bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of eight protocols for genomic DNA extraction of Hypostomus commersoni Valenciennes, 1836 (Loricariidae: Siluriformes)
Authors: Mezzomo P. , Mielniczki-Pereira A. A. , Sausen T. L. , Marinho J. R. , Cansian R. L. 
Published: August 2019

AbstractThe principle and the techniques applied in DNA extraction play a pivotal role in the obtention of a purified genetic material. The present study investigates the efficiency of eight protocols in the DNA extraction of Hypostomus commersoni, an essential component of South American freshwater ichthyofauna. The quality of samples was assessed through spectrophotometry, gel electrophoresis, and PCR-RAPD amplification. The efficiency of DNA extraction was influenced both by the method applied and the target-tissue of choice. Higher concentrations and yield of DNA were obtained from ocular tissue, with a positive spectrum of incubation in lysis buffer for up to 36 hours after sample collection, using fresh tissues and in the presence of a high concentration of Proteinase K (20 mg.ml-1). In these conditions, samples were successfully amplified. To date, there is no record of description for the parameters analyzed in this work, neither the description of RAPD markers for the species H. commersoni.
Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors
Authors: Sartori Geraldo Rodrigues , Leitão Andrei , Montanari Carlos A. , Laughton Charles A. 
Published: August 2019

AbstractCruzain, a cysteine protease of Trypanosoma cruzi, is a validated target for the treatment of Chagas disease. Due to its high similarity in three-dimensional structure with human cathepsins and their sequence identity above 70% in the active site regions, identifying potent but selective cruzain inhibitors with low side effects on the host organism represents a significant challenge. Here a panel of nitrile ligands with varying potencies against cathepsin K, cathepsin L and cruzain, are studied by molecular dynamics simulations as both non-covalent and covalent complexes. Principal component analysis (PCA), identifies and quantifies patterns of ligand-induced conformational selection that enable the construction of a decision tree which can predict with high confidence a low-nanomolar inhibitor of each of three proteins, and determine the selectivity for one against others.
ADC mapping with 12 b values: an improved technique for image quality in diffusion prostate MRI
Authors: Saad Lucas Scatigno , de Queiroz Rosas George , de Farias e Melo Homero José , Gabriele Henrique Armando Azevedo , Szejnfeld Jacob 
Published: August 2019

AbstractPurposeTo compare diffusion images and coefficients obtained with 4 b-value versus 12 b-value apparent diffusion coefficient (ADC) mapping for characterization of prostate lesions and how these coefficients relate and compare to the PI-RADS™ classification and Gleason grading system.MethodsPatients with indications for prostate cancer testing (n=158) underwent multiparametric 3T magnetic resonance imaging (MRI). Two diffusion sequences were acquired, one with 4 b values and one with 12 b values. ADC maps were calculated for each (ADC4 and ADC12) and the respective coefficients were tested for correlation with PI-RADS™ classification and Gleason score.ResultsThe ADC12 sequence produced images of superior quality and sharpness than ADC4. Normal-area means (ADC4, 1793.3×10−6mm2/s; ADC12, 1100×10−6mm2/s) were significantly lower than those of lesion areas (ADC4, 1105.9×10−6mm2/s; ADC12, 689.4×10−6mm2/s) (p<0.001). Both techniques behaved similarly and correlated well with PI-RADS™ classification, distinguishing scores 3, 4, and 5 and with means tending to decline with increasing Gleason grade. ADC12 mapping yielded higher specificity than ADC4 (82.6% vs. 72.3%).ConclusionsDiffusion with 12 values is a viable technique for examination of the prostate. It produced higher-quality images than current techniques and correlates well with PI-RADS™ classification and Gleason score.
The effect of blue-blocking lenses on photostress recovery times for low and high contrast chromatic and achromatic stimuli
Authors: Alzahrani Hind Saeed , Khuu Sieu K. , Ali Adiba , Roy Maitreyee 
Published: August 2019

AbstractThe selective reduction in visible wavelengths transmitted through commercially available blue-blocking lenses (BBLs) is known to influence the appearance and contrast detection of objects, particularly at low light levels which may impact the human retinal receptor response time to dynamic light changes during phostress events. In the present study, we assessed whether BBLs selectively affect photostress recovery times (PSRTs) in 12 participants for chromatic and achromatic stimuli presented under low and high contrast luminance conditions. Four types of commercially available BBLs were evaluated, and their effects on PSRTs were investigated. Our results showed that PSRTs required to detect high contrast chromatic and achromatic stimuli were unaffected by BBLs when compared to a clear control lens. However, PSRTs were significantly affected by BBLs and were longer when chromatic and achromatic stimuli were of low contrast. In addition, BBLs had the greatest impact on the PSRTs of blue coloured targets, and this was dependent on the spectral transmittance profile. These results indicate that wearing BBLs under low contrast conditions can have serious implications for visual behavior, particularly under low-light levels and in situations in which the observer is directly exposed to bright light sources. For example, during night time driving, the driver might be briefly exposed to bright lights by glancing at the headlights of a passing car. This increases the time required for vision to be restored after bright light exposure, resulting in delayed object detection, and therefore stoppage and reaction times, which might pose a safety risk for a driver.
Software for agriculture climate risk management focused in smallholders
Authors: Coltri Priscila Pereira , Pinto Hilton Silveira , de Medeiros Yasmin Onorio , Hashimoto Kaio Shinji , Di Blasio Giovanni Chaves , Alfonsi Eduardo Lauriano , do Valle Gonçalves Renata Ribeiro , Alfonsi Waldenilza Monteiro 
Published: August 2019

AbstractTaking Persimmon (Diospyros kakiL.), Fig (Ficus caricaL.) and Papaya (Carica PapayaL) fruits in São Paulo State, southeast of Brazil, as a case of study, we present here new software that was designed to support smallholders to manage their climate risk on the production area. The main idea of this new software named “Brazilian Mapping for Agricultural Zoning System” (BRAMAZOS) is to transform scientific knowledge into useful information for crop climate risk management, indicating the risk of crop failure and which is the limiting meteorological element for the area unsuitability. The software was developed based on user experience design, focusing on the users facilities with a friendly interface. We simulated these fruits climate risk in current and future scenarios of climate change using ETAHadgem ES Regional Climate Models (RCM), which is a downscaling of the Global Climate Model HadGEM2-ES, based on the IPCC 5th Assessment Report (AR5). We observed changes in the climate risk zone distribution for Persimmon and Papaya cultivation, which could lose almost 30% and 9% of the suitable area respectively. On the other hand, fig did not present significant reduction in the climate risk zone. The results presented here suggested that the temperate fruit examples used here seem to be more sensible to the temperature increase and, the tropical example seems to be more precipitation decrease sensitive. We discussed the significance of BRAMAZOS software as tool to support efficient information to climate risk management, providing agroclimatic information that are efficient to assist decision making, increase food security with the intention to reduce the climate impact on smallholders development and resources management issues.
In vivo sequestration of innate small molecules to promote bone healing
Authors: Zeng Yuze , Shih Yu-Ru V. , Baht Gurpreet S. , Varghese Shyni 
Published: August 2019

AbstractApproaches that enable innate repair mechanisms hold great potential for tissue repair. Herein, we describe biomaterial-assisted sequestration of small molecules to localize pro-regenerative signaling at the injury site. Specifically, we designed a synthetic biomaterial containing boronate molecules to sequester adenosine, a small molecule ubiquitously present in the human body. The biomaterial-assisted sequestration of adenosine leverages the transient surge of extracellular adenosine following injury to prolong local adenosine signaling. We demonstrated that implantation of the biomaterial patch following injury establishes an in-situ stockpile of adenosine, resulting in accelerated healing by promoting both osteoblastogenesis and angiogenesis. The adenosine content within the patch recedes to the physiological level as the tissue regenerates. In addition to sequestering endogenous adenosine, the biomaterial is also able to deliver exogenous adenosine to the site of injury, offering a versatile solution to utilizing adenosine as a potential therapeutic for tissue repair.
A low-cost and easy-to-use cell preservation reagent for 4°C or room temperature sample storage
Authors: Shankar Sidharth , Roy Shreya , Geary-Teeter Ari , Martin George M. , Ladd Paula D. 
Published: August 2019

AbstractCurrent biospecimen storage and preservation methods no longer meet the demands of basic research and clinical diagnostics. Biospecimen preservation methodology has not advanced to accommodate cutting edge molecular analysis technologies that target single cells and full-length transcripts. Traditional methods, such as flash freezing and formalin-fixed paraffin-embedding (FFPE), were designed to provide information on cell structure and spatial relationships in whole tissues. These methods, however, do not maintain the integrity of proteins and nucleic acids. In this proof-of-concept study we examine preservation mechanisms utilized in nature for survival during cold seasons or periods of drought. Plants, brine shrimp, and tardigrades rely on components such as disaccharides or intrinsically disordered proteins to maintain cellular structure and biological activity in the settings of these environmental stresses. Our study demonstrates that these reagents aid in mammalian cell preservation for at least one week when a sample is stored in solution at 4°C, or as a dried sample in a low humidity desiccator.
Deubiquitination of phosphoribosyl-ubiquitin conjugates by PDE domain-containingLegionellaeffectors
Authors: Wan Min , Sulpizio Alan , Akturk Anil , Beck Wendy H.J. , Lanz Michael , Faça Vitor M. , Smolka Marcus B. , Vogel Joseph P. , Mao Yuxin 
Published: August 2019

SummaryPosttranslational protein modification by ubiquitin (Ub) is a central eukaryotic mechanism that regulates a plethora of physiological processes. Recent studies unveiled an unconventional type of ubiquitination mediated by the SidE family ofLegionella pneumophilaeffectors, such as SdeA, that catalyzes the conjugation of Ub to a serine residue of target proteins via a phosphoribosyl linker (hence named PR-ubiquitination). Comparable to the deubiquitinases (DUBs) in the canonical ubiquitination pathway, here we show that twoLegionellaeffectors, named DupA (deubiquitinase forPR-ubiquitination) and DupB, reverse PR-ubiquitination by specific removal of phosphoribosyl-Ub (PR-Ub) from substrates. Both DupA and DupB are fully capable of rescuing the Golgi fragmentation phenotype caused by exogenous expression of SdeA in mammalian cells. We further show that deletion of these two genes results in significant accumulation of PR-ubiquitinated species in host cells infected withLegionella. In addition, we have identified a list of specific PR-ubiquitinated host targets and show that DupA and DupB play a role in modulating the association of PR-ubiquitinated host targets withLegionellacontaining vacuoles (LCV). Together, our data establish a complete PR-ubiquitination and deubiquitination cycle and demonstrate the intricate control thatLegionellahas over this unusual Ub-dependent posttranslational modification.Statement of significanceUbiquitination is a vital posttranslational modification in eukaryotes. A variety of microbial pathogens exploit this pathway during their infection.Legionella pneumophila, the causative bacterial pathogen of Legionnaires’ disease, has been show to hijack host ubiquitination pathway via a large number of effectors. Recent studies revealed a family of effectors catalyzing a novel type of Ub-dependent posttranslational modification, namely PR-ubiquitination. Here we report two new players, DupA and DupB, involved in this unconventional pathway. We found that DupA and DupB function as PR-Ub specific DUBs and play a role in regulating the PR-ubiquitination levels of host targets. Our results not only provide an expanding view of the PR-ubiquitination pathway, but may also facilitate the future identification of PR-ubiquitination pathways in eukaryotes.
Effective anti-collision algorithms for RFID robots system
Authors: Wang Honggang , Wang Shanshan , Yao Jia , Pan Ruoyu , Huang Qiongdan , Zhang Hanlu , Yang Jingfeng 
Published: August 2019

Purpose
The purpose of this paper is to study how to improve the performance of RFID robot system by anti-collision algorithms. For radio frequency identification (RFID) robots operating in mobile scenes, effective anti-collision algorithm not only reduces missed reading but also enhances the speed of RFID robots movement.

Design/methodology/approach
An effective anti-collision algorithm is proposed to accelerate tag identification in RFID robots systems in this paper. The tag collisions in the current time slot are detected by a new method, and then further resolve each small tag collision to improve system throughput, rather than the total tags number estimation. After the reader detected the collision, three different collision resolution methods were described and studied, and the situation of missing tag caused by reader moving is also discussed.

Findings
The proposed algorithm achieves theoretical system throughput of about 0.48, 0.50 and 0.61 and simulates to show that the proposed algorithm performance is significantly improved compared with the existing ALOHA-based algorithm.

Originality/value
The proposed RFID anti-collision algorithm is beneficial to improve the moving speed and identification reliability of the RFID robots in complex environments.
Convergence to shareholder primacy corporate governance: evidence from a leximetric analysis of the evolution of corporate governance regulations in 21 countries, 1995-2014
Authors: Samanta Navajyoti 
Published: August 2019

PurposeFor the past two and half decades, there has been a marked shift in the corporate governance regulations around the world. The change is more remarkable in developing countries where countries with little or no corporate governance regime have adopted “world class” standards. While there can be a debate on whether law in books actually translates into law in action, in the meantime it might be interesting to analyse the law in books to understand how the corporate governance regime has evolved in the past 20 years. This paper quantitatively tracks 21 countries, most of them being developing and emerging economies, over a period of 20 years. The period covers 1995 to 2014; thus, it traverses the pre and post crisis period in 1999 and 2008. Thus, the paper also provides a snapshot of the macrolegal changes that the countries engage in hoping to stave off the next crisis. The paper uses over 50 parameters modelled on the OECD Principles of Corporate Governance. The paper confirms the suspicion that corporate governance norms around the developing economies are converging on shareholder primacy end of the continuum. The rate of convergence was highest just before the financial crisis of 2008 and has since then slowed down.Design/methodology/approachThe paper uses data collected from experts. They filled up detailed questionnaire which quizzed them on the rules relating to corporate governance norms in their country and asked them to retrospectively check their data every five years for the past 20 years. This provided an excellent overview as to how the law has evolved in the past two decades on corporate governance. The data were then tabulated using a scoring sheet and then was put together using item response theory (IRT) which is a Bayesian method similar to factor analysis. The paper then follows a comparative approach using heatmaps to analyse the evolution of corporate governance in developing countries.FindingsCorporate governance norms around the developing economies are converging on shareholder primacy end of the continuum. The rate of convergence was highest just before the financial crisis of 2008 and has since then slowed down.Originality/valueThis is the first time that corporate governance panel data analysis has been carried out on top developing countries across so many parameters for such a long period. This paper also uses Bayesian IRT modelling to analyse the evolution which is novel in its approach especially in the corporate governance literature. The paper thus provides a clear view on the evolution of corporate governance norms and how they are converging on a particular ideology.
Experimental technique for high-frequency conductivity measurement
Authors: Marák Károly , Bilicz Sándor , Pávó József 
Published: August 2019

Purpose
The purpose of this study is to introduce a novel method for the measurement of electromagnetic material parameters.

Design/methodology/approach
The main idea behind the approach is the fact that for slabs with elongated shapes, the intensity of the backscattered field and the electromagnetic resonance frequency corresponding to the length of the sample are dependent on the conductivity of the sample’s material.

Findings
It is shown that for a known scattered field and resonance frequency, it is possible to formulate an inverse problem as to the calculation of the conductivity of the sample’s material at the considered frequencies. To investigate the applicability of the method, demonstrative experiments are performed during which the micro-Doppler effect is used to increase the measurement accuracy. The idea is extended to the case of anisotropic samples, with slight modifications proposed to the experimental setup in the case of significant anisotropy in the investigated material.

Practical implications
The measurement method may prove useful for the investigation of the high-frequency conductive properties of certain materials of interest.

Originality/value
To the best of the authors’ knowledge, this is the first time the use of the micro-Doppler effect is proposed for the purpose of the measurement of material parameters.
Information literacy capabilities of upper secondary students: the case of Vietnam
Authors: Ngo Huyen Thi , Pickard Alison Jane , Walton Geoff 
Published: August 2019

PurposeThis paper aims to focus on investigating information literacy (IL) capabilities and IL self-assessment of Vietnam’s upper secondary students.Design/methodology/approachThe investigation was conducted in two upper secondary schools in the country using a multiple-choice questionnaire. The questionnaire was based on the IL competency-level assessment toolkit of high schools in the USA, the tool for real-time assessment of IL, to measure students’ IL in terms of developing search strategies, evaluating information sources, using information ethically and using English to engage with information effectively.FindingsThe findings reveal that students’ IL has not been well equipped. There is a real need to work toward improving the IL capability of Vietnam’s upper secondary students. The findings also reveal gender differences in IL capabilities.Research limitations/implicationsThe research used a closed-response questionnaire, which is considered appropriate to engage with Vietnamese high-school students, to explore students’ lower-level IL skills and their self-assessment rather than higher-level thinking competencies.Practical implicationsThis research may help Vietnam’s educators understand high-school students’ IL competency and raise their awareness of the importance of IL to encourage the implementation of an IL programme.Originality/valueThis study contributes to the existing knowledge by adding substantially to current understanding of IL level of Vietnamese upper secondary students – a context which has not been explored to date. It also indicates gender inequality in IL capabilities.
Effect of innovativeness on supply chain integration and performance
Authors: Kalyar Masood Nawaz , Shafique Imran , Ahmad Bashir 
Published: August 2019

PurposeThe purpose of this paper is to investigate the potential role of innovativeness in determining supply chain (SC) integration and to foster the SC performance of manufacturing small and medium enterprises (SMEs). The study also proposes that the SC integration–performance relationship is contingent to the degree of environmental uncertainty (EU).Design/methodology/approachThe data were collected from 321 manufacturing SMEs working in Pakistan. Respondents were owners/CEOs/managers of the firms. Considering the formative nature of indicators of SC efficiency and effectiveness, partial least square-based structural equation modeling (SEM) was used to analyze the data.FindingsThe results indicate that innovativeness positively influences the dimensions of SC integration which in turn affects SC efficiency and effectiveness. The results support the presence of moderation for the relationship between the dimensions of both SC integration and performance. The findings suggest that firms should endeavor to accomplish innovativeness and SC integration, as they jointly promote SC performance.Practical implicationsSMEs can use innovativeness as an important tool to increase SC integration and SC performance. For SMEs with a highly volatile and dynamic environment, managers should achieve SC integration and include external integration orientation at the strategic level in order to reap the greatest advantages from SC integration.Originality/valueThis study contributes to the SC literature by exploring the effect of the nascent determinant (innovativeness) of SC practices and performance to expand and deepen current understanding of the potential role of innovativeness in the SC context. Furthermore, considering EU as a moderator opens up new avenues of research to elucidate the SC integration–performance nexus in the emerging market context.