Miracle-dz/UniFAR-FTUs huggingface dataset:
DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool

Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE™ and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data.
Calcium montmorillonite clay reduces urinary biomarkers of fumonisin B1 exposure in rats and humans

Fumonisin B1 (FB1) is often a co-contaminant with aflatoxin (AF) in grains and may enhance AF's carcinogenicity by acting as a cancer promoter. Calcium montmorillonite (i.e. NovaSil, NS) is a possible dietary intervention to help decrease chronic aflatoxin exposure where populations are at risk. Previous studies show that an oral dose of NS clay was able to reduce AF exposure in a Ghanaian population. In vitro analyses from our laboratory indicated that FB1 (like aflatoxin) could also be sorbed onto the surfaces of NS. Hence, our objectives were to evaluate the efficacy of NS clay to reduce urinary FB1 in a rodent model and then in a human population highly exposed to AF. In the rodent model, male Fisher rats were randomly assigned to either FB1 control, FB1 + 2% NS or absolute control group. FB1 alone or with clay was given as a single dose by gavage. For the human trial, participants received NS (1.5 or 3 g day−1) or placebo (1.5 g day−1) for 3 months. Urines from weeks 8 and 10 were collected from the study participants for analysis. In rats, NS significantly reduced urinary FB1 biomarker by 20% in 24 h and 50% after 48 h compared to controls. In the humans, 56% of the urine samples analysed (n = 186) had detectable levels of FB1. Median urinary FB1 levels were significantly (p < 0.05) decreased by >90% in the high dose NS group (3 g day−1) compared to the placebo. This work indicates that our study participants in Ghana were exposed to FB1 (in addition to AFs) from the diet. Moreover, earlier studies have shown conclusively that NS reduces the bioavailability of AF and the findings from this study suggest that NS clay also reduces the bioavailability FB1. This is important since AF is a proven dietary risk factor for hepatocellular carcinoma (HCC) in humans and FB1 is suspected to be a dietary risk factor for HCC and oesophageal cancer in humans.
Oracle's SQL Performance Analyzer

We present the SQL Performance Analyzer, a novel approach in Oracle Database 11g to testing database changes, such as upgrades, parameter changes, schema changes, and gathering optimizer statistics. The SQL Performance Analyzer offers a comprehensive solution to enable users to forecast and analyze how a system change will impact SQL query plans and run time performance, so they can tune their system before they make the change in production. The SQL Performance Analyzer identifies potential problems that may occur and makes suggestions for avoiding any SQL performance degradation. It provides quantitative estimates of the system’s performance in the new environment with high confidence and performs a comparative analysis of the response time of the SQL workload thus allowing for an easy assessment of the change. In this paper we describe the architecture of the SQL Performance Analyzer, its usage model, and its integration points with other Oracle database components to form an end-to-end change management solution.
A Heterodimeric Fc-Based Bispecific Antibody Simultaneously Targeting VEGFR-2 and Met Exhibits Potent Antitumor Activity

Heterodimeric Fc designed by engineering the CH3 homodimeric interface of immunoglobulin G1 serves as an attractive scaffold for the generation of bispecific antibodies (bsAb) due to the favorable properties of the Fc region. In this study, we describe a heterodimeric Fc generated by substituting the conserved electrostatic interactions at the CH3 core interface with asymmetric hydrophobic interactions and introducing asymmetric, long-range electrostatic interactions at the rim of the CH3 interface. Coexpression of Fc proteins carrying the combined CH3 variant pairs in HEK293F cells produced the heterodimer, which was purified with more than 90% yield, and retained wild-type Fc biophysical properties. The heterodimeric Fc was exploited to generate a bsAb simultaneously targeting both the Met receptor tyrosine kinase and the VEGF receptor 2 (VEGFR-2), with two respective antigen-specific, single-chain variable fragments (scFv) into the N-terminus. The Met × VEGFR-2 bsAb bound concurrently to the two target antigens, efficiently inhibited the downstream signaling and tube formation stimulated by the two receptors in human endothelial cells, and exhibited more potent antitumor efficacy in MKN45 human gastric cancer xenograft models than both the parent monospecific antibody alone. Collectively, based on the newly designed heterodimeric Fc-based bsAb, our results provide the therapeutic potential of bsAb targeting both Met and VEGFR-2 simultaneously for the treatment of human cancers. Mol Cancer Ther; 12(12); 2748–59. ©2013 AACR.
Quality of Life and Psychological State in Chinese Breast Cancer Patients Who Received BRCA1/2 Genetic Testing

Background This study aims to understand the quality of life (QOL) and psychological state (PS) of Chinese breast cancer patients who received BRCA1/2 genetic testing; to examine the psychological changes between BRCA1/2 mutation carriers and non-carriers; and to further explore the psychological experience of BRCA1/2 mutation carriers. Methods This study was combined with quantitative and qualitative designs. First, we performed a quantitative investigation using FACT-B (Chinese version) and Irritability, Depression and Anxiety scale (IDA) to assess the QOL and PS in breast cancer patients who received BRCA1/2 genetic testing. Then semi-structured in-depth qualitative interviews among 13 mutation carriers were conducted in hospital. Results Results from the quantitative study showed QOL scores were relatively high and the IDA scores were relatively low among the patients, and there was no significant difference in the QOL or IDA scores between non-carriers and carriers. Based on the qualitative analysis, four main themes emerged: (1) Finding the reason for having breast cancer; (2) Negative emotions; (3) Behavioral changes; (4) Lack of information. Conclusions The present study showed that QOL and PS are good among the breast cancer patients who received genetic testing. Genetic testing itself does not cause long psychosocial effects. BRCA1/2 mutation carriers may have certain negative emotions at the first stage they knew the testing results and may initiate behavioral and lifestyle changes. The patients with a BRCA1/2 mutation desire knowledge with regard to genetic aspects in mainland China. Professional information and advice can be provided to relieve the patients’ negative emotions when they were informed of gene defect.
Streaming Kernel Principal Component Analysis

Kernel principal component analysis (KPCA) provides a concise set of basis vectors which capture non-linear structures within large data sets, and is a central tool in data analysis and learning. To allow for non-linear relations, typically a full $n \times n$ kernel matrix is constructed over $n$ data points, but this requires too much space and time for large values of $n$. Techniques such as the Nystr\"om method and random feature maps can help towards this goal, but they do not explicitly maintain the basis vectors in a stream and take more space than desired. We propose a new approach for streaming KPCA which maintains a small set of basis elements in a stream, requiring space only logarithmic in $n$, and also improves the dependence on the error parameter. Our technique combines together random feature maps with recent advances in matrix sketching, it has guaranteed spectral norm error bounds with respect to the original kernel matrix, and it compares favorably in practice to state-of-the-art approaches.
Conservative Sparsification for efficient and consistent approximate estimation

This paper presents a new technique for sparsification of the information matrix of a multi-dimensional Gaussian distribution. We call this technique Conservative Sparsification (CS) and show that it produces estimates which are consistent with respect to an optimal filter. This technique was applied to the Simultaneous Localisation and Mapping (SLAM) problem, and compared with two existing sparsification approaches; the Sparse Extended Information Filter (SEIF) and the Data Discarding Sparse Extended Information Filter (DDSEIF). Simulation demonstrates that CS is a consistent approach and provides a tighter upper bound than existing conservative methods.
Just nr-Excellent Graphs

In the case of finite dimensional vector spaces, every ordered basis induces a scalar coding of the vectors where the scalars are from the base field. While finite dimensional vector spaces have rich structures, graphs have only one structure namely adjacency. If a graph is connected, the adjacency gives rise to a metric. This metric can be used to define a code for the vertices.
Lessons learned in the abuse of pain-relief medication: a focus on healthcare costs

The increasing prevalence of chronic pain with its major societal impact and the escalating use of opioids in managing it, along with their misuse, abuse, associated fatalities and costs, are epidemics in modern medicine. Over the past two decades, multiple lessons have been learned addressing various issues of abuse. Multiple measures have already been incorporated and more are expected to be incorporated in the future, which in turn may curtail the abuse of drugs and reduce healthcare costs, but these measures may also jeopardize access to appropriate pain treatment. This manuscript describes the lessons learned from the misuse, abuse and diversion of opioids, escalating healthcare costs and the means to control this epidemic.
What Can Asexual Lineage Age Tell Us about the Maintenance of Sex?

Sexual reproduction is both extremely costly and extremely common relative to asexuality, indicating that it must confer profound benefits. This in turn points to major disadvantages of asexual reproduction, which is usually given as an explanation for why almost all asexual lineages are apparently quite short‐lived. However, a growing body of evidence suggests that some asexual lineages are actually quite old. Insight into why sex is so common may come from understanding why asexual lineages persist in some places or taxa but not others. Here, we review the distribution of asexual lineage ages estimated from a diverse array of taxa, and we discuss our results in light of the main mutational and environmental hypotheses for sex. Along with strengthening the case for wide variation in asexual lineage age and the existence of many old asexual taxa, we also found that the distribution of asexual lineage age estimates follows a surprisingly regular distribution, to the extent that asexual taxa viewed as “scandalously” ancient merely fall on the high end of this distribution. We interpret this result to mean that similar mechanisms may determine asexual lineage age across eukaryotic taxa. We also derive some qualitative predictions for asexual lineage age under different theories for sex and discuss empirical evidence for these predictions. Ultimately, we were limited in the extent to which we could use these data to make inferences about the maintenance of sex by the absence of both clear theoretical expectations and estimates of key parameters.
Review of Designs for Haptic Data Visualization

There are many different uses for haptics, such as training medical practitioners, teleoperation, or navigation of virtual environments. This review focuses on haptic methods that display data. The hypothesis is that haptic devices can be used to present information, and consequently, the user gains quantitative, qualitative, or holistic knowledge about the presented data. Not only is this useful for users who are blind or partially sighted (who can feel line graphs, for instance), but also the haptic modality can be used alongside other modalities, to increase the amount of variables being presented, or to duplicate some variables to reinforce the presentation. Over the last 20 years, a significant amount of research has been done in haptic data presentation; e.g., researchers have developed force feedback line graphs, bar charts, and other forms of haptic representations. However, previous research is published in different conferences and journals, with different application emphases. This paper gathers and collates these various designs to provide a comprehensive review of designs for haptic data visualization. The designs are classified by their representation: Charts, Maps, Signs, Networks, Diagrams, Images, and Tables. This review provides a comprehensive reference for researchers and learners, and highlights areas for further research.
DRUM: A Dynamic Range Unbiased Multiplier for approximate applications

Many applications for signal processing, computer vision and machine learning show an inherent tolerance to some computational error. This error resilience can be exploited to trade off accuracy for savings in power consumption and design area. Since multiplication is an essential arithmetic operation for these applications, in this paper we focus specifically on this operation and propose a novel approximate multiplier with a dynamic range selection scheme. We design the multiplier to have an unbiased error distribution, which leads to lower computational errors in real applications because errors cancel each other out, rather than accumulate, as the multiplier is used repeatedly for a computation. Our approximate multiplier design is also scalable, enabling designers to parameterize it depending on their accuracy and power targets. Furthermore, our multiplier benefits from a reduction in propagation delay, which enables its use on the critical path. We theoretically analyze the error of our design as a function of its parameters and evaluate its performance for a number of applications in image processing, and machine classification. We demonstrate that our design can achieve power savings of 54% - 80%, while introducing bounded errors with a Gaussian distribution with near-zero average and standard deviations of 0.45% - 3.61%. We also report power savings of up to 58% when using the proposed design in applications. We show that our design significantly outperforms other approximate multipliers recently proposed in the literature.
Effects of dexamethazone on LPS‐induced activationand migration of mouse dendritic cells revealed by a genome‐wide transcriptional analysis

While lipopolysaccharides (LPS) induce dendritic cell (DC) maturation and migration to lymph nodes, glucocorticoids such as dexamethazone (Dex) have a profound suppressive effect on immune response. The mechanisms that might control this suppressive effect of Dex have been extensively investigated in lymphocytes as possible targets. Much less is known on the effects of Dex on DC, although they are recognized to regulate immunity. To get insights into possible combined effects of Dex and LPS on DC functions, we have undertaken a genome‐wide analysis of differentially expressed genes of DC treated with Dex alone, LPS alone, or both, using high‐density oligonucleotide microarrays. Hierarchical clustering and principal component analysis (PCA) agreed in identifying 24 h as the time point that best discriminated the three treatments. Among the counteracting effects we have observed an inhibition of Dex on the LPS‐induced up‐regulation of the chemokine receptor CCR7. In vivo, Dex treatment blocked the LPS‐induced migration of DC, which lost their ability to reach the draining lymph nodes. In addition, we observed a synergistic effect of Dex and LPS on the expression of the secreted lipocalin 24p3, which has been reported to induce apoptosis in T cells and thus may be related to immune suppression.
Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor.

Vascular endothelial growth factor (VEGF) is a potent endothelial cell-specific mediator of angiogenesis and vasculogenesis. VEGF is involved pathologically in cancer, proliferative retinopathy and rheumatoid arthritis, and as such represents an important therapeutic target. Three classes of disulfide-constrained peptides that antagonize binding of the VEGF dimer to its receptors, KDR and Flt-1, were identified previously using phage display methods. NMR studies of a representative peptide from the most potent class of these peptide antagonists, v107 (GGNECDAIRMWEWECFERL), were undertaken to characterize its interactions with VEGF. v107 has no defined structure free in solution, but binding to VEGF induces folding of the peptide. The solution structure of the VEGF receptor-binding domain-v107 complex was determined using 3940 (1970 per VEGF monomer) internuclear distance and 476 (238 per VEGF monomer) dihedral angle restraints derived from NMR data obtained using samples containing either (13)C/(15)N-labeled protein plus excess unlabeled peptide or (13)C/(15)N-labeled peptide plus excess unlabeled protein. Residual dipolar coupling restraints supplemented the structure determination of the complex and were found to increase significantly both the global precision of VEGF in the complex and the agreement with available crystal structures of VEGF. The calculated ensemble of structures is of high precision and is in excellent agreement with the experimental restraints. v107 has a turn-helix conformation with hydrophobic residues partitioned to one face of the peptide and polar or charged residues at the other face. Contacts between two v107 peptides and the VEGF dimer are mediated by primarily hydrophobic side-chain interactions. The v107-binding site on VEGF overlaps partially with the binding site of KDR and is similar to that for domain 2 of Flt-1. The structure of the VEGF-v107 complex provides new insight into how binding to VEGF can be achieved that may be useful for the design of small molecule antagonists.
A Simple Symbol Estimation for Soft Information Relaying in Cooperative Relay Channels

This paper proposes Symbol-based Soft Forwarding (SSF) protocol for coded transmissions which is based on a simple proposed soft symbol estimation at relay nodes. We present a simple strategy of forwarding soft information based on a simple linear summation of likelihood functions of each symbol. Specifically, with SSF, we demonstrate that exclusion of decoding at the relays costs no significant performance loss. To validate our claims, we examine bit error rate (BER) performance for the proposed scheme against the baseline SF scheme through computer simulations. We find that the proposed scheme can obtain considerable performance gains compared to the conventional relaying protocol.
A Real-Time Angle- and Illumination-Aware Face Recognition System Based on Artificial Neural Network

Automatic authentication systems, using biometric technology, are becoming increasingly important with the increased need for person verification in our daily life. A few years back, fingerprint verification was done only in criminal investigations. Now fingerprints and face images are widely used in bank tellers, airports, and building entrances. Face images are easy to obtain, but successful recognition depends on proper orientation and illumination of the image, compared to the one taken at registration time. Facial features heavily change with illumination and orientation angle, leading to increased false rejection as well as false acceptance. Registering face images for all possible angles and illumination is impossible. In this work, we proposed a memory efficient way to register (store) multiple angle and changing illumination face image data, and a computationally efficient authentication technique, using multilayer perceptron (MLP). Though MLP is trained using a few registered images with different orientation, due to generalization property of MLP, interpolation of features for intermediate orientation angles was possible. The algorithm is further extended to include illumination robust authentication system. Results of extensive experiments verify the effectiveness of the proposed algorithm.
Cardiac output is not a significant source of low frequency mean arterial pressure variability

Spontaneous mean arterial pressure (MAP) variability may be mainly due to fluctuations in cardiac output (CO) and total peripheral resistance (TPR). While high frequency (HF ∼ 0.25 Hz) oscillations in MAP are ultimately driven by respiration, the source of low frequency (LF ∼ 0.1 Hz) fluctuations has not been fully elucidated. It is known that CO buffers these oscillations, but there is no evidence on its potential role in also generating them. The main goal was to determine whether CO is a source of LF variability in MAP. Six dogs were chronically instrumented to obtain beat-to-beat measurements of CO and MAP while the dogs were fully awake and at rest. A causal dynamic model was identified to relate the fluctuations in CO to MAP. The model was then used to predict the MAP fluctuations from the CO fluctuations. The CO fluctuations were able to predict about 70% of the MAP oscillations in the HF band but showed no predictive value in the LF band. Hence, respiration induces CO fluctuations in the HF band that, in turn, cause MAP oscillations, while TPR fluctuations appear to be the dominant mediator of LF fluctuations of MAP. CO is not a significant source of these oscillations, and it may only be responsible for dampening them, likely through the baroreflex.
Relationship between Chromosome Rearrangement and Repeat Sequences in Human Chromosome 7

A various types of repeat patterns are abundant in genomic sequence, and are associated with the biological phenomena at distinct levels. In particular, comparative analyses of whole-genome-sized sequence data reveal that the periodic sequences cause the segmental duplication that is a type of chromosomal structural arrangement [2]. In this study, we analyze the relationships between the large-scale segmental duplication of chromosome and the periodic sequences. For this purpose, the periodic sequences are detected by three tools to detect repeats of genomic sequence, and the distribution of detected periodic sequences is corresponded with the locations on the chromosome where the segmental duplications are observed.