Detection of IUPAC and IUPAC-like chemical names

Motivation: Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures for chemicals like SMILES, InChI, IUPAC or trivial names exist. Only SMILES and InChI names allow a direct structure search, but in biomedical texts trivial names and Iupac like names are used more frequent. While trivial names can be found with a dictionary-based approach and in such a way mapped to their corresponding structures, it is not possible to enumerate all IUPAC names. In this work, we present a new machine learning approach based on conditional random fields (CRF) to find mentions of IUPAC and IUPAC-like names in scientific text as well as its evaluation and the conversion rate with available name-to-structure tools

Mixed-signal circuits and boards for high safety applications

A design methodology for analogue on-line test is presented by means of a real circuit implementation. The test strategy is based on monitoring via a very small analogue checker the inputs of all operational ampliers of a fully di erential circuit. The self-checking properties of the functional circuit are evaluated for a hard/soft fault model. Since the analogue checker outputs a double-rail error indication, the compatibility with digital checkers is ensured and the design of self-checking mixed-signal circuits becomes very simple. The mixed-signal approach is extended toboards through the IEEE Std. 1149.1 digital test bus and a layout rule to avoid interconnect di erential shorts.

Echoic Sensory Substitution Information in a Single Obstacle Circumvention Task.

Accurate motor control is required when walking around obstacles in order to avoid collisions. When vision is unavailable, sensory substitution can be used to improve locomotion through the environment. Tactile sensory substitution devices (SSDs) are electronic travel aids, some of which indicate the distance of an obstacle using the rate of vibration of a transducer on the skin. We investigated how accurately such an SSD guided navigation in an obstacle circumvention task. Using an SSD, 12 blindfolded participants navigated around a single flat 0.6 x 2 m obstacle. A 3-dimensional Vicon motion capture system was used to quantify various kinematic indices of human movement. Navigation performance under full vision was used as a baseline for comparison. The obstacle position was varied from trial to trial relative to the participant, being placed at two distances 25 cm to the left, right or directly ahead. Under SSD guidance, participants navigated without collision in 93% of trials. No collisions occurred under visual guidance. Buffer space (clearance between the obstacle and shoulder) was larger by a factor of 2.1 with SSD guidance than with visual guidance, movement times were longer by a factor of 9.4, and numbers of velocity corrections were larger by a factor of 5 (all p<0.05). Participants passed the obstacle on the side affording the most space in the majority of trials for both SSD and visual guidance conditions. The results are consistent with the idea that SSD information can be used to generate a protective envelope during locomotion in order to avoid collisions when navigating around obstacles, and to pass on the side of the obstacle affording the most space in the majority of trials.Vision and Eye Research Unit, Postgraduate Medical Institute at Anglia Ruskin University; Medical Research Council (Grant ID: G0701870)This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/10.1371/journal.pone.016087

Indoor Air Quality Design and Control in Low-Energy Residential Buildings: Current challenges, selected case studies and innovative solutions covering indoor air quality, ventilation design and control in residences. International Energy Agency Report, Energy in Buildings and Communities Programme, IEA EBC Annex 68

The objective of Subtask 4 in the IEA EBC Annec 68 was to integrate knowledge and results from remaining Subtasks and present them in the context with current knowledge. The focus of the Subtask 4 was on practitioners dealing with ensuring high Indoor Air Quality (IAQ) in modern low-energy residences, the demands and challenges they meet during daily work. This especially includes architects and ventilation designers, facility managers, property developers and employees of public authorities. This publication is a result if Subtask 4’s work. It brings a collection of 24 “case studies” related to IAQ design and control in Low-Energy Residential Buildings. By a “case study” we mean a real life construction project, laboratory investigation or a simulation study that provides innovative approach. The case studies were selected to give the practitioners new insigts, inspiration and motivation to go along new paths leading to sustainable and comfortable homes of the future. The report is organized into three main chapters: “Ways to design residential ventilation in the future” and “Towards better performance and user satisfaction”. The descriptions of case studies are accompanied by “lessons learned” sections aiming directly at practical utilization of results as well as recommended future reading section providing the most important references

Bark beetle population dynamics in the Anthropocene: Challenges and solutions

Tree-killing bark beetles are the most economically important insects in conifer forests worldwide. However, despite N200 years of research, the drivers of population eruptions and crashes are still not fully understood and the existing knowledge is thus insufficient to face the challenges posed by the Anthropocene. We critically analyze potential biotic and abiotic drivers of population dynamics of an exemplary species, the European spruce bark beetle (ESBB) (Ips typographus) and present a multivariate approach that integrates the many drivers governing this bark beetle system. We call for hypothesis-driven, large-scale collaborative research efforts to improve our understanding of the population dynamics of this and other bark beetle pests. Our approach can serve as a blueprint for tackling other eruptive forest insects

A Framework to Account for the Effects of Visual Loss on Human Auditory Abilities

Until recently, a commonly held view was that blindness resulted in enhanced auditory abilities, underpinned by the beneficial effects of cross-modal neuroplasticity. This viewpoint has been challenged by studies showing that blindness results in poorer performance for some auditory spatial tasks. It is now clear that visual loss does not result in a general increase or decrease in all auditory abilities. Although several hypotheses have been proposed to explain why certain auditory abilities are enhanced while others are degraded, these are often limited to a specific subset of tasks. A comprehensive explanation encompassing auditory abilities assessed in fully blind and partially sighted populations and spanning spatial and non-spatial cognition has not so far been proposed. The current article proposes a framework comprising a set of nine principles that can be used to predict whether auditory abilities are enhanced or degraded. The validity of these principles is assessed by comparing their predictions with a wide range of empirical evidence concerning the effects of visual loss on spatial and non-spatial auditory abilities. Developmental findings and the effects of early- versus late-onset visual loss are discussed. Ways of improving auditory abilities for individuals with visual loss and reducing auditory spatial deficits are summarized. A new Perceptual Restructuring Hypothesis is proposed within the framework, positing that the auditory system is restructured to provide the most accurate information possible given the loss of the visual signal and utilizing available cortical resources, resulting in different auditory abilities getting better or worse according to the nine principles

An assessment of auditory-guided locomotion in an obstacle circumvention task

This study investigated how effectively audition can be used to guide navigation around an obstacle. Ten blindfolded normally sighted participants navigated around a 0.6 × 2 m obstacle while producing self-generated mouth click sounds. Objective movement performance was measured using a Vicon motion capture system. Performance with full vision without generating sound was used as a baseline for comparison. The obstacle’s location was varied randomly from trial to trial: it was either straight ahead or 25 cm to the left or right relative to the participant. Although audition provided sufficient information to detect the obstacle and guide participants around it without collision in the majority of trials, buffer space (clearance between the shoulder and obstacle), overall movement times, and number of velocity corrections were significantly (p < 0.05) greater with auditory guidance than visual guidance. Collisions sometime occurred under auditory guidance, suggesting that audition did not always provide an accurate estimate of the space between the participant and obstacle. Unlike visual guidance, participants did not always walk around the side that afforded the most space during auditory guidance. Mean buffer space was 1.8 times higher under auditory than under visual guidance. Results suggest that sound can be used to generate buffer space when vision is unavailable, allowing navigation around an obstacle without collision in the majority of trials

Auditory spatial representations of the world are compressed in blind humans

Compared to sighted listeners, blind listeners often display enhanced auditory spatial abilities such as localization in azimuth. However, less is known about whether blind humans can accurately judge distance in extrapersonal space using auditory cues alone. Using virtualization techniques, we show that auditory spatial representations of the world beyond the peripersonal space of blind listeners are compressed compared to those for normally sighted controls. Blind participants overestimated the distance to nearby sources, and underestimated the distance to remote sound sources, in both reverberant and anechoic environments, and for speech, music and noise signals. Functions relating judged and actual virtual distance were well fitted by compressive power functions, indicating that the absence of visual information regarding the distance of sound sources may prevent accurate calibration of the distance information provided by auditory signals

Automated annotation of chemical names in the literature with tunable accuracy

<p>Abstract</p> <p>Background</p> <p>A significant portion of the biomedical and chemical literature refers to small molecules. The accurate identification and annotation of compound name that are relevant to the topic of the given literature can establish links between scientific publications and various chemical and life science databases. Manual annotation is the preferred method for these works because well-trained indexers can understand the paper topics as well as recognize key terms. However, considering the hundreds of thousands of new papers published annually, an automatic annotation system with high precision and relevance can be a useful complement to manual annotation.</p> <p>Results</p> <p>An automated chemical name annotation system, MeSH Automated Annotations (MAA), was developed to annotate small molecule names in scientific abstracts with tunable accuracy. This system aims to reproduce the MeSH term annotations on biomedical and chemical literature that would be created by indexers. When comparing automated free text matching to those indexed manually of 26 thousand MEDLINE abstracts, more than 40% of the annotations were false-positive (FP) cases. To reduce the FP rate, MAA incorporated several filters to remove "incorrect" annotations caused by nonspecific, partial, and low relevance chemical names. In part, relevance was measured by the position of the chemical name in the text. Tunable accuracy was obtained by adding or restricting the sections of the text scanned for chemical names. The best precision obtained was 96% with a 28% recall rate. The best performance of MAA, as measured with the F statistic was 66%, which favorably compares to other chemical name annotation systems.</p> <p>Conclusions</p> <p>Accurate chemical name annotation can help researchers not only identify important chemical names in abstracts, but also match unindexed and unstructured abstracts to chemical records. The current work is tested against MEDLINE, but the algorithm is not specific to this corpus and it is possible that the algorithm can be applied to papers from chemical physics, material, polymer and environmental science, as well as patents, biological assay descriptions and other textual data.</p