Miracle-dz/UniFAR-FTUs huggingface dataset:
Expansion of growth substrate range in Pseudomonas putida F1 by mutations in both cymR and todS, which recruit a ring-fission hydrolase CmtE and induce the tod catabolic operon, respectively.

Pseudomonas putida F1 can assimilate benzene, toluene and ethylbenzene using the toluene degradation pathway, and can also utilize p-cymene via p-cumate using the p-cymene and p-cumate catabolic pathways. In the present study, P. putida F1 strains were isolated that were adapted to assimilate new substrates such as n-propylbenzene, n-butylbenzene, cumene and biphenyl, and the molecular mechanisms of genetic adaptation to an expanded range of aromatic hydrocarbons were determined. Nucleotide sequence analyses showed that the selected strains have mutations in the cymR gene but not in todF gene. The impairment of the repressor CymR by mutation led to the constitutive expression of CmtE, a meta-cleavage product hydrolase from the cmt operon. This study also showed that CmtE has a broad range of substrates and can hydrolyse meta-cleavage products formed from biphenyl and other new growth substrates via the toluene degradation pathway. However, the artificially constructed strain P. putida F1(cymR : : Tc(r)) and a recombinant P. putida F1, which expressed CmtE constitutively, could not grow on the new substrates. The adapted strains possess the tod operon, which is induced by new growth substrates that are poor inducers of wild-type P. putida F1. When the todS gene from the adapted strains was introduced in a trans manner to P. putida F1(cymR : : Tc(r)), the resulting recombinant strains were able to grow on biphenyl and other new substrates. This finding indicates that the TodS sensor was altered to recognize these substrates and this conclusion was confirmed by nucleotide sequence analyses. Amino acid substitutions were found in the regions corresponding to the receiver domain and the second PAS domain and their boundaries in the TodS protein. These results showed that P. putida F1 adapted strains capable of growth on n-propylbenzene, n-butylbenzene, cumene and biphenyl possess mutations to employ CmtE and to induce the tod catabolic operon by the new growth substrates.
Improving the k-svd facial image compression using a linear deblocking method

The use of sparse representations in signal processing is gradually increasing in the past several years. In a previous work we proposed a new method for compressing facial images using the K-SVD algorithm, which is a novel algorithm for training overcomplete dictionaries that lead to sparse signal representations. This method was shown to be most efficient, surpassing the JPEG2000 performance significantly. In this paper we present a significant addition to our compression algorithm in the form of image deblocking. Since the encoding is done in patches, a visually disturbing artifacts of blockiness appear in the reconstructed images. We eliminate these artifacts using a linear deblocking technique, which is based on local image filters. We construct a linear filter for each relevant pixel independently, and apply these filters as post-processing. This method is limited, but nevertheless it improves the PSNR of the reconstructed images and gives visually appealing results.
Network Management Itineraries for Mobile Agents

Abstract Proposed distributed management architectures, incorporating mobile agent (MA) technology, have not adequately management scalability problems, when monitoring tasks requiring the employment of itinerant agents is considered. Mechanisms building optimal agents itinerary are needed to minimise the total migration cost in terms of the round-trip latency and the incurred traffic. This is of particular importance when the management of networks spanning multiple subnets is involved. On this direction, we have designed and implemented an algorithm which adapts methods usually applied for solving network design problems in the specific problematic of MA itinerary planning. The algorithm not only suggests the optimal number of MAs that minimise the overall cost but also constructs optimal itineraries for each of them. The algorithm implementation has been integrated into our MA framework research prototype and tested into real network environments, demonstrating significant management cost savings.
A Framework for Evaluating Fairness in Input-Queued Switches: Fundamental Principles and Practical Strategies

— Fairness in trafﬁc management can improve the isolation between trafﬁc streams, offer a more predictable performance, eliminate transient bottlenecks, mitigate the effect of certain kinds of denial-of-service attacks, and serve as a critical component of a quality-of-service strategy to achieve certain guaranteed services such as delay bounds and minimum bandwidths. Several research efforts have attempted to achieve fairness in input-queued switches by one measure or another. However, there has not been a unifying framework for evaluating these different fairness strategies against each other. In this paper, we formalize the notion of fairness in input-queued switches through a rigorous framework based on an extension of the max-min notion of fairness. Our framework permits the algorithmic determination of the fair rates to be allocated to the ﬂows through the switch and also permits a quantitative evaluation of strategies that aim to achieve fairness in input-queued switches. We show that our algorithm can be implemented in a distributed fashion to dynamically determine ﬂow rates. We further propose a practical scheduling strategy based on our algorithm. We present simulation results using real gateway trafﬁc traces to evaluate the fairness of a variety of popular scheduling algorithms for input-queued switches. The results show that our scheduling strategy achieves better fairness than other known algorithms for input-queued switches.
Non-Selective Cation Channels Mediate Chloroquine-Induced Relaxation in Precontracted Mouse Airway Smooth Muscle

Bitter tastants can induce relaxation in precontracted airway smooth muscle by activating big-conductance potassium channels (BKs) or by inactivating voltage-dependent L-type Ca2+ channels (VDLCCs). In this study, a new pathway for bitter tastant-induced relaxation was defined and investigated. We found nifedipine-insensitive and bitter tastant chloroquine-sensitive relaxation in epithelium-denuded mouse tracheal rings (TRs) precontracted with acetylcholine (ACH). In the presence of nifedipine (10 µM), ACH induced cytosolic Ca2+ elevation and cell shortening in single airway smooth muscle cells (ASMCs), and these changes were inhibited by chloroquine. In TRs, ACH triggered a transient contraction under Ca2+-free conditions, and, following a restoration of Ca2+, a strong contraction occurred, which was inhibited by chloroquine. Moreover, the ACH-activated whole-cell and single channel currents of non-selective cation channels (NSCCs) were blocked by chloroquine. Pyrazole 3 (Pyr3), an inhibitor of transient receptor potential C3 (TRPC3) channels, partially inhibited ACH-induced contraction, intracellular Ca2+ elevation, and NSCC currents. These results demonstrate that NSCCs play a role in bitter tastant-induced relaxation in precontracted airway smooth muscle.
(Automatic) target detection in synthetic aperture radar imagery via terrain recognition

Surveillance of large areas of the Earth's surface is often undertaken with low resolution synthetic aperture radar (SAR) imagery from either a satellite or a plane. There is a need to process these images with automatic target detection (ATD) algorithms. Typically the targets being searched for are vehicles or small vessels, which occupy only a few resolution cells. Simple thresholding is usually inadequate for detection due to the high amount of noise in the images. Often the background has a discernible texture, and one form of detection is to search for anomalies in the texture caused by the presence of the target pixels. To perform this task a texture model must be able to model a variety of textures at run time, and also model these textures well enough to detect anomalies. We accomplish this with our multiscale nonparametric Markov random field (MRF) texture model.
On hardware solution of dense linear systems via Gauss-Jordan Elimination

Gauss-Jordan Elimination (GJE) is a popular method for solving systems of linear equations. Much work has been done to design high throughput, low cost, FPGA-based architectures for GJE. However, as the interest in energy efficient designs increases, power consumption becomes a prevalent metric that must be considered in any FPGA-based implementation. In this paper, we present a scalable architecture that can efficiently solve any generic system of linear equations using GJE with a single-precision floating-point accuracy and reasonable power and area overheads. Comparisons with two previous implementations show the efficiency of our design.
OFFICE PRODUCTIVITY: A SELF-ASSESSED APPROACH TO OFFICE EVALUATION

The aim of this paper is to provide a validated theoretical framework for the measurement of office productivity. The study’s strength is that it is based on two sizable data sets. The data collected consists of data about the physical characteristics of the office environment and data pertaining to the behavioural environment. One of the key contributions of this study was the development of the components of office productivity, which were: comfort, office layout, informal interaction points, environmental services, designated areas, interaction and distraction. The components were reduced to four in preparation for subsequent analysis. The four distinct components were comfort, office layout, interaction and distraction. This study establishes that it is the behavioural environment that has the greatest impact on office productivity. It demonstrates that it is the dynamic elements of the office environment, interaction and distraction that are perceived as having the greatest positive and negative influences on self assessed productivity.
Genome-wide analysis and environmental response profiling of phosphate-induced-1 family genes in rice (Oryza sativa)

Abstract Phosphate-induced-1 (PHI-1) and phosphate-induced-1-like family genes respond to plant hormones such as abscisic acid (ABA), BR (brassinosteroid) and ethylene. To date, very few researches have been done on abiotic stress for PHI-1 genes. In this work, we report 12 rice PHI-1 genes through genome-wide analysis. The 12 OsPHI-1 genes were tandemly arranged into two clusters and nine conserved motifs were found among their amino acid sequences. Microarray data indicated that all the OsPHI-1 genes exhibited identical expression level but different expression patterns: most OsPHI-1 genes were expressed intensively in panicle development and responded to IAA and BAP treatments; several OsPHI-1 genes responded to trans-zeatin (tZ) and dimethyl sulfoxide (DMSO) treatments; 11 OsPHI-1 genes showed response to abiotic stress. Furthermore, the promoter region analysis showed that all the OsPHI-1 genes contained cis-regulatory elements responding to abiotic stresses. Our study will be helpful to further investigate the biological functions of PHI-1 genes in rice.
Study of the Effects of Monacolin K and Other Constituents of Red Yeast Rice on Obesity, Insulin-Resistance, Hyperlipidemia, and Nonalcoholic Steatohepatitis Using a Mouse Model of Metabolic Syndrome

Purpose. Nonalcoholic fatty liver disease (NAFLD) is a progressive and intractable disease associated with metabolic syndrome. Red yeast rice (RYR) contains monacolin K, a potent inhibitor of HMG-CoA reductase, and its consumption decreases cholesterol and triglyceride levels. We examined the efficacy of RYR constituents using a novel metabolic syndrome-NAFLD mouse model (MSG mice). Methods. Two types of RYR grown under different culture conditions were used. 1P-DU contained only 0.002 g/100 g of monacolin K, whereas 3P-D1 contained 0.131 g/100 g. MSG mice were divided into three groups: control (C) group fed standard food, RYR-C group fed standard food with 1% 1P-DU, and RYR-M group fed standard food with 1% 3P-D1. Mice were examined from 12 to 24 weeks of age. Results. Serum insulin, leptin, and liver damage as well as macrophage aggregation in visceral fat in RYR-C and RYR-M groups were lower than those in C group. The serum adiponectin levels in RYR-C group were significantly higher than those in RYR-M and C groups. Conclusions. RYR was effective against obesity-related inflammation, insulin resistance, and NAFLD in MSG mice irrespective of monacolin K levels. GABA and various peptides produced during fermentation were determined as the active constituents of RYR.
Stream pattern recognition of touching elements of grain mixtures

The paper outlines the problem of stream classification of grain kernels, which involves machine learning methods in cases the images are touching. The applicability of the existing methods of contour separation under real industrial conditions is studied. As a result, a new efficient algorithm is introduced that enables stream separation of grain kernel images. The study has shown that morphological descriptors for restored contours can be used in feature vectors when solving the problem of image classification by means of a neural network with fully connected layers. A program solution is developed that enables classification of the elements of grain mixtures in industrial systems based on the use of 60 the most important morphological, colour and texture descriptors. The paper proposes using the statistical choice of descriptors and the automatic adjustment of the grain mixture flow while performing stream pattern recognition.
Phylogenetic analysis of canine parvovirus isolates from Mathura, India.

1College of Biotechnology, Uttar Pradesh Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishvidhyalaya Evum Go-Anusandhan Sansthan (DUVASU), Mathura, UP, India 2Department of Veterinary Epidemiology and Preventive Medicine, College of Veterinary Sciences and Animal Husbandry, Uttar Pradesh Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishvidhyalaya Evum GoAnusandhan Sansthan (DUVASU), Mathura, UP, India 3Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, Uttar Pradesh Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishvidhyalaya Evum Go-Anusandhan Sansthan (DUVASU), Mathura, UP, India
A CMOS Image Sensor Employing a Double Junction Photodiode

A CMOS image sensor that employs a vertically integrated double junction photodiode structure is presented. This allows colour imaging with only two, wider bandwidth, filters. The sensor uses a 184 x 154 6-transistor pixel array at a 9.6 μm pitch. Results of the device characterisation, and colour image reconstruction using the prototype sensor, are presented.
Francesco Ruggiero 1957-2007

Francesco Ruggiero (1957-2007) was a brilliant acceler- ator physicist, an inventive researcher, a great collaborator, an excellent mentor, and a true gentleman. We here take a look at Francesco's scientific work, and highlight some of his contributions to accelerator physics. More details can be found in the slides presented by the speakers of the Francesco Ruggiero Memorial Symposium held at CERN on 3 October 2007 (2).
Towards a Cyberaide Shell for the TeraGrid

Through the development of advanced middleware, Grid computing has evolved to a mature technology that scientists and researchers can leverage to gain knowledge that was previously unobtainable in a wide variety of scientific domains [2]. However, the ability for new scientists to become involved with Grid computing has become challenging due to its complex nature. This high entry barrier in turn limits the use of Grid computing and advanced cyberinfrastructure as it is unable to trickle down to a more general scientific user group. For example, absence of developer teams in smaller research projects requires the scientist to become an expert in Grid computing themselves. In a typical Grid environment there are obstacles that need to be dealt with such as task management, job scheduling, resource monitoring, and organization management, all of which can overwhelm a domain scientist. Many of these utilities can be abstracted to simplify the scientific user’s experience and enable them to perform their research in a more efficient and productive environment. Our solution is Cyberaide Shell [3], an advanced but simple to use system shell which provides access to the powerful cyberinfrastructure available today [4]. We abstract resources, tasks, and application management tools through a scriptable command line interface. Through a service integration mechanism, the shell’s functionality is exposed to a wide variety of frameworks and programming languages to allow for the scientist to leverage the power of Grid computing within their own applications.
Black Hole Magnetospheres around Thin Disks Driving Inward and Outward Winds

We construct a simple model for stationary, axisymmetric black hole magnetospheres, in which the poloidal magnetic field is generated by a toroidal electric current in a thin disk with an inner edge, by solving the vacuum Maxwell equations in the Schwarzschild background. In this work, to obtain a concise analytical form of the magnetic stream function, we use the approximation that the inner edge is far distant from the event horizon. The global magnetospheric structure with a closed-loop and open field lines threading the inner and outer parts of the disk is explicitly shown, claiming that the model is useful as a starting point to study astrophysical problems involving inward disk-driven winds to a black hole and outward ones to infinity. The asymptotic shape of the field lines at the event horizon becomes nearly cylindrical, while at infinity it becomes conical. The magnetic spot in the disk connected with the black hole through the loop field lines occupies a very narrow region with the ring area roughly equal to the horizon area. By taking account of the existence of a uniform (external) magnetic field, we also obtain a model for collimated open field lines. Then, it is found that the magnetic connection between the black hole and the disk breaks down if the uniform field is strong enough. Considering slow rotation of the magnetosphere and angular momentum transfer by inward winds from the disk, the final discussion is devoted to gradual disruption of the closed loops due to radial accretion of disk plasma toward the black hole.
Automatic cell cutting and nucleus detection

We have developed an automated cell cutting and its nucleus detection technique for automated nucleus transplantation. Animal cells softened by cytochalasin treatment were injected into a microfluidic chip. The microfluidic chip contained 2 orthogonal channels: 1 microchannel was wide, was used to transport cells, and to generate the cutting flow; the other microchannel was thin and used for aspiration, fixing, and stretching of the cell. The injected cell was aspirated and stretched thin into the thin microchannel. Simultaneously, the volume of the cell before and after aspiration was calculated; this volume was used to calculate the fluid flow required to aspirate half the volume of the cell into the thin microchannel. Then, we applied a high-speed flow in the orthogonal microchanel to bisect the cell. Finally, we observed the nucleus of the cut cells to detect the non-nucleus cell. This paper reports the cutting and the detection process and the system, and result of the experiment.
Extending a C-like language for portable SIMD programming

SIMD instructions are common in CPUs for years now. Using these instructions effectively requires not only vectorization of code, but also modifications to the data layout. However, automatic vectorization techniques are often not powerful enough and suffer from restricted scope of applicability; hence, programmers often vectorize their programs manually by using intrinsics: compiler-known functions that directly expand to machine instructions. They significantly decrease programmer productivity by enforcing a very error-prone and hard-to-read assembly-like programming style. Furthermore, intrinsics are not portable because they are tied to a specific instruction set. In this paper, we show how a C-like language can be extended to allow for portable and efficient SIMD programming. Our extension puts the programmer in total control over where and how control-flow vectorization is triggered. We present a type system and a formal semantics of our extension and prove the soundness of the type system. Using our prototype implementation IVL that targets Intel's MIC architecture and SSE instruction set, we show that the generated code is roughly on par with handwritten intrinsic code.
Smile Detection for User Interfaces

The mental state of a person is judged by detecting smiles. The smile detection starts with the facial recognition. The main advantage of the smile detection is it ensures whether smiles are detected by the camera or not. We compare those set of images and determine which image has the best smile. Now, across the mouth region to detect the corners we use Shi-Tomasi corner detection algorithm as reference and explained the results in detail in this paper.
Automatic Pen-and-Ink Illustration of Tone, Gloss, And Texture

We present a method for automatically depicting material appearance using pen and ink. Starting from a classical computer graphics representation -- color map, normal map, illumination, etc. -- we introduce an abstraction layer to bridge between this unsuited input and generic control parameters of pen-and-ink systems, such as primitive shape, size and density. This layer is made of parameters, belonging to tone, gloss and texture categories, that are automatically extracted from the input data. We then demonstrate our approach by presenting how this abstraction layer can easily be used to drive an example pen-and-ink rendering system. We show results on various materials, and validate our choices in a user study.
XHELP: Design of a Cross-Platform Social-Media Application to Support Volunteer Moderators in Disasters

Recent disasters have shown an increase in the significance of social media for both affected citizens and volunteers alike in the coordination of information and organization of relief activities, often independently of and in addition to the official emergency response. Existing research mainly focuses on the way in which individual platforms are used by volunteers in response to disasters. This paper examines the use of social media during the European Floods of 2013 and proposes a novel cross-social-media application for volunteers. Besides comprehensive analysis of volunteer communities, interviews were conducted with "digital volunteers" such as Facebook moderators of disaster-related groups. Based on the challenges identified, we designed and implemented the cross-social-media application "XHELP", which allows information to be both, acquired and distributed cross-media and cross-channel. The evaluation with 20 users leads to further design requirements for applications aiming to support volunteer moderators during disasters.