Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental design schemes for learning Boolean network models

Motivation: A holy grail of biological research is a working model of the cell. Current modeling frameworks, especially in the protein–protein interaction domain, are mostly topological in nature, calling for stronger and more expressive network models. One promising alternative is logic-based or Boolean network modeling, which was successfully applied to model signaling regulatory circuits in human. Learning such models requires observing the system under a sufficient number of different conditions. To date, the amount of measured data is the main bottleneck in learning informative Boolean models, underscoring the need for efficient experimental design strategies. Results: We developed novel design approaches that greedily select an experiment to be performed so as to maximize the difference or the entropy in the results it induces with respect to current best-fit models. Unique to our maximum difference approach is the ability to account for all (possibly exponential number of) Boolean models displaying high fit to the available data. We applied both approaches to simulated and real data from the EFGR and IL1 signaling systems in human. We demonstrate the utility of the developed strategies in substantially improving on a random selection approach. Our design schemes highlight the redundancy in these datasets, leading up to 11-fold savings in the number of experiments to be performed. Availability and implementation: Source code will be made available upon acceptance of the manuscript. Contact: roded@post.tau. ac.il
Measuring Client-Perceived Response Time on the WWW

The response time of a WWW service often plays an important role in its success or demise. From a user's perspective, the response time is the time elapsed from when a request is initiated at a client to the time that the response is fully loaded by the client. This paper presents a framework for accurately measuring the client-perceived response time in a WWW service. Our framework provides feedback to the service provider and eliminates the uncertainties that are common in existing methods. This feedback can be used to determine whether performance expectations are met, and whether additional resources (e.g. more powerful server or better network connection) are needed. The framework can also be used when a consolidator provides Web hosting service, in which case the framework provides quantitative measures to verify the consolidator's compliance to a specified Service Level Agreement. Our approach assumes the existing infrastructure of the Internet with its current technologies and protocols. No modification is necessary to existing browsers or servers, and we accommodate intermediate proxies that cache documents. The only requirement is to instrument the documents to be measured, which can be done automatically using a tool we provide.
Double Pedicle Deep Inferior Epigastric Perforator/Muscle-Sparing TRAM Flaps for Unilateral Breast Reconstruction

Background:Utilizing both rectus abdominis muscles for unilateral breast reconstruction poses significant risks for hernia or bulge formation and decreased abdominal wall strength. We have used the fascial sparing double pedicle deep inferior epigastric artery perforator (DIEP)/DIEP or DIEP/muscle sparing TRAM (MS-TRAM) flap to overcome the disadvantages of the conventional bilateral TRAM or bilateral free TRAM flaps. Methods:Between January 1996 and March 2005, 14 double pedicle free DIEP/DIEP or DIEP/MS-TRAM flaps were performed in 14 patients for unilateral breast reconstruction. The abdominal wall was closed without mesh in all cases. Results:Evaluation of results was conducted through a retrospective chart review and questionnaire. The average hospital stay was 5.4 days. The follow-up period ranged from 9 months to 10 years. There was no flap loss. There were no hernias, although 1 obese patient had lower abdominal wall bulging. Questionnaire was returned by 11 out of 14 patients, with an average rating of 4.5 (1–5), with all but 1 who would recommend it to others. None of the 11 patients had postoperative abdominal pain or back pain, and 9/11 patients returned to daily activities and/or sports. All patients that worked preoperatively returned to work postoperatively. Conclusions:Double pedicle free flaps for unilateral breast reconstruction are a safe option when autologous breast reconstruction is desired, but the volume of tissue required to build a breast exceeds the amount that could be transferred on a single pedicle flap. The double pedicle DIEP (DIEP/DIEP) and/or MS-TRAM (DIEP-MS-TRAM) flap offers good symmetric results for unilateral breast reconstruction and can minimize abdominal wall morbidity.
Learning at every age? Life cycle dynamics of adult education in Europe

Adult learning is seen as a key factor for enhancing employment, innovation and growth. The aim of this paper is to understand the points in the life cycle at which adult learning takes place and whether it leads to reaching a medium or high level of educational attainment. We perform a synthetic panel analysis of adult learning for cohorts aged 25–64 in 27 European countries using the European Union Labour Force Survey. We find that investment across the life cycle by cohorts older than 25 still occurs: participation in education and training as well as educational attainment increase observably across all cohorts. We also find that the decline with age slows down, or is even reversed for older cohorts, for both participation in education and educational attainment. Finally, we can identify cross-country differences in approach. In Nordic countries, adult learning is achieved primarily through participation in education and training without adding to formal educational attainment. In central Europe, adult learning occurs primarily in the form of increasing educational attainment. In Ireland and the UK, a combination of both approaches to adult learning is observable.
On the scalability of SIMD processing for software defined radio algorithms

Software defined radio (SDR) systems require programmable architectures that provide high performance combined with high energy efficiency. Wide single instruction, multiple data (SIMD) architectures could potentially satisfy these demands, but only few publications examine the interdependence between the SIMD width and the performance of typical SDR algorithms. In this paper, we present a detailed analysis of three SDR algorithm classes on a newly developed scalable SIMD architecture, which combines SIMD processing with long instruction word (LIW) execution. Although radix-2 and mixed-radix fast Fourier transform, sphere decoding, and low-density parity-check decoding all benefit from SIMD processing, our results show that there are different constraints on the performance.
Characterization of a functionally important and evolutionarily well- conserved epitope mapped to the short consensus repeats of E-selectin and L-selectin

Selectins represent a new family of adhesion molecules, expressed by leukocytes and endothelial cells, that are involved in the regulation of leukocyte traffic. Here we have characterized a new monoclonal antibody (mAb) (EL-246) that recognizes both human leukocyte L-selectin (previously called LAM-1, LECAM-1, or gp90MEL-14) and endothelial cell E-selectin (previously called ELAM-1). EL-246 recognized a 110-kD protein expressed on cells transfected with E-selectin cDNA and stained many postcapillary venules in inflamed human tonsil. EL-246 also stained human peripheral blood leukocytes and showed identity with anti- L-selectin mAb in two-color flow cytometric analysis. The expression of the leukocyte EL-246 antigen was regulated in the same manner as L- selectin and EL-246 recognized anti-L-selectin mAb affinity-purified antigen in SDS/PAGE Western blot analysis. Further, L-selectin cDNA transfectants were specifically stained by EL-246. EL-246 blocked greater than 95% of lymphocyte adhesion to peripheral lymph node high endothelial venules and greater than 90% of neutrophil adhesion to E- selectin transfectants. In addition to the EL-246 epitope being expressed on two different human selectins, it was detected on L- selectin from a variety of different animals. Interestingly, domain mapping studies localized the EL-246 epitope to the short consensus repeat (SCR) domains of L-selectin. EL-246 is the first mAb that recognizes two different selectins and potentially defines a functional epitope encoded by the SCR domains. Inhibitors of selectin function targeted to this region would be expected to have the added advantage of simultaneously blocking the activity of two distinct adhesion proteins involved in inflammation.
Architecture specification support for component integration

The paper describes an approach to automating the construction of software systems from components. We illustrate how integration-related concerns such as component interfacing, interconnection, distribution and configuration can be modeled with a specification language. We also show how a graphics-based design environment can be used to support visual specification and transformation of integration specifications into implementations. This approach raises the level of architecture specifications to assist the currently labor-intensive and error-prone process of system integration. <<ETX>>
Using Zero-Resource Spoken Term Discovery for Ranked Retrieval

Research on ranked retrieval of spoken content has assumed the existence of some automated (word or phonetic) transcription. Recently, however, methods have been demonstrated for matching spoken terms to spoken content without the need for language-tuned transcription. This paper describes the first application of such techniques to ranked retrieval, evaluated using a newly created test collection. Both the queries and the collection to be searched are based on Gujarati produced naturally by native speakers; relevance assessment was performed by other native speakers of Gujarati. Ranked retrieval is based on fast acoustic matching that identifies a deeply nested set of matching speech regions, coupled with ways of combining evidence from those matching regions. Results indicate that the resulting ranked lists may be useful for some practical similarity-based ranking tasks.
Frateuria terrea sp. nov., isolated from forest soil, and emended description of the genus Frateuria.

A bacterial strain, designated VA24(T), was isolated from forest soil of the Changbai Mountains, Heilongjiang province, China. Cells of strain VA24(T) were Gram-reaction-negative, aerobic, non-spore-forming, long rods, 0.3-0.5×2.0-3.0 μm in size and were motile by means of a subpolar flagellum. Strain VA24(T) was oxidase-positive and catalase-negative. Growth occurred at 21-36 °C, pH 5-10 and in 0-2 % (w/v) NaCl but did not occur at 37 °C. The predominant respiratory quinone was Q-8, the major polar lipids were phosphatidylethanolamine and phosphatidylmonomethylethanolamine and the major cellular fatty acids were iso-C(15 : 0) (14.9 %), iso-C(17 : 1)ω9c (14.1 %), iso-C(17 : 0) (10.8 %) and iso-C(16 : 0) (10.3 %). The DNA G+C content was 67.4 mol% (T(m)). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain VA24(T) was closely related to Frateuria aurantia IFO 13300(T) with 96.9 % sequence similarity. DNA-DNA relatedness of strain VA24(T) to F. aurantia DSM 6220(T) was 15.8 %. Based on its phenotypic and genotypic features, strain VA24(T) represents a novel species of the genus Frateuria, for which the name Frateuria terrea sp. nov. is proposed. The type strain is VA24(T) (=CGMCC 1.7053(T) =NBRC 104236(T)).
Automatic Speaker Identification from Interpersonal Synchrony of Body Motion Behavioral Patterns in Multi-Person Videos

Interpersonal synchrony, i.e. the temporal coordination of persons during social interactions, was traditionally studied by developmental psychologists. It now holds an important role in fields such as social signal processing, usually treated as a dyadic issue. In this paper, we focus on the behavioral patterns from body motion to identify subtle social interactions in the context of multi-person discussion panels, typically involving more than two interacting individuals. We propose a computer-vision based approach for automatic speaker identification that takes advantage of body motion interpersonal synchrony between participants. The approach characterizes human body motion with a novel feature descriptor based on the pixel change history of multiple body regions, which is then used to classify the motor behavioral patterns of the participants into speaking/non-speaking. Our approach was evaluated on a challenging dataset of video segments from discussion panel scenes collected from YouTube. Results are very promising and suggest that interpersonal synchrony of motion behavior is indeed indicative of speaker/listener roles.
Prominence versus Dominance: How Relationships between Alternatives Drive Decision Strategy and Choice

This article argues that the structure of a choice set can influence the extent to which consumers weight a given attribute. The results of seven experiments suggest that the relationship between options under consideration can influence preference ordering by shifting the decision strategy people adopt when constructing their preference. In decisions in which people afford greater importance to one attribute versus another, preference for an option that scores high on this prominent attribute may decrease when decoy options that are clearly better or worse than the focal options are inserted into the choice set. The authors posit that this effect arises because decision makers initially (and spontaneously) use dominance cues rather than prominence when evaluating options, and they continue to use this strategy even when it does not enable them to differentiate the alternatives under consideration. The authors moderate this effect by prompting respondents to consider prominence and by manipulating the order in which respondents evaluate options in the choice set. This article has theoretical implications for research on context effects, contingent decision behavior, and choice architecture as well as practical implications for product-line management.
Dynamic routing with endpoint admission control for V61P networks

In this paper, we propose a dynamic routing with endpoint measurement based admission control (EMBAC) for VoIP networks with mesh topology. The basic idea of this admission control is to use probe flows to measure two routes, which are direct route and one of the two-link routes between each VoIP call's originating-terminating node pair. Based on the probe flow's QoS evaluation, the node decides a route for each call. We compare performance of direct routing, basic dynamic routing and advanced dynamic routing by using simulation. It is shown that an advanced dynamic routing with EMBAC works better for minimizing call blocking probability and packet loss rate than direct routing.
VLSI floorplanning with boundary constraints based on corner block list

In floorplanning of a typical VLSI design, some modules are required to satisfy some placement constraints in the final packing. Boundary constraint is one kind of those placement constraints to pack some modules along one of the four sides: on the left, on the right, at the bottom or at the top of the final floorplan. We implement the boundary constraint algorithm for general floorplan by extending the corner block list (CBL)-a new efficient topology representation for nonslicing floorplan. Our contribution is to find the necessary and sufficient characterization of the modules along the boundary represented by corner block list. We can check the boundary constraints by scanning the intermediate solutions in linear time during the simulated annealing process and fix the corner block list in case the constraints are violated. The experiment results are demonstrated by several examples of MCNC benchmarks and the performance is remarkable.
An Uncleaved Signal Peptide Directs the Malus xiaojinensis Iron Transporter Protein Mx IRT1 into the ER for the PM Secretory Pathway

Malus xiaojinensis iron-regulated transporter 1 (Mx IRT1) is a highly effective inducible iron transporter in the iron efficient plant Malus xiaojinensis. As a multi-pass integral plasma membrane (PM) protein, Mx IRT1 is predicted to consist of eight transmembrane domains, with a putative N-terminal signal peptide (SP) of 1–29 amino acids. To explore the role of the putative SP, constructs expressing Mx IRT1 (with an intact SP) and Mx DsIRT1 (with a deleted SP) were prepared for expression in Arabidopsis and in yeast. Mx IRT1 could rescue the iron-deficiency phenotype of an Arabidopsis irt1 mutant, and complement the iron-limited growth defect of the yeast mutant DEY 1453 (fet3fet4). Furthermore, fluorescence analysis indicated that a chimeric Mx IRT1-eGFP (enhanced Green Fluorescent Protein) construct was translocated into the ER (Endoplasmic reticulum) for the PM sorting pathway. In contrast, the SP-deleted Mx DsIRT1 could not rescue either of the mutant phenotypes, nor direct transport of the GFP signal into the ER. Interestingly, immunoblot analysis indicated that the SP was not cleaved from the mature protein following transport into the ER. Taken together, data presented here provides strong evidence that an uncleaved SP determines ER-targeting of Mx IRT1 during the initial sorting stage, thereby enabling the subsequent transport and integration of this protein into the PM for its crucial role in iron uptake.
Experiences of educational content in Swedish technical vocational education: Examples from the energy and industry programmes

Abstract In this study, teachers and workplace supervisors in two vocational programmes at a Swedish upper secondary school were interviewed about their experiences of what is important to teach and learn during vocational education. The interviews were analysed thematically by the qualitative method analysis of narratives concerning what the informants talked about concerning the educational content. The told experiences of educational content concern five themes: basic knowledge, assessment, different educations, interest and integration of theory and practice. These themes relates to different levels of knowledge, from basic knowledge to learning to learn.
Localized group membership service for ad hoc networks

We present a specification for a new, localized group membership service that maintains the membership status of adjacent nodes-called neighbors-in a mobile distributed system. The service builds on top of a neighborhood service which employs a simple heartbeat mechanism to discover and track neighbors in the mobile network. Both services assume unreliable communication as found in the wireless environment. No knowledge of the network topology is presumed. We impose a deadline for installing views of the membership to force timely deciding protocols. We give a simple implementation of the neighborhood and the group membership service. If the deadline of view installations is at least the heartbeat rate, we can prove the correctness of our suggested implementation. An application in mobile ad hoc networking exemplifies potential areas of deployment for a localized group membership service.
Comparative Study of Classical and Mutually Coupled Switched Reluctance Motors Using Multiphysics Finite-Element Modeling

This paper presents the numerical modeling of a classical switched reluctance motor (SRM) and a mutually coupled SRM (MCSRM); both have three phases with 12 slots and 8 poles. The multiphysics models have been developed, which can take into account the electromagnetic characteristics, mechanical vibration, and acoustic noise of the foregoing machines. A 2-D electromagnetic model has been used to calculate the magnetic force which is the main source of vibration of the entire motor system. The vibration of the motor is calculated by a mode superposition method, while the acoustic noise is predicted by a 3-D finite-element acoustic model. In order to validate the numerical models, experiments have been carried out. A good agreement between measured and numerical results has been observed, and it is found that the vibration and the noise levels of MCSRM are considerably lower than those of classical SRM.
Salinity-Induced Calcium Signaling and Root Adaptation in Arabidopsis Require the Calcium Regulatory Protein Annexin11[W][OPEN]

Arabidopsis root response to salinity requires the calcium regulatory protein annexin1. Salinity (NaCl) stress impairs plant growth and inflicts severe crop losses. In roots, increasing extracellular NaCl causes Ca2+ influx to elevate cytosolic free Ca2+ ([Ca2+]cyt) as a second messenger for adaptive signaling. Amplification of the signal involves plasma membrane reduced nicotinamide adenine dinucleotide phosphate oxidase activation, with the resultant reactive oxygen species triggering Ca2+ influx. The genetic identities of the Ca2+-permeable channels involved in generating the [Ca2+]cyt signal are unknown. Potential candidates in the model plant Arabidopsis (Arabidopsis thaliana) include annexin1 (AtANN1). Here, luminescent detection of [Ca2+]cyt showed that AtANN1 responds to high extracellular NaCl by mediating reactive oxygen species-activated Ca2+ influx across the plasma membrane of root epidermal protoplasts. Electrophysiological analysis revealed that root epidermal plasma membrane Ca2+ influx currents activated by NaCl are absent from the Atann1 loss-of-function mutant. Both adaptive signaling and salt-responsive production of secondary roots are impaired in the loss-of-function mutant, thus identifying AtANN1 as a key component of root cell adaptation to salinity.
A Component-Oriented Metamodel for the Modernization of Software Applications

The modernization of a software system is a complex and expensive task and requires a deep understanding of the existing system. The capability of re-factoring a complex application into some high-level views is mandatory to elicit its structure and start localize possible changes. The high number of different implementation technologies imposes a model-based, neutral approach to reconstruct the structure and hide unnecessary details. OMG supports this view and proposes KDM (Knowledge Discovery Meta model) as means to describe software systems in detail, but unfortunately KDM supports a component-oriented decomposition of the system of interest only partially. To bypass this limitation, the paper proposes the COMO (Component-Oriented MOdernization) meta model to extend KDM, by borrowing recurring concepts from component-based solutions and software architectures, and to support a proper componentization of the system we want to modernize. The paper presents the main elements of the COMO meta model and exemplifies them on a simple case study.