Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple genes coding for precursors of rhodotorucine A, a farnesyl peptide mating pheromone of the basidiomycetous yeast Rhodosporidium toruloides

Haploid cells of mating type A of the basidiomycetous yeast Rhodosporidium toruloides secrete a mating pheromone, rhodotorucine A, which is an undecapeptide containing S-farnesyl cysteine at its carboxy terminus. To analyze the processing and secretion pathway of rhodotorucine A, we isolated both genomic and complementary DNAs encoding the peptide moiety. We identified three distinct genes, RHA1, RHA2, and RHA3, encoding four, five, and three copies of the pheromone peptide, respectively. Complementary DNA clones were classified into two types. One type was homologous to RHA1, and the other type was homologous to RHA2. Transcription start sites were identified by primer extension and S1 nuclease protection, from which the site of the initiator methionine was verified. A primary precursor of rhodotorucine A was detected as a 7-kilodalton protein by immunoprecipitation of in vitro translation products. On the basis of these results, we propose similar three-precursor structures of rhodotorucine A, each containing the amino-terminal peptide sequence Met-Val-Ala. The precursors contain three, four, or five tandem repeats of the pheromone peptide, each separated by a spacer peptide, Thr-Val-Ser(Ala)-Lys, and each precursor has the carboxy-terminal sequence Thr-Val-Ala. This structure suggests that primary precursors of rhodotorucine A do not contain canonical signal sequences.
Epidermal Growth Factor-like Repeats of Thrombospondins Activate Phospholipase Cγ and Increase Epithelial Cell Migration through Indirect Epidermal Growth Factor Receptor Activation*

Thrombospondin (TSP) 1 is a trimeric multidomain protein that contains motifs that recognize distinct host cell receptors coupled to multiple signaling pathways. Selected TSP1-induced cellular responses are tyrosine kinase-dependent, and TSP1 contains epidermal growth factor (EGF)-like repeats. Specific receptor interactions or functions for the EGF-like repeats have not been identified. We asked whether one or more biological responses to TSP1 might be explained through EGF receptor (EGFR) activation. In A431 cells, TSP1 increased autophosphorylation of Tyr-1068 of EGFR in a dose- and time-dependent manner. The ability of TSP1 to activate EGFR was replicated by the tandem EGF-like repeats as a recombinant protein. The three EGF-like repeats alone produced a high level of Tyr-1068 phosphorylation. EGF-like repeats from TSP2 and TSP4 also activated EGFR. Tyr-1068 phosphorylation was less when individual EGF-like repeats were tested or flanking sequences were added to the three EGF-like repeats. TSP1 and its EGF-like repeats also increased phosphorylation of EGFR Tyr-845, Tyr-992, Tyr-1045, Tyr-1086, and Tyr-1173, activated phospholipase Cγ, and increased cell migration. No evidence was found for binding of the EGF-like repeats to EGFR. Instead, EGFR activation in response to TSP1 or its EGF-like repeats required matrix metalloprotease activity, including activity of matrix metalloprotease 9. Access to the ligand-binding portion of the EGFR ectodomain was also required. These findings suggest release of an endogenous EGFR ligand in response to ligation of a second unknown receptor by the TSPs.
Genetic Inactivation of Kcnj16 Identifies Kir5.1 as an Important Determinant of Neuronal PCO2/pH Sensitivity*

The molecular identity of ion channels which confer PCO2/pH sensitivity in the brain is unclear. Heteromeric Kir4.1/Kir5.1 channels are highly sensitive to inhibition by intracellular pH and are widely expressed in several brainstem nuclei involved in cardiorespiratory control, including the locus coeruleus. This has therefore led to a proposed role for these channels in neuronal CO2 chemosensitivity. To examine this, we generated mutant mice lacking the Kir5.1 (Kcnj16) gene. We show that although locus coeruleus neurons from Kcnj16(+/+) mice rapidly respond to cytoplasmic alkalinization and acidification, those from Kcnj16(−/−) mice display a dramatically reduced and delayed response. These results identify Kir5.1 as an important determinant of PCO2/pH sensitivity in locus coeruleus neurons and suggest that Kir5.1 may be involved in the response to hypercapnic acidosis.
Joining contextual information to the intervention in natural language interfaces

We present a dialogue model which has as its main goal to place in context the utterance generated by the speaker. The dialogue model considers that an intervention generates one or more illocutionary acts which are handled as functions. These functions subcategorize to or are subcategorized by other functions in the dialogue. The model uses an exchange schema with the purpose of expressing the different functional subcategorizations. These schemas have properties close to the semantic forms of the verbs in a lexical-functional context. <<ETX>>
The uncoupling of oxidative phosphorylation by ionizing radiation.

Whole body irradiation of rabbits or rats with X-rays or Co60 γ-rays causes uncoupling of oxidative phosphorylation in thymus mitochondria, which is not prevented by the prior administration of AET. Whole body irradiation was not found to affect oxidative phosphorylation in liver or mouse ascites cell mitochondria. The radiation lesion can be repaired in vitro by the addition of cytochrome c, bovine serum albumin, or vitamin K1 to mitochondria. Vitamin E and coenzyme Q10 were without effect. Both phosphorylating steps in the electron transport chain associated with succinate oxidation are affected by irradiation. The diphosphopyridine nucleotide dependent steps in the oxidation of α-ketoglutarate by thymus mitochondria are damaged by in vivo irradiation. Diphosphopyridine nucleotide levels of thymus and spleen but not liver or ascites cells are reduced by in vivo irradiation. No effect of in vitro irradiation on oxidative phosphorylation could be found for thymocyte cell suspensions, isolated thymus or li.
Major Bleeding and Case Fatality Rate with the Direct Oral Anticoagulants in Orthopedic Surgery: A Systematic Review and Meta-Analysis

Abstract The novel direct oral anticoagulants (DOACs) have been proposed as alternatives to low-molecular-weight heparins (LMWHs) for the prevention of venous thromboembolism in orthopedic surgery. However, the clinical impact of postsurgical bleeding with the DOACs has not been extensively evaluated. MEDLINE and EMBASE databases, supplemented with conference abstract books and www.clinicaltrial. gov, were searched up to the first week of March 2015. We included phase II and phase III randomized controlled trials comparing the DOACs with LMWHs in patients undergoing major orthopedic surgery. Data regarding major, fatal, and intracranial bleeding were collected, to calculate the pooled relative risk (RR) and the case-fatality rate (CFR), with 95% confidence interval (CI). We retrieved 25 studies (5 evaluating dabigatran, 4 apixaban, 6 edoxaban, and 10 rivaroxaban), enrolling 42,170 patients. There was no significant difference between the DOACs and LMWHs in the risk of major (1.23 vs. 1.16%; RR: 1.07, 95% CI: 0.89–1.29), fatal (0.02 vs. 0.01%; RR: 1.63, 95% CI: 0.39–6.77), and intracranial bleeding (0 vs. 0.01%; RR: 0.33, 95% CI: 0.03–3.18). The weighted mean CFR of major bleeding was 3.3% (95% CI, 1.5–5.7) and 2.3% (95% CI, 0.7–4.6), respectively. Bleeding complications and the associated CFR during prophylactic anticoagulation in orthopedic surgery were very low and not significantly different between the DOACs and LMWHs.
Image orientation detection using low-level features and faces

Correct image orientation is often assumed by common imaging applications such as enhancement, browsing, and retrieval. However, the information provided by camera metadata is often missing or incorrect. In these cases manual correction is required, otherwise the images cannot be correctly processed and displayed. In this work we propose a system which automatically detects the correct orientation of digital photographs. The system exploits the information provided by a face detector and a set of low-level features related to distributions in the image of color and edges. To prove the effectiveness of the proposed approach we evaluated it on two datasets of consumer photographs.
Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance.

In Gram-negative bacteria, multidrug efflux pumps are responsible for the extrusion of chemicals that are deleterious for growth. Some of these efflux pumps are induced by endogenously produced effectors, while abiotic or biotic signals induce the expression of other efflux pumps. In Pseudomonas putida, the TtgABC efflux pump is the main antibiotic extrusion system that respond to exogenous antibiotics through the modulation of the expression of this operon mediated by TtgR. The plasmid-encoded TtgGHI efflux pump in P. putida plays a minor role in antibiotic resistance in the parental strain; however, its role is critical in isogenic backgrounds deficient in TtgABC. Expression of ttgGHI is repressed by the TtgV regulator that recognizes indole as an effector, although P. putida does not produce indole itself. Because indole is not produced by Pseudomonas, the indole-dependent antibiotic resistance seems to be part of an antibiotic resistance programme at the community level. Pseudomonas putida recognizes indole added to the medium or produced by Escherichia coli in mixed microbial communities. Transcriptomic analyses revealed that the indole-specific response involves activation of 43 genes and repression of 23 genes. Indole enhances not only the expression of the TtgGHI pump but also a set of genes involved in iron homeostasis, as well as genes for amino acid catabolism. In a ttgABC-deficient P. putida, background ampicillin and other bactericidal compounds lead to cell death. Co-culture of E. coli and P. putida ΔttgABC allowed growth of the P. putida mutant in the presence of ampicillin because of induction of the indole-dependent efflux pump.
Implementation issues of a digital control system applied to a PFC boost converter

This paper presents implementation issues of a digital control system applied to a power factor correction (PFC) boost converter rated to a wide range of output power, operating in mixed conduction mode (MCM). The digital control system comprises an input current controller and an output voltage controller. The current controller is formed by two predictive model-based control laws, while the output voltage is regulated through a proportional-integral controller. The implementation requirements of this control system and the executed programming routines, highlighting the inductor current sampling process in different conduction modes are discussed. Experimental results applying a low cost microcontroller are shown to validate the operation of the current and voltage controllers.
Role of different T cells sets in the rejection of syngeneic chemically induced tumors.

This study was designed to investigate the phenotypes of immune cells concerned in the rejection of chemically induced tumors. Counted numbers of viable dissociated cells of a selected C57BL/6 (B6) tumor were combined with counted numbers of peritoneal cells from highly immunized syngeneic B6 donors and inoculated subcutaneously into untreated syngeneic B6 mice. Progressive tumor growth was prevented by nonadherent immune peritoneal cells in numbers less than one-quarter the number of tumor cells, and the cells responsible belonged mainly or entirely to the nonadherent fraction of the peritoneal population. There was no cross-protection between this tumor and a second B6 tumor induced by the same carcinogen, indicating that immunity in this experimental system, as reported previously, is directed to antigens that individually characterize chemically induced tumors. Elimination of Thy-1(+) cells by Thy-1 antiserum and complement abolished the protective capacity of the immune peritoneal cells, showing that immunity under these conditions is mediated by T cells. Protection was also precluded by elimination of Lyt-1(+) cells or of Lyt-2(+) cells, showing that protection could not be attributed to either the Lyt-23 or the Lyt-1 set of T cells alone. Nor was protection conferred by various combinations of these selected Lyt-1 and Lyt-23 cell sets. Thus, participation of the third well defined Lyt cells set, Lyt-123, which is automatically eliminated when the Lyt-23 and Lyt-1 sets are prepared by selective immune cytolysis is evidently necessary to rejection, in these experimental circumstances. Although this might imply that cytotoxicity for syngeneic tumors is effected by Lyt-123 cells, it is emphasized that this assay system allows time for the differentiation and proliferation of cells sets. Thus, the data are also consistent with a uniform hypothesis that cell-mediated cytotoxicity is an exclusive function of Lyt123:CS cells, and that these, and possible Lyt1:H amplifier cells, are generated in the course of the assay from a specifically primed antecedent Lyt123:ARC cell set.
A Triangular Prism Spatial Interpolation Method for Mapping Geological Property Fields

Abstract: The spatial interpolation of property fields in 3D, such as the temperature, salinity, and organic content of ocean water, is an active area of research in the applied geosciences. Conventional interpolation methods have not adequately addressed anisotropy in these data. Thus, in our research we considered two interpolation methods based on a triangular prism volume element, as a triangular prism structure best represents directivity, to express the anisotropy inherent in geological property fields. A linear triangular prism interpolation is proposed for layered stratum that achieves a complete continuity based on the volume coordinates of the triangular prism. A triangular prism quadric interpolation (a unit function of a triangular prism spline with 15 nodes) is designed for a smooth transition between adjacent triangular prisms with approximately continuity, expressing the continuity of the entire model. We designed a specific model which accounts for the different spatial correlations in three dimensions. We evaluated the accuracy of our proposed linear and triangular prism quadric interpolation methods with traditional inverse distance weighting (IDW) and kriging interpolation approaches in comparative experiments. The results show that, in 3D geological modeling, the linear and quadric triangular prism interpolations more accurately represent the changes in the property values of the layered strata than the IDW and kriging interpolation methods. Furthermore, the triangular prism quadric interpolation algorithm with 15 nodes outperforms the other methods. This study of triangular prism interpolation algorithms has implications for the expression of data fields with 3D properties. Moreover, our novel approach will contribute to spatial attribute prediction and representation and is applicable to all 3D geographic information; for example, in studies of atmospheric circulation, ocean circulation, water temperature, salinity, and three-dimensional pollutant diffusion.
Comparison of Antigen‐Specific T‐Cell Responses of Tuberculosis Patients using Complex or Single Antigens of Mycobacterium tuberculosis

We have screened peripheral blood mononuclear cells (PBMC) from tuberculosis (TB) patients for proliferative reactivity and interferon‐γ (IFN‐γ) secretion against a panel of purified recombinant (r) and natural (n) culture filtrate (rESAT‐6, nMPT59, nMPT64 and nMPB70) and somatic‐derived (rGroES, rPstS, rGroEL and rDnaK) antigens of Mycobacterium tuberculosis. The responses of PBMC to these defined antigens were compared with the corresponding results obtained with complex antigens, such as whole‐cell M. tuberculosis, M. tuberculosis culture filtrate (MT‐CF) and cell wall antigens, as well as the vaccine strain, Mycobacterium bovis bacillus Calmette–Guérin (BCG). In addition, M. tuberculosis and MT‐CF‐induced T‐cell lines were tested in the same assays against the panel of purified and complex antigens. The compiled data from PBMC and T‐cell lines tested for antigen‐induced proliferation and IFN‐γ secretion showed that the most frequently recognized antigen was ESAT‐6, followed by MPT59, GroES, MPB70, MPT64, DnaK, GroEL and PstS. The frequency of ESAT‐6 responders, as measured both by proliferation (18/19) and secretion of IFN‐γ (16/19) was comparable to the results obtained with whole‐cell M. tuberculosis, MT‐CF and M. bovis BCG. We also observed that most of the high responders to complex antigens recognized all of the antigens tested (covariation), demonstrating that the repertoire of human T‐cell specificities induced by natural infection is directed towards several unrelated culture filtrate as well as somatic‐derived protein antigens. In conclusion, the results obtained suggest that the cellular immune response in humans is directed against several important target antigens of M. tuberculosis and that some antigens, such as ESAT‐6, are recognized by a high number of individuals. Such antigens represent candidates to be used for development of specific diagnostic reagents or in subunit vaccines.
Calcitonin Gene-Related Peptide is Increased in Hindlimb Motoneurons After Exercise

Calcitonin gene-related peptide (CGRP) is a neuroactive peptide present in some spinal cord motoneurons and at their motor endplates in skeletal muscle. Although detectable levels of CGRP change after surgical and pharmacological interruptions of neuromuscular connectivity, a clear understanding of its physiological role in the motor system is lacking. The purpose of this study was to investigate whether downhill running exercise, which elicits muscle damage and repair, also elicits changes in CGRP levels in hindlimb motoneurons. Twenty female Wistar rats were divided into five groups: control (c), 48 hours post-exercise (48 hr), 72 hours (72 hr), two weeks (2 wks) and four weeks (4 wks). Exercise groups ran downhill for one 30 minute period. Histological examination of muscle from ankle extensors (triceps surae, TS) and flexors (anterior crural, AC) indicated the characteristic presence of histiocytes by 48 hr post-exercise in TS but not in AC. Paraformaldehyde-fixed, 30 microm sections of lumbar spinal cord (L2-L4) from the same animals were incubated with polyclonal antisera to CGRP. The number of CGRP-positive TS motor nuclei increased significantly by 48 hr after exercise (p = 0.001) vs control and returned to baseline values by 4 wks (p > 0.05). In contrast, no significant changes were observed in the AC motoneuron pool at any post-exercise interval (p > 0.05). The temporal changes in CGRP levels in TS motoneurons suggest that expression of this neuropeptide may be differentially regulated by exercise-induced changes in neuromuscular function, possibly as related to muscle tissue damage/repair mechanisms and thus to remodeling at the neuromuscular junction.
Nomadicity: Anytime, Anywhere in a Disconnected World

Nomadic computing and communications is upon us. We are all nomads, but we lack the systems support to assist us in our various forms of mobility. In this paper, we discuss the vision of nomadicity, its technical challenges, and approaches to the resolution of these challenges. One of the key characteristics of this paradigmshift in the way we deal with the information is that we face dramatic and sudden changes in connectivity and latency. Our systems must be “nomadically-enabled” in that mechanisms must be developed that deal with such changes in a natural and transparent fashion. Currently, this is not the case in that our systems typically treat such changes as exceptions or failures; this is unacceptable. Moreover, the industry is producing “piece parts” that are populating our desktops, briefcases and belt-hooks, but that do not interoperate with each other, in general. We require innovative and systemwide solutions to overcome these problems. Such are the issues we address in this paper.
Stabilization of multi-agent systems and complex networks - a unified model using distributed control

In this paper, stability analysis is studied for coupled complex networks using distributed control in a unified model. Under this new model, we combine the multi-agent systems with complex networks nicely, allowing for inherent physical connections between agents and communication transmissions among controllers. Necessary and sufficient conditions under both distributed state feedback and observer-based output feedback control are given for the coupled dynamical systems. A two-step controller design procedure based on a parameter dependent Lyaponov function is presented, which reduces some conservativeness compared to the original direct Lyaponov method. The robustness of the system is also discussed in the presence of disturbances. Finally, some numerical examples are given to illustrate the theoretical results.
Synaptotagmin10-Cre, a Driver to Disrupt Clock Genes in the SCN

Surgical lesion of the suprachiasmatic nuclei (SCN) profoundly affects the circadian timing system. A complication of SCN ablations is the concomitant scission of SCN afferents and efferents. Genetic disruption of the molecular clockwork in the SCN provides a complementary, less invasive experimental approach. The authors report the generation and functional analysis of a new Cre recombinase driver mouse that evokes homologous recombination with high efficiency in the SCN. They inserted the Cre recombinase cDNA into the Synaptotagmin10 (Syt10) locus, a gene strongly expressed in the SCN. Heterozygous Synaptotagmin10-Cre (Syt10Cre) mice have no obvious circadian locomotor phenotype, and homozygous animals show slightly reduced light-induced phase delays. Crosses of Syt10Cre mice with β-galactosidase reporter animals revealed strong Cre activity in the vast majority of SCN cells. Cre activity is not detected in nonneuronal tissues with the exception of the testis. The authors demonstrate that conditionally deleting the clock gene Bmal1 using the Syt10Cre driver renders animals arrhythmic.
Evaluating 2-D grid interpolation techniques for predicting ambient RF power density in automobile factories

This paper evaluates the suitability of existing 2-D interpolation techniques to estimate RF power density levels within an automobile manufacturing plant in the UK. This analysis is based on a measurement campaign carried out at five locations within the plant. Using widely accepted interpolation techniques, a power density grid that provides an estimate of power density distribution for the plant can be created. The interpolation techniques evaluated are: Inverse distance weighting, Kriging and Spline. The analytical results showed that the Kriging technique was more suitable for estimating power density across the entire band (0.2 GHz - 3 GHz). Using the power density grid obtained, an energy profile for a pallet traveling in a predefined production loop was estimated. As a result, it becomes essential to carefully select the estimation technique to adopt, particularly when the measurement dispersion points are sparse.