gebhart/patrepeval huggingface dataset:
Reliability-Based Precancellation of Inter-Carrier Interference for Highly Mobile OFDM Systems (2012)

Orthogonal Frequency Division Multiplexing (OFDM) systems in fast time-varying channels suffer from inter-carrier interference (ICI), which necessitates the use of ICI mitigating equalizers. The performance of the equalizers strongly depends on the channel estimation (CE). Estimating the channel matrix in the frequency domain using pilot estimates can only provide limited performance, because pilots are also corrupted by ICI. We propose two approaches for reliability-based ICI precancellation at the receiver to improve CE. Firstly, a log-likelihood ratio window is used to optimize the interpolation points for CE. Secondly, a post-processor is employed to improve the estimates of the pilots' neighbours. The low-complexity minimum mean squared error decision feedback frequency equalizer, which exploits the banded structure of the channel matrix, showed increased performance gains after ICI precancellation.
Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: Enzymes in the Wbp Pathway Responsible for O-Antigen Assembly in Pseudomonas aeruginosa PAO1 (2009)

The B-band O-antigen of the lipopolysaccharide found in the opportunistic pathogen Pseudomonas aeruginosa PAO1 (serotype O5) comprises a repeating trisaccharide unit that is critical for virulence and protection from host defense systems. One of the carbohydrates in this repeating unit, the rare diacetylated aminuronic acid derivative 2,3-diacetamido-2,3-dideoxy-beta-d-mannuronic acid (ManNAc(3NAc)A), is thought to be produced by five enzymes (WbpA, WbpB, WbpE, WbpD, and WbpI) in a stepwise manner starting from UDP-GlcNAc. Although the genes responsible for the biosynthesis of this sugar are known, only two of the five encoded proteins (WbpA and WbpI) have been thoroughly investigated. In this report, we describe the cloning, overexpression, purification, and biochemical characterization of the three central enzymes in this pathway, WbpB, WbpE, and WbpD. Using a combination of capillary electrophoresis, RP-HPLC, and NMR spectroscopy, we show that WbpB and WbpE are a dehydrogenase/aminotransferase pair that converts UDP-GlcNAcA to UDP-GlcNAc(3NH(2))A in a coupled reaction via a unique NAD(+) recycling pathway. In addition, we confirm that WbpD catalyzes the acetylation of UDP-GlcNAc(3NH(2))A to give UDP-GlcNAc(3NAc)A. Notably, WbpA, WbpB, WbpE, WbpD, and WbpI can be combined in vitro to generate UDP-ManNAc(3NAc)A in a single reaction vessel, thereby providing supplies of this complex glycosyl donor for future studies of lipopolysaccharide assembly. This work completes the biochemical characterization of the enzymes in this pathway and provides novel targets for potential therapeutics to combat infections with drug resistant P. aeruginosa strains.
SARS-CoV-2 infection increases the gene expression profile for Alzheimer’s disease risk (2022)

The coronavirus disease 2019 (COVID-19) pandemic has caused over 600,000,000 infections globally thus far. Up to 30% of individuals with mild to severe disease develop long COVID, exhibiting diverse neurologic symptoms including dementias. However, there is a paucity of knowledge of molecular brain markers and whether these can precipitate the onset of Alzheimer's disease (AD). Herein, we report the brain gene expression profiles of severe COVID-19 patients showing increased expression of innate immune response genes and genes implicated in AD pathogenesis. The use of a mouse-adapted strain of SARS-CoV-2 (MA10) in an aged mouse model shows evidence of viral neurotropism, prolonged viral infection, increased expression of tau aggregator FKBP51, interferon-inducible gene <i>Ifi204</i>, and complement genes C4 and C5AR1. Brain histopathology shows AD signatures including increased tau-phosphorylation, tau-oligomerization, and α-synuclein expression in aged MA10 infected mice. The results of gene expression profiling of SARS-CoV-2-infected and AD brains and studies in the MA10 aged mouse model taken together, for the first time provide evidence suggesting that SARS-CoV-2 infection alters expression of genes in the brain associated with the development of AD. Future studies of common molecular markers in SARS-CoV-2 infection and AD could be useful for developing novel therapies targeting AD.
Detecting Gait Asymmetry with Wearable Accelerometers (2015)

Abstract : Gait asymmetry can be a useful indicator of a variety of medical and pathological conditions, including musculoskeletal injury (MSI), neurological damage associated with stroke or head trauma, and a variety of age-related disorders. Body-worn accelerometers provide the ability for real-time monitoring and detection of changes in gait asymmetry, thereby providing continuous real-time information about medical conditions and enabling timely interventions. We propose practical and robust algorithms for detecting gait asymmetry using features extracted from accelerometers attached to each foot. By registering simultaneous acceleration differences between the two feet, these asymmetry features provide robustness to a variety of confounding factors, such as changes in walking speed and load carriage. Because the algorithms require only summary statistics obtained from each frame (i.e., contiguous block) of accelerometer data, they can potentially be implemented in real-time physiological status monitoring systems, which may operate under severe limitations in power, computation, and communication bandwidth. We evaluate the algorithms on a data collection consisting of 24 subjects with multiple levels of induced gait asymmetries in both indoor and outdoor natural walking conditions. Changes in magnitude and pattern asymmetry features are sensitive to the sign and magnitude of gait asymmetry and provide the ability to detect and track asymmetries during continuous monitoring. By creating individualized background models from short data collections of normal walking, the algorithms are able to reliably detect asymmetrical walking induced by small ankle weights during short duration walking trials. Moreover, the background models and the test data are derived from both indoor and outdoor walking trials, where the outdoor walking contained uphill and downhill grades.
Orthologous Mammalian APOBEC3A Cytidine Deaminases Hypermutate Nuclear DNA (2013)

The human APOBEC3 gene cluster locus encodes polynucleotide cytidine deaminases. Although many act as viral restriction factors through mutation of single-stranded DNA, recent reports have shown that human APOBEC3A was capable of efficiently hypermutating nuclear DNA and inducing DNA breaks in genomic DNA. In addition, the enzyme was unique in efficiently deaminating 5-methylcytidine in single-stranded DNA. To appreciate the evolutionary relevance of these activities, we analyzed A3A-related enzymes from the rhesus and tamarin monkey, horse, sheep, dog, and panda. All proved to be orthologous to the human enzyme in all these activities revealing strong conservation more than 148 My. Hence, their singular role in DNA catabolism is a well-established mechanism probably outweighing any deleterious or pathological roles such as genomic instability and cancer formation.
Role of bone scan in addition to CT in patients with breast cancer selected for systemic staging (2016)

For patients diagnosed with breast cancer, CT-TAP is a satisfactory stand-alone investigation for systemic staging.
Off‐angle dependence of void formation and defect behavior in a ‐plane MOVPE‐GaN on r ‐plane sapphire substrate (2009)

Abstract Transmission electron microscope (TEM) observation was performed to analyze microstructures in a (11 $ \bar 2 $ 0)‐plane GaN thin films grown by metal‐organic vapor‐phase epitaxy (MOVPE) on a r (1 $ \bar 1 $ 02)‐plane sapphire substrate Special attention was paid to an influence of small off‐angle of the substrate plane to morphology of defects in the thin films. From the TEM observation, the following results were drawn. (1) The crystallographic orientation relationship between GaN and sapphire substrate is (11 $ \bar 2 $ 0)[0001][ $ \bar 1 $ 100] GaN // (1 $ \bar 1 $ 02)[ $ \bar 1 $ 101][11 $ \bar 2 $ 0] sapphire . The direction of + c ‐polarity coincides with that reported previously. (2) The pits on the surface are formed on the grain boundaries of GaN. (3) The density of pits is related with the density of nucleation of GaN‐islands on the substrate. The increase in density of pits with the off‐angle can be explained by the increase of nucleation sites provided by atomic steps on the substrate. (4) The side‐wall planes of pits and voids are considered to be closed to ±(0001), ±(11 $ \bar 2 $ 4), and (11 $ \bar 2 $ 2). (5) The formation of pits and voids are attributable to the trend that such inclining planes as (11 $ \bar 2 $ 2) and (11 $ \bar 2 $ 4) are stable compared with + c (0001). A possible technique for reduction of defects is also discussed. (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Design acceleration of embedded RF inductors on a multilayer flip chip package substrate (2011)

The electrical performance and the design challenges associated with radio frequency inductors on advanced multilayer package substrates are evaluated. First, new macro-models are developed and can be used to optimize the performance of RF components under process design rules constraints. Then, a novel scalable compact model that utilizes only frequency independent RLC components is introduced. This model is able to represent non linear frequency dependent effects such as skin effect and internal inductance. This compact model is validated using on-package measurements and also used to design a simple RF low pass filter.
Validation of protein arginine methyltransferase 5 (PRMT5) as a candidate therapeutic target in the spontaneous canine model of non-Hodgkin lymphoma (2021)

Non-Hodgkin lymphoma (NHL) is a heterogeneous group of blood cancers arising in lymphoid tissues that commonly effects both humans and dogs. Protein arginine methyltransferase 5 (PRMT5), an enzyme that catalyzes the symmetric di-methylation of arginine residues, is frequently overexpressed and dysregulated in both human solid and hematologic malignancies. In human lymphoma, PRMT5 is a known driver of malignant transformation and oncogenesis, however, the expression and role of PRMT5 in canine lymphoma has not been explored. To explore canine lymphoma as a useful comparison to human lymphoma while validating PRMT5 as a rational therapeutic target in both, we characterized expression patterns of PRMT5 in canine lymphoma tissue microarrays, primary lymphoid biopsies, and canine lymphoma-derived cell lines. The inhibition of PRMT5 led to growth suppression and induction of apoptosis, while selectively decreasing global marks of symmetric dimethylarginine (SDMA) and histone H4 arginine 3 symmetric dimethylation. We performed ATAC-sequencing and gene expression microarrays with pathway enrichment analysis to characterize genome-wide changes in chromatin accessibility and whole-transcriptome changes in canine lymphoma cells lines upon PRMT5 inhibition. This work validates PRMT5 as a promising therapeutic target for canine lymphoma and supports the continued use of the spontaneously occurring canine lymphoma model for the preclinical development of PRMT5 inhibitors for the treatment of human NHL.
Supplementary Figure 2 from Sangivamycin-like Molecule 6 Exhibits Potent Anti-Multiple Myeloma Activity through Inhibition of Cyclin-Dependent Kinase-9 (2023)

&lt;p&gt;PDF file, 106K, SLM6 toxicity studies in C57BL/6 immunocompetent mice.&lt;/p&gt;
Magnetic field effect on periodic stripe domains in nematic liquid crystals (1995)

Hybrid aligned nematic films placed onto an isotropic fluid substrate exhibit an unusual periodic stripe domain structure that appears only when the thickness of the film is smaller than a few tenths of a micrometer. We investigated the effect of a magnetic field on the threshold between the periodic stripe domains and the aperiodic deformed structure of the director. As experimentally observed, a magnetic field applied along the stripe domains favors a nonperiodic state with the director undistorted in the horizontal plane. The experimental findings are confirmed by a theory that takes into account not only the usual type of the elastic distortions, but also the so-called saddle-splay elasticity. A comparison of the experimental and theoretical data allows one to estimate that the saddle-splay elastic constant ${\mathit{K}}_{24}$ is of the same order of magnitude as the bulk elastic constants; this result agrees with independent studies of confined liquid crystal systems.
Recent challenges in condition monitoring of industrial electric machines (2020)

The limitations of thermal, vibration, or electrical monitoring of electric machines such as false indications, low sensitivity, and difficulty of fault interpretation have recently been exposed. This has led to a shift in the direction in research towards applying new techniques for improving the reliability of condition monitoring. With the changing environment, the purpose of this article is to provide an overview of the recent trend in the industrial demand and research activity in condition monitoring technology. The new developments in insulation testing, electrical testing, flux analysis, transient analysis, and fault prognostics are summarized. The future challenges and recommendations for future work for the new technologies are also stated to support researchers target research/development efforts according to industrial needs.
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection (2021)

SARS-CoV-2 virus has infected more than 92 million people worldwide resulting in the Coronavirus disease 2019 (COVID-19). Using a rhesus macaque model of SARS-CoV-2 infection, we have characterized the transcriptional signatures induced in the lungs of juvenile and old macaques following infection. Genes associated with Interferon (IFN) signaling, neutrophil degranulation and innate immune pathways are significantly induced in macaque infected lungs, while pathways associated with collagen formation are downregulated, as also seen in lungs of macaques with tuberculosis. In COVID-19, increasing age is a significant risk factor for poor prognosis and increased mortality. Type I IFN and Notch signaling pathways are significantly upregulated in lungs of juvenile infected macaques when compared with old infected macaques. These results are corroborated with increased peripheral neutrophil counts and neutrophil lymphocyte ratio in older individuals with COVID-19 disease. Together, our transcriptomic studies have delineated disease pathways that improve our understanding of the immunopathogenesis of COVID-19.
200-fs optical pulse generation and intracavity pulse evolution in a hybrid mode-locked semiconductor diode-laser/amplifier system (1992)

Optical pulses of 200 fs with 165 W of peak power have been generated from an AlGaAs semiconductor diode-laser system. These pulses represent, to our knowledge, both the shortest and most intense ever generated from an all-semiconductor injection diode-laser system. The intracavity pulse evolution in the external cavity is also investigated experimentally. The findings show that the large nonlinearities associated with gain depletion and saturable absorption cause appreciable spectral and temporal modification of the mode-locked optical pulse as it oscillates in the laser cavity.
Temperature sensitive absorption characteristics of polyamides (2009)

We investigate the temperature dependent absorption characteristics of polyamides (PA) in the terahertz frequency range. The absorption spectra can be explained by inter-molecular bonding mechanisms. Experimental data is obtained by terahertz time-domain spectroscopy (THzTDS) on injection-molded specimens as well as on molten polyamides at different temperatures. The THzTDS data is compared to FTIR measurements. Additionally, we present density functional theory simulations of PA66 that clarify the origin of the well-known absorption peaks located at approximately 3 THz and 9 THz, respectively.
Methods for Fast Computation of Integral Transforms (1994)

This paper is concerned with two aspects of the numerical calculation of integral transforms. The first is finding a necessary and sufficient condition that enables converting an integral transform into a correlation (convolution) form. The condition and the transformation that implements it are generalizations of the Gardner transformation and derived in the paper. This technique can be applied to a wide class of integral transforms and is shown to reduce the computational complexity and storage requirements of the resulting algorithm. The second issue addressed in the paper is the accuracy of the calculation of the correlation integral, obtained by the above transformation, for a given number of samples. It is shown how the standard FFT method can be applied in combination with various numerical integration rules. This proves to be an important factor in expediting the computations, reducing the storage requirements, and improving the accuracy.
Amantadine Increases Gait Steadiness in Frontal Gait Disorder due to Subcortical Vascular Encephalopathy: A Double-Blind Randomized Placebo-Controlled Trial Based on Quantitative Gait Analysis (2001)

In a randomized, double-blind placebo-controlled trial, 40 patients diagnosed as subcortical vascular encephalopathy (SVE) were given a daily dose of 500 ml i.v. amantadine vs. placebo for 5 days. Both groups were treated with physiotherapy on a daily basis. Quantitative gait analyses were performed at days 1 and 6 to evaluate gait steadiness from cadence, length of heel-to-toe movements, variability of centre of gravity (COG) and double support time. Both placebo- and amantadine-receiving patient groups showed mild improvement in gait parameters after study, which failed to show the superiority of amantadine, when comparing drug-induced changes between both groups. However, analysing the treatment effects from day 0 to day 6 in both groups separately, statistically significant changes could be found in the amantadine group for cadence, length of heel-to-toe movements in single support phase as well as for variability in double support phase and double support time (two-tailed paired t-test, p < 0.05), whereas in the placebo group, a statistically significant effect could only be seen for double support time (p < 0.05). In this small pilot study, amantadine tends to improve gait steadiness as evaluated by cadence, length of heel-to-toe movements in single support phase, variability in double support phase and double support time, in patients with moderate frontal gait disorder due to SVE. Improvements in the placebo group can be interpreted as physiotherapy effect, which improved gait steadiness slightly, however, this was statistically significant only for double support time.
Experience with the VHDL environment (2003)

The authors present their work in the use of the VHDL (VHSIC Hardware Development Language) environment on three different models of DEC VAX (1, 4, and 5.8 Mips (million instruction per second)). The work included the development of a number of VHDL models and sequences of input stimuli and the gathering of performance data from their execution. Even though the set of benchmarks is not in any way exhaustive, they represent typical applications, making it possible to derive performance models for predicting both time and memory requirements for VHDL modeling and simulation. It is shown that the performances of the VHDL environment on the three computers correlate perfectly with their Mips figures; thus the performance models developed can be normalized to a 1-Mips VAX machine.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Controlled orientation of molecular-beam-epitaxial BaTiO3on Si(001) using thickness engineering of BaTiO3and SrTiO3buffer layers (2017)

Monolithically integrating BaTiO on silicon substrates has attracted attention because of the wide spectrum of potential novel applications ranging from electronics to photonics. For optimal device performance, it is important to control the BaTiO domain orientation during thin film preparation. Here, we use molecular beam epitaxy to prepare crystalline BaTiO on Si(001) substrates using a SrTiO buffer layer. A systematic investigation is performed to understand how to control the BaTiO domain orientation through the thickness engineering of the SrTiO buffer layer and the BaTiO layer itself. This provides different possibilities for obtaining a given BaTiO orientation as desired for a specific device application.
Fungi that Infect Humans (2017)

In its short history of a century and a half, of which the last half-century brought the most dramatic advances, scientific medicine has found ways to cure or to treat millions of ill people who 200 years ago would have died early. Paradoxically, these successes of modern medicine have given rise to large groups of people at risk for fungal infections. Life-saving treatments may now breach normal immune functions, or susceptible patients such as premature newborns now survive long enough to become infected by a fungus. Invasive fungal infections have been very rare over most of our species' history (1), and the fungi that infect healthy humans are a small, if fascinating, group. Many more invasive fungal infections now occur in patients with an underlying serious illness.
A tangent formula derived from Patterson-function arguments. III. Structure determination of zeolitic and layered materials from low-resolution powder diffraction data (1995)

The viability of solving the structure type of zeolitic and layered materials applying multisolution direct methods to low-resolution (~2.2 Å) powder diffraction data is shown. The phases are refined with the tangent formula derived from Patterson-function arguments [Rius (1993). Acta Cryst. A49, 406–409] and the correct phase sets are discriminated with the conventional figures of merit. The two test examples presented are (a) the already known tetragonal zeolite ZSM-11 (space group 1{\bar 4}m2) at 2.3 Å resolution and (b) the hitherto unknown layer silicate RUB-15 (Ibam) at 2.2 Å resolution. In both cases, the tetrahedral Si units appear as resolved peaks in the Fourier maps computed with the phases of the highest-ranked direct-methods solutions.
Adaptive Prediction Model in Prospective Molecular Signature–Based Clinical Studies (2013)

Use of molecular profiles and clinical information can help predict which treatment would give the best outcome and survival for each individual patient, and thus guide optimal therapy, which offers great promise for the future of clinical trials and practice. High prediction accuracy is essential for selecting the best treatment plan. The gold standard for evaluating the prediction models is prospective clinical studies, in which patients are enrolled sequentially. However, there is no statistical method using this sequential feature to adapt the prediction model to the current patient cohort. In this article, we propose a reweighted random forest (RWRF) model, which updates the weight of each decision tree whenever additional patient information is available, to account for the potential heterogeneity between training and testing data. A simulation study and a lung cancer example are used to show that the proposed method can adapt the prediction model to current patients' characteristics, and, therefore, can improve prediction accuracy significantly. We also show that the proposed method can identify important and consistent predictive variables. Compared with rebuilding the prediction model, the RWRF updates a well-tested model gradually, and all of the adaptive procedure/parameters used in the RWRF model are prespecified before patient recruitment, which are important practical advantages for prospective clinical studies.