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Area-selective deposition (ASD) based on self-aligned technology has emerged as a promising solution for resolving misalignment issues during ultrafine patterning processes. Despite its potential, the problems of area-selectivity losing beyond a certain thickness remain critical in ASD applications. This study reports a novel approach to sustain the area-selectivity of Ir films as the thickness increases. Ir films are deposited on Al 2 O 3 as the growth area and SiO 2 as the non-growth area using atomic-layer-deposition with tricarbonyl-(1,2,3-η)-1,2,3-tri(tert-butyl)-cyclopropenyl-iridium and O 3 . O 3 exhibits a dual effect, facilitating both deposition and etching. In the steady-state growth regime, O 3 solely contributes to deposition, whereas in the initial growth stages, longer exposure to O 3 etches the initially formed isolated Ir nuclei through the formation of volatile IrO 3 . Importantly, longer O 3 exposure is required for the initial etching on the growth area(Al 2 O 3 ) compared to the non-growth area(SiO 2 ). By controlling the O 3 injection time, the area selectivity is sustained even above a thickness of 25 nm by suppressing nucleation on the non-growth area. These findings shed light on the fundamental mechanisms of ASD using O 3 and offer a promising avenue for advancing thin-film technologies. Furthermore, this approach holds promise for extending ASD to other metals susceptible to forming volatile species., (© 2024 The Author(s). Small published by Wiley‐VCH GmbH.)

Reconstructing the surface nature of metal-organic frameworks (MOFs) as precatalytic structures is a promising methodology for improving electrocatalytic performance. However, regulating the structural evolution of MOFs during electrolysis remains highly uncontrollable and lacks an in-depth understanding of the role of in situ -derived active sites. Here, we suggest a simple approach to fine-tune the symmetry of Co-MOFs with an oxo-coordinated asymmetric coordination that acts as a prototypical structure motif for the oxygen evolution reaction (OER). Through a facile thermal treatment, the Co-N4 configuration of Co-MOFs transforms to the distorted Co-N3-oxo configuration of defective Co-ligand nanoclusters. By operando spectroscopic characterization, the reconstructed Co-N3-oxo structure enables a rapid structural transition toward homogeneous oxyhydroxides. Moreover, the defective nature of the precatalytic structure regulates the surface Co-O bonding environment with abundant μ 2 -O-Co 3+ sites, thereby exhibiting highly enhanced OER activity with an overpotential of 256 mV at 10 mA cm -2 and excellent durability for 100 h, compared with the pristine Co-MOFs. Atomistic simulations reveal that the effect of OER intermediates on the oxyhydroxides gets distributed among neighboring Co ions, promoting balanced binding of the intermediates. This work highlights an effective strategy to design the MOF-based structure for optimizing the surface nature, thus enhancing the electrocatalytic activity.

Despite extensive research into the phylogenetic relationships of the genus Magnolia , Neotropical taxa have been neglected. This is partly because their numbers have recently doubled and now account for almost half of the global richness. Therefore, by sampling one-third of all Neotropical taxa their relationships were studied using morphological, nuclear, and plastome data. Two major clades were identified: Clade I, comprising Magnolia sect. Talauma, Magnolia sect. Splendentes from the Neotropics, and the Asian Magnolia sect. Gwillimia ; while Clade II included the Neotropical clades Magnolia sect. Macrophylla and Magnolia sect. Magnolia , along with the remaining non-Neotropical sections. Within Clade I, Magnolia sect. Talauma was geographically divided into a northern subclade grouping Mexican and Central American taxa, and a southern subclade comprising South American and Caribbean taxa. Magnolia sect. Splendentes was also dichotomously divided, corresponding to the former Magnolia sect. Talauma subsect. Cubenses and Magnolia sect. Talauma subsect. Dugandiodendron . In Clade II, the relationships within Magnolia sect. Macrophylla and Magnolia sect. Magnolia were unclear, suggesting a species complex in all Magnolia sect. Macrophylla taxa. In total, 25 morphological traits were assessed, and ancestral state reconstructions were carried out. Only the joined clustering of mature follicles was a synapomorphy for the southern subclade of Magnolia sect. Talauma . In conclusion, this highlights the need to re-assess the taxonomic delimitation of certain groups, to update the infrageneric classification of Neotropical clades and to explore morphological traits to support them., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Local adaptation may facilitate range expansion during invasions, but the mechanisms promoting destructive invasions remain unclear. Cheatgrass ( Bromus tectorum ), native to Eurasia and Africa, has invaded globally, with particularly severe impacts in western North America. We sequenced 307 genotypes and conducted controlled experiments. We found that diverse lineages invaded North America, where long-distance gene flow is common. Ancestry and phenotypic clines in the native range predicted those in the invaded range, indicating pre-adapted genotypes colonized different regions. Common gardens showed directional selection on flowering time that reversed between warm and cold sites, potentially maintaining clines. In the Great Basin, genomic predictions of strong local adaptation identified sites where cheatgrass is most dominant. Preventing new introductions that may fuel adaptation is critical for managing ongoing invasions., Competing Interests: Competing interests: Authors declare that they have no competing interests.

Contrary to the prevailing notion that shell structures arise from the intricate chemistry and surface defects of InP quantum dots (QDs), an innovative strategy that remarkably enhances the luminescence efficiency of core-only InP QDs to over 90% is introduced. This paradigm shift is achieved through the concurrent utilization of group 2 and 3 metal-derived ligands, providing an effective remedy for surface defects and facilitating charge recombination. Specifically, a combination of Zn carboxylate and Ga chloride is employed to address the undercoordination issues associated with In and P atoms, leading to the alleviation of in-gap trap states. The intricate interplay and proportional ratio between Ga- and Zn-containing ligands play pivotal roles in attaining record-high luminescence efficiency in core-only InP QDs, as successfully demonstrated across various sizes and color emissions. Moreover, the fabrication of electroluminescent devices relying solely on InP core emission opens a new direction in optoelectronics, demonstrating the potential of the approach not only in optoelectronic applications but also in catalysis or energy conversion by charge transfer., (© 2024 Wiley‐VCH GmbH.)

Lithium (Li) metal has been regarded as the ideal anode for rechargeable batteries due to its low reduction potential and high theoretical capacity. However, the formation of fatal Li dendrites during repeated cycling shortens the battery life and causes serious safety concerns. Functionalized separators with electrically conductive and lithiophilic coating layers potentially inhibit dendrite formation and growth on Li metal anodes by providing nucleation sites for reversible Li deposition/stripping. In this work, we propose functionalized separators incorporating heteroatom-doped (N or B) graphene interlayers to modulate the Li nucleation behavior. The electronegative N-doping and electropositive B-doping were investigated to understand their regulation of the Li deposition behavior. With the heteroatom-doped graphene-coated separators, we observe significantly improved cycling stability along with enhanced charge transfer kinetics and low Li nucleation overpotential. This is attributed to the heteroatom-doped graphene interlayer expanding the surface area of the Li metal anode while providing additional space for uniform Li deposition/stripping, thus preventing undesirable side reactions. As a result, the formation of dendrites and pits on the Li metal anode surface is suppressed, demonstrating the protective effect of the Li metal anode. Interestingly, N-doped graphene-coated separators exhibit lower Li nucleation overpotentials than B-doped graphene-coated separators but rather lower average Coulombic efficiencies and reduced cycling stability. This implies that adequate adsorption on B-based sites, as opposed to the strong adsorption on N-based sites, improves the reversibility. Notably, the Li adsorption strength of the lithiophilic functional groups critically affects the reversibility, as observed by Li nucleation barrier measurements and atomistic simulations. This work suggests that interface engineering using conductive and lithiophilic materials can be a promising strategy for controlling Li deposition in advanced Li metal batteries.

Memristive neuromorphic computing has emerged as a promising computing paradigm for the upcoming artificial intelligence era, offering low power consumption and high speed. However, its commercialization remains challenging due to reliability issues from stochastic ion movements. Here, we propose an innovative method to enhance the memristive uniformity and performance through aliovalent halide doping. By introducing fluorine concentration into dynamic TiO 2- x memristors, we experimentally demonstrate reduced device variations, improved switching speeds, and enhanced switching windows. Atomistic simulations of amorphous TiO 2- x reveal that fluoride ions attract oxygen vacancies, improving the reversible redistribution and uniformity. A number of migration barrier calculations statistically show that fluoride ions also reduce the migration energies of nearby oxygen vacancies, facilitating ionic diffusion and high-speed switching. The detailed Voronoi volume analysis further suggests design principles in terms of the migrating species' electrostatic repulsion and migration barriers. This work presents an innovative methodology for the fabrication of reliable memristor devices, contributing to the realization of hardware-based neuromorphic systems.

Targeted proteomics is widely utilized in clinical proteomics; however, researchers often devote substantial time to manual data interpretation, which hinders the transferability, reproducibility, and scalability of this approach. We introduce DeepMRM, a software package based on deep learning algorithms for object detection developed to minimize manual intervention in targeted proteomics data analysis. DeepMRM was evaluated on internal and public datasets, demonstrating superior accuracy compared with the community standard tool Skyline. To promote widespread adoption, we have incorporated a stand-alone graphical user interface for DeepMRM and integrated its algorithm into the Skyline software package as an external tool., Competing Interests: J.P. is an employee of Bertis, Inc., and C.W., D.A., and S.K. are employees of Bertis Bioscience, Inc., both of which are companies developing proteomics-based diagnostics solutions., (© 2023 The Authors.)

The VIOLA ALBIDA complex is a complicated group with taxonomic problems having continuous leaf variations and composed of taxa related to the following names: Viola albida , V. albida var. takahashii , and V. chaerophylloides. As a first step to understanding the genomic nature of this complex, this study identified the whole chloroplast genome of V. albida . The genome is 157,692 bp in length (36.3% of GC content) and contains four subregions: a large single copy region of 86,220 bp, a small single copy region of 17,248 bp, and a pair of inverted regions of 27,112 bp each. An annotation of the gene identifies 111 unique genes, including 77 protein-coding genes, four rRNA genes, and 30 tRNA genes. The phylogenetic analysis of this genome with selected cp genomes from Viola identifies the close relationship between V. albida and V. ulleungdoensis. It is noteworthy that V. chaerophylloides , traditionally recognized as a member of the VIOLA ALBIDA complex, is genetically distant from V. albida and forms a sister group of all other members of the subsection Patellares . Our genome report is expected to serve as a basis for understanding the identity of the VIOLA ALBIDA complex., Competing Interests: No potential conflict of interest was reported by the authors., (© 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Premise: Developing an effective and easy-to-use high-molecular-weight (HMW) DNA extraction method is essential for genomic research, especially in the era of third-generation sequencing. To efficiently use technologies capable of generating long-read sequences, it is important to maximize both the length and purity of the extracted DNA; however, this is frequently difficult to achieve with plant samples., Methods and Results: We present a HMW DNA extraction method that combines (1) a nuclei extraction method followed by (2) a traditional cetyltrimethylammonium bromide (CTAB) DNA extraction method for plants with optimized extraction conditions that influence HMW DNA recovery. Our protocol produced DNA fragments (percentage of fragments >20 kbp) that were, on average, ca. five times longer than those obtained using a commercial kit, and contaminants were removed more effectively., Conclusions: This effective HMW DNA extraction protocol can be used as a standard protocol for a diverse array of taxa, which will enhance plant genomic research., (© 2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

Reverse electrodialysis (RED) directly harvests renewable energy from salinity gradients, and the achievable potential power heavily relies on the ion exchange membranes. Graphene oxides (GOs) are considered a solid candidate for the RED membrane because the laminated GO nanochannels with charged functional groups provide an excellent ionic selectivity and conductivity. Yet, a high internal resistance and poor stability in aqueous solutions limit the RED performance. Here, we develop a RED membrane that concurrently achieves high ion permeability and stable operation based on epoxy-confined GO nanochannels with asymmetric structures. The membrane is fabricated by reacting epoxy-wrapped GO membranes with ethylene diamine via vapor diffusion, overcoming the swelling properties in aqueous solutions. More importantly, the resultant membrane exhibits asymmetric GO nanochannels in terms of both channel geometry and electrostatic surface charges, leading to the rectified ion transport behavior. The demonstrated GO membrane exhibits the RED performance up to 5.32 W·m -2 with >40% energy conversion efficiency across a 50-fold salinity gradient and 20.3 W·m -2 across a 500-fold salinity gradient. Planck-Nernst continuum models coupled to molecular dynamics simulations rationalize the improved RED performance in terms of the asymmetric ionic concentration gradient within the GO nanochannel and the ionic resistance. The multiscale model also provides the design guidelines for ionic diode-type membranes configuring the optimum surface charge density and ionic diffusivity for efficient osmotic energy harvesting. The synthesized asymmetric nanochannels and their RED performance demonstrate the nanoscale tailoring of the membrane properties, establishing the potentials for 2D material-based asymmetric membranes.

Advancements in deep plasma proteomics are enabling high-resolution measurement of plasma proteoforms, which may reveal a rich source of novel biomarkers previously concealed by aggregated protein methods. Here, we analyze 188 plasma proteomes from non-small cell lung cancer subjects (NSCLC) and controls to identify NSCLC-associated protein isoforms by examining differentially abundant peptides as a proxy for isoform-specific exon usage. We find four proteins comprised of peptides with opposite patterns of abundance between cancer and control subjects. One of these proteins, BMP1, has known isoforms that can explain this differential pattern, for which the abundance of the NSCLC-associated isoform increases with stage of NSCLC progression. The presence of cancer and control-associated isoforms suggests differential regulation of BMP1 isoforms. The identified BMP1 isoforms have known functional differences, which may reveal insights into mechanisms impacting NSCLC disease progression., Competing Interests: OCF. has financial interest in Selecta Biosciences, Tarveda Therapeutics, and Seer. MKRD, YH, JEB, JW, DH, SF, IM, SK, MK, RWB, TLP, SB, OCF, and AS have financial interest in Seer. LAD is a member of Seer’s Scientific Advisor Board and is financially compensated for that role. Only Seer, and no other companies mentioned here, was involved in the study design, data collection and analysis, and manuscript writing/editing. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2023 Donovan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

An innovative autonomous resonance-tuning (ART) energy harvester is reported that utilizes adaptive clamping systems driven by intrinsic mechanical mechanisms without outsourcing additional energy. The adaptive clamping system modulates the natural frequency of the harvester's main beam (MB) by adjusting the clamping position of the MB. The pulling force induced by the resonance vibration of the tuning beam (TB) provides the driving force for operating the adaptive clamp. The ART mechanism is possible by matching the natural frequencies of the TB and clamped MB. Detailed evaluations are conducted on the optimization of the adaptive clamp tolerance and TB design to increase the pulling force. The energy harvester exhibits an ultrawide resonance bandwidth of over 30 Hz in the commonly accessible low vibration frequency range (<100 Hz) owing to the ART function. The practical feasibility is demonstrated by evaluating the ART performance under both frequency and acceleration-variant conditions and powering a location tracking sensor., (© 2022 The Authors. Advanced Science published by Wiley-VCH GmbH.)

Recently, the chloroplast genome of Viola verecunda from a sample collected in Japan has been published. Although the name is often recognized as a taxonomic synonym of Viola arcuata , the genetic identity of the two species has never been compared intensively. We report the complete chloroplast genome sequence of V. arcuata, of which sample was collected from Seoul, Korea. The cp genome of V. arcuata (OM301625) has 157,870 bp in length and is composed of four regions: 86,366 bp of a large single-copy (LSC) region, 17,298 bp of a small single-copy (SSC) region, and 27,103 bp of a pair of inverted repeats (IRs). The complete genome contains 130 genes, including 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. When comparing chloroplast genomes between V. verecunda , and V. arcuata , 34 different loci were recognized: 12 SNPs and 22 indels. In the coding regions, there were two amino acid insertions ( ndhI ) caused by one base deletion, three synonymous substitutions ( ndhF, ccsA, and ndhI ), and six nonsynonymous substitutions ( matK , rpoC2 , ndhF , ycf1 , and two rpl2 s on each IR region). In non-coding regions, variants of 19 polyN sites, one microsatellite, two insertions, and two SNPs were recognized. Phylogenetic analysis confirms a sister or nearly identical relationship between two genomes. This study will provide the genetic basis for solving a taxonomic problem between V. arcuata and V. verecunda ., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Background and Aims: Ongoing global warming is a challenge for humankind. A series of drastic climatic changes have been proven to have occurred throughout the Cenozoic based on a variety of geological evidence, which helps to better understand our planet's future climate. Notably, extant biomes have recorded drastic environmental shifts. The climate in southern Asia, which hosts high biodiversity, is deeply impacted by the Asian monsoon. The origins and evolutionary dynamics of biomes occurring between the tropics and sub-tropics in southern Asia have probably been deeply impacted by climatic changes; however, these aspects remain poorly studied. We tested whether the evolutionary dynamics of the above biomes have recorded the drastic, late Cenozoic environmental shifts, by focusing on Magnolia section Michelia of the family Magnoliaceae., Methods: We established a fine time-calibrated phylogeny of M. section Michelia based on complete plastid genomes and inferred its ancestral ranges. Finally, we estimated the evolutionary dynamics of this section through time, determining its diversification rate and the dispersal events that occurred between tropical and sub-tropical areas., Key Results: The tropical origin of M. section Michelia was dated to the late Oligocene; however, the diversification of its core group (i.e. M. section Michelia subsection Michelia) has occurred mainly from the late Miocene onward. Two key evolutionary shifts (dated approx. 8 and approx. 3 million years ago, respectively) were identified, each of them probably in response to drastic climatic changes., Conclusion: Here, we inferred the underlying evolutionary dynamics of biomes in southern Asia, which probably reflect late Cenozoic climatic changes. The occurrence of modern Asian monsoons was probably fundamental for the origin of M. section Michelia; moreover, the occurrence of asymmetric dispersal events between the tropics and sub-tropics hint at an adaptation strategy of M. section Michelia to global cooling, in agreement with the tropical conservatism hypothesis., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

A biological receptor serves as sensory transduction from an external stimulus to an electrical signal. It allows humans to better match the environment by filtering out repetitive innocuous information and recognize potentially damaging stimuli through key features, including adaptive and maladaptive behaviors. Herein, for the first time, the authors develop substantial artificial receptors involving both adaptive and maladaptive behaviors using diffusive memristor. Metal-oxide nanorods (NR) as a switching matrix enable the electromigration of an active metal along the surface of the NRs under electrical stimulation, resulting in unique surface-dominated switching dynamics with the advantage of fast Ag migration and fine controllability of the conductive filament. To experimentally demonstrate its potential application, a thermoreceptor system is constructed using memristive artificial receptors. The proposed surface-dominated diffusive memristor allows the direct emulation of the biological receptors, which represents an advance in the bioinspired technology adopted in creating artificial intelligence systems., (© 2021 The Authors. Advanced Science published by Wiley-VCH GmbH.)

Decades of research on solute-induced phase transformation of metal hydride systems have shown the possibility to enhance hydrogen storage properties through novel material design such as nanoconfinement engineering. Nevertheless, the fundamentals of mechanical stress effect on confined Pd nanoparticles remain yet to be elucidated due to the difficulty in linking with hydrogen sorption thermodynamics. Here, a thermodynamic tuning of Pd nanocubes associated with hydrogen sorption as a result of encapsulation by reduced graphene oxide (rGO) layers is demonstrated. Pd nanocubes are constrained by rGO to such a degree that the chemical potential and the pressure hysteresis of the system during hydrogen sorption drastically change while showing a size dependence. A thorough thermodynamic analysis elucidates the role of constraints on hydrogen uptake and release; despite the nanoscale regime, the thermodynamic parameters (enthalpy and entropy) during phase transition considerably increase, a phenomenon not seen before in unconstrained Pd nanoparticle systems.

RNA-protein interaction can be captured by crosslinking and enrichment followed by tandem mass spectrometry, but it remains challenging to pinpoint RNA-binding sites (RBSs) or provide direct evidence for RNA-binding. To overcome these limitations, we here developed pRBS-ID, by incorporating the benefits of UVA-based photoactivatable ribonucleoside (PAR; 4-thiouridine and 6-thioguanosine) crosslinking and chemical RNA cleavage. pRBS-ID robustly detects peptides crosslinked to PAR adducts, offering direct RNA-binding evidence and identifying RBSs at single amino acid-resolution with base-specificity (U or G). Using pRBS-ID, we could profile uridine-contacting RBSs globally and discover guanosine-contacting RBSs, which allowed us to characterize the base-specific interactions. We also applied the search pipeline to analyze the datasets from UVC-based RBS-ID experiments, altogether offering a comprehensive list of human RBSs with high coverage (3,077 RBSs in 532 proteins in total). pRBS-ID is a widely applicable platform to investigate the molecular basis of posttranscriptional regulation., (© 2021. The Author(s).)

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta , as well as for unraveling the origin of many cultivars., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Yoo, Lee, Kim and Lim.)

The technologically important frequency range for the application of electrostrictors and piezoelectrics is tens of Hz to tens of kHz. Sm 3+ - and Gd 3+ -doped ceria ceramics, excellent intermediate-temperature ion conductors, have been shown to exhibit very large electrostriction below 1 Hz. Why this is so is still not understood. While optimal design of ceria-based devices requires an in-depth understanding of their mechanical and electromechanical properties, systematic investigation of the influence of dopant size on frequency response is lacking. In this report, the mechanical and electromechanical properties of dense ceria ceramics doped with trivalent lanthanides (RE 0.1 Ce 0.9 O 1.95 , RE = Lu, Yb, Er, Gd, Sm, and Nd) were investigated. Young's, shear, and bulk moduli were obtained from ultrasound pulse echo measurements. Nanoindentation measurements revealed room-temperature creep in all samples as well as the dependence of Young's modulus on the unloading rate. Both are evidence for viscoelastic behavior, in this case anelasticity. For all samples, within the frequency range f = 0.15-150 Hz and electric field E ≤ 0.7 MV/m, the longitudinal electrostriction strain coefficient (| M 33 |) was 10 2 to 10 4 -fold larger than expected for classical (Newnham) electrostrictors. However, electrostrictive strain in Er-, Gd-, Sm-, and Nd-doped ceramics exhibited marked frequency relaxation, with the Debye-type characteristic relaxation time τ ≤ 1 s, while for the smallest dopants-Lu and Yb-little change in electrostrictive strain was detected over the complete frequency range studied. We find that only the small, less-studied dopants continue to produce useable electrostrictive strain at the higher frequencies. We suggest that this striking difference in frequency response may be explained by postulating that introduction of a dopant induces two types of polarizable elastic dipoles and that the dopant size determines which of the two will be dominant.

Premise: Commonly used molecular techniques such as next-generation sequencing require reliable methods to extract DNA quickly and efficiently. Secondary compounds within plant tissues make this requirement all the more challenging, often forcing researchers to test different extraction methods tailored to their particular species of interest in order to obtain large amounts of high-quality genomic DNA. The opportunities provided by high-throughput, next-generation sequencing only exacerbate these problems, especially when trying to extract DNA from multiple species at the same time. Several methods have attempted to resolve the challenges of obtaining suitable DNA from plants; however, a rapid, high-yield, high-quality, and highly scalable DNA extraction method is still needed., Methods and Results: We present a rapid DNA extraction protocol that utilizes a buffer with relatively large amounts of cetyltrimethylammonium bromide (CTAB) and sodium chloride, combined with a silica maxi-column cleanup of the extracted DNA. The new method is easy to implement using standard equipment and inexpensive reagents. The entire procedure (from grinding to the final elution) can be completed in less than two hours for a single sample and can be easily scaled to meet desired research goals. It works on diverse green plants with highly varied secondary chemistries (e.g., ferns, gymnosperms, and phylogenetically divergent angiosperms)., Conclusions: Application of the protocol to various plant species yielded DNA of high quality in less than two hours and can be adjusted to extract DNA at large (maxi-preps) or small (96-well minipreps) scales. We anticipate that our method will be of wide utility for rapidly isolating large quantities of quality genomic DNA from diverse plant species and will have broad applications in phylogenetic studies utilizing PCR and short-read DNA sequencing., (© 2021 Mavrodiev et al. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of the Botanical Society of America.)

Magnolia ofeliae A. Vázquez & Cuevas, a plant species endemic to south Jalisco, Mexico, is a critically endangered (CR) species based on the IUCN Red List. In this study, we assembled its complete chloroplast (cp) genome. The total genome size of M. ofeliae was 159,839 bp including four subregions: a large single-copy (LSC) region of 88,027 bp and a small single-copy (SSC) region of 18,752 bp separated by a pair of identical inverted repeat regions (IRs) of 26,530 bp each. The GC content of the cp genome of M. ofeliae is 39.3%. The cp genome encoded a set of 113 genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis results that M. ofeliae is a sister to all other magnolias in the subfamily Magnolioideae., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Forsythia saxatilis (Nakai) Nakai is an endemic species in Korea. We present the second complete chloroplast genome sequence of F. saxatilis showing that the chloroplast genome is 156,376 bp in length containing four subregions: a large single-copy (LSC) region of 87,097 bp, a small single-copy (SSC) region of 17,859 bp, and a pair of inverted repeat regions (IRs) of 25,710 bp. The genome contains 131 genes including 88 protein-coding genes, 35 tRNA s, and eight rRNAs. We found 40 base differences in 17 sites between our chloroplast genome and the previously reported chloroplast genome sequences of F. saxatilis . All of the differences were found in a region of 832 bp in the LSC region except for one site, which indicated potential sequencing errors in building the previously reported genome because of little substitutions in the homologous region of the other Forsythia species and even of Abeliophyllum distichum , a sister to Forsythia . The new chloroplast genomes of F. saxatilis and those of F. x intermedia and F. viridissima are identical, which suggests that F. saxatilis is maternally closely related to the other two species., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Semiconducting inorganic materials with band gaps ranging between 0 and 5 eV constitute major components in electronic, optoelectronic and photovoltaic devices. Since the band gap is a primary material property that affects the device performance, large band-gap databases are useful in selecting optimal materials in each application. While there exist several band-gap databases that are theoretically compiled by density-functional-theory calculations, they suffer from computational limitations such as band-gap underestimation and metastable magnetism. In this data descriptor, we present a computational database of band gaps for 10,481 materials compiled by applying a hybrid functional and considering the stable magnetic ordering. For benchmark materials, the root-mean-square error in reference to experimental data is 0.36 eV, significantly smaller than 0.75-1.05 eV in the existing databases. Furthermore, we identify many small-gap materials that are misclassified as metals in other databases. By providing accurate band gaps, the present database will be useful in screening materials in diverse applications.

Electromechanically active ceramic materials, piezoelectrics and electrostrictors, provide the backbone of a variety of consumer technologies. Gd- and Sm-doped ceria are ion conducting ceramics, finding application in fuel cells, oxygen sensors, and, potentially, as memristor materials. While optimal design of ceria-based devices requires a thorough understanding of their mechanical and electromechanical properties, reports of systematic study of the effect of dopant concentration on the electromechanical behavior of ceria-based ceramics are lacking. Here we report the longitudinal electrostriction strain coefficient ( M 33 ) of dense RE x Ce 1- x O 2- x /2 ( x ≤ 0.25) ceramic pellets, where RE = Gd or Sm, measured under ambient conditions as a function of dopant concentration within the frequency range f = 0.15-350 Hz and electric field amplitude E ≤ 0.5 MV/m. For >100 Hz, all ceramic pellets tested, independent of dopant concentration, exhibit longitudinal electrostriction strain coefficient with magnitude on the order of 10 -18 m 2 /V 2 . The quasi-static ( f < 1 Hz) electrostriction strain coefficient for undoped ceria is comparable in magnitude, while introducing 5 mol % Gd or 5 mol % Sm produces an increase in M 33 by up to 2 orders of magnitude. For x ≤ 0.1 (Gd)-0.15 (Sm), the Debye-type relaxation time constant (τ) is in the range 60-300 ms. The inverse relationship between dopant concentration and quasi-static electrostrictive strain parallels the anelasticity and ionic conductivity of Gd- and Sm-doped ceria ceramics, indicating that electrostriction is partially governed by ordering of vacancies and changes in local symmetry.

Quantitative proteomic platforms based on precursor intensity in mass spectrometry (MS1-level) uniquely support in vivo metabolic labeling with superior quantification accuracy but suffer from limited multiplexity (≤3-plex) and frequent missing quantities. Here we present a new MS1-level quantification platform that allows maximal multiplexing with high quantification accuracy and precision for the given labeling scheme. The platform currently comprises 6-plex in vivo SILAC or in vitro diethylation labeling with a dedicated algorithm and is also expandable to higher multiplexity (e.g., nine-plex for SILAC). For complex samples with broad dynamic ranges such as total cell lysates, our platform performs highly accurately and free of missing quantities. Furthermore, we successfully applied our method to measure protein synthesis rate under heat shock response in human cells by 6-plex pulsed SILAC experiments, demonstrating the unique biological merits of our in vivo platform to disclose translational regulations for cellular response to stress.

Holmskioldia sanguinea Retz. (Lamiaceae) is a widely cultivated ornamental plant. As a first report in the genus, we present the complete chloroplast genome sequence of H. sanguinea using genome skimming of paired-end NGS data. The total genome size measures 153,273 bp in length containing four subregions: 84,693 bp of large single-copy region, 17,330 bp small single-copy region, and a pair of inverted repeat regions, measuring 25,625 bp. The genome contains 115 genes including 80 protein-coding genes, 4 rRNAs, and 31 tRNAs. Phylogenetic analysis showed that H. sanguinea is a sister to Scutellaria in the subfamily Scutellarioideae of Lamiaceae., Competing Interests: No potential conflict of interest was reported by the authors., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Gastrodia elata is a non-photosynthetic saprophytic plant of medicinal use in the oriental countries. We report the second complete chloroplast (cp) genome of G. elata from a sample collected in Korea. The length of cp genome is only 35,180 bp: there is no inverted repeated region and many photosynthesis genes are missing compared to typical angiosperm cp genomes. It includes 20 protein-coding genes, 3 rRNAs, and 5 tRNAs. The overall GC content of the genome was 26.7%. Relatively, high intra-specific variation (457 SNPs and 670 indels) is detected in the species comparing it with other seed plants., Competing Interests: No potential conflict of interest was reported by the authors., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The development of high performance gas sensors that operate at room temperature has attracted considerable attention. Unfortunately, the conventional mechanism of chemiresistive sensors is restricted at room temperature by insufficient reaction energy with target molecules. Herein, novel strategy for room temperature gas sensors is reported using an ionic-activated sensing mechanism. The investigation reveals that a hydroxide layer is developed by the applied voltages on the SnO 2 surface in the presence of humidity, leading to increased electrical conductivity. Surprisingly, the experimental results indicate ideal sensing behavior at room temperature for NO 2 detection with sub-parts-per-trillion (132.3 ppt) detection and fast recovery (25.7 s) to 5 ppm NO 2 under humid conditions. The ionic-activated sensing mechanism is proposed as a cascade process involving the formation of ionic conduction, reaction with a target gas, and demonstrates the novelty of the approach. It is believed that the results presented will open new pathways as a promising method for room temperature gas sensors., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Premise: A new set of primers was developed for sequencing of whole chloroplast genomes of Magnolia species and gap-filling of unfinished genomes., Methods and Results: Two hundred and fifty primers were newly designed based on two previously reported chloroplast genomes from two different genera in Magnoliaceae. A total of 134 primer pairs, including the ones developed in this study and 18 previously reported ones, were enough to cover the entire chloroplast genome sequences in Magnoliaceae. Four species from different sections of Magnolia ( M. dealbata , M. fraseri var . pyramidata , M. liliiflora , and M. odora ) were used to show the general application of these primers to chloroplast genome sequencing in Magnolia ., Conclusions: Using the developed primers, four Magnolia chloroplast genomes were successfully assembled. These results show the utility of these primers across Magnolia and their potential use for phylogenetic studies, DNA barcoding, and population genetics in this group., (© 2019 Song et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.)

The stress inevitably imposed during electrochemical reactions is expected to fundamentally affect the electrochemistry, phase behavior and morphology of electrodes in service. Here, we show a strong stress-composition coupling in lithium binary alloys during the lithiation of tin-tin oxide core-shell nanoparticles. Using in situ graphene liquid cell electron microscopy imaging, we visualise the generation of a non-uniform composition field in the nanoparticles during lithiation. Stress models based on density functional theory calculations show that the composition gradient is proportional to the applied stress. Based on this coupling, we demonstrate that we can directionally control the lithium distribution by applying different stresses to lithium alloy materials. Our results provide insights into stress-lithium electrochemistry coupling at the nanoscale and suggest potential applications of lithium alloy nanoparticles.

Goodyera schlechtendaliana is a common orchid species in East Asia, providing a case to study phylogeographic structure of understory plants in warm temperate forests. Here, we present the complete chloroplast genome of the Korean G. schlechtendaliana . Its length is 153,801 bp and it has four subregions; 82,683 bp of large-single-copy and 18,048 bp of small-single-copy regions are separated by 26,535 bp of inverted repeat regions, including 133 genes (86 protein-coding genes, eight rRNAs, and 39 tRNAs). Phylogenetic analyses suggest that the chloroplast genomic data should be useful in future phylogeographic and phylogenetic studies of Goodyera ., Competing Interests: No potential conflict of interest was reported by the authors., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Scutellaria indica var. coccinea (Lamiaceae) is an endemic taxon in Jeju Island, Korea. We present the complete chloroplast genome sequence of S. indica var. coccinea . Its genome size is 151,956 bp in length comprising a large single copy of 83,951 bp, a small single copy of 17,539 bp, and a pair of inverted repeats measuring 25,233 bp. The complete genome contains 115 genes including 80 protein-coding genes, four rRNAs, and 31 tRNAs. Phylogenetic analysis of this species with 10 published chloroplast genomes in Lamiaceae showed that S. insignis is a sister to S. indica var. coccinea ., Competing Interests: No potential conflict of interest was reported by the authors., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Morphological evolution accompanying a surface roughening and preferred orientation is an effective way to realize a high-performance gas sensor because of its significant potential as a chemical catalyst through chemical potentials and atomic energy states. In this work, we investigated a heterojunction of double-side-W-decorated NiO nanoigloos fabricated through radio frequency sputtering and a soft-template method. Interestingly, a morphological evolution characterized by a pyramidal rough surface and the preferred orientation of the (111) plane was observed upon decorating the bare NiO nanoigloos with W. The underlying mechanism of the morphological evolution was precisely demonstrated based on the van der Drift competitive growth model originating from the oxygen transport and chemical strain in the lattice. The gas sensing properties of W-decorated NiO show an excellent NO 2 response and selectivity when compared to other gases. In addition, high response stability was evaluated under interference gas and humidity conditions. The synergistic effects on the sensing performance were interpreted on the basis of the morphological evolution of W-decorated NiO nanoigloos.

Agile Earth observation can be achieved with responsiveness in satellite launches, sensor pointing, or orbit reconfiguration. This study presents a framework for designing reconfigurable satellite constellations capable of both regular Earth observation and disaster monitoring. These observation modes are termed global observation mode and regional observation mode, constituting a reconfigurable satellite constellation (ReCon). Systems engineering approaches are employed to formulate this multidisciplinary problem of co-optimizing satellite design and orbits. Two heuristic methods, simulated annealing (SA) and genetic algorithm (GA), are widely used for discrete combinatorial problems and therefore used in this study to benchmark against a gradient-based method. Point-based SA performed similar or slightly better than the gradient-based method, whereas population-based GA outperformed the other two. The resultant ReCon satellite design is physically feasible and offers performance-to-cost(mass) superior to static constellations. Ongoing research on observation scheduling and constellation management will extend the ReCon applications to radar imaging and radio occultation beyond visible wavelengths and nearby spectrums.

The fatigue resistance of piezoelectric PVDF has been under question in recent years. While some report that a significant degradation occurs after 10⁶ cycles of repeated voltage input, others report that the reported degradation originates from the degraded metal electrodes instead of the piezoelectric PVDF itself. Here, we report the piezoelectric response and remnant polarization of PVDF during 10⁷ cycles of repeated compression and tension, with silver paste-based electrodes to eliminate any electrode effect. After applying repeated tension and compression of 1.8% for 10⁷ times, we do not observe any notable decrease in the output voltage generated by PVDF layers. The results from tension experiments show stable remnant polarization of 5.5 μC/cm², however, the remnant polarization measured after repeated compression exhibits a 7% decrease as opposed to the tensed PVDF. These results suggest a possible anisotropic response to stress direction. The phase analyses by Raman spectroscopy reveals no significant change in the phase content, demonstrating the fatigue resistance of PVDF.

Despite the wide applicability of oxynitrides from photocatalysis to refractory coatings, our understanding of the materials has been limited in terms of their thermodynamics. The configurational entropy via randomly mixed O/N or via cation vacancies are known to stabilize oxynitrides, despite the positive formation enthalpies. Here, using tin oxynitrides as a model system, we show by ab initio computations that oxynitrides in seemingly charge-unbalanced composition stabilize by forming pernitrides among metal-(O,N) 6 octahedra. The nitrogen pernitride dimer, =(N-N)=, results in the effective charge of -4, facilitating the formation of nitrogen-rich oxynitrides. We report that the dimer forms only in structures with corner-sharing octahedra, since the N-N bond formation requires sufficient rotational degrees of freedom among the octahedra. X-ray photoemission spectra of the synthesized tin oxynitride films reveal two distinct nitrogen bonding environments, confirming the computation results. This work opens the search space for a novel kind of oxynitrides stabilized by N dimer formation, with specific structural selection rules.

The utilization of edge sites in two-dimensional materials including transition-metal dichalcogenides (TMDs) is an effective strategy to realize high-performance gas sensors because of their high catalytic activity. Herein, we demonstrate a facile strategy to synthesize the numerous edge sites of vertically aligned MoS 2 and larger surface area via SiO 2 nanorod (NRs) platforms for highly sensitive NO 2 gas sensor. The SiO 2 NRs encapsulated by MoS 2 film with numerous edge sites and partially vertical-aligned regions synthesized using simple thermolysis process of [(NH 4 ) 2 MoS 4 ]. Especially, the vertically aligned MoS 2 prepared on 500 nm thick SiO 2 NRs (500MoS 2 ) shows approximately 90 times higher gas-sensing response to 50 ppm NO 2 at room temperature than the MoS 2 film prepared on flat SiO 2 , and the theoretical detection limit is as low as ∼2.3 ppb. Additionally, it shows reliable operation with reversible response to NO 2 gas without degradation at an operating temperature of 100 °C. The use of the proposed facile approach to synthesize vertically aligned TMDs using nanostructured platform can be extended for various TMD-based devices including sensors, water splitting catalysts, and batteries.

We describe Strelka2 ( https://github.com/Illumina/strelka ), an open-source small-variant-calling method for research and clinical germline and somatic sequencing applications. Strelka2 introduces a novel mixture-model-based estimation of insertion/deletion error parameters from each sample, an efficient tiered haplotype-modeling strategy, and a normal sample contamination model to improve liquid tumor analysis. For both germline and somatic calling, Strelka2 substantially outperformed the current leading tools in terms of both variant-calling accuracy and computing cost.

The potential barrier formed at the grain boundaries in Fe-doped SrTiO3 is reported to be one of the main reasons of the exceptionally large grain boundary resistivity of the material. Of particular interest is thus how to accurately quantify the potential barrier height, Ψgb, in such electronic conductors. This study aims to expand the applicability of a linear diffusion model (namely I-V model) to electronic conductors. The I-V model has previously proven its success in accurate determination of Ψgb in popular ionic conductors. By employing 1 mol% Fe-doped SrTiO3 as a model material, the current-voltage characteristics of the grain boundary investigated demonstrate the power law behavior predicted by the I-V model, verifying the applicability of this model. The Ψgb estimated from the I-V model at different temperatures are compared with those from the resistivity ratio of the grain boundary to the bulk. The resistivity ratio has been exclusively used to determine Ψgb in various conductors over several decades and yet has limitations in its accuracy. The Ψgb determined by the I-V model are found to be substantially lower than those from the resistivity ratio; such discrepancy implies that the potential barrier only partially contributes to the high grain boundary resistivity of a lightly doped electron-hole conducting SrTiO3.

The extent of the influence of space charge on the electric current through the grain boundary in solid electrolytes can be parameterized by the grain boundary potential, i.e. the height of the potential barrier formed at the grain boundary. Previously the value of this parameter has been estimated exclusively by the ratio of the grain boundary resistivity to the bulk counterpart over several decades. We recently demonstrated that it can be alternatively determined by analyzing the current-voltage characteristic of the grain boundary. Furthermore, we theoretically justified that the conventional method is in fact a subset of the new method, therefore, the latter is a more reliable and comprehensive approach to determine the grain boundary potential. Here, we present the experimental results that verify our theoretical justification. The values of the grain boundary potential determined for 1 mol% Sr-doped LaGaO3 (LSG1) employing both methods are in excellent agreement with one another. Such a consistency has not been reported for other solid electrolytes to date and we provide an explanation for it. Our data also indicate that for the case of LSG1, the Nernst-Einstein relation is preserved at the electric field exceeding 900 kV cm-1.

As an endangered species, Magnolia kobus is distributed in Jeju island in Korea with only about 500-1000 individuals. In this study, we presented a complete chloroplast genome of M. kobus which is 159,443 bp and has four sub-regions: 87,484 bp of large single copy and 18,783 bp of small single copy regions are separated by 26,588 bp of inverted repeat regions including 113 genes (79 unique genes, four rRNAs and 30 tRNAs). Phylogenetic analysis using chloroplast genomes showed that M. kobus is a sister of M. insignis and M. laevifolia clade., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Top-down proteomics, the analysis of intact proteins in their endogenous form, preserves valuable information about post-translation modifications, isoforms and proteolytic processing. The quality of top-down liquid chromatography-tandem MS (LC-MS/MS) data sets is rapidly increasing on account of advances in instrumentation and sample-processing protocols. However, top-down mass spectra are substantially more complex than conventional bottom-up data. New algorithms and software tools for confident proteoform identification and quantification are needed. Here we present Informed-Proteomics, an open-source software suite for top-down proteomics analysis that consists of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results viewer. We compare our tool with several other popular tools using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.

Summary: We introduce an open-source software, LIQUID, for semi-automated processing and visualization of LC-MS/MS-based lipidomics data. LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species. LIQUID was compared to other freely available software commonly used to identify lipids and other small molecules (e.g. CFM-ID, MetFrag, GNPS, LipidBlast and MS-DIAL), and was found to have a faster processing time to arrive at a higher number of validated lipid identifications., Availability and Implementation: LIQUID is available at http://github.com/PNNL-Comp-Mass-Spec/LIQUID ., Contact: jennifer.kyle@pnnl.gov or thomas.metz@pnnl.gov., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com)

Separation of proteoforms for global intact protein analysis (i.e. top-down proteomics) has lagged well behind what is achievable for peptides in traditional bottom-up proteomic approach and is becoming a true bottle neck for top-down proteomics. Herein, we report use of long (≥1M) columns containing short alkyl (C1-C4) bonded phases to achieve high-resolution RPLC for separation of proteoforms. At a specific operation pressure limit (i.e., 96.5MPa or 14Kpsi used in this work), column length was found to be the most important factor for achieving maximal resolution separation of proteins when 1.5-5μm particles were used as packings and long columns provided peak capacities greater than 400 for proteoforms derived from a global cell lysate with molecular weights below 50kDa. Larger proteoforms (50-110kDa) were chromatographed on long RPLC columns and detected by MS; however, they cannot be identified yet by tandem mass spectrometry. Our experimental data further demonstrated that long alkyl (e.g., C8 and C18) bonded particles provided high-resolution RPLC for <10kDa proteoforms, not efficient for separation of global proteoforms. Reversed-phase particles with porous, nonporous, and superficially porous surfaces were systematically investigated for high-resolution RPLC. Pore size (200-400Å) and the surface structure (porous and superficially porous) of particles was found to have minor influences on high-resolution RPLC of proteoforms. RPLC presented herein enabled confident identification of ∼900 proteoforms (1% FDR) for a low-microgram quantity of proteomic samples using a single RPLC-MS/MS analysis. The level of RPLC performance attained in this work is close to that typically realized in bottom-up proteomics, and broadly useful when applying e.g., the single-stage MS accurate mass tag approach, but less effective when combined with current tandem MS. Our initial data indicate that MS detection and fragmentation inefficiencies provided by current high-resolution mass spectrometers are key challenges for characterization of larger proteoforms., (Copyright © 2017. Published by Elsevier B.V.)

We report a pivotal role for IL-5 as an angiogenic activator. IL-5 increased proliferation, migration and colony tube formation in HUVECs associated with the phosphorylation of ERK and AKT/eNOS, and promoted microvessel sprouting from an angiogenesis animal model. The angiogenic effects were confirmed in IL-5-deficient mice and addition of IL-5 antibody. HSP70-1 was identified via expression profiling following IL-5 stimulation. A siRNA knockdown of HSP70-1 suppressed angiogenic responses and eNOS phosphorylation induced by IL-5. HSP70-1 overexpression enhanced IL-5-induced angiogenic responses. In addition, IL-5-induced neo-vascular formation was verified in both HSP70-1 knockout and HSP70-1 transgenic mice. Furthermore, transcription factor AP-1 was a main factor in IL-5-induced HSP70-1 in response to ERK and AKT signaling pathway. Angiogenic responses induced by VEGF had no effect in either HSP70-1 siRNA in vitro or HSP70-1 knockout mice. IL-5-induced angiogenic responses depended on the binding of IL-5Rα. Our data demonstrate that binding of IL-5 to IL-5Rα receptors enhances angiogenic responses by stimulating the expression of HSP70-1 via the eNOS signaling pathway.

Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments requires a series of computational steps that identify and quantify LC-MS features. It also requires statistical analyses that distinguish systematic changes in abundance between conditions from artifacts of biological and technical variation. The 2015 study of the Proteome Informatics Research Group (iPRG) of the Association of Biomolecular Resource Facilities (ABRF) aimed to evaluate the effects of the statistical analysis on the accuracy of the results. The study used LC-tandem mass spectra acquired from a controlled mixture, and made the data available to anonymous volunteer participants. The participants used methods of their choice to detect differentially abundant proteins, estimate the associated fold changes, and characterize the uncertainty of the results. The study found that multiple strategies (including the use of spectral counts versus peak intensities, and various software tools) could lead to accurate results, and that the performance was primarily determined by the analysts' expertise. This manuscript summarizes the outcome of the study, and provides representative examples of good computational and statistical practice. The data set generated as part of this study is publicly available.

Mass spectrometry (MS)-based proteomics, which uses high-resolution hybrid mass spectrometers such as the quadrupole-orbitrap mass spectrometer, can yield tens of thousands of tandem mass (MS/MS) spectra of high resolution during a routine bottom-up experiment. Despite being a fundamental and key step in MS-based proteomics, the accurate determination and assignment of precursor monoisotopic masses to the MS/MS spectra remains difficult. The difficulties stem from imperfect isotopic envelopes of precursor ions, inaccurate charge states for precursor ions, and cofragmentation. We describe a composite method of utilizing MS data to assign accurate monoisotopic masses to MS/MS spectra, including those subject to cofragmentation. The method, "multiplexed post-experiment monoisotopic mass refinement" (mPE-MMR), consists of the following: multiplexing of precursor masses to assign multiple monoisotopic masses of cofragmented peptides to the corresponding multiplexed MS/MS spectra, multiplexing of charge states to assign correct charges to the precursor ions of MS/MS spectra with no charge information, and mass correction for inaccurate monoisotopic peak picking. When combined with MS-GF+, a database search algorithm based on fragment mass difference, mPE-MMR effectively increases both sensitivity and accuracy in peptide identification from complex high-throughput proteomics data compared to conventional methods.

Peukert's equation is widely used to model the rate dependence of battery capacity, and has recently attracted attention for application to supercapacitors. Here we present a newly developed method to readily determine Peukert's constant using impedance spectroscopy. Impedance spectroscopy is ideal for this purpose as it has the capability of probing electrical performance of a device over a wide range of time-scales within a single measurement. We demonstrate that the new method yields consistent results with conventional galvanostatic measurements through applying it to commercially available supercapacitors. Additionally, the novel method is much simpler and more precise, making it an attractive alternative for the determination of Peukert's constant.