Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular cloning of syndecan, an integral membrane proteoglycan

We describe cDNA clones for a cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. The cDNA encodes a unique core protein of 32,868 D that contains several structural features consistent with its role as a glycosamino-glycan-containing matrix anchor. The sequence shows discrete cytoplasmic, transmembrane, and NH2-terminal extracellular domains, indicating that the molecule is a type I integral membrane protein. The cytoplasmic domain is small and similar in size but not in sequence to that of the beta-chain of various integrins. The extracellular domain contains a single dibasic sequence adjacent to the extracellular face of the transmembrane domain, potentially serving as the protease-susceptible site involved in release of this domain from the cell surface. The extracellular domain contains two distinct types of putative glycosaminoglycan attachment sites; one type shows sequence characteristics of the sites previously described for chondroitin sulfate attachment (Bourdon, M. A., T. Krusius, S. Campbell, N. B. Schwartz, and E. Ruoslahti. 1987. Proc. Natl. Acad. Sci. USA. 84:3194-3198), but the other type has newly identified sequence characteristics that potentially correspond to heparan sulfate attachment sites. The single N-linked sugar recognition sequence is within the putative chondroitin sulfate attachment sequence, suggesting asparagine glycosylation as a mechanism for regulating chondroitin sulfate chain addition. Both 5' and 3' regions of this cDNA have sequences substantially identical to analogous regions of the human insulin receptor cDNA: a 99-bp region spanning the 5' untranslated and initial coding sequences is 67% identical and a 35- bp region in the 3' untranslated region is 81% identical in sequence. mRNA expression is tissue specific; various epithelial tissues show the same two sizes of mRNA (2.6 and 3.4 kb); in the same relative abundance (3:1), the cerebrum shows a single 4.5-kb mRNA. This core protein cDNA describes a new class of molecule, an integral membrane proteoglycan, that we propose to name syndecan (from the Greek syndein, to bind together).
Iterative reliability-based decoding of turbo-like codes

In this paper, the use of a reliability-based decoding algorithm for some concatenated codes with an interleaver, known as turbo-like codes, is examined to address and overcome the suboptimality of iterative decoding. Simulation results show that the suboptimality of iterative decoding for moderate length codes can be at least partially compensated by this combined approach. Some insights about the potential additional coding gains achievable by the combined approach are investigated based on the characteristics of the constituent decoders, which highlights the nature of suboptimality in iterative decoding.
Modeling Software Evolution using Algebraic Graph Rewriting

We show how evolution requests can be formalized using algebraic graph rewriting. In particular, we present a way to convert the UML class diagrams to colored graphs. Since changes in software may effect the relation between the methods of classes, our colored graph representation also employs the relations in UML interaction diagrams. Then, we provide a set of algebraic graph rewrite rules that formalizes the changes that may be caused by an evolution request, using the pushout construction in the category of marked colored graphs.
Leveraging test generation and specification mining for automated bug detection without false positives

Mining specifications and using them for bug detection is a promising way to reveal bugs in programs. Existing approaches suffer from two problems. First, dynamic specification miners require input that drives a program to generate common usage patterns. Second, existing approaches report false positives, that is, spurious warnings that mislead developers and reduce the practicability of the approach. We present a novel technique for dynamically mining and checking specifications without relying on existing input to drive a program and without reporting false positives. Our technique leverages automatically generated tests in two ways: Passing tests drive the program during specification mining, and failing test executions are checked against the mined specifications. The output are warnings that show with concrete test cases how the program violates commonly accepted specifications. Our implementation reports no false positives and 54 true positives in ten well-tested Java programs.
Buffer insertion considering process variation

A comprehensive probabilistic methodology is proposed to solve the buffer insertion problem with the consideration of process variations. In contrast to a recent work, we point out, for the first time, that the correlation between the required arrival time and the downstream loading capacitance must be considered in order to solve the problem "correctly". We develop an efficient bottom-up recursive algorithm to calculate the joint probability density function that accurately captures the above correlation, and propose effective pruning rules to exclude probabilistically inferior solutions. We verify our buffer insertion using timing analysis with both device and interconnect variations, and show that compared to the conventional buffer insertion algorithm using nominal device and interconnect parameters, our new buffer insertion methodology can reduce the probability of timing violation by up to 30%.
Capacity-Achieving Multiwrite WOM Codes

In this paper, we give an explicit construction of a family of capacity-achieving binary t-write WOM codes for any number of writes t, which have polynomial time encoding and decoding algorithms. The block length of our construction is N=(t/ε)<sup>O(t/(δε))</sup> when ε is the gap to capacity and encoding and decoding run in time N<sup>1+δ</sup>. This is the first deterministic construction achieving these parameters. Our techniques also apply to larger alphabets.
Accelerating Volume Visualization by Exploiting Temporal Coherence

In this paper we present two methods for accelerating surface visualizations of volume data, the image cache and the isomap. The image cache allows us to take advantage of temporal coherence during viewpoint changes. The image cache, which maintains intermediate values used to render the previous image, can be queried for visibility and shading information. While changing the isosurface threshold values, an isomap is generated for the current camera position. This new structure allows surface threshold variations to be rendered interactively. These methods perform well with large data sets because they reduce the rendering time dependence on data size.
Study on Incentives on the Construction Contractor Considering the Reputation Effect

By applying principle-agent and reputation theory, combining with the multi-task principle-agent model and agent market reputation model, construction contractor incentive model of construction project considering the reputation effect was established, and the validity of the market reputation incentive to the contractor was analyzed. We obtained: Firstly, reputation incentive can partly substitute explicit incentives; the "market reputation" of the contractor can make the contractors' opportunism behavior less and lower the client's incentive cost even without the "Game reputation" which is formed by the repetitious game between the client/project management company and the contractor. Secondly, the explicit incentives and the implicit incentives are complementary each other; when the reputation incentive is stronger, the explicit incentives can be weaker. Thirdly, the validity and maneuverability of reputation incentive depends on the establishment of construction market credit system and the just evaluation of the contractor's working ability and effort.
Neural-network-based modeling and dynamic policy synthesis for model predictive control of nonlinear systems

A dynamic control policy with optimized dynamics is explored for its use in a model predictive control (MPC) algorithm for a nonlinear system modeled with a feedforward neural network. The nonlinear system is expressed as a polytopic quasi-linear-parameter-varying (quasi-LPV) system over a region of the state-input space and the dynamics of the policy are allowed to depend on the time-varying parameter of the quasi-LPV model. The policy dynamics are optimized off-line to obtain an enlarged domain of attraction which matches with the state-input region over which the polytopic approximation of the system holds good. A complete MPC algorithm using the dynamic policy as the terminal policy ensures stabilization and improved performance over a larger domain without a larger horizon length.
Subspace Classier in the Hilbert Space

To improve the performance of the subspace classi er, it is e ective to reduce the dimensionality of the intersections between subspaces. For this purpose, the feature space is mapped implicitly to the in nite dimensional Hilbert space and the subspace classi er is applied in the Hilbert space.
Evaluation of Quality Attribute Variability in Software Product Families

Software product family or line is a software engineering paradigm that systematizes reuse. In Software Product Line Engineering, two phases are distinguished: Domain Engineering which is in charge of developing a common infrastructure and assets and Application Engineering which makes use of those assets to generate the products. One of the key aspects of product lines is variability and its management. However, the main focus has been on functional variability and quality variability in software product lines has not received so much attention by researchers. In a product line different members of the line may require different levels of a quality requirement, for instance they could differ in terms of their availability, security, reliability, etc. Due to this variability, quality evaluation in software product lines is much more complicated that in single-systems. One alternative is to evaluate all the products of a line but it is very expensive and ways of reducing evaluation efforts are necessary. In this direction, the paper presents a method for facilitating cost-effective quality evaluation of a product line taking into consideration variability on quality attributes.
Graded refractive index silicon oxynitride thin film characterized by spectroscopic ellipsometry

A graded refractive index silicon oxynitride (SiOxNy) thin film was prepared on a silicon substrate by ion assisted deposition. Spectroscopic ellipsometry (SE) was used to optically analyze the film. The measured SE spectra (2500–8200 A) were analyzed with several fitting models, whose construction was based on an Auger depth profile of the film. In each model, the optical response of SiOxNy was described using the Bruggeman effective medium approximation, by modeling it as a physical mixture of two distinct phases: silicon dioxide and silicon nitride. Grading was modeled by varying the silicon nitride volume fraction with depth below the surface, according to an assumed profile. Fitting results were very sensitive to the profile chosen, which was different for each model. Experimentation with the profile led to a model which produced a remarkably good fit, over the entire spectral range. As a result, the film thickness and its refractive index profile were determined. The index profile determined by SE a.
A Comparison of Personality Characteristics and Psychiatric Symptomatology between Upper Airway Resistance Syndrome and Obstructive Sleep Apnea Syndrome

Objective To investigate the personality characteristics of patients with upper airway resistance syndrome (UARS) and those of patients with obstructive sleep apnea syndrome (OSAS). Methods Eighty-eight patients with UARS and 365 patients with OSAS participated. All patients had a diagnostic full-night attended polysomnography (PSG) and completed the Athens Insomnia Scale (AIS), Pittsburgh Sleep Quality Index (PSQI), Epworth Sleepiness Scale (ESS), Symptom Checklist-90-Revision (SCL-90-R) and Eysenck Personality Questionnaire (EPQ). Results The UARS group scored significantly higher than the OSAS group on the ESS, AIS, and PSQI (p<0.001). The scores of all SCL-90-R subscales in the UARS group were significantly higher than those in the OSA group (all p<0.001, except for somatization, p=0.016). Patients with UARS scored lower on EPQ-E (extroversion/introversion) (p=0.006) and EPQ-L (lie) (p<0.001) than those with OSA. UARS patients also showed higher scores on EPQ-P (psychoticism) (p=0.002) and EPQ-N (neuroticism) (p<0.001) than OSAS patients. Conclusion Our results suggest that patients with UARS have worse subjective sleep quality than OSAS patients in spite of their better PSG findings. UARS patients tend to have more neurotic and sensitive personalities than patients with OSAS, which may be a cause of the clinical features of UARS.
An affect detection technique using mobile commodity sensors in the wild

Current techniques to computationally detect human affect often depend on specialized hardware, work only in laboratory settings, or require substantial individual training. We use sensors in commodity smartphones to estimate affect in the wild with no training time based on a link between affect and movement. The first experiment had 55 participants do touch interactions after exposure to positive or neutral emotion-eliciting films; negative affect resulted in faster but less precise interactions, in addition to differences in rotation and acceleration. Using off-the-shelf machine learning algorithms we report 89.1% accuracy in binary affective classification, grouping participants by their self-assessments. A follow up experiment validated findings from the first experiment; the experiment collected naturally occurring affect of 127 participants, who again did touch interactions. Results demonstrate that affect has direct behavioral effect on mobile interaction and that affect detection using common smartphone sensors is feasible.
Utility of Baroreflex Sensitivity as a Marker of Stress

Presently, adaptive systems use various cognitive and cardiovascular measures to evaluate the functional state of the operator. One marker that has been largely ignored as an assessment tool is baroreflex sensitivity (BRS). This study examined the extent to which BRS changed in response to acute psychological and physical stressors. A total of 20 participants underwent 6-min exposures to a psychological stressor and a physical stressor. Baroreceptor sensitivity, blood pressure, heart rate, heart rate variability, stroke volume, cardiac output, mean blood pressure, total peripheral resistance, left ventricular ejection time, and pre-ejection period were continuously measured at rest and throughout the testing period. Compared to rest, BRS significantly decreased during both the psychological and physical stressors. BRS was reduced more with the psychological stressor than the physical stressor. Heart rate and systolic blood pressure significantly increased above rest during the psychological stressor but not during the physical stressor. There were no significant differences from rest or between stressors for the other physiological markers. BRS was more robustly responsive than other cardiovascular measures commonly used to assess the psychophysiological response to stress, suggesting BRS is a useful marker for evaluating operator functional state during psychological and physical tasks.
Pan-supplier stock control in a virtual warehouse

We describe the commercial application of agents to the handling of catalogue and stock-control for the selling of books on the internet. The primary characteristic of the target market is (very) low volumes over a (very) large number of items, thus agility and extremely low overheads are the essential factors for a viable business model. Being a new company (established 2004), without legacy software and with the freedom to make new choices, it was decided that the agent abstraction offered both short-term software engineering and longer-term business advantages. This expectation has been borne out in practice, in that it has been possible to construct an e-trading platform, using a 4-person team over a period of a few months, and that is now part of a live business operation handling just over 12,000 transactions daily. In this paper we explain how agents helped focus attention on the responsibilities of key software functions, how different functions should interact with one another and how to identify and propagate key performance indicator information through the system to detect unexpected behaviour. Agent technology has many potential benefits for dynamic fast-moving businesses where software requirements change quickly and business needs grow rapidly, all within a dynamic environment that has entirely different rules across the axes of geography, market, customer and competitor. Using autonomous agents allowed The Book Depository to build quickly a complex network of P2P relationships with a large number of suppliers and publishers of very different sizes who each utilize a variety of different trading and data interchange standards.
On the refinement of ontologies

Ontologies have emerged as one of the key issues in information integration and interoperability and their application to knowledge management and electronic commerce. A trend towards formal methods for ontology management is obvious. This paper discusses a concept which can be expected to be of great importance to formal ontology management, and which is well-known in traditional software development: the refinement of ontologies. We define and discuss the concept, give illustrating examples, and highlight its advantages as compared to other forms of ontology revision.
Prominent Object Detection and Recognition: A Saliency-based Pipeline

This manuscript introduces the problem of prominent object detection and recognition. The problem deals with finding the most important region of interest, segmenting the relevant item/object in that area, and assigning it an object class label. In other words, we are solving the three problems of saliency modeling, saliency detection, and object recognition under one umbrella. The motivation behind such a problem formulation is 1) the benefits to the knowledge representation-based vision pipelines, and 2) the potential improvements in emulating bio-inspired vision systems by solving these three problems together. We propose a method as a baseline for further research. The proposed model predicts the most important area in the image, segments the associated objects, and labels them. The proposed problem and method are evaluated against human fixations, annotated segmentation masks, and object class categories. We define a chance level for each of the evaluation criterion to compare the proposed algorithm with. Despite the good performance of the proposed baseline, the overall evaluations indicate that the problem of prominent object detection and recognition is a challenging task that is still worth investigating further.
A CSP Approach for Customizing Mobile Service Bundles

To satisfy individual requirements of customers, mobile phone service industries are offering a variety of service modules for customers to build their own customized service packages. In this paper,we present an approach of customizing service bundles using CSP (Constraint Satisfaction Problem), a well-known problem-solving technology in AI domain. Firstly, service customization model containing service elements and rules is represented in a graphical way. Next, the service customization model is transformed as a CSP such that classical constraint solver (such as Choco) can be employed to infer a service configuration. A case of mobile phone service customization in China Mobile is used throughout this paper to demonstrate the effectiveness of the presented approach.
The pH-dependent rate of action of local anesthetics on the node of Ranvier

Local anesthetic solutions were applied suddenly to the outside of single myelinated nerve fibers to measure the time course of development of block of sodium channels. Sodium currents were measured under voltage clamp with test pulses applied several times per second during the solution change. The rate of block was studied by using drugs of different lipid solubility and of different charge type, and the external pH was varied from pH 8.3 to pH 6 to change the degree of ionization of the amine compounds. At pH 8.3 the half-time of action of amine anesthetics such as lidocaine, procaine, tetracaine, and others was always less than 2 s and usually less than 1 s. Lowering the pH to 6.0 decreased the apparent potency and slowed the rate of action of these drugs. The rate of action of neutral benzocaine was fast (1 s) and pH independent. The rate of action of cationic quaternary QX-572 was slow (greater than 200 s) and also pH independent. Other quaternary anesthetic derivatives showed no action when applied outside. The result is that neutral drug forms act much more rapidly than charged ones, suggesting that externally applied local anesthetics must cross a hydrophobic barrier to reach their receptor. A model representing diffusion of drug into the nerve fiber gives reasonable time courses of action and reasonable membrane permeability coefficients on the assumption that the hydrophobic barrier is the nodal membrane. Arguments are given that there may be a need for reinterpretation of many published experiments on the location of the anesthetic receptor and on which charge form of the drug is active to take into account the effects of unstirred layers, high membrane permeability, and high lipid solubility.
Wireless LAN based indoor positioning system WiPS and its simulation

The wireless LAN (Wi-Fi) infrastructure is widely used and many location-aware systems and services are researched. In this paper, wireless LAN based indoor positioning system (WiPS) is proposed. WiPS uses wireless LAN technology to measure the location of each mobile terminal. Mobile terminals equip only wireless LAN device to communicate and measure its location, so it can be made without any additional devices for location sensing. Existing wireless LAN based location systems measure the signal strength by only access points. On WiPS, each mobile terminal also measures the signal strength of neighboring terminals. Thereby WiPS can achieve more precise location estimation than existing systems, where there are many mobile terminals. We simulate the case that distance measurement has probabilistic error. The result shows improvement of accuracy in WiPS.
A “linear logic” Quicksort

The linear style of programming inspired by linear logic has been proposed to reduce garbage collection and synchronization costs in serial and parallel systems. We programmed Quicksort for both lists and arrays in a "linear" fragment of Lisp to estimate the performance impact of linearity on a serial machine. Even though Quicksort is well-tuned for current non-linear architectures, we find that linearity extracts no real penalty. Our "linear" list Quicksort is as fast as any non-linear list Quicksort, and our "linear" vector Quicksort is only 3.5% slower than a non-linear vector Quicksort. The linear style is moderately pleasant, and the redundancy of linearity checking can aid in finding bugs.