Miracle-dz/UniFAR-FTUs huggingface dataset:
SERS Study of Tetrodotoxin (TTX) by Using Silver Nanoparticle Arrays

The optical properties of tetrodotoxin (TTX), a scarce toxin with anesthetic properties, were studied using nanoparticle arrays-assisted surface-enhanced Raman scattering (SERS). The nanoparticles arrays were fabricated using nanosphere lithography and a metallic lift-off process to control the particle size, shape, and spacing in the arrays. Using density functional methods, the Raman spectrum of TTX was also calculated with Gaussian03 software. The main peaks of the spectrum are originated from the vibration of the NH2 molecule group. In the SERS experiment, we were able to measure the Raman spectrum with a TTX concentration as less as 0.9 ng/mL. This sensitivity is comparable to that from high performance liquid chromatography.
Troubleshooting Under Uncertainty

We develop a series of approximations for decision-theoretic troubleshooting under uncertainty. Our approach generates troubleshooting plans in the face of uncertainty in the relationships among components and device status, observations, as well as the affect of actions on device status. Included in our approach is a Bayesian-network representation of these relationships. We have applied our technique successfully to troubleshooting problems with printing, photocopier feeders, automobiles, and gas turbines. We report empirical findings demonstrating the high quality of plans produced by our approach.
Centroidal Voronoi Tessellation-Based Reduced-Order Modeling of Complex Systems

\noindent A reduced-order modeling methodology based on centroidal Voronoi tessellations (CVTs) is introduced. CVTs are special Voronoi tessellations for which the generators of the Voronoi diagram are also the centers of mass (means) of the corresponding Voronoi cells. For discrete data sets, CVTs are closely related to the h-means and k-means clustering techniques. A discussion of reduced-order modeling for complex systems such as fluid flows is given to provide a context for the application of reduced-order bases. Then, detailed descriptions of CVT-based reduced-order bases and how they can be constructed from snapshot sets and how they can be applied to the low-cost simulation of complex systems are given. Subsequently, some concrete incompressible flow examples are used to illustrate the construction and use of CVT-based reduced-order bases. The CVT-based reduced-order modeling methodology is shown to be effective for these examples.
Mutations in both KRAS and BRAF may contribute to the methylator phenotype in colon cancer.

BACKGROUND & AIMS Colorectal cancers (CRCs) with the CpG island methylator phenotype (CIMP) often associate with epigenetic silencing of hMLH1 and an activating mutation in the BRAF gene. However, the current CIMP criteria are ambiguous and often result in an underestimation of CIMP frequencies in CRCs. Because BRAF and KRAS belong to same signaling pathway, we hypothesized that not only mutations in BRAF but mutant KRAS may also associate with CIMP in CRC. METHODS We determined the methylation status in a panel of 14 markers (7 canonical CIMP-related loci and 7 new loci), microsatellite instability status, and BRAF/KRAS mutations in a collection of 487 colorectal tissues that included both sporadic and Lynch syndrome patients. RESULTS Methylation analysis of 7 CIMP-related markers revealed that the mean number of methylated loci was highest in BRAF-mutated CRCs (3.6) vs KRAS-mutated (1.2, P < .0001) or BRAF/KRAS wild-type tumors (0.7, P < .0001). However, analyses with 7 additional markers showed that the mean number of methylated loci in BRAF mutant tumors (4.4) was the same as in KRAS mutant CRCs (4.3, P = .8610). Although sporadic microsatellite instability high tumors had the highest average number of methylated markers (8.4), surprisingly, Lynch syndrome CRCs also demonstrated frequent methylation (5.1). CONCLUSIONS CIMP in CRC may result from activating mutations in either BRAF or KRAS, and the inclusion of additional methylation markers that correlate with mutant KRAS may help clarify CIMP in future studies. Additionally, aberrant DNA methylation is a common event not only in sporadic CRC but also in Lynch syndrome CRCs.
A Hierarchical Bayesian Framework for Score-Informed Source Separation of Piano Music Signals

Here we propose a score-informed monaural source separation system to extract every tone from a mixture of piano tone signals. Two sinusoidal models in our earlier work are employed in the above-mentioned system to represent piano tones: the General Model and the Piano Model. The General Model, a variant of sinusoidal modeling, can represent a single tone with high modeling quality, yet it fails to separate mixtures of tones due to the overlapping partials. The Piano Model, on the other hand, is an instrument-specific model tailored for piano. Its modeling quality is lower but it can learn from training data (consisting entirely of isolated tones), resolve the overlapping partials and thus separate the mixtures. We formulate a new hierarchical Bayesian framework to run both Models in the source separation process so that the mixtures with overlapping partials can be separated with high quality. The results show that our proposed system gives robust and accurate separation of piano tone signal mixtures (including octaves) while achieving significantly better quality than those reported in related work done previously.
Updating LSP dictionaries with collocational information

Despite the big amount of general language dictionaries in electronic form, those coming from specialised areas are still “under construction”. There are two main reasons for this: firstly, the need for these dictionaries was/is less essential than the need for general language dictionaries, since these were/are aiming mainly to specialists, and secondly many specialised areas are changing over time, resulting to dictionaries that need continuing updating. Due to this, techniques that improve the automatic or semiautomatic construction and updating of specialised dictionaries are and will always be welcome. In this work we are concerned with the updating of dictionaries for Languages for Special Purposes (LSPs) with information coming from collocations. The collocations to be used are extracted from LSP corpora of not necessarily big size.
Virtual Screening of Natural and Synthetic Ligands Against Diabetic Retinopathy by Molecular Interaction With Angiopoietin-2

PurposeDiabetic retinopathy (DR) is the most common diabetic eye disease and a leading cause of blindness. The role of angiopoietin-2 a tyrosine kinase receptor is well-reported in angiogenesis during the onset of the disease. The purpose of this study is to screen out more potential herbal molecules which can evidently be used as a better, natural and safe herbal drug against this disease. DesignIn silico virtual screening and molecular interaction studies were performed. MethodsThe current course of work focused on molecular interactions on angiopoietin-2 protein with selected natural ligands, namely allicin, ajoene, D-pinitol and salacinol, along with synthetic ones like nateglinide, biguanide, tolbutamide and tolazamide. There was an attempt to carry out the virtual comparative study between natural and synthetic ligands. Proceeding toward this approach, docking of all molecules was performed using the Autodock 4.2 program. ResultsInference of this interaction study is that D-pinitol, which is the herbal extract of Glycine max, shows a very reliable docking pattern as compared with the synthetic ligand tolazamide. Although the binding energy of a synthetic ligand is lower compared to that of the natural ones, the binding energy of synthetic and natural ligands are at an approximate level. The lower the binding energy, the better the ligand molecular interaction. ConclusionsOur findings suggest that D-pinitol, the natural, safe ligand, can be used in the treatment of diabetic retinopathy with few or no side effects after estimating and calculating proper doses using in vitro approaches.
A new species of Micronycteris (Chiroptera: Phyllostomidae) from Bolivia

Abstract Although significant work has been done to define species relationships within the Neotropical genus Micronycteris, the group has yet to be fully resolved. In Bolivia Micronycteris is represented by 4 species: M. hirsuta, M. megalotis, M. minuta, and M. sanborni. Through examination of morphological characters and analyses of cranial measurements and genetic data, we determine that M. sanborni is not found in Bolivia and describe a new species closely related to it. The new species is morphometrically distinct from its congeners, forming a cluster separate from M. schmidtorum, M. minuta, and M. brosseti along principal component (PC) 1 (explaining 57.3% of the variation and correlated with maxillary toothrow length) and also separate from M. sanborni along PC 2 (explaining 35.4% of the variation and correlated with condylobasal length). The new species forms a statistically supported clade in all phylogenetic analyses; however, a sister relationship to M. sanborni is not supported. Genetic distance values that separate Micronycteris sp. nov. from its closest relatives range from 5.3% (versus M. sanborni) to 10.4% (versus M. minuta from Guyana). We diagnose and describe the new species in detail and name it in honor of the late Terry Lamon Yates for his contributions to Bolivian mammalogy. Micronycteris sp. nov. is Bolivia's 1st endemic bat species and because of its importance, the conservation implications are discussed. Resumen A pesar de que se ha realizado un trabajo significativo para definir las relaciones interespecíficas en el género Micronycteris, estas todavía no han sido plenamente resueltas. En Bolivia, el género Micronycteris está representado por 4 especies: M. hirsuta, M. megalotis, M. minuta y M. sanborni. Mediante el examen de caracteres morfológicos y análisis de medidas craneanas y datos genéticos, determinamos que M. sanborni no se encuentra en Bolivia y describimos una nueva especie cercanamente relacionada a esta. La nueva especie es morfométricamente distinta de sus congéneres, formando un grupo separado de M. schmidtorum, M. minuta y M. brosseti en el componente principal 1 (el cual explica 57.3% de la variación y está correlacionado con el largo dentario del maxilar) y separado de M. sanborni en el componente principal 2 (el cual explica 35.4% de la variación y está correlacionado con la longitud condilobasal). La nueva especie forma un clado con soporte estadístico en todos los análisis filogenéticos, sin embargo su relación de especie hermana con M. sanborni carece de soporte. Los valores de distancias genéticas que separan Micronycteris sp. nov. de sus parientes más cercanos varía de 5.3% (versus M. sanborni) a 10.4% (versus M. minuta de Guyana). Diagnosticamos y describimos la nueva especie en detalle y la nombramos en honor del fallecido Terry Lamon Yates por sus contribuciones a la mastozoología boliviana. Micronycteris sp. nov. es la primera especie de murciélago endémica de Bolivia y debido a su importancia discutimos las implicaciones para su conservación.
A Novel Signal Detection Scheme Based on Wavelet Packet Denoising and Cyclic Spectrum Theory

This paper propose a novel scheme combining wavelet packet denoising and cyclic spectrum feature to detect signal. Since many non-stationary signals existing in communication system have cyclostationnary features, signals can be detected by taking advantage of cyclic spectrum. But when the signal spectrum has more complex structure, the noise component is too large or noise itself has cyclostationary features, the demodulation effect of cyclic spectrum is not satisfactory. In consideration of the limitation of signal identification by employing cyclic spectrum signal identification, this paper introduces a novel scheme combining wavelet packet denoising and cyclic spectrum on the basis of the study of cyclic spectrum principles and the spectrum correlation characteristics of several typical communication signals. In this method, wavelet packet is adopted to delimitate noise using soft threshold and signal is identified according to the feature of its cyclic spectrum afterwards. Simulation results indicate that the method has good noise suppression capability, as well as an excellent signal recognition capability.
Functionalization of polymer powders for SLS-processes using an atmospheric plasma jet in a fluidized bed reactor

Recently additive manufacturing processes such as selective laser sintering (SLS) of polymers have gained more importance for industrial applications [1]. Tailor-made modification of polymers is essential in order to make these processes more efficient and to cover the industrial demands. The so far used polymer materials show weak performance regarding the mechanical stability of processed parts. To overcome this limitation, a new route to functionalize the surface of commercially available polymer particles (PA12; PE-HD; PP) using an atmospheric plasma jet in combination with a fluidized bed reactor has been investigated. Consequently, an improvement of adhesion and wettability [2] of the polymer surface without restraining the bulk properties of the powder is achieved. The atmospheric plasma jet process can provide reactive species at moderate temperatures which are suitable for polymer material. The functionalization of the polymer powders improves the quality of the devices build in a SLS-process.
Security Mechanism for Multi-Domain Vehicle-to-Grid Infrastructure

Plug-in electric vehicles (PEVs) reduce greenhouse gas emission by using power from the electric grid. PEVs are considered distributed energy resources and mobile storage devices, which require two-way communication standards to communicate with emerging Smart Grid infrastructure. Due to frequent mobility of PEVs, inter-utility real-time data communication is critical to the operation of interconnected systems in Vehicle-to-Grid (V2G) infrastructure. Interoperability and security considerations of V2G infrastructure components are decisive for widespread deployment of PEVs. In this paper, we propose multi-domain network architecture for V2G infrastructure which includes comprehensive hybrid public key infrastructure using hierarchical and peer-to-peer cross-certifications. We present system and performance analysis of the proposed security architecture.
The Complexity of Renaming

We study the complexity of renaming, a fundamental problem in distributed computing in which a set of processes need to pick distinct names from a given namespace. We prove an individual lower bound of \Omega( k ) process steps for deterministic renaming into any namespace of size sub-exponential in k, where k is the number of participants. This bound is tight: it draws an exponential separation between deterministic and randomized solutions, and implies new tight bounds for deterministic fetch-and-increment registers, queues and stacks. The proof of the bound is interesting in its own right, for it relies on the first reduction from renaming to another fundamental problem in distributed computing: mutual exclusion. We complement our individual bound with a global lower bound of \Omega( k \log ( k / c ) ) on the total step complexity of renaming into a namespace of size ck, for any c \geq 1. This applies to randomized algorithms against a strong adversary, and helps derive new global lower bounds for randomized approximate counter and fetch-and-increment implementations, all tight within logarithmic factors.
Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition

Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available.
Topological Many-Body States in Quantum Antiferromagnets via Fuzzy Supergeometry

Recent vigorous investigations of topological order have not only discovered new topological states of matter but also shed new light to \already known" topological states. One established example with topological order is the valence bond solid (VBS) states in quantum antiferromagnets. The VBS states are disordered spin liquids with no spontaneous symmetry breaking but most typically manifest topological order known as hidden string order on 1D chain. Interestingly, the VBS models are based on mathematics analogous to fuzzy geometry. We review applications of the mathematics of fuzzy super-geometry in the construction of supersymmetric versions of VBS (SVBS) states, and give a pedagogical introduction of SVBS models and their properties [arXiv:0809.4885, 1105.3529, 1210.0299]. As concrete examples, we present detail analysis of supersymmetric versions of SU(2) and SO(5) VBS states, i:e: UOSp(Nj2) and UOSp(Nj4) SVBS states whose mathematics are closely related to fuzzy twoand four-superspheres. The SVBS states are physically interpreted as hole-doped VBS states with superconducting property that interpolate various VBS states depending on value of a hole-doping parameter. The parent Hamiltonians for SVBS states are explicitly constructed, and their gapped excitations are derived within the single-mode approximation on 1D SVBS chains. Prominent features of the SVBS chains are discussed in detail, such as a generalized string order parameter and entanglement spectra. It is realized that the entanglement spectra are at least doubly degenerate regardless of the parity of bulk (super)spins. Stability of topological phase with supersymmetry is discussed with emphasis on its relation to particular edge (super)spin states.
Localized multiple kernel learning

Recently, instead of selecting a single kernel, multiple kernel learning (MKL) has been proposed which uses a convex combination of kernels, where the weight of each kernel is optimized during training. However, MKL assigns the same weight to a kernel over the whole input space. In this paper, we develop a localized multiple kernel learning (LMKL) algorithm using a gating model for selecting the appropriate kernel function locally. The localizing gating model and the kernel-based classifier are coupled and their optimization is done in a joint manner. Empirical results on ten benchmark and two bioinformatics data sets validate the applicability of our approach. LMKL achieves statistically similar accuracy results compared with MKL by storing fewer support vectors. LMKL can also combine multiple copies of the same kernel function localized in different parts. For example, LMKL with multiple linear kernels gives better accuracy results than using a single linear kernel on bioinformatics data sets.
Acquired somatic TP53 or PIK3CA mutations are potential predictors of when polyps evolve into colorectal cancer

Colorectal cancer (CRC) develops from accumulated mutations. However, which gene determines the malignant transformation from adenoma to carcinoma is still uncertain. Fifty-three formalin fixed paraffin-embedded polyps that had pathological findings from patients with hyperplasia, adenomatous, and tubular adenoma < 1 cm (non-neoplasia polyps, NNP, n = 27) or tubular adenoma ≥ 1 cm, tubulovillous and villous adenoma (neoplastic polyps, NP, n = 26) were recruited. Six paired synchronous polyps and cancer tissues and 50 independent fresh CRC tumors were also collected. All tissues were analyzed for their mutation genomes using next generation sequencing with a 50-gene panel. There were 40 types of somatic variants found in 7 genes, APC (43%), KRAS (28%), TP53 (11%), FBXW7 (8%), GNAS (4%), SMAD4 (2%), and BRAF (2%), and they were detected in 32 (60%) polyps. If combined with the mutation spectrum found in CRC tissues, a significant increase in the mutation rate in TP53 and PIK3CA from NNP, NP, early and late stage carcinoma (7%, 15%, 33.3% and 65% for TP53, p < 0.001; 0%, 0%, 23.3% and 25% for PIK3CA, p = 0.002) were noticed. Furthermore, distinct molecular features can be found in five pairs of synchronous polyps and tumors. However, TP53 or PIK3CA mutations can be found in tumor tissues but not in polyps. By systematically investigating the genome from polyps to tumor tissues, we demonstrated that acquired TP53 or PIK3CA somatic mutations are potential predictors for malignancy development. These results may aid in the identification of high risk individuals with tissues harboring mutations in these two genes.
Response-Time Analysis for Globally Scheduled Symmetric Multiprocessor Platforms

In the last years, a progressive migration from single processor chips to multi-core computing devices has taken place in the general-purpose and embedded system market. The development of multi-processor systems is already a core activity for the most important hardware companies. A lot of different solutions have been proposed to overcome the physical limits of single core devices and to address the increasing computational demand of modern multimedia applications. The real-time community followed this trend with an increasing number of results adapting the classical scheduling analysis to parallel computing systems. This paper will contribute to refine the schedulability analysis for symmetric multi-processor (SMP) real-time systems composed by a set of periodic and sporadic tasks. We will focus on both fixed and dynamic priority global scheduling algorithms, where tasks can migrate from one processor to another during execution. By increasing the complexity of the analysis, we will show that an improvement is possible over existing schedulability tests, significantly increasing the number of schedulable task sets detected. The added computational effort is comparable to the cost of techniques widely used in the uniprocessor case. We believe this is a reasonable cost to pay, given the intrinsically higher complexity of multi-processor devices.
A SIGNAL PROCESSING SYSTEM-LEVEL DESIGN COURSE

We describe a rst-year graduate course in embedded system design. Embedded systems may contain a mixture of signal processing, communication, and control algorithms implemented by a variety of technologies such as digital hardware, software, and analog circuits. The course focuses on how modern design methods and tools handle the heterogeneity and complexity in embedded systems design and covers block diagram modeling, algorithm speci cation, system simulation, and system synthesis. Students gain handson experience by using electronic design automation tools to design and simulate systems. This paper proposes steps to transition this course into the undergraduate curriculum.