Model-based Curvilinear Network Extraction and Tracking toward Quantitative Analysis of Biopolymer Networks

Curvilinear biopolymer networks pervade living systems. They are routinely imaged by fluorescence microscopy to gain insight into their structural, mechanical, and dynamic properties. Image analysis can facilitate understanding the mechanisms of their formation and their biological functions from a quantitative viewpoint. Due to the variability in network geometry, topology and dynamics as well as often low resolution and low signal-to-noise ratio in images, segmentation and tracking networks from these images is challenging. In this dissertation, we propose a complete framework for extracting the geometry and topology of curvilinear biopolymer networks, and also tracking their dynamics from multi-dimensional images. The proposed multiple Stretching Open Active Contours (SOACs) can identify network centerlines and junctions, and infer plausible network topology. Combined with a $k$-partite matching algorithm, temporal correspondences among all the detected filaments can be established. This work enables statistical analysis of structural parameters of biopolymer networks as well as their dynamics. Quantitative evaluation using simulated and experimental images demonstrate its effectiveness and efficiency. Moreover, a principled method of optimizing key parameters without ground truth is proposed for attaining the best extraction result for any type of images. The proposed methods are implemented into a usable open source software ``SOAX\u27\u27. Besides network extraction and tracking, SOAX provides a user-friendly cross-platform GUI for interactive visualization, manual editing and quantitative analysis. Using SOAX to analyze several types of biopolymer networks demonstrates the potential of the proposed methods to help answer key questions in cell biology and biophysics from a quantitative viewpoint

The Analysis of the Fatty Acid Content of Fingerprint Residues Using Gas ChromatographyMass Spectrometry

One of the recurring issues in the practice of forensic science is human subjectivity, especially within the field of fingerprint examination. Smudged fingerprints at crime scenes that contain little to no ridge detail often cause problems for examiners who, in turn, are unable to make identifications or exclusions in the absence of DNA markers. In recent years, researchers have explored the chemical composition of fingerprint residues to either provide an alternative means for including or excluding potential donors, or to provide investigative leads. Research into the chemical composition of fingerprints has shown that it may be possible to determine sex, age, and race from residues that are left behind when a fingerprint is deposited on a surface. However, it is important to first ensure that residues deposited by one individual remain consistent over a period of time.;In this study, five different types of skin residues (natural, eccrine, face, neck, and groomed fingerprints) were collected from six participants over the course of 56 days to assess both intra- and inter-subject variability of the different sample types. Natural prints consisted of any substances that were on the participant\u27s hands upon arrival at each collection event. Eccrine residues were collected after washing hands with soap and water. Groomed prints were collected after rubbing hands across the subject\u27s own face and neck. The measured variables were the relative quantities of fatty acid methyl esters (FAMEs), squalene, and cholesterol in each subject\u27s residues. The fatty acid methyl esters were analyzed using a conventional gas chromatography/mass spectrometry (GC/MS) instrument. Canonical discriminant analysis (CDA) was used to classify the data into known grouping factors to determine if there were sufficient differences between the residues of different samples or subjects to enable classification between groups.;The results show that within an individual, 82% of the original grouped cases were correctly classified and 62% of the cross-validated grouped cases were correctly classified to the correct source of the sample. In other words, there are significant chemical differences between the five types of samples collected from an individual. Natural and eccrine residues generally contained the fewest compounds and in the lowest amounts and were not helpful for discriminating between individuals. Saturated fatty acids such as C16:0 and C18:0 were the most commonly observed compounds in the natural and eccrine residues. Groomed fingerprint residues contained more FAMEs than the natural and eccrine residues, although not as many FAMEs as the face and neck residues. Using leave-one-out cross validation, classifying subjects using a fixed sample type, like face or neck, provided better than 92% and 77% accuracy, respectively, even when including the intra-subject variability over a 56-day period. The results indicate that residues on surfaces like the face and neck are more highly discriminating than eccrine secretions, the latter of which are dominant in fingerprint residues. Although freshly groomed fingerprints contain many of the compounds from the face and neck sebaceous secretions, the chemical composition of groomed prints is significantly different from natural fingerprints

A critical review of the current state of forensic science knowledge and its integration in legal systems

Forensic science has a significant historical and contemporary relationship with the criminal justice system. It is a relationship between two disciplines whose origins stem from different backgrounds. It is trite that effective communication assist in resolving underlying problems in any given context. However, a lack of communication continues to characterise the intersection between law and science. As recently as 2019, a six-part symposium on the use of forensic science in the criminal justice system again posed the question on how the justice system could ensure the reliability of forensic science evidence presented during trials. As the law demands finality, science is always evolving and can never be considered finite or final. Legal systems do not always adapt to the nature of scientific knowledge, and are not willing to abandon finality when that scientific knowledge shifts. Advocacy plays an important role in the promotion of forensic science, particularly advocacy to the broader scientific community for financial support, much needed research and more testing. However, despite its important function, advocacy should not be conflated with science. The foundation of advocacy is a cause; whereas the foundation of science is fact. The objective of this research was to conduct a qualitative literature review of the field of forensic science; to identify gaps in the knowledge of forensic science and its integration in the criminal justice system. The literature review will provide researchers within the field of forensic science with suggested research topics requiring further examination and research. To achieve its objective, the study critically analysed the historical development of, and evaluated the use of forensic science evidence in legal systems generally, including its role regarding the admissibility or inadmissibility of the evidence in the courtroom. In conclusion, it was determined that the breadth of forensic scientific knowledge is comprehensive but scattered. The foundational underpinning of the four disciplines, discussed in this dissertation, has been put to the legal test on countless occasions. Some gaps still remain that require further research in order to strengthen the foundation of the disciplines. Human influence will always be present in examinations and interpretations and will lean towards subjective decision making.JurisprudenceD. Phil

Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica.

The Earth's crust hosts a subsurface, dark, and oligotrophic biosphere that is poorly understood in terms of the energy supporting its biomass production and impact on food webs at the Earth's surface. Dark oligotrophic volcanic ecosystems (DOVEs) are good environments for investigations of life in the absence of sunlight as they are poor in organics, rich in chemical reactants and well known for chemical exchange with Earth's surface systems. Ice caves near the summit of Mt. Erebus (Antarctica) offer DOVEs in a polar alpine environment that is starved in organics and with oxygenated hydrothermal circulation in highly reducing host rock. We surveyed the microbial communities using PCR, cloning, sequencing and analysis of the small subunit (16S) ribosomal and Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RubisCO) genes in sediment samples from three different caves, two that are completely dark and one that receives snow-filtered sunlight seasonally. The microbial communities in all three caves are composed primarily of Bacteria and fungi; Archaea were not detected. The bacterial communities from these ice caves display low phylogenetic diversity, but with a remarkable diversity of RubisCO genes including new deeply branching Form I clades, implicating the Calvin-Benson-Bassham (CBB) cycle as a pathway of CO2 fixation. The microbial communities in one of the dark caves, Warren Cave, which has a remarkably low phylogenetic diversity, were analyzed in more detail to gain a possible perspective on the energetic basis of the microbial ecosystem in the cave. Atmospheric carbon (CO2 and CO), including from volcanic emissions, likely supplies carbon and/or some of the energy requirements of chemoautotrophic microbial communities in Warren Cave and probably other Mt. Erebus ice caves. Our work casts a first glimpse at Mt. Erebus ice caves as natural laboratories for exploring carbon, energy and nutrient sources in the subsurface biosphere and the nutritional limits on life

Forensic Analysis of Fiber Dyes via Surface-Enhanced Raman Spectroscopy

Fibers are a common piece of evidence found at crime scenes that may become a link between the scene and a suspect, or allow for the reconstruction of certain crime events. Although a big portion of fibers are still white cottons, the advancement of commercial fiber production and dyeing in the past century led to an increase in types of synthetic fibers and dye applications that can be found and used in forensic analyses. Nonetheless, the fiber evidentiary value is not fully explored, as for the most part, the separation and analysis of the dye on the fiber is not routinely done. This is mostly because traditional methods for dye analysis require lengthy or expensive procedures, combining extractions or hydrolysis, solvent tailoring, separation procedures such as TLC or HPLC, and potential mass-spectrometry for the extract identification. Currently, the prescribed method of fiber forensic analysis involves the fiber macro and microscopical examination, determination of optical properties, cross-sectioning, and spectrophotometric and infrared analysis. In the case where fibers of same polymer make have similar colors that cannot be separated by spectrophotometric analysis, there is still a chance that those fibers could have been dyed using differing dyes. It is possible to analyze those dyes by surface-enhanced Raman spectroscopy, a method which allows for high enhancements of low concentration, microliter volume samples, allowing the analyst to extract single fibers in small volumes of solvents.b This research focused on the comparison of solvent systems, alongside hydrofluoric acid fuming and in situ SER analysis, to develop a working routine for forensic fiber dye analysis. The research was also expanded to simulate casework, showing that the extraction methods coupled with SERS and statistical analysis can be used to differentiate and successfully classify questioned fibers when compared to known sets. Tweaks and improvements to the method of analysis are presented by either acid-addition, or use of coffee-ring – SERS analysis on high performance thin-layer chromatography plates. Methods of improvement and further research are also presented, with the scope of validating of SERS by both forensic science and the courts. Because this project presents a novel approach to the completion of forensic fiber analyses, it shows that SERS can be a valuable tool and aid in the improvement of forensic science and the criminal justice system. The presented approach shows a successful, rapid and inexpensive technique that can also be expanded and utilized for the analysis of other evidence types

The oldest peracarid crustacean reveals a Late Devonian freshwater colonization by isopod relatives.

Peracarida (e.g. woodlice and side-swimmers) are, together with their sister-group Eucarida (e.g. krill and decapods), the most speciose group of modern crustaceans, suggested to have appeared as early as the Ordovician. While eucarids' incursion onto land consists of mainly freshwater and littoral grounds, some peracarids have evolved fully terrestrial ground-crawling ecologies, inhabiting even our gardens in temperate regions (e.g. pillbugs and sowbugs). Their fossil record extends back to the Carboniferous and consists mainly of marine occurrences. Here, we provide a complete re-analysis of a fossil arthropod-Oxyuropoda-reported in 1908 from the Late Devonian floodplains of Ireland, and left with unresolved systematic affinities despite a century of attempts at identification. Known from a single specimen preserved in two dimensions, we analysed its anatomy using digital microscopy and multispectral macroimaging to enhance the contrast of morphological structures. The new anatomical characters and completeness of Oxyuropoda, together with a phylogenetic analysis with representatives of all major Eumalacostraca groups, indicate that Oxyuropoda is a crown peracarid, part of a clade including amphipods and isopods. As such, Oxyuropoda is the oldest known species Peracarida, and provides evidence that derived peracarids had an incursion into freshwater and terrestrial environments as early as the Famennian, more than 360 Ma

Physical and chemical trace evidence from 3d-printed firearms, and use of a quadcopter for targeted sampling of gaseous mercury in the atmosphere

My forensic research resulted in the first peer-reviepaper to address the forensic challenges presented by 3D-printed polymer firearms. The work involved a systematic approach to the analysis of evidence stemming from 3D-printed firearms filling a critical void in current forensic knowledge. We used DART-MS to characterize the polymer evidence left behind by 3D-printed firearms as well as an evaluation of pre-existing firearm and toolmark techniques and fingerprint analysis. We demonstrated that 3D-printed firearms leave behind characteristic polymer residue on cartridge cases bullets and the receiving surface which can be identified using DART-MS. The culmination of the work includes a database / reference library that can give forensic practitioners the ability to identify and source unknown polymer evidence using chemometric analysis including principle component analysis (PCA) and ongoing work with supervised statistical classification methods. Several novel analytical methods were developed in the course of this dissertation work including forensic analysis of trace chemical evidence from 3D-printed firearms using direct analysis in real time-mass spectrometry (DART-MS) and targeted aerial sampling for quantitation of gaseous mercury. The mercury project utilized a quadcopter unmanned aerial vehicle (UAV) and gold-coated quartz sorbent tubes to target and capture gaseous mercury which was then quantified both in the laboratory and in the field using cold vapor atomic fluorescence spectrometry (CVAFS). This method was verified to effectively capture and quantify mercury in the atmosphere near point sources and was applied near a coal-fired power plants petroleum refinery and municipal landfill. Average concentrations (± standard deviation) immediately downwind of the landfill were higher at ground level and 30 m compared to 60 m and 120 m (5.3 ± 0.5 ng m-3 5.4 ± 0.7 ng m-3 4.2 ± 0.7 ng m-3 and 2.5 ± 0.3 ng m-3 respectively). Concentrations were also higher at an urban/industrial area (Memphis) (3.3 ± 0.9 ng m-3) compared with a rural/background area (1.5 ± 0.2 ng m-3). Overall we shothe method is useful to probe Hg concentrations aloft and quantify emissions from potential point sources in the field using an inexpensive quadcopter and sampling setup. The forensic research was funded by NIJ Graduate Research Fellowship (Award # 2017-IJ-CX-0001). The opinions findings and conclusions or recommendations expressed here are those of the authors and do not necessarily reflect those of the U.S. Department of Justice