julilili42/papers huggingface dataset:
Characterization of the Oxygen-Responsive NreABC Regulon of Staphylococcus aureus
2008-09-27

ABSTRACT Here, we investigate the functionality of the oxygen-responsive nitrogen regulation system NreABC in the human pathogen Staphylococcus aureus and evaluate its role in anaerobic gene regulation and virulence factor expression. Deletion of nreABC resulted in severe impairment of dissimilatory nitrate and nitrite reduction and led to a small-colony phenotype in the presence of nitrate during anaerobic growth. For characterization of the NreABC regulon, comparative DNA microarray and proteomic analyses between the wild type and nreABC mutant were performed under anoxic conditions in the absence and presence of nitrate. A reduced expression of virulence factors was not observed in the mutant. However, both the transcription of genes involved in nitrate and nitrite reduction and the accumulation of corresponding proteins were highly decreased in the nreABC mutant, which was unable to utilize nitrate as a respiratory oxidant and, hence, was forced to use fermentative pathways. These data were corroborated by the quantification of the extracellular metabolites lactate and acetate. Using an Escherichia coli -compatible two-plasmid system, the activation of the promoters of the nitrate and nitrite reductase operons and of the putative nitrate/nitrite transporter gene narK by NreBC was confirmed. Overall, our data indicate that NreABC is very likely a specific regulation system that is essential for the transcriptional activation of genes involved in dissimilatory reduction and transport of nitrate and nitrite. The study underscores the importance of NreABC as a fitness factor for S. aureus in anoxic environments.
Involvement of the auditory brainstem system in spinocerebellar ataxia type 2 (SCA2), type 3 (SCA3) and type 7 (SCA7)
2008-09-29

Aims: The spinocerebellar ataxia type 2 (SCA2), type 3 (SCA3) and type 7 (SCA7) are clinically characterized by progressive and severe ataxic symptoms, dysarthria, dysphagia, oculomotor impairments, pyramidal and extrapyramidal manifestations and sensory deficits. Although recent clinical studies reported additional disease signs suggesting involvement of the brainstem auditory system, this has never been studied in detail in SCA2, SCA3 or SCA7. Methods: We performed a detailed pathoanatomical investigation of unconventionally thick tissue sections through the auditory brainstem nuclei (that is, nucleus of the inferior colliculus, nuclei of the lateral lemniscus, superior olive, cochlear nuclei) and auditory brainstem fibre tracts (that is, lateral lemniscus, trapezoid body, dorsal acoustic stria, cochlear portion of the vestibulocochlear nerve) of clinically diagnosed and genetically confirmed SCA2, SCA3 and SCA7 patients. Results: Examination of unconventionally thick serial brainstem sections stained for lipofuscin pigment and Nissl material revealed a consistent and widespread involvement of the auditory brainstem nuclei in the SCA2, SCA3 and SCA7 patients studied. Serial brainstem tissue sections stained for myelin showed loss of myelinated fibres in two of the auditory brainstem fibre tracts (that is, lateral lemniscus, trapezoid body) in a subset of patients. Conclusions: The involvement of the auditory brainstem system offers plausible explanations for the auditory impairments detected in some of our and other SCA2, SCA3 and SCA7 patients upon bedside examination or neurophysiological investigation. However, further clinical studies are required to resolve the striking discrepancy between the consistent involvement of the brainstem auditory system observed in this study and the comparatively low frequency of reported auditory impairments in SCA2, SCA3 and SCA7 patients.
Die Kristallstrukturen der Komplexe [Ni(en)3][(DMC)2], [Cu(en)2(DMC)][DMC] und [Zn(en)(DMC)2] (en = Ethylendiamin, DMCH = 1,3‐Dimethylcyanursäure); ein Beitrag zur Konkurrenz anionischer und neutraler Liganden um die Koordinationssphäre zweiwertiger 3d‐Metalle
2008-09-29

Abstract The Crystal Structures of the Complexes [Ni(en) 3 ][(DMC) 2 ], [Cu(en) 2 (DMC)][DMC], and Zn(en)(DMC) 2 (en = Ethylenediamine, DMCH = 1,3‐Dimethylcyanuric Acid); a Contribution to the Competition of Anionic and Neutral Ligands for the Coordination Sphere of Divalent 3d‐Metals The complexes [Ni(en) 3 ][(DMC) 2 ] ( 4 ), [Cu(en) 2 (DMC)][DMC] ( 5 ), and [Zn(en)(DMC) 2 ] ( 6 ) are obtained from the reactions of aqueous (LiDMC) 2 ·4 H 2 O solutions with NiCl 2 , CuSO 4 , and ZnCl 2 , respectively, in the presence of ethylenediamine (DMCH = 1,3‐dimethylcyanuric acid, 2 ; en = ethylenediamine). In the solid state, the complexes exhibit both coordinated and uncoordinated DMC anions. The crystal structures of 4 , 5 , and 6 are discussed.
Group diversity and group identification: The moderating role of diversity beliefs
2008-09-30

Research on diversity in teams and organizations has revealed ambiguous results regarding the effects of group composition on workgroup performance. The categorization—elaboration model (van Knippenberg et al., 2004) accounts for this variety and proposes two different underlying processes. On the one hand diversity may bring about intergroup bias which leads to less group identification, which in turn is followed by more conflict and decreased workgroup performance. On the other hand, the information processing approach proposes positive effects of diversity because of a more elaborate processing of information brought about by a wider pool and variety of perspectives in more diverse groups. We propose that the former process is contingent on individual team members' beliefs that diversity is good or bad for achieving the team's aims. We predict that the relationship between subjective diversity and identification is more positive in ethnically diverse project teams when group members hold beliefs that are pro-diversity. Results of two longitudinal studies involving postgraduate students working in project teams confirm this hypothesis. Analyses further reveal that group identification is positively related to students' desire to stay in their groups and to their information elaboration. Finally, we found evidence for the expected moderated mediation model with indirect effects of subjective diversity on elaboration and the desire to stay, mediated through group identification, moderated by diversity beliefs.
Reentrant Condensation of Proteins in Solution Induced by Multivalent Counterions
2008-09-30

Negatively charged globular proteins in solution undergo a condensation upon adding trivalent counterions between two critical concentrations C and C, C <C. This reentrant condensation behavior above C is caused by short-ranged electrostatic interactions between multivalent cations and acidic residues, mechanistically different from the case of DNA. Small-angle x-ray scattering indicates a short-ranged attraction between counterion-bound proteins near C and C. Monte Carlo simulations (under these strong electrostatic coupling conditions) support an effective inversion of charge on surface side chains through binding of the multivalent counterions.
Do long-term results justify decompressive craniectomy after severe traumatic brain injury?
2008-09-30

Object A decompressive craniectomy can be a life-saving procedure to relieve critically increased intracranial pressure. The survival of a patient is important as well as the subsequent and long-term quality of life. In this paper the authors' goal was to investigate whether long-term clinical results justify the use of a decompressive craniectomy. Methods Thirty-three patients (20 males and 13 females) with a mean age of 36.3 years (range 13–60 years) with severe traumatic brain injury (Grades III and IV) and subsequent massive brain swelling were examined. For postoperative assessment the Barthel Index was used. A surgical intervention was based on the following criteria: 1) The intracranial pressure could not be controlled by conservative treatment and constantly exceeded 30 mm Hg (cerebral perfusion pressure &lt; 50 mm Hg). 2) Transcranial Doppler ultrasonography revealed only a systolic flow pattern or systolic peaks. 3) There were no other major injuries. 4) The patient was not older than 60 years. Results One-fifth of all patients died and one-fifth remained in a vegetative state. Mild deficits were seen in 6 of 33 patients. A full rehabilitation (Barthel Index 90–100) was achieved in 13 patients (39.4%). Five patients could resume their former occupation, and another 4 had to change jobs. Conclusions Age remains to be one of the most important exclusion factors. Decompressive craniectomy provided good clinical results in nearly 40% of patients who were otherwise most likely to die. Therefore, long-term results justify the use of decompressive craniectomy in this case series.
From recording linguistic competence to supporting inferences about language acquisition in context
2008-09-30

Abstract Student models for Intelligent Computer Assisted Language Learning (ICALL) have largely focused on the acquisition of grammatical structures. In this paper, we motivate a broader perspective of student models for ICALL that incorporates insights from current research on second language acquisition and language testing. We argue for a student model that includes a representation of the learner's ability to use language in context and to perform tasks, as well as for an explicit activity model that provides information on the language tasks and the inferences for the student model they support. The student model architecture we present is being developed as part of the TAGARELA system, an intelligent workbook supporting the instruction of Portuguese. Keywords: Intelligent Computer-Assisted Language Learning (ICALL)intelligent tutoring systems (ITS)natural language processing (NLP)second language acquisition (SLA)student modellearner modelactivity modeltask appropriatenesstask strategiesL1 transfer Acknowledgements For helpful discussion and suggestions, we would like to thank the ICALL research group (http://purl.org/net/icall) at the Ohio State University, where we developed the work reported here: Susan Bull, Trude Heift, Donna Long, Kathy McCoy, Bob Mislevy, Scott Payne, Mathias Schulze and the reviewers of UserModeling 2007, where an earlier version of our proposal was presented (Amaral & Meurers, Citation2007a). Notes 1. This simplification was necessary at this stage of the project development for purely practical reasons. 2. For expository reasons, this example uses the inverse scenario of TAGARELA, which is used by Americans learning Portuguese.
Smart Camera Based Monitoring System and Its Application to Assisted Living
2008-10-01

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Western societies are aging rapidly. An automated 24/7 surveillance to ensure safety of the elderly while respecting privacy becomes a major challenge. At the same time this is representative of novel and emerging video surveillance applications discovered lately besides the classic surveillance protection applications in airports, government buildings, and industrial plants. Three problems of current surveillance systems are identified. A distributed and automated smart camera based approach is proposed that addresses these problems. The proposed system's goal set is to analyze the real world and reflect all relevant—and only relevant—information live in an integrated virtual counterpart for visualization. It covers georeferenced person tracking and activity recognition (falling person detection). A prototype system installed in a home for assisted living has been running 24/7 for several months now and shows quite promising performance. </para>
Retinal detachment after phacoemulsification in high myopia: Analysis of 2356 cases
2008-10-01

The risk for postoperative RD in this study (1.5% to 2.2%) corresponds to the incidence of pseudophakic RD and idiopathic RD in myopia described in the literature. The risk profile for postoperative RD in this series cannot be distinguished from the risk profile for idiopathic RD in myopia of this extent. The true effect of prophylactic treatment of degenerative lesions remains to be elucidated.
Rooting and Dating Maples (Acer) with an Uncorrelated-Rates Molecular Clock: Implications for North American/Asian Disjunctions
2008-10-01

Abstract.—Simulations suggest that molecular clock analyses can correctly identify the root of a tree even when the clock assumption is severely violated. Clock-based rooting of phylogenies may be particularly useful when outgroup rooting is problematic. Here, we explore relaxed-clock rooting in the Acer/Dipteronia clade of Sapindaceae, which comprises genera of highly uneven species richness and problematic mutual monophyly. Using an approach that does not presuppose rate autocorrelation between ancestral and descendant branches and hence does not require a rooted a priori topology, we analyzed data from up to seven chloroplast loci for some 50 ingroup species. For comparison, we used midpoint and outgroup rooting and dating methods that rely on rooted input trees, namely penalized likelihood, a Bayesian autocorrelated-rates model, and a strict clock. The chloroplast sequences used here reject a single global substitution rate, and the assumption of autocorrelated rates was also rejected. The root was placed between Acer and Dipteronia by all three rooting methods, albeit with low statistical support. Analyses of Acer diversification with a lineage-through-time plot and different survival models, although sensitive to missing data, suggest a gradual decrease in the average diversification rate. The nine North American species of Acer diverged from their nearest relatives at widely different times: eastern American Acer diverged
Long-Term Follow-up of Retinitis Pigmentosa Patients with Multifocal Electroretinography
2008-10-01

The mfERG allows long-term follow-up of disease progression in retinitis pigmentosa. It does not replace, but complements psychophysical methods and could be used as an objective outcome measure in upcoming treatment studies involving patients with advanced retinal diseases.
Giant outburst of EXO 2030+375: pulse-phase resolved analysis of INTEGRAL data
2008-10-01

In June-September 2006 the Be/X-ray binary EXO 2030+375 experienced the second giant outburst since its discovery. The source was shown to have a complicated pulse-averaged X-ray spectral continuum with possible evidence of cyclotron absorption features. In this paper we present the first pulse-phase resolved analysis of the broad band X-ray spectra of EXO 2030+375 obtained with the INTEGRAL observatory close to the maximum and during the decay phase of the giant outburst. We report a strong variability of the spectrum with pulse phase. Alternative spectral continuum models are discussed. The dependence of the spectral parameters on pulse phase during the maximum of the outburst and the evolution of the pulse profiles with time are qualitatively consistent with the pulsar's emission diagram changing from the fan-beam geometry close to the maximum of the outburst to a combination of pencil and fan beams (of comparable intesities) at the end of the decay phase. Evidence of a cyclotron absorption line around 63 keV at the pulse phase interval preceeding the main peak of the pulse profile is present in the spectrum obtained close to the maximum of the outburst.
CD203c is Overexpressed on Neoplastic Mast Cells in Systemic Mastocytosis and is Upregulated upon IgE Receptor Cross-Linking
2008-10-01

The ectoenzyme E-NPP3 (CD203c) has recently been identified as a novel activation-linked cell surface antigen on basophils. In the present study, we examined expression of CD203c on normal mast cells (MC) and bone marrow (bm) MC derived from 85 patients with systemic mastocytosis (SM), including cases with indolent SM (ISM, n=72), SM with associated clonal hematologic non-MC-lineage disease (SM-AHNMD, n=6), aggressive SM (ASM, n=3), and mast cell leukemia (MCL, n=4). Surface expression of CD203c was analyzed by multicolor flow cytometry. In patients with SM, bm MC expressed significantly higher amounts of CD203c compared to normal bm MC (median MFI in controls: 260 versus median MFI in SM: 516, p&lt;0.05). Slightly lower amounts of CD203c were detected on MC in SM-AHNMD and ASM compared to ISM. To demonstrate CD203c expression in MC at the mRNA level, neoplastic MC were highly enriched by cell sorting, and were found to express CD203c mRNA in RT-PCR analysis. Cross-linking of the IgE receptor on MC resulted in a substantial upregulation of CD203c, whereas the KIT-ligand stem cell factor (SCF) showed no significant effects. In conclusion, CD203c is a novel activation-linked surface antigen on MC that is upregulated in response to IgE receptor cross-linking and is overexpressed on neoplastic MC in patients with SM.
T cell-mediated help against tumors
2008-10-01

Adoptive transfer of tumor antigen-specific T helper (Th) cells is a surprisingly potent anti-tumor therapy. Even in RIP1-Tag2 mice with a rapidly growing, aggressive endogenous beta cell tumor Th can significantly extend life time and are more efficient than any other therapy studied. The therapeutic effect of Th cells seems to be independent of tumor cell destruction. It critically relies on three principles: (1) inhibition of tumor angiogenesis, (2) inhibition of beta cell proliferation, and (3) induction of tumor dormancy. As tumor cell destruction by cytotoxic CD8(+) T cells (CTL) largely failed in tumor therapy, induction of tumor dormancy by Th cell-mediated immune responses represents a novel therapeutic option that may be combined with other cytotoxic regimens, e.g., radio- and/or chemotherapy, as it is established for bone marrow transplantation. Importantly, Th cell efficacy strictly requires interferon gamma (IFNgamma) signaling, and in the absence of IFNgamma, Th cells may even worsen tumor diseases. Therefore, using the immune system to control tumor dormancy represents a novel approach, especially as therapy of tumors resistant to conventional therapies. Yet, it is important to underline that Th cell-based antitumor effects critically depend on a functional cytokine network, especially appropriate IFNgamma signaling.
Evolution of microstructure and melt topology in partially molten granitic mylonite: Implications for rheology of felsic middle crust
2008-10-01

The deformation study of midcrustal porphyritic granite reveals exceptionally high strain intensities of feldspar aggregates compared to stronger quartz. Three types of microstructures corresponding to evolutionary stages of deformed granite were recognized: (1) the metagranite marked by viscous flow of plagioclase around strong alkali feldspar and quartz, (2) quartz augen orthogneiss characterized by development of banded mylonitic structure of recrystallized plagioclase and K‐feldspar surrounding augens of quartz, and (3) banded mylonite characterized by alternation of quartz ribbons and mixed aggregates of feldspars and quartz. The original weakening of alkali feldspar is achieved by decomposition into albite chains and K‐feldspar resulting from a heterogeneous nucleation process. The subsequent collapse of alkaline feldspar and development of monomineralic layering is attributed to the onset of syn‐deformational dehydration melting of Mu‐Bi layers associated with production of ∼2% melt. The final deformation stage is marked by mixing of feldspars which is explained by higher melt production due to introduction of external water. An already small amount of melt is responsible for extreme weakening of the feldspar because of Melt Connectivity Threshold effect triggering grain boundary sliding deformation mechanisms. The grain boundary sliding controls diffusion creep at small melt fraction and evolves to particulate flow at high melt fractions. Strong quartz shows a dislocation creep deformation mechanism throughout the whole deformation history marked by variations in the activity of the slip systems, which are attributed to variations in stress and strain rate partitioning with regard to changing rheological properties of the deforming feldspars.
Differential dependency on motion coherence in subregions of the human MT+ complex
2008-10-01

Abstract The detection of coherent motion embedded in noise has been widely used as a measure of global visual motion processing. Animal studies have demonstrated that this performance is closely linked to the responses of direction‐sensitive neurons in the macaque middle temporal (MT) and medial superior temporal (MST) areas. Despite the strong similarities between the visual cortex of human and that of non‐human primates, the human middle temporal complex (area MT+), located in the posterior part of the inferior temporal sulcus and presumably comprising both area MT and area MST, has not consistently been found to share the functional hallmark of MT and MST neurons, i.e. their preference for coherent rather than incoherent visual motion. In order to search for such preferences in human area MT+, blood oxygen level‐dependent responses to random dot kinematograms presented in the right visual hemifield were studied here as a function of stimulus size and dot density. The stimulus extensions were varied in such a way as to cover an area either equaling, exceeding or falling below the mean receptive field size of macaque area MT. Unlike the posterior part of human area MT+, the anterior part and its right‐hemisphere homolog showed significantly stronger responses to coherent than to incoherent motion. These differences were only present for large stimuli that presumably exceeded the receptive field size of neurons in area MT. Our results suggest that functional magnetic resonance imaging may reveal stronger responses to coherent visual motion in human area MST, provided that the stimulus allows for sufficient summation within the receptive fields. In contrast, functional magnetic resonance imaging may fail to reveal the same dependency for human area MT.
Distributed model predictive control for coordinated path following control of omnidirectional mobile robots
2008-10-01

This paper considers the problem of steering and coordinating a group of omnidirectional mobile robots along given paths. Two subproblems, i.e., a path following subproblem and a motion coordination subproblem are solved by using distributed nonlinear model predictive control (NMPC) whose cost function is coupled with neighbors. The distinct features of NMPC are that constraints can be explicitly accommodated, as well as nonlinear and time-varying systems can be easily handled. An idea of morphing is employed to generate intermediate configurations between a source and a target configuration with a desired transition rate. Each mobile robot adjusts its own speed along its reference path to achieve motion coordination. Experiments with three omnidirectional mobile robots are presented to illustrate the validity of our proposed method. Unlike nonholonomic mobile robots, omnidirectional mobile robots have simultaneously and independently controlled rotational and translational motion capabilities.