Miracle-dz/UniFAR-FTUs huggingface dataset:
Shotgun proteomic analysis of S-thiolation sites of guinea pig lens nuclear crystallins following oxidative stress in vivo

Purpose To compare levels of S-glutathiolation and S-cysteinylation occurring at more than 60 cysteine residues of 12 different guinea pig lens water-soluble nuclear crystallins following treatment of the animals with hyperbaric oxygen (HBO). Methods Guinea pigs (initially 18 months old) were treated 30X (3X per week for 10 weeks) with HBO (2.5 atm 100% O2 for 2.5 h) as a model to study the formation of nuclear cataract. This treatment produces a moderate increase in lens nuclear light scatter (compared to denser scatter occurring after 80 HBO treatments), with five- to sixfold increases in levels of protein-bound glutathione (PSSG) and protein-bound cysteine (PSSC). Trypsin digests of lens nuclear water-soluble proteins were analyzed with two-dimensional liquid chromatography and mass spectrometry to identify specific cysteine residues binding either glutathione or cysteine. Lens nuclei of age-matched untreated animals were used as controls. Results All major crystallins, except αB, were modified to some extent by either S-glutathiolation or S-cysteinylation. Overall, 72% of the cysteine residues of guinea pig lens nuclear crystallins were shown to be capable of binding glutathione, cysteine, or both molecules. The crystallin with the highest level of modification was βA1/A3 (six of eight –SH groups), and that with the lowest (two of five –SH groups) was βA2. O2-induced increases in PSSG levels were 2.8, 2.4, and 4.1 times control for γA-, γB-, and γC-crystallins, respectively. Comparable increases in PSSC levels for the three γ-crystallins were 2.3, 2.7, and 2.4 times control, respectively. βB2-crystallin showed the highest amount of O2-induced PSSG formation of any of the crystallins, as well as a substantial level of control PSSG, and nearly all of this was due to a single residue, C67, a site also present in human βB2-crystallin. Overall, 32 of the 44 modified cysteine residues were homologous with the human. Conclusions This large-scale study successfully identified lens crystallin cysteine residues that bound glutathione and/or cysteine under normal or oxidative stress conditions. The high percentage of protein –SH groups that are modified by S-thiolation in the guinea pig lens nucleus demonstrates the substantial protein sulfhydryl redox buffer capability present in the center of the lens. The results suggest that PSSG and PSSC formation may act to delay O2-induced insolubilization of γA-, γB-, and γC-crystallins, and β-crystallins, but with a greater effect on the γ-crystallins at an early stage of oxidative stress. The study has shown that technological approaches are now available to investigate in considerable detail the role of specific lens –SH groups in nuclear cataractogenesis.
Morphosyntactic Tagging of Slovene: Evaluating Taggers and Tagsets

The paper evaluates tagging techniques on a corpus of Slovene, where we are faced with a large number of possible word-class tags and only a small (hand-tagged) dataset. We report on training and testing of four different taggers on the Slovene MULTEXT-East corpus containing about 100.000 words and 1000 different morphosyntactic tags. Results show, first of all, that training times of the Maximum Entropy Tagger and the Rule Based Tagger are unacceptably long, while they are negligible for the Memory Based Taggers and the TnT tri-gram tagger. Results on a random split show that tagging accuracy varies between 86% and 89% overall, between 92% and 95% on known words and between 54% and 55% on unknown words. Best results are obtained by TnT. The paper also investigates performance in relation to our EAGLES-based morphosyntactic tagset. Here we compare the per-feature accuracy on the full tagset, and accuracies on these features when training on a reduced tagset. Results show that PoS accuracy is quite high, while accuracy on Case is lowest. Tagset reduction helps improve accuracy, but less than might be expected.
Identification of a Mouse Cytomegalovirus Gene Selectively Targeting CD86 Expression on Antigen-Presenting Cells

ABSTRACT We and others have shown that infection of dendritic cells with murine cytomegalovirus (MCMV) leads to severe functional impairment of these antigen-presenting cells (D. M. Andrews, C. E. Andoniou, F. Granucci, P. Ricciardi-Castagnoli, and M. A. Degli-Esposti, Nat. Immunol. 2:1077-1084, 2001; S. Mathys, T. Schroeder, J. Ellwart, U. H. Koszinowski, M. Messerle, and U. Just, J. Infect. Dis. 187:988-999, 2003). Phenotypically, reduced surface expression of costimulatory molecules and major histocompatibility complex molecules was detected. In order to identify the molecular basis for the observed effects, we generated MCMV mutants with large deletions of nonessential genes. The study was facilitated by the finding that a monocyte-macrophage cell line displayed similar phenotypic alterations after MCMV infection. By analyzing the expression of cell surface molecules on infected cells, we identified a mutant virus which is no longer able to downmodulate the expression of the costimulatory molecule CD86. Additional mutants with smaller deletions allowed us to pin down the responsible gene to a certain genomic region. RNA analysis led to the identification of the spliced gene m147.5, encoding a protein with 145 amino acids. Experiments with an m147.5 mutant revealed that the protein affects CD86 expression only, suggesting that additional MCMV genes are responsible for downmodulation of the other surface molecules. Identification of viral gene products interfering with functionally important proteins of antigen-presenting cells will provide the basis to dissect the complex interaction of CMV with these important cells and to evaluate the biological importance of these viral genes in vivo.
Skill and automaticity: Relations, implications, and future directions.

Automaticity and skill are closely related but are not identical. Automatic processes are components of skill, but skill is more than the sum of the automatic components. Automaticity and skill are similar in that both are learned through practice; this has implications for (1) current studies of the co-occurrence of properties of automaticity, (2) the relation between multiple resources and automaticity, and (3) the relation between control and automaticity. Many of the issues in automaticity may be resolved or at least revised by considering the role that automatic processes play in performing a skill. RESUME L'automatismeet l'habiletesont relies mais non identiques. Les processus automatiques sont les composantes d'une habilite, mais celle-ci est plus que la somme de ses composantes automatiques. L'automatisme et l'habilete sont similaires en ce sens qu'ils sont tous deux appris par la pratique. Ceci a des implications sur (1) les etudes actuelles sur la co-occurrence des proprietes de Tautomatisme, (2) la relation entre les ressources multiples et l'automatisme et (3) la relation entre le controle et l'automatisme. Plusieurs des questions portant sur l'automatisme pourraient trouver leur reponse ou du moins etre reformulees par l'examen du role que jouent les processus automatiques dans l'exercice d'une habilete. Psychologists have believed there is a strong relation between automaticity and skill since the last century. Bryan and Harter (1899) argued that automaticity was a necessary component of skill, that higher-level aspects of skill could not be acquired until lower level aspects had become automatized. LaBerge and Samuels (1974) echoed Bryan and Hatter's position, arguing that there was not enough attentional capacity to consider higher-level aspects of skill until lower-level aspects had become automatized, thereby freeing attentional capacity for the higher-level aspects. Other researchers may not accept the idea that attentional capacity limits the acquisition of skill (e.g., Spelke, Hirst, & Neisser, 1976) or that automatization should be defined as a reduction in capacity demands (e.g., Kolers, 1975), but most would agree that automatization is an important aspect of skill. The close relation between automaticity and skill raises several questions: Are automaticity and skill the same thing? Is there anything to skill besides automaticity? What does a skills perspective imply for studies of automaticity? The purpose of this article is to suggest possible answers to these questions. * This research was supported by Grant No. U0053 from the Natural Sciences and Engineering Research Council of Canada. Address reprint requests to Gordon D. Logan, Department of Psychological Sciences, Purdue University, West Lafayette, Indiana, 47907, U.S.A.
Image Indexing Technique and Its Parallel Retrieval on PVM

The paper presents the technique for image indexing and its parallel implementation on a parallel virtual machine. The indexing method is the combination of the autocorrelogram method and color difference correlograms method. Color filtering is used for quantization of the RGB colorspace into 64 colors to reduce the complexity and calculation time. Then, both color and spatial information are employed to build the index of each image. Experimental results suggest that the method can index and retrieve images with different views of the same scene or large changes in appearance. The performance of the image retrieval system is also improved significantly when compared with both color histogram and color correlogram method. The scheme is also implemented on PVM with the load balancing technique to speed up its retrieval time. The experimental results also show that it could speed up the processing time significantly.
Scheduling Optimization for Real-Time Services in WCDMA

At the uplink of WCDMA-UMTS systems the User Equipment (UE) sends Scheduling Information (SI) to the Node B at each Transmission Time Interval (TTI) of 2ms. According to 3GPP standards the SI does not include any information regarding the delay sensitivity or the current packet delay of each traffic flow. However, this turns to be a great disadvantage for the scheduling procedure, especially regarding real-time applications, as it does not allow the scheduler to provide delay based QoS differentiation. In this paper, we propose the substitution of the Highest priority Logical channel ID (HLID) field of the SI report with a new metric, namely Mean Logical Channel Priority (MLCP) which furthermore is utilized by a Delay-driven Packet Scheduler (DPS). The performance of the overall MLCP-DPS scheme is evaluated by means of system level simulations.
Forced oscillation techniques for measuring mechanical properties of the respiratory system.

Airway function is usually assessed by tests of forced expiration or, in more specialised laboratories, by measuring airways resistance by whole body plethysmography. Plethysmography depends on the patients' cooperation and requires expensive and bulky apparatus. An alternative non-invasive technique for measuring airflow resistance, using forced oscillation, was introduced by DuBois and colleagues in the 1950s'-almost at the same time as body plethysmography-but did not become as widely established in clinical physiology. The biomechanical principles of forced oscillation are generally less familiar than those underlying conventional measurements of airways resistance and lung compliance, and the technical requirements for obtaining accurate pressure and flow signals and the subsequent signal processing are more demanding. Recent advances in pressure transducer and microcomputer technology, however, have removed many of the earlier problems with signal collection and analysis. Because most oscillation methods require less cooperation from the subject and less bulky apparatus than body plethysmography the balance of advantage between the two methods has altered and we can expect the oscillation technique to become more widely used in clinical physiology. Methods of applying forced oscillation Forced oscillation techniques deduce the mechanical properties of the respiratory system from the response to small externally produced oscillatory forces. From the responsemeasured as the instantaneous pressure-flow relationship (impedance)-flow resistance and the reactance (the combined effect of elastance and inertance) of the respiratory system can be computed. Because these mechanical properties of the lungs are non-linear it is important that only small external forces are applied. Most commonly, forced oscillation is applied at the airway opening by a loudspeaker and the pressure-flow relation is also measured at the airway opening ("input" impedance-see fig 1). Alternative techniques apply an oscillatory signal to the surface of the chest wall and measure the induced flow response at the airway opening or they oscillate at the airway opening and measure flow at the chest wall ("transfer" impedance). 2 Transfer impedance has certain technical advantages but requires the subject to be seated in a head out plethysmograph and will not be further discussed. The simplest form of forced oscillation technique applies a single sinusoidal signal during breath holding (fig 2). The impedance
A tightly-coupled processor-network interface

Careful design of the processor-network interface can dramatically reduce the software overhead of interprocessor communication. Our interface architecture reduces communication overhead five fold in our benchmarks. Most of our performance gain comes from simple, low cost hardware mechanisms for fast dispatching on, forwarding of, and replying to messages. The remaining improvement can be gained by implementing the network interface as part of the processor’s register file. For example, using our hardware mechanisms a register-mapped interface can receive, process, and reply to a remote read request in a total of two RISC instructions. We have implemented an RTL model of an off-chip memory-mapped interface which provides our hardware mechanisms. Our industrial partner, Motorola, is implementing a similar network interface on-chip in an experimental version of the 88110 processor.
Robust overlapping speech recognition based on neural networks

We address issues for improving hands-free speech recognition performance in the presence of multiple simultaneous speakers using multiple distant microphones. In this paper, a log spectral mapping is proposed to estimate the log mel-filterbank outputs of clean speech from multiple noisy speech using neural networks. Both the mapping of the far-field speech and combination of the enhanced speech and the estimated interfering speech are investigated. Our neural network based feature enhancement method incorporates the noise information and can be viewed as a non-linear log spectral subtraction. Experimental studies on MONC corpus showed that MLP-based mapping techniques yields a improvement in the recognition accuracy for the overlapping speech.
aZIBO: A New Descriptor Based in Shape Moments and Rotational Invariant Features

In this work, a descriptor called a ZIBO (absolute Zernike moments with Invariant Boundary Orientation) that describes the shape of objects using the module of Zernike moments and the edge features obtained from an almost rotational invariant version of the Edge Gradient Co-occurrence Matrix (EGCM) is proposed. The two descriptors obtained, the Zernike module as global descriptor and the new version of EGCM as local one, are used to characterize images from three different datasets, Kimia99, MPEG2 and MPEG7. Later on, the concatenation of both local and global descriptors was evaluated using kNN with City block and Chi-square distance metrics. Also, the descriptors are assessed separately with a weight-based method, being the results obtained compared with the ones reached by the baseline method, ZMEG (Zernike Moment Edge Gradient). Using MPEG7, which is the most challenging dataset, and the weight-based classifier, this proposal obtained a success rate of 78.29%, outperforming the 75.86% achieved by ZMEG method. With the MPEG2 dataset, results were even better with an 81.00% of success rate against 77.25% of ZMEG.
3D FEA simulation of segmented reinforcement variable stiffness composites

Reconfigurable and morphing structures may provide significant improvement in overall platform performance through optimization over broad operating conditions. The realization of this concept requires structures, which can accommodate the large deformations necessary with modest weight and strength penalties. Other studies suggest morphing structures need new materials to realize the benefits that morphing may provide. To help meet this need, we have developed novel composite materials based on specially designed segmented reinforcement and shape memory polymer matrices that provide unique combinations of deformation and stiffness properties. To tailor and optimize the design and fabrication of these materials for particular structural applications, one must understand the envelope of morphing material properties as a function of microstructural architecture and constituent properties. Here we extend our previous simulations of these materials by using 3D models to predict stiffness and deformation properties in variable stiffness segmented composite materials. To understand the effect of various geometry tradeoffs and constituent properties on the elastic stiffness in both the high and low stiffness states, we have performed a trade study using a commercial FEA analysis package. The modulus tensor is constructed and deformation properties are computed from representative volume elements (RVE) in which all (6) basic loading conditions are applied. Our test matrix consisted of four composite RVE geometries modeled using combinations of 5 SMP and 3 reinforcement elastic moduli. Effective composite stiffness and deformation results confirm earlier evidence of the essential performance tradeoffs of reduced stiffness for increasing reversible strain accommodation with especially heavy dependencies on matrix modulus and microstructural architecture. Furthermore, our results show these laminar materials are generally orthotropic and indicate that previous calculations of matrix gap and interlaminar strains based on kinematic approximations are accurate to within 10-20% for many material systems. We compare these models with experimental results for a narrow geometry and material set to show the accuracy of the models as compared to physical materials. Our simulations indicate that improved shape memory polymer materials could enable a composite material that can accommodate ~30% strain with a cold state stiffness of ~30GPa. This would improve the current state of the art 5-10x and significantly reduce the weight and stiffness costs of using a morphing component.
Kaposi's Sarcoma-Associated Herpesvirus-Encoded LANA Interacts with Host KAP1 To Facilitate Establishment of Viral Latency

ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) typically displays two different phases in its life cycle, the default latent phase and the lytic phase. There is a short period of lytic gene expression in the early stage of KSHV primary infection. The factors involved in the shutdown process of lytic gene expression are poorly identified. It has been shown that the latency-associated nuclear antigen (LANA) encoded by KSHV plays an important role in the establishment of viral latency. In screening, we identified a host protein, Krüppel-associated box domain-associated protein 1 (KAP1), that bound to LANA. We validated the interaction between LANA and KAP1 in vivo and in vitro, as well as their colocalization in the nucleus. We mapped out that LANA interacted with both the N- and C-terminal domains of KAP1. Based on the interface of LANA-KAP1 interaction determined, we proved that LANA recruited KAP1 to the RTA promoter region of the KSHV genome. We revealed that KAP1 was involved in transcriptional repression by LANA. We found multiple cooccupation sites of LANA and KAP1 on the whole KSHV genome by chromatin immunoprecipitation for sequencing (ChIP-seq) and demonstrated that LANA-recruited KAP1 played a critical role in the shutdown of lytic gene expression during the early stage of KSHV primary infection. Taken together, our data suggest that LANA interacts with KAP1 and represses lytic gene expression to facilitate the establishment of KSHV latency. IMPORTANCE Our study revealed the mechanism of transcriptional repression by LANA during KSHV primary infection, providing new insights into the process of KSHV latency establishment.
Morphology Control of Polysulfone Membranes in Filtration Processes: a Critical Review

Polysulfone (PSU) membranes have been widely applied in microfiltration and ultrafiltration processes due to their excellent properties, such as chemical inertness across the entire pH range, compressive strength, and thermal stability. Despite these advantages, the application of PSU membranes in filtration processes has often been restricted due to their hydrophobic nature, which results in serious membrane fouling and a reduced permeate flux. Moreover, PSU membranes suffer from several disadvantages, including bulky structure, low binding force between fibers, and poor mechanical properties. The key factor in the development and application of polymeric membranes is the control of its polymeric morphology due to the significant influence of membrane morphology on the membrane performance. Effective techniques of controlling PSU membrane morphology are accessed, and the effects of the morphological control on mechanical properties, chemical stability, membrane performance, and membrane fouling are investigated. Findings from various individual studies were analyzed and discussed in order to provide a critical review of this subject. The results emphasized that the membrane pore size and surface porosity mostly governs PSU membrane morphology, which enhances membrane performance and reduces membrane fouling.
Cytoplasmic condensation is both necessary and sufficient to induce apoptotic cell death

Programmed cell death (apoptosis) is important in tissue maintenance. Hallmarks of apoptosis include caspase activation, DNA fragmentation and an overall reduction in cell volume. Whether this apoptotic volume decrease (AVD) is a mere response to initiators of apoptosis or whether it is functionally significant is not clear. In this study, we sought to answer this question using human malignant glioma cells as a model system. In vivo, high grade gliomas demonstrate an increased percentage of apoptotic cells as well as upregulation of death ligand receptors. By dynamically monitoring cell volume, we show that the induction of apoptosis, via activation of either the intrinsic or extrinsic pathways with staurosporine or TRAIL, respectively, resulted in a rapid AVD in D54-MG human glioma cells. This decrease in cell volume could be prevented by inhibiting the efflux of Cl– through channels. Such suppression of AVD also reduced the activation of caspases 3, 8 and 9 and suppressed DNA fragmentation. Importantly, experimental manipulations that reduce the cell volume to 70% of the original volume for periods of at least 3 hours were sufficient to initiate apoptosis even in the absence of death ligands. Hence, this data suggests that cell condensation is both necessary and sufficient for the induction of apoptosis.
ZigBee-based Remote Patient Monitoring

This paper describes a developed continuous patient monitoring system based on the ZigBee protocol. The system was tested in the hospital environment using six sensor devices in two different modes. For electrocardiogram transmission and in the absence of hidden-nodes, the system achieved a mean delivery ratio of 100% and 98.56%, respectively for star and 2-hop tree network topologies. When sensor devices were arranged in a way that three of them were unable to hear the transmissions made by the other three, the mean delivery ratio dropped to 83.96%. However, when sensor devices were reprogrammed to transmit only heart rate values, the mean delivery ratio increased to 99.90%, despite the presence of hidden-nodes.