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1.
Sci Rep ; 11(1): 6482, 2021 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-33753760

RESUMO

This study addresses the core issue facing a surgical team during breast cancer surgery: quantitative prediction of tumor likelihood including estimates of prediction error. We have previously reported that a molecular probe, Laser Raman spectroscopy (LRS), can distinguish healthy and tumor tissue. We now report that combining LRS with two machine learning algorithms, unsupervised k-means and stochastic nonlinear neural networks (NN), provides rapid, quantitative, probabilistic tumor assessment with real-time error analysis. NNs were first trained on Raman spectra using human expert histopathology diagnostics as gold standard (74 spectra, 5 patients). K-means predictions using spectral data when compared to histopathology produced clustering models with 93.2-94.6% accuracy, 89.8-91.8% sensitivity, and 100% specificity. NNs trained on k-means predictions generated probabilities of correctness for the autonomous classification. Finally, the autonomous system characterized an extended dataset (203 spectra, 8 patients). Our results show that an increase in DNA|RNA signal intensity in the fingerprint region (600-1800 cm-1) and global loss of high wavenumber signal (2800-3200 cm-1) are particularly sensitive LRS warning signs of tumor. The stochastic nature of NNs made it possible to rapidly generate multiple models of target tissue classification and calculate the inherent error in the probabilistic estimates for each target.


Assuntos
Inteligência Artificial , Teorema de Bayes , Biomarcadores Tumorais , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/etiologia , Análise Espectral Raman/métodos , Análise de Dados , Feminino , Humanos , Imuno-Histoquímica/métodos , Prognóstico , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Análise Espectral Raman/normas
2.
Sensors (Basel) ; 20(21)2020 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-33147836

RESUMO

Laser Raman spectroscopy (LRS) is a highly specific biomolecular technique which has been shown to have the ability to distinguish malignant and normal breast tissue. This paper discusses significant advancements in the use of LRS in surgical breast cancer diagnosis, with an emphasis on statistical and machine learning strategies employed for precise, transparent and real-time analysis of Raman spectra. When combined with a variety of "machine learning" techniques LRS has been increasingly employed in oncogenic diagnostics. This paper proposes that the majority of these algorithms fail to provide the two most critical pieces of information required by the practicing surgeon: a probability that the classification of a tissue is correct, and, more importantly, the expected error in that probability. Stochastic backpropagation artificial neural networks inherently provide both pieces of information for each and every tissue site examined by LRS. If the networks are trained using both human experts and an unsupervised classification algorithm as gold standards, rapid progress can be made understanding what additional contextual data is needed to improve network classification performance. Our patients expect us to not simply have an opinion about their tumor, but to know how certain we are that we are correct. Stochastic networks can provide that information.


Assuntos
Neoplasias da Mama , Lasers , Redes Neurais de Computação , Análise Espectral Raman , Algoritmos , Neoplasias da Mama/diagnóstico , Humanos
3.
J Vis Exp ; (152)2019 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-31710034

RESUMO

Global warming affects microbial communities in a variety of ecosystems, especially cryospheric habitats. However, little is known about microbial-mediated carbon fluxes in extreme environments. Hence, the methodology of sample acquisition described in the very few studies available implies two major problems: A) high resolution data require a large number of samples, which is difficult to obtain in remote areas; B) unavoidable sample manipulation such as cutting, sawing, and melting of ice cores that leads to a misunderstanding of in situ conditions. In this study, a prototype device that requires neither sample preparation nor sample destruction is presented. The device can be used for in situ measurements with a high spectral and spatial resolution in terrestrial and ice ecosystems and is based on the Laser-Induced Fluorescence Emission (L.I.F.E.) technique. Photoautotrophic supraglacial communities can be identified by the detection of L.I.F.E. signatures in photopigments. The L.I.F.E. instrument calibration for the porphyrin derivates chlorophylla (chla) (405 nm laser excitation) and B-phycoerythrin (B-PE) (532 nm laser excitation) is demonstrated. For the validation of this methodology, L.I.F.E. data were ratified by a conventional method for chla quantification that involved pigment extraction and subsequent absorption spectroscopy. The prototype applicability in the field was proven in extreme polar environments. Further testing on terrestrial habitats took place during Mars analog simulations in the Moroccan dessert and on an Austrian rock glacier. The L.I.F.E. instrument enables high resolution scans of large areas with acceptable operation logistics and contributes to a better understanding of the ecological potential of supraglacial communities in the context of global change.


Assuntos
Biomarcadores/metabolismo , Fluorescência , Aquecimento Global , Camada de Gelo/química , Lasers/normas
4.
Sci Rep ; 9(1): 14639, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31601985

RESUMO

Failure to precisely distinguish malignant from healthy tissue has severe implications for breast cancer surgical outcomes. Clinical prognoses depend on precisely distinguishing healthy from malignant tissue during surgery. Laser Raman spectroscopy (LRS) has been previously shown to differentiate benign from malignant tissue in real time. However, the cost, assembly effort, and technical expertise needed for construction and implementation of the technique have prohibited widespread adoption. Recently, Raman spectrometers have been developed for non-medical uses and have become commercially available and affordable. Here we demonstrate that this current generation of Raman spectrometers can readily identify cancer in breast surgical specimens. We evaluated two commercially available, portable, near-infrared Raman systems operating at excitation wavelengths of either 785 nm or 1064 nm, collecting a total of 164 Raman spectra from cancerous, benign, and transitional regions of resected breast tissue from six patients undergoing mastectomy. The spectra were classified using standard multivariate statistical techniques. We identified a minimal set of spectral bands sufficient to reliably distinguish between healthy and malignant tissue using either the 1064 nm or 785 nm system. Our results indicate that current generation Raman spectrometers can be used as a rapid diagnostic technique distinguishing benign from malignant tissue during surgery.


Assuntos
Neoplasias da Mama/cirurgia , Cuidados Intraoperatórios/métodos , Margens de Excisão , Mastectomia Segmentar , Análise Espectral Raman/métodos , Mama/patologia , Mama/cirurgia , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/patologia , Feminino , Humanos , Cuidados Intraoperatórios/economia , Análise de Componente Principal , Espectroscopia de Luz Próxima ao Infravermelho/instrumentação , Espectroscopia de Luz Próxima ao Infravermelho/métodos , Análise Espectral Raman/instrumentação , Fatores de Tempo
5.
Astrobiology ; 14(5): 391-405, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24823800

RESUMO

Abstract We have developed a portable dual-wavelength laser fluorescence spectrometer as part of a multi-instrument optical probe to characterize mineral, organic, and microbial species in extreme environments. Operating at 405 and 532 nm, the instrument was originally designed for use by human explorers to produce a laser-induced fluorescence emission (L.I.F.E.) spectral database of the mineral and organic molecules found in the microbial communities of Earth's cryosphere. Recently, our team had the opportunity to explore the strengths and limitations of the instrument when it was deployed on a remote-controlled Mars analog rover. In February 2013, the instrument was deployed on board the Magma White rover platform during the MARS2013 Mars analog field mission in the Kess Kess formation near Erfoud, Morocco. During these tests, we followed tele-science work flows pertinent to Mars surface missions in a simulated spaceflight environment. We report on the L.I.F.E. instrument setup, data processing, and performance during field trials. A pilot postmission laboratory analysis determined that rock samples acquired during the field mission exhibited a fluorescence signal from the Sun-exposed side characteristic of chlorophyll a following excitation at 405 nm. A weak fluorescence response to excitation at 532 nm may have originated from another microbial photosynthetic pigment, phycoerythrin, but final assignment awaits development of a comprehensive database of mineral and organic fluorescence spectra. No chlorophyll fluorescence signal was detected from the shaded underside of the samples.


Assuntos
Marte , Simulação de Ambiente Espacial , Espectrometria de Fluorescência/instrumentação , Robótica/instrumentação
6.
Astrobiology ; 11(10): 997-1016, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22149884

RESUMO

Primitive photosynthetic microorganisms, either dormant or dead, may remain today on the martian surface, akin to terrestrial cyanobacteria surviving endolithically in martian analog sites on Earth such as the Antarctic Dry Valleys and the Atacama Desert. Potential markers of martian photoautotrophs include the red edge of chlorophyll reflectance spectra or fluorescence emission from systems of light-harvesting pigments. Such biosignatures, however, would be modified and degraded by long-term exposure to ionizing radiation from the unshielded cosmic ray flux onto the martian surface. In this initial study into this issue, three analytical techniques--absorbance, reflectance, and fluorescence spectroscopy--were employed to determine the progression of the radiolytic destruction of cyanobacteria. The pattern of signal loss for chlorophyll reflection and fluorescence from several biomolecules is characterized and quantified after increasing exposures to ionizing gamma radiation. This allows estimation of the degradation rates of cyanobacterial biosignatures on the martian surface and the identification of promising detectable fluorescent break-down products.


Assuntos
Biomarcadores , Radiação Ionizante , Synechocystis/isolamento & purificação , Exobiologia , Marte , Espectrometria de Fluorescência , Synechocystis/efeitos da radiação
7.
Astrobiology ; 10(10): 989-1000, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21162678

RESUMO

It has been hypothesized in this journal and elsewhere, based on surveys of published data from prebiotic synthesis experiments and carbonaceous meteorite analyses, that basic amino acids such as lysine and arginine were not abundant on prebiotic Earth. If the basic amino acids were incorporated only rarely into the first peptides formed in that environment, it is important to understand what protobiotic chemistry is possible in their absence. As an initial test of the hypothesis that basic amino acid negative [BAA(-)] proteins could have performed at least a subset of protobiotic chemistry, the current work reports on a survey of 13 archaeal and 13 bacterial genomes that has identified 61 modern gene sequences coding for known or putative proteins not containing arginine or lysine. Eleven of the sequences found code for proteins whose functions are well known and important in the biochemistry of modern microbial life: lysine biosynthesis protein LysW, arginine cluster proteins, copper ion binding proteins, bacterial flagellar proteins, and PE or PPE family proteins. These data indicate that the lack of basic amino acids does not prevent peptides or proteins from serving useful structural and biochemical functions. However, as would be predicted from fundamental physicochemical principles, we see no fossil evidence of prebiotic BAA(-) peptide sequences capable of interacting directly with nucleic acids.


Assuntos
Aminoácidos Básicos/análise , Fenômenos Bioquímicos , Planeta Terra , Sequência de Aminoácidos , Aminoácidos Básicos/genética , Archaea/genética , Bactérias/genética , Genes Arqueais , Genes Bacterianos , Filogenia
8.
Astrobiology ; 10(9): 933-51, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21118025

RESUMO

The Panoramic Camera (PanCam) instrument will provide visible-near IR multispectral imaging of the ExoMars rover's surroundings to identify regions of interest within the nearby terrain. This multispectral capability is dependant upon the 12 preselected "geological" filters that are integrated into two wide-angle cameras. First devised by the Imager for Mars Pathfinder team to detect iron oxides, this baseline filter set has remained largely unchanged for subsequent missions (Mars Exploration Rovers, Beagle 2, Phoenix) despite the advancing knowledge of the mineralogical diversity on Mars. Therefore, the geological filters for the ExoMars PanCam will be redesigned to accommodate the astrobiology focus of ExoMars, where hydrated mineral terrains (evidence of past liquid water) will be priority targets. Here, we conduct an initial investigation into new filter wavelengths for the ExoMars PanCam and present results from tests performed on Mars analog rocks. Two new filter sets were devised: one with filters spaced every 50 nm ("F1-12") and another that utilizes a novel filter selection method based upon hydrated mineral reflectance spectra ("F2-12"). These new filter sets, along with the Beagle 2 filter set (currently the baseline for the ExoMars PanCam), were tested on their ability to identify hydrated minerals and biosignatures present in Mars analog rocks. The filter sets, with varying degrees of ability, detected the spectral features of minerals jarosite, opaline silica, alunite, nontronite, and siderite present in these rock samples. None of the filter sets, however, were able to detect fossilized biomat structures and small (<2 mm) mineralogical heterogeneities present in silica sinters. Both new filter sets outperformed the Beagle 2 filters, with F2-12 detecting the most spectral features produced by hydrated minerals and providing the best discrimination between samples. Future work involving more extensive testing on Mars analog samples that exhibit a wider range of mineralogies would be the next step in carefully evaluating the new filter sets.


Assuntos
Exobiologia/instrumentação , Sedimentos Geológicos/análise , Compostos de Alumínio/análise , Compostos de Alumínio/química , Carbonatos/análise , Carbonatos/química , Compostos Férricos/análise , Compostos Férricos/química , Sedimentos Geológicos/química , Geologia/instrumentação , Geologia/métodos , Compostos de Potássio/análise , Compostos de Potássio/química , Sulfatos/análise , Sulfatos/química
9.
Astrobiology ; 9(7): 659-72, 2009 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-19778277

RESUMO

Laser-induced fluorescence emission (L.I.F.E.) images were obtained in situ following 532 nm excitation of cryoconite assemblages in the ice covers of annual and perennially frozen Antarctic lakes during the 2008 Tawani International Expedition to Schirmacher Oasis and Lake Untersee in Dronning Maud Land, Antarctica. Laser targeting of a single millimeter-scale cryoconite results in multiple neighboring excitation events secondary to ice/air interface reflection and refraction in the bubbles surrounding the primary target. Laser excitation at 532 nm of cyanobacteria-dominated assemblages produced red and infrared autofluorescence activity attributed to the presence of phycoerythrin photosynthetic pigments. The method avoids destruction of individual target organisms and does not require the disruption of either the structure of the microbial community or the surrounding ice matrix. L.I.F.E. survey strategies described may be of interest for orbital monitoring of photosynthetic primary productivity in polar and alpine glaciers, ice sheets, snow, and lake ice of Earth's cryosphere. The findings open up the possibility of searching from either a rover or from orbit for signs of life in the polar regions of Mars and the frozen regions of exoplanets in neighboring star systems.


Assuntos
Cianobactérias/isolamento & purificação , Fluorescência , Água Doce/microbiologia , Camada de Gelo/microbiologia , Lasers , Técnicas Microbiológicas , Regiões Antárticas , Sedimentos Geológicos/microbiologia , Federação Russa , Silício , Espectrofotometria Infravermelho , Microbiologia da Água
10.
Astrobiology ; 9(10): 953-64, 2009 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-20041748

RESUMO

The European Space Agency will launch the ExoMars mission in 2016 with a primary goal of surveying the martian subsurface for evidence of organic material. We have recently investigated the utility of including either a 365 nm light-emitting diode or a 375 nm laser light source in the ExoMars rover panoramic camera (PanCam). Such a modification would make it feasible to monitor rover drill cuttings optically for the fluorescence signatures of aromatic organic molecules and map the distribution of polycyclic aromatic hydrocarbons (PAHs) as a function of depth to the 2 m limit of the ExoMars drill. The technique described requires no sample preparation, does not consume irreplaceable resources, and would allow mission control to prioritize deployment of organic detection experiments that require sample destruction, expenditure of non-replaceable consumables, or both. We report here for the first time laser-induced fluorescence emission (L.I.F.E.) imaging detection limits for anthracene, pyrene, and perylene targets doped onto a Mars analog granular peridotite with a 375 nm Nichia laser diode in optically uncorrected wide-angle mode. Data were collected via the Beagle 2 PanCam backup filter wheel fitted with original blue (440 nm), green (530 nm), and red (670 nm) filters. All three PAH species can be detected with the PanCam green (530 nm) filter. Detection limits in the green band for signal-to-noise ratios (S/N) > 10 are 49 parts per million (ppm) for anthracene, 145 ppm for pyrene, and 20 ppm for perylene. The anthracene detection limit improves to 7 ppm with use of the PanCam blue filter. We discuss soil-dependent detection limit constraints; use of UV excitation with other rover cameras, which provides higher spatial resolution; and the advantages of focused and wide-angle laser modes. Finally, we discuss application of L.I.F.E. techniques at multiple wavelengths for exploration of Mars analog extreme environments on Earth, including Icelandic hydrothermally altered basalts and the ice-covered lakes and glaciers of Dronning Maud Land, Antarctica.


Assuntos
Exobiologia/instrumentação , Meio Ambiente Extraterreno/química , Lasers , Marte , Compostos Orgânicos/análise , Raios Ultravioleta , Regiões Antárticas , Cristalização , Fluorescência , Limite de Detecção , Hidrocarbonetos Policíclicos Aromáticos/análise , Erupções Vulcânicas
11.
Astrobiology ; 8(4): 807-21, 2008 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-18498219

RESUMO

"Hairy blobs" are unusual clumps of organic bodies and sulfate crystals that have been found in evaporite minerals grown in acid saline lakes. Here, we document modern hairy blobs in halite and gypsum from 5 modern acid saline lakes in southern Western Australia, and Permian hairy blobs trapped in halite from the mid-Permian Opeche Shale in the subsurface of North Dakota. These are among the first microbial remains described from acid saline lake environments. They give clues about the role of microorganisms in the acidity, geochemistry, and mineralogy of these extreme environments. This study also may add to the inventory of life in extreme environments and help predict possible martian life-forms and the method of preservation.


Assuntos
Sulfato de Cálcio/análise , Sedimentos Geológicos/análise , Cloreto de Sódio/análise , Água/análise , Austrália , Planeta Terra , Microbiologia Ambiental , Meio Ambiente Extraterreno , Concentração de Íons de Hidrogênio , Lasers , Marte , Microscopia Ultravioleta , Análise Espectral Raman , Estados Unidos , Microbiologia da Água
12.
Astrobiology ; 6(1): 17-33, 2006 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-16551224

RESUMO

The relative abundance of the protein amino acids has been previously investigated as a potential marker for biogenicity in meteoritic samples. However, these investigations were executed without a quantitative metric to evaluate distribution variations, and they did not account for the possibility of interdisciplinary systematic error arising from inter-laboratory differences in extraction and detection techniques. Principal component analysis (PCA), hierarchical cluster analysis (HCA), and stochastic probabilistic artificial neural networks (ANNs) were used to compare the distributions for nine protein amino acids previously reported for the Murchison carbonaceous chondrite, Mars meteorites (ALH84001, Nakhla, and EETA79001), prebiotic synthesis experiments, and terrestrial biota and sediments. These techniques allowed us (1) to identify a shift in terrestrial amino acid distributions secondary to diagenesis; (2) to detect differences in terrestrial distributions that may be systematic differences between extraction and analysis techniques in biological and geological laboratories; and (3) to determine that distributions in meteoritic samples appear more similar to prebiotic chemistry samples than they do to the terrestrial unaltered or diagenetic samples. Both diagenesis and putative interdisciplinary differences in analysis complicate interpretation of meteoritic amino acid distributions. We propose that the analysis of future samples from such diverse sources as meteoritic influx, sample return missions, and in situ exploration of Mars would be less ambiguous with adoption of standardized assay techniques, systematic inclusion of assay standards, and the use of a quantitative, probabilistic metric. We present here one such metric determined by sequential feature extraction and normalization (PCA), information-driven automated exploration of classification possibilities (HCA), and prediction of classification accuracy (ANNs).


Assuntos
Aminoácidos/análise , Meteoroides , Aminoácidos/isolamento & purificação , Aminoácidos/normas , Análise por Conglomerados , Planeta Terra , Exobiologia , Meio Ambiente Extraterreno , Marte , Redes Neurais de Computação , Origem da Vida , Análise de Componente Principal , Processos Estocásticos
13.
Astrobiology ; 3(4): 649-55, 2003.
Artigo em Inglês | MEDLINE | ID: mdl-14994715

RESUMO

It has been underappreciated that inorganic processes can produce stromatolites (laminated macroscopic constructions commonly attreibuted to microbiological activity), thus calling into question the long-standing use of stromatolites as de facto evidence for ancient life. Using lossless compression on unmagnified reflectance red-green-blue (RGB) images of matched stromatolite-sediment matrix pairs as a complexity metric, the compressibility index (delta(c), the log ratio of the ratio of the compressibility of the matrix versus the target) of a putative abiotic test stromatolite is significantly less than the delta(c) of a putative biotic test stromatolite. There is a clear separation in delta(c) between the different stromatolites discernible at the outcrop scale. In terms of absolute compressibility, the sediment matrix between the stromatolite columns was low in both cases, the putative abiotic stromatolite was similar to the intracolumnar sediment, and the putative biotic stromatolite was much greater (again discernible at the outcrop scale). We propose tht this metric would be useful for evaluating the biogenicity of images obtained by the camera systems available on every Mars surface probe launched to date including Viking, Pathfinder, Beagle, and the two Mars Exploration Rovers.


Assuntos
Evolução Planetária , Sedimentos Geológicos , Algoritmos , Planeta Terra , Fósseis , Fenômenos Geológicos , Geologia , Processamento de Imagem Assistida por Computador , Marte , Paleontologia
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