SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences.

The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequence-based domains: (i) structure-based using SCOP and (ii) sequence-based using Pfam to avoid conflicts from two domain assignment methodologies. Users can investigate SNPs within protein domains with 2D and 3D maps. We expect this visual annotation of SNPs within protein domains will help scientists select and interpret SNPs associated with diseases. A web interface for the SNP@Domain is freely available at http://snpnavigator.net/ and from http://bioportal.net/.This project was supported by the Korean Ministry of Science and Technology (MOST) under grant number M10508040002-05N0804-00210 and M10407010001-05N0701-00100. Y.B.C. is supported by Biogreen21 program (20050401-034-791-006-03-00 and 20050301-034-481-006-02-00). Funding to pay the Open Access publication charges for this article was provided by M10407010001-05N0701-00100 grant of MOST

The United States COVID-19 Forecast Hub dataset

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages

Performance Characteristics of Automobile Air Conditioning Using the R134a/R1234yf Mixture

In this study, the energy and exergy of an automobile refrigeration system using R134a and R134a/R1234yf were analyzed experimentally with respect to outdoor air temperature and compressor speed. As outdoor air temperature increased from 32.5 °C to 37.5 °C, the coefficient of performance (COP) and total exergy destruction rate of the refrigeration system using Mix30 decreased by 5.19% and 25.8% on average, compared to that of the system using R134a. The exergy efficiency of the Mix30 refrigeration system was on average 21.8% higher than that of the R134a system. As the compressor rotating speed increased from 1000 to 2000 rpm, the cooling capacity of the refrigeration system using R134a and R134a/R1234yf increased, while the COP decreased. The COP and total exergy destruction rate of the refrigeration system using Mix30 decreased by 4.82% and 19.5%, compared to that of the system using R134a. The exergy efficiency of the Mix30 refrigeration system increased on average by 20.7%, compared to that of the R134a system. The total exergy destruction rate of the automobile refrigeration system using R134a/R1234yf decreased with increase in R1234yf, while exergy efficiency increased. In addition, the exergy destruction rate of the automobile refrigeration system decreased as the amount of R1234yf in the R134a/R1234yf automobile refrigeration system increased

Development of Surface-Modified Polyacrylonitrile Fibers and Their Selective Sorption Behavior of Precious Metals

The purpose of this study was to design a powerful fibrous sorbent for recovering precious metals such as Pd(II) and Pt(IV), and moreover for identifying its selectivity toward Pd(II) or Pt(IV) from a binary metal solution. For the development of the sorbent, polyacrylonitrile (PAN) was selected as a model textile because its morphological property (i.e., thin fiber form) is suitable for fast adsorption processes, and a high amount of PAN has been discharged from industrial textile factories. The PAN fiber was prepared by spinning a PAN–dimethylsulfoxide mixture into distilled water, and then its surface was activated through amidoximation so that the fiber surface could possess binding sites for Pd(II) and Pt(IV). Afterwards, by Fourier-transform infrared (FT-IR) and scanning electron microscopy (SEM) analyses, it was confirmed that the amidoximation reaction successfully occurred. The surface-activated fiber, designated as PAN–oxime fiber, was used to adsorb and recover precious metals. In the experiment results, it was clearly observed that adsorption capacity of PAN–oxime fiber was significantly enhanced compared to the raw material form. Actually, the raw material does not have sorption capacity for the metals. In a comparison study with commercial sorbent (Amberjet™ 4200), it was found that adsorption capacity of PAN–oxime was rather lower than that of Amberjet™ 4200, however, in the aspects of sorption kinetics and metal selectivity, the new sorbent has much faster and better selectivity

Overexpression of Golgi Protein CYP21-4s Improves Crop Productivity in Potato and Rice by Increasing the Abundance of Mannosidic Glycoproteins

CYP21-4 is a novel Golgi-localized cyclophilin protein involved in oxidative stress tolerance. Here, we generated transgenic plants overexpressing AtCYP21-4 and OsCYP21-4 in potato and rice, respectively. The stems and roots of AtCYP21-4–overexpressing potato plants were longer than those of wild-type (WT) plants, which resulted in heavier tubers. In vitro tuberization in the transgenic potato also resulted in significantly greater tuber number and weight, as well as a shorter time to microtuber formation. Similarly, OsCYP21-4–overexpressing transgenic rice plants had higher biomass and productivity with longer early-stage internodes than the WT and higher seed weight. Immunoblot analysis with CYP21-4 antibody showed that these productivity-enhancing phenotypes were associated with high CYP21-4s protein expression. Anatomically, transgenic potato stems exhibited higher lignin content in xylem cells and thicker leaves. In addition, relative content of mannosidic glycoproteins per unit of total protein was above 20% in transgenic potato tubers and rice grains. Based on these findings, we propose that CYP21-4s are involved in the growth and development of plant vegetative and storage tissues via their effects on glycoprotein abundance or glycan processing in the Golgi apparatus. Thus, increasing CYP21-4s expression in crops could represent an alternative way to increase crop productivity and yield

Beetroot (Beta vulgaris) rescues mice from γ-ray irradiation by accelerating hematopoiesis and curtailing immunosuppression

Context: Beetroot [Beta vulgaris Linné (Chenopodiaceae)], a vegetable usually consumed as a food or a medicinal plant in Europe, has been reported to have antioxidant and anti-inflammatory properties. Since the lymphohematopoietic system is the most sensitive tissue to ionizing radiation, protecting it from radiation damage is one of the best ways to decrease detrimental effects from radiation exposure. Objective: In this study, we evaluated the radio-protective effects of beetroot in hematopoietic stem cells (HSCs) and progenitor cells. Materials and methods: Beetroot extract was administered at a dose of 400 mg/mouse per os (p.o.) three times into C57BL/6 mice and, at day 10 after γ-ray irradiation, diverse molecular presentations were measured and compared against non-irradiated and irradiated mice with PBS treatments. Survival of beetroot-fed and unfed irradiated animal was also compared. Results: Beetroot not only stimulated cell proliferation, but also minimized DNA damage of splenocytes. Beetroot also repopulated S-phase cells and increased Ki-67 or c-Kit positive cells in bone marrow. Moreover, beetroot-treated mice showed notable boosting of differentiation of HSCs into burst-forming units-erythroid along with increased production of IL-3. Also, beetroot-treated mice displayed enhancement in the level of hematocrit and hemoglobin as well as the number of red blood cell in peripheral blood. Beetroot diet improved survival rate of lethally exposed mice with a dose reduction factor (DRF) of 1.1. Discussion and conclusion: These results suggest that beetroot has the potency to preserve bone marrow integrity and stimulate the differentiation of HSCs against ionizing radiation

Design of a Novel and Selective IRAK4 Inhibitor Using Topological Water Network Analysis and Molecular Modeling Approaches

Protein kinases are deeply involved in immune-related diseases and various cancers. They are a potential target for structure-based drug discovery, since the general structure and characteristics of kinase domains are relatively well-known. However, the ATP binding sites in protein kinases, which serve as target sites, are highly conserved, and thus it is difficult to develop selective kinase inhibitors. To resolve this problem, we performed molecular dynamics simulations on 26 kinases in the aqueous solution, and analyzed topological water networks (TWNs) in their ATP binding sites. Repositioning of a known kinase inhibitor in the ATP binding sites of kinases that exhibited a TWN similar to interleukin-1 receptor-associated kinase 4 (IRAK4) allowed us to identify a hit molecule. Another hit molecule was obtained from a commercial chemical library using pharmacophore-based virtual screening and molecular docking approaches. Pharmacophoric features of the hit molecules were hybridized to design a novel compound that inhibited IRAK4 at low nanomolar levels in the in vitro assay

Fundamental Study of Facile and Stable Hydrogen Evolution Reaction at Electrospun Ir and Ru Mixed Oxide Nanofibers

Electrochemical hydrogen evolution reaction (HER) has been an interesting research topic in terms of the increasing need of renewable and alternative energy conversion devices. In this article, Ir_<i>x</i>Ru_1–<i>x</i>O_<i>y</i> (<i>y</i> = 0 or 2) nanofibers with diverse compositions of Ir/IrO₂ and RuO₂ are synthesized by electrospinning and calcination procedures. Their HER activities are measured in 1.0 M NaOH. Interestingly, the HER activities of Ir_<i>x</i>Ru_1–<i>x</i>O_<i>y</i> nanofibers improve gradually during repetitive cathodic potential scans for HER, and then eventually reach the steady-state consistencies. This cathodic activation is attributed to the transformation of the nanofiber surface oxides to the metallic alloy. Among a series of Ir_<i>x</i>Ru_1–<i>x</i>O_<i>y</i> nanofibers, the cathodically activated Ir_0.80Ru_0.20O_<i>y</i> shows the best HER activity and stability even compared with IrO_<i>y</i> and RuO_<i>y</i>, commercial Pt and commercial Ir (20 wt % each metal loading on Vulcan carbon), where a superior stability is possibly ascribed to the instant generation of active Ir and Ru metals on the catalyst surface upon HER. Density functional theory calculation results for hydrogen adsorption show that the energy and adsorbate–catalyst distance at metallic Ir_0.80Ru_0.20 are close to those at Pt. This suggests that mixed metallic Ir and Ru are significant contributors to the improved HER activity of Ir_0.80Ru_0.20O_<i>y</i> after the cathodic activation. The present findings clearly demonstrate that the mixed oxide of Ir and Ru is a very effective electrocatalytic system for HER