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Catatonia is a complex amalgamation of neuropsychiatric symptoms that can manifest in both psychiatric and neurological conditions. The treatment of catatonia related to psychiatric illnesses is well documented as it typically responds to benzodiazepines and electroconvulsive therapy (ECT). However, the treatment of catatonia related to neurological disorders has shown to be more difficult, particularly when associated with Lewy Body Dementia (LBD). Here, we present the case of a 78-year-old woman with LBD, Bipolar I, depressive type, who successfully underwent twelve ECT sessions to treat catatonia refractory to benzodiazepine therapy. The effectiveness of the treatment was measured using the Bush-Françis Catatonia Scale (BFCS) to measure her catatonic symptoms as she progressed through the therapy. This report highlights the importance of considering ECT as a leading therapeutic approach in this particular subset of patients who do not respond adequately to pharmaceutical therapy and medical titrations., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2024, Sahib Din et al.)

Introduction: To determine if hyperbaric oxygen (HBO2) therapy has an effect on diabetic blood glucose levels (BGL) and, if so, the extent of this effect. Also, to examine factors that exacerbate any observed effect., Methods: This was a retrospective review of prospectively collected quality data on diabetics undergoing HBO2. Pre- and post-treatment BGL were recorded. Pre-treatment BGL ⟨120 mg/dL received glucose supplementation. Hypoglycemia was defined as BGL ⟨70 mg/dL. BGL ⟨90 mg/dL was included as an elevated hypoglycemia threshold., Results: 77 patients representing 1,825 treatments were included for analysis. No patient had deleterious side effects or required emergency care. BGL decreased in 75.4% of treatments in this group, with a median decrease of 25 mg/dL (IQR=54 mg/dL; range of decreased 374 mg/dL to increased 240 mg/dL). A statistically significant greater percentage of treatments of patients with type 2 diabetes resulted in a decrease in BGL (1598 or 77.5%) compared to treatments of patients with type 1 diabetes (169 or 51.5%) (χ2(1, N=1767) =55.37, p⟨0.001). 1.1% of treatments had post-HBO2 serum glucose ⟨90 mg/dL, and 0.2% of treatments had post-HBO2 serum glucose ⟨70 mg/dL. The majority (70%) of patients with post-HBO2 BGL ⟨90 mg/dL were maintained on insulin alone (χ2(2, N=20) =12.4, p=0.002). Well-controlled diabetics (i.e., those with all BGLs within 50 mg/dL over all pre-HBO2 treatments) had no post-HBO2 BGL ⟨70 mg/dL or ⟨90 mg/dL., Conclusion: Our results suggest that HBO2 does not cause a clinically significant decrease in diabetic patient BGL. No patient in our study had deleterious side effects or required emergency care. We found that glucose level of ⟨90 mg/dL occurred more often in those who use insulin. Hyperbaric patients who exhibit consistent BGL values may represent a group who could be managed similarly to the non-diabetic population., Competing Interests: The authors of this paper declare no conflicts of interest exist with this submission., (Copyright© Undersea and Hyperbaric Medical Society.)

Objective: Plasma levels of branched-chain amino acids (BCAA) are consistently elevated in obesity and type 2 diabetes (T2D) and can also prospectively predict T2D. However, the role of BCAA in the pathogenesis of insulin resistance and T2D remains unclear., Methods: To identify pathways related to insulin resistance, we performed comprehensive gene expression and metabolomics analyses in skeletal muscle from 41 humans with normal glucose tolerance and 11 with T2D across a range of insulin sensitivity (SI, 0.49 to 14.28). We studied both cultured cells and mice heterozygous for the BCAA enzyme methylmalonyl-CoA mutase (Mut) and assessed the effects of altered BCAA flux on lipid and glucose homeostasis., Results: Our data demonstrate perturbed BCAA metabolism and fatty acid oxidation in muscle from insulin resistant humans. Experimental alterations in BCAA flux in cultured cells similarly modulate fatty acid oxidation. Mut heterozygosity in mice alters muscle lipid metabolism in vivo, resulting in increased muscle triglyceride accumulation, increased plasma glucose, hyperinsulinemia, and increased body weight after high-fat feeding., Conclusions: Our data indicate that impaired muscle BCAA catabolism may contribute to the development of insulin resistance by perturbing both amino acid and fatty acid metabolism and suggest that targeting BCAA metabolism may hold promise for prevention or treatment of T2D.

Background: The frequency of migraine headaches is higher in women than in men and in susceptible women attacks are related to changes in ovarian hormone levels. Intracranial mast cells (MCs) are likely to have a role in migraine headache genesis, and changes in the dural MC population might influence headache susceptibility. The present study thus tested the hypothesis that sex and ovarian hormones influence the density and phenotypic makeup of dural MCs., Methods: Histochemistry combined with quantitative analyses was used to investigate sex differences, estrous cycle and ovarian hormones on dural MC density, phenotype and degranulation level in male and female rats., Results: Our data show that in female rats, dural MC density fluctuates during the estrous cycle and is overall higher than in males. In ovariectomized rats, estradiol, but not progesterone, promoted an increase in dural MC density. This effect was abolished by a splenectomy, suggesting estrogen-related recruitment of MCs from the spleen. Finally, our data suggest that the phenotypic make up of dural MCs, which represents the level of cellular maturity, is also governed by changes in estrogen levels., Conclusions: Given the potential role of dural MCs in triggering headache, our data suggest that estrogen-related modulation of dural MC density and phenotypic makeup could have a role in mediating the higher frequency and severity of headaches such as migraine, in women.

We would like to respond to Brosch et al. regarding our manuscript "Expression of the Splicing Factor Gene SFRS10 Is Reduced in Human Obesity and Contributes to Enhanced Lipogenesis" (Pihlajamäki et al., 2011b). Brosch performed RT-PCR in liver samples from 13 lean and 34 obese individuals, finding no differences in SFRS10 or LPIN1 expression. We wish to address points raised by Brosch, including experimental strategy and analysis of human SFRS10 expression.

Genome-wide association analyses (GWAS) contributed to the detection of a number of single-nucleotide polymorphisms (SNPs) associated with obesity. However, little is known about the impact of the obesity-risk alleles on weight loss-related phenotypes after lifestyle interventions. A recent meta-analysis of GWAS reported five genomic loci near or in the genes FTO, MC4R, TMEM18, SDCCAG8, TNKS/MSRA that were associated with obesity in children and adolescents. Here, we analyzed the effect of the 10 SNPs representative of the five loci on measures of weight loss and cardiometabolic risk after a 1-year lifestyle intervention in 401 children and adolescents (mean age 10.74 years; 55.4% female; mean BMI 27.42 kg/m(2), mean BMI-standard deviation score (SDS) 2.37). For confirmation of one locus genotyping of three intronic SNPs in SDCCAG8 was performed in 626 obese adults who completed the 10-week hypoenergetic diet program. Intronic variants of SDCCAG8, which are associated with early onset obesity, are associated with reduced weight loss after a 1-year lifestyle intervention in overweight children and adolescents even after adjusting for age, sex, baseline measurement, or multiple testing (all P < 10(-6)). However, our results could not be confirmed in 626 obese adults undertaking a hypoenergetic diet intervention.

Alternative mRNA splicing provides transcript diversity and may contribute to human disease. We demonstrate that expression of several genes regulating RNA processing is decreased in both liver and skeletal muscle of obese humans. We evaluated a representative splicing factor, SFRS10, downregulated in both obese human liver and muscle and in high-fat-fed mice, and determined metabolic impact of reduced expression. SFRS10-specific siRNA induces lipogenesis and lipid accumulation in hepatocytes. Moreover, Sfrs10 heterozygous mice have increased hepatic lipogenic gene expression, VLDL secretion, and plasma triglycerides. We demonstrate that LPIN1, a key regulator of lipid metabolism, is a splicing target of SFRS10; reduced SFRS10 favors the lipogenic β isoform of LPIN1. Importantly, LPIN1β-specific siRNA abolished lipogenic effects of decreased SFRS10 expression. Together, our results indicate that reduced expression of SFRS10, as observed in tissues from obese humans, alters LPIN1 splicing, induces lipogenesis, and therefore contributes to metabolic phenotypes associated with obesity., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Aims: The G-allele of the single nucleotide polymorphism (SNP) rs10830963 in MTNR1B (melatonin receptor 1B gene) is associated with type 2 diabetes mellitus and glucose levels in adults. The aim of this study was to analyze whether there is an allele-dosage effect on glucose metabolism in overweight children and to explore if changes in glucose metabolism in a lifestyle intervention do also depend on genotype., Methods: We genotyped rs10830963 in 1118 overweight children and adolescents [mean age 10.7 yr, mean body mass index (BMI) 27.8 kg/m2]; 340 of these individuals completed a 1-yr lifestyle intervention (mean age 10.7 yr, mean BMI 27.9 kg/m2). The degree of overweight [BMI-SDS (standard deviation score)], fasting insulin, glucose, homeostasis model assessment for insulin resistance (HOMA-IR), and quantitative insulin sensitivity check index (QUICKI) were measured before and after intervention., Results: We showed a significant relationship between rs10830963 and basal glucose levels [β:1.101, 95% confidence interval (CI) 0.316-1.886 mg/dL per risk allele; p = 0.006] by linear regression adjusted for age, age(2), and sex. There was no effect of the allele on insulin or indices of insulin resistance or sensitivity. After the 1-yr lifestyle intervention, we observed a significant reduction of BMI-SDS as well as an improvement of HOMA-IR and QUICKI, but no evidence for an association between rs10830963 genotype and changes of glucose levels., Conclusions: The G-allele of rs10830693 in the MTNR1B gene was significantly related to glucose levels, while an impact of this genetic variant on the changes in glucose metabolism in children participating in a lifestyle intervention was not observable., (© 2011 John Wiley & Sons A/S.)

Insulin resistance in skeletal muscle is a key phenotype associated with type 2 diabetes (T2D) for which the molecular mediators remain unclear. We therefore conducted an expression analysis of human muscle biopsies from patients with T2D; normoglycemic but insulin-resistant subjects with a parental family history (FH(+)) of T2D; and family history-negative control individuals (FH(–)). Actin cytoskeleton genes regulated by serum response factor (SRF) and its coactivator megakaryoblastic leukemia 1 (MKL1) had increased expression in T2D and FH(+) groups. Furthermore, striated muscle activator of Rho signaling (STARS), an activator of SRF, was upregulated in T2D and FH(+) and was inversely correlated with insulin sensitivity. Skeletal muscle from insulin-resistant mice recapitulated this gene expression pattern and showed reduced G-actin and increased nuclear localization of MKL1, each of which regulates SRF activity. Overexpression of MKL1 or reduction in G-actin decreased insulin-stimulated Akt phosphorylation, whereas reduction of STARS expression increased insulin signaling and glucose uptake. Pharmacological SRF inhibition by CCG-1423 reduced nuclear MKL1 and improved glucose uptake and tolerance in insulin-resistant mice in vivo. Thus, SRF pathway alterations are linked to insulin resistance, may contribute to T2D pathogenesis, and could represent therapeutic targets.

Objective: Association with obesity and increased insulin levels have been reported for two variants (rs17782313 and rs12970134) located downstream of the melanocortin-4 receptor gene (MC4R)., Methods: We investigated whether these variants have sex-specific effects on overweight, obesity and 14 related phenotypes in 889 overweight and obese children and adolescents. We also explored the impact of the variants on weight change in 367 of the 889 cases who participated in an intervention program. Prior to these analyses we showed that both variants were associated with overweight/obesity in the analyzed 889 cases versus 442 normal-weight and lean controls (case-control study)., Results: In explorative analyses we observed higher diastolic blood pressure levels in males (rs17782313: β = 2.52 mm Hg per risk allele; p = 0.003) but reduced blood pressure level in females for the same risk allele (β = -1.72 mm Hg; p = 0.039). We also detected a greater BMI standard deviation score (BMI-SDS) reduction in females with the risk allele at rs17782313 (β = 0.086 per risk allele; p = 0.021). Additionally, we observed evidence for an association of the same risk allele with insulin levels (β = 0.029 log (μU/ml); p = 0.044) with no sex-specific effect. For the remaining 11 phenotypes, we observed no evidence for a (sex-specific) association., Conclusions: In sum, our data support the associations of variants rs17782313 and rs12970134 near MC4R with early onset obesity and increased insulin levels. Exploratory evidence for sex-specific effects of the risk alleles were observed for diastolic blood pressure and BMI-SDS reduction., (Copyright © 2011 S. Karger AG, Basel.)

To understand the influence of chromosomal alterations on gene expression in a genome-wide view, chromosomal imbalances detected by single nucleotide polymorphism (SNP) chips were compared with global gene expression in 16 cases of chronic lymphocytic leukemia (CLL). A strong concordance between chromosomal gain or loss and increased or reduced expression of genes in the affected regions was found, respectively. Regions of uniparental disomy (UPD) were rare and had usually no consistent influence on gene expression, but in one instance, a large UPD was associated with a downregulation of most genes in the affected chromosome. The frequently deleted miRNAs, MIRN15A and MIRN16-1, did not show a reduced expression in cases with monoallelic deletions. The BCL2 protein, considered to be downregulated by these miRNAs, was upregulated not only in CLL with biallelic deletion of MIRN15A and MIRN16-1, but also in cases with monoallelic deletion. This suggests a complex regulation of BCL2 levels in CLL cells. Taken together, in CLL, a global gene dosage effect exists for chromosomal gains and deletions and in some instances for UPDs. We did not confirm a consistent correlation between MIRN15A and MIRN16-1 expression levels and BCL2 protein levels, indicating a complex regulation of BCL2 expression., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ∼ 2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 × 10⁻⁸), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.

Objective: To examine the association between genomewide association study-based diabetes mellitus-related single-nucleotide polymorphisms (SNPs) and coronary artery calcification (CAC), a valid risk factor for coronary heart disease, in a large, unselected, population-based cohort., Methods and Results: We genotyped 11 validated genomewide association study-based diabetes SNPs in 4459 participants of the Heinz Nixdorf Recall Study. We applied generalized linear regression models to explore the impact of the diabetes SNPs on CAC and to jointly model the effect of the SNPs and CAC on diabetes status. We observed a significant association between cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/2B) variant rs564398 and quantitative CAC (P=1.81 x 10(-5) and adjusted P=4.02 x 10(-4); odds ratio for the presence of CAC, 1.12 [95% CI, 1.02 to 1.25]). Moreover, we observed no strong impact of CAC on diabetes risk in the presence of the other genetic variants., Conclusions: We show that a genetic variant near CDKN2A/2B that has been reported to be strongly associated with diabetes is strongly associated with CAC. In contrast, variants near insulin-like growth factor-binding protein 2 (IGFBP2), CDK5 regulatory subunit associated protein 1-like 1 (CDKAL1), solute carreir family 30 (zinc transporter), member 8 (SLC30A8), hematopoietically-expressed homeobox (HHEX), and transcription factor 7-like2 (TCF7L2) were clearly associated with diabetes; no evidence for an association to CAC was observable. This differential association pattern underlines the potential of endophenotypes, such as CAC, to extend the scope of disease outcome associations.

Meta-analyses of population-based genome-wide association studies (GWAS) in adults have recently led to the detection of new genetic loci for obesity. Here we aimed to discover additional obesity loci in extremely obese children and adolescents. We also investigated if these results generalize by estimating the effects of these obesity loci in adults and in population-based samples including both children and adults. We jointly analysed two GWAS of 2,258 individuals and followed-up the best, according to lowest p-values, 44 single nucleotide polymorphisms (SNP) from 21 genomic regions in 3,141 individuals. After this DISCOVERY step, we explored if the findings derived from the extremely obese children and adolescents (10 SNPs from 5 genomic regions) generalized to (i) the population level and (ii) to adults by genotyping another 31,182 individuals (GENERALIZATION step). Apart from previously identified FTO, MC4R, and TMEM18, we detected two new loci for obesity: one in SDCCAG8 (serologically defined colon cancer antigen 8 gene; p = 1.85x10(-8) in the DISCOVERY step) and one between TNKS (tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase gene) and MSRA (methionine sulfoxide reductase A gene; p = 4.84x10(-7)), the latter finding being limited to children and adolescents as demonstrated in the GENERALIZATION step. The odds ratios for early-onset obesity were estimated at approximately 1.10 per risk allele for both loci. Interestingly, the TNKS/MSRA locus has recently been found to be associated with adult waist circumference. In summary, we have completed a meta-analysis of two GWAS which both focus on extremely obese children and adolescents and replicated our findings in a large followed-up data set. We observed that genetic variants in or near FTO, MC4R, TMEM18, SDCCAG8, and TNKS/MSRA were robustly associated with early-onset obesity. We conclude that the currently known major common variants related to obesity overlap to a substantial degree between children and adults., Competing Interests: The authors have declared that no competing interests exist.

We report a case-control study with 251 unrelated migraine patients and 192 unrelated healthy controls to evaluate an association between the polymorphisms of the 5-HT transporter (5-HTT) gene rs2066713 and rs1979572 and different migraine phenotypes. We found a genetic association for the A allele of rs1979572 for migraine with aura (MA) especially in women as well as a significant lower prevalence for MA for carrier of the A allele of rs2066713 in women. These findings support previous results suggesting that the 5-HTT gene is involved in the polygenic etiology of MA. These data further suggest that women are more likely to be clinically affected by mutations in the 5-HTT gene than men.

Context: Fatty liver is an important complication of obesity; however, regulatory mechanisms mediating altered gene expression patterns have not been identified., Objective: The aim of the study was to identify novel transcriptional changes in human liver that could contribute to hepatic lipid accumulation and associated insulin resistance, type 2 diabetes, and nonalcoholic steatohepatitis., Design: We evaluated gene expression in surgical liver biopsies from 13 obese (nine with type 2 diabetes) and five control subjects using Affymetrix U133A microarrays. PCR validation was performed in liver biopsies using an additional 16 subjects. We also tested thyroid hormone responses in mice fed chow or high-fat diet., Setting: Recruitment was performed in an academic medical center., Participants: Individuals undergoing elective surgery for obesity or gallstones participated in the study., Results: The top-ranking gene set, down-regulated in obese subjects, was comprised of genes previously demonstrated to be positively regulated by T(3) in human skeletal muscle (n = 399; P < 0.001; false discovery rate = 0.07). This gene set included genes related to RNA metabolism (SNRPE, HNRPH3, TIA1, and SFRS2), protein catabolism (PSMA1, PSMD12, USP9X, IBE2B, USP16, and PCMT1), and energy metabolism (ATP5C1, COX7C, UQCRB). We verified thyroid hormone regulation of these genes in the liver after injection of C57BL/6J mice with T(3) (100 microg/100 g body weight); furthermore, T(3)-induced increases in expression of these genes were abolished by high-fat diet. In agreement, expression of these genes inversely correlated with liver fat content in humans., Conclusions: These data suggest that impaired thyroid hormone action may contribute to altered patterns of gene expression in fatty liver.

Objective: A substantial number of patients with acute aortic syndrome (AAS) require invasive therapy because of disease progression. Our study aimed to assess the impact of positron emission tomography (PET)/computed tomography (CT) and serological markers of inflammation to identify patients at high risk for disease progression., Methods: 33 patients with AAS (thoracic aortic aneurysm 5, thoracic aortic dissection 14, penetrating aortic ulcer 8, intramural haematoma 6) were included. After intravenous administration of [18F] fluorodeoxyglucose a non-contrast enhanced PET/CT of the body trunk and CT angiography of the entire aorta was performed. Serological levels of D-dimers and C-reactive protein (CRP) were measured in all patients. Follow-up imaging was performed to detect disease progression., Results: 11 (33%) of 33 patients showed elevated tracer uptake within the aortic pathology, whereas 22 patients were PET-negative. In 23 patients a CRP level exceeding 1.0 mg/dl or a D-dimer level larger than 250 microg/l was found. The follow-up time was 224 (195) days. Nine of 11 PET-positive patients (82%) showed progression of AAS. In contrast, 55% of PET-negative patients showed stable disease or regression during the follow-up period. Kaplan-Meier analysis showed a clear, but not yet significant trend to longer survival in PET-negative patients, whereas elevated CRP and D-dimers did not allow for distinguishing of high-risk patients., Conclusions: Vessel wall inflammation was found in one-third of the patients with AAS and this patient group seems to have a high risk for disease progression. These initial results needs further investigation.

Background: Hierarchical clustering is a widely applied tool in the analysis of microarray gene expression data. The assessment of cluster stability is a major challenge in clustering procedures. Statistical methods are required to distinguish between real and random clusters. Several methods for assessing cluster stability have been published, including resampling methods such as the bootstrap. We propose a new resampling method based on continuous weights to assess the stability of clusters in hierarchical clustering. While in bootstrapping approximately one third of the original items is lost, continuous weights avoid zero elements and instead allow non integer diagonal elements, which leads to retention of the full dimensionality of space, i.e. each variable of the original data set is represented in the resampling sample., Results: Comparison of continuous weights and bootstrapping using real datasets and simulation studies reveals the advantage of continuous weights especially when the dataset has only few observations, few differentially expressed genes and the fold change of differentially expressed genes is low., Conclusion: We recommend the use of continuous weights in small as well as in large datasets, because according to our results they produce at least the same results as conventional bootstrapping and in some cases they surpass it.

During the 2003 heat wave an increase in mortality was observed in several European countries. Evidence suggests that the heat wave effect on mortality varies based upon underlying disease. In this study we examined the effects of the 2003 heat wave on all-cause and cause-specific mortality (neoplasms, cardiovascular and respiratory diseases) in a large west German city. Daily weather data for Essen was obtained from the German meteorological service. Death certificates for all deaths in Essen from 2002 to 2003 were coded according to the World Health Organization (WHO) guidelines. Mean numbers of daily deaths during and after the heat wave were compared with the average mortality in summer months (reference period). Poisson generalized additive models, adjusted for weekday and season, were fitted for overall and cause-specific mortality for the entire study period. During the 2003 heat wave (August 6-12), daily mortality increased by 15% (neoplasms), 30% (cardiovascular), and 61% (respiratory), with a decrease in the week after the heat wave of 17% for neoplasms and a sustained rise for respiratory mortality (77%). Regression analysis showed an association between heat and overall mortality in 2003 and greatest associations for respiratory mortality. Even the comparatively short heat wave in Essen in the year 2003 was associated with a rise in overall and cause-specific mortality. Different mechanisms appear to influence cause-specific mortality, with strongest associations for respiratory mortality. Harvesting might play a role in mortality due to neoplasms.

T-cell prolymphocytic leukemia (T-PLL) is a rare aggressive lymphoma derived from mature T cells, which is, in most cases, characterized by the presence of an inv(14)(q11q32)/t(14;14)(q11;q32) and a characteristic pattern of secondary chromosomal aberrations. DNA microarray technology was employed to compare the transcriptomes of eight immunomagnetically purified CD3+ normal donor-derived peripheral blood cell samples, with five highly purified inv(14)/t(14;14)-positive T-PLL blood samples. Between the two experimental groups, 734 genes were identified as differentially expressed, including functionally important genes involved in lymphomagenesis, cell cycle regulation, apoptosis and DNA repair. Notably, the differentially expressed genes were found to be significantly enriched in genomic regions affected by recurrent chromosomal imbalances. Upregulated genes clustered on chromosome arms 6p and 8q, and downregulated genes on 6q, 8p, 10p, 11q and 18p. High-resolution copy-number determination using single nucleotide polymorphism chip technology in 12 inv(14)/t(14;14)-positive T-PLL including those analyzed for gene expression, refined chromosomal breakpoints as well as regions of imbalances. In conclusion, combined transcriptional and molecular cytogenetic profiling identified novel specific chromosomal loci and genes that are likely to be involved in disease progression and suggests a gene dosage effect as a pathogenic mechanism in T-PLL.

Objectives: When estimating the expression of genes based on the scanned images from microarrays various algorithms are applied in a so-called low-level analysis which can calculate expression values with an arbitrary number of digits beyond the decimal point. However, too many digits (decimal places) are usually not justified because they do not represent the precision of the measured expression. Thus, there is pseudo-precision and, as a result, there are no tied values., Methods: We suggest avoiding, or omitting, the pseudo-precision: ties can remain, or be created by rounding the computed expression values. Then, average ranks can be used in order to apply nonparametric tests when ties occur. We use two actual data sets and the Wilcoxon rank sum test., Results: We demonstrate that rounding gives a more efficient test, i.e. the average p-value is decreased and the number of p-values smaller than 0.05 is increased., Conclusions: The random noise of pseudo-precision can reduce the efficiency of statistical tests applied to detect differentially expressed genes. This result is, obviously, relevant in many other areas of our digitalized world.

Drug resistance constitutes a considerable problem in the therapy of acute myeloid leukemia (AML). In order to identify genes which might be related to drug resistance, we retrospectively studied gene expression patterns in blast populations of 14 patients with de novo AML, focusing on known or potential resistance mechanisms against cytosine arabinoside and anthracyclines. Following induction and postremission chemotherapy, 7 patients achieved a complete remission (CR) for more than 1 year, while 7 patients showed blast persistence (BP) after induction and salvage chemotherapy. Gene expression analysis was performed using RNA extracted from archived guanidine extracts and Affymetrix HGU133A gene chips. We utilized the Gene Ontology category Biological Process to select genes implicated in DNA metabolism, nucleoside and nucleotide metabolism and transport, reactive oxygen species metabolism, apoptosis and response to drugs and identified 32 differentially expressed genes. From this functional perspective, we found differences between the CR and BP groups with regard to nucleotide metabolism (PBEF1, G6PD; p = 0.048), apoptosis (TNFAIP3, TNFAIP8, MPO, BCL2A1, BAX, SON, BNIP3L; p = 0.039) and reactive oxygen species metabolism (SOD2, KIAA0179; p = 0.048). However, the attempt to construct a predictive model of chemoresistance failed. BP samples had a 2-fold higher expression of CD34 than CR samples. Thus, our findings are in line with reports describing differences in apoptosis resistance between CD34+ and CD34- blast populations. Taken together, our results suggest that drug resistance in AML is a heterogenous phenomenon that might be better defined by means of disturbed biological processes than by focusing on the alteration of the expression of distinct genes., (2007 S. Karger AG, Basel)

Objective: To evaluate the effect of extracorporeal gas exchange (ECMO) on mortality of patients referred with severe acute respiratory distress syndrome (ARDS)., Design and Setting: Prospective observational study in a university hospital ICU., Patients: 150 patients with severe ARDS., Interventions: Multimodal treatment with and without ECMO., Measurements and Main Results: We treated 118 patients (78.7%) conservatively and 32 patients with ECMO. Patients in the ECMO group presented with significantly more severe disease (lung injury score 3.8+/-0.3 vs. 3.3+/-0.4; SOFA score 52+/-14 vs. 43+/-12; and SAPS score 14+/-3.3 vs. 10+/-3.5). Mortality in ECMO-treated patients tended to be higher than that with conservative treatment (46.9% vs. 28.8%, p=0.059). Multivariate logistic regression analyses with backward selection excluded ECMO as predictor of mortality (p=0.79). Independent predictors of mortality were age (odds ratio 1.044, 95% confidence interval 1.014-1.075, p=0.004), mean pulmonary artery pressure (1.082, 1.026-1.141, p=0.036), sequential organ failure assessment score (1.148, 1.018-1.294, p=0.024), and days of mechanical ventilation prior to referral (1.064, 1.008-1.123, p=0.025)., Conclusion: ECMO treatment does not predict mortality in patients with most severe ARDS.

Gene expression studies from hematopoietic stem cell (HSC) populations purified to variable degrees have defined a set of stemness genes. Unexpectedly, results also hinted toward a HSC chromatin poised in a wide-open state. With the aim of providing a robust tool for further studies into the molecular biology of HSCs, the studies herein describe the construction and comparative molecular analysis of lambda-phage cDNA libraries from highly purified HSCs that retained their long-term repopulating activities (long-term HSCs [LT-HSCs]) and from short-term repopulating HSCs that were largely depleted of these activities. Microarray analysis of the libraries confirmed the previous results but also revealed an unforeseen preferential expression of translation- and metabolism-associated genes in the LT-HSCs. Therefore, these data indicate that HSCs are quiescent only in regard of proliferative activities but are in a state of readiness to provide the metabolic and translational activities required after induction of proliferation and exit from the HSC pool.

Objective: To evaluate the prevalence of pulmonary hypertension associated with severe acute respiratory distress syndrome (ARDS) and to asses the value of pulmonary artery trunk diameter (PAT) to predict pulmonary hypertension., Design: Prospective study, Setting: University teaching hospital and ARDS referral center., Patients: 103 patients with ARDS, who received both right heart catheterization and chest computed tomography., Interventions: None., Measurements and Results: 95 patients (92.2%) with ARDS had pulmonary artery hypertension, 16 of them (16.8%) mild, 72 (75.8%) moderate, and 7 (7.4%) severe, as assessed by right heart catheterization. Of the patients with moderate and severe pulmonary hypertension, 43 had a pulmonary artery trunk diameter >or=29 mm yielding a sensitivity of 0.54 and a specificity of 0.63. Pulmonary artery trunk diameter correlated significantly but weakly with mean pulmonary artery pressure (r=0.34, p=0.0004). The positive predictive value was 0.83, and the negative predictive value was 0.28. The diagnosis of pulmonary hypertension by PAT diameter measurements was incorrect in 43.7% of patients with ARDS., Conclusions: Pulmonary artery hypertension has a high prevalence in patients with severe ARDS. Measurement of PAT diameter on admission CT scan is an unreliable tool for identification of ARDS patients with pulmonary hypertension.

Background: One important application of microarray experiments is to identify differentially expressed genes. Often, small and negative expression levels were clipped-off to be equal to an arbitrarily chosen cutoff value before a statistical test is carried out. Then, there are two types of data: truncated values and original observations. The truncated values are not just another point on the continuum of possible values and, therefore, it is appropriate to combine two statistical tests in a two-part model rather than using standard statistical methods. A similar situation occurs when DNA methylation data are investigated. In that case, there are null values (undetectable methylation) and observed positive values. For these data, we propose a two-part permutation test., Results: The proposed permutation test leads to smaller p-values in comparison to the original two-part test. We found this for both DNA methylation data and microarray data. With a simulation study we confirmed this result and could show that the two-part permutation test is, on average, more powerful. The new test also reduces, without any loss of power, to a standard test when there are no null or truncated values., Conclusion: The two-part permutation test can be used in routine analyses since it reduces to a standard test when there are positive values only. Further advantages of the new test are that it opens the possibility to use other test statistics to construct the two-part test and that it avoids the use of any asymptotic distribution. The latter advantage is particularly important for the analysis of microarrays since sample sizes are usually small.

Objectives: The high density oligonucleotide microarrays from Affymetrix (Affymetrix GeneChips) are very popular in biomedical research. They enable to study the expression of thousands of genes simultaneously. In experiments with multiple arrays, normalization techniques are used to reduce the so-called obscuring variation, i.e. the technical variation that is of non-biological origin. Several different normalization methods have been proposed during the last years., Methods: We review published results about the comparison of normalization methods proposed for Affymetrix GeneChips., Results: The quantile normalization seems to perform favorably regarding precision (low variance), accuracy (low bias), and practicability (low computing time). However, according to very recent results, this normalization method can have an impact on the biological variability and, therefore, appears to be less than optimal from this point of view., Conclusion: Although the quantile normalization may be recommendable, more investigations based on more data sets are needed so that the different normalization methods can be evaluated on widely differing data.

Motivation: Loss of chromosomal material is often observed in cancer cells. In this situation the expression of genes is related to their position on the genome. Epigenetic phenomena may also silence several genes in the same region of a chromosome. While cytogenetic or other molecular genetic methods spot changes of DNA copy number, they cannot detect other causes of silencing., Results: We propose a method that utilizes the link from expression information gained from high-density DNA microarrays to the gene locus according to current databases. Statistical methods adequate to spot conspicuous runs of non-expressed genes are introduced and compared to one another by merit of their power and robustness against false positives., Availability: Code for the formulae can be obtained (R code) via http://www.panix.com/~derwisch/hannes/longrun

Microarray technology enables researchers to investigate the expression of several thousand genes simultaneously. The whole transcriptional response of these genes in normal cells or tissue, in disease condition, as an response to biological, genetical or chemical stimuli or during normal biological processes such as cell cycle or embryonic development can be investigated. This leads to a huge amount of data, from which the relevant information has to be extracted by statistical and computational methods. Several software packages for the analysis of gene expression data are available, both commercially and freely. They differ particularly with regard to the implemented analytical methods, the graphical display and the manageability. In this paper the commercial software packages arraySCOUT, GeneSpring and Spotfire DecisionSite for Functional Genomics are compared and their applicability for analysis of gene expression data is studied. Small artificial and application test datasets are used to compare the computational results of the software packages. As far as possible results are verified with standard statistical software package SAS.