bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiatom Catalysts for Energy‐Related Electrocatalysis
Authors: Peng Wei , Feng Yiyang , Yan Xiao , Hou Feng , Wang Liqun , Liang Ji 
Published: November 2020

AbstractMultiatom catalysts (MACs) with isolated monodisperse active sites comprising two to tens of metal atoms have attracted intensive research attention and industrial interest. With the combination of high atom utilization and well‐defined molecule‐like electronic structure, MACs show great potential for applications in a wide range of electrochemical catalytic reactions. This review aims to discuss the recent progress of MACs in energy‐related electrocatalysis. Critical issues, including the synthesis and characterization of the MACs, will be showcased. Moreover, recent advances are highlighted in the design and synthesis of MACs with a well‐controlled structure and composition to achieve enhanced catalytic performance in energy‐related electrocatalysis. Current challenges and future prospects for MACs are also presented to shed light on the rational design of MACs as potential industrialized catalysts in the future.
Assessing methods and obstacles in chemical space exploration
Authors: Reeves Shawn , DiFrancesco Benjamin , Shahani Vijay , MacKinnon Stephen , Windemuth Andreas , Brereton Andrew E. 
Published: November 2020

AbstractBenchmarking the performance of generative methods for drug design is complex and multifaceted. In this report, we propose a separation of concerns for de novo drug design, categorizing the task into three main categories: generation, discrimination and exploration. We demonstrate that changes to any of these three concerns impacts benchmark performance for drug design tasks. In this report, we present Deriver, an open‐source Python package that acts as a modular framework for molecule generation, with a focus on integrating multiple generative methods. Using Deriver, we demonstrate that changing parameters related to each of these three concerns impacts chemical space traversal significantly, and that the freedom to independently adjust each is critical to real‐world applications having conflicting priorities. We find that combining multiple generative methods can improve optimization of molecular properties and lower the chance of becoming trapped in local minima. In addition, filtering molecules for drug‐likeness (based on physicochemical properties and SMARTS pattern matching) before they are scored may hinder exploration, but can also improve the quality of the final molecules. Finally, we demonstrate that any given task has an exploration algorithm best suited to it, though in practice linear probabilistic sampling generally results in the best outcomes, when compared to Monte Carlo sampling or greedy sampling. Deriver is being made freely available, to help others interested in collaboratively improving existing methods in de novo drug design centered around inheritance of molecular structure, modularity, extensibility, and separation of concerns.
Peak values of twist‐to‐bend ratio in triangular flower stalks of Carex pendula: a study on biomechanics and functional morphology
Authors: Speck Olga , Steinhart Feray , Speck Thomas 
Published: November 2020

PremiseBecause of their own weight and additional wind forces, plants are exposed to various bending and torsional loads that sometimes require contradictory structural characteristics and mechanical properties. The resulting trade‐off between flexural and torsional rigidity can be quantified and compared using the dimensionless twist‐to‐bend ratio.MethodsThe flexural rigidity of the stems of Carex pendula was determined by 2‐point bending tests. Additionally, 4‐point bending tests and torsional tests were carried out on segments of two internodes directly below the inflorescences to measure flexural and torsional rigidity. Anatomical investigations were performed to quantify the cross‐sectional distribution of their tissues.ResultsThe flexural rigidity of the stems, segments of the apical internode 1, and the more basal internode 2 differed significantly from each other, whereas the bending elastic moduli were not significantly different. The torsional rigidity of segments of internode 2 was a factor of 3.3 higher than that of internode 1, whereas the torsional moduli did not differ significantly. The twist‐to‐bend ratios of segments of internode 1 and 2 reached values between 85 and 403. Light microscopic investigations revealed a triangular stem possessing individual sclerenchyma strands, with internode 2 having significantly more strands than internode 1.ConclusionsIn the case of Carex pendula, flexural and torsional rigidity are adapted to the given mechanical constraints by significant changes in morphometric variables (axial and polar second moment of area, number of sclerenchyma strands), whereas the material properties (bending and torsional modulus) do not change markedly along the stem.
Light availability influences the intensity of nectar robbery and its effects on reproduction in a tropical shrub via multiple pathways
Authors: Fitch Gordon , Vandermeer John H. 
Published: November 2020

PremiseThe multiple exogenous pathways by which light availability affects plant reproduction (e.g., via influence on attraction of mutualists and antagonists) remain surprisingly understudied. The light environment experienced by a parent can also have transgenerational effects on offspring via these same pathways.MethodsWe evaluated (a) the influence of light availability on floral traits in Odontonema cuspidatum, (b) the relative importance of the pathways by which light influences nectar robbery and reproductive output, and (c) the role of parental light environment in mediating these relationships. We conducted a reciprocal translocation experiment using clonally propagated ramets and field surveys of naturally occurring plants.ResultsLight availability influenced multiple floral traits, including flower number and nectar volume, which in turn influenced nectar robbery. But nectar robbery was also directly influenced by light availability, due to light effects on nectar robber foraging behavior or neighborhood floral context. Parental light environment mediated the link between light availability and nectar robber attraction, suggesting local adaptation to low‐light environments in floral visitor attraction. However, we found no transgenerational effect on reproduction.ConclusionsOur findings demonstrate that exogenous pathways by which light influences plants (particularly through effects on floral antagonists) can complicate the positive relationship between light availability and plant reproduction. Our results are among the first to document effects of light on floral antagonists and clonal transgenerational effects on flower visitor attraction traits.
Accelerated senescence as a cost of reproduction: Testing associations between oxidative stress and reproductive effort in rural and urban women
Authors: Sancilio Amelia , Jasienska Grazyna , Panter‐Brick Catherine , Ziomkiewicz Anna , Nenko Ilona , Bribiescas Richard G. 
Published: November 2020

AbstractObjectivesOxidative stress is hypothesized to contribute to age‐related somatic deterioration. Both reproductive and ecological context may necessitate tradeoffs that influence this outcome. We examined whether measures of lifetime reproductive effort were related to levels of oxidative stress biomarkers in peri‐ and post‐menopausal women and whether associations were moderated by rural or urban residence.MethodsWe surveyed 263 healthy women (age 62.1 ± 10.0 SD) from rural (N = 161) and urban Poland (N = 102), collecting sociodemographic data and urine samples to analyze biomarkers of oxidative stress (8‐oxo‐2′‐deoxyguanosine, 8‐OHdG) and antioxidative defense (copper‐zinc superoxide dismutase, Cu‐Zn SOD). Linear regression models, adjusted for residence, were used to test for associations between reproductive effort and 8‐OHdG and Cu‐Zn SOD.ResultsUnivariate models demonstrated significant associations between gravidity and the biomarkers of oxidative stress (8‐OHdG: R2 = 0.042, P ≤ .001; Cu‐Zn SOD: R2 = 0.123, P ≤ .001). Multivariate models incorporating potential confounding variables, as well as cross‐product interaction terms, indicated that gravidity was associated with 8‐OHdG (P < .01, R2adj = 0.067) and Cu‐Zn SOD (P = .01, R2adj = 0.159). Residence (ie, urban vs rural) did not significantly moderate the associations between the biomarkers and reproductive effort.ConclusionsHigher lifetime reproductive effort contributes to increases in oxidative stress and antioxidative defenses. Our results provide evidence of potential mechanisms underlying the physiological tradeoffs influencing senescence for women with high reproductive effort. We illustrate the value of applying an evolutionary perspective to elucidate variation in human health and senescence.
Electron microscopic study of the median structure of the posterior column of the spinal cord of the adult rat with a special reference to the posterior median septum
Authors: Mii Kimihiko , Yagishita Saburo , Kumabe Toshihiro 
Published: November 2020

AbstractIn neuroanatomy textbooks on humans, the posterior median septum is commonly depicted along the midline of the posterior column of the spinal cord. For intramedullary spinal cord tumors, the standard surgical treatment is posterior midline myelotomy. However, its anatomical basis is still unclear. Therefore, in this study we focused on the ultrastructural characterization of the median structure of the posterior column in an adult rat. In the median part of the fasciculi gracilis, a fine lineal tissue continued from the posterior median sulcus to the 3/4th depth of the fasciculi. At higher magnification, this fine lineal tissue consisted of bundles of astrocytes, which are often disrupted and eventually disappeared. At the junction of the ventral part of the fasciculi cuneatus and the gray commissure, short lineal figures of glial tissues extended dorsally. These lineal figures of glial tissues were morphologically similar to other lineal figures of glial tissues found in the posterior column; bundles of astrocytes extending along the axons that entered the gray commissure and the perivascular lineal figures of glial tissues. In conclusion, this study revealed that the posterior median septum is composed of very fine lineal figures of glial tissues that are often disrupted and eventually disappear. We consider these basic structures to be similar in humans. Therefore, during posterior midline myelotomy, accurately separating along the posterior median septum in the posterior column is extremely difficult.
Odontoblast processes of the mouse incisor are plates oriented in the direction of growth
Authors: Shuhaibar Ninna , Hand Arthur R. , Terasaki Mark 
Published: November 2020

AbstractOdontoblast processes are thin cytoplasmic projections that extend from the cell body at the periphery of the pulp toward the dentin‐enamel junction. The odontoblast processes function in the secretion, assembly and mineralization of dentin during development, participate in mechanosensation, and aid in dentin repair in mature teeth. Because they are small and densely arranged, their three‐dimensional organization is not well documented. To gain further insight into how odontoblast processes contribute to odontogenesis, we used serial section electron microscopy and three‐dimensional reconstructions to examine these processes in the predentin region of mouse molars and incisors. In molars, the odontoblast processes are tubular with a diameter of ~1.8 μm. The odontoblast processes near the incisor tip are similarly shaped, but those midway between the tip and apex are shaped like plates. The plates are radially aligned and longitudinally oriented with respect to the growth axis of the incisor. The thickness of the plates is approximately the same as the diameter of molar odontoblast processes. The plates have an irregular edge; the average ratio of width (midway in the predentin) to thickness is 2.3 on the labial side and 3.6 on the lingual side. The plate geometry seems likely to be related to the continuous growth of the incisor and may provide a clue as to the mechanisms by which the odontoblast processes are involved in tooth development.
Impact of various ecological parameters on the life‐history characteristics of Bufotes viridis sitibundus from Turkey
Authors: Altunışık Abdullah , Gül Serkan , Özdemir Nurhayat 
Published: November 2020

AbstractIn this study, we used the skeletochronology method to estimate various growth parameters, such as age structure, minimum and maximum life span, age of sexual maturity, and the relationship between body size and weight of eight different populations of the variable toad, Bufotes viridis sitibundus, in Turkey. Further, we determined the relationship between these parameters and ecologic factors using the partial Mantel test. A significant difference was found among the populations with respect to age, body size, and body weight in both males and females. On average, the maximum life span was recorded as 10 years for males and 11 years for females. In the studied populations, the average age of sexual maturity ranged between 2 and 4 years for both sexes. Sexual dimorphism in terms of snout‐vent length (SVL) was not observed between males and females in all the populations. Toads from the higher altitudes tended to be significantly larger, older, and heavier than those from lower altitudes. We concluded that altitude and temperature have an impact on the growth rate, body size, and body mass.
Effects of variable domain orientation on anti‐HER2 single‐chain variable fragment antibody expressed in the Escherichia coli cytoplasm
Authors: Koçer İlkay , Cox Emily C. , DeLisa Matthew P. , Çelik Eda 
Published: November 2020

AbstractSingle‐chain variable fragment (scFv) antibodies have great potential for a range of applications including as diagnostic and therapeutic agents. However, production of scFvs is challenging because proper folding and activity depend on the formation of two intrachain disulfide bonds that do not readily form in the cytoplasm of living cells. Functional expression in bacteria therefore involves targeting to the more oxidizing periplasm, but yields in this compartment can be limiting due to secretion bottlenecks and the relatively small volume compared to the cytoplasm. In the present study, we evaluated an anti‐HER2 scFv, which is specific for human epidermal growth receptor 2 (HER2) overexpressed in breast cancer, for functional expression in the cytoplasm of Escherichia coli strains BL21(DE3) and SHuffle T7 Express, the latter of which is genetically engineered for cytoplasmic disulfide bond formation. Specifically, we observed much greater solubility and binding activity with SHuffle T7 Express cells, which likely resulted from the more oxidative cytoplasm in this strain background. We also found that SHuffle T7 Express cells were capable of supporting high‐level soluble production of anti‐HER2 scFvs with intact disulfide bonds independent of variable domain orientation, providing further evidence that SHuffle T7 Express is a promising host for laboratory and preparative expression of functional scFv antibodies.
Consolidated plasmid Design for Stabilized Heterologous Production of the complex natural product Siderophore Yersiniabactin
Authors: Qi Ruiquan , Swayambhu Girish , Bruno Michael , Zhang Guojian , Pfeifer Blaine A. 
Published: November 2020

AbstractYersiniabactin (Ybt) is a hybrid polyketide‐nonribosomal complex natural product also known as a siderophore for its iron chelation properties. The native producer of Ybt, Yersinia pestis, is a priority pathogen responsible for the plague in which the siderophore properties of Ybt are used to sequester iron and other metal species upon host infection. Alternatively, the high metal binding properties of Ybt enable a plethora of potentially valuable applications benefiting from metal remediation and/or recovery. For these applications, a surrogate production source is highly preferred relative to the pathogenic native host. In this work, we present a modification to the heterologous Escherichia coli production system established for Ybt biosynthesis. In particular, the multiple plasmids originally used to express the genetic pathway required for Ybt biosynthesis were consolidated to a single, copy‐amplifiable plasmid. In so doing, plasmid stability was improved from ~30% to ≥80% while production values maintained at 20–30% of the original system, which resulted in titers of 0.5–3 mg/L from shake flask vessels.
Develop a circular RNA–related regulatory network associated with prognosis of gastric cancer
Authors: Wei Shuxun , Teng Shifeng , Yao Jun , Gao Wenchao , Zang Jia , Wang Guangyong , Hu Zhiqian 
Published: November 2020

AbstractBackgroundIn gastric cancer (GC), circular RNAs (circRNAs) mainly play an important role in miRNA sponge, which not only indicate long‐term survival and prognosis but also increase resistance to the apoptosis. The purpose of the study is to explore new circRNAs and their underlying mechanisms in GC.MethodThrough rigorous retrieval strategies, we used the sva package to analyze and identify differentially expressed circRNAs (DECs) from three Gene Expression Omnibus microarray datasets (GSE83521, GSE89143, and GSE78092). Online website CSCD and CircInteractome were used to reveal the binding sites between miRNAs and DECs. The possible target miRNAs of the DECs identified based on miRNAs, and Cytoscape was used to create a regulatory network of circRNA‐miRNA‐mRNA and identified the hub genes which were further validated using The Cancer Genome Atlas database and Human Protein Atlas.ResultsTwenty‐eight DECs were obtained using the sva package. A regulatory network of circRNA‐miRNA‐mRNA (competing endogenous RNA) containing 15 circRNAs, 24 miRNAs, and 158 genes was identified. A protein‐protein interaction network based on the 158 genes was established, and further determined that 10 hub genes (SKA1, ANLN, CHEK1, SKA3, TOP2A, BIRC5, RRM2, NCAPG2, FANCI, and RAD51) were associated with some cancer‐related pathways based on the functional enrichment analysis. Finally, six hub genes (BIRC5, TOP2A, FANCI, NCAPG2, RAD51, and RRM2) were proven to influence the overall survival of GC.ConclusionOur study established a circRNA‐miRNA‐mRNA regulatory network and defined six circRNA‐related hub genes in GC, which could serve as potential therapeutic targets or prognostic biomarker for GC treatment.
Correlation of tumor‐infiltrating immune cells of melanoma with overall survival by immunogenomic analysis
Authors: Huang Lili , Chen Hong , Xu Yu , Chen Jianhua , Liu Zhuqing , Xu Qing 
Published: November 2020

AbstractAimsDifferent types of tumor‐infiltrating immune cells not only augment but also dampen antitumor immunity in the microenvironment of melanoma. Therefore, it is critical to provide an overview of tumor‐infiltrating immune cells in melanoma and explore a novel strategy for immunotherapies.MethodsWe analyzed the immune states of different stages in melanoma patients by the immune, stromal, and estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE) scores. Immune cell types were identified by the estimating relative subsets of RNA transcripts (CIBERSORTx) algorithm in 471 melanoma and 324 healthy tissues. Moreover, we performed a gene set variation analysis (GSVA) to determine the differentially regulated pathways in the tumor microenvironment.ResultsIn melanoma cohorts, we found that ESTIMATE and immune scores were involved in survival or tumor clinical stage. Among the 22 immune cells, CD8+ T cells, M2 macrophages, and regulatory T cells (Tregs) showed significant differences using the CIBERSORTx algorithm. Furthermore, GSVA identified the immune cell‐related pathways; the primary immunodeficiency pathway, intestinal immune network for IgA, and TGF‐β pathways were identified as participants of the crosstalk in CD8+ T cells, Tregs, and M2 macrophages in the melanoma microenvironment.ConclusionThese results reveal the cellular and molecular characteristics of immune cells in melanoma, providing a method for selecting targets of immunotherapies and promoting the efficacy of therapies for the treatment of melanoma.
Corymbia citriodora: A Valuable Resource from Australian Flora for the Production of Fragrances, Repellents, and Bioactive Compounds
Authors: Goodine Tyler , Oelgemöller Michael 
Published: November 2020

AbstractAs global chemical manufacturing has historically relied on inexpensive feedstocks from the petrochemical industry, the identification of new naturally derived feedstocks represents an important and sustainable alternative. This review introduces Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson as an attractive renewable resource of natural compounds for organic chemical transformations. Although native to Australia, this plant species is now grown and harvested worldwide. The chemical composition of citriodora oils varies with location, harvesting season and age of leaves. Beyond their historic uses as fragrances or repellents, the more abundant terpenes found in citriodora oils such as citronellal, citronellol, and isopulegol have notable roles in the manufacture of fine chemicals. This review highlights several industrial processes intimately related to the citriodora terpenes, some advances in fragrances and repellents, as well as the use of these terpenes in the most recently reported synthesis of bioactive compounds. Where relevant, processes highlighting the adoption of green chemistry principles are presented and briefly discussed.
Evaluations of the capacity of an existing brine system and estimation of salt loading profile for increased soft water demand to avoid soil contamination
Authors: Sharma Deepak , Karre Avinashkumar V. , Valsaraj Kalliat T. 
Published: November 2020

AbstractAs part of the expansion of a new chemical manufacturing facility, the debottlenecking of an existing brine system for an increase in soft water demand and the usefulness of the method was studied. Mathematical equations were used to estimate the salt loading profile. The effect of increasing soft water demand on the brine system was studied using parameters such as the amount of salt, the number of refills of brine tank, the brine pump run time, the number of days for the salt pit to empty, and the number of brine truck deliveries. The generalized mathematical equations derived and presented in this study can be used for any debottlenecking studies. The study showed that the existing brine pit and brine pumps can be reused for the future brine demand. The study showed with a good truck delivery logistics and a robust pit maintenance program, the number of regenerations can be increased while utilizing the existing brine pit system. The risk level remained the same as in existing pit systems since an increase in the frequency of pit maintenance was used to account for higher brine levels in the pit. The study methodology can be utilized for similar brine and softener systems in plant expansion operations to avoid a new pit system and to reduce capital costs. Brine seepage through the new concrete walls was avoided effectively. A polyvinyl chloride above ground tank system is recommended for brine service in all future projects where feasible.