The Chemical Space Project

One of the simplest questions that can be asked about molecular diversity is how many organic molecules are possible in total? To answer this question, my research group has computationally enumerated all possible organic molecules up to a certain size to gain an unbiased insight into the entire chemical space. Our latest database, GDB-17, contains 166.4 billion molecules of up to 17 atoms of C, N, O, S, and halogens, by far the largest small molecule database reported to date. Molecules allowed by valency rules but unstable or nonsynthesizable due to strained topologies or reactive functional groups were not considered, which reduced the enumeration by at least 10 orders of magnitude and was essential to arrive at a manageable database size. Despite these restrictions, GDB-17 is highly relevant with respect to known molecules. Beyond enumeration, understanding and exploiting GDBs (generated databases) led us to develop methods for virtual screening and visualization of very large databases in the form of a “periodic system of molecules” comprising six different fingerprint spaces, with web-browsers for nearest neighbor searches, and the MQN- and SMIfp-Mapplet application for exploring color-coded principal component maps of GDB and other large databases. Proof-of-concept applications of GDB for drug discovery were realized by combining virtual screening with chemical synthesis and activity testing for neurotransmitter receptor and transporter ligands. One surprising lesson from using GDB for drug analog searches is the incredible depth of chemical space, that is, the fact that millions of very close analogs of any molecule can be readily identified by nearest-neighbor searches in the MQN-space of the various GDBs. The chemical space project has opened an unprecedented door on chemical diversity. Ongoing and yet unmet challenges concern enumerating molecules beyond 17 atoms and synthesizing GDB molecules with innovative scaffolds and pharmacophores.

Full correction for spatially distributed speed-of-sound in echo ultrasound based on measuring aberration delays via transmit beam steering

Aberrations of the acoustic wave front, caused by spatial variations of the speed-of-sound, are a main limiting factor to the diagnostic power of medical ultrasound imaging. If not accounted for, aberrations result in low resolution and increased side lobe level, over all reducing contrast in deep tissue imaging. Various techniques have been proposed for quantifying aberrations by analysing the arrival time of coherent echoes from so-called guide stars or beacons. In situations where a guide star is missing, aperture-based techniques may give ambiguous results. Moreover, they are conceptually focused on aberrators that can be approximated as a phase screen in front of the probe. We propose a novel technique, where the effect of aberration is detected in the reconstructed image as opposed to the aperture data. The varying local echo phase when changing the transmit beam steering angle directly reflects the varying arrival time of the transmit wave front. This allows sensing the angle-dependent aberration delay in a spatially resolved way, and thus aberration correction for a spatially distributed volume aberrator. In phantoms containing a cylindrical aberrator, we achieved location-independent diffraction-limited resolution as well as accurate display of echo location based on reconstructing the speed-of-sound spatially resolved. First successful volunteer results confirm the clinical potential of the proposed technique.

Swiss Feline Cancer Registry: A Retrospective Study of the Occurrence of Tumours in Cats in Switzerland from 1965 to 2008

Cancer is one of the leading causes of death in companion animals. Information on the epidemiology of cancer is instrumental for veterinary practitioners in patient management; however, spontaneously arising tumours in companion animals also resemble those in man and can provide useful data in combating cancer. Veterinary cancer registries for cats are few in number and have often remained short-lived. This paper presents a retrospective study of tumours in cats in Switzerland from 1965 to 2008. Tumour diagnoses were coded according to topographical and morphological keys of the International Classification of Oncology for Humans (ICD-O-3). Correlations between breed, sex and age were then examined using a multiple logistic regression model. A total of 18,375 tumours were diagnosed in 51,322 cats. Of these, 14,759 (80.3%) tumours were malignant. Several breeds had significantly lower odds ratios for developing a tumour compared with European shorthair cats. The odds of a cat developing a tumour increased with age, up to the age of 16 years, and female cats had higher risk of developing a tumour compared with male cats. Skin (4,970; 27.05%) was the most frequent location for tumours, followed by connective tissue (3,498; 19.04%), unknown location (2,532; 13.78%) and female sexual organs (1,564; 8.51%). The most common tumour types were epithelial tumours (7,913; 43.06%), mesenchymal tumours (5,142; 27.98%) and lymphoid tumours (3,911; 21.28%).

Regional facial asymmetries in unilateral orofacial clefts

OBJECTIVES Assess facial asymmetry in subjects with unilateral cleft lip (UCL), unilateral cleft lip and alveolus (UCLA), and unilateral cleft lip, alveolus, and palate (UCLP), and to evaluate which area of the face is most asymmetrical. METHODS Standardized three-dimensional facial images of 58 patients (9 UCL, 21 UCLA, and 28 UCLP; age range: 8.6-12.3 years) and 121 controls (age range 9-12 years) were mirrored and distance maps were created. Absolute mean asymmetry values were calculated for the whole face, cheek, nose, lips, and chin. One-way analysis of variance, Kruskal-Wallis, and t-test were used to assess the differences between clefts and controls for the whole face and separate areas. RESULTS Clefts and controls differ significantly for the whole face as well as in all areas. Asymmetry is distributed differently over the face for all groups. In UCLA, the nose was significantly more asymmetric compared with chin and cheek (P = 0.038 and 0.024, respectively). For UCL, significant differences in asymmetry between nose and chin and chin and cheek were present (P = 0.038 and 0.046, respectively). In the control group, the chin was the most asymmetric area compared to lip and nose (P = 0.002 and P = 0.001, respectively) followed by the nose (P = 0.004). In UCLP, the nose, followed by the lips, was the most asymmetric area compared to chin, cheek (P < 0.001 and P = 0.016, respectively). LIMITATIONS Despite division into regional areas, the method may still exclude or underrate smaller local areas in the face, which are better visualized in a facial colour coded distance map than quantified by distance numbers. The UCL subsample is small. CONCLUSION Each type of cleft has its own distinct asymmetry pattern. Children with unilateral clefts show more facial asymmetry than children without clefts.

Implementation and Operational Research: Risk Charts to Guide Targeted HIV-1 Viral Load Monitoring of ART: Development and Validation in Patients From Resource-Limited Settings.

BACKGROUND HIV-1 RNA viral load (VL) testing is recommended to monitor antiretroviral therapy (ART) but not available in many resource-limited settings. We developed and validated CD4-based risk charts to guide targeted VL testing. METHODS We modeled the probability of virologic failure up to 5 years of ART based on current and baseline CD4 counts, developed decision rules for targeted VL testing of 10%, 20%, or 40% of patients in 7 cohorts of patients starting ART in South Africa, and plotted cutoffs for VL testing on colour-coded risk charts. We assessed the accuracy of risk chart-guided VL testing to detect virologic failure in validation cohorts from South Africa, Zambia, and the Asia-Pacific. RESULTS In total, 31,450 adult patients were included in the derivation and 25,294 patients in the validation cohorts. Positive predictive values increased with the percentage of patients tested: from 79% (10% tested) to 98% (40% tested) in the South African cohort, from 64% to 93% in the Zambian cohort, and from 73% to 96% in the Asia-Pacific cohort. Corresponding increases in sensitivity were from 35% to 68% in South Africa, from 55% to 82% in Zambia, and from 37% to 71% in Asia-Pacific. The area under the receiver operating curve increased from 0.75 to 0.91 in South Africa, from 0.76 to 0.91 in Zambia, and from 0.77 to 0.92 in Asia-Pacific. CONCLUSIONS CD4-based risk charts with optimal cutoffs for targeted VL testing maybe useful to monitor ART in settings where VL capacity is limited.

Anterior superior alveolar nerve (ASAN): A morphometric-anatomical Analysis

The anterior superior alveolar nerve (ASAN) is a branch of the infraorbital nerve. Only few studies have morphometrically evaluated the course of the ASAN. Midfacial segments of ten hemisectioned fresh adult cadaver heads were dissected to uncover the anterior wall of the maxilla. Specimens were subsequently decalcified and the bone overlying the ASAN was removed under a microscope to expose the ASAN. Its branching pattern from the infraorbital nerve was recorded, and the course of the ASAN within the anterior wall of the maxillary sinus was morphometrically assessed measuring distances to predefined landmarks using a digital caliper. A distinct ASAN was observed in all specimens. It arose lateral (six cases) or inferior (four cases) from the infraorbital nerve. The point of origin was located at a mean distance of 12.2 ± 5.79 mm posterior to the infraorbital foramen. The ASAN was located on average 2.8 ± 5.13 mm lateral to the infraorbital foramen. After coursing medially, the ASAN ran inferior to the foramen at a mean distance of 5.5 ± 3.07 mm. When approaching the nasal aperture, the loop of the ASAN was on average 13.6 ± 3.07 mm above the nasal floor. The horizontal mean distance from the ASAN to the nasal aperture was 4.3 ± 2.74 mm halfway down from the loop, and 3.3 ± 2.60 mm at the floor of the nose, respectively. In conclusion, the present study evaluated the course of the ASAN relative to the infraorbital foramen and nasal aperture. This information is helpful to avoid damage to this anatomical structure during interventions in the infraobrital region of the maxilla. Further, knowledge of the course of the ASAN and of its bony correlate (canalis sinuosus) may be valuable in interpreting anesthetic or radiologic findings in the anterior maxilla.

Dynamics of critical incidents with potentially violent outcomes involving ultra fans: an explorative study

This study examines incidents involving a tense atmosphere combined with higher risk of football fan violence. A systematic description of such critical incidents (CIs) identifying their risk factors and warning signs is yet lacking. This study looks beyond fans’ violent acts per se and focuses on CIs involving ultra fans with a potentially – but not necessarily – violent outcome. A preliminary study involving a focus group was conducted followed by a main study including eight case studies. The focus group comprised five professionals working with football fans who discussed CIs’ observable characteristics. Risk factors and warning signs were coded using content analysis, such as, ‘arrest of a fan’. In the main study, people involved in actual CIs were interviewed to explore these phenomena in more depth. An integrated model of CIs’ dynamics, risk factors and warning signs was compiled using data gathered in both studies.

CHEOPS Performance for Exomoons: The Detectability of Exomoons by Using Optimal Decision Algorithm

Many attempts have already been made to detect exomoons around transiting exoplanets, but the first confirmed discovery is still pending. The experiences that have been gathered so far allow us to better optimize future space telescopes for this challenge already during the development phase. In this paper we focus on the forthcoming CHaraterising ExOPlanet Satellite (CHEOPS), describing an optimized decision algorithm with step-by-step evaluation, and calculating the number of required transits for an exomoon detection for various planet moon configurations that can be observable by CHEOPS. We explore the most efficient way for such an observation to minimize the cost in observing time. Our study is based on PTV observations (photocentric transit timing variation) in simulated CHEOPS data, but the recipe does not depend on the actual detection method, and it can be substituted with, e.g., the photodynamical method for later applications. Using the current state-of-the-art level simulation of CHEOPS data we analyzed transit observation sets for different star planet moon configurations and performed a bootstrap analysis to determine their detection statistics. We have found that the detection limit is around an Earth-sized moon. In the case of favorable spatial configurations, systems with at least a large moon and a Neptune-sized planet, an 80% detection chance requires at least 5-6 transit observations on average. There is also a nonzero chance in the case of smaller moons, but the detection statistics deteriorate rapidly, while the necessary transit measurements increase quickly. After the CoRoT and Kepler spacecrafts, CHEOPS will be the next dedicated space telescope that will observe exoplanetary transits and characterize systems with known Doppler-planets. Although it has a smaller aperture than Kepler (the ratio of the mirror diameters is about 1/3) and is mounted with a CCD that is similar to Kepler's, it will observe brighter stars and operate with larger sampling rate; therefore, the detection limit for an exomoon can be the same as or better, which will make CHEOPS a competitive instruments in the quest for exomoons.

Fear Reduction Processes in Imaginal and In Vivo Flooding: A Comment on James' Review

The research comparing imaginal and in vivo exposure in the treatment of clinically significant fear, recently reviewed by James (1986), is reexamined from the perspective of bioinformational theory and the concept of emotional processing. Fear is assumed to be stored in long term memory as a network of propositionally-coded information, which has to be processed if treatment is to be successful. Emotional processing is indicated by activation of fear responses and their habituation within and across treatment sessions. Consistent with the theory, our review indicates that successful treatment via imaginal and in vivo exposure is indeed related to activation and habituation of fear responses; interference with processing has a negative impact upon fear reduction, regardless of the specific treatment techniques employed. Furthermore, some apparently discrepant findings in the available research literature can be understood in terms of the theories cited. These ideas provide a useful perspective from which to plan future research efforts and to advance our understanding of the processes underlying reduction of pathological fear.

Characterization of HFO2 Capacitors

Hafnium oxide (HfOn) is a promising dielectric for future microelectronic applications. Hf02 thin films (10-75nm) were deposited on Pt/Si02/Si substrates by pulsed DC magnetron reactive sputtering. Top electrodes of Pt were formed by e-beam evapo- ration through an aperture mask on the samples to create MIM (Metal-Insulator-Metal) capacitors. Various processing conditions (Arloz ratio, DC power and deposition rate) and post-deposition annealing conditions (time and temperature) were investigated. The structure of the Hf02 films was characterized by X-ray diffraction (XRD) and the roughness was measured by a profilometer. The electrical properties were characterized in terms of their relative permittivity (E,(T) and ~,.(f)) and leakage behavior (I-V, I-T and I- time). The electrical measurements were performed over a temperature range from -5 to 200°C. For the samples with best experimental results, the relative permittivity of HfOa was found to be -- 27 after anneal and increased by 0.027%/"C with increasing temperature over the measured temperature range. At 25"C, leakage current density was below lop8 ~ l c m ' at 1 volt. The leakage current increased with temperature above a specific threshold temperature below which the leakage current didn't change much. The leakage current increased with voltage. At voltages below lvolt, it's ohmic; at higher voltages, it follows Schottky model. The breakdown field is - 1 . 8 2 ~ lo6 Vlcm. The optical bandgap was measured with samples deposited on quartz substrates to be 5.4eV after anneal.

The Church Music Program: The Effect of Moving from Performance-based to Education-based Emphasis in a Church Music Program

This research project sought to answer the primary research question: What occurs when the music program in a church changes its emphasis from performance to education? This qualitative study of a church choir included participant observation of Wednesday evening and Sunday morning rehearsals over a 12 week period, individual interviews, group interviews, written responses, and written and visual assessment of musical skills. The goal was a rich description of the participants and emerging themes resulting from the shift in emphasis. Analysis of data occurred through inductive processing. Data was initially coded and then the codes were categorized into sub-themes, and finally into major themes. Early analysis of the data began with reflection in a researcher journal. Following the completion of the study the journal was entered into a word processor, as were transcriptions of videotaped rehearsals, and written reflections from the participants. After all data had been reviewed repeatedly and entered into the word processor, it was coded, reexamined, and finally categorized into sub-themes and themes. After coding and identification of major themes and sub-themes the finding were challenged by looking for disconfirming evidence. Finally, after the completion of the analysis stage, member checks were conducted. The results of the analysis of data revealed themes that could be associated either with the choir or the director. The key themes primarily associated with the choir were: Response to the change in rehearsal format; Attitude toward learning; Appropriateness of community learning model; and, Member's perceptions of the results of the program. The key themes associated with the director were identified as: Conductor assuming the role of educator; Conductor recognizing the choir as learners; Conductor treating rehearsals as a time for teaching and learning; and, Conductor's perception of the effectiveness of the change in focus. The study concluded that a change in focus from performance to education did not noticeably improve the sound of the choir after twelve-weeks. There were however, indications that improvements were being made by the individual members. Further study of the effects over a longer period of time is recommended.

A TEMPERATURE-SENSITIVE DEFECT IN THE EXPRESSION OF A SARCOMA VIRUS TRANSFORMING GENE

The viral proteins synthesized by a Moloney murine sarcoma virus (Mo-MuSV) with a temperature-sensitive mutation in a function required for the maintenance of the transformed state (ts110) were examined. Normal rat kidney cells (NRK) were infected with the ts110 virus and a non-virus-producing cell clone, termed 6m2, was isolated. This cell clone had a malignant phenotype at 33(DEGREES), the permissive temperature, but changed to a normal phenotype at 39(DEGREES).^ Two viral proteins were detected in 6m2 cells. A 58,000 dalton protein (P58) was detected at both 33(DEGREES) and 39(DEGREES) and contained only core protein (gag) coded sequences. An 85,000 dalton protein (P85) was detected only at 33(DEGREES) and contained sequences of viral core proteins p15, pp12, and part of p30 as well as protein sequences attributed by peptide mapping to P23 and P38, two candidate viral mouse src (v-mos) gene products. These results provide good evidence that P85 is a gag-mos polyprotein. As expected for a functional mos-gene product, P85 synthesis preceded parameters characteristic of the transformed state, including changes in cell morphology, in the cytoplasmic microtubule complex (CMTC) and in the rate of hexose uptake.^ Other studies were conducted to ascertain the defect which prohibited the synthesis of P85 at 39(DEGREES), the non-permissive temperature. When 6m2 cells were treated with actinomycin D at 39(DEGREES) and shifted to 33(DEGREES), the cells were unable to synthesize P85, but P58 continued to be made. P85 mRNA, active at 33(DEGREES), continued to be translated for two to three hours after shifting to 39(DEGREES) as judged by pulse-labeling experiments. Virus harvested at 33(DEGREES) from ts110 MuSV producer cells packaged both P85 and P58 coding RNAs while virus harvested at 39(DEGREES) was deficient in the amount of P85 coding RNA. Agarose gel electrophoresis of 6m2 cellular RNA showed that RNA harvested at 33(DEGREES) contained the 4.0 and 3.5 kb RNAs. Similar experiments on cells maintained at 39(DEGREES) have detected only the 4.0 kb RNA, suggesting that the 3.5 kb RNA codes for P85. The defect appeared to be in the long term stability of the P85 coding RNA at 39(DEGREES), since, in shift-up experiments (33(DEGREES) (--->) 39(DEGREES)), P85 was translated for only three hours at 39(DEGREES), while P58 was synthesized for at least eight hours. However, at 33(DEGREES) in the presence of actinomycin D, the ratio of P85 and P58 synthesis at hourly intervals was similar throughout a 12 hour period. ^

BIOCHEMICAL CHARACTERIZATION AND GENETIC MAPPING OF WILD TYPE AND MUTANT GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE ALLELES IN CHINESE HAMSTER OVARY CELLS

A UV-induced mutation of the enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPD) was characterized in the CHO clone A24. The asymmetric 4-banded zymogram and an in vitro GAPD activity equal to that of wild type cells were not consistent with models of a mutant heterozygote producing equal amounts of wild type and either catalytically active or inactive mutant subunits that interacted randomly. Cumulative evidence indicated that the site of the mutation was the GAPD structural locus expressed in CHO wild type cells, and that the mutant allele coded for a subunit that differed from the wild type subunit in stability and kinetics. The evidence included the appearance of a fifth band, the putative mutant homotetramer, after addition of the substrate glyceraldehyde-3-phosphate (GAP) to the gel matrix; dilution experiments indicating stability differences between the subunits; experiments with subsaturating levels of GAP indicating differences in affinity for the substrate; GAPD zymograms of A24 x mouse hybrids that were consistent with the presence of two distinct A24 subunits; independent segregation of A24 wild type and mutant electrophoretic bands from the hybrids, which was inconsistent with models of mutation of a locus involved in posttranslational modification; the mapping of both wild type and mutant forms of GAPD to chromosome 8; and the failure to detect any evidence of posttranslational modification (of other A24 isozymes, or through mixing of homogenates of A24 and mouse).^ The extent of skewing of the zymogram toward the wild type band, and the unreduced in vitro activity were inconsistent with models based solely on differences in activity of the two subunits. Comparison of wild type homotetramer bands in wild type cells and A24 suggested the latter had a preponderance of wild type subunits over mutant subunits, and had more GAPD tetramers than did CHO controls.^ Two CHO linkages, GAPD-triose phosphate isomerase, and acid phosphatase 2-adenosine deaminase were reported provisionally, and several others were confirmed. ^

Adolescent Meaning Making of Past Experience

This study examined the meaning making processes of self-defining memories in adolescents, as well as how they co-construct the narratives of these events with their parents. The sample consisted of 53 students, aged 12-14, who came in for recorded laboratory sessions to discuss self-defining memories with their parents. These sessions were later coded on levels of meaning making and co-construction. These codes were, then, analyzed with the adolescents’ questionnaire scores regarding friendship quality, internalizing, and externalizing behaviors. The data revealed that adolescents and parents were both rated higher for more complex levels of meaning making and that those rated higher for more complex meaning making abilities had better friendship qualities. The implications of these findings were discussed in terms of their importance for parents supporting their children’s emotional expressivity, narrative abilities, and meaning making strategies.

Rights at Risk: Refugees in the New South Africa

This thesis seeks to analyze the relationship between public attitudes toward refugees in a refugee receiving state and the realization of the legal rights afforded refugees (de facto rights). I hypothesize that the more negative a host culture is toward refugees, the less refugees are able to realize their rights. Conversely, the more positive a host culture is toward refugees, the more refugees are able to realize their rights. I test the hypothesis through a case study of refugee populations in Cape Town, South Africa, based on research conducted from May to June 2007. The orientation (positive or negative) of the host culture's perceptions toward a refugee group (Independent Variable) is measured through: (1) a coded content analysis of the South African media, (2) a coded content analysis of semi-structured interviews, and (3) an assessment of secondary source public opinion surveys and reports. The realization of refugee rights (Dependent Variable) is operationalized as a function of two rights: (1) the right to personal physical integrity and (2) the right to protection from unlawful detention. These rights are measured by coding (1) media reports and (2) interviews, and by (3) assessing NGO reports and secondary source public opinion surveys. My empirical data shows that the cultural orientation toward refugees is not overwhelmingly negative, and the realization of rights is not conclusively "low." However, the frequency of data coded "negative" and "low" versus "positive" or "high" suggest that South Africans regard refugees somewhat negatively and that rights are not fully realized. This finding is strengthened by the analysis of secondary sources and field notes.