Miracle-dz/UniFAR-FTUs huggingface dataset:
The Regulator of G Protein Signaling Domain of Axin Selectively Interacts with Gα12 but Not Gα13

Axin, a negative regulator of the Wnt signaling pathway, contains a canonical regulator of G protein signaling (RGS) core domain. Herein, we demonstrate both in vitro and in cells that this domain interacts with the α subunit of the heterotrimeric G protein G12 but not with the closely related Gα13 or with several other heterotrimeric G proteins. Axin preferentially binds the activated form of Gα12, a behavior consistent with other RGS proteins. However, unlike other RGS proteins, that of axin (axinRGS) does not affect intrinsic GTP hydrolysis by Gα12. Despite its inability to act as a GTPase-activating protein, we demonstrate that in cells, axinRGS can compete for Gα12 binding with the RGS domain of p115RhoGEF, a known G12-interacting protein that links G12 signaling to activation of the small G protein Rho. Moreover, ectopic expression of axinRGS specifically inhibits Gα12-directed activation of the Rho pathway in MDA-MB 231 breast cancer cells. These findings establish that the RGS domain of axin is able to directly interact with the α subunit of heterotrimeric G protein G12 and provide a unique tool to interdict Gα12-mediated signaling processes.
Transfer of R 388 Derivatives by a Pathogenesis-Associated Type IV Secretion System into both Bacteria and Human Cells

Bacterial type IV secretion systems (T4SSs) are involved in processes such as bacterial conjugation and protein translocation to animal cells. In this work, we have switched the substrates of T4SSs involved in pathogenicity for DNA transfer. Plasmids containing part of the conjugative machinery of plasmid R388 were transferred by the T4SS of human facultative intracellular pathogen Bartonella henselae to both recipient bacteria and human vascular endothelial cells. About 2% of the human cells expressed a green fluorescent protein (GFP) gene from the plasmid. Plasmids of different sizes were transferred with similar efficiencies. B. henselae codes for two T4SSs: VirB/VirD4 and Trw. A virB mutant strain was transfer deficient, while a trwE mutant was only slightly impaired in DNA transfer. DNA transfer was in all cases dependent on protein TrwC of R388, the conjugative relaxase, implying that it occurs by a conjugation-like mechanism. A DNA helicasedeficient mutant of TrwC could not promote DNA transfer. In the absence of TrwB, the coupling protein of R388, DNA transfer efficiency dropped 1 log. The same low efficiency was obtained with a TrwB point mutation in the region involved in interaction with the T4SS. TrwB interacted with VirB10 in a bacterial two-hybrid assay, suggesting that it may act as the recruiter of the R388 substrate for the VirB/VirD4 T4SS. A TrwB ATPase mutant behaved as dominant negative, dropping DNA transfer efficiency to almost null levels. B. henselae bacteria recovered from infected human cells could transfer the mobilizable plasmid into recipient Escherichia coli under certain conditions, underscoring the versatility of T4SSs.
Librando: transparent code randomization for just-in-time compilers

Just-in-time compilers (JITs) are here to stay. Unfortunately, they also provide new capabilities to cyber attackers, namely the ability to supply input programs (in languages such as JavaScript) that will then be compiled to executable code. Once this code is placed and marked as executable, it can then be leveraged by the attacker. Randomization techniques such as constant blinding raise the cost to the attacker, but they significantly add to the burden of implementing a JIT. There are a great many JITs in use today, but not even all of the most commonly used ones randomize their outputs. We present librando, the first comprehensive technique to harden JIT compilers in a completely generic manner by randomizing their output transparently ex post facto. We implement this approach as a system-wide service that can simultaneously harden multiple running JITs. It hooks into the memory protections of the target OS and randomizes newly generated code on the fly when marked as executable. In order to provide "black box" JIT hardening, librando needs to be extremely conservative. For example, it completely preserves the contents of the calling stack, presenting each JIT with the illusion that it is executing its own generated code. Yet in spite of the heavy lifting that librando performs behind the scenes, the performance impact is surprisingly low. For Java (HotSpot), we measured slowdowns by a factor of 1.15x, and for compute-intensive JavaScript (V8) benchmarks, a slowdown of 3.5x. For many applications, this overhead is low enough to be practical for general use today.
MathIOmica: An Integrative Platform for Dynamic Omics

Multiple omics data are rapidly becoming available, necessitating the use of new methods to integrate different technologies and interpret the results arising from multimodal assaying. The MathIOmica package for Mathematica provides one of the first extensive introductions to the use of the Wolfram Language to tackle such problems in bioinformatics. The package particularly addresses the necessity to integrate multiple omics information arising from dynamic profiling in a personalized medicine approach. It provides multiple tools to facilitate bioinformatics analysis, including importing data, annotating datasets, tracking missing values, normalizing data, clustering and visualizing the classification of data, carrying out annotation and enumeration of ontology memberships and pathway analysis. We anticipate MathIOmica to not only help in the creation of new bioinformatics tools, but also in promoting interdisciplinary investigations, particularly from researchers in mathematical, physical science and engineering fields transitioning into genomics, bioinformatics and omics data integration.
Mining Student Behavior Patterns in Reading Comprehension Tasks

Reading comprehension is critical in life-long learning as well as in the workplace. In this paper, we describe how multidimensional k-means clustering combined with Bloom’s Taxonomy can be used to determine positive and negative cognitive skill sets with respect to reading comprehension tasks. This information could be used to inform environments that support students improving their meta-cognitive skills.
Leptin attenuates hypoxia/reoxygenation‐induced activation of the intrinsic pathway of apoptosis in rat H9c2 cells

Cardiomyocyte apoptosis is a component of cardiac remodeling that can contribute to heart failure in obesity. A role for leptin in mediating this process has been suggested and the objective of this work was to investigate the effect of leptin on apoptosis and associated mechanisms in H9c2 cells which were subjected to hypoxia/reoxygenation (HR) to mimic myocardial ischemia/reperfusion. Qualitative immunofluorescent and quantitative laser scanning cytometry approaches demonstrated that exposure of cells to HR increased DNA fragmentation (TUNEL staining) which was attenuated by leptin (6 nM, 1 h) pretreatment. We also found increased annexin‐V binding and caspase‐3 activity in cells exposed to HR, both of which were attenuated by leptin pretreatment. Leptin reduced HR‐induced translocation of the pro‐apoptotic protein Bax to the mitochondrial membrane, which provides a mechanism to explain its protective effect. Consequently, leptin attenuated the HR‐induced decrease in mitochondrial membrane potential and increase in cytochrome c release from mitochondria. Leptin treatment increased the phosphorylation of p38 MAPK and AMPK and respective inhibitors of these kinases, SB203580 and Compound C, prevented the ability of leptin to decrease HR‐induced caspase‐3 activity. In conclusion, we establish mechanisms via which leptin exerts anti‐apoptotic effects that may be of significance in understanding the development of heart failure in obesity. J. Cell. Physiol. 221: 490–497, 2009. © 2009 Wiley‐Liss, Inc.
The Hip Fracture Patient on Warfarin: Evaluating Blood Loss and Time to Surgery

Objectives: To compare blood loss, delay of surgery, and short-term adverse events in (1) patients admitted on warfarin versus nonanticoagulated controls and (2) warfarin patients with day of surgery (DOS) international normalized ratio (INR) of 1.5 or greater versus below 1.5. Design: Retrospective cohort. Setting: Academic Level I trauma center. Patients/Participants: One hundred twenty four patients treated surgically for hip fractures including patients presenting on warfarin (n = 62) and matched controls (n = 62). Intervention: Cephalomedullary nailing (CMN), hemiarthroplasty, or total hip arthroplasty. Main Outcome Measures: The primary outcome was transfusion rate. Secondary outcomes included calculated blood loss, 30-day complication rate, and hours from emergency department presentation to surgery. Results: There was no significant difference in blood transfusion rates between the warfarin and control groups (P = 0.86). Blood transfusion was required in 58.1% of patients in the warfarin group (48.3% of arthroplasties and 65.5% of CMNs) compared with 56.6% of controls (41.9% of arthroplasties and 73.3% of CMNs). There were also no significant differences in calculated blood loss or in complication rates. Patients on warfarin had significantly longer time to surgery (P < 0.01). Subanalysis of the warfarin group showed that patients with DOS INR at or above 1.5 had similar transfusion rates, blood loss, and complications compared with patients with INR below 1.5. Treatment with CMN was the only covariate that was found to be a significant independent predictor of transfusion on multivariable analysis (P = 0.048). Conclusions: Patients with hip fractures admitted on warfarin seem to be at similar risk of transfusion or adverse events compared with nonanticoagulated patients. Awaiting normalization of INR delayed surgery without reducing bleeding or preventing complications. Within reason, surgeons may consider proceeding with surgery in patients with INR above 1.5 if patients are otherwise medically optimized. The upper limit above which surgery causes increased blood loss is currently unknown. Level of Evidence: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Multimedia Learning

This article defines and exemplifies multimedia learning and multimedia instruction, describes theoretical frameworks for multimedia learning and multimedia instruction, summarizes evidence-based principles for how to design multimedia instruction, and suggests future trends in multimedia research. Multimedia design principles for reducing extraneous processing include the coherence principle, signaling principle, redundancy principle, spatial contiguity principle, and temporal contiguity principle. Multimedia design principles for managing essential processing include the pre-training principle, segmenting principle, and modality principle. Multimedia design principles for fostering generative processing include the personalization principle, voice principle, embodiment principle, and generative activity principle. Research on multimedia learning represents an example of applying the science of learning to education, and stands as one of educational psychology’s success stories.
The Raf-like Kinase ILK1 and the High Affinity K+ Transporter HAK5 Are Required for Innate Immunity and Abiotic Stress Response1[OPEN]

Microbe-induced changes in macronutrient content are required to generate immune responses via a kinase and potassium transporter. Plant perception of pathogen-associated molecular patterns (PAMPs) and other environmental stresses trigger transient ion fluxes at the plasma membrane. Apart from the role of Ca2+ uptake in signaling, the regulation and significance of PAMP-induced ion fluxes in immunity remain unknown. We characterized the functions of INTEGRIN-LINKED KINASE1 (ILK1) that encodes a Raf-like MAP2K kinase with functions insufficiently understood in plants. Analysis of ILK1 mutants impaired in the expression or kinase activity revealed that ILK1 contributes to plant defense to bacterial pathogens, osmotic stress sensitivity, and cellular responses and total ion accumulation in the plant upon treatment with a bacterial-derived PAMP, flg22. The calmodulin-like protein CML9, a negative modulator of flg22-triggered immunity, interacted with, and suppressed ILK1 kinase activity. ILK1 interacted with and promoted the accumulation of HAK5, a putative (H+)/K+ symporter that mediates a high-affinity uptake during K+ deficiency. ILK1 or HAK5 expression was required for several flg22 responses including gene induction, growth arrest, and plasma membrane depolarization. Furthermore, flg22 treatment induced a rapid K+ efflux at both the plant and cellular levels in wild type, while mutants with impaired ILK1 or HAK5 expression exhibited a comparatively increased K+ loss. Taken together, our results position ILK1 as a link between plant defense pathways and K+ homeostasis.
A double guarantee kidnapping detection in simultaneous localization and mapping

A double guarantee kidnapping detection (DGKD) method is proposed for determining whether kidnapping has happened and which type of kidnapping it is. The method can be constructed conveniently, with only three metrics and different thresholds. Our method is a hybrid type utilizing selective front-check and verification processes, using the metrics to obtain the best possible accuracy on kidnapping detection. In addition, a convenient method to determine the thresholds on real-time conditions is proposed. Simulation results demonstrate the validity and accuracy of the proposed method.
Localization of glycerate kinase and some enzymes for sucrose synthesis in c(3) and c(4) plants.

The localization of some key enzymes leading to sucrose synthesis in photosynthetic tissue of C(3) and C(4) species was investigated. These included UDP-glucose (UDPG) pyrophosphorylase, sucrose phosphate synthetase, and glycerate kinase. Whether glycerate kinase is localized exclusively in the chloroplast or partly outside the chloroplast could influence the fate of carbon flow to sucrose through the glycolate pathway.In the C(3) species wheat, intact chloroplasts were isolated from protoplasts. Following separation of the chloroplasts by differential centrifugation and by sucrose density gradient centrifugation, UDPG pyrophosphorylase, sucrose phosphate synthetase, and sucrose synthetase were found outside the chloroplast while glycerate kinase was localized in the chloroplast.In the C(4) species (maize, NADP-malic enzyme-type; Panicum miliaceum, NAD-malic enzyme type and Brachiaria erucaeformis, phosphoenolpyruvate carboxykinase type) the distribution of UDPG pyrophosphorylase and glycerate kinase between mesophyll and bundle sheath cells and their intracellular localization in mesophyll protoplasts was determined. Substantial activity of UDPG pyrophosphorylase was found in both mesophyll and bundle sheath cells while glycerate kinase was localized only in mesophyll cells. From C(4) mesophyll protoplasts, UDPG pyrophosphorylase was found to be cytoplasmic while glycerate kinase appears exclusively localized in the chloroplasts as determined by differential centrifugation and sucrose density gradients.It seems that in both C(3) and C(4) plants, the terminal steps of sucrose synthesis occur exclusively in the cytoplasm while carbon flow in the glycolate pathway to sucrose must occur through glycerate kinase in the chloroplasts. The localization of glycerate kinase in mesophyll cells of C(4) plants may have further implications for intercellular flow of carbon during metabolism in the glycolate pathway in these species.
Effects of memory aids on conversations between nursing home residents with dementia and nursing assistants

The effects of personalised memory books on the conversations between four residents with dementia and three nursing assistants (NAs) were evaluated using an experimental, single-subject design. Most residents increased their production of factual utterances, NAs decreased their use of non-facilitative conversational behaviours, and conversational turn-taking became more equitable when residents used their books. The addition of NA instruction resulted in further reduction of non-facilitative NA behaviour. The effects of the intervention were somewhat weaker with residents with greater dementia severity. Social validity measures suggested that this intervention may hold promise for improving conversations between NAs and residents with dementia.
Predicting Future Customers via Ensembling Gradually Expanded Trees

Our LAMDAer team has won the 10th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD) 2006 Data Mining Competition (open category) grand champion. This report presents our solution to the PAKDD 2006 Data Mining Competition. Following a brief description of the task, we discuss the difficulties of the task and explain the motivation of our solution. Then, we propose the Gradually Expanded Tree Ensemble (GetEnsemble) method, which handles the difficulties via ensembling expanded trees. We evaluated the proposed method and several other methods using AUC, and found the proposed method beats others in this task. Besides, we show how to obtain cues on which kind of second generation (2G) customers are likely to become third generation (3G) users with the proposed method.
Outsourcing the deep self: Deep self discordance does not explain away intuitions in manipulation arguments

Abstract According to manipulation arguments for incompatibilism, manipulation might undermine an agent’s responsibility even when the agent satisfies plausible compatibilist conditions on responsibility. According to Sripada (2012), however, empirical data suggest that people take manipulation to undermine responsibility largely because they think that the manipulated act is in discord with the agent’s “deep self,” thus violating the plausible compatibilist condition of deep self concordance. This paper defends Sripada’s general methodological approach but presents data that strongly suggest that, contrary to Sripada’s contention, most of the effect of manipulation on attributions of moral responsibility is unmediated by worries about inadequate information or deep self discordance. Instead, it depends largely on worries that the action is ultimately explained by factors outside the agent’s control, just as proponents of manipulation arguments have proposed. More generally, data suggest that judgments of deep self discordance are themselves explained by worries about responsibility, and that the everyday notion of what an agent wants or is “deep down” is sensitive not only to the agent’s internal psychological structure, but also its source. This casts some doubt on recent claims about the explanatory role of deep self judgments.
Compact clocks for industrial applications: The EMRP project IND 55 MClocks

Vapor cell atomic clocks are an interesting technology because they combine compactness, low power consumption and excellent relative frequency stability. Recently, due to better performing laser sources and innovative techniques to prepare and detect the atoms, several cell-based prototypes exhibiting unprecedented frequency stability have been developed. These techniques allow a reduction in the transfer of laser noise to the atoms, improvement of the signal-to-noise ratio and subsequently the clock's frequency stability. The project IND55 Mclocks funded by the European Metrological Research Programme (EMRP) proposes to develop high performances vapor cell clocks for industrial applications. Three technologies are investigated: 1) the pulsed optical pumping (POP) scheme; 2) the cold atoms approach, and 3) the Coherent Population Trapping (CPT). The results related to the first period of activity are presented.
An experimental analysis of psychometric functions in a threshold discrimination task with four response categories1

An experiment on a threshold discrimination task with four response categories was conducted to check the implicit assumptions of a threshold discrimination task with three response categories. Consideration of a task with three response categories, for example, “stronger,”“don't know,” and “weaker,” leads us to anticipate a relation between position parameters and that between the sizes of scale parameters of a model for a task with four response categories, such as, “stronger,”“probably stronger,”“probably weaker,” and “weaker. ” That is, position parameters will be equidistant between adjacent categories and the middle scale parameter will be the largest. The results of the experiment on a four-category task did not support these anticipated relation, and a possibility of biases in the estimation of point of subjective equality (PSE), using a three-category task is pointed out. As an alternative to a three-category task, a four-category task is suggested when more than two categories are required.
Unsupervised Topic Detection in document collections: an application in marketing and business journals

The rapid increase of publications in marketing and related areas increasingly hampers the realisation of a general idea of what is 'hot' in the respective fields of interest. Topic Detection (TD), based on unsupervised text clustering, is a promising approach to tackle this problem. We introduce a new methodology that facilitates the determination of the number of topics discussed in a given text collection. By applying this approach to a text corpus which includes 12 international marketing and business journals we identify hot spots in marketing science. The approach may help both scientists and practitioners to systematically discover topics in digital information environments, as provided by the internet for instance.
Licensed under Creative Commons Attribution Cc by Energy Efficient Cluster Head Selection in Wireless Sensor Networks

Wireless sensor network consists of several distributed sensor nodes. It is used for several military applications, environmental applications and health related applications. However, a WSN is a power constrained system, since sensors nodes have shorten lifespan because they run on limited power batteries. The lifespan of sensor network depends on battery unit. In WSN, Energy consumption is one of the most crucial design issues. It is essential to design efficient routing protocol for increase the lifetime of the sensor nodes. LEACH (Low Energy Adaptive Clustering Hierarchy) protocol motivates most of the research in energy efficient data gathering in data centric applications of WSN. It allows the rotation of cluster head role among the sensor nodes and tries to distribute the energy consumption over the network. The recent research based on LEACH-B routing protocol. It saves energy consumption by ensuring that the clusters are balanced. This exiting work has limitation that replaces the cluster head after completion of each round. A proposed approach reduced the amount of cluster head and replacement cost. By decreasing this cost, it increase network lifetime compared to existing protocol.