Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasma Membrane Phosphatidylinositol 4,5 Bisphosphate Is Required for Internalization of Foot-and-Mouth Disease Virus and Vesicular Stomatitis Virus

Phosphatidylinositol-4,5-bisphosphate, PI(4,5)P2, is a phospholipid which plays important roles in clathrin-mediated endocytosis. To investigate the possible role of this lipid on viral entry, two viruses important for animal health were selected: the enveloped vesicular stomatitis virus (VSV) − which uses a well characterized clathrin mediated endocytic route − and two different variants of the non-enveloped foot-and-mouth disease virus (FMDV) with distinct receptor specificities. The expression of a dominant negative dynamin, a PI(4,5)P2 effector protein, inhibited the internalization and infection of VSV and both FMDV isolates. Depletion of PI(4,5)P2 from plasma membrane using ionomycin or an inducible system, and inhibition of its de novo synthesis with 1-butanol revealed that VSV as well as FMDV C-S8c1, which uses integrins as receptor, displayed a high dependence on PI(4,5)P2 for internalization. Expression of a kinase dead mutant (KD) of phosphatidylinositol-4-phosphate-5-kinase Iα (PIP5K-Iα), an enzyme responsible for PI(4,5)P2 synthesis that regulates clathrin-dependent endocytosis, also impaired entry and infection of VSV and FMDV C-S8c1. Interestingly FMDV MARLS variant that uses receptors other than integrins for cell entry was less sensitive to PI(4,5)P2 depletion, and was not inhibited by the expression of the KD PIP5K-Iα mutant suggesting the involvement of endocytic routes other than the clathrin-mediated on its entry. These results highlight the role of PI(4,5)P2 and PIP5K-Iα on clathrin-mediated viral entry.
Evaluation of the effect of co-financing on collaboration between health care, social services and social insurance in Sweden

Abstract In this paper, we present an ongoing research project aimed to determine the impact of co-financing on collaboration around patients with musculoskeletal disorders. A trial legislation that allows the social insurance, social services and health care services to unite in co-financing under joint political steering has been tested in different areas in Sweden. In a series of studies, we compare collaboration processes and health outcome for patients with musculoskeletal disorders between health centres with co-financing projects and control health centres without co-financing projects. In this paper the studies are described and some preliminary results are discussed.
NANOEMULSION FORMATION BY LOW-ENERGY METHODS: A REVIEW

The interest in nanoemulsions has experienced a continuous increase in the last years as evidenced by the numerous publications and comprehensive reviews on the subject. This enormous interest is triggered by the wide range of applications, namely in the pharmaceutical, cosmetic, food, chemical industries. Nanoemulsions (submicrometer-size droplets) have advantages over conventional emulsions (micrometer-size droplets) due to their small droplet size; it stipulates their stability against sedimentation or creaming and a transparent or translucent optical aspect (similar to that of microemulsions). Nanoemulsions are commonly prepared by high-energy methods using mechanical devices, which can produce intense disruptive forces, for example, high pressure homogenizers and ultrasound generators. Nanoemulsion formation by these methods is quite straightforward as the higher the energy input is, the smaller is the droplet size. However, the level of energy required to obtain nanometer-scaled droplets is very high, and therefore, cost-inefficient, especially considering that only a small amount of the energy produced is used for emulsification. In contrast, low-energy emul sification methods using the internal chemical energy of the system are often more energy efficient as only simple stirring is needed, and generally allow producing a smaller droplet size than high-energy methods. It has been also claimed that high-energy methods allow preparing nanoemulsions at higher oil-to-surfactant ratios than low-energy methods. The results obtained confirm that both PIT and PIC have the same mechanisms. However, there are still issues to be solved. One of them concerns the possibility to obtain nanoemulsions with the minimum droplet size and low polydispersity by the PIC method. It is likely that the kinetics of the emulsification process plays an important role in this emul sification method, which has not been taken sufficiently into account. Therefore, more research effort needs to be done on this subject. A more comprehensive knowledge on the mechanisms involved in nanoemulsion formation by low-energy methods will allow their optimization and consequently will extend the fields of their application. The interest in nanoemulsions has experienced a con
Bound-Constrained Polynomial Optimization Using Only Elementary Calculations

We provide a monotone nonincreasing sequence of upper bounds fkH(k≥1) converging to the global minimum of a polynomial f on simple sets like the unit hypercube in ℝn. The novelty with respect to the converging sequence of upper bounds in Lasserre [Lasserre JB (2010) A new look at nonnegativity on closed sets and polynomial optimization, SIAM J. Optim. 21:864–885] is that only elementary computations are required. For optimization over the hypercube [0, 1]n, we show that the new bounds fkH have a rate of convergence in O(1/k). Moreover, we show a stronger convergence rate in O(1/k) for quadratic polynomials and more generally for polynomials having a rational minimizer in the hypercube. In comparison, evaluation of all rational grid points with denominator k produces bounds with a rate of convergence in O(1/k2), but at the cost of O(kn) function evaluations, while the new bound fkH needs only O(nk) elementary calculations.
Extraction of Fetal QRS Complex from Abdominal ECG Signals

Background: Extraction of Fetal ECG signal from non-invasive abdominal ECG signal is an important clinical application. Fetal ECG signal provides significant and valuable information about the fetal heart growth and health condition. Objective: Abdominal signals are usually corrupted by high amplitude maternal ECG signals and often found superimposed with the Fetal ECG signal. Suppression of maternal peaks for proper Fetal ECG signal extraction is attempted in our work. Method: A multichannel Fetal ECG signal extraction procedure is proposed in this work using Multivariate Empirical Mode Decomposition (MEMD) and Singular Value Decomposition (SVD). Observation: Patient dataset from three pregnant women is used for evaluating our procedure. The proposed method produced an average detection accuracy of fetal heart rate of 85.33% (min: 75 and max: 100).
On the Use of TCP BBR in Cellular Networks

TCP BBR is a new TCP variant developed at Google, which, as of this year, is fully deployed in Google's internal WANs and used by services such as Google.com and YouTube. In contrast to other commonly used TCP variants, TCP BBR is not loss-based but model-based: It builds a model of the network path between communicating nodes in terms of bottleneck bandwidth and minimum round-trip delay and tries to operate at the point where all available bandwidth is used and the round-trip delay is at a minimum. Although TCP BBR has indeed resulted in lower latency and more efficient usage of bandwidth in fixed networks, its performance over cellular networks is less clear. This article studies TCP BBR in live mobile networks and through emulations, and compares its performance with TCP NewReno and TCP CUBIC, two of the most commonly used TCP variants. The results from these studies suggest that in most cases TCP BBR outperforms both TCP NewReno and TCP CUBIC. However, under precise network conditions, competing TCP BBR flows do not share the available bandwidth in a fair way, something that shows up, for example, when shorter TCP BBR flows struggle to get their fair share from longer ones.
Robust feature tracking for endoscopic pose estimation and structure recovery

Minimally invasive surgery is a highly complex medical discipline with several difficulties for the surgeon. To alleviate these difficulties, augmented reality can be used for intraoperative assistance. For visualization, the endoscope pose must be known which can be acquired with a SLAM (Simultaneous Localization and Mapping) approach using the endoscopic images. In this paper we focus on feature tracking for SLAM in minimally invasive surgery. Robust feature tracking and minimization of false correspondences is crucial for localizing the endoscope. As sensory input we use a stereo endoscope and evaluate different feature types in a developed SLAM framework. The accuracy of the endoscope pose estimation is validated with synthetic and ex vivo data. Furthermore we test the approach with in vivo image sequences from da Vinci interventions.
A knowledge-driven quasi-global registration of thoracic-abdominal CT and CBCT for image-guided interventions

In this work, we have developed a novel knowledge-driven quasi-global method for fast and robust registration of thoracic-abdominal CT and cone beam CT (CBCT) scans. While the use of CBCT in operating rooms has become a common practice, there is an increasing demand on the registration of CBCT with pre-operative scans, in many cases, CT scans. One of the major challenges of thoracic-abdominal CT/CBCT registration is from various fields of view (FOVs) of the two imaging modalities. The proposed approach utilizes a priori knowledge of anatomy to generate 2D anatomy targeted projection (ATP) images that surrogate the original volumes. The use of lower dimension surrogate images can significantly reduce the computation cost of similarity evaluation during optimization and make it practically feasible to perform global optimization based registration for image-guided interventional procedures. Another a priori knowledge about the local optima distribution on energy curves is further used to effectively select multi-starting points for registration optimization. 20 clinical data sets were used to validate the method and the target registration error (TRE) and maximum registration error (MRE) were calculated to compare the performance of the knowledge-driven quasi-global registration against a typical local-search based registration. The local search based registration failed on 60% cases, with an average TRE of 22.9mm and MRE of 28.1mm; the knowledge-driven quasi-global registration achieved satisfactory results for all the 20 data sets, with an average TRE of 3.5mm, and MRE of 2.6mm. The average computation time for the knowledge-driven quasi-global registration is 8.7 seconds.
Speed versus accuracy in neural sequence tagging for natural language processing

Sequence Tagging, including part of speech tagging, chunking and named entity recognition, is an important task in NLP. Recurrent neural network models such as Bidirectional LSTMs have produced impressive results on sequence tagging. In this work, we first present a Bidirectional LSTM neural network model for sequence tagging tasks. Then we show a simple and fast greedy sequence tagging system using a feedforward neural network. We compare the speed and accuracy between the Bidirectional LSTM model and the greedy feedforward model. In addition, we propose two new models based on Mention2Vec by Stratos (2016): Feedforward-Mention2Vec for named entity recognition and chunking, and BPEMention2Vec for part-of-speech tagging. Feedforward-Mention2Vec predicts tag boundaries and corresponding types separately. BPE-Mention2Vec uses the Byte Pair Encoding algorithm to segment words first and then predicts the part-of-speech tags for the subword spans. We carefully design the experiments to demonstrate the speed and accuracy tradeoff in different models. The empirical results reveal that the greedy feedforward model can achieve comparable accuracy and faster speed than recurrent models for sequence tagging, and Feedforward-Mention2Vec is competitive with the fully structured BiLSTM model for named entity recognition while being more scalable in the number of named entity types.
Jointly Private Convex Programming

In this paper we present an extremely general method for approximately solving a large family of convex programs where the solution can be divided between different agents, subject to joint differential privacy. This class includes multi-commodity flow problems, general allocation problems, and multi-dimensional knapsack problems, among other examples. The accuracy of our algorithm depends on the \emph{number} of constraints that bind between individuals, but crucially, is \emph{nearly independent} of the number of primal variables and hence the number of agents who make up the problem. As the number of agents in a problem grows, the error we introduce often becomes negligible. We also consider the setting where agents are strategic and have preferences over their part of the solution. For any convex program in this class that maximizes \emph{social welfare}, there is a generic reduction that makes the corresponding optimization \emph{approximately dominant strategy truthful} by charging agents prices for resources as a function of the approximately optimal dual variables, which are themselves computed under differential privacy. Our results substantially expand the class of problems that are known to be solvable under both privacy and incentive constraints.
Real time stress analysis by a scanning infrared camera.

A method of real time stress analysis by a scanning infrared camera has been developed. The stress concentrations have been measured for the notched and cracked specimens made of aluminium alloy and mild steel. A macroscopic pattern of the stress distribution can be visualized momentarily according to the variation of the applied load. Data of the stress distribution can be stored in a video tape recorder, and accuracy has been improved by smoothing these data. Results are in good agreement with those by the finite element analysis. By means of this system, fatigue crack propagation can be monitored and the hysteresis energy in the cyclic plastic zone at the crack tip can be measured as well.
Role of the p55-gamma subunit of PI3K in ALK-induced cell migration: RNAi-based selection of cell migration regulators

ABSTRACT Recently, unbiased functional genetic selection identified novel cell migration-regulating genes. This RNAi-based functional selection was performed using 63,996 pooled lentiviral shRNAs targeting 21,332 mouse genes. After five rounds of selection using cells with accelerated or impaired migration, shRNAs were retrieved and identified by half-hairpin barcode sequencing using cells with the selected phenotypes. This selection process led to the identification of 29 novel cell migration regulators. One of these candidates, anaplastic lymphoma kinase (ALK), was further investigated. Subsequent studies revealed that ALK promoted cell migration through the PI3K-AKT pathway via the p55γ regulatory subunit of PI3K, rather than more commonly used p85 subunit. Western blot and immunohistochemistry studies using mouse brain tissues revealed similar temporal expression patterns of ALK, phospho-p55γ, and phospho-AKT during different stages of development. These data support an important role for the p55γ subunit of PI3K in ALK-induced cell migration during brain development.
The Evolutionary Legacy of Diversification Predicts Ecosystem Function

Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the “ELDERness surfaces. ” These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.
Semantic Typicality Effects in Primary Progressive Aphasia

Prototypical items within a semantic category are processed faster than atypical items within the same category. This typicality effect reflects normal representation and processing of semantic categories and when absent may be reflective of lexical–semantic deficits. We examined typicality effects in individuals with semantic and nonsemantic variants of primary progressive aphasia (PPA; semantic—PPA-S, agrammatic—PPA-G), a neurodegenerative disorder characterized by specific decline in language function, and age-matched controls. Using a semantic category verification task, where participants were asked to decide whether visual or auditory words (category typical, atypical, or nonmembers) belonged within a specified superordinate category, we found a typicality effect (ie, faster response times for typical vs atypical items) for all participant groups. However, participants with more severe PPA-S did not show a typicality effect in either modality. Findings may reflect increased intracategory semantic blurring as the disease progresses and semantic impairment becomes more severe.
Polypyrimidine Tract Binding Protein (hnRNP I) Is Possibly a Conserved Modulator of miRNA-Mediated Gene Regulation

MiRNAs can regulate gene expression through versatile mechanisms that result in increased or decreased expression of the targeted mRNA and it could effect the expression of thousands of protein in a particular cell. An increasing body of evidence suggest that miRNAs action can be modulated by proteins that bind to the same 3′UTRs that are targeted by miRNAs, suggesting that other factors apart from miRNAs and their target sites determine miRNA-modulation of gene expression. We applied an affinity purification protocol using biotinylated let-7 miRNA inhibitor to isolate proteins that are involved in let-7 mediated gene regulation that resulted in an affinity purification of Polypyrimidine Tract Binding protein (PTB). Here we show that PTB interacts with miRNAs and human Argonaute 2 (hAgo2) through RNA as well as identified potential mammalian cellular targets that are co-regulated by PTB and hAgo2. In addition, using genetic approach, we have demonstrated that PTB genetically interacts with Caenorhabditis elegans let-7 indicating a conserved role for PTB in miRNA-mediated gene regulation.
Impact of Combined Acute Rejection on BK Virus-Associated Nephropathy in Kidney Transplantation

BK virus-associated nephropathy (BKVAN) is one of the major causes of allograft dysfunction in kidney transplant (KT) patients. We compared BKVAN combined with acute rejection (BKVAN/AR) with BKVAN alone in KT patients. We retrospectively analyzed biopsy-proven BKVAN in KT patients from 2000 to 2011 at Seoul National University Hospital. Among 414 biopsies from 951 patients, biopsy-proven BKVAN was found in 14 patients. Nine patients had BKVAN alone, while 5 patients had both BKVAN and acute cellular rejection. BKVAN in the BKVAN alone group was detected later than in BKVAN/AR group (21.77 vs 6.39 months after transplantation, P=0.03). Serum creatinine at diagnosis was similar (2.09 vs 2.00 mg/dL). Histological grade was more advanced in the BKVAN/AR group (P=0.034). Serum load of BKV, dose of immunosuppressants, and tacrolimus level showed a higher tendency in the BKVAN alone group; however it was not statistically significant. After anti-rejection therapy, immunosuppression was reduced in the BKVAN/AR group. Renal functional deterioration over 1 yr after BKVAN diagnosis was similar between the two groups (P=0.665). These findings suggest that the prognosis of BKVAN/AR after anti-rejection therapy followed by anti-BKV therapy might be similar to that of BKVAN alone after anti-BKV therapy.
TLB Shootdown Mitigation for Low-Power Many-Core Servers with L1 Virtual Caches

Power efficiency has become one of the most important design constraints for high-performance systems. In this paper, we revisit the design of low-power virtually-addressed caches. While virtually-addressed caches enable significant power savings by obviating the need for Translation Lookaside Buffer (TLB) lookups, they suffer from several challenging design issues that curtail their widespread commercial adoption. We focus on one of these challenges–cache flushes due to virtual page remappings. We use detailed studies on an ARM many-core server to show that this problem degrades performance by up to 25 percent for a mix of multi-programmed and multi-threaded workloads. Interestingly, we observe that many of these flushes are spurious, and caused by an indiscriminate invalidation broadcast on ARM architecture. In response, we propose a low-overhead and readily implementable hardware mechanism using bloom filters to reduce spurious invalidations and mitigate their ill effects.
Major knowledge gaps and system barriers to guideline implementation among European physicians treating patients with atrial fibrillation: a European Society of Cardiology international educational needs assessment

Aims Guideline-adherent treatment is associated with improved prognosis in atrial fibrillation (AF) patients but is insufficiently implemented in clinical practice. The European Society of Cardiology (ESC) performed a multinational educational needs assessment study among cardiologists, general practitioners/family physicians (GPs/FPs), and neurologists in order to evaluate knowledge and skills of physicians and system factors related to AF care delivery. Methods and results A total of 561 physicians (294 cardiologists, 131 neurologists, and 136 GPs/FPs) from six European countries participated. This mixed-methods study included exploratory semi-structured qualitative interviews (n = 30) and a quantitative survey that included two clinical cases (n = 531). We identified eight key knowledge gaps and system barriers across all domains of AF care. A majority across all specialties reported skills needing improvement to classify AF pathophysiologically, rather than based on duration of episodes, and reported lack of availability of long-term electrocardiogram recording. Skills interpreting the CHA2DS2-VASc and the HAS-BLED scores were reported as needing improvement by the majority of neurologists (52% and 60%, respectively) and GPs/FPs (65% and 74%). Cardiologists calculated the CHA2DS2-VASc and HAS-BLED scores in 94%/70% in a presented case patient, but only 60%/49% of neurologists and 58%/42% of GPs/FPs did. There was much uncertainty on how to deal with anticoagulant therapy in complex patients. There was also a high disparity in using rate or rhythm control strategies, and indications for ablation. Information delivery to patients and communication between different specialties was often considered suboptimal, while national regulations and restrictions often hamper international guideline implementation. Conclusion We identified major gaps in physicians' knowledge and skills across all domains of AF care, as well as system factors hampering guideline-compliant care implementation and communication. These gaps should be addressed by targeted educational and advocacy efforts.