Miracle-dz/UniFAR-FTUs huggingface dataset:
Stimulus-Dependent, Promoter-Specific Binding of Transcription Factor WRKY1 to Its Native Promoter and the Defense-Related Gene PcPR1-1 in Parsleyw⃞

WRKY transcription factors form a large family that plays a role in plant responses to biotic stress and during senescence. Defining in vivo relevant WRKY/promoter relationships has been hampered by the factors' indiscriminate binding to known W box DNA elements and their possible genetic redundance. Employing chromatin immunoprecipitations (ChIP) of cultured cells, we show that parsley (Petroselinum crispum) WRKY1 protein binds to the W boxes of its native promoter as well as to that of PcWRKY3 and the defense-related PR10-class marker gene Pathogenesis-Related1-1 (PcPR1-1). Although present at low concentrations in resting cells, WRKY1 does not appear to play a role in the immediate early gene response upon elicitation because it does not bind to the promoter at this time. Paradoxically, in vivo binding at the PcWRKY1 promoter correlates more with downregulation of gene expression, whereas previous overexpression studies suggested an activating function of WRKY1 on PcWRKY1 expression. By contrast, PcPR1-1 expression remains strong when its promoter is occupied in vivo by WRKY1. Unexpectedly, ChIP revealed that W boxes at promoter sites are constitutively occupied by other WRKY transcription factors, indicating that site recruitment does not seem to play a major role in their regulation. Rather, WRKY proteins very likely act in a network of mutually competing participants with temporal displacement occurring at defined preoccupied sites by other family members in a stimulus-dependent manner.
Only One Protomer Is Active in the Dimer of SARS 3C-like Proteinase*

The severe acute respiratory syndrome coronavirus 3C-like protease has been proposed to be a key target for structurally based drug design against SARS. The enzyme exists as a mixture of dimer and monomer, and only the dimer was considered to be active. In this report, we have investigated, using molecular dynamics simulation and mutational studies, the problems as to why only the dimer is active and whether both of the two protomers in the dimer are active. The molecular dynamics simulations show that the monomers are always inactive, that the two protomers in the dimer are asymmetric, and that only one protomer is active at a time. The enzyme activity of the hybrid severe acute respiratory syndrome coronavirus 3C-like protease of the wild-type protein and the inactive mutant proves that the dimerization is important for enzyme activity and only one active protomer in the dimer is enough for the catalysis. Our simulations also show that the right conformation for catalysis in one protomer can be induced upon dimer formation. These results suggest that the enzyme may follow the association, activation, catalysis, and dissociation mechanism for activity control.
Using relationship to control disclosure in Awareness servers

Awareness servers provide information about a person to help observers determine whether they are available for contact. A tradeoff exists in these systems: more sources of information, and higher fidelity in those sources, can improve people's decisions, but each increase in information reduces privacy. In this paper, we look at whether the type of relationship between the observer and the person being observed can be used to manage this tradeoff. We conducted a survey that asked people what amount of information from different sources that they would disclose to seven different relationship types. We found that in more than half of the cases, people would give different amounts of information to different relationships. We also found that the only relationship to consistently receive less information was the acquaintance -- essentially the person without a strong relationship at all. Our results suggest that awareness servers can be improved by allowing finer-grained control than what is currently available.
Robust Deadlock Avoidance for Sequential Resource Allocation Systems With Resource Outages

While the supervisory control (SC) problem of (maximally permissive) deadlock avoidance for sequential resource allocation systems (RASs) has been extensively studied in the literature, the corresponding results that are able to address potential resource outages are quite limited, both, in terms of their volume and their control capability. This paper leverages the recently developed SC theory for switched discrete event systems (s-DES) in order to provide a novel systematic treatment of this more complicated version of the RAS deadlock avoidance problem. Following the modeling paradigm of s-DES, both the operation of the considered RAS and the corresponding maximally permissive SC policy are decomposed over a number of operational modes that are defined by the running sets of the failing resources. In particular, the target supervisor must be decomposed to a set of “localized predicates,” where each predicate is associated with one of the operational modes. A significant part, and a primary contribution, of this paper concerns the development of these localized predicates that will enable the formal characterization and the effective computation of the sought supervisor. With these predicates available, a distributed representation for the sought supervisor that is appropriate for real-time implementation is eventually obtained through an adaptation of the relevant distributed algorithm that is provided by the current s-DES SC theory. Note to Practitioners—This paper extends the existing theory of deadlock avoidance for buffer-space allocation in flexibly automated production systems so that it accounts for disruptive effects due to potential temporary outages of some of the system servers. The set of the failing servers at any time instant defines the corresponding operational mode for the underlying resource allocation system. The primary problem that is addressed by this paper is the synthesis of a resource allocation policy that will ensure the ability of all process instances that do not require the failing resources in a particular mode, to execute repetitively and complete successfully while the system remains in that mode. In line with some past literature on this problem, we call the corresponding supervisory control problem as “robust deadlock avoidance,” and we leverage results from the recently emerged theory for modeling and control of switched discrete event systems in order to characterize and compute a maximally permissive solution for it.
The Relationship between Brain Oscillations and BOLD Signal during Memory Formation: A Combined EEG–fMRI Study

Previous studies demonstrated that increases in the theta frequency band with concomitant decreases in the alpha/beta frequency band indicate successful memory formation. However, little is known about the brain regions and the cognitive processes that underlie these encoding-related oscillatory memory effects. We investigated this relationship using simultaneous EEG–fMRI recordings in humans during long-term memory encoding. In line with prior studies, we demonstrate that a decrease in beta power and an increase in theta power positively predict subsequent recall. In fMRI, stronger activity in the left inferior prefrontal cortex and the right parahippocampal gyrus correlated with successful memory formation. EEG source localization revealed that the subsequent memory effect in the beta band was localized in the left inferior prefrontal cortex, whereas the effect in the theta band was localized in medial temporal lobe regions. Trial-by-trial correlations between EEG and BOLD activity showed that beta power correlated negatively with left inferior prefrontal cortex activity. This correlation was more pronounced for items that could later be successfully recalled compared to items later forgotten. Based on these findings, we suggest that beta oscillations in the left inferior prefrontal cortex indicate semantic encoding processes, whereas theta oscillations in the medial temporal lobe reflect the binding of an item to its spatiotemporal context.
The transcriptional activator HIyU of Vibrio cholerae: nucleotide sequence and role in virulence gene expression

HlyU upregulates expression of the haemolysin, HlyA, of Vibrio cholerae. DNA sequence analysis indicates that HlyU is an 11.9 kDa protein containing a putative helix‐turn‐helix motif and belonging to a family of small regulatory proteins, including NolR (Rhizobium meliloti), SmtB (Synechococcus PCC 7942) and ArsR (piasmids R773, Escherichia coli; p1258, Staphylococcus aureus; and pSX267, Staphylococcus xylosus). An hlyU mutant was constructed by insertional inactivation, and found to be deficient in the production of both the haemolysin and a 28kDa secreted protein. The mutant was assessed for virulence in the infant mouse cholera model, revealing a 100‐fold increase in the LD50. This suggests that HlyU promotes expression of virulence determinant(s) in vivo.
Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis Isolates with Low Copy Numbers of IS6110 by Using Mycobacterial Interspersed Repetitive Units

ABSTRACT A study set of 180 Mycobacterium tuberculosis and Mycobacterium bovis isolates having low copy numbers of IS6110 were genotyped using the recently introduced method based on the variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR). The results were compared with results of the more commonly used methods, IS6110 restriction fragment length polymorphism (RFLP) and spoligotyping. The isolates were collected in Michigan from 1996 to 1999 as part of a project to genotype all isolates from new cases of tuberculosis in the state. Twelve MIRU loci were amplified, and the amplicons were analyzed by agarose gel electrophoresis to determine the copy number at each MIRU locus. MIRU-VNTR produced more distinct patterns (80 patterns) than did IS6110 RFLP (58 patterns), as would be expected in this study set. Spoligotyping identified 59 patterns. No single method defined all unique isolates, and the combination of all three typing methods generated 112 distinct patterns identifying 90 unique isolates and 90 isolates in 22 clusters. The results confirm the potential utility of MIRU-VNTR typing and show that typing with multiple methods is required to attain maximum specificity.
Wireless interference identification with convolutional neural networks

The steadily growing use of license-free frequency bands requires reliable coexistence management for deterministic medium utilization. For interference avoidance, proper wireless interference identification (WII) is essential. In this work we propose the first WII approach based upon deep convolutional neural networks (CNNs). The CNN naively learns its features through self-optimization during an extensive data-driven GPU-based training process. We propose a CNN example which is based upon sensing snapshots with a limited duration of 12.8 μs and an acquisition bandwidth of 10 MHz. The CNN distinguishes between 15 classes. They represent packet transmissions of IEEE 802.11 b/g, IEEE 802.15. 4 and IEEE 802.15. 1 with overlapping frequency channels within the 2.4 GHz ISM band. We show that the CNN outperforms state-of-the-art WII approaches and has a classification accuracy greater than 95 % for signal-to-noise ratio of at least −5 dB.
Joint Detection and Tracking of Time-Varying Harmonic Components: A Flexible Bayesian Approach

This paper addresses the joint estimation and detection of time-varying harmonic components in audio signals. We follow a flexible viewpoint, where several frequency/amplitude trajectories are tracked in spectrogram using particle filtering. The core idea is that each harmonic component (composed of a fundamental partial together with several overtone partials) is considered a target. Tracking requires to define a state-space model with state transition and measurement equations. Particle filtering algorithms rely on a so-called sequential importance distribution, and we show that it can be built on previous multipitch estimation algorithms, so as to yield an even more efficient estimation procedure with established convergence properties. Moreover, as our model captures all the harmonic model information, it actually separates the harmonic sources. Simulations on synthetic and real music data show the interest of our approach
Substrate and Inhibitor Specificity of Butyrate Uptake in Apical Membrane Vesicles of the Rat Distal Colon

Background/Aims: There is substantial evidence that transcellular flux of short-chain fatty acid (SCFA) absorption, at least in part, is mediated by an anion exchange process with bicarbonate. Methods: This anion exchange system was further characterized in apical membrane vesicles of the rat distal colon by studying substrate and inhibitor specificities of a variety of substituted monocarboxylic acids as well as of known inhibitors of the recently described monocarboxylate transporter MCT1 and MCT2. Results: SCFA transport was significantly reduced in the presence of branched and unbranched SCFAs and several bromo, chloro and mercapto analogues as well as nicotinic acid and L-lactate. In contrast, known inhibitors of monocarboxylate transporter proteins like stilbene derivatives, phloretin and 2-cyano-4-hydroxycinnamate did not inhibit bicarbonate-gradient stimulated butyrate transport. Kinetic analysis of increasing substrate concentrations of 3-mercaptopropionate, L-lactate and nicotinic acid showed saturation kinetics with apparent Ki of 6.1, 18.3 and 14.7 mmol/l, respectively. Conclusions: The data not only confirm earlier results that absorption of SCFAs in apical membranes of the rat distal colon is mediated by a relatively low affinity/high capacity SCFA–/HCO–3 exchange mechanism, but also indicate that although this anion transporter shares some functional similarities, is not identical with the recently cloned MCT isoforms.
Small molecule inhibitor of apoptosis proteins antagonists: a patent review

Introduction: The family of inhibitor of apoptosis proteins (IAPs) plays a key role in the suppression of proapoptotic signaling; hence, a small molecule that disrupts the binding of IAPs with their functional partner should restore apoptotic response to proapoptotic stimuli in cells. The continued publication of new patent applications of IAP antagonists over the past 4 years is a testament to the continued interest surrounding the IAP family of proteins. Areas covered: This review summarizes the IAP antagonist patent literature from 2010 to 2014. Monovalent and bivalent Smac mimetics will be covered as well as two new developments in the field: IAP antagonists coupled to or merged with other targeted agents and new BIR2 selective IAP antagonists. Expert opinion: In addition to the well-explored scaffolds for monovalent and bivalent Smac-mimetics, some companies have taken more drastic approaches to explore new chemical space – for example, fragment-based approaches and macrocyclic inhibitors. Furthermore, other companies have designed compounds with alternative biological profiles – tethering to known kinase binding structures, trying to target to the mitochondria or introducing selective binding to the BIR2 domain. An overview of the status for the four small molecule IAP antagonists being evaluated in active human clinical trials is also provided.
On the Statistical Properties of the Capacity of Spatially Correlated Nakagami-M MIMO Channels

This paper studies the statistical properties of the channel capacity of spatially correlated Nakagami-m multiple- input multiple-output (MIMO) channels. We have derived closed- form expressions for the probability density function (PDF), the cumulative distribution function (CDF), the level-crossing rate (LCR), and the average duration of fades (ADF) of the lower bound on the channel capacity. In order to study the impact of the spatial correlation on the channel capacity, the analysis of the statistical properties of the channel capacity is carried out for different receiver antenna spacings. It is observed that the antenna spacing has a significant influence on the spread and maximum value of the PDF and LCR. The proposed method can be employed to study the statistical properties of the capacity of MIMO channels in different fading environments. The correctness of the analytical expressions is confirmed by simulations.
Under Neutrality, QST ≤ FST When There Is Dominance in an Island Model

TO test whether quantitative traits are under directional or homogenizing selection, it is common practice to compare population differentiation estimates at molecular markers ( F ST) ([Wright 1951][1]) and quantitative traits ( Q ST) ([Spitze 1993][2]). If the trait is neutral and its determinism
Analysis of Extreme Summer Rainfall Using Climate Teleconnections and Typhoon Characteristics in South Korea 1

Abstract: It is now widely acknowledged that climate variability modulates the frequency of extreme hydrological events. Traditional methodologies for hydrologic frequency analysis are not devised to account for variation in the exogenous teleconnections. Flood frequency analysis is further plagued by the assumptions of stationary in the causal structure as well as ergodicity. Here, we propose a dynamical hierarchical Bayesian analysis to account for exogenous forcing that govern the summer season rainfall. The precursors for Korean summer rainfall at different frequencies are identified utilizing wavelet and independent component analyses. The sea surface temperatures, the ensemble of rainfall predictions by General Circulation Model, in addition to the typhoon attributes were found to have direct correlation with extreme rainfall events and were used as inputs to the logistic regression model. The model parameters are estimated using Markov Chain Monte Carlo and the resulting posterior distributions associated with individual inputs are analyzed to advance our understanding of the spatiotemporal impact of the teleconnections. Eight rainfall stations throughout Korea are considered in this analysis. We demonstrate that the probability of occurrence of extreme events could be successfully projected at a 90% rate of correct classification of extreme events.
Effect of Two Different Multimicronutrient Supplements on Vitamin D Status in Women of Childbearing Age: A Randomized Trial

The German Nutrition Society raised in 2012 the recommended daily vitamin D intake from 200 to 800 international units (IU) to achieve 25-hydroxyvitamin D (25(OH)D) levels of at least 50 nmol/L, even when endogenous vitamin D synthesis is minimal such as in winter. We aimed to evaluate this recommendation in women of childbearing age. This is a single-center, randomized, open trial conducted from 8 January to 9 May 2016 in Esslingen, Germany. We randomized 201 apparently healthy women to receive for 8 weeks a daily multimicronutrient supplement containing either 200 IU (n = 100) or 800 IU vitamin D3 (n = 101). Primary outcome measure was serum 25(OH)D. 196 participants completed the trial. Increases in 25(OH)D (median with interquartile range) from baseline to study end were 13.2 (5.9 to 20.7) nmol/L in the 200 IU group, and 35.8 (18.2 to 52.8) nmol/L in the 800 IU group (p < 0.001 for the between group difference). At study end, levels of ≥50 nmol/L were present in 70.4% of the 200 IU group and in 99% of the 800 IU group. Participants on hormonal contraceptives had higher baseline levels and a stronger increase in 25(OH)D. In conclusion, daily supplementation of 800 IU vitamin D3 during wintertime in Germany is sufficient to achieve a 25(OH)D level of at least 50 nmol/L in almost all women of childbearing age, whereas 200 IU are insufficient.
The early Paleozoic oceanic island seamount in the Chencai area, Zhejiang Province: Implication of the Yangtze–Cathaysia amalgamation

Details of the collision between the Cathaysia and Yangtze blocks have long been debated. Detailed geological, geochemical, and C and O isotopic studies were carried out on the plagioclase amphibolite and marble in the Chencai area, Zhuji city, Zhejiang Province. The plagioclase amphibolite yields U–Pb age of 435 ± 11 Ma, which represents the metamorphic age, and the youngest age indicates that the plagioclase amphibolite formed after 463 Ma. The marble in the Chencai area yields U–Pb age of 431 ± 7 Ma and represents the metamorphic age, and the youngest inherited zircon indicates that the marble formed after 457 Ma. Combined with the two ages, we believed that they were both formed at early Paleozoic (after 457 Ma) and suffered metamorphism during the Caledonian (431–435 Ma). Meanwhile, REE and trace‐element characteristics show that the plagioclase amphibolite originated from the mantle source with the characteristics of OIB. The marble C and O isotopic characteristics indicated that the protolith of marble may be marine carbonate. The occurrence of the oceanic island seamount indicates that the Chencai Complex should be a subduction–accretion complex (CSAC), which formed at early Paleozoic. Given the presence of Caledonian granulite and garnet amphibolite in the Longyou area, amalgamation of the Cathaysia and Yangtze blocks was completed after 457 Ma. The CSAC is the product of the Yangtze–Cathaysia collision, with the collision causing widespread amphibolite‐facies metamorphism.
General-Purpose Nonlinear Model-Order Reduction Using Piecewise-Polynomial Representations

We present algorithms for automated macromodeling of nonlinear mixed-signal system blocks. A key feature of our methods is that they automate the generation of general-purpose macromodels that are suitable for a wide range of time- and frequency-domain analyses important in mixed-signal design flows. In our approach, a nonlinear circuit or system is approximated using piecewise-polynomial (PWP) representations. Each polynomial system is reduced to a smaller one via weakly nonlinear polynomial model-reduction methods. Our approach, dubbed PWP, generalizes recent trajectory-based piecewise-linear approaches and ties them with polynomial-based model-order reduction, which inherently captures stronger nonlinearities within each region. PWP-generated macromodels not only reproduce small-signal distortion and intermodulation properties well but also retain fidelity in large-signal transient analyses. The reduced models can be used as drop-in replacements for large subsystems to achieve fast system-level simulation using a variety of time- and frequency-domain analyses (such as dc, ac, transient, harmonic balance, etc.). For the polynomial reduction step within PWP, we also present a novel technique [dubbed multiple pseudoinput (MPI)] that combines concepts from proper orthogonal decomposition with Krylov-subspace projection. We illustrate the use of PWP and MPI with several examples (including op-amps and I/O buffers) and provide important implementation details. Our experiments indicate that it is easy to obtain speedups of about an order of magnitude with push-button nonlinear macromodel-generation algorithms.
Speculation And Wealth When Investors Have Diverse Beliefs And Financial Markets Are Incomplete

In our heterogenous-beliefs incomplete-markets models, precautionary and speculative motives coexist. Missing markets for Arrow securities affect the size and avenues for precautionary savings. Survival dynamics suggested by Friedman (1953) and studied by Blume and Easley (2006) depend on whether agents can trade a disaster-state security. When the market for a disaster-state security is closed, precautionary savings flow into risk-free bonds, prompting less-informed investors to accumulate wealth. Because speculation motives are strongest for the disaster-state Arrow security, opening this market brings outcomes close to those for a complete-markets benchmark where instead it is well-informed investors who accumulate wealth. Speculation is more limited in other cases, and outcomes for wealth dynamics are closer to those in an economy in which only a risk-free bond can be traded.