Miracle-dz/UniFAR-FTUs huggingface dataset:
Explorer Sloppiness in spontaneously active neuronal networks

General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact openaccess@ed.ac. uk providing details, and we will remove access to the work immediately and investigate your claim. Various plasticity mechanisms, including experience-dependent, spontaneous, as well as homeostatic ones, continuously remodel neural circuits. Yet, despite fluctuations in the properties of single neurons and synapses, the behavior and function of neuronal assemblies are generally found to be very stable over time. This raises the important question of how plasticity is coordinated across the network. To address this, we investigated the stability of network activity in cultured rat hippocampal neurons recorded with high-density multielec-trode arrays over several days. We used parametric models to characterize multineuron activity patterns and analyzed their sensitivity to changes. We found that the models exhibited sloppiness, a property where the model behavior is insensitive to changes in many parameter combinations, but very sensitive to a few. The activity of neurons with sloppy parameters showed faster and larger fluctuations than the activity of a small subset of neurons associated with sensitive parameters. Furthermore, parameter sensitivity was highly correlated with firing rates. Finally, we tested our observations from cell cultures on an in vivo recording from monkey visual cortex and we confirm that spontaneous cortical activity also shows hallmarks of sloppy behavior and firing rate dependence. Our findings suggest that a small subnetwork of highly active and stable neurons supports group stability, and that this endows neuronal networks with the flexibility to continuously remodel without compromising stability and function.
Measurement of Muscle Strength in Haemodialysis Patients by Pinch and Hand Grip Strength and Comparison to Lean Body Mass Measured by Multifrequency Bio-Electrical Impedance

Background: Muscle weakness is a risk factor for mortality in haemodialysis (HD) patients; we wished to determine whether measuring the composition of the arm with bioimpedance was associated with arm muscle strength. Methods: We measured pinch strength (PS) and hand grip strength (HGS) in 250 adult HD patients with corresponding post-dialysis multifrequency bioelectrical assessments with segmental body analysis. Results: Mean age 64.0 ± 15.6, 66% male and 45.6% diabetic. The maximum HGS in the dominant or non-fistula arm was 18.9 ± 9.2 kg and PS 4.09 ± 1.96 kg respectively, with a correlation of r = 0.80, p < 0.001. HGS was associated with body cell mass (β 0.37, p < 0.001) and PS with appendicular muscle mass (β 0.06, p < 0.001). Both HGS and PS were independently associated with the ratio of extracellular water (ECW) to total body water (TBW); β -139.5, p = 0.024, β -44.8, p < 0.001 in the arm. The presence of an arterio-venous fistula increased the ECW/TBW ratio in the arm from 0.383 ± 0.009 to 0.390 ± 0.012, p < 0.05. Conclusion: Muscle strength measured by HGS and PS was associated with both markers of whole body and segmental body composition within the arm, particularly ECW/TBW. Bioimpedance measurements and assessment of muscle strength should be measured in the non-fistula arm.
Dynamical Evolution of Globular Cluster Systems Formed in Galaxy Mergers: Deep Hubble Space Telescope Advanced Camera for Surveys Imaging of Old and Intermediate-Age Globular Clusters in NGC 3610

The Advanced Camera for Surveys on board the Hubble Space Telescope has been used to obtain deep, high-resolution images of the giant elliptical galaxy NGC 3610, a well-established remnant of a dissipative galaxy merger. These observations supersede previous, shallower observations that revealed the presence of a population of metal-rich globular clusters of intermediate age (∼1.5-4 Gyr). We detect a total of 580 cluster candidates, 46% more than from the previous WFPC2 images. The new photometry strengthens the significance of the previously found bimodality of the color distribution of clusters. Peak colors in V - I are 0.93 ± 0.01 and 1.09 ± 0.01 for the blue and red subpopulations, respectively. The luminosity function of the inner 50% of the metal-rich ("red") population of clusters differs markedly from that of the outer 50%. In particular, the luminosity function of the inner 50% of the red clusters shows a flattening consistent with a turnover that is about 1.0 mag fainter than the turnover of the blue clusters. This is consistent with predictions of recent models of cluster disruption for the age range mentioned above and for metallicities that are consistent with the peak color of the red clusters, as predicted by population synthesis models. The radial surface density profile of red clusters follows that of the underlying galaxy light more closely than in "normal" elliptical galaxies, which is consistent with the intermediate-age nature of the red clusters. We determine the specific frequency of clusters in NGC 3610 and find a present-day value of SN = 1.4 ± 0.6. Using published age estimates for the diffuse light of NGC 3610, as well as cluster disruption models, we estimate that this value will increase to SN = 3.8 ± 1.7 at an age of 10 Gyr, which is consistent with typical SN values for "normal" elliptical galaxies. Our findings constitute further evidence in support of the notion that metal-rich cluster populations formed during major mergers involving gas-rich galaxies can evolve dynamically (through disruption processes) into the red, metal-rich cluster populations that are ubiquitous in normal giant ellipticals.
Immunological Effects of Bevacizumab-Based Treatment in Metastatic Colorectal Cancer

Objective: The efficacy of bevacizumab in metastatic colorectal cancer (mCRC) could be related not only to its well-known antiangiogenetic properties but also to a hypothetical effect on the immune system of the host. Methods: We enrolled mCRC patients treated with a bevacizumab-based first-line therapy. Lymphocyte and dendritic cell subsets were evaluated at baseline, 3rd and 6th cycle. The clinical efficacy was estimated as response rate and progression-free survival. Forty healthy subjects were used as reference. Results: Fifty-one patients were enrolled. In comparison with healthy subjects, they showed a decrease of T and B cell compartments. Bevacizumab ameliorated the impairment of lymphocyte subsets, especially for T cells. Responders showed a trend toward an increase of CD3 (p = 0.07) and CD4 (p = 0.05). Among patients with a progression-free survival >1 year, only CD19 (p = 0.033) and CD20 (p = 0.013) showed a significant increase. No baseline impairment and no significant modification of dendritic cells were found. Conclusion: Bevacizumab-based therapy is able to increase B and T cell compartments. The expansion of T lymphocytes could imply an amelioration of dendritic cell-presenting capacity. These effects correlate with a more favourable clinical outcome and could be taken into account in clinical protocols aimed at combining antiangiogenetic-therapy with immunotherapy in mCRC.
DSim, a Danish Parallel Corpus for Text Simplification

We present DSim, a new sentence aligned Danish monolingual parallel corpus extracted from 3701 pairs of news telegrams and corresponding professionally simplified short news articles. The corpus is intended for building automatic text simplification for adult readers. We compare DSim to different examples of monolingual parallel corpora, and we argue that this corpus is a promising basis for future development of automatic data-driven text simplification systems in Danish. The corpus contains both the collection of paired articles and a sentence aligned bitext, and we show that sentence alignment using simple tf*idf weighted cosine similarity scoring is on line with state―of―the―art when evaluated against a hand-aligned sample. The alignment results are compared to state of the art for English sentence alignment. We finally compare the source and simplified sides of the corpus in terms of lexical and syntactic characteristics and readability, and find that the one―to―many sentence aligned corpus is representative of the sentence simplifications observed in the unaligned collection of article pairs.
Robust Prostate Segmentation Using Intrinsic Properties of TRUS Images

Accurate segmentation is usually crucial in transrectal ultrasound (TRUS) image based prostate diagnosis; however, it is always hampered by heavy speckles. Contrary to the traditional view that speckles are adverse to segmentation, we exploit intrinsic properties induced by speckles to facilitate the task, based on the observations that sizes and orientations of speckles provide salient cues to determine the prostate boundary. Since the speckle orientation changes in accordance with a statistical prior rule, rotation-invariant texture feature is extracted along the orientations revealed by the rule. To address the problem of feature changes due to different speckle sizes, TRUS images are split into several arc-like strips. In each strip, every individual feature vector is sparsely represented, and representation residuals are obtained. The residuals, along with the spatial coherence inherited from biological tissues, are combined to segment the prostate preliminarily via graph cuts. After that, the segmentation is fine-tuned by a novel level sets model, which integrates 1) the prostate shape prior, 2) dark-to-light intensity transition near the prostate boundary, and 3) the texture feature just obtained. The proposed method is validated on two 2-D image datasets obtained from two different sonographic imaging systems, with the mean absolute distance on the mid gland images only 1.06±0.53 mm and 1.25±0.77 mm, respectively. The method is also extended to segment apex and base images, producing competitive results over the state of the art.
Injectional anthrax at a Scottish district general hospital

SUMMARY This retrospective, descriptive case-series reviews the clinical presentations and significant laboratory findings of patients diagnosed with and treated for injectional anthrax (IA) since December 2009 at Monklands Hospital in Central Scotland and represents the largest series of IA cases to be described from a single location. Twenty-one patients who fulfilled National Anthrax Control Team standardized case definitions of confirmed, probable or possible IA are reported. All cases survived and none required limb amputation in contrast to an overall mortality of 28% being experienced for this condition in Scotland. We document the spectrum of presentations of soft tissue infection ranging from mild cases which were managed predominantly with oral antibiotics to severe cases with significant oedema, organ failure and coagulopathy. We describe the surgical management, intensive care management and antibiotic management including the first description of daptomycin being used to treat human anthrax. It is noted that some people who had injected heroin infected with Bacillus anthracis did not develop evidence of IA. Also highlighted are biochemical and haematological parameters which proved useful in identifying deteriorating patients who required greater levels of support and surgical debridement.
Geographic Aspects of Photovoltaics in Europe: Contribution of the PVGIS Website

The photovoltaic geographic information system (PVGIS) is a web-based knowledge distribution system that provides climate data and tools needed for the performance assessment of photovoltaic (PV) technology in Europe. Geodatabases and simulation models are interlinked with the web interface, thus providing easy-to-use access to users. Interactive maps play an important role in understanding the geographic dependency of the performance of the PV technology. While our previous papers dealt with technical aspects of development and data analysis, here we review lessons learned from the feedback of users. A description of the underlying data and web tools is followed by the analysis of two points that are often discussed when comparing PVGIS with alternative systems: 1) the uncertainty of solar radiation estimates and 2) PV yield predictions. For systems based on the ground observations, such as PVGIS, higher uncertainty of estimates can be expected in mountains, close to the coastline, and in regions with lower density of the meteorological stations. A comparison of PVGIS with other simulation software may show regional differences, which typically reflect: 1) the use of underlying databases that are based on diverse input data (ground-measured or satellite with various observation periods) and that vary in spatial and time resolutions, and 2) the use of different simulation concepts. A cross comparison of the existing systems is needed to identify advantages and limits of their use in solar energy projects.
Is ‘Self-Medication’ a Useful Term to Retrieve Related Publications in the Literature? A Systematic Exploration of Related Terms

Background Self-Medication (SM), i.e. using medications to treat oneself, is a major concern for health researchers and policy makers. The terms “self medication” or “self-medication” (SM terms) have been used to explain various concepts while several terms have also been employed to define this practice. Hence, retrieving relevant publications would require exhaustive literature screening. So, we assessed the current situation of SM terms in the literature to improve the relevancy of search outcomes. Methods In this Systematic exploration, SM terms were searched in the 6 following databases and publisher’s portals till April 2012: Web of Science, Scopus, PubMed, Google scholar, ScienceDirect, and Wiley. A simple search query was used to include only publications with SM terms. We used Relative-Risk (RR) to estimate the probability of SM terms use in related compared to unrelated publications. Sensitivity and specificity of SM terms as keywords in search query were also calculated. Relevant terms to SM practice were extracted and their Likelihood Ratio positive and negative (LR+/-) were calculated to assess their effect on the probability of search outcomes relevancy in addition to previous search queries. We also evaluated the content of unrelated publications. All mentioned steps were performed in title (TI) and title or abstract (TIAB) of publications. Results 1999 related and 1917 unrelated publications were found. SM terms RR was 4.5 in TI and 2.1 in TIAB. SM terms sensitivity and specificity respectively were 55.4% and 87.7% in TI and 84.0% and 59.5% in TIAB. “OTC” and “Over-The-Counter Medication”, with LR+ 16.78 and 16.30 respectively, provided the most conclusive increase in the probability of the relevancy of publications. The most common unrelated SM themes were self-medication hypothesis, drug abuse and Zoopharmacognosy. Conclusions Due to relatively low specificity or sensitivity of SM terms, relevant terms should be employed in search queries and clear definitions of SM applications should be applied to improve the relevancy of publications.
MRI‐based myelin water imaging: A technical review

Multiexponential T2 relaxation time measurement in the central nervous system shows a component that originates from water trapped between the lipid bilayers of myelin. This myelin water component is of significant interest as it provides a myelin‐specific MRI signal of value in assessing myelin changes in cerebral white matter in vivo. In this article, the various acquisition and analysis strategies proposed to date for myelin water imaging are reviewed and research conducted into their validity and clinical applicability is presented. Comparisons between the imaging methods are made with a discussion regarding potential difficulties and model limitations. Magn Reson Med 73:70–81, 2015. © 2014 Wiley Periodicals, Inc.
The Neuroscience Literacy of Trainee Teachers

Background: There is concern about the prevalence of neuromyths in education, but little is known about how teachers think about the brain and how this may influence their practice. Aim: To further understanding of how teachers, at entry to the profession, think about brain development and function. Sample: 158 graduate trainee teachers at the end of their one-year course. Methods: Preliminary semi-structured interviews contributed to the development of a suitable survey instrument. Participants were then surveyed during one of their final lectures. Results: Trainees’ ideas reflected misconceptions in public circulation and notions promoted by popular brain-based educational programmes. Most of the trainee teachers in our survey did not accept, or were unsure, about whether mental activity derives from biological brain function. Trainee teachers place equal importance on home environment and education as determinants of educational outcome, with genetics a significant but smaller influence than either. A follow up survey with a new cohort of trainees confirmed that constructs about development are linked to a sense of agency, with beliefs in strong genetic influence associated with stronger notions of biologically-defined limits on pupil achievement. Conclusions: In the absence of formal training, trainee teachers acquire their own ideas about brain function, many of which are potentially detrimental to their practice as teachers. Neuroscience Literacy 3
A Tale of Two Perspectives: A Conceptual Framework of User Expectations and Experiences of Instructional Fitness Apps

We present a conceptual framework grounded in both users' reviews and HCI theories, residing between practices and theories as a form of intermediate-level knowledge in interaction design. Previous research has examined different forms of intermediary knowledge such as conceptual structures, strong concepts, and bridging concepts. Within HCI, these forms are generic and rise either from theories or particular instances. In this work, we created and evaluated a conceptual framework for a specific domain (instructional fitness apps). We first extracted the particular instances using users' online reviews and conceptualised them as an expectations and experiences framework. Second, within the framework, we evaluated the artefact related constructs using Norman's design principles. Third, we evaluated beyond the artefact related constructs using distributed cognition theory. We present an analysis of such intermediate-level knowledge with the aim of informing future designs.
The Anterior N1 Component as an Index of Modality Shifting

Abstract Processing of a given target is facilitated when it is defined within the same (e.g., visual–visual), compared to a different (e.g., tactile–visual), perceptual modality as on the previous trial [Spence, C. , Nicholls, M. , & Driver, J. The cost of expecting events in the wrong sensory modality. Perception & Psychophysics, 63, 330–336, 2001]. The present study was designed to identify electrocortical (EEG) correlates underlying this “modality shift effect. ” Participants had to discriminate (via foot pedal responses) the modality of the target stimulus, visual versus tactile (Experiment 1), or respond based on the target-defining features (Experiment 2). Thus, modality changes were associated with response changes in Experiment 1, but dissociated in Experiment 2. Both experiments confirmed previous behavioral findings with slower discrimination times for modality change, relative to repetition, trials. Independently of the target-defining modality, spatial stimulus characteristics, and the motor response, this effect was mirrored by enhanced amplitudes of the anterior N1 component. These findings are explained in terms of a generalized “modality-weighting” account, which extends the “dimension-weighting” account proposed by Found and Müller [Searching for unknown feature targets on more than one dimension: Investigating a “dimension-weighting” account. Perception & Psychophysics, 58, 88–101, 1996] for the visual modality. On this account, the anterior N1 enhancement is assumed to reflect the detection of a modality change and initiation of the readjustment of attentional weight-setting from the old to the new target-defining modality in order to optimize target detection.
Discriminative Syntax-Based Word Ordering for Text Generation

Word ordering is a fundamental problem in text generation. In this article, we study word ordering using a syntax-based approach and a discriminative model. Two grammar formalisms are considered: Combinatory Categorial Grammar (CCG) and dependency grammar. Given the search for a likely string and syntactic analysis, the search space is massive, making discriminative training challenging. We develop a learning-guided search framework, based on best-first search, and investigate several alternative training algorithms.The framework we present is flexible in that it allows constraints to be imposed on output word orders. To demonstrate this flexibility, a variety of input conditions are considered. First, we investigate a “pure” word-ordering task in which the input is a multi-set of words, and the task is to order them into a grammatical and fluent sentence. This task has been tackled previously, and we report improved performance over existing systems on a standard Wall Street Journal test set. Second, we tackle the same reordering problem, but with a variety of input conditions, from the bare case with no dependencies or POS tags specified, to the extreme case where all POS tags and unordered, unlabeled dependencies are provided as input (and various conditions in between). When applied to the NLG 2011 shared task, our system gives competitive results compared with the best-performing systems, which provide a further demonstration of the practical utility of our system.
Blur perception throughout the visual field in myopia and emmetropia

We evaluated the ability of emmetropic and myopic observers to detect and discriminate blur across the retina under monocular or binocular viewing conditions. We recruited 39 young (23–30 years) healthy adults (n = 19 myopes) with best-corrected visual acuity 0.0 LogMAR (20/20) or better in each eye and no binocular or accommodative dysfunction. Monocular and binocular blur discrimination thresholds were measured as a function of pedestal blur using naturalistic stimuli with an adaptive 4AFC procedure. Stimuli were presented in a 46° diameter window at 40 cm. Gaussian blur pedestals were confined to an annulus at either 0°, 4°, 8°, or 12° eccentricity, with a blur increment applied to only one quadrant of the image. The adaptive procedure efficiently estimated a dipper shaped blur discrimination threshold function with two parameters: intrinsic blur and blur sensitivity. The amount of intrinsic blur increased for retinal eccentricities beyond 4° (p < 0.001) and was lower in binocular than monocular conditions (p < 0.001), but was similar across refractive groups (p = 0.47). Blur sensitivity decreased with retinal eccentricity (p < 0.001) and was highest for binocular viewing, but only for central vision (p < 0.05). Myopes showed worse blur sensitivity than emmetropes monocularly (p < 0.05) but not binocularly (p = 0.66). As expected, blur perception worsens in the visual periphery and binocular summation is most evident in central vision. Furthermore, myopes exhibit a monocular impairment in blur sensitivity that improves under binocular conditions. Implications for the development of myopia are discussed.