gebhart/patrepeval huggingface dataset:
A Novel Three-Dimensional Culture System Allows Prolonged Culture of Functional Human Granulosa Cells and Mimics the Ovarian Environment (2010)

The development of techniques allowing the growth of primordial follicles to mature follicles in vitro has much potential for both reproductive medicine and developmental research. However, human primordial and preantral follicles fail to grow after isolation from the surrounding ovarian stroma. Granulosa cells, which normally undergo apoptosis after ovulation, contain a subpopulation of ovarian follicular cells remaining viable in vitro over prolonged periods when cultured in the presence of leukemia-inhibiting factor. However, when cultured as monolayers, they progressively lose all their characteristics, such as follicle-stimulating hormone receptor and cytochrome P450-aromatase. Here, we describe a three-dimensional culture system containing type I collagen, which, together with leukemia-inhibiting factor, allowed the survival and growth of a subpopulation of granulosa cells isolated from mature ovarian follicles and supported them to proliferate into spherical structures exhibiting steroidogenic capacity, as demonstrated by P450-aromatase and 3beta-hydroxysteroid dehydrogenase. After transplantation into the ovaries of immunodeficient mice, these cells became localized preferentially within antral follicles and the prolonged expression of follicle-stimulating hormone receptor was confirmed as well. With this optimization of the culture conditions, an environment was created, which acts as a niche closely mimicking the development of early ovarian follicles in vitro.
Technical Report for HW2VEC -- A Graph Learning Tool for Automating\n Hardware Security (2021)

In this technical report, we present HW2VEC [11], an open-source graph\nlearning tool for hardware security, and its implementation details (Figure 1).\nHW2VEC provides toolboxes for graph representation extraction in the form of\nData Flow Graphs (DFGs) or Abstract Syntax Trees (ASTs) from hardware designs\nat RTL and GLN levels. Besides, HW2VEC also offers graph learning tools for\nrepresenting hardware designs in vectors that preserve both structural features\nand behavioral features. To the best of our knowledge, HW2VEC is the first\nopen-source research tool that supports applying graph learning methods to\nhardware designs in different abstraction levels for hardware security. We\norganize the remainder of this technical report as follows: Section 2\nintroduces the architecture of HW2VEC; Section 3 gives information about the\nuse-case implementations; Section 4 provides the experimental results and\ndemonstrates the performance of HW2VEC for two hardware security applications:\nHT detection and IP piracy detection; finally, Section 5 will conclude this\nreport.\n
Development of a VEGFR-2 antagonist based on a novel protein scaffold (AdNectin) (2005)

3150 Background: Shortcomings of traditional antibody technology have prompted the development of antagonists using addressable fibronectin proteins (AdNectins). The benefits of AdNectins include the ability to rapidly identify high affinity binders with tailored binding kinetics, as well as the ability to produce these proteins by economic E. coli-based production Methods: Using this technology an AdNectin antagonist to VEGFR-2 was developed. VEGFR-2 was chosen as a target because of its well validated role in angiogenesis. Methods: The anti-VEGFR-2 AdNectin, CT322, was evaluated pre-clinically for its biophysical characteristics, ability to block VEGFR-2 activity on endothelial cells, pharmacokinetics, inhibition of VEGF activity in vivo, and effects on tumor progression in mouse models. Results: CT322, is a PEGylated 10 kDa monomeric protein that is highly stable at 37°C. CT322 binds human and mouse VEGFR-2 with affinities of 0.2 nM and 4 nM, respectively. CT322 efficiently blocked VEGF-induced endothelial cell proliferation, migration and tube formation. Pharmacokinetic in rats: UnPEGylated CT322 was rapidly cleared (70 ml/hr/kg) via the kidneys. Addition of a 40 kDa polyethylene glycol reduced the clearance rate to 5.2 ml/hr/kg leading to 10 fold increase in bioavailability. No accumulation of CT322 in normal tissues was observed. In vivo, CT322 inhibited VEGF-induced vascular permeability at 5 mg/kg dose indicating an effective blockage of VEGFR-2 activity in mice. CT322 significantly inhibited tumor growth in a range of mouse and human xenografts tumor models at dose range of 10 - 40 mg/kg (i.p. 3x week). Conclusions: CT322 is a VEGFR-2 antagonist based on a novel alternative protein scaffold and has high target specificity and affinity, as well as favorable biophysical properties. CT322 block human VEGFR-2 and murine VEGFR-2 (Flk1). Consequently, CT322 has been shown to be very effective in inhibiting tumor growth in multiple pre-clinical models. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Compound Theraeutics, Gokemeijer
Psychologic Reasons for Patients Preferring Minimally Invasive Total Hip Arthroplasty (2007)

Success of an orthopaedic operation depends on patients achieving their primary goal(s) and having satisfaction with the outcome. The enthusiasm of patients for minimally invasive total hip arthroplasty seems related to satisfaction with the operation. We hypothesized patients' attitude toward a small incision would increase their confidence and satisfaction with the operation but the importance of the incision would dissipate after patients realized their goals of pain relief and functional recovery. One hundred sixty-five patients responded to a 14-question patient-perception questionnaire preoperatively and 6 weeks postoperatively and a followup survey at 6 months to 1 year postoperatively. One hundred nine patients had small incisions (mean, 9.6 cm) and 56 had long incisions (mean, 17.9 cm). Preoperatively patients expected small-incision surgery would positively influence their primary goals and satisfaction; at 6 weeks postoperative they believed more strongly that this was true. By 6 months to 1 year, the importance of the incision diminished because 100% of patients met their primary goals. Forty percent of patients with a long incision were not satisfied and the reasons given were related to the process of reincorporating their injured hip into their whole-body image. We confirmed our first hypothesis that a small incision influences a patient's satisfaction postoperatively; we could not confirm our second hypothesis that incision length did not matter after attaining primary goals.
Direct measurement of molecular level adhesion between poly(ethylene terephthalate) and polyethylene films: determination of surface and interfacial energies (1994)

The strength of an adhesive bond depends on the thermodynamic work of adhesion, among other properties. In this paper, we report the direct measurement of the thermodynamic work of cohesion and adhesion between poly(ethylene terephthalate) (PET) and polyethylene (PE) films. The pull-off force between polymer surfaces was measured using the surface forces apparatus (SFA). Thermodynamic work of adhesion was determined from pull-off force measurements using the theory of contact mechanics developed by Johnson, Kendall, and Roberts (JKR theory). The values of the surface energies of PET and PE, and the interfacial energy between PET and PE were obtained from these measurements. The dependence of the measured values of the work of adhesion on the rate of separation, time in contact, and other variables that could reflect an irreversible contribution to the measured adhesion was found to be negligible. The critical surface tensions of PET and PE were determined from contact angle measurements. The critical surface tension of wetting depends on the characteristics of the probe liquids. The surface energy of PET determined by the direct force measurements is higher than the critical surface tension of wetting. These values are 61.2 mJ/m2 and about 43 mJ/m , respectively. However, in the case of PE the surface energy determined using the SFA and the critical surface tension of wetting are about the same, 33 mJ/m2. The interfacial energy between PET and PE, obtained from direct measurements, is about 17.1 mJ/m2.
PD‐L1 overexpression correlates with JAK2‐V617F mutational burden and is associated with 9p uniparental disomy in myeloproliferative neoplasms (2022)

Myeloproliferative neoplasms (MPN) are chronic stem cell disorders characterized by enhanced proliferation of myeloid cells, immune deregulation, and drug resistance. JAK2 somatic mutations drive the disease in 50-60% and CALR mutations in 25-30% of cases. Published data suggest that JAK2-V617F-mutated MPN cells express the resistance-related checkpoint PD-L1. By applying RNA-sequencing on granulocytes of 113 MPN patients, we demonstrate that PD-L1 expression is highest among polycythemia vera patients and that PD-L1 expression correlates with JAK2-V617F mutational burden (R = 0.52; p < .0001). Single nucleotide polymorphism (SNP) arrays showed that chromosome 9p uniparental disomy (UPD) covers both PD-L1 and JAK2 in all MPN patients examined. MPN cells in JAK2-V617F-positive patients expressed higher levels of PD-L1 if 9p UPD was present compared to when it was absent (p < .0001). Moreover, haplotype-based association analyses provided evidence for germline genetic factors at PD-L1 locus contributing to MPN susceptibility independently of the previously described GGCC risk haplotype. We also found that PD-L1 is highly expressed on putative CD34<sup>+</sup> CD38<sup>-</sup> disease-initiating neoplastic stem cells (NSC) in both JAK2 and CALR-mutated MPN. PD-L1 overexpression decreased upon exposure to JAK2 blockers and BRD4-targeting agents, suggesting a role for JAK2-STAT5-signaling and BRD4 in PD-L1 expression. Whether targeting of PD-L1 can overcome NSC resistance in MPN remains to be elucidated in forthcoming studies.
Photo-Leakage Current of Thin-Film Transistors with ZnO Channels Formed at Various Oxygen Partial Pressures under Visible Light Irradiation (2012)

The effects of the oxygen partial pressure [ p (O 2 )] during ZnO sputtering on the photo-leakage current of a ZnO thin-film transistor (TFT) were investigated. The photo-leakage current increased with decreasing p (O 2 ). When the photon energy of incident light is smaller than the band-gap of the ZnO, electrons are excited from the trapped states existing near the valence band. It was found that the density of the electron traps increased when the p (O 2 ) decreased. Moreover, the trap states were formed at ∼0.5 eV and 2.8–3.2 eV from the conduction band ( E C ) when the p (O 2 ) decreased. The traps formed at ( E C - E ) of ∼0.5 eV affect the subthreshold characteristics in the dark state, while the traps formed at ( E C - E ) of 2.8–3.2 eV affect the photo-leakage current of the ZnO TFTs.
Photovoltaic Properties of a Conjugated Polymer Blend of MDMO−PPV and PCNEPV (2004)

Photovoltaic properties of solution-processed semiconducting polymer blends have been studied. It is demonstrated that photoinduced charge transfer occurs in binary mixtures of poly[2-methoxy-5-(3,7-dimethyloctyloxy)-1,4-phenylenevinylene] (MDMO−PPV) and poly[oxa-1,4-phenylene-(1-cyano-1,2-vinylene)−(2-methoxy-5-(3,7-dimethyloctyloxy)-1,4-phenylene)-1,2-(2-cyanovinylene)-1,4-phenylene] (PCNEPV). Further, it is shown that the photovoltaic performance is improved by a thermal treatment which alters the morphology of the photoactive layer. The temperature necessary to achieve the enhanced performance is related to transition temperatures of the pure polymers. Device optimization yields solar cells with a power conversion efficiency of 0.75% under standard test conditions (AM 1.5, 1000 W/m2).
Fluid Dynamics of a Novel Micro-Fistula Implant for the Surgical Treatment of Glaucoma (2015)

Under flow testing, the XEN micro-fistula implant was able to maintain backpressure above numerical hypotony levels without the use of complex valve systems. This is due to the XEN implant's design, derived from the principles that dictate Newtonian fluids.
Unsteady Flow Control Mechanism of Synthetic Jet on a Low Pressure Turbine Blade (2011)

The three-dimensional viscous unsteady Reynolds-averaged Navier-Stokes equations were solved to simulate the flow on a low pressure turbine blade.The effects of synthetic jet on the flow separation in the suction side of the Pak-B low pressure turbine blade were numerically investigated by the SST(shear stress transport) turbulence model coupled with the Langtry-Menter transition model for turbulent flow.The unsteady flow control mechanism of synthetic jet and the flow structure were also presented.The numerical results show that the flow separation in the blade suction side can be effectively suppressed even eliminated by introducing the synthetic jet with the proper control frequency.At the Reynolds number of 25 000 and the free stream turbulence intensity of 0.08%,the increase in synthetic jet frequency can improve the control effectiveness of the flow separation on the low pressure turbine blade and reduce the flow loss.When the synthetic jet frequency is 10 Hz,the flow loss coefficient relative to the total pressure at the turbine blade exit is 0.42.However,the relative loss coefficient decreases to only 0.41 when the synthetic jet frequency increases to 20 Hz.These results imply that the flow loss does not drop clearly for the low pressure turbine blade at low Reynolds number when the synthetic jet frequency is greater than 10 Hz.
Capsid intermediates assembled in a foot-and-mouth disease virus genome RNA-programmed cell-free translation system and in infected cells (1985)

Structural protein complexes sedimenting at 140S, 70S (empty capsids), and 14S were isolated from foot-and-mouth disease virus-infected cells. The empty capsids were stable, while 14S complexes were relatively short-lived. Radioimmune binding assays involving the use of neutralizing monoclonal antibodies to six distinct epitopes on type A12 virus and polyclonal antisera to A12 structural proteins demonstrated that native empty capsids were indistinguishable from virus. Infected cell 14S particles possessed all the neutralizing epitopes and reacted with VP2 antiserum. Cell-free structural protein complexes sedimenting at 110S, 60S, and 14S containing capsid proteins VP0, VP3, and VP1 are assembled in a rabbit reticulocyte lysate programmed with foot-and-mouth viral RNA. These structures also contain the six epitopes, and cell-free 14S structures like their in vivo counterparts reacted with VP2 antiserum. Capsid structures from infected cells and the cell-free complexes adsorbed to susceptible cells, and this binding was inhibited, to various degrees, by saturating levels of unlabeled virus. These assays and other biochemical evidence indicate that capsid assembly in the cell-free system resembles viral morphogenesis in infected cells. In addition, epitopes on the virus surface possibly involved in interaction with cellular receptor sites are found early in virion morphogenesis.
Broadband Optical Mammography: Chromophore Concentration and Hemoglobin Saturation Contrast in Breast Cancer (2015)

This study reports the optical characterization and quantitative oximetry of human breast cancer using spectrally-resolved images collected with a broadband, continuous-wave optical mammography instrument. On twenty-six cancer patients, we collected two-dimensional optical mammograms and created maps of the concentrations of hemoglobin, water, and lipids, as well as the oxygen saturation of hemoglobin. For each cancerous breast, we analyzed the difference between the tumor region (as identified by x-ray and optical mammography) and the remainder of breast tissue. With respect to the surrounding tissue, we found that cancer regions have significantly higher concentrations of total hemoglobin (+2.4 ± 0.4 μM) and water (+7 ± 1% v/v), and significantly lower lipid concentration (8 ± 2% v/v) and oxygen saturation of hemoglobin (5 ± 1%). We also found a significant correlation between the tumor optical contrast and the grade of breast cancer as quantified by the Nottingham histologic score; this demonstrates how optical signatures may be representative of metabolic and morphological features, as well as the aggressive potential of the tumor.
Exploring novel terahertz detectors and sources with the UCSB free-electron lasers. (2008)

Summary form only given. The UCSB free-electron lasers energize two research thrusts - terahertz resonant detectors, and terahertz Bloch oscillators. Work on terahertz resonant detectors focuses on plasmonic resonances in grating gated field effect transistors. The resonant response, ~ 50 GHz wide, can be tuned with gate voltage and grating geometry. Gating a narrow region of the channel to threshold enhances reponsivity. The pinched off region develops a barrier to electron flow and "Schottky like" characteristics, exhibiting strong bolometric or rectified response with time constants varying from submicroseconds to 10's of microseconds. Efforts to make a Bloch oscillator oscillate use super- superlattices comprised of short period superlattices interleaved by heavily doped n+ regions. Room temperature terahertz photon assisted transport, excited by the radiation from the FEL's, supports the notion that the super-superlattice structure supports uniform Stark ladders when subjected to sufficiently strong electric fields to bring matwerialthe super- superlattice into the Bloch oscillator limit. Current work fabricates metal clad ring resonators and pulse excites them with ~ microsecond long pulses or -microsecond long bursts of intense 9GHz radiation.
On the Byzantine Robustness of Clustered Federated Learning (2020)

Federated Learning (FL) is currently the most widely adopted framework for collaborative training of (deep) machine learning models under privacy constraints. Albeit it's popularity, it has been observed that Federated Learning yields suboptimal results if the local clients' data distributions diverge. The recently proposed Clustered Federated Learning Framework addresses this issue, by separating the client population into different groups based on the pairwise cosine similarities between their parameter updates. In this work we investigate the application of CFL to byzantine settings, where a subset of clients behaves unpredictably or tries to disturb the joint training effort in an directed or undirected way. We perform experiments with deep neural networks on common Federated Learning datasets which demonstrate that CFL (without modifications) is able to reliably detect byzantine clients and remove them from training.
Multistage Distributed Amplifier Design (2016)

This chapter presents how the real frequency technique (RFT) is used in the design of multistage distributed amplifiers. The equalizers are made of transmission lines. The chapter introduces a new variable and formalism better suited for the distributed medium. The modified RFT is able to optimize and synthesize the transmission lines. The chapter provides a method for optimizing the multistage amplifier noise figure. It gives a technique to solve the problem of too high or too low characteristic impedance requirements for the microstrip realizations. The chapter provides a possible transistor bias circuit and shows how it can be used during the optimization process to provide more accurate results. It concludes with realizations of a 1.15-1.5 GHz, a 2-8 GHz, and a 5.925-6.425 GHz distributed amplifiers. For the distributed amplifiers of the chapter, the error function consists of the transducer gain, the voltage standing wave ratio (VSWR), and the noise figure.
Fixed point probability field for complex occlusion handling (2005)

In this paper, we show that in a multi-camera context, we can effectively handle occlusions in real-time at each frame independently, even when the only available data comes from the binary output of a simple blob detector, and the number of present individuals is a priori unknown. We start from occupancy probability estimates in a top view and rely on a generative model to yield probability images to be compared with the actual input images. We then refine the estimates so that the probability images match the binary input images as well as possible. We demonstrate the quality of our results on several sequences involving complex occlusions.
Imaging the magnetic near-field of light with an aperture probe (Conference Presentation) (2017)

The development of innovative photonic devices and metamaterials with tailor-made functionalities depends critically on our capability to characterize them and understand the underlying light-matter interactions. Thus, imaging all components of the electromagnetic light field with nanoscale resolution is of paramount importance in this area. Nowadays, the electric and the vertical magnetic field components of light can be measured with sub-wavelength resolution. This is achieved by scanning the sample surface with specific probes in a method known as scanning near-field optical microscopy (SNOM). However, within this toolbox, an unambiguous way of visualizing the horizontal magnetic field component has been missing. We have answered this challenge by demonstrating experimentally that a hollow-pyramid circular aperture probe SNOM can directly image the horizontal magnetic field of light in simple plasmonic antennas – rod, disk and ring. These results are also confirmed by numerical simulations, showing that the probe can be approximated, in the first order, by a magnetic point-dipole source. This approximation substantially reduces the simulation time and complexity and facilitates the otherwise controversial interpretation of near-field images. Further, we use the validated technique to study complex plasmonic antennas and to explore new opportunities for their engineering and characterization. The applicability of this methodology is currently being extended beyond plasmonics structures. Thus, the presented hollow-pyramid circular aperture based SNOM approach complements the existing techniques for imaging the different electromagnetic field components, by providing an opportunity to explore the tangential magnetic field of light with sub-wavelength resolution.
LLC resonant converters for PHEV battery chargers (2013)

The load-dependent properties of LLC resonant converter leads to enormous difficulty in regular design of the converter, even when the load characteristic is usually assumed to be passive for the design simplification. For a battery charger, the output voltage requirement is quite different and is more challenging compared with the passive load. In this paper, an optimal design methodology for LLC resonant converter is presented and verified in a 400V/4kW charger for plug in hybrid electric vehicle (PHEV) applications with peak efficiency of 97%.