bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rarity patterns of woody plant species are associated with life form and diversification rates in Pacific islands forests
Authors: Ibanez Thomas , Ainsworth Alison , Gross Jacob , Price Jonathan P. , Webb Edward L. , Hart Patrick J. 
Published: June 2021

PremiseRarity is a complex and central concept in ecology and conservation biology. Yet, it is still poorly understood why some species are rare and others common. Here, we aimed to understand the drivers of species rarity patterns in woody plant communities.MethodsWe analyzed the local abundance and landscape frequency of 121 woody plant species across 238 plots on American Samoa and Hawaiian islands. We first assessed whether taxonomy, life form (shrub, small tree, large tree), and dispersal syndrome (dispersed by animals or by other means) are associated with the rarity of species. We then analyzed phylogenetic patterns in plant rarity and tested whether rarity patterns are associated with species evolutionary distinctiveness and the number of species within genera and families.ResultsLarge trees were less abundant but more frequent than shrub species. Animal‐dispersed species tended to be less abundant than species dispersed by other means, while species frequency was not associated with dispersal syndromes. Relative frequency in Hawai′i exhibited a more robust phylogenetic signal than did abundance. Both evolutionary distinctiveness and taxa species richness were significantly associated with the frequency of shrub species in Hawai′i.ConclusionsLife form appears consistently associated with the rarity of species. High diversification rate is probably a key factor explaining landscape‐scale rarity of native species on isolated archipelagos like Hawai′i. At the landscape scale, rarity appears to be inversely associated with evolutionary distinctiveness, but at the local scale, species abundance may be not associated with evolutionary distinctiveness.
History of the methodology of disease gene identification
Authors: Antonarakis Stylianos E. 
Published: June 2021

AbstractThe past 45 years have witnessed a triumph in the discovery of genes and genetic variation that cause Mendelian disorders due to high impact variants. Important discoveries and organized projects have provided the necessary tools and infrastructure for the identification of gene defects leading to thousands of monogenic phenotypes. This endeavor can be divided in three phases in which different laboratory strategies were employed for the discovery of disease‐related genes: (i) the biochemical phase, (ii) the genetic linkage followed by positional cloning phase, and (iii) the sequence identification phase. However, much more work is needed to identify all the high impact genomic variation that substantially contributes to the phenotypic variation.
N‐doped TiO2‐quantum dots tightly anchored on graphene with superior interfacial contact via C–Ti bond
Authors: Dai Yue , Ju Tangtong , Tang Hailong , Wang Meiling , Wang Min , Ma Yongqing , Zheng Ganhong 
Published: June 2021

AbstractA novel composite of N‐doped TiO2‐quantum dots tightly anchored on graphene (denoted as N‐doped TiO2‐QDs@GP) with superior interfacial contact via C–Ti bond was synthesized via the simple one‐pot vapor‐thermal method. The as‐obtained N‐doped TiO2‐QDs@GP includes TiO2 QDs with an average size of 3.28 nm uniformly distributed on the surface of GP. The large specific area and superior interfacial contact via C–Ti bond ensured its potential photocatalytic application. Except for the effective interfacial charge transfer achieved via C–Ti chemical bond between TiO2 QDs and GP, its enhanced visible light absorption and larger oxygen vacancy ratio also make contributions. Electron spin resonance spectra (ESR) were used to study the photocatalytic mechanism, which proved the participation of both superoxide radical (·O2−) and hydroxyl radical (·OH) in the photocatalytic reactions. This work provides a promising one‐pot method for constructing intimately contacted N‐doped TiO2/GP composite with superior interfacial contact via C–Ti bond and excellent photocatalytic activities.
Evaluating the Passivation Layer of Freshly Cleaved Silicon Surfaces by Binary Silane‐Based Electrolytes
Authors: Schneier Dan , Horowitz Yonatan , Kasnatscheew Johannes , Grünebaum Mariano , Wiemhöfer Hans‐Dieter , Winter Martin , Peled Emanuel 
Published: June 2021

AbstractThe expansion of silicon anodes in lithium‐ion batteries during lithiation and the resulting instability of its solid‐electrolyte interphase (SEI) has been its Achilles heel for quite some time. Beyond the mechanical damage, this expansion exposes fresh elemental silicon to the electrolyte solution. The electrolyte readily decomposes on the reactive silicon surface. Researchers that test novel electrolytes find it difficult to separate which of the electrolyte components (solvent or anion) decomposes first and diagnose the respective decomposition products. Here, we utilize a straightforward test protocol that reveals which reduces first on bare silicon. We exposed four electrolyte mixtures to elemental silicon in custom made T‐cells by breaking thin silicon wafers in solution. We analyze the resulting surface film layers and compare their composition to the electrolyte's performance in symmetrical lithium cells, and Si/Li cells. We found that unstable anions rather than reactive solvents lead to poor electrochemical performance.
The gamma‐tubulin ring complex: Deciphering the molecular organization and assembly mechanism of a major vertebrate microtubule nucleator
Authors: Böhler Anna , Vermeulen Bram J.A. , Würtz Martin , Zupa Erik , Pfeffer Stefan , Schiebel Elmar 
Published: June 2021

AbstractMicrotubules are protein cylinders with functions in cell motility, signal sensing, cell organization, intracellular transport, and chromosome segregation. One of the key properties of microtubules is their dynamic architecture, allowing them to grow and shrink in length by adding or removing copies of their basic subunit, the heterodimer αβ‐tubulin. In higher eukaryotes, de novo assembly of microtubules from αβ‐tubulin is initiated by a 2 MDa multi‐subunit complex, the gamma‐tubulin ring complex (γ‐TuRC). For many years, the structure of the γ‐TuRC and the function of its subunits remained enigmatic, although structural data from the much simpler yeast counterpart, the γ‐tubulin small complex (γ‐TuSC), were available. Two recent breakthroughs in the field, high‐resolution structural analysis and recombinant reconstitution of the complex, have revolutionized our knowledge about the architecture and function of the γ‐TuRC and will form the basis for addressing outstanding questions about biogenesis and regulation of this essential microtubule organizer.
Structural and spectroscopic investigations of neodymium‐doped strontium borophosphate glass
Authors: Pagoti Ramakrishna , Panda Sitakanta , Patchapureddy Vinodkumar , Padhi Ranjib Kumar , Subramanian Balakrishnan , Jena Hrudananda , Panigrahi Bhabani Shankar 
Published: June 2021

AbstractNeodymium‐doped glass finds application in lasers with high energy and low pulse width. In the present study, a series of Nd3+ ions (0–2 mol%)‐doped strontium borophosphate (SBP) glass samples was prepared through the conventional melt quench method. A broad peak in the X‐ray diffraction spectrum confirmed the formation of a single‐phase amorphous borophosphate glass. Fourier transform infrared spectra of the doped and undoped glass samples indicated the presence of borate and phosphate groups that form the anionic network. The thermal properties of the glass samples were determined from thermogravimetry/differential thermal analysis. Photoluminescence and ultraviolet–visible light techniques were used to investigate the optical properties of the as‐prepared SBP:Nd glass. The Judd–Ofelt (JO) intensity parameters Ωλ (2, 4, 6), stimulated emission cross‐section, branching ratios, and transition probabilities of the Nd3+‐doped glass were obtained through the JO analysis. Characteristic Nd3+ emission peaks were observed at 1330, 1060, and 876 nm, corresponding to the 4F3/2→4IS/2 (S = 13, 11, and 9) transitions, respectively. The suitability of SBP:Nd (0.5 mol%) glass for use in solid‐state lasers was demonstrated by its intense luminescence, high transition probability, high emission cross‐section, optical gain, and luminescence branching ratio.
1,3‐Benzodioxole‐Modified Noscapine Analogues: Synthesis, Antiproliferative Activity, and Tubulin‐Bound Structure
Authors: Yong Cassandra , Devine Shane M. , Abel Anne‐Catherine , Tomlins Stefan D. , Muthiah Divya , Gao Xuexin , Callaghan Richard , Steinmetz Michel O. , Prota Andrea E. , Capuano Ben , Scammells Peter J. 
Published: June 2021

AbstractSince the revelation of noscapine's weak anti‐mitotic activity, extensive research has been conducted over the past two decades, with the goal of discovering noscapine derivatives with improved potency. To date, noscapine has been explored at the 1, 7, 6′, and 9′‐positions, though the 1,3‐benzodioxole motif in the noscapine scaffold that remains unexplored. The present investigation describes the design, synthesis and pharmacological evaluation of noscapine analogues consisting of modifications to the 1,3‐benzodioxole moiety. This includes expansion of the dioxolane ring and inclusion of metabolically robust deuterium and fluorine atoms. Favourable structural modifications were subsequently incorporated into multi‐functionalised noscapine derivatives that also possessed modifications previously shown to promote anti‐proliferative activity in the 1‐, 6′‐ and 9′‐positions. Our research efforts afforded the deuterated noscapine derivative 14 e and the dioxino‐containing analogue 20 as potent cytotoxic agents with EC50 values of 1.50 and 0.73 μM, respectively, against breast cancer (MCF‐7) cells. Compound 20 also exhibited EC50 values of <2 μM against melanoma, non‐small cell lung carcinoma, and cancers of the brain, kidney and breast in an NCI screen. Furthermore, compounds 14 e and 20 inhibit tubulin polymerisation and are not vulnerable to the overexpression of resistance conferring P‐gp efflux pumps in drug‐resistant breast cancer cells (NCIADR/RES). We also conducted X‐ray crystallography studies that yielded the high‐resolution structure of 14 e bound to tubulin. Our structural analysis revealed the key interactions between this noscapinoid and tubulin and will assist with the future design of noscapine derivatives with improved properties.
Pretreatment neutrophil‐to‐lymphocyte ratio as a potential prognostic biomarker for newly diagnosed patients with metastatic castration‐sensitive prostate cancer
Authors: Salah Samer , Abu‐Hijlih Ramiz , Abuhijla Fawzi , Tamimi Faris , Al‐Tell Abdallah , Shahait Mohammed 
Published: June 2021

AbstractBackgroundAlthough the prognostic role of neutrophil‐to‐lymphocyte ratio (NLR) has been assessed in patients with metastatic castration‐resistant prostate cancer, data on its impact on oncological outcomes of patients with metastatic castration‐sensitive prostate cancer (mCSPC) are scarce.AimThis study aims to examine the influence of elevated pretreatment NLR on time to prostatic‐specific antigen (PSA) progression and overall survival (OS) of patients with mCSPC.MethodsWe retrospectively reviewed patients presenting between June 2007 and June 2019 with mCSPC. Survival was estimated by the Kaplan‐Meier method and compared by the log‐rank test. Multivariate analyses were used to assess the factors influencing time to PSA progression and OS.ResultsA total of 189 patients were included; median age = 69 years, median PSA = 155 ng/mL, 41(22%) had visceral metastasis. Median time to PSA progression was shorter for patients with NLR ≥4 (n = 37) compared to patients with NLR < 4 (n = 146); 11.3 and 18.3 months, respectively, P = .015. Patients with NLR ≥4 also had inferior median OS (23.9 vs 49.5 months, P = .001). On multivariate analysis, NLR ≥4 was not an independent factor for time to PSA progression. However, NLR ≥4 was an independent factor of inferior OS (HR: 2.75, 95% CI: 1.01‐7.87, P = .047). Other independent factors predicting inferior OS included Eastern Cooperative Oncology Group Performance Status ≥1, high‐volume status, and Hb < 12.ConclusionElevated pretreatment NLR independently predicts inferior OS in newly diagnosed patients with mCSPC. However, NLR was not a predictor of time to PSA progression.
Thorough QT/QTc Evaluation of the Cardiac Safety of Enarodustat (JTZ‐951), an Oral Erythropoiesis‐Stimulating Agent, in Healthy Adults
Authors: Pai Sudhakar M. , Yamada Hiroyuki , Kleiman Robert B. , Zhuo Rui , Huang Qingtao (Mike) , Koretomo Ryosuke 
Published: June 2021

AbstractThis study evaluated the effect of enarodustat on cardiac repolarization in healthy subjects. Enarodustat (20 and 150 mg [supratherapeutic dose]), placebo, and moxifloxacin (positive control, 400 mg) were administered orally to males and females (N = 54) in a crossover fashion. Continuous 12‐lead Holter electrocardiogram (ECG) data were obtained before and after dosing, and blood samples were obtained for pharmacokinetic assessments of enarodustat, its circulating metabolite (R)‐M2, and moxifloxacin. Central tendency analysis was performed for relevant ECG parameters, the relationship between individual‐corrected interval from beginning of the QRS complex to end of the T wave in the frontal plane (QTcI, the primary end point) and plasma concentrations of enarodustat and (R)‐M2 were assessed, and ECG waveforms were evaluated for morphological changes. The supratherapeutic dose resulted in 7‐ and 9‐fold higher geometric mean maximum concentrations for enarodustat and (R)‐M2, respectively, than the 20 mg dose. Based on time point analysis, the upper bound of the 2‐sided 90% confidence interval (CI) for QTcI did not exceed 10 milliseconds at any of the time points for either dose. Based on QTcI‐concentration analysis, the slopes for enarodustat and (R)‐M2 were not statistically different than 0, and the upper bounds of the 2‐sided 90% CI for QTcI at the geometric mean maximum concentrations for the supratherapeutic dose were 1.97 and 1.68 milliseconds for enarodustat and (R)‐M2, respectively. The lower bound of the 2‐sided 90% CI for moxifloxacin was ≥5 milliseconds, demonstrating assay sensitivity. The study demonstrated no clinically relevant effect of enarodustat and (R)‐M2 on cardiac repolarization. There was no evidence of any clinically significant effect on the PR interval and QRS duration, and ECG waveforms showed no new clinically relevant morphological changes.
Base and Covariate Population Pharmacokinetic Analyses of Dupilumab in Adolescents and Children ≥6 to <12 Years of Age Using Phase 3 Data
Authors: Kovalenko Pavel , Kamal Mohamed A. , Davis John D. , Huniti Nidal , Xu Christine , Bansal Ashish , Shumel Brad , DiCioccio A. Thomas 
Published: June 2021

AbstractPopulation pharmacokinetic (PK) base and covariate analyses were conducted using data from adolescents with moderate‐to‐severe atopic dermatitis (AD) and children ≥6 to <12 years of age with severe AD. Two phase 3 studies were analyzed (165 adolescents and 241 children on active treatment). A 2‐compartment model with linear and Michaelis‐Menten elimination and 3 transit compartments describing lag time in absorption was utilized. Weight, albumin, body mass index, and Eczema Area and Severity Index score were statistically significant covariates in at least 1 of the age populations. Only body weight had a consequential effect on central volume. Although an absorption rate and target‐mediated clearance somewhat decreased with age, no dose adjustment was needed in addition to the adjustment for weight already implemented in the phase 3 studies. Otherwise, population PK parameters and covariates were similar across the 2 pediatric subpopulations and in adults. No allometric changes in elimination rate and beta half‐life were observed with weight. Parameterization of models in terms of rates was a useful alternative to parameterization in terms of clearances, allowing for an absence of repeated covariates and preventing overparameterization. The model adequately described dupilumab pharmacokinetics in the pediatric populations.
Photoactivatable Circular Caged Oligonucleotides for Transcriptome In Vivo Analysis (TIVA)
Authors: Yang Linlin , von Trentini Dora , Kim HyunBum , Sul Jai‐Yoon , Eberwine James H. , Dmochowski Ivan J. 
Published: June 2021

AbstractLight activation is an effective way to impart spatiotemporal control over oligonucleotide probes that are widely applied for gene expression regulation and target function investigation. Among the major oligonucleotide caging strategies, cyclization with a photocleavable linker is an elegant design, which affords both atom efficiency and stability in many biological environments. Here, we introduce an improved protocol for circular oligonucleotide synthesis requiring only one round of HPLC purification. With a series of poly‐U oligonucleotide strands of different sizes and backbone modifications, the pre‐photolysis caging stability and post‐photolysis target binding affinity were studied through a denaturing gel assay and melting temperature measurements. A 14 U 2'‐OMe RNA probe was selected, with strong potential application in transcriptome in vivo analysis (TIVA) for mRNA isolation.
Practical Methods for Expression of Recombinant Protein in the Pichia pastoris System
Authors: Mohammadzadeh Roghayeh , Karbalaei Mohsen , Soleimanpour Saman , Mosavat Arman , Rezaee Seyed Abdolrahim , Ghazvini Kiarash , Farsiani Hadi 
Published: June 2021

AbstractOne of the most critical challenges of genetic engineering is the expression of recombinant proteins using biological expression systems. Nowadays, different expression systems from bacteria to mammalian tissue culture cells are available for the production of recombinant proteins for medical and industrial purposes. Among various choices, yeast expression systems such as Pichia pastoris are promising candidates. The P. pastoris expression system is a standard tool for the production of biopharmaceuticals and industrial enzymes. It is also considered a unique host for the expression of subunit vaccines which could significantly affect the growing market of medical biotechnology. Using P. pastoris as an expression system for heterologous proteins, this article provides detailed basic protocols for cloning of a recombinant cassette into a suitable expression vector, the transformation of foreign vector DNAs into the yeast by electroporation, and expression and purification of desired recombinant protein. © 2021 Wiley Periodicals LLC.Basic Protocol 1: Cloning of a recombinant cassette into a suitable expression vectorBasic Protocol 2: Transformation of P. pastoris and selection of transformantsBasic Protocol 3: Optimization and large‐scale expression of recombinant proteinsBasic Protocol 4: Purification of recombinant proteins
Sheath formation in the presence of non‐extensive electron distribution
Authors: Moulick Rakesh , Garg Anuj , Kumar Mukesh 
Published: June 2021

AbstractThe main aim of this article is to recognize the sheath formation in the presence of non‐extensive electron distribution. The role of ion–neutral collision parameterKand the non‐extensive parameter “q” has been discussed. Existing literature suggests that the presence of non‐extensive electrons potentially modifies the plasma sheath behaviour. However, numerical calculations over the full plasma range, jointly addressing the sheath and presheath, are rare. Sheath formation, being a very fundamental phenomenon, deserves enough investigation in the region of non‐extensive distribution of particles. This study attempts to bridge the gap in understanding the formation of the sheath in collisional plasma in the light of both Boltzmann andq‐distributed non‐extensive electrons.
Undersampling correction methods to control γ‐dependence for comparing β‐diversity between regions
Authors: Cao Ke , Svenning Jens‐Christian , Yan Chuan , Zhang Jintun , Mi Xiangcheng , Ma Keping 
Published: June 2021

AbstractMeasures of β‐diversity are known to be biased by differences in γ‐diversity (i.e., γ‐dependence), making it challenging to compare β‐diversity across regions. Undersampling corrections have been designed to reduce effects of γ‐dependence on β‐diversity arising from the problem of incomplete sampling. However, no study has systematically tested the effectiveness of these corrections or examined how well they reflect β‐diversity patterns across ecological gradients. Here, we conduct these tests by comparing two undersampling corrections with the widely used individual‐based null model approach, using both simulated communities along an ecological gradient and empirical data across a wide range of γ‐diversity and sample sizes. We found that undersampling corrections using diversity accumulation curves were more effective than the null‐model approaches in removing γ‐dependence. In particular, the corrected β‐Shannon diversity index was least dependent on γ‐diversity, and was the most reflective of the β‐diversity pattern along a simulated ecological gradient. Moreover, a corrected Jaccard–Chao index applied to null model results removed γ‐dependence more effectively than either the correction alone or the null model alone. Undersampling corrections are effective tools for removing γ‐dependence bias, thus facilitating comparisons of β‐diversity across regions.
Proper environmental DNA metabarcoding data transformation reveals temporal stability of fish communities in a dendritic river system
Authors: Laporte Martin , Reny‐Nolin Emilie , Chouinard Victoria , Hernandez Cécilia , Normandeau Eric , Bougas Bérénice , Côté Caroline , Behmel Sonja , Bernatchez Louis 
Published: June 2021

AbstractProtecting freshwater biodiversity is considered an ultimate challenge but depends on reliable surveys of species distribution and abundance which eDNA metabarcoding (environmental DNA metabarcoding) may offer. To do so, a better understanding of the sources of temporal variation among species eDNA abundance and of data transformation in eDNA metabarcoding studies is needed. Here, we show that transformation based on relative abundance is critical to suitable analyses of eDNA metabarcoding data and that Hellinger transformation performed slightly better than other methods. Furthermore, we show that site localities significantly explain eDNA metabarcoding variation, while no variation is explained by time of sampling. This indicates that species communities vary more spatially than temporally within a dendritic system composed of small rivers. We then further documented the community structure in the St. Charles River (Québec City, Canada) and six of its tributaries. This revealed the existence of eight species communities explaining 82.1% of eDNA read variation within this river network. Moreover, variation in environmental variables among sites explained 53.0% of eDNA reads, while sampling events and temporal environmental variation explained no eDNA metabarcoding variation. Altogether, this supports the claim that eDNA metabarcoding is a powerful tool to document and monitor fish communities in watersheds composed of small river dendritic systems.