Geometry of Schroedinger Space-Times II: Particle and Field Probes of the Causal Structure

We continue our study of the global properties of the z=2 Schroedinger space-time. In particular, we provide a codimension 2 isometric embedding which naturally gives rise to the previously introduced global coordinates. Furthermore, we study the causal structure by probing the space-time with point particles as well as with scalar fields. We show that, even though there is no global time function in the technical sense (Schroedinger space-time being non-distinguishing), the time coordinate of the global Schroedinger coordinate system is, in a precise way, the closest one can get to having such a time function. In spite of this and the corresponding strongly Galilean and almost pathological causal structure of this space-time, it is nevertheless possible to define a Hilbert space of normalisable scalar modes with a well-defined time-evolution. We also discuss how the Galilean causal structure is reflected and encoded in the scalar Wightman functions and the bulk-to-bulk propagator.Comment: 32 page

Detection of Perturbation Phases and Developmental Stages in Organisms from DNA Microarray Time Series Data

Available DNA microarray time series that record gene expression along the developmental stages of multicellular eukaryotes, or in unicellular organisms subject to external perturbations such as stress and diauxie, are analyzed. By pairwise comparison of the gene expression profiles on the basis of a translation-invariant and scale-invariant distance measure corresponding to least-rectangle regression, it is shown that peaks in the average distance values are noticeable and are localized around specific time points. These points systematically coincide with the transition points between developmental phases or just follow the external perturbations. This approach can thus be used to identify automatically, from microarray time series alone, the presence of external perturbations or the succession of developmental stages in arbitrary cell systems. Moreover, our results show that there is a striking similarity between the gene expression responses to these a priori very different phenomena. In contrast, the cell cycle does not involve a perturbation-like phase, but rather continuous gene expression remodeling. Similar analyses were conducted using three other standard distance measures, showing that the one we introduced was superior. Based on these findings, we set up an adapted clustering method that uses this distance measure and classifies the genes on the basis of their expression profiles within each developmental stage or between perturbation phases

Automatic mapping of atoms across both simple and complex chemical reactions

Mapping atoms across chemical reactions is important for substructure searches, automatic extraction of reaction rules, identification of metabolic pathways, and more. Unfortunately, the existing mapping algorithms can deal adequately only with relatively simple reactions but not those in which expert chemists would benefit from computer's help. Here we report how a combination of algorithmics and expert chemical knowledge significantly improves the performance of atom mapping, allowing the machine to deal with even the most mechanistically complex chemical and biochemical transformations. The key feature of our approach is the use of few but judiciously chosen reaction templates that are used to generate plausible "intermediate" atom assignments which then guide a graph-theoretical algorithm towards the chemically correct isomorphic mappings. The algorithm performs significantly better than the available state-of-the-art reaction mappers, suggesting its uses in database curation, mechanism assignments, and - above all - machine extraction of reaction rules underlying modern synthesis-planning programs

Perceptions of newly admitted undergraduate medical students on experiential training on community placements and working in rural areas of Uganda

<p>Abstract</p> <p>Background</p> <p>Uganda has an acute problem of inadequate human resources partly due to health professionals' unwillingness to work in a rural environment. One strategy to address this problem is to arrange health professional training in rural environments through community placements. Makerere University College of Health Sciences changed training of medical students from the traditional curriculum to a problem-based learning (PBL) curriculum in 2003. This curriculum is based on the SPICES model (student-centered, problem-based, integrated, community-based and services oriented). During their first academic year, students undergo orientation on key areas of community-based education, after which they are sent in interdisciplinary teams for community placements. The objective was to assess first year students' perceptions on experiential training through community placements and factors that might influence their willingness to work in rural health facilities after completion of their training.</p> <p>Methods</p> <p>The survey was conducted among 107 newly admitted first year students on the medical, nursing, pharmacy and medical radiography program students, using in-depth interview and open-ended self-administered questionnaires on their first day at the college, from October 28-30, 2008. Data was collected on socio-demographic characteristics, motivation for choosing a medical career, prior exposure to rural health facilities, willingness to have part of their training in rural areas and factors that would influence the decision to work in rural areas.</p> <p>Results</p> <p>Over 75% completed their high school from urban areas. The majority had minimal exposure to rural health facilities, yet this is where most of them will eventually have to work. Over 75% of the newly admitted students were willing to have their training from a rural area. Perceived factors that might influence retention in rural areas include the local context of work environment, support from family and friends, availability of continuing professional training for career development and support of co-workers and the community.</p> <p>Conclusion</p> <p>Many first year students at Makerere University have limited exposure to health facilities in rural areas and have concerns about eventually working there.</p

Asymptomatic bacteriuria in sickle cell disease: a cross-sectional study

BACKGROUND: It is known that there is significant morbidity associated with urinary tract infection and with renal dysfunction in sickle cell disease (SCD). However, it is not known if there are potential adverse outcomes associated with asymptomatic bacteriuria (ASB) infections in sickle cell disease if left untreated. This study was undertaken to determine the prevalence of ASB, in a cohort of patients with SCD. METHODS: This is a cross-sectional study of patients in the Jamaican Sickle Cell Cohort. Aseptically collected mid-stream urine (MSU) samples were obtained from 266 patients for urinalysis, culture and sensitivity analysis. Proteinuria was measured by urine dipsticks. Individuals with abnormal urine culture results had repeat urine culture. Serum creatinine was measured and steady state haematology and uric acid concentrations were obtained from clinical records. This was completed at a primary care health clinic dedicated to sickle cell diseases in Kingston, Jamaica. There were 133 males and 133 females in the sample studied. The mean age (mean ± sd) of participants was 26.6 ± 2.5 years. The main outcome measures were the culture of ≥ 10(5 )colony forming units of a urinary tract pathogen per milliliter of urine from a MSU specimen on a single occasion (probable ASB) or on consecutive occasions (confirmed ASB). RESULTS: Of the 266 urines collected, 234 were sterile and 29 had significant bacteriuria yielding a prevalence of probable ASB of 10.9% (29/266). Fourteen patients had confirmed ASB (prevalence 5.3%) of which 13 had pyuria. Controlling for genotype, females were 14.7 times more likely to have confirmed ASB compared to males (95%CI 1.8 to 121.0). The number of recorded visits for symptomatic UTI was increased by a factor of 2.5 (95% CI 1.4 to 4.5, p < 0.005) but serum creatinine, uric acid and haematology values were not different in patients with confirmed ASB compared with those with sterile urine. There was no association with history of gram negative sepsis. CONCLUSION: ASB is a significant problem in individuals with SCD and may be the source of pathogens in UTI. However, further research is needed to determine the clinical significance of ASB in SCD

Erythropoietic protoporphyria

Erythropoietic protoporphyria (EPP) is an inherited disorder of the haem metabolic pathway characterised by accumulation of protoporphyrin in blood, erythrocytes and tissues, and cutaneous manifestations of photosensitivity. EPP has been reported worldwide, with prevalence between 1:75,000 and 1:200,000. It usually manifests in early infancy upon the first sun exposures. EPP is characterised by cutaneous manifestations of acute painful photosensitivity with erythema and oedema, sometimes with petechiae, together with stinging and burning sensations upon exposure to sunlight, without blisters. These episodes have a variable severity depending on the exposure duration and may result in chronic permanent lesions on exposed skin. As protoporphyrin is a lipophilic molecule that is excreted by the liver, EPP patients are at risk of cholelithiasis with obstructive episodes, and chronic liver disease that might evolve to rapid acute liver failure. In most patients, EPP results from a partial deficiency of the last enzyme of the haem biosynthetic pathway, ferrochelatase, EC 4.99.1.1/FECH (encoded by the FECH gene). EPP appears to be inherited as an autosomal dominant disease, the clinical expression of which is modulated by the presence of the hypomorphic FECH IVS3-48C allele trans, but recessive inheritance with two mutated FECH alleles has also been described. In about 2% of patients, overt disease was recently shown to be caused by gain-of-function mutations in the erythroid-specific aminolevulinic acid synthase 2 (ALAS2/ALAS, EC 2.3.1.27) gene and named X-linked dominant protoporphyria. Diagnosis is established by finding increased levels of protoporphyrin in plasma and red blood cells, and detection of a plasma fluorescence peak at 634 nm. Investigations for hepatic involvement, ferrochelatase activity level, genetic analysis (FECH mutations, presence of the hypomorphic FECH IVS3-48C allele trans and ALAS2 mutations) and family studies are advisable. Differential diagnosis includes phototoxic drug reactions, hydroa vacciniforme, solar urticaria, contact dermatitis, angio-oedema and, in some cases, other types of porphyria. Management includes avoidance of exposure to light, reduction of protoporphyrin levels and prevention of progression of possible liver disease to liver failure. As the major risk in EPP patients is liver disease, a regular follow-up of hepatic involvement is essential. Sequential hepatic and bone marrow transplantation should be considered as a suitable treatment for most severe cases of EPP with hepatic involvement. EPP is a lifelong disorder whose prognosis depends on the evolution of the hepatic disease. However, photosensitivity may have a significant impact on quality of life of EPP patients

Candidate gene analysis of spontaneous preterm delivery: New insights from re-analysis of a case-control study using case-parent triads and control-mother dyads

<p>Abstract</p> <p>Background</p> <p>Spontaneous preterm delivery (PTD) has a multifactorial etiology with evidence of a genetic contribution to its pathogenesis. A number of candidate gene case-control studies have been performed on spontaneous PTD, but the results have been inconsistent, and do not fully assess the role of how two genotypes can impact outcome. To elucidate this latter point we re-analyzed data from a previously published case-control candidate gene study, using a case-parent triad design and a hybrid design combining case-parent triads and control-mother dyads. These methods offer a robust approach to genetic association studies for PTD compared to traditional case-control designs.</p> <p>Methods</p> <p>The study participants were obtained from the Norwegian Mother and Child Cohort Study (MoBa). A total of 196 case triads and 211 control dyads were selected for the analysis. A case-parent triad design as well as a hybrid design was used to analyze 1,326 SNPs from 159 candidate genes. We compared our results to those from a previous case-control study on the same samples. Haplotypes were analyzed using a sliding window of three SNPs and a pathway analysis was performed to gain biological insight into the pathophysiology of preterm delivery.</p> <p>Results</p> <p>The most consistent significant fetal gene across all analyses was COL5A2. The functionally similar COL5A1 was significant when combining fetal and maternal genotypes. PON1 was significant with analytical approaches for single locus association of fetal genes alone, but was possibly confounded by maternal effects. Focal adhesion (hsa04510), Cell Communication (hsa01430) and ECM receptor interaction (hsa04512) were the most constant significant pathways.</p> <p>Conclusion</p> <p>This study suggests a fetal association of COL5A2 and a combined fetal-maternal association of COL5A1 with spontaneous PTD. In addition, the pathway analysis implied interactions of genes affecting cell communication and extracellular matrix.</p

Influence of helium-ion bombardment on the optical properties of ZnO nanorods/p-GaN light-emitting diodes

Light-emitting diodes (LEDs) based on zinc oxide (ZnO) nanorods grown by vapor-liquid-solid catalytic growth method were irradiated with 2-MeV helium (He+) ions. The fabricated LEDs were irradiated with fluencies of approximately 2 × 1013 ions/cm2 and approximately 4 × 1013 ions/cm2. Scanning electron microscopy images showed that the morphology of the irradiated samples is not changed. The as-grown and He+-irradiated LEDs showed rectifying behavior with the same I-V characteristics. Photoluminescence (PL) measurements showed that there is a blue shift of approximately 0.0347 and 0.082 eV in the near-band emission (free exciton) and green emission of the irradiated ZnO nanorods, respectively. It was also observed that the PL intensity of the near-band emission was decreased after irradiation of the samples. The electroluminescence (EL) measurements of the fabricated LEDs showed that there is a blue shift of 0.125 eV in the broad green emission after irradiation and the EL intensity of violet emission approximately centered at 398 nm nearly disappeared after irradiations. The color-rendering properties show a small decrease in the color-rendering indices of 3% after 2 MeV He+ ions irradiation

Assessing Recent Smoking Status by Measuring Exhaled Carbon Monoxide Levels

The main expectations of applying proteomics technologies to clinical questions are the discovery of disease related biomarkers. Despite technological advancement to increase proteome coverage and depth to meet these expectations the number of generated biomarkers for clinical use is small. One of the reasons is that found potential biomarkers often are false discoveries. Small sample sizes, in combination with patient sample heterogeneity increase the risk of false discoveries. To be able to extract relevant biological information from such data, high demands are put on the experimental design and the use of sensitive and quantitatively accurate technologies. The overall aim of this thesis was to apply quantitative proteomics methods for biomarker discovery in clinical samples. A method for reducing bias by controlling for individual variation in smoking habits is described in paper I. The aim of the method was objective assessment of recent smoking in clinical studies on inflammatory responses. In paper II, the proteome of alveolar macrophages obtained from smoking subjects with and without the inflammatory lung disease chronic obstructive pulmonary disease (COPD) were quantified by two-dimensional gel-electrophoresis (2-DE). A gender focused analysis showed protein level differences within the female group, with down-regulation of lysosomal pathway and up-regulation of oxidative pathway in COPD patients. Paper III, a mass spectrometry based proteomics analysis of tumour samples, contributes to the molecular understanding of vulvar squamous cell carcinoma (VSCC) and we identified a high risk patient subgroup of HPV-negative tumours based on the expression of four proteins, further suggesting that this subgroup is characterized by an altered ubiquitin-proteasome signalling pathway. Paper III describes a data analysis workflow for the extraction of biological information from quantitative mass spectrometry based proteomics data. High patient-to-patient tumour proteome variability was addressed by using pathway profiling on individual tumour data, followed by comparison of pathway association ranks in a multivariate analysis. We show that pathway data on individual tumour level can detect subpopulations of patients and identify pathways of specific importance in pre-defined clinical groups by the use of multivariate statistics. In paper IV, the potentials and limits of quantitative mass spectrometry on clinical samples was evaluated by defining the quantitative accuracy of isobaric labels and label-free quantification. Quantification by isobaric labels in combination with pI pre-fractionation showed a lower limit of quantification (LOQ) than a label-free analysis without pI pre-fractionation, and 6-plex TMT were more sensitive than 8-plex iTRAQ. Precursor mixing measured by isolation interference (MS1 interference) is more linked to the quantitative accuracy of isobaric labels than reporter ion interference (MS2 interference). Based on that we could define recommendations for how much isolation interference that can be accepted; in our data <30% isolation interference had little effect the quantitative accuracy. In conclusion, getting biological knowledge from proteomics studies requires a careful study design, control of possible confounding factors and the use of clinical data to identify disease subtypes. Further, to be able to draw conclusions from the data, the analysis requires accurate quantitative data and robust statistical tools to detect significant protein alterations. Methods around these issues are developed and discussed in this thesis