Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Chemotaxis Sensory Proteins for Amino Acids in Pseudomonas fluorescens Pf 0-1 and Their Involvement in Chemotaxis to Tomato Root Exudate and Root Colonization

Pseudomonas fluorescens Pf0-1 showed positive chemotactic responses toward 20 commonly-occurring L-amino acids. Genomic analysis revealed that P. fluorescens Pf0-1 possesses three genes (Pfl01_0124, Pfl01_0354, and Pfl01_4431) homologous to the Pseudomonas aeruginosa PAO1 pctA gene, which has been identified as a chemotaxis sensory protein for amino acids. When Pf01_4431, Pfl01_0124, and Pfl01_0354 were introduced into the pctA pctB pctC triple mutant of P. aeruginosa PAO1, a mutant defective in chemotaxis to amino acids, its transformants showed chemotactic responses to 18, 16, and one amino acid, respectively. This result suggests that Pf01_4431, Pfl01_0124, and Pfl01_0354 are chemotaxis sensory proteins for amino acids and their genes were designated ctaA, ctaB, and ctaC, respectively. The ctaA ctaB ctaC triple mutant of P. fluorescens Pf0-1 showed only weak responses to Cys and Pro but no responses to the other 18 amino acids, indicating that CtaA, CtaB, and CtaC are major chemotaxis sensory proteins in P. fluorescens Pf0-1. Tomato root colonization by P. fluorescens strains was analyzed by gnotobiotic competitive root colonization assay. It was found that ctaA ctaB ctaC mutant was less competitive than the wild-type strain, suggesting that chemotaxis to amino acids, major components of root exudate, has an important role in root colonization by P. fluorescens Pf0-1. The ctaA ctaB ctaC triple mutant was more competitive than the cheA mutant of P. fluorescens Pf0-1, which is non-chemotactic, but motile. This result suggests that chemoattractants other than amino acids are also involved in root colonization by P. fluorescens Pf0-1.
Simulating the transient evolution and abrupt change of Northern Africa atmosphere – ocean – terrestrial ecosystem in the Holocene $

We present the first synchronously coupled transient simulation of the evolution of the northern Africa climate-ecosystem for the last 6500 years in a global general circulation ocean–atmosphere–terrestrial ecosystem model. The model simulated the major abrupt vegetation collapse in the southern Sahara at about 5 ka, consistent with the proxy records. Local precipitation, however, shows a much more gradual decline with time, implying a lack of strong positive vegetation feedback on annual rainfall during the collapse. The vegetation change in northern Africa is driven by local precipitation decline and strong precipitation variability. In contrast, the change of precipitation is dominated by internal climate variability and a gradual monsoonal climate response to orbital forcing. In addition, some minor vegetation changes are also simulated in different regions across northern Africa The model also simulated a gradual annual mean surface cooling in the subtropical North Atlantic towards the latest Holocene, as well as a reduced seasonal cycle of SST. The SST response is caused largely by the insolation forcing, while the annual mean cooling is also reinforced by the increased coastal upwelling near the east boundary. The increased upwelling results from a southward retreat of the North Africa monsoon system, and, in turn, an increased northeasterly trade wind. The simulated changes of SST and upwelling are also largely consistent with marine proxy records, albeit with a weaker magnitude in the model. The mismatch between the collapse of vegetation and gradual transition of rainfall suggests that the vegetation collapse is not caused by a strong positive vegetation feedback. Instead, it is suggested that the Mid-Holocene collapse of North African vegetation is caused mainly by a nonlinear response of the vegetation to a precipitation threshold in the presence of strong climate variability. The implication to the modeling and observations is also discussed. r 2007 Elsevier Ltd. All rights reserved.
Hypernymy relations from definiens-definiendum co-occurrence in multiple dictionary definitions

This research was funded by project: “Agrupacion semantica y relaciones lexicologicas en el diccionario”, lead by J. DeCesaris (HUM2009-07588/FILO); APLE: “Procesos de actualizacion del lexico del espanol a partir de la prensa”, 2010-2012, lead by M. T. Cabre (FFI2009-12188-C05-01/FILO).
White Matter Abnormality Correlates with Developmental and Seizure Outcomes in West Syndrome of Unknown Etiology

BACKGROUND AND PURPOSE: West syndrome is an epileptic encephalopathy characterized by epileptic spasms, a specific pattern on electroencephalography of hypsarrhythmia, and developmental regression. Our aim was to assess white matter abnormalities in West syndrome of unknown etiology. We hypothesized that diffusion tensor imaging reveals white matter abnormalities, especially in patients with poor seizure and developmental outcomes. MATERIALS AND METHODS: We enrolled 23 patients with new-onset West syndrome of unknown etiology. DTI was performed at 12 and 24 months of age. Fractional anisotropy images were compared with those of controls by using tract-based spatial statistics. We compared axial, radial, and mean diffusivity between patients and controls in the fractional anisotropy skeleton. We determined correlations of these parameters with developmental quotient, electroencephalography, and seizure outcomes. We also compared DTI with hypometabolism on fluorodeoxyglucose positron-emission tomography. RESULTS: At 12 months of age, patients showed widespread fractional anisotropy reductions and higher radial diffusivity in the fractional anisotropy skeleton with a significant difference on tract-based spatial statistics. The developmental quotient at 12 months of age correlated positively with fractional anisotropy and negatively with radial and mean diffusivity. Patients with seizure and abnormal findings on electroencephalography after initial treatments had lower fractional anisotropy and higher radial diffusivity. At 24 months, although tract-based spatial statistics did not show significant differences between patients and controls, tract-based spatial statistics in the 10 patients with a developmental quotient of <70 had significant fractional anisotropy reduction. In patients with unilateral temporal lobe hypometabolism on PET, tract-based spatial statistics showed greater fractional anisotropy reduction in the temporal lobe ipsilateral to the side of PET hypometabolism. CONCLUSIONS: Diffuse abnormal findings on DTI at 12 months of age suggest delayed myelination as a key factor underlying abnormal findings on DTI. Conversely, asymmetric abnormal findings on DTI at 24 months may reflect underlying focal pathologies.
Environmental Learning without Vision: Effects of Cognitive Load on Interface Design

Blindfolded participants were guided along routes from two display modes: spatial language ("left," "right," or "straight") or spatialized audio (where the perceived sound location indicates the target direction). Half of the route guidance trials were run concurrently with a secondary vibrotactile N-back task. To assess cognitive map development, subjects performed a homing task from the route's terminus. As spatialized audio displays are processed perceptually, we hypothesized they would be less affected by increased cognitive load than language displays, which require cognitive mediation. In corroboration, results showed the secondary task had no effect on cognitive map performance for guidance by spatialized audio but led to significantly worse homing errors for guidance by spatial language. Spatialized audio was also reliably faster and more accurate than language for traversing the route. These results have important implications for the design of future navigation and guidance systems for visually impaired persons.
Are there national risk factors for epidemic cholera? The correlation between socioeconomic and demographic indices and cholera incidence in Latin America.

BACKGROUND From 1991 through 1995, all Latin American countries maintained cholera surveillance systems to track the epidemic that entered the region through Peru in January 1991. These data were used to assess correlations between socioeconomic and demographic indices that might serve as national risk predictors for epidemic cholera in Latin America. METHODS Correlations between country-specific cumulative cholera incidence rates from 1991 through 1995 and infant mortality, the Human Development Index [HDI] a numerical value based on life expectancy, education, and income), gross national product (GNP) per capita, and female literacy were tested using the Pearson correlation coefficient. RESULTS A total of 1,339,834 cholera cases with a cumulative incidence rate of 183 per 100,000 population were reported from affected Western Hemisphere countries from 1991 through 1995. Infant mortality rates were the most strongly correlated with cumulative cholera incidence based on the Pearson correlation coefficient. The HDI had a less strong negative correlation with cumulative cholera incidence. The GNP per capita and female literacy rates were weakly and negatively correlated with cholera cumulative incidence rates. CONCLUSIONS Infant mortality and possibly the HDI may be useful indirect indices of the risk of sustained transmission of cholera within a Latin American country. Cumulative cholera incidence is decreased particularly in countries with infant mortality below 40 per 1000 live births. The lack of reported cholera cases in Uruguay and the Caribbean may reflect a low risk for ongoing transmission, consistent with socioeconomic and demographic indices. Cholera surveillance remains an important instrument for determining cholera trends within individual countries and regions.
Nasal CPAP has become an indispensable part of the primary treatment of newborns with respiratory distress syndrome

Prenatal steroids, early nasal CPAP combined with early surfactant treatment followed by extubation to nasal CPAP, and if necessary mechanical ventilation is a very effective treatment of respiratory distress syndrome. This treatment package is part of the ‘Scandinavian model’ for treatment of very‐low‐birthweight infants which also comprises gentle ventilation at birth; minimal handling; ‘neonatal individualized development care and assessment program’; high priority of breast feeding; and use of kangaroo method and which facilitates observation and nursing of sick premature infants and optimizes the possibility for early mother–child contact.
Climate change and weed adaptation: can evolution of invasive plants lead to greater range expansion than forecasted?

Clements DR & Ditommaso A (2011). Climate change and weed adaptation: can evolution of invasive plants lead to greater range expansion than forecasted? Weed Research51, 227–240. Summary Invasive plants are frequently viewed as harbingers of climate change owing to their potential to cause economic and ecological damage in the process of expanding their ranges. Models are being developed to help predict the range expansion of these plants, based on known tolerance ranges. Success of weeds has often been attributed to an ‘all-purpose genotype’, implying a high level of phenotypic plasticity. However, recent work has shown that many species are capable of relatively rapid genetic change as well, enhancing their ability to invade new areas in response to anthropogenic ecosystem modification. We thus predict that range expansion by many invasive species will exceed that predicted by modelling approaches that do not consider potential evolutionary change. We highlight a number of cases where weeds have expanded their latitudinal ranges or are predicted to do so in response to climatic selection pressures. We also list ten traits as likely targets for natural selection under climate change. The lag phase commonly observed for invasive species may frequently be a result of the time needed for the invader to evolve to fit the new habitat. During this present period of climate change, many invasive plant populations are likely to be in the process of developing adaptations that could lead to exponential population growth in the near future. Thus, assessment of the risk of invasive species owing to changing climate must incorporate evolutionary potential.
Head and neck neoplasms: magnetization transfer analysis.

PURPOSE Magnetization transfer (MT) imaging enables analysis of the contribution of restricted motion protons in the macromolecular pool to magnetic resonance (MR) signal intensity. The authors undertook this study to determine whether MT ratios (MTRs) could be used to predict pathologic characteristics of head and neck neoplasms. MATERIALS AND METHODS Fifty-four patients with pathologically proved neoplasms (squamous cell carcinomas, n = 33; non-squamous cell carcinomas, n = 11; benign masses, n = 10) underwent MT imaging. MTRs were correlated with pathologic findings. RESULTS No statistically significant correlations were noted between MTRs and degree of differentiation, keratinization, cells per high-power field, and rate of mitosis. Statistically significant differences were found between MTRs of malignancies and muscle (P < .01), cerebrospinal fluid (P < .001), fat (P < .001), and benign neoplasms (P < .001). MTRs of muscle were higher than those of benign, squamous cell, and non-squamous cell neoplasms. CONCLUSION MT imaging shows promise in differentiation of benign from malignant head and neck neoplasms. No statistically significant differences in MTRs were noted among malignancies.
A high‐resolution approach to estimating ecosystem respiration at continental scales using operational satellite data

A better understanding of the local variability in land‐atmosphere carbon fluxes is crucial to improving the accuracy of global carbon budgets. Operational satellite data backed by ground measurements at Fluxnet sites proved valuable in monitoring local variability of gross primary production at highly resolved spatio‐temporal resolutions. Yet, we lack similar operational estimates of ecosystem respiration (Re) to calculate net carbon fluxes. If successful, carbon fluxes from such a remote sensing approach would form an independent and sought after measure to complement widely used dynamic global vegetation models (DGVMs).
Optical feedback in vertical-cavity surface-emitting lasers

Optical feedback in a vertical-cavity surface-emitting laser due to a fiber facet of varying position is studied in experiment and theory. Measured spectra and light-current curves show periodic variations in resonant wavelength, threshold current, differential quantum efficiency, and output power as a function of fiber position. Theoretical results were obtained using a 2 /spl times/ 2 vector propagation matrix method which models the laser and fiber in a single structure and shows good agreement with experimental results. A novel method for determining the linewidth enhancement factor /spl alpha/ by analyzing the wavelength variation as a function of fiber position is presented and a value of /spl alpha/ = 2.8 was obtained.
High Bone Turnover Is Intrinsically Harmful: Two Paths to a Similar Conclusion: The Parfitt View

At the 1993 Osteoporosis Conference in Hong Kong, Larry Riggs and myself each proposed that high bone turnover made an independent contribution to vertebral fracture risk that was not captured by bone densitometry. Riggs et al.’s proposal was based on a reanalysis of a controlled trial of dermal estrogen, mine was on a more theoretical analysis of qualitative contributions to bone fragility. We were struck by the similarity of our conclusions reached from different starting points, but our plans to write a joint paper were frustrated by the pressure of other commitments and the infrequency of our meetings. Subsequently, Riggs et al. published a more detailed version of his analysis in a symposium, and I developed my ideas in a book chapter. In their recent editorial, Riggs and Melton revisit their earlier paper and review more recent data supporting the same conclusion—that high bone turnover is intrinsically harmful. I remain in complete agreement with this conclusion, but it is necessary to define more clearly the circumstances in which it applies. Also, I believe that the mechanism I proposed in 1993 is more plausible, more subtle, and more versatile than the perforative resorption described by Drs. Riggs and Melton. For high turnover to constitute what I refer to as a mechanical threat, some horizontally oriented trabeculae must have been removed by the mechanism that our group suggested in 1983, and that was later confirmed by Eriksen et al. and endorsed by Riggs and Melton, which withdraws lateral support from the remaining vertically oriented trabeculae that bear the compressive loads. The resistance to buckling decreases as the square of the increase in unsupported length. A contributory factor is that residual vertical trabeculae slowly become thinner with increasing age. Each episode of bone remodeling that occurs on a thin unsupported vertical trabecula, as found in most women more than 5 years postmenopause, acts as a stress concentrator, and represents a focal weakness that poses a small risk of buckling, because even a normal-sized resorption cavity may penetrate halfway or more through a trabecula. For this effect, it is not necessary for the resorptive process to perforate the trabecula; being present is enough. Consequently, when turnover increases, the risk of buckling will increase within only a few weeks, as the number of resorption sites increases—it is not necessary for additional irreversible bone destruction to occur. Conversely, when turnover falls, the risk of buckling falls within a few weeks, long before there has been any measurable increase in bone mass. Such a modification of the mechanism supports Drs. Riggs and Melton’s suggestion that only a small effective dose of an antiresorptive agent may be sufficient to abrogate the mechanical threat.
Expression of Oncogenic Epidermal Growth Factor Receptor Family Kinases Induces Paclitaxel Resistance and Alters β-Tubulin Isotype Expression*

Oncogenic transformation confers resistance to chemotherapy through a variety of mechanisms, including suppression of apoptosis, increased drug metabolism, and modification of target proteins. Oncogenic epidermal growth factor receptor family members, including EGFRvIII and HER2, are expressed in a broad spectrum of human malignancies. Cell lines transfected with EGFRvIII andHER2 are more resistant to paclitaxel-mediated cytotoxicity, and tubulin polymerization induced by paclitaxel is suppressed compared with cells expressing wild type epidermal growth factor receptor. Because differential expression of β-tubulin isotypes has been proposed to modulate paclitaxel resistance, we analyzed β-tubulin isotypes expressed in cell lines transfected with different oncogenes. EGFRvIII- and HER2-expressing cells demonstrated equivalent total β-tubulin protein compared with cells transfected with wild type receptor or untransfected controls. EGFRvIII-expressing cells demonstrated increases in class IVa (2.5-fold) and IVb (3.1-fold) mRNA, and HER2-expressing cells showed increases in class IVa (2.95-fold) mRNA. Expression of oncogenic Ha-Ras did not change class IV RNA levels significantly. Inhibition of EGFRvIII kinase activity using a mutant allele with an inactivating mutation in the kinase domain decreased expression of class IVa by 50% and partially reversed resistance to paclitaxel. Expression of oncogenic epidermal growth factor receptor family members is associated with modulation of both β-tubulin isotype expression and paclitaxel resistance in cells transformed by expression of the receptor. This effect on tubulin expression may modulate drug resistance in human malignancies that express these oncogenes.
CONSTRAINTS ON SUBDUCTION GEODYNAMICS FROM SEISMIC ANISOTROPY

Much progress has been made over the past several decades in delineating the structure of subducting slabs, but several key aspects of their dynamics remain poorly constrained. Major unsolved problems in subduction geodynamics include those related to mantle wedge viscosity and rheology, slab hydration and dehydration, mechanical coupling between slabs and the ambient mantle, the geometry of mantle flow above and beneath slabs, and the interactions between slabs and deep discontinuities such as the core‐mantle boundary. Observations of seismic anisotropy can provide relatively direct constraints on mantle dynamics because of the link between deformation and the resulting anisotropy: when mantle rocks are deformed, a preferred orientation of individual mineral crystals or materials such as partial melt often develops, resulting in the directional dependence of seismic wave speeds. Measurements of seismic anisotropy thus represent a powerful tool for probing mantle dynamics in subduction systems. Here I review the observational constraints on seismic anisotropy in subduction zones and discuss how seismic data can place constraints on wedge, slab, and sub‐slab anisotropy. I also discuss constraints from mineral physics investigations and geodynamical modeling studies and how they inform our interpretation of observations. I evaluate different models in light of constraints from seismology, geodynamics, and mineral physics. Finally, I discuss some of the major unsolved problems related to the dynamics of subduction systems and how ongoing and future work on the characterization and interpretation of seismic anisotropy can lead to progress, particularly in frontier areas such as understanding slab dynamics in the deep mantle.
Paternity and relatedness in wild chimpanzee communities

The genetic structure of three contiguous wild chimpanzee communities in West Africa was examined to determine the extent to which the community, the mixed-sex social unit of chimpanzees, represents a closed reproductive unit. An analysis of paternity for 41 offspring resulted in 34 cases of paternity assignment to an adult male belonging to the same community. Among the 14 offspring for which all potential within-community fathers have been tested, one likely case of extra-group paternity (EGP) has been identified, suggesting an incidence of EGP of 7%. This more extensive analysis contradicts a previous genetic study of the Taï chimpanzees that inferred 50% extra-group fathers. We suggest, based on direct comparison of results for 33 individuals at 1 microsatellite locus and direct comparison of paternity assignments for 11 offspring, that the error rate in the previous study was too high to produce accurate genotypes and assignments of paternity and hence caused the false inference of a high rate of EGP. Thus, the community is the primary but not exclusive unit for reproduction in wild chimpanzees, and females do not typically reproduce with outside males. Despite the inferred low level of gene flow from extra-community males, relatedness levels among the community males are not significantly higher than among community females, and the distribution of genetic relationships within the group suggests that, rather than a primarily male-bonded social structure, the group is bonded through relationships between males and females. Kinship may explain cooperative behaviors directed against other communities, but is unlikely to explain the high levels of affiliation and cooperation seen for male within-community interactions.
Inhibitory effect of meloxicam, a selective cyclooxygenase‐2 inhibitor, and ciglitazone, a peroxisome proliferator‐activated receptor gamma ligand, on the growth of human ovarian cancers

It was recently reported that high expression of peroxisome proliferator‐activated receptor γ (PPARγ) and low expression of cyclooxygenase‐2 (COX‐2) might be involved in the inhibition of ovarian tumor progression and confirmed that PPARγ activation could suppress COX‐2 expression via the nuclear factor‐κB pathway in ovarian cancer cells.