Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture1[W][OA]

We present in this paper a novel, semiautomated image-analysis software to streamline the quantitative analysis of root growth and architecture of complex root systems. The software combines a vectorial representation of root objects with a powerful tracing algorithm that accommodates a wide range of image sources and quality. The root system is treated as a collection of roots (possibly connected) that are individually represented as parsimonious sets of connected segments. Pixel coordinates and gray level are therefore turned into intuitive biological attributes such as segment diameter and orientation as well as distance to any other segment or topological position. As a consequence, user interaction and data analysis directly operate on biological entities (roots) and are not hampered by the spatially discrete, pixel-based nature of the original image. The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements. The use of the software is illustrated with a time-lapse analysis of cluster root formation in lupin (Lupinus albus) and an architectural analysis of the maize (Zea mays) root system. The software, SmartRoot, is an operating system-independent freeware based on ImageJ and relies on cross-platform standards for communication with data-analysis software.
Brand leadership and product innovation as firm strategies in global food markets

Purpose – This paper aims to understand the motivations for product innovation and brand leadership using a series of case studies focusing on firms with leading market positions of different types.Design/methodology/approach – A qualitative study is presented of three leading food sector firms of different types (large/public, medium/private, and international/cooperative). An analysis of brand leadership is undertaken in the context of a conceptual framework linking process innovation, product innovation, and the firm's resource base and market orientation.Findings – The cases suggest that process innovation supports product innovation as firms implement strategies to differentiate their products. Response to changing demand is a disciplined reaction where firms exploit their specialized resources using superior product knowledge and branding power. Leadership positions are maintained not only by responding to changing demand but by steering the market using innovative products and consumer education.Re.
G1/S Arrest Induced by Histone Deacetylase Inhibitor Sodium Butyrate in E1A + Ras-transformed Cells Is Mediated through Down-regulation of E2F Activity and Stabilization of β-Catenin*

Tumor cells are often characterized by a high and growth factor-independent proliferation rate. We have previously shown that REF cells transformed with oncogenes E1A and c-Ha-Ras do not undergo G1/S arrest of the cell cycle after treatment with genotoxic factors. In this work, we used sodium butyrate, a histone deacetylase inhibitor, to show that E1A + Ras transformants were able to stop proliferation and undergo G1/S arrest. Apart from inducing G1/S arrest, sodium butyrate was shown to change expression of a number of cell cycle regulatory genes. It down-regulated cyclins D1, E, and A as well as c-myc and cdc25A and up-regulated the cyclin-kinase inhibitor p21waf1. Accordingly, activities of cyclin E-Cdk2 and cyclin A-Cdk2 complexes in sodium butyrate-treated cells were decreased substantially. Strikingly, E2F1 expression was also down-modulated at the levels of gene transcription, the protein content, and the E2F transactivating capability. To further study the role of p21waf1 in the sodium butyrate-induced G1/S arrest and the E2F1 down-modulation, we established E1A + Ras transformants from mouse embryo fibroblast cells with deletion of the cdkn1a (p21waf1) gene. Despite the absence of p21waf1, sodium butyrate-treated mERas transformants reveal a slightly delayed G1/S arrest as well as down-modulation of E2F1 activity, implying that the observed effects are mediated through an alternative p21waf1-independent signaling pathway. Subsequent analysis showed that sodium butyrate induced accumulation of β-catenin, a downstream component of the Wnt signaling. The results obtained indicate that the antiproliferative effect of histone deacetylase inhibitors on E1A + Ras-transformed cells can be mediated, alongside other mechanisms, through down-regulation of E2F activity and stabilization of β-catenin.
Plasmonic Metasurface for Directional and Frequency-Selective Thermal Emission

Incandescent sources typically emit broadband light in all directions. Most of this radiation is lost for applications in the infrared region, such as spectroscopy or compositional analysis. Here the authors control both the spatial and temporal coherence of blackbody radiation with a plasmonic metasurface that emits a narrow band of frequencies in a small solid angle. This system operates reliably at 600 \ifmmode^\circ\else\textdegree\fi{}C using CMOS-compatible materials, inviting the development of compact, efficient, and cheap infrared sources and gas detectors.
Determination of toxic carbonyl compounds in cigarette smoke

Toxic carbonyl compounds, including formaldehyde, malonaldehyde, and glyoxal, formed in mainstream cigarette smoke were quantified by derivatization—solid phase extraction—gas chromatography methods. Cigarette smoke from 14 commercial brands and one reference (2R1F) was drawn into a separatory funnel containing aqueous phosphate‐buffered saline. Reactive carbonyl compounds trapped in the buffer solution were derivatized into stable nitrogen containing compounds (pyrazoles for β‐dicarbonyl and α,β‐unsaturated aldehyde; quinoxalines for α‐dicarbonyls; and thiazolidines for alkanals). After derivatives were recovered using C18 solid phase extraction cartridges, they were analyzed quantitatively by a gas chromatograph with a nitrogen phosphorus detector. The total carbonyl compounds recovered from regular size cigarettes ranged from 1.92 mg/cigarette−1 to 3.14 mg/cigarette−1. The total carbonyl compounds recovered from a reference cigarette and a king size cigarette were 3.23 mg/cigarette−1 and 3.39 mg/cigarette−1, respectively. The general decreasing order of the carbonyl compounds yielded was acetaldehyde (1110–2101 μg/cigarette−1) > diacetyl (301–433 μg/cigarette−1), acrolein (238–468 μg/cigarette−1) > formaldehyde (87.0–243 μg/cigarette−1), propanal (87.0–176 μg/cigarette−1) > malonaldehyde (18.9–36.0 μg/cigarette−1), methylglyoxal (13.4–59.6 μg/cigarette−1) > glyoxal (1.93–6.98 μg/cigarette−1). © 2006 Wiley Periodicals, Inc. Environ Toxicol 21: 47–54, 2006.
Design and Evaluation of a Prototype Rear Obstacle Detection and Driver Warning System

This study, concerned with the development of driver interface criteria for a rear obstacle detection system, assessed the appropriateness of alternative warning timing algorithms and evaluated various interface approaches for presenting warning information to drivers. Interface testing used a minivan and a passenger sedan equipped with a prototype rear obstacle detection system. Two different warning timing algorithms and four different interface conditions were examined. The appropriateness of the warning timing algorithms was tested using an alerted backing procedure wherein drivers backed to known obstacles and braked in response to the warning. A surprise event scenario was also included in order to examine driver reaction to the warning under unexpected conditions. Alerted backing results suggest that although both timing algorithms led to few target strikes, one algorithm led to more acceptable ratings, fewer target strikes and close calls, and less urgent braking. None of the interface warning conditions reliably induced avoidance braking under the surprise event condition. Actual or potential applications of this work include the appropriate design of effective backing warning systems.
Repeats, Reformulations, and Emotional Speech: Evidence for the Design of Human-Computer Speech Interfaces

Firstly, the acoustic characteristics of the users’ utterances have been found to be very different if they constitute repetitions or reformulations of previous utterances. That is, if the system claims not to have understood a contribution by the speaker, the speaker will repeat his utterance, however, usually with a different stress pattern, different phrasal intonation, with a strong emphasis on exact pronunciation or even hyper−articulation, and short pauses between the words. Some of these properties may cause severe problems for current automatic speech processing systems; for instance, Levow (1998) describes that the error rate in speech recognition rises from 16% to 44% for repetitions. That means that the characteristics of an utterance are very different if it constitutes a repetition of a previous contribution, and that these differences cannot be neglected in human−computer interaction (HCI).
Retrieval of Cloud Optical Properties From Multiple Infrared Hyperspectral Measurements: A Methodology Based on a Line-by-Line Multiple-Scattering Code

A methodology to retrieve cloud optical properties using high spectral resolution (HSR) infrared (IR) measurements is presented. This new method has the ability to easily adapt to multiple instruments and viewing angles. The retrieval uses a line-by-line multiple-scattering simulation and HSR IR measurements to retrieve spectrally resolved cloud optical depths (ODs). The spectral ODs are compared to a precomputed OD database generated from an ensemble of cloud particle-size distributions and precomputed single-scattering and single-particle optical properties for a variety of ice-crystal habits. Cloud microphysics are retrieved by finding the closest fit to the database. Results are independent of first-guess optical property assumptions on size and habit. The retrieval method has been applied to aircraft, satellite, and uplooking HSR measurements with results evaluated against coincident HSR lidar and radar measurements. Analysis of retrieval errors produced by assumptions and uncertainties in the atmospheric state demonstrates different sensitivities to atmospheric parameters when uplooking or downlooking data are analyzed. For both viewing geometries, the retrieval is most sensitive to the uncertainties in the assumed cloud boundaries. It is also found that nonuniform vertical distribution of cloud OD can result in significant biases in the IR retrieved cloud ODs.
Dissociating between object affordances and spatial compatibility effects using early response components

Perception and action are tightly linked: objects may be perceived not only in terms of visual features, but also in terms of possibilities for action. Previous studies showed that when a centrally located object has a salient graspable feature (e.g., a handle), it facilitates motor responses corresponding with the feature's position. However, such so-called affordance effects have been criticized as resulting from spatial compatibility effects, due to the visual asymmetry created by the graspable feature, irrespective of any affordances. In order to dissociate between affordance and spatial compatibility effects, we asked participants to perform a simple reaction-time task to typically graspable and non-graspable objects with similar visual features (e.g., lollipop and stop sign). Responses were measured using either electromyography (EMG) on proximal arm muscles during reaching-like movements, or with finger key-presses. In both EMG and button press measurements, participants responded faster when the object was either presented in the same location as the responding hand, or was affordable, resulting in significant and independent spatial compatibility and affordance effects, but no interaction. Furthermore, while the spatial compatibility effect was present from the earliest stages of movement preparation and throughout the different stages of movement execution, the affordance effect was restricted to the early stages of movement execution. Finally, we tested a small group of unilateral arm amputees using EMG, and found residual spatial compatibility but no affordance, suggesting that spatial compatibility effects do not necessarily rely on individuals' available affordances. Our results show dissociation between affordance and spatial compatibility effects, and suggest that rather than evoking the specific motor action most suitable for interaction with the viewed object, graspable objects prompt the motor system in a general, body-part independent fashion.
Estimating rigidity index ( IR ) based on CPT measurements

The rigidity index (IR) is defined as the ratio of the shear modulus (G) to the undrained soil strength (su) and is a critical parameter for estimating the consolidation coefficient (ch) using cone data. IR has also been shown to influence the stresses and pore pressures that develop around an advancing cone. The most accurate method to determine IR is through the use of advanced laboratory tests on high quality samples, though simplified methods do exist (such as chart solutions based on stress history and plasticity). Since cone tests and in-situ correlations are commonly used, a new method is proposed that only requires use of cone data; no complimentary laboratory tests or field sampling is required. A database of laboratory and cone tests from several clay sites was used to evaluate existing methods and to develop a new method for predicting IR using only cone test data. 3 International Symposium on Cone Penetration Testing, Las Vegas, Nevada, USA 2014
The spatial distribution of MR imaging abnormalities in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy and their relationship to age and clinical features.

BACKGROUND AND PURPOSE Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a condition causing recurrent subcortical strokes. MR imaging, which shows focal lacunar infarcts and leukoaraiosis, plays a central role in the diagnosis and evaluation. We studied MR imaging abnormalities in a large prospectively recruited cohort of CADASIL patients to describe the spatial distribution of abnormalities, determine how this distribution alters with age, and identify any correlations with the clinical features of the disease. METHODS In this study, 112 CADASIL subjects from 64 families were prospectively recruited. MR imaging scans were graded by a single neuroradiologist, by using the modified Scheltens scale, to quantify the severity of high-signal-intensity changes in different brain regions. RESULTS Lesion load increased progressively with age. Scores were maximal in the frontal, parietal, and anterior temporal cortex, and the external capsule; intermediate in the pons; and relatively low in the corpus callosum, caudate, globus pallidus, cerebellum, midbrain, and medulla. Anterior temporal pole involvement was common at all ages and, when present, usually confluent, but this was absent in 33% of patients 20-29 years of age. A history of stroke correlated with total Scheltens score and internal capsule and pontine scores. Dementia correlated with total Scheltens score and subcortical white matter score, whereas depression correlated with subcortical white matter score but not total Scheltens score. CONCLUSIONS There is a characteristic pattern of MR imaging abnormalities in CADASIL that aids in differential diagnosis; however, some characteristic features, such as anterior temporal pole involvement, can be absent. MR imaging lesion load correlated with some clinical features including stroke and dementia, whereas depression is more common in individuals with deep white matter changes.
Porosity formation mechanisms in cold metal transfer (CMT) gas metal arc welding (GMAW) of zinc coated steels

The porosity formation in cold metal transfer (CMT) gas metal arc welding (GMAW) of zinc coated steel is studied over a wide range of the heat inputs (160–250 J mm− 1), which shows low porosity in weld bead ( < 2% of bead area) in low ( < 250 J mm− 1) and high (>350 J mm− 1) heat inputs and maximum at medium (250–350 J mm− 1) heat inputs. The high speed imaging of weld pool shows that the highest frequency of zinc vapour escapes at high heat inputs compared to other conditions. Numerous experiments show that size and location of pores along with escaping of zinc vapour are the results of competition of viscosity of weld pool against buoyancy and vapour pressure within the time required to reach solidification temperature. Based on this concept, mechanisms involved in porosity formation, growth and escape phenomena are disclosed, which can help select the optimised welding conditions to obtain porosity free welds in CMT-GMAW of zinc coated steels.
How well do final year undergraduate medical students master practical clinical skills?

Introduction: The clinical examination and other practical clinical skills are fundamental to guide diagnosis and therapy. The teaching of such practical skills has gained significance through legislative changes and adjustments of the curricula of medical schools in Germany. We sought to find out how well final year undergraduate medical students master practical clinical skills. Methods: We conducted a formative 4-station objective structured clinical examination (OSCE) focused on practical clinical skills during the final year of undergraduate medical education. Participation was voluntary. Besides the examination of heart, lungs, abdomen, vascular system, lymphatic system as well as the neurological, endocrinological or orthopaedic examination we assessed other basic clinical skills (e.g. interpretation of an ECG, reading a chest X-ray). Participants filled-out a questionnaire prior to the exam, inter alia to give an estimate of their performance. Results: 214 final year students participated in our study and achieved a mean score of 72.8% of the total score obtainable. 9.3% of participants (n=20) scored insufficiently (<60%). We found no influence of sex, prior training in healthcare or place of study on performance. Only one third of the students correctly estimated their performance (35.3%), whereas 30.0% and 18.8% over-estimated their performance by 10% and 20% respectively. Discussion: Final year undergraduate medical students demonstrate considerable deficits performing practical clinical skills in the context of a formative assessment. Half of the students over-estimate their own performance. We recommend an institutionalised and frequent assessment of practical clinical skills during undergraduate medical education, especially in the final year.
On the structure and homogeneity of solid solutions: The limits of conventional X-ray diffraction

Abstract The characterization of solid solutions by conventional X-ray diffraction (XRD) is critically assessed using the example of Cu-Co alloys. In particular, the limits of this technique for investigating compositional inhomogeneities are discussed. Coherent Cu-Co multilayer films are taken as a model for a decomposed solid solution, with the layer thicknesses being taken as representative for the sizes of heterogeneous domains. It is shown that the XRD patterns of these multilayer films continuously change with decreasing layer thickness from that of two bulk phases to a single pattern identical to that of a homogeneous solid solution, the transition occurring at a layer thickness of about 10 nm. Below this layer thickness, the lattice spacing derived from the single diffraction pattern exhibits an average value determined by the overall composition. By definition, this average lattice spacing varies continuously between the pure elements with a Vegard law dependence when the overall composition is c.
Household CO and PM measured as part of a review of China's National Improved Stove Program.

UNLABELLED In 2001-2003, a team of researchers from the United States and China performed an independent, multidisciplinary review of China's National Improved Stove Program carried out since the 1980s. As part of a 3500-household survey, a subsample of 396 rural households were monitored for particulate matter less than 4 microm (PM(4)) in kitchens and living rooms over 24 h, of which 159 were measured in both summer and winter. Carbon monoxide was measured in a 40% subsample. The results of this indoor air quality (IAQ) component indicate that for nearly all household stove or fuel groupings, PM(4) levels were higher than - and sometimes more than twice as high as - the national PM(10) standard for indoor air (150 microg PM(10)/m(3)). If these results are typical, then a large fraction of China's rural population is now chronically exposed to levels of pollution far higher than those determined by the Chinese government to harm human health. Further, we observed highly diverse fuel usage patterns in these regions in China, supporting the observations in the household survey of multiple stoves being present in many kitchens. Improved stoves resulted in reduced PM(4) from biomass fuel combinations, but still not at levels that meet standards, and little improvement was observed in indoor pollution levels when other unimproved stoves were present in the same kitchen. As many households change fuels according to daily and seasonal factors, resulting in different seasonal concentrations in living rooms and kitchens, assessing health implications from fuel use requires longitudinal evaluation of fuel use and IAQ levels, combined with accurate time-activity information. PRACTICAL IMPLICATIONS Leaving aside the difficult issue of enforcement, it is uncertain whether Chinese household IAQ standards represent realistic objectives for current attainment given current patterns of energy consumption in rural China, which rely so heavily on unprocessed solid fuels. Even when used with chimneys, these fuels emit substantial pollution into the household environment. It is probable that low-emission technologies involving gaseous/liquid fuels or high combustion - efficiency biomass stoves need to be promoted in order to achieve these standards for the greater part of the population.
Cigarette Smoking Accelerated Brain Aging and Induced Pre-Alzheimer-Like Neuropathology in Rats

Cigarette smoking has been proposed as a major risk factor for aging-related pathological changes and Alzheimer's disease (AD). To date, little is known for how smoking can predispose our brains to dementia or cognitive impairment. This study aimed to investigate the cigarette smoke-induced pathological changes in brains. Male Sprague-Dawley (SD) rats were exposed to either sham air or 4% cigarette smoke 1 hour per day for 8 weeks in a ventilated smoking chamber to mimic the situation of chronic passive smoking. We found that the levels of oxidative stress were significantly increased in the hippocampus of the smoking group. Smoking also affected the synapse through reducing the expression of pre-synaptic proteins including synaptophysin and synapsin-1, while there were no changes in the expression of postsynaptic protein PSD95. Decreased levels of acetylated-tubulin and increased levels of phosphorylated-tau at 231, 205 and 404 epitopes were also observed in the hippocampus of the smoking rats. These results suggested that axonal transport machinery might be impaired, and the stability of cytoskeleton might be affected by smoking. Moreover, smoking affected amyloid precursor protein (APP) processing by increasing the production of sAPPβ and accumulation of β–amyloid peptide in the CA3 and dentate gyrus region. In summary, our data suggested that chronic cigarette smoking could induce synaptic changes and other neuropathological alterations. These changes might serve as evidence of early phases of neurodegeneration and may explain why smoking can predispose brains to AD and dementia.