Miracle-dz/UniFAR-FTUs huggingface dataset:
Large deformation three-dimensional image registration in image-guided radiation therapy

In this paper, we present and validate a framework, based on deformable image registration, for automatic processing of serial three-dimensional CT images used in image-guided radiation therapy. A major assumption in deformable image registration has been that, if two images are being registered, every point of one image corresponds appropriately to some point in the other. For intra-treatment images of the prostate, however, this assumption is violated by the variable presence of bowel gas. The framework presented here explicitly extends previous deformable image registration algorithms to accommodate such regions in the image for which no correspondence exists. We show how to use our registration technique as a tool for organ segmentation, and present a statistical analysis of this segmentation method, validating it by comparison with multiple human raters. We also show how the deformable registration technique can be used to determine the dosimetric effect of a given plan in the presence of non-rigid tissue motion. In addition to dose accumulation, we describe a method for estimating the biological effects of tissue motion using a linear–quadratic model. This work is described in the context of a prostate treatment protocol, but it is of general applicability.
Cooperative suspended object manipulation using reinforcement learning and energy-based control

Cooperative dynamic object manipulation can extend the manipulation capabilities of robot-robot and human-robot teams. In order to be able to inject energy into various suspended objects of unknown parameters, in this paper we propose an adaptive controller which combines reinforcement learning with energy based swing-up control. The proposed controller is successfully verified in a single robot and human-robot experimental setup for different types of suspended objects.
A perceptual-based rate control for HEVC

In this paper, a perceptual-based rate control algorithm for the high efficiency video coding (HEVC) is proposed. Since the human visual system (HVS) is highly sensitive to edge information inherited in image and video contents, gradient magnitude is considered a very effective attribute on the computation of the spatial perceptual characteristics (SPC) and the temporal perceptual characteristic (TPC). The latter is further computed based on the gradient magnitude similarity deviation (GMSD). The combined perceptual characteristic of SPC and TPC is then used to guide the bit allocation process for each CTU. Experimental results have clearly shown that the proposed perceptual rate control scheme can achieve superior perceptual coding performance, compared with the original R-A rate control adopted in the HEVC.
Entity ranking using click-log information

Log information describing the items the users have selected from the set of answers a query engine returns to their queries constitute an excellent form of indirect user feedback that has been extensively used in the web to improve the effectiveness of search engines. In this work we study how the logs can be exploited to improve the ranking of the results returned by an entity search engine. Entity search engines are becoming more and more popular as the web is changing from a web of documents into a "web of things". We show that entity search engines pose new challenges since their model is different than the one documents are based on. We present a novel framework for feature extraction that is based on the notions of entity matching and attribute frequencies. The extracted features are then used to train a ranking classifier. We introduce different methods and metrics for ranking, we combine them with existing traditional techniques and we study their performance using real and synthetic data. The experiments show that our technique provides better results in terms of accuracy.
Safety and Feasibility of Long-term Intravenous Sodium Nitrite Infusion in Healthy Volunteers

Background Infusion of sodium nitrite could provide sustained therapeutic concentrations of nitric oxide (NO) for the treatment of a variety of vascular disorders. The study was developed to determine the safety and feasibility of prolonged sodium nitrite infusion. Methodology Healthy volunteers, aged 21 to 60 years old, were candidates for the study performed at the National Institutes of Health (NIH; protocol 05-N-0075) between July 2007 and August 2008. All subjects provided written consent to participate. Twelve subjects (5 males, 7 females; mean age, 38.8±9.2 years (range, 21–56 years)) were intravenously infused with increasing doses of sodium nitrite for 48 hours (starting dose at 4.2 µg/kg/hr; maximal dose of 533.8 µg/kg/hr). Clinical, physiologic and laboratory data before, during and after infusion were analyzed. Findings The maximal tolerated dose for intravenous infusion of sodium nitrite was 267 µg/kg/hr. Dose limiting toxicity occurred at 446 µg/kg/hr. Toxicity included a transient asymptomatic decrease of mean arterial blood pressure (more than 15 mmHg) and/or an asymptomatic increase of methemoglobin level above 5%. Nitrite, nitrate, S-nitrosothiols concentrations in plasma and whole blood increased in all subjects and returned to preinfusion baseline values within 12 hours after cessation of the infusion. The mean half-life of nitrite estimated at maximal tolerated dose was 45.3 minutes for plasma and 51.4 minutes for whole blood. Conclusion Sodium nitrite can be safely infused intravenously at defined concentrations for prolonged intervals. These results should be valuable for developing studies to investigate new NO treatment paradigms for a variety of clinical disorders, including cerebral vasospasm after subarachnoid hemorrhage, and ischemia of the heart, liver, kidney and brain, as well as organ transplants, blood-brain barrier modulation and pulmonary hypertension. Clinical Trial Registration Information http://www.clinicaltrials. gov; NCT00103025
Glycan-dependent and -independent Association of Vesicular Stomatitis Virus G Protein with Calnexin*

Calnexin (CNX) is a membrane-bound molecular chaperone that associates with newly synthesized proteins in the endoplasmic reticulum. Although several studies have indicated that it interacts exclusively with glycoproteins that carry monoglucosylated N-linked oligosaccharides, others have reported that it can bind to proteins that have no glycans. To address this discrepancy, we translated wild-type vesicular stomatitis virus G protein and nonglycosylated mutant forms in the presence of microsomes and examined their association with CNX. Individual G protein molecules were found to efficiently associate with CNX when both glycans were present and less efficiently if there was only a single glycan. Nonglycosylated G protein also interacted with CNX, but only when misfolded and present in high molecular weight aggregates. The results indicated that CNX can interact with G protein in two ways: through an oligosaccharide-dependent mechanism that involves individual substrate proteins; and in an oligosaccharide-independent association with large aggregates.
The Epidemiology of Cosmetic Treatments for Corneal Opacities in a Korean Population

Purpose To describe etiologies and clinical characteristics of corneal opacities leading patients to seek cosmetic treatments. Methods The medical records of 401 patients who presented for cosmetic improvement in corneal opacities between May 2004 and July 2007 were retrospectively reviewed. The following parameters were analyzed: age, gender, cause of corneal opacity, time course of the corneal disease, associated diseases, prior and current cosmetic treatments, visual acuity, location and depth of the corneal opacity, and the presence of either corneal neovascularization or band keratopathy. A single practitioner examined all patients. Results The most common causes of corneal opacity were ocular trauma (203 eyes, 50.6%), retinal disease (62 eyes, 15.5%), measles (38 eyes, 9.5%), and congenital etiologies (22 eyes, 5.5%). Prior treatments included iris colored contact lenses (125 eyes, 31.1%) and corneal tattooing (34 eyes, 8.46%). A total of 321 of 401 eyes underwent cosmetic treatment for corneal opacities. The most common treatment performed after the primary visit was corneal tattooing (261 eyes, 64.92%). Conclusions This is the first study to investigate the causes and clinical characteristics of patients presenting for cosmetic treatment of corneal opacities rather than for functional improvement. Various cosmetic interventions are available for patients with corneal opacities, and these should be individualized for the needs of each patient.
A Game with a Purpose to Access Europe's Cultural Treasure

Europeana, the European aggregator for dig- ital cultural heritage objects spends huge ef- fort on providing access to the vast collection of Europe's Culture. While the content has been made available online, it still needs to be disseminated. We propose a \games with a purpose" approach to engage people with this tremendous collection and make them dis- cover European culture. This approach is im- plemented by a question and answering sys- tem, in which players create questions that are answered by speci c Europeana resources. Other players can then use a search interface to Europeana to nd the particular resource that is needed to answer the question. This concept provides a low level entrance to cul- tural heritage for end users. Moreover it re- veals human search strategies on Europeana that can be exploited to support and improve the search experience of other users on Euro- peana and helps to identify objects of interest by analyzing usage data.
Pyrosequencing of TPMT alleles in a general Swedish population and in patients with inflammatory bowel disease.

BACKGROUND Interindividual differences in therapeutic efficacy in patients treated with thiopurines might be explained by the presence of thiopurine S-methyltransferase (TPMT) alleles that encode for reduced TPMT enzymatic activity. It is therefore of value to know an individual's inherent capacity to express TPMT. METHOD We developed a pyrosequencing method to detect 10 single-nucleotide polymorphisms (SNPs) in TPMT. A Swedish population (n = 800) was examined for TPMT*3A, TPMT*3B, TPMT*3C, and TPMT*2. Patients with inflammatory bowel disease (n = 24) and healthy volunteers (n = 6), selected on the basis of TPMT enzymatic activity, were investigated for all 10 SNPs to determine the relationship between TPMT genotype and phenotype. RESULTS In the general population we identified the following genotypes with nonfunctional alleles: TPMT*1/*3A (*3A allelic frequency, 3.75%), TPMT*1/*3C (*3C allelic frequency, 0.44%), TPMT*1/*3B (*3B allelic frequency, 0.13%), and TPMT*1/*2 (*2 allelic frequency, 0.06%). All nine individuals with normal enzymatic activity were wild-type TPMT*1/*1. Thirteen individuals with intermediate activity were either TPMT*1/*3A (n = 12) or TPMT*1/*2 (n = 1). Eight individuals with low enzymatic activity were TPMT*3A/*3A (n = 4), TPMT*3A/*3C (n = 2), or TPMT*1/*3A (n = 2). CONCLUSION Next to wild type, the most frequent alleles in Sweden are TPMT*3A and TPMT*3C. A previously established phenotypic cutoff for distinguishing normal from intermediate metabolizers was confirmed. To identify the majority of cases (90%) with low or intermediate TPMT activity, it was sufficient to analyze individuals for only 3 of the 10 SNPs investigated. Nevertheless, this investigation indicates that other mutations might be of relevance for decreased enzymatic activity.
Social Network Analysis and Visualization

1053-5888/08/$25.00©2008IEEE IEEE SIGNAL PROCESSING MAGAZINE [147] NOVEMBER 2008 T he notion of a social network, and associated methods of analysis, is permeating an increasing number of application domains, including communications, bibliometry, and systems biology. This article provides a short introduction, and an overview of the foundations of this field, focusing primarily, but not excusively, on methods.
Predicting Composition Dependence of Glass Forming Ability in Ternary Al-Cu-Y System by Thermodynamic Calculation

The composition dependence of glass forming ability in the ternary Al-Cu-Y system is predicted by thermodynamic calculations based on the Miedema’s model and Alonso’s method. By comparing the relative energetic status of the amorphous phase versus the solid solution phase, a hexagonal composition region that energetically favoring the metallic glass formation is predicted. The glass formation driving force and crystallization resistance are further calculated and the composition of Al72Cu10Y18 is pinpointed with the largest glass forming ability in the Al-Cu-Y system. The calculation results are well supported by the experimental observations reported in the literature.
A Public-Key Cryptosystem Scheme on Conic Curves over the Ring Zn

A public key cryptosystem scheme is proposed that are based on conic curves over the ring Zn. Our scheme is motivated by KMOV scheme on elliptic curves, but our scheme remove some restrictive condition from KMOV scheme and constructed on conic curves. Its security bases on the difficulty of factoring a composite number n, just like RSA. It can resist some of the known attacks on RSA. We also constructed digital signature and a proxy signature on our scheme. Since encoding and decoding over conic are easily implement, it has enabled our scheme to greatly enhance efficiency. Also, our schemes can be used in the mobile payment system with the limited bandwidth. Key-Words: residue class ring Zn, conic curve, public-key cryptosystem, digital signature, proxy signature
M 2 C ? Deliverable D 2 . 1 A classification of IP traffic models

This deliverable presents a survey of generic models for IP traffic. A fundamental distinction is made between user-oriented models (in which individual users are explicitly models) and black-box models (in which the focus is on modeling the superposition of many users). Notably, it is shown that both are able to capture long-range dependence. A number of provisioning objectives are presented, and resulting guidelines are given. Then it is stressed that accurate provisioning greatly benefits from a reliable estimate of the variance curve. First ideas on estimating this variance curve are presented.
Scheduling Algorithm for Data Flow Model in Real-time Control System

In many real-time control systems, data flow is the base structure of software model. The QoC (Quality of Control) of some systems not only relate to whether the temporal constraints of real-time tasks can be met, but also relate to whether the data flow is non-suspending. While the data flow is suspending, both the control precision and running speed would degrade. For preventing the data flow suspending, we introduce a real-time scheduling algorithm that considers the risk of data flow suspending. We also present an implementation framework for real-time scheduling algorithm based on RTAI. It can simplify the implementation and verification of real-time scheduling algorithm. The results of verification manifest the DFO-RSA algorithm can prevent the data flow suspending effectively while guarantee the temporal constraints of critical tasks. Keyword: Real time control system, real-time scheduling algorithm, data-flow, real-time operating system
Models of type theory with strict equality

This thesis introduces the idea of two-level type theory, an extension of Martin-Lof type theory that adds a notion of strict equality as an internal primitive. A type theory with a strict equality alongside the more conventional form of equality, the latter being of fundamental importance for the recent innovation of homotopy type theory (HoTT), was first proposed by Voevodsky, and is usually referred to as HTS. Here, we generalise and expand this idea, by developing a semantic framework that gives a systematic account of type formers for two-level systems, and proving a conservativity result relating back to a conventional type theory like HoTT. Finally, we show how a two-level theory can be used to provide partial solutions to open problems in HoTT. In particular, we use it to construct semi-simplicial types, and lay out the foundations of an internal theory of (∞, 1)-categories.
Sphingolipids contribute to acetic acid resistance in Zygosaccharomyces bailii

Lignocellulosic raw material plays a crucial role in the development of sustainable processes for the production of fuels and chemicals. Weak acids such as acetic acid and formic acid are troublesome inhibitors restricting efficient microbial conversion of the biomass to desired products. To improve our understanding of weak acid inhibition and to identify engineering strategies to reduce acetic acid toxicity, the highly acetic‐acid‐tolerant yeast Zygosaccharomyces bailii was studied. The impact of acetic acid membrane permeability on acetic acid tolerance in Z. bailii was investigated with particular focus on how the previously demonstrated high sphingolipid content in the plasma membrane influences acetic acid tolerance and membrane permeability. Through molecular dynamics simulations, we concluded that membranes with a high content of sphingolipids are thicker and more dense, increasing the free energy barrier for the permeation of acetic acid through the membrane. Z. bailii cultured with the drug myriocin, known to decrease cellular sphingolipid levels, exhibited significant growth inhibition in the presence of acetic acid, while growth in medium without acetic acid was unaffected by the myriocin addition. Furthermore, following an acetic acid pulse, the intracellular pH decreased more in myriocin‐treated cells than in control cells. This indicates a higher inflow rate of acetic acid and confirms that the reduction in growth of cells cultured with myriocin in the medium with acetic acid was due to an increase in membrane permeability, thereby demonstrating the importance of a high fraction of sphingolipids in the membrane of Z. bailii to facilitate acetic acid resistance; a property potentially transferable to desired production organisms suffering from weak acid stress. Biotechnol. Bioeng. 2016;113: 744–753. © 2015 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
Self-tuning of dEWMA controller parameters for mixed product processes with equipment aging

This paper presents an iterative approach which provides a sub-optimal solution of the best achievement performance in the case of closed-loop aged-based processes applied on semiconductor manufacturing industry. The aim is to provide an online parameter estimation of dEWMA Controller in the case of mixed product Run-to-Run (RtR) control. The online estimation is done without any a priori knowledge of process parameters and noise structure. The best achievement performance improvements is illustrated using a simulation problem from literature. The example is applied on the removal rate control in a Chemical Mechanical Polishing (CMP) process.
Public school choice vs. private school vouchers

In the wake of the U.S. Supreme Court's decision upholding the constitutionality of public funding for private religious schools, the debate over private school vouchers has intensified. At the same time, the federal No Child Left Behind Act has put new emphasis on choice within the public school system. The debate no longer centers around whether we should have more choice in education, but whether choice should occur within public schools or extend to private schools. What are the advantages and disadvantages of each approach? This volume is a compilation of articles, papers, and discussions on public school choice and private school vouchers. Contributors include Christopher Edley of Harvard Law School; former New York Times education editor Edward B. Fiske; Richard Just of the American Prospect; Helen F. Ladd of Duke University; Gordon MacInnes of the New Jersey Department of Education; Eliot Mincberg of People for the American Way; Sean Reardon of Pennsylvania State University; Brent Staples of the New York Times; Adam Urbanski of the American Federation of Teachers; Amy Stuart Wells of Columbia; John Yun of Harvard; and, from The Century Foundation, Thad Hall, Richard D. Kahlenberg, Richard C. Leone, Ruy Teixeira, and Bernard Wasow.
First-Class Relationships for Object-Orientated Programming Languages

The object-oriented paradigm describes a powerful systemwhere complex systems can be modelled by a network of communicating objects. The object model is powerful because it appeals to our understanding of the world, yet it has serious shortcomings where the model doesn’t match our expectations. In particular, relationships are completely ignored by most object-oriented programming languages. Programmers must rely on error prone code using references which are a poor substitute for many of the complex relationships programs must represent. There have been several attempts to add relationships to the objectoriented paradigm and object-oriented design and object-oriented design and specification languages now include relationships, however there has been little progress made in adding relationships at the implementation level. We believe this is because existing attempts have not refined the object-orientedmodel, but simply added relationships to existing systems. In this proposal we present a prototype for a novel model of relationships in the object-oriented paradigm in which relationships, rather than objects, are the dominant constructs. This shift in focus allows programmers to gain more leverage from the object-oriented abstraction by bringing the language closer to the systems which are modelled. In addition, our model produces a stronger hierarchy than existing object-oriented systems which makes program decomposition easier and reduces coupling between objects.
Line Searches in Swift X-Ray Spectra

Prior to the launch of the Swift mission several X-ray line detections were reported in gamma-ray burst afterglow spectra. To date, these pre-Swift era results have not been conclusively confirmed. The most contentious issue in this area is the choice of statistical method used to evaluate the significance of these features. In this paper we compare three different methods already extant in the literature for assessing the significance of possible line features and discuss their relative advantages and disadvantages. The methods are demonstrated by application to observations of 40 bursts from the archive of Swift XRT at early times (<a few kiloseconds posttrigger in the rest frame of the burst). Based on this thorough analysis we found no strong evidence for emission lines. For each of the three methods we have determined detection limits for emission-line strengths in bursts with spectral parameters typical of the Swift-era sample. We also discuss the effects of the current calibration status on emission-line detection.