Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the circulating levels of IL-12 and IL-33 in patients with breast cancer: influences of the tumor stages and cytokine gene polymorphisms

Objective(s): IL-12 as an anti-tumor cytokine and IL-33 a novel identified cytokine with both pro- or anti-tumor activities, play important roles in response against tumor cells. Our aim was to evaluate the IL-12 and IL-33 levels and single nucleotide polymorphisms (SNP) in their genes in patients with breast cancer. Materials and Methods: Blood samples were collected from 100 patients with breast cancer, and 100 healthy women were controls. The serum IL-12 and IL-33 levels were measured by ELISA. The SNP rs3212227 (in IL-12 gene) and rs1929992 (in IL-33 gene) were determined using PCR-RFLP. Results: The IL-12 levels similarly expressed in patients and controls. IL-12 levels in patients at stage I were significantly lower than in the healthy group (P<0.05). IL-33 levels and the IL-33/IL-12 ratio were significantly higher in patients than the control group (P<0.001). The IL-33 levels and IL-33/IL-12 ratio in stage IV patients were significantly higher than other stages and controls (P<0.0001 and P<0.001, respectively). There were no significant differences in the frequencies of genotypes in rs3212227 and rs1929992 between patients and the control group. No significant differences were observed between subjects with various genotypes at rs3212227 and rs1929992 with respect to related cytokine levels. Conclusion: These results indicate that the diminished IL-12 production may contribute to the tumor establishment. The higher IL-33 levels and IL-33/IL-12 ratio in patients also indicate an imbalance in Th1/Th2 responses that may contribute to tumor development. Thus, correcting the imbalance of Th1/Th2 could be an important strategy for cancer immunotherapy.
Albert Schweitzer. A biography

The second edition of this biography of humanitarian Albert Schweitzer has been updated to include documents discovered since the work was originally written, including the letters between Schweitzer and Helene Bresslau written during the ten years before their marriage. This correspondence tells of a complicated love story and throws a completely new light on Schweitzer's personality and the genesis of his decision to go to Africa. The author's ongoing research has also included more recently released documents from the State Department regarding Schweitzer's battle with the United States Atomic Energy Commission to halt H-bomb tests.
Experiences and investigations with Heraklion MESH: an experimental metropolitan multi-radio mesh network

We present our experiences and investigations with an experimental metropolitan multi-radio mesh network that covers an area of approximately 60 Km2 in the city of Heraklion, Crete. The network consists of 14 nodes, among which six are core nodes with up to four 802.11a wireless interfaces each, and an additional wireless interface for management and monitoring. The distance between core mesh nodes varies from 1.6 to 5 Km, and the wireless mesh network contains two gateways that connect it to a fixed network. Our investigations have considered the online monitoring of the links between core nodes, the interference between the wireless interfaces located in the same mesh node, channel assignment procedures, and the use of the metropolitan mesh network for real-time collection of electromagnetic field (EMF) measurements.
Optimal control of affine nonlinear continuous-time systems using an online Hamilton-Jacobi-Isaacs formulation

Solving the Hamilton-Jacobi-Isaacs (HJI) equation, commonly used in H∞ optimal control, is often referred to as a two-player differential game where one player tries to minimize the cost function while the other tries to maximize it. In this paper, the HJI equation is formulated online and forward-in-time using a novel single online approximator (SOLA)-based scheme to achieve optimal regulation and tracking control of affine nonlinear continuous-time systems. The SOLA-based adaptive approach is designed to learn the infinite horizon HJI equation, the corresponding optimal control input, and the worst case disturbance. A novel parameter tuning algorithm is derived which not only achieves the optimal cost function, control input, and the disturbance, but also ensures the system states remain bounded during the online learning. Lyapunov methods are used to show that all signals are uniformly ultimately bounded (UUB) while ensuring the approximated signals approach their optimal values with small bounded error. In the absence of OLA reconstruction errors, asymptotic convergence to the optimal signals is demonstrated, and simulation results illustrate the effectiveness of the approach.
Users lost: reflections on the past, future, and limits of information science

The paper is the acceptance address for the 1997 ACM SIGIR Gerard Salton Award for Excellence in Research. In the preamble, the approach of dealing with the broader context of information science when considering information retrieval (IR) is justified. The first part contains personal reflections of the author related to the major events and issues that formed his professional life and research agenda. The second, and major part, considers the broad aspects of information science as a field: origin, problems addressed, areas of study, structure, specialties, paradigm splits, and education problems. The third part discusses the limits of information science in terms of internal limits imposed by the activities in the field and external limits imposed by the very human nature of information processing and use. Throughout, issues related to users and use are transposed, as being of primary concern.
Pharmacotherapy for post-traumatic stress disorder: systematic review and meta-analysis.

BACKGROUND Pharmacological treatment is widely used for post-traumatic stress disorder (PTSD) despite questions over its efficacy. AIMS To determine the efficacy of all types of pharmacotherapy, as monotherapy, in reducing symptoms of PTSD, and to assess acceptability. METHOD A systematic review and meta-analysis of randomised controlled trials was undertaken; 51 studies were included. RESULTS Selective serotonin reuptake inhibitors were found to be statistically superior to placebo in reduction of PTSD symptoms but the effect size was small (standardised mean difference -0.23, 95% CI -0.33 to -0.12). For individual pharmacological agents compared with placebo in two or more trials, we found small statistically significant evidence of efficacy for fluoxetine, paroxetine and venlafaxine. CONCLUSIONS Some drugs have a small positive impact on PTSD symptoms and are acceptable. Fluoxetine, paroxetine and venlafaxine may be considered as potential treatments for the disorder. For most drugs there is inadequate evidence regarding efficacy for PTSD, pointing to the need for more research in this area.
SIRS: Internet Worm Propagation Model and Application

Internet worms spread fast and destroy strong. An accurate Internet worm model provides insight into worm propagation. It aids in identifying the characteristics in the worm spreading and provides better detection and prevention for a new worm threat. In this paper, based on the classical Kermack-Mckendrick model, we propose a general Internet worm model called SIRS (Susceptible -- Infectious -- Removed -- Susceptible) worm model by accounting for two aspects: one is the increased worm removal rate, the other is that the partial removed hosts become susceptible hosts again due to users' weak secure awareness. Simulation results of the SIRS worm model match the observed data of Code-Red worm pretty well. This model leads to a better understanding and prediction of the scale and speed of Internet worm spreading, and provides effective measures to control the spread of Internet worms.
A General Local Reconstruction Approach Based on a Truncated Hilbert Transform

Exact image reconstruction from limited projection data has been a central topic in the computed tomography (CT) field. In this paper, we present a general region-of-interest/volume-of-interest (ROI/VOI) reconstruction approach using a truly truncated Hilbert transform on a line-segment inside a compactly supported object aided by partial knowledge on one or both neighboring intervals of that segment. Our approach and associated new data sufficient condition allows the most flexible ROI/VOI image reconstruction from the minimum account of data in both the fan-beam and cone-beam geometry. We also report primary numerical simulation results to demonstrate the correctness and merits of our finding. Our work has major theoretical potentials and innovative practical applications.
Simple, standardized incorporation of genetic risk into non-genetic risk prediction tools for complex traits: coronary heart disease as an example

Purpose: Genetic risk assessment is becoming an important component of clinical decision-making. Genetic Risk Scores (GRSs) allow the composite assessment of genetic risk in complex traits. A technically and clinically pertinent question is how to most easily and effectively combine a GRS with an assessment of clinical risk derived from established non-genetic risk factors as well as to clearly present this information to patient and health care providers. Materials and Methods: We illustrate a means to combine a GRS with an independent assessment of clinical risk using a log-link function. We apply the method to the prediction of coronary heart disease (CHD) in the Atherosclerosis Risk in Communities (ARIC) cohort. We evaluate different constructions based on metrics of effect change, discrimination, and calibration. Results: The addition of a GRS to a clinical risk score (CRS) improves both discrimination and calibration for CHD in ARIC. Results are similar regardless of whether external vs. internal coefficients are used for the CRS, risk factor single nucleotide polymorphisms (SNPs) are included in the GRS, or subjects with diabetes at baseline are excluded. We outline how to report the construction and the performance of a GRS using our method and illustrate a means to present genetic risk information to subjects and/or their health care provider. Conclusion: The proposed method facilitates the standardized incorporation of a GRS in risk assessment.
Comprehensive Expression Profiling of Tumor Cell Lines Identifies Molecular Signatures of Melanoma Progression

Background Gene expression profiling has revolutionized our ability to molecularly classify primary human tumors and significantly enhanced the development of novel tumor markers and therapies; however, progress in the diagnosis and treatment of melanoma over the past 3 decades has been limited, and there is currently no approved therapy that significantly extends lifespan in patients with advanced disease. Profiling studies of melanoma to date have been inconsistent due to the heterogeneous nature of this malignancy and the limited availability of informative tissue specimens from early stages of disease. Methodology/Principle Findings In order to gain an improved understanding of the molecular basis of melanoma progression, we have compared gene expression profiles from a series of melanoma cell lines representing discrete stages of malignant progression that recapitulate critical characteristics of the primary lesions from which they were derived. Here we describe the unsupervised hierarchical clustering of profiling data from melanoma cell lines and melanocytes. This clustering identifies two distinctive molecular subclasses of melanoma segregating aggressive metastatic tumor cell lines from less-aggressive primary tumor cell lines. Further analysis of expression signatures associated with melanoma progression using functional annotations categorized these transcripts into three classes of genes: 1) Upregulation of activators of cell cycle progression, DNA replication and repair (CDCA2, NCAPH, NCAPG, NCAPG2, PBK, NUSAP1, BIRC5, ESCO2, HELLS, MELK, GINS1, GINS4, RAD54L, TYMS, and DHFR), 2) Loss of genes associated with cellular adhesion and melanocyte differentiation (CDH3, CDH1, c-KIT, PAX3, CITED1/MSG-1, TYR, MELANA, MC1R, and OCA2), 3) Upregulation of genes associated with resistance to apoptosis (BIRC5/survivin). While these broad classes of transcripts have previously been implicated in the progression of melanoma and other malignancies, the specific genes identified within each class of transcripts are novel. In addition, the transcription factor NF-KB was specifically identified as being a potential “master regulator” of melanoma invasion since NF-KB binding sites were identified as consistent consensus sequences within promoters of progression-associated genes. Conclusions/Significance We conclude that tumor cell lines are a valuable resource for the early identification of gene signatures associated with malignant progression in tumors with significant heterogeneity like melanoma. We further conclude that the development of novel data reduction algorithms for analysis of microarray studies is critical to allow for optimized mining of important, clinically-relevant datasets. It is expected that subsequent validation studies in primary human tissues using such an approach will lead to more rapid translation of such studies to the identification of novel tumor biomarkers and therapeutic targets.
Stability criteria for power amplifiers under mismatch effects

Potential instability of power amplifiers (PAs) under mismatch effects is analyzed, with emphasis on the impact of the PA termination at the fundamental frequency. A large-signal version of the μ factor is derived, considering the lower and upper sideband of the fundamental frequency as virtual observation ports. This requires the application of the conversion matrix approach to each steady-state solution obtained with harmonic balance when varying the fundamental termination. To evaluate the impact of the fundamental output load, a contour technique is used to assemble loads giving the same μ value. A stabilization procedure is provided, based on the mapping of the mismatched load onto the stable region of the fundamental termination Smith chart. The analysis is extended to consider the baseband frequency, using three virtual observation ports.
A joint resource allocation scheme for multi-relay aided uplink multi-user OFDMA system

In this paper, we consider the problem of resource allocation in relay aided uplink multi-user transmission with a single destination node. We adopt the amplify-and-forward (AF) relaying scheme and the orthogonal frequency division multiple access (OFDMA) as the main transmission modulation. The optimization is formulated as maximizing the end-to-end system throughput subject to limited number of sub-carriers and a limited amount of power for each individual user as well as the relay node. The optimization is a mixed integer programming problem over the sub-carrier allocation to each user, sub-carrier pairing at the relay, the power allocation of each user, and the power allocation at the relay. With the aid of dual decomposition, we find the near optimal solutions with acceptable complexity. To further reduce the complexity, we present a suboptimal algorithm which sacrifices very little on the performance. Finally, simulation results are provided to corroborate the proposed studies.
Correlation between Protein and mRNA Abundance in Yeast

ABSTRACT We have determined the relationship between mRNA and protein expression levels for selected genes expressed in the yeastSaccharomyces cerevisiae growing at mid-log phase. The proteins contained in total yeast cell lysate were separated by high-resolution two-dimensional (2D) gel electrophoresis. Over 150 protein spots were excised and identified by capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein spots were quantified by metabolic labeling and scintillation counting. Corresponding mRNA levels were calculated from serial analysis of gene expression (SAGE) frequency tables (V. E. Velculescu, L. Zhang, W. Zhou, J. Vogelstein, M. A. Basrai, D. E. Bassett, Jr., P. Hieter, B. Vogelstein, and K. W. Kinzler, Cell 88:243–251, 1997). We found that the correlation between mRNA and protein levels was insufficient to predict protein expression levels from quantitative mRNA data. Indeed, for some genes, while the mRNA levels were of the same value the protein levels varied by more than 20-fold. Conversely, invariant steady-state levels of certain proteins were observed with respective mRNA transcript levels that varied by as much as 30-fold. Another interesting observation is that codon bias is not a predictor of either protein or mRNA levels. Our results clearly delineate the technical boundaries of current approaches for quantitative analysis of protein expression and reveal that simple deduction from mRNA transcript analysis is insufficient.
High-Resolution Array Comparative Genomic Hybridization in Sporadic and Celiac Disease–Related Small Bowel Adenocarcinomas

Purpose: The molecular pathogenesis of small intestinal adenocarcinomas is not well understood. Understanding the molecular characteristics of small bowel adenocarcinoma may lead to more effective patient treatment. Experimental Design: Forty-eight small bowel adenocarcinomas (33 non–celiac disease related and 15 celiac disease related) were characterized for chromosomal aberrations by high-resolution array comparative hybridization, microsatellite instability, and APC promoter methylation and mutation status. Findings were compared with clinicopathologic and survival data. Furthermore, molecular alterations were compared between celiac disease–related and non–celiac disease–related small bowel adenocarcinomas. Results: DNA copy number changes were observed in 77% small bowel adenocarcinomas. The most frequent DNA copy number changes found were gains on 5p15.33-5p12, 7p22.3-7q11.21, 7q21.2-7q21.3, 7q22.1-7q34, 7q36.1, 7q36.3, 8q11.21-8q24.3, 9q34.11-9q34.3, 13q11-13q34, 16p13.3, 16p11.2, 19q13.2, and 20p13-20q13.33, and losses on 4p13-4q35.2, 5q15-5q21.1, and 21p11.2-21q22.11. Seven highly amplified regions were identified on 6p21.1, 7q21.1, 8p23.1, 11p13, 16p11.2, 17q12-q21.1, and 19q13.2. Celiac disease–related and non–celiac disease–related small bowel adenocarcinomas displayed similar chromosomal aberrations. Promoter hypermethylation of the APC gene was found in 48% non–celiac disease–related and 73% celiac disease–related small bowel adenocarcinomas. No nonsense mutations were found. Thirty-three percent of non–celiac disease–related small bowel adenocarcinomas showed microsatellite instability, whereas 67% of celiac disease–related small bowel adenocarcinomas were microsatellite unstable. Conclusions: Our study characterized chromosomal aberrations and amplifications involved in small bowel adenocarcinoma. At the chromosomal level, celiac disease–related and non–celiac disease–related small bowel adenocarcinomas did not differ. A defect in the mismatch repair pathways seems to be more common in celiac disease–related than in non–celiac disease–related small bowel adenocarcinomas. In contrast to colon and gastric cancers, no APC nonsense mutations were found in small bowel adenocarcinoma. However, APC promoter methylation seems to be a common event in celiac disease–related small bowel adenocarcinoma. Clin Cancer Res; 16(5); 1391–401
Infinite Images: Creating and Exploring a Large Photorealistic Virtual Space

We present a system for generating “infinite” images from large collections of photos by means of transformed image retrieval. Given a query image, we first transform it to simulate how it would look if the camera moved sideways and then perform image retrieval based on the transformed image. We then blend the query and retrieved images to create a larger panorama. Repeating this process will produce an “infinite” image. The transformed image retrieval model is not limited to simple 2-D left/right image translation, however, and we show how to approximate other camera motions like rotation and forward motion/zoom-in using simple 2-D image transforms. We represent images in the database as a graph where each node is an image and different types of edges correspond to different types of geometric transformations simulating different camera motions. Generating infinite images is thus reduced to following paths in the image graph. Given this data structure we can also generate a panorama that connects two query images, simply by finding the shortest path between the two in the image graph. We call this option the “image taxi. ” Our approach does not assume photographs are of a single real 3-D location, nor that they were taken at the same time. Instead, we organize the photos in themes, such as city streets or skylines and synthesize new virtual scenes by combining images from distinct but visually similar locations. There are a number of potential applications to this technology. It can be used to generate long panoramas as well as content aware transitions between reference images or video shots. Finally, the image graph allows users to interactively explore large photo collections for ideation, games, social interaction, and artistic purposes.
Attentional control and the self: The Self-Attention Network (SAN)

Although there is strong evidence that human decision-making is frequently self-biased, it remains unclear whether self-biases mediate attention. Here we review evidence on the relations between self-bias effects in decision-making and attention. We ask: Does self-related information capture attention? Do self-biases modulate pre-attentive processes or do they depend on attentional resources being available? We review work on (1) own-name effects, (2) own-face effects, and (3) self-biases in associative matching. We argue that self-related information does have a differential impact on the allocation of attention and that it can alter the saliency of a stimulus in a manner that mimics the effects of perceptual-saliency. However, there is also evidence that self-biases depend on the availability of attentional resources and attentional expectancies for upcoming stimuli. We propose a new processing framework, the Self-Attention Network (SAN), in which neural circuits responding to self-related stimuli interact with circuits supporting attentional control, to determine our emergent behavior. We also discuss how these-bias effects may extend beyond the self to be modulated by the broader social context—for example, by cultural experience, by an in-group as opposed to an out-group stimulus, and by whether we are engaged in joint actions. Self-biases on attention are modulated by social context.