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Orthogonality, Lommel integrals and cross product zeros of linear combinations of Bessel functions
(2015)
The cylindrical Bessel differential equation and the spherical Bessel differential equation in the interval R\(\leq\)r\(\leq\)\(\gamma\)R with Neumann boundary conditions are considered. The eigenfunctions are linear combinations of the Bessel function \(\Phi\)\(_{n,ν}\)(r) = Y'\(_{ν}\) (\(\lambda\)\(_{n,ν}\))J\(_{ν}\)(\(\lambda\)\(_{n,ν}\) r/R) - J'\(_{ν}\)(\(\lambda\)\(_{n,ν}\))Y\(_{ν}\)(\(\lambda\)\(_{n,ν}\)r/R) or linear combinations of the spherical Bessel functions \(\psi\)\(_{m,ν}\)(r) = y'\(_{ν}\)(\(\lambda\)\(_{m,ν}\))j\(_{ν}\)(\(\lambda\)\(_{m,ν}\)r/R) - j'\(_{ν}\)(\(\lambda\)\(_{m,ν}\))y\(_{ν}\)(\(\lambda\)\(_{m,ν}\)r/R). The orthogonality relations with analytical expressions for the normalization constant are given. Explicit expressions for the Lommel integrals in terms of Lommel functions are derived. The cross product zeros Y'\(_{ν}\)\(\lambda\)\(_{n,ν}\))J'\(_{ν}\)(\(\gamma\)\(\lambda\)\(_{n,ν}\))- J'\(_{ν}\)(\(\lambda\)\(_{n,ν}\))Y'\(_{ν}\)(\(\gamma\)\(\lambda\)\(_{n,ν}\)) = 0 and y'\(_{ν}\)(\(\lambda\)\(_{m,ν}\))j'\(_{ν}\)(\(\gamma\)\(\lambda\)\(_{m,ν}\)) - j'\(_{ν}\)(\(\lambda\)\(_{m,ν}\))y'\(_{ν}\)(\(\gamma\)\(\lambda\)\(_{m,ν}\)) = 0 are considered in the complex plane for real as well as complex values of the index ν and approximations for the exceptional zero \(\lambda\)\(_{1,ν}\) are obtained. A numerical scheme based on the discretization of the twodimensional and three-dimensional Laplace operator with Neumann boundary conditions is presented. Explicit representations of the radial part of the Laplace operator in form of a tridiagonal matrix allow the simple computation of the cross product zeros.
Microbial species (bacteria and archaea) in the gut are important for human health in various ways. Not only does the species composition vary considerably within the human population, but each individual also appears to have its own strains of a given species. While it is known from studies of bacterial pan-genomes, that genetic variation between strains can differ considerably, such as in Escherichia coli, the extent of genetic variation of strains for abundant gut species has not been surveyed in a natural habitat. This is mainly due to the fact that most of these species cannot be cultured in the laboratory. Genetic variation can range from microscale genomic rearrangements such as small nucleotide polymorphism (SNP) to macroscale large genomic rearrangements like structural variations. Metagenomics offers an alternative solution to study genetic variation in prokaryotes, as it involves DNA sequencing of the whole community directly from the environment. However, most metagenomic studies to date only focus on variation in gene abundance and hence are not able to characterize genetic variation (in terms of presence or absence of SNPs and genes) of gut microbial strains of individuals.
The aim of my doctorate studies was therefore to study the extent of genetic variation in the genomic sequence of gut prokaryotic species and its phenotypic effects based on: (1) the impact of SNP variation in gut bacterial species, by focusing on genes under selective pressure and (2) the gene content variation (as a proxy for structural variation) and their effect on microbial species and the phenotypic traits of their human host.
In the first part of my doctorate studies, I was involved in a project in which we created a catalogue of 10.3 million SNPs in gut prokaryotic species, based on metagenomes. I used this to perform the first SNP-based comparative study of prokaryotic species evolution in a natural habitat. Here, I found that strains of gut microbial species in different individuals evolve at more similar rates than the strains within an individual. In addition, I found that gene evolution can be uncoupled from the evolution of its originating species, and that this could be related to selective pressure such as diet, exemplified by galactokinase gene (galK). Despite the individuality (i.e. uniqueness of each individual within the studied metagenomic dataset) in the SNP profile of the gut microbiota that we found, for most cases it is not possible to link SNPs with phenotypic differences. For this reason I also used gene content as a proxy to study structural variation in metagenomes.
In the second part of my doctorate studies, I developed a methodology to characterize the variability of gene content in gut bacterial species, using metagenomes. My approach is based on gene deletions, and was applied to abundant species (demonstrated using a set of 11 species). The method is sufficiently robust as it captures a similar range of gene content variability as has been detected in completely sequenced genomes. Using this procedure I found individuals differ by an average of 13% in their gene content of gut bacterial strains within the same species. Interestingly no two individuals shared the same gene content across bacterial species. However, this variation corresponds to a lower limit, as it is only accounts for gene deletion and not insertions. This large variation in the gene content of gut strain was found to affect important functions, such as polysaccharide utilization loci (PULs) and capsular polysaccharide synthesis (CPS), which are related with digestion of dietary fibers.
In summary, I have shown that metagenomics based approaches can be robust in characterizing genetic variation in gut bacterial species. I also illustrated, using examples both for SNPs and gene content (galK, PULs and CPS), that this genetic variation can be used to predict the phenotypic characteristics of the microbial species, as well as predicting the phenotype of their human host (for example, their capacity to digest different food components). Overall, the results of my thesis highlight the importance of characterizing the strains in the gut microbiome analogous to the emerging variability and importance of human genomics.
Background: Nontraumatic osteonecrosis of the femoral head (NONFH) is a debilitating disease that represents a significant financial burden for both individuals and healthcare systems. Despite its significance, however, its prevalence in the Chinese general population remains unknown. This study aimed to investigate the prevalence of NONFH and its associated risk factors in the Chinese population.
Methods: A nationally representative survey of 30,030 respondents was undertaken from June 2012 to August 2013. All participants underwent a questionnaire investigation, physical examination of hip, and bilateral hip joint X-ray and/or magnetic resonance imaging examination. Blood samples were taken after overnight fasting to test serum total cholesterol, triglyceride, and high-density lipoprotein (HDL) and low-density lipoprotein (LDL) levels. We then used multivariate logistic regression analysis to investigate the associations between various metabolic, demographic, and lifestyle-related variables and NONFH.
Results: NONFH was diagnosed in 218 subjects (0.725%) and the estimated NONFH cases were 8.12 million among Chinese people aged 15 years and over. The prevalence of NONFH was significantly higher in males than in females (1.02% vs. 0.51%, \(\chi^2\) = 24.997, P < 0.001). Among NONFH patients, North residents were subjected to higher prevalence of NONFH than that of South residents (0.85% vs. 0.61%, \(\chi^2\) = 5.847, P = 0.016). Our multivariate regression analysis showed that high blood levels of triglycerides, total cholesterol, LDL-cholesterol, and non-HDL-cholesterol, male, urban residence, family history of osteonecrosis of the femoral head, heavy smoking, alcohol abuse and glucocorticoid intake, overweight, and obesity were all significantly associated with an increased risk of NONFH.
Conclusions: Our findings highlight that NONFH is a significant public health challenge in China and underscore the need for policy measures on the national level. Furthermore, NONFH shares a number of risk factors with atherosclerosis.
Virulent Agrobacterium tumefaciens strains integrate their T-DNA into the plant genome where the encoded agrobacterial oncogenes are expressed and cause crown gall disease. Essential for crown gall development are IaaH (indole-3-acetamide hydrolase), IaaM (tryptophan monooxygenase) and Ipt (isopentenyl transferase), which encode enzymes for the biosynthesis of auxin (IaaH, IaaM) and cytokinin (Ipt). Although these oncogenes are well studied as the tumor-inducing principle, nothing is known about the regulation of oncogene expression in plant cells. Our studies show that the intergenic regions (IGRs) between the coding sequences (CDS) of the three oncogenes function as promoters in plant cells. These promoters possess a eukaryotic sequence organization and cis-regulatory elements for the binding of plant transcription factors. WRKY18, WRKY40, WRKY60 and ARF5 were identified as activators of the Ipt promoter whereas IaaH and IaaM is constitutively expressed and no transcription factor further activates their promoters. Consistent with these results, the wrky triple mutant plants in particular, develops smaller crown galls than wild-type and exhibits a reduced Ipt transcription, despite the presence of an intact ARF5 gene. WRKY40 and WRKY60 gene expression is induced by A. tumefaciens within a few hours whereas the ARF5 gene is transcribed later during crown gall development. The WRKY proteins interact with ARF5 in the plant nucleus, but only WRKY40 together with ARF5 synergistically boosts the activation of the Ipt promoter in an auxin-dependent manner. From our data, we propose that A. tumefaciens initially induces WRKY40 gene expression as a pathogen defense response of the host cell. The WRKY protein is recruited to induce Ipt expression, which initiates cytokinin-dependent host cell division. With increasing auxin levels triggered by ubiquitous expression of IaaH and IaaM, ARF5 is activated and interacts with WRKY40 to potentiate Ipt expression and balance cytokinin and auxin levels for further cell proliferation.
The spin-orbit (SO) coupled optical lattices have attracted considerable interest. In this paper, we investigate the phase diagram of the interacting Fermi gas with Rashba-type spin-orbit coupling (SOC) on a square optical lattice. The phase diagram is investigated in a wide range of atomic interactions and SOC strength within the framework of the cluster dynamical mean-field theory (CDMFT). We show that the interplay between the atomic interactions and SOC results in a rich phase diagram. In the deep Mott insulator regime, the SOC can induce diverse spin ordered phases. Whereas near the metal-insulator transition (MIT), the SOC tends to destroy the conventional antiferromagnetic fluctuations, giving rise to distinctive features of the MIT. Furthermore, the strong fluctuations arising from SOC may destroy the magnetic orders and trigger an order to disorder transition in close proximity of the MIT.
Gemäß 2-Prozess-Modellen der Abhängigkeit resultiert die Reaktion auf suchtassoziierte Reize aus der Interaktion zweier in Verbindung stehender, aber unabhängig voneinander arbeitender Systeme: Aus dem Zusammenspiel eines dominierenden Implizitsystems und eines geschwächten Explizitsystems ergeben sich starke Annäherungstendenzen, die immer wieder zum Konsum der Droge führen. Den genannten Systemen können eigene aber überlappend arbeitende neuronale Schaltkreise zugeordnet werden. Als Anteil des Implizitsystems generieren Impulse des Striatums Annäherungstendenzen. Gegenspieler hierzu ist der Bereich der Amygdala, hier kann Vermeidungs- und Abwendungsverhalten gegenüber präsentierten Stimuli entstehen. Beiden übergeordnet befähigt der präfrontale Cortex zu einer bewussten Entscheidungsfindung und Verhaltenskontrolle (Triadic Modell). Indirekte Mess-methoden wie die Approach-Avoidance Task (AAT) ermöglichen über die Analyse des gezeigten Verhaltens die Erfassung der vorherrschenden Assoziationen zwischen emotionaler Stimuluswertigkeit und aufkommender Verhaltenstendenz des impulsiven Systems. Grundlage der AAT ist es dabei, dass prinzipiell als positiv bewertete Stimuli vorrangig mit Annäherungs-verhalten, Stimuli mit Negativbewertung dagegen eher mit Vermeidungs-verhalten verknüpft werden. Je nach Aufgabenstellung werden Reizvalenz und geforderte motorische Reaktion unterschiedlich kombiniert. So ergeben sich kompatible bzw. inkompatible Kombinationen zwischen dargebotenem Reiz, geforderter Reaktion (Annäherung vs. Vermeidung) und empfundener Assoziation (positiv vs. negativ). Bei Kompatibilität werden schnellere Reaktionen mit niedrigerer Fehlerrate gezeigt als bei inkompatibler Aufgaben-stellung. Dies lässt auf die vorliegenden Verhaltenstendenzen schließen. In der vorliegenden Arbeit entscheidet der Faktor „Gruppe“ (alkoholabhängige Pro-banden bzw. gesunde Kontrollpersonen) über Kompatibilität bzw. Inkompatibilität der Kombination aus Reiz (alkoholassoziierter bzw. nicht-alkoholassoziierter Stimulus) und Verhalten (Annäherung bzw. Vermeidung).
Ziel war es nun die postulierten Annäherungstendenzen gegenüber alkohol-assoziierten Reizen auf Verhaltensebene mittels AAT zu erfassen. Gleichzeitig wurde mittels Nahinfrarot-Spektroskopie (NIRS) die Aktivität der beteiligten kortikalen Strukturen des dorsolateralen Präfrontalcortex (DLPFC), des Orbito-frontalcortex (OFC) sowie des dorsalen fronto-medianen Cortex (DFMC) gemessen und zwischen alkoholabhängigen und gesunden Probanden ver-glichen. Bezüglich der gemessenen Reaktionszeiten ergaben sich wie erwartet bei dem untersuchten Patientenkollektiv Annäherungstendenzen gegenüber alkoholassoziierten Stimuli. Gegenüber nicht-alkoholassoziierten Produkt-bildern waren Vermeidungstendenzen erkennbar. Die Auswertungen der Kontrollgruppe ergaben genau umgekehrte Resultate. Identische Ergebnisse ließen sich für beide Gruppen bei Betrachtung der mittels NIRS gemessenen Hirnaktivität des OFC beschreiben. Diese Ergebnisse werden im Rahmen einer Abhängigkeit als Resultat einer vermehrt positiven Bewertung suchtassoziierter Stimuli mit einem übermäßigen Ansprechen des Belohnungszentrums diskutiert. Unabhängig der Gruppenzugehörigkeit konnten im Bereich des DLPFC durch eine stärkere kortikale Aktivierung bei Vermeidung im Vergleich zur Annäherung der alkoholassoziierten Produktbilder Annäherungspräferenzen gegenüber alkoholischen Produktbildern nachgewiesen werden. Die fehlenden Gruppenunterschiede lassen sich eventuell durch die gegebenen Instruktionen mit Betonung des Bildinhaltes und einem dadurch erzeugten Bewusstsein für die Hypothesen des Experiments erklären. Außerdem bietet eine durch Alkoholabhängigkeit generell verminderte Aktivität des DLPFC einen möglichen Erklärungsansatz. Korrelationsanalysen zwischen DLPFC und OFC unter-stützen die Vorstellung des DLPFC als oberstes Kontrollgremium über sämtlichen dem Belohnungszentrum zuzuordnenden Hirnstrukturen.
Ausblickend lässt sich die klinische Bedeutung der erhaltenen Resultate erörtern. Aktuelle Forschungsarbeiten verwenden die AAT im Rahmen eines Trainings zur Rückfallprävention. Durch viele Wiederholungen der inkompatiblen Reiz-Verhaltenskombination werden vorhandene Annäherungs-tendenzen abgeschwächt und Rückfälle vermieden. Offen bleibt die Erforschung der diesen Trainingserfolgen zugrundeliegenden Mechanismen sowie eine mögliche Eingrenzung der davon profitierenden Patientengruppen.
Aufgrund der gestiegenen Komplexität der Umwelt ist es für den Gesetzgeber unerlässlich, Experten in die Entscheidungsfindungsphase einzubeziehen, um funktionsfähige Regelwerke zu erstellen. Diese Spezialisten sind in der Theorie in Informationslieferanten und Interessensvertreter zu differenzieren. Die Vorgehensweisen "echter" Lobbyisten haben sich im Laufe der Zeit auf eine äußerst diskrete Ebene verschoben, sodass ein Sichtbarmachen nicht legitimierter Handlungen sich als ein äußerst schwieriges Unterfangen darstellt. Die politikwissenschaftlichen Ansätze zum empirischen Nachweis von Lobbyismusaktivitäten im Gesetzgebungsprozess werden daher einerseits auf die Anwendbarkeit im Steuerrecht überprüft und die bestmögliche Methodenkombination auf das europäische Vorhaben einer Gemeinsamen Konsolidierten Körperschaftsteuer-Bemessungsgrundlage (GKKB) angewandt. Es ist hierdurch möglich, eine begrenzte Anzahl von Individuen, Verbänden und Unternehmen aus der Gesamtheit der durch offizielle Dokumente der Europäischen Kommission sichtbaren Akteure herauszufiltern, denen eine erhöhte Beteiligung am Entstehungsprozess des Richtlinienentwurfs nachgesagt wird.
Background
Chronic psychological stress is associated with accelerated aging and increased risk for aging-related diseases, but the underlying molecular mechanisms are unclear.
Results
We examined the effect of lifetime stressors on a DNA methylation-based age predictor, epigenetic clock. After controlling for blood cell-type composition and lifestyle parameters, cumulative lifetime stress, but not childhood maltreatment or current stress alone, predicted accelerated epigenetic aging in an urban, African American cohort (n = 392). This effect was primarily driven by personal life stressors, was more pronounced with advancing age, and was blunted in individuals with higher childhood abuse exposure. Hypothesizing that these epigenetic effects could be mediated by glucocorticoid signaling, we found that a high number (n = 85) of epigenetic clock CpG sites were located within glucocorticoid response elements. We further examined the functional effects of glucocorticoids on epigenetic clock CpGs in an independent sample with genome-wide DNA methylation (n = 124) and gene expression data (n = 297) before and after exposure to the glucocorticoid receptor agonist dexamethasone. Dexamethasone induced dynamic changes in methylation in 31.2 % (110/353) of these CpGs and transcription in 81.7 % (139/170) of genes neighboring epigenetic clock CpGs. Disease enrichment analysis of these dexamethasone-regulated genes showed enriched association for aging-related diseases, including coronary artery disease, arteriosclerosis, and leukemias.
Conclusions
Cumulative lifetime stress may accelerate epigenetic aging, an effect that could be driven by glucocorticoid-induced epigenetic changes. These findings contribute to our understanding of mechanisms linking chronic stress with accelerated aging and heightened disease risk.
Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304\(\pm\)0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of \(\pm\)0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.