bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning, Visualizing and Exploring 16S rRNA Structure Using an Attention-based Deep Neural Network
Authors: Zhao Zhengqiao , Woloszynek Stephen , Agbavor Felix , Mell Joshua Chang , Sokhansanj Bahrad A. , Rosen Gail 
Published: October 2020

AbstractRecurrent neural networks (RNNs) with memory (e.g. LSTMs) and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional networks, recurrent neural networks, and attention mechanisms to perform sample-associated attribute prediction—phenotype prediction—and extract interesting features, such as informative taxa and predictivek-mer context. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We focus on typically short DNA reads of 16s ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. Our deep learning approach enables sample-level attribute and taxonomic prediction, with the aim of aiding biological research and supporting medical diagnosis. We demonstrate that our implementation of a novel attention-based deep network architecture,Read2Pheno, achieves read-level phenotypic prediction and, in turn, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance comparable to conventional approaches. Most importantly, as a further result of the training process, the network architecture will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output on the intermediate layer of the network model, which can provide biological insight when visualized. Finally, we demonstrate that a model with an attention layer can automatically identify informative regions in sequences/reads which are particularly informative for classification tasks. An implementation of the attention-based deep learning network is available athttps://github.com/EESI/sequence_attention.
mutSigMapper: an R package to map spectra to mutational signatures based on shot-noise modeling
Authors: Candia Julián 
Published: October 2020

AbstractSummarymutSigMapper aims to resolve a critical shortcoming of existing software for mutational signature analysis, namely that of finding parsimonious and biologically plausible exposures. By implementing a shot-noise-based model to generate spectral ensembles, this package addresses this gap and provides a quantitative, non-parametric assessment of statistical significance for the association between mutational signatures and observed spectra.Availability and implementationThe mutSigMapper R package is available under GPLv3 license athttps://github.com/juliancandia/mutSigMapper. Its documentation provides additional details and demonstrates applications to biological datasets.
Enhanced Loading of Paclitaxel in Cationic Liposomes by Replacement of Oleoyl with Linoleoyl Lipid Tails with Benefits in Cancer Therapeutics fromIn VitroStudies
Authors: Zhen Yuhong , Ewert Kai K. , Fisher William S. , Steffes Victoria M. , Li Youli , Safinya Cyrus R. 
Published: October 2020

AbstractLipid-based carriers of the hydrophobic drug paclitaxel (PTX) are used in clinical trials as next-generation agents for cancer chemotherapy. Improving the loading capacity of these carriers requires enhanced PTX solubilization. We compared the solubility of PTX in cationic liposomes (CLs) with lipid tails containing one (oleoyl; C18:1 Δ9; DOTAP/DOPC) or two (linoleoyl; C18:2 Δ9; DLinTAP/DLinPC)cisdouble bonds with newly synthesized cationic DLinTAP (2,3-dilinoleoyloxypropyltrimethylammonium methylsufate). We used differential-interference-contrast microscopy to directly observe PTX crystal formation and generate kinetic phase diagrams representing the time-dependence of PTX solubility as a function of PTX content in the membrane. Replacing tails bearing onecisdouble bond (DO lipids) with those bearing two (DLin lipids) significantly increased PTX membrane solubility in CLs. Remarkably, 8 mol% PTX in DLinTAP/DLinPC CLs remained soluble for approximately as long as 3 mol% PTX (the membrane solubility limit which has been the focus of most previous fundamental studies and clinical trials) in DOTAP/DOPC CLs. The large increase in solubility is likely caused by enhanced molecular affinity between lipid tails and PTX upon replacement of oleoyl by linoleoyl tails, rather than by the transition in membrane structure from lipid bilayers to inverse cylindrical micelles observed in small-angle X-ray scattering. Importantly, the efficacy of PTX-loaded CLs against human prostate cancer (PC3) cells from measurements of the IC50 of PTX cytotoxicity was unaffected by changing the lipid tails, and toxicity of the CL carrier alone was negligible. Moreover, efficacy was approximately doubled against human melanoma (M21) cells for PTX-loaded DLinTAP/DLinPC over DOTAP/DOPC CLs. The findings demonstrate the potential of chemical modifications of the lipid tails to increase the PTX membrane loading well over the typically used 3 mol% while maintaining (and in some cases even increasing) the efficacy of CLs. The increased PTX solubility will aid the development of liposomal PTX carriers that require significantly less lipid to deliver a given amount of PTX, reducing side effects and costs.
Structure of the ancestral TRPY1 channel fromSaccharomyces cerevisiaereveals mechanisms of modulation by lipids and calcium
Authors: Ahmed Tofayel , Nisler Collin R. , Fluck Edwin C. , Sotomayor Marcos , Moiseenkova-Bell Vera Y. 
Published: October 2020

ABSTRACTTransient Receptor Potential (TRP) channels have evolved in eukaryotes to control various cellular functions in response to a wide variety of chemical and physical stimuli. This large and diverse family of channels emerged in fungi as mechanosensitive osmoregulators. TheSaccharomyces cerevisiaevacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, but the molecular details of channel modulation remain elusive so far. Here, we describe the full-length cryo-electron microscopy structure of TRPY1 at 3.1 Å resolution. The structure reveals a distinctive architecture for TRPY1 among all eukaryotic TRP channels with an evolutionarily conserved and archetypical transmembrane domain, but distinct structural folds for the cytosolic N- and C-termini. We identified the inhibitory phosphatidylinositol 3-phosphate (PI(3)P) lipid binding site, which sheds light into the lipid modulation of TRPY1 in the vacuolar membrane. The structure also exhibited two Ca2+-binding sites: one in the cytosolic side, implicated in channel activation, and the other in the vacuolar lumen side, involved in channel inhibition. These findings, together with data from molecular dynamics simulations, provide structural insights into the basis of TRPY1 channel modulation by lipids and Ca2+.
The mammalian rod synaptic ribbon is essential for Cavchannel facilitation and ultrafast fusion of the readily releasable pool of vesicles
Authors: Grabner Chad Paul , Moser Tobias 
Published: October 2020

AbstractRod photoreceptors (PRs) use ribbon synapses to transmit visual information. To signal ‘no light detected’ they release glutamate continually to activate post-synaptic receptors, and when light is detected glutamate release pauses. How a rod’s individual ribbon enables this process was studied here by recording evoked changes in whole-cell membrane capacitance from wild type and ribbonless (RIBEYE-ko) rods. Wild type rods created a readily releasable pool (RRP) of 92 synaptic vesicles (SVs) that emptied as a single kinetic phase with a τ < 0.4 msec. Lowering intracellular Ca2+-buffering accelerated Cavchannel opening and facilitated release kinetics, but RRP size was unaltered. In contrast, ribbonless rods created an RRP of 24 SVs, and lacked Cavchannel facilitation; however, Ca2+channel-release coupling remained tight. The release deficits caused a sharp attenuation of rod-driven light responses measured from RIBEYE-ko mice. We conclude that the synaptic ribbon facilitates Ca2+-influx and establishes a large RRP of SVs.
Optimal design of adaptively sampled NMR experiments for measurement of methyl group dynamics with application to a ribosome-nascent chain complex
Authors: Waudby Christopher A. , Burridge Charles , Christodoulou John 
Published: October 2020

AbstractNMR measurements of cross-correlated nuclear spin relaxation provide powerful probes of polypeptide dynamics and rotational diffusion, free from contributions due to chemical exchange or interactions with external spins. Here, we report on the development of a sensitivity-optimized pulse sequence for the measurement of cross-correlated relaxation in methyl spin systems by analysis of the differential relaxation of transitions within the13C multiplet. We describe the application of optimal design theory to implement a real-time ‘on-the-fly’ adaptive sampling scheme that maximizes the accuracy of the measured rate constants. The increase in sensitivity obtained using this approach enables, for the first time, quantitative measurements of rotational diffusion within folded states of translationally-arrested ribosome–nascent chain complexes of the FLN5 filamin domain, and can be used to place strong limits on interactions between the domain and the ribosome surface.
Through-grid wicking enables high-speed cryoEM specimen preparation
Authors: Tan Yong Zi , Rubinstein John L. 
Published: October 2020

Blotting times for conventional cryoEM specimen preparation complicate time-resolved studies and lead to some specimens adopting preferred orientations or denaturing at the air–water interface. Here, it is shown that solution sprayed onto one side of a holey cryoEM grid can be wicked through the grid by a glass-fiber filter held against the opposite side, often called the `back', of the grid, producing a film suitable for vitrification. This process can be completed in tens of milliseconds. Ultrasonic specimen application and through-grid wicking were combined in a high-speed specimen-preparation device that was named `Back-it-up' or BIU. The high liquid-absorption capacity of the glass fiber compared with self-wicking grids makes the method relatively insensitive to the amount of sample applied. Consequently, through-grid wicking produces large areas of ice that are suitable for cryoEM for both soluble and detergent-solubilized protein complexes. The speed of the device increases the number of views for a specimen that suffers from preferred orientations.
Orchestrating internal and external resources to achieve agility and performance: the centrality of market orientation
Authors: Kurniawan Randy , Manurung Adler Haymans , Hamsal Mohammad , Kosasih Wibowo 
Published: October 2020

PurposeThis study examines the collaborative impact of networking capability and balanced agile project management (APM) on firm performance through the mediating role of market orientation and business process agility of medium and large telecommunication technology providers in Indonesia.Design/methodology/approachResearch data were collected from the executive management of telecommunication technology providers in Indonesia via a questionnaire survey to obtain 150 valid questionnaires for analysis. This study analyzed the overall model fit and causal relationship using confirmatory factor analysis (CFA) and structural equation modeling (SEM).FindingsThe results indicate that market orientation fully mediates the link between networking capability-business process agility and balanced APM-business process agility. Furthermore, business process agility mediates the relationship between market orientation and firm performance.Research limitations/implicationsThis study is based on a cross-sectional nature and might fail to capture the dynamic of the studied variables over an extended period.Originality/valueThe study extends the knowledge that dynamic capabilities, represented by networking capability and balanced APM, must be framed by market orientation to create customer value and improve bargaining position. However, market orientation alone is not enough in a highly dynamic business environment. Organization also requires business process agility, responsiveness and adaptability to timely address customers' needs and requirements.
Antecedents of career self-management: home country and international careers in Kuwait
Authors: Abdalla Ikhlas , Al-Zufairi Awad 
Published: October 2020

PurposeThe purpose of this paper is to examine how leadership aspiration mediates the effect of career self-efficacy on employees' engagement in career self-management (CSM; i.e. deployment of career advancement strategies concerning access to power, psychological boundaryless and self-promotion), whether self-efficacy directly influences CSM, and whether these relations are conditional upon nationality (which is a proxy for domestic and international careers in Kuwait).Design/methodology/approachA questionnaire was completed by 615 highly educated young Kuwaitis and self-initiated expatriates (SIEs; Arab and South Asian nationals) working in Kuwait.FindingsThe results demonstrate that self-efficacy, directly and indirectly (mediated by leadership aspiration), influences the three types of career advancement strategies. Moderated-mediation analyses suggest that SIEs and Kuwaitis engage in similar CSM behaviors when it is motivated by self-efficacy, which is mediated by leadership aspiration. Also, self-efficacy has greater direct effect on SIEs' CSM than Kuwaitis', but Kuwaitis have higher tendency for CSM behavior.Practical implicationsInterventions aiming to improve employees' engagement in CSM may focus on enhancing their psychological capital and contexts, while minding the differential effects of nationality and self-efficacy on CSM of Kuwaitis and SIEs.Originality/valueThe study provides unique information about CSM utilizing understudied populations namely, Middle-Eastern and self-initiated expatriate employees. It confirms the effects of self-efficacy and leadership aspiration on CSM and reveals different effects of nationality depending on the motivators at play.
Numerical investigation of friction laws for laminar and turbulent flow in undulated channels
Authors: Benim Ali Cemal , Maddala Sai Bhagavan 
Published: October 2020

Purpose
The purpose of this paper is the numerical investigation of the friction laws for incompressible flow in undulated channels, with emphasis on the applicability of the hydraulic diameter concept. A focal point of the study is the derivation of correlations to increase the accuracy of the hydraulic diameter approach.

Design/methodology/approach
Calculations are performed for laminar and turbulent flow, for Reynolds number ranges between 10–2,000 and 5,000–100,000. For turbulent flow, the shear stress transport (SST) model is used. A simple, sawtooth-like undulation shape is considered, where the channel geometry can be described by means of three length parameters. Letting each to take three values, totally 27 geometries are analyzed.

Findings
It is observed that the hydraulic diameter concept applied via analytical or empirical expressions to obtain friction coefficients does not lead to accurate results. For laminar flow, the maximum deviations of analytical values from predicted are about 70%, while 20% deviation is observed on average. For turbulent flow, deviations of Blasius correlation from predicted ones are smaller, but still remarkable with about 20% for maximum deviation and about 10% on average.

Originality/value
Applicability of the hydraulic diameter concept to undulated channels was not computationally explored. A further original ingredient of the work is the derivation of correlations that lead to improved accuracy in calculating the friction coefficient using hydraulic diameter. For laminar flow, the maximum and average deviations of present correlations from numerical predictions are below 5% and 2%, respectively. For turbulent flow, these numbers turn out to be approximately 12% for the maximum deviation and about 2% for the average.
Hybrid nanofluid flow on a shrinking cylinder with prescribed surface heat flux
Authors: Waini Iskandar , Ishak Anuar , Pop Ioan 
Published: October 2020

Purpose
This study aims to investigate the flow impinging on a stagnation point of a shrinking cylinder subjected to prescribed surface heat flux in Al2O3-Cu/water hybrid nanofluid.

Design/methodology/approach
Using similarity variables, the similarity equations are obtained and then solved using bvp4c in MATLAB. The effects of several physical parameters on the skin friction and heat transfer rate, as well as the velocity and temperature profiles are analysed and discussed.

Findings
The outcomes show that dual solutions are possible for the shrinking case, in the range

λc<λ<−1, where

λc is the bifurcation point of the solutions. Meanwhile, the solution is unique for

λ≥−1. Besides, the boundary layer is detached on the surface at

λc, where the value of

λc is affected by the hybrid nanoparticle

φhnf and the curvature parameter

γ. Moreover, the friction and the heat transfer on the surface increase with the rising values

φhnf and

γ. Finally, the temporal stability analysis shows that the first solution is stable in the long run, whereas the second solution is not.

Originality/value
The present work considers the problem of stagnation point flow impinging on a shrinking cylinder containing Al2O3-Cu/water hybrid nanofluid, with prescribed surface heat flux. This paper shows that two solutions are obtained for the shrinking case. Further analysis shows that only one of the solutions is stable as time evolves.
Influence of customer participation from the employee perspective
Authors: Yoo Jaewon , Chen Jing , Frankwick Gary L. 
Published: October 2020

PurposeTo reduce costs, many banks have increased customer involvement during the creation and delivery of their products and services. Based on a job demands-resources (JD-R) model, this study tests an inverted U-shaped curvilinear relationship between perceived customer participation and employee work engagement. Customer orientation (CO) and service employee perceived fit with customers (PCF) moderate this relationship, which eventually affect both the internal and external benefits of service-employee work engagement.Design/methodology/approachThe authors collected survey data from 518 service employees in the South Korean banking and insurance industries and analyzed the data using structural equation modeling (SEM).FindingsThe results indicate that perceived customer participation (PCP) has a significant inverted U-shape effect on work engagement. Results also suggest that CO and PCF have positive relationships with work engagement. In addition, they moderate the inverted U-shaped relationship between service employee PCP and work engagement, while work engagement positively affects organizational citizenship, job satisfaction and commitment.Research limitations/implicationsThe authors empirically identify a curvilinear effect of PCP on work engagement. In doing so, the authors introduce and operationalize the new construct: PCF and suggest PCF and CO as unique job resources for service employees. The authors also examine these constructs as predictors based on a motivational process and as moderators based on a strain (energetic) process.Practical implicationsFrom a managerial perspective, examining the curvilinear relationships of customer participation and work engagement suggests that front-line employees’ (FLEs’) PCP does not necessarily enhance the economic benefits of productivity gains by using customers as substitutes for portions of employee labor. Another finding with managerial relevance indicates that service employees, who have more CO and PCF, showed more tolerant attitudes toward unnecessary and excessive levels of customer participation and regarded it as a job resource.Originality/valueThis study explains that researchers must consider the positive and negative sides of customer participation simultaneously because frontline employee PCP can be changed depending on the level of participation provided by customers. This study also shows that CO can be assumed as a personal resource and PCF as an environmental resource in the work engagement process.
The strategic design of port services based on a total landed cost approach
Authors: González-Ramírez Rosa G. , Villalobos J. Rene , Meneses Cesar 
Published: October 2020

PurposeThis paper explores the effect of port's service time, particularly the mean and variability, on shippers' total landed costs to determine the competitive position of the port and derive recommendations for the strategic design of port services.Design/methodology/approachThe competitive position of a port is estimated considering the service level offered to the end-users of the port such as port service time, its variability and its effect on the total landed costs observed by the port users. The proposed methodology is meant to help ports to determine the required service time levels to maintain or gain a competitive advantage against other ports, in terms of attracting common hinterland's customers.FindingsResults show the advantages of considering service levels factors to determine the competitive position of a port, and what are the minimum characteristics required to capture more traffic volumes, that can help port managers to take strategic design decisions to better position the port in the current fierce market.Research limitations/implicationsThe proposed methodology is illustrated by considering a case study, which is the Port of Guaymas in Mexico. Data was not directly collected by the port, but based on interviews with shippers and public information, a representative case is presented. Due to a confidentiality agreement with the Port, specific references for most of the data used to estimate the model's parameters are not provided. The analysis is intended to show the potential value of this mechanism and can be used for evaluating the competitive position, from a high-level perspective, of any port to determine potential hinterland by improving the service level of the port.Originality/valueThe existing literature on port choice and port competition has not previously considered the effect of port service levels under the perspective of total landed costs of the users, being this paper a contribution to fulfill this gap.