gebhart/patrepeval huggingface dataset:
Effects of directional antennas at the base station on the Doppler spectrum (1997)

We analyze the effect of directional antennas at the base station on the Doppler spectrum. It is well known that the Doppler spectrum is dependent on the probability density function (pdf) of the angle-of-arrival (AOA) of the multipath components at the mobile unit and the direction of the motion of the mobile. The Doppler spectrum is U-shaped, when the pdf of the AOA of the multipath components at the mobile is uniform. Here, however, we study the Doppler fading at the base station and assume that the scatterers are uniformly located around the mobile within a circle and derive the pdf of the AOA of the multipath components at the mobile when directional antennas are used at the base station.
Connectivity properties of a mobile packet radio network model (2003)

A model of a packet radio network in which transmitters with a transmission range of R units are distributed according to a two-dimensional Poisson point process is examined. It is a widely held belief that an optimal number of nearest neighbors of a transmitter (the magic number) exists that maximizes the throughput of the network. The authors show that no magic number can exist. However, the notion of a magic number is shown to be useful, and an explanation is provided for why computations based on magic numbers give answers that are good in practice.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Long-Haul Dense Space-Division Multiplexed Transmission Over Low-Crosstalk Heterogeneous 32-Core Transmission Line Using a Partial Recirculating Loop System (2016)

In this paper, we present long-haul 32-core dense space-division-multiplexed (DSDM) unidirectional transmission over a single-mode multicore transmission line. We developed a low-crosstalk heterogeneous 32-core fiber with a square lattice arrangement, and a novel partial recirculating loop system. The span crosstalk of the 51.4-km 32-core transmission line was less than -34.5 dB. This allowed the transmission of polarization-division-multiplexed 16 quadrature amplitude modulation (PDM-16QAM) signals through all 32 cores over a long distance exceeding 1000 km. We demonstrate 32-core DSDM 20 wavelength-division-multiplexed PDM-16QAM transmission over 1644.8 km with a high aggregate spectral efficiency of 201.46 b/s/Hz Additionally, we examine the effect of crosstalk on the transmission performance of each core, and show that the Q-penalty has strong correlation with intercore crosstalk.
Evolution of polyketide synthases in bacteria (2008)

The emergence of resistant strains of human pathogens to current antibiotics, along with the demonstrated ability of polyketides as antimicrobial agents, provides strong motivation for understanding how polyketide antibiotics have evolved and diversified in nature. Insights into how bacterial polyketide synthases (PKSs) acquire new metabolic capabilities can guide future laboratory efforts in generating the next generation of polyketide antibiotics. Here, we examine phylogenetic and structural evidence to glean answers to two general questions regarding PKS evolution. How did the exceptionally diverse chemistry of present-day PKSs evolve? And what are the take-home messages for the biosynthetic engineer?
Dark-field imaging on a clinical CT system: performance and potential based on first results (2022)

X-ray computed tomography (CT) has been established as a daily tool in clinical diagnostics and has been continuously refined by more recent innovations in the last years. These systems are, however, limited by fundamental constraints since they are only capable of mapping X-ray attenuation differences in the tissue. Phase-contrast and dark-field imaging provide complementary contrast, which originates from physically different interaction processes of X-rays with matter. Particularly the dark-field signal is considered to have significant diagnostic potential since it is capable to retrieve micro-structural information below the actual resolution limit of the imaging system. This was demonstrated in various laboratory setups and recently also in the fist study with human patients in a clinical radiography system based on a grating interferometer. In a recent work, we presented the first implementation of such an X-ray interferometer into a clinical CT gantry. Upscaling and adapting this technology for a rotating CT gantry involves several challenges and tradeoffs ranging from limitations in interferometer design over fast, continuous signal acquisition requirements to tolerances in applied patient dose. In this work we discuss the performance of the first clinical dark-field CT prototype. For this purpose, we present results of our phantom studies which were designed to evaluate whether and how the dark-field contrast generated by the system is capable to provide additional structural sample information. The key aspects include the possibility of quantitative imaging and a gradual approach to simulate results that come as close as possible to a real application in a human patient.
Investigation of DNA Condensing Properties of Amphiphilic Triblock Cationic Polymers by Atomic Force Microscopy (2010)

Introduction of nucleic acids into cells is an important biotechnology research field which also holds great promise for therapeutic applications. One of the key steps in the gene delivery process is compaction of DNA into nanometric particles. The study of DNA condensing properties of three linear cationic triblock copolymers poly(ethylenimine-b-propylene glycol-b-ethylenimine), namely, LPEI(50)-PPG(36)-LPEI(50), LPEI(19)-PPG(36)-LPEI(19), and LPEI(14)-PPG(68)-LPEI(14), indicates that proper DNA condensation is driven by both the charge and the size of the respective cationic hydrophilic linear polyethylenimine (LPEI) and neutral hydrophobic poly(propylene glycol) (PPG) parts. Atomic force microscopy was used to investigate the interactions of the triblock copolymers with plasmid DNA at the single molecule level and to enlighten the mechanism involved in DNA condensation.
Physically Plausible Spectral Reconstruction (2020)

Spectral reconstruction algorithms recover spectra from RGB sensor responses. Recent methods-with the very best algorithms using deep learning-can already solve this problem with good spectral accuracy. However, the recovered spectra are physically incorrect in that they do not induce the RGBs from which they are recovered. Moreover, if the exposure of the RGB image changes then the recovery performance often degrades significantly-i.e., most contemporary methods only work for a fixed exposure. In this paper, we develop a physically accurate recovery method: the spectra we recover provably induce the same RGBs. Key to our approach is the idea that the set of spectra that integrate to the same RGB can be expressed as the sum of a unique fundamental metamer (spanned by the camera's spectral sensitivities and linearly related to the RGB) and a linear combination of a vector space of metameric blacks (orthogonal to the spectral sensitivities). Physically plausible spectral recovery resorts to finding a spectrum that adheres to the fundamental metamer plus metameric black decomposition. To further ensure spectral recovery that is robust to changes in exposure, we incorporate exposure changes in the training stage of the developed method. In experiments we evaluate how well the methods recover spectra and predict the actual RGBs and RGBs under different viewing conditions (changing illuminations and/or cameras). The results show that our method generally improves the state-of-the-art spectral recovery (with more stabilized performance when exposure varies) and provides zero colorimetric error. Moreover, our method significantly improves the color fidelity under different viewing conditions, with up to a 60% reduction in some cases.
The Coalition Policy Management Portal for Policy Authoring, Verification, and Deployment (2008)

We are investigating computing platform-independent policy frameworks to specify, analyze, and deploy security and networking policies. The goal is to provide easy to use mechanisms for refining high-level user-specified goals into low-level controls. This scenario-based demo of a Coalition Policy Management Portal prototype uses the context of a hostage rescue situation to demonstrate usable and effective policy authoring through either natural language or structured lists that create natural language policy rules; policy visualization; analysis of policies for conflict, dominance, and coverage, and methods to resolve the issues identified; policy transformation from natural language to XML or ACPL SPL for automated enforcement, and deployment of policies onto mission equipment. The prototype builds on the SPARCLE and PONDER2 research projects.
Treatment of aggressive multiple myeloma by high-dose chemotherapy and total body irradiation followed by blood stem cells autologous graft (1989)

Eight patients with stage III aggressive multiple myeloma, refractory to current chemotherapy in six cases, were treated by high-dose chemotherapy (nitrosourea, etoposide, and melphalan) (HDC) and total body irradiation (TBI), followed by autografting with blood stem cells. These cells were previously collected by leukapheresis performed during hematologic recovery following cytotoxic drug-induced bone marrow aplasia. Seven patients were alive 9 to 17 months after HDC-TBI and graft. One died at day 40 from cerebral bleeding. All living patients achieved a 90% or greater reduction in tumor mass. In two cases, a complete remission (CR) has persisted at a follow-up of 15 and 16 months. Three patients have been well and off therapy with stable minimal residual disease (RD) since 10, 11, and 17 months, respectively. A patient in apparent CR and another with RD have relapsed 9 to 12 months posttreatment. Autologous blood-derived hematopoietic stem cells induced successful and sustained engraftment in all living patients. These results, although still preliminary, indicate that HDC and TBI, followed by blood stem cells autograft, which has both practical and theoretical interest over allogeneic or autologous bone marrow transplantation, deserve consideration in selected patients with multiple myeloma.
An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery (2016)

Meeting the increasing food and energy demands of a growing population will require the development of ground-breaking strategies that promote sustainable plant production. Host-induced gene silencing has shown great potential for controlling pest and diseases in crop plants. However, while delivery of inhibitory noncoding double-stranded (ds)RNA by transgenic expression is a promising concept, it requires the generation of transgenic crop plants which may cause substantial delay for application strategies depending on the transformability and genetic stability of the crop plant species. Using the agronomically important barley-Fusarium graminearum pathosystem, we alternatively demonstrate that a spray application of a long noncoding dsRNA (791 nt CYP3-dsRNA), which targets the three fungal cytochrome P450 lanosterol C-14α-demethylases, required for biosynthesis of fungal ergosterol, inhibits fungal growth in the directly sprayed (local) as well as the non-sprayed (distal) parts of detached leaves. Unexpectedly, efficient spray-induced control of fungal infections in the distal tissue involved passage of CYP3-dsRNA via the plant vascular system and processing into small interfering (si)RNAs by fungal DICER-LIKE 1 (FgDCL-1) after uptake by the pathogen. We discuss important consequences of this new finding on future RNA-based disease control strategies. Given the ease of design, high specificity, and applicability to diverse pathogens, the use of target-specific dsRNA as an anti-fungal agent offers unprecedented potential as a new plant protection strategy.
Synthesis of Oligodeoxynucleotides Containing N4-Mercaptoethylcytosine and Their Use in the Preparation of Oligonucleotide−Peptide Conjugates Carrying c-myc Tag-Sequence (1998)

The preparation and properties of oligodeoxynucleotides containing mercaptoethyl groups at position N-4 of cytosine are described. The resulting thiol-oligodeoxynucleotides were reacted with a maleimido-peptide carrying the c-myc tag-sequence. The peptide-oligonucleotide conjugate is specifically recognized by an anti c-myc monoclonal antibody, thus constituting a labeling system with sensitivity similar to other existing methods of nonradioactive labeling.
Codeword Metric Calculation Scheme for Outer Code in Overloaded MIMO-OFDM System (2015)

This paper presents a codeword metric calculation scheme in two step joint decoding of block coded signals in an overloaded multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) system. In the previous literature, the two step joint decoding scheme has been proposed for the complexity reduction of joint maximum likelihood decoding in the overloaded MIMO system. However, the two step decoding scheme has not been combined with an outer code. The selection of the candidate codewords in the inner block code may not always be able to provide the metric of a binary coded symbol for the outer code. The metric of the binary coded symbol calculated in the first stage is used in the proposed scheme. It is shown that the proposed two step decoding scheme shows better performance than a bit flipping based scheme and reduces the complexity by about 0.013 for 4 signal streams with the cost of bit error rate degradation within 0.5dB.
Correlation of Patient Confidence in Attaining Treatment Goals and Outcomes After Knee Arthroplasty (2013)

Introduction: Total knee arthroplasty (TKA) outcomes drive assessment of quality and reinvestment; therefore a risk stratified assessment is paramount for fair evaluation. Stratification can be affected by multiple factors including patient motivation. This study attempted to identify the correlation of patient9s preoperative confidence in their ability to return to desired activity level after TKA and improved function and outcomes. Methods: A continuous series of TKA procedures from 2008 to 2010 in a healthcare system was reviewed retrospectively. Patients included reported pre- and postoperative knee injury and osteoarthritis outcomes scores (KOOS), SF-12 scores, and responded a question regarding the desired activity level, including the level of confidence (0–10 scale) in attaining such goals, after surgery. Gender, age, body mass index, education level, smoking status, length of stay (LOS), 30-day readmission and reoperation, and 1-year infection rates were collected. Correlation of patient confidence in attaining treatment goals and the outcomes collected was established using multiple linear and logistic regression models adjusted for baseline mental and functional scores. Results: A total of 1020 primary, 18 bilateral and 177 revision TKA patients completed their postoperative questionnaires and had an average follow-up of 430, 411 and 376 days, respectively. Patients were confident in achieving treatment goals with an average score of 7.7 ± 2.1, 9.3 ± 0.5 and 6.4 ± 2.6 for primary, bilateral and revision TKA, respectively. There was direct correlation of level of confidence and shorter LOS (p = 0.005), and no correlation with readmission, reoperation and infection. Moreover, confidence was correlated with improved function and pain KOOS (p Conclusion: Patient confidence in attaining treatment goals after primary TKA has a direct correlation with shorter LOS and improved function. Patient motivation should be weighted when measuring TKA outcomes.
High-temperature viscous carbon flow for the growth of single-wall carbon nanotubes (2000)

The growth of soot-like carbonaceous materials were studied by shadowgraphy during 20 ms CO2laser pulse irradiation of a graphite-Co/Ni composite target in an Ar atmosphere at room temperature. Carbonaceous deposits were characterized by Raman scattering and transmission electron microscopy. We discuss the formation process of single-wall carbon nanotubes in a high-temperature viscous carbon flow.
A New High-Performance Gadonanotube-Polymer Hybrid Material for Stem Cell Labeling and Tracking by MRI (2018)

A gentle, rapid method has been developed to introduce a polyacrylic acid (PAA) polymer coating on the surface of gadonanotubes (GNTs) which significantly increases their dispersibility in water without the need of a surfactant. As a result, the polymer, with its many carboxylic acid groups, coats the surface of the GNTs to form a new GNT-polymer hybrid material (PAA-GNT) which can be highly dispersed in water (ca. 20 mg·mL<sup>-1</sup>) at physiological pH. When dispersed in water, the new PAA-GNT material is a powerful MRI contrast agent with an extremely short water proton spin-lattice relaxation time (<i>T</i><sub>1</sub>) which results in a <i>T</i><sub>1</sub>-weighted relaxivity of 150 mM<sup>-1</sup>·s<sup>-1</sup> per Gd<sup>3+</sup> ion at 1.5 T. Furthermore, the PAA-GNTs have been used to safely label porcine bone-marrow-derived mesenchymal stem cells for magnetic resonance imaging. The labeled cells display excellent image contrast in phantom imaging experiments, and transmission electron microscopy images of the labeled cells reveal the presence of highly dispersed PAA-GNTs within the cytoplasm with 10<sup>14</sup> Gd<sup>3+</sup> ions per cell.
Abstract 883: PRDX4 as a novel target for pancreatic cancer (2019)

Abstract Pancreatic cancer (PCa) is a fatal malignancy showing a 5% 5-year survival rate, creating an urgent need for new therapeutic targets. Many cancers have high production of reactive oxygen species (ROS), leaving them potentially vulnerable to targeting proteins involved in ROS metabolism. In line with this, we identified Peroxiredoxin 4 (PRDX4) as an essential gene in 26% of pancreatic cell lines by mining functional genomics datasets. PRDX4 is localized in the endoplasmic reticulum (ER) where it metabolizes H2O2. We validated in nine established PCa cell lines and patient derived primary cell lines that depletion of PRDX4 using siRNA or shRNA leads to inhibition of proliferation and cell death in a subset of pancreatic cancer cells. This was accompanied by increased levels of reactive oxygen species (ROS) as measured by flow cytometry. Dual-Depletion of NADPH oxidase 4 (NOX4) and PRDX4 could rescue the cell death phenotype thereby indicating that increase in ROS was a consequence of NOX4 activity. PRDX4 depletion led to focal accumulation of phosphorylated H2AX (γH2AX) in the cellular nuclei, consistent with DNA damage. Phosphorylation of H2AX was exclusively dependent upon activation of the upstream kinase DNA-PKcs. Cells depleted for PRDX4 were also more sensitive to ionizing radiation. Depleting PRDX4 with inducible shRNA in established xenografts inhibited tumor growth. Finally, using transcriptome data accompanying the functional genomics datasets, we identified a 2-gene expression signature that predicts sensitivity to PRDX4 targeting. This study indicates that depletion of PRDX4 causes increased ROS resulting in DNA damage leading to DNA-PKcs activation, inhibition of proliferation and cell death in a subset of pancreatic cancers. PRDX4 is a potential novel therapeutic target that may act synergistically with radiation therapy. Citation Format: Pallavi Jain, Azin Sayad, Erik Mollen, Michael Xie, Kevin Brown, Jason Moffat, David Hedley, Paul Boutros, Bradley Wouters, Marianne Koritzinsky. PRDX4 as a novel target for pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 883.
Evaluation of Canadian and Other Wheats for Waxy Proteins (1997)

Peer reviewed: Yes
N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses (2019)

A species barrier for the influenza A virus is the differential expression of sialic acid, which can either be α2,3-linked for avians or α2,6-linked for human viruses. The influenza A virus hosts also express other species-specific sialic acid derivatives. One major modification at C-5 is N-glycolyl (NeuGc), instead of N-acetyl (NeuAc). N-glycolyl is mammalian specific and expressed in pigs and horses, but not in humans, ferrets, seals, or dogs. Hemagglutinin (HA) adaptation to either N-acetyl or N-glycolyl is analyzed on a sialoside microarray containing both α2,3- and α2,6-linkage modifications on biologically relevant N-glycans. Binding studies reveal that avian, human, and equine HAs bind either N-glycolyl or N-acetyl. Structural data on N-glycolyl binding HA proteins of both H5 and H7 origin describe this specificity. Neuraminidases can cleave N-glycolyl efficiently, and tissue-binding studies reveal strict species specificity. The exclusive manner in which influenza A viruses differentiate between N-glycolyl and N-acetyl is indicative of selection.
Cherenkov emission from external beam irradiation: proportional to the dose buildup gradient and inversely affected by tissue optical attenuation (2020)

Cherenkov light emission from tissue undergoing radiation therapy is a complex function of the dose deposition and is reduced by the optical attenuation of the tissue. A diffusion theory based integral of the remitted light is presented, using the assumption that only Cherenkov photons from the first 8 mm of tissue are able to appreciably escape from the surface. This depth restriction falls within the linear build-up region for both electron and photon beams used in radiotherapy. The resulting expression for Cherenkov light fluence formulated here indicates that the outgoing intensity is dependent upon the quasi-linear dose build up gradient (k<sub>2</sub>) in the first 8 mm of tissue, is inversely proportional to the optical absorption (&mu;<sub>a</sub>), and is relatively independent of the scattering coefficient (&mu;<sub>s</sub> <sup>/</sup> ). Numerical evaluation suggests that the diffuse component of Cherenkov light emission dominates over any unscattered photons, suggesting that the radiation build-up factor dominates what is imaged off the surface. This observation could allow for linear corrections to Cherenkov images with knowledge of tissue optical properties and for better interpretation of the origin of Cherenkov from tissue.
EFFECT OF BREASTFEEDING ON GASTROINTESTINAL INFECTION IN INFANTS: A TARGETED MAXIMUM LIKELIHOOD APPROACH FOR CLUSTERED LONGITUDINAL DATA (2013)

The PROmotion of Breastfeeding Intervention Trial (PROBIT) cluster-randomized a program encouraging breastfeeding to new mothers in hospital centers. The original studies indicated that this intervention successfully increased duration of breastfeeding and lowered rates of gastrointestinal tract infections in newborns. Additional scientific and popular interest lies in determining the causal effect of longer breastfeeding on gastrointestinal infection. In this study, we estimate the expected infection count under various lengths of breastfeeding in order to estimate the effect of breastfeeding duration on infection. Due to the presence of baseline and time-dependent confounding, specialized "causal" estimation methods are required. We demonstrate the double-robust method of Targeted Maximum Likelihood Estimation (TMLE) in the context of this application and review some related methods and the adjustments required to account for clustering. We compare TMLE (implemented both parametrically and using a data-adaptive algorithm) to other causal methods for this example. In addition, we conduct a simulation study to determine (1) the effectiveness of controlling for clustering indicators when cluster-specific confounders are unmeasured and (2) the importance of using data-adaptive TMLE.