Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased Fitness of Pseudomonas fluorescens Pf0-1 Leucine Auxotrophs in Soil

ABSTRACT The annotation process of a newly sequenced bacterial genome is largely based on algorithms derived from databases of previously defined RNA and protein-encoding gene structures. This process generally excludes the possibility that the two strands of a given stretch of DNA can each harbor a gene in an overlapping manner. While the presence of such structures in eukaryotic genomes is considered to be relatively common, their counterparts in prokaryotic genomes are just beginning to be recognized. Application of an in vivo expression technology has previously identified 22 discrete genetic loci in Pseudomonas fluorescens Pf0-1 that were specifically activated in the soil environment, of which 10 were present in an antisense orientation relative to previously annotated genes. This observation led to the hypothesis that the physiological role of overlapping genetic structures may be relevant to growth conditions outside artificial laboratory media. Here, we examined the role of one of the overlapping gene pairs, iiv19 and leuA2, in soil. Although iiv19 was previously demonstrated to be preferentially activated in the soil environment, its absence did not alter the ability of P. fluorescens to colonize or survive in soil. Surprisingly, the absence of the leuA2 gene conferred a fitness advantage in the soil environment when leucine was supplied exogenously. This effect was determined to be independent of the iiv19 gene, and further analyses revealed that amino acid antagonism was the underlying mechanism behind the observed fitness advantage of the bacterium in soil. Our findings provide a potential mechanism for the frequent occurrence of auxotrophic mutants of Pseudomonas spp. in the lungs of cystic fibrosis patients.
Transceiver Inphase/Quadrature Imbalance, Ellipse Fitting, and the Universal Software Radio Peripheral

In this paper, we introduce a method for inphase/quadrature imbalance parameter estimation based on ellipse fitting. The performance of the method is analytically derived. In particular, it is shown that the method exhibits a small bias (which can be negligible under some standard practical conditions) and a variance slightly above the Cramér-Rao bound. The method is then applied to measurements from a contemporary BiCMOS transceiver which is used on one of the most popular daughterboards of the universal software radio peripheral. In our measurements, the phase skew varies up to 5° with the baseband frequency, while the amplitude imbalance varies between 0 and 0.3 dB over carrier frequencies and across hardware units. The time variation, however, is only 0.004 dB in amplitude and 0.06 ° in phase. This indicates that the units could either be calibrated online when there is no transmission (in a two-antenna MIMO system, one antenna could transmit a calibration signal to the other), or they could be calibrated during production, in which case a table with different carrier and baseband frequencies would be needed. However, there is no need to estimate the parameters on every burst.
e0240 Effects of atorvastatin on the expressions of PECAM-1 and P-selectin in atherosclerotic rabbits

Objective To investigate the effects of atorvastatin on atherosclerotic rabbits serum lipid concentration and the expressions of PECAM-1 and P-selectin in rabbit thoracic aorta. Methods Atherosclerotic rabbit models were made by feeding the rabbits with high cholesterol. Thirty New Zealand big rabbits, weight (2.0±0.2) kg, were randomly divided into three groups. Group A was fed with common forage, Group B was fed with high cholesterol diet, and group C was fed with high cholesterol diet and atorvastatin simultaneously. After 16 weeks feeding, serum TC, TG, LDL-C, VLDL-C were measured. The aortic arteries were isolated and the samples adjacent to aortic arch were harvested for formicroscopy detection. The PECAM-1 and P-selectin gene expressions in rabbit thoracic aorta were detected by RT-PCR. Results The levels of TC, TG, LDL-C, VLDL-C in group B were significantly increased compared with group B and group C (p<0.05), while the levels of TC, TG, LDL-C, VLDL-C in group C were higher than those in group A (p<0.05). The aorta structure in group A was clear, the aortic intimal in group B was significantly thick and infiltrated by a large number of foam and inflammatory cells, but the endothelium in group C only showed focal infiltration of those cells observed under the microscope. The mRNA expression of PECAM-1 and P-selectin in group B were significantly increased than in group A (p<0.01), while those in group C, which were also higher than group A, were significantly decreased than in group B (p<0.05). Conclusions Atorvastatin regulates lipid metabolism effectively and reduces the PECAM-1 and P-selectin expression, which are closely related to atherosclerosis.
Historicizing historical trauma theory: Troubling the trans-generational transmission paradigm

The premise that “trauma” is transmitted across generations is central to the historical trauma discourse currently circulating in indigenous communities and professional networks in Canada. Historical trauma may be understood as the offspring of two older and apparently antithetical discourses: Native healing, and colonial professional critiques of indigenous family life. While the former has maintained a therapeutic focus on restoring intergenerational social relations, the latter has pathologized indigenous parenting and child-rearing practices. The emergence of historical trauma marks a global shift in the moral economy by which victimhood status, acquired through individual experiences of physical and especially sexual abuse, has come to wield greater currency than collective struggles against colonialism. Providers of contemporary indigenous healing programmes are drawing simultaneously on trauma discourse, which is seen to legitimate individual social suffering, and older therapeutic forms centred on sharing local social histories to restore intergenerational continuities and collective identity. But these invocations of historical trauma may continue the colonial discourse of mental health and social welfare professionals, who blamed indigenous parenting practices for children’s social problems and failure to assimilate. Some contemporary mental health and child development professionals have invoked parents’ and grandparents’ transmission of historical trauma in ways which construct indigenous families as pathological, promote an oversimplified, universalizing understanding of Canadian colonialism, and divert attention from the contemporary continuation of colonial structures and relations.
Structural and Functional Characterization of Diffusible Signal Factor Family Quorum-Sensing Signals Produced by Members of the Burkholderia cepacia Complex

ABSTRACT Previous work has shown that Burkholderia cenocepacia produces the diffusible signal factor (DSF) family signal cis-2-dodecenoic acid (C12:Δ2, also known as BDSF), which is involved in the regulation of virulence. In this study, we determined whether C12:Δ2 production is conserved in other members of the Burkholderia cepacia complex (Bcc) by using a combination of high-performance liquid chromatography, mass spectrometry, and bioassays. Our results show that five Bcc species are capable of producing C12:Δ2 as a sole DSF family signal, while four species produce not only C12:Δ2 but also a new DSF family signal, which was identified as cis,cis-11-methyldodeca-2,5-dienoic acid (11-Me-C12:Δ2,5). In addition, we demonstrate that the quorum-sensing signal cis-11-methyl-2-dodecenoic acid (11-Me-C12:Δ2), which was originally identified in Xanthomonas campestris supernatants, is produced by Burkholderia multivorans. It is shown that, similar to 11-Me-C12:Δ2 and C12:Δ2, the newly identified molecule 11-Me-C12:Δ2,5 is a potent signal in the regulation of biofilm formation, the production of virulence factors, and the morphological transition of Candida albicans. These data provide evidence that DSF family molecules are highly conserved bacterial cell-cell communication signals that play key roles in the ecology of the organisms that produce them.
Extracellular Iron Biomineralization by Photoautotrophic Iron-Oxidizing Bacteria

ABSTRACT Iron oxidation at neutral pH by the phototrophic anaerobic iron-oxidizing bacterium Rhodobacter sp. strain SW2 leads to the formation of iron-rich minerals. These minerals consist mainly of nano-goethite (α-FeOOH), which precipitates exclusively outside cells, mostly on polymer fibers emerging from the cells. Scanning transmission X-ray microscopy analyses performed at the C K-edge suggest that these fibers are composed of a mixture of lipids and polysaccharides or of lipopolysaccharides. The iron and the organic carbon contents of these fibers are linearly correlated at the 25-nm scale, which in addition to their texture suggests that these fibers act as a template for mineral precipitation, followed by limited crystal growth. Moreover, we evidence a gradient of the iron oxidation state along the mineralized fibers at the submicrometer scale. Fe minerals on these fibers contain a higher proportion of Fe(III) at cell contact, and the proportion of Fe(II) increases at a distance from the cells. All together, these results demonstrate the primordial role of organic polymers in iron biomineralization and provide first evidence for the existence of a redox gradient around these nonencrusting, Fe-oxidizing bacteria.
Prebiotic Content of Bread Prepared with Flour from Immature Wheat Grain and Selected Dextran-Producing Lactic Acid Bacteria

ABSTRACT In the last few years the need to produce food with added value has fueled the search for new ingredients and health-promoting compounds. In particular, to improve the quality of bakery products with distinct nutritional properties, the identification of new raw materials, appropriate technologies, and specific microbial strains is necessary. In this study, different doughs were prepared, with 10% and 20% flour from immature wheat grain blended with type “0 America” wheat flour. Immature flour was obtained from durum wheat grains harvested 1 to 2 weeks after anthesis. Doughs were obtained by both the straight-dough and sourdough processes. Two selected exopolysaccharide-producing strains of lactic acid bacteria (LAB), Leuconostoc lactis A95 and Lactobacillus curvatus 69B2, were used as starters. Immature flour contained 2.21 g/100 g (dry weight) of fructo-oligosaccharides. Twenty percent immature flour in dough resulted in a shorter leavening time (4.23 ï¿½ 0.03 h) than with the control and dough with 10% immature flour. The total titratable acidity of sourdough with 20% immature flour was higher (12.75 ï¿½ 0.15 ml 0.1 N NaOH) than in the control and sourdough with 10% immature wheat flour (9.20 ml 0.1 N NaOH). Molecular analysis showed that all samples contained three LAB species identified as L. lactis, L. curvatus, and Pediococcus acidilactici. A larger amount of exopolysaccharide was found in sourdough obtained with 20% immature flour (5.33 ï¿½ 0.032 g/kg), positively influencing the exopolysaccharide content of the bread prepared by the sourdough process (1.70 ï¿½ 0.03 g/kg). The addition of 20% immature flour also led to a greater presence of fructo-oligosaccharides in the bread (900 mg/100 g dry weight), which improved its nutritional characteristics. While bread volume decreased as the concentration of immature wheat flour increased, its mechanical characteristics (stress at a strain of 30%) were the same in all samples obtained with different percentages of fructo-oligosaccharides. These data support the use of immature wheat grain flour, and exopolysaccaride-producing lactic acid bacteria in formulating functional prebiotic baked goods whose nutritional value can be suitably improved.
Homonymous hemianopias

Objective: To describe the clinical characteristics and clinical-anatomic correlations of homonymous hemianopia (HH). Background: Homonymous hemianopia impairs visual function and frequently precludes driving. Most knowledge of HH is based on relatively few cases with clinical-anatomic correlations. Methods: The authors reviewed medical records of all patients with HH seen in their service between 1989 and 2004. Demographic characteristics, characteristics of visual field defects, causes of visual field defects, neuroradiologic definition of lesion location, and associated neurologic deficits were recorded. Results: A total of 904 HH were found in 852 patients. A total of 340 HH (37.6%) were complete and 564 HH (62.4%) were incomplete. Homonymous quadrantanopia (264 HH, 29%) was the most common type of incomplete HH, followed by homonymous scotomatous defects (116 HH, 13.5%), partial HH (114 HH, 13%), and HH with macular sparing (66 HH, 7%). A total of 407 HH (45.0%) were isolated. Causes of HH included stroke (629 HH, 69.6%), trauma (123, 13.6%), tumor (102, 11.3%), brain surgery (22, 2.4%), demyelination (13, 1.4%), other rare causes (13, 1.4%), and unknown etiology (2, 0.2%). The lesions were most commonly located in the occipital lobes (45%) and the optic radiations (32.2%). Every type of HH, except for unilateral loss of temporal crescent and homonymous sectoranopia, was found in all lesion locations along the retrochiasmal visual pathways. Conclusion: Homonymous hemianopia is usually secondary to stroke, head trauma, and tumors. Although the characteristics of visual field defects can be helpful in lesion location, specific visual field defects do not always indicate specific brain locations.
VEC3D: a 3-D virtual English classroom for second language learning

The traditional e-learning systems are generally less attractive to students due to their lack of 3D immersion and real voice interaction. The technology of virtual reality can be exploited to compensate these weaknesses. We propose a realistic and interactive virtual English classroom entitled VEC3D by integrating vivid 3D graphics and real-time voice communication. The goal of VEC3D aims to help undergraduate students develop the overall English communicative competence in listening, speaking, reading and writing.
Direct Laser Writing of Nanophotonic Structures on Contact Lenses

Contact lenses are ubiquitous biomedical devices used for vision correction and cosmetic purposes. Their application as quantitative analytical devices is highly promising for point-of-care diagnostics. However, it is a challenge to integrate nanoscale features into commercial contact lenses for application in low-cost biosensors. A neodymium-doped yttrium aluminum garnet (Nd:YAG) laser (1064 nm, 3 ns pulse, 240 mJ) in holographic interference patterning mode was utilized to produce optical nanostructures over the surface of a hydrogel contact lens. One-dimensional (925 nm) and two-dimensional (925 nm × 925 nm) nanostructures were produced on contact lenses and analyzed by spectroscopy and angle-resolve measurements. The holographic properties of these nanostructures were tested in ambient moisture, fully hydrated, and artificial tear conditions. The measurements showed a rapid tuning of optical diffraction from these nanostructures from 41 to 48°. The nanostructures were patterned near the edges of the contact lens to avoid any interference and obstruction to the human vision. The formation of 2D nanostructures on lenses increased the diffraction efficiency by more than 10%. The versatility of the holographic laser ablation method was demonstrated by producing four different 2D nanopattern geometries on contact lenses. Hydrophobicity of the contact lens was characterized by contact angle measurements, which increased from 59.0° at pristine condition to 62.5° at post-nanofabrication. The holographic nanostructures on the contact lens were used to sense the concentration of Na+ ions. Artificial tear solution was used to simulate the conditions in dry eye syndrome, and nanostructures on the contact lenses were used to detect the electrolyte concentration changes (±47 mmol L–1). Nanopatterns on a contact lens may be used to sense other ocular diseases in early stages at point-of-care settings.
Hospital—school liaison: perspectives of health and education professionals supporting children with renal transplants

This article explores collaboration between health and education staff as a key aspect of educational provision for children with chronic medical conditions, drawing upon material from interviews with eight health professionals (paediatric nephrologists and specialist renal nurses) and 11 mainstream schoolteachers involved in the care and schooling of children with renal transplants. Notwithstanding the apparent existence of good practice, a complex interplay of attitudinal, institutional and wider political and economic factors is identified that is likely to undermine the effectiveness of collaboration between health and education professionals. The importance of hospital—school liaison — that is, of a proactive, preventative and hence systematic and strategic nature — is highlighted. Such findings have a particular relevance for policy and practice in the context of the current Every Child Matters agenda, and are likely to have wider applicability to the education of chronically-ill children at large.
Evidence-based Medicine: How to Practice and Teach EBM

Evidence-based Healthcare: How to Make Health Policy and Management Decisions, by J. A. Muir Gray, 270 pp, with illus, paper, $29.95, ISBN 0-443-05721-4, New York, NY, Churchill Livingstone, 1997. We develop clinical expertise with bedside training and experience. How well do we integrate this experience with the best available external evidence for the purpose of direct patient care? I suspect that we do not carry out this function very well. Evidence-based Medicine (EBM) is the practice of applying valid evidence and data to a specific clinical question engendered during patient care. Lately, EBM has been on the lips and pen tips of clinicians, perhaps as a close runner-up to the other shibboleths managed care, gag clause, and networking. Is EBM then another mere mantra, a novel paradigm, or a practicable concept to help with ordinary, day-to-day clinical care? I believe it is the last, but you should be
Morphology, Migration, and Transcriptome Analysis of Schwann Cell Culture on Butterfly Wings with Different Surface Architectures.

It has been shown that material surface topography greatly affects cell attachment, growth, proliferation, and differentiation. However, the underlying molecular mechanisms for cell-material interactions are still not understood well. Here, two kinds of butterfly wings with different surface architectures were employed for addressing such an issue. Papilio ulysses telegonus (P.u.t.) butterfly wing surface is composed of micro/nanoconcaves, whereas Morpho menelaus (M.m.) butterfly wings are decorated with grooves. RSC96 cells grown on M.m. wings showed a regular sorting pattern along with the grooves. On the contrary, the cells seeded on P.u. t. wings exhibited random arrangement. Transcriptome sequencing and bioinformatics analysis revealed that huntingtin (Htt)-regulated lysosome activity is a potential key factor for determining cell growth behavior on M.m. butterfly wings. Gene silence further confirmed this notion. In vivo experiments showed that the silicone tubes fabricated with M.m. wings markedly facilitate rat sciatic nerve regeneration after injury. Lysosome activity and Htt expression were greatly increased in the M.m. wing-fabricated graft-bridged nerves. Collectively, our data provide a theoretical basis for employing butterfly wings to construct biomimetic nerve grafts and establish Htt lysosome as a crucial regulator for cell-material interactions.
Le pharmacien et chimiste Henri Braconnot (Commercy 1780-Nancy 1855)

Henri Braconnot naquit a Commercy en 1780. A l'âge de 13 ans, il est mis en apprentissage chez Graux, apothicaire a Nancy, ou il apprend la pharmacie, la chimie et la botanique jusqu'a son appel aux armees. Affecte a Strasbourg, il y perfectionne ses connaissances jusqu'a son licenciement, et se rend alors a Paris ou il frequente differents etabllissements d'enseignement dont l'Ecole gratuite de pharmacie. De retour a Nancy, qu'il ne quittera plus, en 1802, il devient directeur du jardin botanique, est elu a l'academie locale et commence ses recherches de chimie vegetale qui se poursuivent quasiment jusqu'a son deces, au debut de l'annee 1855. Braconnot a attache son nom a l'extraction des principes des vegetaux et l'essentiel de ses publications y est consacre. Plusieurs themes peuvent etre distingues : les acides, les corps gras, les principes extractifs - qui auraient pu le mener a la decouverte des alcaloides -, le sucre de bois et de chiffon, les constituants vegetaux organiques, la nitration de la cellulose. Ses travaux divers sont consacres aux colorants, a l'analyse des eaux, a la chimie physiologique, a la toxicologie et a la mineralogie. Bien qu'il n'ait jamais ete diplome, la Pharmacie a toujours considere Braconnot comme l'un des siens.
Mechanisms of Fluoroquinolone Resistance in Escherichia coli Isolates from Food-Producing Animals

ABSTRACT Eleven multidrug-resistant Escherichia coli isolates (comprising 6 porcine and 5 bovine field isolates) displaying fluoroquinolone (FQ) resistance were selected from a collection obtained from the University Veterinary Hospital (Dublin, Ireland). MICs of nalidixic acid and ciprofloxacin were determined by Etest. All showed MICs of nalidixic acid of >256 μg/ml and MICs of ciprofloxacin ranging from 4 to >32 μg/ml. DNA sequencing was used to identify mutations within the quinolone resistance-determining regions of target genes, and quantitative real-time PCR (qRT-PCR) was used to evaluate the expression of the major porin, OmpF, and component genes of the AcrAB-TolC efflux pump and its associated regulatory loci. Decreased MIC values to nalidixic acid and/or ciprofloxacin were observed in the presence of the efflux pump inhibitor phenylalanine-arginine-β-naphthylamide (PAβN) in some but not all isolates. Several mutations were identified in genes coding for quinolone target enzymes (3 to 5 mutations per strain). All isolates harbored GyrA amino acid substitutions at positions 83 and 87. Novel GyrA (Asp87 → Ala), ParC (Ser80 → Trp), and ParE (Glu460 → Val) substitutions were observed. The efflux activity of these isolates was evaluated using a semiautomated ethidium bromide (EB) uptake assay. Compared to wild-type E. coli K-12 AG100, isolates accumulated less EB, and in the presence of PAβN the accumulation of EB increased. Upregulation of the acrB gene, encoding the pump component of the AcrAB-TolC efflux pump, was observed in 5 of 11 isolates, while 10 isolates showed decreased expression of OmpF. This study identified multiple mechanisms that likely contribute to resistance to quinolone-based drugs in the field isolates studied.