gebhart/patrepeval huggingface dataset:
A Phase II Randomized Study of CDX-1401, a Dendritic Cell Targeting NY-ESO-1 Vaccine, in Patients with Malignant Melanoma Pre-Treated with Recombinant CDX-301, a Recombinant Human Flt3 Ligand. (2016)

9589 Background: Patients (pts) with high-risk melanoma have a 20-60% recurrence rate with 5-year OS between 45% and 70%. The adjuvant setting is an opportunity to test prevention vaccines that may have efficacy against disease recurrence. We evaluated CDX301, a recombinant human Flt3 ligand (Flt3L), plus vaccination with CDX1401, a fusion protein consisting of human monoclonal IgG1 antibody targeting the dendritic cell (DC) receptor DEC-205 linked to the NY-ESO-1 tumor antigen, in a phase II, open-label, multicenter, randomized study of subjects with resected melanoma, to determine whether immune responses to NY-ESO-1 elicited by vaccination with CDX1401 + poly-ICLC are substantially increased by prior expansion of circulating DC with Flt3L therapy. Methods: 60 pts with resected melanoma were randomized to two cohorts: Cohort 1 received CDX301 pretreatment (25 ug/kg SC x 10 days) in 2 of 4 monthly cycles of vaccination with CDX1401 (1mg IC) + poly-ICLC (2mg SC, days 1 and 2). Cohort 2 received 4 monthly cycles of vaccine with CDX1401 and poly-ICLC without prior CDX301. We also assessed immunogenicity to other melanoma-associated antigens and memory viral responses, character of PBMC subsets, and safety, tolerability and clinical efficacy of the regimens. Results: Both treatments were well tolerated with grade 1-2 AEs of chills, injection site erythema and pain, fever and myalgias most common. Disease recurred in 8 of 60 pts. Two of the 8 pts progressed prior to completing 4 cycles of treatment. Preliminary analyses show substantial (between ~15- to ~200-fold) increases of PBMC innate immune cells (DC, monocytes and NK cells) in subjects from cohort 1 vs cohort 2. Further, there was development of higher anti-NY-ESO-1 antibody titers in cohort 1 vs cohort 2. Comparative immune cell gene expression profiling of PBMC are consistent with these differences. Finally, significant NY-ESO-1 specific immune T cell responses were observed and differences between cohorts are being analyzed. Data from all 60 patients will be presented. Conclusions: DC mobilization with Flt3L is safe and may enhance responses to DC targeted vaccines. Clinical trial information: NCT02129075.
New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing (2012)

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.
Supplementary Figures 1-2, Tables 1-2 from Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 Gene Fusions in Prostate Cancer (2023)

Supplementary Figures 1-2, Tables 1-2 from Characterization of TMPRSS2:ETV5 and SLC45A3:ETV5 Gene Fusions in Prostate Cancer
Performance Evaluation of B5G Moving Networks with Spatial Consistency and Random Blockages (2021)

Moving networks is an emerging paradigm for next-generation communication networks that envisage a technology that could support moving vehicular user equipment (VUE) with high data-rates over a reliable connection under varied mobility scenarios such as high-speed trains, buses on the freeway, etc. However, while operating at mmWave frequencies, the direct base station (BS) to the VUE (BS-to-VUE) link is adversely impacted by penetration losses and frequent link outages. Link outages are caused primarily due to extremely poor Non-Line-of-Sight (NLOS) channel conditions at mmWave frequencies. To address this problem, a novel architecture has been proposed in literature where a vehicular moving-relay (MR) is introduced that serves the VUE via access link while the backhaul to the MR is provided by a BS. In this paper, we exhaustively analyze and numerically quantify the link fragility and outage for spatially consistent channel realizations at 28 and 73 GHz for links between the BS-to-VUE, BS-to-MR, and MR-to-VUE. Furthermore, in this study, we also capture the impact of frequent transitions among LOS and NLOS conditions, human blockage events, and penetration losses. The simulation results reveal that i) the direct link between the BS and VUE would be extremely fragile with link-outage probabilities 17% and 59.5% compared to the relay-aided link with link-outage probabilities 1.1 and 2% for 28 GHz and 73 GHz respectively and that ii) the BS-to-VUE link would be impacted severely by human blockages compared to relay aided links where only the last hop MR-to-VUE link is impacted by human blockages but negligibly due to its relatively short range. Lastly, we have determined closed-form analytical expressions to estimate the link-outage probability of the BS-to-MR link.
Cell–biomaterial interactions (2013)

This succinct textbook gives students the perfect introduction to the world of biomaterials, linking the fundamental properties of metals, polymers, ceramics and natural biomaterials to the unique advantages and limitations surrounding their biomedical applications. Clinical concerns such as sterilization, surface modification, cell-biomaterial interactions, drug delivery systems and tissue engineering are discussed in detail, giving students practical insight into the real-world challenges associated with biomaterials engineering; key definitions, equations and concepts are concisely summarised alongside the text, allowing students to quickly and easily identify the most important information; and bringing together elements from across the book, the final chapter discusses modern commercial implants, challenging students to consider future industrial possibilities. Concise enough to be taught in a single semester, and requiring only a basic understanding of biology, this balanced and accessible textbook is the ideal introduction to biomaterials for students of engineering and materials science.
Recent therapeutic approaches to cystathionine beta‐synthase‐deficient homocystinuria (2022)

Cystathionine beta-synthase (CBS)-deficient homocystinuria (HCU) is the most common inborn error of sulfur amino acid metabolism. The pyridoxine non-responsive form of the disease manifests itself by massively increasing plasma and tissue concentrations of homocysteine, a toxic intermediate of methionine metabolism that is thought to be the major cause of clinical complications including skeletal deformities, connective tissue defects, thromboembolism and cognitive impairment. The current standard of care involves significant dietary interventions that, despite being effective, often adversely affect quality of life of HCU patients, leading to poor adherence to therapy and inadequate biochemical control with clinical complications. In recent years, the unmet need for better therapeutic options has resulted in development of novel enzyme and gene therapies and exploration of pharmacological approaches to rescue CBS folding defects caused by missense pathogenic mutations. Here, we review scientific evidence and current state of affairs in development of recent approaches to treat HCU.
Spiking Sparse Recovery With Non-Convex Penalties (2022)

Sparse recovery (SR) based on spiking neural networks has been shown to be computationally efficient with ultra-low power consumption. However, existing spiking-based sparse recovery (SSR) algorithms are designed for the convex <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\ell _{1}$</tex-math></inline-formula>-norm regularized SR problem, which often underestimates the true solution. This paper proposes an adaptive version of SSR, <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i.e.</i>, A-SSR, to optimize a class of non-convex regularized SR problems and analyze its global asymptotic convergence. The superiority of A-SSR is validated with synthetic simulations and real applications, including image reconstruction and face recognition. Furthermore, it is shown that the proposed A-SSR essentially improves the recovery accuracy by avoiding systematic underestimation and obtains over 4 dB PSNR improvement in image reconstruction quality and around 5% improvement in recognition confidence. At the same time, the proposed A-SSR maintains energy efficiency in hardware implementation. When implemented on the neuromorphic Loihi chip, our method consumes only about 1% of the power of the iterative solver FISTA, enabling applications under energy-constrained scenarios.
3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures (2006)

The acquisition speed of current FD-OCT (Fourier Domain - Optical Coherence Tomography) instruments allows rapid screening of three-dimensional (3D) volumes of human retinas in clinical settings. To take advantage of this ability requires software used by physicians to be capable of displaying and accessing volumetric data as well as supporting post processing in order to access important quantitative information such as thickness maps and segmented volumes. We describe our clinical FD-OCT system used to acquire 3D data from the human retina over the macula and optic nerve head. B-scans are registered to remove motion artifacts and post-processed with customized 3D visualization and analysis software. Our analysis software includes standard 3D visualization techniques along with a machine learning <i>support vector machine</i> (SVM) algorithm that allows a user to semi-automatically segment different retinal structures and layers. Our program makes possible measurements of the retinal layer thickness as well as volumes of structures of interest, despite the presence of noise and structural deformations associated with retinal pathology. Our software has been tested successfully in clinical settings for its efficacy in assessing 3D retinal structures in healthy as well as diseased cases. Our tool facilitates diagnosis and treatment monitoring of retinal diseases.
Dispersion-free VAD single-mode fibers in the 15-μm wavelength region (1983)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text T. Miya, F. Hanawa, K. Chida, and Y. Ohmori, "Dispersion-free VAD single-mode fibers in the 1.5-μm wavelength region," Appl. Opt. 22, 372-373 (1983) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Machine Learning to Detect Alzheimer’s Disease from Circulating Non-Coding RNAs (2019)

Blood-borne small non-coding (sncRNAs) are among the prominent candidates for blood-based diagnostic tests. Often, high-throughput approaches are applied to discover biomarker signatures. These have to be validated in larger cohorts and evaluated by adequate statistical learning approaches. Previously, we published high-throughput sequencing based microRNA (miRNA) signatures in Alzheimer's disease (AD) patients in the United States (US) and Germany. Here, we determined abundance levels of 21 known circulating miRNAs in 465 individuals encompassing AD patients and controls by RT-qPCR. We computed models to assess the relation between miRNA expression and phenotypes, gender, age, or disease severity (Mini-Mental State Examination; MMSE). Of the 21 miRNAs, expression levels of 20 miRNAs were consistently de-regulated in the US and German cohorts. 18 miRNAs were significantly correlated with neurodegeneration (Benjamini-Hochberg adjusted P < 0.05) with highest significance for miR-532-5p (Benjamini-Hochberg adjusted P = 4.8 × 10<sup>-30</sup>). Machine learning models reached an area under the curve (AUC) value of 87.6% in differentiating AD patients from controls. Further, ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted P = 0.0002). Interestingly, the miRNAs with lower abundance in AD were enriched in monocytes and T-helper cells, while those up-regulated in AD were enriched in serum, exosomes, cytotoxic t-cells, and B-cells. Our study represents the next important step in translational research for a miRNA-based AD test.
Close Links between Cold Shock Proteins and Cancer (2023)

Nine of the ten papers published in this Special Issue explore various aspects of the multifunctional protein Y-box binding protein-1 (YB-1) and its role in cancer [...].
Dynamic Response of Battery Tabs Under Ultrasonic Welding (2013)

Ultrasonic metal welding (USMW) for battery tabs must be performed with 100% reliability in battery pack manufacturing as the failure of a single weld essentially results in a battery that is inoperative or cannot deliver the required power due to the electrical short caused by the failed weld. In ultrasonic metal welding processes, high-frequency ultrasonic energy is used to generate an oscillating shear force (sonotrode force) at the interface between a sonotrode and few metal sheets to produce solid-state bonds between the sheets clamped under a normal force. These forces, which influence the power needed to produce the weld and the weld quality, strongly depend on the mechanical and structural properties of the weld parts and fixtures in addition to various welding process parameters, such as weld frequencies and amplitudes. In this work, the effect of structural vibration of the battery tab on the required sonotrode force during ultrasonic welding is studied by applying a longitudinal vibration model for the battery tab. It is found that the sonotrode force is greatly influenced by the kinetic properties, quantified by the equivalent mass, equivalent stiffness, and equivalent viscous damping, of the battery tab and cell pouch interface. This study provides a fundamental understanding of battery tab dynamics during ultrasonic welding and its effect on weld quality, and thus provides a guideline for design and welding of battery tabs from tab dynamics point of view.
Ultra-broadband omnidirectional-distributed Bragg-reflectors for near-IR to longwave-IR thermophotovoltaic devices (2022)

High performance broadband Distributed Bragg Reflectors (DBRs) have become instrumental in the design of high efficiency Thermophotovoltaic devices, improving efficiency by redirecting parasitic photon loss during conversion towards the device for regenerating power. Broadband Bragg Reflectors designed to reflect in the 3-5 micron, 3-12 micron, and 1-12 micron infrared ranges are of crucial importance in such applications to maximize regeneration efficiency in TPV devices, as most parasitic photons fall in these ranges under typical operating temperatures. Additionally, omnidirectional capabilities further improve regeneration efficiency by absorbing parasitic photons at large angles of incidence. In this work, we present a novel inverse design transfer matrix optimization algorithm for designing variable layer thickness broadband DBRs for arbitrary wavelength ranges and angles of incidence, and we showcase the resulting ultra-high reflection DBRs designed with our algorithm, specifically for the 1-12&mu;m IR range. We demonstrate that our DBRs provide very significant increases in average reflection over the IR ranges of interest as compared to state-of-the-art reflective coatings, even at large angles of incidence, and are also optimized to be considerably thinner than quarter wavelength and other state of the art DBRs with comparable reflection spectra. As such, the DBRs designed with our inverse design algorithm have significant applications in the design of very high efficiency TPV systems, while also being thin enough to embed onto devices or windows, and are also easy to fabricate due to their simple multilayer 1-D structure.
Self‐Immolative Activation of β‐Galactosidase‐Responsive Probes for In Vivo MR Imaging in Mouse Models (2019)

Abstract Our lab has developed a new series of self‐immolative MR agents for the rapid detection of enzyme activity in mouse models expressing β‐galactosidase (β‐gal). We investigated two molecular architectures to create agents that detect β‐gal activity by modulating the coordination of water to Gd III . The first is an intermolecular approach, wherein we designed several structural isomers to maximize coordination of endogenous carbonate ions. The second involves an intramolecular mechanism for q modulation. We incorporated a pendant coordinating carboxylate ligand with a 2, 4, 6, or 8 carbon linker to saturate ligand coordination to the Gd III ion. This renders the agent ineffective. We show that one agent in particular (6‐C pendant carboxylate) is an extremely effective MR reporter for the detection of enzyme activity in a mouse model expressing β‐gal.
Novel simultaneous combination chemical thrombolysis/rheolytic thrombectomy therapy for acute critical limb ischemia: The power‐pulse spray technique (2004)

The novel power-pulse spray (P-PS) technique maximizes and combines the advantages and minimizes the disadvantages of both chemical thrombolysis (CT) and rheolytic thrombectomy (RT). Forty-nine consecutive patients with iliofemoral thrombotic occlusion were treated via P-PS technique. Using a 6 Fr RT catheter, saline prime was exchanged for thrombolytic solution [group 1, 10-20 mg tenecteplase (TNK)/50 cc saline, n = 25; group 2, 1,000,000 urokinase (UK)/50 cc saline, n = 24]. The outflow port was closed, then the catheter was advanced at 1 mm increments while pulsing lytic agent. After 30-min lysis time, RT and definitive treatment of the underlying stenosis were performed. Procedure success was 23/25 (92%) and 22/24 (91.6%) for group 1 and 2, respectively. The mean total procedure time was 72 and 75 min in group 1 and 2, respectively. Thirty-day limb salvage was 91% in both groups. There were no major surgical complications. The P-PS technique is safe and effective using either UK or TNK, offering several potential advantages over monotherapy, including more rapid revascularization, decreases systemic lytic exposure and bleeding complications while facilitating both CT and RT capacity and efficacy.
The inverse barycentric displacement problem (2023)

Abstract In this short paper, we analyze the problem of finding the triangular barycentric coordinates of an interpolated ray hitting a given point. This task, which we term the inverse barycentric displacement problem , is general and useful in geometry processing and computer graphics. Concrete applications of the solution include the construction of displacement maps and texture baking. We derive the set of complete, closed-form solutions and discuss the number and existence of solutions. We close with a discussion of implementation-oriented optimizations and a few example applications.
Osteopontin plays a pivotal role in increasing severity of respiratory syncytial virus infection (2018)

The molecular mechanisms underlying susceptibility to severe respiratory syncytial virus (RSV) infection remain poorly understood. Herein, we report on the role of osteopontin (OPN) in regulation of RSV infection in human epithelial cells and how interleukin-1 beta (IL-1β), a cytokine secreted soon after RSV infection, when persistently expressed can induce OPN expression leading to increased viral infection. We first compared OPN expression in two human epithelial cell lines: HEK-293 and HEp-2. In contrast to HEp-2, HEK-293 expresses low levels of pro-caspase-1 resulting in decreased IL-1β expression in response to RSV infection. We found a correlation between low IL-1β levels and a delay in induction of OPN expression in RSV-infected HEK-293 cells compared to HEp-2. This phenomenon could partially explain the high susceptibility of HEp-2 cells to RSV infection versus the moderate susceptibility of HEK-293 cells. Also, HEK-293 cells expressing low levels of pro-caspase-1 exhibit decreased IL-1β expression and delayed OPN expression in response to RSV infection. HEK-293 cells incubated with human rIL-1β showed a dose-dependent increase in OPN expression upon RSV infection. Also, incubation with rOPN increased RSV viral load. Moreover, HEp-2 cells or mice infected with a mucogenic RSV strain RSV-L19F showed elevated levels of OPN in contrast to mice infected with the laboratory RSV strain rA2. This correlated with elevated levels of OPN following infection with RSV-L19F compared to rA2. Together, these results demonstrate that increased OPN expression is regulated in part by IL-1β, and the interplay between IL-1β and OPN signaling may play a pivotal role in the spread of RSV infection.
A new outflow boundary condition (1992)

Abstract Boundary conditions come from Nature. Therefore these conditions exist at natural boundaries. Often, owing to limitations in computing power and means, large domains are truncated and confined between artificial synthetic boundaries. Then the required boundary conditions there cannot be provided naturally and there is a need to fabricate them by intuition, experience, asymptotic behaviour and numerical experimentation. In this work several kinds of outflow boundary conditions, including essential, natural and free boundar conditions, are evaluated for two flow and heat transfer model problems. A new outflow boundary condition, called hereafter the free boundary condition , is introduced and tested. This free boundary condition is equivalent to extending the validity of the weak form of the governing equations to the synthetic outflow instead of replacing them there with unknown essential or natural boundary conditions. In the limit of zero Reynolds number the free boundary condition minimizes the energy functional among all possible choices of outflow boundary conditions. A review of results from applications of the same boundary conditions to several other flow situations is also presented and discussed.
Low-temperature vortex dynamics in a high-temperature superconductor (1994)

Magnetic-field gradients in the mixed state of a type-II superconductor are studied using $^{205}\mathrm{Tl}$ nuclear magnetic resonance (NMR) on ${\mathrm{Tl}}_{2}$${\mathrm{Ba}}_{2}$${\mathrm{Ca}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{10+\mathrm{\ensuremath{\delta}}}$. An anomalous peak was observed in the temperature dependence of the transverse relaxation rate at T/${\mathit{T}}_{\mathit{c}}$\ensuremath{\approxeq}0.25. We attribute this behavior to magnetic-field flucutations from vortex dynamics. We interpret this behavior as a crossover of the principal time scale for vortex dynamics with that of the NMR experiment, approximately 100 \ensuremath{\mu}s. The temperature dependence of this time scale is discussed.
ChemInform Abstract: Unnatural β‐L‐Enantiomers of Nucleoside Analogues as Potent Anti‐Hepatitis B Virus Agents. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.