Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Relationship between Chlorocatechol Catabolic Enzymes from Rhodococcus opacus 1CP and Their Counterparts in Proteobacteria: Sequence Divergence and Functional Convergence

ABSTRACT Biochemical investigations of the muconate and chloromuconate cycloisomerases from the chlorophenol-utilizing strainRhodococcus opacus (erythropolis) 1CP had previously indicated that the chlorocatechol catabolic pathway of this strain may have developed independently from the corresponding pathways of proteobacteria. To test this hypothesis, we cloned the chlorocatechol catabolic gene cluster of strain 1CP by using PCR with primers derived from sequences of N termini and peptides of purified chlorocatechol 1,2-dioxygenase and chloromuconate cycloisomerase. Sequencing of the clones revealed that they comprise different parts of the same gene cluster in which five open reading frames have been identified. The clcB gene for chloromuconate cycloisomerase is transcribed divergently from a gene which codes for a LysR-type regulatory protein, the presumed ClcR. Downstream of clcRbut separated from it by 222 bp, we detected the clcA andclcD genes, which could unambiguously be assigned to chlorocatechol 1,2-dioxygenase and dienelactone hydrolase. A gene coding for a maleylacetate reductase could not be detected. Instead, the product encoded by the fifth open reading frame turned out to be homologous to transposition-related proteins of IS1031 and Tn4811. Sequence comparisons of ClcA and ClcB to other 1,2-dioxygenases and cycloisomerases, respectively, clearly showed that the chlorocatechol catabolic enzymes of R. opacus 1CP represent different branches in the dendrograms than their proteobacterial counterparts. Thus, while the sequences diverged, the functional adaptation to efficient chlorocatechol metabolization occurred independently in proteobacteria and gram-positive bacteria, that is, by functionally convergent evolution.
A Parametric CPS to Sprinkle CIC with Classical Reasoning

Dependent type theory was introduced by Martin-Löf as an alternative foundation for mathematics, stemming from the then-nascent proof-as-program correspondance [8]. Since its inception, it has been designed as an intrinsically intuitionistic system. Meanwhile, in a parallel research path, the proof-as-program correspondance was extended to classical logic by means of control operators [5]. Such operators can be compiled away through a program translation known as continuation-passing style. A natural question that arises is the compatibility of dependent type theory with classical logic, which would typically be implemented using control operators. Twenty years ago, Barthe et al. described a pure type system equipped with such operators [1]. This system requires a strong stratification of the logic, with types living in a pure world. Furthermore, it has also been noticed that dependent elimination does not mix well with computational classical logic [2, 6], a phenomenon that casts a doubt on the feasibility of a dependent CPS. We propose an alternative approach inspired by our recent work on mixing effects with dependent type theory [9]. Our work fits in the paradigm of syntactical models that we have been advocating for [4], i.e. the justification of a given type theory by compilation into a more standard type theory. Here, our target theory is CIC, the calculus of inductive constructions, and our source theory is CIC extended with a modality ‖·‖ : i → i on which classical reasoning is allowed. The syntactical translation is intuitively an enrichment of the Lafont-Streicher-Reus CPS [7] with an additional layer of parametricity in the style of Lasson and Bernardy [3]. It is a close variant of our parametric effectful translation described in our latest paper. Essentially, all the intuitionistic content is pushed back into the parametricity layer. For instance, the translation of a type is somehow a doubly-negated type, which is irrelevant, together with a parametricity proof which embeds the actual type hidden inside this classical type. Similarly, a boolean is translated as a doubly-negated boolean together with a parametricity proof which represents the actual boolean. That is, [[B]] ≡ Σb : ¬¬B. Bε b where Bε is inductively defined as follows.
Abciximab administration and clinical outcomes after percutaneous intervention for in‐stent restenosis

Abciximab therapy improves clinical outcomes after percutaneous interventions for de novo coronary artery disease. We sought to determine whether clinical outcomes after percutaneous intervention for in‐stent restenosis are affected by abciximab administration. Between January 1996 and July 1999, 322 consecutive patients underwent percutaneous intervention for in‐stent restenosis; 157 patients received abciximab and 165 patients were treated without abciximab based on operator discretion. Baseline clinical and angiographic variables and type of percutaneous intervention were recorded. Follow‐up information was obtained and clinical endpoints were recorded. A multivariate analysis was performed to determine the independent variables associated with adverse clinical outcomes. Baseline clinical and angiographic variables were similar in both groups. Patients who received abciximab were more likely to be treated with rotational atherectomy and less likely to have only balloon angioplasty or repeat stenting. Mean follow‐up duration was 19 ± 12 months. There were no significant differences in the incidence of angina/myocardial infarction (29% vs. 30%; P = 0.9), target vessel revascularization (18% vs. 21%; P = 0.5), death (8% vs. 7%; P = 0.4), or major adverse cardiovascular events (38% vs. 39%; P = 0.9) in both groups. Abciximab administration was not an independent variable associated with adverse outcomes. In this observational study, clinical outcomes after percutaneous intervention for in‐stent restenosis did not seem to be affected by abciximab administration. Randomized trials are needed to identify the role of platelet glycoprotein IIb/IIIa inhibitors in the management of in‐stent restenosis. Cathet Cardiovasc Intervent 2002;56:184–187. © 2002 Wiley‐Liss, Inc.
Sensitivity of the Diagnostic Interview Schedule for Children, 2nd edition (DISC-2.1) for specific diagnoses of children and adolescents.

OBJECTIVE The sensitivity of the Diagnostic Interview Schedule for Children, second edition (DISC-2.1) was examined for certain "rare" disorders: eating disorders, major depressive episode, obsessive compulsive disorder, psychosis, tic disorders, and substance use disorders. METHOD Subjects recruited from specialized centers were interviewed with the DISC-2.1; the centers' diagnoses served as the criterion measure. RESULTS Overall the DISC showed good to excellent sensitivity (range = 0.73 to 1.0). Used alone, the DISC-P (parent interview) was generally more sensitive than the DISC-C (child interview). Areas for additional instrument revision were identified. Recommendations about informant choice by diagnosis are offered. CONCLUSIONS The strategy used in this study was useful for assessing the DISC's sensitivity for these disorders. Additional work examining specificity of the DISC remains to be done. The DISC should prove a useful adjunct in clinical settings given the ease and relatively low cost of administration.
Identification of the Receptor-associated Signaling Enzymes That Are Required for Platelet-derived Growth Factor-AA-dependent Chemotaxis and DNA Synthesis*

Activation of the platelet-derived growth factor (PDGF) α receptor (αPDGFR) leads to cell migration and DNA synthesis. These events are preceded by the ligand-induced tyrosine phosphorylation of the receptor and its association with SH2-containing signaling enzymes including Src family members (Src), the phosphotyrosine phosphatase SHP-2, phosphatidylinositol 3-kinase (PI3K), and phospholipase C-γ1 (PLCγ). In this study, we sought to systematically evaluate the relative roles of the signaling enzymes that are recruited to the αPDGFR for DNA synthesis and cell migration. Our approach was to generate and characterize tyrosine to phenylalanine αPDGFR mutants that failed to associate with one or more of the above listed signaling enzymes. In a 3T3-like cell line (Ph cells), PDGF-dependent DNA synthesis was strictly dependent on only one of the receptor-associated proteins, PI3K. In contrast, multiple signaling enzymes were required for maximal chemotaxis, as receptors unable to associate with either Src, PI3K, or PLCγ initiated chemotaxis to 4, 47, or 56% of the wild-type level, respectively. Furthermore, coexpression of mutant receptors revealed that these signaling enzymes do not need to be on the same receptor for a cell to respond chemotactically to PDGF. We conclude that for the αPDGFR, PI3K plays a major role in initiating DNA synthesis, whereas PI3K, PLCγ, and especially Src are required for chemotaxis.
Herpes Simplex Virus Glycoproteins H/L Bind to Cells Independently of αVβ3 Integrin and Inhibit Virus Entry, and Their Constitutive Expression Restricts Infection

ABSTRACT Herpes simplex virus (HSV) fusion with cells requires the gD, gB, and gH/gL glycoprotein quartet. gD serves as a receptor binding glycoprotein. gB and gH/gL execute fusion in an as-yet-unclear manner. To better understand the role of gH/gL in HSV entry, we produced a soluble version of gH/gL carrying a One-STrEP tag (gHt.st/gL). Previous findings implicated integrins as possible ligands to gH/gL (C. Parry et al., J. Gen. Virol. 86:7-10, 2005). We report that (i) gHt.st/gL bound a number of cells in a dose-dependent manner at concentrations similar to those required for the binding of soluble gB or gD. (ii) gHt.st/gL inhibited HSV entry at the same concentrations required for binding. It also inhibited cell-cell fusion in transfected cells. (iii) The absence of β3 integrin did not prevent the binding of gHt.st/gL to CHO cells and infection inhibition. Conversely, integrin-negative K562 cells did not acquire the ability to bind gHt.st/gL when hyperexpressing αVβ3 integrin. (iv) Constitutive expression of wild-type gH/gL (wt-gH/gL) restricted infection in all of the cell lines tested, a behavior typical of glycoproteins which bind cellular receptors. The extent of restriction broadly paralleled the efficiency of gH/gL transfection. RGD motif mutant gH/gL could not be differentiated from wt-gH with respect to restriction of infection. Cumulatively, the present results provide several lines of evidence that HSV gH/gL interacts with a cell surface cognate protein(s), that this protein is not necessarily an αVβ3 integrin, and that this interaction is required for the process of virus entry/fusion.
A simulation study on the wired-equivalent capacity of ad hoc networks

In this paper we demonstrate the concept of wired- equivalent capacity in ad-hoc networks through a large-scale simulation study. A capacity model that mimics conventional experience (e.g. on wired, infrastructured networks) is proposed under a specific, yet realistic and user-oriented, assumption of the maximum fair usage. Capacity is then the maximum throughput capacity per node under which packet loss is similar to that of a conventional wired network, for all nodes. We show how this capacity metric becomes predictable inside ad-hoc networks using a simple power-law while delay is bounded.
Characterization of the Nucleoside Triphosphate Phosphohydrolase and Helicase Activities of the Reovirus λ1 Protein*

Previous studies have shown that the reovirus λ1 core protein harbors a putative nucleotide-binding motif and exhibits an affinity for nucleic acids. In addition, a nucleoside triphosphate phosphohydrolase activity present in reovirus cores has been recently assigned to λ1 using gene reassortment analysis. In this study, it was demonstrated that the recombinant λ1 protein, expressed in the yeast Pichia pastoris, is able to hydrolyze nucleoside 5′-triphosphates or deoxynucleoside 5′-triphosphates. This activity was absolutely dependent on the presence of a divalent cation, Mg2+ or Mn2+. The protein can also unwind double-stranded nucleic acid molecules in the presence of a nucleoside 5′-triphosphate or deoxynucleoside 5′-triphosphate. These results provide the first biochemical evidence that the reovirus λ1 protein is a nucleoside triphosphate phosphohydrolase/helicase and strongly support the idea that λ1 participates in transcription of the viral genome.
Analyse of Fault Tolerant Topology Configuration for More Electric Aircraft Actuation System

This paper presents a modular topology configuration of fault tolerant permanent magnet motor drive for more electric aircraft. Fault tolerant is achieved with each phase electrically, magnetically, thermally and physically independent of all others. It is discussed that must be balanced against the increasing complexity of a high phase number and the inevitably greater of a failure. A flexible motor and drive configuration is proposed to increase the redundancy against drive system failures.
Ca 2 1 Channels Involved in the Generation of the Slow Afterhyperpolarization in Cultured Rat Hippocampal Pyramidal Neurons

Shah, M. and D. G. Haylett.Ca channels involved in the generation of the slow afterhyperpolarization in cultured rat hippocampal pyramidal neurons. J. Neurophysiol.83: 2554–2561, 2000. The advantages of using isolated cells have led us to develop short-term cultures of hippocampal pyramidal cells, which retain many of the properties of cells in acute preparations and in particular the ability to generate afterhyperpolarizations after a train of action potentials. Using perforated-patch recordings, both medium and slow afterhyperpolarization currents (mI AHP and sI AHP, respectively) could be obtained from pyramidal cells that were cultured for 8–15 days. The sIAHP demonstrated the kinetics and pharmacologic characteristics reported for pyramidal cells in slices. In addition to confirming the insensitivity to 100 nM apamin and 1 mM TEA, we have shown that the sIAHP is also insensitive to 100 nM charybdotoxin but is inhibited by 100mM D-tubocurarine. Concentrations of nifedipine (10 mM) and nimodipine (3mM) that maximally inhibit L-type calcium channels reduced the sI AHP by 30 and 50%, respectively. However, higher concentrations of nimodipine (10 mM) abolished the sI AHP, which can be partially explained by an effect on action potentials. Both nifedipine and nimodipine at maximal concentrations were found to reduce the HVA calcium current in freshly dissociated neurons to the same extent. The N-type calcium channel inhibitor, v-conotoxin GVIA (100 nM), irreversibly inhibited the sI AHP by 37%. Together, v-conotoxin (100 nM) and nifedipine (10mM) inhibited the sI AHP by 70%. 10mM ryanodine also reduced the sI AHP by 30%, suggesting a role for calcium-induced calcium release. It is concluded that activation of the sIAHP in cultured hippocampal pyramidal cells is mediated by a rise in intracellular calcium involving multiple pathways and not just entry via L-type calcium channels.
Evolution of chloroplast vesicle transport.

Vesicle traffic plays a central role in eukaryotic transport. The presence of a vesicle transport system inside chloroplasts of spermatophytes raises the question of its phylogenetic origin. To elucidate the evolution of this transport system we analyzed organisms belonging to different lineages that arose from the first photosynthetic eukaryote, i.e. glaucocystophytes, chlorophytes, rhodophytes, and charophytes/embryophytes. Intriguingly, vesicle transport is not apparent in any group other than embryophytes. The transfer of this eukaryotic-type vesicle transport system from the cytosol into the chloroplast thus seems a late evolutionary development that was acquired by land plants in order to adapt to new environmental challenges.
Automatic Cognitive Load Detection from Face, Physiology, Task Performance and Fusion During Affective Interference

Cognitive load is experienced during critical tasks and also while engaged emotional states are induced either by the task itself or by extraneous experiences. Emotions irrelevant to the working memory representation may interfere with the processing of relevant tasks and can influence task performance and behavior, making the accurate detection of cognitive load from nonverbal information challenging. This paper investigates automatic cognitive load detection from facial features, physiology and task performance under affective interference. Data was collected from participants (n=20) solving mental arithmetic tasks with emotional stimuli in the background and a combined classifier was used for detecting cognitive load levels. Results indicate that the face modality for cognitive load detection was more accurate under affective interference, whereas physiology and task performance were more accurate without the affective interference. Multimodal fusion improved detection accuracies, but it was less accurate under affective interferences. More specifically, the accuracy decreased with increasing intensity of emotional arousal.
Microphone array design for spatial audioobject early reflection parametrisation fromroom impulse responses

Room Impulse Responses (RIRs) measured with microphone arrays capture spatial and nonspatial information, e.g. the early reflections’ directions and times of arrival, the size of the room and its absorption properties. The Reverberant Spatial Audio Object (RSAO) was proposed as a method to encode room acoustic parameters from measured array RIRs. As the RSAO is object-based audio compatible, its parameters can be rendered to arbitrary reproduction systems and edited to modify the reverberation characteristics, to improve the user experience. Various microphone array designs have been proposed for sound field and room acoustic analysis, but a comparative performance evaluation is not available. This study assesses the performance of five regular microphone array geometries (linear, rectangular, circular, dual-circular and spherical) to capture RSAO parameters for the direct sound and early reflections of RIRs. The image source method is used to synthesise RIRs at the microphone positions as well as at the centre of the array. From the array RIRs, the RSAO parameters are estimated and compared to the reference parameters at the centre of the array. A performance comparison among the five arrays is established as well as the effect of a rigid spherical baffle for the circular and spherical arrays. The effects of measurement uncertainties, such as microphone misplacement and sensor noise errors, are also studied. The results show that planar arrays achieve the most accurate horizontal localisation whereas the spherical arrays perform best in elevation. Arrays with smaller apertures achieve a higher number of detected reflections, which becomes more significant for the smaller room with higher reflection density.
Relighting of Virtual Objects under Environment Lighting

Current relighting applications often constrain one or several factors of the rendering equation to keep the rendering speed real-time. For example, visibility is often precalculated and animations are not allowed, changes in lighting are limited to simple rotation or the lighting is not very detailed. Other techniques compromise on quality and often coarsely tabulate BRDF functions. In order to solve these problems, some techniques have started to use spherical radial basis functions. However, solving the triple product integral does not guarantee interactivity. In order to dynamically change lighting conditions or alter scene geometry and materials, these three factors need to be converted to the SRBF representation in a fast manner. This paper presents a method to perform the SRBF data construction and rendering in real-time. To support dynamic high-frequency lighting, a multiscale residual transformation algorithm is applied. Area lights are detected through a peak detection algorithm. By using voxel cone tracing and a subsampling scheme, animated geometry casts soft shadows dynamically. We demonstrate the effectiveness of our method with a real-time application. Users can shine with multiple light sources onto a camera and the animated virtual scene is relit accordingly.
ResD signal transduction regulator of aerobic respiration in Bacillus subtilis: ctaA promoter regulation

A two‐component signal transduction system composed of a sensor kinase, ResE, and a response regulator, ResD, encoded by resD and resE genes of the res operon (resABCDE), has a regulatory role in both aerobic and anaerobic respiration. In terms of aerobic respiration, resD functions upstream of ctaA, a gene required for haem A biogenesis and hence for the synthesis of haem A‐containing cytochrome terminal oxidases. Although ResD is probably a transcription factor, there was no direct evidence that ResD protein, either phosphorylated or unphosphorylated, interacts directly with regulatory regions of ResD‐controlled genes. Here, we report the overexpression and purification of ResD and ResE and their role in gene activation. ResD can be phosphorylated by ResE in vitro and is a monomer in solution in either the phosphorylated or unphosphorylated state. The binding activity of ResD to the ctaA promoter was examined by gel shift assays and DNase I footprinting assays. DNase I footprinting showed both unphosphorylated and phosphorylated ResD binding to the ctaA promoter and showed that there are three binding sites (A1, A2 and A3), two (A1 and A2) upstream of the −35 promoter region and one (A3) downstream of the −10 of the promoter. The role of each site in ctaA promoter activity and ResD binding was characterized using deletion analysis, followed by the DNase I footprinting and in vivo transcription assays of promoter–lacZ fusions. Our results showed that the concentration of ResD required to bind at each site is different and that ResD binding at the A1 site is independent of the other two ResD binding sites, but that the concentration of ResD∼P required to protect site A2 is reduced when site A3 is present. In vivo transcription assays from promoter–lacZ fusion constructs showed that DNA containing ResD‐binding site A2 was essential for promoter activity and that promoter constructs containing both binding sites A2 and A3 were sufficient for full promoter activity.
A new source code repository for dynamic storing, browsing, and retrieval of source codes

Software reuse is a solution to reduce the costs of estimation, design, development, and testing. Reuse of source codes can release the coders from the time-killing botheration of doing the same coding again and again for same kind of software projects. If the proposed distribution format (Application→ Module→Class→Function→Sub-function) is followed while storing source codes, then it is easier to fulfill the requests for any level of source codes. In this paper, a source code repository system is proposed that dynamically distributes an application to its smallest level components and stores their information. Besides, it provides an interface to browse and retrieve the desired source codes. During dynamic retrieval, the desired source codes are merged together by a bottom-up integration method. Implementation shows that the proposed repository outperforms the other related research works with providing more features in simpler way.
PCA-based design of a SEPIC converter

The design of fourth order dc-dc converters is discussed in this paper. The Principal Components Analysis is applied to find the set of passive components which allows to avoid double resonance in the control-to-output transfer function. The design of a synchronous SEPIC converter has been studied as an application of the proposed design methodology by using a database of real passive components. The performances of the SEPIC converter designed with the proposed methodology are verified through both time domain and frequency domain simulations and they are compared with those ones achieved by standard ripple-based design procedures.