gebhart/patrepeval huggingface dataset:
4-D ultrafast ultrasound imaging: in vivo quantitative imaging of blood flows and tissue viscoelastic properties (2016)

Very high frame rate ultrasound imaging has enabled the development of novel imaging modalities such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative real-time imaging of the intrinsic mechanical properties of tumors, to name a few. We present here the extension of Ultrafast Ultrasound Imaging in three dimensions based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. High contrast and resolution were achieved while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32X32 matrix-array probe. Its capability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3-D Shear-Wave Imaging, 4-D Ultrafast Doppler Imaging, and 4D vector flow imaging. These results demonstrate the potential of 4-D Ultrafast Ultrasound Imaging for the volumetric real-time mapping of stiffness, tissue motion and flow in humans in vivo and promises new clinical quantitative applications of ultrasound with reduced intra- and inter-observer variability.
Certificate Transparency with Privacy (2017)

Abstract Certificate transparency (CT) is an elegant mechanism designed to detect when a certificate authority (CA) has issued a certificate incorrectly. Many CAs now support CT and it is being actively deployed in browsers. However, a number of privacy-related challenges remain. In this paper we propose practical solutions to two issues. First, we develop a mechanism that enables web browsers to audit a CT log without violating user privacy. Second, we extend CT to support non-public subdomains.
Feasibility of laparoscopic liver resection for liver cavernous hemangioma: A single-institutional comparative study (2020)

Laparoscopic liver resection for liver cavernous hemangioma can be safely performed with improved postoperative recovery. However, surgery for liver cavernous hemangioma should be conducted with informed consent of the patients.
Titanium Carbide (Ti3C2Tx) MXene Ornamented with Palladium Nanoparticles for Electrochemical CO Oxidation (2021)

Abstract Titanium carbide (Ti 3 C 2 T x ) MXene possesses various unique physicochemical and catalytic properties. However, the electrochemical CO oxidation performance is not yet addressed experimentally. Herein, Ti 3 C 2 T x (T X =OH, O, and F) ordered and exfoliated two‐dimensional nanosheets ornamented with semi‐spherical palladium nanoparticles (2.5 Wt. %) with an average diameter of (10±1 nm) (denoted as Pd/Ti 3 C 2 T x ) is rationally designed for the electrochemical CO oxidation. The fabrication process is based on the selective chemical etching of Ti 3 AlC 2 and delamination under sonication to form Ti 3 C 2 Tx nanosheets that are used as a substrate and reducing agent for supporting in situ growth of Pd nanoparticles via impregnation with Pd salt. Interestingly, Pd‐free Ti 3 C 2 T x displayed inferior CO oxidation activity, while Pd/Ti 3 C 2 T x enhanced the CO oxidation activity substantially. This is attributed to the combination of outstanding physicochemical properties of Ti 3 C 2 T x and the catalytic merits of Pd nanoparticles.
Immune age and biological age as determinants of vaccine responsiveness among elderly populations: the Human Immunomics Initiative research program (2021)

The Human Immunomics Initiative (HII), a joint project between the Harvard T.H. Chan School of Public Health and the Human Vaccines Project (HVP), focuses on studying immunity and the predictability of immuneresponsiveness to vaccines in aging populations. This paper describes the hypotheses and methodological approaches of this new collaborative initiative. Central to our thinking is the idea that predictors of age-related non-communicable diseases are the same as predictors for infectious diseases like COVID-19 and influenza. Fundamental to our approach is to differentiate between chronological, biological and immune age, and to use existing large-scale population cohorts. The latter provide well-typed phenotypic data on individuals' health status over time, readouts of routine clinical biochemical biomarkers to determine biological age, and bio-banked plasma samples to deep phenotype humoral immune responses as biomarkers of immune age. The first phase of the program involves 1. the exploration of biological age, humoral biomarkers of immune age, and genetics in a large multigenerational cohort, and 2. the subsequent development of models of immunity in relation to health status in a second, prospective cohort of an aging population. In the second phase, vaccine responses and efficacy of licensed COVID-19 vaccines in the presence and absence of influenza-, pneumococcal- and pertussis vaccines routinely offered to elderly, will be studied in older aged participants of prospective population-based cohorts in different geographical locations who will be selected for representing distinct biological and immune ages. The HII research program is aimed at relating vaccine responsiveness to biological and immune age, and identifying aging-related pathways crucial to enhance vaccine effectiveness in aging populations.
Schlafen family member 5 (SLFN5) regulates LAT1-mediated mTOR activation in castration-resistant prostate cancer (2020)

Abstract Androgen-deprivation therapy (ADT) is the standard of care for the treatment of non-resectable prostate cancer (PCa). Despite high treatment efficiency, most patients ultimately develop lethal castration-resistant prostate cancer (CRPC). In this study, we perform a comparative proteomic analysis of three in vivo, androgen receptor (AR)–driven, orthograft models of CRPC. Differential proteomic analysis reveals that distinct molecular mechanisms, including amino acid (AA) and fatty acid (FA) metabolism, are involved in the response to ADT between the different models. Despite this heterogeneity, we identify SLFN5 as an AR-regulated biomarker in CRPC. SLFN5 expression is high in CRPC tumours and correlates with poor patient outcome. In vivo, SLFN5 depletion strongly impairs tumour growth in castrated condition. Mechanistically, SLFN5 interacts with ATF4 and regulates the expression of LAT1, an essential AA transporter. Consequently, SLFN5 depletion in CRPC cells decreases intracellular levels of essential AA and impairs mTORC1 signalling in a LAT1-dependent manner.
A novel role for survivin in erythroblast enucleation (2012)

This study identified a novel role for survivin in erythroblast enucleation through previously unknown protein partners.
Use of AGS-16M8F as a novel antibody drug conjugate (ADC) for treating renal cancers. (2010)

e15014 Background: AGS-16 is a novel transmembrane antigen discovered by Agensys using transcription profiling that is expressed in kidney and other cancers. A fully human IgG2k monoclonal antibody that binds to AGS-16 with high affinity was conjugated to the anti-microtubulin drug monomethyl auristatin F (MMAF) via a noncleavable maleimidocaproyl (mc) linker to yield the antibody drug conjugate, AGS-16M8F. Methods: In vitro studies were performed to evaluate the binding affinity, species cross reactivity and cell cytotoxicity of AGS-16M8F. The pharmacokinetics (PK) and anti-tumor activity of AGS-16M8F was evaluated using multiple well-established patient-derived and cell line models of renal clear cell carcinomas. In addition, the expression of AGS-16 protein in patient kidney cancer specimens was confirmed using IHC analysis of individual specimens and tissue microarrays. Results: AGS-16M8F bound with high affinity (Kd = 0.3 nM) to both human and cynomolgus monkey AGS-16. Following cell surface binding, AGS-16M8F was internalized and trafficked to lysosomes where catabolism resulted in the release of active drug metabolite. AGS-16M8F mediated potent cell cytotoxicity in vitro and led to significant and prolonged growth inhibition or complete eradication of multiple, large established renal cancer xenograft models, including those grown orthotopically. Results from pharmacokinetic analyses demonstrated that AGS-16M8F was stable in vivo. Finally, IHC analysis confirmed that AGS-16 was highly expressed in more than 80% of renal cancers including both clear cell and papillary carcinomas. Conclusions: When considered together these data indicate that AGS-16M8F is a promising therapeutic ADC for the treatment of renal and other AGS-16 expressing cancers. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Agensys Inc.
Pattern fidelity in nanoimprinted films using critical dimension small angle x-ray scattering (2006)

The primary measure of process quality in nanoimprint lithography (NIL) is the fidelity of pattern transfer, comparing the dimensions of the imprinted pattern to those of the mold. Routine production of nanoscale patterns will require new metrologies capable of nondestructive dimensional measurements of both the mold and the pattern with subnanometer precision. In this work, a rapid, nondestructive technique termed critical dimension small angle x-ray scattering (CD-SAXS) is used to measure the cross sectional shape of both a pattern master, or mold, and the resulting imprinted films. CD-SAXS data are used to extract periodicity as well as pattern height, width, and sidewall angles. Films of varying materials are molded by thermal embossed NIL at temperatures both near and far from the bulk glass transition (TG). The polymer systems include a photoresist and two homopolymers. Our results indicate that molding at low temperatures (T-TG<40°C) produces small-aspect-ratio patterns that maintain periodicity to within a single nanometer, but feature large sidewall angles. While the observed pattern height does not reach that of the mold until very large imprinting temperatures (T-TG70°C), the pattern width of the mold is accurately transferred for T-TG>30°C.
Morphometry and Lymph Dynamics of Swine Thoracic Duct (2020)

<b><i>Background:</i></b> The goal of this study was to characterize the thoracic duct (TD) both morphologically and hemodynamically. <b><i>Methods and Results:</i></b> The lymphatic flow and pressure gradient from the cisterna chyli (CC) to the lymphovenous junction were measured in anesthetized swine (<i>n</i> = 9). After the animals were euthanized, the TD were harvested for histomorphometric analyses in which three samples were perfused with 9% gelatin to obtain the morphometry of the TD valve in both the open and closed configuration. Spectral analyses were performed. An afferent lymphatic vessel of the CC was accessed and cannulated after the animal was euthanized for casting (<i>n</i> = 3) to obtain morphometric data. The <i>in vivo</i> flow rate was 0.7 ± 0.49 mL/minute. Spectral analysis (Fast Fourier Transformation) showed correlation coefficients of 0.858 ± 0.063 and 0.586 ± 0.112 (<i>p</i> < 0.05) for the TD and JVPs, respectively. The average pressure gradient was 8.1 mmHg along the TD. The length of the TD was 35.6 ± 2.2 cm. The maximal width of the CC ranged from 11.4 to 15 mm. The diameter of the TD varied irregularly from 2 to 4.3 mm. The geometry of the TD leaflets was determined to have an area of 1.99 ± 0.53 mm<sup>2</sup>, a leaflet length of 3.26 ± 0.86 mm, a packet depth of 0.66 ± 0.19 mm, and a wall length of 5.46 ± 2.16 mm. The TD media thickness was ∼7 ± 3 μm. The number of valves ranged from 9 to 13 in the full length of the TD. <b><i>Conclusions:</i></b> A relatively constant pressure gradient in the swine TD drives lymph flow from the CC to the jugular vein. The TD is a thin-walled vessel with valves that prevent reflux of lymph flow. This study of morphometric and lymphatic dynamics is important for interventionalists to understand the anatomy and physiology of the TD to design new diagnostic, interventional procedures, and devices.
Mobility Performance of Macrocell-Assisted Small Cells in Manhattan Model (2014)

Macrocell-assisted small cell concepts, such as "Phantom cell concept" and "soft cell concept", have been proposed previously for interference management, flexible cell planning, and energy saving in dense small cell deployments. These concepts require macrocell involvement to improve links between small cell and user. Since target implementation areas of the concepts are crowded urban areas (e.g. downtown New York City) to satisfy the data need, more realistic simulations are needed to be implemented compared to conventional evaluations. In this paper, as a new approach to urban area LTE simulations, Manhattan grid layout is presented and implemented for mobility performance of Macrocell-assisted small Cell concept. The results show that the macrocell involvement to improve mobility performance gives a great advantage compared to using the conventional mobility solution for dense small cell deployments.
Multiparty Non-Interactive Key Exchange and More From Isogenies on Elliptic Curves (2020)

We describe a framework for constructing an efficient non-interactive key exchange (NIKE) protocol for n parties for any n ≥ 2. Our approach is based on the problem of computing isogenies between isogenous elliptic curves, which is believed to be difficult. We do not obtain a working protocol because of a missing step that is currently an open mathematical problem. What we need to complete our protocol is an efficient algorithm that takes as input an abelian variety presented as a product of isogenous elliptic curves, and outputs an isomorphism invariant of the abelian variety.
OP023 A phase 3b open-label multicentre study (VERSIFY) of the efficacy of vedolizumab on endoscopic healing in moderately to severely active Crohn’s disease (CD) (2018)

Vedolizumab (VDZ) is a gut-selective humanised immunoglobulin G1 monoclonal antibody that prevents the trafficking of T-lymphocytes into the gastrointestinal submucosa by antagonising the interaction of alpha4beta7 integrin with its ligand, mucosal addressin cell adhesion molecule 1 (MAdCAM-1).1 VDZ has demonstrated statistically significant differences in clinical remission from placebo in patients (patients) with moderately to severely active Crohn’s disease (CD),2 but endoscopic healing was not previously assessed. The present study evaluated the effect of VDZ on endoscopic remission and healing in patients with CD. Patients with moderately to severely active CD (≥3 months; CD Activity Index [CDAI] 220-450; Simple Endoscopic Score for CD [SES-CD] ≥7; ≥1 mucosal ulceration on centrally read endoscopy) who had previously experienced treatment failure with corticosteroids, immunomodulators, and/or at least one tumour necrosis factor-alpha (TNF) antagonist were enrolled. Patients received VDZ 300 mg intravenously at weeks 0, 2, 6, and then every 8 weeks for 26 weeks, followed by a 26-week treatment extension period. The primary endpoint was endoscopic remission (SES-CD ≤4) at week 26, assessed by centrally read ileocolonoscopy. Key secondary endpoints included endoscopic response (SES-CD ≥50% reduction from baseline) and complete endoscopic healing (absence of ulcerations) at week 26. Subgroup analyses stratified by TNF antagonist exposure status were performed for all endpoints and by disease severity for endoscopic remission only. Of the 101 patients enrolled, 55% had previously failed at least one TNF antagonist (TNF-F), and 46% were categorised as having severe endoscopic activity at entry (SES-CD score of >15). Endoscopic remission rates at week 26 were 12% overall, 20% in TNF antagonist naïve (TNF-N), and 6% in TNF-F patients, respectively (Table 1). Endoscopic remission at week 26 was achieved in 17% of patients with moderate endoscopic activity (SES-CD score of 7–15) compared with 7% of patients with severe disease. Endoscopic response and complete endoscopic healing rates at week 26 are shown in Table 1. Endoscopic outcomes at week 26 by TNF antagonist status. VDZ demonstrated the ability to induce endoscopic remission and healing in a refractory population. TNF-N patients were more likely to achieve endoscopic remission and healing than those with previous treatment failure to a TNF antagonist. 1. Soler D, et al. The binding specificity and selective antagonism of vedolizumab, an anti-α4β7 integrin therapeutic antibody in development for inflammatory bowel diseases. J Pharmacol Exp Ther, 2009:330;864-–75, 330. 2. Sandborn WJ, et al. Vedolizumab as induction and maintenance therapy for Crohn’s disease. N Engl J Med, 2013;369:711–21.
Synchronous frequency comparison of optical lattice clocks to approach the quantum limit (2011)

We demonstrate a synchronous frequency comparison of two optical lattice clocks operated using <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">87</sup> Sr and <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">88</sup> Sr atoms, whose Allan standard deviation achieved 1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-17</sup> in an averaging time of 1,600 s by cancelling out the Dick effect to approach the QPN limit. The scheme manifests an advantage of using a large number N ≈ 2,000 of atoms in optical clocks and paves the way to investigate clocks' inherent uncertainties and relativistic geodesy on a time scale of tens of minutes.
A combined surface and volumetric approach for registration of patient specific models into left atrial cardiac ablation procedures (2009)

Accurate visualization and targeting of specific anatomic locations are key components for successful treatment in catheter based cardiac ablation therapy. In order to augment visualization tools such as bi-plane fluoroscopy and real-time ultrasound, recent work has focussed on registering detailed, patient-specific models into the procedure. Surface based techniques are a popular approach, however, challenges include sensitivity to both the number and as well as locations of selected surface points, thereby making registration accuracy dependent on operator experience as well as patient anatomy. In this work, we propose a new technique for registering preoperative models into patient space by combining a surface based method with a volumetric based approach. The volumetric approach utilizes points from the continuously tracked catheter which is sampled at a rate of five times per second. The technique is tested using data from a canine experiment with five ground truth fiducial markers. The combined registration technique has smaller mean errors for all fiducial markers as compared to using a surface based technique alone. The combined surface and volumetric approach is also more robust to surface point selection, thereby decreasing the sensitivity of point selection on the registration result.
Built‐in Nanostructures in Transparent Oxides for Novel Photonic and Electronic Functions Materials (2009)

This chapter reviews distinct photonic/electronic properties originating from built-in nanostructures in transparent oxide-based materials, emphasizing potential of nanostructures hidden in crystal structure. Materials focused on are oxychalcogenides LaCuOCh (Ch = chalcogen ion) and homologous oxides InGa03 (Zn0) m (m = integer) having naturally formed multi-quantum well structures and 12Ca0-7Al203 (C12A7) with a unique nanoporous structure. Novel functions and devices arising from the built-in nanostructure are: (1) modulation doping of positive holes and room-temperature stable exciton in LaCuOCh, (2) high-performance transparent field-effect transistor fabricated in InGa03(Zn0)5 epitaxial thin films, and (3) conversion of insulator to persistent electronic conductor by carrier doping in 12Ca0-7Al203 (C12A7). These examples demonstrate realization of excellent photonic and electronic features in oxide-based materials applicable for emerging devices. Present attainments open a new frontier of material science, paving a way to “invisible oxide electronics.” UV-LED (light source, transparent PN-junction and transparent conductive line) are key components for invisible circuits.
Software for computer modeling of laser-pulse propagation through an optical system with nonlinear optical elements (1998)

We developed a set of computer codes organized in a software package that allows us to model high-energy laser pulse propagation through bulk nonlinear optical media. Nonlinearities included in the model are two-photon absorption, the electronic Kerr effect, excited-state and free-carrier absorption along with the associated electrostrictive and photo-acoustic refractive index change. The propagation of CW beams, nsec/psec pulses and picosecond pulse trains is determined for various spatial distributions of the input beam. We used a cylindrically symmetric spatial geometry typical for laser outputs to reduce the CPU and memory requirements making modeling a real-time task on PC's, even for significant propagation paths (many Rayleigh ranges). The validity of the numerical outputs was tested against known results for a large range of parameters. In particular the codes are being used to investigate and design optical limiting devices with single or multi-element geometries, as well as limiters using stepped or graded density of nonlinear material. The linear propagation module integrated with the nonlinear beam propagation method (BPM) codes allow the simulation of typical experiments such as Z-scan (sample position changes in a focused beam) and limiting experiments (different input energy values).
Self-trapping of Necklace Beams in Self-Focusing Kerr Media (1999)

Solitons of the cubic Nonlinear Schrodinger Equation (NLSE) are probably the most studied solitons in nature. One of the reasons is the mathematical elegance and simplicity of this equation. But another more important reason is the vast number of physical systems that can be described by this equation.
Data Invariants: On Trust in Data-Driven Systems. (2020)

The reliability and proper function of data-driven applications hinge on the data's continued conformance to the applications' initial design. When data deviates from this initial profile, system behavior becomes unpredictable. Data profiling techniques such as functional dependencies and denial constraints encode patterns in the data that can be used to detect deviations. But traditional methods typically focus on exact constraints and categorical attributes, and are ill-suited for tasks such as determining whether the prediction of a machine learning system can be trusted or for quantifying data drift. In this paper, we introduce data invariants, a new data-profiling primitive that models arithmetic relationships involving multiple numerical attributes within a (noisy) dataset and which complements the existing data-profiling techniques. We propose a quantitative semantics to measure the degree of violation of a data invariant, and establish that strong data invariants can be constructed from observations with low variance on the given dataset. A concrete instance of this principle gives the surprising result that low-variance components of a principal component analysis (PCA), which are usually discarded, generate better invariants than the high-variance components. We demonstrate the value of data invariants on two applications: trusted machine learning and data drift. We empirically show that data invariants can (1) reliably detect tuples on which the prediction of a machine-learned model should not be trusted, and (2) quantify data drift more accurately than the state-of-the-art methods. Additionally, we show four case studies where an intervention-centric explanation tool uses data invariants to explain causes for tuple non-conformance.