gebhart/patrepeval huggingface dataset:
Segmentation under Occlusions Using Selective Shape Prior (2008)

In this work, we address the problem of segmenting multiple objects, under possible occlusions, in a level set framework. A variational energy that incorporates a piecewise constant representation of the image in terms of the object regions and the object spatial order is proposed. To resolve occluded boundaries, prior knowledge of the shape of objects is also introduced within the segmentation energy. By minimizing the above energy, we solve the segmentation with depth problem, i.e., estimating the object boundaries, the object intensities, and the spatial order. The segmentation with depth problem was originally dealt with by the Nitzberg–Mumford–Shiota (NMS) variational formulation, which proposes segmentation energies for each spatial order. We discuss the relationships and show the computational advantages of our formulation over the NMS model, mainly due to our treatment of spatial order estimation within a single energy. A novelty here is that the spatial order information available in the image model is used to dynamically impose prior shape constraints only to occluded boundaries. Also presented are experiments on synthetic and real images that have promising results.
Stochastic Video Long-term Interpolation (2018)

In this paper, we introduce a stochastic dynamics video infilling (SDVI) framework to generate frames between long intervals in a video. Our task differs from video interpolation which aims to produce transitional frames for a short interval between every two frames and increase the temporal resolution. Our task, namely video infilling, however, aims to infill long intervals with plausible frame sequences. Our framework models the infilling as a constrained stochastic generation process and sequentially samples dynamics from the inferred distribution. SDVI consists of two parts: (1) a bi-directional constraint propagation module to guarantee the spatial-temporal coherence among frames, (2) a stochastic sampling process to generate dynamics from the inferred distributions. Experimental results show that SDVI can generate clear frame sequences with varying contents. Moreover, motions in the generated sequence are realistic and able to transfer smoothly from the given start frame to the terminal frame. Our project site is this https URL
Graphene‐Based Intrinsically Stretchable 2D‐Contact Electrodes for Highly Efficient Organic Light‐Emitting Diodes (Adv. Mater. 31/2022) (2022)

Organic Light-Emitting Diodes Intrinsically stretchable light-emitting diodes (ISOLEDs) are becoming increasingly important for wearable electronics. In article number 2203040, Han-Young Woo, Tae-Woo Lee, and co-workers report the design of highly efficient ISOLEDs that use a graphene-based 2D-contact stretchable electrode. As a benefit of a newly designed conjugated polyelectrolyte with efficient electron injection capability, the ISOLED yields an unprecedently high current efficiency of 20.3 cd A−1.
Power And Frequency Measurements From A Uniform Backward Wave Oscillator As A Function Of Length (2005)

The authors describe results from an experiment where the number of ripple periods in the slow wave structure of a backward wave oscillator (BWO) is increased. Both microwave power and frequency measurements are made for each shot. For a given cathode voltage and beam current, the microwave peak power and frequency are plotted as a function of BWO length. In previous investigations, the observation of two power maxima as a function of length was explained by the interaction of the electron beam with the forward traveling wave and reflections at the transition from the slow wave structure into the output waveguide. However, recent numerical calculations using the phase dynamics of electron beam and electromagnetic modes suggest that the power maxima are due to the phase relationship between the electron beam density wave and the backward wave. Experiments were performed on the Sinus-6, a relativistic electron beam accelerator. By adjusting the pressure in the Sinus-6 spark gap switch, cathode voltages between 400 kV to 650 kV can be obtained. The experiment was repeated for different sets of beam parameters. In all cases, the magnetic field used for beam transport was longer than the length of the slow wave structure. The experimentalmore » results are compared with phase model calculations and PIC code simulations using KARAT and TWOQUICK.« less
Therapeutic HIV-1 vaccine (2018)

Major advances in our immunological understanding resulting from basic science and clinical trials studies have paved the way and established a solid platform to jump over the stumbling blocks that prevent the field from developing a therapeutic HIV-1 vaccine. It is time for immuno-modulation and combinatorial strategies towards HIV-1 eradication.
Achievable Rate Region of Quantized Broadcast and MAC Channels (2011)

In this paper, we study the achievable rate region of Gaussian multiuser channels with the messages transmitted being from finite input alphabets and the outputs being {\em quantized at the receiver}. In particular, we focus on the achievable rate region of $i)$ Gaussian broadcast channel (GBC) and $ii)$ Gaussian multiple access channel (GMAC). First, we study the achievable rate region of two-user GBC when the messages to be transmitted to both the users take values from finite signal sets and the received signal is quantized at both the users. We refer to this channel as {\em quantized broadcast channel (QBC)}. We observe that the capacity region defined for a GBC does not carry over as such to QBC. We show that the optimal decoding scheme for GBC (i.e., high SNR user doing successive decoding and low SNR user decoding its message alone) is not optimal for QBC. We then propose an achievable rate region for QBC based on two different schemes. We present achievable rate region results for the case of uniform quantization at the receivers. Next, we investigate the achievable rate region of two-user GMAC with finite input alphabet and quantized receiver output. We refer to this channel as {\em quantized multiple access channel (QMAC)}. We derive expressions for the achievable rate region of a two-user QMAC. We show that, with finite input alphabet, the achievable rate region with the commonly used uniform receiver quantizer has a significant loss compared to the achievable rate region without receiver quantization. We propose a {\em non-uniform quantizer} which has a significantly larger rate region compared to what is achieved with a uniform quantizer in QMAC.
Design and Synthesis of Microscale Opto-Magnetic Trapping Handles (2016)

Thesis (Ph. D.)--University of Rochester. Department of Mechanical Engineering, 2016.
Mutations in KDSR Cause Recessive Progressive Symmetric Erythrokeratoderma (2020)

Supplemental Data Supplemental Data include five figures and three tables and can be found with this article online at http://dx.doi.org/10.1016/j.ajhg.2017.05.003. Supplemental Data Document S1. Figures S1–S5 and Tables S1–S3 Download Document S2. Article plus Supplemental Data Download Web Resources 1000 Genomes, http://www.internationalgenome.org/ ANNOVAR, http://annovar.openbioinformatics.org/en/latest/ BWA-MEM, http://bio-bwa.sourceforge.net/index.shtml Database of Genomic Variants, http://dgv.tcag.ca/dgv/app/home dbSNP, https://www.ncbi.nlm.nih.gov/projects/SNP/ Exome Aggregation Consortium (ExAC) Browser, http://exac.broadinstitute.org/ ExonPrimer, https://ihg.helmholtz-muenchen.de/ihg/ExonPrimer.html GenBank, https://www.ncbi.nlm.nih.gov/genbank/ Genome Analysis Toolkit (GATK), https://software.broadinstitute.org/gatk/ Integrative Genomics Viewer (IGV), http://software.broadinstitute.org/software/igv/ OMIM, https://www.omim.org/ SNPmasker, http://bioinfo.ebc.ee/snpmasker/ UCSC Genome Browser, https://genome.ucsc.edu/index.html Variant Effect Predictor, http://useast.ensembl.org/info/docs/tools/vep/index.html The discovery of new genetic determinants of inherited skin disorders has been instrumental to the understanding of epidermal function, differentiation, and renewal. Here, we show that mutations in KDSR (3-ketodihydrosphingosine reductase), encoding an enzyme in the ceramide synthesis pathway, lead to a previously undescribed recessive Mendelian disorder in the progressive symmetric erythrokeratoderma spectrum. This disorder is characterized by severe lesions of thick scaly skin on the face and genitals and thickened, red, and scaly skin on the hands and feet. Although exome sequencing revealed several of the KDSR mutations, we employed genome sequencing to discover a pathogenic 346 kb inversion in multiple probands, and cDNA sequencing and a splicing assay established that two mutations, including a recurrent silent third base change, cause exon skipping. Immunohistochemistry and yeast complementation studies demonstrated that the mutations cause defects in KDSR function. Systemic isotretinoin therapy has achieved nearly complete resolution in the two probands in whom it has been applied, consistent with the effects of retinoic acid on alternative pathways for ceramide generation.
Critical current properties of multifilament V&lt;inf&gt;3&lt;/inf&gt;Ga wire at temperatures above 4.2 Kelvin (1977)

Studies of the superconducting properties of V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> Ga formed in composite wires by solid state reaction are presented. Multifilament wires were fabricated containing nineteen V-6.1 at.%Ga filaments or thirty V-8.0 at. %Ga filaments in a Cu-17.5 at .%Ga matrix. A study of J <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</inf> as a function of magnetic field and temperature on these wires is reported. At a temperature of 8.6 K, and in a magnetic field of 10 Tesla, a J <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</inf> of 4.2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> amps/ cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> was measured for the thirty filament wire. This is significantly higher than the J <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</inf> of commercially available V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> Ga tape Or Nb <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> Sn wire, These studies indicate that not only does our V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> Ga wire exhibit high magnetic field properties Superior to those for commercially available wire at 4.2 K, but it also retains its superior J <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</inf> values at temperatures in excess of 11 K.
A 4.4 pJ/Access 80 MHz, 128 kbit Variability Resilient SRAM With Multi-Sized Sense Amplifier Redundancy (2011)

An ultra low energy, 128 kbit 6T SRAM in 90 nm LP CMOS with energy consumption of 4.4 pJ/access, operating at 80 MHz for the wireless sensor applications is developed. The variability resilient and low power techniques developed include innovation in the local architecture with the use of local read/write assist circuitry. The energy-efficient hierarchical bit-lines structure includes low swing global bit-lines and VDD/2 pre-charged short local bit-lines. The innovative Multi-Sized SA redundancy (MS-SA-R) calibration technique for the global read sense amplifiers of the SRAM not only adds to the variability resilience but also yields maximum energy reduction compared with existing calibration techniques.
Roles, rights, and responsibilities: Better governance through decision rights automation (2009)

At its essence software development governance is about guiding the development organization so that it produces value that aligns with the needs of the business. As software development platforms mature they provide increasingly sophisticated capabilities for process measurement and guidance. These new capabilities in turn offer an excellent opportunity for governance tools to help guide the development. In this paper we discuss a model of the development organization that includes: roles, responsibilities, decisions, rights, artifacts and their lifecycles. We show how this model can be elicited and deployed as part of a governance solution to guide the development organization and provide a description of a prototype we have built to automate this process. We conclude with a discussion and important directions for future work in the area.
Computer-Aided Design Methodology for Electrostatic Discharge (ESD) Protection Applications (2006)

Physical mechanisms that define the triggering conditions of lateral P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> structures for ESD (electrostatic discharge) protection are identified using 2D numerical simulations. The TCAD (technology computer aided design) allows for accurate prediction of the forward and reverse blocking voltages, necessary for custom ESD protection design. Symmetrical and asymmetrical dual-polarity S-type I-V characteristics are achieved for bipolar input/output ESD protection design. This is realized by using 1) tailored forward-and reverse- blocking junction configurations embedded in coupled (P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> )//(N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> ) structures, and 2) optimized adjustment of the structures' doping implantations and isolation regions
Abstract A32: Pretargeted immunoPET of CEA-expressing in intraperitoneal human colonic tumor xenografts in nude mice (2010)

Abstract Objective: Radiolabeled antibodies were being developed commercially for the detection of several cancer types. However, imaging with radiolabeled antibodies require a relatively long interval between injection and imaging acquisition for adequate contrast to develop. The pretargeting method is a 2-step method: a unlabeled bsMAb with affinity for the tumor and a small radiolabeled molecule is injected, followed by the a radiolabeled compound. This aims to optimize the imaging system by specific tumor accumulation and fast blood clearance of the radiopharmacon, which allows imaging within one hour. Short-lived positron emitting radionuclides, e.g. 68Ga (half life: 68 min) match the pharmacokinetics of the small molecule. In this study, pretargeted immunoPET with a bispecific monoclonal anti-carcinoembryonic antigen (CEA) x anti-histamine-succinyl-glycine (HSG) antibody, TF2, and a radiolabeled peptide, IMP288, was compared to 18F-FDG in detecting CEA-expressing tumors in nude mice. Methods: Groups of five BALB/c nude mice were inoculated with CEA-expressing human colonic tumor cells intraperitoneally. One group received 5 MBq 18F-FDG intravenously (i.v.). Another group received TF2 and 5 MBq 68Ga-IMP288 i.v. 16 h later. After one hour PET/CT images were acquired. One day later this was repeated vice versa. Uptake of 68Ga-IMP288 or 18F-FDG in the tumors and other dissected tissues was determined. Results: High, specific tumor uptake of 68Ga-IMP288 (23.4 ± 7.2% ID/g) was observed, with very low accretion in the normal tissues (intestines: 0.50 ± 0.19 % ID/g; liver: 1.83 ± 0.45 % ID/g). This resulted in high tumor-to-background ratios (e.g. tumor-to-intestines 57.5 ± 22.4) and in the clear visualization of the small intra-abdominal tumor lesions (1.5–5 mm), as soon as one hour after the injection of 68Ga-IMP288. 18F-FDG localized efficiently in the tumors (8.7 ± 3.1 % ID/g), but with physiological uptake in various normal tissues (intestines: 2.15 ± 0.61 % ID/g; liver: 2.78 ± 0.52 % ID/g). The low tumor-to-background ratio (e.g. tumor-to-intestines 4.0 ± 0.9) complicated the detection of the tumors. Conclusions: This study indicated that pretargeted immunoPET with TF2 and 68Ga-IMP288 is a specific and sensitive method for detecting colon cancer. Citation Information: Clin Cancer Res 2010;16(7 Suppl):A32
Diethyl Ethoxymethylenemalonate (2001)

(R = Et) [87-13-8] C10H16O5 (MW 216.23) InChI = 1S/C10H16O5/c1-4-13-7-8(9(11)14-5-2)10(12)15-6-3/h7H,4-6H2,1-3H3 InChIKey = LTMHNWPUDSTBKD-UHFFFAOYSA-N (R = Me) [22398-14-7] C7H10O5 (MW 174.15) InChI = 1S/C7H10O5/c1-10-4-5(6(8)11-2)7(9)12-3/h4H,1-3H3 InChIKey = RHFZTBSULNJWEI-UHFFFAOYSA-N (push–pull alkene;1 1,4-addition–elimination (AdN–E);2 quinoline derivatives;3 1,4-addition;4 [3 + 2] cycloadditions;5 Diels–Alder reaction;6 protecting group for amino sugars7 and amino acids;8 oxo-Meldrum's acid9) Physical Data: R = Et: bp 108–110 °C/0.25 mmHg; d 1.070 g cm−3. R = Me:2h mp 44–45 °C; bp 106 °C/0.7 mmHg. Solubility: sol ethanol and diethyl ether. Form Supplied in: clear liquid; widely available. Analysis of Reagent Purity: n20D = 1.4612–1.4623. Preparative Method: prepared by heating Triethyl Orthoformate, Diethyl Malonate, Acetic Anhydride, and catalytic amounts of Zinc Chloride.10 Purification: fractional vacuum distillation.
Low voltage driven carbon nanotube field emission cathode (2004)

An under-gate CNT cathode structure was fabricated and characterized. The purpose of this work is to fabricate a cathode with micron-sized CNT-to-counter electrode gap, d/sub G/. Scanning electron microscopy was used to characterize the fabricated cathode. Electrical measurements were made in a vacuum chamber. It was found that cathode-to-gate voltage decreases with decreasing d/sub G/. It was also observed that emitting layer made of high purity CNT powder offers higher performance in terms of emission site density.
Correction: Verkade, J.M.M.; et al. A Polar Sulfamide Spacer Significantly Enhances the Manufacturability, Stability, and Therapeutic Index of Antibody–Drug Conjugates. Antibodies 2018, 7, 12 (2018)

The conflict of interest section of the published paper [1] has been updated as follows[...].
Immunogenicity and safety of the 13-valent pneumococcal conjugate vaccine in HIV-infected individuals naive to pneumococcal vaccination (2015)

A three-dose regimen of PCV13 was well tolerated in pneumococcal vaccine-naive, HIV-infected individuals. Significant immune responses to all serotypes were observed following the first dose of PCV13, with only modest increases in antibody titres following subsequent PCV13 or PPSV23 administration.
Disruption of WT1 gene expression and exon 5 splicing following cytotoxic drug treatment: antisense down-regulation of exon 5 alters target gene expression and inhibits cell survival. (2004)

Deregulated expression of the Wilms' tumor gene (WT1) has been implicated in the maintenance of a malignant phenotype in leukemias and a wide range of solid tumors through interference with normal signaling in differentiation and apoptotic pathways. Expression of high levels of WT1 is associated with poor prognosis in leukemias and breast cancer. Using real-time (Taqman) reverse transcription-PCR and RNase protection assay, we have shown up-regulation of WT1 expression following cytotoxic treatment of cells exhibiting drug resistance, a phenomenon not seen in sensitive cells. WT1 is subject to alternative splicing involving exon 5 and three amino acids (KTS) at the end of exon 9, producing four major isoforms. Exon 5 splicing was disrupted in all cell lines studied following a cytotoxic insult probably due to increased exon 5 skipping. Disruption of exon 5 splicing may be a proapoptotic signal because specific targeting of WT1 exon 5-containing transcripts using a nuclease-resistant antisense oligonucleotide (ASO) killed HL60 leukemia cells, which were resistant to an ASO targeting all four alternatively spliced transcripts simultaneously. K562 cells were sensitive to both target-specific ASOs. Gene expression profiling following treatment with WT1 exon 5-targeted antisense showed up-regulation of the known WT1 target gene, thrombospondin 1, in HL60 cells, which correlated with cell death. In addition, novel potential WT1 target genes were identified in each cell line. These studies highlight a new layer of complexity in the regulation and function of the WT1 gene product and suggest that antisense directed to WT1 exon 5 might have therapeutic potential.
TAPAS: A Thresholding Approach for Probability Map Automatic Segmentation in Multiple Sclerosis (2019)

Abstract Total brain white matter lesion (WML) volume is the most widely established magnetic resonance imaging (MRI) outcome measure in studies of multiple sclerosis (MS). To estimate WML volume, there are a number of automatic segmentation methods, yet, manual delineation remains the gold standard approach. These approaches often yield a probability map to which a threshold is applied to create lesion segmentation masks. Unfortunately, few approaches systematically determine the threshold employed; many methods use a manually selected threshold, thus introducing human error and bias into the automated procedure. In this study, we propose and validate an automatic thresholding algorithm, Thresholding Approach for Probability Map Automatic Segmentation in Multiple Sclerosis (TAPAS), to obtain subject-specific threshold estimates for probability map automatic segmentation of T2-weighted (T2) hyperintense WMLs. Using multimodal MRI, the proposed method applies an automatic segmentation algorithm to obtain probability maps. We obtain the true subject-specific threshold that maximizes Sørensen-Dice Similarity Coefficient (DSC). Then the subject-specific thresholds are modeled on a naive estimate of volume using a general additive model. Applying this model, we predict a subject-specific threshold in data not used for training. We ran a Monte Carlo-resampled split-sample cross-validation (100 validation sets) using two data sets: the first obtained from the Johns Hopkins Hospital (JHH) on a Philips 3 Tesla (3T) scanner (n = 94) and a second collected at the Brigham and Women’s Hospital (BWH) using a Siemens 3T scanner (n = 40). By means of the proposed automated technique, in the JHH data, we found an average reduction in subject-level absolute error of 0.1 mL per one mL increase in manual volume. Using Bland-Altman analysis, we found that volumetric bias associated with group-level thresholding is mitigated when applying TAPAS. The BWH data showed similar absolute error estimates using group-level thresholding or TAPAS likely since Bland-Altman analyses indicate no systematic biases associated with group or TAPAS volume estimates. The current study presents the first validated fully automated method for subject-specific threshold prediction to segment brain lesions.