Miracle-dz/UniFAR-FTUs huggingface dataset:
A user-friendly Hypercard interface for human linkage analysis

The availability of a large number of highly informative genetic markers has made human linkage analysis faster and easier to perform. However, current linkage analysis software does not provide an organizational database into which a large body of linkage data can be easily stored and manipulated. This manual entry and editing of linkage data is often time consuming and prone to typing errors. In addition, the large number of alleles in many of these markers must be reduced in order to perform linkage analysis with multiple loci across large genetic distances. This reduction in allele number is often difficult and confusing, especially in large pedigrees. We have taken advantage of the Macintosh-based Hypercard program to develop an interface with which linkage data can be easily stored, retrieved and edited. For each family, the components of the pedigree, including ID numbers, sex and affection status, only need to be entered once. The program (Linkage Interface) retrieves this information each time the data from a new polymorphic marker is entered. Linkage Interface has flexible editing capabilities that allow the user to change any portion of the pedigree, including the addition or deletion of family members, without affecting previously entered genotype data. Linkage Interface can also analyze both the pedigree and marker data and will detect any inconsistencies in inheritance patterns. In addition, the program can reduce the number of alleles for a polymorphic marker. Linkage Interface will then compare the 'reduced' data to the original marker data and assists in maintaining all informative meioses by pointing out which meioses have become non-informative. (ABSTRACT TRUNCATED AT 250 WORDS)
Iron Metallodrugs: Stability, Redox Activity and Toxicity against Artemia salina

Iron metallodrugs comprise mineral supplements, anti-hypertensive agents and, more recently, magnetic nanomaterials, with both therapeutic and diagnostic roles. As biologically-active metal compounds, concern has been raised regarding the impact of these compounds when emitted to the environment and associated ecotoxicological effects for the fauna. In this work we assessed the relative stability of several iron compounds (supplements based on glucoheptonate, dextran or glycinate, as well as 3,5,5-trimethylhexanoyl (TMH) derivatives of ferrocene) against high affinity models of biological binding, calcein and aprotransferrin, via a fluorimetric method. Also, the redox-activity of each compound was determined in a physiologically relevant medium. Toxicity toward Artemia salina at different developmental stages was measured, as well as the amount of lipid peroxidation. Our results show that polymer-coated iron metallodrugs are stable, non-redox-active and non-toxic at the concentrations studied (up to 300 µM). However, TMH derivatives of ferrocene were less stable and more redox-active than the parent compound, and TMH-ferrocene displayed toxicity and lipid peroxidation to A. salina, unlike the other compounds. Our results indicate that iron metallodrugs based on polymer coating do not present direct toxicity at low levels of emission; however other iron species (eg. metallocenes), may be deleterious for aquatic organisms. We suggest that ecotoxicity depends more on metal speciation than on the total amount of metal present in the metallodrugs. Future studies with discarded metallodrugs should consider the chemical speciation of the metal present in the composition of the drug.
Cyclic AMP mediated gene expression in bovine corneal endothelial cells.

PURPOSE Agents that increase intracellular levels of cAMP mediate gene expression associated with cellular morphology, growth, and/or differentiation via the cAMP response element (CRE). The cAMP element binding protein (CREB) is a transcriptional activator that binds and stimulates gene expression from the CRE in the promoters of cAMP responsive genes. This study was designed to characterize the cyclic AMP (cAMP) transcription apparatus in bovine corneal endothelial cells (BCE). METHODS CRE transcriptional activity was determined by transient transfection assays using the CRE-chloramphenicol acetyl transferase gene (CRE-CAT) fusion reporter construct. Western blot analyses were performed to determine whether CREB was present in BCE. Mobility shift DNA-binding assay using gel electrophoresis and DNase I protection assays were performed to exclude the possibility of other CRE-binding factors. RESULTS The authors identified the transcription factor, CREB, in nuclear extracts from BCE by Western blot analysis and showed that its DNA-binding characteristics are identical to the previously characterized CREB protein by DNase I protection and mobility shift DNA-binding studies. Transient transfection studies using the CRE-CAT reporter constructs revealed that the beta-adrenergic receptor agonist, isoproterenol, stimulates gene expression to levels similar to those induced by forskolin, a direct activator of adenylate cyclase (6.0- and 7.2-fold, respectively). CONCLUSIONS The results suggest that agents that modulate receptors coupled to adenylate cyclase may effect the corneal endothelium by altering gene expression through the second messenger, cAMP.
Keyword searching and browsing in databases using BANKS

With the growth of the Web, there has been a rapid increase in the number of users who need to access online databases without having a detailed knowledge of the schema or of query languages; even relatively simple query languages designed for non-experts are too complicated for them. We describe BANKS, a system which enables keyword-based search on relational databases, together with data and schema browsing. BANKS enables users to extract information in a simple manner without any knowledge of the schema or any need for writing complex queries. A user can get information by typing a few keywords, following hyperlinks, and interacting with controls on the displayed results. BANKS models tuples as nodes in a graph, connected by links induced by foreign key and other relationships. Answers to a query are modeled as rooted trees connecting tuples that match individual keywords in the query. Answers are ranked using a notion of proximity coupled with a notion of prestige of nodes based on inlinks, similar to techniques developed for Web search. We present an efficient heuristic algorithm for finding and ranking query results.
Efficient Semantic Video Annoation by Object and Shot Re-Detection

Manual video annotation on shot and on object level is a very time consuming and therefore cost intensive task. Automatic object and shot re-detection is one step forward in order to provide a cost efficient solution for temporally detailed video annotation. In this demonstration a tool will be shown which integrates novel video visualisation, navigation and interactive object re-detection techniques. Automatically re-detected objects and shots can be annotated by reusing operator annotations in a semi-automatic way. Object and shot re-detection capabilities are demonstrated on a variety of content, e.g. anchor person redetection in news content and setting and re-take detection in rushes content.
Flexural behaviour of RC beams strengthened With externally bonded (EB) FRP sheets or Near Surface Mounted (NSM) FRP rods method

Strengthening is a process of upgrading to increase the strength of structural components to carry additional loads. Strengthening methods include externally bonded (EB) Fiber Reinforced Polymer (FRP) plates, (or wet laid-up fabrics) and Near Surface Mounted (NSM) FRP rods. The present investigation study the enhancement in flexural performance of un-cracked RC beams strengthened with either a single ply or a 2-ply wet laid-up carbon fiber reinforced polymer (CFRP) fabric(s) or NSM glass fiber reinforced polymer (GFRP) rods. An identical RC beam in its un-strengthened form is used as the control. A series of RC beams of dimensions 170 mm width × 270 mm depth × 2325 mm length were tested to destruction under four point bending. The variables are the number of carbon plies in a wet laid-up scheme and the number of GFRP rods in a NSM scheme. The RC beams were designed to have excess reinforcement in shear to allow the beams to fail in bending. The flexural performance was assessed in terms of the enhancement in the ultimate load carrying capacity, load-deflection characteristic up to and beyond peak, initial stiffness, and strain development in the RC beams, due to the attached carbon fiber reinforced polymer (CFRP) sheets and GFRP rods. Test results show that the RC beams strengthened with two (2) NSM GFRP rods recorded the highest of about 88% increase in strength capacity over the control beam and 34% increase corresponding to those of strengthened with a GFRP rod. The strength capacity of the beam specimens strengthened with a rod and two (2) rods of NSM GFRP recorded an ultimate load of about 62% higher and 29% respectively than those beams strengthened with a layer and two (2) layers of EB CFRP sheets. The higher performance enhancing ability of the NSM strengthening scheme is therefore evident compared to that of the conventional and industry preferred wet laid up.
Poly(A) Tail Shortening by a Mammalian Poly(A)-specific 3′-Exoribonuclease*

3′-Exonucleolytic removal of the poly(A) tail is the first and often rate-limiting step in the decay of many eucaryotic mRNAs. In a cytoplasmic extract from HeLa cells, the poly(A) tail of mRNA was degraded from the 3′-end. In agreement with earlierin vivo observations, prominent decay intermediates differed in length by about 30 nucleotides. The Mg2+-dependent, poly(A)-specific 3′-exoribonuclease responsible for this poly(A) shortening activity was purified from calf thymus. A polypeptide of 74 kDa copurified with the activity. The deadenylating nuclease (DAN) required a free 3′-OH group, released solely 5′-AMP, degraded RNA in a distributive fashion, and preferred poly(A) as a substrate. At low salt concentration, the activity of purified DAN was strongly dependent on spermidine or other, yet unidentified factors. Under these reaction conditions, DAN was also stimulated by the cytoplasmic poly(A)-binding protein I (PAB I). At physiological salt concentration, the stimulatory effect of spermidine was weak and PAB I was inhibitory. At either salt concentration DAN and PAB I reconstituted poly(A) shortening with the same pattern of intermediates seen in cytoplasmic extract. The properties of DAN suggest that the enzyme might be involved in the deadenylation of mRNA in vivo.
Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi

We have identified a DNA methyltransferase of the Dnmt2 family in Dictyostelium that was denominated DnmA. Expression of the dnmA gene is downregulated during the developmental cycle. Overall DNA methylation in Dictyostelium is approximately 0.2% of the cytosine residues, which indicates its restriction to a limited set of genomic loci. Bisulfite sequencing of specific sites revealed that DnmA is responsible for methylation of mostly asymmetric C-residues in the retrotransposons DIRS-1 and Skipper. Disruption of the gene resulted in a loss of methylation and in increased transcription and mobilization of Skipper. Skipper transcription was also upregulated in strains that had genes encoding components of the RNA interference pathway disrupted. In contrast, DIRS-1 expression was not affected by a loss of DnmA but was strongly increased in strains that had the RNA-directed RNA polymerase gene rrpC disrupted. A large number of siRNAs were found that corresponded to the DIRS-1 sequence, suggesting concerted regulation of DIRS-1 expression by RNAi and DNA modification. No siRNAs corresponding to the standard Skipper element were found. The data show that DNA methylation plays a crucial role in epigenetic gene silencing in Dictyostelium but that different, partially overlapping mechanisms control transposon silencing.
Fast Detection of Dense Subgraphs with Iterative Shrinking and Expansion

In this paper, we propose an efficient algorithm to detect dense subgraphs of a weighted graph. The proposed algorithm, called the shrinking and expansion algorithm (SEA), iterates between two phases, namely, the expansion phase and the shrink phase, until convergence. For a current subgraph, the expansion phase adds the most related vertices based on the average affinity between each vertex and the subgraph. The shrink phase considers all pairwise relations in the current subgraph and filters out vertices whose average affinities to other vertices are smaller than the average affinity of the result subgraph. In both phases, SEA operates on small subgraphs; thus it is very efficient. Significant dense subgraphs are robustly enumerated by running SEA from each vertex of the graph. We evaluate SEA on two different applications: solving correspondence problems and cluster analysis. Both theoretic analysis and experimental results show that SEA is very efficient and robust, especially when there exists a large amount of noise in edge weights.
Evaluating Block Algorithm Variants in LAPACK

The LAPACK software project currently under development is intended to provide a portable linear algebra library for high performance computers. LAPACK will make use of the Level 1, 2, and 3 BLAS to carry out basic operations. A principal focus of this project is to im- plement blocked versions of a number of algorithms to take advantage of the greater parallelism and improved data locality of the Level 3 BLAS. In this paper, we describe our work with vari- ants of some of these algorithms and the performance data we have collected. LAPACK is planned to be a collection of Fortran 77 subroutines for the analysis and solution of systems of simultaneous linear algebraic equations, linear least-squares problems, and matrix eigenvalue problems (1). This project will combine the functionality of LINPACK and EISPACK in a single package, incorporate recent algorithmic improvements, and restructure the algorithms to use the Level 2 and 3 BLAS (Basic Linear Algebra Subprograms) for efficiency on today's high-performance computers. We are investigating variant versions of many of the rou- tines in LAPACK. The building blocks of the LAPACK library are the BLAS, a set of standard subroutines for the most common operations in linear algebra (2,3,4). The original set of BLAS, consisting of vector-vector operations, was used in LINPACK. Recently, specifications have been drawn up for matrix-vector operations (Level 2 BLAS) and matrix-matrix operations (Level 3 BLAS) to meet the demands of multiprocessing, vectorization, and hierarchical memory in today's high-performance computers. In particular, the Level 3 BLAS perform O (n 3 ) operations on O (n 2 ) data elements, which helps to improve the ratio of computation to memory references on machines that have a memory hierarchy. This paper describes some of the block factorization routines in LAPACK. The blocked version calls the Level 3 BLAS and, if necessary, an un- blocked version of the algorithm to do the processing within a block. The unblocked version calls only Level 1 and 2 BLAS routines and is called directly from the blocked routine if the user has set the blocksize to 1. The LU decomposition is derived by equating the product of a unit lower triangular matrix L and an upper triangular matrix U to the original matrix A. As an illus-
A Robust Appearance Model for Object Tracking

Patch strategy is widely adopted in visual tracking to address partial occlusions. However, most patch-based tracking methods either assume all patches sharing the same importance or exploit simple prior for computing the importance of each patch, which may depress the tracking performance when the target object is non-rigid or the background information is included in the initial bounding box. To this end, an importance-aware appearance model with respect to the target patches and background patches is built, which is able to adaptively evaluate the importance of each target/background patch by means of the local self-similarity. In addition, we propose a novel bi-directional multi-voting scheme, which integrates a multi-voting scheme and the two-side agreement scheme, to produce a reliable target-background confidence map. Combining the importance-aware appearance model and the bi-directional multi-voting scheme, a robust patch-based tracking method is proposed. Experimental results demonstrate that the proposed tracking method outperforms other state-of-the-art methods on a set of challenging tracking tasks.
Learning to Diffuse: A New Perspective to Design PDEs for Visual Analysis

Partial differential equations (PDEs) have been used to formulate image processing for several decades. Generally, a PDE system consists of two components: the governing equation and the boundary condition. In most previous work, both of them are generally designed by people using mathematical skills. However, in real world visual analysis tasks, such predefined and fixed-form PDEs may not be able to describe the complex structure of the visual data. More importantly, it is hard to incorporate the labeling information and the discriminative distribution priors into these PDEs. To address above issues, we propose a new PDE framework, named learning to diffuse (LTD), to adaptively design the governing equation and the boundary condition of a diffusion PDE system for various vision tasks on different types of visual data. To our best knowledge, the problems considered in this paper (i.e., saliency detection and object tracking) have never been addressed by PDE models before. Experimental results on various challenging benchmark databases show the superiority of LTD against existing state-of-the-art methods for all the tested visual analysis tasks.
X-Morphising: Review Essay of Bruno Latour's Aramis, or the Love of Technology

An extended review is presented of Bruno Latour's book Aramis, or the Love of Technology (Harvard University Press, 1996). Attention is paid to the textual style and strategies in the book, and also to how it fits in with, and exemplifies, many of the more abstract claims central to Latour's actor-network theory. In particular, consideration is given to the provocative arguments in the book about the status of nonhuman beings in social-scientific research, and to the specific manoeuvre whereby Aramis, this transportation project which never quite made it from being an idea to being a completed object, is accorded agency—and even a voice—in the text. The ‘x-morphising’ which underpins Aramis in this respect is examined, and is subsequently criticised for a flattening out of agency which permits humans and nonhumans to be regarded as ‘social’ equivalents. Although attracted to Latour's radical emancipation of nonhuman things from a social-scientific netherworld, we nonetheless conclude by worrying about the flat and undifferentiated ‘spatial imaginary’ at the heart of what he is attempting to do for actors of all kinds in Aramis.
Optical properties of crystalline Al203 thin films grown by atomic layer deposition

Atomic layer deposition of Al203 thin films on Si and Si02 substrates was investigated in the temperature range of 470- 1030 K. The films grown at 870-1030 K contained crystalline phase while those deposited at temperatures below 870 K were amorphous. The growth rate was 0.03 nm per cycle at 1030 K but it increased with decreasing temperature and reached 0.13 nm per cycle at 470 K. The densities of crystalline films were 3660-3670 kg/m3 while those of amorphous films ranged from 2820 to 3140 kg/m3. The refractive indices of crystalline films (1.75-1.77 at the wavelength of 500 nm) were significantly higher than the refractive indices of amorphous films. A disadvantage of crystalline films compared with amorphous films was somewhat higher surface roughness. Nevertheless, the extinction coefficient of the former films did not exceed 0.004 at the wavelength of 500 nm. Excitation of crystalline films at the wavelengths shorter than 175 nm resulted in a broadband photoluminescence peaking at 350-360 nm. The excitation spectrum indicated dominant excitation of this emission via interband transition. The intrinsic absorption edges of 7.2 and 6.6 eV were estimated for crystalline and amorphous films, respectively, from the long-wavelength edges of the excitation spectra measured at 10 K.
Molecular characterization of two cya mutations, cya-854 and cyaR1

The cya-854 mutation of Escherichia coli K-12 (E. Brickman, L. Soll, and J. Beckwith, J. Bacteriol. 116:582-587, 1973) has been shown to consist of a 200-base-pair deletion generating a new translation start that permits synthesis of the adenylate cyclase carboxy terminus. Contrary to expectations (C. Guidi-Rontani, A. Danchin, and A. Ullmann, J. Bacteriol. 148:753-761, 1981), cyaR1 results from the insertion of an IS1 element into the sequence coding for the catalytic center of the protein.
Applying the model driven generative domain engineering method to develop self-organizing architectural solutions for mobile robot

Model driven generative domain engineering (MDGDE) is a domain engineering method aiming to develop optimized, reusable architectures, components and aspects for application engineering. Agents are regarded in MDGDE as special objects having more autonomy, and taking more initiative. Design of the agent involves three levels of activities: logical analysis and design, physical analysis, physical design. This classification corresponds to domain analysis and design, application analysis, and application design. Agent is an important analysis and design tool for MDGDE because it facilitates development of complex distributed system—the mobile robot. According to MDGDE, we designed a distributed communication middleware and a set of event-driven agents, which enables the robot to initiate actions adaptively to the dynamical changes in the environment. This paper describes our approach as well as its motivations and our practice.
Glutamate and Choline Levels Predict Individual Differences in Reading Ability in Emergent Readers

Reading disability is a brain-based difficulty in acquiring fluent reading skills that affects significant numbers of children. Although neuroanatomical and neurofunctional networks involved in typical and atypical reading are increasingly well characterized, the underlying neurochemical bases of individual differences in reading development are virtually unknown. The current study is the first to examine neurochemistry in children during the critical period in which the neurocircuits that support skilled reading are still developing. In a longitudinal pediatric sample of emergent readers whose reading indicators range on a continuum from impaired to superior, we examined the relationship between individual differences in reading and reading-related skills and concentrations of neurometabolites measured using magnetic resonance spectroscopy. Both continuous and group analyses revealed that choline and glutamate concentrations were negatively correlated with reading and related linguistic measures in phonology and vocabulary (such that higher concentrations were associated with poorer performance). Correlations with behavioral scores obtained 24 months later reveal stability for the relationship between glutamate and reading performance. Implications for neurodevelopmental models of reading and reading disability are discussed, including possible links of choline and glutamate to white matter anomalies and hyperexcitability. These findings point to new directions for research on gene-brain-behavior pathways in human studies of reading disability.