Looking at the Gregory-Laflamme instability through quasinormal modes

We study evolution of gravitational perturbations of black strings. It is well known that for all wave numbers less than some threshold value, the black string is unstable against the scalar type of gravitational perturbations, which is named the Gregory-Laflamme instability. Using numerical methods, we find the quasinormal modes and time-domain profiles of the black string perturbations in the stable sector and also show the appearance of the Gregory-Laflamme instability in the time domain. The dependence of the black string quasinormal spectrum and late-time tails on such parameters as the wave vector and the number of extra dimensions is discussed. There is numerical evidence that at the threshold point of instability, the static solution of the wave equation is dominant. For wave numbers slightly larger than the threshold value, in the region of stability, we see tiny oscillations with very small damping rate. While, for wave numbers slightly smaller than the threshold value, in the region of the Gregory-Laflamme instability, we observe tiny oscillations with very small growth rate. We also find the level crossing of imaginary part of quasinormal modes between the fundamental mode and the first overtone mode, which accounts for the peculiar time domain profiles.

Sub-telomere directed gene expression during initiation of invasive aspergillosis

Aspergillus fumigatus is a common mould whose spores are a component of the normal airborne flora. Immune dysfunction permits developmental growth of inhaled spores in the human lung causing aspergillosis, a significant threat to human health in the form of allergic, and life-threatening invasive infections. The success of A. fumigatus as a pathogen is unique among close phylogenetic relatives and is poorly characterised at the molecular level. Recent genome sequencing of several Aspergillus species provides an exceptional opportunity to analyse fungal virulence attributes within a genomic and evolutionary context. To identify genes preferentially expressed during adaptation to the mammalian host niche, we generated multiple gene expression profiles from minute samplings of A. fumigatus germlings during initiation of murine infection. They reveal a highly co-ordinated A. fumigatus gene expression programme, governing metabolic and physiological adaptation, which allows the organism to prosper within the mammalian niche. As functions of phylogenetic conservation and genetic locus, 28% and 30%, respectively, of the A. fumigatus subtelomeric and lineage-specific gene repertoires are induced relative to laboratory culture, and physically clustered genes including loci directing pseurotin, gliotoxin and siderophore biosyntheses are a prominent feature. Locationally biased A. fumigatus gene expression is not prompted by in vitro iron limitation, acid, alkaline, anaerobic or oxidative stress. However, subtelomeric gene expression is favoured following ex vivo neutrophil exposure and in comparative analyses of richly and poorly nourished laboratory cultured germlings. We found remarkable concordance between the A. fumigatus host-adaptation transcriptome and those resulting from in vitro iron depletion, alkaline shift, nitrogen starvation and loss of the methyltransferase LaeA. This first transcriptional snapshot of a fungal genome during initiation of mammalian infection provides the global perspective required to direct much-needed diagnostic and therapeutic strategies and reveals genome organisation and subtelomeric diversity as potential driving forces in the evolution of pathogenicity in the genus Aspergillus.

Genetic Background of Patients from a University Medical Center in Manhattan: Implications for Personalized Medicine

Background: The rapid progress currently being made in genomic science has created interest in potential clinical applications; however, formal translational research has been limited thus far. Studies of population genetics have demonstrated substantial variation in allele frequencies and haplotype structure at loci of medical relevance and the genetic background of patient cohorts may often be complex. Methods and Findings: To describe the heterogeneity in an unselected clinical sample we used the Affymetrix 6.0 gene array chip to genotype self-identified European Americans (N = 326), African Americans (N = 324) and Hispanics (N = 327) from the medical practice of Mount Sinai Medical Center in Manhattan, NY. Additional data from US minority groups and Brazil were used for external comparison. Substantial variation in ancestral origin was observed for both African Americans and Hispanics; data from the latter group overlapped with both Mexican Americans and Brazilians in the external data sets. A pooled analysis of the African Americans and Hispanics from NY demonstrated a broad continuum of ancestral origin making classification by race/ethnicity uninformative. Selected loci harboring variants associated with medical traits and drug response confirmed substantial within-and between-group heterogeneity. Conclusion: As a consequence of these complementary levels of heterogeneity group labels offered no guidance at the individual level. These findings demonstrate the complexity involved in clinical translation of the results from genome-wide association studies and suggest that in the genomic era conventional racial/ethnic labels are of little value.

Increased Occurrence of Dental Anomalies Associated with Second-Premolar Agenesis

Objective: To evaluate the prevalence of dental anomalies in patients with agenesis of second premolars and compare the findings with the prevalence of these anomalies in the general population. Materials and Methods: A Brazilian sample of 203 patients aged 8 to 22 years was selected. All patients presented agenesis of at least one second premolar. Panoramic and periapical radiographs and dental casts were used to analyze the presence of other associated dental anomalies, including agenesis of other permanent teeth, ectopia of unerupted permanent teeth, infraocclusion of deciduous molars, microdontia of maxillary lateral incisors, and supernumerary teeth. The occurrence of these anomalies was compared with occurrence data previously reported for the general population. Statistical testing was performed using the chi-square test (P < .05) and the odds ratio. Results: The sample with agenesis of at least one second premolar presented a significantly increased prevalence rate of permanent tooth agenesis (21%), excluding third molars. Among the sample segment aged 14 years or greater (N = 77), occurrence of third-molar agenesis (48%) exceeded twice its normal frequency. Significant increases in occurrence of microdontia of maxillary lateral incisors (20.6%), infraocclusion of deciduous molars (24.6%), and distoangulation of mandibular second premolars (7.8%) were observed. Palatally displaced canine anomaly was also significantly elevated (8.1%). Conclusion: The results provide evidence that agenesis of other permanent teeth, microdontia, deciduous molar infraocclusion, and certain dental ectopias are the products of the same genetic mechanisms that cause second-premolar agenesis. (Angle Orthod. 2009;79:436-441.)

Identification and Phylogenetic Analysis of Heme Synthesis Genes in Trypanosomatids and Their Bacterial Endosymbionts

It has been known for decades that some insect-infecting trypanosomatids can survive in culture without heme supplementation while others cannot, and that this capability is associated with the presence of a betaproteobacterial endosymbiont in the flagellate's cytoplasm. However, the specific mechanisms involved in this process remained obscure. In this work, we sequence and phylogenetically analyze the heme pathway genes from the symbionts and from their hosts, as well as from a number of heme synthesis-deficient Kinetoplastida. Our results show that the enzymes responsible for synthesis of heme are encoded on the symbiont genomes and produced in close cooperation with the flagellate host. Our evidence suggests that this synergistic relationship is the end result of a history of extensive gene loss and multiple lateral gene transfer events in different branches of the phylogeny of the Trypanosomatidae.

Search for Active Neutrino Disappearance Using Neutral-Current Interactions in the MINOS Long-Baseline Experiment

We report the first detailed comparisons of the rates and spectra of neutral-current neutrino interactions at two widely separated locations. A depletion in the rate at the far site would indicate mixing between nu(mu) and a sterile particle. No anomalous depletion in the reconstructed energy spectrum is observed. Assuming oscillations occur at a single mass-squared splitting, a fit to the neutral- and charged-current energy spectra limits the fraction of nu(mu) oscillating to a sterile neutrino to be below 0.68 at 90% confidence level. A less stringent limit due to a possible contribution to the measured neutral-current event rate at the far site from nu(e) appearance at the current experimental limit is also presented.

Testing Lorentz Invariance and CPT Conservation with NuMI Neutrinos in the MINOS Near Detector

A search for a sidereal modulation in the MINOS near detector neutrino data was performed. If present, this signature could be a consequence of Lorentz and CPT violation as predicted by the effective field theory called the standard-model extension. No evidence for a sidereal signal in the data set was found, implying that there is no significant change in neutrino propagation that depends on the direction of the neutrino beam in a sun-centered inertial frame. Upper limits on the magnitudes of the Lorentz and CPT violating terms in the standard-model extension lie between 10(-4) and 10(-2) of the maximum expected, assuming a suppression of these signatures by a factor of 10(-17).

Measurement of neutrino oscillations with the MINOS detectors in the NuMI beam

This Letter reports new results from the MINOS experiment based on a two-year exposure to muon neutrinos from the Fermilab NuMI beam. Our data are consistent with quantum-mechanical oscillations of neutrino flavor with mass splitting vertical bar Delta m(2)vertical bar = (2.43 +/- 0.13) x 10(-3) eV(2) (68% C.L.) and mixing angle sin(2)(2 theta) > 0.90 (90% C.L.). Our data disfavor two alternative explanations for the disappearance of neutrinos in flight: namely, neutrino decays into lighter particles and quantum decoherence of neutrinos, at the 3.7 and 5.7 standard-deviation levels, respectively.

Evolution of perturbations of squashed Kaluza-Klein black holes: Escape from instability

The squashed Kaluza-Klien (KK) black holes differ from the Schwarzschild black holes with asymptotic flatness or the black strings even at energies for which the KK modes are not excited yet, so that squashed KK black holes open a window in higher dimensions. Another important feature is that the squashed KK black holes are apparently stable and, thereby, let us avoid the Gregory-Laflamme instability. In the present paper, the evolution of scalar and gravitational perturbations in time and frequency domains is considered for these squashed KK black holes. The scalar field perturbations are analyzed for general rotating squashed KK black holes. Gravitational perturbations for the so-called zero mode are shown to be decayed for nonrotating black holes, in concordance with the stability of the squashed KK black holes. The correlation of quasinormal frequencies with the size of extra dimension is discussed.

Novel pathogenic mutations and skin biopsy analysis in Knobloch syndrome

Purpose: To facilitate future diagnosis of Knobloch syndrome (KS) and better understand its etiology, we sought to identify not yet described COL18A1 mutations in KS patients. In addition, we tested whether mutations in this gene lead to absence of the COL18A1 gene product and attempted to better characterize the functional effect of a previously reported missense mutation. Methods: Direct sequencing of COL18A1 exons was performed in KS patients from four unrelated pedigrees. We used immunofluorescent histochemistry in skin biopsies to evaluate the presence of type XVIII collagen in four KS patients carrying two already described mutations: c. 3277C>T, a nonsense mutation, and c. 3601G>A, a missense mutation. Furthermore, we determined the binding properties of the mutated endostatin domain p.A1381T (c.3601G>A) to extracellular matrix proteins using ELISA and surface plasmon resonance assays. Results: We identified four novel mutations in COL18A1, including a large deletion involving exon 41. Skin biopsies from KS patients revealed lack of type XVIII collagen in epithelial basement membranes and blood vessels. We also found a reduced affinity of p.A1381T endostatin to some extracellular matrix components. Conclusions: COL18A1 mutations involved in Knobloch syndrome have a distribution bias toward the coding exons of the C-terminal end. Large deletions must also be considered when point mutations are not identified in patients with characteristic KS phenotype. We report, for the first time, lack of type XVIII collagen in KS patients by immunofluorescent histochemistry in skin biopsy samples. As a final point, we suggest the employment of this technique as a preliminary and complementary test for diagnosis of KS in cases when mutation screening either does not detect mutations or reveals mutations of uncertain effect, such as the p.A1381T change.

Schistosoma mansoni Tegument Protein Sm29 Is Able to Induce a Th1-Type of Immune Response and Protection against Parasite Infection

Background: Schistosomiasis continues to be a significant public health problem. This disease affects 200 million people worldwide and almost 800 million people are at risk of acquiring the infection. Although vaccine development against this disease has experienced more failures than successes, encouraging results have recently been obtained using membrane-spanning protein antigens from the tegument of Schistosoma mansoni. Our group recently identified Sm29, another antigen that is present at the adult worm tegument surface. In this study, we investigated murine cellular immune responses to recombinant (r) Sm29 and tested this protein as a vaccine candidate. Methods and Findings: We first show that Sm29 is located on the surface of adult worms and lung-stage schistosomula through confocal microscopy. Next, immunization of mice with rSm29 engendered 51%, 60% and 50% reduction in adult worm burdens, in intestinal eggs and in liver granuloma counts, respectively (p<0.05). Protective immunity in mice was associated with high titers of specific anti-Sm29 IgG1 and IgG2a and elevated production of IFN-gamma, TNF-alpha and IL-12, a typical Th1 response. Gene expression analysis of worms recovered from rSm29 vaccinated mice relative to worms from control mice revealed a significant (q<0.01) down-regulation of 495 genes and up-regulation of only 22 genes. Among down-regulated genes, many of them encode surface antigens and proteins associated with immune signals, suggesting that under immune attack schistosomes reduce the expression of critical surface proteins. Conclusion: This study demonstrates that Sm29 surface protein is a new vaccine candidate against schistosomiasis and suggests that Sm29 vaccination associated with other protective critical surface antigens is the next logical strategy for improving protection.

Dynamics of carbon, biomass, and structure in two Amazonian forests

Amazon forests are potentially globally significant sources or sinks for atmospheric carbon dioxide. In this study, we characterize the spatial trends in carbon storage and fluxes in both live and dead biomass (necromass) in two Amazonian forests, the Biological Dynamic of Forest Fragments Project (BDFFP), near Manaus, Amazonas, and the Tapajos National Forest (TNF) near Santarem, Para. We assessed coarse woody debris (CWD) stocks, tree growth, mortality, and recruitment in ground-based plots distributed across the terra firme forest at both sites. Carbon dynamics were similar within each site, but differed significantly between the sites. The BDFFP and the TNF held comparable live biomass (167 +/- 7.6 MgC.ha(-1) versus 149 +/- 6.0 MgC.ha(-1), respectively), but stocks of CWD were 2.5 times larger at TNF (16.2 +/- 1.5 MgC.ha(-1) at BDFFP, versus 40.1 +/- 3.9 MgC.ha(-1) at TNF). A model of current forest dynamics suggests that the BDFFP was close to carbon balance, and its size class structure approximated a steady state. The TNF, by contrast, showed rapid carbon accrual to live biomass (3.24 +/- 0.22 MgC.ha(-1).a(-1) in TNF, 2.59 +/- 0.16 MgC.ha(-1).a(-1) in BDFFP), which was more than offset by losses from large stocks of CWD, as well as ongoing shifts of biomass among size classes. This pattern in the TNF suggests recovery from a significant disturbance. The net loss of carbon from the TNF will likely last 10 - 15 years after the initial disturbance (controlled by the rate of decay of coarse woody debris), followed by uptake of carbon as the forest size class structure and composition continue to shift. The frequency and longevity of forests showing such disequilibruim dynamics within the larger matrix of the Amazon remains an essential question to understanding Amazonian carbon balance.

Hormonal, metabolic and perceptual responses to different resistance training systems

Aim. The purpose of the present study was to compare the effect of different resistance training systems (Multiple-set [MS] and Pyramid [P]) on hormonal, metabolic and perceptual markers of internal load. Methods. Ten healthy men performed two resistance training sessions (MS and P) which consisted of three exercises (bench press, peck deck and decline bench press) with the same total volume of load lifted. The training sessions were performed 14 days apart and allocated in a counter-balanced order. Hormonal (plasma insulin, growth hormone [GH], testosterone and cortisol) and metabolic (blood glucose and lactate) responses were assessed before and after each exercise bout. Session rating of perceived exertion (session RPE) was taken 30-min following each bout. Results. No difference was observed for session-RPE between P and MS bouts (P>0.05). Plasma GH, cortisol and lactate increased significantly after exercise both bouts (P<0.01), but there were no significant changes between MS and P (P>0.05). Conclusion. It is concluded that the acute bout of resistance exercise following MS and P systems provide similar training strain when the total volume of load lifted is matched.

Modeling of Plastic Deformation Effects in Ferromagnetic Thin Films

To explain the magnetic behavior of plastic deformation of thin magnetic films (Fe and permalloy) on an elastic substrate (nitinol), it is noted that unlike in the bulk, the dislocation density does not increase dramatically because of the dimensional constraint. As a result, the resulting residual stress, even though strain hardening is limited, dominates the observed magnetic behavior. Thus, with the field parallel to the stress axis, the compressive residual stress resulting from plastic deformation causes a decrease in remanence and an increase in coercivity; and with the field perpendicular to the stress axis, the resulting compressive residual stress causes an increase in remanence and a decrease in coercivity. These elements have been inserted into the model previously developed for plastic deformation in the bulk, producing the aforementioned behavior, which has been observed experimentally in the films.

Two physically, functionally, and developmentally distinct peritoneal macrophage subsets

The peritoneal cavity (PerC) is a unique compartment within which a variety of immune cells reside, and from which macrophages (Mempty set) are commonly drawn for functional studies. Here we define two Mempty set subsets that coexist in PerC in adult mice. One, provisionally called the large peritoneal Mempty set (LPM), contains approximately 90% of the PerC Mempty set in unstimulated animals but disappears rapidly from PerC following lipopolysaccharide (LPS) or thioglycolate stimulation. These cells express high levels of the canonical Mempty set surface markers, CD11b and F4/80. The second subset, referred to as small peritoneal Mempty set (SPM), expresses substantially lower levels of CD11b and F4/80 but expresses high levels of MHC-II, which is not expressed on LPM. SPM, which predominates in PerC after LPS or thioglycolate stimulation, does not derive from LPM. Instead, it derives from blood monocytes that rapidly enter the PerC after stimulation and differentiate to mature SPM within 2 to 4 d. Both subsets show clear phagocytic activity and both produce nitric oxide (NO) in response to LPS stimulation in vivo. However, their responses to LPS show key differences: in vitro, LPS stimulates LPM, but not SPM, to produce NO; in vivo, LPS stimulates both subsets to produce NO, albeit with different response patterns. These findings extend current models of Mempty set heterogeneity and shed new light on PerC Mempty set diversity, development, and function. Thus, they introduce a new context for interpreting (and reinterpreting) data from ex vivo studies with PerC Mempty set.