Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of Physiological Oscillation Frequencies in a Computer Model of Neocortex

Coordination of neocortical oscillations has been hypothesized to underlie the “binding” essential to cognitive function. However, the mechanisms that generate neocortical oscillations in physiological frequency bands remain unknown. We hypothesized that interlaminar relations in neocortex would provide multiple intermediate loops that would play particular roles in generating oscillations, adding different dynamics to the network. We simulated networks from sensory neocortex using nine columns of event-driven rule-based neurons wired according to anatomical data and driven with random white-noise synaptic inputs. We tuned the network to achieve realistic cell firing rates and to avoid population spikes. A physiological frequency spectrum appeared as an emergent property, displaying dominant frequencies that were not present in the inputs or in the intrinsic or activated frequencies of any of the cell groups. We monitored spectral changes while using minimal dynamical perturbation as a methodology through gradual introduction of hubs into individual layers. We found that hubs in layer 2/3 excitatory cells had the greatest influence on overall network activity, suggesting that this subpopulation was a primary generator of theta/beta strength in the network. Similarly, layer 2/3 interneurons appeared largely responsible for gamma activation through preferential attenuation of the rest of the spectrum. The network showed evidence of frequency homeostasis: increased activation of supragranular layers increased firing rates in the network without altering the spectral profile, and alteration in synaptic delays did not significantly shift spectral peaks. Direct comparison of the power spectra with experimentally recorded local field potentials from prefrontal cortex of awake rat showed substantial similarities, including comparable patterns of cross-frequency coupling.
Multiscale modelling of dislocation/grain boundary interactions. II. Screw dislocations impinging on tilt boundaries in Al

The interaction of dislocations with grain boundaries (GBs) determines a number of important aspects of the mechanical performance of materials, including strengthening and fatigue resistance. Here, the coupled atomistic/discrete-dislocation (CADD) multiscale method, which couples a discrete dislocation continuum region to a fully atomistic region, is used to study screw-dislocations interacting with Σ3, Σ11, and Σ9 symmetric tilt boundaries in Al. The low-energy Σ3 and Σ11 boundaries absorb lattice dislocations and generate extrinsic grain boundary dislocations (GBDs). As multiple screw dislocations impinge on the GB, the GBDs form a pile-up along the GB and provide a back stress that requires increasing applied load to push the lattice dislocations into the GB. Dislocation transmission is never observed, even with large GBD pile-ups near the dislocation/GB intersection. Results are compared with experiments and previous, related simulations. The Σ9 grain boundary, composed from a more complex set of structural units, absorbs screw dislocations that remain localized, with no GBD formation. With increasing applied stress, new screw dislocations are then nucleated into the opposite grain from structural units in the GB that are nearby but not at the location where the original dislocation intersected the boundary. The detailed behaviour depends on the precise location of the incident dislocations and the extent of the pile-up. Transmission can occur on both Schmid and non-Schmid planes and can depend on the shear stresses on the GB plane. A continuum yield locus for transmission is formulated. In general, the overall dissociation and/or transmission behaviour is also determined by the Burgers vectors and associated steps of the primitive vectors of the grain boundary, and the criteria for dislocation transmission formulated by Lee et al . [Scripta Metall. 23 799 (1989); Phil. Mag. A 62 131 (1990); Metall. Trans. A 21 2437 (1990)] are extended to account for these factors.
On the Rule-Based Parsing of Czech

This paper presents various attempts to accustom the Rule-based Approach (RBA) as originally introduced by Eric Brill in 1993 (Brill 1993a), on the problem of parsing of Czech (a highly inflective language) within a dependency based syntactic framework (Sgall et al 1986). It is experimentally supported in this paper that the modification of RBA for the stated aim is neither simple nor straightforward for all attempts fail to produce such a set of rules that parses Czech with a comparable success rate to the one obtained for English or the one obtained for the currently best parser (statistical) for Czech (Collins et al. 1999).
Information Processing in Digital Holographic Microscopy

Digital holography is a new three-dimensional imaging technology. The recording conditions of hologram in off-axis Fresnel transform digital holography with pre-magnification are analyzed. The experimental setup used for recording the digital hologram of microscopic object is built. The numerical reconstruction methods of digital hologram disturbed by strong noise are studied experimentally. The intensity and phase image of the USAF test target is obtained by Fresnel transform algorithm. The lateral resolution of and axial resolution of no larger than 10 nm are achieved. The results show that for strong noisy hologram the automatic phase compensation method must be combined with manual adjusting parameter in order to obtain accurate phase image.
De Novo Computational Design of Retro-Aldol Enzymes

The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.
Genomic Prediction of Breeding Values when Modeling Genotype × Environment Interaction using Pedigree and Dense Molecular Markers

Genomic selection (GS) has become an important aid in plant and animal breeding. Multienvironment (multitrait) models allow borrowing of information across environments (traits), which could enhance prediction accuracy. This study presents multienvironment (multitrait) models for GS and compares the predictive accuracy of these models with: (i) multienvironment analysis without pedigree and marker information, and (ii) multienvironment pedigree or/and marker-based models. A statistical framework for incorporating pedigree and molecular marker information in models for multienvironment data is described and applied to data that originate from wheat (Triticum aestivum L.) multienvironment trials. Two prediction problems relevant to plant breeders are considered: (CV1) predicting the performance of untested genotypes ("newly" developed lines), and (CV2) predicting the performance of genotypes that have been evaluated in some environments but not in others. Results confi rmed the superiority of models using both marker and pedigree information over those based on pedigree information only. Models with pedigree and/or markers had better predictive accuracy than simple linear mixed models that do not include either of these two sources of information. We concluded that the evaluation of such trials can benefi t greatly from using multienvironment GS models.
Deriving Linear and Adjoint Codes for CFD using Automatic Dierentiation

Sensitivity analysis is a research area of increasing interest within CFD. Recent developments in Automatic Differentiation software (AD) make the discrete adjoint methods particularly attractive. We outline the theory of adjoint sensitivities and discuss how to use AD to derive adjoint versions from CFD codes. In particular we review the properties of the four major AD packages, we explain how to prepare the code for AD, how to treat Runge-Kutta timestepping, how to validate the derived code and how to optimise the CFD code such as to improve the performance of the derived code
External Validation of the MRI-DRAGON Score: Early Prediction of Stroke Outcome after Intravenous Thrombolysis

Background and Purpose The aim of our study was to validate in an independent cohort the MRI-DRAGON score, an adaptation of the (CT-) DRAGON score to predict 3-month outcome in acute ischemic stroke patients undergoing MRI before intravenous thrombolysis (IV-tPA). Methods We reviewed consecutive (2009–2013) anterior circulation stroke patients treated within 4.5 hours by IV-tPA in the Lille stroke unit (France), where MRI is the first-line pretherapeutic work-up. We assessed the discrimination and calibration of the MRI-DRAGON score to predict poor 3-month outcome, defined as modified Rankin Score >2, using c-statistic and the Hosmer-Lemeshow test, respectively. Results We included 230 patients (mean ±SD age 70.4±16.0 years, median [IQR] baseline NIHSS 8 [5]–[14]; poor outcome in 78(34%) patients). The c-statistic was 0.81 (95%CI 0.75–0.87), and the Hosmer-Lemeshow test was not significant (p = 0.54). Conclusions The MRI-DRAGON score showed good prognostic performance in the external validation cohort. It could therefore be used to inform the patient's relatives about long-term prognosis and help to identify poor responders to IV-tPA alone, who may be candidates for additional therapeutic strategies, if they are otherwise eligible for such procedures based on the institutional criteria.
Back to the Future: Modeling Time Dependence in Binary Data

Since Beck, Katz, and Tucker (1998), the standard method for modeling time dependence in binary data has been to incorporate time dummies or splined time in logistic regressions. Although we agree with the need for modeling time dependence, we demonstrate that time dummies can induce estimation problems due to separation. Splines do not suffer from these problems. However, the complexity of splines has led substantive researchers (1) to use knot values that may be inappropriate for their data and (2) to ignore any substantive discussion concerning temporal dependence. We propose a relatively simple alternative: including t, t 2, and t 3 in the regression. This cubic polynomial approximation is trivial to implement—and, therefore, interpret—and it avoids problems such as quasi-complete separation. Monte Carlo analysis demonstrates that, for the types of hazards one often sees in substantive research, the polynomial approximation always outperforms time dummies and generally performs as well as splines or even more flexible autosmoothing procedures. Due to its simplicity, this method also accommodates nonproportional hazards in a straightforward way. We reanalyze Crowley and Skocpol (2001) using nonproportional hazards and find new empirical support for the historical-institutionalist perspective.
No-Load Losses in Transformer under Overexcitation/Inrush-Current Conditions: Tests and a New Model

Tests were conducted on several transformers rated 100 kVA or less and on a power transformer rated 370 MVA in an aim to characterize the no-load losses and magnetizing resistance for transformers subjected to overexcitation and inrush current. Analysis of the results revealed that the magnetizing resistance changes as a function of the peak magnetization flux or the amplitude of the magnetic field. A new model of the instantaneous magnetizing resistance (IMR) as a function of the instantaneous flux has been developed and its dynamic use in EMTP allows the form of the hysteresis cycle and the mean losses in overexcitation to be reproduced with a high degree of accuracy. The same model also allows account to be taken of losses due to the harmonics superimposed on the fundamental. The results showed that the IMR calculated under inrush current conditions is higher than that in overexcitation conditions.
Cytogenetic stability of chicken T‐cell line transformed with Marek's disease virus: atomic force microscope, a new tool for investigation

The Marek's disease virus (MDV) integration may induce a novel organization of chromatin architecture with a modified genetic expression. In our opinion it is worthwhile trying to relate cytogenetic stability to functional modifications. Recently, atomic force microscopy technique was applied to study the structure of chromosomes at a nanoscale level. This high resolution allows to investigate the different structure of chromatin in order to study cytogenetic stability and chromosome aberrations due to MDV insertion. In this paper data are presented indicating a duplication [78,WZ,dup(1p)(p22–p23)] and a deletion [78,WZ cht del(3)(q2.10)] of Chromosomes 1 and 3 relatively. Relationships between GTG (G‐bands by Trypsin using Giemsa) bands and the topography of chromosomes are also discussed, naming them Topographic Banding. The architecture of chromosomes observed by AFM can be related to the data obtained with classic banding techniques thus overcoming the optical resolution limits. The presence of chromatin bridges between sister chromatids at most of the heterochromatic regions is also evidenced. Besides, we present different studies of the longitudinal and transversal symmetry of the hetero and euchromatic regions to clearly demonstrate a different underlying architecture of these regions. It is indeed evident that the heterochromatic bands are more symmetrical than euchromatic bands. Copyright © 2010 John Wiley & Sons, Ltd.
Electronic Commerce and Competitive First-Degree Price Discrimination

As consumer e-commerce matures on-line retailers are adopting personalisation technologies which significantly increase their ability to undertake first-degree price discrimination by offering different prices to different consumers. We present a model of duoplolistic competition between firms capable of using such technologies. Using firstdegree price discrimination firms are able to extract more surplus from their customers, but also face more intense competition, because they compete, in effect, for each and every consumer in the market. Whether or not firms will choose to use this new technology will depend on whether or not the enhanced surplus extraction effect dominates the intensified competition effect. We present a model which makes these ideas precise, and characterise the conditions under which firms will choose to employ firstdegree price discrimination technologies. Acknowledgements We are grateful to John Beath and Avner Shaked for useful discussions. Both authors thank the financial support of the ESRC grant no. R000222642.
Accelerometer-derived physical activity and sedentary time by cancer type in the United States

The 2003–2004 and 2005–2006 cycles of the National Health and Nutrition Examination Survey (NHANES) were among the first population-level studies to incorporate objectively measured physical activity and sedentary behavior, allowing for greater understanding of these behaviors. However, there has yet to be a comprehensive examination of these data in cancer survivors, including short- and long-term survivors of all cancer types. Therefore, the purpose of this analysis was to use these data to describe activity behaviors in short- and long-term cancer survivors of various types. A secondary aim was to compare activity patterns of cancer survivors to that of the general population. Cancer survivors (n = 508) and age-matched individuals not diagnosed with cancer (n = 1,016) were identified from a subsample of adults with activity measured by accelerometer. Physical activity and sedentary behavior were summarized across cancer type and demographics; multivariate regression was used to evaluate differences between survivors and those not diagnosed with cancer. On average, cancer survivors were 61.4 (95% CI: 59.6, 63.2) years of age; 57% were female. Physical activity and sedentary behavior patterns varied by cancer diagnosis, demographic variables, and time since diagnosis. Survivors performed 307 min/day of light-intensity physical activity (95% CI: 295, 319), 16 min/day of moderate-vigorous intensity activity (95% CI: 14, 17); only 8% met physical activity recommendations. These individuals also reported 519 (CI: 506, 532) minutes of sedentary time, with 86 (CI: 84, 88) breaks in sedentary behavior per day. Compared to non-cancer survivors, after adjustment for potential confounders, survivors performed less light-intensity activity (P = 0.01), were more sedentary (P = 0.01), and took fewer breaks in sedentary time (P = 0.04), though there were no differences in any other activity variables. These results suggest that cancer survivors are insufficiently active. Relative to adults of similar age not diagnosed with cancer, they engage in more sedentary time with fewer breaks. As such, sedentary behavior and light-intensity activity may be important intervention targets, particularly for those for whom moderate-to-vigorous activity is not well accepted.
Evaluation of corneal thickness and topography in normal eyes using the Orbscan corneal topography system

AIMS To map the thickness, elevation (anterior and posterior corneal surface), and axial curvature of the cornea in normal eyes with the Orbscan corneal topography system. METHODS 94 eyes of 51 normal subjects were investigated using the Orbscan corneal topography system. The anterior and posterior corneal elevation maps were classified into regular ridge, irregular ridge, incomplete ridge, island, and unclassified patterns, and the axial power maps were grouped into round, oval, symmetric bow tie, asymmetric bow tie, and irregular patterns. The pachymetry patterns were designated as round, oval, decentred round, and decentred oval. RESULTS The thinnest point on the cornea was located at an average of 0.90 (SD 0.51) mm from visual axis and had an average thickness of 0.55 (0.03) mm. In 69.57% of eyes, this point was located in the inferotemporal quadrant, followed by the superotemporal quadrant in 23.91%, the inferonasal quadrant in 4.35%, and the superonasal quadrant in 2.17%. Among the nine regions of the cornea evaluated (central, superotemporal, temporal, inferotemporal, inferior, inferonasal, nasal, superonasal, and superior) the central cornea had the lowest average thickness (0.56 (0.03) mm) and the superior cornea had the greatest average thickness (0.64 (0.03) mm). The mean simulated keratometry (SimK) was 44.24 (1.61)/43.31 (1.66) dioptres (D) and the mean astigmatism was 0.90 (0.41) D. Island (71.74%) was the most common elevation pattern observed in the anterior corneal surface, followed by incomplete ridge (19.57%), regular ridge (4.34%), irregular ridge (2.17%), and unclassified (2.17%). Island (32.61%) was the most common topographic pattern in the posterior corneal surface, following by regular ridge (30.43%), incomplete ridge (23.91%), and irregular ridge (13.04%) patterns. Symmetric bow tie was the most common axial power pattern in the anterior cornea (39.13%), followed by oval (26.07%), asymmetric bow tie (23.91%), round (6.52%), and irregular (4.53%) patterns. In the pachymetry maps, 47.83% of eyes had an oval pattern, and round, decentred oval, and decentred round were observed in 41.30%, 8.70%, and 2.18% of eyes, respectively. CONCLUSION The information on regional corneal thickness, corneal elevation and axial corneal curvature obtained with the Orbscan corneal topography system from normal eyes provides a reference for comparison with diseased corneas. The Orbscan corneal topography system is a useful tool to evaluate both corneal topography and corneal thickness.
The Influence of Forums and Multilevel Governance on the Climate Adaptation Practices of Australian Organizations

To date, there are few regulations and policies relating to climate change in Australia. Uncertainty about the timing, structure, and potential impact of proposed legislation such as a national carbon abatement scheme, is leading to planning delays across the country. To assist with these policy uncertainties, organizations can embed themselves in multilevel governance frameworks that inform, structure, and facilitate strategic development, planning, and action. As part of these networks, organizational representatives also engage in formal and informal forums, a type of interorganizational relationship, which can include industry task forces, policy development committees, interagency groups, and specific climate change committees. Forums constitute an additional level of governance that influences decision making. The patterns of relationships within these multilevel governance frameworks are examined in this paper, with a focus on the forum level of organizational cooperation. Specifically, we investigate the type of forums operating and their role in supporting organizational responses to climate change. A series of interviews and focus groups were conducted in two study areas, the Swan Canning region of Western Australia and the Hunter / Central Coast region of New South Wales. The results indicate that organizations participate in a diverse range of forums. Further, forums appear to play a key role in the everyday business of organizations by enhancing their ability to plan and address a range of issues, including those associated with climate change. In addition the research highlights some of the barriers and drivers for the development and implementation of climate adaptation practices that emerge from forum discussions. For example, a lack of government guidance in interpreting climate change policy was described as a barrier yet access to the knowledge and expertise of participants was highlighted as a potential driver. The paper discusses how an ability to create new forums and utilize existing nonclimate related forums assists organizations in addressing climate change impacts. We contend that forums constitute a level of governance deeply embedded in organizational practice that influences both their capacity and motivation to undertake climate adaptation. Our findings suggest that research investigating the rules that govern forums and the structural properties of the networks in which they are embedded is required to further understand the role of multilevel governance in shaping organizational responses to climate change.