Miracle-dz/UniFAR-FTUs huggingface dataset:
– Lessons and Recommendations for Closed Source

Although the effectiveness of software inspection (formal peer review) has a long and mostly supportive history, the thought of reviewing a large, unfamiliar software artifact over a period of weeks is something dreaded by both the author and the reviewers. The dislike of this cumbersome process is natural, but neither the formality nor the aversion are fundamental characteristics of peer review. The core idea of review is simply to get an expert peer to examine your work for problems that you are blind to. The actual process is much less important for finding defects than the expertise of the people involved [1]. While developers will acknowledge the value of inspection, most avoid it and adoption of traditional inspection practices remains relatively low [2], [3]. Surprisingly, peer review is a prevalent practice in Open Source Software (OSS) projects, which have minimalist processes and consist of intrinsically motivated developers. We examined over 100K peer reviews in case studies on the Apache httpd server, Subversion, Linux, FreeBSD, KDE, and Gnome and noted an “efficient fit” between the needs of OSS developers and the evolution and minimalist structure of the peer review processes they use [4]. On these OSS projects, changes are asynchronously broadcast (usually on a mailing list) to the development team, and reviewers self-select changes that they are invested in and competent to review. Changes that are uninteresting often remain unreviewed. To find changes in what can be an overwhelming broadcast of information, OSS developers rely on simple email filters, descriptive email subjects, and detailed change logs. These change logs represent the “the heart beat of the project. ” Through them, developers maintain a conceptual understanding of the whole system and participate in the threaded email discussions and reviews for which they have the required expertise. This natural fit contrasts sharply with an enforced, but Figure 1. The spectrum of peer review techniques: From formal inspection to minimal-process OSS review. Tool supported, lightweight review provides a flexible, but traceable middle ground.
LMS coupled adaptive prediction and system identification: a statistical model and transient mean analysis

The LMS algorithm has been successfully used in many system identification problems. However, when the input data covariance matrix is ill-conditioned, the algorithm converges slowly. To overcome the slow convergence, an adaptive structure is studied, which incorporates an LMS adaptive predictor (prewhitener) prior to the LMS algorithm for system identification (canceler). Since the prewhitener is also adaptive, the input to the LMS canceler is nonstationary, even when the input is stationary. Because of the coupling and the nonstationarity of LMS canceler input, analysis of the performance of the two adaptations is extremely difficult. A simple theoretical model of the coupled adaptations is presented and analyzed. First and second moment analysis indicates that the adaptive predictor significantly speeds up the LMS canceler as compared to a system without prewhitening and enlarges the stability domain of the canceler (larger allowable /spl mu/). Monte-Carlo simulations are presented which are in good agreement with the predictions of the mathematical model. >
An analysis of value function learning with piecewise linear control

Reinforcement learning (RL) algorithms attempt to learn optimal control actions by iteratively estimating a long-term measure of system performance, the so-called value function. For example, RL algorithms have been applied to walking robots to examine the connection between robot motion and the brain, which is known as embodied cognition. In this paper, RL algorithms are analysed using an exemplar test problem. A closed form solution for the value function is calculated and this is represented in terms of a set of basis functions and parameters, which is used to investigate parameter convergence. The value function expression is shown to have a polynomial form where the polynomial terms depend on the plant's parameters and the value function's discount factor. It is shown that the temporal difference error introduces a null space for the differenced higher order basis associated with the effects of controller switching (saturated to linear control or terminating an experiment) apart from the time of the switch. This leads to slow convergence in the relevant subspace. It is also shown that badly conditioned learning problems can occur, and this is a function of the value function discount factor and the controller switching points. Finally, a comparison is performed between the residual gradient and TD(0) learning algorithms, and it is shown that the former has a faster rate of convergence for this test problem.
Mo-sleep: Unobtrusive sleep and movement monitoring via Wi-Fi signal

Sleep monitoring system helps to diagnose various health problems. Traditional solutions for sleep monitoring are usually invasive or limited to medical facilities. Radio Frequency (RF) based methods require specialized devices or dedicated wireless sensors. Recently, Wi-Fi based methods without any wearable or dedicated devices obtain more attention, however, they all assume that all the users are in a relatively quiet environment without moving targets. In this paper, we develop a system called Mo-Sleep, which adopts off-the-shelf Wi-Fi devices to continuously collect fine-grained wireless Channel State Information (CSI) in a room. We introduce a motion detection module in our system to identify whether the CSI information has been interfered by a moving target. We then use Principal Component Analysis (PCA) to obtain accurate breath signal. Our prototypic system demonstrates that the proposed scheme can not only remove interfered CSI, but also obtain real time breath rate every five seconds.
Ex Vivo Expansion of CD4+CD25+FoxP3+ T Regulatory Cells Based on Synergy between IL-2 and 4-1BB Signaling1

Naturally occurring CD4+CD25+FoxP3+ T regulatory (Treg) cells require three distinct signals transduced via TCR, CD28, and IL-2R for their development and maintenance. These requirements served as the basis for several recently developed ex vivo expansion protocols that relied on the use of solid support-bound Abs to CD3 and CD28 in the presence of high dose IL-2. We report in this study that Treg cells up-regulate the expression of inducible costimulatory receptor 4-1BB in response to IL-2, and stimulation using this receptor via a novel form of 4-1BB ligand (4-1BBL) fused to a modified form of core streptavidin (SA-4-1BBL) was effective in expanding these cells up to 110-fold within 3 wk. Expanded cells up-regulated CD25, 4-1BB, and membranous TGF-β, suppressed T cell proliferation, and prevented the rejection of allogeneic islets upon adoptive transfer into graft recipients. Importantly, SA-4-1BBL rendered CD4+CD25− T effector cells refractive to suppression by Treg cells. This dual function of signaling via 4-1BB, vis-à-vis Treg cell expansion and licensing T effector cells resistant to Treg cell suppression, as well as the up-regulation of 4-1BB by IL-2 may serve as important regulatory mechanisms for immune homeostasis following antigenic challenge. Stimulation using a soluble form of SA-4-1BBL represents a novel approach to expand Treg cells with potential therapeutic applications in autoimmunity and transplantation.
The pNNx files: re-examining a widely used heart rate variability measure

Objective: To re-examine the standard pNN50 heart rate variability (HRV) statistic by determining how other thresholds compare with the commonly adopted 50 ms threshold in distinguishing physiological and pathological groups. Design: Retrospective analysis of Holter monitor databases. Subjects: Comparison of HRV data between 72 healthy subjects and 43 with congestive heart failure (CHF); between sleeping and waking states in the 72 healthy subjects; and between 20 young and 20 healthy elderly subjects. Main outcome measures: Probability values for discriminating between groups using a family of pNN values ranging from pNN4 to pNN100. Results: For all three comparisons, pNN values substantially less than 50 ms consistently provided better separation between groups. For the normal versus CHF groups, p < 10−13 for pNN12 versus p < 10−4 for pNN50; for the sleeping versus awake groups, p < 10−21 for pNN12 versus p < 10−10 for pNN50; and for the young versus elderly groups, p < 10−6 for pNN28 versus p < 10−4 for pNN50. In addition, for the subgroups of elderly healthy subjects versus younger patients with CHF, p < 0.007 for pNN20 versus p < 0.17 for pNN50; and for the subgroup of New York Heart Association functional class I–II CHF versus class III–IV, p < 0.04 for pNN10 versus p < 0.13 for pNN50. Conclusions: pNN50 is only one member of a general pNNx family of HRV statistics. Enhanced discrimination between a variety of normal and pathological conditions is obtained by using pNN thresholds as low as 20 ms or less rather than the standard 50 ms threshold.
Flexible dynamic information flow control in Haskell

We describe a new, dynamic, floating-label approach to language-based information flow control, and present an implementation in Haskell. A labeled IO monad, LIO, keeps track of a current label and permits restricted access to IO functionality, while ensuring that the current label exceeds the labels of all data observed and restricts what can be modified. Unlike other language-based work, LIO also bounds the current label with a current clearance that provides a form of discretionary access control. In addition, programs may encapsulate and pass around the results of computations with different labels. We give precise semantics and prove confidentiality and integrity properties of the system.
Subtle conformational changes between CX3CR1 genetic variants as revealed by resonance energy transfer assays

The chemokine CX3CL1 is expressed as a membrane protein that forms a potent adhesive pair with its unique receptor CX3CR1. This receptor has 3 natural variants, V249‐T280 (VT), I249‐T280 (IT), and I249‐M280 (IM), whose relative frequencies are significantly associated with the incidence of various inflammatory diseases. To assess the adhesive potency of CX3CR1 and the molecular diversity of its variants, we assayed their clustering status and their possible structural differences by fluorescence/bioluminescence resonance energy transfer (FRET or BRET) techniques. FRET assays by flow cytometry showed that the CX3CR1 variants cluster, in comparison with appropriate controls. BRET assays showed low nonspecific signals for VT and IT variants and high specific signals for IM, and thus pointed out a structural difference in this variant. We used molecular modeling to show how natural point mutations of CX3CR1 affect the packing of the 6th and 7th helices of this G‐protein coupled receptor. Moreover, we found that the BRET technique is sensitive enough to detect these tiny changes. Consistently with our previous finding that CX3CL1 aggregates, our data here indicate that CX3CR1 clustering may contribute to the adhesiveness of the CX3CL1‐CX3CR1 pair and may thus represent a new target for anti‐inflammatory therapies. —Darbandi‐Tehrani, K. , Hermand, P., Carvalho, S. , Dorgham, K. , Couvineau, A. , Lacapère, J.‐J., Combadière, C. , Deterre, P. Subtle conformational changes between CX3CR1 genetic variants as revealed by resonance energy transfer assays. FASEB J. 24, 4585–4598 (2010). www.fasebj. org
G protein‐coupled receptor kinase 2 mediates µ‐opioid receptor desensitization in GABAergic neurons of the nucleus raphe magnus

Nucleus raphe magnus (NRM) sends the projection to spinal dorsal horn and inhibits nociceptive transmission. Analgesic effect produced by µ‐opioid receptor agonists including morphine partially results from activating the NRM‐spinal cord pathway. It is generally believed that µ‐opioid receptor agonists disinhibit spinally projecting neurons of the NRM and produce analgesia by hyperpolarizing GABAergic interneurons. In the present study, whole‐cell patch‐clamp recordings combined with single‐cell RT‐PCR analysis were used to test the hypothesis that DAMGO ([D‐Ala2,N‐methyl‐Phe4,Gly‐ol5]enkephalin), a specific µ‐opioid receptor agonist, selectively hyperpolarizes NRM neurons expressing mRNA of glutamate decarboxylase (GAD67). Homologous desensitization of µ‐opioid receptors in NRM neurons could result in the development of morphine‐induced tolerance. G protein‐coupled receptor kinase (GRK) is believed to mediate µ‐opioid receptor desensitization in vivo. Therefore, we also investigated the involvement of GRK in mediating homologous desensitization of DAMΑΜGO‐induced electrophysiological effects on NRM neurons by using two experimental strategies. First, single‐cell RT‐PCR assay was used to study the expression of GRK2 and GRK3 mRNAs in individual DAMGO‐responsive NRM neurons. Whole‐cell recording was also performed with an internal solution containing the synthetic peptide, which corresponds to Gβγ‐binding domain of GRK and inhibits Gβγ activation of GRK. Our results suggest that DAMGO selectively hyperpolarizes NRM GABAergic neurons by opening inwardly rectifying K+ channels and that GRK2 mediates short‐term homologous desensitization of µ‐opioid receptors in NRM GABAergic neurons.
Experiences with Clean I/O

The Clean system is a powerful functional programming tool. It contains experiments in a number of different areas of functional language design. In particular, it has a novel proposal for the organization of input and output, and contains impressive libraries of facilities for programming graphical user interfaces. Clean I/O is based on collections of operations that act to cause side effects on multiple explicit abstract values representing physical I/O entities, such as files and graphical interfaces. A system of unique types is used to ensure that these values are individually single threaded through the program; and the side effecting I/O operations are therefore well controlled. This approach is distinct from monadic I/O, which is being widely adopted; monadic I/O schemes are based on a single, implicit environment, and guarantee that this is single threaded. In this paper we will show that the Clean and monadic approaches to I/O merge nicely. The functionality provided by the Clean and its I/O libraries allows libraries for monadic I/O to be implemented. The paper presents an implementation of a basic I/O monad library in Clean that can serve for future development. In itself, the fact that the monadic approach can be implemented in Clean is unsurprising. However, some interesting technical difficulties arose during implementation of the monad; these and their solutions are discussed. The opportunity to express programs using the implicit environments of monadic I/O allows us to simplify Clean programs by removing some of the spaghetti, whilst retaining the generality of the explicit environments where it is the most appropriate approach.
Context-Aware Data Processing to Enhance Quality of Measurements in Wireless Health Systems: An Application to MET Calculation of Exergaming Actions

Wireless health systems enable remote and continuous monitoring of individuals, with applications in elderly care support, chronic disease management, and preventive care. The underlying sensing platform provides constructs that consider the quality of information driven from the system and ensure the reliability/validity of the outcomes to support the decision-making processes. In this paper, we present an approach to integrate contextual information within the data processing flow in order to improve the quality of measurements. We focus on a pilot application that uses wearable motion sensors to calculate metabolic equivalent of task (MET) of exergaming movements. Exergames need to show energy expenditure values, often using accelerometer approximations applied to general activities. We focus on two contextual factors, namely “activity type” and “sensor location,” and demonstrate how these factors can be used to enhance the measured values, since allocating larger weights to more informative sensors can improve the final measurements. Further, designing regression models for each activity provides better results than any generalized model. Indeed, the averaged R2 value for the movements using simple sensor location improve from a general 0.71 to as high as 0.84 for an individual activity type. The different methods present a range of R2 value averages across activity type from 0.64 for sensor location to 0.89 for multidimensional regression, with an average game play MET value of 7.93. Finally, in a leaveone-subject-out cross validation, a mean absolute error of 2.231 METs is found when predicting the activity levels using the best models.
Caspase-3 as an important factor in the early cytotoxic effect of nickel on oral mucosa cells in patients treated orthodontically.

INTRODUCTION The effect of fixed orthodontic appliances on biochemical changes in saliva and pathophysiological status of the oral cavity is not clear. Recent data showed that nickel (Ni) released from orthodontic appliances can decrease cellular viability, induce DNA damage and apoptosis in oral mucosa cells. Since the mechanism of these Ni effects is unknown, the aim of our study was to analyze the expression of caspase-3 in epithelial cells of oral mucosa in healthy individuals treated orthodontically. MATERIAL AND METHODS Twenty-eight volunteers participated in the study. Epithelial cells were collected from oral mucosa directly before appliance insertion, one week after the insertion, and 24 four weeks after the insertion of fixed appliances. Cellular identification and measurements were conducted by light microscopy. Caspase-3 expression was evaluated immunochemically. Nickel concentration in saliva was also determined. RESULTS A significantly higher number of oral epithelial cells with caspase-3 immunoreactivity in was found one week, but not 24 weeks, after orthodontic treatment. The enhanced expression of caspase-3 was accompanied by increased nickel concentration in saliva. CONCLUSIONS Our data suggests that nickel released from orthodontic appliances can activate caspase-3 and this mechanism may be partially responsible for the cytotoxic action of nickel in the oral cavity of orthodontically-treated individuals.
Hardware-Assisted Secure Resource Accounting under a Vulnerable Hypervisor

With the proliferation of cloud computing to outsource computation in remote servers, the accountability of computational resources has emerged as an important new challenge for both cloud users and providers. Among the cloud resources, CPU and memory are difficult to verify their actual allocation, since the current virtualization techniques attempt to hide the discrepancy between physical and virtual allocations for the two resources. This paper proposes an online verifiable resource accounting technique for CPU and memory allocation for cloud computing. Unlike prior approaches for cloud resource accounting, the proposed accounting mechanism, called Hardware-assisted Resource Accounting (HRA), uses the hardware support for system management mode (SMM) and virtualization to provide secure resource accounting, even if the hypervisor is compromised. Using a secure isolated execution support of SMM, this study investigates two aspects of verifiable resource accounting for cloud systems. First, this paper presents how the hardware-assisted SMM and virtualization techniques can be used to implement the secure resource accounting mechanism even under a compromised hypervisor. Second, the paper investigates a sample-based resource accounting technique to minimize performance overheads. Using a statistical random sampling method, the technique estimates the overall CPU and memory allocation status with 99%~100% accuracies and performance degradations of 0.1%~0.5%.
Effects of Changes in Colored Light on Brain and Calf Muscle Blood Concentration and Oxygenation

Color light therapy is a therapeutic method in complementary medicine. In color therapy, light of two contrasting colors is often applied in a sequential order. The aim of this study was to investigate possible physiological effects, i.e., changes in the blood volume and oxygenation in the brain and calf muscle of healthy subjects who were exposed to red and blue light in sequential order. The hypothesis was that if a subject is first exposed to blue and then red light, the effect of the red light will be enhanced due to the contrastingly different characteristics of the two colors. The same was expected for blue light, if first exposing a subject to red and then to blue light. Twelve healthy volunteers (six male, six female) were measured twice on two different days by near-infrared spectroscopy during exposure to colored light. Two sequences of colored light were applied in a controlled, randomized, crossover design: first blue, then red, and vice versa. For the brain and muscle, the results showed no significant differences in blood volume and oxygenation between the two sequences, and a high interindividual physiological variability. Thus, the hypothesis had to be rejected. Comparing these data to results from a previous study, where subjects were exposed to blue and red light without sequential color changes, shows that the results of the current study appear to be similar to those of red light exposure. This may indicate that the exposure to red light was preponderant and thus effects of blue light were outweighed.
Army of Botnets

The trend toward smaller botnets may be more dangerous than large botnets, in terms of large-scale attacks like distributed denials of service. We examine the possibility of “super-botnets,” networks of independent botnets that can be coordinated for attacks of unprecedented scale. For an adversary, super-botnets would also be extremely versatile and resistant to countermeasures. As such, superbotnets must be examined by the research community, so that defenses against this threat can be developed proactively. Our simulation results shed light on the feasibility and structure of super-botnets and some properties of their command-and-control mechanism. New forms of attack that super-botnets can launch are explored, and possible defenses against the threat of super-botnets are suggested.