Miracle-dz/UniFAR-FTUs huggingface dataset:
SoxS Increases the Expression of the Zinc Uptake System ZnuACB in an Escherichia coli Murine Pyelonephritis Model

ABSTRACT Paralogous transcriptional regulators MarA, Rob, and SoxS act individually and together to control expression of more than 80 Escherichia coli genes. Deletion of marA, rob, and soxS from an E. coli clinical isolate prevents persistence beyond 2 days postinfection in a mouse model of pyelonephritis. We used microarray analysis to identify 242 genes differentially expressed between the triple deletion mutant and its parent strain at 2 days postinfection in the kidney. One of these, znuC of the zinc transport system ZnuACB, displayed decreased expression in the triple mutant compared to that in the parental strain, and deletion of znuC from the parental strain reduced persistence. The marA rob soxS triple deletion mutant was less viable in vitro under limited-Zn and Zn-depleted conditions, while disruption of znuC caused a reduction in the growth rates for the parental and triple mutant strains to equally low levels under limited-Zn or Zn-depleted conditions. Complementation of the triple mutant with soxS, but not marA or rob, restored the parental growth rate in Zn-depleted medium, while deletion of only soxS from the parental strain led to low growth in Zn-depleted medium. Both results suggested that SoxS is a major regulator responsible for growth under Zn-depleted conditions. Gel shift experiments failed to show direct binding of SoxS to the znuCB promoter, thus suggesting indirect control of znuCB expression by SoxS. While SoxS expression in the triple mutant fully restored persistence, increased expression of znuACB via a plasmid in this mutant only partially restored wild-type levels of persistence in the kidney. This work implicates SoxS control of znuCB expression as a key factor in persistence of E. coli in murine pyelonephritis.
An Analysis of Multi-type Relational Interactions in FMA Using Graph Motifs with Disjointness Constraints

The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions for detecting logical inconsistencies as well as other anomalies represented by the motifs. MOCH represents patterns of multi-type interaction as small labeled (with multiple types of edges) sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology, we performed exhaustive analyses of a variety of labeled sub-graph motifs. The quality assurance feature of MOCH comes from the distinct use of a subset of the edges of the graph motifs as constraints for disjointness, whereby bringing in rule-based flavor to the approach as well. With possible disjointness implied by antonyms, we performed manual inspection of the resulting FMA fragments and tracked down sources of abnormal inferred conclusions (logical inconsistencies), which are amendable for programmatic revision of the FMA. Our results demonstrate that MOCH provides a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation.
Toward Automated Testing of Geo-Distributed Replica Selection Algorithms

Many geo-distributed systems rely on a replica selection algorithms to communicate with the closest set of replicas. Unfortunately, the bursty nature of the Internet traffic and ever changing network conditions present a problem in identifying the best choices of replicas. Suboptimal replica choices result in increased response latency and reduced system performance. In this work we present GeoPerf, a tool that tries to automate testing of geo-distributed replica selection algorithms. We used GeoPerf to test Cassandra and MongoDB, two popular data stores, and found bugs in each of these systems.
Ultrasonic Tissue Characterization of Carotid Plaque Improves the Prediction of Cardiovascular Events in Diabetic Patients

OBJECTIVE The aim of this study is to evaluate whether noninvasive ultrasonic tissue characterization of carotid plaque using integrated backscatter (IBS) analysis can be a predictor of future cardiovascular events (CVE) in asymptomatic type 2 diabetic patients. RESEARCH DESIGN AND METHODS We prospectively evaluated the association between Calibrated-IBS value, an ultrasonic marker for tissue characteristics of carotid plaque, and CVE in 85 asymptomatic type 2 diabetic patients with carotid plaque. RESULTS The median follow-up period was 7.9 years, and there were 20 new CVE. The risk of CVE was significantly higher in the subjects with low Calibrated-IBS values (<−17.1 dB; n = 42) as compared with those with high values (≥−17.1 dB; n = 43) (P = 0.004, log-rank test). Cox proportional hazards regression analysis revealed that both Calibrated-IBS value (hazard ratio [HR] 0.802 [95% CI 0.710–0.906]; P < 0.0001) and plaque thickness (1.938 [1.170–3.213]; P = 0.010) were independently associated with CVE, even after adjustment for the 10-year risk for a general cardiovascular disease estimated by Framingham risk scoring (FRS). Time-dependent receiver operating characteristic curve analysis for CVE at 10 years after the baseline examinations revealed that area under the curve for Calibrated-IBS was 0.76 (0.60–0.90) and substantially higher than those for plaque thickness (0.60 [0.45–0.79]) and FRS (0.60 [0.40–0.78]). These analyses also revealed that the addition of both plaque thickness and Calibrated-IBS value to conventional risk factors significantly improved the event prediction. CONCLUSIONS Calibrated-IBS value could improve the risk prediction of CVE in asymptomatic type 2 diabetic patients with carotid plaque.
Time-and-Energy-Aware Computation Offloading in Handheld Devices to Coprocessors and Clouds

Running sophisticated software on smart phones could result in poor performance and shortened battery lifetime because of their limited resources. Recently, offloading computation workload to the cloud has become a promising solution to enhance both performance and battery life of smart phones. However, it also consumes both time and energy to upload data or programs to the cloud and retrieve the results from the cloud. In this paper, we develop an offloading framework, named Ternary Decision Maker (TDM), which aims to shorten response time and reduce energy consumption at the same time. Unlike previous works, our targets of execution include an on-board CPU, an on-board GPU, and a cloud, all of which combined provide a more flexible execution environment for mobile applications. We conducted a real-world application, i.e., matrix multiplication, in order to evaluate the performance of TDM. According to our experimental results, TDM has less false offloading decision rate than existing methods. In addition, by offloading modules, our method can achieve, at most, 75% savings in execution time and 56% in battery usage.
Multiple suppression in the image space: A Mahogany eld example

A compensation circuit is disclosed for compensating bias levels of an operational circuit in response to variations in a supply voltage. The compensation mechanism identifies variations in the supply voltage by comparing the voltage of a selected node of the operation circuit with a relatively constant or fixed reference voltage. Based on the results of the comparison, the compensation mechanism adjusts selected bias levels in the operational circuit, preferably using current stealing circuitry, so that the functionality and performance of the operational circuit can be substantially maintained. A biasing circuit for biasing one or more differential pairs is also disclosed.
New ghrelin agonist, HM01 alleviates constipation and L‐dopa‐delayed gastric emptying in 6‐hydroxydopamine rat model of Parkinson's disease

Constipation and L‐dopa‐induced gastric dysmotility are common gastrointestinal (GI) symptoms in Parkinson's disease (PD). We investigated the novel ghrelin agonist, HM01 influence on GI motor dysfunctions in 6‐hydroxydopamine (6‐OHDA) rats.
Closed-form solution of Lindblad master equations without gain

We present a closed form solution to the eigenvalue problem of a class of master equations that describe open quantum system with loss and dephasing but without gain. The method relies on the existence of a conserved number of excitation in the Hamiltonian part and that none of the Lindblad operators describe an excitation of the system. In the absence of dephasing Lindblad operators, the eigensystem of the Liouville operator can be constructed from the eigenvalues and eigenvectors of the effective non-Hermitian Hamiltonian used in the quantum jump approach. Open versions of spin chains, the Tavis-Cummings model and coupled Harmonic oscillators without gain can be solved using this technique.
Interviewing Suspects in Denial: On How Different Evidence Disclosure Modes Affect the Elicitation of New Critical Information

This study examines how different evidence disclosure modes affect the elicitation of new critical information. Two modes derived from the Strategic Use of Evidence (SUE) framework were compared against an early disclosure mode (i.e., the evidence was disclosed at the outset of the interview). Participants (N = 88) performed a mock crime consisting of several actions before they were interviewed as suspects. In both SUE conditions the interviewer elicited and disclosed statement-evidence inconsistencies in two phases after an introductory phase. For the SUE-Confrontation (SUE-C) condition, the interview was introduced in a business-like manner, and the interviewer confronted the suspects with the in/consistencies without giving them a chance to comment on these. For the SUE-Introduce-Present-Respond (SUE-IPR) condition, the interviewer introduced the interview in a non-guilt-presumptive way, presented the in/consistencies and allowed the suspects to comment on these, and then responded to their comments; at all times in a non-judgmental manner. Both SUE conditions generated comparatively more statement-evidence inconsistencies. The SUE-IPR condition resulted in more new critical information about the phase of the crime for which the interviewer lacked information, compared to the Early disclosure condition. A likely explanation for this was that (for the SUE-IPR condition) the interviewer used the inconsistencies to create a fostering interview atmosphere and made the suspects overestimate the interviewer's knowledge about the critical phase of the crime. In essence, this study shows that in order to win the game (i.e., obtaining new critical information), the interviewer needs to keep the suspect in the game (i.e., by not being too confrontational and judgmental).
Parenting and Temperament as Interacting Agents in Early Language Development

Objective. This study investigated relations among parenting, temperament, and early language, especially parenting as a moderator of the temperament-language association. Design. Measures of temperament, parenting (maternal responsiveness), and language were obtained from a sample of 102 predominantly European American, middle-class mother - infant dyads who were studied when the infants were 12 and 16 months of age. Results. The interaction between infant distress to novelty and maternal responsiveness at 12 months was related to 16-month language, such that when infants were low in distress to novelty, more responsive parenting was associated with better language abilities. Moreover, for boys only, greater maternal responsiveness was related to better language abilities only when boys displayed less smiling and laughter. Conclusions. The effects of emotionality and parenting on language acquisition depend on the level of the other.
Analysis and evaluation of driving behavior recognition based on a 3-axis accelerometer using a random forest approach: poster abstract

Understanding human drivers' behavior is critical for the self-driving cars, and has been intensively studied in the past decade. We exploit the widely available camera and motion sensor data from car recorders, and propose a hybrid method of recognizing driving events based on the random forest approach. The classification results are analyzed by comparing different features, classifiers and filters. A high accuracy of 98.1% on driving behavior classification is obtained and the robustness is verified on a dataset including 2400 driving events.
Association of the Myosin-binding Subunit of Myosin Phosphatase and Moesin: Dual Regulation of Moesin Phosphorylation by Rho-associated Kinase and Myosin Phosphatase

The small GTPase Rho is believed to regulate the actin cytoskeleton and cell adhesion through its specific targets. We previously identified the Rho targets: protein kinase N, Rho-associated kinase (Rho- kinase), and the myosin-binding subunit (MBS) of myosin phosphatase. We found that in MDCK epithelial cells, MBS accumulated at the tetradecanoylphorbol-13-acetate (TPA)-induced membrane ruffling area, where moesin, a member of the ERM (ezrin, radixin, and moesin) family, was localized. Neither membrane ruffling nor an accumulation of moesin and MBS at the free-end plasma membrane was induced when MDCK cells were stimulated with TPA after the microinjection of C3, which ADP-ribosylates and inactivates Rho. MBS was colocalized with moesin at the cell–cell contact sites in MDCK cells. We also found that moesin was coimmunoprecipitated with MBS from MDCK cells. Recombinant MBS interacted with the amino-terminal domains of moesin and ezrin. Myosin phosphatase composed of the catalytic subunit and MBS showed phosphatase activity toward moesin, which was phosphorylated by Rho-kinase. The phosphatase activity was inhibited when MBS was phosphorylated by Rho-kinase. These results suggest that MBS is recruited with moesin to the plasma membrane and that myosin phosphatase and Rho-kinase regulate the phosphorylation state of moesin downstream of Rho.
Malathion Pesticide Degradation by Advanced Oxidation Process ( UV-Irradiation )

This study investigated the degradation of commercially used organophosphorous pesticide malathion in aqueous solution by UV-Irradiation process. The process was optimized by varying different parameters such as operating pH, TiO2 loading, H2O2 concentration and initial pollutant concentration. It was observed that COD removal were 91.6 % for 2 ppm initial concentration of malathion and under optimized condition TiO2 loading 3gm/L, pH 6, and H2O2 concentration of 0.625 ml/50ml solution in 16 hours. This study indicates that degradation by UV-Irradiation process could be used as efficient and environmental friendly technique for the degradation of bio-recalcitrant organic pollutants. Keywords— Pesticide, malathion, Aqueous solution, degradation, UV-irradiation, COD,UV Spectophotometer, TiO2,
Toxicity and mutagenicity of plumbagin and the induction of a possible new DNA repair pathway in Escherichia coli

Actively growing Escherichia coli cells exposed to plumbagin, a redox cycling quinone that increases the flux of O2- radicals in the cell, were mutagenized or killed by this treatment. The toxicity of plumbagin was not found to be mediated by membrane damage. Cells pretreated with plumbagin could partially reactivate lambda phage damaged by exposure to riboflavin plus light, a treatment that produces active oxygen species. The result suggested the induction of a DNA repair response. Lambda phage damaged by H2O2 treatment were not reactivated in plumbagin-pretreated cells, nor did H2O2-pretreated cells reactivate lambda damaged by treatment with riboflavin plus light. Plumbagin treatment did not induce lambda phage in a lysogen, nor did it cause an increase in beta-galactosidase production in a dinD::Mu d(lac Ap) promoter fusion strain. Cells pretreated with nonlethal doses of plumbagin showed enhanced survival upon exposure to high concentrations of plumbagin, but were unchanged in their susceptibility to far-UV irradiation. polA and recA mutants were not significantly more sensitive than wild type to killing by plumbagin. However, xth-1 mutants were partially resistant to plumbagin toxicity. It is proposed that E. coli has an inducible DNA repair response specific for the type of oxidative damage generated during incubation with plumbagin. Furthermore, this response appears to be qualitatively distinct from the SOS response and the repair response induced by H2O2.
Examining the relationship between alcohol-energy drink risk profiles and high-risk drinking behaviors.

BACKGROUND The mixing of alcohol and energy drinks (AMEDs) is a trend among college students associated with higher rates of heavy episodic drinking and negative alcohol-related consequences. The goals of this study were to take a person-centered approach to identify distinct risk profiles of college students based on AMED-specific constructs (expectancies, attitudes, and norms) and examine longitudinal associations between AMED use, drinking, and consequences. METHODS A random sample of incoming freshmen (n = 387, 59% female) completed measures of AMED use, AMED-specific expectancies, attitudes, and normative beliefs, and drinking quantity and alcohol-related consequences. Data were collected at 2 occasions: spring semester of freshmen year and fall semester of sophomore year. RESULTS Latent profile analysis identified 4 subgroups of individuals: occasional AMED, anti-AMED, pro-AMED, and strong peer influence. Individuals in the pro-AMED group reported the most AMED use, drinking, and consequences. There was a unique association between profile membership and AMED use, even after controlling for drinking. CONCLUSIONS Findings highlighted the importance of AMED-specific expectancies, attitudes, and norms. The unique association between AMED risk profiles and AMED use suggests AMED use is a distinct behavior that could be targeted by AMED-specific messages included in existing brief interventions for alcohol use.
Teachers’ funds of knowledge: a challenge to evidence-based practice

The spontaneous nature of much early childhood teaching makes it vital to understand the range of knowledge that teachers draw on in their curricular and pedagogical decision-making. Hammersley argued that teaching practice cannot be based directly on research evidence because it needs to be filtered through teachers’ experiences and understandings. Models of professional knowledge have rarely highlighted teachers’ personal knowledge. Drawing on an interpretivist study that investigated children’s interests as a foundation for curriculum and pedagogy in New Zealand, this paper supports Hammersley’s argument and proposes that the concept of teachers’ funds of knowledge has the potential to explain aspects of teachers’ knowledge. The paper argues that such informal knowledge, gained from life experience, is a primary influence and likely to be prioritised over theory and research in teachers’ pedagogical decision-making in early childhood education. Some implications of this argument for teacher education and teachers’ professional learning are suggested.
Evolution of the Drosophila Feminizing Switch Gene Sex-lethal

In Drosophila melanogaster, the gene Sex-lethal (Sxl) controls all aspects of female development. Since melanogaster males lacking Sxl appear wild type, Sxl would seem to be functionally female specific. Nevertheless, in insects as diverse as honeybees and houseflies, Sxl seems not to determine sex or to be functionally female specific. Here we describe three lines of work that address the questions of how, when, and even whether the ancestor of melanogaster Sxl ever shed its non-female-specific functions. First, to test the hypothesis that the birth of Sxl's closest paralog allowed Sxl to lose essential ancestral non-female-specific functions, we determined the CG3056 null phenotype. That phenotype failed to support this hypothesis. Second, to define when Sxl might have lost ancestral non-female-specific functions, we isolated and characterized Sxl mutations in D. virilis, a species distant from melanogaster and notable for the large amount of Sxl protein expression in males. We found no change in Sxl regulation or functioning in the 40+ MY since these two species diverged. Finally, we discovered conserved non-sex-specific Sxl mRNAs containing a previously unknown, potentially translation-initiating exon, and we identified a conserved open reading frame starting in Sxl male-specific exon 3. We conclude that Drosophila Sxl may appear functionally female specific not because it lost non-female-specific functions, but because those functions are nonessential in the laboratory. The potential evolutionary relevance of these nonessential functions is discussed.
A routine method for the determination of phosphoglucose isomerase activity in body fluid

A simple, rapid colorimetric method for the estimation of phosphoglucose isomerase activity, using the determination of fructose by the method of Roe, Epstein, and Goldstein (1949), is described. An arbitrary fructose standard is advocated and normal values for human serum and cerebrospinal fluid are presented.
A substrate-integrated-waveguide (SIW) quadrature hybrid-junction for low cost millimeter-wave planar antenna array

Couplers are critical elements in microwave and millimeter-wave frequency range systems and circuits [1]. Metallic rectangular waveguide couplers have been widely used in various millimeter-wave and microwave applications. However, metallic waveguide is not only a relatively high cost technology but also difficult to be integrated with planar circuits. The substrate integrated waveguide (SIW) is a planar technology that provides an attractive low- cost and low- loss alternative [2]. Planar circuits can be integrated into the same SIW substrate using planar transitions. In this paper, a SIW quadrature hybrid (−3 dB branch[3] line coupler) is presented and designed for millimeter- wave applications. Furthermore, a simple circuit model is proposed for fast design optimization of the presented junction. Simulated S-parameters results using both the proposed circuit model and HFSS package are provided for verification of the proposed model.
Agile dynamic provisioning of multi-tier Internet applications

Dynamic capacity provisioning is a useful technique for handling the multi-time-scale variations seen in Internet workloads. In this article, we propose a novel dynamic provisioning technique for multi-tier Internet applications that employs (1) a flexible queuing model to determine how much of the resources to allocate to each tier of the application, and (2) a combination of predictive and reactive methods that determine when to provision these resources, both at large and small time scales. We propose a novel data center architecture based on virtual machine monitors to reduce provisioning overheads. Our experiments on a forty-machine Xen/Linux-based hosting platform demonstrate the responsiveness of our technique in handling dynamic workloads. In one scenario where a flash crowd caused the workload of a three-tier application to double, our technique was able to double the application capacity within five minutes, thus maintaining response-time targets. Our technique also reduced the overhead of switching servers across applications from several minutes to less than a second, while meeting the performance targets of residual sessions.