Furthermore, we demonstrate on-chip detection of C580Y, the most prevalent single-nucleotide polymorphism associated to artemisinin-resistant malaria. Real-time non-optical DNA sensing is facilitated using Ion-Sensitive Field-Effect Transistors, fabricated in unmodified complementary metal-oxide-semiconductor technology, coupled with loop-mediated isothermal amplification. This work holds significant potential for the development of a fully portable and quantitative malaria diagnostic that can be used as a rapid point-of-care test.
Real-time optoacoustic tracking of single moving micro-objects in deep tissue-mimicking phantoms
Authors: Aziz Azaam , Medina-Sánchez Mariana , Claussen Jing , Schmidt Oliver G. 
Published: May 2019

ABSTRACTMedical imaging plays an important role in diagnosis and treatment of multiple diseases. It is a field under continuous development which seeks for improved sensitivity and spatiotemporal resolution to allow the dynamic monitoring of diverse biological processes that occur at the micro- and nanoscale. Emerging technologies for targeted diagnosis and therapy such as nanotherapeutics, micro-implants, catheters and small medical tools also need to be precisely located and monitored while performing their function inside the human body. In this work, we show for the first time the real-time tracking of moving single micro-objects below centimeter thick tissue-mimicking phantoms, using multispectral optoacoustic tomography (MSOT). This technique combines the advantages of ultrasound imaging regarding depth and resolution with the molecular specificity of optical methods, thereby facilitating the discrimination between the spectral signatures of the micro-objects from those of intrinsic tissue molecules. The resulting MSOT signal is further improved in terms of contrast and specificity by coating the micro-objects’ surface with gold nanorods, possessing a unique absorption spectrum, which will allow their discrimination from surrounding biological tissues when translated to in vivo settings.
Abnormal morphology biases haematocrit distribution in tumour vasculature and contributes to heterogeneity in tissue oxygenation
Authors: Bernabeu Miguel O. , Köry Jakub , Grogan James A. , Markelc Bostjan , Beardo Albert , d’Avezac Mayeul , Enjalbert Romain , Kaeppler Jakob , Daly Nicholas , Hetherington James , Krüger Timm , Maini Philip K. , Pitt-Francis Joe M. , Muschel Ruth J. , Alarcón Tomás , Byrne Helen M. 
Published: May 2019

AbstractOxygen heterogeneity in solid tumours is recognised as a limiting factor for therapeutic efficacy. This heterogeneity arises from the abnormal vascular structure of the tumour, but the precise mechanisms linking abnormal structure and compromised oxygen transport are only partially understood. In this paper, we investigate the role that RBC transport plays in establishing oxygen heterogeneity in tumour tissue. We focus on heterogeneity driven by network effects, which are challenging to observe experimentally due to the reduced fields of view typically considered. Motivated by our findings of abnormal vascular patterns linked to deviations from current RBC transport theory, we calculate average vessel lengths and diameters from tumour allografts of three cancer cell lines and observe a substantial reduction in the ratio compared to physiological conditions. Mathematical modelling reveals that small values of the ratio λ (i.e. λ < 6) can bias haematocrit distribution in tumour vascular networks and drive heterogeneous oxygenation of tumour tissue. Finally, we show an increase in the value of λ in tumour vascular networks following treatment with the anti-angiogenic cancer agent DC101. Based on our findings, we propose λ as an effective way of monitoring the efficacy of antiangiogenic agents and as a proxy measure of perfusion and oxygenation in tumour tissue undergoing anti-angiogenic treatment.Significance statementOxygen heterogeneity in solid tumours is recognised as a limiting factor for therapeutic efficacy. This heterogeneity arises from the abnormal tumour vascular structure. We investigate the role that anomalies in RBC transport play in establishing oxygen heterogeneity in tumour tissue. We introduce a metric to characterise tumour vasculature (mean vessel length-to-diameter ratio, λ) and demonstrate how it predicts tissue oxygen heterogeneity. We also report an increase in λ following treatment with the antiangiogenic agent DC101. Together, we propose λ as an effective way of monitoring the action of anti-angiogenic agents and a proxy measure of oxygen heterogeneity in tumour tissue. Unravelling the causal relationship between tumour vascular structure and tissue oxygenation will pave the way for new personalised therapeutic approaches.
The calcium channel subunit α2δ-3 organizes synapses via a novel activity-dependent, autocrine BMP signaling pathway
Authors: Hoover Kendall M. , Gratz Scott J. , Herrmann Kelsey A. , Qi Nova , Liu Alexander , Perry-Richardson Jahci J. , Vanderzalm Pamela J. , O’Connor-Giles Kate M. , Broihier Heather T. 
Published: May 2019

AbstractSynapses are highly specialized for neurotransmitter signaling, yet activity-dependent growth factor release also plays critical roles at synapses. While efficient neurotransmitter signaling is known to rely on precise apposition of release sites and neurotransmitter receptors, molecular mechanisms enabling high-fidelity growth factor signaling within the synaptic microenvironment remain obscure. Here we show that the auxiliary calcium channel subunit α2δ-3 promotes the function of a novel activity-dependent autocrine BMP signaling pathway at the Drosophila NMJ. α2δ proteins have conserved synaptogenic activity, although how they execute this function has remained elusive. We find that α2δ-3 provides an extracellular scaffold for autocrine BMP signaling, suggesting a new mechanistic framework for understanding α2δ’s conserved role in synapse organization. We further establish a transcriptional requirement for activity-dependent, autocrine BMP signaling in determining synapse density, structure, and function. We propose that activity-dependent, autocrine signals provide neurons with continuous feedback on their activity state and are thus well poised to modulate synapse structure and function.
ARGONAUTE5 Mediates Fine-Tuning of Vegetative-to-Reproductive Phase Transition Through Its Interaction with miR156 in Arabidopsis
Authors: Roussin-Léveillée Charles , Silva-Martins Guilherme , Moffett Peter 
Published: May 2019

ABSTRACTVegetative-to-reproductive phase change is a finely tuned process in plants, largely controlled by the age-regulated microRNA156 (miR156), which functions by suppressing the transcripts of SQUAMOSA-PROMOTER BINDING LIKE (SPL) transcription factors. ARGONAUTE proteins (AGO) are essential effectors of miRNA-mediated gene regulation. However, which AGO(s) mediate(s) the control of flowering time remains unclear. Here, we demonstrate a role for AGO5 in vegetative-to-reproductive phase transition through the modulation of SPL transcription factors. We show that AGO5 interacts physically and functionally with miR156 and that ago5 mutants present an early flowering phenotype in Arabidopsis. Furthermore, in ago5 mutants, the repression of flowering caused by miR156 overexpression is largely reversed, whereas leaf morphology remains unaffected. Our results thus indicate a specific role for AGO5 in mediating miR156 activity in meristematic, but not vegetative, tissue. As such, our data suggest a spatiotemporal regulation of the miR156 aging pathway, mediated through different AGO proteins in different tissues.
Impact of food safety training on the knowledge, practice, and attitudes of food handlers working in fast-food restaurants
Authors: Elobeid Tahra , Savvaidis Ioannis , Ganji Vijay 
Published: May 2019

Purpose
In many developing countries, the main source of food related illness is the fast foods restaurants. Health inspections of fast-food restaurants may not be sufficient to ensure and enforce the food safety regulations. The purpose of this paper is to investigate the food safety knowledge, attitudes and practices (KAP) of fast food handlers in Qatar.

Design/methodology/approach
Data were collected from 102 fast-food handlers through a structured survey. The questionnaire comprised questions on food safety KAP. The association between scores for KAP among the food handlers was measured with Spearman’s rank correlation.

Findings
A significant direct association was found throughout the different criteria of food safety KAP. In total, 90 percent of fast food handlers had undergone formal training on food safety. Although fast food handlers thought they had overall good knowledge on food safety (93.9 percent), results showed that they had a poor knowledge on proper cleaning of equipment, cross-contamination, foodborne diseases, food danger zone and correct procedures for thawing of frozen food. Only (34.7 percent) of the food handlers correctly identified Salmonella as a food pathogen.

Originality/value
Based on the current findings, the authors believe that continuous food safety and hygiene training should be implemented in all food service operations especially in fast-food restaurants in Qatar to ensure that all food handlers have the knowledge and the skill to provide safe food.
Understanding the consumption of traditional-local foods through the experience perspective
Authors: Savelli Elisabetta , Bravi Laura , Murmura Federica , Pencarelli Tonino 
Published: May 2019

PurposeThe purpose of this paper is to understand whether an experiential perspective can be usefully adopted in the context of traditional-local foods (TLFs) by assuming a consumer perspective that analyses attitudes and behaviours of young people towards truffles. In particular, it examines which values drive the consumption of truffles and whether they are perceived as an experiential-based food or simply a nutritional-based one.Design/methodology/approachThe research was carried out through a survey conducted on a sample of 720 Italian university students from January to May 2016. The data were processed using analysis of variance, principal component analysis and a two-step cluster analysis.FindingsThe results show that the search for pleasure and gratification can be very important for young consumers and that gratification plays a critical role in the consumption of fresh truffles along with convenience. This confirms that TLFs, like truffles, can be highly appreciated by young consumers for their emotional content, which allows them to have a personal experience when buying and consuming them.Originality/valueThe study contributes to the literature by enriching the overall understanding of young people’s food behaviour and by deepening the adoption of the experiential perspective within the TLF business. Moreover, it has practical and useful implications for promoting the consumption of TLFs among the young and for managing TLFs as well as the rural areas from where they originate.
Cultural and contextual influences on corporate social responsibility
Authors: Ling Ya-Hui 
Published: May 2019

PurposeThe purpose of this paper is to examine the influence of managerial cultural values and the contextual environment (country of origin and country of operation) on corporate social responsibility (CSR) investments in three Asian countries.Design/methodology/approachA total of 150 questionnaires were collected from 150 companies located in Taiwan, Malaysia and Singapore. The potential influence of ethnicity on cultural values was controlled by collecting data from ethnic Chinese managers.FindingsThe results show that senior managers, especially their cultural values, play a crucial role in directing Asian companies’ CSR investments. In addition, the context (a firm’s country of origin and country of operation) also differentiates the cultural values and CSR investments in these three countries.Originality/valueThe study adds to the understanding of the influence of managerial cultural values and context on various aspects of CSR. Especially, the study offers valuable managerial implications for CSR implementation from the Chinese management perspective. Considering the fast global expansion of Chinese companies, the results concerning how Chinese managers’ cultural values influence their CSR investments priority offer valuable managerial implications. The comparisons of cultural values and CSR investments priority among ethnic Chinese managers in different contextual environments also serve as good starting points for future studies.
Performance assessment of shooting methods using parallel cloud computing
Authors: Agundis-Tinajero Gibran , Peña Gallardo Rafael , Segundo-Ramírez Juan , Visairo-Cruz Nancy , Guerrero Josep M. 
Published: May 2019

Purpose
The purpose of this study is to present the performance evaluation of three shooting methods typically applied to obtain the periodic steady state of electric power systems, with the aim to check the benefits of the use of cloud computing regarding relative efficiency and computation time.

Design/methodology/approach
The mathematical formulation of the methods is presented, and their parallelization potential is explained. Two case studies are addressed, and the solution is computed with the shooting methods using multiple computer cores through cloud computing.

Findings
The results obtained show a reduction in the computation time and increase in the relative efficiency by the application of these methods with parallel cloud computing, in the problem of obtainment of the periodic steady state of electric power systems in an efficient way. Additionally, the characteristics of the methods, when parallel cloud computing is used, are shown and comparisons among them are presented.

Originality/value
The main advantage of employment of parallel cloud computing is a significant reduction of the computation time in the solution of the problem of a heavy computational load caused by the application of the shooting methods.