Miracle-dz/UniFAR-FTUs huggingface dataset:
Vortex and Strain Skeletons in Eulerian and Lagrangian Frames

We present an approach to analyze mixing in flow fields by extracting vortex and strain features as extremal structures of derived scalar quantities that satisfy a duality property: They indicate vortical as well as high-strain (saddle-type) regions. Specifically, we consider the Okubo-Weiss criterion and the recently introduced MZ criterion. Although the first is derived from a purely Eulerian framework, the latter is based on Lagrangian considerations. In both cases, high values indicate vortex activity, whereas low values indicate regions of high strain. By considering the extremal features of those quantities, we define the notions of a vortex and a strain skeleton in a hierarchical manner: The collection of maximal zero-dimensional, one-dimensional, and 2D structures assemble the vortex skeleton; the minimal structures identify the strain skeleton. We extract those features using scalar field topology and apply our method to a number of steady and unsteady 3D flow fields.
Magnetic resonance imaging-defined areas of microvascular obstruction after acute myocardial infarction represent microvascular destruction and haemorrhage.

AIMS Lack of gadolinium-contrast wash-in on first-pass perfusion imaging, early gadolinium-enhanced imaging, or late gadolinium-enhanced (LGE) cardiovascular magnetic resonance (CMR) imaging after revascularized ST-elevation myocardial infarction (STEMI) is commonly referred to as microvascular obstruction (MVO). Additionally, T2-weighted imaging allows for the visualization of infarct-related oedema and intramyocardial haemorrhage (IMH) within the infarction. However, the exact histopathological correlate of the contrast-devoid core and its relation to IMH is unknown. METHODS AND RESULTS In eight Yorkshire swine, the circumflex coronary artery was occluded for 75 min by a balloon catheter. After 7 days, CMR with cine imaging, T2-weighted turbospinecho, and LGE was performed. Cardiovascular magnetic resonance images were compared with histological findings after phosphotungstic acid-haematoxylin and anti-CD31/haematoxylin staining. These findings were compared with CMR findings in 27 consecutive PCI-treated STEMI patients, using the same scanning protocol. In the porcine model, the infarct core contained extensive necrosis and erythrocyte extravasation, without intact vasculature and hence, no MVO. The surrounding-gadolinium-enhanced-area contained granulation tissue, leucocyte infiltration, and necrosis with morphological intact microvessels containing microthrombi, without erythrocyte extravasation. Areas with IMH (median size 1.92 [0.36-5.25] cm(3)) and MVO (median size 2.19 [0.40-4.58] cm(3)) showed close anatomic correlation [intraclass correlation coefficient (ICC) 0.85, r = 0.85, P = 0.03]. Of the 27 STEMI patients, 15 had IMH (median size 6.60 [2.49-9.79] cm(3)) and 16 had MVO (median size 4.31 [1.05-7.57] cm(3)). Again, IMH and MVO showed close anatomic correlation (ICC 0.87, r = 0.93, P < 0.001). CONCLUSION The contrast-devoid core of revascularized STEMI contains extensive erythrocyte extravasation with microvascular damage. Attenuating the reperfusion-induced haemorrhage may be a novel target in future adjunctive STEMI treatment.
Disrupted Interhemispheric Synchrony in Default Mode Network Underlying the Impairment of Cognitive Flexibility in Late-Onset Depression

The intuitive association between cognitive impairment and aberrant functional activity in the brain network has prompted interest in exploring the role of functional connectivity in late-onset depression (LOD). The relationship of altered voxel-mirrored homotopic connectivity (VMHC) and cognitive dysfunction in LOD is not yet well understood. This study was designed to examine the implicit relationship between the disruption of interhemispheric functional coordination and cognitive impairment in LOD. LOD patients (N = 31) and matched healthy controls (HCs; N = 37) underwent neuropsychological tests and functional magnetic resonance imaging (fMRI) in this study. The intergroup difference of interhemispheric coordination was determined by calculating VMHC value in the whole brain. The neuro-behavioral relevancy approach was applied to explore the association between disrupted VMHC and cognitive measures. Receiver operating characteristic (ROC) curve analysis was used to determine the capability of disrupted regional VMHC to distinguish LOD. Compared to the HC group, significantly attenuated VMHC in the superior frontal gyrus (SFG), superior temporal gyrus (STG), posterior cerebellar lobe (CePL) and post- and precentral gyri were observed in the bilateral brain of LOD patients. The interhemispheric asynchrony in bilateral CePLs was positively correlated with the performance of trail making test B (TMT-B) in LOD patients (r = 0.367, P = 0.040). ROC analysis revealed that regions with abnormal VMHC could efficiently distinguish LOD from HCs (Area Under Curve [AUC] = 0.90, P < 0.001). Altered linkage patterns of intrinsic homotopic connectivity and impaired cognitive flexibility was first investigated in LOD, and it would provide a novel clue for revealing the neural substrates underlying cognitive impairment in LOD.
Analytics in sustainable precision animal nutrition

The global population, resource, and climate dynamics suggest we must improve sustainability of food production systems (Ohlsson, 2014; Kleinman et al., 2018). Improving livestock production sustainability is particularly important because a significant portion of the projected increases in global food demand is anticipated to come from livestock (Thornton, 2010). Improving sustainability of livestock production systems can be achieved through optimized reproductive, genetic, nutritional, and health management (White et al., 2014, 2015). Management decisions within livestock production can be thought of as two interleaved feedback loops. The first feedback loop is between the animal and the environment: the animal is influenced by its environment and, in turn, influences its environment. The second feedback loop is between the animal and the manager: the manager takes information about the animal’s behavior and attempts to influence the environment to optimize the animal’s performance (Figure 1). Managers make management decisions on different timescales ranging from immediate to relaxed. An example of an immediate management decision would be a farmer identifying an animal as sick, isolating the animal, and treating the animal for the illness. We term this immediate because the farmer must identify the sick animal as soon as possible and must react to the diagnosis as soon as possible. An example of a relaxed management decision would be the farmer electing to change the feed provided to his animals in response to something observed about their production (i.e., the cows are producing poorly, so change the ration to provide higher nutrient density to correct a nutrient shortfall). This decision is more relaxed because its formulation and response are subjected to natural, biological delays (i.e., it may take days to weeks to see a production response to a new diet). Improving the precision of these decision-making processes and reducing the burden of decision making on farmers are two critical steps toward improving sustainability of livestock production. Precision agricultural technologies have been identified as one possible solution (Berckmans, 2014; Tullo et al., 2019). Open in a separate window Figure 1. Depiction of the feedback loops between the farm manager, animal, and environment. The animal and environment influence each other, as do the animal and the manager’s decisions about the animal. Additionally, the manager can make decisions about the environment that will influence the animal.
A Wavelet-Based Joint Estimator of the Parameters of Long-Range Dependence

A joint estimator is presented for the two parameters that define the long-range dependence phenomenon in the simplest case. The estimator is based on the coefficients of a discrete wavelet decomposition, improving a wavelet-based estimator of the scaling parameter (Abry and Veitch 1998), as well as extending it to include the associated power parameter. An important feature is its conceptual and practical simplicity, consisting essentially in measuring the slope and the intercept of a linear fit after a discrete wavelet transform is performed, a very fast (O(n)) operation. Under well-justified technical idealizations the estimator is shown to be unbiased and of minimum or close to minimum variance for the scale parameter, and asymptotically unbiased and efficient for the second parameter. Through theoretical arguments and numerical simulations it is shown that in practice, even for small data sets, the bias is very small and the variance close to optimal for both parameters. Closed-form expressions are given for the covariance matrix of the estimator as a function of data length, and are shown by simulation to be very accurate even when the technical idealizations are not satisfied. Comparisons are made against two maximum-likelihood estimators. In terms of robustness and computational cost the wavelet estimator is found to be clearly superior and statistically its performance is comparable. We apply the tool to the analysis of Ethernet teletraffic data, completing an earlier study on the scaling parameter alone.
The prognostic value of serum uric acid in the acute phase of hemorrhagic stroke patients in black Africans

Introduction Very few studies have been conducted to evaluate the prevalence of hyperuricemia and its impact on the prognosis amongst acute hemorrhagic stroke (AHS) patients. The objectives was to determine the prevalence of hyperuricemia in AHS patients and examined the association between hyperuricemia and stroke outcomes in the Douala General Hospital (DGH). Methods This was a hospital based prospective cohort which included AHS patients with baseline SUA levels and 3 months post stroke follow-up data. SUA values were divided into quintiles. Associations between hyperuricemia and stroke outcomes were analyzed using multiple logistic regression and survival analysis (cox regression and Kaplan Meier). Results A total of 221 AHS patients were reviewed with a mean age of 55.8±11.8 years. The prevalence of hyperuricemia among AHS patients was 34.4% with mean SUA level of 376.8±131.9 μmol/l. On multivariate analysis, hyperuricemia was not independently associated with early death [(OR = 1.072 (CI: 0.370-3.056; p = 0.897)] and poor functional outcome [(OR=2.487 (CI: 0.771-8.699; p = 0.154)] after hemorrhagic stroke. No significant increase in stroke deaths was observed across higher SUA quintiles amongst hemorrhagic stroke patients (p = 0.326). No statistically significant correlation was observed between SUA level and NIHSS (r = 0.063, p = 0.353) and between SUA level and mRS (r = 0.030, p = 0.662) in hemorrhagic stroke. Conclusion About one third of patients present with hyperuricemia in the acute phase of hemorrhagic stroke. Hyperuricemia can act as risk factor for stroke because of its relationship with CVRFs but hyperuricemia has no impact on the severity and short-term outcome amongst black African hemorrhagic stroke patients.
Primary cell wall composition of bryophytes and charophytes.

Major differences in primary cell wall (PCW) components between non-vascular plant taxa are reported. (1) Xyloglucan: driselase digestion yielded isoprimeverose (the diagnostic repeat unit of xyloglucan) from PCW-rich material of Anthoceros (a hornwort), mosses and both leafy and thalloid liverworts, as well as numerous vascular plants, showing xyloglucan to be a PCW component in all land plants tested. In contrast, charophycean green algae (Klebsormidium flaccidium, Coleochaete scutata and Chara corallina), thought to be closely related to land plants, did not contain xyloglucan. They did not yield isoprimeverose; additionally, charophyte material was not digestible with xyloglucan-specific endoglucanase or cellulase to give xyloglucan-derived oligosaccharides. (2) Uronic acids: acid hydrolysis of PCW-rich material from the charophytes, the hornwort, thalloid and leafy liverworts and a basal moss yielded higher concentrations of glucuronic acid than that from the remaining land plants including the less basal mosses and all vascular plants tested. Polysaccharides of the hornwort Anthoceros contained an unusual repeat-unit, glucuronic acid-alpha(1-->3)-galactose, not found in appreciable amounts in any other plants tested. Galacturonic acid was consistently the most abundant PCW uronic acid, but was present in higher concentrations in acid hydrolysates of bryophytes and charophytes than in those of any of the vascular plants. Mannuronic acid was not detected in any of the species surveyed. (3) Mannose: acid hydrolysis of charophyte and bryophyte PCW-rich material also yielded appreciably higher concentrations of mannose than are found in vascular plant PCWs. (4) Mixed-linkage glucan (MLG) was absent from all algae and bryophytes tested; however, upon digestion with licheninase, PCW-rich material from the alga Ulva lactuca and the leafy liverwort Lophocolea bidentata yielded penta- to decasaccharides, indicating the presence of MLG-related polysaccharides. Our results show that major evolutionary events are often associated with changes in PCW composition. In particular, the acquisition of xyloglucan may have been a pre-adaptive advantage that allowed colonization of land.
Methods for computing color anaglyphs

A new computation technique is presented for calculating pixel colors in anaglyph images. The method depends upon knowing the RGB spectral distributions of the display device and the transmission functions of the filters in the viewing glasses. It requires the solution of a nonlinear least-squares program for each pixel in a stereo pair and is based on minimizing color distances in the CIEL*a*b* uniform color space. The method is compared with several techniques for computing anaglyphs including approximation in CIE space using the Euclidean and Uniform metrics, the Photoshop method and its variants, and a method proposed by Peter Wimmer. We also discuss the methods of desaturation and gamma correction for reducing retinal rivalry.
New Statistical Learning Methods for Estimating Optimal Dynamic Treatment Regimes

Dynamic treatment regimes (DTRs) are sequential decision rules for individual patients that can adapt over time to an evolving illness. The goal is to accommodate heterogeneity among patients and find the DTR which will produce the best long-term outcome if implemented. We introduce two new statistical learning methods for estimating the optimal DTR, termed backward outcome weighted learning (BOWL), and simultaneous outcome weighted learning (SOWL). These approaches convert individualized treatment selection into an either sequential or simultaneous classification problem, and can thus be applied by modifying existing machine learning techniques. The proposed methods are based on directly maximizing over all DTRs a nonparametric estimator of the expected long-term outcome; this is fundamentally different than regression-based methods, for example, Q-learning, which indirectly attempt such maximization and rely heavily on the correctness of postulated regression models. We prove that the resulting rules are consistent, and provide finite sample bounds for the errors using the estimated rules. Simulation results suggest the proposed methods produce superior DTRs compared with Q-learning especially in small samples. We illustrate the methods using data from a clinical trial for smoking cessation. Supplementary materials for this article are available online.
Hydraulic Erosion Using Smoothed Particle Hydrodynamics

This paper presents a new technique for modification of 3D terrains by hydraulic erosion. It efficiently couples fluid simulation using a Lagrangian approach, namely the Smoothed Particle Hydrodynamics (SPH) method, and a physically‐based erosion model adopted from an Eulerian approach. The eroded sediment is associated with the SPH particles and is advected both implicitly, due to the particle motion, and explicitly, through an additional velocity field, which accounts for the sediment transfer between the particles. We propose a new donor‐acceptor scheme for the explicit advection in SPH. Boundary particles associated to the terrain are used to mediate sediment exchange between the SPH particles and the terrain itself. Our results show that this particle‐based method is efficient for the erosion of dense, large, and sparse fluid. Our implementation provides interactive results for scenes with up to 25,000 particles.
An evolutionary robotics model of visually-guided braking: Testing optical variables

This paper presents results from a series of evolutionary robotics simulations that were designed to investigate the informational basis of visually-guided braking. Evolutionary robotics techniques were used to develop models of visually-guided braking behavior in humans to aid in resolving existing questions in the literature. Based on a well-used experimental paradigm from psychology, model agents were evolved to solve a driving-like braking task in a simple 2D environment involving one object. Agents had five sensors to detect image size of the object, image expansion rate, tau, tau-dot and proportional rate, respectively. These optical variables were those tested in experimental investigations of visually-guided braking in humans. The aim of the present work was to investigate which of these optical variables were used by the evolved agents to solve the braking task when all variables were available to control braking. Our results indicated that the agent with the highest performance used exclusively .
A Submodule Clustering Method for Multi-way Data by Sparse and Low-Rank Representation

A new submodule clustering method via sparse and low-rank representation for multi-way data is proposed in this paper. Instead of reshaping multi-way data into vectors, this method maintains their natural orders to preserve data intrinsic structures, e.g., image data kept as matrices. To implement clustering, the multi-way data, viewed as tensors, are represented by the proposed tensor sparse and low-rank model to obtain its submodule representation, called a free module, which is finally used for spectral clustering. The proposed method extends the conventional subspace clustering method based on sparse and low-rank representation to multi-way data submodule clustering by combining t-product operator. The new method is tested on several public datasets, including synthetical data, video sequences and toy images. The experiments show that the new method outperforms the state-of-the-art methods, such as Sparse Subspace Clustering (SSC), Low-Rank Representation (LRR), Ordered Subspace Clustering (OSC), Robust Latent Low Rank Representation (RobustLatLRR) and Sparse Submodule Clustering method (SSmC).
Parametric modeling and linear estimation of elastic deformations

We present a novel method to model and estimate elastic geometric deformations of an observed object, whether they are caused by the object's own dynamic behavior, or by the dynamic behavior of the imaging device, or both. A procedure for estimating the space of possible deformations the object may undergo based only on a set of observations is derived. This information is then employed to derive a linear estimator of the elastic deformation in any given observation. Application to change detection is presented.
Identification of amino acids recognized by syncytium-inhibiting and neutralizing monoclonal antibodies to the human parainfluenza type 3 virus fusion protein

Neutralizing monoclonal antibodies specific for the fusion (F) glycoprotein of human parainfluenza type 3 virus (PIV3) were used to select neutralization-resistant antigenic variants. Sequence analysis of the F genes of the variants indicated that their resistance to antibody binding, antibody-mediated neutralization or to both was a result of specific amino acid substitutions within the neutralization epitopes of the F1 and F2 subunits. Comparison of the locations of PIV3 neutralization epitopes with those of Newcastle disease and Sendai viruses indicated that the antigenic organization of the fusion proteins of paramyxoviruses is similar. Furthermore, some of the PIV3 epitopes recognized by syncytium-inhibiting monoclonal antibodies are located in an F1 cysteine cluster region which corresponds to an area of the measles virus F protein involved in fusion activity.
Simple and Efficient Nonparametric Method for Estimating the Number of Signals Without Eigendecomposition

Inspired by the computational simplicity and numerical stability of QR decomposition, a nonparametric method for estimating the number of signals without eigendecomposition (MENSE) is proposed for the coherent narrowband signals impinging on a uniform linear array (ULA). By exploiting the array geometry and its shift invariance property to decorrelate the coherency of signals through subarray averaging, the number of signals is revealed in the rank of the QR upper-trapezoidal factor of the autoproduct of a combined Hankel matrix formed from the cross correlations between some sensor data. Since the infection of additive noise is defused, signal detection capability is improved. A new detection criterion is then formulated in terms of the row elements of the QR upper-triangular factor when finite array data are available, and the number of signals is determined as a value of the running index for which this ratio criterion is maximized, where the QR decomposition with column pivoting is also used to improve detection performance. The statistical analysis clarifies that the MENSE detection criterion is asymptotically consistent. Furthermore, the proposed MENSE algorithm is robust against the array uncertainties including sensor gain and phase errors and mutual coupling and against the deviations from the spatial homogeneity of noise model. The effectiveness of the MENSE is verified through numerical examples, and the simulation results show that the MENSE is superior in detecting closely spaced signals with a small number of snapshots and/or at relatively low signal-to-noise ratio (SNR)
Trends in the Practice of Parental Presence During Induction of Anesthesia and the Use of Preoperative Sedative Premedication in the United States, 1995–2002: Results of a Follow-Up National Survey

Both parental presence during induction of anesthesia and sedative premedication are currently used to treat preoperative anxiety in children. A survey study conducted in 1995 demonstrated that most children are taken into the operating room without the benefit of either of these two interventions. In 2002 we conducted a follow-up survey study. Five thousand questionnaires were mailed to randomly selected physician members of the American Society of Anesthesiologists. Mailings were followed by a nonresponse bias assessment. Twenty-seven percent (n = 1362) returned the questionnaire after 3 mailings. We found that a significantly larger proportion of young children undergoing surgery in the United States were reported to receive sedative premedication in 2002 as compared with 1995 (50% vs 30%, P = 0.001). We also found that in 2002 there was significantly less geographical variability in the use of sedative premedication as compared with the 1995 survey (F = 8.31, P = 0.006). Similarly, we found that in 2002 parents of children undergoing surgery in the United States were allowed to be present more often during induction of anesthesia as compared with 1995 (χ2 = 26.3, P = 0.0001). Finally, similar to our findings in the 1995 survey, midazolam was uniformly selected most often to premedicate patients before surgery.