gebhart/patrepeval huggingface dataset:
Time reversal optical tomography locates fluorescent targets in a turbid medium (2013)

A fluorescence optical tomography approach that extends time reversal optical tomography (TROT) to locate fluorescent targets embedded in a turbid medium is introduced. It uses a multi-source illumination and multi-detector signal acquisition scheme, along with TR matrix formalism, and multiple signal classification (MUSIC) to construct pseudo-image of the targets. The samples consisted of a single or two small tubes filled with water solution of Indocyanine Green (ICG) dye as targets embedded in a 250 mm × 250 mm × 60 mm rectangular cell filled with Intralipid-20% suspension as the scattering medium. The ICG concentration was 1μM, and the Intralipid-20% concentration was adjusted to provide ~ 1-mm transport length for both excitation wavelength of 790 nm and fluorescence wavelength around 825 nm. The data matrix was constructed using the diffusely transmitted fluorescence signals for all scan positions, and the TR matrix was constructed by multiplying data matrix with its transpose. A pseudo spectrum was calculated using the signal subspace of the TR matrix. Tomographic images were generated using the pseudo spectrum. The peaks in the pseudo images provided locations of the target(s) with sub-millimeter accuracy. Concurrent transmission TROT measurements corroborated fluorescence-TROT findings. The results demonstrate that TROT is a fast approach that can be used to obtain accurate three-dimensional position information of fluorescence targets embedded deep inside a highly scattering medium, such as, a contrast-enhanced tumor in a human breast.
Classification of breast masses and normal tissues in digital tomosynthesis mammography (2008)

Digital tomosynthesis mammography (DTM) can provide quasi-3D structural information of the breast by reconstructing the breast volume from projection views (PV) acquired in a limited angular range. Our purpose is to design an effective classifier to distinguish breast masses from normal tissues in DTMs. A data set of 100 DTM cases collected with a GE first generation prototype DTM system at the Massachusetts General Hospital was used. We reconstructed the DTMs using a simultaneous algebraic reconstruction technique (SART). Mass candidates were identified by 3D gradient field analysis. Three approaches to distinguish breast masses from normal tissues were evaluated. In the 3D approach, we extracted morphological and run-length statistics texture features from DTM slices as input to a linear discriminant analysis (LDA) classifier. In the 2D approach, the raw input PVs were first preprocessed with a Laplacian pyramid multi-resolution enhancement scheme. A mass candidate was then forward-projected to the preprocessed PVs in order to determine the corresponding regions of interest (ROIs). Spatial gray-level dependence (SGLD) texture features were extracted from each ROI and averaged over 11 PVs. An LDA classifier was designed to distinguish the masses from normal tissues. In the combined approach, the LDA scores from the 3D and 2D approaches were averaged to generate a mass likelihood score for each candidate. The A<sub>z</sub> values were 0.87±0.02, 0.86±0.02, and 0.91±0.02 for the 3D, 2D, and combined approaches, respectively. The difference between the A<sub>z</sub> values of the 3D and 2D approaches did not achieve statistical significance. The performance of the combined approach was significantly (p<0.05) better than either the 3D or 2D approach alone. The combined classifier will be useful for false-positive reduction in computerized mass detection in DTM.
Detection of Friction Stir Welding Defects of AA1060 Aluminum Alloy Using Specific Damping Capacity (2018)

The demand for nondestructive testing has increased, especially in welding testing. In the current study, AA1060 aluminum plates were jointed using the friction stir welding (FSW) process. The fabricated joints were subjected to free vibration impact testing in order to investigate the dynamic properties of the welded joint. Damping capacity and dynamic modulus were used in the new prediction method to detect FSW defects. The data acquired were processed and analyzed using a dynamic pulse analyzer lab shop and ME'Scope's post-processing software, respectively. A finite element analysis using ANSYS software was conducted on different types of designed defects to predict the natural frequency. The results revealed that defective welded joints significantly affect the specific damping capacity. As the damping ratio increased, so did the indication of opportunities to increase the presence of defects. The finite element simulation model was consistent with experimental work. It was therefore revealed that natural frequency was insufficient to predict smaller defects.
Detection, Synchronization, and Doppler Scale Estimation with Multicarrier Waveforms in Underwater Acoustic Communication (2008)

In this paper, we propose a novel method for detection, synchronization and Doppler scale estimation for underwater acoustic communication using orthogonal frequency division multiplex (OFDM) waveforms. This new method involves transmitting two identical OFDM symbols together with a cyclic prefix, while the receiver uses a bank of parallel self-correlators. Each correlator is matched to a different Doppler scaling factor with respect to the waveform dilation or compression. We characterize the receiver operating characteristic in terms of probability of false alarm and probability of detection. We also analyze the impact of Doppler scale estimation accuracy on the data transmission performance. These analytical results provide guidelines for the selection of the detection threshold and Doppler scale resolution. In addition to computer-based simulations, we have tested the proposed method with real data from an experiment at Buzzards Bay, MA, Dec. 15, 2006. Using only one preamble, the proposed method achieves similar performance on the Doppler scale estimation and the bit error rate as an existing method that uses two linearly-frequencymodulated (LFM) waveforms, one as a preamble and the other as a postamble, around each data burst transmission. Compared with the LFM based method, the proposed method works with a constant detection threshold independent of the noise level and is suited to handle the presence of dense multipath channels. More importantly, the proposed approach does not need to buffer the whole data packet before data demodulation, which facilitates future development of online realtime receivers for multicarrier underwater acoustic communications.
Improving the performance of turbo codes through concatenation with rectangular parity check codes (2002)

We show that a concatenated code with a simple rectangular-parity-check outer code and a turbo inner code performs significantly better than a turbo code alone.
Diversity of Type II restriction endonucleases that require two DNA recognition sites (2003)

Orthodox Type IIP restriction endonucleases, which are commonly used in molecular biological work, recognize a single palindromic DNA recognition sequence and cleave within or near this sequence. Several new studies have reported on structural and biochemical peculiarities of restriction endonucleases that differ from the orthodox in that they require two copies of a particular DNA recognition sequence to cleave the DNA. These two sites requiring restriction endonucleases belong to different subtypes of Type II restriction endonucleases, namely Types IIE, IIF and IIS. We compare enzymes of these three types with regard to their DNA recognition and cleavage properties. The simultaneous recognition of two identical DNA sites by these restriction endonucleases ensures that single unmethylated recognition sites do not lead to chromosomal DNA cleavage, and might reflect evolutionary connections to other DNA processing proteins that specifically function with two sites.
Environmentally friendly refining: Fischer–Tropsch versus crude oil (2006)

Projected changes in crude oil refinery design to meet future fuel specifications require that intermediates are produced that are already present in Fischer–Tropsch syncrude. A qualitative comparison is made between syncrude and crude oil, and the refinery designs needed to convert these raw materials into transportation fuels. Syncrude is sulfur free, nitrogen free and contains no heteroatom rich residues, making its purification and separation less complex than that of crude oil. The conversion units needed to produce motor-gasoline, jet fuel and diesel from syncrude are of similar complexity to that of crude oil, but crude oil residue conversion is much more involved. Furthermore, cleaner conversion technologies can be used to upgrade syncrude. A Fischer–Tropsch refinery consequently has a smaller environmental footprint than a crude oil refinery.
Fast dose optimization for rotating shield brachytherapy (2017)

POGS reduced treatment plan optimization time approximately 18 times for RSBT with similar HR-CTV D<sub>90</sub> , organ at risk (OAR) D<sub>2cc</sub> values, and EQD2 values compared to CPLEX, which is significant progress toward clinical translation of RSBT.
45.4L: <i>Late‐News Paper:</i> Retardation Film Made of Polymerisable Liquid Crystal without Rubbing (2005)

Abstract A retardation film of polymerisable liquid crystal has been developed. It is a negative C‐plate, which compensates for the optical retardation of a vertical‐alignment (VA) mode cell by using the characteristics of cholesteric liquid crystal. It is made by a simple process using a non‐rubbed alignment layer and exhibits good optical characteristic.
A New Nonestrogenic Steroidal Inhibitor of 17β-Hydroxysteroid Dehydrogenase Type I Blocks the Estrogen-Dependent Breast Cancer Tumor Growth Induced by Estrone (2012)

17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) converts estrone (E1) into estradiol (E2) and is expressed in many steroidogenic tissues and breast cancer cell lines. Because the potent estrogen E2 stimulates the growth and development of hormone-dependent diseases, inhibition of the final step of E2 synthesis is considered a promising strategy for the treatment of breast cancer. On the basis of our previous study identifying 16β-(m-carbamoylbenzyl)-E2 (CC-156) as a lead compound for the inhibition of 17β-HSD1, we conducted a number of structural modifications to reduce its undesired residual estrogenic activity. The steroid derivative PBRM [3-(2-bromoethyl)-16β-(m-carbamoylbenzyl)-17β-hydroxy-1,3,5(10)-estratriene] emerged as a potent inhibitor of 17β-HSD1 with an IC(50) value of 68 nmol/L for the transformation of E1 into E2. When tested in the estrogen-sensitive breast cancer cell line T-47D and in mice, PBRM showed no estrogenic activity in the range of concentrations tested. Furthermore, with the purpose of evaluating the bioavailability of PBRM and CC-156 injected subcutaneously (2.3 mg/kg), we measured their plasmatic concentrations as a function of time, calculated the area under the curve (AUC(0-12h)) and showed a significant improvement for PBRM (772 ng*h/mL) compared with CC-156 (445 ng*h/mL). We next tested the in vivo efficiency of PBRM on the T-47D xenograft tumor model in female ovariectomized athymic nude mice. After a treatment with PBRM, tumor sizes in mice stimulated with exogenous E1 were completely reduced at the control group level (without E1 treatment). As a conclusion, PBRM is a promising nonestrogenic inhibitor of 17β-HSD1 for the treatment of estrogen-dependent diseases such as breast cancer.
Low-Power Switching in Phase-Change Memory using New Superlattice : SnTe/Sb 2 Te 3 System (2012)

A new material SnTe for a superlattice (SL) phase-change device is proposed as the substitute of GeTe. XRD results showed that a SnTe(111)/Sb2Te3(001) SL formed, though SnSbTe-alloy peaks were greatly dominant. The switching power of this device was approximately 1/10th－1/15th that of a Ge2Sb2Te5 device, and, almost equivalent to or lower than that of a GeTe/Sb2Te3 SL device. The endurance was confirmed to be higher than 10 5 cycles. For the mechanism of the low switching power, Sn switching might work. This is, however, still a supposition.
Chloride Conductance Expressed by ΔF508 and Other Mutant CFTRs In <i>Xenopus</i> Oocytes (1991)

The cystic fibrosis transmembrane conductance regulator (CFTR) is associated with expression of a chloride conductance that is defective in cystic fibrosis (CF). Xenopus oocytes injected with RNA coding for CFTR that contained mutations in the first nucleotide binding fold (NBF1) expressed chloride currents in response to raising adenosine 3',5'-monophosphate (cAMP) with forskolin and 3-isobutyl-1-methylxanthine (IBMX). The mutant CFTRs were less sensitive than wild-type CFTR to this activating stimulus, and the reduction in sensitivity correlated with the severity of cystic fibrosis in patients carrying the corresponding mutations. This demonstration provides the basis for detailed analyses of NBF1 function and suggests potential pharmacologic treatments for cystic fibrosis.
Low Power ASIC GPS Tracking Loops: Quantifying the Trade-Offs Between Area, Power and Accuracy (2012)

High power consumption of existing GPS receiver chips limits continuous GPS operation in mobile devices. In order to pave the way for advances in areas such as location-aware applications and micro robotics navigation, we have to reduce the power consumed in GPS receivers. A microprocessor-based design is highly reconfigurable and easy to develop and debug but not low power enough for mobile applications. The software overhead in tracking loops implemented on a microprocessor can be avoided with hardware implementation of the tracking loops on an Application-Specific Integration Circuit (ASIC). The low power asynchronous GPS baseband processor architecture in [1] achieves low power by allowing each subsystem to operate at its natural frequency without clocking and by employing arbitrated hardware tracking loops. On power-up, a host system initializes the receiver with system configurations, tracking loops parameters, and Doppler frequencies and acquisition power thresholds of six available satellites. An asymmetric acquisition scheme allows each channel to perform just code phase acquisition after initialization and to then track continuously. In this paper, we will describe and analyze the performance and robustness of the asymmetric acquisition algorithm introduced in [1] in greater detail. With such an acquisition scheme, the receiver does not need a dedicated bank of correlators for full acquisition but can re-use the same correlators used for tracking, resulting in minimal hardware footprint on a GPS ASIC. We will also describe the architecture of the asynchronous ASIC implementation of the Phase-Locked Loop (PLL) and Delay-Locked Loop (DLL) and present an analysis of the power, size and accuracy trade-offs for the tracking loops.
Insulation failure detection in the stator windings of ASD-driven induction machines using standard deviation of line currents (2002)

This paper develops a straightforward, current-based scheme to detect stator turn faults that have occurred due to insulation failure in an ASD-driven, three-phase induction machine. The method employs simple statistical analysis to detect turn shorts in the stator of the machine. It is shown that the standard deviation of the calibrated, RMS line currents reveals a change in the machine's electrical symmetry that can be caused by turn shorts. To account for inherent machine imbalance, calibration is performed with the machine in a known fault-free state; additionally, current normalization accounts for varying loads. The method is sensitive to source balance, and is thus proposed only for inverter-fed machines.
Design of spring actuators made of ferromagnetic shape memory alloy and composites (2003)

Design of ferromagnetic shape memory alloy (FSMA) based spring actuators is discussed where a variety of design parameters are included, design of FSMA and FSMA composite, that of compact electromagnet, and the mode of deformation of a helical spring. Advantages of FSMA and FSMA composite are simple design, faster actuation speed large axial stroke and magnetic force.
<title>Measurement of the anterior structures of the human eye by partial coherence interferometry</title> (1995)

In the past few years a new technique for measuring intraocular distances has been developed, which is based on interferometry using partially coherent light beams and the Doppler principle. It has been shown that this technique is capable of measuring corneal thickness, axial eye length, and retinal thickness in human eyes in vivo with unprecedented precision. This technique has now been further extended to measure the anterior chamber depth and the thickness of the lens. A precision of 10 micrometers is obtained for both intraocular distances. This is more than one order of magnitude better than with conventional techniques.
Self-Template Growth of Ferroelectric Bi<sub>4</sub>Ti<sub>3</sub>O<sub>12</sub> Nanoplates via Flux-Mediated Epitaxy with VO<sub><i>x</i></sub> (2010)

Flux-mediated epitaxy of self-assembled ferroelectric Bi4Ti3O12 (BIT) nanoplates on SrTiO3 (001) is investigated with vanadium oxide (VOx) as the flux medium. It is shown that precoverage of a SrTiO3 (001) substrate with VOx helps to nucleate thin rutile TiO2 (001) crystallites that act as templates for the subsequent growth of (110)-oriented BIT nanoplates. Piezoresponse force microscopy reveals the presence of 90° domain walls even within a single BIT nanoplate, similar to BIT bulk single crystals.
Erbium:YAG laser resonator which reduces laser damage to the cavity high reflector (2000)

A rod of solid state gain material centered between two flat end mirrors (i.e. the flat-flat resonator) is a common laser resonator configuration. Positive dioptric power in the rod, thermally induced by the pumping of the gain medium, enables the resonator to operate in the stable regime. A typical problem that may ultimately limit maximum power in lasers of this type is the susceptibility of the cavity end mirrors to laser-induced damage. A technique that mitigates this damage by increasing the intra-cavity spot width at the end mirror location is described. The resulting modified resonator is equivalent to the flat-flat resonator with regard to its output laser beam propagation parameters and to the symmetrical mode fill of the gain medium.
ChemInform Abstract: Hydroboration. Part 81. Synthesis of 2‐(Dialkylamino)boronic Esters and Acids via Hydroboration of Enamines. A Convenient Preparation of β‐Dialkylamino Alcohols. (1988)

Abstract Hydroboration of the enamines (I) with borane‐dimethyl sulfide (II) gives the corresponding alkylboranes (III) which are converted to the boronic esters (V) on methanolysis.
Strategies to maximize the performance of a STED microscope (2012)

In stimulated emission depletion (STED) microscopy, the spatial resolution scales as the inverse square root of the STED beam's intensity. However, to fully exploit the maximum effective resolution achievable for a given STED beam's intensity, several experimental precautions have to be considered. We focus our attention on the temporal alignment between the excitation and STED pulses and the polarization state of the STED beam. We present a simple theoretical framework that help to explain their influence on the performance of a STED microscope and we validate the results by imaging calibration and biological samples with a custom made STED architecture based on a supercontinuum laser source. We also highlight the advantages of using time gating detection in terms of temporal alignment.
A Three-Layer Virtual Director Model for Supporting Automated Multi-Site Distributed Education (2006)

In multi-site distributed education (MSDE), video streams from multiple sites are available. To best utilize the limited screen space at each site, we develop a customizable, automated display management system in this paper, i.e., only user-preferred streams will be shown as triggered by events and timers. The configuration of such user preference, however, is challenging because it has to be both human-friendly and machine-friendly. To address this challenge, we propose a three-layer virtual director model. In the user layer, we identify three categories of parameters that can represent a wide range of user preferences yet are easy to use. These preferences are then automatically translated into a machine-friendly timed automaton in the execution layer. The automaton is simulated dynamically, which selects a subset of streams to show on the screen through a display layer. Evaluation results demonstrate the correctness and efficiency of the proposed framework
miR-19, miR-345, miR-519c-5p Serum Levels Predict Adverse Pathology in Prostate Cancer Patients Eligible for Active Surveillance (2014)

Serum microRNAs hold great promise as easily accessible and measurable biomarkers of disease. In prostate cancer, serum miRNA signatures have been associated with the presence of disease as well as correlated with previously validated risk models. However, it is unclear whether miRNAs can provide independent prognostic information beyond current risk models. Here, we focus on a group of low-risk prostate cancer patients who were eligible for active surveillance, but chose surgery. A major criteria for the low risk category is a Gleason score of 6 or lower based on pre-surgical biopsy. However, a third of these patients are upgraded to Gleason 7 on post surgical pathological analysis. Both in a discovery and a validation cohort, we find that pre-surgical serum levels of miR-19, miR-345 and miR-519c-5p can help identify these patients independent of their pre-surgical age, PSA, stage, and percent biopsy involvement. A combination of the three miRNAs increased the area under a receiver operator characteristics curve from 0.77 to 0.94 (p<0.01). Also, when combined with the CAPRA risk model the miRNA signature significantly enhanced prediction of patients with Gleason 7 disease. In-situ hybridizations of matching tumors showed miR-19 upregulation in transformed versus normal-appearing tumor epithelial, but independent of tumor grade suggesting an alternative source for the increase in serum miR-19a/b levels or the release of pre-existing intracellular miR-19a/b upon progression. Together, these data show that serum miRNAs can predict relatively small steps in tumor progression improving the capacity to predict disease risk and, therefore, potentially drive clinical decisions in prostate cancer patients. It will be important to validate these findings in a larger multi-institutional study as well as with independent methodologies.
A C‐terminally amidated analogue of ShK is a potent and selective blocker of the voltage‐gated potassium channel Kv1.3 (2012)

ShK, a 35-residue peptide from a sea anemone, is a potent blocker of potassium channels. Here we describe a new ShK analogue with an additional C-terminus Lys residue and amide. ShK-K-amide is a potent blocker of Kv1.3 and, in contrast to ShK and ShK-amide, is selective for Kv1.3. To understand this selectivity, we created complexes of ShK-K-amide with Kv1.3 and Kv1.1 using docking and molecular dynamics simulations, then performed umbrella sampling simulations to construct the potential of mean force of the ligand and calculate the corresponding binding free energy for the most stable configuration. The results agree well with experimental data.