Algorithms to automatically quantify the geometric similarity of anatomical surfaces

We describe new approaches for distances between pairs of 2-dimensional surfaces (embedded in 3-dimensional space) that use local structures and global information contained in inter-structure geometric relationships. We present algorithms to automatically determine these distances as well as geometric correspondences. This is motivated by the aspiration of students of natural science to understand the continuity of form that unites the diversity of life. At present, scientists using physical traits to study evolutionary relationships among living and extinct animals analyze data extracted from carefully defined anatomical correspondence points (landmarks). Identifying and recording these landmarks is time consuming and can be done accurately only by trained morphologists. This renders these studies inaccessible to non-morphologists, and causes phenomics to lag behind genomics in elucidating evolutionary patterns. Unlike other algorithms presented for morphological correspondences our approach does not require any preliminary marking of special features or landmarks by the user. It also differs from other seminal work in computational geometry in that our algorithms are polynomial in nature and thus faster, making pairwise comparisons feasible for significantly larger numbers of digitized surfaces. We illustrate our approach using three datasets representing teeth and different bones of primates and humans, and show that it leads to highly accurate results.Comment: Changes with respect to v1, v2: an Erratum was added, correcting the references for one of the three datasets. Note that the datasets and code for this paper can be obtained from the Data Conservancy (see Download column on v1, v2

Cyclic AMP-associated shape change in mesangial cells and its reversal by prostaglandin E2

Cyclic AMP-associated shape change in mesangial cells and its reversal by prostaglandin E2. The mesangial cell is a glomerular cell type with smooth muscle-like (contractile) properties. The responses evoked in cultured mesangial cells by catecholamines were examined in the presence or absence of prostaglandin E2 (PGE2) with or without a phosphodiesterase inhibitor. Exposure to 10-4M norepinephrine, epinephrine, or isoproterenol elevated intracellular cyclic AMP (cAMP) levels in mesangial cells (25th to 30th passages) nearly threefold. If isobutylmethylxanthine (MIX) was also included, the hormones caused marked further increases in cAMP (after a 20-min incubation, control with MIX, 64.2 ± 5.2 pmoles/mg protein; 10-4M norepinephrine, 4266 ± 284 pmoles/mg protein; 10-4M epinephrine, 5812 ± 173 pmoles/mg protein; and 10-4M isoproterenol, 3136 ± 114 pmoles/mg protein). Under both of these circumstances (that is, catecholamines with or without MIX) greater than 50% of the cells underwent a change in shape (that is, had a round cell body with long, thin tapered processes). The cAMP and shape change response was independent of extracellular calcium ions and appeared to be due to β-adrenergic stimulation. Isoproterenol with MIX stimulated an alteration in morphology and cAMP production at concentrations of 10-4M to 10-9M. Within 10 min following β-adrenergic stimulation (10-4M isoproterenol plus MIX) cAMP was maximum; at this time a shape change was first evident. Eighty-five to one hundred percent of the cells had undergone a shape change by 40 min. Dibutyryl cAMP (10-3M) also induced a shape change in cultured mesangial cells. The addition of PGE2 to either morphologically altered cells or to the isoproterenol incubation medium (with or without MIX) prior to treating the cells, resulted in complete restoration to the normal flat appearance of mesangial cells or no shape change, respectively. PGE2 attenuated but did not abolish hormone-induced elevations in intracellular cAMP. Thus, catecholamines caused mesangial cells to change their shape in association with elevations of intracellular cAMP. PGE2 markedly inhibited the shape change as well as markedly attenuated cAMP generation.La modification de la forme associé l'PAMP cyclique dans les cellules mésangiales et sa interversion par prostaglandine E2. La cellule mésangiale est un type cellulaire glomérulaire ayant despropriétés voisines du muscle lisse (contractile). Les réponses évoquées dans des cellules mésangiales en culture par les catécholamines ont été examinées en présence ou en l'absence de prostaglandine E2 (PGE2) avec ou sans un inhibiteur des phosphodiestérases. L'exposition à 10-4M de noradrénaline, d'adrénaline, ou d'isoprotérénol a élevé les niveaux d'AMP cyclique intracellulaires (cAMP) dans les cellules mésangiales (25ème à 30ème passages) de presque troisfois. Si de l'isobutylméthylxanthine (MIX) était également inclue, les hormones entraînaient des augmentations plus fortes de cAMP (après 20 min d'incubation, contrôles avec MIX, 64,2 ± 5,2 pmoles/mg protéines; 10-4M noradrénaline, 4266 ± 284 pmoles/g protéines; 10-4M adrénaline, 5812 ± 173 pmoles/mg protéines; et 10-4M isoprotérénol, 3136 ± 114 pmoles/mg protéines). Dans chacune de ces circontances (c'est-à-dire catécholamines avec ou sans MIX), plus de 50% cellules subissaient une modification de forme (c'est-à-dire avaient un corps cellulaire rond, avec des expansions rubannées longues et fines). Les réponses cAMP et de modification de forme étaient indépendantes des ions calcium extracellulaires, et paraîssaient être dues à la stimulation β-adrénergique. L'isoprotérénol avec MIX stimulait une altération de la morphologie et de la production de cAMP pour des concentrations de 10-4M à 10-9M. En 10 min, après stimulation β-adrénergique (10-4M d'isoprotérénol plus MIX), cAMP était maximum; à ce moment, la modification de forme était évidente. Quatre-vingt-cinq à cent pour cent des cellules avaient subi une modification de forme en 40 min. Le dibutyryl cAMP (10-3M) induisait également une modification de forme dans les cellules mésangiales en culture. L'addition de PGE2 soit à des cellules morphologiquement altérées, soit au milieu d'incubation de l'isoprotérénol (avec ou sans MIX), avant de traiter les cellules, entraînait une restauration complète de l'apparence normale, plate, des cellules mésangiales, ou l'absence de modification, respectivement. PGE2 a atténué, mais n'a pas aboli les élévations induites par les hormones du cAMP intracellulaire. Ainsi, les catécholamines faisaient changer de forme les cellules mésangiales en association avec des élévations du cAMP intracellulaire. La PGE2 inhibait de façon marquée la modification de changement, et atténuait sensiblement la génération de cAMP

Melt conditioning by advanced shear technology (MCAST) for refining solidification microstructures

MCAST (melt conditioning by advanced shear technology) is a novel processing technology developed recently by BCAST at Brunel University for conditioning liquid metal prior to solidification processing. The MCAST process uses a twin screw mechanism to impose a high shear rate and a high intensity of turbulence to the liquid metal, so that the conditioned liquid metal has uniform temperature, uniform chemical composition and well-dispersed and completely wetted oxide particles with a fine size and a narrow size distribution. The microstructural refinement is achieved through an enhanced heterogeneous nucleation rate and an increased nuclei survival rate during the subsequent solidification processing. In this paper we present the MCAST process and its applications for microstructural refinement in both shape casting and continuous casting of light alloys

Use of the tetrazolium salt MTT to measure cell viability effects of the bacterial antagonist Lysobacter enzymogenes on the filamentous fungus Cryphonectria parasitica

Despite substantial interest investigating bacterial mechanisms of fungal growth inhibition, there are few methods available that quantify fungal cell death during direct interactions with bacteria. Here we describe an in vitro cell suspension assay using the tetrazolium salt MTT as a viability stain to assess direct effects of the bacterial antagonist Lysobacter enzymogenes on hyphal cells of the filamentous fungus Cryphonectria parasitica. The effects of bacterial cell density, fungal age and the physiological state of fungal mycelia on fungal cell viability were evaluated. As expected, increased bacterial cell density correlated with reduced fungal cell viability over time. Bacterial effects on fungal cell viability were influenced by both age and physiological state of the fungal mycelium. Cells obtained from 1-week-old mycelia lost viability faster compared with those from 2-week-old mycelia. Likewise, hyphal cells obtained from the lower layer of the mycelial pellicle lost viability more quickly compared with cells from the upper layer of the mycelial pellicle. Fungal cell viability was compared between interactions with L. enzymogenes wildtype strain C3 and a mutant strain, DCA, which was previously demonstrated to lack in vitro antifungal activity. Addition of antibiotics eliminated contributions to MTT-formazan production by bacterial cells, but not by fungal cells, demonstrating that mutant strain DCA had lost complete capacity to reduce fungal cell viability. These results indicate this cell suspension assay can be used to quantify bacterial effects on fungal cells, thus providing a reliable method to differentiate strains during bacterial/fungal interactions

Spin and e-e interactions in quantum dots: Leading order corrections to universality and temperature effects

We study the statistics of the spacing between Coulomb blockade conductance peaks in quantum dots with large dimensionless conductance g. Our starting point is the ``universal Hamiltonian''--valid in the g->oo limit--which includes the charging energy, the single-electron energies (described by random matrix theory), and the average exchange interaction. We then calculate the magnitude of the most relevant finite g corrections, namely, the effect of surface charge, the ``gate'' effect, and the fluctuation of the residual e-e interaction. The resulting zero-temperature peak spacing distribution has corrections of order Delta/sqrt(g). For typical values of the e-e interaction (r_s ~ 1) and simple geometries, theory does indeed predict an asymmetric distribution with a significant even/odd effect. The width of the distribution is of order 0.3 Delta, and its dominant feature is a large peak for the odd case, reminiscent of the delta-function in the g->oo limit. We consider finite temperature effects next. Only after their inclusion is good agreement with the experimental results obtained. Even relatively low temperature causes large modifications in the peak spacing distribution: (a) its peak is dominated by the even distribution at kT ~ 0.3 Delta (at lower T a double peak appears); (b) it becomes more symmetric; (c) the even/odd effect is considerably weaker; (d) the delta-function is completely washed-out; and (e) fluctuation of the coupling to the leads becomes relevant. Experiments aimed at observing the T=0 peak spacing distribution should therefore be done at kT<0.1 Delta for typical values of the e-e interaction.Comment: 15 pages, 4 figure

A YOLOv5-based network for the detection of a diffuse reflectance spectroscopy probe to aid surgical guidance in gastrointestinal cancer surgery

PURPOSE: A positive circumferential resection margin (CRM) for oesophageal and gastric carcinoma is associated with local recurrence and poorer long-term survival. Diffuse reflectance spectroscopy (DRS) is a non-invasive technology able to distinguish tissue type based on spectral data. The aim of this study was to develop a deep learning-based method for DRS probe detection and tracking to aid classification of tumour and non-tumour gastrointestinal (GI) tissue in real time. METHODS: Data collected from both ex vivo human tissue specimen and sold tissue phantoms were used for the training and retrospective validation of the developed neural network framework. Specifically, a neural network based on the You Only Look Once (YOLO) v5 network was developed to accurately detect and track the tip of the DRS probe on video data acquired during an ex vivo clinical study. RESULTS: Different metrics were used to analyse the performance of the proposed probe detection and tracking framework, such as precision, recall, mAP 0.5, and Euclidean distance. Overall, the developed framework achieved a 93% precision at 23 FPS for probe detection, while the average Euclidean distance error was 4.90 pixels. CONCLUSION: The use of a deep learning approach for markerless DRS probe detection and tracking system could pave the way for real-time classification of GI tissue to aid margin assessment in cancer resection surgery and has potential to be applied in routine surgical practice

Linear conductance in Coulomb-blockade quantum dots in the presence of interactions and spin

We discuss the calculation of the linear conductance through a Coulomb-blockade quantum dot in the presence of interactions beyond the charging energy. In the limit where the temperature is large compared with a typical tunneling width, we use a rate-equations approach to describe the transitions between the corresponding many-body states. We discuss both the elastic and rapid-thermalization limits, where the rate of inelastic scattering in the dot is either small or large compared with the elastic transition rate, respectively. In the elastic limit, we find several cases where a closed solution for the conductance is possible, including the case of a constant exchange interaction. In the rapid-thermalization limit, a closed solution is possible in the general case. We show that the corresponding expressions for the linear conductance simplify for a Hamiltonian that is invariant under spin rotations.Comment: 11 pages, no figures, revtex

Pion decay constant in quenched QCD with Kogut-Susskind quarks

We present a non-perturbative calculation for the pion decay constant with quenched Kogut-Susskind quarks. Numerical simulations are carried out at $\beta = 6.0$ and 6.2 with various operators extending over all flavors. The renormalization correction is applied for each flavor by computing non-perturbative renormalization constants, and it is compared with a perturbative calculation. We also study the behavior of $f_\pi$ in the continuum limits for both non-perturbative and perturbative calculations. The results in the continuum limit is also discussed.Comment: LATTICE99(matrix elements) 3 pages, 4 eps figure

Coulomb Blockade Fluctuations in Strongly Coupled Quantum Dots

Quantum fluctuations of Coulomb blockade are investigated as a function of the coupling to reservoirs in semiconductor quantum dots. We use fluctuations in the distance between peaks $\Delta N$ apart to characterize both the amplitude and correlation of peak motion. For strong coupling, peak motion is greatly enhanced at low temperature, but does not show an increase in peak-to-peak correlation. These effects can lead to anomalous temperature dependence in the Coulomb valleys, similar to behavior ascribed to Kondo physics.Comment: figures made smaller so download works. Revised, including new data. Related papers at http://www.stanford.edu/group/MarcusLab/grouppubs.htm

Spectroscopy of the Potential Profile in a Ballistic Quantum Constriction

We present a theory for the nonlinear current-voltage characteristics of a ballistic quantum constriction. Nonlinear features first develop because of above-barrier reflection from the potential profile, created by impurities in the vicinity of the constriction. The nonlinearity appears on a small voltage scale and makes it possible to determine distances between impurities as well as the magnitude of the impurity potentials.Comment: 3 pages, 4 figures (availiable upon request), REVTEX, Applied Physics Report 93-5