Unified detection and tracking of instruments during retinal microsurgery

Methods for tracking an object have generally fallen into two groups: tracking by detection and tracking through local optimization. The advantage of detection-based tracking is its ability to deal with target appearance and disappearance, but it does not naturally take advantage of target motion continuity during detection. The advantage of local optimization is efficiency and accuracy, but it requires additional algorithms to initialize tracking when the target is lost. To bridge these two approaches, we propose a framework for unified detection and tracking as a time-series Bayesian estimation problem. The basis of our approach is to treat both detection and tracking as a sequential entropy minimization problem, where the goal is to determine the parameters describing a target in each frame. To do this we integrate the Active Testing (AT) paradigm with Bayesian filtering, and this results in a framework capable of both detecting and tracking robustly in situations where the target object enters and leaves the field of view regularly. We demonstrate our approach on a retinal tool tracking problem and show through extensive experiments that our method provides an efficient and robust tracking solution.

Quantitative PCR for the diagnosis of cutaneous leishmaniasis from formalin-fixed and paraffin-embedded skin sections.

The present report describes a real-time PCR-based procedure to reliably determine the quantity of Leishmania amastigotes in relation to the amount of host tissue in histological skin sections from canine and equine cases of cutaneous leishmaniasis. The novel diagnostic Leishmania-PCR has a detection limit of <0.02 amastigotes per μg tissue, which corresponds well to the detection limit of immunohistochemistry and is far beyond that of conventional histology. Our results emphasise the importance of PCR to complement routine histology of cutaneous leishmaniasis cases, particularly in laboratories in which no immunohistochemical assay is available.

Development of a rapid column-switching LC-MS/MS method for the quantification of THCCOOH and THCCOOH-glucuronide in whole blood for assessing cannabis consumption frequency

The concentration of 11-nor-9-carboxy-Δ(9)-tetrahydrocannabinol (THCCOOH) in whole blood is used as a parameter for assessing the consumption behavior of cannabis consumers. The blood level of THCCOOH-glucuronide might provide additional information about the frequency of cannabis use. To verify this assumption, a column-switching liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the rapid and direct quantification of free and glucuronidated THCCOOH in human whole blood was newly developed. The method comprised protein precipitation, followed by injection of the processed sample onto a trapping column and subsequent gradient elution to an analytical column for separation and detection. The total LC run time was 4.5 min. Detection of the analytes was accomplished by electrospray ionization in positive ion mode and selected reaction monitoring using a triple-stage quadrupole mass spectrometer. The method was fully validated by evaluating the following parameters: linearity, lower limit of quantification, accuracy and imprecision, selectivity, extraction efficiency, matrix effect, carry-over, dilution integrity, analyte stability, and re-injection reproducibility. All acceptance criteria were analyzed and the predefined criteria met. Linearity ranged from 5.0 to 500 μg/L for both analytes. The method was successfully applied to whole blood samples from a large collective of cannabis consumers, demonstrating its applicability in the forensic field.

Influence of contact points on the performance of caries detection methods in approximal surfaces of primary molars: an in vivo study

This in vivo study aimed to evaluate the influence of contact points on the approximal caries detection in primary molars, by comparing the performance of the DIAGNOdent pen and visual-tactile examination after tooth separation to bitewing radiography (BW). A total of 112 children were examined and 33 children were selected. In three periods (a, b, and c), 209 approximal surfaces were examined: (a) examiner 1 performed visual-tactile examination using the Nyvad criteria (EX1); examiner 2 used DIAGNOdent pen (LF1) and took BW; (b) 1 week later, after tooth separation, examiner 1 performed the second visual-tactile examination (EX2) and examiner 2 used DIAGNOdent again (LF2); (c) after tooth exfoliation, surfaces were directly examined using DIAGNOdent (LF3). Teeth were examined by computed microtomography as a reference standard. Analyses were based on diagnostic thresholds: D1: D 0 = health, D 1 –D 4 = disease; D2: D 0 , D 1 = health, D 2 –D 4 = disease; D3: D 0 –D 2 = health, D 3 , D 4 = disease. At D1, the highest sensitivity/specificity were observed for EX1 (1.00)/LF3 (0.68), respectively. At D2, the highest sensitivity/ specificity were observed for LF3 (0.69)/BW (1.00), respectively. At D3, the highest sensitivity/specificity were observed for LF3 (0.78)/EX1, EX2 and BW (1.00). EX1 showed higher accuracy values than LF1, and EX2 showed similar values to LF2. We concluded that the visual-tactile examination showed better results in detecting sound surfaces and approximal caries lesions without tooth separation. However, the effectiveness of approximal caries lesion detection of both methods was increased by the absence of contact points. Therefore, regardless of the method of detection, orthodontic separating elastics should be used as a complementary tool for the diagnosis of approximal noncavitated lesions in primary molars.

AN INVESTIGATION OF THE EFFECT OF FORMALDEHYDE SPECIES ON ENVIRONMENTAL MEASUREMENT METHODS UNDER AMBIENT CONDITIONS

Species variations in formaldehyde solutions and gases were investigated by means of infrared spectral analysis. Double beam infrared spectrometry in conjunction with sodium chloride wafer technique and solvent compensation technique were employed. Formaldehyde species in various solutions were investigated. Formalin 37% was stable for many months. Refrigeration had no effects on its stability. Spectral changes were detected in 1000 ppm formaldehyde solutions. The absorbances of very diluted solutions up to 100 ppm were lower than the detection limit of the instruments. Solvent compensation improved resolution, but was associated with an observed lack of repeatability. Formaldehyde species in animal chambers containing animals and in mobile home air were analyzed with the infrared spectrophotometer equipped with a 10 cm gas cell. Spectra were not different from the spectrum of clean air. A portable single beam infrared spectrometer with a 20 meter pathlength was used for reinvestigation. Indoor formaldehyde could not be detected in the spectral; conversely, an absorption peak at 3.58 microns was found in the spectra of 3 and 15 ppm formaldehyde gas in animal chambers. This peak did not appear in the spectrum of the control chamber. Because of concerns over measurement bias among various analytical methods for formaldehyde, side-by-side comparisons were conducted in both laboratory and field measurements. The chromotropic acid method with water and 1% sodium bisulfite as collection media, the pararosaniline method, and a single beam infrared spectrometer were compared. Measurement bias was elucidated and the extent of the effects of temperature and humidity was also determined. The problems associated with related methods were discussed. ^

Ground truthing the Cd/Ca-carbon isotope relationship in foraminifera of the Greenland-Iceland-Norwegian Seas

In order to examine whether the paleoceanographic nutrient proxies, d13C and cadmium/calcium in foraminiferal calcite, are well coupled to nutrients in the region of North Atlantic Deep Water formation, we present da ta from two transects of the Greenland-Iceland-Norwegian Seas. Along Transect A (74.3°N, 18.3°E to 75.0°N, 12.5°W, 15 stations), we measured phosphate and Cd concentrations of modern surface sea water. Along Transect B (64.5°N, 0.7°W to 70.4°N, 18.2°W, 14 stations) we measured Cd/Ca ratios and d13C of the planktonic foraminifera Neogloboquadrina pachyderma sinistral in core top sediments. Our results indicate that Cd and phosphate both vary with surface water mass and are well correlated along Transect A. Our planktonic foraminiferal d13C data indicate similar nutrient variation with water mass along Transect B. Our Cd/Ca data hint at the same type of nutrient variability, but interpretations are hampered by low values close to the detection limit of this technique and therefore relatively large error bars. We also measured Cd and phosphate concentrations in water depth profiles at three sites along Transect A and the d13C of the benthic foraminifera Cibicidoides wuellerstorfi along Transect B. Modern sea water depth profiles along Transect A have nutrient depletions at the surface and then constant values at depths greater than 100 meters. The d13C of planktonic and benthic foraminifera from Transect B plotted versus depth also reflect surface nutrient depletion and deep nutrient enrichment as seen at Transect A, with a small difference between intermediate and deep waters. Overall we see no evidence for decoupling of Cd/Ca ratio and d13C in foraminiferal calcite from water column nutrient concentrations along these transects in a region of North Atlantic Deep Water formation.

Sr-Nd isotopic analyses of sand-sized sediment from the San Francisco Bay coastal system

A diverse suite of geochemical tracers, including 87Sr/86Sr and 143Nd/144Nd isotope ratios, the rare earth elements (REEs), and select trace elements were used to determine sand-sized sediment provenance and transport pathways within the San Francisco Bay coastal system. This study complements a large interdisciplinary effort (Barnard et al., 2012) that seeks to better understand recent geomorphic change in a highly urbanized and dynamic estuarine-coastal setting. Sand-sized sediment provenance in this geologically complex system is important to estuarine resource managers and was assessed by examining the geographic distribution of this suite of geochemical tracers from the primary sources (fluvial and rock) throughout the bay, adjacent coast, and beaches. Due to their intrinsic geochemical nature, 143Nd/144Nd isotopic ratios provide the most resolved picture of where sediment in this system is likely sourced and how it moves through this estuarine system into the Pacific Ocean. For example, Nd isotopes confirm that the predominant source of sand-sized sediment to Suisun Bay, San Pablo Bay, and Central Bay is the Sierra Nevada Batholith via the Sacramento River, with lesser contributions from the Napa and San Joaquin Rivers. Isotopic ratios also reveal hot-spots of local sediment accumulation, such as the basalt and chert deposits around the Golden Gate Bridge and the high magnetite deposits of Ocean Beach. Sand-sized sediment that exits San Francisco Bay accumulates on the ebb-tidal delta and is in part conveyed southward by long-shore currents. Broadly, the geochemical tracers reveal a complex story of multiple sediment sources, dynamic intra-bay sediment mixing and reworking, and eventual dilution and transport by energetic marine processes. Combined geochemical results provide information on sediment movement into and through San Francisco Bay and further our understanding of how sustained anthropogenic activities which limit sediment inputs to the system (e.g., dike and dam construction) as well as those which directly remove sediments from within the Bay, such as aggregate mining and dredging, can have long-lasting effects.

Major, trace and rare earth element concentrations of sediments from ODP Leg 207 sites

The Cretaceous and Paleogene sediments recovered during Ocean Drilling Program Leg 207 can be divided into three broad modes of deposition: synrift clastics (lithologic Unit V), organic matter-rich, laminated black shales (Unit IV), and open-marine chalk and calcareous claystones (Units III-I). The aim of this study is to provide a quantitative geochemical characterization of sediments representing these five lithologic units. For this work we used the residues (squeeze cakes) obtained from pore water sampling. Samples were analyzed for bulk parameters (total inorganic carbon, total organic carbon, and S) and by X-ray fluorescence for major (Si, Ti, Al, Fe, Mn, Mg, Ca, Na, K, and P) and selected minor (As, Ba, Co, Cr, Cu, Mo, Ni, Pb, Rb, Sr, U, V, Y, Zn, and Zr) elements. Inductively coupled plasma-mass spectrometry analyses for rare earth elements (REEs) were performed on acid digestions of the squeeze cake samples from Site 1258. The major element composition is governed by the mixture of a terrigenous detrital component of roughly average shale (AS) composition with biogenous carbonate and silica. The composition of the terrigenous detritus is close to AS in Units II-IV. For Unit I, a more weathered terrigenous source is suggested. Carbonate contents reach >60 wt% on average in chalks and calcareous claystones of Units II-IV. The SiO2 contribution in excess of the normal terrigenous-detrital background indicates the presence of biogenous silica, with highest amounts in Units II and III. The contents of coarse-grained material (quartz) are enhanced in Unit V, where Ti and Zr contents are also high. This indicates a high-energy depositional environment. REE patterns are generally similar to AS. A more pronounced negative Ce anomaly in Unit IV may indicate low-oxygen conditions in the water column. The Cretaceous black shales of Unit IV are clearly enriched in redox-sensitive and stable sulfide-forming elements (Mo, V, Zn, and As). High phosphate contents point toward enhanced nutrient supply and high bioproductivity. Ba/Al ratios are rather high throughout Unit IV despite the absence of sulfate in the pore water, indicating elevated primary production. Manganese contents are extremely low for most of the interval studied. Such an Mn depletion is only possible in an environment where Mn was mobilized and transported into an expanded oxygen minimum zone ("open system"). The sulfur contents show a complete sulfidation of the reactive iron of Unit IV and a significant excess of sulfur relative to that of iron, which indicates that part of the sulfur was incorporated into organic matter. We suppose extreme paleoenvironmental conditions during black shale deposition: high bioproductivity like in recent coastal upwelling settings together with severe oxygen depletion if not presence of hydrogen sulfide in the water column.

Geochemistry of dark-light rhythm sediments of the Japan Sea

Ocean Drilling Program Legs 127 and 128 in the Japan Sea have revealed the existence of numerous dark-light rhythms of remarkable consistency in sediments of late Miocene, latest Pliocene, and especially Pleistocene age. Light-colored units within these rhythms are massive or bioturbated, consist of diatomaceous clays, silty clays, or nannofossil-rich clays, and are generally poor in organic matter. Dark-colored units are homogeneous, laminated, or thinly bedded and include substantial amounts of biogenic material such as well-preserved diatoms, planktonic foraminifers, calcareous nannofossils, and organic matter (maximum 7.4 wt%). The dark-light rhythms show a similar geometrical pattern on three different scales: First-order rhythms consist of a cluster dominated by dark-colored units followed by a cluster dominated by light-colored units (3-5 m). Spectral analysis of a gray-value time series suggests that the frequencies of the first-order rhythms in sediments of latest Pliocene and Pleistocene age correlate to the obliquity and the eccentricity cycles. The second-order dark-light rhythms include a light and a dark-colored unit (10-160 cm). They were formed in time spans of several hundred to several ten thousand years, with variance centering around 10,500 yr. This frequency may correspond to half the precessional cycle. Third-order rhythms appear as laminated or thinly bedded dark-light couplets (2-15 mm) within the dark-colored units of the second-order rhythms and may represent annual frequencies. In interpreting the rhythms, we have to take into account that (1) the occurrence of the first- and second-order rhythms is not necessarily restricted to glacial or interglacial periods as is shown by preliminary stable-isotope analysis and comparison with the published d18O record; (2) they appear to be Milankovitch-controlled; and (3) a significant number of the rhythms are sharply bounded. The origin of the dark-light rhythms is probably related to variations in monsoonal activity in the Japan Sea, which show annual frequencies, but also operates in phase with the orbital cycles.

Experimental comparison of FBARs and SMRs responsitivities to mass loadings

The utilisation of thin film technology to develop film bulk acoustic resonators (FBARs) and solidly mounted resonators (SMRs), offers great potential to outperform the sensitivity and minimum detection limit of gravimetric sensors. Up to now, the choice between FBARs and SMRs depends primarily on the users' ability to design and fabricate Bragg reflectors and/or membranes, because neither of these two types of resonators has been demonstrated to be superior to the other. In the work reported here, it is shown that identically designed FBARs and SMRs resonating at the same frequency exhibit different responsitivities, Rm, to mass loadings, being the FBARs more responsive than the SMRs. For the specific device design and resonant frequency (~2 GHz) of the resonators presented, FBARs' mass responsitivity is ~20% greater than that of SMRs, and although this value should not be taken as universal for all possible device designs, it clearly indicates that FBAR devices should be favoured over SMRs in gravimetric sensing applications.

Suppression of protein synthesis in brain during hibernation involves inhibition of protein initiation and elongation

Protein synthesis (PS) has been considered essential to sustain mammalian life, yet was found to be virtually arrested for weeks in brain and other organs of the hibernating ground squirrel, Spermophilus tridecemlineatus. PS, in vivo, was below the limit of autoradiographic detection in brain sections and, in brain extracts, was determined to be 0.04% of the average rate from active squirrels. Further, it was reduced 3-fold in cell-free extracts from hibernating brain at 37°C, eliminating hypothermia as the only cause for protein synthesis inhibition (active, 0.47 ± 0.08 pmol/mg protein per min; hibernator, 0.16 ± 0.05 pmol/mg protein per min, P < 0.001). PS suppression involved blocks of initiation and elongation, and its onset coincided with the early transition phase into hibernation. An increased monosome peak with moderate ribosomal disaggregation in polysome profiles and the greatly increased phosphorylation of eIF2α are both consistent with an initiation block in hibernators. The elongation block was demonstrated by a 3-fold increase in ribosomal mean transit times in cell-free extracts from hibernators (active, 2.4 ± 0.7 min; hibernator, 7.1 ± 1.4 min, P < 0.001). No abnormalities of ribosomal function or mRNA levels were detected. These findings implicate suppression of PS as a component of the regulated shutdown of cellular function that permits hibernating ground squirrels to tolerate “trickle” blood flow and reduced substrate and oxygen availability. Further study of the factors that control these phenomena may lead to identification of the molecular mechanisms that regulate this state.

Frequency of migrants and migratory activity are genetically correlated in a bird population: Evolutionary implications

Most migratory bird populations are composed of individuals that migrate and individuals that remain resident. While the role of ecological factors in maintaining this behavioral dimorphism has received much attention, the importance of genetic constraints on the evolution of avian migration has not yet been considered. Drawing on the recorded migratory activities of 775 blackcaps (Sylvia atricapilla) from a partially migratory population in southern France, we tested two alternative genetic models about the relationship between incidence and amount of migratory activity. The amount of migratory activity could be the continuous variable “underlying” the phenotypic expression of migratory urge, or, alternatively, the expression of both traits could be controlled by two separate genetic systems. The distributions of migratory activities in five different cohorts and the inheritance pattern derived from selective breeding experiments both indicate that incidence and amount of migratory activity are two aspects of one trait. Thus, all birds without measurable activity have activity levels at the low end of a continuous distribution, below the limit of expression or detection. The phenotypic dichotomy “migrant–nonmigrant” is caused by a threshold which may not be fixed but influenced both genetically and environmentally. This finding has profound implications for the evolution of migration: the transition from migratoriness to residency should not only be driven by selection favoring resident birds but also by selection for lower migratory activity. This potential for selection on two aspects, residency and migration distance, of the same trait may enable extremely rapid evolutionary changes to occur in migratory behavior.

Quantitation of Pseudomonas aeruginosa in wound biopsy samples: from bacterial culture to rapid `real-time' polymerase chain reaction

We developed a real-time detection (RTD) polymerase chain reaction (PCR) with rapid thermal cycling to detect and quantify Pseudomonas aeruginosa in wound biopsy samples. This method produced a linear quantitative detection range of 7 logs, with a lower detection limit of 103 colony-forming units (CFU)/g tissue or a few copies per reaction. The time from sample collection to result was less than 1h. RTD-PCR has potential for rapid quantitative detection of pathogens in critical care patients, enabling early and individualized treatment.

Coordination of aproximations in secondary school students’ understanding of limit concept

The aim of this research is to characterize the coordination of the processes of approximation related to the understanding of the limit of a function. We analyze the answers of 64 post-secondary school students to 7 problems considering the dynamic and metric conception of limit of a function. Results indicate that the metric understanding of the limit in terms of inequality supports that the student is capable of coordinating the approximations in the domain and in the range when lateral approximations coincide. However, the student is not capable of this coordination when lateral approximations do not coincide. This indicates that the metric understanding of the limit begins with the previous construction of the dynamic conception in case of coincidence of the lateral approximations in the range.

Algorithm for the detection of outliers based on the theory of rough sets

Outliers are objects that show abnormal behavior with respect to their context or that have unexpected values in some of their parameters. In decision-making processes, information quality is of the utmost importance. In specific applications, an outlying data element may represent an important deviation in a production process or a damaged sensor. Therefore, the ability to detect these elements could make the difference between making a correct and an incorrect decision. This task is complicated by the large sizes of typical databases. Due to their importance in search processes in large volumes of data, researchers pay special attention to the development of efficient outlier detection techniques. This article presents a computationally efficient algorithm for the detection of outliers in large volumes of information. This proposal is based on an extension of the mathematical framework upon which the basic theory of detection of outliers, founded on Rough Set Theory, has been constructed. From this starting point, current problems are analyzed; a detection method is proposed, along with a computational algorithm that allows the performance of outlier detection tasks with an almost-linear complexity. To illustrate its viability, the results of the application of the outlier-detection algorithm to the concrete example of a large database are presented.