Miracle-dz/UniFAR-FTUs huggingface dataset:
Sustained baculovirus‐mediated expression in myogenic cells

Baculovirus has emerged as a promising gene delivery vector due to its low cytotoxicity and nonreplication nature in mammalian cells. However, baculovirus‐mediated expression is transient and generally lasts less than 14 days, which could restrict its application in the treatment of diseases requiring stable transgene expression.
The Timing of Initial Public Offerings

Abstract In this paper, we study the dynamics of initial public offerings (IPOs) by examining the tradeoff between an entrepreneur’s private benefits, which are lost whenever the firm is publicly traded, versus the advantages from diversification. We characterize the timing dimension of the decision to go public, derive a function for firm value, and describe their effect on the evolution of firm risk over time. Our model, which endogenizes the timing of the decision to stay private or to go public, is able explain two puzzling phenomena: the clustering of IPOs and buyouts in time and the long-run underperformance of recently issued stock relative to the shares of longer-listed companies.
Autonomous Agent for Deception Detection

Autonomous agents can be of assistance in detecting and reducing deception in computerized forums and chat-rooms. Although some deception detection methods exist they heavily rely on audio and visual information. Our focus is on text-based environments where there is no data of this type to use. We have developed DIG, an innovative machine learning-based autonomous agent, which joins a group of players as a regular member and assists them in catching a deceiver. We introduce “the pirate game” as a platform for deploying this agent. Our experimental study shows that although humans display difficulty detecting deception, DIG is not only capable of finding a deceptive player, but it also helps increase the entire group’s success.
Effect of Treadmill Exercise on Circulating Thyroid Hormone Measurements

Objectives: Effects of exercise on circulating thyroid hormone (TH) values remain controversial. We sought to observe the effect of treadmill exercise on serum TH values in highly selected subjects. Methods: Twenty-six healthy male military recruits aged 23–27 (mean, 25) years were studied. All had maintained identical diet and physical activity for a week before the test. Serum samples were drawn before (baseline) and immediately, 1, 4, 24, 24 and 48 h after maximal exercise (on a treadmill, Bruce protocol). All subjects completed the protocol with normal ECG results. Specimens were analyzed to measure 3,3′,5-triiodothyronine (T3), thyroxine (T4), free T4 (FT4), free T3 and thyroid-stimulating hormone (TSH) in the same assays. To determine the possible effect of hemodynamic changes, hematocrit (Hct)-adjusted data were also compared. Results: Hemoconcentration, as reflected by increased Hct, was found immediately after exercise. No significant changes of serum mean TH values before and after exercise were found except for TSH, which increased significantly immediately after exercise (1.72 vs. baseline 1.42 IU/l, p < 0.01). Values for T3, T4, and TSH increased significantly immediately after exercise, as compared to other postexercise values. However, the changes became insignificant after Hct adjustment. The FT4 values showed a reciprocal increase after exercise that became significant after Hct correction. Significantly negative correlation was found between FT4 and TSH values, but these values were still well within the normal range. Conclusions: Maximal treadmill exercise does not greatly affect the determination of concentrations of circulating THs.
A Shaped Temporal Filter Camera

Digital movie cameras only perform a discrete sampling of real-world imagery. While spatial sampling effects are well studied in the literature, there has not been as much work in regards to temporal sampling. As cameras get faster and faster, the need for conventional frame-rate video that matches the abilities of human perception remains. In this article, we introduce a system with controlled temporal sampling behavior. It transforms a high fps input stream into a conventional speed output video in real-time. We investigate the effect of different temporal sampling kernels and demonstrate that extended, overlapping kernels can mitigate aliasing artifacts. Furthermore, NPR effects, such as enhanced motion blur, can be achieved. By applying Fourier transforms in the temporal domain, we can also obtain novel tools for analyzing and visualizing time dependent effects. We demonstrate the effect of different sampling kernels in creating enhanced movies and stills of fast motion.
Constructing Short-Length Irregular LDPC Codes with Low Error Floor

Trapping sets (TSs) are known to cause error floors in regular and irregular low-density parity-check (LDPC) codes. By avoiding major error-contributing TSs during the code construction process, codes with low error floors can effectively be built. In it has been shown that TSs labeled as [w;u] are considered as being equivalent under the automorphism of the graph and are therefore contributing equally to the error floor. However, TSs with the same label [w;u] are not identical in general, particularly for the case of irregular LDPC codes. In this paper, we introduce a parameter e that can identify the number of "distinguishable" cycles in the connected subgraph induced by an elementary trapping set. Further, we propose a code construction algorithm, namely the Progressive-Edge-Growth Approximate-minimum-Cycle-Set-Extrinsic-message-degree (PEG-ACSE) method, that aims to avoid small elementary trapping sets (ETSs), particularly detrimental ETSs. We also develop theorems evaluating the minimum possible ETSs formed by PEG construction algorithms in general. We compare the characteristics of the codes built using the proposed method and those built using PEG-only or PEG-Approximate-minimum-Cycle-Extrinsic-message-degree (PEG-ACE) methods. Results from simulations show that the codes constructed using the proposed PEG-ACSE method produce lower error rates, particularly at the high signal-to-noise (SNR) region, compared with codes constructed using other PEG-based algorithms.
Deviation management during process execution

Software development companies have been putting a lot of effort in adopting process models, however two main issues remain. On the one hand, process models are inherently incomplete, since companies can not capture all possible situations in a single model. On the other hand, managers can not force process participants (agents) to strictly follow these models. The effect of both issues is that companies need to be able to handle deviations during process enactment. In order to make sure that process agents follow the process model and that their deviations get detected and handled, they adopt the so-called Process-centered Software Engineering Environments (PSEEs). Unfortunately, the options proposed by these tools, when it comes to handling a deviation, are rather limited to basically ignoring or forbidding it. In the present work, we face this limitation by presenting an approach for detecting, managing and tolerating agent deviations. Besides, in this paper we present the formal specification for this approach in the Linear Temporal Logic (LTL). It has been used as a the basis of our PSEE prototype.
Animal-Protein Intake Is Associated with Insulin Resistance in Adventist Health Study 2 (AHS-2) Calibration Substudy Participants: A Cross-Sectional Analysis

Abstract Background: High intakes of total and animal protein are associated with the risk of type 2 diabetes (T2D). The influence of protein type on insulin resistance, a key precursor of T2D, has not been extensively studied. Objective: The aim of this study was to determine the associations between dietary total, animal, and plant protein intakes as well as the animal-to-plant protein (AP) intake ratio with insulin resistance in middle-aged and older adults. Methods: This was a cross-sectional analysis in 548 participants (mean ± SD age: 66.2 ± 13.7 y) from the calibration substudy of the AHS-2 (Adventist Health Study 2) cohort. Participants consumed diets with a low AP intake ratio. Dietary intakes of total and particular types of protein were calculated from six 24-h dietary recalls. Participants completed a self-administered questionnaire on demographic, lifestyle, health, diet intake, and physical activity characteristics. Anthropometric variables including weight, height, and waist circumference were measured. Homeostasis model assessment of insulin resistance (HOMA-IR) was calculated by using fasting serum glucose and insulin. Multiple linear regression models were used to test the relations between total and specific protein intakes with insulin resistance. Results: The ranges of dietary intakes of animal and plant protein and the AP intake ratio were 0.4–87.4 and 14.0–79.2 g/d and 0.02–4.43, respectively. Dietary intakes per 10-g/d increments of total protein (β: 0.11; 95% CI: 0.02, 0.21) and animal protein (β: 0.11; 95% CI: 0.01, 0.20) and the AP intake ratio (β: 1.82; 95% CI: 0.80, 2.84) were positively related to HOMA-IR. Plant protein was not significantly related to insulin resistance. Conclusion: Total and animal protein intakes and the AP intake ratio were positively associated with HOMA-IR in adults with relatively a low intake of animal protein and a high consumption of plant protein.
The rph1 Gene Is a Common Contributor to the Evolution of Phosphine Resistance in Independent Field Isolates of Rhyzopertha Dominica

Phosphine is the only economically viable fumigant for routine control of insect pests of stored food products, but its continued use is now threatened by the world-wide emergence of high-level resistance in key pest species. Phosphine has a unique mode of action relative to well-characterised contact pesticides. Similarly, the selective pressures that lead to resistance against field sprays differ dramatically from those encountered during fumigation. The consequences of these differences have not been investigated adequately. We determine the genetic basis of phosphine resistance in Rhyzopertha dominica strains collected from New South Wales and South Australia and compare this with resistance in a previously characterised strain from Queensland. The resistance levels range from 225 and 100 times the baseline response of a sensitive reference strain. Moreover, molecular and phenotypic data indicate that high-level resistance was derived independently in each of the three widely separated geographical regions. Despite the independent origins, resistance was due to two interacting genes in each instance. Furthermore, complementation analysis reveals that all three strains contain an incompletely recessive resistance allele of the autosomal rph1 resistance gene. This is particularly noteworthy as a resistance allele at rph1 was previously proposed to be a necessary first step in the evolution of high-level resistance. Despite the capacity of phosphine to disrupt a wide range of enzymes and biological processes, it is remarkable that the initial step in the selection of resistance is so similar in isolated outbreaks.
A feasible user story tool for agile software development?

User stories form the heart of the Extreme Programming methodology planning game. In its turn, Extreme Programming is one of the supporting pillars of the wider agile software development process. The user stories form a set of central work products that determine the software development processes. In the spirit of Extreme Programming the production of user stories is kept as simple as possible. Traditionally, user stories are hand written on index cards as they are easy to store, display, rearrange and distribute to the co-located development team. However, virtually all other work products of an application development team are in electronic format, and agile software development is increasingly being adopted by teams working from remote locations. In these circumstances distributed development teams look to software solutions for creating and using user stories. This paper surveys some of the tools that are being used and examines their suitability for the task using a set of requirements. As a result of this investigation the author has produced a prototype user story software tool for Agile Software Development called DotStories. The paper concludes by discussing the features of DotStories and its how closely it can approach the ideal user story software tool. Indeed, the proposition that software tools can ever improve on index cards is considered in the light of experience to date.
Are Cloud Enabled Virtual Labs Economical? - A Case Study Analyzing Cloud based Virtual Labs for Educational Purposes

Cost efficiency is an often mentioned strength of cloud computing (Talukader et al., 2010). In times of decreasing educational budgets virtual labs provided by cloud computing might be an interesting alternative for higher education organizations or IT training facilities. This contribution analyzes the cost advantage of virtual educational labs provided via cloud computing means and compare these costs to costs of classical educational labs provided in a dedicated manner. This contribution develops a four step decision making model which might be interesting for colleges, universities or other IT training facilities planning to implement cloud based training facilities. Furthermore this contribution provides interesting findings when cloud computing has economical advantages in education and when not. The developed four step decision making model of general IaaSa applicability can be used to find out whether an IaaS cloud based virtual IT lab approach is more cost efficient than a dedicated approach. aInfrastructure as a Service. This contribution follows the IaaS, PaaS and SaaS definition of NIST (Mell and Grance, 2011).
Metamaterial-inspired high-absorption surfaces for thermal infrared applications

We present design, fabrication, and characterization results of a highly absorptive surface in the thermal infrared that draws on concepts from the frequency selective surface and metamaterials communities. At normal incidence this optically thin surface has an absorption of over 99%. Furthermore, it has a broad angular range (over 90% absorption at 60 degrees from normal). The simple structure is composed of a reflective metal layer, a roughly quarter-wave layer of lossy dielectric, and a top metal layer that is patterned with an array of subwavelength apertures. The design of the aperture allows spectral and angular control of the absorption/emission band. We will present simulation and measured results. Change in waveband and polarization could easily be changed from pixel to pixel in a focal plane array.
File systems deserve verification too!

File systems are too important, and current ones are too buggy, to remain unverified. Yet the most successful verification methods for functional correctness remain too expensive for current file system implementations --- we need verified correctness but at reasonable cost. This paper presents our vision and ongoing work to achieve this goal for a new high-performance flash file system, called BilbyFs. BilbyFs is carefully designed to be highly modular, so it can be verified against a high-level functional specification one component at a time. This modular implementation is captured in a set of domain specific languages from which we produce the design-level specification, as well as its optimised C implementation. Importantly, we also automatically generate the proof linking these two artefacts. The combination of these features dramatically reduces verification effort. Verified file systems are now within reach for the first time.
Analysis of Genes Involved in Body Weight Regulation by Targeted Re-Sequencing

Introduction Genes involved in body weight regulation that were previously investigated in genome-wide association studies (GWAS) and in animal models were target-enriched followed by massive parallel next generation sequencing. Methods We enriched and re-sequenced continuous genomic regions comprising FTO, MC4R, TMEM18, SDCCAG8, TKNS, MSRA and TBC1D1 in a screening sample of 196 extremely obese children and adolescents with age and sex specific body mass index (BMI) ≥ 99th percentile and 176 lean adults (BMI ≤ 15th percentile). 22 variants were confirmed by Sanger sequencing. Genotyping was performed in up to 705 independent obesity trios (extremely obese child and both parents), 243 extremely obese cases and 261 lean adults. Results and Conclusion We detected 20 different non-synonymous variants, one frame shift and one nonsense mutation in the 7 continuous genomic regions in study groups of different weight extremes. For SNP Arg695Cys (rs58983546) in TBC1D1 we detected nominal association with obesity (pTDT = 0.03 in 705 trios). Eleven of the variants were rare, thus were only detected heterozygously in up to ten individual(s) of the complete screening sample of 372 individuals. Two of them (in FTO and MSRA) were found in lean individuals, nine in extremely obese. In silico analyses of the 11 variants did not reveal functional implications for the mutations. Concordant with our hypothesis we detected a rare variant that potentially leads to loss of FTO function in a lean individual. For TBC1D1, in contrary to our hypothesis, the loss of function variant (Arg443Stop) was found in an obese individual. Functional in vitro studies are warranted.
HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status

Overexpression of HER2 is an important prognostic marker, and the only predictive biomarker of response to HER2-targeted therapies in invasive breast cancer. HER2-HER3 dimer has been shown to drive proliferation and tumor progression, and targeting of this dimer with pertuzumab alongside chemotherapy and trastuzumab, has shown significant clinical utility. The purpose of this study was to accurately quantify HER2-HER3 dimerisation in formalin fixed paraffin embedded (FFPE) breast cancer tissue as a novel prognostic biomarker. FFPE tissues were obtained from patients included in the METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) study. HER2-HER3 dimerisation was quantified using an improved fluorescence lifetime imaging microscopy (FLIM) histology-based analysis. Analysis of 131 tissue microarray cores demonstrated that the extent of HER2-HER3 dimer formation as measured by Förster Resonance Energy Transfer (FRET) determined through FLIM predicts the likelihood of metastatic relapse up to 10 years after surgery (hazard ratio 3.91 (1.61–9.5), p = 0.003) independently of HER2 expression, in a multivariate model. Interestingly there was no correlation between the level of HER2 protein expressed and HER2-HER3 heterodimer formation. We used a mathematical model that takes into account the complex interactions in a network of all four HER proteins to explain this counterintuitive finding. Future utility of this technique may highlight a group of patients who do not overexpress HER2 protein but are nevertheless dependent on the HER2-HER3 heterodimer as driver of proliferation. This assay could, if validated in a group of patients treated with, for instance pertuzumab, be used as a predictive biomarker to predict for response to such targeted therapies.
Thermal activation of PBTI-related stress and recovery processes in GaN MIS-HEMTs using on-wafer heaters

Threshold voltage instabilities are investigated in GaN-based metal-insulator-semiconductor (MIS) high-electron-mobility-transistors (HEMTs) with specially designed on-wafer heaters structures. The heaters are based on metal lines or 2-dimensional electron gas (2DEG) resistors and enable to choose the temperature during stress and recovery in the stress-recovery experiments independently. It allows to decouple thermal activation of capture (<; 0.9 eV) and emission (0.4-0.9 eV) processes at the dielectric/nitride interface, which is not possible in stress-recovery experiments performed at a common ambient temperature.
Seattle: a platform for educational cloud computing

Cloud computing is rapidly increasing in popularity. Companies such as RedHat, Microsoft, Amazon, Google, and IBM are increasingly funding cloud computing infrastructure and research, making it important for students to gain the necessary skills to work with cloud-based resources. This paper presents a free, educational research platform called Seattle that is community-driven, a common denominator for diverse platform types, and is broadly deployed. Seattle is community-driven -- universities donate available compute resources on multi-user machines to the platform. These donations can come from systems with a wide variety of operating systems and architectures, removing the need for a dedicated infrastructure. Seattle is also surprisingly flexible and supports a variety of pedagogical uses because as a platform it represents a common denominator for cloud computing, grid computing, peer-to-peer networking, distributed systems, and networking. Seattle programs are portable. Students' code can run across different operating systems and architectures without change, while the Seattle programming language is expressive enough for experimentation at a fine-grained level. Our current deployment of Seattle consists of about one thousand computers that are distributed around the world. We invite the computer science education community to employ Seattle in their courses.
The Irrevocable Multi-Armed Bandit Problem

This paper considers the multi-armed bandit problem with multiple simultaneous arm pulls and the additional restriction that we do not allow recourse to arms that were pulled at some point in the past but then discarded. This additional restriction is highly desirable from an operational perspective and we refer to this problem as the ‘Irrevocable Multi-Armed Bandit’ problem. We observe that natural modifications to well known heuristics for multi-armed bandit problems that satisfy this irrevocability constraint have unsatisfactory performance, and thus motivated introduce a new heuristic: the ‘packing’ heuristic. We establish through numerical experiments that the packing heuristic oers excellent performance, even relative to heuristics that are not constrained to be irrevocable. We also provide a theoretical analysis that studies the ‘price’ of irrevocability i.e. the performance loss incurred in imposing the constraint we propose on the multi-armed bandit model. We show that this performance loss is uniformly bounded for a general class of multi-armed bandit problems, and also indicate its dependence on various problem parameters. Finally, we obtain a computationally fast algorithm to implement the packing heuristic; the algorithm renders the packing heuristic computationally cheaper than methods that rely on the computation of Gittins indices.
The R+-Tree: A Dynamic Index for Multi-Dimensional Objects

The problem of indexing multidimensional objects is considered. First, a classification of existing methods is given along with a discussion of the major issues involved in multidimensional data indexing. Second, a variation to Guttman’s Rtrees (R+-trees) that avoids overlapping rectangles in intermediate nodes of the tree is introduced. Algorithms for searching, updating, initial packing and reorganization of the structure are discussed in detail. Finally, we provide analytical results indicating that R+-trees achieve up to 50% savings in disk accesses compared to an R-tree when searching files of thousands of rectangles.