Miracle-dz/UniFAR-FTUs huggingface dataset:
Hydrolysis of 4-methylumbelliferyl N-acetyl-chitotrioside catalyzed by hen and turkey lysozymes. pH dependence of the kinetics constants.

The binding constants of 4-methylumbelliferyl-beta-glycosides of (GlcNAc)2 ((GlcNAc)2-MeU) and of (GlcNAc)3 ((GlcNAc)3-MeU) to hen lysozyme [EC 3.2. 1.17] were determined by measuring changes in the fluorescence at 375 nm. It was shown that (GlcNAc)2-MeU and (GlcNAc)3-MeU bind mainly at subsites B, C, and D, and A, B, C, and D, respectively, with the terminal MeU group bound at subsite D. The rate of hydrolysis of (GlcNAc)3-MeU catalyzed by hen and turkey lysozymes was determined at 0.1 ionic strength and 42 degrees C in the pH range of 2 to 8. The release of 4-methylumbelliferone was followed fluorimetrically. The pH dependences of kcat, kcat/Km, and Km were analyzed assuming that that nonproductive binding occurs competitively and that the molecular species with ionized Asp 52 and protonated Glu 35 is active. Comparison of the pH dependences of the kinetic constants for hen lysozyme with those for turkey lysozyme, in which Asp 101 of hen lysozyme is replaced by Gly, made it possible to determine the pK values of Asp 52, Glu 35, and Asp 101. The pK values of Asp 52 and Glu 35 were 3.60 and 6.20, respectively, for hen and turkey lysozymes and 3.95 and 6.55, respectively, for their nonproductive complexes. The pK value of Asp 101 of hen lysozyme was 4.20 for the free enzyme, 3.30 for the nonproductive complex, and 3.95 for the productive complex. These pK values, except for the pK value of Asp 52 of the nonproductive complex, are in excellent agreement with those determined by spectroscopic methods in our laboratory (Kurasmitsu et al. (1974) J. Biochem. 76, 671--683; (1975) ibid. 77, 291--301; (1977) ibid. 82, 585--597; (1978) ibid. 83, 159--170). This demonstrates that lysozyme-catalyzed hydrolysis can be fully explained in terms of the proposal based on the X-ray data (Blake et al. (1967) Proc. Roy. Soc. B167, 378--388), with regard to the participation of Asp 52 and Glu 35.
Way-predicting set-associative cache for high performance and low energy consumption

This paper proposes a new approach using way prediction for achieving high performance and low energy consumption of set-associative caches. By accessing only a single cache way predicted, instead of accessing all the ways in a set, the energy consumption can be reduced. This paper shows that the way-predicting set-associative cache improves the ED (energy-delay) product by 60-70% compared to a conventional set-associative cache,.
Automatic speculative DOALL for clusters

Automatic parallelization for clusters is a promising alternative to time-consuming, error-prone manual parallelization. However, automatic parallelization is frequently limited by the imprecision of static analysis. Moreover, due to the inherent fragility of static analysis, small changes to the source code can significantly undermine performance. By replacing static analysis with speculation and profiling, automatic parallelization becomes more robust and applicable. A naïve automatic speculative parallelization does not scale for distributed memory clusters, due to the high bandwidth required to validate speculation. This work is the first automatic speculative DOALL (Spec-DOALL) parallelization system for clusters. We have implemented a prototype automatic parallelization system, called Cluster Spec-DOALL, which consists of a Spec-DOALL parallelizing compiler and a speculative runtime for clusters. Since the compiler optimizes communication patterns, and the runtime is optimized for the cases in which speculation succeeds, Cluster Spec-DOALL minimizes the communication and validation overheads of the speculative runtime. Across 8 benchmarks, Cluster Spec-DOALL achieves a geomean speedup of 43.8x on a 120-core cluster, whereas DOALL without speculation achieves only 4.5x speedup. This demonstrates that speculation makes scalable fully-automatic parallelization for clusters possible.
TSV-constrained micro-channel infrastructure design for cooling stacked 3D-ICs

Micro-channel based liquid cooling has significant capability of removing high density heat in 3D-ICs. The conventional micro-channel structures investigated for cooling 3D-ICs use straight channels. However, the presence of TSVs which form obstacles to the micro-channels prevents distribution of straight micro-channels. In this paper, we investigate the methodology of designing TSV-constrained micro-channel infrastructure. Specifically, we decide the locations and geometry of micro-channels with bended structure so that the cooling effectiveness is maximized. Our micro-channel structure could achieve up to 87% pumping power savings compared with the structure using straight micro-channels.
Carboxyl‐terminal truncation of leucine76 converts heparin‐binding EGF‐like growth factor from a heparin‐enhancible to a heparin‐suppressible growth factor

Previous studies have indicated that heparin differentially regulates heparin‐binding EGF‐like growth factor (HB‐EGF) and amphiregulin (AR) mitogenic activity. To further explore this phenomenon, these mitogens were compared under identical cell culture conditions in two different assays. The results of our present investigation demonstrated that AR‐mediated mitogenic activity in the murine AKR‐2B fibroblast‐like cell line was inhibited by heparin, while HB‐EGF activity was enhanced. However, the absolute effect of heparin appeared to be cell type specific since HB‐EGF mitogenic activity was not dramatically affected by coincubation with heparin when tested on human dermal fibroblasts. Several studies have indicated that mutation of a conserved leucine in the carboxyl‐terminal region of both EGF and transforming growth factor‐α results in decreased affinity for EGF receptors. Since this leucine is present in the analogous position of HB‐EGF, but absent in AR, we examined the effect of deleting this residue by carboxyl‐terminal truncation of HB‐EGF. Analysis of recombinant forms of HB‐EGF demonstrated that HB‐EGF can be converted to a heparin‐inhibited growth factor if the putative mature form of the protein is truncated by two residues (leucine76 and proline77) at the carboxyl terminus. Further analysis demonstrated that only leucine76 appears to be required for heparin‐dependent enhancement of HB‐EGF‐mediated mitogenic activity, indicating that this amino acid may play a pivotal role in controlling the response of HB‐EGF to heparin or related glycosaminoglycan sulfates. Our results also suggest that expression of different HB‐EGF forms in vivo could result in the production of HB‐EGFs with divergent responses to sulfated glycosaminoglycans and proteoglycans. © 1995 Wiley‐Liss, Inc.
Elective medium for the direct count of vibrio (campylobacter) fusobacteria, bacteroides, selenomonas and veillonella in the gingival crevice flora.

A modified reinforced clostridial agar with blood and china blue permitted the recognition of Vibrio(Campylobacter)sputorum, Fusobacterium nucleatum, Bacteroides ochraceus, Selenomonas sputigena and Veillonella species by colony form and colour. Microscopy and biochemical tests confirmed the relation between colonial morphology and species. The medium facilitates identification and permits differential counts of these five gram-negative anaerobes in the gingival crevice flora.
Sensation-Seeking and Differentially Arousing Television Commercials

Abstract The authors predicted (a) that disinhibited consumers would react more favorably to advertising that was high in arousal and (b) that inhibited consumers would react more favorably to advertising that was low in arousal. They tested these predictions by having U.S. college students evaluate both the commercial and the product being marketed in 1 of 2 beer commercials. The prospective buyers then completed a measure of dispositional sensation-seeking tendencies. Although the participants who differed in disinhibition reacted differently to the 2 commercials, the nature of their responses was more complex than predicted.
Handling Unstructured Data for Semantic Web – A Natural Language Processing Approach

World Wide Web is a large repository of structured data and un-structured data. Structured data has a wellfixed structure thus is easy to analyze and use with computational machinery. On the other side handling of unstructured data is a challenging task for knowledge base. This paper describes Natural Language Processing techniques for handling unstructured data and its usefulness for semantic Web so that knowledge extracted from un-structured data can be useful for searchers ease of access and extraction of relevant documents.
Hybridization of Photogrammetry and Laser Scanning Technology for As-Built 3D CAD Models

Digital Mockups (Virtual Prototypes) significantly reduce risk and cost on large aerospace programs, but their accuracy hinges on the creation of 3D models of existing facilities, based on "as-built" field conditions instead of less-accurate design blueprints. Methods for creating as-built models vary from tedious hand-measurements, to photograph-rectification-survey techniques (collectively known as photogrammetry), to the evolving technology of terrestrial laser scanning. Lockheed Martin has proven through robust field testing that the accuracy of each technology is variable to specific applications. Therefore, we have developed a hybrid method that leverages the strengths of each technology, including edge recognition, targeting accuracy, and complex-surface collection. This hybridization has helped to identify key technical deficiencies in the current state-of- practice for as-built CAD modeling, such as automatic modeling and feature extraction. In addition, Lockheed Martin has refined a statistical evaluation technique to objectively measure the accuracy of the final model against the field conditions, regardless of the technology utilized. The advantages and disadvantages of each technology are presented here, as well as methodologies for effectively combining the technologies into a more-accurate and efficient hybrid process. This overall capability is crucial to Lockheed Martin for reducing reliance on physical prototypes, and optimizing project return on cost, schedule, and risk.
Dissociable Processes of Cognitive Control during Error and Non-Error Conflicts: A Study of the Stop Signal Task

Background Conflict detection and subsequent behavioral adjustment are critical to daily life, and how this process is controlled has been increasingly of interest. A medial cortical region which includes the anterior cingulate cortex (ACC) has been theorized to act as a conflict detector that can direct prefrontal activity for behavioral adjustments. This conflict monitoring hypothesis was supported by many imaging studies of the Stroop task, with a focus on non-error processes. Here we sought to examine whether this circuit could be generalized to the stop signal task (SST), another behavioral paradigm widely used to study cognitive control. In particular, with a procedure to elicit errors in the SST, we examined whether error and non-error control were mediated by the same pathways. Methodology/Principal Findings In functional magnetic resonance imaging of 60 healthy adults, we demonstrated that the medial cortical activity during stop success (SS) as compared to go success (G) trials is correlated with increased prefrontal activity in post-stop SS as compared to post-go SS trials, though this correlation was not specific to the medial cortical region. Furthermore, thalamic and insular rather than medial cortical activation during stop error (SE) as compared to G trials correlated with increased prefrontal activity in post-stop SS as compared to post-go SS trials. Conclusions/Significance Taken together, these new findings challenge a specific role of the ACC and support distinct pathways for error and non-error conflict processing in cognitive control.
Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images

We make an analogy between images and statistical mechanics systems. Pixel gray levels and the presence and orientation of edges are viewed as states of atoms or molecules in a lattice-like physical system. The assignment of an energy function in the physical system determines its Gibbs distribution. Because of the Gibbs distribution, Markov random field (MRF) equivalence, this assignment also determines an MRF image model. The energy function is a more convenient and natural mechanism for embodying picture attributes than are the local characteristics of the MRF. For a range of degradation mechanisms, including blurring, nonlinear deformations, and multiplicative or additive noise, the posterior distribution is an MRF with a structure akin to the image model. By the analogy, the posterior distribution defines another (imaginary) physical system. Gradual temperature reduction in the physical system isolates low energy states (``annealing''), or what is the same thing, the most probable states under the Gibbs distribution. The analogous operation under the posterior distribution yields the maximum a posteriori (MAP) estimate of the image given the degraded observations. The result is a highly parallel ``relaxation'' algorithm for MAP estimation. We establish convergence properties of the algorithm and we experiment with some simple pictures, for which good restorations are obtained at low signal-to-noise ratios.
Long-term outcome and efficacy of endoscopic hemorrhoid ligation for symptomatic internal hemorrhoids.

AIM To assess the long-term outcome of endoscopic hemorrhoid ligation (EHL) for the treatment of symptomatic internal hemorrhoids. METHODS A total of 759 consecutive patients (415 males and 344 females) were enrolled. Clinical presentations were rectal bleeding (593 patients) and mucosal prolapse (166 patients). All patients received EHL at outpatient clinics. Hemorrhoid severity was classified by Goligher's grading. The mean follow-up period was 55.4 mo (range, 45-92 mo). RESULTS The number of band ligations averaged 2.35 in the first session for bleeding and 2.69 for prolapsed patients. Bleeding was controlled in 587 (98.0%) patients, while prolapse was reduced in 137 (82.5%) patients. After treatment, 93 patients experienced anal pain and 48 patients had mild bleeding. Patient subjective satisfaction was 93.6%. Repeat treatment or surgery was performed if symptoms were not relieved in the first session. In the bleeding group, the recurrence rate was 3.7% (22 patients) at 1 year, and 6.6% and 13.0% at 2 and 5 years. In the prolapsed group, the recurrence rate was 3.0%, 9.6% and 16.9% at 1, 2 and 5 years, respectively. CONCLUSION EHL is an easy and well-tolerated procedure for the treatment of symptomatic internal hemorrhoids, with good long-term results.
Downregulation of PCAF by miR-181a/b Provides Feedback Regulation to TNF-α–Induced Transcription of Proinflammatory Genes in Liver Epithelial Cells

Aberrant cellular responses to proinflammatory cytokines, such as TNF-α, are pathogenic features in most chronic inflammatory diseases. A variety of extracellular and intracellular feedback pathways has evolved to prevent an inappropriate cellular reaction to these proinflammatory cytokines. In this study, we report that TNF-α treatment of human and mouse cholangiocytes and hepatocytes downregulated expression of p300/CBP-associated factor (PCAF), a coactivator and an acetyltransferase that promotes histone acetylation and gene transcription. Of these upregulated microRNAs in TNF-α–treated cells, miR-181a/b (miR-181a and miR-181b) suppressed translation of PCAF mRNA. Functional manipulation of miR-181a/b caused reciprocal alterations in PCAF protein expression in cultured cholangiocytes and hepatocytes. Inhibition of miR-181a/b function with anti-miRs blocked TNF-α–induced suppression of PCAF expression. Promoter recruitment of PCAF was shown to be associated with TNF-α–induced transcription of inflammatory genes. Intriguingly, pretreatment of cells with TNF-α inhibited transcription of inflammatory genes in response to subsequent TNF-α stimulation. Overexpression of PCAF or inhibition of miR-181a/b function with anti-miRs attenuated the inhibitory effects of TNF-α pretreatment on epithelial inflammatory response to subsequent TNF-α stimulation. Downregulation of PCAF and the inhibitory effects of TNF-α pretreatment on liver epithelial inflammatory response were further confirmed in a mouse model of TNF-α i.p. injection. These data suggest that PCAF is a target for miR-181a/b, and downregulation of PCAF by TNF-α provides negative feedback regulation to inflammatory reactions in liver epithelial cells, a process that may be relevant to the epigenetic fine-tuning of epithelial inflammatory processes in general.
Minkowski Distance based Feature Selection Algorithm for Effective Intrusion Detection

Intrusion Detection System (IDS) plays a major role in the provision of effective security to various types of networks. Moreover, Intrusion Detection System for networks need appropriate rule set for classifying network bench mark data into normal or attack patterns. Generally, each dataset is characterized by a large set of features. However, all these features will not be relevant or fully contribute in identifying an attack. Since different attacks need various subsets to provide better detection accuracy. In this paper an improved feature selection algorithm is proposed to identify the most appropriate subset of features for detecting a certain attacks. This proposed method is based on Minkowski distance feature ranking and an improved exhaustive search that selects a better combination of features. This system has been evaluated using the KDD CUP 1999 dataset and also with EMSVM (1) classifier. The experimental results show that the proposed system provides high classification accuracy and low false alarm rate when applied on the reduced feature subsets.
Estimating Diffusion Probability Changes for AsIC-SIS Model

We address the problem of estimating changes in diffusion probability over a social network from the observed information diffusion results, which is possibly caused by an unknown external situation change. For this problem, we focused on the asynchronous independent cascade (AsIC) model in the SIS (Susceptible/Infected/Susceptible) setting in order to meet more realistic situations such as communication in a blogosphere. This model is referred to as the AsIC-SIS model. We assume that the diffusion parameter changes are approximated by a series of step functions, and their changes are reflected in the observed diffusion results. Thus, the problem is reduced to detecting how many step functions are needed, where in time each one starts and how long it lasts, and what the hight of each one is. The method employs the derivative of the likelihood function of the observed data that are assumed to be generated from the AsIC-SIS model, adopts a divideand-conquer type greedy recursive partitioning, and utilizes an MDL model selection measure to determine the adequate number of step functions. The results obtained using real world network structures confirmed that the method works well as intended. The MDL criterion is useful to avoid overfitting, and the found pattern is not necessarily the same in terms of the number of step functions as the one assumed to be true, but the error is always reduced to a small value.
Split brain: divided perception but undivided consciousness

In extensive studies with two split-brain patients we replicate the standard finding that stimuli cannot be compared across visual half-fields, indicating that each hemisphere processes information independently of the other. Yet, crucially, we show that the canonical textbook findings that a split-brain patient can only respond to stimuli in the left visual half-field with the left hand, and to stimuli in the right visual half-field with the right hand and verbally, are not universally true. Across a wide variety of tasks, split-brain patients with a complete and radiologically confirmed transection of the corpus callosum showed full awareness of presence, and well above chance-level recognition of location, orientation and identity of stimuli throughout the entire visual field, irrespective of response type (left hand, right hand, or verbally). Crucially, we used confidence ratings to assess conscious awareness. This revealed that also on high confidence trials, indicative of conscious perception, response type did not affect performance. These findings suggest that severing the cortical connections between hemispheres splits visual perception, but does not create two independent conscious perceivers within one brain.
Cerebral acetylcholinesterase activity is not decreased in MS patients with cognitive impairment

Background: Neuropsychological studies have extensively described the presence of cognitive dysfunction in MS patients. One possible pharmacological treatment of the impairment could be based on acetylcholinesterase inhibitors (AChEIs), which have shown efficacy in alleviating cognitive impairment in many other disorders. The findings on the efficacy of AChEI medication in MS associated cognitive symptoms are preliminary and no studies concerning cerebral acetylcholinesterase (AChE) activity in these patients have been published. Objective: The objective of the study was to examine cerebral AChE activity in cognitively deteriorated MS patients. Cerebral AChE activity of 10 MS patients with secondary progressive disease and marked cognitive impairment, and 10 healthy controls, was studied with positron emission tomography using tracer 11C-MP4A. Methods: The cognitive profile of the patients was assessed with CERAD (Consortium to Establish a Registry for Alzheimer’s Disease). Results: No differences in cortical AChE activity between MS patients and controls were seen. Conclusions: In the patient group regional AChE activities had inverse correlations with Word learning and MMSE (Mini-Mental State Examination) scores. In the group of cognitively deteriorated MS patients no change in cerebral AChE activity, compared with controls, was observed, but within the patient group more pronounced cognitive symptoms were associated with higher cerebral AChE activity.
Computationally easy outlier detection via projection pursuit with finitely many directions

Outlier detection is fundamental to data analysis. Desirable properties are affine invariance, robustness, low computational burden, and nonimposition of elliptical contours. However, leading methods fail to possess all of these features. The Mahalanobis distance outlyingness (MD) imposes elliptical contours. The projection outlyingness, powerfully involving projections of the data onto all univariate directions, is highly computationally intensive. Computationally easy variants using projection pursuit with but finitely many directions have been introduced, but these fail to capture at once the other desired properties. Here, we develop a ‘robust Mahalanobis spatial outlyingness on projections’ (RMSP) function, which indeed satisfies all the four desired properties. Pre-transformation to a strong invariant coordinate system yields affine invariance, ‘spatial trimming’ yields robustness, and ‘spatial Mahalanobis outlyingness’ is used to obtain computational ease and smooth, unconstrained contours. From empirical study using artificial and actual data, our findings are that SUP is outclassed by MD and RMSP, that MD and RMSP are competitive, and that RMSP is especially advantageous in describing the intermediate outlyingness structure when elliptical contours are not assumed.