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Conventional histopathology involves expensive and labor intensive processes that often consume tissue samples, rendering them unavailable for other analysis. We present a novel end-to-end workflow for pathology powered by hyperspectral microscopy and deep learning. First, we developed a custom hyperspectral microscope to non-destructively image the autofluorescence of unstained tissue sections. We then train a deep learning model to use the autofluorescence to generate virtual histological stains, which avoids the cost and variability of chemical staining procedures and conserves tissue samples. We showed that the virtual images reproduce the histological features present in the real stained images using a randomized nonalcoholic steatohepatitis (NASH) scoring comparison study where both real and virtual stains are scored by pathologists. The test showed moderate to good concordance between pathologists’ scoring on corresponding real and virtual stains. Finally, we developed deep learning-based models for automated NASH clinical research network (NASH CRN) score prediction. We showed that the end-to-end automated pathology platform is comparable to pathologists for NASH CRN scoring when evaluated against the expert pathologist consensus scores. This study provides proof of concept for this virtual staining strategy, which could improve cost, efficiency, and reliability in pathology, and enable novel approaches to spatial biology research.

Droplet microfluidics is a commercially successful technology, widely used in single cell sequencing and droplet PCR. Combining droplet making with droplet sorting has also been demonstrated, but so far found limited use, partly due to difficulties in scaling manufacture with injection molded plastics. We introduce a droplet sorting system with several new elements, including: 1) an electrode design combining metallic and ionic liquid parts, 2) a modular, multi-sorting fluidic design with features for keeping inter-droplet distances constant, 3) using timing parameters calculated from fluorescence or scatter signal triggers to precisely actuate dozens of sorting electrodes, 4) droplet collection techniques, including ability to collect a single droplet, and 5) a new emulsion breaking method to collect aqueous samples for downstream analysis. We use these technologies to build a fluorescence based cell sorter that sorts with high purity. We also show that these microfluidic designs can be translated into injection molded thermoplastic, suitable for industrial production. Finally, we tally the advantages and limitations of these devices.

Metagenomic studies have revolutionized the study of novel phages. However these studies trade the depth of coverage for breadth. In this study we show that the targeted sequencing of a phage genomic region as small as 200-300 base pairs, can provide sufficient sequence diversity to serve as an individual-specific barcode or “Phageprint”. The targeted approach reveals a high-resolution view of phage communities that is not available through metagenomic datasets. By creating instructional videos and collection kits, we enabled citizen scientists to gather ∼700 oral samples spanning ∼100 individuals residing in different parts of the world. In examining phage communities at 6 different oral sites, and by comparing phage communities of individuals living across the globe, we were able to study the effect of spatial separation, ranging from several millimeters to thousands of kilometers. We found that the spatial separation of just a few centimeters (the distance between two oral sites) can already result in highly distinct phage community compositions. For larger distances, spanning the phage communities of different individuals living in different parts of the world, we did not observe any correlation between spatial distance and phage community composition as individuals residing in the same city did not have any more similar phage communities than individuals living on different continents. Additionally, we found that neither genetics nor cohabitation seem to play a role in the relatedness of phage community compositions across individuals. Cohabitating siblings and even identical twins did not have phage community compositions that were any more similar than those of unrelated individuals. The primary factor contributing to phage community composition relatedness is direct contact between two habitats, as is demonstrated by the similarity between oral phage community compositions of partners. Furthermore, by exploring phage communities across the span of a month, and in some cases several years, we observed highly stable community compositions. These studies consistently point to the existence of remarkably diverse and personal phage families that are stable in time and apparently present in people around the world.

The uterine cervix softens, shortens, and dilates throughout pregnancy in response to progressive disorganization of its layered collagen microstructure. This process is an essential part of normal pregnancy, but premature changes are associated with preterm birth. Clinically, there are no reliable noninvasive methods to objectively measure cervical softening or assess cervical microstructure. The goal of these preliminary studies was to evaluate the feasibility of using an intracavity ultrasound array to generate acoustic radiation force impulse (ARFI) excitations in the uterine cervix through simulation, and to optimize the acoustic radiation force (ARF) excitation for shear wave elasticity imaging (SWEI) of the tissue stiffness. The cervix is a unique soft tissue target for SWEI because it has significantly greater acoustic attenuation (α = 1.3 to 2.0 dB·cm(-1)·MHz(-)1) than other soft tissues, and the pathology being studied tends to lead to an increase in tissue compliance, with healthy cervix being relatively stiff compared with other soft tissues (E ≈ 25 kPa). Additionally, the cervix can only be accessed in vivo using a transvaginal or catheter-based array, which places additional constraints on the excitation focal characteristics that can be used during SWEI. Finite element method (FEM) models of SWEI show that larger-aperture, catheter-based arrays can utilize excitation frequencies up to 7 MHz to generate adequate focal gain up to focal depths 10 to 15 mm deep, with higher frequencies suffering from excessive amounts of near-field acoustic attenuation. Using full-aperture excitations can yield ~40% increases in ARFI-induced displacements, but also restricts the depth of field of the excitation to ~0.5 mm, compared with 2 to 6 mm, which limits the range that can be used for shear wave characterization of the tissue. The center-frequency content of the shear wave particle velocity profiles ranges from 1.5 to 2.5 kHz, depending on the focal configuration and the stiffness of the material being imaged. Overall, SWEI is possible using catheter-based imaging arrays to generate adequate displacements in cervical tissue for shear wave imaging, although specific considerations must be made when optimizing these arrays for this shear wave imaging application.

We demonstrate a successful selective growth of Si0.3Ge0.7 quantum dots (QDs) over array of p+-Si nanopillars using a low-pressure chemical vapor deposition technique, and hereafter realized high-performance QD broadband photodiodes for visible to near-infrared photodetection based on heterostructures of indium tin oxide/Si0.3Ge0.7 QD/Si pillar. Thanks to effective hole confinement and thus a built-in electric field within the SiGe QD, high ratios of photocurrent to dark current of ~2200, 100, and 30, respectively, were measured on our SiGe QDs-based photodiodes under illumination of 9 mW/cm2 at wavelength of 500-800, 1300, and 1500 nm. The QD photodiode exhibits a very low dark current density of 3.2 × 10-8 A/cm2 and a tunable power-dependent linearity by applied voltage through the competition of electron drift and carrier recombination processes.

Anterior cruciate ligament (ACL) disruption is a common injury that is detrimental to an athlete's quality of life. Determining the mechanisms that cause ACL injury is important in order to develop proper interventions. A failure locus defined as various combinations of loadings and movements, internal/external rotation of femur and valgus and varus moments at a 25(o) knee flexion angle leading to ACL failure was obtained. The results indicated that varus and valgus movements were more dominant to the ACL injury than femoral rotation. Also, Von Mises stress in the lateral tibial cartilage during the valgus ACL injury mechanism was 83% greater than that of the medial cartilage during the varus mechanism of ACL injury. The results of this study could be used to develop training programmes focused on the avoidance of the described combination of movements which may lead to ACL injury.

We present the results of recent investigations into the fabrication and characterization of high-Q, small mode volume one-dimensional photonic crystal nanobeam cavities in Si and two-dimensional photonic crystal slab nanocavities in GaAs. The nanobeam cavity modes are investigated in transmission by means of a microfiber taper loop apparatus. The spectral transmission profile of the cavity modes is investigated as a function of input polarization into the fiber. The Q of the cavity for different positions and orientations of the fiber taper is investigated. The results are compared to measurements by resonant scattering. The slab nanocavities are investigated by means of quantum dot photoluminescence excitation spectroscopy. We present recent progress in growth and fabrication of such slab nanocavities.

We investigated four unique methods for achieving scalable, deterministic integration of quantum emitters into ultra-high Q{V photonic crystal cavities, including selective area heteroepitaxy, engineered photoemission from silicon nanostructures, wafer bonding and dimensional reduction of III-V quantum wells, and cavity-enhanced optical trapping. In these areas, we were able to demonstrate site-selective heteroepitaxy, size-tunable photoluminescence from silicon nanostructures, Purcell modification of QW emission spectra, and limits of cavity-enhanced optical trapping designs which exceed any reports in the literature and suggest the feasibility of capturing- and detecting nanostructures with dimensions below 10 nm. In addition to process scalability and the requirement for achieving accurate spectral- and spatial overlap between the emitter and cavity, these techniques paid specific attention to the ability to separate the cavity and emitter material systems in order to allow optimal selection of these independently, and eventually enable monolithic integration with other photonic and electronic circuitry. We also developed an analytic photonic crystal design process yielding optimized cavity tapers with minimal computational effort, and reported on a general cavity modification which exhibits improved fabrication tolerance by relying exclusively on positional- rather than dimensional tapering. We compared several experimental coupling techniques for device characterization. Significant efforts were devoted to optimizing cavity fabrication, including the use of atomic layer deposition to improve surface quality, exploration into factors affecting the design fracturing, and automated analysis of SEM images. Using optimized fabrication procedures, we experimentally demonstrated 1D photonic crystal nanobeam cavities exhibiting the highest Q/V reported on substrate. Finally, we analyzed the bistable behavior of the devices to quantify the nonlinear optical response of our cavities.

This Letter features a new, scalable fabrication method and experimental characterization of glass-filled apertures exhibiting extraordinary transmission. These apertures are fabricated with sizes, aspect ratios, shapes, and side-wall profiles previously impossible to create. The fabrication method presented utilizes top-down lithography to etch silicon nanostructures. These nanostructures are oxidized to provide a transparent template for the deposition of a plasmonic metal. Gold is deposited around these structures, reflowed, and the surface is planarized. Finally, a window is etched through the substrate to provide optical access. Among the structures created and tested are apertures with height to diameter aspect ratios of 8:1, constructed with rectangular, square, cruciform, and coupled cross sections, with tunable polarization sensitivity and displaying unique properties based on their sculpted side-wall shape. Transmission data from these aperture arrays is collected and compared to examine the role of spacing, size, and shape on their overall spectral response. The structures this Letter describes can have a variety of novel applications from the creation of new types of light sources to massively multiplexed biosensors to subdiffraction limit imaging techniques.

In order to expand the use of nanoscaled silicon structures we present a new etching method that allows us to shape silicon with sub-10 nm precision. This top-down, CMOS compatible etching scheme allows us to fabricate silicon devices with quantum behavior without relying on difficult lateral lithography. We utilize this novel etching process to create quantum dots, quantum wires, vertical transistors and ultra-high-aspect ratio structures. We believe that this etching technique will have broad and significant impacts and applications in nano-photonics, bio-sensing, and nano-electronics.

We show that, taking a two-dimensional photonic-crystal slab system as an example, surprisingly high quality factors (Q) over 10^5 are achievable, even in the absence of a rigorous photonic-band-gap. We find that the density of in-plane Bloch modes can be controlled by creating additional photon feedback from a finite-size photonic-crystal boundary that serves as a low-Q resonator. This mechanism enables significant reduction in the coupling strength between the bound state and the extended Bloch modes by more than a factor of 40., 5 pages, 4 figures

We show that the properties of silicon can be changed profoundly when nanofabricated to below 5nm, resulting in larger bandgap emission and more efficient light generation. Moreover, three-dimensional nanostructures can be fabricated at these nanoscale dimensions by dynamic control over the dry etching process.

This study characterizes a common antigen recognized by two monoclonal antibodies (mAbs) that immunoreact with the principal piece of the human sperm flagellum. By means of immunofluorescence microscopy, mAbs S69 (IgM) and S70 (IgG1) (WHO Task-force nomenclature) were observed to bind to the principal piece of methanol- or detergent-permeabilized human spermatozoa, but did not react with live swimming spermatozoa as assessed by immunofluorescence microscopy. Faint immunofluorescence was also seen on the connecting piece in approximately 40% of the spermatozoa. Immunoreactivity in both regions was resistant to sequential extraction with Triton X-100, sodium thiocyanate, and urea. Pre-embedding electron microscopic immunogold labeling of ejaculated spermatozoa with mAb S69 showed gold particles located on the fibrous sheath. Immunoreactive peptides of 68, 53, and 45 kDa were recognized by both S69 and S70 mAbs on immunoblots of nonreduced human sperm extracts, while a 68-kDa band and a strongly immunoreactive triplet from 54 to 51 kDa were recognized in reduced sperm extracts. Human fibrous sheaths were isolated by differential solubilization and centrifugation and characterized by transmission electron microscopy. The 68-kDa and 54-51-kDa bands were enriched and found to be major polypeptides in the isolated fibrous sheath fraction. These results suggest that the S69/S70 antigen, which we term SP (sperm protein) (68 kDa, 54-51 kDa), is a component of the human fibrous sheath.

Visible and near-IR photoluminescence (PL) is reported from sub-10 nm silicon nanopillars. Pillars were plasma etched from single crystal Si wafers and thinned by utilizing strain-induced, self-terminating oxidation of cylindrical structures. PL, lifetime, and transmission electron microscopy were performed to measure the dimensions and emission characteristics of the pillars. The peak PL energy was found to blue shift with narrowing pillar diameter in accordance with a quantum confinement effect. The blue shift was quantified using a tight binding method simulation that incorporated the strain induced by the thermal oxidation process. These pillars show promise as possible complementary metal oxide semiconductor compatible silicon devices in the form of light-emitting diode or laser structures.

We investigate high-Q, small mode volume photonic crystal nanobeam cavities using a curved, tapered optical microfiber loop. The strength of the coupling between the cavity and the microfiber loop is shown to depend on the contact position on the nanobeam, angle between the nanobeam and the microfiber, and polarization of the light in the fiber. The results are compared to a resonant scattering measurement.

A full or partial tear of the anterior cruciate ligament (ACL) is a common and painful injury that has been estimated to occur approximately 250,000 times annually in the U.S. [1]. Articular cartilage and meniscal injuries are also associated with ACL injuries [2]. ACL injuries can often lead to degenerative osteoarthritis of the articular cartilage [2]. An epidemiology study of athletic injuries by Majewski et al. [3] determined that out of 19,530 sports injuries, 20% were ACL injuries and 8% were medial collateral ligament (MCL) injuries.Copyright © 2010 by ASME

Anterior cruciate ligament (ACL) disruption is a common injury that is detrimental to an athlete’s quality of life. Determining the mechanisms that cause ACL injury is important in order to develop proper interventions. This study was conducted to provide insight into the specific knee orientations associated with ACL injuries. A failure locus for the ACL was developed by simulating multiple loading scenarios using a 3-D finite element analysis (FEA) model of the knee. The results indicated varus and valgus were more dominant to the ACL injury compared to femoral rotation. The order of MCL failure, ACL failure, and maximum meniscus stress was also determined with respect to time during loading. The results of this study could be used to develop training programs focused on the avoidance of the described combination of movements, which may lead to ACL injury.

Sperm antigens recognized by monoclonal antibodies (mAbs), S19, S69, S71, S72 and S77 submitted to the World Health Organization (WHO)-Sponsored Sperm Monoclonal Antibody Workshops were immunolocalized by light (LM) and transmission electron microscopy (TEM). S19 was surface reactive while mAbs S69, S71, S72 and S77 recognized internal antigens. Indirect immunofluorescence staining of permeabilized sperm with the mAbs revealed that S69 recognized an internal tail antigen, while S71, S72 and S77 recognized acrosomal proteins. Preservation of immunoreactivity after fixation in various combinations of glutaraldehyde, paraformaldehyde and tannic acid was evaluated for mAbs S69 to S77 using immunofluorescence microscopy. The epitopes recognized by these mAbs were adversely affected by these fixatives; therefore, pre-embedding immunogold staining was employed, prior to fixation, osmication, dehydration and embedding. Using this approach, the antigen recognized by mAb S19 was found associated with the plasmalemma of the head and tail of intact sperm. Monoclonal antibody S69 localized to the fibrous sheath. The mAbs S71, S72 and S77, which required sperm permeabilization to expose their acrosomal locus by LM, did not immunoreact with the plasmalemma at the TEM level. Ultrastructural examination of acrosome-reacted sperm revealed the localization of S71 and S77 on the inner and outer acrosomal membranes and with acrosomal matrix. The S72 antigen was associated with the inner and outer acrosomal membranes.

We introduce using sputtered aluminum oxide (alumina) as a resilient etch mask for fluorinated silicon reactive ion etches. Achieving selectivity of 5000:1 for cryogenic silicon etching and 68:1 for SF(6)/C(4)F(8) silicon etching, we employ this mask for fabrication of high-aspect-ratio silicon micropillars and nanopillars. Nanopillars with diameters ranging from below 50 nm up to several hundred nanometers are etched to heights greater than 2 microm. Micropillars of 5, 10, 20, and 50 microm diameters are etched to heights of over 150 microm with aspect ratios greater than 25. Processing and characterization of the sputtered alumina is also discussed.

It is sent economic useful parameters of geese of Obroshyn selection. It is shown results of the made researches on four groups of birds of different populations. Efficiency of their use in conditions of agricultural enterprises of Lviv region is determined.

The human sperm protein SP-10 was previously defined as a "primary vaccine candidate" by a World Health Organization Taskforce on Contraceptive Vaccines. By one- and two-dimensional immunoblots, we show that SP-10, extracted from ejaculated human sperm, demonstrated a polymorphism of immunogenic peptides from 18 to 34 kDa, a pattern that was conserved from individual to individual and was not altered by reducing agents. The majority of the antigenic peptides possessed isoelectric points of approximately 4.9. Immunocytochemistry on testis sections indicated that SP-10 was localized to round spermatids and spermatozoa within the adluminal compartment of the seminiferous epithelium. Immunofluorescence showed that SP-10 was not associated with the surface of acrosome-intact, ejaculated sperm. Light and electron microscopic immunocytochemistry localized SP-10 throughout the acrosome, and electron microscopic evidence demonstrated a bilaminar array in association with the inner aspect of the outer acrosomal membrane and the outer aspect of the inner acrosomal membrane. After induction of the acrosome reaction with the ionophore A23187, SP-10 remained displayed on the sperm head in association with the inner acrosomal membrane and equatorial segment. The results indicate that the MHS-10 monoclonal antibody may be used as a marker of acrosome development in the human and as a probe to evaluate acrosome status. The results also support the hypothesis that inhibition of sperm-egg interaction by anti-SP-10 monoclonal antibody may occur as a result of antigen exposure following the acrosome reaction.

In 2006, the Charlottesville Waldorf School (CWS) is building a new elementary school facility on thirteen acres in Charlottesville. The building is being designed by SOURCE architects to achieve a LEED “platinum” certification. The Community Design Assistance Center (CDAC) joined the site design process to develop a conceptual site master plan a multi-layered trail system that traverses the site includes walking paths that connect the school to different areas of the site and that connect the site to its surroundings (park and trail systems, neighbors, etc.). It was envisioned that a section of the trail would include a “Medicinal Plant Trail” and be planted with indigenous plants that could be labeled for educational walks.

This paper describes an experimental modular distributed manipulation system upon which one can implement a variety of control schemes. We have shown elsewhere that when one includes the nonsmooth effects of friction into a model of distributed manipulation, nonsmooth feedback laws must generally be used to control distributed manipulators. We summarize results obtained with this experimental system that confirm the validity of control schemes proposed by the authors in recent papers. We describe the control algorithms in some detail and include specifics of the experimental set-up and experimental results.