Miracle-dz/UniFAR-FTUs huggingface dataset:
Endocytic proteins drive vesicle growth via instability in high membrane tension environment

Significance Biological cells are engaged in an incessant uptake of macromolecules for nutrition and inter- and intracellular communication; this entails significant local bending of the plasma membrane and formation of cargo-carrying vesicles executed by a designated set of membrane-deforming proteins. The energetic cost incurred in forming vesicles is directly related to the stressed state of the membrane and, hence, that of the cell. In this study, we reveal a protein-induced “snap-through instability” that offsets tension and drives vesicle growth during clathrin-mediated endocytosis, the main pathway for the transport of macromolecules into cells. Because these proteins (actin and BAR proteins) are involved in other interfacial rearrangements in cells, the predicted instability could be at play in cells at-large. Clathrin-mediated endocytosis (CME) is a key pathway for transporting cargo into cells via membrane vesicles; it plays an integral role in nutrient import, signal transduction, neurotransmission, and cellular entry of pathogens and drug-carrying nanoparticles. Because CME entails substantial local remodeling of the plasma membrane, the presence of membrane tension offers resistance to bending and hence, vesicle formation. Experiments show that in such high-tension conditions, actin dynamics is required to carry out CME successfully. In this study, we build on these pioneering experimental studies to provide fundamental mechanistic insights into the roles of two key endocytic proteins—namely, actin and BAR proteins—in driving vesicle formation in high membrane tension environment. Our study reveals an actin force-induced “snap-through instability” that triggers a rapid shape transition from a shallow invagination to a highly invaginated tubular structure. We show that the association of BAR proteins stabilizes vesicles and induces a milder instability. In addition, we present a rather counterintuitive role of BAR depolymerization in regulating the shape evolution of vesicles. We show that the dissociation of BAR proteins, supported by actin–BAR synergy, leads to considerable elongation and squeezing of vesicles. Going beyond the membrane geometry, we put forth a stress-based perspective for the onset of vesicle scission and predict the shapes and composition of detached vesicles. We present the snap-through transition and the high in-plane stress as possible explanations for the intriguing direct transformation of broad and shallow invaginations into detached vesicles in BAR mutant yeast cells.
Quantification of Subdural Electrode Shift Between Initial Implantation, Postimplantation Computed Tomography, and Subsequent Resection Surgery.

BACKGROUND Subdural electrodes are often implanted for localization of epileptic regions. Postoperative computed tomography (CT) is typically acquired to locate electrode positions for planning any subsequent surgical resection. Electrodes are assumed to remain stationary between CT acquisition and resection surgery. OBJECTIVE To quantify subdural electrode shift that occurred between the times of implantation (Crani 1), postoperative CT acquisition, and resection surgery (Crani 2). METHODS Twenty-three patients in this case series undergoing subdural electrode implantation were evaluated. Preoperative magnetic resonance and postoperative CT were acquired and coregistered, and electrode positions were extracted from CT. Intraoperative positions of electrodes and the cortical surface were digitized with a coregistered stereovision system. Movement of the exposed cortical surface was also tracked, and change in electrode positions was calculated relative to both the skull and the cortical surface. RESULTS In the 23 cases, average shift of electrode positions was 8.0 ± 3.3 mm between Crani 1 and CT, 9.2 ± 3.7 mm between CT and Crani 2, and 6.2 ± 3.0 mm between Crani 1 and Crani 2. The average cortical shift was 4.7 ± 1.4 mm with 2.9 ± 1.0 mm in the lateral direction. The average shift of electrode positions relative to the cortical surface between Crani 1 and Crani 2 was 5.5 ± 3.7 mm. CONCLUSION The results show that electrodes shifted laterally not only relative to the skull, but also relative to the cortical surface, thereby displacing the electrodes from their initial placement on the cortex. This has significant clinical implications for resection based upon seizure activity and functional mapping derived from intracranial electrodes.
Validation of the DAPT score in patients randomized to 6 or 12 months clopidogrel after predominantly second-generation drug-eluting stents

Summary The DAPT score is a recently-proposed decision tool for guiding optimal duration of dual antiplatelet therapy (DAPT). It showed modest accuracy in prior derivation and validation cohorts of patients with ≥12 months DAPT. This study was aimed to evaluate the validity of the DAPT score in a cohort of patients with 6 or 12 months DAPT after implantation of predominantly second-generation drug-eluting stents. We analyzed data of patients enrolled in the ISAR-SAFE trial. Patients were classified into low (<2) or high (≥2) DAPT score groups. Primary ischaemic (all-cause death, myocardial infarction, definite stent thrombosis or stroke) and bleeding (TIMI major or minor) outcomes were analyzed in the low and high DAPT score groups. Data of 3976 patients were available for DAPT score calculation. 2407 patients (60.5%) were classified in the low DAPT score group and 1569 patients (39.5%) in the high DAPT score group. In the low DAPT score group there were no significant differences between 6 and 12 months DAPT regarding ischaemic (1.0% vs. 1.4%, HR=0.74, 95% CI, 0.35–1.57; p=0.43) or bleeding outcomes (0.3% vs. 0.8%, HR=0.44, 95% CI, 0.13–1.42; p=0.17). In the high DAPT score group there were also no significant differences between 6 and 12 months DAPT regarding ischaemic (1.9% vs. 1.8%, HR=1.02, 95% CI, 0.49–2.14; p=0.96) or bleeding (0.3% vs. 0.5%, HR=0.51, 95% CI, 0.09–2.78; p=0.44) outcomes. In conclusion, the DAPT score failed to show a differential treatment effect in patients receiving 6 or 12 months DAPT after contemporary drug-eluting stent implantation.
Initiation of Hepatitis C Virus Infection Is Dependent on Cholesterol and Cooperativity between CD81 and Scavenger Receptor B Type I

ABSTRACT In the past several years, a number of cellular proteins have been identified as candidate entry receptors for hepatitis C virus (HCV) by using surrogate models of HCV infection. Among these, the tetraspanin CD81 and scavenger receptor B type I (SR-BI), both of which localize to specialized plasma membrane domains enriched in cholesterol, have been suggested to be key players in HCV entry. In the current study, we used a recently developed in vitro HCV infection system to demonstrate that both CD81 and SR-BI are required for authentic HCV infection in vitro, that they function cooperatively to initiate HCV infection, and that CD81-mediated HCV entry is, in part, dependent on membrane cholesterol.
Battery Aging Study Using Field Use Data

Regarded as the future of the automotive industry, electric cars are not far from a worldwide deployment. However some drawbacks still slow down this deployment such as batteries lifetime and autonomy which have to be increased in order to compete conventional internal combustion engine vehicles (ICE). Therefore, a well understanding of the battery aging phenomena is mandatory regarding the development of new hybrid achitectures and their energy management. In order to study those phenomena and understand the causes, ten fuel cell hybrid electric vehicles developed for postal delivery purpose among the european Mobypost project have been monitored during three years. This experimentation led to create a rich database. Using this database the remaining capacity of an entire fleet of vehicule have been calculated. Consequently the capacity fades could be estimated and illustrated in function of the temperature and the batteries cycle number, through a non linear regression with an error NRMSE of 0.129.
Lessons Learned from Designing a 65 nm ASIC for Evaluating Third Round SHA-3 Candidates

In this paper we present the implementation results for all five SHA-3 third round candidate algorithms, BLAKE, Grøstl, JH, Keccak, and Skein in a standard-cell-based ASIC realized using 65nm CMOS technology. The ASIC includes two sets of implementations developed independently and with different optimization targets, and includes a reference SHA-2 implementation as well. We believe that having the results of two separate sets of implementations allows us to better identify the valid design space for all candidate algorithms. We present data showing the evolution of the solution space for each algorithm from simple synthesis estimations to the final implementation on the ASIC and show that post-layout results can differ by as much as 50% from synthesis results.
Epigenetics: A New Link Between Nutrition and Cancer

Emerging studies suggest that dietary components can affect gene expression through epigenetic mechanisms. Epigenetic modifications are heritable and potentially reversible changes in gene expression that do not require changes in the DNA sequence. The main mechanisms of epigenetic control in mammals are DNA methylation, histone modifications, and RNA silencing. The potential reversibility of epigenetic changes suggests that they could be modulated by nutrition and bioactive food compounds. Thus, epigenetic modifications could mediate environmental signals and provide a link between susceptibility genes and environmental factors in the etiology of cancer. Elucidating the impact of nutrition on epigenetic mechanisms may serve as a tool to predict an individuals’ susceptibility to cancer, provide dietary recommendations, or provide therapeutic applications of natural compounds against cancer. The optimal duration and the dose necessary for a chemopreventive effect require further studies. There is limited information about tissue specificity and temporal aspects of dietary treatments. Species differences need to be considered when interpreting results from various models. Importantly, molecular mechanisms of bioactive dietary components should be investigated in greater detail in human intervention studies. Although some of these issues remain controversial, this review mainly focuses on promising data that support the developing field of Nutritional Epigenetics.
Application of cardiac impedance signal in the reservoir-wave model of circulatory system in humans

Reservoir-wave model assumes that aortic blood pressure curve (Pao (t)) is a sum of two pressure components: first related to change in the blood volume within aorta(Pwk(t)), second related to axial velocity of blood along the aorta (Pex(t)). If impedance cardiography (ICG) signal tracks changes of blood volume within segment of thorax, it can be used to estimate Pwk(t) noninvasively in humans. During late diastole, according to reservoir-wave model Pao(t)= Pwk(t). Moreover, Pwk(t) in aorta and pressure in peripheral arteries should be similar. If these assumptions hold true, during late diastole, shapes of Pao(t), of pressure in peripheral arteries, and of impedance cardiography signal should be exponential decay curves with the same time constant. Parameters of exponential decay curves of radial pressure obtained with Finapres and of cardiac impedance were compared in 4 subjects. Different locations of ICG sensing electrodes were tested We found that degree of similarity between ICG and Finapres signals depends on the location of ICG sensing electrodes. Motion artifacts and O wave distorted ICG curves and diminished the similarity between the two curves. Least effected and most similar to decaying portion of radial pressure curve was the impedance signal obtained with sensing electrodes localized upon the abdominal aorta, but the shape of two signals still considerably varied. Thus, we conclude that impedance signal can be used to determine the parameters of Pwk(t) curve in humans only if essential improvement in gaining and processing of this signal will be applied.
Slope and $G$-set characterization of set-valued functions and applications to non-differentiable optimization problems

In this paper we derive a generalizing concept of G-norms, which we call G-sets, which is used to characterize minimizers of non-difierentiable regularization functionals. Moreover, the concept is closely related to the deflnition of slopes as published in a recent book by Ambrosio, Gigli, Savare. A paradigm of regularization models fltting in this framework is robust bounded variation regularization. Two essential properties of this regularization technique are documented in the literature and it is shown that these properties can also be achieved with metric regularization techniques.
Niches, models, and climate change: Assessing the assumptions and uncertainties

As the rate and magnitude of climate change accelerate, understanding the consequences becomes increasingly important. Species distribution models (SDMs) based on current ecological niche constraints are used to project future species distributions. These models contain assumptions that add to the uncertainty in model projections stemming from the structure of the models, the algorithms used to translate niche associations into distributional probabilities, the quality and quantity of data, and mismatches between the scales of modeling and data. We illustrate the application of SDMs using two climate models and two distributional algorithms, together with information on distributional shifts in vegetation types, to project fine-scale future distributions of 60 California landbird species. Most species are projected to decrease in distribution by 2070. Changes in total species richness vary over the state, with large losses of species in some “hotspots” of vulnerability. Differences in distributional shifts among species will change species co-occurrences, creating spatial variation in similarities between current and future assemblages. We use these analyses to consider how assumptions can be addressed and uncertainties reduced. SDMs can provide a useful way to incorporate future conditions into conservation and management practices and decisions, but the uncertainties of model projections must be balanced with the risks of taking the wrong actions or the costs of inaction. Doing this will require that the sources and magnitudes of uncertainty are documented, and that conservationists and resource managers be willing to act despite the uncertainties. The alternative, of ignoring the future, is not an option.
Intrusion Risk Analysis and the Power Law Distribution of Attacks

Risk analysis is the first essential step in the risk management process. In order to do an effective risk analysis, is necessary to identify and quantify the threats to information technology assets. Then statistical models of information security threats are required to develop effective risk analysis methodologies. We present experimental evidence suggesting that network intrusion attacks follows a power law distribution and then we explore some implications for intrusion risk analysis.
Fe<sub>3</sub>O<sub>4</sub> and Fe Nanoparticles by Chemical Reduction of Fe(acac)<sub>3</sub> by Ascorbic Acid: Role of Water

Nanoparticles of Fe3O4 and Fe are chemically synthesized by reduction of Fe(acac)3 using ascorbic acid in controlled condition. It was observed that addition of water during the chemical synthesis process yields Fe3O4 nanoparticles, whereas if the reaction is carried out in absence of water yields Fe nanoparticles—which get oxidized upon exposure to air atmosphere. Fe3O4 (15 ± 5 nm) and Fe/iron oxide nanoparticles (7 ± 1 nm) were successfully synthesized in the comparative study reported herewith. Mechanism for formation/synthesis of Fe3O4 and Fe/iron oxide nanoparticles is proposed herewith in which added water acts as an oxygen supplier. Physico-chemical characterization done by SEM, TEM, EDAX, and XPS supports the proposed mechanism.
Cognitive Biases and Emotional Wisdom in the Evolution of Conflict Between the Sexes

Two recent theories within evolutionary psychology have produced novel insights into conflict between the sexes. According to error management theory (EMT), asymmetries over evolutionary time in the cost-benefit consequences of specific social inferences have produced predictable cognitive biases. Women, for example, appear to underinfer commitment in response to signals of resource display. Men often overinfer a woman's sexual desire when she merely smiles at or casually touches them. These inferential biases, according to EMT, represent functional adaptations rather than markers of irrationality in information processing. According to strategic interference theory, certain “negative emotions' function to motivate action to reduce conflict produced by impediments to preferred social strategies. Emotions such as jealousy and anger, rather than reducing rationality, may embody inherited ancestral wisdom functional in dealing with interference inflicted by other individuals. These evolution-based theories have produced novel empirical discoveries and challenge traditional theories anchored in the premise that cognitive biases and negative emotions necessarily lead to irrationality.
Cytokine production by CD4+ T cells specific for coagulation factor VIII in healthy subjects and haemophilia A patients

Summary HaemophiliaA patients treated with human factorVIII (fVIII) may develop antibody (Ab) inhibitors to fVIII. FVIII-specific CD4+ T cells are common in haemophilia A patients, but also in healthy subjects who do not have a sustained anti-fVIII Ab response. Here, we examined the fVIII-induced IFNγ -, IL-4- and TGF- β 1-producing CD4+ T blasts by culturing peripheral blood mononuclear cells (PBMC) from controls and patients with recombinant fVIII. FVIII exposure significantly increased IFNγ - and IL-4-, but not TGF-β 1-producing CD4+ T blasts in patients with inhibitors. Patients without inhibitors had fVIII-induced IFNγ - andTGF-β 1-,but not IL-4-producing CD4+ T blasts.Controls did not have IL-4-producing CD4+ T blasts. However, controls whose PMBC proliferated in response to fVIII had fVIII-induced CD4+ T blasts that produced IFN-γ, the number of which correlated with the intensity of the proliferative response to fVIII of their PMBC, whereas controls whose PMBC did not proliferate to fVIII had predominantly fVIII-induced CD4+ T blasts that producedTGF- β 1.The presence in controls and patients without inhibitors of fVIII-induced IFN-γ -producing CD4 + T cells, but not IL-4-producing CD4+ T cells, which are abundant in inhibitor patients, suggests a role of Th1 cells in initiating the immune response to fVIII, and of Th2 cells in the development of strong inhibitor production. The polarized high ratios of Th3/Th1 and Th3/Th2 in controls and patients without inhibitors suggest that a preponderance ofTh3 cells in the response to fVIII may help to maintain tolerance to fVIII.
Epidemiology of human African trypanosomiasis

Human African trypanosomiasis (HAT), or sleeping sickness, is caused by Trypanosoma brucei gambiense, which is a chronic form of the disease present in western and central Africa, and by Trypanosoma brucei rhodesiense, which is an acute disease located in eastern and southern Africa. The rhodesiense form is a zoonosis, with the occasional infection of humans, but in the gambiense form, the human being is regarded as the main reservoir that plays a key role in the transmission cycle of the disease. The gambiense form currently assumes that 98% of the cases are declared; the Democratic Republic of the Congo is the most affected country, with more than 75% of the gambiense cases declared. The epidemiology of the disease is mediated by the interaction of the parasite (trypanosome) with the vectors (tsetse flies), as well as with the human and animal hosts within a particular environment. Related to these interactions, the disease is confined in spatially limited areas called “foci”, which are located in Sub-Saharan Africa, mainly in remote rural areas. The risk of contracting HAT is, therefore, determined by the possibility of contact of a human being with an infected tsetse fly. Epidemics of HAT were described at the beginning of the 20th century; intensive activities have been set up to confront the disease, and it was under control in the 1960s, with fewer than 5,000 cases reported in the whole continent. The disease resurged at the end of the 1990s, but renewed efforts from endemic countries, cooperation agencies, and nongovernmental organizations led by the World Health Organization succeeded to raise awareness and resources, while reinforcing national programs, reversing the trend of the cases reported, and bringing the disease under control again. In this context, sustainable elimination of the gambiense HAT, defined as the interruption of the transmission of the disease, was considered as a feasible target for 2030. Since rhodesiense HAT is a zoonosis, where the animal reservoir plays a key role, the interruption of the disease’s transmission is not deemed feasible.
Blood Flow Clustering and Applications inVirtual Stenting of Intracranial Aneurysms

Understanding the hemodynamics of blood flow in vascular pathologies such as intracranial aneurysms is essential for both their diagnosis and treatment. Computational fluid dynamics (CFD) simulations of blood flow based on patient-individual data are performed to better understand aneurysm initiation and progression and more recently, for predicting treatment success. In virtual stenting, a flow-diverting mesh tube (stent) is modeled inside the reconstructed vasculature and integrated in the simulation. We focus on steady-state simulation and the resulting complex multiparameter data. The blood flow pattern captured therein is assumed to be related to the success of stenting. It is often visualized by a dense and cluttered set of streamlines.We present a fully automatic approach for reducing visual clutter and exposing characteristic flow structures by clustering streamlines and computing cluster representatives. While individual clustering techniques have been applied before to streamlines in 3D flow fields, we contribute a general quantitative and a domain-specific qualitative evaluation of three state-of-the-art techniques. We show that clustering based on streamline geometry as well as on domain-specific streamline attributes contributes to comparing and evaluating different virtual stenting strategies. With our work, we aim at supporting CFD engineers and interventional neuroradiologists.
A Case Study on Example-Based Parsing

The paper describes an example-based parser for Chinese: Tree structure whose size is equal or smaller than the sentence to be parsed are retrieved from a treebank and aligned with the sentence. Subsequent structural adaptations handle unknown words, type shifting and metaphorical extensions of words. Derivational adaptations reanalyze awkward subtrees in order to auto-correct badly matched trees and insert unmatched, previously deleted words. This strategy is crucial for parsing long sentences. We try to illustrate the function of the parser through the analysis of one example sentence in different parsing models. The main concern is to find an optimal strategy for the retrieval of appropriate tree structures and to demonstrate the advantages of fuzzy matches.