Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-scale Asymmetries in the DNA of E . coli

Compositional asymmetries in circular bacterial chromosomes exist on a large-scale. Using a sliding window to take the average concentration of nucleotides across a length equal to one-half of the chromosome (~2.3 million characters), it is possible to to split the E. Coli genome into two distinct region: one with a bias in C concentration and the other with a bias in G concentration. This genome wide asymmetry is known as GC skew and is due to the two-stranded structure of the chromosome. What drives this difference in composition? How is it actualized in a given sequence? A generic method is presented using regular expressions and mutual information to find embedded structure in these two regions. This technique should be able to identify the still debated explanation of third codon position bias responsible for GC skew, but might also identify other possible explanations should they exist.
Sequential Bayesian Decision Making for Multi-Armed Bandit

Most approaches to multiple agent decision making, or single agent multi-action decisions, tacitly assume a stationary reward environment in which -greedy approaches can asymptotically give valid information regarding action-value policies. We extend this approach by taking a Bayesian methodology to multi-armed bandits in which natural balance between exploitation and exploration takes place. Crucially we do not collapse information until all unknowns can be integrated out together. Uncertainty at all levels is automatically incorporated into the decision process, occasionally resulting in decisions being made which differ from the standard maximum likelihood approach. This framework can be extended with ease to incorporate utility functions which combine expected future reward and penalise model ignorance as well as offering a game theoretic framework in which multiple agents interact.
Conservation of the Keap1-Nrf2 System: An Evolutionary Journey through Stressful Space and Time

The Keap1-Nrf2 system is an evolutionarily conserved defense mechanism against oxidative and xenobiotic stress. Its regulatory mechanisms, e.g., stress-sensing mechanism, proteasome-based regulation of Nrf2 activity and selection of target genes, have been elucidated mainly in mammals. In addition, emerging model animals, such as zebrafish, fruit fly and Caenorhabditis elegans, have been shown to have similar anti-stress systems to mammals, suggesting that analogous defense systems are widely conserved throughout the animal kingdom. Experimental evidence in lower animals provides important information beyond mere laboratory-confined utility, such as regarding how these systems transformed during evolution, which may help characterize the mammalian system in greater detail. Recent advances in genome projects of both model and non-model animals have provided a great deal of useful information toward this end. We herein review the research on Keap1-Nrf2 and its analogous systems in both mammals and lower model animals. In addition, by comparing the amino acid sequences of Nrf2 and Keap1 proteins from various species, we can deduce the evolutionary history of the anti-stress system. This combinatorial approach using both experimental and genetic data will suggest perspectives of approach for researchers studying the stress response.
Phase I study of chimeric anti-CD20 monoclonal antibody in Chinese patients with CD20-positive non-Hodgkin's lymphoma

Objective: This study was designed to determine the safety, pharmacokinetics and biologic effects of a human-mouse chimeric anti-CD20 monoclonal antibody (SCT400) in Chinese patients with CD20-positive B-cell non-Hodgkin's lymphoma (CD20+ B-cell NHL). SCT400 has an identical amino acid sequence as rituximab, with the exception of one amino acid in the CH1 domain of the heavy chain, which is common in Asians. Methods: Fifteen patients with CD20+ B-cell NHL received dose-escalating SCT400 infusions (250 mg/m2: n=3; 375 mg/m2: n=9; 500 mg/m2: n=3) once weekly for 4 consecutive weeks with a 24-week follow-up period. The data of all patients were collected for pharmacokinetics and pharmacodynamics analyses. Results: No dose-limiting toxicities were observed. Most drug-related adverse events were grade 1 or 2. Two patients had grade 3 or 4 neutropenia. Under premedication, the drug-related infusion reaction was mild. A rapid, profound and durable depletion of circulating B cells was observed in all dose groups without significant effects on T cell count, natural killer (NK) cell count or immunoglobulin levels. No patient developed anti-SCT400 antibodies during the course of the study. SCT400 serum half-life (T1/2), maximum concentration (Cmax) and area under the curve (AUC) generally increased between the first and fourth infusions (P<0.05). At the 375 mg/m2 dose, the T1/2 was 122.5±46.7 h vs. 197.0±75.0 h, respectively, and the Cmax was 200.6±20.2 g/mL vs. 339.1±71.0 g/mL, respectively. From 250 mg/m2 to 500 mg/m2, the Cmax and AUC increased significantly in a dose-dependent manner (P<0.05). Patients with a high tumor burden had markedly lower serum SCT400 concentrations compared with those without or with a low tumor burden. Of the 9 assessable patients, 1 achieved complete response and 2 achieved partial responses. Conclusions: SCT400 is well-tolerated and has encouraging preliminary efficacy in Chinese patients with CD20+ B-cell NHL.
Sentence Processing in Parkinson's Disease

Parkinson's disease (PD) is a neurodegenerative condition that is associated with the depletion of dopamine (DA)-containing neurons in specific brain regions. This article reviews one consequence of this defect-sentence comprehension difficulty in nondemented patients with PD. The first section describes the pattern of cognitive deficits seen in patients with PD, focusing specifically on their difficulties with language processing. Subsequent sections relate the profile of cognitive impairments in PD to studies investigating compromised DA metabolism in fronto-striatal brain regions. The findings suggest that the sentence comprehension deficit in PD is due in large part to limitations in the strategic distribution of cognitive resources such as selective attention that contribute to the processing of complex material. The physiological basis for this deficit appears to be associated with the disruption of a fronto-striatal cerebral network that is compromised following degradation of the DA projection system.
Capacity Evaluation of a Multi-Hop Wireless Ad hoc Network Using Minimum Impact Routing

We measure and evaluate the capacity of an asymmetric multi-hop wireless ad hoc network from a new perspective using minimum impact routing, which selects a route based on total interference impact measured with total disturbed nodes along an asymmetrical transmission path. Wireless nodes use this local interference measure as the threshold to adjust the variable transmit power in order to achieve optimal number of relays and spatial reuse, hence reducing the impact of multi-hop interference and relaying on capacity. Our result shows minimum impact routing coupled with variable transmit power that optimizing spatial reuse has a significant reduction in total disturbed nodes compared with shortest-path routing, furthermore a dramatic impact on network capacity performance
Speed and Texture: An Empirical Study on Optical-Flow Accuracy in ADAS Scenarios

Increasing mobility in everyday life has led to the concern for the safety of automotives and human life. Computer vision has become a valuable tool for developing driver assistance applications that target such a concern. Many such vision-based assisting systems rely on motion estimation, where optical flow has shown its potential. A variational formulation of optical flow that achieves a dense flow field involves a data term and regularization terms. Depending on the image sequence, the regularization has to appropriately be weighted for better accuracy of the flow field. Because a vehicle can be driven in different kinds of environments, roads, and speeds, optical-flow estimation has to be accurately computed in all such scenarios. In this paper, we first present the polar representation of optical flow, which is quite suitable for driving scenarios due to the possibility that it offers to independently update regularization factors in different directional components. Then, we study the influence of vehicle speed and scene texture on optical-flow accuracy. Furthermore, we analyze the relationships of these specific characteristics on a driving scenario (vehicle speed and road texture) with the regularization weights in optical flow for better accuracy. As required by the work in this paper, we have generated several synthetic sequences along with ground-truth flow fields.
Defects in Hemopoietic Stem Cell Activity in Ikaros Mutant Mice

Here we provide evidence that the Ikaros family of DNA binding factors is critical for the activity of hemopoietic stem cells (HSCs) in the mouse. Mice homozygous for an Ikaros null mutation display a >30-fold reduction in long-term repopulation units, whereas mice homozygous for an Ikaros dominant negative mutation have no measurable activity. The defect in HSC activity is also illustrated by the ability of wild-type marrow to repopulate unconditioned Ikaros mutants. A progressive reduction in multipotent CFU-S14 (colony-forming unit-spleen) progenitors and the earliest erythroid-restricted precursors (BFU-E [burst-forming unit-erythroid]) is also detected in the Ikaros mutant strains consistent with the reduction in HSCs. Nonetheless, the more mature clonogenic erythroid and myeloid precursors are less affected, indicating either the action of a compensatory mechanism to provide more progeny or a negative role of Ikaros at later stages of erythromyeloid differentiation. In Ikaros mutant mice, a decrease in expression of the tyrosine kinase receptors flk-2 and c-kit is observed in the lineage-depleted c-kit+Sca-1+ population that is normally enriched for HSCs and may in part contribute to the early hemopoietic phenotypes manifested in the absence of Ikaros.
A Partial Taxonomy of Knowledge about Actions

An incomplete taxonomy is proposed for the knowledge of actions a computer must have if it is to understand stories about people performing these actions. The classification is along two dimensions, Force - why a person should follow the rule, and Form - what the rule looks like. Four kinds of force are distinguished, Strict, Social, Suggested,and Regulatory, while six forms are distinguished, Subactions, Substates, Side Conditions, Methods, Time Orderings, and Do-Whiles. For the most part it seems that any force type may combine with any form type in producing a rule. One example, how to use an umbrella, is examined in detail although facts about many human activities, from playing bridge to washing one's hair, are used as examples.
Measuring how far a controllable system is from an uncontrollable one

The main goal of this note is to explore some of the properties of a controllable system which, in a precise sense to be defined, is near an uncontrollable pair. To do this, we first discuss the notion of the distance between a controllable system and the nearest uncontrollable one in both real and complex cases [2]-[5]. When this distance is relatively small, we show to what extent this distance corresponds to certain properties of the uncontrollability matrix and the reachability Grammian.
Square Roots of Total Boolean Matrices: Enumeration Issues

This paper studies the square roots of total Boolean matrices. The basic matrices are introduced and it is proved that all the square roots of the total Boolean matrix can be constructed from the basic ones. Next the basic matrices of order 2, 3, 4, 5 are enumerated and they are connected with directed graphs. Finally some issues are discussed concerning applications of self-organization and routing in wireless sensor networks.
Cavity opening by a giant planet in a protoplanetary disc and effects on planetary migration

We study the effect of a Jovian planet on the gas distribution of a protoplanetary disc, using a new numerical scheme that allows us to take into consideration the global evolution of the disc, down to an arbitrarily small inner physical radius. We find that Jovian planets do not open cavities in the inner part of the disc (i.e. interior to their orbits) unless (a) the inner physical edge of the disc is close to the planet’s location or (b) the planet is much more massive than the disc. In all other cases the planet simply opens a gap in the gas density distribution, whose global profile is essentially unchanged relative to the one that it would have if the planet were absent. We recognize, though, that the dust distribution can be significantly different from the gas distribution and that dust cavities might be opened in some situations, even if the gas is still present in the inner part of the disc. Concerning the migration of the planet, we find that classical type II migration (with speed proportional to the viscosity of the disc) occurs only if the gap opened by the planet is deep and clean. If there is still a significant amount of gas in the gap, the migration of the planet is generally slower than the theoretical type II migration rate. In some situations, migration can be stopped or even reversed. We develop a simple model that reproduces satisfactorily the migration rate observed in the simulations, for a wide range of disc viscosities and planet masses and locations relative to the inner disc edge. Our results are relevant for extrasolar planetary systems, as they explain (a) why some hot Jupiters did not migrate all the way down to their parent stars and (b) why the outermost of a pair of resonant planets is typically the most massive one.
Load Balancing By Using Paging Technique for Cellular Network

: Practical load balancing framework that improves upon existing strategies. These techniques are portable to a broad range of prevalent architectures, including massively parallel machines as well as a task selection mechanism that can preserve or improve communication locality. To provide a multiple coverage area, the different tiers are associated with each cell. Each mobile terminal can be paged in any tier of a multi tier hierarchical cellular network. Paging requests are balanced in different waiting queues of different tiers, and the load balancing among them is achieved probabilistically among n tiers. In the process of paging schemes are the hierarchical pipeline paging scheme, the hierarchical sequential paging scheme, and the hierarchical blanket paging scheme can be apply to minimize the delay constraint and paging cost.
Efficient Top-K Fuzzy Interactive Query Expansion While Formulating a Query: From a Performance Perspective

Interactive query expansion and fuzzy search are two efficient techniques for assisting a user in an information retrieval process. Interactive query expansion helps the user refine a query by giving suggestions on how a query might be extended to further specify the actual information need of the user. Fuzzy search, on the other hand, supports the user by including results for terms that approximately equals the query string. This avoids reformulating queries with slight misspellings and will retrieve results for indexed terms not spelled as expected. This study will look at the performance aspects of combining these concepts to give the user real time suggestions on how to complete query as the query is formulated letter by letter. These suggestions will be a set of terms from the index that are fuzzy matches of the query string terms, and are chosen based on the individual rank of the term, the semantic correlation between the individual term and the edit distance between the query and the suggestion. The combination of these techniques is challenging from a performance aspect because each of them requires a lot of computation, and their relationship is such that these computations will be multiplicative when combined. Giving suggestions letter by letter as the user types requires a lookup for each letter and fuzzy search will expand each of these lookups with the fuzzy matches of the prefix to match against the index. For each of these different completions of the fuzzy matched prefixes, we will need to calculate the semantic correlation it has to the previous matched terms. This study will present three algorithms to give top-k suggestions for the single term case and then extend these in three ways to handle multi term queries. These algorithms will use a trie based term index with some extensions to enable fast lookup of top-k terms that match a given prefix and to assess the semantic correlation between the terms in the suggestion. The performance review will demonstrate that our approach will be viable to use for presenting the user with suggestions in real time even with a fairly large number of terms.
Validación de instrumentos para la medición de Resiliencia y Síndrome de Burnout en estudiantes del programa de Ingeniería Industrial de la Universidad de Córdoba

El Síndrome Burnout y la resiliencia son temas muy tratados en la actualidad, el primer concepto es un factor de riesgo psicosocial habitual en la sociedad y el segundo es la capacidad de superar positivamente las adversidades. El objetivo principal del estudio es validar las características psicométricas de los instrumentos Maslach Burnout Inventory – Student Survey (MBI-SS) y Connor – Davindson Scale 10 itmes (CD-RISC 10), en estudiantes de Ingeniería Industrial de la Universidad de Córdoba, obteniendo como resultado la validación psicométrica. Palabras clave: Burnout académico, resiliencia académica, validez de características psicométricas ABSTRACT:
Application Of Polymer-Coated Magnetic Nanoparticles For Oil Separation

Large oil spills and oily wastewater discharges from ships and industrial activities can have serious impacts on the environment with potentially major economic impacts. Current oil remediation techniques are inefficient and may have deleterious environmental consequences. However, nanotechnology offers a new route to potentially remediate oil pollution. In this study, a cheap and facile hydrothermal method was developed to synthesize polyvinylpyrrolidone-coated magnetite nanoparticles to separate a reference MC252 oil from oil–water mixture under environmentally relevant conditions. Fluorescence and Proton nuclear magnetic resonance spectroscopy results showed near 100% oil removal from oil–water mixture in the ultrapure water under optimum condition. Based on gas chromatography–mass spectrometry data, approximately 100% of lower molecular mass alkanes (C9–C21) were removed within 10 min of magnetic separation and by increasing the separation time to 40 min, greater than 67% of C22–25 alkanes were removed. Moreover, nanoparticles removed near 100% oil from synthetic seawater solutions in the presence and absence of fulvic acid showing excellent oil removal capacity of the nanoparticles under different conditions. Results show that these nanoparticles can be utilized to remove oil over a short time with a high removal efficiency under environmentally relevant conditions.
State Justification Using Genetic Algorithms in Sequential Circuit Test Generation

Complex VLSI circuits impose constraints on a test generator which are very difficult to handle using deterministic algorithms. Thus, a major goal in de­ veloping a new test generator is to have the capability of handling constraints, but without sacrificing the performance and effectiveness of deterministic ap­ proaches. In this paper, we describe a hybrid sequential circuit test generator which combines deterministic algorithms for fault excitation and propagation with genetic algorithms for state justification. The hybrid test generator re­ stricts state justification for complex circuits to the genetic approach, which is better able to handle constraints. High fault coverages were obtained for the ISCAS89 sequential benchmark circuits and several synthesized circuits, and in many cases the results are better than those for purely deterministic approaches. Results were further augmented by preceding the hybrid test generation by a fast run of simulation-based test generation controlled by a genetic algorithm. T h is research was supported in part by ARPA under Contract DABT63-95-C-0069, in part by the Semiconductor Research Corporation under Contract SRC 94-DP-109, and in part by Hewlett-Packard under an equipment grant.
Steganography and Broadcasting

Informally, steganography is the process of exchanging a secret message between two communicating entities so that an eavesdropper may not know that a message has been sent. After a review of some steganographic systems, we found that these systems have some defects. First, there are situations in which some concealment algorithms do not properly hide a secret message. Second, to conceal one bit of a secret message, some ask at least five documents and make at least two sampling operations, thus increasing their run-times. Considering the different ways to communicate with the receiver, we propose two steganographic systems adapted to the email communication whose algorithms are deterministic. To hide one bit of a secret message, our steganographic systems need only one document and performs one sampling operation and therefore significantly reduces the run-time.
SWAPART : Synthetic Object Creation by Part Substitution

An artistic, semi-automatic modeling scheme, called SWAPART, is presented. It allows a user to swap parts of existing geometry using similarly-looking geometry. The new scheme, which can be viewed as a computerized analogy of the traditional art technique known as assemblage, draws heavily on recent results in the area of 3D geometric search engines, and is geared toward novice or artistic end-users. Given a 3D model that the user may obtain from any source, a novice end-user can extract different parts from the model and query a server that holds information about a large database of 3D parts for possible substitutions. The end-user works in an interactive client environment that provides the needed interaction capabilities and the transparent server connections. The output geometry (with the selected substituting parts) is a 3D model that can be further processed by any computer graphics tool, including this client-server system.
Presence of a bi-directional S phase-specific transcription regulatory element in the promoter shared by testis-specific TH2A and TH2B histone genes

During mammalian spermatogenesis, somatic histones are replaced by testis-specific variants. The synthesis of the variants occurs primarily in the germ cells undergoing meiosis in the absence of DNA replication. We have cloned the genes encoding rat somatic and testis-specific H2A (TH2A) histones. The two genes share 300 bp of 5' upstream region with respective H2B genes: somatic H2A with somatic H2B and testis-specific TH2A with testis-specific TH2B gene. The deduced amino acid sequences show that H2A and TH2A histones have eight amino acid differences in the first half of the molecules and three consecutive changes in the C-terminal region. TH2A gene is expressed only in testis. Although synthesis of TH2A and TH2B histones is independent of DNA replication and insensitive to inhibitors of DNA synthesis in testis, the regulatory region shared by the two genes contain a bi-directional S phase-specific transcription regulatory element. In addition, TH2A gene, like TH2B gene, contains the consensus sequence element in the 3' non-coding region which is involved in the S phase-specific stabilization of histone mRNA.