bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity of filamentous fungi associated with coral and sponges in coastal reefs of northeast Brazil
Authors: Paulino Gustavo V. B. , Félix Ciro R. , Landell Melissa F.
Published: November 2019

Fungi are known to form associations with various marine organisms and substrata such as sponges and corals, both as potential symbionts or pathogens. These microorganisms occupy an ecological niche that has recently attracted great attention due to their potential in either ecological or pharmaceutical advances. However, the interaction between marine invertebrates and fungi is still poorly understood, including how they are affected by anthropogenic actions. Here, we identified 89 fungal isolates through sequencing of the ITS rDNA region obtained from the various sponge and coral species collected at two northeast Brazilian reefs. We found 43 species of fungi from 16 genera, all belonging to phylum Ascomycota. The sponges and coral shared four genera: Aspergillus, Penicillium, Trichoderma, and Cladosporium, all commonly found in terrestrial habitats and associated with marine invertebrates. We observed some unusual species in relation to the marine environment, such as Clonostachys rosea and Neopestalotiopsis clavispora, most of them related to plants, either as saprophytic or pathogenic, suggesting that these species were transported from the surrounding terrestrial environment to the reefs. In addition, some isolates represent possible undescribed species, reinforcing the importance of studying the marine environment in relation to its ecological and biotechnological importance.
The MRL/MpJ Mouse Strain Is Not Protected From Muscle Atrophy and Weakness After Rotator Cuff Tear
Authors: Talarek Jeffrey R. , Piacentini Alex N. , Konja Alexis C. , Wada Susumu , Swanson Jacob B. , Nussenzweig Samuel C. , Dines Joshua S. , Rodeo Scott A. , Mendias Christopher L.
Published: November 2019

Chronic rotator cuff tears are a common source of shoulder pain and disability. Patients with rotator cuff tears often have substantial weakness, fibrosis, and fat accumulation, which limit successful surgical repair and postoperative rehabilitation. The Murphy Roths Large (MRL) strain of mice have demonstrated superior healing and protection against pathological changes in several disease and injury conditions. We tested the hypothesis that, compared with the commonly used C57Bl/6 (B6) strain, MRL mice would have less muscle fiber atrophy and fat accumulation, and be protected against the loss in force production that occurs after cuff tear. Adult male B6 and MRL mice were subjected to a rotator cuff tear, and changes in muscle fiber contractility and histology were measured. RNA sequencing and shotgun metabolomics and lipidomics were also performed. The muscles were harvested one month after tear. B6 and MRL mice had a 40% reduction in relative muscle force production after rotator cuff tear. RNA sequencing identified an increase in fibrosis‐associated genes and a reduction in mitochondrial metabolism genes. The markers of glycolytic metabolism increased in B6 mice, while MRL mice appeared to increase amino acid metabolism after tear. There was an accumulation of lipid after injury, although there was a divergent response between B6 and MRL mice in the types of lipid species that accrued. There were strain‐specific differences between the transcriptome, metabolome, and lipidome of B6 and MRL mice, but these differences did not protect MRL mice from weakness and pathological changes after rotator cuff tear. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:811‐822, 2020
Development and Application of a Novel Metric to Characterize Comprehensive Range of Motion of Reverse Total Shoulder Arthroplasty
Authors: Elwell Josie A. , Athwal George S. , Willing Ryan
Published: November 2019

Active range of motion (ROM) of reverse total shoulder arthroplasty (rTSA) can be limited by bony impingement, muscle inability, and joint instability. The aim of this study was to develop a novel metric representative of comprehensive ROM of rTSA, which is evaluated in the context of all three factors. It was hypothesized that the metric, termed global circumduction ROM (GC‐ROM), would capture differences resulting from directional changes in rTSA design parameters known to increase ROM. GC‐ROM was calculated for a set of 18 rTSA configurations with humeral polyethylene cup depths of 6 and 8.1 mm, glenosphere lateralization (GLat) distances of 0, 5, and 10 mm, and neck‐shaft angles (NSA) of 135°, 145°, and 155°. For any implant configuration, arm positions were defined by internal/external (IE) rotation angle and two spherical coordinates representing the elevation plane angle and elevation angle. At each IE rotation angle, incremental positions with variable elevation plane and elevation angles were checked for feasibility based on impingement, muscle ability, and risk of instability. Coordinates of feasible positions were mapped to unit spheres and connected to form regions, of which the surface area was calculated to represent allowable circumduction ROM. ROMs were averaged across all IE rotation angles to produce a single metric, GC‐ROM. The results showed that decreasing cup depth and increasing GLat and NSA increased GC‐ROM. In conclusion, a novel metric to characterize comprehensive ROM, evaluated based on several ROM‐limiting factors, was developed as a performance metric through which rTSA designs can be compared. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:880‐887, 2020
Determination, residue analysis, risk assessment and processing factors of tebufenozide in okra fruits under field conditions
Authors: Luo Xiaoshuang , Qin Xinxian , Chen Dan , Liu Zhengyi , Zhang Kankan , Hu Deyu
Published: November 2019

BACKGROUND

Ensuring the yield, quality, and profitability of okra by preventing and controlling pests with the application of insecticides has increased in the last decade. Some insecticide residues might remain in edible parts of okra (fruits) and lead to several potential human health problems. Therefore, research on the residue behaviour, risk assessment and removal approach of insecticides on okra fruits is important for food safety, together with the proper application and residual elimination of insecticides in okra.

RESULTS

A simple liquid chromatography with tandem mass spectrometry (LC–MS/MS) method was established and validated for determining the tebufenozide residues in okra fruits. The recoveries of tebufenozide in okra fruits were >72% with relative standard deviations of 0.6 to 6.1%. The dissipation rates of tebufenozide were different in okra fruits cultivated under open land and glasshouse field conditions because of the discriminating humidity and temperature conditions. The dietary intake of the tebufenozide residues from okra fruit consumption for Chinese consumers was fairly low, with approximately no potential health risk. The processing factor values of washing, blanching, washing + blanching and soaking were all less than one, which indicated that these processes could effectively reduce the residual hydrazide in the okra fruit.

CONCLUSION

The developed method for analysing tebufenozide in okra fruits was applicable for field studies on this insecticide. The potential health risk of tebufenozide in okra fruits could be negligible to the health of different age groups of Chinese consumers. The soaking process effectively removed tebufenozide residues from okra fruits. The obtained data will help Chinese governments establish a maximum residue limit of tebufenozide in okra and provide data for the risk assessment and removal of tebufenozide in other crops. © 2019 Society of Chemical Industry
Identification and characterization of antioxidant peptides from Chinese dry‐cured mutton ham
Authors: Wang Jingyun , Lu Shiling , Li Ruiting , Wang Yuan , Huang Liyuan
Published: November 2019

BACKGROUND

Chinese mutton ham is a dry‐cured meat product with a long ripening time. The aim of this study was to identify and characterize antioxidant peptides from Chinese mutton ham.

RESULTS

Mutton ham peptides (MHPs) were purified by gel filtration, anion exchange and reversed‐phase high‐performance liquid chromatography steps. The 2,2′‐azino‐bis (3‐ethylbenzothiazoline‐6‐sulfonic acid) diammonium salt (ABTS) free radical scavenging capacity was used to guide the purification of MHPs. Three antioxidant peptides were identified by liquid chromatography with tandem mass spectrometry (LC–MS/MS) as Met‐Trp‐Thr‐Asp (MWTD), Ala‐Pro‐Tyr‐Met‐Met (APYMM) and Phe‐Trp‐Ile‐Ile‐Glu (FWIIE), with molecular weights 551.61, 611.76, and 706.84 Da, respectively. Among them, APYMM exhibited the highest ABTS radical scavenging activity. The three peptides had the ability to inhibit lipid oxidation and Fenton's reagent‐induced protein oxidation and DNA damage. After simulated gastrointestinal digestion, FWIIE and APYMM showed increased antioxidant activity, while MWTD showed decreased activity.

CONCLUSION

Three novel peptides isolated from Chinese mutton ham had strong biological activity. Chinese mutton ham is potentially a functional food and an excellent source of natural antioxidants. © 2019 Society of Chemical Industry
Temperature sensitivity of decomposition of soil organic matter fractions increases with their turnover time
Authors: Jia Yufu , Kuzyakov Yakov , Wang Guoan , Tan Wenbing , Zhu Biao , Feng Xiaojuan
Published: November 2019

Soil organic carbon (SOC) is an indicator of soil fertility. Global warming accelerates SOC decomposition, consequently, resulting in land degradation. Characterization of the response of SOC decomposition to temperature is important for predicting land development. A simulation model based on temperature sensitivity (Q10) of SOC decomposition has been used to predict SOC response to climate warming. However, uncertain Q10 leads to substantial uncertainties in the predictions. A major uncertainty comes from the interference of rainfall. To minimize this interference, we sampled surface (0–5 cm) soils along an isohyet across a temperature gradient in the Qinghai–Tibetan Plateau. The Q10 of bulk soil and the four soil fractions, such as light fraction (LightF), particulate organic matter (POM), hydrolyzable fraction (HydrolysF), and recalcitrant fraction (RecalcitF), were studied by 14C dating. Turnover time follows the order: LightF < POM < bulk soil < HydrolysF < RecalcitF. The Q10 follows the order: LightF (1.0) = POM (1.0) < HydrolysF (3.63) < bulk soil (5.93) < RecalcitF (7.46). This indicates that stable fractions are much more sensitive to temperature than labile fractions. We also suggest that protection mechanisms rather than molecular composition regulate SOC turnover. A new concept 'protection sensitivity' of SOC decomposition was proposed. Protection sensitivity relates to protection type and primarily controls Q10 variation. A simulation model based on the Q10 of individual fractions predicted SOC change and land development in the Qinghai–Tibetan Plateau in the next 100 years much effectively as compared to simulations based on one‐pool model (Q10 = 2) or bulk soil (Q10 = 5.93).
Structural changes of the microplankton community following a pulse of inorganic nitrogen in a eutrophic river
Authors: Kleinteich Julia , Hilt Sabine , Hoppe Andreas , Zarfl Christiane
Published: November 2019

Global change will increase the number and severity of extreme events resulting in strongly pulsed nutrient loading to rivers. Recent studies indicate the potential for rapid plankton shifts as short‐term response to storm events and highlight the need for high‐frequency methods to understand these complex processes. Here, we studied the effects of a strong short‐term pulse of ammonium nitrate in a eutrophic temperate river that elevated nitrate‐N concentrations from 3.1 to 10–55 mg L−1. An intense phytoplankton bloom increased chlorophyll a concentrations from below 10 μg L−1 to over 140 μg L−1 despite of high background N concentrations and followed the N‐pulse downstream. High‐throughput sequencing revealed the temporal dynamics of the bacterial (16S rRNA gene) and microeukaryotic (18S rRNA gene) community throughout the event. Bacterial and microeukaryotic community richness was reduced, and community composition changed significantly during the bloom. Few microeukaryote taxa (e.g., Cyclotella meneghiniana, Chlamydomonas) dominated the bloom and replaced the rich summer phytoplankton community. Long‐term monitoring data (2008–2016) using classical microscope analyses showed that seasonal shifts in phytoplankton community composition were linked to physical parameters and nutrient availability with P‐limitation observed in spring but not in summer. We conclude that a disturbance in abiotic and biotic control factors, such as caused by a nutrient pulse, can induce structural shifts in the microplankton community leading to a phytoplankton bloom, even in eutrophic waters.
Cash, credit, or phone? An empirical study on the adoption of mobile payments in the United States
Authors: Zhang Jing , Mao En
Published: November 2019

The purpose of this study is to investigate the effects of consumer factors on behavioral intention to adopt mobile payments. We focus on the proximity mobile payment, which is made feasible by the near‐field communications (NFCs) technology. Building upon the theory of reasoned action and technology acceptance model (TAM), a behavioral intention model was established consisting of enhanced cognitive antecedents as well as affective and social antecedents. Cognitive antecedents encompass the factors including relative advantage, perceived usefulness and ease of use in the TAM, and technology characteristics (e.g., responsiveness and mobility); affective antecedents focus on positive and negative emotions associated with using NFC mobile payments. Both antecedents are expected to affect attitudes. In addition, social antecedents examine subjective norms and the influence of network externalities. Data were collected from 394 adult nonusers of NFC mobile payments in the United States via an online survey. The research model was tested using structural equation modeling. The results showed that all three antecedents significantly affected individual consumers’ intention to adopt NFC mobile payments, explaining a significant amount of variance. Both theoretical and marketing implications are discussed in the context of NFC mobile payments.
Thermodynamic Analysis of the Uptake of a Protein in a Spherical Polyelectrolyte Brush
Authors: Walkowiak Jacek , Lu Yan , Gradzielski Michael , Zauscher Stefan , Ballauff Matthias
Published: November 2019

A thermodynamic study of the adsorption of Human Serum Albumin (HSA) onto spherical polyelectrolyte brushes (SPBs) by isothermal titration calorimetry (ITC) is presented. The SPBs are composed of a solid polystyrene core bearing long chains of poly(acrylic acid). ITC measurements done at different temperatures and ionic strengths lead to a full set of thermodynamicbinding constants together with the enthalpies and entropies of binding. The adsorption of HSA onto SPBs is described with a two‐step model. The free energy of binding ΔGb depends only weakly on temperature because of a marked compensation of enthalpy by entropy. Studies of the adsorbed HSA by Fourier transform infrared spectroscopy (FT‐IR) demonstrate no significant disturbance in the secondary structure of the protein. The quantitative analysis demonstrates that counterion release is the major driving force for adsorption in a process where proteins become multivalent counterions of the polyelectrolyte chains upon adsorption. A comparison with the analysis of other sets of data related to the binding of HSA to polyelectrolytes demonstrates that the cancellation of enthalpy and entropy is a general phenomenon that always accompanies the binding of proteins to polyelectrolytes dominated by counterion release.
Reconfigurable wide band wearable multiple input multiple output antenna with hanging resonator
Authors: Biswas Ashim Kumar , Chakraborty Ujjal
Published: November 2019

This letter presents a two‐element textile‐based multiple input multiple output (MIMO) antenna with switchable dual wide band characteristics. The antenna is integrated with two switches enabled hanging resonators and a partial ground plane with funnel‐shaped DGS. It covers the spectra from 3.11 to 5.15 GHz in one and 4.81 to 7.39 GHz in another switching condition. The antenna satisfies the WiMAX/C‐band downlink (3.2‐3.8/3.7‐4.2 GHz) and WLAN/C‐band uplink (5.15‐5.35/5.72‐5.825/5.925‐6.425 GHz) application bands. The resonator structures provide very high port isolation of >19.5 and >21 dB in the lower and upper band, respectively. The proposed antenna offers suitable values of diversity parameters which include envelope correlation coefficient (ECC < 0.18), diversity gain (DG > 9.9 dB), and channel capacity loss (CCL < 0.2 BPS/Hz). The simulated results are found to be in close agreement with the measured outcomes from the experiments. The proposed antenna proves to be promising for wearable MIMO applications.
Navigator‐based reacquisition and estimation of motion‐corrupted data: Application to multi‐echo spin echo for carotid wall MRI
Authors: Frost Robert , Biasiolli Luca , Li Linqing , Hurst Katherine , Alkhalil Mohammad , Choudhury Robin P. , Robson Matthew D. , Hess Aaron T. , Jezzard Peter
Published: November 2019

Purpose

To assess whether artifacts in multi‐slice multi‐echo spin echo neck imaging, thought to be caused by brief motion events such as swallowing, can be corrected by reacquiring corrupted central k‐space data and estimating the remainder with parallel imaging.

Methods

A single phase‐encode line (ky = 0, phase‐encode direction anteroposterior) navigator echo was used to identify motion‐corrupted data and guide the online reacquisition. If motion corruption was detected in the 7 central k‐space lines, they were replaced with reacquired data. Subsequently, GRAPPA reconstruction was trained on the updated central portion of k‐space and then used to estimate the remaining motion‐corrupted k‐space data from surrounding uncorrupted data. Similar compressed sensing‐based approaches have been used previously to compensate for respiration in cardiac imaging. The g‐factor noise amplification was calculated for the parallel imaging reconstruction of data acquired with a 10‐channel neck coil. The method was assessed in scans with 9 volunteers and 12 patients.

Results

The g‐factor analysis showed that GRAPPA reconstruction of 2 adjacent motion‐corrupted lines causes high noise amplification; therefore, the number of 2‐line estimations should be limited. In volunteer scans, median ghosting reduction of 24% was achieved with 2 adjacent motion‐corrupted lines correction, and image quality was improved in 2 patient scans that had motion corruption close to the center of k‐space.

Conclusion

Motion‐corrupted echo‐trains can be identified with a navigator echo. Combined reacquisition and parallel imaging estimation reduced motion artifacts in multi‐slice MESE when there were brief motion events, especially when motion corruption was close to the center of k‐space.
The Pond Dye, Aquashade, Does Not Prevent Cyanobacterial Off-Flavors in Pond-Grown Channel Catfish
Authors: Tucker Craig S , Mischke Charles C
Published: November 2019

Aquashade is a dye that is used to control the growth of underwater weeds by reducing light penetration through water. We applied four, monthly applications of 1 μL/L Aquashade to three Channel Catfish Ictalurus punctatus ponds during the summer growing season to determine its effects on water quality and incidence of off-flavor in catfish. Three ponds were untreated controls. Dye treatments had no effect on nitrite or total ammonia concentrations, hours of supplemental aeration, phytoplankton standing crops, or fish production. Cyanobacteria that are known to produce odorous metabolites were found in all of the ponds at some time during the study. On the sampling date immediately before fish harvest, two ponds in each treatment contained populations of the odor-producing cyanobacterium, Planktothrix perornata and contained fish that would not be acceptable for processing because of musty off-flavors. The mechanism of action of the dye—reducing water-column penetration of light in wavelengths of ~600–650 nm—will have little effect on odor-producing species of cyanobacteria because those species have physiological adaptations (nonchlorophyll accessory pigments and the ability to regulate their position in the water column), which allow them to thrive in low-light environments.
Vitamin A and Wound Healing
Authors: Zinder Roman , Cooley Rachel , Vlad Lucian G. , Molnar Joseph A.
Published: November 2019

Vitamin A is a general term for retinoids. Vitamin A deficiency leads to a variety of cutaneous manifestations. It also functions as a hormone through retinoic acid receptors altering the activity of multiple cell lines. Pancreatic vitamin A levels are critical for retinoid signaling and normal pancreatic control of glucose. Vitamin A deficiency is more common during infection, and supplementation reduces severe morbidity and mortality from infectious diseases. Vitamin A modulates activities at the cellular level and, via its interrelationship with hormones such as thyroid, insulin, and corticosteroids, has diffuse metabolic effects on the body. It plays an important role in all stages of wound healing. Vitamin A is known for its ability to stimulate epithelial growth, fibroblasts, granulation tissue, angiogenesis, collagen synthesis, epithelialization, and fibroplasia. Local (topical) and systemic supplementation with vitamin A has been proven to increase dermal collagen deposition. There are numerous animal studies and limited human studies regarding physiologic effect of vitamin A on acute or chronic wounds via systemic or topical administration. The most common use of vitamin A supplementation is to offset steroids’ effect. When considering supplementation, the potential benefits must be weighed against the risk of harm. Vitamin A toxicity can be critical and even result in death. The evidence for supplementation with vitamin A is currently limited to expert opinion and is not backed up by rigorous trials. There is an acute need for therapeutic trials with vitamin A supplementations.
Bounds approximation of limit‐state surface based on active learning Kriging model with truncated candidate region for random‐interval hybrid reliability analysis
Authors: Yang Xufeng , Wang Tai , Li Jincheng , Chen Zhang
Published: November 2019

This article reports a brand‐new methodology based on active learning Kriging model for hybrid reliability analysis (HRA) with both random and interval variables. Unlike probabilistic reliability analysis, the limit state surface (LSS) of HRA is projected into a banded region in the domain of random variables. Only approximating the bounds of the banded region is able to meet the accuracy requirement of HRA. In the proposed methodology, the HRA problem is innovatively transformed into a traditional system reliability analysis (SRA) problem with numerous failure modes. And then a basic idea from the field of SRA is borrowed into HRA, and the so‐called truncated candidate region (TCR) for HRA is proposed. In each iteration, the negligible region which probably does not influence the bounds estimation of failure probability is truncated from the original candidate region, and the optimal training point is chosen from the TCR. After several iterations, the TCR will converge to the true ideal candidate region, that is, the candidate region without the inner part of LSS, and the added training points will be driven to the region around the bounds of LSS. The performance of the proposed method is compared with relevant methods by five case studies.
Donors’ Responses to Profit Incentives in the Social Sector: The Entrepreneurial Orientation Reward and the Profit Penalty
Authors: Faulk Lewis , Pandey Sheela , Pandey Sanjay K. , Scott Kennedy Kristen
Published: November 2019

This study uses an online survey experiment to test whether the pairing of profit‐seeking with mission‐related programs in the social sector attracts or deters donations from individual donors. We test individuals’ response to three types of profit incentives allowed under current U.S. public policy: (1) non‐distributed profit to an organization, which is allowed for nonprofit entities; (2) profit to the organization's equity investors and owners, which is allowed under for‐profit social enterprise governance charters; and (3) profit to lending investors, which is introduced by social impact bonds, a pay‐for‐success policy tool. We test trust theory, under which profit incentives deter donors against entrepreneurial orientation (EO) theory, which suggests that donors are attracted to organizations that use innovative, market‐driven programs. Findings indicate support for both theories, but the support depends on how the specific profit incentive is structured. Donors support organizations that use profit‐generating social enterprise programs—but only when the profits are non‐distributable; donors’ support is significantly lower for social enterprises in which owners and equity investors may profit. Importantly however, this negative effect is not found for pay‐for‐success policy tools where lending investors, rather than equity investors and owners, receive profits.
Preparation and characterization of collagen/chitosan composites with silver nanoparticles
Authors: Sionkowska Alina , Walczak Maciej , Michalska‐Sionkowska Marta
Published: November 2019

In this work, thin films made from the blends of collagen and chitosan with silver nanoparticles were prepared and their properties, which are important for potential biomedical applications, were studied. Thin biopolimeric film was obtained by solvent evaporation from collagen/chitosan mixture containing silver nanoparticles. Mechanical properties of the composites were tested in dry condition using a mechanical testing machine. Microstructure of films was analyzed by Atomic Force Microscope. The surface properties were analyzed by contact angle measurements using hydrophilic and hydrophobic liquids. In addition, antimicrobial properties of collagen/chitosan/silver composites were tested during the microbiological test. It was found that the addition of silver nanoparticles to collagen/chitosan film affects several of its properties. Microbiological studies showed that obtained collagen/chitosan/silver nanoparticles materials possess bacteriostatic activity against Staphylococcus aureus.
Effect of particle type and its surface characteristics on the mechanical properties of particle‐filled polymer composite for precision machine tools
Authors: Yin Jicai , Meng Xiaojun , Bian Bingchuan , Zhang Jianhua , Yin Yingyue
Published: November 2019

For excellent damping properties, polymer composite (PC) has drawn particular attention in the field of modern ultra‐precision machining (UPM). However, applications of PC are restricted due to its inferior mechanical strength. In this paper, different granite coarse aggregate, different fine aggregate, and different filler were added into PC to increase its mechanical strength. The effects of coarse aggregate type, fine aggregate type, filler type on the mechanical strength of particle‐filled polymer composite (PFPC) were investigated systematically. Experimental results show that the best mechanical strength was obtained when the coarse aggregate type is Jinan clay granite, the fine aggregate is Jinan clay granite, and the filler is fly ash (FA). Results also show that the compressive strength of PFPC was closely correlated with the compressive strength of aggregate rock, and the compressive strength of PFPC increases with the increasing compressive strength of the aggregate rock. In order to further improve the mechanical strength of PFPC, the aggregate was subsequently treated by ultrasonication, direct mixing silanization, nebulizing silanization, macerating silanization. And four types of PFPC were obtained, that is, U‐PFPC, D‐PFPC, N‐PFPC, M‐PFPC, respectively. Among these four types of PFPC, the M‐PFPC exhibited the best mechanical strength. And the compressive strength and flexural strength of M‐PFPC are 146.97 MPa and 37.33 MPa, respectively; increased by 8.31% and 13.53% compared with PFPC produced by standard pouring technologies. In addition, the mechanism of the influence of the aggregate whose surfaces were treated on the mechanical strength of PFPC was revealed by scanning electron microscopy and contact angle test. The test results show that the M‐PFPC exhibited the favorable interface bond. This study was of great significance to increase the mechanical properties of PC and improve its application in precision machine tools.
Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38‐46
Authors: Christoffer Charles , Terashi Genki , Shin Woong‐Hee , Aderinwale Tunde , Maddhuri Venkata Subramaniya Sai Raghavendra , Peterson Lenna , Verburgt Jacob , Kihara Daisuke
Published: November 2019

We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI) rounds 38‐46. The pipeline integrates programs developed in our group as well as other existing scoring functions. The core of the pipeline is the LZerD protein‐protein docking algorithm. If templates of the target complex are not found in PDB, the first step of our docking prediction pipeline is to run LZerD for a query protein pair. Meanwhile, in the case of human group prediction, we survey the literature to find information that can guide the modeling, such as protein‐protein interface information. In addition to any literature information and binding residue prediction, generated docking decoys were selected by a rank aggregation of statistical scoring functions. The top 10 decoys were relaxed by a short molecular dynamics simulation before submission to remove atom clashes and improve side‐chain conformations. In these CAPRI rounds, our group, particularly the LZerD server, showed robust performance. On the other hand, there are failed cases where some other groups were successful. To understand weaknesses of our pipeline, we analyzed sources of errors for failed targets. Since we noted that structure refinement is a step that needs improvement, we newly performed a comparative study of several refinement approaches. Finally, we show several examples that illustrate successful and unsuccessful cases by our group.
Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDock
Authors: Torchala Mieczyslaw , Gerguri Tereza , Chaleil Raphael A. G. , Gordon Patrick , Russell Francis , Keshani Miriam , Bates Paul A.
Published: November 2019

The formation of specific protein‐protein interactions is often a key to a protein's function. During complex formation, each protein component will undergo a change in the conformational state, for some these changes are relatively small and reside primarily at the sidechain level; however, others may display notable backbone adjustments. One of the classic problems in the protein‐docking field is to be able to a priori predict the extent of such conformational changes. In this work, we investigated three protocols to find the most suitable input structure conformations for cross‐docking, including a robust sampling approach in normal mode space. Counterintuitively, knowledge of the theoretically best combination of normal modes for unbound‐bound transitions does not always lead to the best results. We used a novel spatial partitioning library, Aether Engine (see Supplementary Materials), to efficiently search the conformational states of 56 receptor/ligand pairs, including a recent CAPRI target, in a systematic manner and selected diverse conformations as input to our automated docking server, SwarmDock, a server that allows moderate conformational adjustments during the docking process. In essence, here we present a dynamic cross‐docking protocol, which when benchmarked against the simpler approach of just docking the unbound components shows a 10% uplift in the quality of the top docking pose.
Crystal structure of pantoate kinase from Thermococcus kodakarensis
Authors: Kita Akiko , Kishimoto Asako , Shimosaka Takahiro , Tomita Hiroya , Yokooji Yuusuke , Imanaka Tadayuki , Atomi Haruyuki , Miki Kunio
Published: November 2019

The coenzyme A biosynthesis pathways in most archaea involve two unique enzymes, pantoate kinase and phosphopantothenate synthetase, to convert pantoate to 4′‐phosphopantothenate. Here, we report the first crystal structure of pantoate kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complex with ATP and a magnesium ion. The electron density for the adenosine moiety of ATP was very weak, which most likely relates to its broad nucleotide specificity. Based on the structure of the active site that contains a glycerol molecule, the pantoate binding site and the roles of the highly conserved residues are suggested.
Photoluminescence Intensity Enhancement of Single Silicon Quantum Dots on a Metal Membrane with a Spacer
Authors: Zhou Jingjian , Pevere Federico , Gatty Hithesh K. , Linnros Jan , Sychugov Ilya
Published: November 2019

Silicon quantum dots (Si QDs) featuring high photoluminescence (PL) intensity are necessary for the realization of different photonic and photovoltaic devices, such as light‐emitting diodes (LEDs) and luminescent solar concentrators (LSCs). Herein, Si QDs on a ≈100–200 nm thin silicon dioxide membrane with a metal back‐coating are prepared. The dots are formed from the device layer of a silicon‐on‐insulator (SOI) wafer by etching and thermal oxidation. Aluminum is sputtered on the backside of the membrane, acting as a back‐surface mirror, changing the local density of optical modes, as well as the local excitation field. The PL properties of such Si QDs are then characterized at the single‐particle level. It is found that the PL yield of single Si QDs on the membrane is enhanced by approximately one order of magnitude, compared with that of Si QDs outside the membrane under the same excitation power. These results indicate that advances in nanofabrication can substantially improve the optical properties of Si QDs, thus paving the way for their application.
Improved Laser‐Based Photoluminescence on Single‐Walled Carbon Nanotubes
Authors: Kollarics Sándor , Palotás Julianna , Bojtor András , Márkus Bence Gábor , Rohringer Philip , Pichler Thomas , Simon Ferenc
Published: November 2019

Photoluminescence (PL) is a common tool to characterize various properties of single‐walled carbon nanotube (SWCNT) chirality distribution and the level of tube individualization in SWCNT samples. Most PL studies use conventional lamp light sources whose spectral distribution is filtered with a monochromator, but this results in a still impure spectrum with a low spectral intensity. Tunable dye lasers offer a tunable light source which cover the desired excitation wavelength range with a high spectral intensity, but their operation is often cumbersome. Herein, the design and properties of an improved dye‐laser system which is based on a Q‐switch pump laser are presented. The high peak power of the pump provides an essentially threshold‐free lasing of the dye laser, which substantially improves the operability. It allows operation with laser dyes, such as Rhodamin 110 and Pyridin 1, which are otherwise on the border of operation of the laser. The system allows to cover the 540–730 nm wavelength range with four dyes. In addition, the dye laser output pulses closely follow the properties of the pump, which directly provides a time‐resolved and tunable laser source. The performance of the system by measuring the PL map of a HiPco SWCNTs sample is demonstrated.
Investigations of the Solid Electrolyte Interphase Using X‐Ray Photoelectron Spectroscopy In situ Experiment on the Lithium‐Based Solid Electrolyte LiPSON
Authors: Michel Fabian , Becker Martin , Janek Juergen , Polity Angelika
Published: November 2019

Lithium phosphorus sulfuric oxide nitride (LiPSON) is prepared by radio frequency (RF) sputtering using a sputter target with compositions of 50 wt% Li3PO4 and 50 wt% Li2SO4. Knowledge about the present phases at the solid electrolyte–lithium anode interface, the so‐called solid electrolyte interphase (SEI), is achieved by performing an in situ sputtering of metallic lithium on the electrolyte and subsequently measuring the chemical bonding by X‐ray photoelectron spectroscopy (XPS). Information about the SEI is of essential interest to understand the process of lithium‐ion conduction in the half cell. Therefore, the information about the formation of lithium phases in the SEI is crucial.
The Influence of Ga–OH Bond at Initial GaN Surface on the Electrical Characteristics of SiO2/GaN Interface
Authors: Uenuma Mutsunori , Ando Ryota , Furukawa Masaaki , Uraoka Yukiharu
Published: November 2019

Herein, the influence of the Ga–OH bond at the GaN surface on the electrical characteristics of the SiO2/GaN metal‐oxide semiconductor structure is investigated. The GaN surface is modified by three different surface treatments (O2 annealing, wet annealing, and ultraviolet [UV]/O3 treatment). The Ga–OH bond is evaluated by X‐ray photoelectron spectroscopy and characterized by capacitance–voltage (CV) measurements and a positive bias stress test. Increasing the ratio of Ga–OH bonds at the SiO2/GaN interface decreases the net fixed charge at the SiO2/GaN interface in the CV measurements and increases the voltage shift in the stress test. Therefore, the Ga–OH bond at the SiO2/GaN interface develops a negative charge and behaves as an electron trap. The undesirable influence of the Ga–OH‐related traps is reduced by low‐temperature annealing.
Dopamine Loaded SiO2 Coated Fe3O4 Magnetic Nanoparticles: A New Anticancer Agent in pH‐Dependent Drug Delivery
Authors: Dey Chaitali , Das Arpita , Goswami Madhuri Mandal
Published: November 2019

In this present study, we have shown dopamine acts as very good agent in killing cancer cells with very high rate. We have used silica coated iron oxide magnetic particles as dopamine drug delivery agent. We have synthesized iron oxide (Fe3O4) magnetic nanoparticles (MNPs), and coated it with silicon dioxide (SiO2), then loaded it with dopamine (DA) which has been used here as anticancer drug. Here a significant improvement was found in case of drug release under acidic pH than normal blood pH. The MNPs are characterized using X‐ray diffraction (XRD), Energy Dispersive Analysis of X‐rays (EDAX), Fourier transform infrared (FTIR), Field Emission Scanning Electron Microscopy (FESEM), Transmission Electron Microscopy (TEM), High Resolution Transmission Electron Microscopy (HRTEM), Selected Area Electron Diffraction (SAED) and vibrating sample magnetometer (VSM) to confirm its structural, morphological and magnetic properties. Particles after characterization were involved in investigation of DA drug release by altering pH for better treatment of cancer. The results are very important and promising.
The effects of multimarket contact on partner selection for technology cooperation
Authors: Ryu Wonsang , Reuer Jeffrey J. , Brush Thomas H.
Published: November 2019

Research summary

We investigate how multimarket contact between prospective partners affects their partner selection for technology cooperation. Drawing on the multimarket competition literature, we argue that multimarket contact generates mutual forbearance from opportunism by enabling broad retaliation across the shared markets against opportunism. As a result, multimarket contact between potential partners makes them prefer each other as partners for technology cooperation. We also claim that this positive effect of multimarket contact on the formation of cooperative agreements is more pronounced when the partners have reciprocal contacts rather than nonreciprocal ones.

Managerial summary

This article explains one of the reasons why rival firms can be good partners to each other for technology cooperation. Managers might conjecture that firms tend to avoid partnering with rival firms for R&D because they may be more opportunistic than those without product market overlap. However, our theory suggests a counter‐intuitive argument that market overlap between partners rather deters them from engaging in opportunistic behaviors because market overlap enables them to broadly retaliate against such behaviors across the shared product markets. Consistent with this idea, our empirical results show that global top 200 biopharmaceutical companies are more likely to choose each other for technology cooperation as they share more product markets and this tendency is reinforced when their important markets are different.
Effect of Hydroxyapatite Nanorods on the Fate of Human Adipose‐Derived Stem Cells Assessed In Situ at the Single Cell Level with a High‐Throughput, Real‐Time Microfluidic Chip
Authors: Hao Min , He Jianlong , Wang Chunhua , Wang Chao , Ma Baojin , Zhang Shan , Duan Jiazhi , Liu Feng , Zhang Yu , Han Lin , Liu Hong , Sang Yuanhua
Published: November 2019

The fate of stem cells at the single cell level with limited communication with other cells is still unknown due to the lack of an efficient tool for highly accurate molecular detection. Moreover, the conditional sensitivity of biological experiments requires a sufficient number of parallel experiments to support a conclusion. In this work, a microfluidic single cell chip is designed for use with a protein chip to investigate the effect of hydroxyapatite (HAp) on the osteogenic differentiation of human adipose‐derived stem cells (hADSCs) in situ at the single cell level. By successfully detecting secretory proteins in situ, it is found that the HAp nanorods enhance osteogenic differentiation at the single cell level. In the chip, the single cell seeding approach confirms the osteogenic differentiation of the hADSCs, which endocytoses HAp, by reducing the influence of the factors secreted by neighboring differentiating cells. Most importantly, more than 7000 microchambers provide a sufficient number of parallel experiments for statistical analysis, which ensure a high level of repeatability of the HAp nanorod‐induced osteogenic differentiation. The microfluidic chip comprising single cell culture microchambers with in situ detection capability is a promising tool for research on cell behavior or cell fate at the single cell level.
A security feature framework for programming languages to minimize application layer vulnerabilities
Authors: Khwaja Amir A. , Murtaza Muniba , Ahmed Hafiz F.
Published: November 2019

Pervasiveness of Internet‐based applications and computing devices has increased cybersecurity threats for wide range of users. Studies have shown that application security flaws have their roots in programming languages used for application development. Some vulnerabilities are due to programmer's negligence and others are due to the vulnerabilities present in the programming languages and their libraries. Developers may not be aware of the existing flaws in the programming languages and do not have time to take necessary measures as they develop applications. To cope with the challenge, this article proposes a security feature framework for programming languages to understand various exploitations and possible mitigations in programming languages. This security feature framework can be used to evaluate existing programming languages for potential vulnerabilities, level of security support, and the language features needed to mitigate these vulnerabilities. Moreover, language designers may use this framework as a guide to ensure that the language being designed has necessary and sufficient security feature set. The proposed security feature framework is then applied to several popular programming languages to evaluate the level of security feature coverage and gaps in these languages along with some recommendations on how to address these gaps.
Micromechanisms of leading edge erosion of wind turbine blades: X‐ray tomography analysis and computational studies
Authors: Mishnaevsky Leon , Fæster Søren , Mikkelsen Lars P. , Kusano Yukihiro , Bech Jakob Ilsted
Published: November 2019

Micromechanisms of leading edge erosion of wind turbine blades are studied with the use of X‐ray tomography and computational micromechanics simulations. Computational unit cell micromechanical models of the coatings taking into account their microscale and nanoscale structures have been developed and compared with microscopy studies. It was observed that the heterogeneities, particles, and voids in the protective coatings have critical effect on the crack initiation in the coatings under multiple liquid impact. The damage criterion for the formation of initial defects in the top coating is determined, and it is maximum principal stress criterion. Porosity or stiff particles in the coatings change the damage initiation sites, moving it from the contact surface to the pores or particles closest to the surface. Increasing the thickness of the polymer coatings allows reducing the stress amplitude, thus delaying the damage.
Nanotechnology platforms for cancer immunotherapy
Authors: Yang Zhaogang , Ma Yifan , Zhao Hai , Yuan Yuan , Kim Betty Y. S.
Published: November 2019

Various cancer therapies have advanced remarkably over the past decade. Unlike the direct therapeutic targeting of tumor cells, cancer immunotherapy is a new strategy that boosts the host's immune system to detect specific cancer cells for efficient elimination. Nanoparticles incorporating immunomodulatory agents can activate immune cells and modulate the tumor microenvironment to enhance antitumor immunity. Such nanoparticle‐based cancer immunotherapies have received considerable attention and have been extensively studied in recent years. This review thus focuses on nanoparticle‐based platforms (especially naturally derived nanoparticles and synthetic nanoparticles) utilized in recent advances; summarizes delivery systems that incorporate various immune‐modulating agents, including peptides and nucleic acids, immune checkpoint inhibitors, and other small immunostimulating agents; and introduces combinational cancer immunotherapy with nanoparticles, especially nanoparticle‐based photo‐immunotherapy and nanoparticle‐based chemo‐immunotherapy. Undoubtedly, the recent studies introduced in this review prove that nanoparticle‐incorporated cancer immunotherapy is a highly promising treatment modality for patients with cancer. Nonetheless further research is needed to solve safety concerns and improve efficacy of nanoplatform‐based cancer immunotherapy for future clinical application.

This article is categorized under:

Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease
Free Will & Empirical Arguments for Epiphenomenalism
Authors: Elzein Nadine
Published: November 2019

While philosophers have worried about mental causation for centuries, worries about the causal relevance of conscious phenomena are also increasingly featuring in neuroscientific literature. Neuroscientists have regarded the threat of epiphenomenalism as interesting primarily because they have supposed that it entails free will scepticism. However, the steps that get us from a premise about the causal irrelevance of conscious phenomena to a conclusion about free will are not entirely clear. In fact, if we examine popular philosophical accounts of free will, we find, for the most part, nothing to suggest that free will is inconsistent with the presence of unconscious neural precursors to choices. It is only if we adopt highly non-naturalistic assumptions about the mind (e.g. if we embrace Cartesian dualism and locate free choice in the non-physical realm) that it seems plausible to suppose that the neuroscientific data generates a threat to free will.