Smart local orbitals for efficient calculations within density functional theory and beyond.

Localized basis sets in the projector augmented wave formalism allow for computationally efficient calculations within density functional theory (DFT). However, achieving high numerical accuracy requires an extensive basis set, which also poses a fundamental problem for the interpretation of the results. We present a way to obtain a reduced basis set of atomic orbitals through the subdiagonalization of each atomic block of the Hamiltonian. The resulting local orbitals (LOs) inherit the information of the local crystal field. In the LO basis, it becomes apparent that the Hamiltonian is nearly block-diagonal, and we demonstrate that it is possible to keep only a subset of relevant LOs that provide an accurate description of the physics around the Fermi level. This reduces to some extent the redundancy of the original basis set, and at the same time, it allows one to perform post-processing of DFT calculations, ranging from the interpretation of electron transport to extracting effective tight-binding Hamiltonians, very efficiently and without sacrificing the accuracy of the results.

Increased expression of the proprotein convertase enzyme FURIN in rheumatoid arthritis.

OBJECTIVE: FURIN is a proprotein convertase enzyme that inhibits the proinflammatory function of T cells and myeloid cells. Elevated FURIN expression levels have been reported in immune-mediated diseases, such as primary Sjögren's syndrome. Here, we investigated the levels of FURIN in peripheral blood (PB) and synovial fluid (SF) leucocytes from patients with rheumatoid arthritis (RA). METHOD: FURIN mRNA expression in PB and SF cells was determined by quantitative reverse transcription-polymerase chain reaction and FURIN plasma levels were measured using enzyme-linked immunosorbent assay. Associations between FURIN levels and demographic and clinical characteristics of the patients were determined. RESULTS: FURIN levels were significantly elevated in PB and SF mononuclear cells, T cells, and monocytes from RA patients compared to healthy controls. High FURIN levels were significantly associated with the prevailing prednisolone treatment, higher prednisolone doses, and increased C-reactive protein levels and Health Assessment Questionnaire values. CONCLUSION: FURIN is significantly upregulated in RA PB and SF leucocytes, suggesting that it may have a role in the pathogenesis of RA. In addition, our results suggest that elevated FURIN expression is associated with the indicators of more severe RA.

Mass vaccination response to a measles outbreak is not always possible. Lessons from a London prison.

In this study, we describe a contained measles outbreak in a London prison, the second such outbreak in a custodial setting. Once vaccination commenced, just under a third of eligible prisoners were immunised due to a low uptake of the vaccine. We conducted a root-cause analysis in order to identify factors which may have prevented or altered the course of the outbreak. Our analysis revealed that many of the factors identified are those that cannot be easily changed. It is unlikely that mass vaccination at the time, even in the absence of some of the more easily rectifiable issues, could have fully avoided further cases in the event of a mass outbreak. Both measles outbreaks in a custodial setting started with a member of staff and immunisation status of the staff were largely unknown. We argue that mass vaccination following an outbreak in a prison is unlikely to fully prevent a mass outbreak, and that implementing opt-out testing, empirical vaccination and insisting on full immunisation of staff are most likely to both prevent and contain outbreaks in the future.

Size control of charge-orbital order in half-doped manganite La0.5Ca0.5MnO3.

Motivated by recent experimental results, we study the effect of size reduction on half-doped manganite, La(0.5)Ca(0.5)MnO(3), using the combination of density-functional theory (DFT) and dynamical mean-field theory (DMFT). We find that upon size reduction the charge-ordered antiferromagnetic phase, observed in bulk, is destabilized, giving rise to the stability of a ferromagnetic metallic state. Our theoretical results, carried out on a defect-free nanocluster in isolation, establish the structural changes that follow upon size reduction to be responsible for this. Our study further points out the effect of size reduction to be distinctively different from application of hydrostatic pressure. Interestingly, our DFT+DMFT study additionally reports the correlation-driven stability of the charge-orbitally ordered state in bulk La(0.5) Ca(0.5) MnO(3), even in the absence of long-range magnetic order.

Exogenous peptides compete for the presentation of endogenous antigens to major histocompatibility complex class II-restricted T cells.

Antigen-presenting cells (APC) transfected with a construct encoding the hen egg-white lysozyme (HEL) amino acid sequence 1-80 constitutively present HEL peptides complexed to major histocompatibility complex (MHC) class II molecules to specific T cell hybridomas, indicating that endogenous cellular antigens can be efficiently presented to class II-restricted T cells. Here we show that exogenous peptide competitors added to HEL-transfected APC can inhibit the presentation of endogenous HEL peptides to class II-restricted T cells. The inhibition is specific for the class II molecule binding the competitor peptide, and it affects to the same extent presentation of exogenous or endogenous HEL peptides. These results, demonstrating that an exogenous competitor can inhibit class II-restricted T cell activation induced by endogenous as well as exogenous antigen, suggest lack of strict compartmentalization between endogenous and exogenous pathways of antigen presentation. Since autoreactive T cells may recognize endogenous, as well as exogenous antigens, the results have implications for the treatment of autoimmune diseases by MHC blockade.

Dynamical vertex approximation for nanoscopic systems.

With an increasing complexity of nanoscopic systems and the modeling thereof, new theoretical tools are needed for a reliable calculation of complex systems with strong electronic correlations. To this end, we propose a new approach based on the recently introduced dynamical vertex approximation. We demonstrate its reliability already on the one-particle vertex (i.e., dynamical mean field theory) level by comparison with the exact solution. Modeling a quantum point contact with 110 atoms, we show that the contact becomes insulating already before entering the tunneling regime due to a local Mott-Hubbard transition occurring on the atoms which form the point contact.

mTOR phosphorylated at S2448 binds to raptor and rictor.

In mammalian cells, the mammalian target of rapamycin (mTOR) forms an enzyme complex with raptor (together with other proteins) named mTOR complex 1 (mTORC1), of which a major target is the p70 ribosomal protein S6 kinase (p70S6K). A second enzyme complex, mTOR complex 2 (mTORC2), contains mTOR and rictor and regulates the Akt kinase. Both mTORC1 and mTORC2 are regulated by phosphorylation, complex formation and localization. So far, the role of p70S6K-mediated mTOR S2448 phosphorylation has not been investigated in detail. Here, we report that endogenous mTOR phosphorylated at S2448 binds to both, raptor and rictor. Experiments with chemical inhibitors of the mTOR kinase and of the phosphatidylinositol-3-kinase revealed that downregulation of mTOR S2448 phosphorylation correlates with decreased mTORC1 activity but can occur decoupled of effects on mTORC2 activity. In addition, we found that the correlation of the mTOR S2448 phosphorylation status with mTORC1 activity is not a consequence of effects on the assembly of mTOR protein and raptor. Our data allow new insights into the role of mTOR phosphorylation for the regulation of its kinase activity.

CDKs as therapeutic targets for the human genetic disease tuberous sclerosis?

The tuberous sclerosis gene 2 product tuberin is an important regulator of the mammalian target of rapamycin (mTOR). In addition, tuberin is known to bind to the cyclin-dependent kinase (CDK) inhibitor p27(Kip1) (p27) and to regulate its stability and localization via mTOR-independent mechanisms. Recently, evidence has been provided that tuberin also affects p27 localization via regulating mTOR's potential to activate the serum- and glucocorticoid-inducible kinase (SGK1) to phosphorylate p27. Taken together, these findings strengthen the argument that besides mTOR-inhibitors, such as rapamycin analogues, p27 and CDKs could also be considered targets for hamartoma therapeutics in tuberous sclerosis.

Skp2 inversely correlates with p27 and tuberin in transformed cells.

The cyclin-dependent kinase inhibitor p27Kip1 (p27) is a major gatekeeper of the mammalian cell cycle progression known to be regulated by both, its subcellular localization and its degradation. To allow entrance into S phase and thereby mammalian cell cycle progression p27 must be degraded by a skp2-containing E3 ubiquitin ligase whose task is to target p27 for degradation by the proteasome. The tumor suppressor gene product tuberin directly binds to p27 and protects it from degradation via skp2. Whereas, p27 and tuberin are known to be localized to both, the cytoplasm and the nucleus, the localization of skp2 remained elusive. Here we demonstrate that skp2 is a cytoplasmic and nuclear protein. In addition we found an inverse correlation of the endogenous protein levels of skp2 with p27 and tuberin in different transformed cells and under different growth conditions. These data allow new important insights into this molecular network of cell cycle control.

Tuberin, p27 and mTOR in different cells.

Mutations in the genes TSC1 or TSC2 cause the autosomal dominantly inherited tumor suppressor syndrome tuberous sclerosis, which is characterized by the development of tumors, named hamartomas, in different organs. The TSC gene products, hamartin and tuberin, form a complex, of which tuberin is assumed to be the functional component. Both, hamartin and tuberin have been implicated in the control of the cell cycle by activating the cyclin-dependent kinase inhibitor p27 and in cell size regulation by inhibiting the mammalian target of rapamycin (mTOR) a regulator of the p70 ribosomal protein S6 kinase (p70S6K) and its target the ribosomal protein S6. The tuberin/hamartin complex was shown to protect p27 from protein degradation. Within the mTOR signaling pathway tuberin harbors GTPase activating (GAP) potential toward Rheb, which is a potent regulator of mTOR. In this study, we have analyzed the protein levels of tuberin, p27, cyclin D1, mTOR and phospho mTOR Ser2448 (activated mTOR), S6 and phospho S6 Ser240/244 (activated S6) and as controls alpha-tubulin and topoisomerase IIbeta, in ten different cells, including primary normal cells, immortalized and transformed cell lines.

Binding of myelin basic protein peptides to human histocompatibility leukocyte antigen class II molecules and their recognition by T cells from multiple sclerosis patients.

Multiple sclerosis (MS) is an autoimmune disease in which myelin proteins have been implicated as autoantigens recognized by pathogenic autoreactive T cells. To study the relationship between human myelin basic protein (hMBP) and HLA alleles associated to MS susceptibility, such as DRB1*1501, the binding of synthetic peptides spanning the entire hMBP sequence to 10 purified HLA-DR molecules was determined. All the hMBP peptides tested showed binding affinity for at least one of the DR molecules analyzed, but three hMBP peptides, included in sequences 13-32, 84-103, and 144-163 were found capable of binding to three or more DR molecules. The hMBP peptide 84-103 was the most degenerate in binding, in that it bound to 9 out of 10 DR molecules tested. Interestingly, it bound with highest affinity to DRB1*1501 molecules. To correlate the binding pattern of hMBP peptides to HLA class II molecules with their recognition by T cells, 61 hMBP-specific T cell lines (TCL) were established from the peripheral blood of 20 MS patients, who were homozygous, heterozygous, or negative for DRB1*1501. Analysis of hMBP epitopes recognized by these TCL and their HLA restriction demonstrated a very good correlation between binding data and T cell proliferation to hMBP peptides. Although virtually all hMBP peptides tested could be recognized by at least one TCL from MS patients, three immunodominant T cell epitopes were apparent among the TCL examined, corresponding exactly to the hMBP peptides capable of binding to several DR molecules. No major difference could be detected in the recognition of immunodominant hMBP peptides by TCL from DRB1*1501 positive or negative MS patients. These results have implications for the role of hMBP as relevant autoantigen, and of DRB1*1501 as susceptibility allele in MS.

The preS1 antigen of hepatitis B virus is highly immunogenic at the T cell level in man.

14 hepatitis B vaccine recipients who showed high titers of anti-hepatitis B surface antibodies in serum after booster immunization with a polyvalent hepatitis B surface antigen vaccine that contained trace amounts of hepatitis B virus (HBV) preS1 and preS2 envelope antigens were studied for their in vitro T cell response to these antigens. All 14 subjects displayed a significant proliferative T cell response to the S/p25 envelope region encoded polypeptide; 8 also responded to preS1, while only 1 showed a significant level of T cell proliferation to preS2. Limiting dilution analysis demonstrated that the frequency of preS-specific T cells in two of these vaccine recipients was higher than that of S/p25-specific T cells. T cell cloning was then performed and a total of 29 HBV envelope antigen-reactive CD4+ cloned lines were generated from two preS-responsive vaccines. 21 of these lines were S/p25 specific, 7 preS1 specific, and 1 preS2 specific. Taken together, all these results suggest that the preS1 antigen may function as a strong T cell immunogen in man.

Different clinical behaviors of acute hepatitis C virus infection are associated with different vigor of the anti-viral cell-mediated immune response.

The anti-viral T cell response is believed to play a central role in the pathogenesis of hepatitis C virus infection. Since chronic evolution occurs in > 50% of HCV infections, the sequential analysis of the T cell response from the early clinical stages of disease may contribute to define the features of the T cell response associated with recovery or chronic viral persistence. For this purpose, 21 subjects with acute hepatitis C virus infection were sequentially followed for an average time of 44 wk. Twelve patients normalized transaminase values that remained normal throughout the follow-up period; all but two cleared hepatitis C virus-RNA from serum. The remaining nine patients showed persistent viremia and elevated transaminases. Analysis of the peripheral blood T cell proliferative response to core, E1, E2, NS3, NS4, and NS5 recombinant antigens and synthetic peptides showed that responses to all hepatitis C virus antigens, except E1, were significantly more vigorous and more frequently detectable in patients who normalized transaminase levels than in those who did not. By sequential evaluation of the T cell response, a difference between the two groups of patients was already detectable at the very early stages of acute infection and then maintained throughout the follow-up period. The results suggest that the vigor of the T cell response during the early stages of infection may be a critical determinant of disease resolution and control of infection.

Identification of immunodominant T cell epitopes of the hepatitis B virus nucleocapsid antigen.

Several lines of experimental evidence suggest that inclusion of core sequences in the hepatitis B vaccine may represent a feasible strategy to increase the efficacy of the vaccination. In order to identify immunodominant core epitopes, peripheral blood T cells purified from 23 patients with acute hepatitis B and different HLA haplotypes were tested with a panel of 18 short synthetic peptides (15 to 20 amino acids [AA]) covering the entire core region. All patients except one showed a strong T cell proliferative response to a single immunodominant 20 amino acid sequence located within the aminoterminal half of the core molecule. Two additional important sequences were also identified at the aminoterminal end and within the carboxyterminal half of the core molecule. These sequences were able to induce significant levels of T cell proliferation in 69 and 73% of the patients studied, respectively. T cell response to these epitopes was HLA class II restricted. The observations that (a) polyclonal T cell lines produced by PBMC stimulation with native HBcAg were specifically reactive with the relevant peptides and that (b) polyclonal T cell lines produced with synthetic peptides could be restimulated with native HBcAg, provide evidence that AA sequences contained within the synthetic peptides represent real products of the intracellular processing of the native core molecule. In conclusion, the identification of immunodominant T cell epitopes within the core molecule provides the molecular basis for the design of alternative and hopefully more immunogenic vaccines.

Identification of a plum pox virus CI-interacting protein from chloroplast that has a negative effect in virus infection.

The cylindrical inclusion (CI) protein of potyviruses is involved in virus replication and cell-to-cell movement. These two processes should rely on multiple plant-virus interactions; however, little is known about the host factors that are involved in, or that may interfere with, CI functions. By using a yeast two-hybrid system, the CI protein from Plum pox virus (PPV) was found to interact with the photosystem I PSI-K protein, the product of the gene psaK, of Nicotiana benthamiana. Coexpression of PPV CI was shown to cause a decrease in the accumulation level of PSI-K transiently expressed in N. benthamiana leaves. To test the biological relevance of this interaction, we have analyzed the infection of PPV in N. benthamiana plants in which psaK gene expression has been silenced by RNA interference, as well as in Arabidopsis thaliana psaK knockout plants. Our results show that downregulation of the psaK gene leads to higher PPV accumulation, suggesting a role for the CI-PSI-K interaction in PPV infection.

[Metabolic acidosis in patients with chronic kidney diseases: why and when to treat it?]. / Acidosi nell'insufficienza renale: perche' e quando trattarla.

Metabolic acidosis is a common complication in patients with advanced chronic renal diseases and dialytic treatments are unable to correct it completely. In hemodialysis (HD) patients, severe metabolic acidosis is associated with an increased risk of death. Evidence from several experimental studies suggests that even mild metabolic acidosis is associated with systemic effects. Acidosis is implicated in endocrine changes and has negative repercussions on bone and protein metabolism. In addition, recent observations suggest that acidosis triggers inflammation and accelerates the progression of chronic kidney diseases. As a contradictory finding, acidosis can reduce circulating leptin. Clinical studies on the nutritional effects of metabolic acidosis correction have shown mildly favorable effects. Taking into account the systemic effects of metabolic acidosis it is suggested that even mild metabolic acidosis is corrected. However, the new findings concerning the systemic effects of acidosis must be evaluated in controlled trials.

Fine specificity of the human T cell response to hepatitis B virus core antigen.

The fine specificity of the human T cell response to the hepatitis B virus core antigen (HBcAg) was investigated in 23 patients with acute hepatitis B virus (HBV) infection using a panel of short synthetic peptides covering the entire core region. An immunodominant T cell epitope which was recognized by all except one patient, was identified within the core sequence 50-69. Two further important T cell recognition sites were represented by the amino acid sequences 1-20 and 117-131, which were stimulatory for the T cells of 69% and 73% of the patients, respectively. T cell recognition of the synthetic peptides was HLA class II restricted because the peptide-induced T cell proliferation was inhibited by anti-HLA class II but not by anti-HLA class I monoclonal antibodies. These findings may be relevant to the development of future preventive and therapeutic strategies against HBV infection.

Immune pathogenesis of hepatitis B.

Available information about the immune pathogenesis of HBV infection in man is very limited. However, the present availability of recombinant sources of the different HBV antigens expressed in the appropriate forms to induce activation of either HLA class I or HLA class II-restricted T cells, provides the necessary tools to investigate directly the mechanisms of liver damage, the role of the different cellular components of the immune system in HBV clearance and the specific nature of the immune defects potentially responsible for the chronic evolution of HBV infection. In addition, improved knowledge of HBV biology suggests a dynamic interpretation of the HBV-immune system interactions, based on which viral mutations as well as direct interferences of HBV with specific immune functions are believed to play a relevant role with respect to the outcome of HBV infection.

Antiviral cell-mediated immune responses during hepatitis B and hepatitis C virus infections.

Cell-mediated immune responses to hepatitis B (HBV) and hepatitis C virus (HCV) antigens are vigorous and multispecific in acute, self-limited infections. Moreover, the prevalent cytokine pattern of circulating virus-specific T cells from patients who recover spontaneously from acute hepatitis is Th1-like. Longitudinal analysis of the T cell response to HCV antigens from the early stages of HCV infection in patients who recover from hepatitis and those who do not indicates that weaker responses and a prevalent Th2 pattern of cytokine production is associated with viral persistence and chronic evolution of disease. Although similar sequential studies are missing in hepatitis B, the observation that HBV-specific T cell responses are very weak or totally undetectable in the peripheral blood of patients with long-lasting chronic hepatitis B suggests that strength and quality of virus-specific T cell responses at the early stages of infection may influence the final outcome of both hepatitis B and C. While T cell hyporesponsiveness seems to be an important determinant for HBV persistence once chronic hepatitis has developed, this mechanism appears to be less critical in chronic HCV infection, because the vigor and quality of HCV-specific T cell responses seem to improve as a function of the duration of infection. This is shown by the finding that HCV-specific CD4- and CD8-mediated responses are easily detectable in the peripheral blood of patients with long-lasting chronic hepatitis C and that production of Th1 cytokines predominates within their livers. HCV therefore seems to be able to persist even in the face of an active T cell response and to acquire the capacity to survive within a host environment apparently unfavorable to its persistence. The high variability of HCV may explain its efficiency in escaping immune surveillance.

Visual capture and understanding of hand pointing actions in a 3-D environment.

We present a nonintrusive system based on computer vision for human-computer interaction in three-dimensional (3-D) environments controlled by hand pointing gestures. Users are allowed to walk around in a room and manipulate information displayed on its walls by using their own hands as pointing devices. Once captured and tracked in real-time using stereo vision, hand pointing gestures are remapped onto the current point of interest, thus reproducing in an advanced interaction scenario the "drag and click" behavior of traditional mice. The system, called PointAt (patent pending), enjoys a careful modeling of both user and optical subsystem, and visual algorithms for self-calibration and adaptation to both user peculiarities and environmental changes. The concluding sections provide an insight into system characteristics, performance, and relevance for real applications.