Miracle-dz/UniFAR-FTUs huggingface dataset:
Interhemispheric Difference Images from Postoperative Diffusion Tensor Imaging of Gliomas

Introduction Determining the full extent of gliomas during radiotherapy planning can be challenging with conventional T1 and T2 magnetic resonance imaging (MRI). The purpose of this study was to develop a method to automatically calculate differences in the fractional anisotropy (FA) and mean diffusivity (MD) values in target volumes obtained with diffusion tensor imaging (DTI) by comparing with values from anatomically homologous voxels on the contralateral side of the brain. Methods Seven patients with a histologically confirmed glioma underwent postoperative radiotherapy planning with 1.5 T MRI and computed tomography. DTI was acquired using echo planar imaging for 20 noncolinear directions with b = 1000 s/mm2 and one additional image with b = 0, repeated four times for signal averaging. The distribution of FA and MD was calculated in the gross tumor volume (GTV), shells 0-5 mm, 5-10 mm, 10-15 mm, 15-20 mm, and 20-25 mm outside the GTV, and the GTV mirrored in the left-right direction (mirGTV). All images were aligned to a template image, and FA and MD interhemispheric difference images were calculated. The difference in mean FA and MD between the regions of interest was statistically tested using two-sided paired t-tests with α = 0.05. Results The mean FA in mirGTV was 0.20 ± 0.04, which was larger than the FA in the GTV (0.12 ± 0.03) and shells 0-5 mm (0.15 ± 0.03) and 5-10 mm (0.17 ± 0.03) outside the GTV. The mean MD (×10-3 mm2/s) in mirGTV was 0.93 ± 0.09, which was smaller than the MD in the GTV (1.48 ± 0.19) and the peritumoral shells. The distribution of FA and MD interhemispheric differences followed the same trends as FA and MD values. Conclusions This study successfully implemented a method for calculation of FA and MD differences by comparison of voxel values with anatomically homologous voxels on the contralateral side of the brain. Further research is warranted to determine if radiotherapy planning using these images can be used to improve target delineation.
Estimating 3D Human Pose from Single Images Using Iterative Refinement of the Prior

This paper proposes a generative method to extract 3D human pose using just a single image. Unlike many existing approaches we assume that accurate foreground background segmentation is not possible and do not use binary silhouettes. A stochastic method is used to search the pose space and the posterior distribution is maximized using Expectation Maximization (EM). It is assumed that some knowledge is known a priori about the position, scale and orientation of the person present and we specifically develop an approach to exploit this. The result is that we can learn a more constrained prior without having to sacrifice its generality to a specific action type. A single prior is learnt using all actions in the Human Eva dataset [9] and we provide quantitative results for images selected across all action categories and subjects, captured from differing viewpoints.
An image edge mask for face identity verification

In this paper, we propose an image edge mask method for face identity verification. The method uses a mask matrix arising from edge detection to extract essential facial information via a Hadamard-Schur product to form a feature template. Several edge detectors have been experimented and our empirical observations show encouraging results. Apart from using an edge mask, the proposed method is generic in the sense that it can be easily extended using different image masks for direct and fast feature extraction.
Knowledge Management and Polanyi

In this paper, I assess the impact of Polanyi’s epistemology on the business discipline of knowledge management (KM). Polanyi’s epistemology has been misunderstood and misapplied in KM literature because of the influence of Ikujiro Nonaka. This misunderstanding is rooted in the misidentification of Nonaka’s tacit knowledge with Polanyi’s tacit knowing, a conflation of a shallow bifurcation of categories of knowledge with a rich process of knowing. I explore these misunderstandings as myths about Polanyi in KM literature. Finally, I conclude by arguing that indwelling is the best way of explaining and advancing Polanyi’s epistemology and attempt to provide the essentials of Polanyi’s epistemology in one sentence, one paragraph, and one page.
Why Likelihood ?

The Likelihood Principle has been defended on Bayesian grounds, on the grounds that it coincides with and systematizes intuitive judgments about example problems, and by appeal to the fact that it generalizes what is true when hypotheses have deductive consequences about observations. Here we divide the Principle into two parts -one qualitative, the other quantitative -and evaluate each in the light of the Akaike information criterion. Both turn out to be correct in a special case (when the competing hypotheses have the same number of adjustable parameters), but not otherwise.
Experience Without Qualities: Boredom and Modernity

Although boredom appears to be a perennial feature of the human condition, it is linked to ways of experiencing time and thinking about human existence that are recognizably modern. By tracing the emergence and evolution of the modern discourse on boredom in French and German literary, philosophical, and sociological texts, Experience Without Qualities makes a contribution to the intellectual and cultural history of European modernity. In interpreting that discourse as the reflection of a specifically modern crisis of meaning, it contributes to the theorization of modernity and modern experience. And in bringing these historical and theoretical dimensions into conversation, it develops analytic strategies that are of broader application in interdisciplinary inquiry-for the methodological problems that arise in thinking about boredom as a phenomenon of both philosophical and more broadly cultural significance illuminate the constraints that confront any attempt to reflect historically on subjective experience in modernity.
Collaborative Web Service QoS Prediction with Location-Based Regularization

Predicting the Quality of Service (QoS) values is important since they are widely applied to Service-Oriented Computing (SOC) research domain. Previous research works on this problem do not consider the influence of user location information carefully, which we argue would contribute to improving prediction accuracy due to the nature of Web services invocation process. In this paper, we propose a novel collaborative QoS prediction framework with location-based regularization (LBR). We first elaborate the popular Matrix Factorization (MF) model for missing values prediction. Then, by taking advantage of the local connectivity between Web services users, we incorporate geographical information to identify the neighborhood. Different neighborhood situations are considered to systematically design two location-based regularization terms, i.e. LBR1 and LBR2. Finally we combine these regularization terms in classic MF framework to build two unified models. The experimental analysis on a large-scale real-world QoS dataset shows that our methods improve 23.7% in prediction accuracy compared with other state-of-the-art algorithms in general cases.
A Journey in Entity Related Retrieval for TREC 2009

The focus of this paper is to present the results obtained as a result of performing entity information retrieval, namely the home pages of products, organizations and persons. The preliminary results, based on the Indri Search Engine, of this study and experimentation were presented at the Entity Track in TREC 2009. Indri Search Engine is an efficient and effective open source tool, which is operated by indri query language in any windows or UNIX based platform. Indri is based on the inference network framework and supports structured queries.
gMark: Schema-Driven Generation of Graphs and Queries

Massive graph data sets are pervasive in contemporary application domains. Hence, graph database systems are becoming increasingly important. In the experimental study of these systems, it is vital that the research community has shared solutions for the generation of database instances and query workloads having predictable and controllable properties. In this paper, we present the design and engineering principles of <inline-formula> <tex-math notation="LaTeX">$\mathsf {gMark}$</tex-math><alternatives> <inline-graphic xlink:href="ciucanu-ieq1-2633993.gif"/></alternatives></inline-formula>, a domain- and query language-independent graph instance and query workload generator. A core contribution of <inline-formula> <tex-math notation="LaTeX">$\mathsf {gMark}$</tex-math><alternatives> <inline-graphic xlink:href="ciucanu-ieq2-2633993.gif"/></alternatives></inline-formula> is its ability to target and control the diversity of properties of both the generated instances and the generated workloads coupled to these instances. Further novelties include support for regular path queries, a fundamental graph query paradigm, and schema-driven selectivity estimation of queries, a key feature in controlling workload chokepoints. We illustrate the flexibility and practical usability of <inline-formula><tex-math notation="LaTeX">$\mathsf {gMark}$ </tex-math><alternatives><inline-graphic xlink:href="ciucanu-ieq3-2633993.gif"/></alternatives></inline-formula> by showcasing the framework's capabilities in generating high quality graphs and workloads, and its ability to encode user-defined schemas across a variety of application domains.
A Monadic Formalization of ML5

ML5 is a programming language for spatially distributed computing, based on a Curry-Howard correspondence with the modal logic S5. Despite being designed by a correspondence with S5 modal logic, the ML5 programming language differs from the logic in several ways. In this paper, we explain these discrepancies between ML5 and S5 by translating ML5 into a slightly different logic: intuitionistic S5 extended with a lax modality that encapsulates effectful computations in a monad. This translation both explains the existing ML5 design and suggests some simplifications and generalizations. We have formalized our translation within the Agda proof assistant. Rather than formalizing lax S5 as a proof theory, we \emph{embed} it as a universe within the the dependently typed host language, with the universe elimination given by implementing the modal logic's Kripke semantics. This representation technique saves us the work of defining a proof theory for the logic and proving it correct, and additionally allows us to inherit the equational theory of the meta-language, which can be exploited in proving that the semantics validates the operational semantics of ML5.
Interaction of the Neisseria gonorrhoeae PilA protein with the pilE promoter involves multiple sites on the DNA

PilA is the putative DNA-binding component of a two-component system that regulates transcription of the pilin expression locus (pilE) of Neisseria gonorrhoeae. Here we report the purification of the PilA protein and characterization of its DNA-binding activity. PilA was overproduced in Escherichia coli with an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible expression vector. Cell extracts were prepared by sonication and fractionated by anion-exchange chromotography, followed by dye affinity chromatography with Cibacron Blue. Proteins were eluted by using a gradient of KCl, and PilA-containing fractions were identified by immunoblot analysis with a polyclonal anti-PilA antiserum. Purified PilA was judged to be > 90% pure, as determined by Coomassie blue staining and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. PilA purified in this manner was used to develop a gel retardation assay with a 301-bp fragment containing the pilE promoter (PpilE) and upstream sequences as a probe. A fragment of similar size containing the E. coli aroH promoter was used as a negative control. Competition experiments using a 100- to 1,000-fold excess of unlabelled DNA fragments confirmed the specificity of PilA binding to the pilE promoter. To localize the PilA binding site within the 301-bp PpilE fragment, stepwise deletions were generated by PCR and the fragments were examined in the gel shift assay. The results of these experiments show that there are two regions upstream of PpilE that are required for binding by PilA. Taken together, these data indicate that while PilA binds specifically to the upstream region of the pilE gene, this interaction is complex and likely involves multiple regions of this DNA sequence.
Essential Role of Gamma Interferon in Survival of Colon Ascendens Stent Peritonitis, a Novel Murine Model of Abdominal Sepsis

ABSTRACT Despite considerable progress, peritonitis and sepsis remain life-threatening conditions. To improve the understanding of the pathophysiology encountered in sepsis, a new standardized and highly reproducible murine model of abdominal sepsis termed colon ascendens stent peritonitis (CASP) was developed. In CASP, a stent is inserted into the ascending colon, which generates a septic focus. CASP employing a stent of 14-gauge diameter (14G stent) results in a mortality of 100% within 18 to 48 h after surgery. By inserting stents of small diameters, mortality can be exactly controlled. Thus, CASP surgery with insertion of a 22G or 18G stent (22G or 18G CASP surgery) results in 38 or 68% mortality, respectively. 14G CASP surgery leads to a rapid invasion of bacteria into the peritoneum and the blood. As a consequence, endotoxemia occurs, inflammatory cells are recruited, and a systemic inflammatory response syndrome develops. Interestingly, the most pronounced upregulation of inflammatory cytokines (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α] and interleukin-12) is observed in spleen and lungs. CASP surgery followed by stent removal at specific time intervals revealed that all animals survived if intervention was performed after 3 h, whereas removal of the septic focus after 9 h did not prevent death, suggesting induction of autonomous mechanisms of a lethal inflammatory response syndrome. 18G CASP surgery in IFN-γ receptor-deficient (IFNγR−/−) mice revealed an essential role of IFN-γ in survival of sepsis, whereas TNF receptor p55-deficient (TNFRp55−/−) mice did not show altered survival rates. In summary, this study describes a novel animal model that closely mimics human sepsis and appears to be highly suitable for the study of the pathophysiology of abdominal sepsis. Importantly, this model demonstrates a protective role of IFN-γ in survival of bacterial sepsis.
Multi-Objective Control-Relevant Demand Modeling for Supply Chain Management

The development of control-oriented decision policies for inventory management in supply chains has received considerable interest in recent years, and demand modeling to supply forecasts for these policies is an important component of an effective solution to this problem. Drawing from the problem of control-relevant identification, we present an approach for demand modeling based on data that relies on a control-relevant prefilter to tailor the emphasis of the fit to the intended purpose of the model, which is to provide forecast signals to a tactical inventory management policy based on Model Predictive Control. Integrating the demand modeling and inventory control problems offers the opportunity to obtain reduced-order models that exhibit superior performance, with potentially lower user effort relative to traditional “open-loop” methods. A systematic approach to generating these prefilters is presented and the benefits resulting from their use are demonstrated on a representative production/inventory system case study. A multi-objective formulation is developed that allows the user to emphasize minimizing inventory variance, minimizing starts variance, or their combination.
Realtime Fire Simulation

Flame simulation is nothing new to computer graphics. As early as 1996, researchers Nick Foster and Dimitri Metaxas were presenting the algorithms and techniques needed for fluid simulation [3]. Three years later, researcher Joe Stam was proposing modified techniques for use in computer graphics that would later become the basis for many iterations of calculating the behavior of fire [6] [5]. Many later attempts would get realistic results, but at the cost of being far from real time, needing minutes to calculate the state of the fluid after many physics iterations and performing the costly render. Other attempts, like Marc de Kruijf’s Firestarter program whose is in real time, but may not behave in believable ways [2]. Many early game applications would use to run either pre-baked calculations or a series of flat, animated textures rotated for their normals to face the player to provide the illusion of flame. Nvidia was one of the only groups to have a flame simulation that was both real time and fairly believable. Their algorithm ended up very similar to our own [1], and was announced less than one year before the
Validation of the Parlay API through prototyping

The desire within the telecommunications world for new and faster business growth has been a major drive towards the development of open network API. Over the past 7 years several (semi) standardization groups have announced work on network API, including TINA-C, JAIN, IEEE P1520, INforum, 3GPP, JAIN, Parlay. The Parlay group seems most successful in attracting industry awareness with their API, called the Parlay API. The rational behind the Parlay API is that it attracts innovation from third parties that are outside the network operator's domain to build and deploy new network-hosted applications. This also means that the public telecommunication network is opened for niche and short-lived applications as well as for applications that possibly integrate telephones with other terminals such as PC. The Parlay group has successfully passed the first two phases of success, namely publishing their API on the right moment in time and attracting a critical mass within the telecommunication industry with their results. Prototyping the API on a real network execution platform is the only way to show its technical feasibility. Such an exercise was executed internally within Lucent Technologies and raised a number of questions as well as recommendations on both the technical and the semantical behavior for systems that will be interconnected via the Parlay API. We share these results, showing the drawbacks and advantages as well as challenges for this API.
New Algorithms and Architectures for Post-Silicon Validation

To identify design errors that escape pre-silicon verification, post-silicon validation is becoming an important step in the implementation flow of digital integrated circuits. While many debug problems are tackled on testers, there are hard-to-find design errors that are activated only in-system. A key challenge during in-system debugging is to acquire data from internal circuit’s nodes in real-time. In this thesis, we propose several techniques to address this problem, ranging from resource-efficient and programmable trigger units to automated selection of trace signals to a distributed architecture for embedded logic analysis. Deciding when to acquire data on-chip is done using trigger units. Because there is an inherent tradeoff between the size of the trigger units and the types of events that can be programmed into them, we first explore a resource-efficient and programmable trigger unit implementation. We show how the on-chip buffers used for data acquisition can be leveraged to store information regarding the logic functions that are programmed at runtime as the trigger events. This reduces the requirement in terms of logic resources for the trigger unit, while enlarging the set of programmable trigger events supported by these resources. We also propose a new algorithm to automatically map trigger events onto the proposed trigger unit. Next we shift the focus from the trigger units to the sample units available onchip. Once the real-time debug experiment has been completed, the amount of data available to the user is limited by the capacity of the on-chip trace buffers. For logic bugs, where the circuit implementation matches the physical prototype, we show how the structural information from the circuit netlist can be leveraged to expand the amount of data made available off-line to the user. To ensure that data expansion
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information

The Localizome server predicts the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein and presents the result as an intuitive graphic representation. It utilizes hmmpfam to detect the presence of Pfam domains and a prediction algorithm, Phobius, to predict the TM helices. The results are combined and checked against the TM topology rules stored in a protein domain database called LocaloDom. LocaloDom is a curated database that contains TM topologies and TM helix numbers of known protein domains. It was constructed from Pfam domains combined with Swiss-Prot annotations and Phobius predictions. The Localizome server corrects the combined results of the user sequence to conform to the rules stored in LocaloDom. Compared with other programs, this server showed the highest accuracy for TM topology prediction: for soluble proteins, the accuracy and coverage were 99 and 75%, respectively, while for TM protein domain regions, they were 96 and 68%, respectively. With a graphical representation of TM topology and TM helix positions with the domain units, the Localizome server is a highly accurate and comprehensive information source for subcellular localization for soluble proteins as well as membrane proteins. The Localizome server can be found at .
Risk-constrained Markov decision processes

We propose a new constrained Markov decision process framework with risk-type constraints. The risk metric we use is Conditional Value-at-Risk (CVaR), which is gaining popularity in finance. It is a conditional expectation but the conditioning is defined in terms of the level of the tail probability. We propose an iterative offline algorithm to find the risk-contrained optimal control policy. A stochastic approximation-inspired ‘learning’ variant is also sketched.
Simple Culture System for Bobwhite Quail and Japanese Quail Embryos from the Blastoderm Stage to Hatching using a Single Surrogate Eggshell

The ex vivo culture of avian embryos is a technique for the long-term culturing of embryos outside of their own shell and shell membrane. It allows easy access to the developing embryos and embryo manipulation. The two-step system is widely applied when the culture is performed after oviposition. Japanese quail as well as bobwhite quail are used as models for avian safety assessment as recommended by the Organisation for Economic Co-operation and Development (OECD) guidelines. However, biological studies on the bobwhite quail have been more limited than those on the Japanese quail. We have developed a more simplified ex vivo culture protocol for the two species of quail embryos from the blastoderm stage through to hatching using a single surrogate eggshell. Hatchabilities of 31% and 27% were obtained in bobwhite quail and Japanese quail embryos, respectively. The simple system described in the present study is an easy and acceptable procedure.
Dimensionality Decrease Heuristics for NP Complete Problems

The vast majority of scientific community believes that P! =NP, with countless supporting arguments. The number of people who believe otherwise probably amounts to as few as those opposing the 2nd Law of Thermodynamics. But isn't nature elegant enough, not to resource to brute-force search? In this article, a novel concept of dimensionality is presented, which may lead to a more efficient class of heuristic implementations to solve NP complete problems. Thus, broadening the universe of man-machine tractable problems. Dimensionality, as defined here, will be a closer analog of strain energy in nature.