Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-Term Immunological Memory Induced by Recombinant Oral Salmonella Vaccine Vectors

ABSTRACT We have previously shown that Salmonella entericaserovar Typhimurium expressing the hagB hemagglutinin gene from Porphyromonas gingivalis can induce primary and recall immune responses in serum and secretions in mice; however, the longevity of memory induced by oral Salmonella carriers has not been adequately demonstrated. In this study, we examined the capacity of mice to mount a recall response 52 weeks after primary immunization. Recall responses were seen in serum immunoglobulin G (IgG) and IgA following boosting at week 52, and in most cases, they were equal to or greater than the primary responses. Significant mucosal IgA recall responses in saliva and vaginal wash were also detected following boosting at week 52. In addition, there was a considerable residual response in secretions at week 51, prior to boosting. These results indicate that oral Salmonellavectors can induce long-term memory to recombinant HagB and are particularly effective at inducing long-lasting mucosal responses as well as at inducing the capacity for mucosal recall responses.
Effect of Synthetic Surfactants on the Solubilization and Distribution of PAHs in Water/Soil-Water Systems

The present study examined the effects of four surfactants, including three non-ionic surfactants (Tween 80, Triton X-100 and Brij 35) and an anionic surfactant SDS on the solubilization and distribution of phenanthrene (Phe) and pyrene (Pyr) in soil-water systems. All four surfactants could enhance the solubilization of Phe and Pyr in aqueous phase linearly when surfactant concentrations exceeded their respective critical micelle concentrations (CMC). Molar solubilization ratio (MSR) which indicated surfactant's solubilization capacity for Phe and Pyr, was highest for Tween 80 for both PAHs, and SDS had the lowest among the four surfactants, while Triton X-100 and Brij 35 had about the same MSR for both PAHs. Moreover, all the surfactants could provide a strong micelle partitioning phase for the more hydrophobic Pyr than Phe as revealed by their high micelle - aqueous phase partition coefficient, K mc. Batch desorption studies also demonstrated that Tween 80 had the best capacity for the desorption of both Phe and Pyr in the soil-water systems, and followed by Triton X-100 and Brij 35, while SDS seems to have no positive effect on the desorption of PAHs probably due to its relatively high CMC value. Therefore, from the application standpoint, the results obtained in this study suggest that Tween 80 would be the most suitable candidate among the four surfactants in improving solubilization and desorption of PAHs in soil-water system, which are believed to be the prerequisites for successful bioremediation technology for PAH contaminated soil.
Combined Bone Allograft and Adipose-Derived Stem Cell Autograft in a Rabbit Model

Currently available options for the repair of bony defects have substantial limitations. Much work has looked to the possibility of engineering bone using stem cells. These tissue-engineering efforts have focused on calvarial defect models, which have the advantages of minimal load-bearing and a large surface area. This study aims to solve the somewhat more challenging problem of repairing segmental bony defects such as those of the mandible and long bones. Four groups of decellularized bone tubes with cortical perforations were implanted subcutaneously in a rabbit model: empty bone tubes, bone tubes containing fibrin glue alone, bone tubes containing fibrin glue and freshly isolated autologous adipose-derived stem cells (ASCs), and bone tubes containing fibrin glue and predifferentiated autologous ASCs. Results showed a foreign body response characterized by fibrous capsule formation with minimal angiogenesis and no evidence of osteoblastic activity. Substantial changes are needed if this model is to become viable.
Activation of the Prefrontal Cortex during the Wisconsin Card Sorting Test (Keio Version) as Measured by Two-Channel Near-Infrared Spectroscopy in Patients with Traumatic Brain Injury

To investigate brain activation in the prefrontal cortex (PFC) during the Wisconsin Card Sorting Test (Keio Version) (KWCST), we examined changes in total hemoglobin volume (THV) in 8 patients with traumatic brain injury (TBI) and 20 healthy control subjects using two-channel near-infrared spectroscopy. As a result, average THV in the right PFC during KWCST in TBI patients (–0.131 ± 0.127) was significantly lower than in control subjects (0.016 ± 0.135) (2 × 3 ANOVA; p < 0.05). These results demonstrated that the TBI patients had lower circulation of hemoglobin in the right PFC during the KWCST than the control subjects.
Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1

The flagellar protein FlgJ, a member of glycoside hydrolase family 73, has N‐ and C‐terminal domains that are responsible for flagellar rod assembly and peptidoglycan hydrolysis, respectively. The crystal structure of the C‐terminal domain of SPH1045 (SPH1045‐C), the FlgJ from Sphingomonas sp. strain A1, showed a long cleft formed by two lobes, α and β. In this study, seven site‐specific mutants of residues in the cleft were prepared and analyzed. Enzyme activity was reduced most significantly in mutants E185A and Y281A, followed by E224A. A comparison of the crystal structure of the inactive mutant E185A with that of other related enzymes revealed that Glu185 is structurally reasonable as the proton donor and that Tyr281 is close to Glu185. Glu224 is, however, far from the catalytic site, which is inconsistent with the decreased activity exhibited by E224A. The structural flexibility of Glu224 and its neighboring residues observed in SPH1045‐C may indicate that this region is able to change its conformation upon substrate binding. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A post-nonlinear mixture model approach to binary matrix factorization

In this paper, we address the Binary Matrix Factorization (BMF) problem which is the restriction of the nonnegative matrix factorization (NMF) to the binary matrix case. A necessary and sufficient condition for the identifiability for the BFM model is given. We propose to approach the BMF problem by the NMF problem using a nonlinear function which guarantees the binarity of the reconstructed data. Two new algorithms are introduced and compared in simulations with the state of art BMF algorithms.
Will Nintendo ‘ ‘ Wii Fit ’ ’ Get You Fit ? An Evaluation of the Energy Expenditure from Active-Play Videogames

Objective: This study aimed to determine whether Nintendo (Redmond, WA) ‘‘Wii Fit ’’ games can help individuals meet physical activity recommendations. Subjects and Methods: Thirty young healthy volunteers were recruited for this randomized crossover study to evaluate the energy expenditure associated with (1) a 30-minute ‘‘Wii Fit Free Run,’’ (2) three 10-minute bouts of ‘‘Wii Fit’’ aerobic games (‘‘Rhythm Boxing,’’ ‘‘Super Hula Hoop,’’ and ‘‘Advanced Steps’’), and (3) 30minute treadmill running/walking. Energy expenditure was measured by indirect calorimetry using breath-bybreath analyses of O2 consumption and CO2 production. Results: The ‘‘Wii Fit’’ conditions produced a moderate exercise intensity (5.0, 4.1, 3.9, and 3.8 metabolic equivalents [METs] in ‘‘Free Run,’’ ‘‘Rhythm Boxing,’’ ‘‘Super Hula Hoop,’’ and ‘‘Advanced Steps’’), whereas the treadmill running/walking produced a vigorous exercise intensity (METs = 8.0). Based on federal guidelines, an individual could achieve the minimum weekly goal of 500 MET-minutes by playing selected ‘‘Wii Fit’’ aerobics games for 20–26 minutes a day, 5 days a week. Conclusions: Although not as vigorous as the treadmill, active-play videogames such as ‘‘Wii Fit’’ may provide an alternative way to encourage exercise and increase adoption and adherence to the physical activity guidelines.
Transformations and multi-scale optimisation in biological adaptive networks

The natural energy minimisation behaviour of a dynamical system can be interpreted as a simple optimisation process, finding a locally optimal resolution of constraints between system variables. In human problem solving, high-dimensional problems are often made much easier by inferring a low-dimensional model of the system in which search is more effective. But this is an approach that seems to require top-down domain knowledge; not one amenable to the spontaneous energy minimisation behaviour of a natural dynamical system. However, in recent work we investigated the ability of distributed dynamical systems to improve their constraint resolution ability over time by self-organisation. Using a ‘self-modelling’ Hopfield network with a particular type of associative connection we illustrated how slowly changing relationships between system components results in a transformation into a new system, a low-dimensional caricature of the original system, in which the energy minimisation behaviour is significantly more effective at globally resolving system constraints. This uses only very simple and fully-distributed positive feedback mechanisms that are relevant to other ‘active linking’ and adaptive networks. Here we overview the implications of this neural network model for understanding transformations and emergent collective behaviour in various non-neural adaptive networks such as social, genetic and in particular, ecological networks.
Proximal Sequences of the Aldolase A Fast Muscle-specific Promoter Direct Nerve- and Activity-dependent Expression in Transgenic Mice*

Muscle activity is known to modulate the muscle fiber phenotype. Changes in muscle activity (normal or experimentally induced) lead to modifications of the expression status of several muscle-specific genes. However, the transcription regulatory elements involved in the adaptative response are mainly unknown. The aldolase A muscle-specific promoter, pM, is expressed in adult fast twitch muscle with a preferential expression in fast glycolytic-2B fibers. Its activity is induced during postnatal muscle maturation, suggesting a role of nerve and/or muscle activity. Indeed, denervation of gastrocnemius in newborn mice prevented the activation of the promoter in this muscle, despite the nerve-independent formation of 2B fibers. Although the nerve was necessary for pM onset during development, denervating the gastrocnemius in adults had only mild effects on pM activity. By contrast, a transgene including the pM proximal regulatory sequences that are sufficient to reproduce the 2B fiber-specific expression of the endogenous promoter was shown to be highly sensitive to both neonatal and adult denervation. Transgenes containing muscle-specific pM proximal promoter elements were used to delineate the regulatory elements involved in this response to innervation and changes in the contractile activity pattern. Nerve- and activity-dependent elements could be localized in the 130-base pair-long proximal promoter region of the human aldolase A gene.
Efficacy of Rikkunshito, a traditional Japanese medicine (Kampo), in treating functional dyspepsia.

BACKGROUND Rikkunshito, a traditional Japanese (Kampo) medicine, is widely prescribed as an oral preparation for the treatment of functional dyspepsia (FD). In our previous study, we reported that extracorporeal ultrasonography (US) is a useful technique for the assessment of the gastric accommodation reflex (AR) and duodenogastric motility. In this study, we examined the effects of Rikkunshito on the gastroduodenal function in patients with FD. METHODS Sixteen FD patients (median age, 45 y) underwent US, before and after 14 days of treatment with Rikkunshito (7.5 g b.d.). For assessment of the AR, a cross-sectional area of the proximal stomach was measured after incremental ingestion of a liquid meal up to 400-mL. The expansion rate was used as the parameter to determine the AR. Then, the gastric emptying rate (GER), motility index (MI), and reflux index (RI) were evaluated using previously reported methods. RESULTS Although no significant changes were observed in the total score of the Gastrointestinal Symptom Rating Scale (GSRS), the scores of 3 of the 15 symptoms of GSRS decreased significantly after treatment with Rikkunshito. The expansion rate of the proximal stomach was significantly greater after treatment with Rikkunshito than before the treatment. Although the GER and MI increased significantly, no significant differences in the RI were observed after treatment with Rikkunshito. CONCLUSION These observations suggested that Rikkunshito may be beneficial for the treatment of FD patients with impaired AR and gastric motility. These results also suggested that Rikkunshito has a therapeutic potential for FD and GERD.
HUMAN STRATEGIES IN THE CONTROL OF TIME CRITICAL UNSTABLE SYSTEMS

The purpose of this study is to investigate the human manual control strategy when balancing an inverted pendulum under time critical constraints. The strategy was assessed through the quantification and evaluation of human response while performing tasks that require fast reaction from the human operator. The results show that as the task becomes more difficult due to increased time delay or shortened pendulum length, the human operator adopts a more discrete-type strategy. Additionally, dissimilarities between control of a short pendulum and a delayed pendulum are identified and discussed. Finally, the discrete-control mechanism is interpreted by relating the observed human responses to human-performance models. These results can be applied to systems requiring human interaction, such as teleoperation, which could be designed to maximize human response.
BMP/Smad signaling and embryonic cerebellum development: Stem cell specification and heterogeneity of anterior rhombic lip

The canonical bone morphogenetic proteins (BMPs) signaling have been shown to mediate many embryonic developmental processes. Due to its complexity, there are still many unknowns about this signal pathway including the Smad usage and requirement. Cerebellum, one of the most studied neural organs in development biology, requires canonical BMP signaling for stem cell specification. Here we review the role of canonical BMP signaling during the embryonic cerebellum development. Also, we raise several unsolved issues concerning the BMP signaling including the co‐Smad independency of this signaling pathway. Besides, we also propose two models for explaining the cerebellar anterior rhombic lip (ARL) specification mechanisms. In addition, we review the heterogeneity of the ARL stem cells, which may provide new insight into understanding the neural stem cell specification process of the embryonic cerebellum.
Mutations within the Catalytic Motif of DNA Adenine Methyltransferase (Dam) of Aeromonas hydrophila Cause the Virulence of the Dam-Overproducing Strain To Revert to That of the Wild-Type Phenotype

ABSTRACT In this study, we demonstrated that the methyltransferase activity associated with Dam was essential for attenuation of Aeromonas hydrophila virulence. We mutated aspartic acid and tyrosine residues to alanine within the conserved DPPY catalytic motif of Dam and transformed the pBAD/damD/A, pBAD/damY/A, and pBAD/damAhSSU (with the native dam gene) recombinant plasmids into the Escherichia coli GM33 (dam-deficient) strain. Genomic DNA (gDNA) isolated from either of the E. coli GM33 strains harboring the pBAD vector with the mutated dam gene was resistant to DpnI digestion and sensitive to DpnII restriction endonuclease cutting. These findings were contrary to those with the gDNA of E. coli GM33 strain containing the pBAD/damAhSSU plasmid, indicating nonmethylation of E. coli gDNA with mutated Dam. Overproduction of mutated Dam in A. hydrophila resulted in bacterial motility, hemolytic and cytotoxic activities associated with the cytotoxic enterotoxin (Act), and protease activity similar to that of the wild-type (WT) bacterium, which harbored the pBAD vector and served as a control strain. On the contrary, overproduction of native Dam resulted in decreased bacterial motility, increased Act-associated biological effects, and increased protease activity. Lactone production, an indicator of quorum sensing, was increased when the native dam gene was overexpressed, with its levels returning to that of the control strain when the dam gene was mutated. These effects of Dam appeared to be mediated through a regulatory glucose-inhibited division A protein. Infection of mice with the mutated Dam-overproducing strains resulted in mortality rates similar to those for the control strain, with 100% of the animals dying within 2 to 3 days with two 50% lethal doses (LD50s) of the WT bacterium. Importantly, immunization of mice with a native-Dam-overproducing strain at the same LD50 did not result in any lethality and provided protection to animals after subsequent challenge with a lethal dose of the control strain.
Mechanism of induction of rat hepatic CYP2B and 3A by the pesticide methoxychlor

Our earlier investigation demonstrated that methoxychlor treatment induced hepatic cytochrome P450 2B1/2B2 and 3A proteins in rats and enhanced their respective enzymatic activities. To determine the mechanism of the methoxychlor‐mediated induction and whether methoxychlor acts as a frank inducer and not merely by causing stabilization of the cytochrome P450 proteins or of their mRNAs, we assessed the effect of methoxychlor treatment on the transcriptional rate and mRNA levels of these hemeproteins by nuclear run‐on and northern blot analyses. Methoxychlor treatment markedly elevated the transcriptional rates of cytochrome P4502B1/2B2 and 3A. Also, higher levels of mRNA of these CYPs were observed. By contrast, mRNA levels of CYP1A1/1A2 were not affected. Using a nuclear run‐on method that apparently measures specifically the transcription initiation rate of CYP2B1 and 2B2, we observed that the transcriptional rate of 2B2 was increased substantially more than that of CYP2B1. This differential induction of CYP2B2 versus 2B1 may account for the discrepancy between the levels of induced CYP2B protein and the much lower‐than‐expected CYP2B‐mediated enzymatic activity observed in our earlier study. © 1998 John Wiley & Sons, Inc. J Biochem Mol Toxicol 12: 315–323, 1998
Optimization of Microtextured Light-Management Films for Enhanced Light Trapping in Organic Solar Cells Under Perpendicular and Oblique Illumination Conditions

To improve light absorption in organic solar cells, microscale surface-textured light-management (LM) films are applied on top of the front glass substrate. In this study, numerical simulations are employed to determine the optimal texture of the LM films that would result in the highest short-circuit current density of the solar cells in perpendicular, as well as oblique, illumination conditions. Different types of 2-D periodic surface textures are analyzed (pyramidal, parabolic, sinusoidal), and the effects of the period and groove height sizes are investigated. Numerical simulations are based on a model that combines geometric optics and wave optics and, thus, enables simulation of light propagation through the thick microtextured LM film and glass, as well as thin layers of the device, respectively. Results show that parabolic textures are the most advantageous for the solar cells to achieve high performance operating in changing illumination conditions. When properly optimized, they enable over 14% boost of the short-circuit current density in a broad range of illumination incident angles, with the maximum of 22% for perpendicular incidence, with respect to that of the nontextured cell.
Screening for mental disorders in cardiology outpatients

The objective of the study was to compare the frequency of mental disorders in cardiology outpatients to the number of patients with psychological problems identified by cardiologists. In a cardiology outpatient service, 103 consecutive patients were asked to participate in the study. Of these 86 were included and screened for mental disorder with the Primary Care Evaluation of Mental Disorders (PRIME-MD), Structured Clinical Interview for DSM-IV (SCID) psychosis screening, the Clock Drawing Test, and the WHO-5 Well-being Index. The cardiologists were asked to rate the severity of somatic and mental problems in each patient on visual analogue scales (VAS-som and VAS-men). The current treatments, including psychiatric and psychological treatments, were noted, and the survival was followed for 3 years. Of the 86 patients included, 34 (40%) had a diagnosis of mental disorder. Eleven (12.8%) had major depression, six (7.0%) minor depression, six (7.0%) anxiety disorder, two unspecified somatoform disorder, seven (8.1%) dementia, one alcohol abuse and one psychosis. Three of the patients were in long-term psychopharmacological treatment. Although the cardiologists predicted mental disorder significantly better than chance, none of the patients was in relevant treatment for their mental disorder. At 3-year follow-up, 20 (24%) of the patients had died. Age and severity of heart disease predicted mortality, while the presence of a mental disorder did not. Mental disorders, especially depression, were frequent in cardiology outpatients. Even in cases where the cardiologists identified psychological problems, the diagnosis had no consequence, as none of the patients was offered relevant treatment.
Evidence for a weakening of tropical surface wind extremes in response to atmospheric warming

The changes of extreme winds and its links with precipitation are assessed over the past two decades using daily satellite observations and climate model simulations. Both observations and models indicate a decrease in the frequency of the strongest wind events and an increase in the frequency of light wind events in response to a warming of the tropical oceans. The heaviest precipitation events are found to be more frequent when the tropical oceans warm, but the surface winds associated with these extreme rainfall events weaken. These results add further evidence to suggest that the atmospheric circulation becomes less energetic as the climate warms. It further suggests that the enhancement of the extreme precipitation events is mainly a result of increasing atmospheric water vapor and occurs despite a weakening of the large‐scale circulation, which acts to diminish the mass convergence toward the precipitating zones.
A temperature‐sensitive adenylyl cyclase mutant of Dictyostelium

Dictyostelium development starts with the chemotactic aggregation of up to 106 amoebae in response to propagating cAMP waves. cAMP is produced by the aggregation stage adenylyl cyclase (ACA) and cells lacking ACA (aca null) cannot aggregate. Temperature‐sensitive mutants of ACA were selected from a population of aca null cells transformed with a library of ACA genes, a major segment of which had been amplified by error‐prone PCR. One mutant (tsaca2) that can complement the aggregation null phenotype of aca null cells at 22°C but not at 28°C was characterized in detail. The basal catalytic activity of the enzyme in this mutant was rapidly and reversibly inactivated at 28°C. Using this mutant strain we show that cell movement in aggregates and mounds is organized by propagating waves of cAMP. Synergy experiments between wild‐type and tsaca2 cells, shifted to the restrictive temperature at various stages of development, showed that ACA plays an important role in the control of cell sorting and tip formation.