Miracle-dz/UniFAR-FTUs huggingface dataset:
Very rapid phosphorylation kinetics suggest a unique role for Lhcb2 during state transitions in Arabidopsis

Light-harvesting complex II (LHCII) contains three highly homologous chlorophyll-a/b-binding proteins (Lhcb1, Lhcb2 and Lhcb3), which can be assembled into both homo- and heterotrimers. Lhcb1 and Lhcb2 are reversibly phosphorylated by the action of STN7 kinase and PPH1/TAP38 phosphatase in the so-called state-transition process. We have developed antibodies that are specific for the phosphorylated forms of Lhcb1 and Lhcb2. We found that Lhcb2 is more rapidly phosphorylated than Lhcb1: 10 sec of ‘state 2 light’ results in Lhcb2 phosphorylation to 30% of the maximum level. Phosphorylated and non-phosphorylated forms of the proteins showed no difference in electrophoretic mobility and dephosphorylation kinetics did not differ between the two proteins. In state 2, most of the phosphorylated forms of Lhcb1 and Lhcb2 were present in super- and mega-complexes that comprised both photosystem (PS)I and PSII, and the state 2-specific PSI–LHCII complex was highly enriched in the phosphorylated forms of Lhcb2. Our results imply distinct and specific roles for Lhcb1 and Lhcb2 in the regulation of photosynthetic light harvesting.
Modelling the layer-specific three-dimensional residual stresses in arteries, with an application to the human aorta

This paper provides the first analysis of the three-dimensional state of residual stress and stretch in an artery wall consisting of three layers (intima, media and adventitia), modelled as a circular cylindrical tube. The analysis is based on experimental results on human aortas with non-atherosclerotic intimal thickening documented in a recent paper by Holzapfel et al. ( Holzapfel et al. 2007 Ann. Biomed. Eng. 35, 530–545 (doi:10.1007/s10439-006-9252-z)). The intima is included in the analysis because it has significant thickness and load-bearing capacity, unlike in a young, healthy human aorta. The mathematical model takes account of bending and stretching in both the circumferential and axial directions in each layer of the wall. Previous analysis of residual stress was essentially based on a simple application of the opening-angle method, which cannot accommodate the three-dimensional residual stretch and stress states observed in experiments. The geometry and nonlinear kinematics of the intima, media and adventitia are derived and the associated stress components determined explicitly using the nonlinear theory of elasticity. The theoretical results are then combined with the mean numerical values of the geometrical parameters and material constants from the experiments to illustrate the three-dimensional distributions of the stretches and stresses throughout the wall. The results highlight the compressive nature of the circumferential stress in the intima, which may be associated with buckling of the intima and its delamination from the media, and show that the qualitative features of the stretch and stress distributions in the media and adventitia are unaffected by the presence or absence of the intima. The circumferential residual stress in the intima increases significantly as the associated residual deformation in the intima increases while the corresponding stress in the media (which is compressive at its inner boundary and tensile at its outer boundary) is only slightly affected. The theoretical framework developed herein enables the state of residual stress to be calculated directly, serves to improve insight into the mechanical response of an unloaded artery wall and can be extended to accommodate more general geometries, kinematics and states of residual stress as well as more general constitutive models.
Imitation learning of non-linear point-to-point robot motions using dirichlet processes

In this paper we discuss the use of the infinite Gaussian mixture model and Dirichlet processes for learning robot movements from demonstrations. Starting point of this work is an earlier paper where the authors learn a non-linear dynamic robot movement model from a small number of observations. The model in that work is learned using a classical finite Gaussian mixture model (FGMM) where the Gaussian mixtures are appropriately constrained. The problem with this approach is that one needs to make a good guess for how many mixtures the FGMM should use. In this work, we generalize this approach to use an infinite Gaussian mixture model (IGMM) which does not have this limitation. Instead, the IGMM automatically finds the number of mixtures that are necessary to reflect the data complexity. For use in the context of a non-linear dynamic model, we develop a Constrained IGMM (CIGMM). We validate our algorithm on the same data that was used in [5], where the authors use motion capture devices to record the demonstrations. As further validation we test our approach on novel data acquired on our iCub in a different demonstration scenario in which the robot is physically driven by the human demonstrator.
Robust artifactual independent component classification for BCI practitioners

Objective. EEG artifacts of non-neural origin can be separated from neural signals by independent component analysis (ICA). It is unclear (1) how robustly recently proposed artifact classifiers transfer to novel users, novel paradigms or changed electrode setups, and (2) how artifact cleaning by a machine learning classifier impacts the performance of brain–computer interfaces (BCIs). Approach. Addressing (1), the robustness of different strategies with respect to the transfer between paradigms and electrode setups of a recently proposed classifier is investigated on offline data from 35 users and 3 EEG paradigms, which contain 6303 expert-labeled components from two ICA and preprocessing variants. Addressing (2), the effect of artifact removal on single-trial BCI classification is estimated on BCI trials from 101 users and 3 paradigms. Main results. We show that (1) the proposed artifact classifier generalizes to completely different EEG paradigms. To obtain similar results under massively reduced electrode setups, a proposed novel strategy improves artifact classification. Addressing (2), ICA artifact cleaning has little influence on average BCI performance when analyzed by state-of-the-art BCI methods. When slow motor-related features are exploited, performance varies strongly between individuals, as artifacts may obstruct relevant neural activity or are inadvertently used for BCI control. Significance. Robustness of the proposed strategies can be reproduced by EEG practitioners as the method is made available as an EEGLAB plug-in.
Mining for Quality Control of Court Records ∗

Attorneys across the United States use government-provided electronic databases to submit docket entries and associated case files for processing and archival in public judicial records. Data entry errors in these repositories, while rare, can disrupt the court process, confuse the public record, or breach privacy and confidentiality. Docket quality assurance is thus a high priority for the courts, but manual review remains resource-intensive. We have developed a prototype application of text mining and human language technologies to partially automate quality assurance review of electronic court documents. This solution uses document classification and named entity recognition to extract metadata directly from documents. Discrepancies between the extracted metadata and the userprovided metadata indicate a possible data entry error. On two independent samples of publicly available court documents, we find that for a small number of classes with a sufficient number of training documents, the document class can be automatically classified with greater than 94% accuracy in one case, but only 81% in the other. Our attempts to extract case numbers and the names of parties from documents via a conditional random field model met with less success. Future work with more extensive training data is necessary to more accurately evaluate both applications.
Language: A Pernicious and Powerful Tool

Two principles guide Parker’s teaching: first is the belief that curriculum should connect with life, and second, is that she has an obligation to promote tolerance and acceptance of homosexuality. An important aspect of this is revealing to her students her own sexual orientation. In this article, she explains why she exposes her personal life, and describes how she creates a dialogue with her students about homosexuality, beginning with how the word “gay” is used in everyday language, specifically as a term to belittle peers. She also explains how infuses gay and lesbian literature with studies of canonical literature.
The impact of metabolism on stable isotope dynamics: a theoretical framework

Stable isotope analysis is a powerful tool used for reconstructing individual life histories, identifying food-web structures and tracking flow of elemental matter through ecosystems. The mechanisms determining isotopic incorporation rates and discrimination factors are, however, poorly understood which hinders a reliable interpretation of field data when no experimental data are available. Here, we extend dynamic energy budget (DEB) theory with a limited set of new assumptions and rules in order to study the impact of metabolism on stable isotope dynamics in a mechanistic way. We calculate fluxes of stable isotopes within an organism by following fluxes of molecules involved in a limited number of macrochemical reactions: assimilation, growth but also structure turnover that is here explicitly treated. Two mechanisms are involved in the discrimination of isotopes: (i) selection of molecules occurs at the partitioning of assimilation, growth and turnover into anabolic and catabolic sub-fluxes and (ii) reshuffling of atoms occurs during transformations. Such a framework allows for isotopic routing which is known as a key, but poorly studied, mechanism. As DEB theory specifies the impact of environmental conditions and individual state on molecule fluxes, we discuss how scenario analysis within this framework could help reveal common mechanisms across taxa.
Tooth size discrepancies in Irish orthodontic patients among different malocclusion groups.

OBJECTIVE To determine the prevalence of tooth size discrepancies (TSDs) in an Irish orthodontic population among different malocclusion groups. MATERIALS AND METHODS From 850 pretreatment sets of orthodontic models at a university clinic, 240 were selected with 30 female and 30 male sets for each malocclusion (Class I, Class II division 1, Class II division 2, and Class III). Digital models were produced, and the mesial and distal contact points were digitized to calculate overall and anterior tooth size ratios. The differences between the male and female groups and among the malocclusion groups were analyzed using two-way analysis of variance (ANOVA) (P < .05). RESULTS A clinically significant anterior TSD (more than two standard deviations from the Bolton means) existed in 37.9% of the subjects. No differences existed in the prevalence of overall TSDs between the male and female groups (P = .5913) or among the malocclusion groups (P = .0809). For the mean anterior tooth size ratios in the male group, the values for Class III and Class II division 2 were higher than in Class II division 1, and the value for Class II division 2 was higher than in Class I (P = .0184). CONCLUSIONS The prevalence of anterior tooth size discrepancies in this sample of Irish orthodontic patients was 37.9%. There were no statistically significant differences in the prevalence of mean overall TSDs with regard to malocclusion or gender. In the male group, the mean anterior tooth size ratio was higher in Class III and in Class II division 2 malocclusion than in Class II division 1 and higher in Class II division 2 malocclusion than in Class I malocclusion.
Data-Parallel Spatial Join Algorithms

Efficient data-parallel spatial join algorithms for bucket PMR quadtrees and R-trees, common spatial data structures, are given. The domain consists of planar line segment data (i.e., Bureau of the Census TIGER/Line files). Parallel algorithms for map intersection and a spatial range query are described. The algorithms are implemented using the scan model of parallel computation on the hypercube architecture of the Connection Machine.
Robust Arbitrary-View Gait Recognition Based on 3D Partial Similarity Matching

Existing view-invariant gait recognition methods encounter difficulties due to limited number of available gait views and varying conditions during training. This paper proposes gait partial similarity matching that assumes a 3D object shares common view surfaces in significantly different views. Detecting such surfaces aids the extraction of gait features from multiple views; 3D parametric body models are morphed by pose and shape deformation from a template model using 2D gait silhouette as observation. The gait pose is estimated by a level set energy cost function from silhouettes including incomplete ones. Body shape deformation is achieved via Laplacian deformation energy function associated with inpainting gait silhouettes. Partial gait silhouettes in different views are extracted by gait partial region of interest elements selection and re-projected onto 2D space to construct partial gait energy images. A synthetic database with destination views and multi-linear subspace classifier fused with majority voting is used to achieve arbitrary view gait recognition that is robust to varying conditions. Experimental results on CMU, CASIA B, TUM-IITKGP, AVAMVG, and KY4D data sets show the efficacy of the propose method.
Cardiac output during exercise by the open circuit acetylene washin method: comparison with direct Fick.

An open-circuit (OpCirc) acetylene uptake cardiac output (QT) method was modified for use during exercise. Two computational techniques were used. OpCirc1 was based on the integrated uptake vs. end-tidal change in acetylene, and OpCirc2 was based on an iterative finite difference modeling method. Six subjects [28-44 yr, peak oxygen consumption (VO(2)) = 120% predicted] performed cycle ergometry exercise to compare QT using OpCirc and direct Fick methods. An incremental protocol was repeated twice, separated by a 10-min rest, and subsequently subjects exercised at 85-90% of their peak work rate. Coefficient of variation of the OpCirc methods and Fick were highest at rest (OpCirc1, 7%, OpCirc2, 12%, Fick, 10%) but were lower at moderate to high exercise intensities (OpCirc1, 3%, OpCirc2, 3%, Fick, 5%). OpCirc1 and OpCirc2 QT correlated highly with Fick QT (R(2) = 0.90 and 0.89, respectively). There were minimal differences between OpCirc1 and OpCirc2 compared with Fick up to moderate-intensity exercise (<70% peak VO(2)); however, both techniques tended to underestimate Fick at >70% peak VO(2). These differences became significant for OpCirc1 only. Part of the differences between Fick and OpCirc methods at the higher exercise intensities are likely related to inhomogeneities in ventilation and perfusion matching (R(2) = 0.36 for Fick - OpCirc1 vs. alveolar-to-arterial oxygen tension difference). In conclusion, both OpCirc methods provided reproducible, reliable measurements of QT during mild to moderate exercise. However, only OpCirc2 appeared to approximate Fick QT at the higher work intensities.
Adaptive Neural Control of a Class of Output-Constrained Nonaffine Systems

In this paper, we present a novel tracking controller for a class of uncertain nonaffine systems with time-varying asymmetric output constraints. Firstly, the original nonaffine constrained (in the sense of the output signal) control system is transformed into a output-feedback control problem of an unconstrained affine system in normal form. As a result, stabilization of the transformed system is sufficient to ensure constraint satisfaction. It is subsequently shown that the output tracking is achieved without violation of the predefined asymmetric time-varying output constraints. Therefore, we are capable of quantifying the system performance bounds as functions of time on both transient and steady-state stages. Furthermore, the transformed system is linear with respect to a new input signal and the traditional backstepping scheme is avoided, which makes the synthesis extremely simplified. All the signals in the closed-loop system are proved to be semi-globally, uniformly, and ultimately bounded via Lyapunov synthesis. Finally, the simulation results are presented to illustrate the performance of the proposed controller.
Fracture resistance of cementum-extended composite fillings in severely damaged deciduous incisors: An in vitro study

Objective: The aim of this study was to comparatively assess the fracture resistance of the cementum-extended and conventional composite fillings with or without intracanal composite posts in severely damaged deciduous incisors. Materials and Methods: This in vitro study was performed on 60 extracted deciduous maxillary incisors that were randomly divided into four groups: Group 1: Composite filling (CF); Group 2: Composite filling with composite posts (CF + CP); Group 3: Composite filling extended 0.5 mm to cementum (ceCF); Group 4: Composite filling extended 0.5 mm to cementum with composite posts (ceCF + CP). The fracture resistance was assessed by exerting a progressively increasing load with a cross-head speed of 0.5 mm/min in a Universal Testing Machine. Statistical Analysis: Data were analyzed by SPSS-18 using one-way analysis of variance at α < 0.05. Results: The mean fracture resistance (MFR) values of the experimental groups were 410.57 ± 139.44 N, 564.44 ± 92.63 N, 507.5 ± 76.37 N and 601.08 ± 96.04 N. A significant difference was found between the MFR of Groups 1 and 2, Groups 1 and 4 and Groups 3 and 4 (P < 0.05). Conclusion: A superior outcome was achieved by intracanal composite posts in both conventional and cementum-extended composite fillings.
Cognitive Deterioration in Bilateral Asymptomatic Severe Carotid Stenosis

Background and Purpose— This study aimed to monitor cognitive performance during a 3-year period in subjects with bilateral asymptomatic severe internal carotid artery stenosis and to explore the role of cerebral hemodynamics and atherosclerotic disease in the development of cognitive dysfunction. Methods— One hundred fifty-nine subjects with bilateral asymptomatic severe internal carotid artery stenosis were included and prospectively evaluated for a 3-year period. At entry, demographics, vascular risk profile, and pharmacological treatments were defined. Cognitive status was evaluated using the Mini-Mental State Examination at baseline and at follow-up. Cerebral hemodynamics was assessed by transcranial Doppler–based breath-holding index test. As a measure of the extent of systemic atherosclerotic disease, common carotid artery intima-media thickness was measured. A cutoff for pathological values was set at 0.69 for breath-holding index and 1.0 mm for intima-media thickness. Results— The risk of decreasing in Mini-Mental State Examination score increased progressively from patients with bilaterally normal to those with unilaterally abnormal breath-holding index, reaching the highest probability in patients with bilaterally abnormal breath-holding index (P<0.0001). Pathological values of intima-media thickness did not influence the risk of Mini-Mental State Examination score change. Conclusions— Our findings suggest that patients with asymptomatic bilateral severe internal carotid artery stenosis may be at risk of developing cognitive impairment. The evaluation of the hemodynamic status, besides providing insights about the possible mechanism behind the cognitive dysfunction present in carotid atherosclerotic disease, may be of help for the individuation of subjects deserving earlier and more aggressive treatments.
Consideration of Epstein-Barr Virus-Encoded Noncoding RNAs EBER1 and EBER2 as a Functional Backup of Viral Oncoprotein Latent Membrane Protein 1

ABSTRACT The Epstein-Barr virus (EBV)-encoded noncoding RNAs EBER1 and EBER2 are highly abundant through all four latency stages of EBV infection (III-II-I-0) and have been associated with an oncogenic phenotype when expressed in cell lines cultured in vitro. In vivo, EBV-infected B cells derived from freshly isolated lymphocytes show that EBER1/2 deletion does not impair viral latency. Based on published quantitative proteomics data from BJAB cells expressing EBER1 and EBER2, we propose that the EBERs, through their activation of AKT in a B-cell-specific manner, are a functionally redundant backup of latent membrane protein 1 (LMP1)—an essential oncoprotein in EBV-associated malignancies, with a main role in AKT activation. Our proposed model may explain the lack of effect on viral latency establishment in EBER-minus EBV infection.
Effect of Tourniquet Application on Postoperative Functional Outcome Following Total Knee Arthroplasty: A Prospective Cohort Study

Background: A pneumatic tourniquet is often used during total knee arthroplasty (TKA). However, tourniquet application is often associated with an increased incidence of adverse events and soft tissue damage due to high mechanical pressure. This could potentially result in delayed recovery. The aim of the present study was to evaluate the effect of tourniquet use during TKA on the postoperative functional outcome. Methods: In this prospective cohort study, patients were eligible for inclusion when they were scheduled for primary TKA due to osteoarthritis, age between 50 and 75 years and Dutch language proficiency. Exclusion criteria were inflammatory arthritis, severe cardiac complaints, severe pulmonary disorders, Body Mass Index (BMI) >35, severe coagulation disorders or hospitalization in the previous two months before surgery. The Knee Osteoarthritis Outcome Score (KOOS) questionnaire was obtained at baseline and eight weeks postoperative to evaluate the functional outcome. In addition, muscle strength of the upper and lower limb, range of motion (ROM) of the knee joint and Visual Analogue Scale (VAS) were assessed as secondary outcomes. Length of stay, analgesic consumption and adverse events were also recorded. Results: In total, 96 consecutive patients undergoing TKA met the inclusion criteria. They received usual care according to the surgeon’s preferences whereas 49 patients received no tourniquet (non-tourniquet group) during surgery and in 47 patients a tourniquet was standard applied (tourniquet group). There were no significant differences between both groups in terms of KOOS 1) pain (p=0.398), 2) symptoms (p=0.514), 3) daily living (p=0.904), 4) sport/ recreation (p=0.635) and 5) knee-related quality of life (p=0.970) scores eight weeks after surgery. Also no significant differences were found in respect to knee ROM (p=0.982) and muscle strength (p=≤0.300) during follow-up. We found however, less pain in the tourniquet group compared to the non-tourniquet group but this was only significant during the first days after surgery (p=≤0.043). Conclusion: Our results show that tourniquet application during TKA did not significantly affect the short-term functional outcome as assessed by KOOS scores, ROM of the knee joint and muscle strength of the upper and lower limb. However, there were minor differences in respect to knee related pain between both groups during the first days after surgery.