Miracle-dz/UniFAR-FTUs huggingface dataset:
Measures of Compositional Strand Bias Related to Replication Machinery and its Applications

The compositional asymmetry of complementary bases in nucleotide sequences implies the existence of a mutational or selectional bias in the two strands of the DNA duplex, which is commonly shaped by strand-specific mechanisms in transcription or replication. Such strand bias in genomes, frequently visualized by GC skew graphs, is used for the computational prediction of transcription start sites and replication origins, as well as for comparative evolutionary genomics studies. The use of measures of compositional strand bias in order to quantify the degree of strand asymmetry is crucial, as it is the basis for determining the applicability of compositional analysis and comparing the strength of the mutational bias in different biological machineries in various species. Here, we review the measures of strand bias that have been proposed to date, including the ∆GC skew, the B1 index, the predictability score of linear discriminant analysis for gene orientation, the signal-to-noise ratio of the oligonucleotide bias, and the GC skew index. These measures have been predominantly designed for and applied to the analysis of replication-related mutational processes in prokaryotes, but we also give research examples in eukaryotes.
An efficient data replication method for data access applications in vehicular ad-hoc networks

Due to the high vehicle mobility, the topology of vehicular ad hoc networks (VANETs) dynamically changes, and disconnections may frequently occur. When two vehicles are disconnected, they are not able to access data from each other. Data replication has been widely used to reduce the effect of intermittent connectivity and improve data access performance in distributed systems. However, many nodes in VANET may only have limited storage space, and thus cannot replicate all the data such as large music files or video clips. To address this problem, we propose an efficient data replication method for data access applications in VANETs. In this method the vehicles are grouped into a platoon and they contribute part of their buffers to replicate data for others in the same platoon and share data with them. When a vehicle leaves the platoon, it prefetches interested data and transfers its buffered data to other vehicles in advance so that they can still access the data after it leaves. We implement this algorithm in NS-2 and GrooveNet Simulators. The GroveNet Simulator is used to generate the vehicle mobility trace file, which is used in the ns-2 simulations. Extensive simulation results show that this method provides high data availability, low data access overhead, and low false alarm rate.
Fault Detection for Networked Control Systems Based on Wireless Sensor Networks

Focusing on a class of networked control systems built around wireless sensor networks (WSN), the controller and the actuator in systems are assumed to be time-driven and the clocks are fully synchronized. The observer based on discrete switched systems is designed to detect faults which occur in the system. Firstly, by studying the transmission characteristics of data with wireless sensor networks, the augmented fault observer is constructed, and the observer is equivalent to the discrete switched system. Secondly, based on Lyapunov stability theory, the stability condition of observer can be viewed as a linear matrix inequality and the stability of system is proved. When the system is normal, if the given inequality condition is satisfied, the observer system is stable. When a fault occurs, the observer can detect the fault by the rapid change of residue. Finally, an illustrative example is given to demonstrate the effectiveness of the proposed method. Copyright © 2013 IFSA.
Small Ruminant Nor98 Prions Share Biochemical Features with Human Gerstmann-Sträussler-Scheinker Disease and Variably Protease-Sensitive Prionopathy

Prion diseases are classically characterized by the accumulation of pathological prion protein (PrPSc) with the protease resistant C-terminal fragment (PrPres) of 27–30 kDa. However, in both humans and animals, prion diseases with atypical biochemical features, characterized by PK-resistant PrP internal fragments (PrPres) cleaved at both the N and C termini, have been described. In this study we performed a detailed comparison of the biochemical features of PrPSc from atypical prion diseases including human Gerstmann-Sträussler-Scheinker disease (GSS) and variably protease-sensitive prionopathy (VPSPr) and in small ruminant Nor98 or atypical scrapie. The kinetics of PrPres production and its cleavage sites after PK digestion were analyzed, along with the PrPSc conformational stability, using a new method able to characterize both protease-resistant and protease-sensitive PrPSc components. All these PrPSc types shared common and distinctive biochemical features compared to PrPSc from classical prion diseases such as sporadic Creutzfeldt-Jakob disease and scrapie. Notwithstanding, distinct biochemical signatures based on PrPres cleavage sites and PrPSc conformational stability were identified in GSS A117V, GSS F198S, GSS P102L and VPSPr, which allowed their specific identification. Importantly, the biochemical properties of PrPSc from Nor98 and GSS P102L largely overlapped, but were distinct from the other human prions investigated. Finally, our study paves the way towards more refined comparative approaches to the characterization of prions at the animal–human interface.
A Mixed Generative-Discriminative Based Hashing Method

Hashing methods have proven to be useful for a variety of tasks and have attracted extensive attention in recent years. Various hashing approaches have been proposed to capture similarities between textual, visual, and cross-media information. However, most of the existing works use a bag-of-words methods to represent textual information. Since words with different forms may have similar meaning, semantic level text similarities can not be well processed in these methods. To address these challenges, in this paper, we propose a novel method called semantic cross-media hashing (SCMH), which uses continuous word representations to capture the textual similarity at the semantic level and use a deep belief network (DBN) to construct the correlation between different modalities. To demonstrate the effectiveness of the proposed method, we evaluate the proposed method on three commonly used cross-media data sets are used in this work. Experimental results show that the proposed method achieves significantly better performance than state-of-the-art approaches. Moreover, the efficiency of the proposed method is comparable to or better than that of some other hashing methods.
A Practical Location-aided Energy-aware Routing Method for UWB-based Sensor Networks

In this paper, a practical location-aided routing method for sensor networks based on ultra-wideband (UWB) technique is proposed and evaluated. This method makes use of the positioning function of UWB and takes info account the energy consumption in the network. By modeling the property of energy consumption, we find that energy and quality-of-service (QOS) issues are greatly influenced by the route selected. Accordingly, a new routing algorithm is derived to search for energy-efficient routes that can support adequate QOS requirements. The simulation results have proved the advantages of this routing scheme
T L  C S C W S?

Sets play a key role in foundations of mathematics. Why? To what extent is it an accident of history? Imagine that you have a chance to talk to mathematicians from a far away planet. Would their mathematics be setbased? What are the alternatives to the set-theoretic foundation of mathematics? Besides, set theory seems to play a significant role in computer science, in particular in database theory and formal methods. Is there a good justification for that? We discuss these and some related issues. 1 Sets in Computer Science Quisani: I wonder why sets play such a prominent role in foundations of mathematics. To what extent is it an accident of history? And I have questions about the role of sets in computer science. ∗Partially supported by NSF grant DMS–0070723 and by a grant from Microsoft Research. Address: Mathematics Department, University of Michigan, Ann Arbor, MI 48109–1109, U.S.A. , ablass@umich.edu. This paper was written during a visit to Microsoft Research. Authors: Have you studied set theory? Q: Not really but I came across set theory when I studied discrete mathematics and logic, and I looked into Lévy’s book [38] years ago. I remember that ZFC, first-order Zermelo-Fraenkel set theory with the axiom of choice, became for all practical purposes the foundation of mathematics. I can probably reconstruct the ZFC axioms. A: Do you remember the intuitive model for ZFC. Q: Let me see. You consider the so-called cumulative hierarchy of sets. It is a transfinite hierarchy, so that you have levels 0 ,1, . , ω, ω + 1, . On the level zero, you have the empty set and possibly some atoms. On any other level α you have the sets of objects that occur on levels < α. Intuitively the process never ends. To model ZFC, you just go far enough in this hierarchy so that all axioms are satisfied. Is that correct, more or less?
Speech , Music and Hearing Quarterly Progress and Status Report Parametric model of VT area functions : vowels and consonants

This is an extension of earlier work on vocal tract area function modelli ng (Fant, 1960, 1992, 1993; Lin, 1990) retaining a minimum of three independent control parameters in a more complex, physiologically oriented model providing a flexible choice of detail structure. Systematic perturbation analysis of vocal tract boundary conditions and of values of the independent control parameters have been carr ied out. These data supplement calculated transfer functions and nomograms of formant frequencies as a function of the place, Xc ,and the area, Ac, of a vocal tract constriction and the lip-parameter lo/Ao. Compensatory articulations providing almost the same formant frequency patterns with substantiall y different choice of control parameters are discussed. Additional vocal tract area function structures and control parameters for simulating consonantal articulations are introduced. Essential properties of laterals, nasals and retroflex articulations have been simulated Inversion experiments on steady state vowels have been successful but there remains to define and test possible constraints for the handling of variations in
Outcomes Linked to High-Quality Afterschool Programs: Longitudinal Findings from the Study of Promising Afterschool Programs

Summary A new study by researchers at the University of California, Irvine, the University of Wisconsin-Madison and Policy Studies Associates, Inc. finds that regular participation in high-quality afterschool programs is linked to significant gains in standardized test scores and work habits as well as reductions in behavior problems among disadvantaged students. These gains help offset the negative impact of a lack of supervision after school. The two-year study followed almost 3,000 low-income, ethnically diverse elementary and middle school students from eight states in six major metropolitan centers and six smaller urban and rural locations. About half of the young people attended high-quality afterschool programs at their schools or in their communities. Background on the Study The Study of Promising Afterschool Programs was designed to examine relations between high-quality afterschool programs and desired academic and behavioral outcomes for low-income students. The study was grounded in an assets orientation, which understands that all young people, including those living in poverty, have capacities to make healthy, positive choices if given the opportunity. The research team reviewed previous research on child and youth development in order to depict the processes that lead to positive student outcomes, as shown in Exhibit 1.
Food transport in the C. elegans pharynx

SUMMARY Pumping of the C. elegans pharynx transports food particles (bacteria) posteriorly. We examined muscle motions to determine how this posterior transport is effected. We find that the motions of the middle section of the pharynx, the anterior isthmus, are delayed relative to the anterior section, the corpus. Simulations in which particles are assumed to move at mean fluid velocity when not captured by the walls of the pharyngeal lumen show that delayed isthmus motions do indeed cause net particle transport; however, the amount is much less than in the real pharynx. We propose that the geometry of the pharyngeal lumen forces particles to the center, where they move faster than mean fluid velocity. When this acceleration is incorporated into the simulation, particles are transported efficiently. The transport mechanism we propose explains past observations that the timing of muscle relaxation is important for effective transport. Our model also makes a prediction, which we confirm, that smaller bacteria are better food sources for C. elegans than large ones.
Perinatal Cat and Dog Exposure and the Risk of Asthma and Allergy in the Urban Environment: A Systematic Review of Longitudinal Studies

Background. The literature is contradictory concerning pet exposure and the risk of development of asthma and other allergic diseases. Using longitudinal studies, we aimed to systematically review the impact of pet ownership in the critical perinatal period as a risk factor for allergies in childhood. Methods. Medline database was searched for urban cohort studies with perinatal exposure to cats and/or dogs and subsequent asthma or allergic disease. Results. Nine articles, comprising 6498 participants, met inclusion criteria. Six found a reduction in allergic disease associated with perinatal exposure to dogs or, cats or dogs. One study found no association. Two found increased risk only in high-risk groups. Conclusion. Longitudinal studies in urban populations suggest that perinatal pets, especially dogs, may reduce the development of allergic disease in those without a family history of allergy. Other unmeasured factors such as pet-keeping choices in allergic families may be confounding the association seen in these high-risk families, and further study is required.
Managed care for Brazil's banks

The focus on financial sector reform in emerging market economies often centers on the need to reduce government involvement in markets. Individual countries have taken many different approaches toward reaching this goal. In Brazil, financial sector reform has entailed the need for a large governmental role in structuring reforms, especially in the banking sector. This article explores a key aspect of Brazil's financial liberalization-the reform and opening of the domestic banking sector. ; Efforts to liberalize trade that began in the late 1980s and early 1990s in Brazil were hampered by economic and political concerns, chiefly inflation. The Real Plan, introduced in 1994, provided economic stabilization but did not automatically improve the outlook for the financial sector. Instead, policymakers were forced to initiate a managed restructuring of the private and public banking sectors. ; This article first discusses policy choices facing government decision makers in opening domestic financial sectors and then examines the basic features of Brazil's banking sector reform within the context of other changes and policy objectives taking place in Brazil. The author concludes that Brazil's banking reform promoted a sweeping reorganization of the banking sector and effectively averted a banking crisis. At the same time, deepening and consolidation of reform in the banking sector will remain incomplete until new legislation can be passed and fiscal reform is further advanced.
P2V and V2P communication for Pedestrian warning on the basis of Autonomous Vehicles

The use of smartphones in a road context by drivers and Vulnerable Road Users (VRU) is rapidly increasing. To reduce the risks related to the influence of smartphone usage in a situation where traffic needs to be considered, a collision prediction algorithm is proposed based on Pedestrian to Vehicle (P2V) and Vehicle to Pedestrian (V2P) communication technologies, which increases the visual situational awareness of VRU regarding the nearby location of both autonomous and manually-controlled vehicles in a user-friendly form. The proposed application broadcasts the device's position to the vehicles nearby, and reciprocally, the vehicles nearby broadcast their position to the device in use, supporting pedestrians and other VRU to minimize potential dangers and increase the acceptance of autonomous vehicles on our roads. Results regarding the evaluation of the proposed approach showed a good performance and high detection rate, as well as a high user satisfaction derived from the interaction with the system.
Elevated dNTP levels suppress hyper-recombination in Saccharomyces cerevisiae S-phase checkpoint mutants

MEC1, the essential yeast homolog of the human ATR/ATM genes, controls the S-phase checkpoint and prevents replication fork collapse at slow zones of DNA replication. The viability of hypomorphic mec1-21 is reduced in the rad52 mutant, defective in homologous recombination, suggesting that replication generates recombinogenic lesions. We previously observed a 6-, 10- and 30-fold higher rate of spontaneous sister chromatid exchange (SCE), heteroallelic recombination and translocations, respectively, in mec1-21 mutants compared to wild-type. Here we report that the hyper-recombination phenotype correlates with lower deoxyribonucleoside triphosphate (dNTP) levels, compared to wild-type. By introducing a dun1 mutation, thus eliminating inducible expression of ribonucleotide reductase in mec1-21, rates of spontaneous SCE increased 15-fold above wild-type. All the hyper-recombination phenotypes were reduced by SML1 deletions, which increase dNTP levels. Measurements of dNTP pools indicated that, compared to wild-type, there was a significant decrease in dNTP levels in mec1-21, dun1 and mec1-21 dun1, while the dNTP levels of mec1-21 sml1, mec1-21 dun1 sml1 and sml1 mutants were ∼2-fold higher. Interestingly, higher dNTP levels in mec1-21 dun1 sml1 correlate with ∼2-fold higher rate of spontaneous mutagenesis, compared to mec1-21 dun1. We suggest that higher dNTP levels in specific checkpoint mutants suppress the formation of recombinogenic lesions.
Sequential Test Generation Based on Preferred Primary Input Cubes

It was shown earlier that certain primary input values have a negative effect on the fault coverage of a functional test sequence when they appear repeatedly in the sequence. A gate-level sequential test generation procedure based on this observation computed a primary input cube <inline-formula> <tex-math notation="LaTeX">${c}$ </tex-math></inline-formula> with preferred values, and generated random functional test sequences that conformed to <inline-formula> <tex-math notation="LaTeX">${c}$ </tex-math></inline-formula> with a high probability <inline-formula> <tex-math notation="LaTeX">$ {0.5 \leq p < 1}$ </tex-math></inline-formula>. This procedure selected values for <inline-formula> <tex-math notation="LaTeX">${p}$ </tex-math></inline-formula> out of a set of possible values, and assigned the same value of <inline-formula> <tex-math notation="LaTeX">${p}$ </tex-math></inline-formula> to all the primary inputs. Motivated by the low computational complexity of this procedure, this paper addresses the selection of <inline-formula> <tex-math notation="LaTeX">${p}$ </tex-math></inline-formula> and the possibility of using different values of <inline-formula> <tex-math notation="LaTeX">${p}$ </tex-math></inline-formula> for different primary inputs. The goal is to increase the fault coverage and reduce the number of functional test sequences. The procedure described in this paper adjusts a functional test sequence to a circuit by complementing values that conflict with <inline-formula> <tex-math notation="LaTeX">${c}$ </tex-math></inline-formula>. The procedure requires fewer functional test sequences to reach or exceed the fault coverage of the earlier procedure for benchmark circuits. The procedure can be applied to any functional test sequence or set of functional test sequences.
A RBAC extended model and its application in unified access control for web application systems

On the basis of analyzing the access control demands of web application systems, this paper proposed an extended role-based access control model: RBAC4WAS, and gives the formal descriptions of the extended parts. At the same time this paper shows an application of RBAC4WAS and proposes a unified access control solution (UACS), discusses principles of UACS and its implement methods in detail.
Stability of tramadol with three 5-HT3 receptor antagonists in polyolefin bags for patient-controlled delivery systems

Background Mixing 5-hydroxytryptamine-3 (5-HT3) receptor antagonists with patient-controlled analgesia (PCA) solutions of tramadol has been shown to decrease the incidence of nausea and vomiting associated with the use of tramadol PCA for postoperative pain. However, such mixtures are not commercially available, and the stability of the drug combinations has not been duly studied. The study aimed to evaluate the stability of tramadol with three 5-HT3 receptor antagonists in 0.9% sodium chloride injection for PCA administration. Materials and methods Test samples were prepared by adding 1,000 mg tramadol hydrochloride, 8 mg ondansetron hydrochloride, and 6 mg granisetron hydrochloride or 5 mg tropisetron hydrochloride to 100 mL of 0.9% sodium chloride injection in polyolefin bags. The samples were prepared in triplicates, stored at either 25°C or 4°C for 14 days, and assessed using the following compatibility parameters: precipitation, cloudiness, discoloration, and pH. Chemical stability was also determined using a validated high-pressure liquid chromatography method. Results All of the mixtures were clear and colorless throughout the initial observation period. No change in the concentration of tramadol hydrochloride occurred with any of the 5-HT3 receptor antagonists during the 14 days. Similarly, little or no loss of the 5-HT3 receptor antagonists occurred over the 14-day period. Conclusion Our results suggest that mixtures of tramadol hydrochloride, ondansetron hydrochloride, granisetron hydrochloride, or tropisetron hydrochloride in 0.9% sodium chloride injection were physically and chemically stable for 14 days when stored in polyolefin bags at both 4°C and 25°C.
EXTRACTION AND TRACKING OF ORIENTATION CODED FEATURES BEING ROBUST AGAINST ILLUMINATION CHANGES

: We present a feature extraction and tracking method which is based on pure rich texture analysis and has robustness under irregular conditions, such as illumination change, deformation of objects and so on. The method is composed mainly of two algorithms: Entropy Filtering and Orientation Code Matching (OCM). Entropy ﬁlter points up areas of images being messy distribution of orientation codes. The orientation code is determined by detecting the orientation of maximum intensity change around neighboring eight pixels. The areas being extracted by the entropy ﬁlter doesn’t depend on edges and gradations of images and has robustness against illumination change and motion of objects. Therefore, we can say the areas have ”pure rich texture” and are suitable for tracking based on visual information. And then, OCM, a template matching method using the orientation code, is applied to track templates being centered on the features and updates the templates each frame. OCM is speeded up by using the information of texture richness and motion of objects. Because of their large robustness, we can track the templates robustly under irregular conditions.