Virtual screening is a well-established part of computer-aided drug design, which heavily employs similarity search and similarity modeling methods. Most of the popular methods are target agnostic, leaving space for design of new methods that would take into account the specifics of the particular molecular target. Additionally, newly developed methods suffer from two related issues: benchmarking and availability. Benchmarking in the domain often suffers from the use of inappropriate reference methods, lack of reproducibility, and the use of nonstandard benchmark datasets. Although there have been several benchmarking studies in the domain that aim at addressing these issues, mainly by offering a standardized comparison, they often suffer from similar drawbacks. For these reasons, new methods fail to gain trust and therefore fail to become a part of the standard toolbox, which thus consists mostly of older methods. In this work, we address the above-described issues. First, we introduce new adaptive methods for virtual screening. Then, to make our and other newly developed methods readily available, we have designed and implemented a virtual screening tool. To address the benchmarking issue, we have compiled a publicly available collection of benchmarking datasets and proposed a platform offering a...

Cieľom tejto diplomovej práce je vygenerovanie datasetu syntetických snímkov odtlačkov prstov, ktoré vykazujú známky kožných ochorení. Práca sa zaoberá poškodením spôsobeným kožnými ochoreniami v odtlačkoch prstov a generovaním syntetických odtlačkov prstov. Odtlačky prstov s prejavom kožných ochorení boli generované s využitím modelu založeného na Wasserstein GAN s penalizáciou gradientu. Na trénovanie GAN modelu bola použitá unikátna databáza odtlačkov prstov s prejavom kožných ochorení vytvorená na FIT VUT. Daný model bol trénovaný na troch typoch kožných ochorení: atopický ekzém, psoriáza a dyshidrotický ekzém. Sieť generátoru z natrénovaného WGAN-GP modelu bola použitá na vygenerovanie datasetov syntetických odtlačkov prstov. Tieto syntetické odtlačky boli porovnané s reálnymi odtlačkami s využitím NFIQ a FiQiVi nástrojov na určenie kvality spoločne s porovnaním rozložení lokácií a orientácii markantov v snímkoch odtlačkov prstov.

The research was prompted by constant criticism of the Independent Electoral Commission (IEC) because of its poor voter registration and voters’ roll. Free and fair elections are the strong arm of democracy. The identified research problem was investigated by means of qualitative research. A thorough literature study from various sources of information, a case file analysis and structured interviews were used to gather the required data. The interviews were conducted with fingerprint experts, a data processor and constituency electoral assistants from the Lesotho Mounted Police Service, the National Identity and Civil Registry at the Ministry of Home Affairs and the IEC respectively. It was found that using fingerprints and the Automated Fingerprint Identification System (AFIS) can assist in investigations and in combating voter’s fraud, as fingerprints are unique. AFIS can be utilised for various purposes by institutions in the private and public sectors. Like any apparatus, AFIS has its own strengths and weaknesses. / Criminology and Security Science / M. Tech. (Forensic investigation)

Baigiamajame magistro darbe nagrinėjamas genetinių algoritmų taikymas biometrijoje. Išnagrinėta plačiausiai naudojama biometrinė informacija, aprašytos labiausiai paplitusios biometrinės sistemos, genetiniai algoritmai bei jų pritaikymas biometrinių sistemų optimizavimui. Baigiamajame darbe pasiūlytas naujas rankos atpažinimo metodas. Šiam metodui pritaikyti genetiniai algoritmai. Darbą sudaro 7 dalys: įvadas, biometrija, genetiniai algoritmai, genetinių algoritmų taikymas biometrinėse sistemose, genetinių algoritmų taikymas rankos atpažinimui, išvados ir literatūra. Darbo apimtis – 51 p. teksto be priedų, 30 pav., 4 lent., 32 bibliografiniai šaltiniai. / In the graduation thesis to receive the master‘s degree the application of genetic algorithms in biometrics is analysed. The most widely used biometric information have been examined, the most common biometric systems, genetic algorithms and their customization in biometric systems optimization have been described. A new method is proposed for hand recognition. Genetic algorithms have been customized for this method. Structure: introduction, biometry, genetic algorithms, application of genetic algorithms in biometric systems, application of genetic algorithms for hand recognition, the conclusions and bibliography. Thesis consist of: 51 p. text without appendixes, 30 pictures, 4 tables, 32 bibliographical entries.

This work aims to study the procedures of fingerprint identification system and to present some efficient algorithms for pre-processing and minutiae extraction. Most pre-processing steps consist of normalization, segmentation and orientation estimation, and background which focus on decreasing the variance of fingerprints, separating fore and background areas and tracking the direction of ridge lines, respectively. Minutiae extractionis typically divided into two approaches: binarization based method and directgray scale extraction. However, we put emphasis on binarization based method in thisresearch since it is more commonly used method in research papers. The results of simulationbased on a set of fingerprints downloaded from FVC 2006 database showed thatalgorithms we used are accurate and reliable.

[Truncated abstract] The collection of buccal cells is common practise in the epidemiological and forensic science. Unlike venipuncture collection of blood; it is a safer, non-invasive method for collection of biological material. The methods by which these cells are collected from the inner cheek of an individual and stored are the key elements in preserving DNA. Typically, forensic samples require long term storage. Samples are commonly collected on cotton swabs and stored moist at low to ultra-low temperatures (less than -20oC). Although this is the method of choice in most forensic facilities, there are drawbacks. The samples are inherently contaminated with microflora within the oral cavity and the moisture allows a plethora of microorganisms to grow. As the time frame that has elapsed from collection to storage increases, there is an exponential increase in bacterial cells. Storage of containers containing swabs coated with cells at temperatures below 20oC is also costly due to requirements for large freezers which are running and monitored over 24 hours. In the pass 10 to 15 years, researchers have focussed on alternative ways to store buccal cells. The FTA card system by Whatman is one such development. The FTA card is unique in that it provides a means for the collection of buccal cells for storage at room temperature. DNA profiling from samples stored in this way for 11 years has been successfully achieved. The filter paper matrix of the FTA card binds and subsequently lyses cells. ... (2) The second component of this thesis describes a study which subjected cells on buccal swabs to various conditions of increased temperature over periods of time to establish if DNA could be amplified. The aim was to mimic exposure to the vigours of field conditions, particularly in the extreme local environments that prevail in the United Arab Emirates. a. Initially, buccal cells stored at -20oC over 360 days were used to mimic standard archiving procedures. The cells were subsequently transferred to FTA cards, amplified and profiled by using ABI AmpFLSTR Identifiler PCR Amplification Kit (Applied Biosystems, Foster City, CA). Complete STR profiles were successfully recovered from the archived swabs. In most cases 100% of alleles were recovered, suggesting that it is feasible to transfer DNA from properly archived buccal swabs to FTA cards. b. The second phase involved the storage of fresh swabs that had been artificially aged by using incubation temperatures ranging from 40oC to 100oC. Partial profiles resulted from artificially aged samples, indicating that the prevailing conditions prior to low temperature storage of the swabs plays an important role in ensuring cellular integrity and thus, DNA quality. Results from this study suggest that it is possible for biological samples stored under correct conditions to be transferred from swabs to FTA card. In combination, the two chapters presented in this study show that it is feasible to transfer achieved forensic biology samples from swabs to the FTA card system. However, it is necessary to ensure that the samples are treated in the correct manner so as to minimise contamination from external sources and to maintain the correct environmental state to maintain intact cells and usable DNA.

Thesis (MScFoodSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The phenolic composition of Cyclopia species is believed to be partially responsible for the numerous health promoting properties associated with their extracts. Current quality control measures do not accommodate variation in phenolic profiles of Cyclopia species. In this study, comprehensive high performance liquid chromatography (HPLC) methods were developed for the improved characterisation of the phenolic composition of aqueous extracts of two Cyclopia species (C. subternata and C. maculata). The methods were developed to be suitable for both routine quantitative analysis on conventional HPLC instrumentation, and the construction of chromatographic fingerprints for further data analysis. The latter entailed similarity analysis and prediction of total antioxidant capacity (TAC). Using a methodical approach, two separate HPLC methods, using diode array detection (DAD), were developed and validated for the analysis of aqueous extracts prepared from unfermented (green) and fermented plant material of C. subternata and C. maculata. Separation was achieved using the same method parameters (column, temperature, mobile phases), except for differing mobile phase gradients. Hyphenation of the developed HPLC methods with mass spectrometry (MS) and tandem MS allowed the confirmation of phenolic compounds previously identified in Cyclopia, and the tentative identification of several additional compounds in Cyclopia species, which are reported here for the first time. These included apigenin-6,8-di- C-glucoside, 3-hydroxyphloretin-30,50-di-C-hexoside, eriodictyol-di-C-glucoside, iriflophenone-di-O,C-hexoside, hydroxymangiferin and hydroxyisomangiferin. Subsequently, a large number of aqueous extracts of randomly selected green C. subternata (n = 64) and C. maculata (n = 50) plant material samples were analysed. Large quantitative variations were observed on intra- and inter-species levels. Cyclopia maculata extracts contained almost six times more mangiferin than extracts from C. subternata. HPLC-DAD analysis produced duplicate fingerprints for each extract which were consequently used for further analysis. The chromatographic fingerprint of a bioactive extract of each species was included in the respective data sets. Similarity analysis was conducted between the fingerprints from the randomly selected extracts and the corresponding active extract. For each species several extracts were determined to have similar “activity” as that of the active extract (n = 15 for C. subternata and n = 45 for C. maculata). Compounds potentially responsible for the activity were tentatively identified with the aid of principal component analysis (PCA) in combination with similarity analysis. PCA was more effective in identifying small differences between fingerprints than similarity analysis based on the correlation coefficients (r) alone. Furthermore, multivariate data analysis was used to construct partial least squares (PLS) regression models for the prediction of TAC from fingerprint data of each species, and available data from two microplate TAC assays. The construction of the models was successful with reasonable errors (< 10%), and permitted the determination of compounds of interest for future research. These included compounds of known identity that had large positive contributions toward the predictions of TAC, or unknown compounds that had small UV signals, but relatively large positive contributions to the models. / AFRIKAANSE OPSOMMING: Die talle gesondheidbevorderingseienskappe van ekstrakte van Cyclopia spesies word gedeeltelik geassosieer met hul fenoliese samestelling. Huidige kwaliteitskontrolemaatreëls is nie in staat om die variasie wat in die fenoliese profiele van die spesies voorkom, te akkommodeer nie. Omvattende hoë druk vloeistof chromatografiese (HPLC) metodes is vir twee Cyclopia spesies, naamlik C. subternata en C. maculata, in hierdie studie ontwikkel vir beter karakterisering van die fenoliese samestelling van waterekstrakte van dié spesies. Die metodes moes ook geskik wees vir roetine analise van C. subternata en C. maculata ekstrakte op konvensionele HPLC instrumentasie, en vir die opstel van chromatografiese vingerafdrukke (fenoliese samestellingsprofiele) vir verdere data analise, soos gelykvormigheidsanalise en die voorspelling van die totale antioksidantkapasiteit (TAC). Twee HPLC metodes, wat van ’n ultraviolet-diode detektor (DAD) gebruik maak, is ontwikkel deur ’n sistematiese benadering te volg. Die onderskeie metodes is vir die ontleding van waterekstrakte van groen (ongefermenteerde) en gefermenteerde plantmateriaal van C. subternata en C. maculata gevalideer. Ongeag die spesie is optimale skeiding met dieselfde kolom, mobiele fase en kolom-temperatuur bereik, maar met verskillende mobiele fase gradiënte. Analise met massaspektrometrie (MS) en tandem MS het die teenwoordigheid van fenoliese verbindings, wat voorheen in Cyclopia spesies geidentifiseer is, bevestig. Verder is ook ’n aantal verbindings vir die eerste keer in Cyclopia tentatief geidentifiseer. Dit sluit apigenien-6,8-di-C-glukosied, 3- hidroksiefloretien-30,50-di-C-heksosied, eriodiktiol-di-C-glukosied, iriflofenoon-di-O,C-heksosied, hidroksiemangiferien en hidroksie-isomangiferien in. Vervolgens is ’n groot aantal ewekansig gekose waterekstrakte van beide groen C. subternata (n = 64) en C. maculata (n = 50) plantmateriaal geanaliseer, en groot kwantitatiewe variasie op intra- en inter-spesievlak waargeneem. Cyclopia maculata ekstrakte het byvoorbeeld byna ses maal die mangiferieninhoud van C. subternata ekstrakte gehad. HPLC-DAD analise van die ekstrakte het duplikaat vingerafdrukke van elke ekstrak geproduseer, wat vir verdere data analise gebruik is. Die chromatografiese vingerafdruk van ’n bioaktiewe ekstrak van elke spesie was by die onderskeie datastelle ingesluit. Gelykvormigheidsanalise is tussen vingerafdrukke van die ewekansig gekose ekstrakte en die ooreenstemmende aktiewe ekstrak uitgevoer. Vir elke spesie is ’n aantal “aktiewe” ekstrakte aangewys (n = 15 vir C. subternata en n = 45 vir C. maculata). Die verbindings wat potensieel verantwoordelik kan wees vir die aktiwiteite is met behulp van hoofkomponentontleding (PCA) in kombinasie met gelykvormigheidsanalise, tentatief aangewys. PCA was egter meer effektief om klein verskille tussen vingerafdrukke aan te dui, in vergelyking met gelykvormigheidsanalise wat slegs op die korrelasie koëffisiënt (r) gebaseer is. Meerveranderlike data analiese is gebruik om “gedeeltelike kleinste kwadrate” (PLS) regressiemodelle, vir die voorspelling van die TAC van beide spesies te bou. Die voorspelling is gebaseer op hul vingerafdruk data en TAC data van twee TAC mikroplaat metodes. Die model-konstruksie was suksesvol met aanvaarbare voorspellingsfoute (< 10%). Verbindings van belang kon ook bepaal word. Dit sluit bekende verbindings in wat groot positiewe bydraes ten opsigte van die voorspelling van TAC getoon het, asook ongeidentifiseerde verbindings wat klein UV-seine getoon het, maar relatiewe groot bydraes tot die modelle gehad het.

Dans un monde de plus en plus ouvert, les flux de personnes sont amenés à exploser dans les prochaines années. Fluidifier et contrôler ces flux, tout en respectant de fortes contraintes sécuritaires, apparaît donc comme un élément clef pour favoriser le dynamisme économique mondial. Cette gestion des flux passe principalement par la connaissance et la vérification de l’identité des personnes. Pour son aspect pratique et a priori sécurisé, la biométrie, et en particulier celle des empreintes digitales, s’est imposée comme une solution efficace, et incontournable. Néanmoins, elle souffre de deux sévères limitations. La première concerne les mauvaises performances obtenues avec des doigts détériorés. Ces détériorations peuvent être involontaires (travailleurs manuels par exemple), ou bien volontaires, à des fins d’anonymisation. La deuxième concerne les failles de sécurité des capteurs. En particulier, ils sont vulnérables à des attaques avec de fausses empreintes, réalisées par des personnes mal intentionnées dans un but d’usurpation d’identité. D’après nous, ces limitations sont dues à la faible quantité d’information exploitée par les capteurs usuels. Elle se résume souvent à une simple image de la surface du doigt. Pourtant, la complexité biologique des tissus humains est telle qu’elle offre une information très riche, unique, et difficilement reproductible. Nous avons donc proposé une approche d’imagerie, basée sur la Tomographique par Cohérence Optique, un capteur 3D sans contact, permettant de mesurer finement cette information. L’idée majeure de la thèse consiste à étudier divers moyens de l’exploiter, afin de rendre la biométrie plus robuste et vraiment sécurisée / In an increasingly open world, the flows of people are brought to explode in the coming years. Facilitating, streamlining, and managing these flows, by maintaining strict security constraints, therefore represent a key element for the global socio-economic dynamism. This flows management is mainly based on knowledge and verification of person identity. For its practicality and a priori secured, biometrics, in particular fingerprints biometrics, has become an effective and unavoidable solution.Nevertheless, it still suffers from two severe limitations. The first one concerns the poor performances obtained with damaged fingers. This damage can be involuntary (e.g. manual workers) or volunteers, for purposes of anonymity. The second limitation consists in the vulnerability of the commonly used sensors. In particular, they are vulnerable to copies of stolen fingerprints, made by malicious persons for identity theft purpose. We believe that these limitations are due to the small amount of information brought by the usual biometric sensors. It often consists in a single print of the finger surface. However, the biological complexity of human tissue provides rich information, unique to each person, and very difficult to reproduce. We therefore proposed an imaging approach based on Optical Coherence Tomography (OCT), a 3D contactless optical sensor, to finely measure this information. The main idea of the thesis is therefore to explore novel ways to exploit this information in order to make biometrics more robust and truly secured. In particular, we have proposed and evaluated different fingerprint imaging methods, based on the phase of the OCT signal

[pt] A busca por novas técnicas para a revelação de impressões digitais latentes é constante por conta da importância para a área de Ciências Forenses, em especial, na elucidação de crimes. O objetivo do presente estudo é avaliar o potencial da 4,7- di-m-toluilbenzo[c][1,2,5]tiadiazola (BTD 206) como novo marcador para aplicação na identificação dos grupos fundamentais e pontos característicos dos desenhos das impressões digitais, visando melhor contraste de imagem em substratos de diferentes cores, como capa de celular. Seis matrizes diferentes foram testadas para a análise preliminar do desenvolvimento do pó revelador. A matriz escolhida, carbonato de cálcio foi a que apresentou maior intensidade de luminescência no substrato. Esse pó revelador foi desenvolvido e avaliado através da espectrometria de luminescência em três diferentes concentrações. O programa Image J foi utilizado para o processamento das imagens. O pó revelador impregnado com a BTD 206 em metanol, na matriz carbonato de cálcio apresentou características que auxiliaram na melhoria da qualidade do contraste, que foi realizada a partir do histograma de imagem, que descreve a estatística dos níveis de cinza. Dessa forma, em uma imagem com melhor qualidade, é possível extrair informações da impressão digital, como grupos fundamentais e minúncias. O que auxilia em um confronto e identificação de um possível suspeito de um crime. O pó revelador desenvolvido com a BTD 206 teve um desempenho satisfatório para aplicação pretendida. / [en] The search for new techniques for revealing latent fingerprints is constant due to the importance for the area of Forensic Sciences, in particular, in the elucidation of crimes. The objective of the present study is to evaluate the potential of 4,7-di-m-toluylbenzo[c][1,2,5]thiadiazole (BTD 206) as a new marker for application in the identification of fundamental groups and characteristic points of drawings of digital prints, aiming at better image contrast on substrates of different colors, such as cell phone cases. Six different matrices were tested for the preliminary analysis of the developer powder development. The matrix chosen, calcium carbonate, was the one that presented the highest intensity of luminescence in the substrate. This developer powder was developed and evaluated through luminescence spectrometry at three different concentrations. The Image J program was used for image processing. The developer powder impregnated with BTD 206 in methanol, in the calcium carbonate matrix, showed characteristics that helped to improve the quality of the contrast, which was performed from the image histogram, which describes the gray levels statistics. In this way, in a better quality image, it is possible to extract information from the fingerprint, such as fundamental groups and minutiae. Which helps in a confrontation and identification of a possible suspect of a crime. The developer powder developed with BTD 206 performed satisfactorily for the intended application.

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