Miracle-dz/UniFAR-FTUs huggingface dataset:
The napF and narG Nitrate Reductase Operons in Escherichia coli Are Differentially Expressed in Response to Submicromolar Concentrations of Nitrate but Not Nitrite

ABSTRACT Escherichia coli synthesizes two biochemically distinct nitrate reductase enzymes, a membrane-bound enzyme encoded by thenarGHJI operon and a periplasmic cytochromec-linked nitrate reductase encoded by thenapFDAGHBC operon. To address why the cell makes these two enzymes, continuous cell culture techniques were used to examinenapF and narG gene expression in response to different concentrations of nitrate and/or nitrite. Expression of thenapF-lacZ and narG-lacZ reporter fusions in strains grown at different steady-state levels of nitrate revealed that the two nitrate reductase operons are differentially expressed in a complementary pattern. The napF operon apparently encodes a “low-substrate-induced” reductase that is maximally expressed only at low levels of nitrate. Expression is suppressed under high-nitrate conditions. In contrast, the narGHJI operon is only weakly expressed at low nitrate levels but is maximally expressed when nitrate is elevated. The narGHJI operon is therefore a “high-substrate-induced” operon that somehow provides a second and distinct role in nitrate metabolism by the cell. Interestingly, nitrite, the end product of each enzyme, had only a minor effect on the expression of either operon. Finally, nitrate, but not nitrite, was essential for repression of napF gene expression. These studies reveal that nitrate rather than nitrite is the primary signal that controls the expression of these two nitrate reductase operons in a differential and complementary fashion. In light of these findings, prior models for the roles of nitrate and nitrite in control ofnarG and napF expression must be reconsidered.
Statistical characterization of the Sinclair matrix: Application to polarimetric image segmentation

This paper focuses on the flexibility of a multidimensional model of probability density function (pdf) to describe distribution of complex data in polarimetric SAR images. This model is based on Copulas Theory for characterizing the dependence between the polarimetric channels (HH, VV, HV, VH). This corresponds to finding a model based on multidimensional copulas to describe the behavior of the target vector. The advantage in using copulas theory is to extend correlation concept to a wider dependence one, which may be non-linear, especially when processing high-resolution data. So, from this point of view, the model is more flexible than the classical Wishart distribution since no speckle filtering is required as preprocessing step to model accurately the pdfs. The other advantage of copulas is to split dependence concept and marginal distributions. Then, this multidimensional characterization may be linked to pdf which are not necessary of circular Gaussian law. So, specific parametric distribution may be choosen to fit each component (modulus and phase) of the Sinclair matrix. It yields a flexible model, for characterizing statistical behavior of the polarimetric SAR data, that may be derived to produce a segmentation algorithm.
Structure of a Burkholderia pseudomallei Trimeric Autotransporter Adhesin Head

Background Pathogenic bacteria adhere to the host cell surface using a family of outer membrane proteins called Trimeric Autotransporter Adhesins (TAAs). Although TAAs are highly divergent in sequence and domain structure, they are all conceptually comprised of a C-terminal membrane anchoring domain and an N-terminal passenger domain. Passenger domains consist of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region. Methodology/Principal Findings Pathogenic species of Burkholderia contain an overabundance of TAAs, some of which have been shown to elicit an immune response in the host. To understand the structural basis for host cell adhesion, we solved a 1.35 Å resolution crystal structure of a BpaA TAA head domain from Burkholderia pseudomallei, the pathogen that causes melioidosis. The structure reveals a novel fold of an intricately intertwined trimer. The BpaA head is composed of structural elements that have been observed in other TAA head structures as well as several elements of previously unknown structure predicted from low sequence homology between TAAs. These elements are typically up to 40 amino acids long and are not domains, but rather modular structural elements that may be duplicated or omitted through evolution, creating molecular diversity among TAAs. Conclusions/Significance The modular nature of BpaA, as demonstrated by its head domain crystal structure, and of TAAs in general provides insights into evolution of pathogen-host adhesion and may provide an avenue for diagnostics.
On relative coobservability of discrete-event systems

We study a new concept of relative coobservability in decentralized supervisory control of discrete-event systems under partial observation. This extends our previous work on relative observability from a centralized setup to a decentralized one. A fundamental concept in decentralized supervisory control is coobservability (and its several variations); this property is not, however, closed under set union, and hence there generally does not exist the supremal element. Our proposed relative coobservability, although stronger than coobservability, is algebraically well-behaved, and the supremal relatively coobservable sublanguage of a given language exists. We present an algorithm to compute this supremal sublanguage. Moreover, relative coobservability is weaker than conormality, which is also closed under set union; unlike conormality, relative coobservability imposes no constraint on disabling unobservable controllable events.
Salesforce Socialization Tactics: Building Organizational Value Congruence

The authors explore salesforce socialization tactics as a means of building organizational value congruence—an important dimension of salesforce culture strength. An empirical study is presented in which six socialization tactics are measured and it is found that certain socialization tactics have a greater effect than others on organizational value congruence. The findings have important implications for salesforce managers and suggest future research direction.
A quantitative approach for analysing bone modelling patterns from craniofacial surfaces in hominins

Bone size and shape arise throughout ontogeny as a result of the coordinated activity of osteoblasts and osteoclasts, responsible for bone deposition and resorption, and growth displacements. The modelling processes leave specific microstructural features on the bone surface, which can be used to infer the mechanisms shaping craniofacial traits in extinct and extant species. However, the analysis of bone surfaces from fossils and archaeological samples faces some difficulties related to the bone loss caused by taphonomic factors, and the lack of formal methods for estimating missing information and comparing the patterns of bone modelling among several specimens and samples. The present study provides a new approach for the quantitative analysis of bone formation and resorption patterns obtained from craniofacial surfaces. First, interpolation techniques were used to estimate missing data on high‐resolution replicas of the left maxilla in a sample of sub‐adult and adult modern humans and sub‐adult fossil hominins. The performance of this approach was assessed by simulating variable amounts of missing data. Then, we applied measures of dispersion and central tendency to represent the variation and average pattern of bone modelling within samples. The spatial interpolation resulted in reliable estimations of the type of cell activity (deposition or resorption) in the missing areas, even when large extensions of the bone surface were lost. The quantification of the histological data allowed us to integrate the information of different specimens and depict the areas with higher and lower variation in the bone modelling pattern of the maxilla among specimens. Overall, the main advantages of the quantitative approach used here for generating bone modelling patterns are the high replicability and the possibility of incorporating variation among specimens into the comparisons among samples.
Comparative proteomic analysis to study molecular events during gonad development in mice

Sex determination represents a critical bifurcation in the road of embryonic development. It is based on a finely regulated network of gene activity, as well as protein–protein interactions and activation or silencing of signaling pathways. Despite the identification of a number of critical genes, many aspects of the molecular cascade that drives the differentiation of the embryonic gonad into either a testis or an ovary remain poorly understood. To identify new proteins involved in this cascade, we employed two‐dimensional gel electrophoresis and mass spectrometry to compare the protein expression profiles of fetal mouse testes and ovaries. Three proteins, hnRPA1, TRA1, and HSC71, were found to be expressed in a male‐specific manner and this expression was confirmed by real‐time reverse transcriptase polymerase chain reaction (RT‐PCR) and in situ hybridization. Moreover, HSC71 was found to be hyperphosphorylated in male compared to female gonads, emphasizing the advantage of the proteomic approach in allowing the detection of posttranslational modifications. genesis 44:168–176, 2006. © 2006 Wiley‐Liss, Inc.
Generating Plans from Proofs

We present algorithms for answering queries making use of information about source integrity constraints, access restrictions, and access costs. Our method can exploit the integrity constraints to find plans even when there is no direct access to relations appearing in the query. We look at different kinds of plans, depending on the kind of relational operators that are permitted within their commands. To each type of plan, we associate a semantic property that is necessary for having a plan of that type. The key idea of our method is to move from a search for a plan to a search for a proof of the corresponding semantic property, and then generate a plan from a proof. We provide algorithms for converting proofs to plans and show that they will find a plan of the desired type whenever such a plan exists. We show that while discovery of one proof allows us to find a single plan that answers the query, we can explore alternative proofs to find lower-cost plans.
“A Mixed Blessing”: Social Support as a Coping Resource for Parents Who Lost a Child in Terrorist Attacks in Israel

This article deals with the issue of perceived social support among 40 bereaved parents who have lost a child in a terrorist attack in Israel. The aim is to gain a better understanding of the nature and quality of the formal and informal support that the parents received. The parents were interviewed using semistructured in-depth interviews. The content analysis revealed that alongside the positive aspects, the parents also emphasized the negative side of the encounter with the social environment. The positive aspects included feeling of appreciation for the assistance in the coping process. The negative aspects included a sense of abandonment and distress. The dialectic nature of the domain, together with a recognition of its importance, points to the need to reconcile between the desire on the part of the social environment to assist the bereaved parent on one hand and ways to implement it on the other hand.
High-Throughput Chemical Screening Identifies Compounds that Inhibit Different Stages of the Phytophthora agathidicida and Phytophthora cinnamomi Life Cycles

Oomycetes in the genus Phytophthora are among the most damaging plant pathogens worldwide. Two important species are Phytophthora cinnamomi, which causes root rot in thousands of native and agricultural plants, and Phytophthora agathidicida, which causes kauri dieback disease in New Zealand. As is the case for other Phytophthora species, management options for these two pathogens are limited. Here, we have screened over 100 compounds for their anti-oomycete activity, as a potential first step toward identifying new control strategies. Our screening identified eight compounds that showed activity against both Phytophthora species. These included five antibiotics, two copper compounds and a quaternary ammonium cation. These compounds were tested for their inhibitory action against three stages of the Phytophthora life cycle: mycelial growth, zoospore germination, and zoospore motility. The inhibitory effects of the compounds were broadly similar between the two Phytophthora species, but their effectiveness varied widely among life cycle stages. Mycelial growth was most successfully inhibited by the antibiotics chlortetracycline and paromomycin, and the quaternary ammonium salt benzethonium chloride. Copper chloride and copper sulfate were most effective at inhibiting zoospore germination and motility, whereas the five antibiotics showed relatively poor zoospore inhibition. Benzethonium chloride was identified as a promising antimicrobial, as it is effective across all three life cycle stages. While further testing is required to determine their efficacy and potential phytotoxicity in planta, we have provided new data on those agents that are, and those that are not, effective against P. agathidicida and P. cinnamomi. Additionally, we present here the first published protocol for producing zoospores from P. agathidicida, which will aid in the further study of this emerging pathogen.
Photoperiod Regulates Corticosterone Rhythms by Altered Adrenal Sensitivity via Melatonin-Independent Mechanisms in Fischer 344 Rats and C57BL/6J Mice

Most species living in temperate zones adapt their physiology and behavior to seasonal changes in the environment by using the photoperiod as a primary cue. The mechanisms underlying photoperiodic regulation of stress-related functions are not well understood. In this study, we analyzed the effects of photoperiod on the hypothalamic-pituitary-adrenal axis in photoperiod-sensitive Fischer 344 rats. We first examined how photoperiod affects diurnal variations in plasma concentrations of adrenocorticotropic hormone (ACTH) and corticosterone. ACTH levels did not exhibit diurnal variations under long- and short-day conditions. On the other hand, corticosterone levels exhibited a clear rhythm under short-day condition with a peak during dark phase. This peak was not observed under long-day condition in which a significant rhythm was not detected. To analyze the mechanisms responsible for the photoperiodic regulation of corticosterone rhythms, ACTH was intraperitoneally injected at the onset of the light or dark phase in dexamethasone-treated rats maintained under long- and short-day conditions. ACTH induced higher corticosterone levels in rats examined at dark onset under short-day condition than those maintained under long-day condition. Next, we asked whether melatonin signals are involved in photoperiodic regulation of corticosterone rhythms, and rats were intraperitoneally injected with melatonin at late afternoon under long-day condition for 3 weeks. However, melatonin injections did not affect the corticosterone rhythms. In addition, photoperiodic changes in the amplitude of corticosterone rhythms were also observed in melatonin-deficient C57BL/6J mice, in which expression profiles of several clock genes and steroidgenesis genes in adrenal gland were modified by the photoperiod. Our data suggest that photoperiod regulates corticosterone rhythms by altered adrenal sensitivity through melatonin-independent mechanisms that may involve the adrenal clock.
Visual search for a target changing in synchrony with an auditory signal

We examined whether the detection of audio–visual temporal synchrony is determined by a pre-attentive parallel process, or by an attentive serial process using a visual search paradigm. We found that detection of a visual target that changed in synchrony with an auditory stimulus was gradually impaired as the number of unsynchronized visual distractors increased (experiment 1), whereas synchrony discrimination of an attended target in a pre-cued location was unaffected by the presence of distractors (experiment 2). The effect of distractors cannot be ascribed to reduced target visibility nor can the increase in false alarm rates be predicted by a noisy parallel processing model. Reaction times for target detection increased linearly with number of distractors, with the slope being about twice as steep for target-absent trials as for target-present trials (experiment 3). Similar results were obtained regardless of whether the audio–visual stimulus consisted of visual flashes synchronized with amplitude-modulated pips, or of visual rotations synchronized with frequency-modulated up–down sweeps. All of the results indicate that audio–visual perceptual synchrony is judged by a serial process and are consistent with the suggestion that audio–visual temporal synchrony is detected by a ‘mid-level’ feature matching process.
Optic nerve head drusen

Optic disc drusen are congenital and developmental anomalies of the optic nerve head seen commonly in clinical practice, often as an incidental ophthalmologic finding during routine exams. Optic disc drusen are a form of calcific degeneration in some of the axons of the optic nerve. Visual acuity is often not affected but the visual fields of these patients can be abnormal and deteriorate over time. Optic disc drusen are familial and are not uncommon. They are thought to be the result of pathology at the level of the optic nerve head itself. The diagnosis can be made with clinical findings combined with B scan ultrasound and computed tomography. In addition, newer modalities using optic nerve head tomography are proving to be very useful. Since children as well as adults are affected, it is important to consider optic nerve head drusen in the differential diagnosis of papilledema or optic nerve swelling.
Factor Validation of the Consideration of Future Consequences Scale: Evidence for a Short Version

Abstract The author examined the factor structure of the 12-item Consideration of Future Consequences (CFC) Scale (A. Strathman, F. Gleicher, D. S. Boninger, & S. Edwards, 1994) among 664 undergraduate university students enrolled in human development courses. A principal-components factor analysis with varimax rotation yielded 2 factors. The author used confirmatory factor analysis procedures to examine the fit of 4 models, according to the principal-components factor analysis findings, with the observed covariance. The author used a number of fit indices to compare the 4 models. Both sets of analysis provided the greatest support for an 8-item short version of the CFC Scale. The author discussed findings in regard to the CFC Scale as an instrument to measure future time perspective.
Synthesizing State-Based Object Systems from LSC Specifications

Live sequence charts (LSCs) have been defined recently as an extension of message sequence charts (MSCs; or their UML variant, sequence diagrams) for rich inter-object specification. One of the main additions is the notion of universal charts and hot, mandatory behavior, which, among other things, enables one to specify forbidden scenarios. LSCs are thus essentially as expressive as statecharts. This paper deals with synthesis, which is the problem of deciding, given an LSC specification, if there exists a satisfying object system and, if so, to synthesize one automatically. The synthesis problem is crucial in the development of complex systems, since sequence diagrams serve as the manifestation of use cases -- whether used formally or informally -- and if synthesizable they could lead directly to implementation. Synthesis is considerably harder for LSCs than for MSCs, and we tackle it by defining consistency, showing that an entire LSC specification is consistent iff it is satisfiable by a state-based object system, and then synthesizing a satisfying system as a collection of finite state machines or statecharts.
A Novel Regulatory Mechanism of Map Kinases Activation and Nuclear Translocation Mediated by Pka and the Ptp-Sl Tyrosine Phosphatase

Protein tyrosine phosphatase PTP-SL retains mitogen-activated protein (MAP) kinases in the cytoplasm in an inactive form by association through a kinase interaction motif (KIM) and tyrosine dephosphorylation. The related tyrosine phosphatases PTP-SL and STEP were phosphorylated by the cAMP-dependent protein kinase A (PKA). The PKA phosphorylation site on PTP-SL was identified as the Ser231 residue, located within the KIM. Upon phosphorylation of Ser231, PTP-SL binding and tyrosine dephosphorylation of the MAP kinases extracellular signal–regulated kinase (ERK)1/2 and p38α were impaired. Furthermore, treatment of COS-7 cells with PKA activators, or overexpression of the Cα catalytic subunit of PKA, inhibited the cytoplasmic retention of ERK2 and p38α by wild-type PTP-SL, but not by a PTP-SL S231A mutant. These findings support the existence of a novel mechanism by which PKA may regulate the activation and translocation to the nucleus of MAP kinases.
Decision support via automated metric comparison for the palladio-based performance blame analysis

When developing component-based systems, we incorporate third-party black-box components. For each component, performance contracts have been specified by their developers. If errors occur when testing the system built from these components, it is very important to find out whether components violate their performance contracts or whether the composition itself is faulty. This task is called performance blame analysis. In our previous work we presented a performance blame analysis approach that blames components based on a comparison of response time values from the failed test case to expected values derived from the performance contract. In that approach, the system architect needs to manually assess if the test data series shows faster or slower response times than the data derived from the contract. This is laborious as the system architect has to do this for each component operation. In this paper we present an automated comparison of each pair of data series as decision support. In contrast to our work, other approaches do not achieve fully automated decision support, because they do not incorporate sophisticated contracts. We exemplify our performance blame analysis including the automated decision support using the "Common Component Modeling Example" (CoCoME) benchmark.
Psychometric properties of the Malay version of the job satisfaction survey among Malaysian military personnel

Job satisfaction is directly related to a number of positive outcomes at work and in certain other aspects of life. In the past few years, job satisfaction among the armed forces has received much attention, but the results of research have been contradictory, in view of the lack of psychometrically robust instrument. Due to its multidimensional orientation, Job Satisfaction Survey has been widely used to assess job satisfaction across different types of job. Although JSS is a promising measure, it has never been validated in the armed forces context. Thus, the aim of this study was to examine the psychometric properties of the Malay version of the Job Satisfaction Survey (Spector, 1965) using data from Malaysian military personnel . With this is mind, a group of male navy personnel from selected navy bases were recruited to be respondents. Through exploratory factor analyses (EFA), results yielded a five-subscale model with 28 items, namely: recognition, affection, fairness, expectation, and workload. In addition, the validity and stability of the five-dimensional structure of the scale were evident in this study using confirmatory factor analyses (CFA). In summary, this study confirmed the psychometric properties of the scale and can further be used to measure job satisfaction in the armed force setting.