Miracle-dz/UniFAR-FTUs huggingface dataset:
CAG repeat instability in a mouse model for myotonic dystrophy type 1 is associated with changes in cell nuclearity and DNA ploidy

Background: Trinucleotide instability is a hallmark of degenerative neurological diseases like Huntington's disease, some forms of spinocerebellar ataxia and myotonic dystrophy type 1 (DM1). To investigate the effect of cell type and cell state on the behavior of the DM1 CTG•CAG repeat, we studied a knock-in mouse model for DM1 at different time points during ageing and followed how repeat fate in cells from liver and pancreas is associated with polyploidization and changes in nuclearity after the onset of terminal differentiation. Results: After separation of liver hepatocytes and pancreatic acinar cells in pools with 2n, 4n or 8n DNA, we analyzed CTG•CAG repeat length variation by resolving PCR products on an automated PAGE system. We observed that somatic CTG•CAG repeat expansion in our DM1 mouse model occurred almost uniquely in the fraction of cells with high cell nuclearity and DNA ploidy and aggravated with aging. Conclusion: Our findings suggest that post-replicative and terminal-differentiation events, coupled to changes in cellular DNA content, form a preconditional state that influences the control of DNA repair or recombination events involved in trinucleotide expansion in liver hepatocytes and pancreatic acinar cells. Background Instability of CTG•CAG trinucleotide repeats forms an important class of mutations on an ever-growing list of inheritable degenerative neurological diseases, including Huntington's disease, several spinocerebellar ataxias (SCAs 1, 2, 3, 6, 7, 8, 12 and 17) and myotonic dystrophy type 1 (DM1) [1-3]. Depending on disease type, pathogenic mechanisms may vary, but all disorders have in common that the transition to illness appears to be a cellintrinsic process, which is initiated by intergenerational or somatic repeat expansion or both. Although substantial progress has been made by the study of expansion behavior and associated pathophysiological events in repeatcontaining bacterial and yeast model systems [4], translation of findings to the mammalian system is not easy and there is still disagreement over the contribution to CTG•CAG repeat expansion by new strand synthesis during DNA replication or DNA repair and recombination in Published: 23 July 2007 BMC Molecular Biology 2007, 8:61 doi:10.1186/1471-2199-8-61 Received: 12 October 2006 Accepted: 23 July 2007 This article is available from: http://www.biomedcentral. com/1471-2199/8/61 © 2007 van den Broek et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Legion: The Next Logical Step Toward a Nationwide Virtual Computer

The coming of giga-bit networks makes possible the realization of a single nationwide virtual computer comprised of a variety of geographically distributed high-performance machines and workstations. T o realize the potential that the physical infrastructure provides, software must be developed that is easy to use, supports lar ge degrees of parallelism in applications code, and manages the complexity of the underlying physical system for the user . This paper describes our approach to constructing and exploiting such “metasystems”. Our approach inherits features of earlier work on parallel processing systems and heterogeneous distributed computing systems. In particular , we are building on Mentat, an object-oriented parallel processing system developed at the University of V irginia. This report is a preliminary document. W e expect changes to occur as the architecture and design of the system mature.
Weighted sum rate optimization for multicell MIMO systems with hardware-impaired transceivers

Physical transceivers exhibit distortions from hardware impairments, of which traces remain even after compensation and calibration. Multicell MIMO coordinated beamforming methods that ignore these residual impairments may suffer from severely degraded performance. In this work, we consider a general model for the aggregate effect of the residual hardware impairments, and propose an iterative algorithm for finding locally optimal points to a weighted sum rate optimization problem. The importance of accounting for the residual hardware impairments is verified by numerical simulation, and a substantial gain over traditional time-division multiple access with impairments-aware resource allocation is observed.
A Study of Data Quality Requirements for Empirical Data in the food Sciences

Data quality is a critical issue in scientific databases since the reliability of empirical data can have a major impact on the formation of scientific theories and policy decisions. Yet while several conceptual frameworks for data quality have been proposed, there is still a lack of general tools and metrics to measure and control the quality of empirical data in practice. As a first step in this direction, we carried out a detailed study of data quality requirements in a system designed to support food scientists by managing data about food composition. Our users included system designers and developers as well as food compilers and project managers. In addition to determining which dimensions of data quality specified in existing conceptual frameworks users consider important in assessing the reliability of data, we also asked users to assess the importance of various criteria related specifically to empirical data. These factors were based around the four steps typical in the life-cycle of empirical data, namely sampling, analysis, data acquisition and data processing. Another novel feature of our study was to investigate not only the different dimensions of data quality considered to be important but also how this depends on the role of users.
Straight to the point: Discovering themes for summary generation

This paper presents our approach to the problem of single sentence summarisation. We investigate the use of Singular Value Decomposition (SVD) to guide the generation of a summary towards the theme that is the focus of the document to be summarised. In doing so, the intuition is that the generated summary will more accurately reflect the content of the source document. Currently, we operate in the news domain and at present, our summaries are modelled on headlines. This paper presents SVD as an alternative method to determine if a word is a suitable candidate for inclusion in the headline. The results of a recall based evaluation comparing three different strategies to word selection, indicate that thematic information does help improve recall.
Robust Solutions by using Evolutionary Computations on Dynamic Max-Sat Problems

In this paper, optimization problems such that the landscape of the objective function changes over time are treated. Conventional approaches for such time-varying functions by using evolutionary computations are designed to track moving optimal solutions. On the contrary, the proposed method in this paper tries to find out stable solutions, i.e., robust solutions, which may not be optimal at each time step but exhibit better performance for all time steps. Such stable solutions are useful if the acquired solutions are operated by human
Ni-SiO2 Catalysts for the Carbon Dioxide Reforming of Methane: Varying Support Properties by Flame Spray Pyrolysis

Silica particles were prepared by flame spray pyrolysis (FSP) as a support for nickel catalysts. The impact of precursor feed rate (3, 5 and 7 mL/min) during FSP on the silica characteristics and the ensuing effect on catalytic performance for the carbon dioxide, or dry, reforming of methane (DRM) was probed. Increasing the precursor feed rate: (i) progressively lowered the silica surface area from ≈340 m2/g to ≈240 m2/g; (ii) altered the silanol groups on the silica surface; and (iii) introduced residual carbon-based surface species to the sample at the highest feed rate. The variations in silica properties altered the (5 wt %) nickel deposit characteristics which in turn impacted on the DRM reaction. As the silica surface area increased, the nickel dispersion increased which improved catalyst performance. The residual carbon-based species also appeared to improve nickel dispersion, and in turn catalyst activity, although not to the same extent as the change in silica surface area. The findings illustrate both the importance of silica support characteristics on the catalytic performance of nickel for the DRM reaction and the capacity for using FSP to control these characteristics.
Kinetochore microtubules in PTK cells

We have analyzed the fine structure of 10 chromosomal fibers from mitotic spindles of PtK1 cells in metaphase and anaphase, using electron microscopy of serial thin sections and computer image processing to follow the trajectories of the component microtubules (MTs) in three dimensions. Most of the kinetochore MTs ran from their kinetochore to the vicinity of the pole, retaining a clustered arrangement over their entire length. This MT bundle was invaded by large numbers of other MTs that were not associated with kinetochores. The invading MTs frequently came close to the kinetochore MTs, but a two-dimensional analysis of neighbor density failed to identify any characteristic spacing between the two MT classes. Unlike the results from neighbor density analyses of interzone MTs, the distributions of spacings between kinetochore MTs and other spindle MTs revealed no evidence for strong MT-MT interactions. A three-dimensional analysis of distances of closest approach between kinetochore MTs and other spindle MTs has, however, shown that the most common distances of closest approach were 30-50 nm, suggesting a weak interaction between kinetochore MTs and their neighbors. The data support the ideas that kinetochore MTs form a mechanical connection between the kinetochore and the pericentriolar material that defines the pole, but that the mechanical interactions between kinetochore MTs and other spindle MTs are weak.
eNVy: a NonVolatile main memory storage system

We are designing a machine with a very large amount of nonvolatile solid state memory. While some mechanical storage device may remain present to handle overflow and to protect against catastrophic (software) failures, the nonvolatile solid state memory is the primary repository of permanent data. Benefits of this approach include much improved access times, and, hopefully, simplified storage system software. We argue that technological advances will soon make it possible to build high-end file servers and database servers with large nonvolatile solid state memories, at a price/performance ratio competitive with disk- or RAID-based designs. The eNVy project comprises two largely separate aspects. In terms of software, we are investigating how to write a storage server that can take advantage of a large nonvolatile memory, regardless of what technology is used. In terms of hardware, we are looking at different ways of building such a memory system. <<ETX>>
Salt Bridges and Gating in the COOH-terminal Region of HCN2 and CNGA1 Channels

Hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels and cyclic nucleotide-gated (CNG) channels are activated by the direct binding of cyclic nucleotides. The intracellular COOH-terminal regions exhibit high sequence similarity in all HCN and CNG channels. This region contains the cyclic nucleotide-binding domain (CNBD) and the C-linker region, which connects the CNBD to the pore. Recently, the structure of the HCN2 COOH-terminal region was solved and shown to contain intersubunit interactions between C-linker regions. To explore the role of these intersubunit interactions in intact channels, we studied two salt bridges in the C-linker region: an intersubunit interaction between C-linkers of neighboring subunits, and an intrasubunit interaction between the C-linker and its CNBD. We show that breaking these salt bridges in both HCN2 and CNGA1 channels through mutation causes an increase in the favorability of channel opening. The wild-type behavior of both HCN2 and CNGA1 channels is rescued by switching the position of the positive and negative residues, thus restoring the salt bridges. These results suggest that the salt bridges seen in the HCN2 COOH-terminal crystal structure are also present in the intact HCN2 channel. Furthermore, the similar effects of the mutations on HCN2 and CNGA1 channels suggest that these salt bridge interactions are also present in the intact CNGA1 channel. As disrupting the interactions leads to channels with more favorable opening transitions, the salt bridges appear to stabilize a closed conformation in both the HCN2 and CNGA1 channels. These results suggest that the HCN2 COOH-terminal crystal structure contains the C-linker regions in the resting configuration even though the CNBD is ligand bound, and channel opening involves a rearrangement of the C-linkers and, thus, disruption of the salt bridges. Discovering that one portion of the COOH terminus, the CNBD, can be in the activated configuration while the other portion, the C-linker, is not activated has lead us to suggest a novel modular gating scheme for HCN and CNG channels.
Synopsis diffusion for robust aggregation in sensor networks

Previous approaches for computing duplicate-sensitive aggregates in sensor networks (<i>e.g.</i>, in TAG) have used a tree topology, in order to conserve energy and to avoid double-counting sensor readings. However, a tree topology is not robust against node and communication failures, which are common in sensor networks. In this paper, we present <i>synopsis diffusion</i>, a general framework for achieving signi.cantly more accurate and reliable answers by combining energy-efficient multi-path routing schemes with techniques that avoid double-counting. Synopsis diffusion avoids double-counting through the use of <i>order- and duplicate-insensitive (ODI) synopses</i> that compactly summarize intermediate results during in-network aggregation. We provide a surprisingly simple test that makes it easy to check the correctness of an ODI synopsis. We show that the properties of ODI synopses and synopsis di.usion create <i>implicit</i> acknowledgments of packet delivery. We show that this property can, in turn, enable the system to adapt message routing to dynamic message loss conditions, even in the presence of asymmetric links. Finally, we illustrate, using extensive simulations, the significant robustness, accuracy, and energy-efficiency improvements of synopsis diffusion over previous approaches.
Polyamine biosynthesis of apple callus under salt stress: importance of the arginine decarboxylase pathway in stress response.

To clarify the involvement of the arginine decarboxylase (ADC) pathway in the salt stress response, the polyamine titre, putrescine biosynthetic gene expression, and enzyme activities were investigated in apple [Malus sylvestris (L.) Mill. var. domestica (Borkh.) Mansf. ] in vitro callus under salt stress, during recovery after stress, and when ADC was inhibited by D-arginine, an inhibitor of ADC. Salt stress (200 mM NaCl) caused an increase in thiobarbituric acid-reactive substances (TBARS) and electrolyte leakage (EL) of the callus, which was accompanied by an increase in free putrescine content, during 7 d of treatment. Conjugated putrescine was also increased, but this increase was limited to the early stage of salt stress. Accumulation of putrescine was in accordance with induction of ADC activity and expression of the apple ADC gene (MdADC). When callus that had been treated with 200 mM NaCl was transferred to fresh medium with (successive stress) or without (recovery) NaCl, TBARS and EL were significantly reduced in the recovery treatment, indicating promotion of formation of new callus cells, compared with the successive stress treatment. Meanwhile, MdADC expression and ADC activity were also decreased in the callus undergoing recovery, whereas those of the callus under successive stress were increased. Ornithine decarboxylase (ODC) activity showed a pattern opposite to that of ADC in these conditions. D-Arginine treatment led to more serious growth impairment than no treatment under salt stress. In addition, accumulation of putrescine, induction of MdADC, and activation of ADC in D-arginine-treated callus were not comparable with those of the untreated callus. Exogenous addition of putrescine could alleviate salt stress in terms of fresh weight increase and EL. All of these findings indicated that the ADC pathway was tightly involved in the salt stress response. Accumulation of putrescine under salt stress, the possible physiological role of putrescine in alleviating stress damage, and involvement of MdADC and ADC in response to salt stress are discussed.
The Cell Wall-Associated Kinase (WAK) andWAK-Like Kinase Gene Family1

We have identified a large family of genes with sequence similarity to the cell wall-associated kinase ( WAK ) genes ([He et al., 1999][1]). Like the WAK s, these genes exist in multiple gene clusters, and our analyses suggest that they encode functional protein kinases that are associated with the
Neural Networks with Dynamic Synapses

Transmission across neocortical synapses depends on the frequency of presynaptic activity (Thomson & Deuchars, 1994). Interpyramidal synapses in layer V exhibit fast depression of synaptic transmission, while other types of synapses exhibit facilitation of transmission. To study the role of dynamic synapses in network computation, we propose a unified phenomenological model that allows computation of the postsynaptic current generated by both types of synapses when driven by an arbitrary pattern of action potential (AP) activity in a presynaptic population. Using this formalism, we analyze different regimes of synaptic transmission and demonstrate that dynamic synapses transmit different aspects of the presynaptic activity depending on the average presynaptic frequency. The model also allows for derivation of mean-field equations, which govern the activity of large, interconnected networks. We show that the dynamics of synaptic transmission results in complex sets of regular and irregular regimes of network activity.
Autoantibodies in type 2 diabetes induce stress fiber formation and apoptosis in endothelial cells.

CONTEXT Macular edema contributes to visual impairment, and albuminuria is associated with increased cardiovascular mortality in adults with type 2 diabetes mellitus. These microvascular complications result from increased capillary leakage of plasma proteins whose causation is not completely understood. OBJECTIVE The objective of the present study was to test whether plasma from type 2 diabetes with maculopathy/albuminuria or control subjects contains autoantibodies that can induce apoptosis or activate Rho kinase (ROCK) in endothelial cells. DESIGN A cohort of Veterans Affairs Diabetes Trial adults (>40 yr of age) was randomized to standard vs. intensive glycemic treatment lasting 5-7.5 yr. SETTING The study was conducted in outpatient clinics. PATIENTS Case and age-matched control subjects who differed for the baseline presence of significant diabetic maculopathy and/or progression to macro-albuminuria were included in the study. INTERVENTION Pharmacological and lifestyle interventions in the Veterans Affairs Diabetes Trial generally resulted in substantially improved glycemic, blood pressure, and lipid levels. RESULTS Autoantibodies from patients with macular edema or progression to albuminuria potently induced caspase-dependent apoptosis in endothelial cells (up to 60%), whereas IgG from age-matched normal plasma caused much less apoptosis (<10%; P < 0.0001). The active inhibitory autoantibodies triggered stress fiber formation in endothelial cells likely through the activation of Rho guanosine 5'-triphosphatase, which could be nearly completed inhibited by 10 microm Y27632, a specific ROCK inhibitor. CONCLUSIONS These results suggest that autoantibodies from a subset of advanced type 2 diabetes may contribute to diabetic vascular complications by activating ROCK, inducing stress fiber formation and apoptosis in endothelial cells.
Research on the nomenclature relations of conceptual system in fundamental theory of Traditional Chinese Medicine

Objective: Extracting on the medical terminology system will associate TCM with intelligent system and propel TCM informatization. Method: Extracting the term relation by artificial drawing and comparative analysis with UMLS. Results: Obtained 26 kinds of term relations on Nomenclature Relations of Conceptual System in Fundamental Theory of TCM and enriched UMLS. Conclusion: We should further study on Nomenclature Relations of Conceptual System in Fundamental Theory of TCM owing its characters.
Formal Concept Analysis and Rough Set Theory in Clustering

This paper is concerned with the fundamental role of two mathematical theories in some clustering problems. Formal concept analysis provides the algebraic structure and properties of possible concepts from a given context, and rough set theory provides a mathematical tool to deal with imprecise and incomplete data. Based on these theories, we developed models and algorithms for solving three clustering problems: conceptual clustering, approximate conceptual clustering, and text clustering. 1 Formal Concept Analysis and Rough Set Theory A theory of concept lattices has been studied under the name formal concept analysis (FCA) by Wille and his colleagues [1, 11]. Considers a context as a triple (O,D,R) where O be a set of objects, D be a set of primitive descriptors and R be a binary relation between O and D, i.e., R ⊆ O×D and (o, d) ∈ R is understood as the fact that object o has the descriptor d. For any object subset X ⊆ O, the largest tuple common to all objects in X is denoted by λ(X). For any tuple S ∈ T , the set of all objects satisfying S is denoted by ρ(S). A tuple S is closed if λ(ρ(S)) = S. Formally, a concept C in the classical view is a pair (X, S), X ⊆ O and S ⊆ T , satisfying ρ(S) = X and λ(X) = S. X and S are called extent and intent of C, respectively. Concept (X2, S2) is a subconcept of concept (X1, S1) if X2 ⊆ X1 which is equivalent to S2 ⊇ S1, and (X1, S1) is then a superconcept of (X2, S2). It was shown that λ and ρ define a Galois connection between the power sets ℘(O) and ℘(D), i.e., they are two order-reversing one-to-one operators. As a consequence, the following properties hold which will be exploited in the learning process: if S1 ⊆ S2 then ρ(S1) ⊇ ρ(S2) and λρ(S1) ⊆ λρ(S2) if X1 ⊆ X2 then λ(X1) ⊇ λ(X2) and ρλ(X1) ⊆ ρλ(X2) S ⊆ λρ(S), X ⊆ ρλ(X) ρλρ = ρ, λρλ = λ, λρ(λρ(S)) = λρ(S) ρ( ⋃ j Sj) = ⋂ j ρ(Sj), λ( ⋃ j Xj) = ⋂ j λ(Xj) The basic theorem in formal concept analysis [11] states that the set of all possible concepts from a context (O,D,R) is a complete lattice L, called Galois lattice, in which infimum and supremum can be described as follows: ∧