Miracle-dz/UniFAR-FTUs huggingface dataset:
Stability and performance of adaptive algorithms for multichannel blind separation and deconvolution

The problem of blind source separation is reviewed and the properties of stability and performance of the classic adaptive algorithms are derived. In case of an unstable separating solution, a stabilization procedure is proposed. These findings are then extended to the problems of single-channel and multichannel blind deconvolution. It is shown that the algorithms for all these problems can be stabilized for any situation of nonlinearities and source distributions.
Enhancing Identifications of Lipid-embedded Proteins by Mass Spectrometry for Improved Mapping of Endothelial Plasma Membranes in Vivo*

Lipid membranes structurally define the outer surface and internal organelles of cells. The multitude of proteins embedded in lipid bilayers are clearly functionally important, yet they remain poorly defined. Even today, integral membrane proteins represent a special challenge for current large scale shotgun proteomics methods. Here we used endothelial cell plasma membranes isolated directly from lung tissue to test the effectiveness of four different mass spectrometry-based methods, each with multiple replicate measurements, to identify membrane proteins. In doing so, we substantially expanded this membranome to 1,833 proteins, including >500 lipid-embedded proteins. The best method combined SDS-PAGE prefractionation with trypsin digestion of gel slices to generate peptides for seamless and continuous two-dimensional LC/MS/MS analysis. This three-dimensional separation method outperformed current widely used two-dimensional methods by significantly enhancing protein identifications including single and multiple pass transmembrane proteins; >30% are lipid-embedded proteins. It also profoundly improved protein coverage, sensitivity, and dynamic range of detection and substantially reduced the amount of sample and the number of replicate mass spectrometry measurements required to achieve 95% analytical completeness. Such expansion in comprehensiveness requires a trade-off in heavy instrument time but bodes well for future advancements in truly defining the ever important membranome with its potential in network-based systems analysis and the discovery of disease biomarkers and therapeutic targets. This analytical strategy can be applied to other subcellular fractions and should extend the comprehensiveness of many future organellar proteomics pursuits.
Annals of the New York Academy of Sciences Central Role of the Brain in Stress and Adaptation: Links to Socioeconomic Status, Health, and Disease

The brain is the key organ of stress reactivity, coping, and recovery processes. Within the brain, a distributed neural circuitry determines what is threatening and thus stressful to the individual. Instrumental brain systems of this circuitry include the hippocampus, amygdala, and areas of the prefrontal cortex. Together, these systems regulate physiological and behavioral stress processes, which can be adaptive in the short-term and maladaptive in the long-term. Importantly, such stress processes arise from bidirectional patterns of communication between the brain and the autonomic, cardiovascular, and immune systems via neural and endocrine mechanisms underpinning cognition, experience, and behavior. In one respect, these bidirectional stress mechanisms are protective in that they promote short-term adaptation (allostasis). In another respect, however, these stress mechanisms can lead to a long-term dysregulation of allostasis in that they promote maladaptive wear-and-tear on the body and brain under chronically stressful conditions (allostatic load), compromising stress resiliency and health. This review focuses specifically on the links between stress-related processes embedded within the social environment and embodied within the brain, which is viewed as the central mediator and target of allostasis and allostatic load.
A Scheduling Tool for Conditionally Independent Temporal Preferences

It is well known that the problem of finding a feasible schedule for a partially ordered set of tasks can be formulated as a Disjunctive Temporal Problem (DTP). In case we want to find a schedule by taking preferences into account, there exist extensions to DTPs that augment them by associating numeric costs to the violation of individual temporal constraints, however, such extensions make the restrictive assumption that the costs associated with constraints are independent of one another. In this paper we propose a further extension, which enables the designer to specify (directional) dependencies between the preferences associated with the constraints. Such preferences are represented by exploiting Utility Difference Networks (UDNs), that define objective functions whose structure reflects conditional independencies among the nodes of the network. The paper describes the branch-and-bound algorithm at the core of the scheduling tool we have implemented for solving this new class of problems. We also present and discuss encouraging experimental results collected in two different test domains.
DNA origami as a nanoscopic ruler for super-resolution microscopy.

The possibility of highly parallel formation of nanostructures using self-assembly of DNA molecules provides a powerful tool for bottom-up fabrication. The DNA origami technique, involves folding a long single-stranded DNA scaffold using short DNA staple strands that can only bind at particular points along this scaffold. With this technique large numbers of identical structures can be assembled simultaneously in a single experiment. One of the most attractive features of the origami technique is the precise addressability of the DNA structures formed. Each staple strand can serve as an attachment point for many different kinds of molecules or other objects.Due to their small size, DNA nanostructures are commonly imaged using atomic force microscopy or electron microscopy, but with recent advances in far-field fluorescence microscopy beyond the diffraction limit (super-resolution microscopy), structures in the sub-200 nm regime become amenable also to optical analysis.We here show that the distance between fluorescently labeled staple strands bound on specific positions of rectangular DNA origami structures can be accurately determined using a variety of super-resolution techniques such as single-molecule high-resolution imaging with photo-bleaching (SHRImP), direct stochastic optical reconstruction microscopy (dSTORM), and Blink-Microscopy.
Viewpoint Evaluation for Online 3-D Active Object Classification

We present an end-to-end method for active object classification in cluttered scenes from RGB-D data. Our algorithms predict the quality of future viewpoints in the form of entropy using both class and pose. Occlusions are explicitly modeled in predicting the visible regions of objects, which modulates the corresponding discriminatory value of a given view. We implement a one-step greedy planner and demonstrate our method online using a mobile robot. We also analyze the performance of our method compared to similar strategies in simulated execution using the Willow Garage dataset. Results show that our active method usefully reduces the number of views required to accurately classify objects in clutter as compared to traditional passive perception.
Use of subgenomic poliovirus DNA hybridization probes to detect the major subgroups of enteroviruses

Three nucleic acid hybridization probes were derived from DNA clones of the poliovirus type 1 genome. Used in dot hybridization experiments, the probes successfully detected members of each of the major enteroviral subgroups. The hybridization patterns obtained with the three probes suggested that a highly conserved nucleotide sequence existed among the enteroviruses tested, mapping between bases 220 and 1809 in the poliovirus genome. Two new antiviral agents capable of inhibiting enterovirus replication in tissue culture were used to demonstrate the specificity of the probes for viral RNA.
Web Crawling as an AI Project

This paper argues for the introduction of real-world programming projects into AI curricula, specifically using Python as an implementation language. We describe a modular set of projects centered around a focused web crawler, along with potential extensions. The author’s experiences using this project in a class of undergraduates and Master’s students are also discussed.
Design and Proposal of a Next Generation Digital Cable Broadcasting Service-Based System Using Cloud Storage Computing Environments

Although CATV businesses provide temporary (VOD) video-on-demand services and limited supplementary services as similar as web services by launching high definition digital broadcasting, they do not provide bi-directional services and personal services through exceeding the conventional TV without applying the characteristics of IP networks. It becomes the cause of continuous weakness in the aspect of services for the stiff competition with IPTV providers. This study customized a server virtualization system for adopting it to the infrastructure of CATV providers based on Xen, which is a type of Open Source, in order to activate the next generation digital cable broadcasting service. Also, this study designs and proposes a virtualized cloud storage system through applying a HDFS (hadoop distributed file system) that has been attracted as a recent issue.
The gravitational and hydrodynamical interaction between the Large Magellanic Cloud and the Galaxy

We use high-resolution N-body/smoothed particle hydrodynamic simulations to study the hydrodynamical and gravitational interaction between the Large Magellanic Cloud (LMC) and the Milky Way Galaxy. We model the dark and hot extended halo components as well as the stellar/gaseous discs of the two galaxies. Both galaxies are embedded in extended cuspy �CDM dark matter haloes. We follow the previous 4 Gyr of the LMC’s orbit such that it ends up with the correct location and orientation on the sky. Tidal forces elongate the LMC’s disc, forcing a bar and creating a strong warp and diffuse stellar halo, although very few stars become unbound. The stellar halo may account for some of the microlensing events observed towards the LMC. Ram pressure from a low-density ionized halo is then sufficient to remove
Investigations On Hydrothermally Synthesized Co3O4@MnxCo3-xO4 Core-Shell Nanoparticles

Two different morphologies (pseudo-spherical shaped or PS type and hexagonal nanoplate shaped or NP type) and two different concentrations (0.07 M and 0.1 M) of manganese incorporated Co3O4@MnxCo3-xO4 core-shell nanoparticles (CSNs) were investigated, respectively. The motivation of this work is to investigate the magnetic properties of, and specifically the exchange bias, between different shaped CSNs and between different Mn-doped CSNs. A two-step synthesis method was utilized to obtain the CSNs: a soft chemical approach was used to obtain Co3O4 nanoparticles and a hydrothermal nano-phase epitaxy was used to obtain inverted bimagnetic core-shell nanoparticles. XRD results showed that F4̅3m crystal symmetry persists throughout the core region and the shell region for both of PS type and NP type CSNs. TEM-EDX results confirmed that manganese ions were successfully incorporated into the Co3O4 spinel structure of the CSNs. TEM and SEM result confirmed that there is no change in shape after the hydrothermal treatment. HRTEM results showed that the core and the shell can be easily distinguished by the interface between the two regions. Magnetic measurements showed that PS type CSNs have a higher coercivity and exchange bias than NP type CSNs at 5K. The XPS results confirmed that Mn ions were incorporated in the 2+ oxidation state in the CSNs.
A P300 Brain-Computer Interface Based on a Modification of the Mismatch Negativity Paradigm

The P300-based brain-computer interface (BCI) is an extension of the oddball paradigm, and can facilitate communication for people with severe neuromuscular disorders. It has been shown that, in addition to the P300, other event-related potential (ERP) components have been shown to contribute to successful operation of the P300 BCI. Incorporating these components into the classification algorithm can improve the classification accuracy and information transfer rate (ITR). In this paper, a single character presentation paradigm was compared to a presentation paradigm that is based on the visual mismatch negativity. The mismatch negativity paradigm showed significantly higher classification accuracy and ITRs than a single character presentation paradigm. In addition, the mismatch paradigm elicited larger N200 and N400 components than the single character paradigm. The components elicited by the presentation method were consistent with what would be expected from a mismatch paradigm and a typical P300 was also observed. The results show that increasing the signal-to-noise ratio by increasing the amplitude of ERP components can significantly improve BCI speed and accuracy. The mismatch presentation paradigm may be considered a viable option to the traditional P300 BCI paradigm.
A case study in building layered DHT applications

Recent research has shown that one can use Distributed Hash Tables (DHTs) to build scalable, robust and efficient applications. One question that is often left unanswered is that of simplicity of implementation and deployment. In this paper, we explore a case study of building an application for which ease of deployment dominated the need for high performance. The application we focus on is Place Lab, an end-user positioning system. We evaluate whether it is feasible to use DHTs as an application-independent building block to implement a key component of Place Lab: its "mapping infrastructure. " We present Prefix Hash Trees, a data structure used by Place Lab for geographic range queries that is built entire on top of a standard DHT. By strictly layering Place Lab's data structures on top of a generic DHT service, we were able to decouple the deployment and management of Place Lab from that of the underlying DHT. We identify the characteristics of Place Lab that made it amenable for deploying in this layered manner, and comment on its effect on performance.
The Evolution of Three-Dimensional Cell Cultures Towards Unimpeded Regenerative Medicine and Tissue Engineering

The idea that cellular survival and growth could be maintained outside the body was recog‐ nized as possible almost hundred years ago when the German zoologist Wilhelm Roux described a successful experiment where he cultured chick neural crest in warm saline for a few days [1]. Nobel Prize winner Alexis Carrel performed numerous experiments clearly showing that tissue explants, including connective tissue and heart tissue, could be cultured in vitro preserving their characteristics for prolonged periods of time [2] supporting the notion that entire organs could be cultured in vitro. A defined synthetic mixture of amino acids, salts, carbohydrates, vitamins and serum was shown to support cells in vitro[3], thus unifying a major variable in cell culturing experiments and providing a possibility for rapid development of this novel method. Since the establishment of the first cell line by Gey et al.[4] in 1951 cell culturing has become one of the most widely used methods with exceptional contribution to the advances in almost all fields of contemporary biology – cell biology, genetics, cell bio‐ chemistry, physiology etc. Significant progress in the field made possible numerous achieve‐ ments that were believed to be the foundations of personalized medicine. Among these is the isolation of the first line of murine stem cells [5, 6] in 1981, followed by establishment of the first human embryonic stem cell lines by Thompson [7].
Urea Transport by Nitrogen-Regulated Tonoplast Intrinsic Proteins in Arabidopsis1

Urea is the major nitrogen (N) form supplied as fertilizer in agricultural plant production and also an important N metabolite in plants. Because urea transport in plants is not well understood, the aim of the present study was to isolate urea transporter genes from the model plant Arabidopsis. Using heterologous complementation of a urea uptake-defective yeast (Saccharomyces cerevisiae) mutant allowed to isolate AtTIP1;1, AtTIP1;2, AtTIP2;1, and AtTIP4;1 from a cDNA library of Arabidopsis. These cDNAs encode channel-like tonoplast intrinsic proteins (TIPs) that belong to the superfamily of major intrinsic proteins (or aquaporins). All four genes conferred growth of a urea uptake-defective yeast mutant on 2 mm urea in a phloretin-sensitive and pH-independent manner. Uptake studies using 14C-labeled urea into AtTIP2;1-expressing Xenopus laevis oocytes demonstrated that AtTIP2;1 facilitated urea transport also in a pH-independent manner and with linear concentration dependency. Expression studies showed that AtTIP1;2, AtTIP2;1, and AtTIP4;1 genes were up-regulated during early germination and under N deficiency in roots but constitutively expressed in shoots. Subcellular localization of green fluorescent protein-fused AtTIPs indicated that AtTIP1;2, AtTIP2;1, and AtTIP4;1 were targeted mainly to the tonoplast and other endomembranes. Thus, in addition to their role as water channels, TIP transporters may play a role in equilibrating urea concentrations between different cellular compartments.
Exploring a Model of Symbolic Social Communication

We propose a model of symbolic social communication to explain the process whereby sociocultural identity mediates relationships among receivers, sources and messages to shape message effects. This exploratory study examines how two at-risk groups of African American men responded to various HIV prevention messages delivered by celebrity and professional sources. We interviewed 47 men from a homeless shelter and 50 male college students. Members of both groups were likely to select Johnson as the best person to deliver HIV prevention messages among a list of African American celebrity and professional sources. Results suggest the symbolic meanings embedded in celebrities and message topics are important and enduring influences on message effects. The images and ideas that a source represents are transferred to the advocated behavior, attitude or knowledge change and thus shape how messages are interpreted and received. Further understanding of how culture influences the effects of persuasive messages is critical for the improvement of health-communication campaigns.
The Expanded Human Kallikrein (KLK) Gene Family: Genomic Organisation, Tissue-Specific Expression and Potential Functions

Abstract The tissue kallikreins are serine proteases encoded by highly conserved multigene families. The rodent kallikrein (KLK) families are particularly large, consisting of 13 26 genes clustered in one chromosomal locus. It has been recently recognised that the human KLK gene family is of a similar size (15 genes) with the identification of another 12 related genes (KLK4-KLK15) within and adjacent to the original human KLK locus (KLK1-3) on chromosome 19q13.4. The structural organisation and size of these new genes is similar to that of other KLK genes except for additional exons encoding 5 or 3 untranslated regions. Moreover, many of these genes have multiple mRNA transcripts, a trait not observed with rodent genes. Unlike all other kallikreins, the KLK4-KLK15 encoded proteases are less related (25–44%) and do not contain a conventional kallikrein loop. Clusters of genes exhibit high prostatic (KLK2-4, KLK15) or pancreatic (KLK6-13) expression, suggesting evolutionary conservation of elements conferring tissue specificity. These genes are also expressed, to varying degrees, in a wider range of tissues suggesting a functional involvement of these newer human kallikrein proteases in a diverse range of physiological processes.
On the effectiveness of address-space randomization

Address-space randomization is a technique used to fortify systems against buffer overflow attacks. The idea is to introduce artificial diversity by randomizing the memory location of certain system components. This mechanism is available for both Linux (via PaX ASLR) and OpenBSD. We study the effectiveness of address-space randomization and find that its utility on 32-bit architectures is limited by the number of bits available for address randomization. In particular, we demonstrate a <i>derandomization attack</i> that will convert any standard buffer-overflow exploit into an exploit that works against systems protected by address-space randomization. The resulting exploit is as effective as the original exploit, although it takes a little longer to compromise a target machine: on average 216 seconds to compromise Apache running on a Linux PaX ASLR system. The attack does not require running code on the stack. We also explore various ways of strengthening address-space randomization and point out weaknesses in each. Surprisingly, increasing the frequency of re-randomizations adds at most 1 bit of security. Furthermore, compile-time randomization appears to be more effective than runtime randomization. We conclude that, on 32-bit architectures, the only benefit of PaX-like address-space randomization is a small slowdown in worm propagation speed. The cost of randomization is extra complexity in system support.
Htab2RDF: Mapping HTML Tables to RDF Triples

The Web has become a tremendously huge data source hidden under linked documents. A signiﬁcant number of Web documents include HTML tables generated dynamically from relational databases. Often, there is no direct public access to the databases themselves. On the other hand, RDF (Resource Description Framework) gives an eﬃcient mechanism to represent directly data on the Web based on a Web-scalable architecture for identiﬁcation and interpretation of terms. This leads to the concept of Linked Data on the Web. To allow direct access to data on the Web as Linked Data, we propose in this paper an approach to transform HTML tables into RDF triples. It consists of three main phases: reﬁning, pre-treatment and mapping. The whole process is assisted by a domain ontology and the WordNet lexical database. A tool called Htab2RDF has been implemented. Experiments have been carried out to evaluate and show eﬃciency of the proposed approach.
Adaptive implicit hybrid force/pose control of industrial manipulators: compliant motion experiments

The major purpose of this paper is to combine results of current robot force control research with scientific approaches in compliant motion, which are based on Mason's task frame formalism. The embedding of adaptive implicit hybrid force/pose control in a robot control architecture for compliant motion control is described. By the usage of adaptive force control, the practicability of compliant motion applications is improved. The applied control concept is constituted in a theoretical as well as in a practical manner. To highlight the meaning for practical implementations, experimental results with industrial manipulators under adaptive force control in three degrees of freedom are finally shown.
Risk Aversion in Inventory Management

Traditional inventory models focus on risk-neutral decision makers, i.e., characterizing replenishment strategies that maximize expected total profit, or equivalently, minimize expected total cost over a planning horizon. In this paper, we propose a framework for incorporating risk aversion in multiperiod inventory models as well as multiperiod models that coordinate inventory and pricing strategies. We show that the structure of the optimal policy for a decision maker with exponential utility functions is almost identical to the structure of the optimal risk-neutral inventory (and pricing) policies. These structural results are extended to models in which the decision maker has access to a (partially) complete financial market and can hedge its operational risk through trading financial securities. Computational results demonstrate that the optimal policy is relatively insensitive to small changes in the decision-maker's level of risk aversion.