Miracle-dz/UniFAR-FTUs huggingface dataset:
Pignistic Probability Transforms for Mixes of Low- and High-Probability Events

In some real world information fusion situations, time critical decisions must be made with an incomplete information set. Belief function theories (e.g., Dempster-Shafer theory of evidence, Transferable Belief Model) have been shown to provide a reasonable methodology for processing or fusing the quantitative clues or information measurements that form the incomplete information set. For decision making, the pignistic (from the Latin pignus, a bet) probability transform has been shown to be a good method of using Beliefs or basic belief assignments (BBAs) to make decisions. For many systems, one need only address the most-probable elements in the set. For some critical systems, one must evaluate the risk of wrong decisions and establish safe probability thresholds for decision making. This adds a greater complexity to decision making, since one must address all elements in the set that are above the risk decision threshold. The problem is greatly simplified if most of the probabilities fall below this threshold. Finding a probability transform that properly represents mixes of low- and high-probability events is essential. This article introduces four new pignistic probability transforms with an implementation that uses the latest values of Beliefs, Plausibilities, or BBAs to improve the pignistic probability estimates. Some of them assign smaller values of probabilities for smaller values of Beliefs or BBAs than the Smets pignistic transform. They also assign higher probability values for larger values of Beliefs or BBAs than the Smets pignistic transform. These probability transforms will assign a value of probability that converges faster to the values below the risk threshold. A probability information content (PIC) variable is also introduced that assigns an information content value to any set of probability. Four operators are defined to help simplify the derivations.
Molecular identification and quantification of bacteria from endodontic infections using real-time polymerase chain reaction.

INTRODUCTION It was the aim of the present study to evaluate root canal samples for the presence and numbers of specific species as well as for total bacterial load in teeth with chronic apical periodontitis using quantitative real-time polymerase chain reaction (PCR). METHODS Forty adult patients with one radiographically documented periapical lesion were included. Twenty teeth presented with primary infections and 20 with secondary infections, requiring retreatment. After removal of necrotic pulp tissue or root canal filling, a first bacterial sample was obtained. Following chemo-mechanical root canal preparation a second sample was taken and a third sample was obtained after 14 days of intracanal dressing with calcium hydroxide. Analysis by real-time PCR enabled the quantification of total bacterial counts and of nine selected species. RESULTS Root canals with primary infections harbored significantly more bacteria (by total bacterial count) than teeth with secondary infections (P < 0.05). Mean total bacterial count in the retreatment group was 2.1 x 10(6) and was significantly reduced following root canal preparation (3.6 x 10(4)) and intracanal dressing (1.4 x 10(5)). Corresponding values for primary infections were: 4.6 x 10(7), 3.6 x 10(4), and 6.9 x 10(4). The numbers of the selected bacteria and their detection frequency were also significantly reduced. CONCLUSION Root canals with primary infections contained a higher bacterial load. Chemo-mechanical root canal preparation reduced bacterial counts by at least 95%.
Late endosomal transport and tethering are coupled processes controlled by RILP and the cholesterol sensor ORP1L

Summary Late endosomes and lysosomes are dynamic organelles that constantly move and fuse to acquire cargo from early endosomes, phagosomes and autophagosome. Defects in lysosomal dynamics cause severe neurodegenerative and developmental diseases, such as Niemann–Pick type C disease and ARC syndrome, yet little is known about the regulation of late endosomal fusion in a mammalian system. Mammalian endosomes destined for fusion need to be transported over very long distances before they tether to initiate contact. Here, we describe that lysosomal tethering and transport are combined processes co-regulated by one multi-protein complex: RAB7–RILP–ORP1L. We show that RILP directly and concomitantly binds the tethering HOPS complex and the p150Glued subunit of the dynein motor. ORP1L then functions as a cholesterol-sensing switch controlling RILP–HOPS–p150Glued interactions. We show that RILP and ORP1L control Ebola virus infection, a process dependent on late endosomal fusion. By combining recruitment and regulation of both the dynein motor and HOPS complex into a single multiprotein complex, the RAB7–RILP–ORP1L complex efficiently couples and regulates the timing of microtubule minus-end transport and fusion, two major events in endosomal biology.
Transparent motion perception as detection of unbalanced motion signals. III. Modeling

In the preceding two companion articles we studied the conditions under which transparent motion perception occurs through psychophysical experiments, and investigated the underlining neural mechanisms through physiological recordings. The main finding of our perceptual experiments was that whenever a display has finely balanced motion signals in all local areas, it is perceptually nontransparent, and that transparent displays always contain motion signals in different directions that are either spatially unbalanced, or unbalanced in their disparity or spatial frequency contents. In the physiological experiments, we found two stages in the processing of transparent stimuli. The first stage is located primarily in area V1. At this stage motion measurements are made and V1 cells respond well to both the balanced, nontransparent stimuli and the unbalanced, perceptually transparent stimuli. The second stage is located primarily in area MT. MT cells show strong suppression between opposite directions of motion. The suppression for the unbalanced, transparent stimuli is significantly less than that for the balanced, nontransparent stimuli. Therefore, the activity in the second, MT stage correlates better with the perception of motion transparency than the first, V1 stage, which does not distinguish reliably between transparent and nontransparent motion. The above experiments suggest a two-stage model of motion perception with a motion measurement stage in V1 and an opponent- direction suppression stage in area MT. In this article we explicitly test this model through analysis and computer simulations, and compare the response of the model to the perceptual and physiological results using the same balanced and unbalanced stimuli we used in the experiments. In the first stage of the computational model, motion energies in different spatial frequency and disparity ranges are extracted from each local region. Similar to V1, this stage does not distinguish between the balanced and unbalanced stimuli. In the subsequent stage motion energies of opposite directions but with same spatial frequency and disparity contents suppress each other using subtractive or divisive inhibition. This stage responds significantly better to the transparent stimuli than to the nontransparent ones, in agreement with MT activity.
Enhanceosome-Dependent Manner Expression in an MHC NLRC 5 Controls Basal MHC Class I Gene and

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins play important roles in innate immune responses as pattern-recognition receptors. Although most NLR proteins act in cell autonomous immune pathways, some do not function as classical pattern-recognition receptors. One such NLR protein is the MHC class II transactivator, the master regulator of MHC class II gene transcription. In this article, we report that human NLRC5, which we recently showed to be involved in viral-mediated type I IFN responses, shuttles to the nucleus and activates MHC class I gene expression. Knockdown of NLRC5 in different human cell lines and primary dermal fibroblasts leads to reduced MHC class I expression, whereas introduction of NLRC5 into cell types with very low expression of MHC class I augments MHC class I expression to levels comparable to those found in lymphocytes. Expression of NLRC5 positively correlates with MHC class I expression in human tissues. Functionally, we show that both the N-terminal effector domain of NLRC5 and its C-terminal leucine-rich repeat domain are needed for activation of MHC class I expression. Moreover, nuclear shuttling and function depend on a functional Walker A motif. Finally, we identified a promoter sequence in the MHC class I promoter, the X1 box, to be involved in NLRC5-mediated MHC class I gene activation. Taken together, this suggested that NLRC5 acts in a manner similar to class II transactivator to drive MHC expression and revealed NLRC5 as an important regulator of basal MHC class I expression. H ost cells have evolved a variety of pathogen-recognition receptors, such as the membrane-bound TLRs (1). A second important group of pathogen-recognition receptors , the nucleotide-binding domain leucine-rich repeat (NLR) proteins mediate recognition of pathogen-associated molecular patterns (PAMPs) in the cytosol. NLR proteins share a typical tripartite structure, consisting of an N-terminal death fold effector domain, a central NACHT ATPase domain, and a C-terminal leucine-rich repeat (LRR) domain (2). NLRs can be divided into two main functional groups: the inflammasome and nodosome families. The pyrin-like domain (PYD)-containing inflammasome NLR proteins, of which the two most prominent members are NLRP1 and NLRP3, react to PAMPs and danger-associated molecular patterns by inducing caspase-1 activation and subsequent IL-1b processing (3). In contrast, the caspase activation and recruitment domain (CARD)-containing NLRs, of which the two most prominent members are Nod1 and Nod2, trigger the ca-nonical NF-kB pathway in a receptor interacting kinase 2-and inhibitor of IkB kinase-dependent manner upon exposure to bacterial peptidoglycan …
MRI measurement of the temporal evolution of relative CMRO2 during rat forepaw stimulation

This study reports the first measurement of the relative cerebral metabolic rate of oxygen utilization (rCMRO2) during functional brain activation with sufficient temporal resolution to address the dynamics of blood oxygen level‐dependent (BOLD) MRI signal. During rat forepaw stimulation, rCMRO2 was determined in somatosensory cortex at 3‐sec intervals, using a model of BOLD signal and measurements of the change in BOLD transverse relaxation rate, the resting state BOLD transverse relaxation rate, relative cerebral blood flow (rCBF), and relative cerebral blood volume (rCBV). Average percentage changes from 10 to 30 sec after onset of forepaw stimulation for rCBF, rCBV, rCMRO2, and BOLD relaxation rate were 62 ± 16, 17 ± 2, 19 ± 17, and −26 ± 12, respectively. A poststimulus undershoot in BOLD signal was quantitatively attributed to the temporal mismatch between changes in blood flow and volume, and not to the role of oxygen metabolism. Magn Reson Med 42:944–951, 1999. © 1999 Wiley‐Liss, Inc.
Single trial recognition of anticipatory slow cortical potentials: The role of spatio-spectral filtering

Single trial recognition of slow cortical potentials (SCPs) from full-band EEG (FbEEG) faces different challenges to classical EEG such as noisy, high magnitude (~ ±100 μV) infra slow oscillations (ISO) with f ≤ 0.1 Hz and high frequency spatial noise from a variety of artifacts. We analyze offline the anticipation related SCPs recorded from 11 subjects over two days in a variation of the Contingent Negative Variation (CNV) paradigm with Go and No-go conditions in an assistive technology framework. The results suggest that widely used spatial filters such as Common Average Referencing (CAR) and Laplacian are sub-optimal for the single trial analysis of SCPs. We show that a spatial smoothing filter (SSF), which in combination with CAR enhances the spatially distributed SCP while attenuating high frequency spatial noise. We report, first, that a narrow band filter in the range [0.1 1] Hz captures anticipation related SCP better and effectively reduces ISOs. Second, the SSF in combination with CAR outperforms CAR-alone and Laplacian spatial filters. Third, we compare linear and quadratic classifiers calculated using optimally filtered Cz electrode potentials and report that the best methods resulted in single trial classification accuracies of 83 ±4%, where classifiers were trained on day 1 and tested using data from day 2, to ensure generalization capabilities across days (1-7 days).
Warped-Compression: Enabling power efficient GPUs through register compression

This paper presents Warped-Compression, a warp-level register compression scheme for reducing GPU power consumption. This work is motivated by the observation that the register values of threads within the same warp are similar, namely the arithmetic differences between two successive thread registers is small. Removing data redundancy of register values through register compression reduces the effective register width, thereby enabling power reduction opportunities. GPU register files are huge as they are necessary to keep concurrent execution contexts and to enable fast context switching. As a result register file consumes a large fraction of the total GPU chip power. GPU design trends show that the register file size will continue to increase to enable even more thread level parallelism. To reduce register file data redundancy warped-compression uses low-cost and implementationefficient base-delta-immediate (BDI) compression scheme, that takes advantage of banked register file organization used in GPUs. Since threads within a warp write values with strong similarity, BDI can quickly compress and decompress by selecting either a single register, or one of the register banks, as the primary base and then computing delta values of all the other registers, or banks. Warped-compression can be used to reduce both dynamic and leakage power. By compressing register values, each warp-level register access activates fewer register banks, which leads to reduction in dynamic power. When fewer banks are used to store the register content, leakage power can be reduced by power gating the unused banks. Evaluation results show that register compression saves 25% of the total register file power consumption.
Characterization of Profilin Polymorphism in Pollen with a Focus on Multifunctionality

Profilin, a multigene family involved in actin dynamics, is a multiple partners-interacting protein, as regard of the presence of at least of three binding domains encompassing actin, phosphoinositide lipids, and poly-L-proline interacting patches. In addition, pollen profilins are important allergens in several species like Olea europaea L. (Ole e 2), Betula pendula (Bet v 2), Phleum pratense (Phl p 12), Zea mays (Zea m 12) and Corylus avellana (Cor a 2). In spite of the biological and clinical importance of these molecules, variability in pollen profilin sequences has been poorly pointed out up until now. In this work, a relatively high number of pollen profilin sequences have been cloned, with the aim of carrying out an extensive characterization of their polymorphism among 24 olive cultivars and the above mentioned plant species. Our results indicate a high level of variability in the sequences analyzed. Quantitative intra-specific/varietal polymorphism was higher in comparison to inter-specific/cultivars comparisons. Multi-optional posttranslational modifications, e.g. phosphorylation sites, physicochemical properties, and partners-interacting functional residues have been shown to be affected by profilin polymorphism. As a result of this variability, profilins yielded a clear taxonomic separation between the five plant species. Profilin family multifunctionality might be inferred by natural variation through profilin isovariants generated among olive germplasm, as a result of polymorphism. The high variability might result in both differential profilin properties and differences in the regulation of the interaction with natural partners, affecting the mechanisms underlying the transmission of signals throughout signaling pathways in response to different stress environments. Moreover, elucidating the effect of profilin polymorphism in adaptive responses like actin dynamics, and cellular behavior, represents an exciting research goal for the future.
The value of serum antibodies in differentiating inflammatory bowel disease, predicting disease activity and disease course in the newly diagnosed patient

Abstract Background: Data on serum antibodies in untreated adult inflammatory bowel disease (IBD) patients at diagnosis are scarcely available, and results on the stability of antibody presence over time are inconsistent. Our aim was to investigate antibodies in newly diagnosed, untreated IBD patients in relation to disease phenotype and course. Furthermore, we analyzed antibody presence over time. Methods: Baseline anti-Saccharomyces cerevisiae antibodies (ASCA), anti-chitobioside carbohydrate antibodies (ACCA), anti-laminaribioside carbohydrate antibodies (ALCA) and anti-mannobioside carbohydrate antibodies (AMCA) were measured with enzyme-linked immunosorbent assays and perinuclear anti-neutrophilic cytoplasmic antibodies (pANCA) was measured by indirect immunofluorescence in serum of 120 untreated IBD patients at diagnosis and 19 healthy controls. Antibodies were related to disease outcomes. Serial measurements were available in 71 patients. Results: The combination of pANCA and ASCA enabled good discrimination between UC and CD (p = .004). Antibody presence was relatively stable over time, even though there were significant changes in concentrations. There was a trend towards larger fluctuations in concentration with immunosuppressive medication. Baseline pANCA in UC patients correlated with calprotectin values (rho = .545, p = .019) and change in pANCA status over time was associated with disease activity at that moment. No associations were found with antibodies at diagnosis and disease outcomes. Conclusion: Antibody profiles at diagnosis support the distinction between CD and UC. Anti-glycan antibodies are reasonably stable over time, but may fluctuate under the influence of immunosuppressive treatment which may explain the inconsistency in findings hitherto. The appearance or disappearance of pANCA antibodies during follow-up correlated with disease activity in UC and may be used in disease monitoring.
Next-Generation Digital Information Storage in DNA

Digital information can be stored in DNA at densities higher than digital media such as flash memory or quantum holography. Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing.
Forensix: a robust, high-performance reconstruction system

When computer intrusions occur, one of the most costly, time-consuming, and human-intensive tasks is the analysis and recovery of the compromised system. At a time when the cost of human resources dominates the cost of CPU, network, and storage resources, we argue that computing systems should, in fact, be built with automated analysis and recovery as a primary goal. Towards this end, we describe the design, implementation, and evaluation of Forensix: a robust, high-precision reconstruction and analysis system for supporting the computer equivalent of "TiVo". Forensix uses three key mechanisms to improve the accuracy and reduce the human overhead of performing forensic analysis. First it performs comprehensive monitoring of the execution of a target system at the kernel event level, giving a high-resolution, application-independent view of all activity. Second, it streams the kernel event information, in real-time, to append-only storage on a separate, hardened, logging machine, making the system resilient to a wide variety of attacks. Third, it uses database technology to support high-level querying of the archived log, greatly reducing the human cost of performing forensic analysis.
Development of function-related groups version 2.0: a classification system for medical rehabilitation.

OBJECTIVE To present a new version (2.0) of the Functional Independence Measure-Function Related Group (FIM-FRG) case-mix measure. DATA SOURCE/STUDY SETTING 85,447 patient discharges from 252 freestanding facilities and hospital units contained in the 1992 Uniform Data System for Medical Rehabilitation. STUDY DESIGN Patient impairment category, functional status at admission to rehabilitation, and patient age were used to develop groups that were homogeneous with respect to length of stay. Within each impairment category patients were randomly assigned to one data set to create the system (through recursive partitioning) or a second set for validation. Clinical and statistical criteria were used to increase the percentage of patients classified, expand the impairment categories of FIM-FRGs Version 1.1, and evaluate the incremental predictive ability of coexisting medical diagnoses. Predictive stability over time was evaluated using 1990 discharges. PRINCIPAL FINDINGS In Version 2.0, the percentage of patients classified was increased to 92 percent. Version 2.0 includes two new impairment categories and separate groups for patients admitted to rehabilitation for evaluation only. Coexisting medical diagnoses did not improve LOS prediction. The system explains 31.7 percent of the variance in the logarithm of LOS in the 1992 validation sample, and 31.0 percent in 1990 discharges. CONCLUSIONS FIM-FRGs Version 2.0 includes more specific impairment categories, classifies a higher percentage of patient discharges, and appears sufficiently stable over time to form the basis of a payment system for inpatient medical rehabilitation.