Miracle-dz/UniFAR-FTUs huggingface dataset:
Root growth and function of three Mojave Desert grasses in response to elevated atmospheric CO2 concentration

summary Root growth and physiological responses to elevated CO # were investigated for three important Mojave Desert grasses: the C $ perennial Achnatherum hymenoides, the C % perennial Pleuraphis rigida and the C $ annual Bromus madritensis ssp. rubens. Seeds of each species were grown at ambient (360 l ll ’") or elevated (1000 l ll ’" )C O # in a glasshouse and harvested at three phenological stages: vegetative, anthesis and seed fill. Because P. rigida did not flower during the course of this study, harvests for this species represent three vegetative stages. Primary productivity was increased in both C $ grasses in response to elevated CO # (40 and 19% for A. hymenoides and B. rubens, respectively), but root biomass increased only in the C $ perennial grass. Neither above-ground nor belowground biomass of the C % perennial grass was significantly aected by the CO # treatment. Elevated CO # did not significantly aect root surface area for any species. Total plant nitrogen was also not statistically dierent between CO # treatments for any species, indicating no enhanced uptake of N under elevated CO # . Physiological uptake capacities for NO $ and NH % were not aected by the CO # treatment during the second harvest; measurements were not made for the first harvest. However, at the third harvest uptake capacity was significantly decreased in response to elevated CO # for at least one N form in each species. NO $ uptake rates were lower in A. hymenoides and P. rigida, and NH % uptake rates were lower in B. rubens at elevated CO # . Nitrogen uptake on a whole rootsystem basis (NO $ ›NH % uptake capacity‹root biomass) was influenced positively by elevated CO # only for A. hymenoides after anthesis. These results suggest that elevated CO # may result in a competitive advantage for A. hymenoides relative to species that do not increase root-system N uptake capacity. Root respiration measurements normalized to 20∞C were not significantly aected by the CO # treatment. However, specific root respiration was significantly correlated with either root C:N ratio or root water content when all data per species were included within a simple regression model. The results of this study provide little evidence for up-regulation of root physiology in response to elevated CO # and indicate that root biomass responses to CO # are species-specific.
Cloning, expression and purification of orthologous membrane proteins: a general protocol for preparation of the histidine sensor kinase ETR1 from different species

Abstract Orthologous proteins do not necessarily share the same function in all species and those sharing the same function might employ a modified catalytic mechanism. Thus, comparative analysis of homologous or orthologous proteins from different organisms can provide detailed information on the function and the mechanism of an entire protein family. The sensor kinase ETR1 from Arabidopsis thaliana has been well characterized by genetic, physiological and biochemical studies. However, as further model plants are coming into focus for plant hormone research, a general protocol for isolation and purification of orthologous ETR1 proteins seems instrumental for a detailed molecular analysis of this protein family. In this study, we describe the native purification of recombinant ETR1 from Arabidopsis thaliana by mild solubilization with the zwitter-ionic detergent Fos-Choline-14 and single-step purification by immobilized metal ion affinity chromatography. The same protocol was successfully applied for the purification of the orthologous proteins from the moss Physcomitrella patens subsp. patens and the tomato Lycopersicon esculentum. The successful transfer of the purification protocol to proteins of the same family which share sequence identity of 63–80% only suggests that this protocol presents a general purification strategy which is likely to apply also to the purification of other members of the sensor histidine kinase family.
Directional relay based on traveling-wave comparison using intrinsic mode function for EHV transmission lines

This paper presents a high-speed directional relay for EHV transmission line. The basic principle of the directional relay is based on comparing high-frequency component energy of directional traveling waves of each bus outgoing line. The relay comparison scheme is designed with intrinsic mode function (IMF) from empirical mode decomposition. The IMF is used to extract transient features from fault-generated traveling-wave signals propagating along transmission lines during a post-fault period. And the arithmetic differential of the IMF first layer can represent the time instant corresponding to the initial traveling-wave arriving at the directional relay. An actual 500-kV extra high voltage (EHV) transmission system has been simulated by PSCAD/EMTDC to evaluate the scheme. The analysis and simulation results show that the scheme is capable of providing correct responses under various fault conditions, and confirm the validity of this proposed scheme as a fast and secure protection scheme.
Wideband Circularly Polarized Antenna Realizing Omnidirectional Radiation in the Wider Azimuth Planes

A novel circularly polarized (CP) antenna realizing omnidirectional radiation in the wider azimuth planes is proposed in this letter. By introducing curved branches at both the patch and ground plane and making an angle of <italic>α</italic> between them, the amplitude and phase characteristic of the antenna are improved. Meanwhile, the omnidirectional CP field is obtained in the wider azimuth planes. The measured results show that the proposed antenna has a −10-dB impedance bandwidth of 19.6% and a 3-dB axial-ratio bandwidth of 27.4%. Moreover, the omnidirectional CP fields can be obtained in the azimuth planes of <inline-formula> <tex-math notation="LaTeX">$\theta \,= \,50^\circ{-}\text{130}^\circ $</tex-math></inline-formula>.
An Epstein-Barr virus DNA fragment encodes messages for the two major envelope glycoproteins (gp350/300 and gp220/200)

The genes encoding the two major Epstein-Barr virus glycoproteins (gp350/300 and gp220/200) have been mapped to a 5-kilobase fragment of the viral genome (BamHI-L). This fragment encodes 3.4- and 2.8-kilobase RNAs which translate proteins of 135 and 100 kilodaltons, respectively. Both proteins react with antiserum specific for gp350/300 and gp220/200. The 135-kilodalton protein is identical in size to the nascent polypeptide precursor to gp350/300, and the 100-kilodalton protein is the expected size of the polypeptide precursor to gp220/200.
Safety and Efficacy of Sorafenib in Patients With Advanced Hepatocellular Carcinoma in Consideration of Concomitant Stage of Liver Cirrhosis

Goals and Background The multikinase inhibitor sorafenib provides survival benefit for patients with advanced hepatocellular carcinoma (HCC) and liver cirrhosis (LCI) Child-Pugh A. We report our experiences with sorafenib in advanced HCC, particularly in patients with LCI Child-Pugh B/C, where only limited data are available in regard to safety and efficacy of sorafenib. Methods Thirty-four patients with advanced HCC were treated with sorafenib regardless of liver function and prior anticancer therapy. Adverse events (AEs) were graded using Common Toxicity Criteria version 3.0, tumor response was assessed according to Response Evaluation Criteria in Solid Tumors. Results Fifteen patients presented without LCI or with LCI Child-Pugh A, 15/4 patients had LCI Child-Pugh B/C. Barcelona Clinic Liver Cancer stage was B/C/D in 4/22/8 patients. During treatment period (median 2.2 mo), therapy was discontinued in 61.8% of patients due to tumor progression (32.3%), death (17.6%), AEs (8.8%), or noncompliance (2.9%). Most common grade 3/4 AEs included liver dysfunction (23.5%), diarrhea (14.7%), increased lipase (8.8%), fatigue (8.8%), and hand-foot skin reaction (5.9%). Worsening liver dysfunction/failure was more frequent (P=0.036) in patients with LCI Child-Pugh B/C compared with patients with maintained liver function (no LCI/LCI Child-Pugh A). Median overall survival was 7.2 months for patients with maintained liver function versus 3.3/3.4 months for patients with LCI Child-Pugh B/C. Conclusions These data do not support the use of sorafenib in patients with LCI Child-Pugh C, and patients with LCI Child-Pugh B should be treated with caution until larger trials provide more safety data and a clinically relevant survival benefit under sorafenib therapy.
Fit Functions for Relativistic, Single-Species and Bipolar, and Space-Charge-Limited Current Densities

This technical note reviews solutions for planar, relativistic space-charge-limited (SCL) flow both for the single species case with electrons and for bipolar flow with electrons and protons. In most cases, numerical integration or evaluation of special functions is needed to obtain values for these solutions. Here, fit functions for these solutions are derived so that they can be used to calculate 1-D SCL electron and proton current densities and the bipolar enhancement factor for any voltage, including the range transitioning from nonrelativistic to relativistic behavior (approximately 0.1-2 MV, γ = 1.2-5 for electrons and 102-105 MV, γ = 1.1-100 for protons). These fit functions reproduce the exact values to within a few percent, or with an error correction, to within a fraction of 1%. These functions should be useful for evaluating SCL current densities for a range of problems where relativistic effects are important and the 1-D approximation is applicable.
agr System of Listeria monocytogenes EGD-e: Role in Adherence and Differential Expression Pattern

ABSTRACT In this study, we investigated the agrBDCA operon in the pathogenic bacterium Listeria monocytogenes EGD-e. In-frame deletion of agrA and agrD resulted in an altered adherence and biofilm formation on abiotic surfaces, suggesting the involvement of the agr system of L. monocytogenes during the early stages of biofilm formation. Real-time PCR experiments indicated that the transcript levels of agrBDCA depended on the stage of biofilm development, since the levels were lower after the initial attachment period than during biofilm growth, whereas transcription during planktonic growth was not growth phase dependent. The mRNA quantification data also suggested that the agr system was autoregulated and pointed to a differential expression of the agr genes during sessile and planktonic growth. Although the reverse transcription-PCR experiments revealed that the four genes were transcribed as a single messenger, chemical half-life and 5′ RACE (rapid amplification of cDNA ends) experiments indicated that the full size transcript underwent cleavage followed by degradation of the agrC and agrA transcripts, which suggests a complex regulation of agr transcription.
The Impact of Insomnia and Sleep Disturbances on Depression and Suicidality

Previous research has demonstrated an association between suicidality and sleep, suggesting that sleep disturbances may exacerbate mood dysregulation in participants suffering from mood disorders. The purpose of this study was to investigate the impact of sleep disturbances and insomnia on depression and suicidality in a nontreatment seeking sample of college students. Results indicated that insomnia and nightmares were significant predictors of symptoms of depression, while only nightmares significantly predicted suicidal ideation. Further analysis indicated that participants with elevated scores on insomnia, nightmares, or both experienced differing levels of depression and suicidal ideation. Future directions and treatment implications are discussed.
SH3 Domain-mediated Interaction of Dystroglycan and Grb2(*)

Dystroglycan is a novel laminin receptor that links the extracellular matrix and sarcolemma in skeletal muscle. The dystroglycan complex containing α- and β-dystroglycan also serves as an agrin receptor in muscle, where it may regulate agrin-induced acetylcholine receptor clustering at the neuromuscular junction. β-Dystroglycan has now been expressed in vitro and shown to directly interact with Grb2, an adapter protein involved in signal transduction and cytoskeletal organization. Protein binding assays with two Grb2 mutants, Grb2/P49L and Grb2/G203R, which correspond to the loss-of-function mutants in the Caenorhabditis elegans sem -5, demonstrated that the dystroglycan-Grb2 association is through β-dystroglycan C-terminal proline-rich domains and Grb2 Src homology 3 domains. Affinity chromatography has also shown endogenous skeletal muscle Grb2 interacts with β-dystroglycan. Immunoprecipitation experiments have demonstrated that Grb2 associates with α/β-dystroglycan in vivo in both skeletal muscle and brain. The specific dystroglycan-Grb2 interaction may play an important role in extracellular matrix-mediated signal transduction and/or cytoskeleton organization in skeletal muscle that may be essential for muscle cell viability.
Involvement of Dominant-negative Spliced Variants of the Intermediate Conductance Ca2+-activated K+ Channel, KCa3.1, in Immune Function of Lymphoid Cells*

The intermediate conductance Ca2+-activated K+ channel (IKCa channel) encoded by KCa3.1 is responsible for the control of proliferation and differentiation in various types of cells. We identified novel spliced variants of KCa3.1 (human (h) KCa3.1b) from the human thymus, which were lacking the N-terminal domains of the original hKCa3.1a as a result of alternative splicing events. hKCa3.1b was significantly expressed in human lymphoid tissues. Western blot analysis showed that hKCa3.1a proteins were mainly expressed in the plasma membrane fraction, whereas hKCa3.1b was in the cytoplasmic fraction. We also identified a similar N terminus lacking KCa3.1 variants from mice and rat lymphoid tissues (mKCa3.1b and rKCa3.1b). In the HEK293 heterologous expression system, the cellular distribution of cyan fluorescent protein-tagged hKCa3.1a and/or YFP-tagged hKCa3.1b isoforms showed that hKCa3.1b suppressed the localization of hKCa3.1a to the plasma membrane. In the Xenopus oocyte translation system, co-expression of hKCa3.1b with hKCa3.1a suppressed IKCa channel activity of hKCa3.1a in a dominant-negative manner. In addition, this study indicated that up-regulation of mKCa3.1b in mouse thymocytes differentiated CD4(+)CD8(+) phenotype thymocytes into CD4(−)CD8(−) ones and suppressed concanavalin-A-stimulated thymocyte growth by down-regulation of mIL-2 transcripts. Anti-proliferative effects and down-regulation of mIL-2 transcripts were also observed in mKCa3.1b-overexpressing mouse thymocytes. These suggest that the N-terminal domain of KCa3.1 is critical for channel trafficking to the plasma membrane and that the fine-tuning of IKCa channel activity modulated through alternative splicing events may be related to the control in physiological and pathophysiological conditions in T-lymphocytes.
Effects of Radio Collars on Survival and Lekking Behavior of Male Greater Sage-Grouse

Abstract. Monitoring of birds often requires the use of very-high-frequency radios or satellite telemetry to enhance detectability of individuals. An assumption implicit in such studies is that radio-marked individuals are representative of the population at whole, which requires that radios do not influence an individual's behavior or demographics. We present results from a capture—mark—recapture study of male Greater Sage-Grouse (Centrocercus urophasianus), some radio collared, others only banded, in an experimental framework to assess whether radio collars influenced the birds' behavior or survival. We generated encounter histories of 906 male Greater Sage-Grouse and used a robust-design framework in program Mark to estimate probabilities of annual survival, detection, and temporary emigration from the lek for the radio-collared and banded segments of the sample population. Results of models suggested that seasonal detection rates at leks the year after capture were 3–5 times higher for males only banded than for males equipped with radio collars. These results also suggested a possible negative influence of radio collars on males' annual survival and annual lek attendance. We suggest researchers should exercise caution when designing studies or analyzing data that rely on radio-collared male Greater Sage-Grouse.
Transparent force control for Body Extender

The Body Extender is a whole-body exoskeleton designed to operate in unknown and difficult environments, for instance in disaster areas. The Body Extender allows the wearing operator to increase its force while maintaining a high level of perception. The present work describes a novel control system for the Body Extender. We designed the control loop in such a way the interaction forces are perceived as a fraction of the overall external forces. These percentages can be decided at design time as a trade-off between sensitivity and force extension. To realize control, the algorithm includes an on-line estimation of the transported mass. The algorithm has been implemented for one arm of the Body Extender. The identification, the performances and the stability limits has been tested on a simpler structure with only one joint. In the following we will show the basis of the developed algorithm as well as the results achieved on the test platform.
Real-time PCR detection and frequency of 16S rDNA mutations associated with resistance and reduced susceptibility to tetracycline in Helicobacter pylori from England and Wales.

OBJECTIVES To investigate the occurrence of 16S rDNA mutations associated with resistance or reduced susceptibility to tetracycline in Helicobacter pylori isolated in England and Wales, and to develop a real-time PCR assay to detect these DNA polymorphisms from culture and gastric biopsies. METHODS Tetracycline susceptibility was determined by disc diffusion. The MIC of isolates with reduced susceptibility was determined by Etest and agar dilution methods. The 16S rDNA of these isolates was sequenced and resistance-associated mutations identified. A LightCycler assay developed to detect these mutations was applied to DNA extracted from culture and gastric biopsies. RESULTS From 1006 isolates of H. pylori examined, 18 showed reduced susceptibility to tetracycline. Of these, three were resistant (>or=4 mg/L). Mutations in 16S rDNA were detected in 10 of the reduced susceptibility isolates: one double base mutation of A926T/A928C, one A926C, one A928C; and seven A926G. The first two polymorphisms were novel and had not been reported from clinical isolates previously. The LightCycler assay identified each of the 10 isolates with 16S rDNA mutations, but did not detect polymorphisms in 100 tetracycline-susceptible H. pylori isolates. The assay correctly determined the tetracycline susceptibility of H. pylori in 20 gastric biopsy samples. CONCLUSIONS Mutations in 16S rDNA were detected in H. pylori isolated in England and Wales with reduced susceptibility to tetracycline, but resistance to this antibiotic was uncommon. We show molecular-based susceptibility testing for tetracycline is possible direct from biopsy material.
Stability and hopf bifurcation of genetic regulatory networks with multiple delays

In this paper, we study the stability for a triple-gene expression model. We choose the sum of the delays as the bifurcation parameter. The bifurcation will occur when the sum of the delays passes through a critical value. The critical value of the delays is determined. Thus the triple-gene model can remain stable when the sum of the delays is smaller than the critical value. Finally, we verify the correctness of the theoretical results through the numerical simulations.
On verification and controller synthesis for probabilistic systems at runtime

Probabilistic model checking is a technique employed for verifying the correctness of computer systems that exhibit probabilistic behaviour. A related technique is controller synthesis, which generates controllers that guarantee the correct behaviour of the system. Not all controllers can be generated offline, as the relevant information may only be available when the system is running, for example, the reliability of services may vary over time. In this thesis, we propose a framework based on controller synthesis for stochastic games at runtime. We model systems using stochastic two-player games parameterised with data obtained from monitoring of the running system. One player represents the controllable actions of the system, while the other player represents the hostile uncontrollable environment. The goal is to synthesize, for a given property specification, a controller for the first player that wins against all possible actions of the environment player. Initially, controller synthesis is invoked for the parameterised model and the resulting controller is applied to the running system. The process is repeated at runtime when changes in the monitored parameters are detected, whereby a new controller is generated and applied. To ensure the practicality of the framework, we focus on its three important aspects: performance, robustness, and scalability. We propose an incremental model construction technique to improve performance of runtime synthesis. In many cases, changes in monitored parameters are small and models built for consecutive parameter values are similar. We exploit this and incrementally build a model for the updated parameters reusing the previous model, effectively saving time. To address robustness, we develop a technique called permissive controller synthesis. Permissive controllers generalise the classical controllers by allowing the system to choose from a set of actions instead of just one. By using a permissive controller, a computer system can quickly adapt to a situation where an action becomes temporarily unavailable while still satisfying the property of interest. We tackle the scalability of controller synthesis with a learning-based approach. We develop a technique based on real-time dynamic programming which, by generating random trajectories through a model, synthesises an approximately optimal controller. We guide the generation using heuristics and can guarantee that, even in the cases where we only explore a small part of the model, we still obtain a correct controller. We develop a full implementation of these techniques and evaluate it on a large set of case studies from the PRISM benchmark suite, demonstrating significant performance gains in most cases. We also illustrate the working of the framework on a new case study of an open-source stock monitoring application.
Multilocus Sequence Typing Scheme for Enterococcus faecalis Reveals Hospital-Adapted Genetic Complexes in a Background of High Rates of Recombination

ABSTRACT A multilocus sequence typing (MLST) scheme based on seven housekeeping genes was used to investigate the epidemiology and population structure of Enterococcus faecalis. MLST of 110 isolates from different sources and geographic locations revealed 55 different sequence types that grouped into four major clonal complexes (CC2, CC9, CC10, and CC21) by use of eBURST. Two of these clonal complexes, CC2 and CC9, are particularly fit in the hospital environment, as CC2 includes the previously described BVE clonal complex identified by an alternative MLST scheme and CC9 includes exclusively isolates from hospitalized patients. Identical alleles were found in genetically diverse isolates with no linkage disequilibrium, while the different MLST loci gave incongruent phylogenetic trees. This demonstrates that recombination is an important mechanism driving genetic variation in E. faecalis and suggests an epidemic population structure for E. faecalis. Our novel MLST scheme provides an excellent tool for investigating local and short-term epidemiology as well as global epidemiology, population structure, and genetic evolution of E. faecalis.