Solutions to common issues in widefield microscopy: vignetting, mosaicing and depth of focus

In this thesis we have developed solutions to common issues regarding widefield microscopes, facing the problem of the intensity inhomogeneity of an image and dealing with two strong limitations: the impossibility of acquiring either high detailed images representative of whole samples or deep 3D objects. First, we cope with the problem of the non-uniform distribution of the light signal inside a single image, named vignetting. In particular we proposed, for both light and fluorescent microscopy, non-parametric multi-image based methods, where the vignetting function is estimated directly from the sample without requiring any prior information. After getting flat-field corrected images, we studied how to fix the problem related to the limitation of the field of view of the camera, so to be able to acquire large areas at high magnification. To this purpose, we developed mosaicing techniques capable to work on-line. Starting from a set of overlapping images manually acquired, we validated a fast registration approach to accurately stitch together the images. Finally, we worked to virtually extend the field of view of the camera in the third dimension, with the purpose of reconstructing a single image completely in focus, stemming from objects having a relevant depth or being displaced in different focus planes. After studying the existing approaches for extending the depth of focus of the microscope, we proposed a general method that does not require any prior information. In order to compare the outcome of existing methods, different standard metrics are commonly used in literature. However, no metric is available to compare different methods in real cases. First, we validated a metric able to rank the methods as the Universal Quality Index does, but without needing any reference ground truth. Second, we proved that the approach we developed performs better in both synthetic and real cases.

[Herd problem: udder health. Retrospective study of farms assessed by the Swiss Bovine Health Service (BHS) from 1999 to 2004]

Data from 59 farms with complaints of udder health problems and insufficient quality of delivered milk that had been assessed by the Swiss Bovine Health Service (BHS) between 1999 and 2004 were retrospectively analysed. Data evaluated included farm characteristics such as farm size, herd size, average milk yield, milking system and housing system, deficits of the milking equipment and the milking practices, and bacteriological results of milk samples from all cows in lactation. The average size of the farms assessed by the BHS was larger than the size of the were evaluated, 42 showed obvious failures which the farm managers could have noticed. Only 5 of the 57 milkers carried out their work according to the generally valid guidelines of the National Mastitis Council. More than 2 basic mistakes were observed in the milking practices of 36 milkers. In 51 farms, mixed infections with several problem bacteria (those present in at least 20 % of the tested cows on a farm) were found. Staphylococcus aureus proved to be the most common problem germ. As the bacteria responsible for the herd problem (the sole problem bacteria detectable on a particular farm) Staphylococcus aureus was detected in 4 farms. The current study revealed that education in the area of milking techniques and milking practices of farmers should be improved in order to reduce the incidence of udder health problems on herd level. Staphylococcus aureus is the most important problem bacteria involved in herds with udder health problems in Switzerland. Staphylococcus aureus might be used in practice as the indicator germ for early recognition of management problems in dairy farms.

Vaginal voiding: a common cause of daytime urinary leakage in girls

STUDY OBJECTIVE: To estimate the frequency of vaginal voiding as the cause of daytime urinary leakage in girls, and to study the effect of instructions intended to alleviate the problem. SETTING: Girls with vaginal voiding were identified in a group of girls referred because of daytime urinary leakage. They were evaluated by a noninvasive screening protocol. Girls with vaginal voiding were instructed on how to achieve better toilet habits. PARTICIPANTS: Twelve girls with vaginal voiding. RESULTS: Vaginal voiding was found in 12 of 39 girls with daytime urinary leakage. Their age ranged between 8.5 and 13.9 years. They all had history of small leakage immediately after voiding. A body mass index greater than the corresponding 85th percentile was noted in 5 girls, and labial fusion was noted in 2 girls. The complaint disappeared in 10 girls and improved in the remaining 2 girls after instructions on how to achieve better toilet habits. CONCLUSIONS: Vaginal voiding is common in girls. It occurs in girls at risk of overweight, in girls with labial fusion, and in girls adopting a hairpin posture while sitting on the toilet. The diagnosis is obtained by an adequate history. Proper voiding instructions resolve the problem.

Canine noninflammatory alopecia: a comprehensive evaluation of common and distinguishing histological characteristics

BACKGROUND Noninflammatory alopecia is a frequent problem in dogs, and the pathogenesis is still unclear. OBJECTIVE The objective of this study was a comparative histological description of skin biopsies from dogs with different alopecic disorders and control dogs matched for coat type, season and disease duration. ANIMALS Twenty-one cases of alopecia X in plush-coated dogs, 12 cases of recurrent flank alopecia, three cases of hyperestrogenism, 15 cases of hyperadrenocorticism, 12 cases of hypothyroidism and 12 cases of primary alopecic disorders of unknown cause were evaluated. The controls were biopsies from 38 dogs of different coat types. METHODS We evaluated five serial sections of each biopsy histologically and immunohistologically to compare the histological findings within the disease groups and with the control. RESULTS All the dogs with hair cycle disorders had a significant increase in the number of hairless hair follicles, which we assigned to kenogen. In addition, dogs with alopecia X had the lowest percentage of anagen follicles and the highest percentage of telogen follicles. CONCLUSIONS The marked increase in kenogen follicles is a strong indication that the induction of the new anagen phase is impaired in hair cycle disorders. The findings in dogs with alopecia X further suggest that premature catagen is also involved in the pathogenesis. Further work to investigate the stem cell compartment and possible initiating factors for the different cycle phases is required to elucidate the exact pathogenesis.

Dermatopathology in sub-Saharan Africa: a systematic 5-year analysis of all histopathological diagnoses from the Regional Dermatology Training Centre (RDTC) in Moshi, Tanzania.

BACKGROUND Proper diagnosis of skin diseases relies on dermatopathology, the most important diagnostic technique in dermatology. Unfortunately, there are few dermatopathology institutions in sub-Saharan Africa, where little is known about the spectrum of histopathological features observed. OBJECTIVES To investigate the spectrum of dermatopathological diagnoses made in a sub-Saharan African reference centre of a large, mainly rural area. PATIENTS/METHODS To retrospectively evaluate all dermatopathological diagnoses made over a period of 5 years at the Regional Dermatology Training Centre (RDTC) in Moshi, Tanzania. RESULTS There were a total of 1554 skin biopsy specimens. In 45% of cases, there were inflammatory diseases, most frequently lichenoid conditions. Cutaneous neoplasms represented 30.4% of all diagnoses, with Kaposi's sarcoma (KS) and, less frequently, squamous cell carcinoma (SCC) being the two most common neoplastic conditions. The latter also reflected the intensive management of persons with albinism in the RDTC. The distribution of histological diagnoses seemed to correlate with the overall clinical spectrum of cutaneous diseases managed in the RDTC. CONCLUSIONS In this African study inflammatory conditions are the main burden of skin diseases leading to a diagnostic biopsy. Our findings provide further evidence that KS, primarily related to the high prevalence of HIV infection is an epidemiological problem. Both SCC and basal cell carcinoma represent another relatively common malignant cutaneous neoplasms, reflecting the presence of specific populations at risk. The challenging spectrum of histological diagnoses observed in this specific African setting with basic working conditions shows that development of laboratory services of good standards and specific training in dermatopathology are urgently needed.

Risk of severe hypoglycemia in sulfonylurea-treated patients from diabetes centers in Germany/Austria: how big is the problem? which patients are at risk?

BACKGROUND We investigated the rate of severe hypoglycemic events and confounding factors in patients with type-2-diabetes treated with sulfonylurea (SU) at specialized diabetes centers, documented in the German/Austrian DPV-Wiss-database. METHODS Data from 29,485 SU-treated patients were analyzed (median[IQR] age 70.8[62.2-77.8]yrs, diabetes-duration 8.2[4.3-12.8]yrs). The primary objective was to estimate the event-rate of severe hypoglycemia (requiring external help, causing unconsciousness/coma/convulsion and/or emergency.hospitalization). Secondary objectives included exploration of confounding risk-factors through group-comparison and Poisson-regression. RESULTS Severe hypoglycemic events were reported in 826(2.8%) of all patients during their most recent year of SU-treatment. Of these, n = 531(1.8%) had coma, n = 501(1.7%) were hospitalized at least once. The adjusted event-rate of severe hypoglycemia [95%CI] was 3.9[3.7-4.2] events/100 patient-years (coma: 1.9[1.8-2.1]; hospitalization: 1.6[1.5-1.8]). Adjusted event-rates by diabetes-treatment were 6.7 (SU + insulin), 4.9 (SU + insulin + other OAD), 3.1 (SU + other OAD), and 3.8 (SU only). Patients with ≥1 severe event were older (p < 0.001) and had longer diabetes-duration (p = 0.020) than patients without severe events. Participation in educational diabetes-programs and indirect measures of insulin-resistance (increased BMI, plasma-triglycerides) were associated with fewer events (all p < 0.001). Impaired renal function was common (N = 3,113 eGFR ≤30 mL/min) and associated with an increased rate of severe events (≤30 mL/min: 7.7; 30-60 mL/min: 4.8; >60 mL/min: 3.9). CONCLUSIONS These real-life data showed a rate of severe hypoglycemia of 3.9/100 patient-years in SU-treated patients from specialized diabetes centers. Higher risk was associated with known risk-factors including lack of diabetes-education, older age, and decreased eGFR, but also with lower BMI and lower triglyceride-levels, suggesting that SU-treatment in those patients should be considered with caution. This article is protected by copyright. All rights reserved.

The winner takes it all? Characteristics of adolescents at-risk/problem gamblers in Switzerland

Background: Gambling has and still entertains people in almost all societies throughout the world. Western societies have faced considerable changes in the amount and accessibility of gambling possibilities during the last decades, and the rates of both adolescent gamblers and problem gamblers have increased significantly. Objective: To determine the characteristics of at-risk and problem adolescent gamblers in Switzerland. Subjects: The study population consisted of 3134 students (1669 females) attending post-mandatory education in 15 randomly chosen centres. Participants were divided into non- (n=2207), non-problematic (n=754) and at-risk/ problematic gamblers (n=176). Methods: Both gambling groups were compared to non-gamblers on socio-demographic measures, substance use and Internet use. Overall, 29.6% had gambled during the past year and 5.6% had gambled in a risky or problematic way. Compared to non-gamblers and after controlling for potential confounders, non-problem gamblers were significantly more likely to be male, apprentices and to misuse alcohol. At-risk/problematic gamblers were additionally more likely to smoke cannabis, to be problematic Internet users and to be non-Swiss than non-gamblers. Conclusion: At-risk and problematic adolescent gambling is associated with other health risk behaviours. Health practitioners should include gambling in the psycho-social screening and preventive counselling of adolescents.

Spatial and Temporal Analyses of Expansion and Cell Cycle in Sunflower Leaves1 : A Common Pattern of Development for All Zones of a Leaf and Different Leaves of a Plant

We have investigated the spatial distributions of expansion and cell cycle in sunflower (Helianthus annuus L.) leaves located at two positions on the stem, from leaf initiation to the end of expansion. Relative expansion rate (RER) was analyzed by following the deformation of a grid drawn on the lamina; relative division rate (RDR) and flow-cytometry data were obtained in four zones perpendicular to the midrib. Calculations for determining in situ durations of the cell cycle and of S-G2-M in the epidermis are proposed. Area and cell number of a given leaf zone increased exponentially during the first two-thirds of the development duration. RER and RDR were constant and similar in all zones of a leaf and in all studied leaves during this period. Reduction in RER occurred afterward with a tip-to-base gradient and lagged behind that of RDR by 4 to 5 d in all zones. After a long period of constancy, cell-cycle duration increased rapidly and simultaneously within a leaf zone, with cells blocked in the G0-G1 phase of the cycle. Cells that began their cycle after the end of the period with exponential increase in cell number could not finish it, suggesting that they abruptly lost their competence to cross a critical step of the cycle. Differences in area and in cell number among zones of a leaf and among leaves of a plant essentially depended on the timing of two events, cessation of exponential expansion and of exponential division.

Earth’s Rotation: A Challenging Problem in Mathematics and Physics

A suitable knowledge of the orientation and motion of the Earth in space is a common need in various fields. That knowledge has been ever necessary to carry out astronomical observations, but with the advent of the space age, it became essential for making observations of satellites and predicting and determining their orbits, and for observing the Earth from space as well. Given the relevant role it plays in Space Geodesy, Earth rotation is considered as one of the three pillars of Geodesy, the other two being geometry and gravity. Besides, research on Earth rotation has fostered advances in many fields, such as Mathematics, Astronomy and Geophysics, for centuries. One remarkable feature of the problem is in the extreme requirements of accuracy that must be fulfilled in the near future, about a millimetre on the tangent plane to the planet surface, roughly speaking. That challenges all of the theories that have been devised and used to-date; the paper makes a short review of some of the most relevant methods, which can be envisaged as milestones in Earth rotation research, emphasizing the Hamiltonian approach developed by the authors. Some contemporary problems are presented, as well as the main lines of future research prospected by the International Astronomical Union/International Association of Geodesy Joint Working Group on Theory of Earth Rotation, created in 2013.