Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-Scale Phosphoprotein Analysis in Medicago truncatula Roots Provides Insight into in Vivo Kinase Activity in Legumes1[W]

Nitrogen fixation in legumes requires the development of root organs called nodules and their infection by symbiotic rhizobia. Over the last decade, Medicago truncatula has emerged as a major model plant for the analysis of plant-microbe symbioses and for addressing questions pertaining to legume biology. While the initiation of symbiosis and the development of nitrogen-fixing root nodules depend on the activation of a protein phosphorylation-mediated signal transduction cascade in response to symbiotic signals produced by the rhizobia, few sites of in vivo phosphorylation have previously been identified in M. truncatula. We have characterized sites of phosphorylation on proteins from M. truncatula roots, from both whole cell lysates and membrane-enriched fractions, using immobilized metal affinity chromatography and tandem mass spectrometry. Here, we report 3,457 unique phosphopeptides spanning 3,404 nonredundant sites of in vivo phosphorylation on 829 proteins in M. truncatula Jemalong A17 roots, identified using the complementary tandem mass spectrometry fragmentation methods electron transfer dissociation and collision-activated dissociation. With this being, to our knowledge, the first large-scale plant phosphoproteomic study to utilize electron transfer dissociation, analysis of the identified phosphorylation sites revealed phosphorylation motifs not previously observed in plants. Furthermore, several of the phosphorylation motifs, including LxKxxs and RxxSxxxs, have yet to be reported as kinase specificities for in vivo substrates in any species, to our knowledge. Multiple sites of phosphorylation were identified on several key proteins involved in initiating rhizobial symbiosis, including SICKLE, NUCLEOPORIN133, and INTERACTING PROTEIN OF DMI3. Finally, we used these data to create an open-access online database for M. truncatula phosphoproteomic data.
A new web service model of hybrid personalized recommendation

In recent years, personalized recommendation has become a research focus on the Web services recommendation. The current recommendation system can be improved in the prediction accuracy and recommendation quality. This paper proposes a hybrid personalized recommendation model based on users' behaviors context-aware, which combines content-based filtering with collaborative filtering methods. First, we have selected m service subclasses by using content-based filtering method according to classify characteristics and current user-state. Next, users' specific ratings are predicted by K-nearest neighbor method. Finally, the Top-N services in the subclass will be recommended. Through the final experiment, we can draw a conclusion that the improved algorithm has good recommendation effect and high accuracy.
A Robust Steering Assistance System for Road Departure Avoidance

A driver-assistance system (DAS) that combines an automatic road departure avoidance (RDA) system with the driver's steering input is presented. The system is based on a closed-loop driver decision estimator (DDE), which establishes the risk of road departure. If a road departure is likely to occur, the RDA system intervenes by correcting the steering angle. Robustness is guaranteed by an Hinf controller designed to take into consideration the main uncertainties affecting the dynamics. Driver-in-the-loop tests evaluate the performance of the system in terms of robustness, risk of road departure, and driving experience. Experiments show that the system is effective in reducing the risk of road departure without impeding maneuverability.
Use of a dot enzyme-linked immunosorbent assay on absorbed sera for the diagnosis of bovine paratuberculosis.

This study describes the response of cattle to a dot enzyme-linked immunosorbent assay (ELISA) using sera absorbed with Mycobacterium phlei. Results obtained by visual observation are compared with those obtained using a densitometer. Infection status of cattle was determined by faecal culture. Cattle of different levels of exposure and disease manifestation were examined. A significantly higher dot ELISA response was observed (using both absorbed and non-absorbed sera) in animals with heavy shedding of M. paratuberculosis than in animals which tested negative by faecal culture or shed M. paratuberculosis at lower levels (P < 0.05). Paratuberculosis was diagnosed by visual determination of dot ELISA results using non-absorbed sera in 29 of 44 (65.9%) clinically-suspect animals giving positive results by faecal culture, and 85 of 93 (91.4%) cattle testing negative by faecal culture. With absorbed sera, the sensitivity of visual determination decreased to 15 of 44 (34.1%), while specificity increased to 91 of 93 (97.8%). Approximately 75% of cattle yielding positive results by dot ELISA were heavy bacterial shedders (> 1,500 colonies/g of faeces) at the time of serological testing. Comparison of the dot ELISA results determined visually with results obtained by objective densitometric measurement showed compatible specificity. Sensitivity of the dot ELISA was 65.9% for non-absorbed sera using visual evaluation and 87.5% using densitometric evaluation at a cut-off optical density value of 0.2. For absorbed sera, the values were 34.1% and 82.5%, respectively.
Baseline Q waves as a prognostic modulator in patients with ST-segment elevation: insights from the PLATO trial

Background: Baseline Q waves may provide additional value compared with time from the onset of symptoms in predicting outcomes for patients with ST-segment elevation. We evaluated whether baseline Q waves superseded time from symptom onset as a prognostic marker of one-year mortality in patients with ST-segment elevation acute coronary syndrome. Our study was derived from data from patients undergoing primary percutaneous coronary intervention within 24 hours in the PLATelet inhibition and patient Outcomes trial Methods: Q waves on the baseline electrocardiogram were evaluated by a blinded core laboratory. We assessed the associations between baseline Q waves and time from symptom onset to percutaneous coronary intervention with peak biomarkers, ST-segment resolution on the discharge electrocardiogram, and one-year all-cause and vascular mortality. Results: Of 4341 patients with ST-segment elevation, 46% had baseline Q waves. Compared to those without Q waves, those with baseline Q waves were older, more frequently male, had higher heart rates, more advanced Killip class and had a longer time between the onset of symptoms and percutaneous coronary intervention. They also had higher one-year all-cause mortality than patients without baseline Q waves (baseline Q waves: 4.9%; no baseline Q waves: 2.8%; hazard ratio [HR] 1.78, 95% confidence interval [CI] 1.29–2.45, p < 0.001). Complete ST-segment resolution was greatest and all-cause mortality lowest among those with symptom onset three hours or less before percutaneous coronary intervention and no baseline Q waves. After multivariable adjustment, baseline Q waves, but not time from symptom onset, were associated with a significant increase in all-cause mortality (adjusted HR 1.42, 95% CI 1.10–2.01, p = 0.046) and vascular mortality (adjusted HR 1.58, 95% CI 1.09–2.28, p = 0.02). Interpretation: The presence of baseline Q waves provides useful additional prognostic insight into the clinical outcome of patients with ST-segment elevation. Clinical Trials.gov registration no. NCT00391872
Biosynthesis of the Unique Wall Teichoic Acid of Staphylococcus aureus Lineage ST395

ABSTRACT The major clonal lineages of the human pathogen Staphylococcus aureus produce cell wall-anchored anionic poly-ribitol-phosphate (RboP) wall teichoic acids (WTA) substituted with d-Alanine and N-acetyl-d-glucosamine. The phylogenetically isolated S. aureus ST395 lineage has recently been found to produce a unique poly-glycerol-phosphate (GroP) WTA glycosylated with N-acetyl-d-galactosamine (GalNAc). ST395 clones bear putative WTA biosynthesis genes on a novel genetic element probably acquired from coagulase-negative staphylococci (CoNS). We elucidated the ST395 WTA biosynthesis pathway and identified three novel WTA biosynthetic genes, including those encoding an α-O-GalNAc transferase TagN, a nucleotide sugar epimerase TagV probably required for generation of the activated sugar donor substrate for TagN, and an unusually short GroP WTA polymerase TagF. By using a panel of mutants derived from ST395, the GalNAc residues carried by GroP WTA were found to be required for infection by the ST395-specific bacteriophage Φ187 and to play a crucial role in horizontal gene transfer of S. aureus pathogenicity islands (SaPIs). Notably, ectopic expression of ST395 WTA biosynthesis genes rendered normal S. aureus susceptible to Φ187 and enabled Φ187-mediated SaPI transfer from ST395 to regular S. aureus. We provide evidence that exchange of WTA genes and their combination in variable, mosaic-like gene clusters have shaped the evolution of staphylococci and their capacities to undergo horizontal gene transfer events. IMPORTANCE The structural highly diverse wall teichoic acids (WTA) are cell wall-anchored glycopolymers produced by most Gram-positive bacteria. While most of the dominant Staphylococcus aureus lineages produce poly-ribitol-phosphate WTA, the recently described ST395 lineage produces a distinct poly-glycerol-phosphate WTA type resembling the WTA backbone of coagulase-negative staphylococci (CoNS). Here, we analyzed the ST395 WTA biosynthesis pathway and found new types of WTA biosynthesis genes along with an evolutionary link between ST395 and CoNS, from which the ST395 WTA genes probably originate. The elucidation of ST395 WTA biosynthesis will help to understand how Gram-positive bacteria produce highly variable WTA types and elucidate functional consequences of WTA variation. The structural highly diverse wall teichoic acids (WTA) are cell wall-anchored glycopolymers produced by most Gram-positive bacteria. While most of the dominant Staphylococcus aureus lineages produce poly-ribitol-phosphate WTA, the recently described ST395 lineage produces a distinct poly-glycerol-phosphate WTA type resembling the WTA backbone of coagulase-negative staphylococci (CoNS). Here, we analyzed the ST395 WTA biosynthesis pathway and found new types of WTA biosynthesis genes along with an evolutionary link between ST395 and CoNS, from which the ST395 WTA genes probably originate. The elucidation of ST395 WTA biosynthesis will help to understand how Gram-positive bacteria produce highly variable WTA types and elucidate functional consequences of WTA variation.
Memory in Chains: Modeling Primacy and Recency Effects in Memory for Order

Memory for order is fundamental in everyday cognition, supporting basic processes like causal inference. However, theories of order memory are narrower, if anything, than theories of memory generally. The memory-in-chains (MIC) model improves on existing theories by explaining a family of order memory effects, by explaining more processes, and by making strong predictions. This paper examines the MIC model’s explanation of primacy and recency effects, and the prediction that primacy should dominate recency. This prediction is supported by existing data sets, suggesting that Estes’s (1997) perturbation model, dominant among theories of order memory, is incorrect. Fits to data are presented and compared with fits of other models.
Morphonology in the Lexicon

In this paper we present a means of defining morphonological phenomena in an inheritance based lexicon. We make use of the theory behind the formal language MOLUSC, in which morphological alternations were defined as mappings between sequences of tree-structured syllables. We discuss how the alternations can be defined in the inheritance-based lexical representation language DATR, and how the phonological aspects can be built upon to bring it closer to an integrated lexicon with representations which can be used by both the morphology and phonology of a language.
Micro‐/Nanostructured Mechanical Metamaterials

Mechanical properties of materials have long been one of the most fundamental and studied areas of materials science for a myriad of applications. Recently, mechanical metamaterials have been shown to possess extraordinary effective properties, such as negative dynamic modulus and/or density, phononic bandgaps, superior thermoelectric properties, and high specific energy absorption. To obtain such materials on appropriate length scales to enable novel mechanical devices, it is often necessary to effectively design and fabricate micro‐/nano‐ structured materials. In this Review, various aspects of the micro‐/nano‐structured materials as mechanical metamaterials, potential tools for their multidimensional fabrication, and selected methods for their structural and performance characterization are described, as well as some prospects for the future developments in this exciting and emerging field.
Development of a Model to Estimate 24‐Hour Urinary Creatinine Excretion

The accuracy of the spot urine analyte/creatinine ratio in estimating 24‐hour excretion of the analyte is compromised because it is not adjusted for 24‐hour creatinine excretion. The authors developed a model for conveniently estimating 24‐hour creatinine excretion. The model was derived from 24‐hour urine collections using multiple linear regression, including sex, weight, race, and age. The model was then evaluated in a validation cohort, assessing the correlation between estimated and measured 24‐hour creatinine excretion and by comparing their correlation with muscle mass. Estimated creatinine excretion correlated strongly with measured creatinine excretion (r=0.80 in the entire cohort and 0.93 after eliminating patients with incomplete collections), and correlated at least as strongly as measured creatinine excretion with lean muscle mass (r=0.94 vs r=0.82, respectively). Adjusting spot urine analyte/creatinine ratios using the estimated 24‐hour creatinine excretion by this convenient method can improve the accuracy of estimating 24‐hour excretion of albumin, sodium, and other analytes.
Cerebral Toxoplasmosis Combined with Disseminated Tuberculosis

A 24-year-old man presented with mental change, fever, abdominal pain, tenderness and palpable mass on the lower abdomen. He was a non-Korean engineer and did not accompany a legal guardian, so medical history taking was difficult due to his mental status. Brain magnetic resonance imaging showed multiple rim-enhanced lesions of the brain, and abdominal computed tomography showed huge paraspinal abscess. Chest X-ray and computed tomography showed poorly defined nodular opacities. We initially thought that this patient was infected with toxoplasmosis with typical cerebral image finding and immunoglobulin laboratory finding of cerebrospinal fluid and serum study. The abdominal abscess was confirmed as tuberculosis through the pathologic finding of caseous necrosis. We used anti-tuberculosis medication and anti-toxoplasmosis medication for almost 4 months, and then his clinical state and radiological findings were considerably improved.
Neuronal polarization

Neurons are highly polarized cells with structurally and functionally distinct processes called axons and dendrites. This polarization underlies the directional flow of information in the central nervous system, so the establishment and maintenance of neuronal polarization is crucial for correct development and function. Great progress in our understanding of how neurons establish their polarity has been made through the use of cultured hippocampal neurons, while recent technological advances have enabled in vivo analysis of axon specification and elongation. This short review and accompanying poster highlight recent advances in this fascinating field, with an emphasis on the signaling mechanisms underlying axon and dendrite specification in vitro and in vivo. Summary: This short review and accompanying poster highlight recent advances in our understanding of the molecular mechanisms underlying axon and dendrite specification in vitro and in vivo.
Update on Chlamydia trachomatis Vaccinology

ABSTRACT Attempts to produce a vaccine to protect against Chlamydia trachomatis-induced trachoma were initiated more than 100 years ago and continued for several decades. Using whole organisms, protective responses were obtained. However, upon exposure to C. trachomatis, disease exacerbation developed in some immunized individuals, precluding the implementation of the vaccine. Evidence of the role of C. trachomatis as a sexually transmitted pathogen started to emerge in the 1960s, and it soon became evident that it can cause acute infections and long-term sequelae in women, men, and newborns. The main focus of this minireview is to summarize recent findings and discuss formulations, including antigens, adjuvants, routes, and delivery systems for immunization, primarily explored in the female mouse model, with the goal of implementing a vaccine against C. trachomatis genital infections.
ProNodal acts via FGFR3 to govern duration of Shh expression in the prechordal mesoderm

The secreted glycoprotein sonic hedgehog (Shh) is expressed in the prechordal mesoderm, where it plays a crucial role in induction and patterning of the ventral forebrain. Currently little is known about how Shh is regulated in prechordal tissue. Here we show that in the embryonic chick, Shh is expressed transiently in prechordal mesoderm, and is governed by unprocessed Nodal. Exposure of prechordal mesoderm microcultures to Nodal-conditioned medium, the Nodal inhibitor CerS, or to an ALK4/5/7 inhibitor reveals that Nodal is required to maintain both Shh and Gsc expression, but whereas Gsc is largely maintained through canonical signalling, Nodal signals through a non-canonical route to maintain Shh. Further, Shh expression can be maintained by a recombinant Nodal cleavage mutant, proNodal, but not by purified mature Nodal. A number of lines of evidence suggest that proNodal acts via FGFR3. ProNodal and FGFR3 co-immunoprecipitate and proNodal increases FGFR3 tyrosine phosphorylation. In microcultures, soluble FGFR3 abolishes Shh without affecting Gsc expression. Further, prechordal mesoderm cells in which Fgfr3 expression is reduced by Fgfr3 siRNA fail to bind to proNodal. Finally, targeted electroporation of Fgfr3 siRNA to prechordal mesoderm in vivo results in premature Shh downregulation without affecting Gsc. We report an inverse correlation between proNodal-FGFR3 signalling and pSmad1/5/8, and show that proNodal-FGFR3 signalling antagonises BMP-mediated pSmad1/5/8 signalling, which is poised to downregulate Shh. Our studies suggest that proNodal/FGFR3 signalling governs Shh duration by repressing canonical BMP signalling, and that local BMPs rapidly silence Shh once endogenous Nodal-FGFR3 signalling is downregulated. Highlighted article: In the chick prechordal mesoderm, the Nodal precursor proNodal acts via a non-canonical route to inhibit BMP signalling and thus maintain Shh expression
Correlation neglect, voting behaviour and polarization

We analyse a voting model with voters who have correlation neglect, that is, they sometimes fail to appreciate that different sources of information might be correlated. While correlation neglect has the effect of polarising opinions, we show that this doesn’t translate directly to ineffi cient outcomes. Indeed we show that compared with a rational electorate, when the distribution of preferences in society is heterogeneous and suffi ciently balanced, a society composed of voters with correlation neglect may aggregate information in a more effi cient way. Moreover, we show that the polarisation in opinions does not necessarily translate into policy polarisation.
The Twin Study of Negative Valence Emotional Constructs

The Twin Study of Negative Valence Emotional Constructs is a multi-site study designed to examine the relationship between a broad selection of potential measures designed to assess putative endophenotypes for negative valence systems (NVS) and early symptoms of internalizing disorders (IDs). In this article, we describe the sample characteristics, data collection protocols, and measures used. Pre-adolescent Caucasian twin pairs were recruited through the Mid-Atlantic Twin Registry; data collection began in February of 2013. Enrolled twins completed various dimensional self-report measures along with cognitive, emotional, and psychophysiological tasks designed to assess NVS function. Parents also completed surveys about their twins and themselves. In addition, a subset of the twins also participated in a neuroimaging protocols. Data collection is in the final stages, and preliminary analyses are underway. The findings will potentially expand our understanding of the mechanisms by which genetic and environmental factors contribute to individual differences in NVS phenotypes and provide new insights into underlying risk factors for IDs.
Attack Models for Advanced Persistent Threats in Smart Grid Wide Area Monitoring

Wide Area Monitoring Systems (WAMSs) provide an essential building block for Smart Grid supervision and control. Distributed Phasor Measurement Units (PMUs) allow accurate clock-synchronized measurements of voltage and current phasors (amplitudes, phase angles) and frequencies. The sensor data from PMUs provide situational awareness in the grid, and are used as input for control decisions. A modification of sensor data can severely impact grid stability, overall power supply, and physical devices. Since power grids are critical infrastructures, WAMSs are tempting targets for all kinds of attackers, including well-organized and motivated adversaries such as terrorist groups or adversarial nation states. Such groups possess sufficient resources to launch sophisticated attacks. In this paper, we provide an in-depth analysis of attack possibilities on WAMSs. We model the dependencies and building blocks of Advanced Persistent Threats (APTs) on WAMSs using attack trees. We consider the whole WAMS infrastructure, including aggregation and data collection points, such as Phasor Data Concentrators (PDCs), classical IT components, and clock synchronization. Since Smart Grids are cyber-physical systems, we consider physical perturbations, in addition to cyber attacks in our models. The models provide valuable information about the chain of cyber or physical attack steps that can be combined to build a sophisticated attack for reaching a higher goal. They assist in the assessment of physical and cyber vulnerabilities, and provide strategic guidance for the deployment of suitable countermeasures.
Comparison of the Efficiency of Deterministic and Stochastic Algorithms for Visual Reconstruction

Piecewise continuous reconstruction of real-valued data can be formulated in terms of nonconvex optimization problems. Both stochastic and deterministic algorithms have been devised to solve them. The simplest such reconstruction process is the weak string. Exact solutions can be obtained for it and are used to determine the success or failure of the algorithms under precisely controlled conditions. It is concluded that the deterministic algorithm (graduated nonconvexity) outstrips stochastic (simulated annealing) algorithms both in computational efficiency and in problem-solving power. >