Miracle-dz/UniFAR-FTUs huggingface dataset:
The Association of RAS Association Domain Family Protein1A (RASSF1A) Methylation States and Bladder Cancer Risk: A Systematic Review and Meta-Analysis

RAS association domain family protein 1a (RASSF1A) is a putative tumor suppressor gene located on 3p21, has been regarded playing important roles in the regulation of different types of human tumors. Previous reports demonstrated that the frequency of RASSF1A methylation was significantly higher in patients group compared with controls, but the relationship between RASSF1A promoter methylation and pathological features or the tumor grade of bladder cancer remains controversial. Therefore, A meta-analysis of published studies investigating the effects of RASSF1A methylation status in bladder cancer occurrence and association with both pTNM (p, pathologic stage; T, tumor size; N, node status; M, metastatic status) and tumor grade in bladder cancer was performed in the study. A total of 10 eligible studies involving 543 cases and 217 controls were included in the pooled analyses. Under the fixed-effects model, the OR of RASSF1A methylation in bladder cancer patients, compared to non-cancer controls, was 8. 40 with 95%CI = 4. 96–14. 23. The pooled OR with the random-effects model of pTNM and tumor grade in RASSF1A methylated patients, compared to unmethylated patients, was 0. 75 (95%CI = 0. 28–1. 99) and 0. 39 (95%CI = 0. 14–1. 09). This study showed that RASSF1A methylation appears to be an independent prognostic factor for bladder cancer. The present findings also require confirmation through adequately designed prospective studies.
Heightened Responses of the Parahippocampal and Retrosplenial Cortices during Contextualized Recognition of Congruent Objects

Context sometimes helps make objects more recognizable. Previous studies using functional magnetic resonance imaging (fMRI) have examined regional neural activity when objects have strong or weak associations with their contexts. Such studies have demonstrated that activity in the parahippocampal cortex (PHC) generally corresponds with strong associations between objects and their spatial contexts while retrosplenial cortex (RSC) activity is linked with episodic memory. However these studies investigated objects viewed in associated contexts, but the direct influence of scene on the perception of visual objects has not been widely investigated. We hypothesized that the PHC and RSC may only be engaged for congruent contexts in which the object could typically be found but not for neutral contexts. While in an fMRI scanner, 15 participants rated the recognizability of 152 photographic images of objects, presented within congruent and incongruent contexts. Regions of interest were created to examine PHC and RSC activity using a hypothesis-driven approach. Exploratory analyses were also performed to identify other regional activity. In line with previous studies, PHC and RSC activity emerged when objects were viewed in congruent contexts. Activity in the RSC, inferior parietal lobe (IPL) and fusiform gyrus also emerged. These findings indicate that different brain regions are employed when objects are meaningfully contextualized.
Synchronous One Time Biometrics with Pattern Based Authentication

One time passwords are commonly used for authentication purposes in electronic transactions. Nevertheless, providing such a one time password is not really a strong authentication proof %as it can be given by an impostor. because the token generating the passwords can be given by an impostor. In order to cope with this problem, biometric recognition is more and more employed. Even if biometric data are strongly linked with the user, their revocability nor diversity is possible, without an adapted post-processing. Biometric template protection schemes, including the BioHashing algorithm, are used to manage the underlying privacy and security issues. These schemes are used for the protection of several biometric modalities, but are not necessary adapted for all of them. In this paper, we propose a new protocol combining protected biometric data and a classical synchronous one time password to enhance the security of user authentication while preserving usability and privacy. Behavioral biometrics is used to provide a fast and a usable solution for users. We show through experimental results the efficiency of the proposed method.
Effects of Caste on the Expression of Genes Associated with Septic Injury and Xenobiotic Exposure in the Formosan Subterranean Termite

As social insects, termites live in densely populated colonies with specialized castes under conditions conducive to microbial growth and transmission. Furthermore, termites are exposed to xenobiotics in soil and their lignocellulose diet. Therefore, termites are valuable models for studying gene expression involved in response to septic injury, immunity and detoxification in relation to caste membership. In this study, workers and soldiers of the Formosan subterranean termite, Coptotermes formosanus, were challenged by bacterial injection or by no-choice feeding with a sublethal concentration (0.5%) of phenobarbital. Constitutive and induced expression of six putative immune response genes (two encoding for lectin-like proteins, one for a ficolin-precursor, one for the Down syndrome cell adhesion molecule, one for a chitin binding protein, and one for the gram-negative binding protein 2) and four putative detoxification genes (two encoding for cytochrome P450s, one for glutathione S-transferase, and one for the multi antimicrobial extrusion protein), were measured via quantitative real time polymerase chain reaction and compared within and among 1) colonies, 2) treatment types and 3) castes via ANOVA. Eight genes were inducible by septic injury, feeding with phenobarbital or both. Colony origin had no effect on inducibility or differential gene expression. However, treatment type showed significant effects on the expression of the eight inducible genes. Caste effects on expression levels were significant in five of the eight inducible genes with constitutive and induced expression of most target genes being higher in workers than in soldiers.
A mimetic discretization of elliptic obstacle problems

We develop a Finite Element Method (FEM) which can adopt very general meshes with polygonal elements for the numerical approximation of elliptic obstacle problems. These kinds of methods are also known as mimetic discretization schemes, which stem from the Mimetic Finite Difference (MFD) method. The first-order convergence estimate in a suitable (mesh-dependent) energy norm is established. Numerical experiments confirming the theoretical results are also presented.
FtsZ Polymerization Assays: Simple Protocols and Considerations

During bacterial cell division, the essential protein FtsZ assembles in the middle of the cell to form the so-called Z-ring. FtsZ polymerizes into long filaments in the presence of GTP in vitro, and polymerization is regulated by several accessory proteins. FtsZ polymerization has been extensively studied in vitro using basic methods including light scattering, sedimentation, GTP hydrolysis assays and electron microscopy. Buffer conditions influence both the polymerization properties of FtsZ, and the ability of FtsZ to interact with regulatory proteins. Here, we describe protocols for FtsZ polymerization studies and validate conditions and controls using Escherichia coli and Bacillus subtilis FtsZ as model proteins. A low speed sedimentation assay is introduced that allows the study of the interaction of FtsZ with proteins that bundle or tubulate FtsZ polymers. An improved GTPase assay protocol is described that allows testing of GTP hydrolysis over time using various conditions in a 96-well plate setup, with standardized incubation times that abolish variation in color development in the phosphate detection reaction. The preparation of samples for light scattering studies and electron microscopy is described. Several buffers are used to establish suitable buffer pH and salt concentration for FtsZ polymerization studies. A high concentration of KCl is the best for most of the experiments. Our methods provide a starting point for the in vitro characterization of FtsZ, not only from E. coli and B. subtilis but from any other bacterium. As such, the methods can be used for studies of the interaction of FtsZ with regulatory proteins or the testing of antibacterial drugs which may affect FtsZ polymerization.
Decision-Making with Unknown Priors in Supervised Classication

In this work, we examine minimum expected cost decision making in the presence of uncertainty about the class priors. More precisely, a classier is trained on a training set and, once the parameters are estimated, it is applied on new real-world data that have to be labeled. We then examine the situation in which the a priori probabilities of the classes (priors) in the real-world data sets are unknown and are suspected to be dierent from those encountered in the training set (new sampling conditions), while the within-class densities remain unchanged. Various scenarios are considered, according to whether estimates of the new priors are available, and are discussed from a decision-making point of view, aiming to optimize the expected cost in the new sampling conditions. In particular, we show that when no information at all is available about the priors of the data sets on which the classier will be applied, the optimal decision rule is based on the likelihood; that is, equal priors for all classes. This helps to provide a clear interpretation to the \rule of thumb" that is usually applied in this situation: to train the classier with equal proportions of observations from each class (see, e.g., [30]). The analysis method is quite generic and could easily be adapted to various other situations.
A pattern language for interactive tabletops in collaborative workspaces

In this paper, we present a Human-Computer Interaction (HCI) design pattern language that bundles existing knowledge on tabletop design and offers solutions to recurring problems. Our patterns enable not only developers, designers, and domain experts to improve their existing systems and facilitate the design process of new systems, we also encourage novice users to comprehend the variety of tabletop research and commercial products in this domain. We consider our language as a starting point to create a sustainable body of knowledge that will be extended and refined by the community.
Sγ3 switch sequences function in place of endogenous Sγ1 to mediate antibody class switching

Immunoglobulin heavy chain (IgH) class switch recombination (CSR) replaces the initially expressed IgH Cμ exons with a set of downstream IgH constant region (CH) exons. Individual sets of CH exons are flanked upstream by long (1–10-kb) repetitive switch (S) regions, with CSR involving a deletional recombination event between the donor Sμ region and a downstream S region. Targeting CSR to specific S regions might be mediated by S region–specific factors. To test the role of endogenous S region sequences in targeting specific CSR events, we generated mutant B cells in which the endogenous 10-kb Sγ1 region was replaced with wild-type (WT) or synthetic 2-kb Sγ3 sequences or a synthetic 2-kb Sγ1 sequence. We found that both the inserted endogenous and synthetic Sγ3 sequences functioned similarly to a size-matched synthetic Sγ1 sequence to mediate substantial CSR to IgG1 in mutant B cells activated under conditions that stimulate IgG1 switching in WT B cells. We conclude that Sγ3 can function similarly to Sγ1 in mediating endogenous CSR to IgG1. The approach that we have developed will facilitate assays for IgH isotype–specific functions of other endogenous S regions.
A Framework for Expressing the Relationships Between Multiple Views in Requirements Specification

Composite systems are generally comprised of heterogeneous components whose specifications are developed by many development participants. The requirements of such systems are invariably elicited from multiple perspectives that overlap, complement, and contradict each other. Furthermore, these requirements are generally developed and specified using multiple methods and notations, respectively. It is therefore necessary to express and check the relationships between the resultant specification fragments. We deploy multiple ViewPoints that hold partial requirements specifications, described and developed using different representation schemes and development strategies. We discuss the notion of inter-ViewPoint communication in the context of this ViewPoints framework, and propose a general model for ViewPoint interaction and integration. We elaborate on some of the requirements for expressing and enacting inter-ViewPoint relationships-the vehicles for consistency checking and inconsistency management. Finally, though we use simple fragments of the requirements specification method CORE to illustrate various components of our work, we also outline a number of larger case studies that we have used to validate our framework. Our computer-based ViewPoints support environment, The Viewer, is also briefly described. >
Evaluating architecture impact on system energy efficiency

As the energy consumption has been surging in an unsustainable way, it is important to understand the impact of existing architecture designs from energy efficiency perspective, which is especially valuable for High Performance Computing (HPC) and datacenter environment hosting tens of thousands of servers. One obstacle hindering the advance of comprehensive evaluation on energy efficiency is the deficient power measuring approach. Most of the energy study relies on either external power meters or power models, both of these two methods contain intrinsic drawbacks in their practical adoption and measuring accuracy. Fortunately, the advent of Intel Running Average Power Limit (RAPL) interfaces has promoted the power measurement ability into next level, with higher accuracy and finer time resolution. Therefore, we argue it is the exact time to conduct an in-depth evaluation of the existing architecture designs to understand their impact on system energy efficiency. In this paper, we leverage representative benchmark suites including serial and parallel workloads from diverse domains to evaluate the architecture features such as Non Uniform Memory Access (NUMA), Simultaneous Multithreading (SMT) and Turbo Boost. The energy is tracked at subcomponent level such as Central Processing Unit (CPU) cores, uncore components and Dynamic Random-Access Memory (DRAM) through exploiting the power measurement ability exposed by RAPL. The experiments reveal non-intuitive results: 1) the mismatch between local compute and remote memory node caused by NUMA effect not only generates dramatic power and energy surge but also deteriorates the energy efficiency significantly; 2) for multithreaded application such as the Princeton Application Repository for Shared-Memory Computers (PARSEC), most of the workloads benefit a notable increase of energy efficiency using SMT, with more than 40% decline in average power consumption; 3) Turbo Boost is effective to accelerate the workload execution and further preserve the energy, however it may not be applicable on system with tight power budget.
An opposition-based repair operator for multi-objective evolutionary algorithm in constrained optimization problems

In this paper, we design a set of multi-objective constrained optimization problems (MCOPs) and propose a new repair operator to address them. The proposed repair operator is used to fix the solutions that violate the box constraints. More specifically, it employs a reversed correction strategy that can effectively avoid the population falling into local optimum. In addition, we integrate the proposed repair operator into two classical multi-objective evolutionary algorithms MOEA/D and NSGA-II. The proposed repair operator is compared with other two kinds of commonly used repair operators on benchmark problems CTPs and MCOPs. The experiment results demonstrate that our proposed approach is very effective in terms of convergence and diversity.
Effects of temperature and particles on nitrification in a eutrophic coastal bay in southern China

Despite being the only link between reduced and oxidized nitrogen, the impact of environmental factors on nitrification, temperature and particles, in particular, remains unclear for coastal zones. By using the 15NH4+‐labeling technique, we determined nitrification rates in bulk (NTRB) and free‐living (NTRF, after removing particles >3 μm) for water samples with varying particle concentrations (as sampled at different tidal stages) during autumn, winter, and summer in a eutrophic coastal bay in southern China. The highest NTRB occurred in autumn, when particle concentrations were highest. In general, particle‐associated nitrification rates (NTRP, >3 μm) were higher than NTRF and increased with particle abundance. Regardless of seasonally distinctive temperature and particle concentrations, nitrification exhibited consistent temperature dependence in all cases (including bulk, particle‐associated, and free‐living) with a Q10 value of ~2.2. Meanwhile, the optimum temperature for NTRP was ~29°C, 5°C higher than that for NTRF although the causes for such a difference remained unclear. Strong temperature dependence and particle association suggest that nitrification is sensitive to temperature change (seasonality and global warming) and to ocean dynamics (wave and tide). Our results can potentially be applied to biogeochemical models of the nitrogen cycle for future predictions.
A Conflict Resolution Method in Context-Aware Computing

The creation of various mobile devices speeded up the development of context-aware computing. Context-aware applications are able to adjust execution policies at any moment according to context information such as equipment's position, electric power, network bandwidth, and so on. In various context-aware systems, an important solution is to isolate executable codes in different context into a number of program segments and to select different execution policies according to the context in the process of operation, thus increasing the programming flexibility. However, the method can result in conflicts, making the system unable to select correct execution policy. This paper proposes a kind of algorithm designed to resolve conflicts. The algorithm calculates the selection center of each policy and the offset value of each conflicting policy under the current context environment. The algorithm will select execution policies through comparing offsets of policies, thus eliminating conflicts. To avoid the problem of policy thrashing resulting from frequent changes of context environment within a small scope, the algorithm modifies the calculate method of offset through the introduction of persistence coefficient. Experiments testify that the algorithm can effectively eliminate conflicts and well manifest the intention of policy definition, making policy selection more reasonable. Meanwhile the algorithm can avoid the thrashing of policy selection, providing more satisfaction to user.
Power priority selection and adaptive clipping with peak reduction signal for MUDiv/OFDMA

In recent, orthogonal frequency division multiple access (OFDMA) has been used for a multiuser wireless communication. In a wireless network, the transmitted signal of each user has independent channel fluctuation characteristics. By using this characteristic, the multiuser diversity (MUDiv) can be obtained, and a MUDiv/OFDMA has been proposed. Until this time, to achieve a low complexity and performance improvement, the adaptive subcarrier block (ASB) and frequency symbol spreading (FSS) methods have been proposed. However, the system performance in a low Eb/N0 is worse than that of maximal sum capacity (MSC) and peak to average power ratio (PAPR) does not decrease greatly. To solve these problems, in this paper, we propose the subcarrier allocation with the power priority selection (PSS) and the adaptive clipping (AC) with the peak reduction signal to improve the system and PAPR performance.
An Electron Acceptor Challenging Fullerenes for Efficient Polymer Solar Cells

A novel non-fullerene electron acceptor (ITIC) that overcomes some of the shortcomings of fullerene acceptors, for example, weak absorption in the visible spectral region and limited energy-level variability, is designed and synthesized. Fullerene-free polymer solar cells (PSCs) based on the ITIC acceptor are demonstrated to exhibit power conversion efficiencies of up to 6.8%, a record for fullerene-free PSCs.
Concordant Gene Expression in Leukemia Cells and Normal Leukocytes Is Associated with Germline cis-SNPs

The degree to which gene expression covaries between different primary tissues within an individual is not well defined. We hypothesized that expression that is concordant across tissues is more likely influenced by genetic variability than gene expression which is discordant between tissues. We quantified expression of 11,873 genes in paired samples of primary leukemia cells and normal leukocytes from 92 patients with acute lymphoblastic leukemia (ALL). Genetic variation at >500,000 single nucleotide polymorphisms (SNPs) was also assessed. The expression of only 176/11,783 (1.5%) genes was correlated (p<0.008, FDR = 25%) in the two tissue types, but expression of a high proportion (20 of these 176 genes) was significantly related to cis-SNP genotypes (adjusted p<0.05). In an independent set of 134 patients with ALL, 14 of these 20 genes were validated as having expression related to cis-SNPs, as were 9 of 20 genes in a second validation set of HapMap cell lines. Genes whose expression was concordant among tissue types were more likely to be associated with germline cis-SNPs than genes with discordant expression in these tissues; genes affected were involved in housekeeping functions (GSTM2, GAPDH and NCOR1) and purine metabolism.
Facial expression recognition using depth map estimation of Light Field Camera

Facial expressions recognition has gained a growing attention from industry and also academics, because it could be widely used in many field such as Human Computer Interface (HCI) and medical assessment. In this paper, we evaluate the strength of the Light Field Camera for facial expression recognition. The light filed camera can capture the directions of the incoming light rays which is not possible with a conventional 2D camera. In addition, the light filed camera could estimates depth maps which provide further information to handle the facial expression recognition problem. Firstly, a new facial expression dataset is collected by the light field camera. The depth map is estimated and applied on Histogram Oriented Gradient (HOG) to encode these facial components as features. Then, a linear SVM is trained to perform the facial expression classification. Performance of the proposed approach is evaluated using the new dataset with estimated depth map. Experimental results show that significant improvements on accuracy are achieved as compared to the traditional approach.
Interpreting TDR Signal Propagation through Soils with Distinct Layers of Nonaqueous‐Phase Liquid and Water Content

The TDR response in the presence of NAPL transport was investigated in a homogeneous soil. The experimental framework was designed to simulate sharp NAPL fronts that moved in the soil. The TDR waveforms were analyzed to deduce the influence of NAPLs on TDR signal propagation. A general procedure to determine the location of an NAPL‐contaminated front was developed.