Miracle-dz/UniFAR-FTUs huggingface dataset:
A compensatory mutagenesis study of a conserved hairpin in the M gene segment of influenza A virus shows its role in virus replication

ABSTRACT RNA structures are increasingly recognized to be of importance during influenza A virus replication. Here, we investigated a predicted conserved hairpin in the M gene segment (nt 967-994) within the region of the vRNA 5′ packaging signal. The existence of this RNA structure and its possible role in virus replication was investigated using a compensatory mutagenesis approach. Mutations were introduced in the hairpin stem, based on natural variation. Virus replication properties were studied for the mutant viruses with disrupted and restored RNA structures. Viruses with structure-disrupting mutations had lower virus titers and a significantly reduced median plaque size when compared with the wild-type (WT) virus, while viruses with structure restoring-mutations replicated comparable to WT. Moreover, virus replication was also reduced when mutations were introduced in the hairpin loop, suggesting its involvement in RNA interactions. Northern blot and FACS experiments were performed to study differences in RNA levels as well as production of M1 and M2 proteins, expressed via alternative splicing. Stem-disruptive mutants caused lower vRNA and M2 mRNA levels and reduced M2 protein production at early time-points. When the RNA structure was restored, vRNA, M2 mRNA and M2 protein levels were increased, demonstrating a compensatory effect. Thus, this study provides evidence for functional importance of the predicted M RNA structure and suggests its role in splicing regulation.
Women's Health: New Frontiers in Advocacy & Social Justice Research–Introduction

Public health research and practice today faces many new challenges. Major threats to human security have occurred, including: natural disasters from tsunamis, hurricanes and earthquakes; violent deaths from civil unrest and population displacement; terrorism; new, emerging and continuing pandemics ranging from HIV/AIDS to Avian influenza; and persistent and chronic disease from worsening poverty and social inequalities. These challenges create and sustain vulnerabilities that require new and innovative interventions, which take account of the importance of the power differentials between the vulnerable and marginalized populations most affected by these threats. The challenges also require the expertise and efforts of researchers, practitioners and policy-makers whose role it is to explore and address these issues. Recent events, such as the catastrophic hurricanes along the Gulf coast of the United States brought into stark reality the non-randomness of the
The Effect of Creatine Intake on Renal Function

OBJECTIVE: To examine the effect of creatine supplementation on renal function and estimates of creatinine clearance. DATA SOURCES: A MEDLINE search was conducted (1966—September 2004) using the key terms creatine, creatinine, kidney function tests, drug toxicity, and exercise. Relevant articles were cross-referenced to screen for additional information. DATA SYNTHESIS: Supplementation with creatine, an unregulated dietary substance, is increasingly common in young athletes. To date, few studies have evaluated the impact of creatine on renal function and estimates of creatinine clearance. Because creatine is converted to creatinine in the body, supplementation with large doses of creatine may falsely elevate creatinine concentrations. Five studies have reported measures of renal function after acute creatine ingestion and 4 after chronic ingestion. All of these studies were completed in young healthy populations. Following acute ingestion (4–5 days) of large amounts of creatine, creatinine concentrations increased slightly, but not to a clinically significant concentration. Creatinine is also only minimally affected by longer creatine supplementation (up to 5.6 y). CONCLUSIONS: Creatine supplementation minimally impacts creatinine concentrations and renal function in young healthy adults. Although creatinine concentrations may increase after long periods of creatine supplementation, the increase is extremely limited and unlikely to affect estimates of creatinine clearance and subsequent dosage adjustments. Further studies are required in the elderly and patients with renal insufficiency.
Isolation of Campylobacter fetus ss jejuni in adult patients with diarrheal syndrome.

Etude faite a partir de 300 echantillons de feces. La sensibilite aux antimicrobiens est etudiee. L'etude directe du morphotype est positive dans 4 cas et des lymphocytes polymorphonucleaires sont vus dans 4 autres cas. Dans 6 cas, c'est le seul agent etiologique. La sensibilite aux antimicrobiens montre une dose inhibitrice minimale de 1,8 μg/ml pour l'erythomycine et de 32 ou plus pour le chloramphenicol
Acute Airsacculitis in Untreated and Cyclophosphamide-pretreated Broiler Chickens Inoculated with Escherichia coli or Escherichia coli Cell-free Culture Filtrate

Ninety commercial broiler chickens were divided into three equal groups; 30 were injected with brain-heart-infusion broth into the cranial thoracic air sacs (controls), 30 were similarly inoculated with a culture of Escherichia coli, and 30 were similarly inoculated with E. coli cell-free culture filtrate. Birds were examined from 0 to 6 hours post-inoculation. E. coli-inoculated and cell-free culture filtrate-inoculated chickens reacted similarly, with exudation of heterophils into the air sac. Microscopically, heterophils were present in low numbers perivascularly 0.5 hour after inoculation and became more numerous by 3 hours post-inoculation. By 6 hours post-inoculation, there was severe swelling of air sac epithelial cells and thickening of the air sac by proteinaceous fluid and heterophils. Ultrastructurally, air sac epithelial cells were swollen and vacuolated, and interdigitating processes were separated. Histologically and ultrastructurally, all features in control chickens were normal, with only rare heterophils in the air sac interstitium. In E. coli-inoculated and cell-free culture filtrate-inoculated chickens, cell counts (predominantly heterophils) in air sac lavage fluids increased markedly at 3 and 6 hours, with only slight increases in counts from lavages of controls. Heteropenia was observed in E. coli-inoculated chickens, whereas heterophilia was observed in cell-free filtrate chickens and controls. Ninety additional chickens were pretreated with cyclophosphamide, subdivided into three equal groups, and inoculated and examined similarly as above. Cyclophosphamide pretreatment reduced inflammatory changes in air sacs, lowered cell numbers in lavage fluids, and abolished hematologic changes; however, it did not prevent epithelial cell changes. These results indicate that cell-free culture filtrate of E. coli induces changes similar to those induced by cultures of E. coli.
Ensemble Registration of Multisensor Images by a Variational Bayesian Approach

In this paper, a novel image registration method, called ensemble image registration, is proposed. We use an infinite Gaussian mixture model (IGMM), which is based on a joint Gaussian mixture model and a Dirichlet process (DP), to model the joint intensity scatter plot (JISP) of the unregistered images. The DP is the cornerstone of nonparametric Bayesian statistics, and has capability of determining a proper number of mixing components. To simultaneously register a group of images, the cost function of reducing the dispersion in the JISP is preformed by a Bayesian method using IGMM. A variational Bayesian framework is developed to inference the posterior distribution of the parameters in the IGMM. To evaluate the performance of the proposed method, experiments of ensemble image registration are presented. The results show that the proposed method has improved performance compared with conventional methods.
Capacity and Fairness of Quality-Based Channel State Feedback Scheme for Wireless Multicast Systems in Non-Identical Fading Channels

In multi-group multicast systems with greedy scheduling and quality-based channel state information feedback (QCF), a novel scheme to determine group-specific QCF thresholds is proposed for non-identical Rayleigh fading channels. Unlike the conventional schemes using a single common QCF threshold, the proposed scheme using group-specific QCF thresholds provides a trade-off between system capacity and fairness. Hence, it can enhance the fairness for multicast groups at the cost of system capacity. We analyze the capacity, fairness, and feedback overhead of the multi-group multicast systems with greedy scheduling and group-specific QCF to validate the effectiveness of the proposed scheme.
Food Web Structure Shapes the Morphology of Teleost Fish Brains

Previous work showed that teleost fish brain size correlates with the flexible exploitation of habitats and predation abilities in an aquatic food web. Since it is unclear how regional brain changes contribute to these relationships, we quantitatively examined the effects of common food web attributes on the size of five brain regions in teleost fish at both within-species (plasticity or natural variation) and between-species (evolution) scales. Our results indicate that brain morphology is influenced by habitat use and trophic position, but not by the degree of littoral-pelagic habitat coupling, despite the fact that the total brain size was previously shown to increase with habitat coupling in Lake Huron. Intriguingly, the results revealed two potential evolutionary trade-offs: (i) relative olfactory bulb size increased, while relative optic tectum size decreased, across a trophic position gradient, and (ii) the telencephalon was relatively larger in fish using more littoral-based carbon, while the cerebellum was relatively larger in fish using more pelagic-based carbon. Additionally, evidence for a within-species effect on the telencephalon was found, where it increased in size with trophic position. Collectively, these results suggest that food web structure has fundamentally contributed to the shaping of teleost brain morphology.
The antinociceptive properties of the novel compound (±)-trans-4-hydroxy-6-propyl-1-oxocyclohexan-2-one in acute pain in mice

The compound (±)-trans-4-hydroxy-6-propyl-1-oxocyclohexan-2-one [(±)-&dgr;-lactone] was isolated from the plant Vitex cymosa Bertero, and determined to be the active principle. The present study aimed to evaluate the antinociceptive effect of (±)-&dgr;-lactone and to elucidate its mechanism of action. Mice were subjected to in-vivo models of acute pain (acetic acid-induced abdominal writhing, formalin and hot-plate tests) and the open-field test. (±)-&dgr;-Lactone, administered orally (6–900 µmol/kg), exerted a dose-dependent antinociceptive effect in the acetic acid-induced abdominal writhing, formalin and hot-plate tests. (±)-&dgr;-Lactone administered by the intrathecal (i.t.) and subplantar (s.p.) routes (10–600 nmol) exerted concentration-dependent antinociceptive effects in the formalin test, showing its spinal and peripheral activity, respectively. In the hot-plate test, (±)-&dgr;-lactone was also active when administered i.t. , confirming its spinal effect. The previous intraperitoneal (i.p.) application of naloxone, yohimbine, mecamylamine or glibenclamide did not alter the effect produced by the i.t. administration of (±)-&dgr;-lactone, whereas the previous application of atropine and L-arginine significantly reduced its effects in the formalin and hot-plate tests. The previous i.p. application of L-NAME enhanced the antinociceptive effect of the i.t. administration of (±)-&dgr;-lactone in the formalin and hot-plate tests. The previous i.p. application of L-NAME and L-arginine increased and decreased, respectively, the activity of (±)-&dgr;-lactone administered by s.p. administration. These results indicate that (±)-&dgr;-lactone has significant spinal and peripheral antinociceptive activity, and that its effects are at least partially mediated by a reduced nitric oxide production/release, most likely through mechanisms involving the cholinergic system.
Fluxes of energy, water, and carbon dioxide from mountain ecosystems at Niwot Ridge, Colorado

Background: The eddy covariance (EC) technique provides a direct measure of water vapour and carbon dioxide fluxes between ecosystems and the atmosphere. Aims: This review article highlights the findings of various studies that have integrated EC observations into basic meteorological, hydrological and ecological research questions in two ecosystems near Niwot Ridge, Colorado, and synthesises these studies into a catchment-scale model of water and carbon cycling, within the context of regional disturbance and environmental change. Methods: EC was implemented continuously over subalpine forest and alpine tundra vegetation at Niwot Ridge, and resulting data were compared with discrete measurements and modelling studies. Results: Sensible heat fluxes were generally in excess of latent heat fluxes, indicating that the forest and tundra ecosystems were moisture limited. Snow cover regulated the annual sum of primary productivity in the forest, and beneath-snow respiration represented a significant portion of ecosystem respiration at both locations. Conclusions: Changes in the magnitude, timing, or spatial distribution of snow are likely to have the greatest impact on ecological processes in these semi-arid mountain catchments, but possibly in compensatory ways. Ultimately, the degree to which net carbon losses from alpine tundra offset forest carbon sequestration will determine the future magnitude of the Western United States carbon sink.
Interaction of Rab31 and OCRL‐1 in oligodendrocytes: Its role in transport of mannose 6‐phosphate receptors

Rab31, a protein that we cloned from an oligodendrocyte cDNA library, is required for transport of mannose 6‐phosphate receptors (MPRs) from the trans‐Golgi network (TGN) to endosomes and for Golgi/TGN organization. Here we extend the knowledge of the mechanism of action of Rab31 by demonstrating its interaction with OCRL‐1, a phosphatidylinositol 4,5‐diphosphate 5‐phosphatase (PI(4,5)P2 5‐phosphatase) that regulates the levels of PI(4,5)P2 and PI(4)P, molecules involved in transport and Golgi/TGN organization. We show that Rab31 interacts with OCRL‐1 in a yeast two‐hybrid system, GST‐Rab31 pull‐down experiments, and coimmunoprecipitation of OCRL‐1 using oligodendrocyte culture lysates. Rab31 and OCRL‐1 colocalize in the TGN, post‐TGN carriers, and endosomes. Cation‐dependent MPR (CD‐MPR) is sorted to OCRL‐1‐containing carriers, but CD63 and vesicular stomatitis virus G (VSVG) are not. siRNA‐mediated depletion of endogenous Rab31 causes collapse of the TGN apparatus and markedly decreases the levels of OCRL‐1 in the TGN and endosomes. Our observations indicate that the role of Rab31 in the Golgi/TGN structure and transport of MPRs depends on its capability to recruit OCRL‐1 to domains of the TGN where the formation of carriers occurs. The importance of our observations is highlighted by the fact that mutation of OCRL‐1 causes demyelination in humans. © 2009 Wiley‐Liss, Inc.
Inadequacy of Colominic Acid as an Absorbent Intended To Facilitate Use of Complement-Preserved Baby Rabbit Serum in the Neisseria meningitidis Serogroup B Serum Bactericidal Antibody Assay

ABSTRACT The surrogate of protection against Neisseria meningitidis serogroup B (MenB) is the serum bactericidal antibody (SBA) assay, which measures the functional activity of antibody by using an exogenous complement source. Despite baby rabbit complement having been used in meningococcal serogroup A, C, Y, and W135 SBA assays, it is not recommended for use in the MenB SBA assay due to elevated SBA titers caused by low-avidity anti-MenB capsular antibody in test sera. Therefore, the possibility of absorbing anti-MenB capsular antibody from test sera to enable the use of baby rabbit complement in the MenB SBA assay was investigated by comparing the results with those gained using human complement. Colominic acid from Escherichia coli K1, which shares the same linkage residue as MenB polysaccharide, was used as an absorbent due to the commercial unavailability of purified MenB polysaccharide. Inclusion of soluble colominic acid as an absorbent with baby rabbit complement resulted in a general reduction in SBA titers compared with those obtained using baby rabbit complement alone. However, these were not comparable to human SBA titers for all samples. Further optimization and investigations demonstrated that for some samples, colominic acid reduced titers to less than those achieved with human complement, and for others, it was not possible to inhibit titers by using colominic acid. The results suggested that the use of colominic acid will not result in the ability to use baby rabbit complement in the MenB SBA assay, thus not alleviating the difficulties in procuring human complement. However, alternative absorbents, such as purified MenB polysaccharide, may warrant further evaluation.
Position estimation of a mobile robot using optical fiber gyroscope (OFG)

Recognition of the actual position is very important for a mobile robot to move around in its environment. The most common method of position estimation is dead reckoning usually achieved by integrating wheel rotation along the path. This method, however, has a serious problem that the estimation errors are accumulated. In this paper we propose using an optical fiber gyroscope (OFG) combined with the information provided by the wheel encoders to improve the accuracy of position estimation. The formulation using a Kalman filter to combine the information of the encoders with that of the OFG is described. The simulation results and the experimental results show the effectiveness of the proposed method. <<ETX>>
Acquisition of Nosocomial Pathogens on Hands After Contact With Environmental Surfaces Near Hospitalized Patients

Abstract We examined the frequency of acquisition of bacterial pathogens on investigators' hands after contacting environmental surfaces near hospitalized patients. Hand imprint cultures were positive for one or more pathogens after contacting surfaces near 34 (53%) of 64 study patients, with Staphylococcus aureus and vancomycin-resistant Enterococcus being the most common isolates.
Enhanced Axonal Regeneration Following Combined Demyelination plus Schwann Cell Transplantation Therapy in the Injured Adult Spinal Cord

We have treated spinal cord injured rats with demyelination plus Schwann cell transplantation and assessed neurite outgrowth in a quantifiable model of axonal regeneration. Axonal injuries of differing severity were induced in the dorsal funiculus of adult rats using a micromanipulator-controlled Scouten knife. Demyelinated regions were produced so as to overlap with the injury site by the injection of galactocerebroside antibodies plus complement one segment cranial to the axonal injury site. Schwann cells were isolated from the sciatic nerve, expanded in vitro, and transplanted into the injury site 1 day later. Animals were killed after an additional 7 days. Schwann cells were evenly distributed throughout the region of demyelination, which extended 6-7 mm cranial to the axonal injury site. The severity of axonal injury was quantified by counting degenerate axons in transverse resin sections. The degree of axonal regeneration was assessed by an electron microscopic analysis of growth cone frequency and distribution relative to the site of axonal injury. Quantification of growth cones at a distance from the site of axonal injury indicated a strong linear relationship (P < 0.001) between the number of growth cones and the number of severed axons; the ratio of growth cones to severed axons was increased by 26.5% in demyelinated plus transplanted animals compared to demyelinated animals without a transplant. Furthermore, only the demyelinated plus transplanted animals contained growth cones associated with myelin in white matter immediately outside of the region of complete demyelination. Growth cones were absent in transplanted-only animals at a distance from the site of axonal injury. These findings indicate that combined demyelination plus Schwann cell transplantation therapy enhances axonal regeneration following injury and suggests that growth cones are able to overcome myelin-associated inhibitors of neurite outgrowth in the presence of trophic support.
Dark periods and revivals of entanglement in a two-qubit system

In a recent paper Yu and Eberly [Phys. Rev. Lett. 93, 140404 (2004)] have shown that two initially entangled and afterward not interacting qubits can become completely disentangled in a finite time. We study transient entanglement between two qubits coupled collectively to a multimode vacuum field, assuming that the two-qubit system is initially prepared in an entangled state produced by the two-photon coherences, and find the unusual feature that the irreversible spontaneous decay can lead to a revival of the entanglement that has already been destroyed. The results show that this feature is independent of the coherent dipole-dipole interaction between the atoms but it depends critically on whether or not collective damping is present.
Ecological Aspects of Amphibian Metamorphosis

A synthetic theory of the ecology of amphibian metamorphosis is founded on the observation that the large variation in length of larval period and body size at metamorphosis typical of a particular species of amphibian cannot be directly explained by differences in dates of hatching or egg sizes. It is proposed that as development proceeds, variation in exponential growth coefficients causes a trend from a normal distribution to a skewed distribution of body sizes. The degree of skewing increases and the median of the distribution decreases with increasing initial densities of populations. The relative advantages of the largest members of a cohort may arise from a variety of mechanisms including the production of growth inhibitors, interference competition, and size-selective feeding behavior. These mechanisms result in a nonnormal distribution of competitive ability, a possible source of the density-dependent competition coefficient found in systems with many species (1). In our model the ranges of body sizes and dates of metamorphosis are determined by a minimum body size that must be obtained and a maximum body size that will not be exceeded at metamorphosis. Between these two size thresholds the endocrinological initiation of metamorphosis is expected to be related to the recent growth history of the individual larva. Species that exploit uncertain environments will have a wide range of possible sizes at metamorphosis. Species exploiting relatively certain environments will have a narrower range. The evolution of neoteny and direct development logically follow from the application of these ideas to the ecological context of the evolution of amphibian life histories. Species that live in constant aquatic habitats surrounded by hostile environments (desert ponds, caves, high-altitude lakes) may evolve permanent larvae genetically incapable of metamorphosis. Other populations may evolve a facultative metamorphosis such that populations are a mixture of neotenes and terrestrial adults. Direct development results from selection to escape the competition, predation, and environmental uncertainty characteristic of some aquatic habitats and is usually accompanied by parental care. The relation between our ecological model and the physiological mechanisms that initiate metamorphosis can only be suggested and it remains an open problem for developmental biologists.