gebhart/patrepeval huggingface dataset:
Partial Reconstitution of a Replication-Competent Retrovirus in Helper Cells with Partial Overlaps Between Vector and Helper Cell Genomes (1996)

Contamination of retroviral vector preparations with replication-competent retroviruses is a major safety concern in human gene therapy. These can arise by recombination between retroviral vectors and packaging cell sequences. Recently, we constructed new packaging lines, derived from spleen necrosis virus (SNV) that do not contain overlapping regions of homology between these two components (DSH134G and DSH29B cells). These cell lines were tested for the presence of recombination products and replication-competent viruses in comparison to a similar packaging line (DSN) that contains a partial overlap between vector and viral protein coding regions. No recombination products were detected in DSH cells. However, we found that recombination had occurred in DSN cells, partially reconstituting a provirus-like structure that was capable of being spread, although inefficiently, through an infected cell culture. Our data indicate that even small regions of sequence homology eventually allow homologous recombination between vector and helper cell genomes.
A phase I first-in-human study of REGN910 (SAR307746), a fully human and selective angiopoietin-2 (Ang2) monoclonal antibody (MAb), in patients with advanced solid tumor malignancies. (2013)

2517 Background: REGN910 is a selective, fully human Ang2 MAb that potently blocks signaling through the Tie2 receptor regulating tumor angiogenesis and growth. In multiple mouse xenograft models of human solid tumors, REGN910 inhibits tumor growth. Methods: This first-in-human phase I study (3+3 design) explored the safety, recommended phase II dose (RP2D), pharmacokinetics (PK), pharmacodynamics (PD) and antitumor activity of REGN910 as a single agent. REGN910 was given IV at escalating doses. At RP2D, expansion cohorts were initiated to confirm safety and assess anti-tumor activity in about 20 patients (pts). Results: 37 pts [17M/20F; median age 57 (range 22-82); ECOG PS 0(9)/1(28)] were enrolled. Twenty-three (23) pts were enrolled in the dose escalation cohorts. No DLTs were reported, and a MTD was not reached. Most common G1/2 treatment-related adverse events (TRAEs) were fatigue 7(19%), peripheral edema 6(17%), diarrhea 5(14%), abdominal distension 4(11%), and decreased appetite 4(11%). There were no ≥ Grade 3 TRAEs. A confirmed sustained PR (16 wks) was observed in 1 pt with adrenocortical cancer treated at 1 mg/kg. SD (range 6.9-46.8 wks) was reported for 17 of 32 (53%) pts evaluable for efficacy. Fourteen pts received treatment &gt;16 wks. One pt with thyroid cancer had SD for 46 wks, and 1 pt with hepatocellular cancer had SD for 16 wks with ≥50% decline in alpha-fetoprotein. Across all dose levels, REGN910 pharmacokinetics appeared linear and dose-proportional. The PK profile was characterized by an initial distribution and a single mono-exponential elimination phase. Total circulating serum Ang2 levels appeared saturated following treatment in all cohorts, indicating systemic target engagement at all doses tested. Conclusions: Administration of REGN910 in patients with advanced cancer is well tolerated, with generally mild and moderate TRAEs. Dose escalation is completed, and enrollment to the expansion cohorts continues. The safety profile supports combination with chemotherapy and/or other anti-angiogenic agents. Clinical trial information: NCT01271972.
Risk of Cardiovascular Disease in a Cohort of HIV-Infected Adults: A Study Using Carotid Intima-Media Thickness and Coronary Artery Calcium Score (2006)

Our participants had more abnormal surrogate markers than expected at a relatively young age, but those were not associated with use of highly active antiretroviral therapy or protease inhibitors. At present, the positive associations were primarily with traditional and novel cardiovascular risk factors. Some HIV-specific (not treatment-specific) factors were observed; they may become more evident with prolonged HIV infection and treatment.
A targeted secretome profiling by multiplexed immunoassay revealed that secreted chemokine ligand 2 (MCP‐1/CCL2) affects neural differentiation in mesencephalic neural progenitor cells (2014)

Chemokines and cytokines, primarily known for their roles in the immune and inflammatory response, have also been identified as key components of the neurogenic niche where they are involved in the modulation of neural stem cell proliferation and differentiation. However, a complete understanding of the functional role played in neural differentiation and a comprehensive profiling of these secreted molecules are lacking. By exploiting the multiplexing capability of magnetic bead-based immunoassays, we have investigated the changes of the expression levels of a set of chemokines and cytokines released from the pluripotent neural cell line mes-c-myc A1 following its differentiation from a proliferating phenotype (A1P) toward a neural (A1D) phenotype. We found a subset of molecules exclusively released from A1P, whereas others were differentially detected in A1P and A1D conditioned media. Among them, we identified monocyte chemoattractant protein-1/chemokine ligand 2 (MCP-1/CCL2) as a proneurogenic factor able to affect neuronal differentiation of A1 cells as well as of neuroblasts from primary cultures and to induce the elongation and/or formation of neuritic processes. Altogether, data are suggestive of a main role played by the CCL2/CCR2 signaling pathway and in general of the network of secreted cytokines/chemokines in the differentiation of neural progenitor cells toward a neural fate.
Combined crystal plasticity and grain boundary modeling of creep in ferritic-martensitic steels: II. The effect of stress and temperature on engineering and microstructural properties (2019)

Abstract This paper describes a series of physically-based crystal plasticity finite element method (CPFEM) simulations of long-term creep and creep rupture of Grade 91 steel. It is Part 2 of a two part series of papers. Part 1 describes the simulation framework; this part focuses on specific simulations and on how the predicted long-term creep properties of Grade 91 compare to the assumptions used in current high temperature design practices. This work extends the model developed in Part 1 to look at creep properties at different temperatures, principal stresses, and multiaxial stress states. The simulations show that empirically extrapolating creep rupture stresses from short-term experimental data may substantially over predict the actual long-term creep properties of Grade 91. Additionally, the CPFEM calculations predict a transition from notch strengthening creep behavior for high values of maximum principal stress and moderate notch severity to notch weakening behavior for low principal stresses and more severe notches. The latter regime better categorizes conditions in engineering components designed for long term elevated temperature use, which implies Grade 91 may be a notch weakening material in actual service. This would have a significant impact on high temperature design practices, though confirmatory test data on long-life, low stress notched specimens is difficult to obtain. Finally, one advantage of the physically-based modeling approach adopted here is that the simulation results also elucidate the microstructural mechanisms causing the macroscopic trends in engineering properties predicted by the simulations. This paper shows that the detailed micromechanical mechanisms predicted by the CPFEM simulations can be abstracted with a simple micromechanical model that can be used to both explain the detailed results and make improved predictions of engineering properties from experimental data.
Teaching Professionalism in Orthopaedic Surgery Residency Programs (2012)

Zuckerman, Joseph D. MD; Holder, Justin P. BA; Mercuri, John J. BS, MA; Phillips, Donna P. MD; Egol, Kenneth A. MD Author Information
Reproducibility of parameters of postocclusive reactive hyperemia measured by diffuse optical tomography (2016)

The application of near-infrared spectroscopy (NIRS) to assess microvascular function has shown promising results. An important limitation when using a single source-detector pair, however, is the lack of depth sensitivity. Diffuse optical tomography (DOT) overcomes this limitation using an array of sources and detectors that allow the reconstruction of volumetric hemodynamic changes. This study compares the key parameters of postocclusive reactive hyperemia measured in the forearm using standard NIRS and DOT. We show that while the mean parameter values are similar for the two techniques, DOT achieves much better reproducibility, as measured by the intraclass correlation coefficient (ICC). We show that DOT achieves high reproducibility for muscle oxygen consumption (ICC: 0.99), time to maximal HbO2 (ICC: 0.94), maximal HbO2 (ICC: 0.99), and time to maximal HbT (ICC: 0.99). Absolute reproducibility as measured by the standard error of measurement is consistently smaller and close to zero (ideal value) across all parameters measured by DOT compared to NIRS. We conclude that DOT provides a more robust characterization of the reactive hyperemic response and show how the availability of volumetric hemodynamic changes allows the identification of areas of temporal consistency, which could help characterize more precisely the microvasculature.
Energy balanced routing for latency minimized wireless sensor networks (2018)

We present a communication and routing protocol to balance energy consumption among wireless sensor and actuator nodes under the constraint of minimizing end-to-end latency. Minimized and nearly deterministic end-to-end latency allows centralized real time data recording and actuator control. Moreover, defined latency improves security and safety mechanisms to come closer to the trustworthiness of a cable while realizing the advantages of wireless networks. Battery powered or energy harvesting wireless nodes are inevitable to avoid power lines and therefore, we cope with limited energy budgets. In order to balance the communication load among sufficiently supplied nodes, the energy budget is part of the routing path metric. We show that the time domain multiple access scheme is crucial to enable defined latency and improve energy efficiency by avoiding collisions. If the energy distribution among the nodes is known, this novel protocol allows to calculate latency and round-trip time in advance. An asymmetric timing scheme can limit multi-hop latency for either upstream or downstream communication by one superframes (SF) duration. The presented ruleset is able to reconfigure the routing focused on energy constraints of involved nodes.
Evolutionary Algorithm for Noun Phrase Detection in Natural Language Processing (2005)

Noun phrases of a document usually are the main information bearers. Thus, the detection of these units is crucial in many applications related to information retrieval, such as collecting relevant documents by search engines according to a user query, text summarizing, etc. We present an evolutionary algorithm for obtaining a probabilistic finite-state automaton, able to recognize valid noun phrases defined as a sequence of lexical categories. This approach is highly flexible in the sense that the automaton is able to recognize noun phrases similar enough to the ones given by the inferred noun phrase grammar. This flexibility can be allowed thanks to the very accurate set of probabilities provided by the evolutionary algorithm. It works with both, positive and negative examples of the language, thus improving the system coverage, while maintaining its precision. Experimental results show a clear improvement of the performance with respect to others systems
<title>Miniature optical-fiber-based spectrometer employing a compact tandem fiber probe</title> (1993)

We present a novel miniature spectrometer in combination with a compact tandem optical fiber DIP probe. The system is designed to use single strand fibers to obtain high resolution spectral information for the determination of absorbance, transmission and scattering in liquids, or for measuring pH or toxic metal concentrations using immobilized indicator materials. The performance of the CCD array spectrometer in terms of spectral resolution, stray light, noise and dynamic range is shown to equal typical non-fiber analytical instruments. The mode containment optical design of the spectrometer results in excellent light throughput, and fibers as small as 50 micrometers can be used for routine applications. Tandem fiber probes were made by cutting and polishing the distal tips of two parallel fibers at a 45 degree(s) angle. A description of the tandem fiber probe (DIP probe) is presented which includes the probe's construction. Suggestions are made in geometric variations to adapt the probe to perform in other sampling tasks. Optical coupling efficiencies and refractive index effects are evaluated. Methods to construct ruggedized extension or field optical fiber cables are also discussed.
Physiology and behavior of pigs before and after castration: effects of two topical anesthetics (2010)

Surgical castration of male piglets is a common management practice conducted on commercial swine farms to prevent the occurrence of boar taint and aggressive behavior. However, the procedure of surgical castration causes acute pain-induced distress, which is an animal welfare concern. The objective of this study was to evaluate the use of two topical anesthetics to alleviate the pain caused by castration in piglets as measured by physiological and behavior indices of stress. At 3 days of age, 40 weight-matched piglets were allocated to one of four treatment groups. Treatments included: (i) sham castration (CON), (ii) surgical castration (CAS), (iii) castration and short-acting local anesthetic applied topically to the castration wound (SHORT) and (iv) castration and long-acting local anesthetic applied topically to the castration wound (LONG). Blood samples were collected from piglets before and 30, 60, 120 and 180 min after castration to measure leukocyte and differential counts and cortisol concentrations. The above experiment was repeated without blood collection and behavior was recorded for 30 min before and 180 min after castration or handling. Stress vocalizations were recorded during castration and handling. All piglets were weighed before and 24 h after castration and wound healing was recorded daily for the first 14 days after castration. Leukocyte counts and differentials did not differ (P > 0.05) among any of the treatments. Cortisol concentrations were elevated (P < 0.06) in CAS, SHORT and LONG piglets compared with controls 30 and 60 min after castration. The percentage of stress vocalizations was greater (P < 0.05) among castrated piglets compared with CON piglets, regardless of anesthetic treatment. Piglets that were castrated and not given a topical anesthetic spent more time (P < 0.05) lying without contact compared with piglets castrated and given a topical anesthetic, regardless of the topical anesthetic administered. Body weight change did not differ (P > 0.05) among treatments 24 h after castration or control handling and wound healing scores were greater (P < 0.05) in SHORT compared with CAS and LONG piglets 9 to 14 days after castration. In this study, the use of a short- or long-acting topical anesthetic was not effective in reducing the pain-induced distress caused by castration in piglets. Further research is needed to evaluate alternative practical methods to reduce the pain caused by the on-farm castration of piglets.
The Polar Format Imaging Algorithm for Forward-looking Bistatic SAR (2008)

A new effective PFA (Polar Format Algorithm) imaging algorithm for forward looking bistatic SAR is presented in this paper, Non-linear interpolation and sampling are adopted during converting polar coordinate to Cartesian coordinate according to the characteristics of space frequency samples in raw data domain. The algorithm preserves the character of conventional PFA of separating 2D interpolation to two 1D interpolations. The processing flow, efficiency and performance of the new algorithm are as same as conventional PFA for mono-static spotlight SAR. The limited conditions to realize forward looking bistatic SAR are also discussed and the algorithm is validated through point target simulations.
Novel Mechanical Magnetic Shutter Antenna for ELF /VLF Radiation (2018)

Electromagnetic radiation from 3 Hz to 30 kHz in the ELF/ULF/VLF bands sees continued and even renewed interest, despite significant engineering challenges in creating portable radiation systems in this frequency range. A novel mechanical shutter-based antenna with fixed permanent magnets is presented that allows for broadband radiation from a handheld source without the excessive mechanical requirements that have made traditional mechanical antenna concepts impractical. The validated prototype is a mechanical alternative to an electrically short antenna.
Mimic The Raw Domain: Accelerating Action Recognition in the Compressed Domain (2020)

Video understanding usually requires expensive computation that prohibits its deployment, yet videos contain significant spatiotemporal redundancy that can be exploited. In particular, operating directly on the motion vectors and residuals in the compressed video domain can significantly accelerate the compute, by not using the raw videos which demand colossal storage capacity. Existing methods approach this task as a multiple modalities problem. In this paper we are approaching the task in a completely different way; we are looking at the data from the compressed stream as a one unit clip and propose that the residual frames can replace the original RGB frames from the raw domain. Furthermore, we are using teacher-student method to aid the network in the compressed domain to mimic the teacher network in the raw domain. We show experiments on three leading datasets (HMDB51, UCF1, and Kinetics) that approach state-of-the-art accuracy on raw video data by using compressed data. Our model MFCD-Net outperforms prior methods in the compressed domain and more importantly, our model has 11X fewer parameters and 3X fewer Flops, dramatically improving the efficiency of video recognition inference. This approach enables applying neural networks exclusively in the compressed domain without compromising accuracy while accelerating performance.
Compressive Hyperspectral Imaging With Side Information (2015)

A blind compressive sensing algorithm is proposed to reconstruct hyperspectral images from spectrally-compressed measurements. The wavelength-dependent data are coded and then superposed, mapping the three-dimensional hyperspectral datacube to a two-dimensional image. The inversion algorithm learns a dictionary in situ from the measurements via global-local shrinkage priors. By using RGB images as side information of the compressive sensing system, the proposed approach is extended to learn a coupled dictionary from the joint dataset of the compressed measurements and the corresponding RGB images, to improve reconstruction quality. A prototype camera is built using a liquid-crystal-on-silicon modulator. Experimental reconstructions of hyperspectral datacubes from both simulated and real compressed measurements demonstrate the efficacy of the proposed inversion algorithm, the feasibility of the camera and the benefit of side information.
Bimetallic catalysis in the highly enantioselective ring–opening reactions of aziridines (2013)

Structural and kinetic evidence for bimetallic mechanism.
Measurement of Dead Space Fraction Upon ICU Admission Predicts Length of Stay and Clinical Outcomes Following Bidirectional Cavopulmonary Anastomosis* (2017)

Following bidirectional cavopulmonary anastomosis, alveolar dead space fraction in excess of 0.28 or arterial oxyhemoglobin saturation less than 78% upon ICU admission indicates an increased likelihood of requiring intervention prior to hospital discharge. Increasing alveolar dead space fraction and decreasing arterial oxyhemoglobin saturation are associated with increased lengths of stay.
WLS-based partially decentralized adaptive control for coupled ARMAX multi-agent dynamical system (2009)

In this paper, partially decentralized adaptive control for a multi-agent dynamic system is studied. There are many agents in the system, and each agent's state evolves like an ARMAX model with unknown parameters while being intervened by its neighborhood agents, in form of unknown linear interactions. Each agent adopts recursive WLS (weighted least-square) algorithm to estimate its local unknown parameters and designs its local adaptive controller by ldquocertainty equivalencerdquo principle. Generally speaking, it is a question whether such local adaptive controllers can guarantee stability of whole system. In this paper, we not only give the affirmative answer to this question, but also rigorously prove the optimality of decentralized WLS adaptive controller.
A small-molecule inhibitor of SHIP1 reverses age- and diet-associated obesity and metabolic syndrome (2016)

Low-grade chronic inflammation is a key etiological phenomenon responsible for the initiation and perpetuation of obesity and diabetes. Novel therapeutic approaches that can specifically target inflammatory pathways are needed to avert this looming epidemic of metabolic disorders. Genetic and chemical inhibition of SH2-containing inositol 5' phosphatase 1 (SHIP1) has been associated with systemic expansion of immunoregulatory cells that promote a lean-body state; however, SHIP1 function in immunometabolism has never been assessed. This led us to investigate the role of SHIP1 in metabolic disorders during excess caloric intake in mice. Using a small-molecule inhibitor of SHIP1 (SHIPi), here we show that SHIPi treatment in mice significantly reduces body weight and fat content, improves control of blood glucose and insulin sensitivity, and increases energy expenditure, despite continued consumption of a high-fat diet. Additionally, SHIPi reduces age-associated fat in mice. We found that SHIPi treatment reverses diet-associated obesity by attenuating inflammation in the visceral adipose tissue (VAT). SHIPi treatment increases IL-4-producing eosinophils in VAT and consequently increases both alternatively activated macrophages and myeloid-derived suppressor cells. In addition, SHIPi decreases the number of IFN-γ-producing T cells and NK cells in VAT. Thus, SHIPi represents an approach that permits control of obesity and diet-induced metabolic syndrome without apparent toxicity.
FuwaFuwa (2011)

Soft objects are widely used in our day-to-day lives, and provide both comfort and safety in contrast to hard objects. Also, soft objects are able to provide a natural and rich haptic sensation. In human-computer interaction, soft interfaces have been shown to be able to increase emotional attachment between human and machines, and increase the entertainment value of the interaction. We propose the FuwaFuwa sensor, a small, flexible and wireless module to effectively measure shape deformation in soft objects using IR-based directional photoreflectivity measurements. By embedding multiple FuwaFuwa sensors within a soft object, we can easily convert any soft object into a touch-input device able to detect both touch position and surface displacement. Furthermore, since it is battery-powered and equipped with wireless communication, it can be easily installed in any soft object. Besides that, because the FuwaFuwa sensor is small and wireless, it can be inserted into the soft object easily without affecting its soft properties.