Miracle-dz/UniFAR-FTUs huggingface dataset:
Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean

Planktonic Crenarchaea are thought to play a key role in chemolithotrophic ammonia oxidation, a critical step of the marine nitrogen (N) cycle. In this study, we examined the spatial distributions of ammonia-oxidizing Crenarchaea across a large (∼5200 km) region of the central Pacific Ocean. Examination of crenarchaeal 16S rRNA, ammonia monooxygenase subunit A (amoA) genes, and amoA transcript abundances provided insight into their spatial distributions and activities. Crenarchaeal gene abundances increased three to four orders of magnitude with depth between the upper ocean waters and dimly lit waters of the mesopelagic zone. The resulting median value of the crenarchaeal amoA: 16S rRNA gene ratio was 1.3, suggesting the majority of Crenarchaea in the epi- and mesopelagic regions of the Pacific Ocean have the metabolic machinery for ammonia oxidation. Crenarchaeal amoA transcript abundances typically increased one to two orders of magnitude in the transitional zone separating the epipelagic waters from the mesopelagic (100–200 m), before decreasing into the interior of the mesopelagic zone. The resulting gene copy normalized transcript abundances revealed elevated amoA expression in the upper ocean waters (0–100 m) where crenarchaeal abundances were low, with transcripts decreasing into the mesopelagic zone as crenarchaeal gene abundances increased. These results suggest ammonia-oxidizing Crenarchaea are active contributors to the N cycle throughout the epi- and mesopelagic waters of the Pacific Ocean.
Preparation and Use of Nano Zinc Oxide in Neoprene Rubber

Zinc oxide (ZnO) of nanometer particle size was prepared by solid-state pyrolytic method. TEM, XRD, and surface area studies showed that the prepared zinc oxide had particle size in the range of 15–30 nm and surface area in the range of 12–30 m2/g. This nano zinc oxide was used as a curing agent in neoprene rubber. The optimum dosage of ZnO was found to be low compared to commercial ZnO. The cure characteristic and mechanical properties were compared with those containing conventional ZnO. It was found that a low dosage of zinc oxide was enough to give equivalent curing and mechanical properties compared to one containing a higher dosage (5 phr) of commercial zinc oxide in neoprene rubber.
Nitrogen-ion-implanted planar optical waveguides in Er-doped tellurite glass: fabrication and characterization

Fabrication of channel waveguides in Er-doped tungsten-tellurite glasses was recently demonstrated. In order to get a deeper understanding of the process and to optimize the characteristics of the waveguides, we fabricated a set of planar waveguides, each of 7 mm × 7 mm lateral dimensions, in an Er-doped tellurite glass sample by implantation of 1.5 MeV nitrogen ions. Doses of the implanting ions ranged from 1 · 1016 to 8 · 1016 ions/cm2. The samples were studied using interference phase contrast microscopy (Interphako), m-line spectroscopy and spectroscopic ellipsometry. The results show that a barrier layer of reduced refractive index was created around the range of the implanted ions at every dose. It is hoped that combination of the results obtained in these experiments with simulations for channel waveguides will make it possible to optimize ion-implanted fabrication of integrated optical components in this tellurite glass.
Design of fault-tolerant solid state mass memory

This paper presents the flow used for the design of a fault-tolerant solid state mass memory (SSMM) based on commercial off the shelf (COTS) 64 Mb DRAMs. The effects of high-energy radiations on these devices are often complex. In particular, in the paper we consider heavy ion and proton induced soft and hard errors in DRAM devices. In our work, these errors are mitigated at system level rather at device level. In fact the mass memory is based on a suitable ECC code that improves its tolerance with respect to errors induced in DRAMs. The definition of a SSMM architecture is very complex since the design has to take into account the radiation environment and the different system constraints. In this paper we presents the methodology, derived from the operational research theory, used to select the codes and the memory architecture, taking into account the different design constraints.
Measuring distance by angular domain filtering

In this paper a paraxial imaging system with incoherent illumination is interpreted as a signal processing system in which a thin lens performs a forward angular transform on light rays traveling through it. Inverse angular transform exists and could be performed by another thin lens which coincides its focus plane with the first. The common focus plane acts as an angular domain, on which filtering is possible by placing aperture stops. A symmetrically angular filtering results in a direct correspondence between a recorded signal and its object distance. Such a “transform-filtering-inverse transform” system could be understood as a modified tele-centric system, with which a novel concept for measuring a distance without focusing on the target is suggested.
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo. cipf.es/projects/cellbase.
Protein Aggregation in the Brain: The Molecular Basis for Alzheimer’s and Parkinson’s Diseases

Developing effective treatments for neurodegenerative diseases is one of the greatest medical challenges of the 21st century. Although many of these clinical entities have been recognized for more than a hundred years, it is only during the past twenty years that the molecular events that precipitate disease have begun to be understood. Protein aggregation is a common feature of many neurodegenerative diseases, and it is assumed that the aggregation process plays a central role in pathogenesis. In this process, one molecule (monomer) of a soluble protein interacts with other monomers of the same protein to form dimers, oligomers, and polymers. Conformation changes in three-dimensional structure of the protein, especially the formation of β-strands, often accompany the process. Eventually, as the size of the aggregates increases, they may precipitate as insoluble amyloid fibrils, in which the structure is stabilized by the β-strands interacting within a β-sheet. In this review, we discuss this theme as it relates to the two most common neurodegenerative conditions—Alzheimer’s and Parkinson’s diseases.
Places Clustering of Full-Length Film Key-Frames Using Latent Aspect Modeling Over SIFT Matches

An improved unsupervised classification method to extract and link places features and cluster recurrent physical locations (key-places) within a movie is presented. Our approach finds links between key frames of a common key-place based on the use of a probabilistic latent space model over the possible local matches between the key frames image set. This allows the extraction of significant groups of local matching descriptors that may represent characteristic elements of a key-place. An exhaustive evaluation of our approach was conducted on in-house and public image datasets, as well as on full-length movies. Results revealed that our method is very efficient for near-duplicate object/background detection with weak overlap. Performance measurements on full-length movies indicate a recognition rate of about 75% on the key-places clustering with a false alarm rate (FAR) of approximately 2%.
Metabolome Analyses Uncovered a Novel Inhibitory Effect of Acyclic Retinoid on Aberrant Lipogenesis in a Mouse Diethylnitrosamine-Induced Hepatic Tumorigenesis Model

Acyclic retinoid (ACR) is a promising drug under clinical trials for preventing recurrence of hepatocellular carcinoma. The objective of this study was to gain insights into molecular basis of the antitumorigenic action of ACR from a metabolic point of view. To achieve this, comprehensive cationic and lipophilic liver metabolic profiling was performed in mouse diethylnitrosamine (DEN)-induced hepatic tumorigenesis model using both capillary electrophoresis time-of-flight mass spectrometry and liquid chromatography time-of-flight mass spectrometry. ACR significantly counteracted against acceleration of lipogenesis but not glucose metabolism in DEN-treated mice liver, suggesting an important role of lipid metabolic reprogramming in the initiation step of hepatic tumorigenesis. Knowledge-based pathway analysis suggested that inhibition of linoleic acid metabolites such as arachidonic acid, a proinflammatory precursor, played a crucial role in the prevention by ACR of DEN-induced chronic inflammation–mediated tumorigenesis of the liver. As a molecular mechanism of the ACR's effect to prevent the aberrant lipogenesis, microarray analysis identified that a key transcription regulator of both embryogenesis and tumorigenesis, COUP transcription factor 2, also known as NR2F2, was associated with the metabolic effect of ACR in human hepatocellular carcinoma cells. Our study provided potential therapeutic targets for the chemoprevention of hepatocellular carcinoma as well as new insights into the mechanisms underlying prevention of hepatic tumorigenesis. Cancer Prev Res; 9(3); 205–14. ©2016 AACR.
A transition model for the reflection coefficient in surface scattering

A transition function for estimating the Fresnel reflection coefficient over the active frequency range is proposed based on two-dimensional moment method simulation. It naturally connects two approximations of the Fresnel coefficients R(/spl theta/) and R(/spl theta/sp). In the authors' comparisons, the model predictions by the integral equation model (IEM) with the modified Fresnel reflection coefficient are in excellent agreement with simulated data in angular, frequency and polarization dependence.
Multi-Level Discriminative Dictionary Learning With Application to Large Scale Image Classification

The sparse coding technique has shown flexibility and capability in image representation and analysis. It is a powerful tool in many visual applications. Some recent work has shown that incorporating the properties of task (such as discrimination for classification task) into dictionary learning is effective for improving the accuracy. However, the traditional supervised dictionary learning methods suffer from high computation complexity when dealing with large number of categories, making them less satisfactory in large scale applications. In this paper, we propose a novel multi-level discriminative dictionary learning method and apply it to large scale image classification. Our method takes advantage of hierarchical category correlation to encode multi-level discriminative information. Each internal node of the category hierarchy is associated with a discriminative dictionary and a classification model. The dictionaries at different layers are learnt to capture the information of different scales. Moreover, each node at lower layers also inherits the dictionary of its parent, so that the categories at lower layers can be described with multi-scale information. The learning of dictionaries and associated classification models is jointly conducted by minimizing an overall tree loss. The experimental results on challenging data sets demonstrate that our approach achieves excellent accuracy and competitive computation cost compared with other sparse coding methods for large scale image classification.
A new approach to design safe and reliable electrical stimulator

In this paper, a new active charge-balancing technique for functional electrical stimulation is presented. In this method, electrode voltage is monitored after each stimulation period and a charge-balancing circuit keeps the electrode voltage in the safe range. Also, a dynamic comparator is utilised to reduce the total power consumption. This method is adopted in a microstimulator which is used in a functional electrical stimulation application. Simulation in a high-voltage 0.18 μm CMOS technology validates the feasibility of the approach and its low power consumption. The power consumption of the charge-balancing circuits contributes 3.4% of the overall power consumption of the system.
Face Tracking Using Two Cooporative Static and Moving Cameras

In this paper, we present a new stereo approach for tracking human face by using only two cameras in system. One pan-tilt camera is used for tracking person focused on face. One static camera cooperate with pan-tilt camera are used as a stereo system to estimate face 3D position. We propose to update relative position between cameras to reflect camera moving and the change of relative position. Experimental results shows that our proposed system is able to track one person in camera viewing and can estimate the 3D moving path of interesting person
Marketing, R&D, and Startup Valuation

The problem focus is on startup decisions associated with staged venture financing, where both R&D and marketing are significant percentages of overall expenses. When should a startup owner acquire working capital, and how should she/he distribute that capital between R&D (to improve product quality) and marketing (to increase sales) to ultimately grow valuation? Also, should the startup owner cap the total R&D and marketing budgets to increase profitability during staged venture financing? We develop a model to study resource acquisition and allocation decisions across successive stages of startup growth. The model incorporates a funding process whereby the startup valuation is positively impacted by improved product quality and market growth. This model provides insights on optimal acquisition and allocation practices and characterizes the impact of changes in productivity, along with the evolution rate of R&D and marketing payoffs, on the underlying decisions. Our results also illustrate conditions for optimal capping of R&D and marketing expenses as a percentage of revenues.
An Investigation of Differential Power Analysis Attacks on FPGA-based Encryption Systems

Hardware devices implementing cryptographic algorithms are finding their way into many applications. As this happens, the ability to keep the data being processed or stored on the device secure grows more important. Power analysis attacks involve cryptographic hardware leaking information during encryption because power consumption is correlated to the key used for encryption. Power analysis attacks have proven successful against public and private key cryptosystems in a variety of form factors. The majority of the countermeasures that have been proposed for this attack are intended for software implementations on a microcontroller. This project focuses on the development of a VHDL tool for investigating power analysis attacks on FPGAs and exploring countermeasures that might be used. The tool developed here counted the transitions of CLB output signals to estimate power and was used to explore the impact of possible gate-level countermeasures to differential power analysis. Using this tool, it was found that only a few nodes in the circuit have a high correlation to bits of the key. This means that modifying only a small portion of the circuit could dramatically increase the difficulty of mounting a differential power analysis attack on the hardware. Further investigation of the correlation between CLB outputs and the key showed that a tradeoff exists between the amount of space required for decorrelation versus the amount of decorrelation that is desired, allowing a designer to determine the amount of correlation that can be removed for available space. Filtering of glitches on CLB output signals slightly reduced the amount of correlation each CLB had. Finally, a decorrelation circuit was proposed and shown capable of decorrelating flip-flop outputs of a CLB, which account for less than 10% of the CLB outputs signals.
Rapid identification of polymethoxylated flavonoids in traditional Chinese medicines with a practical strategy of stepwise mass defect filtering coupled to diagnostic product ions analysis based on a hybrid LTQ-Orbitrap mass spectrometer.

INTRODUCTION The methodology of stepwise mass defect filtering (MDF) approach coupled to diagnostic product ions (DPIs) analysis on a hybrid linear trap quadrupole (LTQ)/orbitrap mass spectrometer was the first to be established to screen and identify structural analogues from complex herbal extracts. OBJECTIVE To develop an analytical methodology that could be adopted to screen and identify structural analogues in traditional Chinese medicines (TCMs) rapidly and accurately. METHODS Taking polymethoxylated flavonoids (PMFs) in the leaves of Citrus reticulata Blanco as an example, high-resolution mass data were acquired by high-performance liquid chromatography (HPLC) coupled with a LTQ/orbitrap mass spectrometer. The stepwise MDF with multiple mass defect windows or mass windows enabled the original data to be analysed much faster and more accurately by reducing the potential interferences of matrix ions. Additionally, analysis of DPIs could provide a criterion to classify the target constituents detected into certain chemical families. RESULTS In total, 81 PMFs, including 50 polymethoxyflavones and 31 polymethoxyflavanones or polymethoxychalcones, were screened and identified from the original data and preliminarily identified. CONCLUSION The analytical methodology developed could be used as a rapid, effective technique to screen and identify compounds from TCM extracts and other organic matter mixtures with compounds that can also be classified into families based on the common carbon skeletons.
Lexical Access With a Statistically-Derived Phonetic Network

A probabilistic approach to lexical access from a recognized phone sequence is presented. Lexical access is seen as finding the word sequence that maximizes the lexical likelihood of a sequence of phones and durations as recognized by a phone recognizer. This is theoretically correct for minimum error rate recognition within the model presented and is intuitively pleasing since it means that the "confusion matrix" of the phone recognizer will be learned and its regularities exploited. The lexical likelihoods are estimated from training data provided by the phone recognizer using statistical decision trees. Classification trees are used to estimate the phone realiziation distributions and regression trees are used to estimate the phone duration distributions. We find they can capture effectively allophonic variation, alternative pronunciation, word co-articulation and segmental durations. We describe a simpified, but efficient implementation of these models to lexical access in the DARPA resource management recognitiion task.
Modeling and Prolonging Techniques on Operational Lifetime of Wireless Sensor Networks

Power consumption is an essentially important issue and an interesting challenge to prolong the lifetime of wireless sensor network (WSN). Sensors closer to a sink node have a larger forwarding traffic burden and consume more energy than nodes further away from the sink. The whole operational lifetime of WSN is deteriorated because of such an uneven node power consumption patterns, leading to what is known as an energy hole problem (EHP) around the sink node. In this article, we propose a novel power-saving scheme to alleviate the EHP based on the Min(N, T) policy M/G/1 queuing model. With little management cost, the proposed queue-based power-saving technique can be applied to prolong the lifetime of sensor network economically and effectively. For the proposed queue-based model, mathematical framework on performance measures have been formulated. And also we analyze the average traffic load per node for concentric sensor network. Focusing on the nodes located in the innermost shell of WSN, numerical and NS2 network simulation results validate that the proposed approach indeed provides a feasibly cost-effective approach for lifetime elongation of sensor networks.
Chiral Optical Fibres and Gratings

The focal purpose of this thesis is to study chirality specifically in telecommunications area, through the pure chiral fibres (optical fibres constituted by chiral material) and chiral fibre grating (twisted optical fibre), analysing also its behaviour and applications. Nevertheless we shall also address this theme from an economical perspective. The study begins by giving a brief introduction of the history behind optical fibre and chiral fibres, followed by an explanation about chirality, using the constitutive relations. While analysing the constitutive relations of the bi-isotropic medium, we will also study the polarization and its rotation. To better understand this chiral medium, we will verify how a plane wave behaved when it focus on the dielectric-chiral medium interface. Then we shall analyse a pure chiral fibre (optical fibre built with chiral material) and with it study the semileaky and surface modes. Afterwards, we will introduce chiral fibre grating, explaining how they are built and their properties. Through these characteristics, we will be able to divide these fibres in three groups: chiral short period gratings, chiral intermediate period grating and chiral long period grating, but also sub-divide each one into two types, double-helix and single-helix. Finally we shall end by analysing the viability of this new technology, not only as the breakthrough innovations that bring telecommunication systems, but also from an economical point of view.
Ethnic diversity and informal intra- and inter-ethnic contacts with neighbours in The Netherlands

We have examined the extent to which ethnic diversity in neighbourhoods and municipalities in The Netherlands is related to personal contact with neighbours from ethnic in-groups and out-groups among the native majority as well as among ethnic minorities. The results indicate that ethnic diversity is negatively related to personal contacts with native neighbours, but positively to personal contacts with neighbours from other ethnic groups. This applies equally to native respondents and Turks and Moroccans, rejecting Putnam’s hunkering-down hypothesis and ethnic competition theory. Instead, ethnic diversity increases meeting opportunities with ethnic minorities while decreasing meeting opportunities with the native majority.