Miracle-dz/UniFAR-FTUs huggingface dataset:
Iron- and Quorum-sensing Signals Converge on Small Quorum-regulatory RNAs for Coordinated Regulation of Virulence Factors in Vibrio vulnificus*

Vibrio vulnificus is a marine bacterium that causes human infections resulting in high mortality. This pathogen harbors five quorum-regulatory RNAs (Qrr1–5) that affect the expression of pathogenicity genes by modulating the expression of the master regulator SmcR. The qrr genes are activated by phosphorylated LuxO to different degrees; qrr2 is strongly activated; qrr3 and qrr5 are moderately activated, and qrr1 and qrr4 are marginally activated and are the only two that do not respond to cell density-dependent regulation. Qrrs function redundantly to inhibit SmcR at low cell density and fully repress when all five are activated. In this study, we found that iron inhibits qrr expression in three distinct ways. First, the iron-ferric uptake regulator (Fur) complex directly binds to qrr promoter regions, inhibiting LuxO activation by competing with LuxO for cis-acting DNA elements. Second, qrr transcription is repressed by iron independently of Fur. Third, LuxO expression is repressed by iron independently of Fur. We also found that, under iron-limiting conditions, the five Qrrs functioned additively, not redundantly, to repress SmcR, suggesting that cells lacking iron enter a high cell density mode earlier and could thereby modulate expression of virulence factors sooner. This study suggests that iron and quorum sensing, along with their cognate regulatory circuits, are linked together in the coordinated expression of virulence factors.
Effect of water-filled pore space on carbon dioxide and nitrous oxide production in tilled and nontilled soils [Maize; Illinois; Kentucky; Minnesota; Nebraska]

The percentage of soil pore space filled with water (percent water-filled pores, % WFP), as determined by water content and total porosity, appears to be closely related to soil microbial activity under different tillage regimes. Soil incubated in the laboratory at 60% WFP supported maximum aerobic microbial activity as determined by CO production and O uptake. In the field, % WFP of surface no-tillage soils (0–75 mm) at four U.S. locations averaged 62% at time of sampling, whereas that for plowed soils was 44%. This difference in % WFP was reflected in 3.4 and 9.4 times greater CO and NO production, respectively, from surface no-tillage soils over a 24-h period as compared to plowed soils. At a depth of 75 to 150 mm, % WFP values increased in both no-tillage and plowed soils, averaging approximately 70% for no tillage compared with 50 to 60% for plowed soils. Production of CO in the plowed soils was enhanced by the increased % WFP, resulting in little or no difference in CO production between tillage treatments. Nitrous oxide production, however, remained greater under no-tillage conditions. Substantially greater amounts of NO were produced from the N-fertilized soils, regardless of tillage practice. Production of CO and NO was primarily related to the % WFP of tillage treatments although, in several instances, soil-water-soluble C and NO levels were important as well. Calculations of relative aerobic microbial activity between no-tillage and plowed soils, based on differences in % WFP relative to maximum activity at 60%, indicated linear relationships for CO and NO production between WFP values of 30 to 70%. Below 60% WFP, water limits microbial activity, but above 60%, aerobic microbial activity decreases—apparently the result of reduced aeration.
Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1

ABSTRACT Multiply antibiotic-resistant Acinetobacter baumannii isolate D36 was recovered in Australia in 2008 and belongs to a distinct lineage of global clone 1 (GC1). Here, we present the complete 4.13 Mbp genome sequence (chromosome plus 4 plasmids), generated via long read sequencing (PacBio).
A Nuclear Magnetic Resonance Spectroscopy as a Method for Evaluation of In Vivo Poly-l-Lactide Biodegradation Kinetics From Stent-Polymer Matrices

Objectives: We aimed to comprehensively evaluate poly-lactide polymer degradation and sirolimus release kinetics from a drug-eluting stent matrix in the in vivo setting using a nuclear magnetic resonance (NMR) method. Methods: In 22 domestic swine, 18 biodegradable polymer-only coated stents (BPSs) and 36 biodegradable polymer-coated sirolimus-eluting stents (BP-SES) were implanted in coronary arteries with 115% overstretch. The animals were sacrificed at 1, 3, 7, 14, 28, and 56 days following baseline procedures. Vessel segments with BPS were harvested to evaluate polymer degradation with a NMR method, whereas BP-SES to analyze sirolimus tissue uptake and retention. Additionally, 8 BP-SES were implanted for histological analysis for 90 days of follow-up. Results: The NMR showed a gradual absorption of the polymer over the 6 consecutive time points, from 5.48 µg of the polymer on the stent at 1-day follow-up, through 4.33 µg at 3 days, 3.16 µg at 7 days, 2.42 µg at 14 days, 1.92 µg at 28 days to 1.24 µg in the last day of the study. The curve of polymer degradation corresponds well with the pharmacokinetic profile of sirolimus eluted from its surface and measured at identical time points. In histopathology, at 90 days, complete healing and biocompatibility were reported. Conclusions: The utilization of NMR method for BP absorption kinetics evaluation is a useful tool, which may be widely adopted to test other biodegradable implants. Further, it may substantially improve their safety and efficacy by facilitating programmed polymer and drugs elution.
A hybrid vector parabolic equation/ray-tracing propagation modeling technique for rail transportation systems

The deployment of modern communication-based train control (CBTC) systems along a guideway requires a careful study of the radio-wave propagation characteristics of the corresponding wireless channel. Carrying out this study via experimental means can be both expensive and time consuming, considering that current rail transportation networks extend over tens to hundreds of kilometers. Hence, research on numerical techniques that can assist and accelerate, though not replace, the experimental survey of a guideway as a communication channel, is as timely as ever, notwithstanding the large volume of pre-existing work on the subject.
Perception of Pressure on Foot

This study attempted to identify the factors that affect the pressure pain threshold (PPT) on the heel region of the foot. Using dimensional analysis, it was found that probe area (A), indentation speed (V) and their interaction contribute towards PPT. A power form of these factors can be used to model PPT with an exponent of 0.63.
Energy Analysis for Graphics Processors using Novel Methods & Efficient Multi-View Rendering

Real-time rendering is increasingly being performed on battery powered devices, such as laptops and mobile phones. As a result, performance in rendering time is not the only important factor, but the energy consumption is also becoming more and more important, as a lower energy usage directly translates to longer battery time. The main topic of this thesis is energy consumption of graphics processors. To examine this, we perform high-frequency measurements of a number of graph- ics devices’ power consumption. Simultaneously, we render real-time graphics workloads to analyze the power consumption for a number of devices, algorithms, and settings. We draw a number of conclusions for different platforms, e.g., that it is incorrect to assume a direct correlation between rendering time and per-frame energy consumption. We also present a method for evaluating if there is such a correlation on a specific, efficiently utilized, platform. This method uses Pareto frontiers to filter out measurements that are inefficient, with respect to render- ing time and energy consumption, and analyses only measured data points with a possible trade-off. Our long-term goal is to use our conclusions for developing energy-efficient algorithms, as well as raising awareness in the developer commu- nity to consider rendering time and energy consumption while developing real- time graphics algorithms. Furthermore, we develop and improve methods for cor- relating energy consumption on a per-frame basis with other information collected for specific frames, to enable improved analysis regarding real-time graphics en- ergy consumption. Our second topic is efficient multi-view rendering. We have developed an opti- mized algorithm for multi-view ray tracing, targeting auto-stereoscopic displays, which performs up to an order of magnitude faster than previous state of the art algorithms. In addition, we have examined the feasibility of enabling a proposed higher-dimensional rasterizer implemented in hardware to render multi-view and stereoscopic image sets in a single pass. We find it straightforward to adapt a higher-dimensional rasterizer to support multi-view rendering, and propose im- provements to enhance the rendering performance for such applications. (Less)
Estrogen reduces myointimal proliferation after balloon injury of rat carotid artery.

BACKGROUND Vascular disease progresses more slowly in females with functional ovaries than in males. The mechanisms of this vasoprotective effect of female sex are incompletely understood. This study tested (1) whether there is a sex difference in the development of myointimal proliferation after balloon injury of the rat carotid artery in vivo, (2) whether this response is estrogen or androgen dependent, and (3) whether there is a sexual dimorphism in expression of the c-myc proto-oncogene in intact and/or damaged rat carotid arteries. METHODS AND RESULTS Ten-week-old male and female Sprague-Dawley rats were either gonadectomized or studied intact. Gonadectomized rats of both sexes were implanted with estradiol, testosterone, or nothing (control) 3 days before vascular injury. Two weeks later, the rats were killed by overdose of pentobarbital, and the injured right and uninjured control left carotid arteries were fixed and subjected to morphometric analysis for evaluation of the degree of myointimal thickening. Separate groups of intact male and female rats were killed at 1 and 2 hours after vascular injury, and total RNA from injured and uninjured vessels was subjected to Northern blot analysis for assessment of steady state c-myc mRNA levels. Neointimal area and the ratio of neointimal to medial area were significantly less in intact female rats than in intact male rats (P < .05). Gonadectomy of female rats was associated with a greater increase in neointima formation after balloon injury than that observed in intact females (P < .05), but testosterone replacement did not further enhance this response. Estradiol treatment significantly inhibited myointimal proliferation after vascular injury in gonadectomized rats of both sexes (P < .05). Neither gonadectomy nor gonadectomy plus testosterone replacement altered the myointimal proliferative response to balloon injury in male rats. Steady state c-myc mRNA levels were detectable in undamaged carotid arteries in intact rats of both sexes and were significantly greater in males than in females; c-myc mRNA levels were increased in both sexes after carotid injury, but the response was significantly larger in magnitude and more rapid in males than in females. CONCLUSIONS These data indicate that the sex difference in myointimal proliferation after vascular injury is estrogen dependent. C-myc gene expression is greater in the undamaged carotid artery of the male than in that of the female, and the responsiveness of this gene to balloon injury of the artery is more rapid and more robust in the male than in the female rat. These findings have direct implications for the prevention and treatment of vascular disease in humans.
Pancreatic fat is negatively associated with insulin secretion in individuals with impaired fasting glucose and/or impaired glucose tolerance: a nuclear magnetic resonance study

The pathogenesis of type 2 diabetes is characterized by insulin resistance and β‐cell dysfunction. Pancreatic fat load may add to the development of β‐cell dysfunction. The aim was to thoroughly quantify the fat content of pancreas sections (caput, corpus, and cauda) and to compare the impact of pancreatic, intrahepatic, and visceral fat on insulin secretion in humans.
Do you Blend? Huntley High School Does

Huntley High School in Huntley, Illinois has recently implemented a blended learning initiative to meet needs of their learners in the 21st century, infusing technology into the school s curriculum and teachers instructional practices, and preparing students for college and career. Huntley 's unique mix of traditional and blended learning provides a variety of ways for students to learn in both elective and core classes. We share Huntley s unique model of blended learning, focusing on four lessons learned.
Découverte non supervisée de lexique à partir d'un corpus multimodal pour la documentation des langues en danger

De nombreuses langues disparaissent tous les ans et ce a un rythme jamais atteint auparavant. Les linguistes de terrain manquent de temps et de moyens afin de pouvoir toutes les documenter et decrire avant qu’elles ne disparaissent a jamais. L’objectif de notre travail est donc de les aider dans leur tâche en facilitant le traitement des donnees. Nous proposons dans ce memoire des methodes d’extraction non supervisees de lexique a partir de corpus multimodaux incluant des signaux de parole et des images. Nous proposons egalement une methode issue de la recherche d’information afin d’emettre des hypotheses de signification sur les elements lexicaux decouverts. Ce memoire presente en premier lieu la constitution d’un corpus multimodal parole-image de grande taille. Ce corpus simulant une langue en danger permet ainsi de tester les approches computationnelles de decouverte non supervisee de lexique. Dans une seconde partie, nous appliquons un algorithme de decouverte non supervisee de lexique utilisant de l’alignement dynamique temporel segmental (S-DTW) sur un corpus multimodal synthetique de grande taille ainsi que sur un corpus multimodal d’une vraie langue en danger, le Mboshi.
PGE2 Promotes the Migration of Mesenchymal Stem Cells through the Activation of FAK and ERK1/2 Pathway

A critical step of MSCs therapy is dependent on its ability to migrate into the sites of injury, so various approaches have been introduced to boost the migratory ability of MSCs. PGE2 is the major prostaglandin generated by COX enzymes and has been implicated in inflammatory response. Evidence indicates that PGE2 can facilitate MSCs migration. Further exploration of the underlying molecular mechanism participating in the promigratory ability of PGE2 may provide a novel strategy to improve MSC transplantation efficacy. In this study, our findings suggested that EP2 prostanoid receptor promotes MSCs migration through activation of FAK and ERK1/2 pathways. Furthermore, MSCs migration induced by PGE2 was blunted by FAK or ERK1/2 inhibitors. EP2-mediated MSCs migration depends on the activation of FAK and ERK1/2. However, the current study did not investigate the migration of MSCs over a blood vessel endothelial barrier. In conclusion, our findings reveal EP2-mediated FAK and ERK1/2 activation was essential for MSCs migration induced by PGE2, indicating that activation of EP2 receptor and FAK/ERK pathways may be a promising strategy to accelerate homing efficiency of MSCs, which in turn enhances therapeutic potential of MSCs transplantation.
Comparison of the Ileal Digestibility of Amino Acids in Meat and Bone Meal for Broiler Chickens and Growing Rats

The apparent ileal amino acid digestibility in 15 meat and bone samples was compared in growing broiler chickens and growing laboratory rat. The animals were given a diet containing meat and bone meal as the sole source of protein. All diets contained chromic oxide as the indigestible marker to calculate the digestibility estimates. Comparison of digestibility data shows that, for all dispensable amino acids, apparent ileal amino acid digestibility was similar (p>0.05) between broiler chicken and the growing rat. However, the ileal amino acid digestibility was similar (p>0.05) between the two species for only four (histidine, methionine, threonine and valine) of the nine indispensable amino acids. Significant differences (p<0.01 to 0.05) were observed between the estimates in the broiler chicken and the rat for arginine, leucine, lysine, phenylalanine and cystine. Differences approaching statistical significance were observed for isoleucine (p=0.06) and tyrosine (p=0.10). For the amino acids, which differed between the species, the values obtained for broilers were consistently 4 to 7 percentage units lower than those in the rats. The exception was cystine, with digestibility in broilers being 17 percentage units lower than in the rat. The present data do not support the use of the growing rat as a model for growing chickens in the determination of ileal amino acid digestibility.
A Review of the Existing Grading Schemes and a Proposal for a Modified Grading Scheme for Prostatic Lesions in TRAMP Mice

The transgenic adenocarcinoma of the mouse prostate (TRAMP) model is well established and offers several advantages for the study of chemopreventive agents, including its well-defined course of disease progression and high incidence of poorly differentiated carcinomas within a relatively short length of time. However, there is no consensus on the grading of prostatic lesions in these mice. In particular, agreement is lacking on the criteria for differentiating prostatic intraepithelial neoplasia (PIN) from well-differentiated adenocarcinoma, specifically as it relates to evidence of invasion. This differentiation is critical for evaluating the effects of putative chemopreventive agents on progression to neoplasia. Moreover, only one of the published grading schemes assigns numerical grades to prostatic lesions, which facilitate statistical analysis. Here, we review five currently available grading schemes and propose a refined scheme that provides a useful definition of invasion for the differentiation of PIN from well-differentiated adenocarcinoma and includes a numerical scoring system that accounts for both the most severe and most common histopathological lesions in each of the lobes of the prostate and their distributions. We expect that researchers will find this refined grading scheme to be useful for chemoprevention studies in TRAMP mice.
Health‐related physical fitness in children and adolescents with Down syndrome and response to training

Physical fitness is related to health at all ages. Information about physical fitness in the Down syndrome (DS) population, however, is scarce, especially when we consider children and adolescents. A review of the current data available on this topic would be both timely and important as it would serve as a starting point to stimulate new research perspectives. The data we reviewed from the literature showed a general trend toward lower values of physical fitness parameters and worse body composition variables in children and adolescents with DS compared with the population without intellectual disability (ID) or even with the population with ID without DS. Notably, children and adolescents with DS have been described as less active or overprotected; however, these factors may not be the cause of their poor physical fitness. Many of the training programs carried out in children and adolescents with DS did not yield the desired responses, and the reasons are still unknown. The purpose of this review is to summarize the current available literature on health‐related physical fitness in children and adolescents with DS, and the effect of training on these variables. From the literature available, it is clear that more data on this population are necessary.
Analysis of the PROFIBUS token passing protocol over wireless links

For the PROFIBUS, a standardized and well-known fieldbus system, it is attractive to use wireless media. A natural approach in creating such a system is to re-use as much existing technology, as possible. In the area of wireless local area networks (WLANs) clearly the IEEE 802.11 standard is the leading technology. Hence, the question comes up, how this technology can be used in the creation of a wireless PROFIBUS. In this paper, the authors consider the solution of running the existing PROFIBUS MAC and link-layer protocol directly on top of an IEEE 802.11 DSSS PHY, without the 802.11 MAC functionality. They show that the PROFIBUS MAC protocol (a token-passing scheme on top of a broadcast medium, stations organized in a logical ring) is vulnerable against bit errors and packet losses. Specifically, the membership of a station in the logical ring is harmed by loss of token frames. Ring membership is important, since only ring members are allowed to transmit data. Lost stations can't do so, no matter how time-critical and important their data is. Their re-inclusion into the ring takes some time. The problems are serious and they conclude that for creation of a wireless PROFIBUS alternative solutions for MAC- and link-layer protocols should be investigated.
Oxidative Stress in Patients with End-Stage Renal Disease prior to the Start of Renal Replacement Therapy

Background/Aim: In patients with end-stage renal disease (ESRD), cardiovascular complications are the main cause of death. Increased oxidative stress is one of the risk factors for enhanced atherosclerosis in this population. Literature data vary partially dependent on differences in methodology. The present study compares three different methods: plasma lipid peroxides, the newly developed measurement of circulating oxidized LDL (Ox-LDL) particles and the frequently used copper-induced LDL oxidation lag time. Methods: We assessed plasma lipid peroxides, circulating Ox-LDL and in vitro copper-induced LDL oxidation lag time in 47 non-diabetic patients with ESRD, at the start of renal replacement therapy, and compared these with 41 age- and sex-matched controls. Results: In ESRD, total cholesterol (4.6 ± 1.1 vs. 5.6 ± 0.9 mmol/l; p < 0.001), LDL cholesterol (2.8 ± 0.8 vs. 3.5 ± 0.7 mmol/l; p < 0.001) and HDL cholesterol (1.0 ± 0.3 vs. 1.4 ± 0.4 mmol/l; p < 0.001) were lower compared to controls. Plasma lipid peroxides were higher (1.1 ± 0.5 vs. 0.8 ± 0.5 µmol/l; p = 0.003) in ESRD. No differences were observed in plasma Ox-LDL (63.1 ± 62.0 vs. 55.3 ± 48.0 mg/l). However, due to the lower plasma LDL cholesterol in ESRD, LDL oxidation level was increased in ESRD (7.1 ± 0.1 vs. 4.2 ± 0.3%; p = 0.03). LDL lag time was slightly longer (89 ± 11 vs. 84 ± 11 min; p = 0.04) in ESRD. There were no significant differences regarding the amount and rate of dienes produced. Conclusions: Elevated levels of lipid peroxides and higher LDL oxidation levels support the theory that ESRD is associated with increased oxidative stress, which may explain the accelerated atherosclerosis. The measured amount of oxidative stress is not reflected by in vitro oxidizability of LDL.