Miracle-dz/UniFAR-FTUs huggingface dataset:
Rice Mitogen-Activated Protein Kinase Interactome Analysis Using the Yeast Two-Hybrid System1[C][W]

Mitogen-activated protein kinase (MAPK) cascades support the flow of extracellular signals to intracellular target molecules and ultimately drive a diverse array of physiological functions in cells, tissues, and organisms by interacting with other proteins. Yet, our knowledge of the global physical MAPK interactome in plants remains largely fragmented. Here, we utilized the yeast two-hybrid system and coimmunoprecipitation, pull-down, bimolecular fluorescence complementation, subcellular localization, and kinase assay experiments in the model crop rice (Oryza sativa) to systematically map what is to our knowledge the first plant MAPK-interacting proteins. We identified 80 nonredundant interacting protein pairs (74 nonredundant interactors) for rice MAPKs and elucidated the novel proteome-wide network of MAPK interactors. The established interactome contains four membrane-associated proteins, seven MAP2Ks (for MAPK kinase), four MAPKs, and 59 putative substrates, including 18 transcription factors. Several interactors were also validated by experimental approaches (in vivo and in vitro) and literature survey. Our results highlight the importance of OsMPK1, an ortholog of tobacco (Nicotiana benthamiana) salicyclic acid-induced protein kinase and Arabidopsis (Arabidopsis thaliana) AtMPK6, among the rice MAPKs, as it alone interacts with 41 unique proteins (51.2% of the mapped MAPK interaction network). Additionally, Gene Ontology classification of interacting proteins into 34 functional categories suggested MAPK participation in diverse physiological functions. Together, the results obtained essentially enhance our knowledge of the MAPK-interacting protein network and provide a valuable research resource for developing a nearly complete map of the rice MAPK interactome.
Integrated technologies for indexing spoken language

because it is impossible to efficiently locate information in large audio archives. By itself, speech does not permit content-based searches for information like those commonly employed for text documents over the Internet. But now, after more than a decade of steady advances in speech recognition, speaker identification, and language understanding, it is possible to begin building usable automatic content-based indexing tools for spoken language by integrating these emerging technologies. Once these tools become Integrated Technologies FOR Indexing Spoken Language
BID Mediates Oxygen-Glucose Deprivation-Induced Neuronal Injury in Organotypic Hippocampal Slice Cultures and Modulates Tissue Inflammation in a Transient Focal Cerebral Ischemia Model without Changing Lesion Volume

The BH3 interacting-domain death agonist (BID) is a pro-apoptotic protein involved in death receptor-induced and mitochondria-mediated apoptosis. Recently, it has also been suggested that BID is involved in the regulation of inflammatory responses in the central nervous system. We found that BID deficiency protected organotypic hippocampal slice cultures in vitro from neuronal injury induced by oxygen-glucose deprivation. In vivo, BID-knockout (KO) mice and wild type (WT) mice were subjected to 60 min of transient middle cerebral artery occlusion (tMCAO) to induce focal cerebral ischemia, and allowed to recover for 24 h. Infarct volumes and functional outcome were assessed and the inflammatory response was evaluated using immunofluorescence, Western blotting, quantitative PCR (qPCR) and Mesoscale multiplex analysis. We observed no difference in the infarct volume or neurological outcome between BID-KO and WT mice. The inflammatory response was reduced by BID deficiency as indicated by a change in microglial/leukocyte response. In conclusion, our data suggest that BID deficiency is neuroprotective in an in vitro model and modulates the inflammatory response to focal cerebral ischemia in vivo. However, this is not translated into a robust neuroprotection in vivo.
Spontaneous somatic embryogenesis on in vitro root segment cultures of Rauvolfia micrantha Hook. F.—A rare medicinal plant

SummaryPlant regeneration through direct somatic embryogenesis was achieved from root segments derived from in vitro shoots of Rauvolfia micrantha Hook. f. (Apocynaceae) grown for 6 wk in half-strength Murashige and Skoog (MS) medium with 3% sucrose, 100 mgl−1 myo-inositol, and 0.5 mgl−1 α-naphthaleneacetic acid (NAA). The effects of photoperiod and plant growth regulators (PGRs) in half-strength MS medium were studied for the rapid and maximum induction of somatic embryos. The characteristic globular or heart-shaped stages of somatic embryogenesis were not found and cotyledonary stage embryos occasionally appeared without the intervention of callus in total darkness and 16-h photoperiod. Root segments cultured in the medium containing 0.1 mgl−1 NAA and 0.2 mgl−1 6-benzyladenine (BA) under 16-h photoperiod showed the maximum frequency (39%) of embryogenesis. The frequency of embryo formation was increased to 63% when they were cultured in medium with 0.1 mgl−1 NAA and 0.2 mgl−1 BA in the dark for 4wk, then grown under the 16-h photoperiod. Explants with developing embryos developed into plants after transfer to half-strength MS medium supplemented with 0.1 mgl−1 BA and 0.05 mgl−1 NAA. The well-developed plants were hardened and most plants (80%) survived and were phenotypically similar to the mother plants.
K+ channel cAMP activated in guinea pig gallbladder epithelial cells.

In guinea pig gallbladder epithelial cells, an increase in intracellular cAMP levels elicits the rise of anion channel activity. We investigated by patch-clamp techniques whether K(+) channels were also activated. In a cell-attached configuration and in the presence of theophylline and forskolin or 8-Br-cAMP in the cellular incubation bath, an increase of the open probability (P(o)) values for Ca(2+)-activated K(+) channels with a single-channel conductance of about 160 pS, for inward current, was observed. The increase in P(o) of these channels was also seen in an inside-out configuration and in the presence of PKA, ATP, and cAMP, but not with cAMP alone; phosphorylation did not influence single-channel conductance. In the inside-out configuration, the opioid loperamide (10(-5) M) was able to reduce P(o) when it was present either in the microelectrode filling solution or on the cytoplasmic side. Detection in the epithelial cells by RT-PCR of the mRNA corresponding to the alpha subunit of large-conductance Ca(2+)-activated K(+) channels (BK(Ca)) indicates that this gallbladder channel could belong to the BK family. Immunohistochemistry experiments confirm that these cells express the BK alpha subunit, which is located on the apical membrane. Other K(+) channels with lower conductance (40 pS) were not activated either by 8-Br-cAMP (cell-attached) or by PKA + ATP + cAMP (inside-out). These channels were insensitive to TEA(+) and loperamide. The data demonstrate that under conditions that induce secretion, phosphorylation activates anion channels as well as Ca(2+)-dependent, loperamide-sensitive K(+) channels present on the apical membrane.
Community acquired methicillin sensitive Staphylococcus aureus bacteremia, meningitis and brain abscess: A unique presentation

Introduction: ＂Staphylococcus aureus＂ causing isolate central nervous system (CNS) infection is rare. It is mostly related to either neurosurgical intervention or previous local or systemic infection rather than spontaneous isolated infection in adults. Case Report: We report a case of a previously healthy 19-year-old male with no risk factors of ＂Staphylococcus aureus＂ infection, who was found to have methicillin sensitive ＂Staphylococcus aureus＂ (MSSA) bacteremia, meningitis and cerebral abscess, without an apparent source of infection. Conclusion: Our case is a unique presentation of a young male presenting with isolated CNS infection by MSSA. This case highlights the challenge of early diagnosis of brain abscess, an entity that presents very often with non-specific signs, the diagnosis of which can be easily missed, with repercussions on long-term disability and mortality.
Alizarin red in the study of the apposition and resorption on bone.

Alizarin red is given intraperitoneally in dosages of 50–200 mg per kg. It then stains visibly only one generation of bone. Its deposition is studied in gross specimens and in undecalcified sections, and is controlled by comparison with serial decalcified sections. Apposition of white bone can be followed in relation to red bone on periosteal surfaces (where it presents appearances corresponding to different growth rates), on endosteal surfaces, in osteons, and in the interstitial compaction of cancellous bone. Red surfaces may be sites of deposition, stasis, or resorption. Measurements may be made from red lines, provided microscopic control is available. Removal of red bone always implies resorption. It is closely correlated with the presence of osteoclasts in control sections and with areas of surface pitting grossly. Resorbing surfaces may be precisely delimited by studying a graded series of animals. Whole surfaces or zones of stained bone are seen to “drift” toward other situations, undergoing resorptive dissolution or consolidating anew as they move relative to the newer layers. The usefulness of the dye lies in its simplicity of administration, its ready visibility, and in the fact that its persistence in bone enables the fate of areas of bone to be followed over long periods. The preparation of undecalcified sections is a problem common to many other techniques.
How does scale mean? A critical approach to scale in the study of policy

ABSTRACT This article argues that a critical engagement with the categories and concepts of scale has been absent in policy studies. Integrating insights from post-structuralist human geography and policy analysis, the article reveals the multiple meanings actors assign to scales as they make sense of and construct their policy worlds, and also questions the implications of this for the practices and politics of policy. This analytical lens is applied to an empirical example of the policy work involved in implementing England’s academy schools policy in a local authority case study. Four scalar practices emerge from the analysis: dissolving boundaries of scale, shifting between scales, constructing boundaries between scales and emphasizing the interconnectedness of scales. Analysis reveals how critically engaging with how actors construct and mobilize scale can develop a new angle on the political logics shaping policy practices and thus enhance understandings of political struggles over meaning in policy-making.
The tiresias effect: feedforward using light versus temperature in a tangible user interface

In this paper we discuss how light and temperature information can be designed to affect feedforward in a tangible user interface (TUI). In particular we focus on temperature, which has not been widely considered as a mode of information representation in feedback or feedforward. We describe a prototype that implements both information modes in a TUI. Finally, we outline a user study in which these modes are explored as feedforward coaching devices for a decision-making task. The expected outcomes are an understanding of the role of temperature as information for feedforward in TUIs and a set of design guidelines for designers of tangibles working with these physical characteristics.
Ryanodine sensitizes the cardiac Ca2+ release channel (ryanodine receptor isoform 2) to Ca2+ activation and dissociates as the channel is closed by Ca2+ depletion

In single-channel recordings, the rabbit cardiac Ca2+ release channel (RyR2) is converted to a fully open subconductance state with about 50% of full conductance by micromolar concentrations of ryanodine. At +30 mV, corresponding to a luminal to cytoplasmic cation current, the probability of opening (Po) of ryanodine-modified channels was only marginally altered at pCa 10 (pCa = −log10 Ca concentration). However, at −30 mV, the Po was highly sensitive to Ca2+ added to the cis (cytoplasmic) side and, at pCa 10, was reduced to less than 0.27. The EC50 value for channel opening was about pCa 8. No significant Ca2+ inactivation was observed for ryanodine-modified channels at either −30 mV or +30 mV. The opening of unmodified Ca2+ channels is Ca2+ sensitive, with an EC50 value of about pCa 6 (two orders of magnitude less sensitive than ryanodine-modified channels) and IC50 values of pCa 2.2 at −30 mV and 2.5 at +30 mV. Mg2+ decreased the Po of ryanodine-modified channels at low Ca2+ concentrations at both −30 and +30 mV. Caffeine, ATP, and ruthenium red were modulators of the Po of ryanodine-modified channels. In a [3H]ryanodine binding assay, [3H]ryanodine dissociation from the high-affinity binding site was found to be Ca2+ sensitive, with an IC50 of pCa 7.1. High concentrations of unlabeled ryanodine prevented [3H]ryanodine dissociation, but ruthenium red accelerated dissociation. These results suggest that ryanodine sensitizes Ca2+ activation of the Ca2+ release channel and desensitizes Ca2+ inactivation through an allosteric interaction. [3H]Ryanodine dissociates from the high-affinity site when the channel is closed by removal of Ca2+, implying that high-affinity ryanodine and Ca2+ binding sites are linked through either short- or long-range interactions, probably involving conformational changes.
Association of hepsin gene variants with prostate cancer risk and prognosis

Hepsin (HPN) is one of the most consistently overexpressed genes in prostate cancer and there is some evidence supporting an association between HPN gene variants and prostate cancer risk. We report results from a population‐based case–control genetic association study for six tagging single nucleotide polymorphisms (tagSNPs) in the HPN gene.
Nonlinear Control of Systems Preceded by Preisach Hysteresis Description: A Prescribed Adaptive Control Approach

When systems are preceded by hysteresis nonlinearities, many controller strategies have been developed with various hysteresis models, especially in the past decade. Among the hysteresis models, the Preisach model has a very general and well-established mathematical structure. However, designs of controllers that guarantee the closed-loop stability of nonlinear systems having the Preisach hysteresis representation are still a challenging issue in the literature. In this paper, we will attempt to demonstrate a solution in which a stable controller can be designed for nonlinear systems that couple with Preisach hysteresis model. The key is that by utilizing the so-called Preisach plane, the Preisach model is reexpressed into a control-oriented form, in which the input signal is explicitly expressed. It is then possible to fuse available control techniques with the Preisach model designing stable controllers. As an illustration to show the advantage of the developed control-oriented form, a prescribed adaptive control approach is adopted to ensure the transient and steady-state performance of the tracking error. The effectiveness of the control scheme is validated by the experimental results.
Evaluation of Tubular Poly(Trimethylene Carbonate) Tissue Engineering Scaffolds in a Circulating Pulsatile Flow System

Tubular scaffolds (internal diameter approximately 3 mm and wall thickness approximately 0.8 mm) with a porosity of approximately 83% and an average pore size of 116 μm were prepared from flexible poly(trimethylene carbonate) (PTMC) polymer by dip-coating and particulate leaching methods. PTMC is a flexible and biocompatible polymer that crosslinks upon irradiation; porous network structures were obtained by irradiating the specimens in vacuum at 25 kGy before leaching soluble salt particles. To assess the suitability of these scaffolds in dynamic cell culturing for cardiovascular tissue engineering, the scaffolds were coated with a thin (0.1 to 0.2 mm) non-porous PTMC layer and its performance was evaluated in a closed pulsatile flow system (PFS). For this, the PFS was operated at physiological conditions at liquid flows of 1.56 ml/s with pressures varying from 80–120 mmHg at a frequency of 70 pulsations per minute. The mechanical properties of these coated porous PTMC scaffolds were not significantly different than non-coated scaffolds. Typical tensile strengths in the radial direction were 0.15 MPa, initial stiffness values were close to 1.4 MPa. Their creep resistance in cyclic deformation experiments was excellent. In the pulsatile flow setup, the distention rates of these flexible and elastic scaffolds were approximately 0.10% per mmHg, which is comparable to that of a porcine carotid artery (0.11% per mmHg). The compliance and stiffness index values were close to those of natural arteries. In long-term deformation studies, where the scaffolds were subjected to physiological pulsatile pressures for one week, the morphology and mechanical properties of the PTMC scaffolds did not change. This suggests their suitability for application in a dynamic cell culture bioreactor.
Tuning the halogen/hydrogen bond competition: a spectroscopic and conceptual DFT study of some model complexes involving CHF2I.

Insight into the key factors driving the competition of halogen and hydrogen bonds is obtained by studying the affinity of the Lewis bases trimethylamine (TMA), dimethyl ether (DME), and methyl fluoride (MF) towards difluoroiodomethane (CHF(2) I). Analysis of the infrared and Raman spectra of solutions in liquid krypton containing mixtures of TMA and CHF(2) I and of DME and CHF(2) I reveals that for these Lewis bases hydrogen and halogen-bonded complexes appear simultaneously. In contrast, only a hydrogen-bonded complex is formed for the mixtures of CHF(2) I and MF. The complexation enthalpies for the C-H⋅⋅⋅Y hydrogen-bonded complexes with TMA, DME, and MF are determined to be -14.7(2), -10.5(5) and -5.1(6) kJ mol(-1), respectively. The values for the C-I⋅⋅⋅Y halogen-bonded isomers are -19.0(3) kJ mol(-1) for TMA and -9.9(8) kJ mol(-1) for DME. Generalization of the observed trends suggests that, at least for the bases studied here, softer Lewis bases such as TMA favor halogen bonding, whereas harder bases such as MF show a substantial preference for hydrogen bonding.
A Dynamic Description Logic for Semantic Web Service

This paper presents a dynamic description logic and a sound and complete tableau-based satisfiability-checking algorithm for it. This logic is a combination of a typical action theory and the description logic ALCO@, with a feature that actions are treated as citizens. On the one hand, actions are represented over ontologies expressed in description logic; On the other hand, actions can be used as modal operators for the construction of concepts. Therefore, not only actions but also concepts with dynamic meanings can be described. Furthermore, actions can also be used as modal operators for the construction of formulas, so that many reasoning tasks on actions and concepts can be realized with the help of the satisfiability-checking algorithm for formulas. These properties make this logic more capable for the semantic web service.
Improving the Generation of Ground Truths Based on Partially Ordered Lists

G round truths based on partially ordered lists have been used for some years now to evaluate the effectiveness of Music Information Retrieval systems, especially in tasks related to symbolic melodic similarity. However, there has been practically no meta-evaluation to measure or improve the correctness of these evaluations. In this paper we revise the methodology used to generate these ground truths and disclose some issues that need to be addressed. In particular, we focus on the arrangement and aggregation of the relevant results, and show that it is not possible to ensure lists completely consistent. We develop a measure of consistency based on Average Dynamic Recall and propose several alternatives to arrange the lists, all of which prove to be more consistent than the original method. The results of the MIREX 2005 evaluation are revisited using these alternative ground truths.
Automatic extraction of microorganisms and their habitats from free text using text mining workflows

Summary In this paper we illustrate the usage of text mining workflows to automatically extract instances of microorganisms and their habitats from free text; these entries can then be curated and added to different databases. To this end, we use a Conditional Random Field (CRF) based classifier, as part of the workflows, to extract the mention of microorganisms, habitats and the inter-relation between organisms and their habitats. Results indicate a good performance for extraction of microorganisms and the relation extraction aspects of the task (with a precision of over 80%), while habitat recognition is only moderate (a precision of about 65%). We also conjecture that pdf-to-text conversion can be quite noisy and this implicitly affects any sentence-based relation extraction algorithms.
Very low bit rate speech coding based on HMM with speaker adaptation

This paper discusses the speaker adaptation method in the HMM-based phonetic vocoder, which is a very low bit rate speech coding system, based on speech recognition and speech synthesis using HMM. In the HMM-based phonetic vocoder, the speech quality is governed entirely by the speech synthesis HMM in the decoder. Consequently, in order to adapt to an unspecified input speaker, the HMM of the decoder must be adapted to the input speech. Consequently, this paper proposes the following adaptation to input speech. The HMM is matched by speech recognition to the input parameter sequence. Then, the mean vector of the HMM output distribution sequence is translated uniformly in the parameter space for each segment. The quantity expressing the translation is called the translation vector in this paper. The encoder determines the translation vector, which is then quantized and transmitted. A subjective evaluation experiment shows that when the translation vector is quantized by the proposed method at approximately 100 bits/s and speaker-independent HMM is adapted using the translation vector, almost the same speech quality is obtained as when the speaker-dependent model is trained by the speech data of the input speaker. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(2): 67–78, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10503
Influence of Fog Parameters on Withstand Voltage of Contaminated Insulators

This paper describes the investigation results of fog parameters which affect the withstand voltage of contaminated insulators. As a result, the guideline is proposed on fog conditions such as density, droplet size distribution, temperature rise in the fog room, and so on, basing upon the comparison between natural and artificial fog conditions and the relation between fog condition and power-frequency withstand voltage.
IIT TREC 2005: Genomics Track

For the TREC-2005 Genomics Track ad-hoc retrieval task, we report on the development of a scalable information retrieval engine based on a relational data model for the integration of structured data and text. Our objectives are to meet the need for the integrated search of heterogeneous data sets of biomedical literature and structured data found in biological databases, and to demonstrate the efficacy of using a relational database for a large biomedical information retrieval application.