Miracle-dz/UniFAR-FTUs huggingface dataset:
Self-adjusting stack machines

Self-adjusting computation offers a language-based approach to writing programs that automatically respond to dynamically changing data. Recent work made significant progress in developing sound semantics and associated implementations of self-adjusting computation for high-level, functional languages. These techniques, however, do not address issues that arise for low-level languages, i.e., stack-based imperative languages that lack strong type systems and automatic memory management. In this paper, we describe techniques for self-adjusting computation which are suitable for low-level languages. Necessarily, we take a different approach than previous work: instead of starting with a high-level language with additional primitives to support self-adjusting computation, we start with a low-level intermediate language, whose semantics is given by a stack-based abstract machine. We prove that this semantics is sound: it always updates computations in a way that is consistent with full reevaluation. We give a compiler and runtime system for the intermediate language used by our abstract machine. We present an empirical evaluation that shows that our approach is efficient in practice, and performs favorably compared to prior proposals.
Mechanical Properties of Conjugated Polymers and Polymer‐Fullerene Composites as a Function of Molecular Structure

Despite the importance of mechanical compliance in most applications of semiconducting polymers, the effects of structural parameters of these materials on their mechanical properties are typically not emphasized. This paper examines the effect of length of the pendant group on the tensile modulus and brittleness for a series of regioregular poly(3‐alkylthiophenes) (P3ATs) and their blends with a soluble fullerene derivative, PCBM. The tensile modulus decreases with increasing length of the alkyl side‐chain, from 1.87 GPa for butyl side chains to 0.16 GPa for dodecyl chains. The moduli of P3AT:PCBM blends films are greater than those of the pure polymers by factors of 2–4. A theoretical model produces a trend in the effect of alkyl side chain on tensile modulus that follows closely to the experimental measurements. Tensile modulus correlates with brittleness, as the strain at which cracks appear is 6% for P3BT and >60% for P3OT. Adhesion of the P3AT film to a polydimethylsiloxane (PDMS) substrate is believed to play a role in an apparent increase in brittleness from P3OT to P3DDT. The additive 1,8‐Diiodooctane (DIO) reduces the modulus of P3HT:PCBM blend by a factor of 3. These results could enable mechanically robust, flexible, and stretchable electronics.
Oracle Analysis of Sparse Automatic Music Transcription

We have previously proposed a structured sparse approach to piano transcription with promising results recorded on a challenging dataset. The approach taken was measured in terms of both frame-based and onset-based metrics. Close inspection of the results revealed prob- lems in capturing frames displaying low-energy of a given note, for exam- ple in sustained notes. Further problems were also noticed in the onset detection, where for many notes seen to be active in the output tran- cription an onset was not detected. A brief description of the approach is given here, and further analysis of the system is given by considering an oracle transcription, derived from the ground truth piano roll and the given dictionary of spectral template atoms, which gives a clearer indi- cation of the problems which need to be overcome in order to improve the proposed approach.
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells

Motivation: Dynamic simulation of genome-scale molecular interaction networks will enable the mechanistic prediction of genotype–phenotype relationships. Despite advances in quantitative biology, full parameterization of whole-cell models is not yet possible. Simulation methods capable of using available qualitative data are required to develop dynamic whole-cell models through an iterative process of modelling and experimental validation. Results: We formulate quasi-steady state Petri nets (QSSPN), a novel method integrating Petri nets and constraint-based analysis to predict the feasibility of qualitative dynamic behaviours in qualitative models of gene regulation, signalling and whole-cell metabolism. We present the first dynamic simulations including regulatory mechanisms and a genome-scale metabolic network in human cell, using bile acid homeostasis in human hepatocytes as a case study. QSSPN simulations reproduce experimentally determined qualitative dynamic behaviours and permit mechanistic analysis of genotype–phenotype relationships. Availability and implementation: The model and simulation software implemented in C++ are available in supplementary material and at http://sysbio3.fhms. surrey.ac. uk/qsspn/. Contact: a.kierzek@surrey.ac. uk Supplementary information: Supplementary data are available at Bioinformatics online.
Marjolin’s ulcer in chronic wounds – review of available literature

Marjolin’s ulcer is a rare, aggressive skin cancer developing in scar tissue, chronic ulcers and areas affected by inflammations. Its incidence is estimated to range from 1% to 2% of all burn scars. It most frequently takes the form of squamous cell carcinoma which sometimes is diagnosed during examination of lesions developing in scars and hard-to-heal chronic wounds (pressure sores, leg ulcers). Therapeutic management of Marjolin’s ulcer requires well-designed treatment plan to ensure optimal medical care and good quality of life for the patient. The high risk of metastases and damage to the structure of vitally important organs determines the need for early diagnosis and prompt surgical intervention with supplementary therapy. The purpose of the study was to examine etiopathogenesis of Marjolin’s ulcer and principles of its treatment. The authors focused on the aspect of malignant degeneration in chronic wounds (leg ulcers, pressure sores) as a very rare, aggressive form of Marjolin’s ulcer. A review of the available literature on the issue of Marjolin ulcers was conducted using the key words; Marjolin ulcers, pressure sore, chronic wound. Malignant degeneration in chronic wounds is a very rare aggressive form of Marjolin ulcer. Increased oncological alertness should be displayed by nursing and medical personnel taking care of patients with chronic wounds.
Sport-specific nutrition: Practical strategies for team sports

Abstract Implementation of a nutrition programme for team sports involves application of scientific research together with the social skills necessary to work with a sports medicine and coaching staff. Both field and court team sports are characterized by intermittent activity requiring a heavy reliance on dietary carbohydrate sources to maintain and replenish glycogen. Energy and substrate demands are high during pre-season training and matches, and moderate during training in the competitive season. Dietary planning must include enough carbohydrate on a moderate energy budget, while also meeting protein needs. Strength and power team sports require muscle-building programmes that must be accompanied by adequate nutrition, and simple anthropometric measurements can help the nutrition practitioner monitor and assess body composition periodically. Use of a body mass scale and a urine specific gravity refractometer can help identify athletes prone to dehydration. Sports beverages and caffeine are the most common supplements, while opinion on the practical effectiveness of creatine is divided. Late-maturing adolescent athletes become concerned about gaining size and muscle, and assessment of maturity status can be carried out with anthropometric procedures. An overriding consideration is that an individual approach is needed to meet each athlete's nutritional needs.
Omitting Types, Bounded Width and the Ability to Count

We say that a finite algebra 𝔸 = 〈A; F〉 has the ability to count if there are subalgebras C of 𝔸3 and Z of 𝔸 such that the structure 〈A; C, Z〉 has the ability to count in the sense of Feder and Vardi. We show that for a core relational structure A the following conditions are equivalent: (i) the variety generated by the algebra 𝔸 associated to A contains an algebra with the ability to count; (ii) 𝔸2 has the ability to count; (iii) the variety generated by 𝔸 admits the unary or affine type. As a consequence, for CSP's of finite signature, the bounded width conjectures stated in Feder–Vardi [10], Larose–Zadori [17] and Bulatov [5] are identical.
Estimation of creatinine by the Jaffe reaction. A comparison of three methods.

Total chromogen, true, and AutoAnalyzer methods of measuring serum and urine creatinine by the Jaffe reaction were investigated. Some factors influencing this reaction were examined. These included wavelength, blank, linearity, and conditions of color development. Modifications of the three methods were made and their precision, recovery, and sample stability determined. The interference of ketones and glucose were measured. Finally, the values obtained by the three methods on the same samples of serum and urine were compared statistically.
A Dynamical Systems Account of Sensorimotor Contingencies

According to the sensorimotor approach, perception is a form of embodied know-how, constituted by lawful regularities in the sensorimotor flow or in sensorimotor contingencies (SMCs) in an active and situated agent. Despite the attention that this approach has attracted, there have been few attempts to define its core concepts formally. In this paper, we examine the idea of SMCs and argue that its use involves notions that need to be distinguished. We introduce four distinct kinds of SMCs, which we define operationally. These are the notions of sensorimotor environment (open-loop motor-induced sensory variations), sensorimotor habitat (closed-loop sensorimotor trajectories), sensorimotor coordination (reliable sensorimotor patterns playing a functional role), and sensorimotor strategy (normative organization of sensorimotor coordinations). We make use of a minimal dynamical model of visually guided categorization to test the explanatory value of the different kinds of SMCs. Finally, we discuss the impact of our definitions on the conceptual development and empirical as well as model-based testing of the claims of the sensorimotor approach.
Gesture-recognizing hand-held interface with vibrotactile feedback for 3D interaction

This article presents a hand-held interface system for 3D interaction with digital media contents. The system is featured with 1) tracking of the full 6 degrees-of-freedom position and orientation of a hand-held controller, 2) robust gesture recognition using continuous hidden Markov models based on the acceleration and position measurements, and 3) dual-mode vibrotactile feedback using both vibration motor and voice-coil actuator. We also demonstrate the advantages of the system through a usability experiment.
Internal Initiation of Translation Directed by the 5′-Untranslated Region of the mRNA for eIF4G, a Factor Involved in the Picornavirus-induced Switch from Cap-dependent to Internal Initiation (*)

The eIF4 group initiation factors carry out recognition of the mRNA cap, unwinding of mRNA secondary structure, and binding of mRNA to the 43 S preinitiation complex. Infection by picornaviruses results in proteolytic cleavage of one of these factors, eIF4G, an event that severely restricts cap-dependent translation but permits cap-independent initiation to proceed from internal ribosome entry sequences in picornaviral RNAs. The 5′-untranslated region (5′-UTR) of eIF4G mRNA resembles such picornaviral sequences in being unusually long and containing multiple open reading frames and a polypyrimidine tract. When inserted upstream of a luciferase reporter gene, this 5′-UTR served as a translational enhancer in four different cell lines. Mutation of all four upstream ATG codons to AAG did not alter the translational enhancement. The presence of the eIF4G 5′-UTR between an RNA hairpin and the luciferase cistron stimulated expression 119-fold. Similarly, the presence of the 5′-UTR between the two cistrons of a bicistronic mRNA stimulated expression of the downstream cistron 42-fold. These results indicate that the eIF4G 5′-UTR directs internal initiation. The ability to continue synthesis of eIF4G when the cell is unable to carry out normal cap-dependent translation may represent an autoregulatory mechanism or be part of the cellular response to stresses that interrupt cap-dependent translation.
The role of motivation and the regulation of eating on the physical and psychological health of patients with cardiovascular disease

This study tested a longitudinal motivation model for healthy eating in patients with cardiovascular disease, using self-determination and social-cognitive theories. A total of 513 patients completed measures of eating habits, global motivation, motivation for eating, self-efficacy for eating and life satisfaction, immediately after a major cardiac incident and at three times during a year (e.g. 2008–2009). Physiological indicators were measured to examine how they predicted the participants’ physical health. Results found participants with self-determined motivation were more likely to develop a sense of self-efficacy towards eating and a healthy diet, which had beneficial effects on their physical health and life satisfaction.
Temporally Coherent Adaptive Sampling for Imperfect Shadow Maps

We propose a new adaptive algorithm for determining virtual point lights (VPL) in the scope of real‐time instant radiosity methods, which use a limited number of VPLs. The proposed method is based on Metropolis‐Hastings sampling and exhibits better temporal coherence of VPLs, which is particularly important for real‐time applications dealing with dynamic scenes. We evaluate the properties of the proposed method in the context of the algorithm based on imperfect shadow maps and compare it with the commonly used inverse transform method. The results indicate that the proposed technique can significantly reduce the temporal flickering artifacts even for scenes with complex materials and textures. Further, we propose a novel splatting scheme for imperfect shadow maps using hardware tessellation. This scheme significantly improves the rendering performance particularly for complex and deformable scenes. We thoroughly analyze the performance of the proposed techniques on test scenes with detailed materials, moving camera, and deforming geometry.
Interferometer methods for tissue dosimetry and determination of material properties

We propose that displacement, velocity, and double-pulse holographic interferometry can be used to measure the dynamic response of tissue to pulsed lasers. Tissue material properties and dosimetry for pulsed laser interactions with tissue can then be addressed with these tools. The present use of fiber-optic coupled interferometric devices for biomedical applications suggests that these methods can be successfully adapted for the measurement of tissue material properties such as Gruneisen parameters, total energy absorption, energy deposition profiles, characteristics of multi-dimensional stress wave propagation, and heterogeneous effects. In this paper I will show (1) how Michelson interferometry was used to in stress confinement experiments with non-biological materials to make direct measurements of the Gruneisen parameters of a complex, composite material; (2) the advantages of velocity interferometry for determination of the energy deposition profile; and (3) the use of double-pulse holographic interferometry for multi-dimensional stress wave propagation and heterogeneous effects. We will propose a fiber-optic interferometer which is uniquely adapted for in-vivo biomedical applications.
Visualizing and Assessing a Compositional Approach to Service-Oriented Business Process Design Using Unified Modelling Language (UML)

In the context of Service-Oriented Architecture (SOA), complex systems can be realized through the visualization of business driven processes. The automation of Service Supported Systems (SSS) is the future integral part of core SOA which provides preprocessed information and solution suggestions for the Cloud Computing Users (CCU). CCU requires compact and fast decision supporting displays and user interface in order to handle the increasing work load. This requires intelligent, intuitive and robust preprocessing system as a backbone for automation lifecycle management. Complex business management processes often entail complex environmental decision-making procedures. This process can be greatly enhanced if it is based on an exploratory-envisioning system such as Information Exploration and Visualization Environment. Current scientific research has taken advantage of e-science to enhance distributed simulation, analysis and visualization. Many of these infrastructures use one or more collaborative software paradigms like Grid Computing, High Level Architecture (HLA) and Service Oriented Architecture (SOA), which together provide an optimal environment for heterogeneous and distant, real-time collaboration. While significant progress has been made using these collaborative platforms, often there is no particular software suite that fulfils all requirements for an entire organization or case study. End-user must cope manually with a collection of tools and its exporting/importing capabilities to obtain the output needed for a particular purpose. We presents how service oriented architecture can be utilized in automation services support system using RCD framework as underlying composition platform. The introduced framework combines rapid analysis development and intelligent process state visualization for CCU and discusses the challenges met in building reliable cloud computing services for web services. Unified Modeling Language (UML) is used as a specification technique for the system analysis
Differential factor binding at the promoter of early baculovirus gene PE38 during viral infection: GATA motif is recognized by an insect protein

Regulatory elements interacting with DNA-binding proteins have been investigated in the promoter sequence of the early PE38 gene in the Autographa californica nuclear polyhedrosis virus (AcNPV). A GATA motif located 50 nucleotides upstream of the PE38 transcriptional start site is recognized differentially in the course of infection. As demonstrated by footprint and gel mobility shift assays, the GATA sequences TTATCT are protected by nuclear extracts from uninfected Spodoptera frugiperda cells and from S. frugiperda cells early postinfection (p.i.) but not by S. frugiperda cell extracts isolated 40 h p.i. We have compared the binding capacity of the insect GATA-like protein with that of the vertebrate GATA-1 factor identified as erythroid-specific factor. Our results indicate that a factor present in mouse erythroleukemia cells, presumably GATA-1, can bind to the insect GATA motif and vice versa. Evidence from transient expression studies suggests that the mutated GATA sequences do not influence PE38 promoter activity in cell culture.
Factors Affecting the Short-Term Prognosis of Alcohol Dependent Patients Undergoing Inpatient Detoxification

Stable measures of psychological functioning require a considerable period of abstinence. However, the duration of inpatient detoxification programs has decreased dramatically in most health care systems, posing a novel challenge for clinical evaluation of patients. The present study was carried out to examine whether factors predicting short-term prognosis can be identified in alcohol dependent subjects during early stages of inpatient detoxification. Self-reports of mood states were obtained, and executive cognitive functioning was examined. Outcome was studied at 2–3 months. No correlation was found between self-reported symptoms of depression, hopelessness, and anxiety, and percentage of nondrinking days. A significant positive correlation was found between Wisconsin Card Sorting Test (WCST) performance and short-term prognosis measured by this parameter. Thus, in addition to transient withdrawal-related effects, impairments of WCST performance in early stages of alcohol detoxification may reflect more long standing deficits in problem-solving strategies, of possible relevance for matching patients to treatment services.
Molecular assembly, secretion, and matrix deposition of type VI collagen

Monoclonal antibodies reactive with the tissue form of type VI collagen were used to isolate the type VI collagen polypeptides from cultured fibroblasts and muscle cells. Two [35S]methionine-labeled polypeptides of 260 and 140 kD were found intracellularly, in the medium, and in the extracellular matrix of metabolically labeled cells. These polypeptides were disulfide cross-linked into very large complexes. The 260- and 140- kD polypeptides were intimately associated and could not be separated from each other by reduction without denaturation. In the absence of ascorbic acid, both polypeptides accumulated inside the cell, and their amounts in the medium and in the matrix were decreased. These results suggest that both the 260- and the 140-kD polypeptides are integral parts of the type VI collagen molecule. Examination of type VI collagen isolated from the intracellular pool by electron microscopy after rotary shadowing revealed structures corresponding to different stages of assembly of type VI collagen. Based on these images, a sequence for the intracellular assembly of type VI collagen could be discerned. Type VI collagen monomers are approximately 125 nm long and are composed of two globules separated by a thin strand. The monomers assemble into dimers and tetramers by lateral association. Only tetramers were present in culture media, whereas both tetramers and multimers were found in extracellular matrix extracts. The multimers appeared to have assembled from tetramers by end-to-end association into filaments that had prominent knobs and a periodicity of approximately 110 nm. These results show that, unlike other collagens, type VI collagen is assembled into tetramers before it is secreted from the cells, and they also suggest an extracellular aggregation mechanism that appears to be unique to this collagen.
Query-oriented Unsupervised Multi-document Summarization on Big Data

Real time document summarization is a critical need nowadays, owing to the large volume of information available for our reading, and our inability to deal with this entirely due to limitations of time and resources. Oftentimes, information is available in multiple sources, offering multiple contexts and viewpoints on a single topic of interest. Automated multi-document summarization (MDS) techniques aim to address this problem. However, current techniques for automated MDS suffer from low precision and accuracy with reference to a given subject matter, when compared to those summaries prepared by humans and takes large time to create the summary when the input given is too huge. In this paper, we propose a hybrid MDS technique combining feature based algorithms and dynamic programming for generating a summary from multiple documents based on user provided query. Further, in real-world scenarios, Web search serves up a large number of URLs to users, and the work of making sense of these with reference to a particular query is left to the user. In this context, an efficient parallelized MDS technique based on Hadoop is also presented, for serving a concise summary of multiple Webpage contents for a given user query in reduced time duration.