Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamite: A Flexible Code Generating Language for Dynamic Programming Methods Used in Sequence Comparison

We have developed a code generating language, called Dynamite, specialised for the production and subsequent manipulation of complex dynamic programming methods for biological sequence comparison. From a relatively simple text definition file Dynamite will produce a variety of implementations of a dynamic programming method, including database searches and linear space alignments. The speed of the generated code is comparable to hand written code, and the additional flexibility has proved invaluable in designing and testing new algorithms. An innovation is a flexible labelling system, which can be used to annotate the original sequences with biological information. We illustrate the Dynamite syntax and flexibility by showing definitions for dynamic programming routines (i) to align two protein sequences under the assumption that they are both poly-topic transmembrane proteins, with the simultaneous assignment of transmembrane helices and (ii) to align protein information to genomic DNA, allowing for introns and sequencing error.
Approximate Explicit MPC and Closed-loop Stability Analysis based on PWA Lyapunov Functions

Model Predictive Control (MPC) is the de facto standard in advanced industrial automation systems. There are two main formulations of the MPC algorithm: an implicit one and an explicit MPC one. The first requires an optimization problem to be solved on-line, which is the main limitation when dealing with hard real-time applications. As the implicit MPC algorithm cannot be guaran- teed in terms of execution time, in many applications the explicit MPC solution is preferable. In order to deal with systems integrating mixed logic and dynam- ics, the class of the hybrid and piecewise affine models (PWA) were introduced and tackled by the explicit MPC strategy. However, the resulting controller complexity leads to a requirement on the CPU/memory combination which is as strict as the number of states, inputs and outputs increases. To reduce drasti- cally the complexity of the explicit controller while preserving the controller’s performance, a strategy combining switched MPC with discontinuous simpli- cial PWA models is introduced in this thesis. The latter is proven to be circuit implementable, e.g., in FPGA. To ensure that closed-loop stability properties are guaranteed, a stability analysis tool is proposed which exploits suitable and possibly discontinuous PWA Lyapunov-like functions. The tool requires solving offline a linear programming problem. Moreover, the tool is able to compute an invariant set for the closed-loop system, as well as ultimate boundedness and input-to-state stability properties.
Lexical Disambiguation in a Discourse Context

Les AA. examinent la maniere dont la structure du discours affecte le sens des mots et comment le sens des mots affecte la structure du discours. Ils integrent trois elements: = une theorie de la structure du discours appelee SDRT, qui represente le discours en termes de relations rhetoriques; = une theorie de l'attachement du discours appelee DICE, qui evalue les relations rhetoriques qui s'etablissent entre les constituants; = un langage formel pour la specification de la connaissance lexicale, aussi bien syntaxique que semantique, appele LKB
Efficient and Scalable Consistency Maintenance for Heterogeneous Peer-to-Peer Systems

Consistency maintenance mechanism is necessary for the emerging peer-to-peer applications due to their frequent data updates. Centralized approaches suffer single point of failure, while previous decentralized approaches incur too many duplicate update messages because of locality-ignorant structures. To address this issue, we propose a scalable and efficient consistency maintenance scheme for heterogeneous P2P systems. Our scheme takes the heterogeneity nature into account and forms the replica nodes of a key into a locality-aware hierarchical structure, in which the upper layer is DHT-based and consists of powerful and stable replica nodes, while a replica node at the lower layer attaches to a physically close upper layer node. A d-ary update message propagation tree (UMPT) is dynamically built upon the upper layer for propagating the updated contents. As a result, the tree structure does not need to be maintained all the time, saving a lot of cost. Through theoretical analyses and comprehensive simulations, we examine the efficiency and scalability of this design. The results show that, compared with previous designs, especially locality-ignorant ones, our approach is able to reduce the cost by about 25-67 percent.
Experimental investigation of psychophysiological stress-reactions induced by different system response times in human-computer interaction.

In human-computer interaction, system response times are considered to have important effects on operator performance and stress response. To evaluate the effects of short (2s) and long (8s), as well as constant and variable, system response times, a laboratory study was conducted with 68 subjects in four independent groups working at a simulated computer workplace. Subjects had to perform a simple detection and correction task at a visual display terminal in six trials of 20min each, the first being a training trial with identical conditions for all subjects. Performance and physiological measures (heart rate, electrodermal activity, and blood pressure) were taken during the trials, and subjective measures of mood and physical state as well as physiological measures were done in the resting periods iiftcr the trials. In addition to a general adaptation effect over the trials, experimental effects were shown mainly for the duration factor: subjects under conditions of long, as compared to those under shor.
Integrative Modeling of Mitochondrial Metabolism

We are in the process of constructing a kinetic model of mitochondrial metabolism including the electron transport (respiratory chain), the TCA cycle, the fatty acid metabolism (β oxidation), the inner-membrane metabolite carriers, the protein carriers, and the mitochondrial gene expression system. In this work, we report a model of these metabolic pathways that has been recently completed using the E-CELL system [2], a generic simulation environment for cellular simulation based on multiple ordinary differential equations.
A segmented iterative approach to estimation of the coherence spectrum from unevenly sampled sequences

We develop a non-parametric Capon-based magnitude squared coherence (MSC) estimator that utilizes a segmented reformulation of the recently introduced iterative adaptive approach (IAA) to provide high resolution MSC spectrum estimates. The proposed estimator, termed segmented-IAA-MSC (or SIAA-MSC, for short), allows for unevenly sampled data as well as for sequences with arbitrarily missing samples. The estimator first uses segmented-IAA to find accurate estimates of the auto- and cross-covariance matrices of the given sequences. These estimates are then used in a Capon-based MSC estimator reformulated to allow for non-uniformly sampled sequences. The proposed SIAA-MSC estimator is found to yield improved estimates as compared to the more commonly used least squares Fourier transform (LSFT) based MSC estimator.
On subspace-based methods for frequency estimation of random amplitude sinusoidal signals

Sinusoidal signals with random time-varying amplitude show up in many signal processing applications. Amplitude modulation results in degeneracy of the signal subspace, i.e. the signal subspace corresponding to one amplitude modulated sinusoid is no longer spanned by one vector. In this paper, we propose modifications of two subspace-based techniques, namely ESPRIT and MODE for estimating the center frequency of a sinusoidal signal with random time-varying ARMA amplitude. Numerical simulations illustrate the good performance of the methods. Finally, a robust scheme of the proposed methods is described and successfully applied to real radar data.
Shelf life of iceberg lettuce affected by hydro cooling and temperature of storage

Pre cooling is applied to remove the field heat of harvested horticultural produces. The goal of this work was to determine the cooling curve and the effects of hydro cooling on quality and shelf life of iceberg lettuce ‘Lucy Brown’ stored at 5°C and 22°C. Through shelf life, it was determined the changes on accumulated fresh weight loss, leaf relative water content and total chlorophyll, total soluble sugars, reducing and non-reducing sugars, and starch. The field heat from iceberg lettuce heads was removed within the first 10 min when submerged into cooled water at 4°C. Hydro cooled lettuce heads accumulated water over the leaf surfaces resulting in higher rate of fresh weight loss during storage when compared to control. Lettuce stored at 5°C kept higher relative water content in the leaves throughout the shelf life. Hydro cooling treatment delayed the wilting of the external leaves in three and two days when stored at 5 and 22°C, respectively. Hydro cooling did not influence the decrease on total soluble sugars, reducing sugars, non-reducing sugars and starch throughout shelf life, but affected the leaf chlorophyll content. Independent of the temperature in which the ‘Lucy Brown’ iceberg lettuce will be stored, hydro cooling is recommended to prolong quality and shelf life.
A Roadmap to Proliferate Open Source Software Usage within SA Government Servers

Open source software (OSS) is increasingly being recognized by the government sector around the world as a viable choice to proprietary software, particularly in a number of areas of information technology (IT) such as on the network servers. In the OSS domain, it is perceived that OSS has the potential to deliver better value for money, high quality software, secure, flexible, stable and reliable network applications. The South African (SA) government acknowledges that OSS is a viable alternative to proprietary software especially on the servers. According to the data collected (survey) from various SA government departments and agencies, indications are that OSS is not fully implemented on the network servers, although the global trends indicate high usage of OSS within the network environment. The main aim of this paper is to propose a roadmap that can be used to aid SA ministries to increase OSS usage.
Localization of the structural gene for threonine dehydrogenase in Escherichia coli

The threonine dehydrogenase (tdh) gene of Escherichia coli, cloned within the plasmid pDR121, was inactivated in vitro by inserting a segment of DNA carrying the chloramphenicol acetyltransferase (cat) gene. The insertionally inactivated tdh gene was then transferred by homologous recombination into the E. coli chromosome by the procedure of Winans et al. (J. Bacteriol. 161:1219-1221, 1985). Mating experiments, followed by P1-mediated two- and three-point crosses, enabled us to localize tdh near min 81.2. The order with respect to known markers is mtl-cysE-tdh-pyrE.
Estimating labels from label proportions

Consider the following problem: given sets of unlabeled observations, each set with known label proportions, predict the labels of another set of observations, also with known label proportions. This problem appears in areas like e-commerce, spam filtering and improper content detection. We present consistent estimators which can reconstruct the correct labels with high probability in a uniform convergence sense. Experiments show that our method works well in practice.
A New Scheme for Information Hiding Based on Digital Images

Digital steganography is a kind of data security technique. In this paper, a new information hiding scheme was proposed. In this scheme, we embed secret message into still digital images based on (7,4) Hamming Code and Wet Paper Codes. It embeds seven secret bits into a pixel-group of seven cover pixels at a time at first, if that is unsuccessful, it embeds the first three secret bits into that pixel-group once again. The simulation experiments show that the proposed scheme can achieve high embedding efficiency and large embedding payload.
Spectral mixture analysis based citrus greening disease detection using satellite image of florida

The citrus industry in Florida is being threatened by some devastating diseases, one of which is called citrus greening, also known as Huanglongbing (HLB). Timely and location-specific detection and monitoring of the infected citrus trees are required for efficient disease control, while reducing risks of the disease being spread. Satellite images were used to detect citrus greening disease over large areas in this paper, because it has larger view scale and less costly compared to airborne hyperspectral (HS) and multispectral (MS) images. Firstly, normalized difference vegetation index (NDVI) was used to remove water and bare soil from the image. Then, support vector machine (SVM) was used to separate citrus groves from other natural vegetation. Two different endmember extraction methods, vertex component analysis (VCA) and iterated constrained endmember detection (ICE) were used to extract endmembers for soil, grass, HLB infected citrus trees, and healthy citrus trees from endmember candidates identified from a Landsat 5 Thematic Mapper (TM) image with the help of a WorldView-2 image. These endmembers were then used as an input of multiple endmember spectral mixture analysis (MESMA), in order to obtain the fraction map of the citrus trees. The results were compared and evaluated. It was demonstrated that there is a great potential for citrus greening disease detection using a satellite image.
Pre-Treatment Whole Blood Gene Expression Is Associated with 14-Week Response Assessed by Dynamic Contrast Enhanced Magnetic Resonance Imaging in Infliximab-Treated Rheumatoid Arthritis Patients

Approximately 30% of rheumatoid arthritis patients achieve inadequate response to anti-TNF biologics. Attempts to identify molecular biomarkers predicting response have met with mixed success. This may be attributable, in part, to the variable and subjective disease assessment endpoints with large placebo effects typically used to classify patient response. Sixty-one patients with active RA despite methotrexate treatment, and with MRI-documented synovitis, were randomized to receive infliximab or placebo. Blood was collected at baseline and genome-wide transcription in whole blood was measured using microarrays. The primary endpoint in this study was determined by measuring the transfer rate constant (Ktrans) of a gadolinium-based contrast agent from plasma to synovium using MRI. Secondary endpoints included repeated clinical assessments with DAS28(CRP), and assessments of osteitis and synovitis by the RAMRIS method. Infliximab showed greater decrease from baseline in DCE-MRI Ktrans of wrist and MCP at all visits compared with placebo (P<0.001). Statistical analysis was performed to identify genes associated with treatment-specific 14-week change in Ktrans. The 256 genes identified were used to derive a gene signature score by averaging their log expression within each patient. The resulting score correlated with improvement of Ktrans in infliximab-treated patients and with deterioration of Ktrans in placebo-treated subjects. Poor responders showed high expression of activated B-cell genes whereas good responders exhibited a gene expression pattern consistent with mobilization of neutrophils and monocytes and high levels of reticulated platelets. This gene signature was significantly associated with clinical response in two previously published whole blood gene expression studies using anti-TNF therapies. These data provide support for the hypothesis that anti-TNF inadequate responders comprise a distinct molecular subtype of RA characterized by differences in pre-treatment blood mRNA expression. They also highlight the importance of placebo controls and robust, objective endpoints in biomarker discovery. Trial Registration: ClinicalTrials.gov NCT01313520
A High Gain, High Power K-Band Frequency Doubler in 0.18 $\mu{\rm m}$ CMOS Process

A K-band frequency doubler with a current-reuse technique implemented using 0.18 μm CMOS process is presented in this letter. This frequency doubler exhibits a high conversion gain of -0.5 ~ -4.5 dB from 18 to 26 GHz with 0 dBm input drive power, and good fundamental rejection of 30 to 50 dB. The dc power consumption is 18.2 to 20.8 mW, and the chip size is 0.54 × 0.53 mm2. To the author's knowledge, this frequency doubler achieves the highest conversion gain and output power among all K-band CMOS frequency doublers to date.
Process-Oriented Non-intrusive Recovery for Sporadic Operations on Cloud

Cloud-based systems get changed more frequently than traditional systems. These frequent changes involve sporadic operations such as installation and upgrade. Sporadic operations may fail due to the uncertainty of cloud platforms. Each sporadic operation manipulates a number of cloud resources. The accessibility of resources manipulated makes it possible to build an accurate process model of the correct behavior for an operation and its desired effects. This paper proposes a non-intrusive recovery approach for sporadic operations on cloud, called POD-Recovery. POD-Recovery utilizes the above-mentioned process model of the operation. When needed, it triggers recovery actions based on the model through non-intrusive means, i.e., without modifying the code which implements the sporadic operation. POD-Recovery employs an efficient artificial intelligence (AI) planning technique for generating recovery plans. We implement POD-Recovery and evaluate it by recovering from faults injected into 920 runs of five representative sporadic operations.
The Gap Property in Doubling Metrics

We introduce the weak gap property as a variant of the gap property. We show that in any metric space of bounded doubling dimension, any directed graph whose vertex set S has size n and which satisfies the weak gap property has total weight O(wt(MST (S)) log n), where wt(MST (S)) denotes the weight of a minimum spanning tree of S. We show that 2-optimal TSP tours and greedy spanners satisfy the weak gap property. Parts of these notes are based on discussions with Hubert Chan, Anupam Gupta, and Giri Narasimhan, during the workshop Geometric Networks and Metric Space Embeddings, which was held in Dagstuhl (Germany) in November 2006.
Complete Identification Methods for the Causal Hierarchy

We consider a hierarchy of queries about causal relationships in graphical models, where each level in the hierarchy requires more detailed information than the one below. The hierarchy consists of three levels: associative relationships, derived from a joint distribution over the observable variables; cause-effect relationships, derived from distributions resulting from external interventions; and counterfactuals, derived from distributions that span multiple “parallel worlds” and resulting from simultaneous, possibly conflicting observations and interventions. We completely characterize cases where a given causal query can be computed from information lower in the hierarchy, and provide algorithms that accomplish this computation. Specifically, we show when effects of interventions can be computed from observational studies, and when probabilities of counterfactuals can be computed from experimental studies. We also provide a graphical characterization of those queries which cannot be computed (by any method) from queries at a lower layer of the hierarchy.
Long-Run Consequences of Labor Coercion: Evidence from Russian Serfdom

This paper examines the long-run consequences of Russian serfdom. We use novel data measuring the intensity of labor coercion at the district level in 1861. Our results show that a greater legacy of serfdom is associated with lower economic well-being today. We apply an IV strategy that exploits the transfer of serfs from monastic lands in 1764 to establish causality. Exploring mechanisms, we find a positive correlation between the earlier experience of serfdom and pre-Soviet urbanization and land inequality, with negative implications for human capital investment and agglomeration over the long-run.
Growth Comparison of Israeli Carp (Cyprinus carpio) to Different Breeding Combination

ABSTRACT The purpose of this study was to investigate the improvement of growth in Israeli carp (Cyprinus carpio), and the cross experiment was carried out with two strains of Israeli carp. Four combinations of Israeli carp from Jeonbuk fisheries farm and Songpu mirror carp from Heilong Jiang, China (KK; Jeonbuk ♀ × Jeonbuk ♂, KC; Jeonbuk ♀ × China ♂, CC; China ♀ × China ♂ and CK; China ♀ × Jeonbuk ♂) were developed and reared. Body length, body weight and condition factor were determined at 20, 40, 60 and 170 days post-hatch (DPH). The results showed that there were differences in growth rate of the four groups. Body length of four groups were CK > CC > KC > KK and body weight were CC > CK > KC > KK at 170 DPH. The growth perfomance of four groups were statistically significant difference (P<0.05). During the rearing, CC group had longer length and higher weight at 170 DPH compared to other three groups and also condition factor was highest in the CC group, but there was no significant difference in a survival rate. These results indicated that the growth performance mainly depended upon brooder combination but survival rate could not significantly affect brooder.
Assessing the Effectiveness of Drop Chain Footgear at Reducing Bottom Contact in the Newfoundland and Labrador Shrimp Trawler Fishery

This study compared the effectiveness of a reduced seabed impact footgear versus a traditional rockhopper footgear on identical bottom trawls targeting northern shrimp (Pandalus borealis) in Newfoundland and Labrador, Canada. The experimental trawl used in this study was designed to be low seabed impact through the reduction of contact area of the footgear by replacing traditional heavy rockhopper footgear with only a few drop chains lightly in contact with the seabed (i.e., drop chain footgear). Two variants of the experimental drop chain footgear (9-drop chain and 5-drop chain) were designed, evaluated in a flume tank to estimate contact area with the seabed, and then briefly tested at sea for engineering performance and catchability. Results from the flume tank tests were encouraging, demonstrating that the traditional and experimental trawls were similar in performance, but with the experimental drop chain footgears producing substantial reductions in the predicted contact area with the seabed. Comparative commercial fishing trials were then subsequently made with a total of five pairs of tows (10 tows) for the 9-drop chain and six pairs of tows (12 tows) for the 5-drop chain. Though only briefly tested at sea, the results revealed that the drop chain footgears were promising in both engineering and catch performance. Underwater video observations demonstrated that the drop chain trawling system, with greatly reduced bottom contact on the seabed, could help reduce potential disturbance of marine ecosystems, in particular minimizing encounters with snow crab (Chionoecetes opilio).
Entity-Focused Sentence Simplification for Relation Extraction

Relations between entities in text have been widely researched in the natural language processing and information-extraction communities. The region connecting a pair of entities (in a parsed sentence) is often used to construct kernels or feature vectors that can recognize and extract interesting relations. Such regions are useful, but they can also incorporate unnecessary distracting information. In this paper, we propose a rule-based method to remove the information that is unnecessary for relation extraction. Protein-protein interaction (PPI) is used as an example relation extraction problem. A dozen simple rules are defined on output from a deep parser. Each rule specifically examines the entities in one target interaction pair. These simple rules were tested using several PPI corpora. The PPI extraction performance was improved on all the PPI corpora.