Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of atmospheric ozone on microarray data quality.

A data anomaly was observed that affected the uniformity and reproducibility of fluorescent signal across DNA microarrays. Results from experimental sets designed to identify potential causes (from microarray production to array scanning) indicated that the anomaly was linked to a batch process; further work allowed us to localize the effect to the posthybridization array stringency washes. Ozone levels were monitored and highly correlated with the batch effect. Controlled exposures of microarrays to ozone confirmed this factor as the root cause, and we present data that show susceptibility of a class of cyanine dyes (e.g., Cy5, Alexa 647) to ozone levels as low as 5-10 ppb for periods as short as 10-30 s. Other cyanine dyes (e.g., Cy3, Alexa 555) were not significantly affected until higher ozone levels (> 100 ppb). To address this environmental effect, laboratory ozone levels should be kept below 2 ppb (e.g., with filters in HVAC) to achieve high quality microarray data.
Conformational Plasticity of the 2A Proteinase from Enterovirus 71

ABSTRACT The 2A proteinase (2Apro) is an enterovirally encoded cysteine protease that plays essential roles in both the processing of viral precursor polyprotein and the hijacking of host cell translation and other processes in the virus life cycle. Crystallographic studies of 2Apro from enterovirus 71 (EV71) and its interaction with the substrate are reported here. EV71 2Apro was comprised of an N-terminal domain of a four-stranded antiparallel β sheet and a C-terminal domain of a six-stranded antiparallel β barrel with a tightly bound zinc atom. Unlike in other 2Apro structures, there is an open cleft across the surface of the protein in an open conformation. As demonstrated by the crystallographic studies and modeling of the complex structure, the open cleft could be fitted with the substrate. On comparison 2Apro of EV71 to those of the human rhinovirus 2 and coxsackievirus B4, the open conformation could be closed with a hinge motion in the bII2 and cII β strands. This was supported by molecular dynamic simulation. The structural variation among different 2Apro structures indicates a conformational flexibility in the substrate-binding cleft. The open structure provides an accessible framework for the design and development of therapeutics against the viral target.
Wiener-System Subspace Identification for Mobile Wireless mm-Wave Networks

We discuss the feasibility of wireless terahertz communications links deployed in a metropolitan area and model the large-scale fading of such channels. The model takes into account reception through direct line of sight, ground and wall reflection, as well as diffraction around a corner. The movement of the receiver is modeled by an autonomous dynamic linear system in state space, whereas the geometric relations involved in the attenuation and multipath propagation of the electric field are described by a static nonlinear mapping. A subspace algorithm in conjunction with polynomial regression is used to identify a single-output Wiener model from time-domain measurements of the field intensity when the receiver motion is simulated using a constant angular speed and an exponentially decaying radius. The identification procedure is validated by using the model to perform q-step ahead predictions. The sensitivity of the algorithm to small-scale fading, detector noise, and atmospheric changes are discussed. The performance of the algorithm is tested in the diffraction zone assuming a range of emitter frequencies (2, 38, 60,100,140, and 400 GHz). Extensions of the simulation results to situations where a more complicated trajectory describes the motion of the receiver are also implemented, providing information on the performance of the algorithm under a worst case scenario. Finally, a sensitivity analysis to model parameters for the identified Wiener system is proposed.
AFM nanoindentation of viscoelastic materials with large end‐radius probes

We used atomic force microscopy (AFM) nanoindentation to measure mechamcal properties of polymers. Although AFM is generally acknowleaged as a high-resolution imaging tool, accurate quantification of AFM nanoindentation results is challenging. Two main challenges are determination of the projected area for objects as small as AFM tips and use of appropriate analysis methods for viscoelastic materials. We report significant accuracy improvements for modulus measurements when large end-radius tips with appropriate cantilever stiffnesses are used for indentation. Using this approach, the instantaneous elastic modulus of four polymers we studied was measured within 30 to 40% of Dynamic Mechanical Analysis (DMA) results. The probes can, despite their size and very high stiffnesses, be used for imaging of very small domains in heterogeneous materials. For viscoelastic materials, we developed an AFM creep test to determine the instantaneous elastic modulus. The AFM method allows application of a nearly perfect stepload that facilitates data analysis based on hereditary integrals. Results for three polymers suggest that the observed creep in the materials has a strong plastic flow component even at small loads. In this respect, the spherical indenter tips behave like "sharp" indenters used in indentation studies with instrumented indenters.
Research on analyzing sentiment of texts based on semantic comprehension

Text sentimental mining is aim to obtain the orientation information of text, and studying users' opinion is relevant because through it concerned departments could make correct responses. In this paper, we introduce methods to discriminatively learn semantic comprehension for use as features in text classification. Based on the existed HowNet Knowledge, we consider improving algorithm for calculating Chinese term semantic value. Then, conditions of adverbs, conjunctions and text-structure are added step by step. And the experimental results show that the proposed approach is suitable for judging texts' sentimental orientation.
Model-based clustering with genes expression dynamics for time-course gene expression data

Microarray technologies are emerging as a promising tool for genomic studies. A huge body of time-course gene expression data has been and will continuously be produced by microarray experiments. Such gene expression data contains important information and has been proven useful in medical diagnosis, treatment, and drug design. The challenge now is how to analyze such data to obtain the inherent information. Cluster analysis has played an important role in analyzing time-course gene expression data. However, most clustering techniques do not take into consideration the inherent time dependence (dynamics) of time-course gene expression patterns. Accounting for the inherent dynamics of such data in cluster analysis should lead to higher quality clustering. This paper presents a model-based clustering method for time-course gene expression data. The presented method uses Markov chain models (MCMs) to account for the inherent dynamics of time-course gene expression patterns and assumes that expression patterns in the same cluster were generated by the same MCM. For the given number of clusters, the presented method computes cluster models using an EM algorithm and an assignment of genes to these models that maximizes their posterior probabilities. Further, this study employs the average adjusted Rand index (AARI) to evaluate the quality of clustering. The improved performance of the presented method is demonstrated by comparing to the k-means method on a publicly available dataset.
A reprocessing tool for quantitative data analysis in a virtual environment

This paper presents an approach to help speed up and unify the exploration and analysis of time-dependent, volumetric data sets by easily incorporating new qualitative and quantitative information into an exploratory virtual environment (VE). The new information is incorporated through one or more expedited offline "reprocessing" steps, which compute properties of objects extracted from the data. These objects and their properties are displayed in the exploratory VE. A case study involving atmospheric data is presented to demonstrate the utility of the method.
Stochastic Direct Reinforcement: Application to Simple Games with Recurrence

We investigate repeated matrix games with stochastic players as a microcosm for studying dynamic, multi-agent interactions using the Stochastic Direct Reinforcement (SDR) policy gradient algorithm. SDR is a generalization of Recurrent Reinforcement Learning (RRL) that supports stochastic policies. Unlike other RL algorithms, SDR and RRL use recurrent policy gradients to properly address temporal credit assignment resulting from recurrent structure. Our main goals in this paper are to (1) distinguish recurrent memory from standard, non-recurrent memory for policy gradient RL, (2) compare SDR with Q-type learning methods for simple games, (3) distinguish reactive from endogenous dynamical agent behavior and (4) explore the use of recurrent learning for interacting, dynamic agents. We find that SDR players learn much faster and hence outperform recently-proposed Q-type learners for the simple game Rock, Paper, Scissors (RPS). With more complex, dynamic SDR players and opponents, we demonstrate that recurrent representations and SDR’s recurrent policy gradients yield better performance than non-recurrent players. For the Iterated Prisoners Dilemma, we show that non-recurrent SDR agents learn only to defect (Nash equilibrium), while SDR agents with recurrent gradients can learn a variety of interesting behaviors, including cooperation.
Packaging of large and low-pitch size 2D ultrasonic transducer arrays

The successful packaging and electronics integration of large 2D array devices with small pitch-sizes, such as fully populated 2D ultrasonic transducer arrays, require a flexible, simple, and reliable integration approach. One example for such electronics integration is based on through silicon vias (TSVs) with under-bump metallization (UBM) stack for solder bumping. In this paper, we demonstrate such an approach by successfully integrating a fully populated 2D ultrasonic transducer array. Our integration is based on a previously reported TSV technology (trench-frame technology), based on trench-isolated interconnects with supporting frame. We successfully combined the trench-frame technology with a simple UBM preparation technique - electro plating or chemical plating techniques with passivation layers for UBM pad definition are not required. Our results show high shear strength (26.5 g) of the UBM, which is essential for successful flip-chip bonding. The yield of the interconnections is 100% with excellent solder-ball-height uniformity (¿ = 0.9 ¿m). As demonstrated in this paper, this allows for a large-scale assembly of a tiled array by using an interposer. A design guideline for finer element-pitch design was developed suggesting that fusion bonding strength and the length of pillars are the main design parameters.
Exploring deep Markov models in genomic data compression using sequence pre-analysis

The pressure to find efficient genomic compression algorithms is being felt worldwide, as proved by several prizes and competitions. In this paper, we propose a compression algorithm that relies on a pre-analysis of the data before compression, with the aim of identifying regions of low complexity. This strategy enables us to use deeper context models, supported by hash-tables, without requiring huge amounts of memory. As an example, context depths as large as 32 are attainable for alphabets of four symbols, as is the case of genomic sequences. These deeper context models show very high compression capabilities in very repetitive genomic sequences, yielding improvements over previous algorithms. Furthermore, this method is universal, in the sense that it can be used in any type of textual data (such as quality-scores).
The Cell Surface Receptor DC-SIGN Discriminates betweenMycobacterium Species through Selective Recognition of the Mannose Caps on Lipoarabinomannan*

Interactions between dendritic cells (DCs) and Mycobacterium tuberculosis, the etiological agent of tuberculosis, most likely play a key role in anti-mycobacterial immunity. We have recently shown that M. tuberculosis binds to and infects DCs through ligation of the DC-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) and that M. tuberculosis mannose-capped lipoarabinomannan (ManLAM) inhibits binding of the bacilli to the lectin, suggesting that ManLAM might be a key DC-SIGN ligand. In the present study, we investigated the molecular basis of DC-SIGN ligation by LAM. Contrary to what was found for slow growing mycobacteria, such as M. tuberculosis and the vaccine strainMycobacterium bovis bacillus Calmette-Guérin, our data demonstrate that the fast growing saprophytic speciesMycobacterium smegmatis hardly binds to DC-SIGN. Consistent with the former finding, we show that M. smegmatis-derived lipoarabinomannan, which is capped by phosphoinositide residues (PILAM), exhibits a limited ability to inhibit M. tuberculosis binding to DC-SIGN. Moreover, using enzymatically demannosylated and chemically deacylated ManLAM molecules, we demonstrate that both the acyl chains on the ManLAM mannosylphosphatidylinositol anchor and the mannooligosaccharide caps play a critical role in DC-SIGN-ManLAM interaction. Finally, we report that DC-SIGN binds poorly to the PILAM and uncapped AraLAM-containing species Mycobacterium fortuitum and Mycobacterium chelonae, respectively. Interestingly, smooth colony-formingMycobacterium avium, in which ManLAM is capped with single mannose residues, was also poorly recognized by the lectin. Altogether, our results provide molecular insight into the mechanisms of mycobacteria-DC-SIGN interaction, and suggest that DC-SIGN may act as a pattern recognition receptor and discriminate between Mycobacterium species through selective recognition of the mannose caps on LAM molecules.
Men with negative results of guaiac‐based fecal occult blood test have higher prevalences of colorectal neoplasms than women with positive results

Guaiac‐based fecal occult blood tests (gFOBTs) are the most commonly applied tests for colorectal cancer screening globally but have relatively poor sensitivity to detect colorectal neoplasms. Men have higher prevalences of colorectal neoplasms than women. In case of a positive gFOBT result, participants are referred to colonoscopy, independent of sex. To assess performance of gFOBT in routine screening practice, we assessed age and sex specific prevalences (age groups: 55–59, 60–64, 65–69 and 70–74) of colorectal neoplasms in 182,956 women and men undergoing colonoscopy for primary screening and in 20,884 women and men undergoing colonoscopy to follow‐up a positive gFOBT in Bavaria, Germany, in 2007–2009. We conducted model calculations to estimate prevalences among gFOBT negative individuals. Analogous model calculations were performed for women and men tested positive or negative with fecal immunochemical tests. In all age groups (55–59, 60–64, 65–69 and 70–74 years), men undergoing colonoscopy for primary screening had substantially higher prevalences of any colorectal neoplasms and essentially the same prevalences of advanced colorectal neoplasms compared to women undergoing colonoscopy to follow‐up a positive gFOBT. Model calculations suggest that men with negative gFOBT likewise have substantially higher prevalences of colorectal neoplasms than gFOBT positive women in each age group. Model calculations further indicate that no such sex paradoxon occurs, and a much clearer risk stratification can be achieved with fecal immunochemical tests. Our findings underline need to move forward from and overcome shortcomings of gFOBT‐based colorectal cancer screening.
TLR4 Is the Signaling but Not the Lipopolysaccharide Uptake Receptor12

TLR4 is the primary recognition molecule for inflammatory responses initiated by bacterial LPS (endotoxin). Internalization of endotoxin by various cell types is an important step for its removal and detoxification. Because of its role as an LPS-signaling receptor, TLR4 has been suggested to be involved in cellular LPS uptake as well. LPS uptake was investigated in primary monocytes and endothelial cells derived from TLR4 and CD14 knockout C57BL/6 mice using tritiated and fluorescein-labeled LPS. Intracellular LPS distribution was investigated by deconvolution confocal microscopy. We could not observe any difference in LPS uptake and intracellular LPS distribution in either monocytes or endothelial cells between TLR4−/− and wild-type cells. As expected, CD14−/− monocytes showed a highly impaired LPS uptake, confirming CD14-dependent uptake in monocytes. Upon longer incubation periods, the CD14-deficient monocytes mimicked the LPS uptake pattern of endothelial cells. Endothelial cell LPS uptake is slower than monocyte uptake, LBP rather than CD14 dependent, and sensitive to polyanionic polymers, which have been shown to block scavenger receptor-dependent uptake mechanisms. We conclude that TLR4 is not involved in cellular LPS uptake mechanisms. In membrane CD14-positive cells, LPS is predominantly taken up via CD14-mediated pathways, whereas in the CD14-negative endothelial cells, there is a role for scavenger receptor-dependent pathways.
Efficient Algorithms for the Computational Design of Optimal Tiling Arrays

The representation of a genome by oligonucleotide probes is a prerequisite for the analysis of many of its basic properties, such as transcription factor binding sites, chromosomal breakpoints, gene expression of known genes and detection of novel genes, in particular those coding for small RNAs. An ideal representation would consist of a high density set of oligonucleotides with similar melting temperatures that do not cross-hybridize with other regions of the genome and are equidistantly spaced. The implementation of such design is typically called a tiling array or genome array. We formulate the minimal cost tiling path problem for the selection of oligonucleotides from a set of candidates. Computing the selection of probes requires multi-criterion optimization, which we cast into a shortest path problem. Standard algorithms running in linear time allow us to compute globally optimal tiling paths from millions of candidate oligonucleotides on a standard desktop computer for most problem variants. The solutions to this multi-criterion optimization are spatially adaptive to the problem instance. Our formulation incorporates experimental constraints with respect to specific regions of interest and trade offs between hybridization parameters, probe quality and tiling density easily.
Effect of Volume Fraction of Primary Alpha Phase on Solid Particle Erosion Behavior of Ti-6Al-4V Alloy

The present article evaluates the influence of independent control factors such as percentage of primary alpha phase, impact velocity, impingement angle, and erodent size on solid particle erosion behavior of Ti-6Al-4V alloy using a statistical approach. Microstructural variation in terms of different percentage of primary alpha phase of investigated alloy has been introduced by solution annealing it at different temperatures followed by thermal aging. Solid particle erosion tests have been carried out using a sand blast–type test rig following an experimental schedule based on Taguchi's orthogonal arrays. It is observed that erosion rate and the value of percentage elongation decreased with an increase in the content of primary alpha phase from 10 to 20% and then increased for the value corresponding to the content of 30% primary alpha phase in this alloy. We observed that the solid particle erosion behavior of the investigated alloy consisting of various percentages of primary alpha phase is related to their ductility. Among all four control factors, impact velocity of the erodent has been found to be the most significant control factor influencing the solid particle erosion behavior of this alloy followed by impingement angle, percentage of primary alpha phase, and erodent size. Impact velocity has greatest static influence of 91.35%, impingement angle has an influence of 4.69%, percentage of primary alpha phase has an influence of 2.28%, and erodent size has an influence of 0.42% on solid particle erosion having R2 = 0.99. Material loss during solid particle erosion of this alloy was found to be ductile in nature. Ploughing or pile-up leading to platelet formation is the primary mechanism of material loss during erosion of the alloy.
Critical Assessment of Theoretical Calculations of Atomic Structure and Transition Probabilities: An Experimenter’s View

The interpretation of atomic observations by theory and the testing of computational predictions by experiment are interactive processes. It is necessary to gain experience with “the other side” before claims of achievement can be validated and judged. The discussion covers some general problems in the field as well as many specific examples, mostly organized by isoelectronic sequence, of what level of accuracy recently has been reached or which atomic structure or level lifetime problem needs more attention.
Belief Tracking with Stacked Relational Trees

We describe a new model for Dialog State Tracking called a Stacked Relational Tree, which naturally models complex relationships between entities across user utterances. It can represent multiple conversational intents and the change of focus between them. Updates to the model are made by a rule-based system in the language of tree regular expressions. We also introduce a probabilistic version that can handle ASR/NLU uncertainty. We show how the parameters can be trained from log data, showing gains on a variety of standard Belief Tracker metrics, and a measurable impact on the success rate of an end-to-end dialog system for TV program discovery.
University of Birmingham Configuring of extero- and interoceptive senses in actions on food

This paper reviews all the published evidence on the theory that the act of selecting a piece of food or drink structurally coordinates quantitative information across several sensory modalities. The existing data show that the momentary disposition to consume the item is strengthened or weakened by learnt configurations of stimuli perceived through both exteroceptive and interoceptive senses. The observed configural structure of performance shows that the multimodal stimuli are interacting perceptually, rather than merely combining quantities of information from the senses into the observed response.
Staphylococcus aureus antigens reactive with milk immunoglobulin G of naturally infected dairy cows

A 14- to 26-kilodalton fraction of Staphylococcus aureus exoproteins isolated by molecular sieve chromatography and electroelution from polyacrylamide gels was shown to specifically react with antibodies in milk of naturally infected dairy cows. Silver staining of the antigen preparation electrophoresed in polyacrylamide gels showed the strongest reactivity in the 24- to 26-kilodalton region with lesser staining at lower apparent molecular sizes. An enzyme-linked immunosorbent assay was developed to differentiate infected from uninfected cows for diagnostic purposes. Samples from S. aureus-infected cows reacted in the assay, and samples from uninfected cows did not. There was no correlation between numbers of somatic cells in the samples and reactivity to the antigens. Samples from cows infected with coagulase-negative staphylococci did not react with the antigens. It was found, however, that some samples from uninfected cows that were recently postpartum or producing low amounts of milk contained antibodies which bound the antigens. This was believed to be due to transport from blood to the mammary gland of antibodies which were generated by previous intramammary infections or infections at other sites.