Miracle-dz/UniFAR-FTUs huggingface dataset:
Opacity vs TMS 2 : Expectations and Reality [ Technical Report ]

Most of the popular Transactional Memory (TM) algorithms are known to be safe because they satisfy opacity, the well-known correctness criterion for TM algorithms. Recently, it has been shown that they are even more conservative, and that they satisfy TMS2, a strictly stronger property than opacity. This paper investigates the theoretical and practical implications of relaxing those algorithms in order to allow histories that are not TMS2. In particular, we present four impossibility results on TM implementations that are not TMS2 and are either opaque or strictly serializable, and one practical TM implementation that extends TL2, a high-performance state-of-the-art TM algorithm, to allow non-TMS2 histories. By matching our theoretical findings with the results of our performance evaluation, we conclude that designing and implementing TM algorithms that are not TMS2, but safe, has inherent costs that limit any possible performance gain.
LedPred: Learning from DNA to Predict enhancers

2 Description 2 2.1 Data . 2 2.2 Learning from CRM-contained information to predict new regulatory features . 2 2.2.1 Building the training set . 2 2.2.2 Optimization of support vector machine model . 3 2.2.3 Definition of the optimal SVM parameters (γ and C) . 3 2.2. 4 Sorting and selecting features according to their importance in the traing set description . 4 2.2. 5 Plotting the performances of the model . 4 2.3 Function description . 5 2.3. 1 From bed CRM genomic coordinates to training set matrix 5 2.3. 2 Scaling of the CRM feature matrix . 5 2.3. 3 SVM parameter optimization . 5 2.3. 4 Features ranking . 6 2.3. 5 Selecting features . 7 2.3. 6 Creating the best model . 7 2.3. 7 Plotting model perfomance . 8 2.3. 8 Using the model to score unknown sequences . 8 2.3. 9 From the matrix to the model in one function . 9
Efficient robot-based energy maintenance in Wireless Sensor Networks

Energy management is one of the main hurdles in the quest for autonomous and reliable sensor networks. We present a cluster-based model for energy management in networks with static sensors and mobile robots that act as maintenance entities. The objective is to increase network availability by recharging, replacing or redeploying ”depleted” sensors with the help of mobile robots. The problem is to find a network partition where (1) workload is balanced (i.e. an equipartition) and (2) the movements of the maintenance robots in their partition is minimized. This should be done efficiently at least for the weakest elements of the system, the sensors; that is (3) the number of sensor communications should be kept small. While finding the optimal partition is a NP-hard problem, we show a simple and efficient distributed solution that provides partitions of remarkable quality. The simulation results show a rapid progression towards convergence with the quality of the partition similar to a centralized clustering benchmark (K-means). The analysis of our solutions also shows that sensor message cost remains constant as the size of the network increases.
Multi-agent reinforcement learning: an approach based on the other agent's internal model

In a multi-agent environment, whether one agent's action is good or not depends on the other agents' actions. In traditional reinforcement learning methods, which assume stationary environments, it is hard to take into account of the other agent's actions which may change due to learning. In this article, we consider a two-agent cooperation problem, and propose a multi-agent reinforcement learning method based on estimation of the other agent's actions. In our learning method, one agent estimates the other agent's action based on the internal model of the other agent. The internal model is acquired by the observation of the other agent's actions. Through experiments, we demonstrate that good cooperative behaviors are achieved by our learning method.
A Particle Swarm Optimization Approach for Optimum Design of First-Order Controllers in TCP/AQM Network Systems

This paper proposes a Particle Swarm Optimization (PSO) method for determining the optimal parameters of a first-order controller for TCP/AQM system. The model TCP/AQM is described by a second-order system with time delay. First, the analytical approach, based on the D-decomposition method and Lemma of Kharitonov, is used to determine the stabilizing regions of a first-order controller. Second, the optimal parameters of the controller are obtained by the PSO algorithm. Finally, the proposed method is verified and compared with the PI controller using the Network Simulator, NS-2. General Terms Time Delay, Stability, First-Order Controller, TCP/AQM.
Copy‐number variation of MCL1 predicts overall survival of non‐small‐cell lung cancer in a Southern Chinese population

BCL2L1 and MCL1 are key anti‐apoptotic genes, and critical for cancer progression. The prognostic values of BCL2L1 and MCL1 copy‐number variations (CNVs) in non‐small‐cell lung cancer (NSCLC) remain largely unknown. Somatic CNVs in BCL2L1 and MCL1 genes were tested in tumor tissues from 516 NSCLC patients in southern China; afterward, survival analyses were conducted with overall survival (OS) as outcome. Additionally, the associations between CNVs and mRNA expression levels were explored using data from 986 NSCLC patients in the Cancer Genome Atlas project. It was found that amplifications of BCL2L1 and MCL1 were associated with unfavorable OS of NSCLC, with adjusted hazards ratio of 1.62 (95% confident interval [CI] = 1.10–2.40; P = 0.015) and 1.39 (95% CI = 1.05–1.84; P = 0.020), respectively. Amplifications of MCL1, but not BCL2L1, were related with higher mRNA expression levels of corresponding gene, compared with non‐amplifications (P = 0.005). Interestingly, after incorporating with MCL1 CNV status, clinical variables (age, sex, TNM stage, and surgical approach) showed an improved discriminatory ability to classify OS (area under curve increased from 72.2% to 74.1%; P = 0.042, DeLong's test). Overall, MCL1 CNV might be a prognostic biomarker for NSCLC, and additional investigations are needed to validate our findings.
Influence of impaired chaperone or secretion function on SecB production in Escherichia coli

The efficient export of proteins through the cytoplasmic membrane of Escherichia coli requires chaperones to maintain protein precursors in a translocation-competent conformation. In addition to SecB, the major chaperone facilitating export of particular precursors, heat shock-induced chaperones DnaK-DnaJ and GroEL-GroES are also involved in this process. By use of secB'-lacZ gene fusions and immunoprecipitation experiments, SecB production was studied in E. coli strains containing conditional lethal mutations in chaperone or sec genes. While the loss of heat shock chaperones resulted in an increased production of SecB, mutations in sec genes showed only minor effects on SecB synthesis. Neither the plasmid-mediated overexpression of precursors of exoproteins nor the overexpression of secB altered the synthesis of SecB. These results suggest that under conditions where chaperones become depleted, E. coli responds by raising the expression of secB. These data confirm the supposed synergy of different chaperones involved in protein export.
Interaction of NADPH oxidase 1 with Toll-like receptor 2 induces migration of smooth muscle cells.

AIMS NADPH oxidase (Nox) isozymes that generate intracellular reactive oxygen species (ROS) and Toll-like receptor 2 (TLR2), an inflammatory mediator, are both involved in the development of atherosclerotic lesions. To identify the molecular connection between TLR2 and Nox isozymes in vascular remodelling, we analysed generation of ROS and pro-inflammatory cytokines in aortic smooth muscle cells from Nox1-deficient mice in response to the synthetic triacylated lipoprotein Pam3CSK, a TLR2 agonist. METHODS AND RESULTS We showed that TLR2 signalling stimulates progression of the pro-inflammatory phenotype in mouse aortic smooth muscle cells (MASMCs) through activation of Nox1. We demonstrated the interaction of TLR2 with Nox1 using yeast two-hybrid and co-immunoprecipitation assays. MASMCs from Nox1-deficient mice failed to generate of ROS in response to Pam3CSK4, indicating that Nox1 is essential for TLR2-dependent production of ROS. We also found that Pam3CSK4 stimulated migration of MASMCs from wild-type mice in a Transwell system, but MASMCs from Nox1-deficient mice failed to show this response. Wild-type MASMCs produced matrix metalloprotease 2 in response to Pam3CSK4, whereas Nox1-deficient MASMCs failed to generate this protease. Moreover, stimulation of MASMCs with Pam3CSK4 resulted in increased expression of the pro-inflammatory cytokine macrophage inflammatory protein 2 in a Nox1-dependent manner, leading to enhanced monocyte-endothelial cell adhesion and trans-endothelial migration of U937 cells. CONCLUSION These data suggest that Nox1 plays an important role in TLR2-mediated intracellular H2O2 generation, activation of matrix metalloprotease 2, and secretion of pro-inflammatory cytokines, which in turn stimulate MASMC migration and vascular remodelling.
Automatic Recognition of Cantonese-English Code-Mixing Speech

Code-mixing is a common phenomenon in bilingual societies. It refers to the intra-sentential switching of two different languages in a spoken utterance. This paper presents the first study on automatic recognition of Cantonese-English code-mixing speech, which is common in Hong Kong. This study starts with the design and compilation of code-mixing speech and text corpora. The problems of acoustic modeling, language modeling, and language boundary detection are investigated. Subsequently, a large-vocabulary code-mixing speech recognition system is developed based on a two-pass decoding algorithm. For acoustic modeling, it is shown that cross-lingual acoustic models are more appropriate than language-dependent models. The language models being used are character tri-grams, in which the embedded English words are grouped into a small number of classes. Language boundary detection is done either by exploiting the phonological and lexical differences between the two languages or is done based on the result of cross-lingual speech recognition. The language boundary information is used to re-score the hypothesized syllables or words in the decoding process. The proposed code-mixing speech recognition system attains the accuracies of 56.4% and 53.0% for the Cantonese syllables and English words in code-mixing utterances.
WLAN-Based Pedestrian Tracking Using Particle Filters and Low-Cost MEMS Sensors

Indoor positioning systems based on wireless LAN (WLAN) are being widely investigated in academia and industry. Meanwhile, the emerging low-cost MEMS sensors can also be used as another independent positioning source. In this paper, we propose a pedestrian tracking framework based on particle filters, which extends the typical WLAN-based indoor positioning systems by integrating low-cost MEMS accelerometer and map information. Our simulation and real world experiments indicate a remarkable performance improvement by using this fusion framework.
Exfoliative cytology: A possible tool in age estimation in forensic odontology

Introduction: Age determination of unknown human bodies is important in the setting of a crime investigation or a mass disaster because the age at death, birth date, and year of death as well as gender can guide investigators to the correct identity among a large number of possible matches. Objective: The study was undertaken with an aim to estimate the age of an individual from their buccal smears by comparing the average cell size using image analysis morphometric software. Materials and Methods: Buccal smears were collected from 100 apparently healthy individuals. After fixation in 95% alcohol, the smears were stained using standard Papanicolaou laboratory procedure. The average cell size was measured using Dewinter's image analysis software version 4.3. Statistical analysis of the data was done using one-way ANOVA, Bonferroni procedures. Results: The results showed significant decrease in average cell size of individual with increase in age. The difference was highly significant in age group of above 60 years. Conclusion: Age-related alterations are observed in buccal smears.
Ripple-based adaptive constant on-time control with adjustable virtual ripple for buck converter

Ripple-based adaptive constant on-time (RBACOT) control with virtual ripple are conceptually simple, fast dynamic transient responses at lower duty cycle application, and lower component count. This control schema solves instability issue of sub-harmonic oscillation when ceramic capacitors are used. These characteristics make the regulators well-suited, especially for power management applications in portable electronic devices and computers. However, this control schema has some drawbacks of poor dynamic transient response at specified duty cycle range and inherent output voltage offset problem. This paper discussed mentioned shortcomings. A new method called ripple-based adaptive constant on-time control with adjustable virtual ripple was proposed to improve dynamic transient response. Simulation and experiment results show that the proposed concept achieved fast dynamic transient response.
Enhancing Identity Prediction Using a Novel Approach to Combining Hard- and Soft-Biometric Information

The effectiveness with which individual identity can be predicted in, for example, an antiterrorist scenario can benefit from seeking a broad base of identity evidence. The issue of improving performance can be addressed in a number of ways, but system configurations based on integrating different information sources (often involving more than one biometric modality) are a widely adopted means of achieving this. This paper presents a new approach to improving identification performance, where both direct biometric samples and “soft-biometric” knowledge are combined. Specifically, however, we propose a strategy based on an intelligent agent-based decision-making process, which predicts both absolute identity and also other individual characteristics from biometric samples, as a basis for a more refined and enhanced overall identification decision based on flexible negotiation among class-related agents.
A Fair Payment System with Online Anonymous Transfer

Physical cash can be anonymously transfered. Transferability is a desirable property because it allows for flexible, private commerce where neither the seller nor the buyer must identify themselves to the bank. In some cases, however, anonymity can be abused and lead to problems such as blackmail and money laundering. In 1996, Camenisch, Piveteau, and Stadler introduced the concept of fairness for (non-transferable) ECash, where a trusted authority can revoke the anonymity of certain transactions as needed. To our knowledge, no current ECash system supports both anonymous transfer and fairness. We have designed and implemented such a system. Also, we formally describe a set of desirable properties for ECash systems and prove that our system meets all of these properties under the Strong RSA assumption and the Decisional Diffie-Hellman assumption in the random oracle model. Furthermore, we provide extensions for our system that could allow it to deal with offline payments and micropayments. Our system has been implemented in java. Tests have shown that it performs and scales well, as expected. Thesis Supervisor: Ronald Rivest Title: Viterbi Professor of EECS Thesis Co-Supervisor: Susan Hohenberger Department: Electrical Engineering and Computer Science
Mutual Authentication and Key Exchange Protocols for Roaming Services in Wireless Mobile Networks

Two novel mutual authentication and key exchange protocols with anonymity are proposed for different roaming scenarios in the global mobility network. The new features in the proposed protocols include identity anonymity and one-time session key renewal. Identity anonymity protects mobile users privacy in the roaming network environment. One-time session key progression frequently renews the session key for mobile users and reduces the risk of using a compromised session key to communicate with visited networks. It has demonstrated that the computation complexity of the proposed protocols is similar to the existing ones, while the security has been significantly improved
Toxicological and Histopathological Effects of Cheese Wood, Alstonia boonei De Wild Stem Bark Powder used as Cowpea Protectant against Cowpea Bruchid, Callosobruchus maculatus (Fab.) [Coleoptera: Chrysomelidae] on Albino Rats.

Toxicological and histopathological effects of Alstonia boonei stem bark powder on albino rats liver and kidney functions were investigated using standard methods. After two weeks of acclimatization, the rats were randomly divided into four (I - IV) groups of six animals each. Group I was fed with Basal diet, group II - IV were for 30 days with basal diet containing 1%, 4% and 10% A. boonei stem bark powder, respectively. Blood was rapidly collected by direct heart puncture and the plasma aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), total protein, urea and creatinine contents were determined using commercially-available kits. The levels of these biochemical functions were also determined in the liver and kidney. The A. boonei stem bark powder at 10% concentration caused oxidative liver and kidney damages. Histopathological results of the liver shows that the group fed with 4% A. boonei stem bark powder had normal hepatocytes. The group fed with 10% A. boonei stem bark powder had necrosis. The results of the present study showed that the supplementation of 1% and 4% A. boonei stem bark powder to the diets of rats for 30 days did not change the biochemical parameters of liver and kidney as well as histopathological investigation which illustrated normal architecture of liver and kidney.
Proinflammatory Cytokines Predict the Incidence and Progression of Distal Sensorimotor Polyneuropathy: KORA F4/FF4 Study

OBJECTIVE Experimental and epidemiological studies have implicated inflammatory processes in the pathogenesis of distal sensorimotor polyneuropathy (DSPN), but prospective studies are lacking. We hypothesized that biomarkers of inflammation predict the development and progression of DSPN in a population-based cohort. RESEARCH DESIGN AND METHODS This study was based on participants aged 62–81 years from the Cooperative Health Research in the Region of Augsburg (KORA) F4/FF4 cohort, with a mean follow-up of 6.5 years. The predictive value of systemic levels of eight biomarkers of inflammation was assessed for incident DSPN in 133 incident case subjects and 397 individuals without incident DSPN, and for DSPN progression in 57 patients with prevalent DSPN at both time points. RESULTS Higher hs-CRP, interleukin (IL)-6, tumor necrosis factor (TNF)-α, IL-1 receptor antagonist (IL-1RA), and soluble intercellular adhesion molecule (sICAM-1) and lower adiponectin levels were associated with incident DSPN in age- and sex-adjusted analysis; IL-18 and omentin were not. IL-6 (odds ratio 1.31 [95% CI 1.00–1.71]) and TNF-α (odds ratio 1.31 [95% CI 1.03–1.67]) remained associated with incident DSPN after adjusting for known DSPN risk factors. The addition of both cytokines to a clinical risk model improved model fit and reclassification. sICAM-1 and IL-1RA were positively associated with progression of DSPN. CONCLUSIONS Systemic subclinical and vascular inflammation predicted both the onset and progression of DSPN over 6.5 years in an older general population. Thus modulation of inflammatory processes may be relevant to prevent and/or treat diabetic neuropathy.
The nucleotide sequence of the lacC and lacD genes of Staphylococcus aureus.

The nucleotide sequence of two determinants of the heptacistronic lactose operon of Staphylococcus aureus is presented. The genetic organization of this operon is /acABCDFEG. Repression of the lactose operon is mediated, at least in part, by the product of lacR, which is immediately 5' proximal to lacA (1). Additionally, lacF and lacE encode components of the lactose-specific phospho-enol-pyruvate dependent phosphotransferase system (2), while lacG encodes phospho-3-galactosidase (3). binding are underiined.
Extensive Natural Epigenetic Variation at a De Novo Originated Gene

Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5′end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation.
A Survey on Bandwidth Resource Allocation and Scheduling in Wireless Sensor Networks

Bandwidth resource allocation and scheduling has posed a challenging problem in wireless sensor networks. This paper provides a survey on the current state-of-the-art researches in this important area. Bandwidth reservation is considered in terms of time slot allocation in a pure TDMA or TDMA/CSMA based networks. We first overview different approaches for time slot allocation in a star network topology, and then elaborate the problem of time slot allocation and scheduling in a multihop wireless communication network in the presence of interference. Since the problem in multihop wireless network is proved to be NP-complete, most of the exiting solutions use different heuristics to resolve this problem. We address some of these heuristics and algorithms and their impact in wireless sensor networks. Finally, we provide some of the advantages, limitations and possible extensions in the context of IEEE 802.15. 4 communications protocol which is being widely used for wireless sensor networks.