Using natural language processing techniques to inform research on nanotechnology

Literature in the field of nanotechnology is exponentially increasing with more and more engineered nanomaterials being created, characterized, and tested for performance and safety. With the deluge of published data, there is a need for natural language processing approaches to semi-automate the cataloguing of engineered nanomaterials and their associated physico-chemical properties, performance, exposure scenarios, and biological effects. In this paper, we review the different informatics methods that have been applied to patent mining, nanomaterial/device characterization, nanomedicine, and environmental risk assessment. Nine natural language processing (NLP)-based tools were identified: NanoPort, NanoMapper, TechPerceptor, a Text Mining Framework, a Nanodevice Analyzer, a Clinical Trial Document Classifier, Nanotoxicity Searcher, NanoSifter, and NEIMiner. We conclude with recommendations for sharing NLP-related tools through online repositories to broaden participation in nanoinformatics

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

There is a critical opportunity in the field of nanoscience to compare and integrate information across diverse fields of study through informatics (i.e., nanoinformatics). This paper is one in a series of articles on the data curation process in nanoinformatics (nanocuration). Other articles in this series discuss key aspects of nanocuration (temporal metadata, data completeness, database integration), while the focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository. In particular, the article discusses: 1) the rationale and importance of a defined workflow in nanocuration, 2) the influence of organizational goals or purpose on the workflow, 3) established workflow practices in other fields, 4) current workflow practices in nanocuration, 5) key challenges for workflows in emerging fields like nanomaterials, 6) examples to make these challenges more tangible, and 7) recommendations to address the identified challenges. Throughout the article, there is an emphasis on illustrating key concepts and current practices in the field. Data on current practices in the field are from a group of stakeholders active in nanocuration. In general, the development of workflows for nanocuration is nascent, with few individuals formally trained in data curation or utilizing available nanocuration resources (e.g., ISA-TAB-Nano). Additional emphasis on the potential benefits of cultivating nanomaterial data via nanocuration processes (e.g., capability to analyze data from across research groups) and providing nanocuration resources (e.g., training) will likely prove crucial for the wider application of nanocuration workflows in the scientific community

The Influence of Start Position, Initial Step Type, and Usage of a Focal Point on Sprinting Performance

International Journal of Exercise Science 6(4) : 320-327, 2013. For many athletes, sprinting acceleration is vital to sport performance. The purpose of this study was to observe the influences of starting position, type of initial step taken, and a focal point on sprinting velocity, stride length, and acceleration over a 9.1 m distance. Two trials of four conditions were video recorded in which subjects had no focal point (n = 10) or a lateral focal point (n = 9). The four conditions were: forwards (control), backwards, 90° left (90°L), and 90° right (90°R). Lower velocities (p \u3e 0.05) were observed with focal point usage from the 90°R and 90°L starting positions. Four initial steps were observed during the forwards, 90°L, and 90°R conditions: backwards step, anterior tilt with forward step, pivot-crossover step, and lateral side step. The use of a backwards step resulted in an increased velocity (+0.80 m·s-1, p \u3c 0.01) for the 90° turn trials and increased acceleration (+ 0.37 m·s-2,p \u3c 0.01). Our results indicate that looking at a target can cause a decline in sprint velocity and acceleration over a short distance. Moreover, utilizing a backwards step to initiate a 90° turn may generate more power and force, increasing their velocity for short sprints. We recommend training athletes with a target or focal points to help combat the reduced speed and initiate movement with initial backwards step

Interactions between Magnetic Nanowires and Living Cells : Uptake, Toxicity and Degradation

We report on the uptake, toxicity and degradation of magnetic nanowires by NIH/3T3 mouse fibroblasts. Magnetic nanowires of diameters 200 nm and lengths comprised between 1 {\mu}m and 40 {\mu}m are fabricated by controlled assembly of iron oxide ({\gamma}-Fe2O3) nanoparticles. Using optical and electron microscopy, we show that after 24 h incubation the wires are internalized by the cells and located either in membrane-bound compartments or dispersed in the cytosol. Using fluorescence microscopy, the membrane-bound compartments were identified as late endosomal/lysosomal endosomes labeled with lysosomal associated membrane protein (Lamp1). Toxicity assays evaluating the mitochondrial activity, cell proliferation and production of reactive oxygen species show that the wires do not display acute short-term (< 100 h) toxicity towards the cells. Interestingly, the cells are able to degrade the wires and to transform them into smaller aggregates, even in short time periods (days). This degradation is likely to occur as a consequence of the internal structure of the wires, which is that of a non-covalently bound aggregate. We anticipate that this degradation should prevent long-term asbestos-like toxicity effects related to high aspect ratio morphologies and that these wires represent a promising class of nanomaterials for cell manipulation and microrheology.Comment: 21 pages 12 figure

Multicenter study evaluating the Vitek MS system for identification of medically important yeasts

The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates, including 58 C. albicans, 62 C. glabrata, and 53 C. krusei isolates), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n = 58) identified as Candida dubliniensis, one isolate of Candida parapsilosis (n = 73) identified as Candida pelliculosa, and three isolates of Geotrichum klebahnii (n = 6) identified as Geotrichum candidum. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation

Nanoparticles introduced in living cells are capable of strongly promoting the aggregation of peptides and proteins. We use here molecular dynamics simulations to characterise in detail the process by which nanoparticle surfaces catalyse the self- assembly of peptides into fibrillar structures. The simulation of a system of hundreds of peptides over the millisecond timescale enables us to show that the mechanism of aggregation involves a first phase in which small structurally disordered oligomers assemble onto the nanoparticle and a second phase in which they evolve into highly ordered beta-sheets as their size increases

Thyroid research: stepping forward.

It is eight years since Thyroid Research was launched with an aim to enhance opportunities for scientists and clinicians, working in the rapidly advancing field of thyroidology, to publish their research (Thyroid Res 1(1):1, 2008). Right from the outset, Thyroid Research aspired to become a prominent journal in thyroidology with high quality publications. Over the years, the journal has not only survived in the increasingly competitive field of open-access academic journal publication, it has also been making a steady progress towards achieving this ambitious goal. Now, Thyroid Research is ready to step forward to begin a new chapter in its publication.This article is freely available via Open Access. Click on the 'Additional Link' above to access the full-text from the publisher's site.Published

1,8-Bis(silylamido)naphthalene complexes of magnesium and zinc synthesized through alkane elimination reactions

The reactions between magnesium or zinc alkyls and 1,8-bis(triorganosilyl)diaminonaphthalenes afford the 1,8-bis(triorganosilyl)diamidonaphthalene complexes with elimination of alkanes. The reaction between 1,8-C10H6(NSiMePh2H)2 and one or two equivalents of MgnBu2 affords two complexes with differing coordination environments for the magnesium; the reaction between 1,8-C10H6(NSiMePh2H)2 and MgnBu2 in a 1:1 ratio affords 1,8-C10H6(NSiMePh2)2{Mg(THF)2} (1), which features a single magnesium centre bridging both ligand nitrogen donors, whilst treatment of 1,8-C10H6(NSiR3H)2 (R3 = MePh2, iPr3) with two equivalents of MgnBu2 affords the bimetallic complexes 1,8-C10H6(NSiR3)2{nBuMg(THF)}2 (R3 = MePh2 2, R3 = iPr3 3), which feature four-membered Mg2N2 rings. Similarly, 1,8-C10H6(NSiiPr3)2{MeMg(THF)}2 (4) and 1,8-C10H6(NSiMePh2)2{ZnMe}2 (5) are formed through reactions with the proligands and two equivalents of MMe2 (M = Mg, Zn). The reaction between 1,8-C10H6(NSiMePh2H)2 and two equivalents of MeMgX affords the bimetallic complexes 1,8-C10H6(NSiMePh2)2(XMgOEt2)2 (X = Br 6; X = I 7). Very small amounts of [1,8-C10H6(NSiMePh2)2{IMg(OEt2)}]2 (8), formed through the coupling of two diamidonaphthalene ligands at the 4-position with concomitant dearomatisation of one of the naphthyl arene rings, were also isolated from a solution of 7

Assessing Graphical Robot Aids for Interactive Co-working

The shift towards more collaborative working between humans and robots increases the need for improved interfaces. Alongside robust measures to ensure safety and task performance, humans need to gain the confidence in robot co-operators to enable true collaboration. This research investigates how graphical signage can support human–robot co-working, with the intention of increased productivity. Participants are required to co-work with a KUKA iiwa lightweight manipulator on a manufacturing task. The three conditions in the experiment differ in the signage presented to the participants – signage relevant to the task, irrelevant to the task, or no signage. A change between three conditions is expected in anxiety and negative attitudes towards robots; error rate; response time; and participants’ complacency, suggested by facial expressions. In addition to understanding how graphical languages can support human–robot co-working, this study provides a basis for further collaborative research to explore human–robot co-working in more detail

Multicenter evaluation of the vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of gram-positive aerobic bacteria

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting