gebhart/patrepeval huggingface dataset:
Hematopoietic Stem and Progenitor Cells from Human Pluripotent Stem Cells Via Transcription Factor Conversion of Hemogenic Endothelium (2016)

Abstract A variety of tissues can be differentiated from pluripotent stem cells (PSCs) in vitro through stepwise exposure to morphogens, or by conversion of one differentiated cell type into another by enforced expression of master transcription factors (TFs). Despite considerable effort, neither approach has yielded functional human hematopoietic stem cells (HSCs). Building upon recent evidence that HSCs derive from definitive hemogenic endothelium (HE), we performed morphogen-directed differentiation of human PSCs into HE followed by screening of 26 candidate HSC-specifying TFs for the capacity to promote multi-lineage hematopoietic engraftment in irradiated immune deficient murine hosts. From genomic PCR of engrafted cells, we recovered seven TFs (ERG, HOXA5, HOXA9, HOXA10, LCOR, RUNX1, SPI1) that were sufficient to convert HE into hematopoietic stem and progenitor cells (HSPCs) that engraft GLY-A+ erythrocytes, CD33+ myeloid, CD15+ CD31+ neutrophils, CD19+ IgM+ B and CD3+ T cells in primary and secondary murine recipients for 12-14 weeks. Limiting dilution analysis indicated that the frequency of repopulating cells generated by this method was 1 in 4,707-15,029, lower than the frequency in CD34+ cord blood cells (1 in 1,819-5,173). Functional characterization of terminally differentiated cells demonstrated features of definitive erythropoiesis (expression of adult beta globin and enucleation). Engrafted neutrophils responded to cytokine stimuli by activation of myeloperoxidase. Human IgM and IgG could be detected in the serum of engrafted mice, and titers of ovalbumin specific antibody increased in response to protein immunization, indicating boostable immunity. T-cells responded to PMA/Ionomycin stimuli by activation of IFNγ, and sequencing of the T cell receptor revealed a broad clonotype diversity. Proviral integration analysis demonstrated derivation of myeloid and lymphoid progeny from common clones in secondary animals, indicating generation of self-renewing, multipotential HSC-like cells from PSCs. Mechanistically, the seven TFs induced HOXA target genes (LMO2, SOX4, MEIS1 and ID2); upregulated expression of homing-related genes (CXCR4, VLA5 and S1PR1); and enhanced the endothelial to hematopoietic transition (EHT), as indicated by a 2.4-fold induction of a RUNX1c-reporter. Our combined approach of morphogen-driven differentiation and TF-mediated cell fate conversion produced HSPCs from PSCs that hold promise for modeling hematopoietic disease in humanized mice and for therapeutic strategies in genetic blood disorders. Disclosures No relevant conflicts of interest to declare.
Conjugate backprojection approach for cone beam artifact reduction (2006)

With the introduction of volumetric computed tomography (VCT), many studies have been conducted on the cone beam reconstruction algorithms. Majority of the research efforts was devoted to the reduction of cone beam artifacts by designing special weighting functions that treat the projection samples differently based on their cone angles. The selection of weighting function can be quite complex due to the cone beam helical geometry and is often designed through trial-and-error. In this paper, we present a conjugate backprojection approach (CBA) that is capable of significantly reducing cone beam artifacts without the application of a pre-backprojection weighting function. Our approach utilizes CBA operation which simultaneously backprojects and interpolates conjugate sampling pairs. Unlike the conventional backprojection, the final backprojected value depends not only on the distance of these samples to the point-of-intersection, but also on the cone angles of these samples. Consequently, optimization can be performed on a pixel by pixel basis and is independent of the acquisition protocols, such as helical pitches or acquisition modes. The proposed approach is applicable to cone beam helical as well as step-and-shoot acquisitions. Extensive computer simulation and phantom experiments were conducted to demonstrate the efficacy of our approach. Results have shown that the proposed approach significantly reduces the cone beam artifacts.
Efficient Source of Single Photons: A Single Quantum Dot in a Micropost Microcavity (2002)

We have demonstrated efficient production of triggered single photons by coupling a single semiconductor quantum dot to a three-dimensionally confined optical mode in a micropost microcavity. The efficiency of emitting single photons into a single-mode traveling wave is approximately 38%, which is nearly 2 orders of magnitude higher than for a quantum dot in bulk semiconductor material. At the same time, the probability of having more than one photon in a given pulse is reduced by a factor of 7 as compared to light with Poissonian photon statistics.
Engagement of Toll‐like receptor‐2 on cytotoxic T‐lymphocytes occurs <i>in vivo</i> and augments antitumor activity (2008)

Toll‐like receptors (TLRs) are among the fundamental molecules that alert the immune system to the presence of an infection by recognizing pathogen‐associated molecules. Much of our understanding regarding TLR function stems from the study of innate immune cells. Recent studies by several groups, including ours, have shown that TLRs can function as costimulatory receptors for antigen‐specific T cells, resulting in enhanced T‐cell survival and increased expression of effector molecules. We report that the ligation of the TLR1/2 heterodimer on OT‐1 cytotoxic T‐lymphocytes (CTL) but not TLR2 –/– OT‐1 T cells increased cytolytic activity in vitro and in vivo. On the basis of these data, we tested the hypothesis that TLR1/2 stimulation on CTLs would enhance antitumor activity in a therapeutic model of B16‐Ova melanoma. Adoptive OT‐1 T‐cell transfer into wild‐type and MyD88 –/– mice, followed by injection with TLR1/2 ligand, resulted in a synergistic antitumor effect, which correlated with the induction of CD8 T cells specific to various tumor antigens. In contrast, mice receiving TLR2 –/– OT‐1 T cells and TLR1/2 ligand showed minimal therapeutic efficacy. These findings emphasize the physiological significance of TLR2 engagement on CTLs and could make possible new approaches for the development of effective immunotherapies by manipulating TLR signaling within CTLs.—Asprodites, N., Zheng, L., Geng, D., Velasco‐Gonzalez, C., Sanchez‐ Perez, L., Davila, E. Engagement of Toll‐like receptor‐2 on cytotoxic T‐lymphocytes occurs in vivo and augments antitumor activity. FASEB J. 22, 3628–3637 (2008)
A Reduced-Order Model of Mistuning Using a Subset of Nominal System Modes (1999)

Reduced-order models have been reported in the literature that can be used to predict the harmonic response of mistuned bladed disks. It has been shown that in many cases they exhibit structural fidelity comparable to a finite element analysis of the full bladed disk system while offering a significant improvement in computational efficiency. In these models the blades and disk are treated as distinct substructures. This paper presents a new, simpler approach for developing reduced-order models in which the modes of the mistuned system are represented in terms of a subset of nominal system modes. It has the following attributes: the input requirements are relatively easy to generate; it accurately predicts mistuning effects in regions where frequency veering occurs; as the number of degrees-of-freedom increases it converges to the exact solution; it accurately predicts stresses as well as displacements; and it accurately models the deformation and stresses at the blades’ bases.
<title>Integrated wave propagation devices for quality control or diagnostics of pavements</title> (1996)

Seismic Pavement Analyzer and a portable version of it have been extensively used for quality control and monitoring the structural condition of pavements. With them, a pavement can be tested at closely spaced points and at a fraction of the cost and time of coring. The main tests used are the impact echo for determining the thickness of the slab, ultrasonic body wave and ultrasonic surface wave for determining the moduli of top layer, impulse response for determining the condition of subgrade, and SASW method for determining the modulus profile of pavement. Based on extensive field testing on numerous types of base and subgrade,the techniques in general, and the two devices in particular are quite suitable for many quality and pavement evaluation projects.
Basic Blue 54: a New Colorant for Monocytes (1992)

C.I. basic blue 54, a sulfur containing azo textile dye, stained the nucleus and cytoplasm of normal and leukemic monocytes bright red-violet. Essential for the staining reaction was a brief final rinse in a pH 3.6 acetic acid-sodium acetate buffer. Coloration of the type found in monocytes was not observed in other types of mature and immature leukocytes.
Efficient SAT-based unbounded symbolic model checking using circuit cofactoring (2005)

We describe an efficient approach for SAT-based quantifier elimination that significantly improves the performance of pre-image and fixed-point computation in SAT-based unbounded symbolic model checking (UMC). The proposed method captures a larger set of new states per SAT-based enumeration step during quantifier elimination, in comparison to previous approaches. The novelty of our approach is in the use of circuit-based cofactoring to capture a large set of states, and in the use of a functional hashing based simplified circuit graph to represent the captured states. We also propose a number of heuristics to further enlarge the state set represented per enumeration, thereby reducing the number of enumeration steps. We have implemented our techniques in a SAT-based UMC framework where we show the effectiveness of SAT-based existential quantification on public benchmarks, and on a number of large industry designs that were hard to model check using purely BDD-based techniques. We show several orders of improvement in time and space using our approach over previous CNF-based approaches. We also present controlled experiments to demonstrate the role of several heuristics proposed in the paper. Importantly, we were able to prove using our method the correctness of a safety property in an industry design that could not be proved using other known approaches.
Modeling of active shimming of metallic needles for interventional MRI (2020)

Simulations predict that it is possible to minimize metallic probe induced ΔB<sub>0</sub> and signal losses using externally supplied direct current shim coil inserts in arbitrary orientations for potential benefits in many interventional MRI applications.
Nanotube Alignment Mechanism in Floating Evaporative Self-Assembly (2017)

The challenge of assembling semiconducting single-wall carbon nanotubes (s-SWCNTs) into densely packed, aligned arrays has limited the scalability and practicality of high-performance nanotube-based electronics technologies. The aligned deposition of s-SWCNTs via floating evaporative self-assembly (FESA) has promise for overcoming this challenge; however, the mechanisms behind FESA need to be elucidated before the technique can be improved and scaled. Here, we gain a deeper understanding of the FESA process by studying a stationary analogue of FESA and optically tracking the dynamics of the organic ink/water/substrate and ink/air/substrate interfaces during the typical FESA process. We observe that the ink/water interface serves to collect and confine the s-SWCNTs before alignment and that the deposition of aligned bands of s-SWCNTs occurs at the ink/water/substrate contact line during the depinning of both the ink/air/substrate and ink/water/substrate contact lines. We also demonstrate improved control over the interband spacing, bandwidth, and packing density of FESA-aligned s-SWCNT arrays. The substrate lift rate (5-15 mm min<sup>-1</sup>) is used to tailor the interband spacing from 90 to 280 μm while maintaining a constant aligned s-SWCNT bandwidth of 50 μm. Varying the s-SWCNT ink concentration (0.75-10 μg mL<sup>-1</sup>) allows the control of the bandwidth from 2.5 to 45 μm. A steep increase in packing density is observed from 11 s-SWCNTs μm<sup>-1</sup> at 0.75 μg mL<sup>-1</sup> to 20 s-SWCNTs μm<sup>-1</sup> at 2 μg mL<sup>-1</sup>, with a saturated packing density of ∼24 s-SWCNTs μm<sup>-1</sup>. We also demonstrate the scaling of FESA to align s-SWCNTs on a 2.5 × 2.5 cm<sup>2</sup> scale while preserving high-quality alignment on the nanometer scale. These findings help realize the scalable fabrication of well-aligned s-SWCNT arrays to serve as large-area platforms for next-generation semiconductor electronics.
Fiber Optic Flexural Disk Microphone (1989)

A microphone consisting of a hollow cylinder whose flexible, circular endplates are bonded to pairs of flat spiral wound coils of optical fiber is described. When the endplate/disk is deformed due to a pressure difference, the outer and inner fiber coils experience opposite strains resulting in a "push-pull" optical path length difference which is detected in an all-fiber Michelson interferometer. The close proximity of the interferometric fiber coils, separated by the thin thermally conducting end plate, rejects thermal gradient induced signals. The addition of a second identical endplate and fiber coil pair at the opposite end of the cylinder doubles the acoustic sensitivity while canceling acceleration induced signals. The calculated and measured optical strain of a single plate, single coil sensor using static pressure, acoustic pressure, and acceleration are in good agreement and yield a sensitivity of 21 milliradians per Pascal per meter of optical fiber for an 8.0 cm diameter, 3.0 mm thick plate below its resonance frequency of 3 KHz.
Hot-pressed ceramic Cr<sup>2+</sup>:ZnSe gain-switched laser (2006)

The technology of hot-pressed Cr(2+):ZnSe ceramic preparation is reported. Comparative gain-switched lasing of hot-pressed ceramic and CVD grown Cr(2+):ZnSe samples with slope efficiencies up to 10% and output energies up to 2 mJ were demonstrated. This is a milestone in the development of future large scale mid-IR laser systems based on ceramic TM(2+):II-VI materials. This evolving technology has excellent potential as media for practical low cost, high power mid-IR laser applications.
Generating multiple-pulse bursts for enhanced fluorescence detection (2014)

The signal-to-background ratio is the limiting factor for fluorescence based detection, sensing, and imaging. A typical background signal will include direct scattering of excitation and Raman scattering of the sample as well as autofluorescence from the sample and additives. To improve the signal-to-background ratio, fluorophores of high brightness and/or high concentration of the fluorophores need to be used. Most of the background is instantaneous and short-lived (picosecond to nanosecond time scale), and using long-lived fluorescence probes combined with time-gated detection allows for significant suppression of unwanted background. Unfortunately, this approach requires substantial sacrifice of the probe signal in order to sufficiently filter the background unless the fluorescence lifetime of the probe is very long. However, long lived probes like ruthenium bipyridyl have relatively low brightness compared to probes that have shorter, 10-30 ns fluorescence lifetimes.We recently presented an approach based on bursts of multiple pulses that allowed for high probe signal amplification using long-lived ruthenium based probe (Ru) and an 80 MHz repetition-rate laser excitation. Unfortunately, Ru represents an extreme case for probe lifetime, and a probe with a shorter lifetime of 20 ns will require excitation from a pulsed source with much higher repetition rate to significantly enhance its signal. Such high repetition rates are not possible to generate with most of today's available electronics. In this report we present new approaches to optimize and generate bursts of pulses with high repetition rate within the burst and no need for new or improved electronics. The high repetition rates originate from a low-repetition source and are highly tunable. We demonstrate that a burst of 2-10 pulses spaced 3 ns apart (corresponding to a 'burst repetition rate' of 330 MHz) allows for high signal enhancement of the 20 ns probe over the sub-nanosecond/nanosecond background. Such an approach can be applied for any sensing format, allowing much higher sensitivity for detection. Since the energy of a single pulse is spread over a few pulses in the burst, the fluorophore's photostability also improves.
A Spectrally Adaptive Noise Filling Tool for Perceptual Transform Coding of Still Images (2018)

Modern perceptual image coders reach impressively high subjective quality even at low bit-rates but tend to denoise or “detexturize” the coded pictures. Traditionally, two independent parametric approaches, known as texture and film grain synthesis, have been applied in the spatial domain as pre and post-processors around the codec to counteract such effects. In this work, a unified alternative, operating directly within the spectral domain of conventional transform codecs with tight coupling to the transform coefficient quantizer, is proposed. Due to its design, this spectrally adaptive noise filling tool (SANFT) enables highly input adaptive realizations by reusing the coder's existing optimized spatial and spectral partitioning algorithms. Formal subjective evaluation in the context of a main still picture” High Emciency Video Coding (HEVC) implementation confirms the benefit of the proposal.
Enhanced Sensing Performance of Integrated Gas Sensor Devices (2018)

Semiconducting metal oxide (SMO) gas sensors, dedicated to wearable devices were designed, fabricated, and characterized in terms of power consumption, thermal distribution, and sensing capability. The sensors demonstrate a sensitivity down to ppb-level VOC concentrations at a low power consumption of 10.5 mW. To further enhance the baseline stability and sensing response characteristics at low power consumption, a new sensor structure is proposed. The design implements novel aspects in terms of fabrication and microheater geometry, leading to improved sensor performance which enables new applications for SMO gas sensors. In this work, two designs were analyzed using experimental characterization and simulation. The results of the analyses of the two sensors are comparatively reported.
Chemoenzymatic Syntheses of ω‐Ureido <scp>D</scp>‐Amino Acids (1991)

D-Amino acids can be prepared chemoenzymatically in very high yields with high enantioselectivity by cleavage of the corresponding hydantoins with Agrobacterium radiobacter bacterial culture. Hydantoins with highly functionalized side chains are also accepted. The synthetic concept is discussed taking D-citrulline (1) as example.
Microfluidic-Based DNA Purification in a Two-Stage, Dual-Phase Microchip Containing a Reversed-Phase and a Photopolymerized Monolith (2007)

In this report, we show that a novel capillary-based photopolymerized monolith offering unprecedented efficiency (approximately 80%) for DNA extraction from submicroliter volumes of whole blood (Wen, J.; Guillo, C.; Ferrance, J. P.; Landers, J. P. Anal. Chem. 2006, 78, 1673-1681) can be translated to microfluidic devices. However, owing to the large mass of protein present in blood, both DNA binding capacity and extraction efficiency were significantly decreased when extraction of DNA was carried out directly from whole blood (38+/-1%). To circumvent this, a novel two-stage microdevice was developed, consisting in a C18 reversed-phase column for protein capture (stage 1) in series with a monolithic column for DNA extraction (stage 2). The two-stage, dual-phase design improves the capability of the monolith for whole blood DNA extraction by approximately 100-fold. From a 10-microL load of whole blood containing 350 ng of DNA, 99% (340+/-10 ng) traverses the C18 phase while approximately 70% (1020+/-45 ug) of protein is retained. A total of 240+/-2 ng of DNA was eluted from the second-stage monolith, resulting in an overall extraction efficiency of 69+/-1%. This provided not only an improvement in extraction efficiency over other chip-based DNA extraction solid phases but also the highest extraction efficiency reported to-date for such sample volumes in a microfluidic device. As an added bonus, the two-stage, dual-phase microdevice allowed the 2-propanol wash step, typically required to remove proteins from the DNA extraction phase for successful PCR, to be completely eliminated, thus streamlining the process without affecting the PCR amplifiability of the extracted DNA.
Detection of tunnel excavation using fiber optic reflectometry: experimental validation (2013)

Cross-border smuggling tunnels enable unmonitored movement of people and goods, and pose a severe threat to homeland security. In recent years, we have been working on the development of a system based on fiber- optic Brillouin time domain reflectometry (BOTDR) for detecting tunnel excavation. In two previous SPIE publications we have reported the initial development of the system as well as its validation using small-scale experiments. This paper reports, for the first time, results of full-scale experiments and discusses the system performance. The results confirm that distributed measurement of strain profiles in fiber cables buried at shallow depth enable detection of tunnel excavation, and by proper data processing, these measurements enable precise localization of the tunnel, as well as reasonable estimation of its depth.
Structural analysis of the lipopolysaccharide from nontypeable <i>Haemophilus influenzae</i> strain 1003 (2002)

Structural analysis of the lipopolysaccharide (LPS) of nontypeable Haemophilus influenzae strain 1003 has been achieved by the application of high-field NMR techniques, ESI-MS, capillary electrophoresis coupled to ESI-MS, composition and linkage analyses on O-deacylated LPS and core oligosaccharide material. It was found that the LPS contains the common structural element of H. influenzae, l-alpha-D-Hepp-(1-->2)-[PEtn-->6]-l-alpha-D-Hepp-(1-->3)-[beta-D-Glcp-(1-->4)]-l-alpha-D-Hepp-(1-->5)-[PP Etn-->4]-alpha-Kdop-(2-->6)-Lipid A, in which the beta-D-Glcp residue is substituted by phosphocholine at O-6 and an acetyl group at O-4. A second acetyl group is located at O-3 of the distal heptose residue (HepIII). HepIII is chain elongated at O-2 by either a beta-D-Glcp residue (major), lactose or sialyllactose (minor, i.e. alpha-Neu5Ac-(2-->3)-beta-D-Galp-(1-->4)-beta-D-Glcp), where a third minor acetylation site was identified at the glucose residue. Disialylated species were also detected. In addition, a minor substitution of ester-linked glycine at HepIII and Kdo was observed.
Table S3 from PF-06804103, A Site-specific Anti-HER2 Antibody–Drug Conjugate for the Treatment of HER2-expressing Breast, Gastric, and Lung Cancers (2023)

<p>Conjugation of vc0101 does not alter anti-HER2 mAb binding.</p>
Aperture Supervision for Monocular Depth Estimation (2018)

We present a novel method to train machine learning algorithms to estimate scene depths from a single image, by using the information provided by a camera's aperture as supervision. Prior works use a depth sensor's outputs or images of the same scene from alternate viewpoints as supervision, while our method instead uses images from the same viewpoint taken with a varying camera aperture. To enable learning algorithms to use aperture effects as supervision, we introduce two differentiable aperture rendering functions that use the input image and predicted depths to simulate the depth-of-field effects caused by real camera apertures. We train a monocular depth estimation network end-to-end to predict the scene depths that best explain these finite aperture images as defocus-blurred renderings of the input all-in-focus image.