Visualizing protein big data using Python and Jupyter notebooks.

This article reports a workshop from the 2021 IUBMB/ASBMB Teaching Science with Big Data conference held virtually in June 2021 where participants learned to explore and visualize large quantities of protein PBD data using Jupyter notebooks and the Python programming language. This activity instructs participants using Jupyter notebooks, Python functions, loading data with Python, and visualize data using the matplotlib and seaborn Python plotting libraries. It also allows participants to explore large quantities of data to discover trends such amino acid abundance, dihedral angles patterns, and secondary protein structure trends.

Toward bioinspired polymer adhesives: activation assisted via HOBt for grafting of dopamine onto poly(acrylic acid).

The design of bioinspired polymers has long been an area of intense study, however, applications to the design of concrete admixtures for improved materials performance have been relatively unexplored. In this work, we functionalized poly(acrylic acid) (PAA), a simple analogue to polycarboxylate ether admixtures in concrete, with dopamine to form a catechol-bearing polymer (PAA-g-DA). Synthetic routes using hydroxybenzotriazole (HOBt) as an activating agent were examined for their ability in grafting dopamine to the PAA backbone.

Rapid Sentinel Surveillance for COVID-19 - Santa Clara County, California, March 2020.

On February 27, 2020, the Santa Clara County Public Health Department (SCCPHD) identified its first case of coronavirus disease 2019 (COVID-19) associated with probable community transmission (i.e., infection among persons without a known exposure by travel or close contact with a patient with confirmed COVID-19).

Assessing the sustainability of advanced materials using multicriteria decision analysis and the triple bottom line.

Although advanced materials (AdMs) are beneficial in many applications, questions remain as to whether they are more or less sustainable than the conventional materials that they may replace. Currently, there is no available tool to provide clarity to these questions. Traditional approaches for evaluating the sustainability of a chemical or material are usually not standardized, and as a result, the metrics used in sustainability measurements are subjective and often vary from assessor to assessor.

Effect of Cellulose Nanofibrils and TEMPO-mediated Oxidized Cellulose Nanofibrils on the Physical and Mechanical Properties of Poly(vinylidene fluoride)/Cellulose Nanofibril Composites.

Cellulose nanofibrils (CNFs) are high aspect ratio, natural nanomaterials with high mechanical strength-to-weight ratio and promising reinforcing dopants in polymer nanocomposites. In this study, we used CNFs and oxidized CNFs (TOCNFs), prepared by a 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO)-mediated oxidation process, as reinforcing agents in poly(vinylidene fluoride) (PVDF). Using high-shear mixing and doctor blade casting, we prepared free-standing composite films loaded with up to 5 wt % cellulose nanofibrils.

A Definition and Categorization System for Advanced Materials: The Foundation for Risk-Informed Environmental Health and Safety Testing.

Novel materials with unique or enhanced properties relative to conventional materials are being developed at an increasing rate. These materials are often referred to as advanced materials (AdMs) and they enable technological innovations that can benefit society. Despite their benefits, however, the unique characteristics of many AdMs, including many nanomaterials, are poorly understood and may pose environmental safety and occupational health (ESOH) risks that are not readily determined by traditional risk assessment methods.

Effects of soot by-product from the synthesis of engineered metallofullerene nanomaterials on terrestrial invertebrates.

The synthesis of carbon-based nanomaterials is often inefficient, generating large amounts of soot with metals as waste by-product. Currently, there are no specific regulations for disposal of engineered nanomaterials or the waste by-products resulting from their synthesis, so it is presumed that by-products are disposed of in the same way as the parent (bulk) materials. We studied the terrestrial toxicity of soot from gadolinium metallofullerene nanomanufacturing on earthworms (Eisenia fetida) and isopods (Porcellio scaber).

A weight-of-evidence approach to identify nanomaterials in consumer products: a case study of nanoparticles in commercial sunscreens.

Nanoscale ingredients in commercial products represent a point of emerging environmental concern due to recent findings that correlate toxicity with small particle size. A weight-of-evidence (WOE) approach based upon multiple lines of evidence (LOE) is developed here to assess nanomaterials as they exist in consumer product formulations, providing a qualitative assessment regarding the presence of nanomaterials, along with a baseline estimate of nanoparticle concentration if nanomaterials do exist. Electron microscopy, analytical separations, and X-ray detection methods were used to identify and characterize nanomaterials in sunscreen formulations.

Increasing the rate of hydrogen oxidation without increasing the overpotential: a bio-inspired iron molecular electrocatalyst with an outer coordination sphere proton relay.

Oxidation of hydrogen (H) to protons and electrons for energy production in fuel cells is currently catalyzed by platinum, but its low abundance and high cost present drawbacks to widespread adoption. Precisely controlled proton removal from the active site is critical in hydrogenase enzymes in nature that catalyze H oxidation using earth-abundant metals (iron and nickel). Here we report a synthetic iron complex, (Cp)Fe(PN P)(Cl), that serves as a precatalyst for the oxidation of H, with turnover frequencies of 290 s in fluorobenzene, under 1 atm of H using 1,4-diazabicyclo[2.

Nickel phosphine catalysts with pendant amines for electrocatalytic oxidation of alcohols.

Nickel phosphine complexes with pendant amines have been found to be electrocatalysts for the oxidation of primary and secondary alcohols, with turnover frequencies as high as 3.3 s(-1). These complexes are the first electrocatalysts for alcohol oxidation based on non-precious metals, which will be critical for use in fuel cells.

On the Teaching of Science, Technology and International Affairs.

Despite the ubiquity and critical importance of science and technology in international affairs, their role receives insufficient attention in traditional international relations curricula. There is little literature on how the relations between science, technology, economics, politics, law and culture should be taught in an international context. Since it is impossible even for scientists to master all the branches of natural science and engineering that affect public policy, the learning goals of students whose primary training is in the social sciences should be to get some grounding in the natural sciences or engineering, to master basic policy skills, to understand the basic concepts that link science and technology to their broader context, and to gain a respect for the scientific and technological dimensions of the broader issues they are addressing.

Synthesis and reactivity of molybdenum and tungsten bis(dinitrogen) complexes supported by diphosphine chelates containing pendant amines.

Molybdenum and tungsten bis(dinitrogen) complexes of the formula M(N(2))(2)(PNP)(2) (M = Mo and W) and W(N(2))(2)(dppe)(PNP), supported by diphosphine ligands containing a pendant amine of the formula (CH(2)PR(2))(2)NR' = P(R)N(R')P(R) (R = Et, Ph; R' = Me, Bn), have been prepared by Mg reduction of metal halides under an N(2) atmosphere. The complexes have been characterized by NMR and IR spectroscopy, X-ray crystallography, and cyclic voltammetry. Reactivity of the target Mo and W bis(dinitrogen) compounds with CO results in the formation of dicarbonyl complexes.

Efficacy of non-toxic surfaces to reduce bioadhesion in terrestrial gastropods.

Background: Invasive species are described as the greatest threat to biodiversity, after habitat destruction and climate change, potentially imposing economic impacts and indigenous species impairment. Commonly applied chemical controls present the potential for legacy contamination and non-target organism injury. This study investigated the effects of different substrates and novel topographical surfaces on the behavioral and mechanical associations of the terrestrial gastropod Otala lactea.

Skin and soft-tissue infections in suburban primary care: epidemiology of methicillin-resistant Staphylococcus aureus and observations on abscess management.

Background: Reports from urban medical centers suggest that methicillin-resistant Staphylococcus aureus (MRSA) has become the most common cause of skin and soft-tissue infections (SSTIs). Risk factors for MRSA have been identified but have not been clinically useful.

Findings: From May 2006-April 2007, we performed an observational study of 529 SSTIs among ambulatory patients in the urgent care departments of a large suburban primary-care practice.

Desorption of nitramine and nitroaromatic explosive residues from soils detonated under controlled conditions.

Potentially toxic nitroaromatic and nitramine compounds are introduced onto soils during detonation of explosives. The present study was conducted to investigate the desorption and transformation of explosive compounds loaded onto three soils through controlled detonation. The soils were proximally detonated with Composition B, a commonly used military explosive containing 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX).

Assessing the fate and effects of nano aluminum oxide in the terrestrial earthworm, Eisenia fetida.

Nano-sized aluminum is currently being used by the military and commercial industries in many applications including coatings, thermites, and propellants. Due to the potential for wide dispersal in soil systems, we chose to investigate the fate and effects of nano-sized aluminum oxide (Al2O3), the oxidized form of nano aluminum, in a terrestrial organism. The toxicity and bioaccumulation potential of micron-sized (50-200 microm, nominal) and nano-sized (11 nm, nominal) Al2O3 was comparatively assessed through acute and subchronic bioassays using the terrestrial earthworm, Eisenia fetida.

Sediment toxicity and bioaccumulation of nano and micron-sized aluminum oxide.

Nano-aluminum oxide (Al(2)O(3)) is used commercially in coatings and abrasives. Nano-Al(2)O(3) can also be generated through the oxidation of nano-aluminum in military propellants and energetics. The purpose of the present study was to assess toxicity and bioaccumulation of nano-Al(2)O(3) to a variety of sediment organisms (Tubifex tubifex, Hyalella azteca, Lumbriculus variegatus, and Corbicula fluminea).

Organozirconium complexes as catalysts for Markovnikov-selective intermolecular hydrothiolation of terminal alkynes: scope and mechanism.

The efficient and selective organozirconium(IV)-mediated, intermolecular hydrothiolation of terminal alkynes by aliphatic, benzylic, and aromatic thiols using CGCZrMe(2) (CGC = Me(2)SiCp'' NCMe(3), Cp'' = C(5)Me(4)), Cp*ZrBn(3) (Cp* = C(5)Me(5), Bn = benzyl), Cp*ZrCl(2)NMe(2), Cp*(2)ZrMe(2), and Zr(NMe(2))(4) precatalysts is reported. These transformations are shown to be highly Markovnikov-selective, with selectivities up to 99%, and typically in greater than 90% yields. The reaction has been demonstrated on the preparative scale with 72% isolated yield and 99% Markovnikov selectivity.

Organo-f-element catalysts for efficient and highly selective hydroalkoxylation and hydrothiolation.

Lanthanide and actinide catalysts have made significant contributions to many areas of homogeneous catalysis with hydroelementation of C-C unsaturation being a notable area of success. In this Perspective, we review recent advances in f-element hydroelementation for highly selective hydroalkoxylation and hydrothiolation processes. As will be discussed, f-element hydroalkoxylation and hydrothiolation catalysts exhibit selectivities unobtainable by many late transition metal complexes.

Investigating the fate of nitroaromatic (TNT) and nitramine (RDX and HMX) explosives in fractured and pristine soils.

Explosives compounds, known toxins, are loaded to soils on military training ranges predominantly during explosives detonation events that likely fracture soil particles. This study was conducted to investigate the fate of explosives compounds in aqueous slurries containing fractured and pristine soil particles. Three soils were crushed with a piston to emulate detonation-induced fracturing.

Release of metal impurities from carbon nanomaterials influences aquatic toxicity.

Few studies have considered the environmental impacts of impurities and byproducts associated with low-efficiency nanomanufacturing processes. Here, we study the composition and aquatic toxicity of low-purity, as-produced fullerenes (C60) and metallofullerene waste solids, both of which were generated via arc-discharge synthesis. Scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) and inductively coupled plasma mass spectroscopy (ICP-MS) were used to characterize the metals composition of the solid test materials and of aqueous leachates prepared by mixing test materials with waters of varying pH, hardness, and salinity.

Organoactinide-mediated hydrothiolation of terminal alkynes with aliphatic, aromatic, and benzylic thiols.

Atom-efficient organoactinide-catalyzed intermolecular hydrothiolation of terminal alkynes is achieved by Th(IV) and U(IV) complexes to yield vinyl sulfides. The conversion is highly Markovnikov selective and is capable of utilizing aromatic, benzylic, and aliphatic thiols. Kinetic measurements of the transformation mediated by Me(2)SiCp(2)''Th[CH(2)(TMS)](2) (1a; Cp'' = eta(5)-Me(4)C(5)) shows the reaction is zero-order in [thiol], first-order in [1a], first-order in [alkyne] at lower alkyne concentrations, and zero-order at higher [alkyne].

Factors influencing the partitioning and toxicity of nanotubes in the aquatic environment.

Carbon nanotubes (NTs) may be among the most useful engineered nanomaterials for structural applications but could be difficult to study in ecotoxicological evaluations using existing tools relative to nanomaterials with a lower aspect ratio. Whereas the hydrophobicity and van der Waals interactions of NTs may suggest aggregation and sedimentation in aquatic systems, consideration regarding how engineered surface modifications influence their environmental fate and toxicology is needed. Surface modifications (e.