Miracle-dz/UniFAR-FTUs huggingface dataset:
A simple model for Lutz and Bujard’s controllable promoters and its application for analyzing a simple genetic oscillator

Abstract We develop an exact and flexible mathematical model for Lutz and Bujard’s controllable promoters. It can be used as a building block for modeling genetic systems based on them. Special attention is paid to deduce all the model parameters from reported (in vitro) experimental data. We validate our model by comparing the regulatory ranges measured in vivo by Lutz and Bujard against the ranges predicted by the model, and which are calculated as the reporter activity obtained under inducing conditions divided by the activity measured under maximal repression. In particular, we verify Bond et al. assertion that the cooperativity between two lac operators can be assumed to be negligible when their central base pairs are separated by 22 or 32 bp [Gene repression by minimal lac loops in vivo, Nucleic Acids Res, 38 (2010) 8072–8082]. Moreover, we also find that the probability that two repressors LacI bind to these operators at the same time can be assumed to be negligible as well. We finally use the model for the promoter PLlacO-1 to analyze a synthetic genetic oscillator recently build by Stricker et al. [A fast, robust and tunable synthetic gene oscillator, Nature, 456 (2008) 516–519].
Characterization of Kinetoplast DNA from Phytomonas serpens

ABSTRACT. The restriction enzyme digestion of kinetoplast DNA from four Phytomonas serpens isolates shows an overall similar band pattern. One minicircle from isolate 30T was cloned and sequenced, showing low levels of homology but the same general features and organization as described for minicircles of other trypanosomatids. Extensive regions of the minicircle are composed by G and T on the H strand. These regions are very repetitive and similar to regions in a minicircle of Crithidia oncopelti and to telomeric sequences of Saccharomyces cerevisiae. Conserved Sequence Block 3, present in all trypanosomatids, is one nucleotide different from the consensus in P. serpens and provides a basis to differentiate P. serpens from other trypanosomatids. Electron microscopy of kinetoplast DNA evidenced a network with organization similar to other trypanosomatids and the measurement of minicircles confirmed the size of about 1.45 kb of the sequenced minicircle.
The Weight Hierarchy of Some Reducible Cyclic Codes

The generalized Hamming weights (GHWs) of linear codes are fundamental parameters, the knowledge of which is of great interest in many applications. However, to determine the GHWs of linear codes is difficult in general. In this paper, we study the GHWs for a family of reducible cyclic codes and obtain the complete weight hierarchy in several cases. This is achieved by extending the idea of Yang et al. into higher dimension and by employing some interesting combinatorial arguments. It shall be noted that these cyclic codes may have arbitrary number of nonzeros.
From spontaneous total order to uniform total order: different degrees of optimistic delivery

A total order protocol is a fundamental building block in the construction of distributed fault-tolerant applications. Unfortunately, the implementation of such a primitive can be expensive both in terms of communication steps and of number of messages exchanged. This problem is exacerbated in large-scale systems, where the performance of the algorithm may be limited by the presence of high-latency links.Optimistic total order protocols have been proposed to alleviate this problem. However, different optimistic protocols offer quite distinct services. This paper makes an overview of different optimistic approaches and shows how they can be combined in a single adaptive protocol.
Comparison of surgical condition in endoscopic sinus surgery using remifentanil combined with propofol, sevoflurane, or desflurane

Background Various maneuvers are commonly used to achieve the ideal operative field necessary for successful endoscopic sinus surgery (ESS). There are a few contradictory reports on this subject and the consensus is that propofol anesthesia results in a better or similar surgical field and less or similar amount of bleeding than volatile anesthesia. The aim of this study was to compare the surgical field in patients in whom intravenous anesthesia is used as opposed to balanced general anesthesia. Methods Sixty patients undergoing ESS were randomly assigned into three groups, each of which used a different type of anesthesia: propofol/remifentanil (PRO/REM) group, sevoflurane/remifentanil (SEV/REM) group, and desflurane/remifentanil (DES/REM) group. We aimed to maintain the intraoperative mean blood pressure (MBP) at 65 mmHg and the heartrate (HR) at about 75 beats per minute. The quality of visibility of the surgical field was graded, using a validated scoring system, 60 minutes after the start of the operation. Results All groups had a similar MBP and mean HR at 60 minutes after the operation started. There was no significant differences among the three groups for surgical grade score (P = 0.83). Conclusions In this comparative study of three anesthetic combinations (PRO/REM, SEV/REM, and DES/REM) in patients undergoing ESS with controlled BP and HR, we did not observe any significant differences in the surgical grade scores.
Protective effects of glucosamine on oxidative-stress and ischemia/reperfusion-induced retinal injury.

PURPOSE To investigate the protective effects of glucosamine (GlcN) using oxidative stress and rat models of ischemia-reperfusion (I/R) injury and to determine the antiapoptotic and anti-inflammatory mechanisms of GlcN treatment. METHODS We determined the effects of GlcN and the levels of O-linked N-acetylglucosamine (O-GlcNAc) in in vitro retinal ganglion cells (RGCs) treated with or without H₂O₂. The survival and apoptosis rates of RGCs were compared after the addition of GlcN, glucose, or O-(2-acetamido-2-deoxy-Dglucopyranosylidene) amino-N-phenylcarbamate (PUGNAc). Retinal I/R injury was induced in Sprague-Dawley rats by elevating the IOP to 110 mm Hg for 60 minutes. An intraperitoneal injection of GlcN (1000 mg/kg) or normal saline was administered in the different groups, including a control group, a GlcN group, an I/R group, a GlcN+I/R group (1000 mg/kg GlcN 24 hours before I/R injury), and an I/R+GlcN group (7-day period of 1000 mg/kg GlcN 24 hours after I/R injury). The rats were killed 7 days after the I/R injury, and the retinas were collected from each rat for thickness measurements. Quantitative analysis of RGC survival was further determined using labeling with FluoroGold. RESULTS The GlcN increased levels of O-GlcNAc in a dose-dependent manner in the RGCs treated with or without H₂O₂. The GlcN resulted in increased cell survival and reduced apoptosis in the RGCs under oxidative stress conditions. In the rat model of I/R injury, GlcN significantly protected against I/R-induced retinal thinning and suppressed the I/R-induced reductions in a- and b-wave amplitudes of the ERG. In terms of RGC survival, significant incremental density of RGCs was found in the I/R+GlcN group compared with the I/R group. Notably, the use of GlcN in the rat retina decreased apoptosis and the formation of reactive oxygen species (ROS) after I/R injury. We also found that mitogen-activated protein kinase signal pathways played a critical role in the GlcN-mediated attenuation of ROS-induced damage in vitro and I/R injury in vivo. CONCLUSIONS Glucosamine treatment provides multiple levels of retinal protection, including antiapoptotic, anti-inflammatory, and antioxidative benefits. More research on the role of GlcN as a potential agent for the prevention and treatment of glaucoma is warranted.
A New Hybrid GMM/SVM for Speaker Verification

This paper proposes a new combination approach between Gaussian mixture model (GMM) and support vector machine (SVM) by feature extraction based on adapted GMM for SVM in text-independent speaker verification. Because of excellent scalability, adapted GMM was used to extract a small quantity of typical feature vectors from large numbers of speech data for SVM speaker verification. Using this new combination approach, our speaker verification system performed significantly better than the current state-of-the-art GMM-UBM system on the NIST'04 Iside-Iside database
A novel two-port 6T CMOS SRAM cell structure for low-voltage VLSI SRAM with single-bit-line simultaneous read-and-write access (SBLSRWA) capability

This paper reports a two-port 6T CMOS SRAM cell structure for low-voltage VLSI SRAM with single-bit-line simultaneous read-and-write access (SBLSRWA) capability. With a unique structure connecting the source terminal of an NMOS device in the SRAM cell to the write word line, this SRAM cell can be used to provide SBLSRWA capability for 1V two-port VLSI SRAM as verified by SPICE results.
Making Data Mining Models Useful to Model Non-paying Customers of Exchange Carriers

Due to both limitations of technologies and the nature of the problems, data mining may not be able to solve a problem completely in a way as one wishes. When this happens, we need to first understand the actual need of business, characteristic of available partial solution, and then make compromises between the technology solution and business needs. A majority of the papers published in data mining conferences and journals seem to concentrate only on the success side of the story. In this paper, we discuss our experiences and the complete process from near failure to success when applying inductive learning techniques to predict non-paying customers of competitive local exchange carriers (CLEC’s), currently at 20%. Experiments with a number of stateof-the-art methods and algorithms found that most customers were labeled as paying on time. Cost-sensitive learning is not possible since the target company cannot define a cost-model. Finally, after discussing with the billing department, a compromised but still useful solution is to predict the probability that someone will default. The billing team can use the predicted score to prioritize collection efforts as well as to predict cash flow. We have found that two randomized decision tree ensemble methods (Fan’s random decision tree and a probabilistic extension of Breiman’s random forest) are consistently more accurate in posterior probability estimation than single decision tree based probability calibration methods. The software, both Fan’s RDT and probabilistic extension of random forest, as well as a longer version of this paper will be made available by the contacting author.
AXES-RESEARCH — A user-oriented tool for enhanced multimodal search and retrieval in audiovisual libraries

AXES, Access for Audiovisual Archives, is a research project developing tools for new engaging ways to interact with audiovisual libraries, integrating advanced audio and video analysis technologies. The presented prototype is targeted at academic researchers and journalists. The tool allows them to search and retrieve video segments through metadata, audio analysis, as well as visual concepts and similarity searches. Presented here is a user-based vision on the research-oriented tool provided by AXES.
Bilateral Asymmetry Detection in Digital Mammography Using B-Spline Interpolation

Digital mammography allows detection of breast abnormalities in early stage of breast cancer development. One of the abnormalities that may indicate breast cancer in its early stage is bilateral asymmetry. This paper presents computer-aided detection algorithm for bilateral asymmetry that uses B-spline interpolation for breast alignment. Alignment of the right and left breast is important step in computer-aided detection algorithm in order to allow comparison of corresponding points in right and left breast. Differential analysis of breasts is based on simple subtraction technique. The results are highlighted with color in each image and presented on a computer monitor thereby indicating radiologist the regions that need to have a second look and be further investigated. We found that our approach can be a very useful tool for radiologists in detection and diagnosis of bilateral asymmetry.
Designing Proxy Bidders for Online Combinatorial Auctions

The last few years have witnessed a high rate of growth in revenue from single-item online auctions popularized by eBay and similar websites. But implementations of online combinatorial auctions are rare because of the high cost incurred by the seller in solving the WDP, and the high participation and monitoring costs that have to be borne by the bidders. Recently, an incremental dynamic programming formulation for the WDP has made this problem more tractable when the number of items is not too large. In an effort to ease the burden of the bidder, we propose the use of a proxy agent that will bid on the bidder's behalf. In our algorithmic scheme, PRACA, a main process coordinates the activities of a number of autonomous proxy agents, one for each bidder, by means of signals. We derive some interesting theoretical results, and describe how we verified the operational correctness of PRACA.
Assessment of Light Environment Variability in Broadleaved Forest Canopies Using Terrestrial Laser Scanning

Light availability inside a forest canopy is of key importance to many ecosystem processes, such as photosynthesis and transpiration. Assessment of light availability and within-canopy light variability enables a more detailed understanding of these biophysical processes. The changing light-vegetation interaction in a homogeneous oak (Quercus robur L.) stand was studied at different moments during the growth season using terrestrial laser scanning datasets and ray tracing technology. Three field campaigns were organized at regular time intervals (24 April 2008; 07 May 2008; 23 May 2008) to monitor the increase of foliage material. The laser scanning data was used to generate 3D representations of the forest stands, enabling structure feature extraction and light interception modeling, using the Voxel-Based Light Interception Model (VLIM). The VLIM is capable of estimating the relative light intensity or Percentage of Above Canopy Light (PACL) at any arbitrary point in the modeled crown space. This resulted in a detailed description of the dynamic light environments inside the canopy. Mean vertical light extinction profiles were calculated for the three time frames, showing significant differences in light attenuation by the canopy between April 24 on the one hand, and May 7 and May 23 on the other hand. The proposed methodology created the opportunity to link these within-canopy light distributions to the increasing amount of photosynthetically active leaf material and its distribution in the considered 3D space.
Induction of nitric oxide synthase mRNA in coronary resistance arteries isolated from exercise-trained pigs.

The purpose of this study was to develop a method by which endothelial cell nitric oxide synthase (ecNOS) mRNA expression could be measured in single coronary resistance arteries and to test the hypothesis that ecNOS gene expression is upregulated by exercise training. Yucatan miniature swine were randomly assigned to exercise-trained (ET; n = 5) or sedentary (Sed; n = 4) groups for 16 wk. Individual coronary resistance arteries (50-100 μm) were dissected, frozen in liquid nitrogen, and homogenized in a LiCl buffer. mRNA was isolated from each vessel, and ecNOS gene expression was assessed using reverse transcriptase (RT)-polymerase chain reaction (PCR) standardized by coamplifying ecNOS with glyceraldehyde 3-phosphate dehydrogenase (GAPDH). The ecNOS-to-GAPDH amplicon ratio was significantly greater in coronary resistance arteries isolated from ET pigs than in Sed controls. On the basis of these data, it is concluded that RT-PCR can be used on single coronary resistance arteries to assess cell-specific mRNA expression and that ecNOS gene expression is upregulated by exercise training in porcine coronary resistance arteries.
Evaluate fire behavior GRP panel

A series of experiments were conducted to study the fundamental fire and thermal properties of glass-reinforced polyester (GRP) panel material. Both bench-scale and room-scale tests were performed. The GRP was characterized using TGA, DSC, and cone calorimetry. Several predicting models, such as heat release index model, FO-categories model, and minimum energy release rate for flashover model, were used to classify the GRP and forecast the flashover time based on the test results in the cone calorimeter at 50 kW/m2 irradiance. Four experiments were conducted in GRP panels lined ISO 9705 room with a small wooden crib as an ignition source. Flashover time and panel burning time was compared with model study and thermal analysis results.
Blind Separation of Sources from Their Delayed Mixtures

We give a near real-time algorithm for the blind separation of sources from mixtures of delayed sources. Many successful algorithms have been proposed for blind separation of instantaneous mixtures. For delayed mixtures only a few algorithms have been reported, and they assume only cross delays between mixed sources. Moreover, the weights and cross delays are updated in a batch mode, which is not suitable for real-time operation. The algorithm given here allows for delays of all the sources in the mixtures, which is necessary for most practical blind source separation problems. A near realtime procedure to update delays and weights is also proposed. Furthermore, in the presence of sensor noise, previously reported algorithms converge to incorrect cross delay values. This paper gives a wavelet based denoising method that significantly improves convergence to correct delays, thereby improving convergence to correct delays and weights.
Subversion of cellular functions by Listeria monocytogenes

Listeria monocytogenes is a Gram‐positive bacterium that is able to invade and multiply within eukaryotic cells. Its intracellular life‐cycle includes pathogen‐induced phagocytosis, lysis of the phagocytic vacuole, movement in the cytoplasmic environment, and a cell‐to‐cell spread mechanism. Many L. monocytogenes virulence factors have been studied in detail, certain of which subvert specific eukaryotic cell functions in order to favour infection. During entry, the invasion protein InlA takes advantage of the adhesion molecule E‐cadherin and the adherens junction machinery to adhere to target and invade polarized epithelial cells. Another invasion protein of the internalin family, InlB, subverts the signalling pathway of the hepatocyte growth factor receptor Met to induce endocytosis of the receptor and also to favour internalization of the bacteria in non‐polarized epithelial cells. Once inside the cell, the haemolysin of L. monocytogenes—the listeriolysin O or LLO—is secreted to lyse the phagocytic vacuole, and when the bacteria is freed in the cytoplasm, the activity of the LLO is in part regulated by the infected cell itself, taking advantage of the pH sensitivity of the LLO that leads to its inactivation in the neutral eukaryotic cell cytoplasm. Finally, to induce bacterial movement in the cytoplasm, the L. monocytogenes surface protein ActA mimics the activity of the eukaryotic WASP family of proteins to recruit to the bacteria the actin nucleation machinery required for actin polymerization and for the formation of the actin structures (called ‘actin comet tails’) that propel the parasite in the cytosol and help it to invade neighbouring cells. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Cocaine‐ or stress‐induced metaplasticity of LTP in the dorsal and ventral hippocampus

Despite the well documented role of the hippocampus in various modes of drug reinstatement behavior, the persisting effects of in vivo cocaine exposure on hippocampal synaptic plasticity are not sufficiently understood. In this report we investigated the effects of cocaine conditioning on long‐term potentiation (LTP) in the CA1 region of hippocampus along its septotemporal axis. Male Sprague‐Dawley rats experienced a behavioral protocol, in which locomotor activity was monitored in response to various conditioning treatments. LTP was measured in ex vivo slice preparations taken 1–2 weeks after the last behavioral session from the ventral (vH) and dorsal (dH) sectors of hippocampus. Unexpectedly, experiencing the minor intermittent stimuli of the behavioral protocol caused stress‐induced metaplastic changes in both vH (increased LTP) and dH (decreased LTP) in the saline conditioned rats relative to behaviorally naïve controls. These stress effects in the vH and dH were blocked by conditioning with either mineralocorticoid (spironolactone) or glucocorticoid (mifepristone) antagonists, respectively. Stress‐induced metaplasticity in the vH was also prevented by prior administration of the kappa opioid antagonist nor‐binaltorphimine. Cocaine conditioning induced locomotor sensitization and significantly increased LTP in the vH without causing significant change in LTP in the dH. Cocaine‐induced metaplasticity in the vH was prevented by co‐administration of the dopamine D2‐like antagonist eticlopride during cocaine conditioning, but not by co‐administration of the D1/5 antagonist SCH 23390. Our results suggest that the functional connectivity of hippocampus is altered by metaplastic triggers such as exposure to drugs of abuse and/or stressors, thereby shifting the efferent output of hippocampus from dH (cortical) toward vH (limbic) influenced circuits. © 2014 Wiley Periodicals, Inc.
Physical-Layer p-Cycles Adapted for Router-Level Node Protection: A Multi-Layer Design and Operation Strategy

We study an idea for efficient integrated protection of an IP over WDM network using the spare capacity of span-protecting p-cycles to provide protection against both optical link failures and router node failures in the IP/MPLS layer. Previously, networks using span-protecting p-cycles were designed from the point of view of a single-layer physical transport network. Also separately, it has been known how to plan capacity allocations to IP-layer logical links to support controlled levels of bandwidth oversubscription on transiting traffic flows through a failed router or ATM node. To address both failure types, however, it is unattractive to simply combine the two investments in added protection capacity. Accordingly, we have studied ways to plan a 100% span-restorable set of physical-layer p-cycles so that very high levels of transiting traffic flow can also be restored upon MPLS router node failure, with controlled worst-case oversubscription of LSP capacity allocations. In test cases it was found that the spare capacity provided by span-protecting p-cycles can provide a high level of node protection depending on the strategy used for exploring the p-cycle capacity. We think this leads to novel and efficient strategies for multi-service and multi-layer survivable traffic engineering and bandwidth management
Replica allocation for correlated data items in ad hoc sensor networks

To improve data accessibility in ad hoc networks, in our previous work we proposed three methods of replicating data items by considering the data access frequencies from mobile nodes to each data item and the network topology. In this paper, we extend our previously proposed methods to consider the correlation among data items. Under these extended methods, the data priority of each data item is de-fined based on the correlation among data items, and data items are replicated at mobile nodes with the data priority. We employ simulations to show that the extended methods are more efficient than the original ones.