Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations

Population linkage disequilibrium occurs as a consequence of mutation, selection, genetic drift, and population substructure produced by admixture of genetically distinct ethnic populations. African American and Hispanic ethnic groups have a history of significant gene flow among parent groups, which can be of value in affecting genome scans for disease-gene discovery in the case-control and transmission/disequilibrium test designs. Disease-gene discovery using mapping by admixture linkage disequilibrium (MALD) requires a map of polymorphic markers that differentiate between the founding populations, along with differences in disease-gene allele frequencies. We describe markers appropriate for MALD mapping by assessing allele frequencies of 744 short tandem repeats (STRs) in African Americans, Hispanics, European Americans, and Asians, by choosing STR markers that have large differences in composite delta, log-likelihood ratios, and/or I*(2) for MALD. Additional markers can be added to this MALD map by utilization of the rapidly growing single-nucleotide-polymorphism databases and the literature, to achieve a 3-10-cM scanning scale. The map will be useful for studies of diseases, including prostate and breast cancer, diabetes, hypertension, and end-stage renal disease, that have large differences in incidence between the founding populations of either Hispanics or African Americans.

Performance of the ATLAS trigger system in 2015

During 2015 the ATLAS experiment recorded [Formula: see text] of proton-proton collision data at a centre-of-mass energy of [Formula: see text]. The ATLAS trigger system is a crucial component of the experiment, responsible for selecting events of interest at a recording rate of approximately 1 kHz from up to 40 MHz of collisions. This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton-proton collision data.

Endemicity and clinical picture of liver disease due to obstruction of the hepatic portion of the inferior vena cava in Nepal

Obstructive lesion of the hepatic portion of the inferior vena cava is common in Nepal. The clinical data on 150 patients who were seen at the Liver Unit, Bir Hospital, Kathmandu, in three years from 1990 to 1992 were analysed. Although the majority of patients were over 20 years of age, 25 patients were below 10 years of age; there were more males than females in this study. This disease accounted for 17% of 866 patients with chronic liver disease and for nearly one quarter of 267 biopsies performed on this patient group during the same period. Obstructive lesions of the inferior vena cava seem to be more common among poor people with malnutrition. Clinically, our patient group could be divided into acute (n = 27), subacute (n = 43) and chronic (n = 80) cases. The important clinical features are hepatomegaly and/or ascites and, in chronic cases, prominent dilated superficial veins over the body trunk with cephalad flow. Ultrasound is the most helpful diagnostic procedure, especially in subacute and chronic cases, as it frequently demonstrates caval obstruction, thrombosis, dilated hepatic veins and intrahepatic collaterals. Diagnosis is confirmed by cavography, which shows a caval obstruction of varying lengths at the cavo-atrial junction or a marked narrowing of the hepatic portion of the vena cava. In subacute and chronic cases cavography also demonstrates collateral veins, such as the ascending lumbar, hemiazygos and azygos that drain into the superior vena cava. Chronic cases had periods of exacerbation often associated with bacterial infection. The aetiology of inferior vena cava obstruction at its hepatic portion is not known, but there seems to be a frequent association of bacterial infection with the disease.

Skeletal muscle anabolism is a side effect of therapy with the MEK inhibitor: selumetinib in patients with cholangiocarcinoma

BACKGROUND

Cancer cachexia is characterised by skeletal muscle wasting; however, potential for muscle anabolism in patients with advanced cancer is unproven.

METHODS

Quantitative analysis of computed tomography images for loss/gain of muscle in cholangiocarcinoma patients receiving selumetinib (AZD6244; ARRY-142886) in a Phase II study, compared with a separate standard therapy group. Selumetinib is an inhibitor of mitogen-activated protein/extracellular signal-regulated kinase and of interleukin-6 secretion, a putative mediator of muscle wasting.

RESULTS

Overall, 84.2% of patients gained muscle after initiating selumetinib; mean overall gain of total lumbar muscle cross-sectional area was 13.6 cm(2)/100 days (∼2.3 kg on a whole-body basis). Cholangiocarcinoma patients who began standard treatment were markedly catabolic, with overall muscle loss of -7.3 cm(2)/100 days (∼1.2 kg) and by contrast only 16.7% of these patients gained muscle.

CONCLUSION

Our findings suggest that selumetinib promotes muscle gain in patients with cholangiocarcinoma. Specific mechanisms and relevance for cachexia therapy remain to be investigated.

Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group

Five isolates of hepatitis C virus (HCV) RNA from patients with chronic liver disease in Nepal were not classifiable into the known genotypes I/1a, II/1b, III/2a, IV/2b or V/3a using PCR with type-specific primers deduced from the HCV core gene. Their nucleotide sequences were determined for the 5'-terminal 1.5 kilobases and 3'-terminal 1.2 kilobases, covering 30% of the entire genome, and compared with each other and with reported sequences of HCV isolates of various genotypes. They were more similar to a reported HCV isolate (NZL1) of genotype V/3a (in 81.6 to 84.1% of their nucleotides and 85.7 to 88.7% of the deduced amino acid sequence) compared with the genotypes I/1a to IV/2b (in 69.3 to 74.7% and 72.3 to 77.4%, respectively). Hence they were considered to be variants of the third major group (group 3). The five HCV isolates shared 81.3 to 85.2% of nucleotide sequence and 85.4 to 89.3% of deduced amino acid sequence. Thus they were substantially different from each other. One of them was classified as genotype VI/3b due to an 88.2% similarity in nucleotide sequence to that of the reported HCV isolates of this genotype, whereas the remaining four were classified into provisional genotypes 3c, 3d, 3e and 3f. These HCV variants have evolved and remained in Nepal, and have not been observed in the other areas of the world.

Muon reconstruction performance of the ATLAS detector in proton-proton collision data at [Formula: see text]=13 TeV

This article documents the performance of the ATLAS muon identification and reconstruction using the LHC dataset recorded at [Formula: see text] TeV in 2015. Using a large sample of [Formula: see text] and [Formula: see text] decays from 3.2 fb[Formula: see text] of pp collision data, measurements of the reconstruction efficiency, as well as of the momentum scale and resolution, are presented and compared to Monte Carlo simulations. The reconstruction efficiency is measured to be close to [Formula: see text] over most of the covered phase space ([Formula: see text] and [Formula: see text] GeV). The isolation efficiency varies between 93 and [Formula: see text] depending on the selection applied and on the momentum of the muon. Both efficiencies are well reproduced in simulation. In the central region of the detector, the momentum resolution is measured to be [Formula: see text] ([Formula: see text]) for muons from [Formula: see text] ([Formula: see text]) decays, and the momentum scale is known with an uncertainty of [Formula: see text]. In the region [Formula: see text], the [Formula: see text] resolution for muons from [Formula: see text] decays is [Formula: see text] while the precision of the momentum scale for low-[Formula: see text] muons from [Formula: see text] decays is about [Formula: see text].

Henoch Schönlein purpura with nephritis in adults: adverse prognostic indicators in a UK population

BACKGROUND

Henoch Schönlein purpura with nephritis (HSN) in adults may cause severe organ injury, but its rarity has contributed to a lack of data.

AIM

To evaluate clinical outcomes and risk factors in adult HSN patients.

DESIGN

Retrospective analysis.

METHODS

Thirty-seven patients with adult HSN attending the Regional Vasculitis Clinic between 1974 and 2004 were assessed. For inclusion, a renal biopsy showing predominant mesangial IgA immune deposits was required, plus at least two of: purpuric rash, arthralgia, abdominal pain.

RESULTS

Ten patients (27%) progressed to end-stage renal failure (ESRF). Renal failure rates were highest in the first decade, with survival rate 72% at 5 years, 68% at 10 years and 46% at final review. Risk factors for ESRF were: proteinuria > or =1 g/day during follow-up (RR 83.8, p = 0.0006); hypertension at presentation (RR = 53.3, p = 0.0045) and during follow-up (RR = 5.9, p = 0.05); renal impairment at presentation (RR 8.0, p = 0.0015); age <30 years (RR 7.6, p = 0.02); and male sex (RR = 6.0, p = 0.05). Biopsies frequently showed crescents, mostly affecting <50% of glomeruli; their presence predicted ESRF, as did interstitial fibrosis and tubular atrophy. Renal remission, in contrast, was also high (43%). Cytotoxics were used in 32%, with no clear effect on outcome. Relapses affecting the classical extra-renal systems were common, but were not associated with declines in renal function. A high proportion of patients (41%) also suffered vasculitic organ injuries outside the classical systems.

DISCUSSION

HSN in adults is a serious relapsing disease, causing renal failure as frequently as in small-vessel ANCA-positive vasculitides. Prognosis and risks differed in this series from those in other countries, including a higher risk of ESRF than in previous series. Distinct groups developed either ESRF, or remitted. The absence of clear benefit suggests that corticosteroids should be reserved for patients with serious disease, and that cytotoxics may not be merited for those at high risk of renal failure.

3pK, a new mitogen-activated protein kinase-activated protein kinase located in the small cell lung cancer tumor suppressor gene region

NotI linking clones, localized to the human chromosome 3p21.3 region and homozygously deleted in small cell lung cancer cell lines NCI-H740 and NCI-H1450, were used to search for a putative tumor suppressor gene(s). One of these clones, NL1G210, detected a 2.5-kb mRNA in all examined human tissues, expression being especially high in the heart and skeletal muscle. Two overlapping cDNA clones containing the entire open reading frame were isolated from a human heart cDNA library and fully characterized. Computer analysis and a search of the GenBank database to reveal high sequence identity of the product of this gene to serine-threonine kinases, especially to mitogen-activated protein kinase-activated protein kinase 2, a recently described substrate of mitogen-activated kinases. Sequence identitiy was 72% at the nucleotide level and 75% at the amino acid level, strongly suggesting that this protein is a serine-threonine kinase. Here we demonstrate that the new gene, referred to as 3pK (for chromosome 3p kinase), in fact encodes a mitogen-activated protein kinase-regulated protein serine-threonine kinase with a novel substrate specificity.

Transverse-momentum and pseudorapidity distributions of charged hadrons in pp collisions at square root of s = 7 TeV

Charged-hadron transverse-momentum and pseudorapidity distributions in proton-proton collisions at square root of s = 7  TeV are measured with the inner tracking system of the CMS detector at the LHC. The charged-hadron yield is obtained by counting the number of reconstructed hits, hit pairs, and fully reconstructed charged-particle tracks. The combination of the three methods gives a charged-particle multiplicity per unit of pseudorapidity dN(ch)/dη|(|η|<0.5) = 5.78 ± 0.01(stat) ± 0.23(syst) for non-single-diffractive events, higher than predicted by commonly used models. The relative increase in charged-particle multiplicity from square root of s = 0.9 to 7 TeV is [66.1 ± 1.0(stat) ± 4.2(syst)]%. The mean transverse momentum is measured to be 0.545 ± 0.005(stat) ± 0.015(syst)  GeV/c. The results are compared with similar measurements at lower energies.

Topological cell clustering in the ATLAS calorimeters and its performance in LHC Run 1

The reconstruction of the signal from hadrons and jets emerging from the proton-proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting topological cell clusters have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS.

Primary angiitis of the central nervous system: emerging variants

BACKGROUND

Primary angiitis of the central nervous system (PACNS), a serious disease, has not featured prominently in the spectrum of multi-organ disease seen in vasculitis clinics.

AIM

To evaluate the presentation, natural history and features of PACNS variants and compare to those of systemic vasculitides.

DESIGN

Retrospective analysis.

METHODS

Patients (n=105) presented during 1988-2003 to a tertiary regional vasculitis clinic receiving unselected disease types. Data were collected from a clinical database, patient and laboratory records.

RESULTS

The frequency of PACNS presentation rose over the study period, compared with most of the other vasculitides. When PACNS was divided into small- and middle-sized vessel disease (SVD/MVD), their clinical courses differed substantially. SVD PACNS was responsive to immunosuppressive drugs, but relapsed during prolonged periods in all patients on maintenance immunosuppressives, or after withdrawal of treatment, causing recurrent, severe and irreversible CNS injury. MVD PACNS had isolated episodes at presentation, with a paucity of relapses during prolonged follow-up.

DISCUSSION

Similarities between SVD PACNS and microscopic polyarteritis suggest the former may represent a limited form of the latter. MVD PACNS has a distinctly more benign relapse pattern than its multisystem counterpart polyarteritis nodosa. Acute-phase serology was useful in designating inflammatory processes at presentation of patients presenting with encephalopathy caused by SVD only, but were unhelpful in defining relapses in this form of PACNS, the definition of which in all cases rested on clinical assessment and MR scanning. Direct cerebral angiography was not diagnostic in any case of SVD PACNS; positive brain biopsy is diagnostically unequivocal, but the total clinical syndrome with imaging may establish a diagnosis with highest probability. In MVD PACNS, angiography with MR scan proved diagnostic. We suggest an algorithm for a rational, minimally invasive approach to investigation. In PACNS, SVD and MVD are important variants, and decisions about therapy should incorporate these distinctions.

Development of a heat vulnerability index for New York State

OBJECTIVES

The frequency and intensity of extreme heat events are increasing in New York State (NYS) and have been linked with increased heat-related morbidity and mortality. But these effects are not uniform across the state and can vary across large regions due to regional sociodemographic and environmental factors which impact an individual's response or adaptive capacity to heat and in turn contribute to vulnerability among certain populations. We developed a heat vulnerability index (HVI) to identify heat-vulnerable populations and regions in NYS.

STUDY DESIGN

Census tract level environmental and sociodemographic heat-vulnerability variables were used to develop the HVI to identify heat-vulnerable populations and areas.

METHODS

Variables were identified from a comprehensive literature review and climate-health research in NYS. We obtained data from 2010 US Census Bureau and 2011 National Land Cover Database. We used principal component analysis to reduce correlated variables to fewer uncorrelated components, and then calculated the cumulative HVI for each census tract by summing up the scores across the components. The HVI was then mapped across NYS (excluding New York City) to display spatial vulnerability. The prevalence rates of heat stress were compared across HVI score categories.

RESULTS

Thirteen variables were reduced to four meaningful components representing 1) social/language vulnerability; 2) socioeconomic vulnerability; 3) environmental/urban vulnerability; and 4) elderly/ social isolation. Vulnerability to heat varied spatially in NYS with the HVI showing that metropolitan areas were most vulnerable, with language barriers and socioeconomic disadvantage contributing to the most vulnerability. Reliability of the HVI was supported by preliminary results where higher rates of heat stress were collocated in the regions with the highest HVI.

CONCLUSIONS

The NYS HVI showed spatial variability in heat vulnerability across the state. Mapping the HVI allows quick identification of regions in NYS that could benefit from targeted interventions. The HVI will be used as a planning tool to help allocate appropriate adaptation measures like cooling centers and issue heat alerts to mitigate effects of heat in vulnerable areas.