Miracle-dz/UniFAR-FTUs huggingface dataset:
A chaperone‐like HrpG protein acts as a suppressor of HrpV in regulation of the Pseudomonas syringae pv. syringae type III secretion system

The cloned hrp/hrc cluster of Pseudomonas syringae pv. syringae 61 (Pss61) contains 28 proteins, and many of those are assembled into a type III secretion system (TTSS) that is responsible for eliciting the hypersensitive response (HR) in non‐host plants and causing diseases on host plants ( Huang et al., 1995 ). hrpG, the second gene in the hrpC operon, encodes a 15.4 kDa cytoplasmic protein whose predicted structure is similar to SicP (E‐value: 0.19), a TTSS chaperone of Salmonella typhimurium. Two non‐polar hrpG mutants, Pss61‐N826 and Pss61‐N674, were produced to investigate the biological function of hrpG gene. Pss61‐N826, generated by replacing the coding sequence of hrpG with an nptII gene lacking both the promoter and the terminator, was found to be capable of eliciting the wild‐type HR; whereas Pss61‐N674 generated by replacement of a terminatorless nptII gene in the hrpG coding sequence showed the delayed HR phenotype. Northern and Western blotting analyses showed that the expression of hrpZ, hrcJ and hrcQb genes residing on two different operons in Pss61‐N674 was reduced due to the nptII promoter‐driven constitutive expression of hrpV that codes for a negative regulator. Interestingly, a plasmid‐borne hrpG can derepress the hrp expression in Pss61‐N674 and in Pss61 overexpressing HrpV without decreasing the hrpV transcript. Moreover, results of yeast two‐hybrid assay, pull‐down assay and far Western analysis show that HrpG and HrpV interact with each other in vivo and in vitro. Additionally, HrpV interacts with a positive regulator HrpS according to analysis of a yeast two‐hybrid system. Based on the results presented in this study, we propose that HrpG acts as a suppressor of the negative regulator HrpV mediated via protein–protein interaction, leading to modulation of hrp/hrc expression subsequently freeing HrpS to promote the activation of other downstream hrp/hrc genes.
Feature-oriented programming with family polymorphism

In feature-oriented programming (FOP), code clones are also important issue. Although an approach called a software product line (SPL) enables to implement products efficiently by reusing most of their code, SPLs implemented by FOP contain a lot of code clones. Code clones are often caused by alternative features and we also found clones in derivatives among alternative features. To resolve this problem, we propose a new FOP language named FeatureGluonJ, which supports family polymorphism with revisers. The code clones among alternative features are separated into another feature and can be shared among the alternative features by extending that feature. Furthermore, clones in derivatives can be removed as well.
Reduced-rate retransmissions for spread-spectrum packet radio multimedia networks

A reduced-rate retransmission (RRR) scheme is proposed for improving the throughput performance of spread-spectrum packet radio networks. The scheme takes advantages of the available multi-rate scalable source coding techniques. It assumes that several versions of a data packet with different sizes (number of information bits) are available. The transmission of a packet starts from its full-size version. If the full-size version is not correctly received, its half-size version is used in the retransmission. If further retransmissions are needed, the quarter-size version and so on are used. The shrunk packets are transmitted either in a minislot if the processing gain is kept the same, or occupying a slot duration by increasing the processing gain proportionally. In both cases, the effective signal to interference ratio for a packet is increased. As a result, the system throughput is improved. Theoretical and numerical results are provided in this paper which illustrate the throughput improvement. Another advantage of the proposed RRR scheme is that the packet-size reduction provides finer granules for link adaptation. Therefore, it is especially suitable for multimedia applications for which codes of variable rate for the source data are available and which can tolerate gracefully degraded quality of service. The performance of the proposed scheme in fading channels is also addressed.
MRI of blood flow of the human retina

This study reports a high‐resolution MRI approach to image basal blood flow and hypercapnia‐induced blood‐flow changes in the unanesthetized human retina on a 3‐T MRI scanner. Pseudocontinuous arterial spin labeling technique with static tissue suppression was implemented to minimize movement artifacts and improve blood‐flow sensitivity. Turbo spin–echo acquisition was used to achieve high spatial resolution free of susceptibility artifacts. The size, shape, and position of a custom‐made receive radiofrequency coil were optimized for sensitivity in the posterior retina. Synchronized eye blink and respiration to the end of each data readout minimized eye movement and physiological fluctuation. Robust high‐contrast blood‐flow MRI of the unanesthetized human retina was obtained at 500 × 800 μm2 in‐plane resolution. Blood flow in the posterior retina was 93 ± 31 mL/(100 mL min) (mean ± standard deviation, N = 5). Hypercapnic inhalation (5% CO2) increased blood flow by 12 ± 4% relative to air (P < 0.01, N = 5). This study demonstrates the feasibility of blood‐flow MRI of the retina of unanesthetized human. Because blood flow is tightly coupled to metabolic function under normal conditions and it is often perturbed in diseases, this approach could provide unique insights into retinal physiology and serve as an objective imaging biomarker for disease staging and testing of novel therapeutic strategies. This approach could open up new avenue of retinal research. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Learning to Use a Software Library through User-Selected Examples

Once a software library has been selected for a project, there is still the substantial problem of training developers to use it. This process is complicated by the fact that using a software library often requires some understanding of its fundamental components, their relationships, and various interactions between them. This is particularly true with frameworks which tend to impose a structure on the application. In this paper, we present a tool-based approach that demonstrates reuse of the software library through userselected example applications. In this way, a developer can learn about fundamental library components and their relationships. An important aspect of our approach is that it requires no extra effort on the part of the library developer and can be used with any existing software library. Our approach facilitates learning to use a library by: (1) guiding the developer towards important components of general utility; (2) guiding the developer towards components particularly useful for a specific class of applications; and (3) providing access to the relevant source code in each example for further inspection. Our approach is supported by CodeWeb, a reuse tool we have built for C, C++, and Java libraries.
Global expression changes of constitutive and hormonally regulated genes during endometrial neoplastic transformation.

OBJECTIVE Endometrioid endometrial carcinoma is caused by a combination of mutational events and hormonal factors. We used large-scale messenger RNA expression analysis to discover genes that distinguish neoplastic transformation and examine the patterns of tumor expression of those genes which are normally regulated during the menstrual cycle. METHODS Expression of approximately 6000 unique genes was quantified in 4 normal (2 proliferative, 2 secretory) and 10 malignant endometria using Affymetrix Hu6800 GeneChip probe arrays. Expression differences between normal and malignant tissue groups were measured by a test of statistical significance comparing the individual t statistic for each gene to the distribution of maximum t statistics among all genes following 1001 permutations of the tissue group assignments (Permax test). Hormonally responsive genes, selected by comparison of proliferative and secretory subsets of normal endometria using a combination of filters applied to the group means and t test rankings, were then examined in the tumors. RESULTS Fifty genes with a Permax <0.50 provided excellent discrimination between normal and malignant groups and were predominantly characterized by diminished expression levels in the cancers. We found that 100 genes which are hormonally regulated in normal tissues are expressed in a disordered and heterogeneous fashion in cancers, with tumors resembling proliferative more than secretory endometrium. CONCLUSION Neoplastic transformation is accompanied by predominant loss of activity of many genes constitutively expressed in normal source tissues and absence of expression profiles which characterize the antitumorigenic progestin response.
Probabilistic collocation method for uncertainty analysis of soil infiltration in flood modelling

The probabilistic collocation method (PCM) based on the Karhunen-Loeve expansion (KLE) and Polynomial chaos expansion (PCE) is applied for uncertainty analysis of flood inundation modelling. The floodplain hydraulic conductivity (KS) is considered as one of the important parameters in a 2-dimensional (2D) physical model FLO-2D (with Green-Ampt infiltration method) and has a nonlinear relationship with the flood simulation results, such as maximum flow depths (hmax). In this study, due to the spatial heterogeneity of soil, log-transformed Ks was assumed a random field in spatiality with normal distribution and decomposed with KLE in pairs of corresponding eigenvalues and eigenfuctions. The hmax random field is expanded by a second-order PCE approximation and the deterministic coefficients in PCE are solved by FLO-2D. To demonstrate this method, a simplified flood inundation case was used, where the mean and variance of the simulation outputs were compared with those from direct Monte Carlo Simulation. The comparison indicates that PCM could efficiently capture the statistics of flow depth in flood modelling with much less computational requirements.
Calcification and growth processes in planktonic foraminifera complicate the use of B / Ca and U / Ca as carbonate chemistry proxies

The Open University's repository of research publications and other research outputs Calcification and growth processes in planktonic foraminifera complicate the use of B/Ca and U/Ca as carbonate chemistry proxies Journal Article (2016). Calcification and growth processes in planktonic foraminifera complicate the use of B/Ca and U/Ca as carbonate chemistry proxies. Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online's data policy on reuse of materials please consult the policies page. Calcification and growth processes in planktonic foraminifera complicate the use of B/Ca and U/Ca as carbonate chemistry proxies a r t i c l e i n f o a b s t r a c t Keywords: planktonic foraminifera boron uranium proxy sediment trap Although boron and uranium to calcium ratios (B/Ca, U/Ca) in planktonic foraminifera have recently received much attention as potential proxies for ocean carbonate chemistry, the extent of a carbonate chemistry control on these ratios remains contentious. Here, we use biweekly sediment trap samples collected from the subtropical North Atlantic in combination with measured oceanographic data from the same location to evaluate the dominant oceanographic controls on B/Ca and U/Ca in three depth-stratified species of planktonic foraminifera. We also test the control of biological, growth-related, processes on planktonic foraminiferal B and U incorporation by using foraminifer test area density (µg/µm 2) (a monitor of test thickness) and test size from the same samples. B/Ca and U/Ca show little or no significant correlation with carbonate system parameters both within this study and in comparison with other published works. We provide the first evidence for a strong positive relationship between area density (test thickness) and B/Ca, and reveal that this is consistent in all species studied, suggesting a likely role for calcification in controlling boron partitioning into foraminiferal calcite. This finding is consistent with previous observations of less efficient discrimination against trace element 'impurities' (such as B), at higher calcification rates. We observe little or no dependency of B/Ca on test size. In marked contrast, we find that U/Ca displays a strong species-specific dependency on test size in all species, but no relationship with test thickness, implicating some other biological control (possibly related to growth), rather than a calcification control, on U incorporation into foraminiferal calcite. Our results caution against the use of B/Ca and U/Ca in planktonic foraminifera as …
Control of Robotic Manipulators Under Input/Output Communication Delays: Theory and Experiments

Input/output delays in a control system can pose significant impediments to the stabilization problem and potentially degrade the performance of the closed-loop system. In this paper, we study the classical set-point control problem for rigid robots with input-output communication delays in the closed-loop system. We demonstrate that if there are transmission delays between the robotic system and the controller, then the use of the scattering variables can stabilize an otherwise unstable system for arbitrary unknown constant delays. It is also demonstrated that the proposed algorithm results in guaranteed set-point tracking. In the case of time-varying delays, scattering variables together with additional gains can be utilized to stabilize the closed-loop system that is composed of the robotic manipulator and the controller. Furthermore, a scattering representation-based design with position feedback is proposed to improve closed-loop performance under time-varying delays. The proposed algorithms are validated via experiments in this paper.
Spatial reuse strategy in mmWave WPANs with directional antennas

In this paper, we propose a spatial reuse strategy for millimeter-wave (mmWave) wireless personal area networks (WPANs) with directional antennas. By this strategy, two or more transmissions can be appropriately scheduled for spatial sharing based on the beamforming (BF) information. Moreover, we analyze the performance of this strategy with consideration of the difference between idealistic and realistic directional antennas. Simulation results show that the strategy efficiency is related to antenna types, configurations and network topologies, and that the spatial multiplexing gain can be increased accordingly.
hiHMM: Bayesian non-parametric joint inference of chromatin state maps

Motivation: Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications. Results: Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets. Conclusion: The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chromatin landscape analysis. Availability and implementation: Source codes are available at https://github.com/kasohn/hiHMM. Chromatin data are available at http://encode-x.med.harvard.edu/data_sets/chromatin/. Contact: peter_park@harvard.edu or juhan@snu.ac. kr Supplementary information: Supplementary data are available at Bioinformatics online.
Dietary Diversity within Food Groups: An Indicator of Specific Nutrient Adequacy in Tehranian Women

Objective: To determine the relationship between dietary diversity within food groups and dietary diversity score and the probability of nutrient adequacy in Tehranian women. Design: Cross-sectional study assessing food intake by two 24-hour recalls questionnaires on two different occasions. Dietary diversity was defined according to diet quality index revised. The mean probability of adequacy across 14 nutrients was calculated using the Dietary Reference Intakes. Setting: District 13 of Tehran, Iran. Subjects: 286 females aged 18–80 years. Results: Whole grain diversity score mostly correlated with protein and vitamin B2 (r = 0.35, p < 0.05). Fruit diversity score was correlated with vitamin C (r = 0.44, p < 0.05). Dairy diversity score was correlated with calcium intake (r = 0.54, p < 0.05). Meat diversity score was correlated with protein intake (r = 0.34, p < 0.05). Most subjects failed to meet vitamin B6, zinc, magnesium, calcium, copper, and vitamin B12 adequacy. Energy intake was a strong predictor of the mean probability of adequacy in models controlled for age, BMI, education level and job status (model R2 = 0.53). Adding the number of servings from each of the food group to the models significantly improved the model fit (model R2 = 0.59). Adding the dietary diversity score improved the model fit significantly (model R2 = 0.64). Dairy diversity score had the strongest association with improved nutrient adequacy. Conclusion: Dietary diversity score is a useful indicator of specific nutrient adequacy in Tehranian women. However, to determine the adequacy of a specific nutrient, the diversity scores of specific food groups might be taken into account.
Complementary and alternative medicine: oncology nurses' experiences, educational interests, and resources.

PURPOSE/OBJECTIVES To describe oncology nurses' experiences with patients communicating interest in or use of complementary and alternative medicine (CAM) therapies along with oncology nurses' CAM resources and educational interests. DESIGN National mailed survey. SETTING A national medical center and research institute. SAMPLE A random sample of 850 Oncology Nursing Society (ONS) members who are RNs involved in direct patient care. METHODS Respondents completed a demographic questionnaire and the Nurse Complementary and Alternative Medicine Knowledge and Attitude Survey. Initial analysis compared the demographics of the sample to the ONS membership. Descriptive analysis was used to further describe nurses' experiences with patients communicating interest in or use of CAM, nurses' interest in CAM education, and nurses' use of CAM resources. MAIN RESEARCH VARIABLES Experiences, resources, interests, and CAM therapies. FINDINGS Oncology nurses reported their experiences with patients who communicated interest in or use of CAM therapies. Respondents demonstrated considerable interest in learning more about specific CAM therapies and used a variety of resources to find information on CAM therapies. CONCLUSIONS Assessing oncology nurses' experiences, resources used, and interest in learning about CAM therapies is the first step in determining the learning needs of oncology nurses in the direct patient care environment. The next step is to obtain baseline information on oncology nurses' CAM knowledge and attitudes for developing and providing appropriate education. CAM education will provide nurses with knowledge to support and advocate for their patients. IMPLICATIONS FOR NURSING Oncology nurses are the bridge to help patients safely integrate evidence-based CAM therapies into conventional treatment.
Flies as the ointment: Drosophila modeling to enhance drug discovery

Development of a drug and its safe therapeutic application necessitates using animal models for testing purposes. While testing with mammalian models is essential prior to approval for human trials, the use of invertebrate animal models that are amenable to molecular genetic manipulations provide experimental and biological advantages that can streamline the discovery and testing process. Among the benefits of a genetics-based approach is the ability to screen for genes/proteins that may be novel drug targets, and the expedited development of genetic backgrounds that more accurately reflect a specific disease state. An invertebrate model may provide a more robust phenotype for screening, a situation that may arise when there is unanticipated genetic redundancy present in the mammalian model. Finally, the comparatively short generation time and fecundity of invertebrate models allows for increased experimental throughput. Together, these factors may contribute towards savings in time and cost during the drug discovery process.
Simultaneous Learning of Trees and Representations for Extreme Classification, with Application to Language Modeling

This paper addresses the problem of multi-class classification with an extremely large number of classes, where the class predic-tor is learned jointly with the data representation , as is the case in language modeling problems. The predictor admits a hierarchical structure, which allows for efficient handling of settings that deal with a very large number of labels. The predictive power of the model however can heavily depend on the structure of the tree. We address this problem with an algorithm for tree construction and training that is based on a new objective function which favors balanced and easily-separable node partitions. We describe theoretical properties of this objective function and show that it gives rise to a boosting algorithm for which we provide a bound on classification error, i.e. we show that if the objective is weakly optimized in the internal nodes of the tree, then our algorithm will amplify this weak advantage to build a tree achieving any desired level of accuracy. We apply the algorithm to the task of language mod-eling by re-framing conditional density estimation as a variant of the hierarchical classification problem. We empirically demonstrate on text data that the proposed approach leads to high-quality trees in terms of perplexity and computational running time compared to its non-hierarchical counterpart.
Cytokines in nasal fluids from school children with seasonal allergic rhinitis

Allergic rhinitis is a particularly good model for studies of cytokine pro‐duction in vivo, in this study the occurrence of the cytokines IL‐4, IL‐5. IL‐10 and IFN‐yas well as the soluble receptor tbr IL‐4 in nasal lavage flu‐ids were assayed in 38 school children, with seasonal allergic rhinitis, and 19 healthy age matched, non atopic controls, using highly sensitive enzyme immunossays. IL‐4 levels in patients with seasonal allergie rhinitis were markedly increased in comparison with those in non‐atopic controls or in atopic pa‐tients before the start of the pollen season. In controls, but not in the atopic patients, levels of IFN‐yand IL‐5 were significantly higher in specimens obtained during the pollen season than in those obtained outside the season. The IL‐4/IFN‐y ratios were significantly higher in atopic than in nonalopic subjects and further increased in atopic patients during the season. In addition to IL‐4, elevated levels of IL‐10 were observed in association with seasonal rhinitis. Following treatment with a topical steroid (budeso nide) there was a statistically significant increase of the levels of soluble IL‐4 receptor. These findings indicate that nonatopic and atopic individuals react to pollen exposure with distinct cytokine patterns in agreement with the Thl/ Th2 concept. Topical steroids may possibly decrease inflammation by increasing the formation of soluble IL‐4 receptor.