Assessment of a rigorous transitive profile based search method to detect remotely similar proteins

Profile-based sequence search procedures are commonly employed to detect remote relationships between proteins. We provide an assessment of a Cascade PSI-BLAST protocol that rigorously employs intermediate sequences in detecting remote relationships between proteins. In this approach we detect using PSI-BLAST, which involves multiple rounds of iteration, an initial set of homologues for a protein in a 'first generation' search by querying a database. We propagate a 'second generation' search in the database, involving multiple runs of PSI-BLAST using each of the homologues identified in the previous generation as queries to recognize homologues not detected earlier. This non-directed search process can be viewed as an iteration of iterations that is continued to detect further homologues until no new hits are detectable. We present an assessment of the coverage of this 'cascaded' intermediate sequence search on diverse folds and find that searches for up to three generations detect most known homologues of a query. Our assessments show that this approach appears to perform better than the traditional use of PSI-BLAST by detecting 15% more relationships within a family and 35% more relationships within a superfamily. We show that such searches can be performed on generalized sequence databases and non-trivial relationships between proteins can be detected effectively. Such a propagation of searches maximizes the chances of detecting distant homologies by effectively scanning protein "fold space".

A comparison between long-term survivors of Hodgkin's disease and their siblings on fatigue level and factors predicting for increased fatigue

PURPOSE

To compare the level of fatigue in survivors of Hodgkin's disease and their siblings, and to explore factors associated with increased fatigue.

METHODS

Survivors of Hodgkin's disease 5 years or more from diagnosis and their siblings completed a questionnaire study. Fatigue level was measured using the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F) instrument, with lower scores reflecting increased fatigue. Multiple regression models were used to identify factors associated with fatigue level in the two populations.

RESULTS

Five hundred and eleven survivors (median age 44 years; range 16-82) and 224 siblings (median age 44 years; range 16-79) returned the completed questionnaire. The response rates were 61% and 58%, respectively. Compared with siblings, survivors were significantly more likely to report the presence of cardiac disease (26% versus 16%; P = 0.001) and hypothyroidism (65% versus 3%; P <0.001), and had a significantly lower mean FACIT-F score (40.7 and 42.2; P = 0.05). On multivariable analysis, factors significantly associated with increased fatigue in survivors were reports of cardiac disease (P <0.001), psychiatric condition (P <0.001), history of tobacco use (P = 0.004) and low exercise frequency (P = 0.03). For siblings, the only independent factor associated with increased fatigue was low exercise frequency (P = 0.03).

CONCLUSIONS

Survivors of Hodgkin's disease were more fatigued than their siblings. The difference was modest but statistically significant. The significant association between fatigue and cardiac disease suggests the importance of screening for underlying cardiac dysfunction in survivors with symptoms of fatigue. The association between fatigue and smoking history may be due to exacerbation of late medical complications of Hodgkin's disease by tobacco use.

Sarcoma-like mural nodules in ovarian mucinous cystadenomas--a report of two cases

Sarcoma-like mural nodule is a very rare occurrence in a mucinous tumour of the ovary. Two such nodules having morphologically benign features with osteoclastic giant cells, in the wall of mucinous cystadenoma are described. In addition, these nodules exhibited reactive vascular proliferations. The sarcoma-like nodules are associated with a favourable outcome and must be distinguished from other malignant nodules composed of sarcoma or anaplastic carcinoma that may also occur in the wall of mucinous ovarian tumours.

Glucose-induced Akt1 activation mediates fibronectin synthesis in endothelial cells

AIMS/HYPOTHESIS

Increased expression and decreased degradation of extracellular matrix (ECM) proteins are key features of chronic diabetic complications. Fibronectin, a predominant ECM protein, has been shown to be overexpressed in all target organs of diabetic complications and in endothelial cells cultured in high levels of glucose. The present study was designed to elucidate the role of protein kinase B (Akt/PKB) in glucose-induced fibronectin mRNA expression and protein production in vascular endothelial cells.

METHODS

Human umbilical vein endothelial cells were cultured in the presence of high glucose to study Akt/PKB activation. The upstream and downstream mediators in the Akt/PKB pathway were also investigated using dominant negative transfections and specific inhibitors of signalling pathways. Cells were subjected to real time RT-PCR, western blotting, and confocal microscopy to assess Akt1/PKBalpha activation and fibronectin mRNA expression and protein production. To detect transcription factor activation, electrophoretic mobility shift assay was carried out.

RESULTS

Our data demonstrate that fibronectin mRNA expression and protein production that are induced by high glucose are mediated via activation of Akt/PKB, which is modulated by mitogen-activated protein kinase, phosphatidylinositol 3-kinase, and protein kinase C. Glucose-induced fibronectin mRNA expression and protein production are also mediated by Akt1/PKBalpha-dependent activation of the transcription factors nuclear factor-kappaB and activating protein-1.

CONCLUSIONS/INTERPRETATION

Our study provides insight into the mechanical basis of glucose-induced increases in fibronectin mRNA expression and protein production. High levels of glucose may increase fibronectin mRNA expression and protein production by activating Akt/PKB.

Catastrophic microangiopathy induced by high-titre factor VIII inhibitors after liver transplantation for haemophilia A with cirrhosis

Liver transplantation may induce immune tolerance to factor VIII inhibitors but de novo development of inhibitors after transplantation may cause intractable haemorrhage. We report a patient with mild haemophilia A and high-titre FVIII inhibitors who received an orthotopic liver transplantation for complications of hepatitis C virus cirrhosis. Recombinant activated FVII was used in addition to routine haemostatic agents. Conventional immunosuppression was supplemented with antithymocyte globulin and cyclophosphamide. FVIII inhibitors disappeared from the circulation with liver transplantation but they were found to have bound to the graft endothelium, which became activated and induced catastrophic microangiopathy. A subsequent anamnestic response resulted in FVIII inhibitor titres of 1000 Bethesda Units. Uncontrollable haemorrhage persisted until the recipient's death. In patients with high-titre FVIII inhibitors resilient desensitization is required before liver transplantation.

Measurement of the lifetime difference in the B0(s) system

We present a study of the decay B0(s) --> J/psiphi. We obtain the CP-odd fraction in the final state at time zero, Rperpendicular = 0.16 +/- 0.10(stat) +/- 0.02 (syst), the average lifetime of the (B0(s), B0(s)) system, tau(B0(s)) = 1.39(+0.13)(-0.16)(stat)(+0.01)(-0.02)(syst) ps, and the relative width difference between the heavy and light mass eigenstates, DeltaGamma/Gamma tripple bond (GammaL - GammaH)/Gamma = 0.24(+0.28)(-0.38)(stat)(+0.03)(-0.04)(syst). With the additional constraint from the world average of the lifetime measurements using semileptonic decays, we find tau(B0(s)) = 1.39 +/- 0.06 ps and DeltaGamma/Gamma = 0.25(+0.14)(-0.15). For the ratio of the B0(s) and B0 lifetimes we obtain tau(B0(s))/tau(B0) = 0.91 +/- 0.09(stat) +/- 0.003(syst).

Measurement of semileptonic branching fractions of B mesons to narrow D** states

Using the data accumulated in 2002-2004 with the D0 detector in proton-antiproton collisions at the Fermilab Tevatron collider with a center-of-mass energy of 1.96 TeV, the branching fractions of the decays B --> D0(1)(2420)mu+ vmuX and B --> D2(*0)(2460)mu+ vmuX and their ratio have been measured: B(b --> B) x B(B --> D0(1)mu+ vmuX) x B(D0(*0) --> D*- pi+) = [0.087 +/- 0.007(stat) +/- 0.014(syst)]%; B(b --> B) x B(B --> D2(*0) mu+ vmuX) x B(D2(*0) --> D*- pi+) = [0.035 +/- 0.007(stat) +/- 0.008(syst)]% and [B(B --> D2(*0)mu+ vmuX) x B(D2(*0) --> D*- pi+)]/[B(B --> D0(1)mu+ vmuX) x B(D0(1) --> D*- pi+)] = 0.39 +/- 0.09(stat) +/- 0.12 (syst), where the charge conjugated states are always implied.

Search for large extra spatial dimensions in dimuon production with the d0 detector

We present the results of a search for the effects of large extra spatial dimensions in pp collisions at sqrt[s] = 1.96 TeV in events containing a pair of energetic muons. The data correspond to 246 pb(-1) of integrated luminosity collected by the D0 experiment at the Fermilab Tevatron Collider. Good agreement with the expected background was found, yielding no evidence for large extra dimensions. We set 95% C.L. lower limits on the fundamental Planck scale between 0.85 and 1.27 TeV within several formalisms. These are the most stringent limits achieved in the dimuon channel to date.

Search for supersymmetry via associated production of charginos and neutralinos in final states with three leptons

A search for associated production of charginos and neutralinos is performed using data recorded with the D0 detector at a pp center-of-mass energy of 1.96 TeV at the Fermilab Tevatron Collider. This analysis considers final states with missing transverse energy and three charged leptons, of which at least two are electrons or muons. No evidence for supersymmetry is found in a data set corresponding to an integrated luminosity of 320 pb-1. Limits on the product of the production cross section and leptonic branching fraction are set. For the minimal supergravity model, a chargino lower mass limit of 117 GeV at the 95% C.L. is derived in regions of parameter space with enhanced leptonic branching fractions.

Search for neutral supersymmetric Higgs Bosons in multijet events at sqrt[s]=1.96 TeV

We have performed a search for neutral Higgs bosons produced in association with bottom quarks in pp collisions, using 260 pb-1 of data collected with the D0 detector in Run II of the Fermilab Tevatron Collider. The cross sections for these processes are enhanced in many extensions of the standard model (SM), such as in its minimal supersymmetric extension at large tanbeta. The results of our analysis agree with expectations from the SM, and we use our measurements to set upper limits on the production of neutral Higgs bosons in the mass range of 90 to 150 GeV.

Ion detection with photonic crystal microcavities

We have experimentally demonstrated a cation and anion sensor by using short linear photonic crystal microcavities with an embedded quantum dot active region. The photonic crystal microcavity covered with an ion-selective polymer forms a submicrometer optical detection system sensitive to small changes of perchlorate anion (ClO4(-)) and calcium cation (Ca2+) concentrations.

Understanding cardiac arrhythmias

This review highlights the applied science intrinsic to the interpretation of the electrocardiogram and cardiac arrhythmias in children.

Clear cell carcinoid tumour of lung--a case report

An unusual case of pulmonary clear cell carcinoid tumour in a fifteen year old boy is being described. The differential diagnoses considered in this case are described. This is one of the uncommon varieties of carcinoid of lung reported in the world literature.

Cost of ambulatory care of diabetes mellitus: a study from north India

BACKGROUND

Diabetes mellitus is a chronic and potentially disabling disease that represents an important public health and clinical concern because of the economic burden it imposes on the person, family, and society. Despite this, data regarding cost of care of diabetes mellitus from developing countries are scarce. This study aimed to assess the cost of care of Indian patients with diabetes mellitus.

METHODS

Cost of illness in 50 outpatients with diabetes mellitus (diagnosed according to WHO criteria, Expert Committee, 1997) was assessed over a six month period using a specially designed questionnaire, together with structured assessments of disability.

RESULTS

Total annual cost of care was 14 508 rupees (263.78 euros). The largest proportion of the total cost was made up of direct costs (68%), followed by indirect costs (28.76%) and provider's costs (2.8%). Drug costs were high. Total treatment cost was significantly higher in those who were more educated, those who visited the hospital more often, and those receiving a greater number of drugs.

CONCLUSION

From this study it can be concluded that diabetes mellitus is an expensive illness to treat even in developing countries. The main brunt of financial burden is borne by the family. Any efforts at cost reduction should, therefore, have the family as its focus, and relieving the family of this financial burden needs to be prioritised.

Production of WZ events in pp collisions at square root(s) = 1.96 TeV and limits on anomalous WWZ couplings

We present results from a search for WZ production with subsequent decay to l nu l' l' (l and l' = e or mu) using 0.30 fb(-1) of data collected by the D0 experiment between 2002 and 2004 at the Fermilab Tevatron. Three events with WZ decay characteristics are observed. With an estimated background of 0.71 +/- 0.08 events, we measure the WZ production cross section to be 4.5(-2.6)(+3.8) pb, with a 95% C.L. upper limit of 13.3 pb. The 95% C.L. limits for anomalous WWZ couplings are found to be -2.0 < delta kappaZ < 2.4 for form factor scale lambda = 1 TeV, and -0.48 < lambdaZ < 0.48 and -0.49 < delta g(1)(Z) < 0.66 for lambda = 1.5 TeV.

Search for Randall-Sundrum gravitons in dilepton and diphoton final states

We report the first direct search for the Kaluza-Klein (KK) modes of Randall-Sundrum gravitons using dielectron, dimuon, and diphoton events observed with the D0 detector operating at the Fermilab Tevatron pp(-) Collider at sqrt[s]=1.96 TeV. No evidence for resonant production of gravitons has been found in the data corresponding to an integrated luminosity of approximately equal to 260 pb(-1). Lower limits on the mass of the first KK mode at the 95% C.L. have been set between 250 and 785 GeV, depending on its coupling to standard model particles.

Study of Zgamma events and limits on anomalous ZZgamma and Zgammagamma couplings in pp collisions at square root s = 1.96 TeV

We present a measurement of the Zgamma production cross section and limits on anomalous ZZgamma and Zgammagamma couplings for form-factor scales of lambda = 750 and 1000 GeV. The measurement is based on 138 (152) candidates in the eegamma (mumugamma) final state using 320(290) pb(-1) of pp(-1) collisions at square root of s = 1.96 TeV. The 95% C.L. limits on real and imaginary parts of individual anomalous couplings are /h(10,30)Z/ < 0.23, /h(20,40)Z/ < 0.020, /h(10,30)gamma/ < 0.23, and /h(20,40)gamma/ < 0.019 for lambda = 1000 GeV.

Cost of care of schizophrenia: a study of Indian out-patient attenders

OBJECTIVE

To assess the cost of care of Indian out-patients with schizophrenia.

METHOD

Cost of illness in 50 out-patients with schizophrenia was assessed over a 6-month period together with structured assessments of psychopathology and disability, and compared with 50 out-patients with diabetes mellitus.

RESULTS

Total annual costs of care of schizophrenia were 274 US dollars; these were not significantly different from diabetes mellitus. Indirect costs (63%) were higher than direct costs. Drug costs were high. The main brunt of financial burden was borne by the family. Total treatment costs in schizophrenia were significantly higher in those who were unemployed, those who visited the hospital more often, and were more severely ill and disabled.

CONCLUSION

Schizophrenia is an expensive illness to treat even in developing countries. Costs of care are similar to those of chronic physical illness, such as diabetes mellitus. Costs are higher in severely ill and disabled patients.

Glucose-induced up-regulation of CD36 mediates oxidative stress and microvascular endothelial cell dysfunction

AIMS/HYPOTHESIS

Hyperglycaemia-induced oxidative stress is implicated in the pathogenesis of chronic diabetic complications. Glucose-mediated oxidation of LDL may result in increased oxidative stress and vascular endothelial cell dysfunction via interaction with a cell surface scavenger receptor, CD36. In this study, we investigated the role of CD36 in cultured microvascular endothelial cells (MVECs) and in the heart by using an animal model of chronic diabetes.

METHODS

Cultured MVECs were subjected to varying glucose concentrations and assayed for alteration in CD36 gene expression and protein levels. To assess for oxidised LDL (ox-LDL) uptake, MVECs exposed to low and high glucose were treated with ox-LDL (80 microg/ml), a ligand for CD36. Haem oxygenase-1 (HO-1) and endothelin-1 (ET-1) induction, as well as oxidative stress were determined. The role of glucose-induced CD36 alteration in ox-LDL uptake was also assayed following post-transcriptional CD36 gene silencing. For in vivo studies, CD36 mRNA and oxidative DNA and protein damage were measured in heart tissues of 1-month-old diabetic Sprague-Dawley rats.

RESULTS

We found that glucose increased CD36 mRNA and protein levels in MVECs. High levels of glucose also augmented ox-LDL uptake, in association with increasing HO-1 and ET-1 mRNA levels. CD36 gene silencing prevented glucose-induced CD36 alteration, reduced ox-LDL uptake, and prevented HO-1 and ET-1 up-regulation. Similar to in vitro studies, diabetic heart tissues exhibited increased CD36 mRNA levels and increased oxidative DNA and protein damage.

CONCLUSIONS/INTERPRETATION

Our results provide evidence that up-regulation of CD36 may have a role in increasing oxidative stress in MVECs and the heart in chronic diabetes.

Measurement of inclusive differential cross sections for pp collisions at (square root)s = 1.96 TeV

We present measurements of the inclusive production cross sections of the Gamma(1S) bottomonium state in pp collisions at (square root)s = 1.96 TeV. Using the Gamma(1S) --> mu(+)mu(-) decay mode for a data sample of 159 +/- 10 pb(-1) collected by the D0 detector at the Fermilab Tevatron collider, we determine the differential cross sections as a function of the Gamma(1S) transverse momentum for three ranges of the Gamma(1S) rapidity: 0 < y(Gamma) < or = 0.6, 0.6 < y(Gamma) < or = 1.2, and 1.2 < y(Gamma) < or = 1.8.

Myocilin gene implicated in primary congenital glaucoma

Primary congenital glaucoma (PCG) has been associated with CYP1B1 gene (2p21), with a predominantly autosomal recessive mode of inheritance. Our earlier studies attributed CYP1B1 mutations to only 40% of Indian PCG cases. In this study, we included 72 such PCG cases where CYP1B1 mutations were detected in only 12 patients in heterozygous condition, implying involvement of other gene(s). On screening these patients for mutations in myocilin (MYOC), another glaucoma-associated gene, using denaturing high-performance liquid chromatography followed by sequencing, we identified a patient who was double heterozygous at CYP1B1 (c.1103G>A; Arg368His) and MYOC (c.144G>T; Gln48His) loci, suggesting a digenic mode of inheritance of PCG. In addition, we identified the same MYOC mutation, implicated for primary open angle glaucoma, in three additional PCG patients who did not harbor any mutation in CYP1B1. These observations suggest a possible role of MYOC in PCG, which might be mediated via digenic interaction with CYP1B1 and/or an yet unidentified locus associated with the disease.

Polymorphism of HIV-1 gag (p17) gene from female sex workers in Calcutta, India

HIV-1 subtype C is the major subtype in India as evidenced from the analysis of specific regions within envelope and gag gene. The matrix protein (p17) of HIV-1 which is involved in several functions like the viral RNA transport, nuclear localization, assembly of pre-integration complex into host nucleus has been used to study the strain diversity among female sexworkers in Calcutta. The gene encoding for the HIV-1 matrix protein, p17 was amplified by nested polymerase chain reaction (PCR) from blood samples of HIV-1 seropositive female sex workers (FSW) in Calcutta, India. Genes of twenty-two samples were sequenced and the phylogenetic analysis with different global strains showed that the majority (seventeen) was clustered with Indian type C. A few samples were found to be close to other C subtypes isolated from South Africa, China and Myanmar. The comparison of Calcutta samples with the samples from other regions of India along with other non-asian subtype C sequences clearly revealed a different cluster of Indian sequences. The two samples, cal 242 and cal 709 was found to be the most divergent type and showed close relatedness with African C subtypes.

Measurement of dijet azimuthal decorrelations at central rapidities in pp collisions at sqrt s =1.96 TeV

Correlations in the azimuthal angle between the two largest transverse momentum jets have been measured using the D0 detector in p (-)p collisions at a center-of-mass energy sqrt[s]=1.96 TeV. The analysis is based on an inclusive dijet event sample in the central rapidity region corresponding to an integrated luminosity of 150 pb(-1). Azimuthal correlations are stronger at larger transverse momenta. These are well described in perturbative QCD at next-to-leading order in the strong coupling constant, except at large azimuthal differences where contributions with low transverse momentum are significant.

Measurement of the ratio of B+ and B0 meson lifetimes

The ratio of the B+ and B0 meson lifetimes was measured using data collected in 2002-2004 by the D0 experiment in Run II of the Fermilab Tevatron Collider. These mesons were reconstructed in B-->mu(+)nuD(*-)X decays, which are dominated by B0 and B-->mu(+)nuD 0X decays, which are dominated by B+. The ratio of lifetimes is measured to be tau(+)/tau(0)=1.080+/-0.016(stat)+/-0.014(syst).

Measurement of the ratio of inclusive cross sections sigma(pp --> Z + b jet)/sigma(pp --> Z + jet) at square root(s) = 1.96 TeV

Using the data collected with the D0 detector at square root(s) = 1.96 TeV, for integrated luminosities of about 180 pb(-1), we have measured the ratio of inclusive cross sections for pp --> Z + b jet to pp --> Z + jet production. The inclusive Z + b-jet reaction is an important background to searches for the Higgs boson in associated ZH production at the Fermilab Tevatron collider. Our measurement is the first of its kind, and relies on the Z --> e+ e- and Z --> mu+ mu- modes. The combined measurement of the ratio yields 0.021+/-0.005 for hadronic jets with transverse momenta pT > 20 GeV/c and pseudorapidities absolute value(eta) < 2.5, consistent with next-to-leading-order predictions of the standard model.