gebhart/patrepeval huggingface dataset:
Ultrastructure of myotendinous junctions in tendon-skeletal muscle constructs engineered in vitro. (2009)

During development, the interaction between tenocytes and myotubes leads to the formation of highly specialized muscle-tendon structural interfaces: myotendinous junctions (MTJs). Structural integrity of MTJs is critical for force transmission from contracting muscle through tendon to bone. We recently developed an in vitro model of three-dimensional (3-D) skeletal muscle-tendon constructs to address mechanisms of the MTJs development. We hypothesized that engineered in vitro 3-D skeletal muscle-tendon constructs would develop MTJs ultrastructurally resembling those found during fetal development in vivo. To test this hypothesis we compared MTJs structures in vivo to those developed in 3-D skeletal muscle constructs co-cultured with engineered self-organized tendon constructs (SOT), or segments of adult (ART) or fetal rat tail (FRT) by means of electron microscopy. Our study showed that at sites of termination some of the myofibers of the engineered 3-D skeletal muscle-FRT and -SOT constructs displayed emerging finger-like sarcolemmal projections surrounded by collagen fibers. These structures resemble fetal MTJs in vivo. Muscle-ART constructs did not develop MTJs. Muscle-FRT constructs in addition to muscle and tendon also demonstrated well developed cartilage, possessing high potential for development into bone. The muscle-FRT construct model could be used for studies of developmental mechanisms involved in the establishment of interfaces among all four muscular-skeletal tissues: muscle, tendon and cartilage/bone.
Characterization of the anti-apoptotic mechanism of Bcl-B (2003)

Bcl-B protein is an anti-apoptotic member of the Bcl-2 family protein that contains all the four BH (Bcl-2 homology) domains (BH1, BH2, BH3 and BH4) and a predicted C-terminal transmembrane domain. Our previous results showed that Bcl-B binds Bax and suppresses apoptosis induced by over-expression of Bax; however, Bcl-B does not bind or suppress Bak. To explore the molecular basis for the differential binding and suppression of Bax and Bak, we studied the BH3 dimerization domains of Bax and Bak. Chimeric mutants of Bax and Bak were generated that swapped the BH3 domains of these pro-apoptotic proteins. Bcl-B associated with and blocked apoptosis induced by mutant Bak containing the BH3 domain of Bax, but not mutant Bax containing the BH3 domain of Bak. In contrast, Bcl-X(L) protein bound and suppressed apoptosis induction by Bax, Bak and both BH3-domain chimeras. A strong correlation between binding and apoptosis suppression was also obtained using a series of alanine substitutions spanning the length of the Bax BH3 domain to identify critical residues for Bcl-B binding. Conversely, using structure-based modelling to design mutations in the BH3-binding pocket of Bcl-B, we produced two Bcl-B mutants (Leu86-->Ala and Arg96-->Gln) that failed to bind Bax and that also were unable to suppress apoptosis induced by Bax over-expression. In contrast, other Bcl-B mutants that still bound Bax retained protective activity against Bax-induced cell death, thus serving as a control. We conclude that, in contrast with some other anti-apoptotic Bcl-2-family proteins, a strong correlation exists for Bcl-B between binding to pro-apoptotic multidomain Bcl-2 family proteins and functional apoptosis suppression.
A low-power multi-bit ΔΣ modulator in 90nm digital cmos without DEM (2005)

A 2/sup nd/-order 4b /spl Delta//spl Sigma/ modulator uses 3- and 5-level DAC. Truncating the ADC output while shaping and cancelling the error enables the use of low-resolution DAC and avoids DEM. The prototype is implemented in a 90nm digital CMOS technology and uses 2.1 mW from a 1.3V supply with a 40MHz clock. The SNDR is 52dB, 61dB and 72dB for an OSR of 10, 20 and 50, respectively.
Noncontrast‐enhanced time‐resolved 4D dynamic intracranial MR angiography at 7T: A feasibility study (2017)

2 Technical Efficacy Stage 2 J. Magn. Reson. Imaging 2017.
A Comparative Study Of Cross-Correlation Methods For Alignment Of Dna Sequences Containing Repetitive Patterns (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
A Byzantine resilient processor with an encoded fault-tolerant shared memory (1990)

The memory requirements for ultra-reliable computers are expected to increase due to future increases in mission functionality and operating-system requirements. This increase will have a negative effect on the reliability and cost of the system. Increased memory size will also reduce the ability to reintegrate a channel after a transient fault, since the time required to reintegrate a channel in a conventional fault-tolerant processor is dominated by memory realignment time. A Byzantine Resilient Fault-Tolerant Processor with Fault-Tolerant Shared Memory (FTP/FTSM) is presented as a solution to these problems. The FTSM uses an encoded memory system, which reduces the memory requirement by one-half compared to a conventional quad-FTP design. This increases the reliability and decreases the cost of the system. The realignment problem is also addressed by the FTSM. Because any single error is corrected upon a read from the FTSM, a faulty channel's corrupted memory does not need realignment before reintegration of the faulty channel. A combination of correct-on-access and background scrubbing is proposed to prevent the accumulation of transient errors in the memory. With a hardware-implemented scrubber, the scrubbing cycle time, and therefore the memory fault latency, can be upper-bounded at a small value. This technique increases the reliability of the memory system and facilitates validation of its reliability model.
Disruption of the mycobacterial cell entry gene of<i>Mycobacterium bovis</i>BCG results in a mutant that exhibits a reduced invasiveness for epithelial cells (1999)

Mycobacteria belonging to the Mycobacterium tuberculosis complex have the ability to invade and replicate in non-phagocytic cells, an event that requires the presence of bacterial surface components capable of triggering a cell response and the subsequent internalization of the microorganism. In this study, we report the sequencing of the mycobacterial cell entry gene (mce) of Mycobacterium bovis bacillus Calmette-Guérin (BCG) and the generation and characterization of a mutant BCG strain with an inactivated mce gene, by homologous recombination with double cross-over. This mutant strain does not express the mycobacterial cell entry protein (Mce) and exhibits a reduced ability to invade the non-phagocytic epithelial cell line HeLa as compared to wild-type BCG.
Low prevalence of antibodies to glucose‐6‐phosphate isomerase in patients with rheumatoid arthritis and a spectrum of other chronic autoimmune disorders (2003)

No disease-specific pattern of antibody positivity to GPI was apparent. While the antibody-mediated mechanism at play in the mouse model may exemplify a generic mechanism for some forms of arthritis in humans, GPI itself does not appear to be a target common to the majority of RA patients.
Die-to-Die Adhesive Bonding Procedure for Evanescently-Coupled Photonic Devices (2011)

Recently demonstrated evanescent hybrid III-V/Si lasers are mostly based on molecular bonding of a III-V die on an SOI photonic wafer. This procedure requires ultra-clean and smooth bonding surfaces and might be difficult to implement in an industry-scale fabrication process. As an alternative, we present a die-to-die adhesive bonding procedure, using a DVS-BCB polymer. We achieved less than 100 nm-thick bonding layers that enable evanescent coupling between III-V and silicon. The process shows good robustness and bonding strength, with a break-down shear stress of 2 MPa. The process can be scaled-up to a multiple die-to-wafer bonding procedure.
A dual function TAR Decoy serves as an anti-HIV siRNA delivery vehicle (2010)

The TAR RNA of HIV was engineered as an siRNA delivery vehicle to develop a combinatorial therapeutic approach. The TAR backbone was found to be a versatile backbone for expressing siRNAs. Upon expression in human cells, pronounced and specific inhibition of reporter gene expression was observed with TARmiR. The resulting TARmiR construct retained its ability to bind Tat and mediate RNAi. TARmiR was able to inhibit HIV gene expression as a TAR decoy and by RNA interference when challenged with infectious proviral DNA. The implications of this dual function therapeutic would be discussed.
A Controlled, Randomized, Double-Blind Trial of Prophylaxis Against Jaundice Among Breastfed Newborns (2005)

Use of minimal aliquots of L-aspartic acid and EHC for beta-glucuronidase inhibition results in increased fecal bilirubin excretion and less jaundice, without disruption of the breastfeeding experience. Decreased jaundice in the W/C group, which lacked a beta-glucuronidase inhibitor, suggests a different mechanism.
A survey of small molecule glucagon receptor antagonists from recent patents (2006 – 2010) (2011)

The novel small molecule GCGR antagonists reviewed here represent many diverse structural motifs. Some molecules are very potent antagonists of the GCGR in in vitro assays with acceptable selectivity. Some have intriguing in vivo activity in models of T2DM in a variety of preclinical species. It is to be hoped that clinical developments following these preclinical discoveries might result in a long-awaited new treatment for T2DM.
Distributed high-precision time transfer through passive optical networks (2014)

We propose a one-point to multipoint distributed time transfer through passive optical networks using a time division multiple access (TDMA) based two-way time transfer. The clock at each clock user node is, in turn, compared with the high-precision reference clock at a master node by a two-way time transfer during assigned subperiods. The corresponding TDMA control protocol and time transfer units for the proposed scheme are designed and implemented. A 1×8 experimental system with a 20 km single-mode fiber in each subpath is demonstrated. The results show that a standard deviation of <60 ps can be reached in each comparison subperiod.
Wide-field computational imaging of pathology slides using lens-free on-chip microscopy (2014)

Optical examination of microscale features in pathology slides is one of the gold standards to diagnose disease. However, the use of conventional light microscopes is partially limited owing to their relatively high cost, bulkiness of lens-based optics, small field of view (FOV), and requirements for lateral scanning and three-dimensional (3D) focus adjustment. We illustrate the performance of a computational lens-free, holographic on-chip microscope that uses the transport-of-intensity equation, multi-height iterative phase retrieval, and rotational field transformations to perform wide-FOV imaging of pathology samples with comparable image quality to a traditional transmission lens-based microscope. The holographically reconstructed image can be digitally focused at any depth within the object FOV (after image capture) without the need for mechanical focus adjustment and is also digitally corrected for artifacts arising from uncontrolled tilting and height variations between the sample and sensor planes. Using this lens-free on-chip microscope, we successfully imaged invasive carcinoma cells within human breast sections, Papanicolaou smears revealing a high-grade squamous intraepithelial lesion, and sickle cell anemia blood smears over a FOV of 20.5 mm(2). The resulting wide-field lens-free images had sufficient image resolution and contrast for clinical evaluation, as demonstrated by a pathologist's blinded diagnosis of breast cancer tissue samples, achieving an overall accuracy of ~99%. By providing high-resolution images of large-area pathology samples with 3D digital focus adjustment, lens-free on-chip microscopy can be useful in resource-limited and point-of-care settings.
Origami Segmented Helical Antenna With Switchable Sense of Polarization (2017)

Anew design of a segmented helical antenna (SHA), which can switch its sense of polarization by rotating around its center axis is presented. Two implementation methods, one based on origami folding and the other one based on skeleton scaffolding are developed. Example bifilar SHA designs are presented for the UHF frequency band. The performance of the antennas is studied and validated through simulations and measurements. Specifically, the reflection coefficient, axial ratio, realized gain, and radiation pattern beamwidth of the proposed SHAs are investigated and compared with the ones of a conventional bifilar helical antenna. The proposed SHA has two stable states of operation, one with right-hand circular polarization and the other one with left-hand circular polarization. The sense of the polarization of this antenna can be controlled and switched using mechanical rotation. Therefore, this antenna exhibits reconfigurable polarization performance.
Novel local evanescent field detection waveguide multianalyte biosensor (2004)

A novel waveguide sensor capable of sensing multiple analytes directly and in real time with label-free, local detection has been investigated. Numerical simulations agree with analytical calculations of the sensor sensitivity. The waveguide parameters including detector to core distance, adlayer length, and surface roughness have been extensively analyzed. Initial experimental realization efforts are summarized.
TH‐A‐220‐03: On the Dosimetric Effect and Correction of Inverse Consistency and Transitivity Errors in Dose Accumulation (2011)

Purpose: To investigate the dosimetric effect of deformable image registration (DIR) inverse consistency and transitivity errors in dose accumulation and to propose a correction strategy to reduce the impact of these errors. Methods: Given three images, A, B and C, deformation maps are defined as third‐order transitive if the deformation A‐>B‐>C‐>A results in the image A. Four tomotherapy MVCT images from a head and neck treatment were selected representing the anatomical change over the duration of the treatment course. A research version of the Pinnacle RTPS (v9.1) was used for all planning, DIR and dose warping. A seven‐field IMRT plan was created delivering 69.3Gy, 60 & 56Gy to the high, intermediate and low‐dose PTVs respectively. This plan was copied to each of the other three images and the dose calculated on all images. All images were deformed to each other using the fast symmetric Demons algorithm. This algorithm is not inverse‐consistent or transitive error‐free. The dose from each image was warped to and accumulated on the fourth image to result in ‘D_AC1’. The dose from each image was then warped to and accumulated on the third image to result in ‘C_AC1’. ‘C_AC1’ was then warped to the fourth image to result in ‘DAC2’. The difference in between ‘D ACT’ and ‘D_AC2’ was measured. This dose accumulation process was then repeated after all deformation maps were made inverse consistent and then transitive. Results: Inverse consistency and transitivity errors lead to an observable difference between ‘D_AC1’ and ‘D_AC2’. The difference decreased with inverse‐consistent DVFs and decreased further with transitive DVFs. Conclusion: Inverse consistency and transitivity errors lead to discrepancies between doses warped to the same image via different pathways. These discrepancies can be significantly reduced by enforcing inverse consistency and transitivity between all DVFs used in dose accumulation. N Hardcastle is funded by Philips Healthcare
Exploring Grammatical Error Correction with Not-So-Crummy Machine Translation (2012)

To date, most work in grammatical error correction has focused on targeting specific error types. We present a probe study into whether we can use round-trip translations obtained from Google Translate via 8 different pivot languages for whole-sentence grammatical error correction. We develop a novel alignment algorithm for combining multiple round-trip translations into a lattice using the TERp machine translation metric. We further implement six different methods for extracting whole-sentence corrections from the lattice. Our preliminary experiments yield fairly satisfactory results but leave significant room for improvement. Most importantly, though, they make it clear the methods we propose have strong potential and require further study. 1
A Voltage-Edge-Rate-Limiting Soft-Switching Inverter Based on Auxiliary Resonant Pole (2019)

To increase switching frequencies while limiting switching losses in voltage-source inverters, power switches have been made significantly faster with achievable switching times now less than 100 ns. However, faster switches generate larger inverter output voltage edge rates (dv/dt) and result in deleterious effects in variable-speed drive systems including transient overvoltages at motor terminals, electromagnetic interference, and bearing failures due to microarcs. A common approach for limiting peak dv/dt involves using a dv/dt filter. However, the dv/dt filter introduces extra power losses and increases the overall size and weight of the system. Soft-switching circuits, which were originally developed to reduce switching losses, can help reduce dv/dt, but using soft-switching to accurately control dv/dt has not been fully explored. In this paper, a new soft-switching circuit, entitled the auxiliary resonant soft-edge pole (ARSEP), is set forth. ARSEP improves the available softs witching circuits so that dv/dt can be accurately controlled through the circuit parameter design. An ARSEP inverter prototype was designed, simulated, and constructed to verify its performance and benefits. Compared to a conventional hardswitched inverter with a dv/dt filter, the ARSEP inverter prototype results in a significant reduction in overall power loss, inductor volume, and weight.
Acoustic holography for calibration of ultrasound sources and <i>in situ</i> fields in therapeutic ultrasound (2019)

Therapeutic ultrasound sources, which are typically piezoelectric transducers, are intended to deliver known acoustic pressures to targeted tissue sites. Each transducer vibrates in a unique way and radiates a corresponding 3D ultrasound field. Accordingly, transducer vibrations should be known accurately in order to characterize the pressures delivered to the patient. Acoustic holography is a technique that relies on hydrophone measurements to reconstruct a source hologram that characterizes transducer vibrations [Sapozhnikov et al., JASA, 138(3), 1515–1532 (2015)]. In this way, a hologram is a signature of each transducer that can be monitored over time for quality assurance. Using holography-defined source boundary conditions, numerical forward projection of the ultrasound field based on the nonlinear wave equation can be used to accurately predict in situ temperatures and pressures in heterogeneous media for treatment planning. As such, acoustic holography goes beyond simple hydrophone scans and is uniquely suited to meet clinical needs for quantifying therapeutic ultrasound fields. In this paper, several examples of acoustic holography implementation are presented, including the characterization of single-element and multi-element flat and spherically curved sources working in linear and nonlinear regimes and in continuous and pulsed modes. [Work supported by NIH 1R01EB025187, R01EB007643, and R21CA219793; RFBR 17-02-00261 and 17-54-33034.]
Clinical Refraction in Three-Dimensional Dioptric Space Revisited (1997)

The traditional clinical designation of spherocylindrical power unambiguously specifies the refractive properties of a thin lens or refractive surface. This representation of dioptric power is not, however, optimum in mathematical terms, as is apparent when, for example, two spherocylindrical lens powers are added. Alternative systems have been described which are not subject to this same type of difficulty, and the essential feature of these other systems is that spherocylindrical power is defined in terms of a three-dimensional dioptric space in which the axes are usually orthogonal. The advantages of this orthogonality can be exploited in the practice of clinical refraction, provided lens powers in these three dimensions can be physically implemented. Systems using these characteristics have been introduced in the past, but the clinical community has not adopted them on a widespread basis. However, systems which take advantages of these features do have unique advantages relative to traditional clinical refraction procedures. These characteristics, and refractive procedures which exploit their advantages, are described.
Identification of Novel Roles of the Cytochrome P450 System in Early Embryogenesis: Effects on Vasculogenesis and Retinoic Acid Homeostasis (2003)

The cytochrome P450-dependent monooxygenase system catalyzes the metabolism of xenobiotics and endogenous compounds, including hormones and retinoic acid. In order to establish the role of these enzymes in embryogenesis, we have inactivated the system through the deletion of the gene for the electron donor to all microsomal P450 proteins, cytochrome P450 reductase (Cpr). Mouse embryos homozygous for this deletion died in early to middle gestation (approximately 9.5 days postcoitum [dpc]) and exhibited a number of novel phenotypes, including the severe inhibition of vasculogenesis and hematopoiesis. In addition, defects in the brain, limbs, and cell types where CPR was shown to be expressed were observed. Some of the observed abnormalities have been associated with perturbations in retinoic acid homeostasis in later embryogenesis. Consistent with this possibility, embryos at 9.5 dpc had significantly elevated levels of retinoic acid and reduced levels of retinol. Further, some of the observed phenotypes could be either reversed or exacerbated by decreasing or increasing maternal retinoic acid exposure, respectively. Detailed analysis demonstrated a close relationship between the observed phenotype and the expression of genes controlling vasculogenesis. These data demonstrate that the cytochrome P450 system plays a key role in early embryonic development; this process appears to be, at least in part, controlled by regional concentrations of retinoic acid and has profound effects on blood vessel formation.
Automated analysis for microcalcifications in high resolution digital mammograms (1994)

Digital mammography offers the promise of significant advances in early detection of breast cancer. Our overall goal is to design a digital system which improves upon every aspect of current mammography technology: the x-ray source, detector, visual presentation of the mammogram and computer-aided diagnosis capabilities. This paper will discuss one part of our whole-system approach -- the development of a computer algorithm using gray-scale morphology to automatically analyze and flag microcalcifications in digital mammograms in hopes of reducing the current percentage of false-negative diagnoses, which is estimated at 20%. The mamrnograms used for developing this ``mammographers assistant`` are film mammograms which we have digitized at either 70{mu}m or 35{mu}m per pixel resolution with 4096(12 bits) of gray level per pixel. For each potential microcalcification detected. in these images, we compute a number of features in order to distinguish between the different kinds of objects detected.