Miracle-dz/UniFAR-FTUs huggingface dataset:
Deforming meshes that split and merge

We present a method for accurately tracking the moving surface of deformable materials in a manner that gracefully handles topological changes. We employ a Lagrangian surface tracking method, and we use a triangle mesh for our surface representation so that fine features can be retained. We make topological changes to the mesh by first identifying merging or splitting events at a particular grid resolution, and then locally creating new pieces of the mesh in the affected cells using a standard isosurface creation method. We stitch the new, topologically simplified portion of the mesh to the rest of the mesh at the cell boundaries. Our method detects and treats topological events with an emphasis on the preservation of detailed features, while simultaneously simplifying those portions of the material that are not visible. Our surface tracker is not tied to a particular method for simulating deformable materials. In particular, we show results from two significantly different simulators: a Lagrangian FEM simulator with tetrahedral elements, and an Eulerian grid-based fluid simulator. Although our surface tracking method is generic, it is particularly well-suited for simulations that exhibit fine surface details and numerous topological events. Highlights of our results include merging of viscoplastic materials with complex geometry, a taffy-pulling animation with many fold and merge events, and stretching and slicing of stiff plastic material.
The Plasmodium PHIST and RESA-Like Protein Families of Human and Rodent Malaria Parasites

The phist gene family has members identified across the Plasmodium genus, defined by the presence of a domain of roughly 150 amino acids having conserved aromatic residues and an all alpha-helical structure. The family is highly amplified in P. falciparum, with 65 predicted genes in the genome of the 3D7 isolate. In contrast, in the rodent malaria parasite P. berghei 3 genes are identified, one of which is an apparent pseudogene. Transcripts of the P. berghei phist genes are predominant in schizonts, whereas in P. falciparum transcript profiles span different asexual blood stages and gametocytes. We pursued targeted disruption of P. berghei phist genes in order to characterize a simplistic model for the expanded phist gene repertoire in P. falciparum. Unsuccessful attempts to disrupt P. berghei PBANKA_114540 suggest that this phist gene is essential, while knockout of phist PBANKA_122900 shows an apparent normal progression and non-essential function throughout the life cycle. Epitope-tagging of P. falciparum and P. berghei phist genes confirmed protein export to the erythrocyte cytoplasm and localization with a punctate pattern. Three P. berghei PEXEL/HT-positive exported proteins exhibit at least partial co-localization, in support of a common vesicular compartment in the cytoplasm of erythrocytes infected with rodent malaria parasites.
Perceived partner support and psychosexual adjustment to breast cancer

Support from a partner can play a key role in a woman's emotional adjustment to breast cancer. However, little is known about the influence of partner behaviours on a woman's sexual adjustment. This study examined the prospective relationship between baseline levels of several types of perceived partner support (instrumental, informational, emotional and negative) and psychosexual adjustment (sexual functioning and relationship satisfaction) over the course of 12 months post-surgery in a sample of 130 women with breast cancer. Results indicated that perceptions of greater emotional and informational support from the partner at baseline were associated with less sexual difficulties among breast cancer patients concurrently and 6 months post-surgery. Baseline perceptions of greater emotional and instrumental support from a partner were associated with greater relationship satisfaction at all time points. Perceptions of informational support at baseline were related to greater concurrent relationship satisfaction. Baseline perceptions of negative partner support were related to less relationship satisfaction, but only concurrently. These findings suggest that the perception of a partner's provision of emotional, instrumental and informational support may each play a role in facilitating sexual adjustment and relationship satisfaction.
Hypercrossing Number: A New and Effective Cost Function for Cell Placement Optimization

{ Traditionally, the algorithms that optimize placement of cells in a VLSI layout rely on a cost function that includes a distance metric. The choice of a cost function may limit the choices in devising new, more e(cid:14)cient and more e(cid:11)ective algorithms. The metric we propose relies on the interval graph of net nodes, induced by each speci(cid:12)c placement of cells into a row. Nominally, the metric associated with this graph is the chromatic number ((cid:31)). The new cost function, proposed in this paper, is the hypercrossing number (HC), de(cid:12)ned by the cardinality of the edge-set of the interval graph. This metric relates to the edge crossing number (EC) in the corresponding bipartite graph, depends on cell and net order only, and is independent of the target technology.
Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile

MOTIVATION Bicoid protein molecules, translated from maternally provided bicoid mRNA, establish a concentration gradient in Drosophila early embryonic development. There is experimental evidence that the synthesis and subsequent destruction of this protein is regulated at source by precise control of the stability of the maternal mRNA. Can we infer the driving function at the source from noisy observations of the spatio-temporal protein profile? We use non-parametric Gaussian process regression for modelling the propagation of Bicoid in the embryo and infer aspects of source regulation as a posterior function. RESULTS With synthetic data from a 1D diffusion model with a source simulated to model mRNA stability regulation, our results establish that the Gaussian process method can accurately infer the driving function and capture the spatio-temporal dynamics of embryonic Bicoid propagation. On real data from the FlyEx database, too, the reconstructed source function is indicative of stability regulation, but is temporally smoother than what we expected, partly due to the fact that the dataset is only partially observed. To be in line with recent thinking on the subject, we also analyse this model with a spatial gradient of maternal mRNA, rather than being fixed at only the anterior pole. CONTACT m.niranjan@southampton.ac. uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
AESOP: Expressing Concurrency in High-Performance System Software

High-performance computing (HPC) and distributed systems rely on a diverse collection of system soft-ware to provide application services, including file systems, schedulers, and web services. Such system software services must manage highly concurrent requests, interact with a wide range of resources, and scale well in order to be successful. Unfortunately, no single programming model for distributed system software currently offers optimal performance and productivity for all these tasks. While numerous libraries, languages, and language extensions have been developed in recent years to simplify parallel computation, they do not address the challenges of distributed system software in which concurrency control involves a variety of hardware and network devices, not just computational resources. In this work we present AESOP, a new programming language and programming model designed to implement distributed system software with high development productivity and run-time efficiency. AESOP is a superset of the C language that describes blocks of code to be executed concurrently without dictating whether that concurrency will be provided by a threading, event, or other model. This decoupling enables system software to adjust to different architectures, device APIs, and workloads without any change to the core algorithm implementation. AESOP also provides additional language constructs to simplify common system software development tasks. We evaluate AESOP by implementing a basic file server and comparing its performance, memory efficiency, and developer productivity with several thread-based and event-based implementations. AESOP is shown to provide competitive performance to traditional distributed system software development models while at the same time reducing code complexity and enhancing developer productivity.
Immunotolerant Properties of Mesenchymal Stem Cells: Updated Review

Stem cell transplantation is a potential therapeutic option to regenerate damaged myocardium and restore function after infarct. Current research is focused on the use of allogeneic mesenchymal stem cells (MSCs) due to their unique immunomodulatory characteristics and ability to be harvested from young and healthy donors. Both animal and human studies support the immunoprivileged state of MSCs and even demonstrate improvements in cardiac function after transplantation. This research continues to be a topic of interest, as advances will ultimately enable the clinical use of these universal cells for therapy after a myocardial infarction. Updated in vitro, in vivo, and clinical trial studies are discussed in detail in the following review.
The Information Contained in the Exercise of Executive Stock Options

This paper investigates the use by insiders of private information in their decision to exercise executive stock options. It is the first to categorise the exercise of an executive stock option by the proportion of stock sold at exercise. Consistent with existing research, exercises overall do not yield subsequent abnormal returns. However, we find a marked and significant difference in subsequent performance between exercises categorised as ‘high’ and ‘low’ sale proportion respectively. Therefore, while the exercise decision may appear uninformed, this study demonstrates that executives do use private information in their exercise and corresponding sale decisions. Further, near-the-money exercises produce negative abnormal returns, consistent with such exercises being relatively expensive. These results need to be reflected in the valuation of executive stock options, and hence the compensation executives derive from them.
On Enhancing Concurrency in Distributed Software Transactional Memory

Distributed software transactional memory (STM) promises to alleviate difficulties with lockbased (distributed) synchronization and object performance bottlenecks in distributed systems. The existing distributed STM model based on globally-consistent contention management policies may abort many transactions that could potentially commit without violating correctness. To reduce unnecessary aborts and increase concurrency, we propose the distributed dependencyaware (DDA) model for distributed STM, which adopts different conflict resolution strategies based on the types of transactions.In the DDA model, read-only transactions never abort by keeping a set of versions for each object. Each transaction only keeps precedence relations based on its local knowledge of precedence relations.The DDA model that, when a transaction reads from or writes to an object based on its local knowledge, the underlying precedence graph remains acyclic. We propose starvation-free multi-version (SF-MV)-permissiveness, which ensures that: 1) read-only transactions never abort; and 2) every transaction eventually commits. The DDA model satisfies SF-MV-permissiveness with high probability. We present a set of algorithms to support the DDA model, prove its correctness and permissiveness, and show that is supports invisible reads and efficiently garbage collects useless object versions. Our experimental results show that the DDA model outperforms existing contention management policies by 30%-40% in average in high contention environments.
Quantifying the Clinical Significance of Cannabis Withdrawal

Background and Aims Questions over the clinical significance of cannabis withdrawal have hindered its inclusion as a discrete cannabis induced psychiatric condition in the Diagnostic and Statistical Manual of Mental Disorders (DSM IV). This study aims to quantify functional impairment to normal daily activities from cannabis withdrawal, and looks at the factors predicting functional impairment. In addition the study tests the influence of functional impairment from cannabis withdrawal on cannabis use during and after an abstinence attempt. Methods and Results A volunteer sample of 49 non-treatment seeking cannabis users who met DSM-IV criteria for dependence provided daily withdrawal-related functional impairment scores during a one-week baseline phase and two weeks of monitored abstinence from cannabis with a one month follow up. Functional impairment from withdrawal symptoms was strongly associated with symptom severity (p = 0.0001). Participants with more severe cannabis dependence before the abstinence attempt reported greater functional impairment from cannabis withdrawal (p = 0.03). Relapse to cannabis use during the abstinence period was associated with greater functional impairment from a subset of withdrawal symptoms in high dependence users. Higher levels of functional impairment during the abstinence attempt predicted higher levels of cannabis use at one month follow up (p = 0.001). Conclusions Cannabis withdrawal is clinically significant because it is associated with functional impairment to normal daily activities, as well as relapse to cannabis use. Sample size in the relapse group was small and the use of a non-treatment seeking population requires findings to be replicated in clinical samples. Tailoring treatments to target withdrawal symptoms contributing to functional impairment during a quit attempt may improve treatment outcomes.
A linear signal combination model for UWB applications

Systems that use UWB technology based on communication with baseband signals of very short duration recently attract attention in communication and radar application, and thereof have been improving rapidly. Because UWB signals occupy a spectrum that is spread about very wide frequency band, one of the principal issues that need to be considered in UWB applications is the frequency allocation. In order to minimize or prevent possible distorting interferences with existing communication systems, spectral distribution of mandatory EIRP limit values has been determined by FCC in UWB applications. In this study, a linear signal combination model has been established and on mathematical expressions have been provided for production of wave forms are suitable UWB emission mask specified by FCC.
Voronoi coverage control with time-driven communication for mobile sensing networks with obstacles

It is known that the optimal sensor coverage of a mission space is performed by the Voronoi coverage. Aside from the energy required to move, communication among sensors consumes a large amount of their limited energy. So, to reduce communication energy, we propose a distributed control method that deploys sensors avoiding the obstacles by means of time-driven communication. We apply a potential field method to avoid obstacles. We propose a control method that consists of two processes: Voronoi update process and position update process. In the Voronoi update process, the sensor communicates with the other sensors and exchange information about their positions, periodically. Then, the sensing area of the sensor is updated using their positions. On the other hand, in the position update process, each sensor moves to the optimal position to increase its sensing performance on its sensing area which is fixed in the process. Thus, it does not need to communicate with the other sensors in the process. We show that a locally optimal sensor position is a locally uniformly asymptotically stable equilibrium point by the proposed method.
Cortical and Clonal Contribution of Tbr2 Expressing Progenitors in the Developing Mouse Brain

The individual contribution of different progenitor subtypes towards the mature rodent cerebral cortex is not fully understood. Intermediate progenitor cells (IPCs) are key to understanding the regulation of neuronal number during cortical development and evolution, yet their exact contribution is much debated. Intermediate progenitors in the cortical subventricular zone are defined by expression of T-box brain-2 (Tbr2). In this study we demonstrate by using the Tbr2Cre mouse line and state-of-the-art cell lineage labeling techniques, that IPC derived cells contribute substantial proportions 67.5% of glutamatergic but not GABAergic or astrocytic cells to all cortical layers including the earliest generated subplate zone. We also describe the laminar dispersion of clonally derived cells from IPCs using a recently described clonal analysis tool (CLoNe) and show that pair-generated cells in different layers cluster closer (142.1 ± 76.8 μm) than unrelated cells (294.9 ± 105.4 μm). The clonal dispersion from individual Tbr2 positive intermediate progenitors contributes to increasing the cortical surface. Our study also describes extracortical contributions from Tbr2+ progenitors to the lateral olfactory tract and ventromedial hypothalamic nucleus.
Joint Beam Selection and Power Allocation for Multiple Target Tracking in Netted Colocated MIMO Radar System

In this paper, a joint beam selection and power allocation (JBSPA) strategy is developed for multiple target tracking in netted colocated multiple-input multiple-output radar system. Each radar in this network adopts a multibeam working mode, in which multiple simultaneous transmit beams are synthesized. The basis of the JBSPA strategy is to use the optimization technique to control the limited beam and power resource of each radar in order to achieve accurate target state estimation. The Bayesian Cramér-Rao lower bound is derived, normalized, and subsequently utilized, as the optimization criterion for the JBSPA strategy. The resulting optimization problem consists of two adaptable parameters, one for beam selection and the other for power allocation. By introducing an auxiliary vector, a fast two-step solution technique is presented to jointly decide the number of beams generated by each radar, as well as the assignment and transmit power of each beam, subject to some resource constraints. Simulation results verify the superiority of the proposed JBSPA algorithm, in terms of the worst-case tracking accuracy of the multiple targets.
It’s a Book! It’s a Bookstore! Theories of Reading in the Worlds of Childhood and Adolescence

We believe in five-year-olds inking their names in big letters on the flyleaf. We believe in becoming someone else for four hundred pages. We believe in turning off the screens and unplugging the networks once in a while. We believe in meeting the author, reading the footnotes, looking up the words and checking the references. We believe in holding our children on our laps and turning the pages together.
In-Band Full-Duplex Communications for Cellular Networks with Partial Uplink/Downlink Overlap

In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization in cellular networks. However, the explicit impact of spatial interference, imposed by FD communications, on uplink and downlink transmissions has been overlooked in the literature. This paper presents an extensive study of the explicit effect of FD communications on the uplink and downlink performances. For the sake of rigorous analysis, we develop a tractable framework based on stochastic geometry toolset. The developed model accounts for uplink truncated channel inversion power control in FD cellular networks. The study shows that FD communications improve the downlink throughput at the expense of significant degradation in the uplink throughput. Therefore, we propose a novel fine-grained duplexing scheme, denoted as α-duplex scheme, which allows a partial overlap between uplink and downlink frequency bands. To this end, we show that the amount of the overlap can be optimized via adjusting α to achieve a certain design objective.
OMG - Emotion Challenge Solution

This short paper describes our solution to the 2018 IEEE World Congress on Computational Intelligence One-Minute Gradual-Emotional Behavior Challenge, whose goal was to estimate continuous arousal and valence values from short videos. We designed four base regression models using visual and audio features, and then used a spectral approach to fuse them to obtain improved performance.
Adult height variants affect birth length and growth rate in children

Previous studies identified 180 single nucleotide polymorphisms (SNPs) associated with adult height, explaining ∼10% of the variance. The age at which these begin to affect growth is unclear. We modelled the effect of these SNPs on birth length and childhood growth. A total of 7768 participants in the Avon Longitudinal Study of Parents and Children had data available. Individual growth trajectories from 0 to 10 years were estimated using mixed-effects linear spline models and differences in trajectories by individual SNPs and allelic score were determined. The allelic score was associated with birth length (0.026 cm increase per ‘tall’ allele, SE = 0.003, P = 1 × 10−15, equivalent to 0.017 SD). There was little evidence of association between the allelic score and early infancy growth (0–3 months), but there was evidence of association between the allelic score and later growth. This association became stronger with each consecutive growth period, per ‘tall’ allele per month effects were 0.015 SD (3 months–1 year, SE = 0.004), 0.023 SD (1–3 years, SE = 0.003) and 0.028 SD (3–10 years, SE = 0.003). By age 10, the mean height difference between individuals with ≤170 versus ≥191 ‘tall’ alleles (the top and bottom 10%) was 4.7 cm (0.8 SD), explaining ∼5% of the variance. There was evidence of associations with specific growth periods for some SNPs (rs3791675, EFEMP1 and rs6569648, L3MBTL3) and supportive evidence for previously reported age-dependent effects of HHIP and SOCS2 SNPs. SNPs associated with adult height influence birth length and have an increasing effect on growth from late infancy through to late childhood. By age 10, they explain half the height variance (∼5%) of that explained in adults (∼10%).
An important constraint on tropical cloud ‐ climate feedback

Tropical convective anvil clouds detrain preferentially near 200 hPa. It is argued here that this occurs because clear‐sky radiative cooling decreases rapidly near 200 hPa. This rapid decline of clear‐sky longwave cooling occurs because radiative emission from water vapor becomes inefficient above 200 hPa. The emission from water vapor becomes less important than the emission from CO2 because the saturation vapor pressure is so very low at the temperatures above 200 hPa. This suggests that the temperature at the detrainment level, and consequently the emission temperature of tropical anvil clouds, will remain constant during climate change. This constraint has very important implications for the potential role of tropical convective clouds in climate feedback, since it means that the emission temperatures of tropical anvil clouds and upper tropospheric water vapor are essentially independent of the surface temperature, so long as the tropopause is colder than the temperature where emission from water vapor becomes relatively small.