gebhart/patrepeval huggingface dataset:
Structure–Activity Relationship for the 4(3<i>H</i>)-Quinazolinone Antibacterials (2016)

We recently reported on the discovery of a novel antibacterial (2) with a 4(3H)-quinazolinone core. This discovery was made by in silico screening of 1.2 million compounds for binding to a penicillin-binding protein and the subsequent demonstration of antibacterial activity against Staphylococcus aureus. The first structure-activity relationship for this antibacterial scaffold is explored in this report with evaluation of 77 variants of the structural class. Eleven promising compounds were further evaluated for in vitro toxicity, pharmacokinetics, and efficacy in a mouse peritonitis model of infection, which led to the discovery of compound 27. This new quinazolinone has potent activity against methicillin-resistant (MRSA) strains, low clearance, oral bioavailability and shows efficacy in a mouse neutropenic thigh infection model.
Invariant particle filtering with application to localization (2014)

The recently introduced Invariant Extended Kalman Filter (IEKF) is an extended Kalman filter designed for systems admitting symmetries, that possesses interesting convergence properties, and a relative independence of the filter behavior with respect to the system's trajectory. In the present paper, the ideas are extended to a broad class of systems introducing the notion of “conditional invariance”, that is, invariance properties of the system once some of the state variables are known. We exploit this structure by devising an Invariant Rao-Blackwellized Particle Filter: those state variables are sampled, and the rest are marginalized out using IEKFs. The striking property of the obtained particle filter is that the Kalman gains are identical for all particles, leading to a drastic reduction of the computational burden. The strong potential of the method is illustrated by the challenging and realistic problem of localization from noisy inertial sensors and a noisy GPS having a randomly jumping bias.
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis (2015)

Abstract Enhancers, critical determinants of cellular identity, are commonly recognized by correlative chromatin marks and gain-of-function potential, although only loss-of-function studies can demonstrate their requirement in the native genomic context. Previously, we identified an erythroid enhancer of human BCL11A, subject to common genetic variation associated with the fetal haemoglobin level, the mouse orthologue of which is necessary for erythroid BCL11A expression. Here we develop pooled clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 guide RNA libraries to perform in situ saturating mutagenesis of the human and mouse enhancers. This approach reveals critical minimal features and discrete vulnerabilities of these enhancers. Despite conserved function of the composite enhancers, their architecture diverges. The crucial human sequences appear to be primate-specific. Through editing of primary human progenitors and mouse transgenesis, we validate the BCL11A erythroid enhancer as a target for fetal haemoglobin reinduction. The detailed enhancer map will inform therapeutic genome editing, and the screening approach described here is generally applicable to functional interrogation of non-coding genomic elements.
Buried ion-exchanged glass waveguides using field-assisted annealing (2004)

Theoretical and experimental studies on buried ion-exchanged waveguides using field-assisted annealing (FAA) in erbium-doped phosphate glasses are reported. The procedure for making buried waveguides with the use of a two-step process is demonstrated. An analytical model for the FAA process was developed to simulate the experimental conditions, and both the refractive index profiles and the effective buried depths of these waveguides are predicted. The mode intensity profiles as well as the buried depths are measured, and the measured data are in good agreement with the simulated results.
Raman Spectroscopy of Atherosclerosis (2002)

Raman spectroscopy can provide detailed, quantitative information about the chemical composition of an atherosclerotic plaque. Recent development of compact clinical Raman systems and specially developed Raman catheters allow the remote, intravascular application of the technique. This shows prospects for the detection of coronary plaques that are prone to rupture and for the quantitative study of atherosclerosis in terms of chemical composition. This review discusses the basic principles and advances of Raman spectroscopy in the field of atherosclerosis, and its future directions in cardiovascular medicine.
Potential Threat of a New Pathotype of<i>Papaya leaf distortion mosaic virus</i>Infecting Transgenic Papaya Resistant to<i>Papaya ringspot virus</i> (2008)

A virus identified as a new pathotype of Papaya leaf distortion mosaic virus (PLDMV, P-TW-WF) was isolated from diseased papaya in an isolated test-field in central Taiwan, where transgenic papaya lines resistant to Papaya ringspot virus (PRSV) were evaluated. The infected plants displayed severe mosaic, distortion and shoe-stringing on leaves; stunting in apex; and water-soaking on petioles and stems. This virus, which did not react in enzyme-linked immunosorbent assay with the antiserum to the PRSV coat protein, infected only papaya, but not the other 18 plant species tested. Virions studied under electron microscope exhibited morphology and dimensions of potyvirus particles. Reverse transcription-polymerase chain reaction conducted using potyvirus-specific primers generated a 1,927-nucleotide product corresponding to the 3' region of a potyvirus, showing high sequence identity to the CP gene and 3' noncoding region of PLDMV. Search for similar isolates with the antiserum against CP of P-TW-WF revealed scattered occurrence of PLDMV in Taiwan. Phylogenetic analysis of PLDMV isolates of Taiwan and Japan indicated that the Taiwan isolates belong to a separate genetic cluster. Since all the Taiwan isolates infected only papaya, unlike the cucurbit-infecting Japanese P type isolates, the Taiwan isolates are considered a new pathotype of PLDMV. Susceptibility of all our PRSV-resistant transgenic papaya lines to PLDMV indicates that the virus is an emerging threat for the application of PRSV-resistant transgenic papaya in Taiwan and elsewhere.
Axially - And Side - Radiating Optical Fibres For Medical Applications (1985)

Laser surgery and photoradiation therapy are still rapidly developing: they are therefore placing new requirements and conditions on the associated technology. Thus, optical fibers are often requested to have a particular output which matches the needs of the considered applications. Integral fibre tips are a very convenient solution to many optical systems. The fabrication techniques and the experimental characteristics of different kinds of fibre tips are described.
End-to-end distortion estimation for RD-based robust delivery of pre-compressed video (2001)

Applications where packetized video is streamed over the Internet, must be designed to achieve robustness to packet loss as well as compression efficiency. Whenever possible, the ideal solution to this problem is to jointly optimize the adaptation of the compression and error protection strategies to the network status, so as to minimize the expected end-to-end distortion of reconstructed video at the receiver. However, in the case of pre-compressed video streaming, compression is performed without knowledge of the network condition, and conversely the delivery is performed without access to the original signal. It is hence difficult for the transmitter to estimate and minimize the end-to-end distortion during delivery. This paper addresses this problem by deriving an algorithm which enables the transmitter, or other intermediate nodes, to estimate the overall end-to-end distortion while delivering pre-compressed video. This estimate fully accounts for the effects of (prior) quantization, packet loss and error propagation, as well as error concealment. The accuracy of the estimate is demonstrated by simulation results. The algorithm requires storage of minimal side-information that is computed during compression. The algorithm is of low complexity, and is applicable to virtually all coding techniques, including the standard (predictive) video coders. The paper also discusses the use of this estimate to adapt a variety of packet-loss resilience techniques for pre-compressed video streaming. The considerable potential gains of this approach are illustrated via the example of an FEC-based streaming video system.
MLN8237: an orally active small molecule inhibitor of Aurora A kinase in phase I clinical trials (2008)

237 Aurora A kinase regulates the activity of a number of proteins essential to the proper execution of mitosis. Perturbation of Aurora A results in aberrant mitoses leading to cell death. We have developed a selective Aurora A kinase inhibitor, MLN8237; to be used for the therapeutic intervention of human cancers. MLN8237 displays potent activity against Aurora A in both enzymes and cell assays. In cells, MLN8237 proved to be more than 200 fold more selective for Aurora A than the structurally related kinase Aurora B. Treatment of cultured human tumor cells with MLN8237 results in mitotic spindle abnormalities, mitotic accumulation, inhibition of cell proliferation and apoptosis. MLN8237 is orally bioavailable and has a favorable pharmacokinetic profile. A single oral administration of MLN8237 to nude mice bearing subcutaneous human tumor xenografts resulted in a time dependent accumulation of mitotic cells, consistent with the pharmacological effect being mediated through Aurora A inhibition. Repeat oral administration of MLN8237 at well tolerated doses to nude mice bearing subcutaneous human tumor xenografts resulted in dramatic tumor growth inhibition in all models evaluated. In these models, MLN8237 induced mitotic accumulation and apoptosis. MLN8237 did not appreciably inhibit Aurora B at efficacious concentrations, as indicated by measuring phosphorylated histone H3 Ser10 staining. MLN8237 is currently in Phase I clinical trials in patients with advanced malignancies.
Perfect lens makes a perfect trap (2006)

In this work, we present for the first time a new and realistic application of the "perfect lens", namely, electromagnetic traps (or tweezers). We combined two recently developed techniques, 3D negative refraction flat lenses (3DNRFLs) and optical tweezers, and experimentally demonstrated the very unique advantages of using 3DNRFLs for electromagnetic traps. Super-resolution and short focal distance of the flat lens result in a highly focused and strongly convergent beam, which is a key requirement for a stable and accurate electromagnetic trap. The translation symmetry of 3DNRFL provides translation-invariance for imaging, which allows an electromagnetic trap to be translated without moving the lens, and permits a trap array by using multiple sources with a single lens. Electromagnetic trapping was demonstrated using polystyrene particles in suspension, and subsequent to being trapped to a single point, they were then accurately manipulated over a large distance by simple movement of a 3DNRFL-imaged microwave monopole source.
Finding Bent-double Radio Galaxies: A Case Study in Data Mining (2000)

This paper presents our early results in applying data mining techniques to the problem of finding radioemitting galaxies with a bent-double morphology. In the past, astronomers on the FIRST (Faint Images of the Radio Sky at Twenty-cm) survey have detected such galaxies by first inspecting the radio images visually to identify probable bent-doubles, and then conducting observations to confirm that the galaxy is indeed a bentdouble. Our goal is to replace this visual inspection by a semi-automated approach. In this paper, we present a brief overview of data mining, describe the features we use to discriminate bent-doubles from non-bent-doubles, and discuss the challenges faced in defining meaningful features in a robust manner. Our experiments show that data mining, using decision trees, can indeed be a viable alternative to the visual identification of bent-double galaxies.
One Packet Suffices - Highly Efficient Packetized Network Coding With Finite Memory (2011)

Random Linear Network Coding (RLNC) has emerged as a powerful tool for robust high-throughput multicast. Projection analysis - a recently introduced technique - shows that the distributed packetized RLNC protocol achieves (order) optimal and perfectly pipelined information dissemination in many settings. In the original approach to RNLC intermediate nodes code together all available information. This requires intermediate nodes to keep considerable data available for coding. Moreover, it results in a coding complexity that grows linearly with the size of this data. While this has been identified as a problem, approaches that combine queuing theory and network coding have heretofore not provided a succinct representation of the memory needs of network coding at intermediates nodes. This paper shows the surprising result that, in all settings with a continuous stream of data, network coding continues to perform optimally even if only one packet per node is kept in active memory and used for computations. This leads to an extremely simple RLNC protocol variant with drastically reduced requirements on computational and memory resources. By extending the projection analysis, we show that in all settings in which the RLNC protocol was proven to be optimal its finite memory variant performs equally well. In the same way as the original projection analysis, our technique applies in a wide variety of network models, including highly dynamic topologies that can change completely at any time in an adversarial fashion.
p-i-n germanium photodetectors integrated on silicon substrates (2001)

We report on the integration of Ge p-i-n heterojunction photodiodes on Si substrates. The crucial role of interface defects at the Ge/Si interface on the performance of photodetectors is analyzed and taken into account in the design of the devices. We have designed and fabricated high performance p-i-n Ge photodiodes for the near infrared. Pure Ge is grown by ultra-high-vacuum CVD followed by a cyclic thermal annealing and ion implantation. Devices are fabricated using standard photolithography. The photodiodes exhibit maximum responsivity of 0.8 A/W at 1.3 micrometers and 0.7 A/W at 1.55 micrometers , reverse dark currents in the 20 mA/cm<SUP>2</SUP> range at 1V and response times as short as 520 ps. Our devices are the first p-i-n Ge on Si photodetectors fabricated by CVD and exhibit high performances for a wide range of applications.
Novel dual wavelength (1050nm + 800nm) pumping scheme for thulium doped fiber amplifiers (2003)

We demonstrate that simultaneously pumping a thulium doped fiber amplifier with 800nm and 1050nm significantly reduces the required pump powers. 180mW total pump power yielded 27dB gain and less than 5dB noise figure.
A green recycling process designed for LiFePO<sub>4</sub> cathode materials for Li-ion batteries (2015)

A green process route is proposed to recycle LiFePO<sub>4</sub> cathode materials from FePO<sub>4</sub>·2H<sub>2</sub>O metastrengite I intermediate phase.
PTP1B and TC-PTP: novel roles in immune-cell signalingThis paper is one of a selection of papers published in this Special issue, entitled Second Messengers and Phosphoproteins—12th International Conference. (2006)

It has recently been demonstrated that the protein tyrosine phosphatase (PTP) PTP1B and the T-cell PTP (TC-PTP) target several substrates involved in immune cell signaling. Recent data have furthered the view of these 2 PTP members as key regulators of the immune response. This review will focus on the substrate specificities of PTP1B and TC-PTP and their roles in immune cell signaling, and will discuss some new data implicating PTP1B and TC-PTP in myeloid development.
Keratocyte survival following a controlled-rate freeze. (1985)

One of the major drawbacks of cryorefractive surgery is the delay in the postoperative recovery of corneal clarity. The authors have hypothesized that this delay is due to the death of graft keratocytes caused by the freezing process, and the need for subsequent repopulation by host keratocytes to restore corneal clarity. By using a slow, controlled-rate freeze on a modified Barraquer cryolathe, the authors are able to maintain keratocyte viability in the graft corneal tissue, as assessed by standard histologic methods and by collagenase digestion. Maintenance of keratocyte viability results in the rapid return of corneal clarity following lamellar keratoplasty in the rabbit, with few of the histopathologic changes seen following standard rapid freezing of corneal tissue.
<title>Monte Carlo investigations of elastic scattering spectroscopy applied to latex spheres used as tissue phantoms</title> (1995)

An optical-fiber-coupled, elastic-scatter spectrometer has proven effective in discriminating between malignant and nonmalignant tissue in the human bladder and gastrointestinal tract. The system injects broadband light into the tissue with an optical fiber and spectrally analyzes the returning light collected by an adjacent fiber. The collected photons have experienced multiple scattering events and therefore arrive at the analysis fiber after traveling varied paths. The diameter of the source fiber is comparable to its separation from the collection fiber. The diffusion model is inappropriate for this geometry; therefore, Monte Carlo simulations are used. In addition, the size of the scattering sites in tissue are expected to be of the same order as the excitation wavelengths, and Mie theory is expected to provide the best description of the scattering and extinction. We will present and compare the results of simulations and measurements of the elastic scatter signal for suspensions of latex spheres in hemoglobin solutions of varying concentrations.
Analysis of physical characteristics of Tumor Treating Fields for human glioblastoma (2017)

Tumor Treating Fields (TTFields) therapy is an approved treatment that has known clinical efficacy against recurrent and newly diagnosed glioblastoma. However, the distribution of the electric fields and the corresponding pattern of energy deposition in the brain are poorly understood. To evaluate the physical parameters that may influence TTFields, postacquisition MP-RAGE, T1 and T2 MRI sequences from a responder with a right parietal glioblastoma were anatomically segmented and then solved using finite-element method to determine the distribution of the electric fields and rate of energy deposition at the gross tumor volume (GTV) and other intracranial structures. Electric field-volume histograms (EVH) and specific absorption rate-volume histograms (SARVH) were constructed to numerically evaluate the relative and/or absolute magnitude volumetric differences between models. The electric field parameters E<sub>AUC</sub> , V<sub>E</sub><sub>150</sub> , E<sub>95%</sub> , E<sub>50%</sub> , and E<sub>20%</sub> , as well as the SAR parameters SAR<sub>AUC</sub> , V<sub>SAR</sub><sub>7.5</sub> , SAR<sub>95%</sub> , SAR<sub>50%</sub> , and SAR<sub>20%</sub> , facilitated comparisons between models derived from various conditions. Specifically, TTFields at the GTV were influenced by the dielectric characteristics of the adjacent tissues as well as the GTV itself, particularly the presence or absence of a necrotic core. The thickness of the cerebrospinal fluid on the convexity of the brain and the geometry of the tumor were also relevant factors. Finally, the position of the arrays also influenced the electric field distribution and rate of energy deposition in the GTV. Using EVH and SARVH, a personalized approach for TTFields treatment can be developed when various patient-related and tumor-related factors are incorporated into the planning procedure.
MO‐A‐BRD‐06: In Vivo Cherenkov Video Imaging to Verify Whole Breast Irradiation Treatment (2014)

Purpose: To show in vivo video imaging of Cherenkov emission (Cherenkoscopy) can be acquired in the clinical treatment room without affecting the normal process of external beam radiation therapy (EBRT). Applications of Cherenkoscopy, such as patient positioning, movement tracking, treatment monitoring and superficial dose estimation, were examined. Methods: In a phase 1 clinical trial, including 12 patients undergoing post‐lumpectomy whole breast irradiation, Cherenkov emission was imaged with a time‐gated ICCD camera synchronized to the radiation pulses, during 10 fractions of the treatment. Images from different treatment days were compared by calculating the 2‐D correlations corresponding to the averaged image. An edge detection algorithm was utilized to highlight biological features, such as the blood vessels. Superficial dose deposited at the sampling depth were derived from the Eclipse treatment planning system (TPS) and compared with the Cherenkov images. Skin reactions were graded weekly according to the Common Toxicity Criteria and digital photographs were obtained for comparison. Results: Real time (fps = 4.8) imaging of Cherenkov emission was feasible and feasibility tests indicated that it could be improved to video rate (fps = 30) with system improvements. Dynamic field changes due to fast MLC motion were imaged in real time. The average 2‐D correlation was about 0.99, suggesting the stability of this imaging technique and repeatability of patient positioning was outstanding. Edge enhanced images of blood vessels were observed, and could serve as unique biological markers for patient positioning and movement tracking (breathing). Small discrepancies exists between the Cherenkov images and the superficial dose predicted from the TPS but the former agreed better with actual skin reactions than did the latter. Conclusion: Real time Cherenkoscopy imaging during EBRT is a novel imaging tool that could be utilized for patient positioning, movement tracking, treatment monitoring, superficial dose and skin reaction estimation and prediction.
State Feedback Control of Electrorheological Fluids (1996)

Abstract Electrorheological (ER) fluids have electrically controllable stiffness, viscosity, and heat transfer properties. Since the 1940s researchers have attempted to model the properties of ER fluids and have proposed applications which attempt to utilize their special characteristics in the operation of hydraulic valves, soft clutches, and active suspension systems. Early attempts to make these applications commercially successful were hampered by the relatively slow, nonlinear response of ER fluids under on-off control of high electric fields. Successful applications will require fast, precise control of the response of ER fluids, independent of application at low field strengths. This study presents a new approach to the control of ER fluids that overcomes the problems of imprecise, slow, nonlinear response and high electric fields. An optical sensor was used to indicate the ER fluid state in a layered composite window. Feedback control of ER fluid state was developed and compared to conventionally actuated ER fluids. Feedback control employs the state sensor and high initial electric field strength to speed ER state response, then lowers the field strength to the minimum level required to achieve the desired ER fluid state. Predicted responses were compared to experimentally measured responses and showed excellent agreement. Laboratory measurements showed a proportional state feedback control system yielded an electrorheological fluid that responded 35 times faster and 21 times more accurately than possible with a conventional open-loop fluid control system. Although the use of ER fluids in feedback control systems have been proposed in the past, this work is the first application of feedback control to the fluid itself.