Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of Thioredoxin Reductases in Brain Development

The thioredoxin-dependent system is an essential regulator of cellular redox balance. Since oxidative stress has been linked with neurodegenerative disease, we studied the roles of thioredoxin reductases in brain using mice with nervous system (NS)-specific deletion of cytosolic (Txnrd1) and mitochondrial (Txnrd2) thioredoxin reductase. While NS-specific Txnrd2 null mice develop normally, mice lacking Txnrd1 in the NS were significantly smaller and displayed ataxia and tremor. A striking patterned cerebellar hypoplasia was observed. Proliferation of the external granular layer (EGL) was strongly reduced and fissure formation and laminar organisation of the cerebellar cortex was impaired in the rostral portion of the cerebellum. Purkinje cells were ectopically located and their dendrites stunted. The Bergmann glial network was disorganized and showed a pronounced reduction in fiber strength. Cerebellar hypoplasia did not result from increased apoptosis, but from decreased proliferation of granule cell precursors within the EGL. Of note, neuron-specific inactivation of Txnrd1 did not result in cerebellar hypoplasia, suggesting a vital role for Txnrd1 in Bergmann glia or neuronal precursor cells.
The muc genes of pKM101 are induced by DNA damage

A gene fusion was constructed in vitro that resulted in the synthesis of a hybrid protein consisting of the amino-terminal segment of the MucB protein of the mutagenesis-enhancing plasmid pKM101 joined to an enzymatically active carboxy-terminal segment of the beta-galactosidase protein. In strains bearing this fusion, beta-galactosidase activity was induced by UV radiation and other DNA-damaging agents. A genetic analysis of the regulation of expression of the phi (mucB'-lacZ') fusion was consistent with the LexA protein acting as the direct repressor of the mucB gene. Examination of the expression of the mucA and phi (mucB'-lacZ') gene products in maxicells in the presence and absence of a high-copy-number plasmid carrying the lexA+ gene demonstrated that lexA regulated both the mucA and mucB genes, thus supporting our conclusion that the two genes are organized in an operon with the mucA gene transcribed first. An analysis of the effects of the recA430(lexB30) mutation on muc expression led to the discovery of the differential ability of the recA430 gene product to induce expression of a dinB::Mu d1(Ap lac) fusion located on the chromosome and the same phi (dinB'-lacZ+) fusion cloned into plasmid pBR322. Models to account for the role of the recA430 allele on the expression of damage-inducible genes and on mutagenesis are discussed.
MR Angiographic Follow-Up of Intracranial Aneurysms Treated with Detachable Coils: Evaluation of a Blood-Pool Contrast Medium

BACKGROUND AND PURPOSE: Blood-pool agents are promising in the imaging of small vessels with slow or complex flow. Our aim was to compare blood-pool contrast-enhanced MR angiography (BPCE-MRA) using gadofosveset trisodium (Vasovist) with 3D time-of-flight MRA (TOF-MRA) in the follow-up of intracranial aneurysms after endovascular therapy. MATERIALS AND METHODS: We included 32 patients with a total of 37 coiled aneurysms. MRAs in the early steady-state phase were performed on a 1.5T scanner within 8 days of digital subtraction angiography (DSA). Two radiologists independently analyzed TOF-MRA and BPCE-MRA images. Consensus was reached by review involving a third neuroradiologist. DSA images were interpreted separately by an interventional radiologist. Findings were assigned to 1 of 3 categories: 1) complete occlusion, 2) residual neck, and 3) residual aneurysm. RESULTS: Follow-up DSA demonstrated 13 complete obliterations (class 1), 13 residual necks (class 2), and 11 residual aneurysms (class 3). Weighted κ statistics showed substantial concordance of TOF-MRA and DSA (0.664) as well as BPCE-MRA and DSA (0.724) ratings. Comparison between TOF-MRA and BPCE-MRA found excellent agreement (0.818) with only 6 (16.2%) discrepancies. For detecting residual flow, the difference in accuracy of both MRA techniques (83.8% versus 91.9%) was not significant (McNemar, P = 1.000). BPCE-MRA showed a tendency towards higher sensitivity and specificity (91.7% and 92.3%, respectively) compared with TOF-MRA (87.5% and 76.9%). CONCLUSIONS: In classifying the completeness of endovascular cerebral aneurysm therapy, we found that BPCE-MRA and 3D TOF-MRA showed very good agreement. The use of Vasovist did not lead to a significantly increased accuracy of MRA follow-up.
Ergodic capacity of a 2 /spl times/ 2 MIMO system under phase uncertainty at the transmitter

In this paper, we find an expression for the ergodic capacity of a 2 /spl times/ 2 multi-input multi-output (MIMO) flat fading channel for a particular case of partial channel state information at the transmitter: we focus our study on the case where the transmitter is informed just with the modulus of the channel matrix coefficients. First, we prove that a simple power allocation strategy between transmitting antennas is the optimal scheme, in the sense that is a capacity achieving architecture. Next, we derive an expression to calculate the optimal power assigned to each antenna, and find out that it can be expressed as a function of one of the roots of a fourth order polynomial. Finally, some conclusions are presented.
Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

Motivation: Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance. Here, theoretical modeling is powerful to formulate hypotheses for pathways and the dynamics of the metabolism, even if the biological data are incomplete. To develop reliable mathematical models they have to be proven for consistency. This is still a challenging task because many verification techniques fail already for middle-sized models. Consequently, new methods, like decomposition methods or reduction approaches, are developed to circumvent this problem. Methods: We present a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. We used the Petri net formalism to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency we applied concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs. Results: We formulated the core metabolism of Arabidopsis thaliana based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism. By applying network decomposition and reduction techniques at steady-state conditions, we suggest a straightforward mathematical modeling process. We demonstrate that potential steady-state pathways exist, which provide the fixed carbon to nearly all parts of the network, especially to the citric acid cycle. There is a close cooperation of important metabolic pathways, e.g., the de novo synthesis of uridine-5-monophosphate, the γ-aminobutyric acid shunt, and the urea cycle. The presented approach extends the established methods for a feasible interpretation of biological network models, in particular of large and complex models.
The influence of psychological contracts on the adjustment and organisational commitment among expatriates: An empirical study in Taiwan

Purpose - The purpose of this research is to investigate the influence of psychological contracts on the adjustment and organisational commitment of expatriates during international business assignments. The study also aims to investigate the influence of psychological barriers to expatriate adjustment. Design/methodology/approach - A unique survey questionnaire was developed to collect data from 219 Taiwanese business expatriates during the first quarter of 2007. A LISREL analysis is used to test the hypotheses of the research framework. Findings - The study finds that: perceived fulfilment of the psychological contracts of expatriates significantly influences both their adjustment to foreign situations and their organisational commitment; psychological barriers to adjustment have a negative influence on both socio-cultural adjustment and psychological adjustment; and expatriate psychological adjustment has both a direct and an indirect influence on organisational commitment. Practical implications - International managers should implement appropriate human resource measures to meet expatriates' expectations for their psychological contracts. Managers should ensure that expatriates receive adequate counsel and training to assist them in minimizing any psychological barriers they might have to adjustment in a foreign environment. Originality/value - The study extends concepts from organisational behaviour theory and applies them to the process of international manpower management.
Reworking Gender: A Feminist Communicology of Organization

Introduction: Situating Gender in Critical Organization Studies Chapter 1: Feminist Organization Studies in the Wake of the Discursive Turn Chapter 2: Feminism and the Discourses of Modernism: Articulating an Organizational Voice Chapter 3: Postmodernism and Organization Studies: Complicating the Conversation Chapter 4: Organizing at the Intersection of Feminism and Postmodernism Chapter 5: A Feminist Communicology of Organization Chapter 6: A Feminist Communicology of the Airline Pilot: Gender and the Organization of Professional Identity Chapter 7: Conclusion: Reworking Gender in Organization Studies Notes and References
Speech morphing by gradually changing spectrum parameter and fundamental frequency

The paper proposes a new application of speech modification called "speech morphing". In image processing, morphing is a well known technique that gradually changes one person's face to that of someone else. Speech morphing produces similar results for speech; i.e., one person's speech is gradually changed to that of someone else. Speech morphing makes it possible to create movies or multimedia entertainment together with image morphing. The proposed algorithm pitch-synchronously modifies fundamental frequency (F/sub 0/) and DFT spectrum and outputs high quality speech. To clarify the balance of F/sub 0/ modification and spectrum modification, listening tests were carried out using 20 male speakers. The results yielded the relationship between the amount of modification and speaker identity. In terms of overall performance, listening tests show that the proposed algorithm successfully generates smooth, high quality voice changes.
A HYBRID CLONAL SELECTION ALGORITHM FOR QUALITY OF SERVICE-AWARE WEB SERVICE SELECTION PROBLEM

It is imperative to provide service consumers with facilities for selecting re- quired web services according to their Quality of Service (QoS). Several heuristics, which are local adaptation preemptive strategy, elitist perturbation guiding strategy and global tournament strategy for directed localne-tuning, and a hybrid clonal selection algorithm (CSPLPT) are proposed for QoS-aware web service selection problem. It combines the population-based local search mechanism of clonal selection algorithm and population- based elitist learning mechanism of particle swarm optimization algorithm. The hy- bridization idea and the efficacy of the proposed strategies are veried and analyzed step by step with web service selection problem. The proposed algorithm CSPLPT is further compared with recent genetic algorithm-based CoDiGA and particle swarm optimization- based iPSOA algorithms with various scales of composite web services. The comprehen- sive experiments demonstrate the necessity and superiority of the proposed strategies. It also shows that the hybrid algorithm CSPLPT consistently and signicantly outperforms CoDiGA and iPSOA in better QoS performance and average evolutionary behaviors while selecting the composite web services with global QoS constraints.
Production of Mucosally Transmissible SHIV Challenge Stocks from HIV-1 Circulating Recombinant Form 01_AE env Sequences

Simian-human immunodeficiency virus (SHIV) challenge stocks are critical for preclinical testing of vaccines, antibodies, and other interventions aimed to prevent HIV-1. A major unmet need for the field has been the lack of a SHIV challenge stock expressing circulating recombinant form 01_AE (CRF01_AE) env sequences. We therefore sought to develop mucosally transmissible SHIV challenge stocks containing HIV-1 CRF01_AE env derived from acutely HIV-1 infected individuals from Thailand. SHIV-AE6, SHIV-AE6RM, and SHIV-AE16 contained env sequences that were >99% identical to the original HIV-1 isolate and did not require in vivo passaging. These viruses exhibited CCR5 tropism and displayed a tier 2 neutralization phenotype. These challenge stocks efficiently infected rhesus monkeys by the intrarectal route, replicated to high levels during acute infection, and established chronic viremia in a subset of animals. SHIV-AE16 was titrated for use in single, high dose as well as repetitive, low dose intrarectal challenge studies. These SHIV challenge stocks should facilitate the preclinical evaluation of vaccines, monoclonal antibodies, and other interventions targeted at preventing HIV-1 CRF01_AE infection.
Combination of Root Surface Modification with BMP-2 and Collagen Hydrogel Scaffold Implantation for Periodontal Healing in Beagle Dogs

Objective : Biomodification of the root surface plays a major role in periodontal wound healing. Root surface modification with bone morphogenetic protein (BMP) stimulates bone and cementum-like tissue formation; however, severe ankylosis is simultaneously observed. Bio-safe collagen hydrogel scaffolds may therefore be useful for supplying periodontal ligament cells and preventing ankylosis. We examined the effects of BMP modification in conjunction with collagen hydrogel scaffold implantation on periodontal wound healing in dogs. Material and Methods: The collagen hydrogel scaffold was composed of type I collagen sponge and collagen hydrogel. One-wall infrabony defects (5 mm in depth, 3 mm in width) were surgically created in six beagle dogs. In the BMP/Col group, BMP-2 was applied to the root surface (loading dose; 1 µg/µl), and the defects were filled with collagen hydrogel scaffold. In the BMP or Col group, BMP-2 coating or scaffold implantation was performed. Histometric parameters were evaluated at 4 weeks after surgery. Results: Single use of BMP stimulated formation of alveolar bone and ankylosis. In contrast, the BMP/Col group frequently enhanced reconstruction of periodontal attachment including cementum-like tissue, periodontal ligament and alveolar bone. The amount of new periodontal ligament in the BMP/Col group was significantly greater when compared to all other groups. In addition, ankylosis was rarely observed in the BMP/Col group. Conclusion: The combination method using root surface modification with BMP and collagen hydrogel scaffold implantation facilitated the reestablishment of periodontal attachment. BMP-related ankylosis was suppressed by implantation of collagen hydrogel.
Relay selection for energy-efficient cooperative media access control

In this paper, we design an energy-efficient cooperative Medium Access Control (MAC) protocol combined with physical layer power / rate control in order to minimize the energy consumption. Based on the Channel State Information (CSI) and relay-to-destination distance, the potential candidate relays carry out autonomous decisions for minimizing the transmission power required for forwarding their data, when relying on their cooperation. Simulation results demonstrate that our scheme is capable of providing considerable energy savings, while maintaining the target Frame Error Ratio (FER), which is achieved at the cost of introducing a modest additional MAC overhead.
Multi-MetaRing Protocol: Fairness in Optical Packet Ring Networks

We focus on metropolitan area networks operating in packet mode and exploiting a single-hop wavelength division multiplexing (WDM) architecture. First, we briefly describe a specific slotted WDM optical network, based on a folded bus topology. Then, we address the fairness problem arising in this architecture and propose an extension of the MetaRing protocol to a WDM scenario. Two possible strategies are defined and analyzed. Finally, we show that both fair access and high aggregate network throughput can be achieved by properly handling node access through all WDM channels.
Determining what individual SUS scores mean: adding an adjective rating scale

The System Usability Scale (SUS) is an inexpensive, yet effective tool for assessing the usability of a product, including Web sites, cell phones, interactive voice response systems, TV applications, and more. It provides an easy-to-understand score from 0 (negative) to 100 (positive). While a 100-point scale is intuitive in many respects and allows for relative judgments, information describing how the numeric score translates into an absolute judgment of usability is not known. To help answer that question, a seven-point adjective-anchored Likert scale was added as an eleventh question to nearly 1,000 SUS surveys. Results show that the Likert scale scores correlate extremely well with the SUS scores (r=0.822). The addition of the adjective rating scale to the SUS may help practitioners interpret individual SUS scores and aid in explaining the results to non-human factors professionals.
A single amino acid change in the cytoplasmic domain of the simian immunodeficiency virus transmembrane molecule increases envelope glycoprotein expression on infected cells

We have described a virus termed CP-MAC, derived from the BK28 molecular clone of simian immunodeficiency virus, that was remarkable for its ability to infect Sup-T1 cells with rapid kinetics, cell fusion, and CD4 down-modulation (C. C. LaBranche, M. M. Sauter, B. S. Haggarty, P. J. Vance, J. Romano, T. K. Hart, P. J. Bugelski, and J. A. Hoxie, J. Virol. 68:5509-5522, 1994 [Erratum 68:7665-7667]). Compared with BK28, CP-MAC exhibited a number of changes in its envelope glycoproteins, including a highly stable association between the external (SU) and transmembrane (TM) molecules, a more rapid electrophoretic mobility of TM, and, of particular interest, a marked increase in the level of envelope protein expression on the surface of infected cells. These changes were shown to be associated with 11 coding mutations in the env gene (5 in SU and 6 in TM). In this report, we demonstrate that a single amino acid mutation of a Tyr to a Cys at position 723 (Y723C) in the TM cytoplasmic domain of CP-MAC is the principal determinant for the increased expression of envelope glycoproteins on the cell surface. When introduced into the env gene of BK28, the Y723C mutation produced up to a 25-fold increase in the levels of SU and TM on chronically infected cells, as determined by fluorescence-activated cell sorter analysis with monoclonal and polyclonal antibodies. A similar effect was observed when a Tyr-to-Cys change was introduced at the analogous position (amino acid 721) in the SIVmac239 molecular clone, which, unlike BK28 does not contain a premature stop codon in its TM cytoplasmic tail. Substituting other amino acids, including Ala, Ile, and Ser, at this position produced increases in surface envelope glycoproteins that were similar to that observed for the Cys substitution, while a Tyr-to-Phe mutation produced a smaller increase. These results could not be accounted for by differences in the kinetics or efficiency of envelope glycoprotein processing or by shedding of SU from infected cells. However, immunoelectron microscopy demonstrated that the Y723C mutation in BK28 produced a striking redistribution of cell surface envelope molecules from localized patches to a diffuse pattern that covered the entire plasma membrane. This finding suggests that mutation of a Tyr residue in the simian immunodeficiency virus TM cytoplasmic domain may disrupt a structural element that can modulate envelope glycoprotein expression on the surface of infected cells.
Estimating SRS-22 Quality of Life Measures With SF-36: Application in Idiopathic Scoliosis

Study Design. Comparison of a generic- with a disorder-specific health-related quality of life (HRQL) questionnaire. Objectives. To determine the association between generic- and disorder-specific questionnaire domains of similar construct. Summary of Background Data. Short Form-36 (SF-36), a general HRQL questionnaire, has been widely used to evaluate patients with scoliosis and related spine deformity. How it relates to the disorder-specific Scoliosis Research Society-22 (SRS-22) questionnaire is currently unknown. Methods. Seventy-eight patients, operated at a mean age 14.5 years for idiopathic scoliosis with a mean largest Cobb of 60°, completed both questionnaires at a mean of 9.25 years after surgery. Results. The predictability of the SRS-22 Mental Health domain is excellent using the SF-36 Mental Health domain, from which it was adapted (R2 = 0.81). The SRS-22 Pain domain predictability using the SF-36 Bodily Pain domain is also excellent (R2 = 0.79). The SRS-22 Function domain predictability using the SF-36 Physical Component Summary domain is good (R2 = 0.64). The SRS-22 Self-Image and Management Satisfaction/Dissatisfaction domains are poorly predicted by the SF-36 General Health and Physical Component Summary domains, respectively, R2 = 0.52 and 0.54. Conclusion. SRS-22 Mental Health and Pain domain scores can be accurately calculated from correlating SF-36 domain scores. SRS-22 Function scores can be fairly well predicted from correlated SF-36 domain scores. Self-Image and Management Satisfaction/Dissatisfaction domain scores cannot be approximated from SF-36 domain scores.
3 Deep Neural Networks with Matrix Variate Gaussian Priors

Deep neural networks (DNNs) are increasingly popular in modern machine learning. Bayesian learning affords the opportunity to quantify posterior uncertainty on DNN model parameters. Most existing work adopts independent Gaussian priors on the model weights, ignoring possible structural information. In this paper, we consider the matrix variate Gaussian (MVG) distribution to model structured correlations within the weights of a DNN. To make posterior inference feasible, a reparametrization is proposed for the MVG prior, simplifying the complex MVG-based model to an equivalent yet simpler model with independent Gaussian priors on the transformed weights. Consequently, we develop a scalable Bayesian online inference algorithm by adopting the recently proposed probabilistic backpropagation framework. Experiments on several synthetic and real datasets indicate the superiority of our model, achieving competitive performance in terms of model likelihood and predictive root mean square error. Importantly, it also yields faster convergence speed compared to related Bayesian DNN models.