bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heptose I Glycan Substitutions onNeisseria gonorrhoeaeLipooligosaccharide Influence C4b-Binding Protein Binding and Serum Resistance
Authors: Ram Sanjay , Ngampasutadol Jutamas , Cox Andrew D. , Blom Anna M. , Lewis Lisa A. , St. Michael Frank , Stupak Jacek , Gulati Sunita , Rice Peter A. 
Published: May 2007

ABSTRACTLipooligosaccharide (LOS) heptose (Hep) glycan substitutions influence gonococcal serum resistance. Several gonococcal strains bind the classical complement pathway inhibitor, C4b-binding protein (C4BP), via their porin (Por) molecule to escape complement-dependent killing by normal human serum (NHS). We show that the proximal glucose (Glc) on HepI is required for C4BP binding to Por1B-bearing gonococcal strains MS11 and 1291 but not to FA19 (Por1A). The presence of only the proximal Glc on HepI (lgtEmutant) permitted maximal C4BP binding to MS11 but not to 1291. Replacing 1291 lgtE Por with MS11 Por increased C4BP binding to levels that paralleled MS11 lgtE, suggesting that replacement of the Por1B molecule dictated the effects of HepI glycans on C4BP binding. The remainder of the strain background did not affect C4BP binding; replacing the Por of strain F62 with MS11 Por (F62 PorMS11) and truncating HepI mirrored the findings in the MS11 background. C4BP binding correlated with resistance to killing by NHS in most instances. F62 PorMS11 and itslgtEmutant were sensitive to NHS despite binding C4BP, secondary to kinetically overwhelming classical pathway activation and possibly increased alternative pathway activation (measured by factor Bb binding) by the F62 background. FA19 lgtF (HepI unsubstituted) resisted killing by only 10% NHS, not 50% NHS, despite binding levels of C4BP similar to those of FA19 and FA19 lgtE (both resistant to 50% serum), suggesting a role for the proximal Glc in serum resistance independently of C4BP binding. This study provides mechanistic insights into how HepI LOS substitutions affect the serum resistance ofN. gonorrhoeae.
Thermoregulation ofEscherichia coli hchATranscript Stability
Authors: Rasouly Aviram , Shenhar Yotam , Ron Eliora Z. 
Published: May 2007

ABSTRACTThe conserved chaperone Hsp31 ofEscherichia coliis transcribed at low temperatures by σSand repressed by H-NS, whereas at high temperature, transcription is by σ70independently of both σSand H-NS. Here we present evidence for an additional, novel, temperature-dependent control of Hsp31 expression by increased transcript stability.
Detection of the c-kit D816V mutation in systemic mastocytosis by allele-specific PCR
Authors: Schumacher J A , Elenitoba-Johnson K S J , Lim M S 
Published: May 2007

Aims:Thec-kitD816V activating mutation is found in >80% of cases of systemic mastocytosis (SM) and represents a potential drug target. Furthermore, because D816V is one of the diagnostic criteria for SM, it is clinically relevant to determine whether the mutation is present. Traditional techniques such as DNA sequencing are often not sensitive enough to detect mutations in low-abundance tumour cells, including SM. Here, an allele-specific assay to detect the D816V mutation in DNA from archived formalin-fixed paraffin-embedded tissues is described.Methods:A two-tube PCR format was employed to amplifyc-kitexon 17 as a control and an allele-specific reaction to selectively amplify the D816V mutant allele using standard oligonucleotides. A D816V-mutant plasmid control was generated by site-directed mutagenesis of wild-type cells. 14 cases of SM, one D816V-positive seminoma sample, and 35 cases without SM were analysed using the assay.Results:The assay successfully amplified D816V in the mutant plasmid control, 13/14 cases of SM, and confirmed D816V in a seminoma sample. In addition, D816V was not amplified in 35/35 cases without SM. Serial dilution experiments demonstrated sensitivity down to <1%.Conclusion:A sensitive, specific and cost-effective assay to detect the D816V mutation in archived formalin-fixed paraffin-embedded tissues from cases of SM has been developed.
Potential of the volatile-producing fungus Muscodor albus for control of building molds
Authors: Mercier Julien , Jiménez Jorge I. 
Published: May 2007

The possibility of using the volatile-producing fungus Muscodor albus for biofumigation against building molds was investigated. Several species of Aspergillus and Penicillium as well as fungi belonging to nine other genera were inhibited or killed in vitro by volatiles produced by potato dextrose agar or rye grain cultures of M. albus. Trichoderma viride was the only fungus that was not inhibited by M. albus volatiles. To test biofumigation as a preventative treatment against fungal colonization of building material, dry pieces of gypsum drywall were fumigated with grain cultures of M. albus in closed boxes. After a simulated water damage and incubation under saturated humidity for 2 weeks, untreated drywall developed natural fungal populations of about 105–106 cfu/cm2, while drywall fumigated with M. albus culture (20 g/11 L) had nondetectable fungal populations. To test for curative ability, moist pieces of drywall heavily colonized with Cladosporium cladosporioides , Aspergillus niger , or Stachybotrys chartarum were fumigated for 48 h with grain cultures of M. albus. Cladosporium cladosporioides was eliminated within 48 h, while A. niger and S. chartarum were usually more resistant. However, a longer curative fumigation of 96 h was effective in reducing A. niger or naturally occurring mold populations by about 5 log values. The production of volatile organic compounds from 20 g of rye grain culture in 11 L containers was monitored by solid-phase micro extraction and gas chromatography. Concentrations of isobutyric acid, the most abundant volatile, increased gradually in the headspace until it reached 25 μg/L (m/v) within 96 h. The second and third most abundant compounds, 2-methyl-1-butanol and isobutanol, peaked at about 10 and 5 μg/L (m/v), respectively, within the first 24 h and declined gradually afterwards.
The phytopathogenic fungi Leptosphaeria maculans and Leptosphaeria biglobosa: chemotaxonomical characterization of isolates and metabolite production in different culture media
Authors: Pedras M.  Soledade C. , Chumala Paulos B. , Yu Yang 
Published: May 2007

Previous molecular chemotaxonomic analyses of isolates of the plant pathogenic fungus Leptosphaeria maculans (Desm.) Ces. et de Not. (asexual stage Phoma lingam (Tode ex Fr.) Desm.) in a chemically defined medium suggested that this species complex was composed of at least three distinct groups. Subsequently, a group within L. maculans was classified as Leptosphaeria biglobosa , on the basis of morphologic characteristics and the lack of sexual crossing. To obtain clarification regarding the metabolite profiles of the various groups or species of blackleg fungi, the objectives of this work were (i) to determine the chemical structures of metabolites produced by Canadian V isolates and Polish-type isolates in potato dextrose broth (PDB) and (ii) to determine the chemotaxonomic relationship among French isolates of L. biglobosa and among Canadian W isolates and Thlaspi isolates of L. maculans. Here, we report for the first time that Canadian V isolates grown in PDB produced 2,4-dihydroxy-3,6-dimethylbenzaldehyde, a metabolite never reported from L. maculans, but none of the usual phytotoxins (sirodesmins). In addition, we report a new metabolite, 2-[2-(5-hydroxybenzofuranyl)]-3-(4-hydroxyphenyl)propanenitrile, from Polish-type isolates of L. maculans grown in PDB and the metabolite profiles of 16 Thlaspi isolates. The metabolite profiles of Thlaspi isolates indicate that these are part of two distinct groups, the Polish W group and the Canadian W group, i.e., L. biglobosa. Finally, we demonstrate that the metabolite profiles of the French isolates classified as L. biglobosa are similar to those of Canadian W isolates.
Detection of virulence factors in high-level gentamicin-resistant Enterococcus faecalis and Enterococcus faecium isolates from a Tunisian hospital
Authors: Klibi N. , Ben Slama K. , Sáenz Y. , Masmoudi A. , Zanetti S. , Sechi L.A. , Boudabous A. , Torres C. 
Published: May 2007

Phenotypic and genotypic determination of virulence factors were carried out in 46 high-level gentamicin-resistant (HLGR) clinical Enterococcus faecalis (n = 34) and Enterococcus faecium (n = 12) isolates recovered from different patients in La Rabta Hospital in Tunis, Tunisia, between 2000 and 2003 (all these isolates harboured the aac(6′)–aph(2″) gene). The genes encoding virulence factors (agg, gelE, ace, cylLLS, esp, cpd, and fsrB) were analysed by PCR and sequencing. The production of gelatinase and hemolysin, the adherence to caco-2 and hep-2 cells, and the capacity for biofilm formation were investigated in all 46 HLGR enterococci. The percentages of E. faecalis isolates harbouring virulence genes were as follows: gelE, cpd, and ace (100%); fsrB (62%); agg (56%); cylLLS (41.2%); and esp (26.5%). The only virulence gene detected among the 12 HLGR E. faecium isolates was esp (58%). Gelatinase activity was detected in 22 of the 34 E. faecalis isolates (65%, most of them with the gelE+–fsrB+ genotype); the remaining 12 isolates were gelatinase-negative (with the gelE+–fsrB– genotype and the deletion of a 23.9 kb fragment of the fsr locus). Overall, 64% of the cylLLS-containing E. faecalis isolates showed β-hemolysis. A high proportion of our HLGR E. faecalis isolates, in contrast to E. faecium, showed moderate or strong biofilm formation or adherence to caco-2 and hep-2 cells.
Modeling Orienting Behavior and Its Disorders with “Ecological” Neural Networks
Authors: Di Ferdinando Andrea , Parisi Domenico , Bartolomeo Paolo 
Published: May 2007

Abstract
Computational modeling is a useful tool for spelling out hypotheses in cognitive neuroscience and testing their predictions in artificial systems. Here we describe a series of simulations involving neural networks that learned to perform their task by self-organizing their internal connections. The networks controlled artificial agents with an orienting eye and an arm. Agents saw objects with various shapes and locations and learned to press a key appropriate to their shape. The results showed the following: (1) Despite being able to see the entire visual scene without moving their eye, agents learned to orient their eye toward a peripherally presented object. (2) Neural networks whose hidden layers were previously partitioned into units dedicated to eye orienting and units dedicated to arm movements learned the identification task faster and more accurately than did nonmodular networks. (3) Nonetheless, even nonmodular networks developed a similar functional segregation through self-organization of their hidden layer. (4) After partial disconnection of the hidden layer from the input layer, the lesioned agents continued to respond accurately to single stimuli, wherever they occurred, but on double simultaneous stimulation they oriented toward and responded only to the right-sided stimulus, thus simulating extinction/neglect. These results stress the generality of the advantages provided by orienting processes. Hard-wired modularity, reminiscent of the distinct cortical visual streams in the primate brain, provided further evolutionary advantages. Finally, disconnection is likely to be a mechanism of primary importance in the pathogenesis of neglect and extinction symptoms, consistent with recent evidence from animal studies and brain-damaged patients.
The Role of the Dorsolateral Prefrontal Cortex in Bimodal Divided Attention: Two Transcranial Magnetic Stimulation Studies
Authors: Johnson Jennifer Adrienne , Strafella Antonio P. , Zatorre Robert J. 
Published: May 2007

Abstract
The neural processes underlying the ability to divide attention between multiple sensory modalities remain poorly understood. To investigate the role of the dorsolateral prefrontal cortex (DLPFC) in bimodal divided attention, we completed two repetitive transcranial magnetic stimulation (rTMS) studies. We tested the hypothesis that the DLPFC is necessary in the ability to divide attention across modalities. This hypothesis originated as a result of a previous fMRI study in which the posterior DLPFC was active during a bimodal divided attention condition [Johnson, J. A., & Zatorre, R. J. Neural substrates for dividing and focusing attention between simultaneous auditory and visual events. Neuroimage, 2006]. In the current experiments, two separate groups of subjects underwent 10 min of slow rTMS to temporarily disrupt function of the DLPFC. In both groups, the ability to divide attention between unrelated auditory and visual stimuli decreased following DLPFC disruption compared to control site stimulation. Specifically, the ability to divide attention between modalities was hindered, leading to a pattern of behavior similar to bimodal selective attention (ability to attend to one or the other modality but not both). We discuss possible roles of the posterior DLPFC in bimodal divided attention and conclude that the area may be functioning to support the increased working memory load associated with divided, compared to selective attention.
Induced Gamma Band Responses Predict Recognition Delays during Object Identification
Authors: Martinovic Jasna , Gruber Thomas , Müller Matthias M. 
Published: May 2007

Abstract
Neural mechanisms of object recognition seem to rely on activity of distributed neural assemblies coordinated by synchronous firing in the gamma-band range (&gt;20 Hz). In the present electroencephalogram (EEG) study, we investigated induced gamma band activity during the naming of line drawings of upright objects and objects rotated in the image plane. Such plane-rotation paradigms elicit view-dependent processing, leading to delays in recognition of disoriented objects. Our behavioral results showed reaction time delays for rotated, as opposed to upright, images. These delays were accompanied by delays in the peak latency of induced gamma band responses (GBRs), in the absence of any effects on other measures of EEG activity. The latency of the induced GBRs has thus, for the first time, been selectively modulated by an experimental manipulation that delayed recognition. This finding indicates that induced GBRs have a genuine role as neural markers of late representational processes during object recognition. In concordance with the view that object recognition is achieved through dynamic learning processes, we propose that induced gamma band activity could be one of the possible cortical markers of such dynamic object coding.
Individual Differences in the Effects of Perceived Controllability on Pain Perception: Critical Role of the Prefrontal Cortex
Authors: Salomons Tim V. , Johnstone Tom , Backonja Misha-Miroslav , Shackman Alexander J. , Davidson Richard J. 
Published: May 2007

Abstract
The degree to which perceived controllability alters the way a stressor is experienced varies greatly among individuals. We used functional magnetic resonance imaging to examine the neural activation associated with individual differences in the impact of perceived controllability on self-reported pain perception. Subjects with greater activation in response to uncontrollable (UC) rather than controllable (C) pain in the pregenual anterior cingulate cortex (pACC), periaqueductal gray (PAG), and posterior insula/SII reported higher levels of pain during the UC versus C conditions. Conversely, subjects with greater activation in the ventral lateral prefrontal cortex (VLPFC) in anticipation of pain in the UC versus C conditions reported less pain in response to UC versus C pain. Activation in the VLPFC was significantly correlated with the acceptance and denial subscales of the COPE inventory [Carver, C. S., Scheier, M. F., & Weintraub, J. K. Assessing coping strategies: A theoretically based approach. Journal of Personality and Social Psychology, 56, 267–283, 1989], supporting the interpretation that this anticipatory activation was associated with an attempt to cope with the emotional impact of uncontrollable pain. A regression model containing the two prefrontal clusters (VLPFC and pACC) predicted 64% of the variance in pain rating difference, with activation in the two additional regions (PAG and insula/SII) predicting almost no additional variance. In addition to supporting the conclusion that the impact of perceived controllability on pain perception varies highly between individuals, these findings suggest that these effects are primarily top-down, driven by processes in regions of the prefrontal cortex previously associated with cognitive modulation of pain and emotion regulation.
Climate Response to Rapid Urban Growth: Evidence of a Human-Induced Precipitation Deficit
Authors: Kaufmann Robert K. , Seto Karen C. , Schneider Annemarie , Liu Zouting , Zhou Liming , Wang Weile 
Published: May 2007

Abstract
The authors establish the effect of urbanization on precipitation in the Pearl River Delta of China with data from an annual land use map (1988–96) derived from Landsat images and monthly climate data from 16 local meteorological stations. A statistical analysis of the relationship between climate and urban land use in concentric buffers around the stations indicates that there is a causal relationship from temporal and spatial patterns of urbanization to temporal and spatial patterns of precipitation during the dry season. Results suggest an urban precipitation deficit in which urbanization reduces local precipitation. This reduction may be caused by changes in surface hydrology that extend beyond the urban heat island effect and energy-related aerosol emissions.
Relationships between Marine Stratus Cloud Optical Depth and Temperature: Inferences from AVHRR Observations
Authors: Chang Fu-Lung , Coakley James A. 
Published: May 2007

AbstractStudies using International Satellite Cloud Climatology Project (ISCCP) data have reported decreases in cloud optical depth with increasing temperature, thereby suggesting a positive feedback in cloud optical depth as climate warms. The negative cloud optical depth and temperature relationships are questioned because ISCCP employs threshold assumptions to identify cloudy pixels that have included partly cloudy pixels. This study applies the spatial coherence technique to one month of Advanced Very High Resolution Radiometer (AVHRR) data over the Pacific Ocean to differentiate overcast pixels from the partly cloudy pixels and to reexamine the cloud optical depth–temperature relationships. For low-level marine stratus clouds studied here, retrievals from partly cloudy pixels showed 30%–50% smaller optical depths, 1°–4°C higher cloud temperatures, and slightly larger droplet effective radii, when they were compared to retrievals from the overcast pixels. Despite these biases, retrievals for the overcast and partly cloudy pixels show similar negative cloud optical depth–temperature relationships and their magnitudes agree with the ISCCP results for the midlatitude and subtropical regions. There were slightly negative droplet effective radius–temperature relationships, and considerable positive cloud liquid water content–temperature relationships indicated by aircraft measurements. However, cloud thickness decreases appear to be the main reason why cloud optical depth decreases with increasing temperature. Overall, cloud thickness thinning may explain why similar negative cloud optical depth–temperature relationships are found in both overcast and partly cloudy pixels. In addition, comparing the cloud-top temperature to the air temperature at 740 hPa indicates that cloud-top height generally rises with warming. This suggests that the cloud thinning is mainly due to the ascending of cloud base. The results presented in this study are confined to the midlatitude and subtropical Pacific and may not be applicable to the Tropics or other regions.
Onset and End of the Rainy Season in South America in Observations and the ECHAM 4.5 Atmospheric General Circulation Model
Authors: Liebmann Brant , Camargo Suzana J. , Seth Anji , Marengo José A. , Carvalho Leila M. V. , Allured Dave , Fu Rong , Vera Carolina S. 
Published: May 2007

AbstractRainfall in South America as simulated by a 24-ensemble member of the ECHAM 4.5 atmospheric general circulation model is compared and contrasted with observations (in areas in which data are available) for the period 1976–2001. Emphasis is placed on determining the onset and end of the rainy season, from which its length and rain rate are determined.It is shown that over large parts of the domain the onset and ending dates are well simulated by the model, with biases of less than 10 days. There is a tendency for model onset to occur early and ending to occur late, resulting in a simulated rainy season that is on average too long in many areas. The model wet season rain rate also tends to be larger than observed.To estimate the relative importance of errors in wet season length and rain rate in determining biases in the annual total, adjusted totals are computed by substituting both the observed climatological wet season length and rate for those of the model. Problems in the rain rate generally are more important than problems in the length.The wet season length and rain rate also contribute substantially to interannual variations in the annual total. These quantities are almost independent, and it is argued that they are each associated with different mechanisms.The observed onset dates almost always lie within the range of onset of the ensemble members, even in the areas with a large model onset bias. In some areas, though, the model does not perform well. In southern Brazil the model ensemble average onset always occurs in summer, whereas the observations show that winter is often the wettest period. Individual members, however, do occasionally show a winter rainfall peak. In southern Northeast Brazil the model has a more distinct rainy season than is observed. In the northwest Amazon the model annual cycle is shifted relative to that observed, resulting in a model bias.No interannual relationship between model and observed onset dates is expected unless onset in the model and observations has a mutual relationship with SST anomalies. In part of the near-equatorial Amazon, there does exist an interannual relationship between onset dates. Previous studies have shown that in this area there is a relationship between SST anomalies and variations in seasonal total rainfall.
Experimental Forecasts of the Indian Ocean Dipole Using a Coupled OAGCM
Authors: Luo Jing-Jia , Masson Sebastien , Behera Swadhin , Yamagata Toshio 
Published: May 2007

Abstract
The Indian Ocean Dipole (IOD) has profound socioeconomic impacts on not only the countries surrounding the Indian Ocean but also various parts of the world. A forecast system is developed based on a relatively high-resolution coupled ocean–atmosphere GCM with only sea surface temperature (SST) information assimilated. Retrospective ensemble forecasts of the IOD index for the past two decades show skillful scores with up to a 3–4-month lead and a winter prediction barrier associated with its intrinsic strong seasonal phase locking. Prediction skills of the SST anomalies in both the eastern and western Indian Ocean are higher than those of the IOD index; this is because of the influences of ENSO, which is highly predictable. The model predicts the extreme positive IOD event in 1994 at a 2–3-season lead. The strong 1997 cold signal in the eastern pole, however, is not well predicted owing to errors in model initial subsurface conditions. The real-time forecast system with more ensembles successfully predicted the weak negative IOD event in the 2005 boreal fall and La Niña condition in the 2005/06 winter. Recent experimental real-time forecasts showed that a positive IOD event would appear in the 2006 summer and fall accompanied by a possible weak El Niño condition in the equatorial Pacific.