A clustering approach to improve our understanding of the genetic and phenotypic complexity of chronic kidney disease.

Chronic kidney disease (CKD) is a complex disorder that causes a gradual loss of kidney function, affecting approximately 9.1% of the world's population. Here, we use a soft-clustering algorithm to deconstruct its genetic heterogeneity. First, we selected 322 CKD-associated independent genetic variants from published genome-wide association studies (GWAS) and added association results for 229 traits from the GWAS catalog. We then applied nonnegative matrix factorization (NMF) to discover overlapping clusters of related traits and variants. We computed cluster-specific polygenic scores and validated each cluster with a phenome-wide association study (PheWAS) on the BioMe biobank (n = 31,701). NMF identified nine clusters that reflect different aspects of CKD, with the top-weighted traits signifying areas such as kidney function, type 2 diabetes (T2D), and body weight. For most clusters, the top-weighted traits were confirmed in the PheWAS analysis. Results were found to be more significant in the cross-ancestry analysis, although significant ancestry-specific associations were also identified. While all alleles were associated with a decreased kidney function, associations with CKD-related diseases (e.g., T2D) were found only for a smaller subset of variants and differed across genetic ancestry groups. Our findings leverage genetics to gain insights into the underlying biology of CKD and investigate population-specific associations.

A clustering approach to improve our understanding of the genetic and phenotypic complexity of chronic kidney disease.

Chronic kidney disease (CKD) is a complex disorder that causes a gradual loss of kidney function, affecting approximately 9.1% of the world's population. Here, we use a soft-clustering algorithm to deconstruct its genetic heterogeneity. First, we selected 322 CKD-associated independent genetic variants from published genome-wide association studies (GWAS) and added association results for 229 traits from the GWAS catalog. We then applied nonnegative matrix factorization (NMF) to discover overlapping clusters of related traits and variants. We computed cluster-specific polygenic scores and validated each cluster with a phenome-wide association study (PheWAS) on the BioMe biobank (n=31,701). NMF identified nine clusters that reflect different aspects of CKD, with the top-weighted traits signifying areas such as kidney function, type 2 diabetes (T2D), and body weight. For most clusters, the top-weighted traits were confirmed in the PheWAS analysis. Results were found to be more significant in the cross-ancestry analysis, although significant ancestry-specific associations were also identified. While all alleles were associated with a decreased kidney function, associations with CKD-related diseases (e.g., T2D) were found only for a smaller subset of variants and differed across genetic ancestry groups. Our findings leverage genetics to gain insights into the underlying biology of CKD and investigate population-specific associations.

[Nihil certum: historical development of the term prurigo]. / Nihil certum: Historische Entwicklung des Begriffs Prurigo.

The term prurigo is still used to designate primary dermatoses and secondary reaction patterns. A clear definition of the term is not available nor a clear clinical classification of diseases categorized under the term. Furthermore, there is no certainty about the entity it was primarily used to refer to, and whether it should always be considered in relation to pruritus. The concept appears already in very early medical treatises. From the very beginning, it was used in dermatology in a non-uniform way, and was alternately accorded and denied the status of an independent disease entity. Moreover, prurigo was subdivided into many different forms, but their descriptions are partly very similar, so that, for instance, it is quite difficult today to draw any conclusions about the clinical entities the frequently used terms prurigo mitis and prurigo formicans referred to. In contrast, the term prurigo nodularis is still commonly used. This article traces exemplarily the use of the term prurigo in the standard medical textbooks up to the definition of prurigo nodularis.

[Prurigo. Clinical definition and classification]. / Prurigo. Klinische Definition und Klassifikation.

BACKGROUND: There is no consistent definition of the term prurigo and a clear classification is unavailable. OBJECTIVES: Definition of the current forms of prurigo and a new approach to a specific classification. METHODS: Review of the types of prurigo as presented in current textbooks and publications. RESULTS: Pruritus is the main symptom of prurigo and shows an intensely pruritic papule or nodule as the main efflorescence. The term prurigo is not only used for secondary lesions, but also for primary dermatoses. The different forms of prurigo obtain their names depending on etiology, onset and duration of lesions or the clinical appearance. CONCLUSIONS: The term prurigo has not been used consistently. A revision of the classification with a clear distinction between primary dermatoses and secondary lesions seems reasonable. In secondary prurigo, a clinical classification and the cause should be mentioned.

Quantitative analysis of the intra- and inter-subject variability of the whole salivary proteome.

BACKGROUND AND OBJECTIVE: Interest in human saliva is increasing for disease-specific biomarker discovery studies. However, protein composition of whole saliva can grossly vary with physiological and environmental factors over time and it comprises human as well as bacterial proteins. MATERIAL AND METHODS: We compared intra- and inter-subject variabilities using complementary gel-based (two-dimensional difference gel electrophoresis, 2-D DIGE) and gel-free (liquid chromatography tandem mass spectrometry, LC-MS/MS) proteomics profiling of saliva. Unstimulated whole saliva of four subjects was examined at three different time-points (08.00 h, 12.00 h and 17.00 h) and variability of the saliva proteome was analyzed on two successive days by LC-MS/MS. RESULTS: In the 2-D DIGE experiment, the median coefficient of variation (CV) for intra-subject variability was significantly lower (CV of 0.39) than that for inter-subject variability (CV of 0.57; CV of technical replicates 0.17). LC-MS/MS data confirmed the significantly lower variation within subjects over time (CV of 0.37) than the inter-subject variability (CV of 0.53; CV of technical replicates 0.11), and that the inter-subject variability was not time-dependent. CONCLUSION: Both techniques revealed similar trends of variations on technical, intra- and inter-subject level but provided peptide and protein focused information and should thus be used as complementary approaches. The data presented indicate that 2-D DIGE as well as LC-MS/MS approaches are suitable for biomarker screening in saliva.

Invariom modeling of ceftazidime pentahydrate: molecular properties from a 200 second synchrotron microcrystal experiment.

The structure of ceftazidime pentahydrate, a third generation cephalosporin antibiotic, is reported. Data collection was carried out in a remarkably short time with synchrotron radiation and the latest detector technology, illustrating that single-crystal X-ray diffraction can be used as a technique for screening hundreds of compounds in a short amount of time. Structure refinement made use of invarioms, namely non-spherical scattering factors, which allow more information to be derived from a diffraction experiment. Properties that can be screened are bond-topological parameters, empirical hydrogen-bond energies, molecular dipole moments and electrostatic potentials.

The androgen receptor CAG repeat polymorphism as a risk factor of low serum testosterone and its cardiometabolic effects in men.

Previous studies reported correlations of CAG repeat length with sex hormone serum concentrations and cardiometabolic risk factors, but were limited by small cross-sectional samples. We used data of 1859 men aged 20-79 years from the population-based Study of Health in Pomerania (SHIP) to investigate the direct and modulating effects of CAG repeat length on androgen action and cardiometabolic risk factors. We performed cross-sectional and longitudinal linear and Poisson regression models adjusted for age, smoking, physical activity, alcohol consumption and body mass index. The CAG repeat length was categorized into quartiles and low total testosterone (TT) defined according to the age-specific (by decades) 10th percentile, respectively. Age-adjusted cross-sectional linear regression models showed a positive association between CAG repeat length and serum testosterone concentrations [ß coefficient for TT, 0.099 (p = 0.028) and for free T, 0.002 (p = 0.001), respectively]. After a 5.0 year median follow-up period, men with CAG repeat length in the lowest quartile had an increased risk of incident low TT concentrations [relative risk (RR), 2.31; 95% confidence interval (CI), 1.18-4.55]. We found no direct association between CAG repeat length and cardiometabolic risk factors in cross-sectional and longitudinal multivariable linear regression analyses; whereas men with longer CAG repeat length and low TT concentrations showed the highest risk of incident MetS (RR, 1.51; 95% CI, 1.05-2.16). CAG repeat length is a risk factor of incident low TT concentrations and a contributing factor of testosterone-related cardiometabolic effects. The added clinical value of a combined assessment of CAG repeat length and serum TT concentrations merits further investigation.

Role of wound macrophages in skin flap loss or survival in an experimental diabetes model.

BACKGROUND: Tightly controlled wound inflammation is a central determinant of skin flap survival in healthy mice. This study investigated inflammatory response patterns in caudally pedicled skin flaps in diabetic mice during severely impaired conditions of necrotic skin flap tissue loss. METHODS: Skin flap biopsies were analysed by RNase protection assay, quantitative real-time polymerase chain reaction, immunohistochemistry, enzyme-linked immunosorbent assay and immunoblotting. RESULTS: Skin flaps were characterized by the necrotic loss of tissue starting from distal areas of the flaps in diabetic mice. Decay of epidermal and dermal structures within skin flap tissue was paralleled by an immune cell-mediated expression of chemokines (macrophage inflammatory protein 2, macrophage chemoattractant protein 1), cyclo-oxygenase (COX) 2 and inducible nitric oxide synthase (iNOS). Distal regions of necrotic skin flap tissue were infiltrated by excess numbers of neutrophils and macrophages, and the latter were polarized towards a proinflammatory state as they expressed COX-2 and iNOS. Experimental depletion of inflammatory macrophages inhibited necrotic destruction of the distal skin flap tissue in diabetic mice despite the persistence of neutrophil infiltration and inflammation. CONCLUSION: Wound macrophages play a pivotal role in determining the survival or loss of skin flap tissue under disturbed wound healing conditions in obese diabetic mice.

[Immune reconstitution inflammatory syndrome (IRIS) of the small bowel in an immunocompromised patient suffering from systemic lupus erythematosus and non-tuberculous mycobacteriosis]. / Immunrekonstitutionssyndrom des Dünndarms bei einer immunsupprimierten Patientin mit systemischem Lupus erythematodes und nichttuberkulöser Mykobakteriose.

An overwhelming immune reaction resulting in granulomatous inflammation after infection with opportunistic pathogens is termed immune reconstitution inflammatory syndrome (IRIS). It has mainly been described in patients with human immunodeficiency virus (HIV) infection on highly active antiretroviral therapy (HAART) who show a significant increase of low CD4 T cells (initially <50/microl). IRIS may lead to organ damage and differential diagnosis is often difficult. We report the case of a 38-year-old female patient who developed a Mycobacteria genavense infection of the liver and the bowel after several immunosuppressive therapies for systemic lupus erythematosus. CD4 T cell counts as low as 17/microl were found and immunosuppressive therapy was stopped. Despite several courses of antibiotic treatment and rising CD4 T cell counts, severe malabsorption persisted. Upper endoscopy revealed a continuous inflammation with pseudopolyps of the small bowel and histologically, a granulomatous infiltrate was detected. After exclusion of a persisting infection by Mycobacteria genavense, IRIS of the small bowel was suspected and treatment with prednisolone was started. The clinical and histological picture improved significantly, the number of CD25(+)CD4(+) cells decreased in the lamina propria of the duodenum under treatment with prednisolone and Foxp3+ regulatory T cells (Treg) accumulated around granulomas. This case shows that IRIS is not restricted to HIV patients but may also occur in otherwise immunosuppressed patients. Due to different treatment strategies, distinguishing IRIS from infectious diseases is essential. The role of Treg in IRIS has to be elucidated.

Life history of wild Sumatran orangutans (Pongo abelii).

We present life history data on wild Sumatran orangutans gleaned from a 32-year and a 5.5-year study. Estimated age at first reproduction was 15.4 years. At 9.3 years, the average interbirth interval for this population is the longest ever recorded for any great ape population, significantly longer than that of a Bornean orangutan population. We find that age-specific mortality of Sumatran orangutans does not differ between sexes and is significantly lower than that of wild chimpanzees. We conclude that orangutan life history is the slowest among extant great apes. In accordance with their slow life history, longevity in the wild is estimated to be at least 58 years for males and at least 53 for females. We find no evidence for menopause. These data suggest that compared to the ancestral state, humans have undergone less of an increase in longevity than commonly assumed, and have experienced selection on earlier cessation of reproduction.

Annoyance from multiple transportation noise: statistical models and outlier detection.

OBJECTIVE: Statistical models for the annoyance from multiple transportation noise are needed to understand and predict the annoyance resulting from specific noise exposures. METHODS: Models from the class of generalized linear models are suggested and discussed. Observations which are not well explained by the considered model are regarded as outliers. Outlier detection methods are applied to the data modelled by robust estimates using different link functions. RESULTS: The discussed methods are applied to data from a laboratory experiment using generalized linear models. While considering outliers, a generalized linear model with a complementary log-log link is found to be a good choice in modelling the exposure-response relationship between noise levels and annoyance.

FH-Freiburg: a novel missense mutation (C317Y) in growth factor repeat A of the low density lipoprotein receptor gene in a German patient with homozygous familial hypercholesterolemia.

We describe the characterization of a novel mutation in the low density lipoprotein receptor (LDL-R) gene in a patient with true homozygous familial hypercholesterolemia (FH). The combined use of denaturing gradient gel electrophoresis (DGGE) and sequencing of genomic DNA revealed a guanine to adenine base substitution at nucleotide position 1013 of the LDL-R cDNA. This point mutation results in a change from cysteine to tyrosine at amino acid residue 317 of repeat A of the epidermal growth factor (EGF) precursor homology domain. Binding, uptake and degradation of iodinated LDL in skin fibroblasts from the homozygous patient were less than 10% of normal. In contrast, binding, uptake and degradation of iodinated VLDL was reduced by only 60, 30, and 38%, respectively. Incubation of the patient's fibroblasts in the presence of cholesterol diminished the residual binding of VLDL by 50%, suggesting that the loss of the highly conserved cysteine at position 317 results in a LDL-R that fails to bind LDL, but retains some ability to bind VLDL by interacting with the apolipoprotein E. Both parents were heterozygous for the C317Y mutation. Interestingly, however, the father presented with markedly elevated levels of triglycerides and VLDL cholesterol, whereas his LDL cholesterol was unexpectedly low. The mother of the index patient had only slightly elevated LDL cholesterol. These observations testify to the biological complexity of genotype-environment interactions in individuals carrying mutations at the LDL-R locus and indicate that genetic analysis importantly complements the clinical and biochemical diagnosis of patients with hyperlipidemia.

Interleukin-6 stimulates LDL receptor gene expression via activation of sterol-responsive and Sp1 binding elements.

Inflammatory or malignant diseases are associated with elevated levels of cytokines and abnormal low density lipoprotein (LDL) cholesterol metabolism. In the acute-phase response to myocardial injury or other trauma or surgery, total and LDL cholesterol levels are markedly decreased. We investigated the effects of the proinflammatory cytokine interleukin (IL)-6 on LDL receptor (LDL-R) function and gene expression in HepG2 cells. IL-6 dose-dependently increased the binding, internalization, and degradation of (125)I-LDL. IL-6-stimulated HepG2 cells revealed increased steady-state levels of LDL-R mRNA. In HepG2 cells transiently transfected with reporter gene constructs harboring the sequence of the LDL-R promoter extending from nucleotide -1563 (or from nucleotide -234) through -58 relative to the translation start site, IL-6 dose-dependently increased promoter activity. In the presence of LDL, a similar relative stimulatory effect of IL-6 was observed. Studies using a reporter plasmid with a functionally disrupted sterol-responsive element (SRE)-1 revealed a reduced stimulatory response to IL-6. In gel-shift assays, nuclear extracts of IL-6-treated HepG2 cells showed an induced binding of SRE binding protein (SREBP)-1a and SRE binding protein(SREBP)-2 to the SRE-1 that was independent of the cellular sterol content and an induced binding of Sp1 and Sp3 to repeat 3 of the LDL-R promoter. Our data indicate that IL-6 induces stimulation of the LDL-R gene, resulting in enhanced gene transcription and LDL-R activity. This effect is sterol independent and involves, on the molecular level, activation of nuclear factors binding to SRE-1 and the Sp1 binding site in repeat 2 and repeat 3 of the LDL-R promoter, respectively.

Endobronchial drug administration: does deep endobronchial delivery have advantages in comparison with simple injection through the endotracheal tube?

Endobronchial administration of drugs is a valuable alternative to intravenous delivery when venous access cannot be established quickly enough. Some authors propose that deep endobronchial administration through a catheter or similar auxiliary device should give better absorption than simple injection through the endotracheal tube. To test this proposal in the present study two groups of each 6 patients during general anesthesia were administered 3 ml aqueous lidocaine solution at a dose of 2 mg/kg, either deep endobronchially through a catheter or simply through the endotracheal tube. The unusually low volume of administration of 3 ml was chosen because it was thought that the advantages of deep endobronchial administration would then be particularly apparent as 3 ml would lead to a more localized deposit with deep endobronchial administration thus being clearly different from simple injection. No difference in the PaO2 between the two groups could be statistically established. However, the mean lidocaine plasma concentration in the group with the deep endobronchially administered drug was in tendency lower than in the control group (P less than 0.05 at 5 min after delivery). Presumably because of the low volume of administration the mean lidocaine plasma concentrations in both groups always remained under the therapeutic level of at least 1.5 micrograms/ml. Thus, at least for small volumes and stable circulation the results after deep endobronchial administration through a catheter were somewhat worse than after simple injection through the endotracheal tube.

Plasma lidocaine levels and PaO2 with endobronchial administration: dilution with normal saline or distilled water?

STUDY OBJECTIVE: To determine whether water or 0.9% saline should be used as diluent for endobronchial drug administration. PARTICIPANTS: Twelve adult patients. INTERVENTIONS: Patients were endobronchially administered 2 mg/kg lidocaine as marker substance in either 10 mL 0.9% saline or 10 mL distilled water during general anesthesia. MEASUREMENTS AND MAIN RESULTS: The differences in mean lidocaine plasma levels at five minutes (water vs saline, 2.35 vs 1.59 micrograms/mL) and ten minutes (water vs saline: 2.67 vs 1.88 micrograms/mL) were significant (P less than .05). With the initial mean PaO2 being almost (157 mm Hg; F1O2, 0.3) in the two groups, there was a mean drop of about 60 mm Hg in the saline-diluent group, but only about 40 mm Hg in the water-diluent group one minute after administration (P less than .05). CONCLUSION: The use of water resulted in better absorption of lidocaine and less impairment of the PaO2.

What is the optimal volume of administration for endobronchial drugs?

During general anesthesia, three groups of six patients each received 2 mg/kg lidocaine as a marker substance endobronchially in either 10, 5, or 3 mL distilled water. It was found that the group receiving 10 mL initially exhibited the highest lidocaine plasma concentration with a mean of 2.01 micrograms/mL, in comparison with 1.25 micrograms/mL in the 5 mL group and 0.95 micrograms/mL in the 3 mL group. After about 10 minutes, concentration courses were almost the same in the 10 mL and the 5 mL groups. The PaO2 in the 10 mL group dropped initially by approximately 40 mm Hg on average and remained low over 60 minutes. By this time the PaO2 in the 5 mL group (initial drop 46 mm Hg) had come back to the original value (P less than .05). The 3 mL group exhibited even more favorable courses in the PaO2 (initial drop 16 mm Hg on average). However, the lidocaine plasma concentration was at the lowest at all times in this group and, moreover, under the therapeutic level of 1.5 micrograms/mL with the dosage used.

Oligomerization of simian virus 40 tumor antigen may be involved in viral DNA replication.

Biological implications of the oligomerization of simian virus 40 (SV40) large T antigen for viral DNA replication were studied by using two temperature-sensitive SV40 A-gene mutants, tsA 58 and tsA 1499. Both mutants are defective at elevated temperature for viral DNA replication whereas tsA 58 is like most other tsA mutants additionally heat sensitive for cell transformation. We found that in contrast to tsA 58 encoded T antigen, tsA 1499 T antigen is thermostable in the ability to bind specifically to the origin of replication of SV40 DNA. Detailed structural analysis of tsA 1499 T antigen by sucrose density gradient centrifugation revealed that it is strictly temperature sensitive for the formation of homologous oligomers but, as we reported previously (M. Montenarh, M. Kohler, and R. Henning, 1984, J. Virol, 49, 658-664), not for the association with the cellular phosphoprotein p53. These observations are compatible with the idea that, in addition to the specific origin-binding ability as well as other functional features, the oligomerization of T antigen may be essential for viral DNA replication.

Growth of myxococci in suspension in liquid media.

Growth of different strains of myxococci in various liquid media was studied in Erlenmeyer flasks and in small fermentors. Medium containing a small concentration of agar allowed the myxobacteria to grow in the liquid phase in suspension. The dry weight of the cells increased about 100 to 200%. Substitution of other thickening substances for agar caused increased growth with all of eight tested agents.