Miracle-dz/UniFAR-FTUs huggingface dataset:
GAPWM: a genetic algorithm method for optimizing a position weight matrix

MOTIVATION Position weight matrices (PMWs) are simple models commonly used in motif-finding algorithms to identify short functional elements, such as cis-regulatory motifs, on genes. When few experimentally verified motifs are available, estimation of the PWM may be poor. The resultant PWM may not reliably discriminate a true motif from a false one. While experimentally identifying such motifs remains time-consuming and expensive, low-resolution binding data from techniques such as ChIP-on-chip and ChIP-PET have become available. We propose a novel but simple method to improve a poorly estimated PWM using ChIP data. METHODOLOGY Starting from an existing PWM, a set of ChIP sequences, and a set of background sequences, our method, GAPWM, derives an improved PWM via a genetic algorithm that maximizes the area under the receiver operating characteristic (ROC) curve. GAPWM can easily incorporate prior information such as base conservation. We tested our method on two PMWs (Oct4/Sox2 and p53) using three recently published ChIP data sets (human Oct4, mouse Oct4 and human p53). RESULTS GAPWM substantially increased the sensitivity/specificity of a poorly estimated PWM and further improved the quality of a good PWM. Furthermore, it still functioned when the starting PWM contained a major error. The ROC performance of GAPWM compared favorably with that of MEME and others. With increasing availability of ChIP data, our method provides an alternative for obtaining high-quality PWMs for genome-wide identification of transcription factor binding sites. AVAILABILITY The C source code and all data used in this report are available at http://dir.niehs. nih.gov/dirbb/gapwm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
HCI Design for pervasive computing

This paper describes the main assets to be considered in the design of non-invasive and ubiquitous personal communication, with particular emphasis on the use of multi-channel and multi-access devices for ubiquitous applications and services. Mobile technologies are adopted for personal communication and collaborative work and learning and several European projects demonstrated their contribution in economic and cultural development areas due to their versatility and low cost (when compared to other wired communication technologies). Experiments in remote rural schools using handhelds to enhance the learning experience (Arnedillo Sanchez 2002) are examples of such a contribution. The aim of this paper is firstly to overview the development and diffusion of mobile communication technologies, and secondly to focus on the main aspects to consider when designing successful applications and services for mobile and ubiquitous environments.
The trophic significance of bacterial carbon in a marine intertidal sediment: Results of an in situ stable isotope labeling study

We report the results of an in situ tracer experiment in an intertidal sediment, where bacterial carbon was tagged with stable carbon‐isotope label, after the injection of 13C‐glucose. The appearance of label in bacteria (based on label incorporation in bacteria‐specific, phospholipid‐derived fatty acids) and subsequent transfer to meiobenthos (group level) and macrobenthos (species level) was followed for 36 days. The label dynamics of benthic taxa were either fitted with a simple‐isotope model or evaluated against enrichment in bacteria, to derive the importance of bacterially derived carbon for the meiobenthos and macrobenthos. Although selective uptake of bacteria was evident, as 2.4 times more bacterial carbon was grazed as expected from indiscriminate feeding, bacterial carbon accounted on average for only 0.08 and 0.11 of the carbon requirements of meiobenthic and macrobenthic taxa, respectively. Additionally, the contribution of bacterial carbon to total carbon requirements did not depend on the living/feeding depth in the sediment or organism size (evaluated over a size range of four orders of magnitude). The observed overall low contribution of bacterial carbon implies that most intertidal benthic fauna depend primarily on other carbon resources that may assert a stronger control on the structure of intertidal‐sediment communities.
Death Certificates Underestimate Infections as Proximal Causes of Death in the U.S

Background Death certificates are a primary data source for assessing the population burden of diseases; however, there are concerns regarding their accuracy. Diagnosis-Related Group (DRG) coding of a terminal hospitalization may provide an alternative view. We analyzed the rate and patterns of disagreement between death certificate data and hospital claims for patients who died during an inpatient hospitalization. Methods We studied respondents from the Health and Retirement Study (a nationally representative sample of older Americans who had an inpatient death documented in the linked Medicare claims from 1993–2007). Causes of death abstracted from death certificates were aggregated to the standard National Center for Health Statistics List of 50 Rankable Causes of Death. Centers for Medicare and Medicaid Services (CMS)-DRGs were manually aggregated into a parallel classification. We then compared the two systems via 2×2, focusing on concordance. Our primary analysis was agreement between the two data sources, assessed with percentages and Cohen's kappa statistic. Results 2074 inpatient deaths were included in our analysis. 36.6% of death certificate cause-of-death codes agreed with the reason for the terminal hospitalization in the Medicare claims at the broad category level; when re-classifying DRGs without clear alignment as agreements, the concordance only increased to 61%. Overall Kappa was 0.21, or “fair. ” Death certificates in this cohort redemonstrated the conventional top 3 causes of death as diseases of the heart, malignancy, and cerebrovascular disease. However, hospitalization claims data showed infections, diseases of the heart, and cerebrovascular disease as the most common diagnoses for the same terminal hospitalizations. Conclusion There are significant differences between Medicare claims and death certificate data in assigning cause of death for inpatients. The importance of infections as proximal causes of death is underestimated by current death certificate-based strategies.
Assistive classification for improving the efficiency of avian species richness surveys

Avian species richness surveys, which measure the total number of unique avian species, can be conducted via remote acoustic sensors. An immense quantity of data can be collected, which, although rich in useful information, places a great workload on the scientists who manually inspect the audio. To deal with this big data problem, we calculated acoustic indices from audio data at a one-minute resolution and used them to classify one-minute recordings into five classes. By filtering out the non-avian minutes, we can reduce the amount of data by about 50% and improve the efficiency of determining avian species richness. The experimental results show that, given 60 one-minute samples, our approach enables to direct ecologists to find about 10% more avian species.
Identification of Methylated Genes Associated with Aggressive Clinicopathological Features in Mantle Cell Lymphoma

Background Mantle cell lymphoma (MCL) is genetically characterized by the t(11;14)(q13;q32) translocation and a high number of secondary chromosomal alterations. The contribution of DNA methylation to MCL lymphomagenesis is not well known. We sought to identify epigenetically silenced genes in these tumours that might have clinical relevance. Methodology/Principal Findings To identify potential methylated genes in MCL we initially investigated seven MCL cell lines treated with epigenetic drugs and gene expression microarray profiling. The methylation status of selected candidate genes was validated by a quantitative assay and subsequently analyzed in a series of primary MCL (n = 38). After pharmacological reversion we identified 252 potentially methylated genes. The methylation analysis of a subset of these genes (n = 25) in the MCL cell lines and normal B lymphocytes confirmed that 80% of them were methylated in the cell lines but not in normal lymphocytes. The subsequent analysis in primary MCL identified five genes (SOX9, HOXA9, AHR, NR2F2, and ROBO1) frequently methylated in these tumours. The gene methylation events tended to occur in the same primary neoplasms and correlated with higher proliferation, increased number of chromosomal abnormalities, and shorter survival of the patients. Conclusions We have identified a set of genes whose methylation degree and gene expression levels correlate with aggressive clinicopathological features of MCL. Our findings also suggest that a subset of MCL might show a CpG island methylator phenotype (CIMP) that may influence the behaviour of the tumours.
Compact Modeling of Nonlinear Analog Circuits using System Identification via Semi-Definite Programming and Robustness Certification

—This paper presents a system identiﬁcation technique for generating stable compact models of typical analog circuit blocks in radio frequency systems. The identiﬁcation procedure is based on minimizing the model error over a given training data set subject to an incremental stability constraint, which is formulated as a semideﬁnite optimization problem. Numerical results are presented for several analog circuits, including a distributed power ampliﬁer, as well as a MEM device. It is also shown that our dynamical models can accurately predict important circuit performance metrics, and may thus, be useful for design optimization of analog systems.
Spatial Reasoning in Indeterminate Worlds

A possible worlds semantics for model-based spatial reasoning is presented. In this semantics, worlds are characterized by the alternative states that result from indeterminacy or partial knowledge. A world is represented as a set of symbolic arrays, where symbols in the array map to entities in the world and the relative locations of symbols correspond to the relative locations of entities. Deduction is carried out using a model-theoretic approach in which array representations are "inspected" using primitive array functions. Nonmonotonic reasoning using array representations is also discussed.
Effective Steganalytic Algorithm based on Residual Value of Pixels in an Image

Steganalysis is the art and science of detecting the presence of secret information in the cover object. In this work, we propose a steganalytic algorithm, which differentiates the normal image from the stego image. To achieve this, we train a set of images by applying a model that finds all the dependencies among pixels. This model, then calculates the residual value along 0, 45, 90 and 135 degrees. The calculated residual value is then converted into a single digit for memory reduction. These residual values are considered as features. In testing phase, the residual value is calculated for all the pixels and the training feature value is loaded. SVM classifier is employed to differentiate between the training and testing feature. On the basis of minimal distance value, it is decided whether or not the image is stego.
CEA TCB: A novel head-to-tail 2:1 T cell bispecific antibody for treatment of CEA-positive solid tumors

ABSTRACT Carcinoembryonic antigen T cell bispecific antibody (CEA TCB) is a bispecific antibody used to recognize CEA and CD3e via a novel molecular format (2:1) that induces T cell-mediated killing of CEA over-expressing tumors while sparing primary cells with low CEA expression. CEA TCB treatment inhibits tumor growth and generates a highly inflamed tumor microenvironment.
Quantum Effects for the Neutrino Mixing Matrix in a Democratic-Type Model

We investigate the quantum effects for the democratic-type neutrino mass matrix given at the right-handed neutrino mass scale $m_R$ in order to see (i) whether $\theta_{23}=-\pi/4$ predicted by the model is stable to explain the atmospheric neutrino anomaly, (ii) how $\theta_{12}$ and $\theta_{13}$ behave, and (iii) whether the predicted Dirac CP phase $\delta$ keeps maximal size, at the weak scale $m_Z$. We find that, for the (inversely) hierarchical mass spectrum with $m_1\sim m_2$, $\theta_{23}$ and $\theta_{13}$ are stable, while $\theta_{12}$ is not so, which leads to the possibility that the solar neutrino mixing angle can become large at $m_Z$ even if it is taken small at $m_R$. We also show that $\delta$ keeps almost maximal for the above mass spectrum, and our model can give the large CP violation effect in the future neutrino oscillation experiments if the solar neutrino puzzle is explained by the large mixing angle MSW solution.
Modelling prokaryote gene content

The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical evidence for multi-gene events. We compare birth-death models (currently the only widely-used models, in which only one gene can be gained or lost at a time) to blocks models (allowing gain and loss of multiple genes within a family). We analyze two pairs of genomes: two E. coli strains, and the distantly-related Archaeoglobus fulgidus (archaea) and Bacillus subtilis (gram positive bacteria). Blocks models describe the data much better than birth-death models. Our models suggest that lateral transfers of multiple genes from the same family are rare (although transfers of single genes are probably common). For both pairs, the estimated median time that a gene will remain in the genome is not much greater than the time separating the common ancestors of the archaea and bacteria. Deep phylogenetic reconstruction from sequence data will therefore depend on choosing genes likely to remain in the genome for a long time. Phylogenies based on the blocks model are more biologically plausible than phylogenies based on the birth-death model.
Ieee Transactions on Wireless Communications, Accepted for Publication Optimal Two-dimensional Lattices for Precoding of Linear Channels

—Consider the communication system model y = HFx+n, where H and F are the channel and precoder matrices, x is a vector of data symbols drawn from some lattice-type constellation, such as M-QAM, n is an additive white Gaussian noise vector and y is the received vector. It is assumed that both the transmitter and the receiver have perfect knowledge of the channel matrix H and that the transmitted signal Fx is subject to an average energy constraint. The columns of the matrix HF can be viewed as the basis vectors that span a lattice, and we are interested in the precoder F that maximizes the minimum distance of this lattice. This particular problem remains open within the theory of lattices and the communication theory. This paper provides the complete solution for any non-singular M × 2 channel matrix H. For real-valued matrices and vectors, the solution is that HF spans the hexagonal lattice. For complex-valued matrices and vectors, the solution is that HF, when viewed in four-dimensional real-valued space, spans the Schläfli lattice D4.
Leveraging large-scale weakly-tagged images to train inter-related classifiers for multi-label annotation

In this paper, we have developed a new multi-label multi-task learning framework to leverage large-scale weakly-tagged images for inter-related classifier training. A novel image and tag cleansing algorithm is developed for tackling the issues of spam, synonymous, loose and ambiguous tags and obtain more relevant images. The visual concept network is generated to characterize the inter-concept visual similarity contexts precisely and determine the inter-related learning tasks automatically. Through a multi-label multi-task learning paradigm, our structured max-margin learning algorithm can leverage both large-scale weakly-tagged images and the visual concept network to learn large amounts of inter-related classifiers for supporting multi-label image annotation.
Identification of Retinal Ganglion Cells and Their Projections Involved in Central Transmission of Information about Upward and Downward Image Motion

The direction of image motion is coded by direction-selective (DS) ganglion cells in the retina. Particularly, the ON DS ganglion cells project their axons specifically to terminal nuclei of the accessory optic system (AOS) responsible for optokinetic reflex (OKR). We recently generated a knock-in mouse in which SPIG1 (SPARC-related protein containing immunoglobulin domains 1)-expressing cells are visualized with GFP, and found that retinal ganglion cells projecting to the medial terminal nucleus (MTN), the principal nucleus of the AOS, are comprised of SPIG1+ and SPIG1− ganglion cells distributed in distinct mosaic patterns in the retina. Here we examined light responses of these two subtypes of MTN-projecting cells by targeted electrophysiological recordings. SPIG1+ and SPIG1− ganglion cells respond preferentially to upward motion and downward motion, respectively, in the visual field. The direction selectivity of SPIG1+ ganglion cells develops normally in dark-reared mice. The MTN neurons are activated by optokinetic stimuli only of the vertical motion as shown by Fos expression analysis. Combination of genetic labeling and conventional retrograde labeling revealed that axons of SPIG1+ and SPIG1− ganglion cells project to the MTN via different pathways. The axon terminals of the two subtypes are organized into discrete clusters in the MTN. These results suggest that information about upward and downward image motion transmitted by distinct ON DS cells is separately processed in the MTN, if not independently. Our findings provide insights into the neural mechanisms of OKR, how information about the direction of image motion is deciphered by the AOS.
Expected External Profile of PATRICIA Tries

We consider PATRICIA tries on n random binary strings generated by a memoryless source with parameter p ≥ 1/2. For both the symmetric (p = 1/2) and asymmetric cases, we analyze asymptotics of the expected value of the external profile at level k = k(n), defined to be the number of leaves at level k. We study three natural ranges of k with respect to n. For k bounded, the mean profile decays exponentially with respect to n. For k growing logarithmically with n, the parameter exhibits polynomial growth in n, with some periodic fluctuations. Finally, for k = Θ(n), we see super-exponential decay, again with periodic fluctuations. Our derivations rely on analytic techniques, including Mellin transforms, analytic depoissonization, and the saddle point method. To cover wider ranges of k and n and provide more intuitive insights, we also use methods of applied mathematics, including asymptotic matching and linearization.
Associations between Physical Activity and Submaximal Cardiorespiratory and Pulmonary Responses in Men.

BACKGROUND: Habitual physical activity (PA) is associated with higher cardiorespiratory fitness values, but additional information is needed on the contributions of specific types and amounts of PA. Therefore the main aim of this study was to analyze the heart and lung function of a large cohort of men and compare these outcomes with various modes and volumes of PA. METHODS: We used data from 30,594 men from the Aerobics Center Longitudinal Study who were categorized into sedentary, swimmer, walker, and runner groups using self-report PA data collected during 1970-2005. Additional PA categories using MET-minutes/week were used to group men into 5 distinct levels of activity (0 MET-min, 1-499 MET-min, 500-999 MET-min, 1000-1499 MET-min, and ≥ 1500 MET-min). Each participant also completed a maximal treadmill exercise test to quantify their fitness level. Cross-sectional analyses included general linear modeling and multiple comparisons adjusted for age, smoking status, and histories of myocardial infarction, stroke, diabetes, and hypertension. RESULTS: A dose-response linear effect was found for heart function variables across PA MET-min categories. Stronger associations for resting heart rate (HR), heart rate recovery (HRR), exercise HR, and exercise blood pressure were found with the runner and swimming groups when compared to the walkers and sedentary groups. Walkers had significantly better heart function than the sedentary group but only about half the effect seen in the swimmers and runners. Lung function findings showed greater absolute values in FVC and FEV1 across PA categories, but found no difference in lung function ratios (e.g FEV1/FVC%). CONCLUSIONS: We found beneficial linear associations with resting HR, exercise HR, HRR, fitness values, FVC, and FEV1 over increasing MET-min categories. This implies that habitual PA, such as walking, but especially swimming and running, when performed with adequate volume, are viable ways to gain benefits for heart health.
The Unemployment Gender Gap

Women fared decidedly better than men during the most recent recession. By August 2009, the unemployment rate for men had hit 11.0 percent, while that for women held at 8.3 percent. This 2.7 percentage point unemployment gender gap—the largest in the postwar era—appears to refl ect two factors: First, men were much more heavily represented in the industries that suffered the most during the downturn. Second, there was a much sharper increase in the percentage of men who—prompted, perhaps, by a decline in household liquidity—rejoined the labor force but failed to fi nd a job.
Rapid Identification and Multiple Susceptibility Testing of Pathogens from Positive-Culture Sterile Body Fluids by a Combined MALDI-TOF Mass Spectrometry and Vitek Susceptibility System

Infections of the bloodstream, central nervous system, peritoneum, joints, and other sterile areas are associated with high morbidity and sequelae risk. Timely initiation of effective antimicrobial therapy is crucial to improving patient prognosis. However, standard final identification and antimicrobial susceptibility tests (ASTs) are reported 16–48 h after a positive alert. For a rapid, effective and low-cost diagnosis, we combined matrix-assisted laser desorption/ionization time of flight mass spectrometry with a Vitek AST system, and performed rapid microbial identification (RMI) and rapid multiple AST (RMAST) on non-duplicated positive body fluid cultures collected from a hospital in Shanghai, China. Sterile body fluid positive culture and blood positive culture caused by Gram negative (GN) or polymicrobial were applied to the MALDI–TOF measurement directly. When positive blood culture caused by Gram positive (GP) bacteria or yeasts, they were resuspended in 1 ml brain heart infusion for 2 or 4 h enrichment, respectively. Regardless of enrichment, the RMI (completed in 40 min per sample) accurately identified GN and GP bacteria (98.9 and 87.2%, respectively), fungi (75.7%), and anaerobes (94.7%). Dominant species in multiple cultures and bacteria that failed to grow on the routing plates were correctly identified in 81.2 and 100% of cases, respectively. The category agreements of RMAST results, determined in the presence of various antibiotics, were similarly to previous studies. The RMI and RMAST results not only reduce the turnaround time of the patient report by 18–36 h, but also indicate whether a patient's antibiotic treatment should be accelerated, ceased or de-escalated, and adjusted the essential drugs modification for an optimized therapy.