Miracle-dz/UniFAR-FTUs huggingface dataset:
A Geometric Approach to Quadratic Optimization in Computerized Tomography

The problem of image reconstruction from projections in computerized tomography, when cast as a system of linear equations, leads to an inconsistent system. The problem is studied under very adverse conditions, consisting of low-contrast images and a strongly underdetermined system, where the number of equations is only about 25% of the number of variables (fewer equations enable the use of less radiation). Various algorithms are examined with respect to their performance in such cases: ART (Algebraic Reconstruction Technique), quadratic optimization (QUAD – a method that minimizes the L 2 -norm of the residual) and the relatively new component-averaging (CAV) and BICAV algorithms. A variant of QUAD, called NQUAD, is obtained by normalizing the equations before applying QUAD. This has a geometric signiﬁcance since the resulting system is independent of any particular algebraic representation of the equations – a property shared by ART, CAV and BI-CAV. Experiments with phantom reconstructions show that NQUAD is always preferable to QUAD. Under the stated adverse conditions, NQUAD is much better than the other studied algorithms, in terms of image quality, runtime efﬁ-ciency, and the achieved error measures.
Interactive searching and visualization of patterns in attributed graphs

Searching for patterns in graphs and visualizing the search results is an active area of research with numerous applications. With the continual growth of database size, querying these databases often results in multiple solutions. Text-based systems present search results as a list, and going over all solutions can be tedious. In this paper, we present an interactive visualization system that helps users find patterns in graphs and visualizes the search results. The user draws a source pattern and labels it with attributes. Based on these attributes and connectivity constraints, simplified subgraphs are generated, containing all the possible solutions. The system is quite generic and capable of searching patterns and approximate solutions in a variety of data sets.
Suppression of Smooth Muscle Cell Proliferation by a c-myc RNA-cleaving Deoxyribozyme*

A small catalytic DNA molecule targeting c-myc RNA was found to be a potent inhibitor of smooth muscle cell (SMC) proliferation. The catalytic domain of this molecule was based on that previously derived by in vitro selection (Santoro, S. W., and Joyce, G. F. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 4262–4266) and is known as the “10-23” general purpose RNA-cleaving deoxyribozyme. In addition to inhibiting SMC proliferation at low concentration, this molecule (targeting the translation initiation region of c-myc RNA) was found to efficiently cleave its full-length substrate in vitro and down-regulate c-myc gene expression in smooth muscle cells. The serum nuclease stability of this molecule was enhanced without substantial loss of kinetic efficiency by inclusion of a 3′-3′-internucleotide inversion at the 3′-terminal. The extent of SMC suppression was found to be influenced by the length of the substrate binding arms. This correlated to some extent with catalytic activity in both the short substrate under multiple turnover conditions and the full-length substrate under single turnover conditions, with the 9 + 9 base arm molecule producing the greatest activity.
Do difference scores make a difference on the third-person effect?

ABSTRACTResearchers from different fields have been intrigued but also confused with regard to the ways of conceptualizing and operationalizing difference. This article critically reviewed a number of existing means of operationalizing difference and mathematically explicated and empirically tested why difference scores were problematic and why the diamond model that aimed to replace difference scores was equally troublesome. Ultimately, this article recommended polynomial regression as an alternative to difference scores.
Effects of electromagnetic radiation on spatial memory and synapses in rat hippocampal CA1

In this study, we investigated the effects of mobile phone radiation on spatial learning, reference memory, and morphology in related brain regions. After the near-field radiation (0.52–1.08 W/kg) was delivered to 8-week-old Wistar rats 2 hours per day for 1 month, behavioral changes were examined using the Morris water maze. Compared with the sham-irradiated rats, the irradiated rats exhibited impaired performance. Morphological changes were investigated by examining synaptic ultrastructural changes in the hippocampus. Using the physical dissector technique, the number of pyramidal neurons, the synaptic profiles, and the length of postsynaptic densities in the CA1 region were quantified stereologically. The morphological changes included mitochondrial degenerations, fewer synapses, and shorter postsynaptic densities in the radiated rats. These findings indicate that mobile phone radiation can significantly impair spatial learning and reference memory and induce morphological changes in the hippocampal CA1 region.
Risk of Violent Crime in Individuals with Epilepsy and Traumatic Brain Injury: A 35-Year Swedish Population Study

Seena Fazel and colleagues report findings from a longitudinal follow-up study in Sweden that evaluated the risks of violent crime subsequent to hospitalization for epilepsy, or traumatic brain injury. The researchers control for familial confounding with sibling controls. The analyses call into question an association between epilepsy and violent crime, although they do suggest that there may be a relationship between traumatic brain injury and violent crime.
DOCUMENT TRANSLATION RETRIEVAL BASED ON STATISTICAL MACHINE TRANSLATION TECHNIQUES

We compare different strategies to apply statistical machine translation techniques in order to retrieve documents that are a plausible translation of a given source document. Finding the translated version of a document is a relevant task; for example, when building a corpus of parallel texts that can help to create and evaluate new machine translation systems. In contrast to the traditional settings in cross-language information retrieval tasks, in this case both the source and the target text are long and, thus, the procedure used to select which words or phrases will be included in the query has a key effect on the retrieval performance. In the statistical approach explored here, both the probability of the translation and the relevance of the terms are taken into account in order to build an effective query.
Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships

One key element in understanding the molecular machinery of the cell is to understand the structure and function of each protein encoded in the genome. A very successful means of inferring the structure or function of a previously unannotated protein is via sequence similarity with one or more proteins whose structure or function is already known. Toward this end, we propose a means of representing proteins using pairwise sequence similarity scores. This representation, combined with a discriminative classification algorithm known as the support vector machine (SVM), provides a powerful means of detecting subtle structural and evolutionary relationships among proteins. The algorithm, called SVM-pairwise, when tested on its ability to recognize previously unseen families from the SCOP database, yields significantly better performance than SVM-Fisher, profile HMMs, and PSI-BLAST.
Auxin Regulates Arabidopsis Anther Dehiscence, Pollen Maturation, and Filament Elongation[W]

We provide evidence on the localization, synthesis, transport, and effects of auxin on the processes occurring late in Arabidopsis thaliana stamen development: anther dehiscence, pollen maturation, and preanthesis filament elongation. Expression of auxin-sensitive reporter constructs suggests that auxin effects begin in anthers between the end of meiosis and the bilocular stage in the somatic tissues involved in the first step of dehiscence as well as in the microspores and in the junction region between anther and filament. In situ hybridizations of the auxin biosynthetic genes YUC2 and YUC6 suggest that auxin is synthesized in anthers. In agreement with the timing of auxin effects, the TIR1, AFB1, AFB2, and AFB3 auxin receptor-encoding genes are transcribed in anthers only during late stages of development starting at the end of meiosis. We found that in tir1 afb triple and quadruple mutants, anther dehiscence and pollen maturation occur earlier than in the wild type, causing the release of mature pollen grains before the completion of filament elongation. We also assessed the contribution of auxin transport to late stamen developmental processes. Our results suggest that auxin synthesized in anthers plays a major role in coordinating anther dehiscence and pollen maturation, while auxin transport contributes to the independent regulation of preanthesis filament elongation.
Monitoring and controlling QoS network domains

Increased performance, fairness, and security remain important goals for service providers. In this work, we design an integrated distributed monitoring, traffic conditioning, and flow control system for higher performance and security of network domains. Edge routers monitor (using tomography techniques) a network domain to detect quality of service (QoS) violations—possibly caused by underprovisioning—as well as bandwidth theft attacks. To bound the monitoring overhead, a router only verifies service level agreement (SLA) parameters such as delay, loss, and throughput when anomalies are detected. The marking component of the edge router uses TCP flow characteristics to protect ‘fragile’ flows. Edge routers may also regulate unresponsive flows, and may propagate congestion information to upstream domains. Simulation results indicate that this design increases application‐level throughput of data applications such as large FTP transfers; achieves low packet delays and response times for Telnet and WWW traffic; and detects bandwidth theft attacks and service violations. Copyright © 2004 John Wiley & Sons, Ltd.
Efficient Image Evidence Analysis of CNN Classification Results

Convolutional neural networks (CNNs) define the current state-of-the-art for image recognition. With their emerging popularity, especially for critical applications like medical image analysis or self-driving cars, confirmability is becoming an issue. The black-box nature of trained predictors make it difficult to trace failure cases or to understand the internal reasoning processes leading to results. In this paper we introduce a novel efficient method to visualise evidence that lead to decisions in CNNs. In contrast to network fixation or saliency map methods, our method is able to illustrate the evidence for or against a classifier's decision in input pixel space approximately 10 times faster than previous methods. We also show that our approach is less prone to noise and can focus on the most relevant input regions, thus making it more accurate and interpretable. Moreover, by making simplifications we link our method with other visualisation methods, providing a general explanation for gradient-based visualisation techniques. We believe that our work makes network introspection more feasible for debugging and understanding deep convolutional networks. This will increase trust between humans and deep learning models.
Nonce-based Kerberos is a Secure Delegated AKE Protocol

Kerberos is one of the most important cryptographic protocols, first because it is the basisc authentication protocol in Microsoft’s Active Directory and shipped with every major operating system, and second because it served as a model for all Single-Sign-On protocols (e.g. SAML, OpenID, MS Cardspace, OpenID Connect). Its security has been confirmed with several Dolev-Yao style proofs [1–12], and attacks on certain versions of the protocol have been described [13,14]. However despite its importance, despite its longevity, and despite the wealth of Dolev-Yao-style security proofs, no reduction based security proof has been published until now. This has two reasons: (1) All widely accepted formal models either deal with two-party protocols, or group key agreement protocols (where all entities have the same role), but not with 3-party protocols where each party has a different role. (2) Kerberos uses timestamps and nonces, and formal security models for timestamps are not well understood up to now. As a step towards a full security proof of Kerberos, we target problem (1) here: We propose a variant of the Kerberos protocol, where nonces are used instead of timestamps. This requires one additional protocol message, but enables a proof in the standard Bellare-Rogaway (BR) model. The key setup and the roles of the different parties are identical to the original Kerberos protocol. For our proof, we only require that the authenticated encryption and the message authentication code (MAC) schemes are secure. Under these assumptions we show that the probability that a client or server process oracle accepts maliciously, and the advantage of an adversary trying to distinguish a real Kerberos session key from a random value, are both negligible. One main idea in the proof is to model the Kerberos server a a public oracle, so that we do not have to consider the security of the connection client–Kerberos. This idea is only applicable to the communication pattern adapted by Kerberos, and not to other 3-party patterns (e.g. EAP protocols).
Multi-scale based Simulation of Shear Critical Reinforced Concrete Beams Subjected to Drying

The impact of drying at both material and structural levels is discussed based on the multi-scale thermo-mechanistic modeling. The effects of hygral states at nano to micro scales on the macro scale mechanics are focused on. It is quanti- tatively confirmed that the moisture state-dependent tensile strength and crack-dependent moisture diffusivity models play a key role in tackling with the responses of reinforced concrete (RC) members subjected to combined hygro- mechanical actions. Full 3D thermo-mechanics simulation of shear critical RC beams with effective depths, which ranges from 250mm to 1000mm, is carried out from the onset of casting. It is found that the impact of drying increases with the increasing effective depth at the constant beam width. Overall, it is emphasized that linkage of material science and structural mechanics is indispensable for holistic understanding of RC members under coupled mechanical loading and drying. The multi-scale analytical scheme is proved to be applicable for the performance assessment of RC mem- bers at ultimate states as well.
Formulation and evaluation of Folic acid conjugated gliadin nanoparticles of curcumin for targeting colon cancer cells

Preparation of folic acid (FA) conjugated (FA-CUR-GNPs) and non-conjugated (CUR-GNPs) gliadin nanoparticles of curcumin were successfully formulated by desolvation method for oral delivery of drug for targeting colon cancer cell. F1, F3, F5 (conjugated) and F2, F4, F6 (Non-conjugated) were formulated using various drug-polymer ratio (1:2). They were further characterized by FTIR, Mass spectroscopy, NMR, solubility studies, entrapment efficiency, TEM, particle size, surface charge, In-vitro release studies, In vivo toxicity studies and simultaneously evaluated. F3 (curcumin 10mg, gliadin 20mg and FA 5mg) and F4 (curcumin 10mg and gliadin 20mg) were found as the optimized formulation among both the categories. For F3 and F4 formulations; average particle size (168.1 and 195.7nm), zeta potential (-16.5 and -24.4mV), cumulative % drug release (92.92 and 94%) and In vivo toxicity studies were conducted and compared with the control (phosphate-buffer saline, pH 6.8) reveals no toxicity. From the characterization and evaluation studies it was identified that F4 (FA-CUR-GNPs) had better solubility, In vitro release profile and no specified In-vivo toxicity than F3 (CUR-GNPs) formulation with nano-range particle size throughout the experiment. Improved bioavailability and increase targeting capacity toward colon cancer tumor cells were successfully achieved.
Subdiffraction-limited axial imaging of live cells using linear nanoaperture arrays based on extraordinary transmission

We have considered linear nanoaperture arrays for super-resolved live cell imaging. The nanoaperture arrays consist of nanoholes of varying diameter. Each nanohole localizes near-field distribution and produces extraordinary optical transmission (EOT) by surface plasmon localization. Much deeper light penetration was achieved in EOT than under total internal reflection. The results can be used to implement subdiffraction-limited axial resolution when applied to microscopy.
Temporal Stability of the Dutch Version of the Wechsler Memory Scale—Fourth Edition (WMS-IV-NL)

Objective: The Wechsler Memory Scale—Fourth Edition (WMS-IV) is one of the most widely used memory batteries. We examined the test–retest reliability, practice effects, and standardized regression-based (SRB) change norms for the Dutch version of the WMS-IV (WMS-IV-NL) after both short and long retest intervals. Method: The WMS-IV-NL was administered twice after either a short (M = 8.48 weeks, SD = 3.40 weeks, range = 3–16) or a long (M = 17.87 months, SD = 3.48, range = 12–24) retest interval in a sample of 234 healthy participants (M = 59.55 years, range = 16–90; 118 completed the Adult Battery; and 116 completed the Older Adult Battery). Results: The test–retest reliability estimates varied across indexes. They were adequate to good after a short retest interval (ranging from .74 to .86), with the exception of the Visual Working Memory Index (r = .59), yet generally lower after a long retest interval (ranging from .56 to .77). Practice effects were only observed after a short retest interval (overall group mean gains up to 11 points), whereas no significant change in performance was found after a long retest interval. Furthermore, practice effect-adjusted SRB change norms were calculated for all WMS-IV-NL index scores. Conclusions: Overall, this study shows that the test–retest reliability of the WMS-IV-NL varied across indexes. Practice effects were observed after a short retest interval, but no evidence was found for practice effects after a long retest interval from one to two years. Finally, the SRB change norms were provided for the WMS-IV-NL.
Dynamic causal modeling for EEG and MEG

We present a review of dynamic causal modeling (DCM) for magneto‐ and electroencephalography (M/EEG) data. DCM is based on a spatiotemporal model, where the temporal component is formulated in terms of neurobiologically plausible dynamics. Following an intuitive description of the model, we discuss six recent studies, which use DCM to analyze M/EEG and local field potentials. These studies illustrate how DCM can be used to analyze evoked responses (average response in time), induced responses (average response in time‐frequency), and steady‐state responses (average response in frequency). Bayesian model comparison plays a critical role in these analyses, by allowing one to compare equally plausible models in terms of their model evidence. This approach might be very useful in M/EEG research; where correlations among spatial and neuronal model parameter estimates can cause uncertainty about which model best explains the data. Bayesian model comparison resolves these uncertainties in a principled and formal way. We suggest that DCM and Bayesian model comparison provides a useful way to test hypotheses about distributed processing in the brain, using electromagnetic data. Hum Brain Mapp, 2009. © 2009 Wiley‐Liss, Inc.
The Plastidic Bile Acid Transporter 5 Is Required for the Biosynthesis of Methionine-Derived Glucosinolates in Arabidopsis thaliana[W]

Aliphatic glucosinolate biosynthesis is highly compartmentalized, requiring import of 2-keto acids or amino acids into chloroplasts for side chain elongation and export of the resulting compounds into the cytosol for conversion into glucosinolate. Aliphatic glucosinolate biosynthesis in Arabidopsis thaliana is regulated by three R2R3-MYB transcription factors, the major player being High Aliphatic Glucosinolate 1 (HAG1/MYB28). Here, we show that BAT5, which belongs to the putative bile acid transporter family, is the only member of this family that is transactivated by HAG1/MYB28, HAG2/MYB76, and HAG3/MYB29. Furthermore, two isopropylmalate isomerases genes, IPMI1 and IPMI2, and the isopropylmalate dehydrogenase gene, IPMDH1, were identified as targets of HAG1/MYB28 and the corresponding proteins localized to plastids, suggesting a role in plastidic chain elongation reactions. The BAT proteins also localized to plastids; however, only mutants defective in BAT5 function contained strongly reduced levels of aliphatic glucosinolates. The bat5 mutant chemotype was rescued by induced overexpression of BAT5. Feeding experiments using 2-keto acids and amino acids of different chain length suggest that BAT5 is a plastidic transporter of (chain-elongated) 2-keto acids. Mechanical stimuli and methyl jasmonate transiently induced BAT5 expression in inflorescences and leaves. Thus, BAT5 was identified as the first transporter component of the aliphatic glucosinolate biosynthetic pathway.
Use of Expert Knowledge for Decision Tree Pruning

Decision tree technology has been proven to be a valuable way of capturing human decision making within a computer. One main problem for many traditional decision tree pruning methods is that it is always assumed that all misclassifications are equally probable and equally serious. However, in a real-world classification problem, there may be a cost associated with misclassifying examples from each class. Cost-sensitive classification allows one to assign different costs to different types of misclassifications. But few studies deal with how to decide misclassification cost. In this paper, we introduce a cost-sensitive decision tree pruning algorithm CC4.5 which is based on the C4.5 algorithm (Quinlan 1993) and uses expert knowledge to define misclassification costs. This paper is outlined as follows: Section 2 illustrates three different cost-sensitive pruning methods implemented in CC4.5. In section 3, we describe how we use expert knowledge to define the misclassification costs. The evaluation of CC4.5 is done via a comparative analysis between these three pruning methods in CC4.5 and C4.5 as described in section 4.