Miracle-dz/UniFAR-FTUs huggingface dataset:
3D Reconstruction of VZV Infected Cell Nuclei and PML Nuclear Cages by Serial Section Array Scanning Electron Microscopy and Electron Tomography

Varicella-zoster virus (VZV) is a human alphaherpesvirus that causes varicella (chickenpox) and herpes zoster (shingles). Like all herpesviruses, the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus particles in the cytoplasm. Our recent work showed that VZV nucleocapsids are sequestered in nuclear cages formed from promyelocytic leukemia protein (PML) in vitro and in human dorsal root ganglia and skin xenografts in vivo. We sought a method to determine the three-dimensional (3D) distribution of nucleocapsids in the nuclei of herpesvirus-infected cells as well as the 3D shape, volume and ultrastructure of these unique PML subnuclear domains. Here we report the development of a novel 3D imaging and reconstruction strategy that we term Serial Section Array-Scanning Electron Microscopy (SSA-SEM) and its application to the analysis of VZV-infected cells and these nuclear PML cages. We show that SSA-SEM permits large volume imaging and 3D reconstruction at a resolution sufficient to localize, count and distinguish different types of VZV nucleocapsids and to visualize complete PML cages. This method allowed a quantitative determination of how many nucleocapsids can be sequestered within individual PML cages (sequestration capacity), what proportion of nucleocapsids are entrapped in single nuclei (sequestration efficiency) and revealed the ultrastructural detail of the PML cages. More than 98% of all nucleocapsids in reconstructed nuclear volumes were contained in PML cages and single PML cages sequestered up to 2,780 nucleocapsids, which were shown by electron tomography to be embedded and cross-linked by an filamentous electron-dense meshwork within these unique subnuclear domains. This SSA-SEM analysis extends our recent characterization of PML cages and provides a proof of concept for this new strategy to investigate events during virion assembly at the single cell level.
Tele-monitoring techniques to support recovery at home for survivors of a critical illness

This paper proposes and explores the design of a system that includes sensor-based procedures and techniques for remote physiological sensing and functional assessment for these individuals. The remote monitoring (e.g. heart rate, SpO2 level) and assessment system (6-minute walk test) was developed to support the recovery of survivors following a critical illness after their hospital discharge. The paper suggests a new model of care, through a clinician-patient remote monitoring loop, that will enable minimisation of the cost of frequent home visits and allow patients to recover safely in their home environment.
Improved Complexity Bounds for Computing with Planar Algebraic Curves

In this paper, we give improved bounds for the computational complexity of computing with planar algebraic curves. More specifically, for arbitrary coprime polynomials $f$, $g \in \mathbb{Z}[x,y]$ and an arbitrary polynomial $h \in \mathbb{Z}[x,y]$, each of total degree less than $n$ and with integer coefficients of absolute value less than $2^\tau$, we show that each of the following problems can be solved in a deterministic way with a number of bit operations bounded by $\tilde{O}(n^6+n^5\tau)$, where we ignore polylogarithmic factors in $n$ and $\tau$: (1) The computation of isolating regions in $\mathbb{C}^2$ for all complex solutions of the system $f = g = 0$, (2) the computation of a separating form for the solutions of $f = g = 0$, (3) the computation of the sign of $h$ at all real valued solutions of $f = g = 0$, and (4) the computation of the topology of the planar algebraic curve $\mathcal{C}$ defined as the real valued vanishing set of the polynomial $f$. Our bound improves upon the best currently known bounds for the first three problems by a factor of $n^2$ or more and closes the gap to the state-of-the-art randomized complexity for the last problem.
“I Like English Better”: Latino Dual Language Students’ Investment in Spanish, English, and Bilingualism

ABSTRACT This mixed-methodology study surveys 63 fifth graders in a one-way dual language school. Findings alarmingly indicate that although these students are native Spanish speakers in a school that delivers 50% of their instruction in Spanish, they prefer English both academically and socially. Subsequent interviews with 10 sample students of the larger study generate deeper understandings about how these students view their languages. If dual language programs are going to be maximally successful, then they must foster an environment that encourages students’ attitudes and investments toward both of their languages, taking particular care to protect and promote the minority language.
Predictors for Stroke and Death in Non-Anticoagulated Asian Patients with Atrial Fibrillation: The Fushimi AF Registry

Background Atrial fibrillation (AF) increases the risk of stroke and death. Data on the predictors for stroke and death in ‘real-world’ AF patients are limited, especially from large prospective Asian cohorts. Methods The Fushimi AF Registry is a community-based prospective survey designed to enroll all AF patients who visited the participating medical institutions in Fushimi-ku, Kyoto, Japan. Follow-up data were available for 3,304 patients (median follow-up period 741 days). We explored the predictors for ‘death, stroke, and systemic embolism (SE)’ during follow-up in 1,541 patients not receiving oral anticoagulants (OAC) at baseline. Results The mean age was 73.1 ± 12.5 years, and 673 (44%) patients were female. The mean CHADS2 and CHA2DS2-VASc scores were 1.76 and 3.08, respectively. Cumulative events were as follows: stroke/SE in 61 (4%) and death in 230 (15%), respectively. On multivariate analysis, advanced age (hazard ratio (HR): 1.68, 95% confidence interval (CI): 1.24–2.29), underweight (body mass index <18.5 kg/m2) (HR: 1.71, 95% CI: 1.25–2.32), previous stroke/SE/transient ischemic attack (HR: 1.70, 95% CI: 1.25–2.30), heart failure (HR: 1.59, 95% CI: 1.17–2.15), chronic kidney disease (HR: 1.53, 95% CI: 1.16–2.02), and anemia (HR: 2.41, 95% CI: 1.78–3.28) were independent predictors for death/stroke/SE. Cumulative numbers of these 6 risk predictors could stratify the incidence of death/stroke/SE in patients without OAC, as well as those with OAC in our registry. Conclusions Advanced age, underweight, previous stroke/SE/transient ischemic attack, heart failure, chronic kidney disease, and anemia were independently associated with the risk of death/stroke/SE in non-anticoagulated Japanese AF patients.
Sociodemographic factors and patient perceptions are associated with attitudes to kidney transplantation among haemodialysis patients.

BACKGROUND Treatment decisions made by patients with chronic kidney disease are crucial in the renal transplantation process. These decisions are influenced, amongst other factors, by attitudes towards different treatment options, which are modulated by knowledge and perceptions about the disease and its treatment and many other subjective factors. Here we study the attitude of dialysis patients to renal transplantation and the association of sociodemographic characteristics, patient perceptions and experiences with this attitude. METHODS In a cross-sectional study, all patients from eight dialysis units in Budapest, Hungary, who were on haemodialysis for at least 3 months were approached to complete a self-administered questionnaire. Data collected from 459 patients younger than 70 years were analysed in this manuscript. RESULTS Mean age of the study population was 53 +/- 12 years, 54% were male and the prevalence of diabetes was 22%. Patients with positive attitude to renal transplantation were younger (51 +/- 11 versus 58 +/- 11 years), better educated, more likely to be employed (11% versus 4%) and had prior transplantation (15% versus 7%)(P < 0.05 for all). In a multivariate model, negative patient perceptions about transplantation, negative expectations about health outcomes after transplantation and the presence of fears about the transplant surgery were associated, in addition to increasing age, with unwillingness to consider transplantation. CONCLUSIONS Negative attitudes to renal transplantation are associated with potentially modifiable factors. Based on this we suggest that it would be necessary to develop standardized, comprehensible patient information systems and personalized decision support to facilitate modality selection and to enable patients to make fully informed treatment decisions.
Helicase and Capping Enzyme Active Site Mutations in Brome Mosaic Virus Protein 1a Cause Defects in Template Recruitment, Negative-Strand RNA Synthesis, and Viral RNA Capping

ABSTRACT Brome mosaic virus (BMV) encodes two RNA replication proteins: 1a, which contains RNA capping and helicase-like domains, and 2a, which is related to polymerases. BMV 1a and 2a can direct virus-specific RNA replication in the yeast Saccharomyces cerevisiae, which reproduces the known features of BMV replication in plant cells. We constructed single amino acid point mutations at the predicted capping and helicase active sites of 1a and analyzed their effects on BMV RNA3 replication in yeast. The helicase mutants showed no function in any assays used: they were strongly defective in template recruitment for RNA replication, as measured by 1a-induced stabilization of RNA3, and they synthesized no detectable negative-strand or subgenomic RNA. Capping domain mutants divided into two groups. The first exhibited increased template recruitment but nevertheless allowed only low levels of negative-strand and subgenomic mRNA synthesis. The second was strongly defective in template recruitment, made very low levels of negative strands, and made no detectable subgenomes. To distinguish between RNA synthesis and capping defects, we deleted chromosomal geneXRN1, encoding the major exonuclease that degrades uncapped mRNAs. XRN1 deletion suppressed the second but not the first group of capping mutants, allowing synthesis and accumulation of large amounts of uncapped subgenomic mRNAs, thus providing direct evidence for the importance of the viral RNA capping function. The helicase and capping enzyme mutants showed no complementation. Instead, at high levels of expression, a helicase mutant dominantly interfered with the function of the wild-type protein. These results are discussed in relation to the interconnected functions required for different steps of positive-strand RNA virus replication.
Final Report: Unlocking Housing Equity in Japan

Previous literature on asset patterns by age has mostly overlooked housing wealth as a determinant of retiree wealth. Most of these studies focused on Western countries; only sparse literature is available on this issue in the Japanese context, despite its clear relevance to the challenge this nation faces in financing retirement. Releasing equity in housing may be a natural mechanism to boost consumption, reduce public pension liability, and mitigate the demand for long-term care facilities in Japan. In order to implement reverse mortgages (RMs), our analysis suggests that much could be done to remove inhibitors. Policies might include exempting RMs from capital gains tax and transactions tax. In addition, more favourable policies could be adopted regarding the tax status of annuity income flows and interest rate deductions for RMs. Clearly, housing market reforms to enhance information flows would be needed, particularly regarding new and existing housing trades. This would enable the securitization of housing loans and lines of credit. Finally, improvements in other aspects of capital markets would also serve the desired end, including the establishment of reinsurance mechanisms to help lenders offer these reverse mortgages while having some protection against crossover risk. The infrastructure required to build RM markets is not simple, and in the Japanese case, the demand will be dampened by the fact that residential housing values appear to be declining. This fact, plus low interest rates, imply that lenders will find reverse mortgages less appealing than otherwise. Nevertheless, RMs can be a good way to finance elderly consumption in Japan, particularly against the backdrop of governmental financial stringencies.
LONG-TERM INTEGRATION OF THE BAROTROPIC EQUATIONS BY THE LAX-WENDROFF METHOD*

Abstract The system of equations describing the motion of a barotropic fluid with a free surface is solved by using finite-difference methods which are based on the two-step Lax-Wendroff scheme proposed by Richtmyer. The model has rigid boundaries along two latitude circles and the beta-plane approximation is adopted. Initial conditions are given for an ageostrophic jet flow and computations are carried out up to 100 days or 19,200 time steps in order to observe the long-term stability and truncation error properties of the numerical schemes. A series of integrations is performed using different numerical formulations for the Coriolis term and the boundary conditions. A Fickian type smoothing is introduced to control truncation errors for some of the cases. It is found that the numerical results depend critically upon the method for handling the Coriolis term. One scheme gives a relatively constant total energy during the entire 100 days while the rest of the schemes either develop instability or give dam.
Integrated behavior models for factory automation systems

Despite the large amount of models for different aspects of factory automation systems, many of these models target at individual and in most cases static aspects of the system, such as the geometry or its electric parts. There is a lack of suitable description methods, which integrate these individual models to a behavior model including spatial aspects and the handling of material. Furthermore, it is important that this model keeps the link to the more detailed individual models and is sufficiently formal in order to allow an automated analysis. This paper provides a solution to this problem by introducing a model which addresses both spatial structure and behavior and is based on a thorough mathematical theory. Complementary, we report on a tool realization of the modelling theory and explain how the model supports the development of mechatronic systems.
When the shark bites the stingray : The night sky in the construction of the Manus world

It is argued that to understand the Manus' construction of their environment their view of the night sky has to be taken into account. In Manus thought, celestial bodies and constellations were believed to reside at the edge of a saucer-shaped world, being able to permeate sea and sky and interact with the peoples' immediate environment. While only a small number of constellations had been named, these were sufficient to function as a calendar, a visualization of the seasonal cycle and a metaphorical explanation of the seasons. As such, they made the Manus world autonomous in the sense that the causes supposed to bring about seasonal change were situated within this world or at its edge.
On the Robustness of Coordinated Beamforming to Uncoordinated Interference and CSI Uncertainty

As network deployments become denser, interference arises as a dominant performance degradation factor. To confront with this trend, Long Term Evolution (LTE) incorporated features aiming at enabling cooperation among different base stations, a technique termed as Coordinated Multi Point (CoMP). Recent field trial results and theoretical studies of the performance of CoMP schemes revealed, however, that their gains are not as high as initially expected, despite their large coordination overhead. In this paper, we review recent advanced Coordinated Beamforming (CB) schemes, a special family of CoMP that reduces the coordination overhead through a joint choice of transmit and receive linear filters. We focus on assessing their resilience to uncoordinated interference and Channel State Information (CSI) imperfections, which both severely limit the performance gains of all CoMP schemes. We present a simple yet encompassing system model that aims at incorporating different parameters of interest in the relative interference power and CSI errors, and then utilize it for the performance evaluation of the state-of-the-art in CB schemes. It is shown that blindly applying CB in all system scenarios can indeed be counter-productive.
Social Relations in Lebanon: Convoys Across the Life Course.

OBJECTIVES This study systematically analyzed convoys of social relations to investigate the ways in which gender and income shape patterns of social relations across the life course in Lebanon. METHODS Data were drawn from a representative sample of adults aged 18 and older in Greater Beirut, Lebanon (N = 500). Multiple linear regression and multilevel models were conducted to examine main and interactive effects of age, gender, and income on social relations. RESULTS Findings indicate main effects of age, income, and gender on network structure and relationship quality. Older age was associated with larger network size, greater proportion of kin in network, higher positive and lower negative relationship quality. Higher income was associated with larger network size and decreased contact frequency. Female gender was also associated with decreased contact frequency. Gender interacted with income to influence network size and network composition. Higher income was associated with a larger network size and higher proportion of kin for women. DISCUSSION Findings suggest diversity in the experience of social relations. Such nuance is particularly relevant to the Lebanese context where family is the main source of support in old age. Policy makers and program planners may need to refrain from viewing social relations simplistically.
Accelerating Simulation of Large-Scale IP Networks: A Network Invariant Preserving Approach

In this paper, we propose a simulation framework, TranSim, that reduces the rate at which packet-events are generated, in order to accelerate large-scale simulation of IP networks with TCP/UDP traffic. Conceptually, we transform an IP network into an alternate network that generates a smaller number of packet events, carry out simulation in the “transformed” network, and then extrapolate simulation results for the original network from those obtained in the “transformed” network. We formally prove that if the network invariant — the bandwidthdelay product — is preserved, the network dynamics, such as the queue dynamics and the packet dropping probability at each link, and TCP dynamics, such as the congestion window, RTTs, and rate dynamics, remain unchanged in the process of network transformation. We have implemented TranSim in ns-2, and conducted an empirical study to evaluate it against packet level simulation, with respect to the capability of capturing transient, packet level network dynamics, the reduction in the execution time and the memory usage, and the discrepancy in the system throughput. The simulation results indicate maximally two orders of magnitude improvement in the execution time and the performance improvement becomes more prominent as the network size increases (in terms of the number of nodes, the number of flows, the complexity of topology, and link capacity) or as the degree of downsizing increases. The memory usage incurred in TranSim is comparable to that in packet level simulation. The error discrepancy between TranSim and packet level simulation, on the other hand, is between 1-10 % in a wide variety of network topologies, inclusive of randomly generated topologies, and traffic loads with various AQM strategies.
Using eye tracking to compare how adults and children learn to use an unfamiliar computer game

The learnability principle was originally formulated with computer-based applications mainly for adults in mind. In this paper we compare how children and adults learn to use an unfamiliar computer game to determine whether learnability has different meanings across generations. We recorded eye tracking data while users taught themselves to play a computer game. Comparison of the on-screen focus points and eye gazing patterns showed that adults and children have different tactics when confronted with an unfamiliar game. It revealed aspects of software interfaces that adults and children approach differently. For example, children will focus on the game elements and use a trial-and-error approach instead of reading on-screen instructions, while adults are more willing to interrupt game play to read the instructions. The knowledge gained through this research will help designers to distinguish between the needs of users in different age groups and improve the learnability of their products.
Measurement and Management of the Lane Markings' Stripping Ratio from In-vehicle Camera Image

Natural weathering and time-related deterioration by running of vehicles can be seen in road markings. By deterioration of compartment lines, not only the drivers' visibility and the function of visual guidance are reduced but also the line recognition becomes non-functional in spite of important role for the autonomous driving. In this study, we aim to measure and manage the state of deterioration of lane markings. The stripping ratio is measured by image processing technique such as comparison between the pixels of white lines of the road image and the theoretical image that we generate. The road images are continuously synthesized with projection transform from road images taken by an in-vehicle camera and CAN (Controller Area Network) data logged when the vehicle is being driven. The theoretical images are automatically generated by seeking pixels where lane markings should be placed in the synthesis image. The Stripping ratio and the synthesized road images are managed by GIS (Geographic Information System). It is useful to survey the stripping ratio distribution for repainting. This paper, also confirmed the effectiveness of our proposed method through an experiment where the stripping ratio of lane markings was calculated from data obtained by a running vehicle.
Multiple Imputation by Ordered Monotone Blocks With Application to the Anthrax Vaccine Research Program

Multiple imputation (MI) has become a standard statistical technique for dealing with missing values. The CDC Anthrax Vaccine Research Program (AVRP) dataset created new challenges for MI due to the large number of variables of different types and the limited sample size. A common method for imputing missing data in such complex studies is to specify, for each of J variables with missing values, a univariate conditional distribution given all other variables, and then to draw imputations by iterating over the J conditional distributions. Such fully conditional imputation strategies have the theoretical drawback that the conditional distributions may be incompatible. When the missingness pattern is monotone, a theoretically valid approach is to specify, for each variable with missing values, a conditional distribution given the variables with fewer or the same number of missing values and sequentially draw from these distributions. In this article, we propose the “multiple imputation by ordered monotone blocks” approach, which combines these two basic approaches by decomposing any missingness pattern into a collection of smaller “constructed” monotone missingness patterns, and iterating. We apply this strategy to impute the missing data in the AVRP interim data. Supplemental materials, including all source code and a synthetic example dataset, are available online.