Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Conservation of C-terminal Domains of Primary Sigma70-type Transcription Factors between Plants and Bacteria*

Three different cDNAs coding for putative plant plastid sigma70-type transcription initiation factors have recently been cloned and sequenced from Arabidopsis thaliana. We have analyzed the evolutionary conservation of function(s) of the N-terminal and C-terminal halves of these three sigma factors by in vitro transcription studies using heterologous transcription systems and by complementation assays usingEscherichia coli thermosensitive rpoD mutants. Our results indicate differences and similarities of the three plant factors and their prokaryotic ancestors. The functions of the N-terminal parts of the plant sigma factors are considerably different from the function of the N-terminal part of the principal sigma70 factor of E. coli. On the other hand, the C-terminal parts have kept at least two characteristics when compared with their prokaryotic ancestors: 1) they can distinguish between different promoter structures, and 2) one of them is capable of fully complementing E. coli rpoD mutants, i.e.recognizing all essential E. coli promoters that are used by the E. coli principal sigma70 factor. This shows for the first time in vivo a strong evolutionary conservation of cis- and trans-acting elements between the prokaryotic and the plant plastid transcriptional machinery.
Exploring the affordances of online chat for learning

Text-based interaction is one of the frequently used modes of computer mediated communication connecting users via computer networks. Text chat has been and is still an important technology component of online distributed learning environments where students communicate synchronously amongst themselves and with other learning partners such as teachers and experts. Text chat provides several affordances that make it an effective medium for useful online interactions, despite its limitations and the advent of newer technologies like avatar or graphic chat, audio and video conferencing. In this paper, we explore the properties of online text chat, and discuss the limitations and problems of conversations supported by the chat medium. We discuss ways of making the conversations better, enabling more natural and coherent conversations, facilitating conversations with a learning nature, providing aggregate views of chat conversations, and providing chat participants with a social sense of the context or the dynamics of the conversation flow. We review work on technological innovations that support, analyse, and visualise chat conversations.
Commande événementielle : applications aux systèmes robotiques

La theorie du controle a d'abord ete concue pour des controleurs analogiques. Il etait alors pertinent de synthetiser un controleur dans une representation continue. De nos jours, les systemes numeriques ont majoritairement remplaces les systemes analogiques pour differentes raisons (cout, resistance au bruit, integration,.). Les signaux sont alors maintenus constants entre le cadencement periodique fixe par une horloge numerique.La commande evenementielle vise a ameliorer l’echantillonnage periodique en proposant une methode dans laquelle les mises a jour sont declenchees par une fonction evenement.Dans cette these, de nouvelles methodes de synthese de controleurs evenementiels sont presentes et testes sur des systemes temps-reels.La contribution la plus originale etant l'utilisation d'une commande evenementielle appliquee a un probleme d'anticollision entre une quadrirotor et un environnement suppose connu.
Towards Profile-Based Document Summarisation for Interactive Search Assistance

This paper presents an investigation into the utility of profile-based summarisation in the context of site and enterprise search. We employ log analysis to acquire continuously updated profiles to provide profile-based summarisations of search results with the intention of highlighting aspects of the documents that best fit the general user profile. We first introduce the wider context of the research and then focus on a first task-based evaluation using TREC Interactive Track guidelines that compares a search system that uses the outlined profile-based summarisation with two baseline systems to assess whether such summaries could be helpful in a realistic search setting.
Copper and nickel nanoparticles: synthesis by electrochemical discharges

The unique optical, electronic, chemical and biological properties of metal nanoparticles have stimulated a large research activity into manufacturing methods of these nano-structures. An example of copper and nickel nanoparticle synthesis using electrochemical discharges in aqueous solutions is described. This low-cost template technique is a facile procedure to fabricate large quantities of metallic nano-sized particles. The resulting particles are characterized using an electrochemical method (cyclic voltammetry), Energy Dispersive X-ray Spectroscopy (EDS) analysis and Transmission Electron Microscopy (TEM).
The swappable logic unit: a paradigm for virtual hardware

Swappable Logic Units (SLUs) were introduced by the author previously (1996) to play a role in virtual hardware subsystems that is analogous to the role of pages or segments in virtual memory subsystems. The intention is that a conventional operating system can be extended to manage SLU circuitry implemented using FPGA real estate. In order to minimise operating system overheads, two particular SLU-based virtual hardware models were deemed practical: a "sea of accelerators" model and a "parallel harness" model. This paper looks in some detail at how SLUs will fit within the overall environment of a fairly conventional hardware/software system. First, there is a discussion of the FPGA-based hardware environment for SLUs, followed by a discussion of the software environment from which SLUs might be used. After this, there is a description of the operational properties that SLUs can have, and how these fit in with the two virtual hardware models. Finally, proposals for standard interfaces between SLUs and their environment are discussed. These interfaces can be regarded as constraints on the designers of SLU circuitry or, more positively, as suppliers of an enriched context within which such circuitry operates. The overall impact of the work presented in the paper is to show that it is feasible to incorporate configurable hardware within traditional computer systems that use high-level language programs and computer operating systems. That is, it should not always be necessary to devise special-purpose hardware/software systems to realise custom computing.
A New Mechanism of Phosphoregulation in Signal Transduction Pathways

A protein kinase phosphorylates arginine residues in a transcriptional factor during the bacterial heat shock response. Histidine protein kinases and serine, threonine, or tyrosine protein kinases play essential roles in signal transduction in prokaryotes and eukaryotes. A third type of protein kinase, an arginine protein kinase, has been identified. McsB of Bacillus subtilis phosphorylates the heat shock transcriptional regulator CtsR and can be regarded as the founding member of arginine protein kinases.
BMPR 2 mutation alters the lung macrophage endothelin-1 cascade in a mouse model and patients with heritable pulmonary artery hypertension

Talati M, West J, Blackwell TR, Loyd JE, Meyrick B. BMPR2 mutation alters the lung macrophage endothelin-1 cascade in a mouse model and patients with heritable pulmonary artery hypertension. Am J Physiol Lung Cell Mol Physiol 299: L363–L373, 2010. First published June 18, 2010; doi:10.1152/ajplung.00295. 2009. —Macrophage derived-endothelin-1 (ET-1) has been suggested to contribute to a number of chronic lung diseases. Whether the ET-1 cascade from non-vascular sources (inflammatory cells) also contributes to pulmonary artery hypertension (PAH) and in particular to heritable PAH (HPAH) with known bone morphogenetic protein type 2 receptor (BMPR2) mutations is not known. We tested this notion using bone marrow-derived macrophages (BMDM; precursors of tissue macrophages) isolated from ROSA26rtTAXTetO7-tet-BMPR2 mice (model of PAH with universal expression of a mutated BMPR2 gene) with and without activation by LPS and in human lung tissue from HPAH with BMPR2 mutations and idiopathic PAH (IPAH). At baseline ETA and ETB receptors and endothelin converting enzyme (ECE) gene expression was reduced in BMPR2 mutant BMDM compared with controls. In control BMDM, LPS resulted in increased ppET-1 gene expression and ET-1 in culture media, whereas ETA and ETB receptor and ECE gene expression was decreased. These findings were more severe in BMPR2 mutant BMDM. Antagonism of the ETB receptor resulted in increased ET-1 in the media, suggesting that decreased ET-1 uptake by the ETB receptor contributes to the elevation. While ET-1 expression was demonstrated in lung macrophages from controls and IPAH and HPAH patients, ETA and ETB expression was decreased in the HPAH, but not IPAH, patients compared with controls. We conclude that reduced expression of macrophage ET-1 receptors in HPAH increases lung ET-1 and may contribute to the pathogenesis and maintenance of HPAH. This is the first description of protein expression that distinguishes HPAH from IPAH in patients.
Consumption of whole eggs promotes greater stimulation of postexercise muscle protein synthesis than consumption of isonitrogenous amounts of egg whites in young men.

Background: Protein in the diet is commonly ingested from whole foods that contain various macro- and micronutrients. However, the effect of consuming protein within its natural whole-food matrix on postprandial protein metabolism remains understudied in humans.Objective: We aimed to compare the whole-body and muscle protein metabolic responses after the consumption of whole eggs with egg whites during exercise recovery in young men.Design: In crossover trials, 10 resistance-trained men [aged 21 ± 1 y; 88 ± 3 kg; body fat: 16% ± 1% (means ± SEMs)] received primed continuous l-[ring-2H5]phenylalanine and l-[1-13C]leucine infusions and performed a single bout of resistance exercise. After exercise, participants consumed intrinsically l-[5,5,5-2H3]leucine-labeled whole eggs (18 g protein, 17 g fat) or egg whites (18 g protein, 0 g fat). Repeated blood and muscle biopsy samples were collected to assess whole-body leucine kinetics, intramuscular signaling, and myofibrillar protein synthesis.Results: Plasma appearance rates of protein-derived leucine were more rapid after the consumption of egg whites than after whole eggs (P = 0.01). Total plasma availability of leucine over the 300-min postprandial period was similar (P= 0.75) between the ingestion of whole eggs (68% ± 1%) and egg whites (66% ± 2%), with no difference in whole-body net leucine balance (P = 0.27). Both whole-egg and egg white conditions increased the phosphorylation of mammalian target of rapamycin complex 1, ribosomal protein S6 kinase 1, and eukaryotic translation initiation factor 4E-binding protein 1 during postexercise recovery (all P < 0.05). However, whole-egg ingestion increased the postexercise myofibrillar protein synthetic response to a greater extent than did the ingestion of egg whites (P= 0.04). Conclusions: We show that the ingestion of whole eggs immediately after resistance exercise resulted in greater stimulation of myofibrillar protein synthesis than did the ingestion of egg whites, despite being matched for protein content in young men. Our data indicate that the ingestion of nutrient- and protein-dense foods differentially stimulates muscle anabolism compared with protein-dense foods. This trial was registered at clinicaltrials.gov as NCT03117127.
Biodegradation of naphthalene in aqueous nonionic surfactant systems

The principal objective of this study was to quantify the bioavailability of micelle-solubilized naphthalene to naphthalene-degrading microorganisms comprising a mixed population isolated from contaminated waste and soils. Two nonionic surfactants were used, an alkylethoxylate, Brij 30 (C12E4), and an alkylphenol ethoxylate, Triton X-100 (C8PE9.5). Batch experiments were used to evaluate the effects of aqueous, micellized nonionic surfactants on the microbial mineralization of naphthalene and salicylic acid, an intermediate compound formed in the pathway of microbial degradation of naphthalene. The extent of solubilization and biodegradation under aerobic conditions was monitored by radiotracer and spectrophotometric techniques. Experimental results showed that surfactant concentrations above the critical micelle concentration were not toxic to the naphthalene-degrading bacteria and that the presence of surfactant micelles did not inhibit mineralization of naphthalene. Naphthalene solubilized by micelles of Brij 30 or Triton X-100 in liquid media was bioavailable and degradable by the mixed culture of bacteria.
Molecular Markers in Patients with Chronic Wounds to Guide Surgical Debridement

Chronic wounds, such as venous ulcers, are characterized by physiological impairments manifested by delays in healing, resulting in severe morbidity. Surgical debridement is routinely performed on chronic wounds because it stimulates healing. However, procedures are repeated many times on the same patient because, in contrast to tumor excision, there are no objective biological/molecular markers to guide the extent of debridement. To develop bioassays that can potentially guide surgical debridement, we assessed the pathogenesis of the patients’ wound tissue before and after wound debridement. We obtained biopsies from three patients at two locations, the nonhealing edge (prior to debridement) and the adjacent, nonulcerated skin of the venous ulcers (post debridement), and evaluated their histology, biological response to wounding (migration) and gene expression profile. We found that biopsies from the nonhealing edges exhibit distinct pathogenic morphology (hyperproliferative/hyperkeratotic epidermis; dermal fibrosis; increased procollagen synthesis). Fibroblasts deriving from this location exhibit impaired migration in comparison to the cells from adjacent nonulcerated biopsies, which exhibit normalization of morphology and normal migration capacity. The nonhealing edges have a specific, identifiable, and reproducible gene expression profile. The adjacent nonulcerated biopsies have their own distinctive reproducible gene expression profile, signifying that particular wound areas can be identified by gene expression profiling. We conclude that chronic ulcers contain distinct subpopulations of cells with different capacity to heal and that gene expression profiling can be utilized to identify them. In the future, molecular markers will be developed to identify the nonimpaired tissue, thereby making surgical debridement more accurate and more efficacious.
Children and Microbial Foodborne Illness

Consumption of food contaminated with microbial pathogens (bacteria, fungi, parasites, viruses, and their toxins) causes an estimated 76 million illnesses, 325,000 hospitalizations, and 5,000 deaths each year in the United States. People who face relatively higher risks from foodborne illness and associated complications, such as kidney failure, include the very young, the very old, and the immunocompromised, such as those with AIDS and cancer. Children deserve added attention in the study of microbial foodborne illness because the risks of some foodborne illnesses, such as salmonellosis, are relatively higher for children than for other demographic groups. Children’s immune systems are not fully developed, placing them at a relatively higher risk for some foodborne illnesses. A child’s lower weight means that it takes a smaller quantity of pathogens to make a child sick than it would a healthy adult. Also, children have limited control of food safety risks because their meals are usually prepared by others. This article focuses on some of the more common or serious foodborne illnesses, namely illnesses from Campylobacter, Salmonella, E. coli O157:H7, E. coli non-O157:H7 STEC, Listeria, and Toxoplasma gondii. Children are usually exposed to these pathogens not only by contaminated food but also by secondary sources of exposure, such as ill family members or ill classmates in a day care center. A pregnant woman who becomes newly infected with Listeria or Toxoplasma gondii can pass the infection to her fetus. USDA’s Economic Research Service (ERS) estimates that the five foodborne illnesses covered in this article cause $6.9 billion in medical costs, lost productivity, and premature deaths in the United States each year. Using FoodNet data on the proportion of all confirmed and reported illnesses attributed to children for the different pathogens, our preliminary estimate is that about one-third of total costs—$2.3 billion—are the result of illnesses in children under the age of 10. Children and Microbial Foodborne Illness
Role of Sevelamer Hydrochloride in the Coronary Artery Calcification Score

Abstract: The coronary artery calcification score (CACS) is higher in hemodialysis (HD) patients than in non‐HD patients for each age group from the fifth to the eighth decade of life. In order to clarify the relationship between the rate of change in the CACS and several factors related to calcium (Ca) and phosphate (P) metabolism in HD patients, we determined the CACS twice in 144 HD outpatients at an interval of approximately 12 months (2003 and 2004). The dosage of vitamin D formulations (alfacalcidol or maxacalcitol) was reduced or ceased if the serum Ca concentration exceeded 5.0 mEq/L, or the serum P concentration exceeded 6.0 mg/dL, and the dosage of combined sevelamer hydrochloride (SH) and calcium carbonate (CaCO3), as the phosphate binder, was adjusted to maintain the concentrations below these levels. The study parameters were: (1) the total dosage of alfacalcidol (µg), maxacalcitol (µg), SH (mg), and CaCO3 at the time of each CACS measurement; and (2) serum concentrations of Ca, P, alkaline phosphatase, high‐sensitivity parathyroid hormone (HS‐PTH), total protein, albumin, total cholesterol, triglycerides (TG). Regression analysis showed a significant correlation among the total SH dosage, TG, and αCACS. Future investigations will include the differences in αCACS between patients treated with SH who experience a rise in Ca and/or P and those with a decrease in Ca and/or P.
Unsupervised Morphological Segmentation Based on Segment Predictability and Word Segments Alignment

Word segments are relevant cues for the automatic acquisition of semantic relationships from morphologically related words. Indeed, morphemes are the smallest meaning-bearing units. We present an unsupervised method for the segmentation of words into sub-units devised for this objective. The system relies on segment predictability to discover a set of prefixes and suffixes and performs word segments alignment to detect morpheme boundaries.
Spatial Orientation in Weightless Environments

Illusions of body inversion and of vehicle inversion can be evoked by exposure to weightlessness in the microgravity conditions of orbital and parabolic flight. Such illusions can involve all possible combinations of self-inversion and vehicle inversion. In the absence of any patterns of external stimulation, individuals may lose all sense of body orientation to their surroundings while retaining a sense of their overall body configuration and cognitive awareness of their actual position. Touch and pressure cues provide a perceptual ‘down’ in the absence of visual input. When vision is allowed, apparent orientation is influenced by a variety of factors including the direction of gaze, the architectural layout of the vehicle, and sight of the body. The relative importance of the various factors affecting orientation changes with repeated exposure. The virtual absence of sensations of falling during exposure to free-fall emphasizes the role of cognitive factors in experienced orientation.
Geographical distributions in tropical trees: can geographical range predict performance and habitat association in co‐occurring tree species?

Aim A major floristic and climatic transition from aseasonal to seasonal evergreen tropical forest (the Kangar–Pattani Line; KPL) exists in the Indo‐Sundaic region of Southeast Asia. Mechanisms constraining species distribution here are at present poorly understood, but it is hypothesized that species differ in their tolerances of abiotic factors, in particular water availability. Under this hypothesis, we anticipate differences in performance or habitat preferences, or both, of species differing in distribution with respect to the KPL. The aim of this study is to test whether geographical distributions can be used to explain variation in growth, mortality and habitat preferences in co‐occurring tree species differing in their distribution in relation to the KPL.
Results of Long-Term Follow-Up in Patients Undergoing Anterior Screw Fixation for Type II and Rostral Type III Odontoid Fractures

Study Design. Retrospective analysis of the fusion rate of a group of 38 patients having undergone anterior screw fixation for type II and “shallow” type III odontoid fractures. Objective. To determine primarily the long-term fusion rate after anterior screw fixation and to study the clinical characteristics of patients that have a statistically significant or nonsignificant influence on successful outcome. Summary of Background Data. Long-term outcome of anterior screw fixation for odontoid fractures has been evaluated in very few studies. This information should be critical for further establishing this technique as a major therapeutic strategy for these cases. Methods. Thirty-eight patients, 25 males and 13 females (with mean age 48.4 ± 0.4 years), with type II and rostral type III odontoid fractures, underwent anterior cannulated screw fixation during a 62-month period. Radiologic examination of the cervical spine with plain radiographs was performed at 6 weeks, and 2, 6, 12, and 24 months, while computerized tomography of the upper cervical spine (C1–C3) was obtained at 6 months after surgery. Follow-up was available for 31 patients, and the follow-up time ranged from 39 to 87 months (mean 58.4). Results. Radiographic evaluation of the follow-up group showed satisfactory bony fusion and no evidence of abnormal movement at the fracture site in 27 (87.1%) patients. Pseudarthrosis developed in 4 (12.9%) patients; however, 3 (9.6%) of them without instability and 1 (3.2%) with instability. One (3.2%) patient had an instrumentation failure without instability. Conclusions. In our series, anterior odontoid screw fixation comprised a safe therapeutic modality with high stability and low mechanical failure rates during short-term and long-term follow-up.