gebhart/patrepeval huggingface dataset:
Identification of RNA editing sites in the SNP database (2005)

The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications.
3D Point Cloud Registration for Localization Using a Deep Neural Network Auto-Encoder (2017)

We present an algorithm for registration between a large-scale point cloud and a close-proximity scanned point cloud, providing a localization solution that is fully independent of prior information about the initial positions of the two point cloud coordinate systems. The algorithm, denoted LORAX, selects super-points-local subsets of points-and describes the geometric structure of each with a low-dimensional descriptor. These descriptors are then used to infer potential matching regions for an efficient coarse registration process, followed by a fine-tuning stage. The set of super-points is selected by covering the point clouds with overlapping spheres, and then filtering out those of low-quality or nonsalient regions. The descriptors are computed using state-of-the-art unsupervised machine learning, utilizing the technology of deep neural network based auto-encoders. Abstract This novel framework provides a strong alternative to the common practice of using manually designed key-point descriptors for coarse point cloud registration. Utilizing super-points instead of key-points allows the available geometrical data to be better exploited to find the correct transformation. Encoding local 3D geometric structures using a deep neural network auto-encoder instead of traditional descriptors continues the trend seen in other computer vision applications and indeed leads to superior results. The algorithm is tested on challenging point cloud registration datasets, and its advantages over previous approaches as well as its robustness to density changes, noise, and missing data are shown.
Prognostic factors for patients with localized soft‐tissue sarcoma treated with conservation surgery and radiation therapy (2003)

Soft-tissue sarcoma comprises a heterogeneous group of diseases. Prognostic factors for local recurrence, metastatic recurrence, lymph node recurrence, disease free survival, and disease specific survival are different, and optimal treatment strategies need to take this complexity into account.
Devices for launching 0. 1-g projectiles to 150 km/s or more to initiate fusion. Part 2. Railgun accelerators (1979)

The possibility of using a railgun accelerator to launch 0.1-g projectiles to hypervelocities (150 km/s or more) to initiate thermonuclear fusion is studied. The analysis revealed that a railgun with a plasma-arc armature is a viable approach to the goal. When calculating the railgun's probable performance, it was discovered that this launch system might possibly be designed to avoid adverse effects from boundary layer drag. An appendix provided by A.C. Buckingham summarizes his calculations that predict the amount of erosive drag between projectile and rail. Finally, it was found that certain properties of railgun and projectile materials can impose operational limits. Using these limits, single- and multistage accelerators were designed. Within such limits, a railgun could accelerate a 0.1-g projectile to hypervelocities.
Control of Second-Harmonic Generation in Dielectric Polaritonic Metasurfaces Using χ(2) Polarity Switching (2021)

We demonstrate microscopic control of optical nonlinearities in an intersubband polaritonic all-dielectric metasurface comprising of Mie resonators embedded with semiconductor heterostructures. Through heterostructure design, we control the polarity of the resonant χ (2) leading to suppression or enhancement of second-harmonic generation.
Percentage of the positive area of bone metastasis is an independent predictor of disease death in advanced prostate cancer (2003)

We addressed in this study whether quantifying the extent of disease on bone scans can predict the disease death of patients with advanced prostate cancer using computer-assisted image analysis. Pretreatment radionuclide bone scans were reviewed in 56 patients with bone metastases from prostate cancer, and the percentage of the positive area on a bone scan (%PABS) was quantified automatically using a personal computer with the NIH Image program for estimation of the accurate extent of metastatic bone lesions on a bone scan. The significance of the %PABS as well as the other known prognostic factors was evaluated using univariate and multivariate Cox proportional hazards analysis. In univariate regression analysis, the %PABS (P=0.0155), serum alkaline phosphatase (P=0.0272), the tumour grade based on biopsy (P=0.044) and the number of bone lesions on bone scans (P=0.0388) were well associated with disease-specific survival. In multivariate analysis, the %PABS (P=0.0155, relative risk ratio 2.603), but not the other factors, was the independent predictor of the disease death. These results suggest that the %PABS is a novel parameter for predicting the prognosis of patients with advanced prostatic cancer.
A novel sustained‐release matrix based on biodegradable poly(ester amide)s and impregnated with bacteriophages and an antibiotic shows promise in management of infected venous stasis ulcers and other poorly healing wounds (2002)

Healing of poorly vascularized and venous stasis ulcers is often refractory to therapy, particularly when they are infected. Systemic antibiotic therapy may be of little benefit in this setting because of poor penetration of the antibiotic into the wound and the frequent associated emergence of bacterial strains resistant to common antimicrobial agents. Given the clinical significance of these problems, there is a need to explore alternative management approaches for these difficult-to-treat wounds. PhagoBioDerm is a novel wound-healing preparation consisting of a biodegradable polymer impregnated with an antibiotic and lytic bacteriophages, which was recently licensed for sale in the Republic of Georgia (one of the former Soviet Union republics). In 1999-2000, in Tbilisi, Georgia, 107 patients who had ulcers that had failed to respond to conventional therapy were treated with PhagoBioDerm alone or in combination with other interventions. The wounds/ulcers healed completely in 67 (70%) of 96 patients for whom follow-up data were available. In 22 cases in which microbiologic data were available, healing was associated with the concomitant elimination of, or a reduction in, specific pathogenic bacteria in the ulcers. Our findings suggest that this slow-release biopolymer is safe and of possible benefit in the management of refractory wounds, and they support the apparent utility of bacteriophages in this setting. Further studies, including carefully designed clinical trials, will be required to rigorously evaluate the efficacy of this novel wound dressing preparation.
Supporting reusable Web design with HDM-Edit (2005)

As online and off-line electronic publishing is increasingly becoming a massive industrial activity, the design of Web applications, and of hypermedia applications in general, needs to become a well-organized and efficient process. If a good design model is the first item on the agenda, then immediately afterwards, design tools become necessary. This paper describes HDM-Edit (Hypermedia Design Model Editor), a schema editor that supports the conceptual design of Web (and, more generally, hypermedia) applications. HDM-Edit is a component of the JWeb system which supports all the phases of Web prototyping development. HDM-Edit can be used on its own, to support the design activity and the production of high-quality design documentation, or in conjunction with other JWeb modules. HDM-Edit promotes design reuse by supporting several navigation patterns as built-in modelling primitives and by allowing designers to derive the schema of a specific application as a set of hyperviews on the design of a family of applications (an application framework). This paper analyses the requirements for a design tool, outlines JWeb, describes HDM-Edit, discusses experiences of use, and finally compares the requirements with the current version of the tool.
Covering radius 1985-1994 (2002)

We survey important developments in the theory of covering radius during the period 1985-1994. We present lower bounds, constructions and upper bounds, the linear and nonlinear cases, density and asymptotic results, normality, specific classes of codes, covering radius and dual distance, tables, and open problems.
Review of printed Marchand and double Y baluns: characteristics and application (1994)

A review of printed baluns is presented. This is divided into two main groups; Marchand baluns (band pass networks) and double Y baluns (all pass networks). For each of these groups of baluns, three different realizations are given: microstrip-slot line, CPW-slot line and CPW/sub FGP/-CPS and their theoretical and experimental characteristics are compared. Simple expressions for the design of Marchand baluns with Chebyshev response, which replace the complicated synthesis proposed by Cloete are derived. Superior broadbandwidth features of double Y baluns are demonstrated in the design of two uniplanar double balanced mixers. Both the double Y mixer and the CPW/sub FGP/-CPS mixer have a frequency bandwidth 1:6, whilst maintaining other performance similar to that achieved with classical double balanced mixers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Specific serum and CSF microRNA profiles distinguish sporadic behavioural variant of frontotemporal dementia compared with Alzheimer patients and cognitively healthy controls (2018)

Information on circulating miRNAs in frontotemporal lobar degeneration is very limited and conflicting results have complicated an interpretation in Alzheimer's disease thus far. In the present study we I) collected samples from multiple clinical centers across Germany, II) defined 3 homogenous patient groups with high sample sizes (bvFTD n = 48, AD n = 48 and cognitively healthy controls n = 44), III) compared expression levels in both CSF and serum samples and IV) detected a limited set of miRNAs by using a MIQE compliant protocol based on SYBR-green miRCURY assays that have proven reliable to generate reproducible results. We included several quality controls that identified and reduced technical variation to increase the reliability of our data. We showed that the expression levels of circulating miRNAs measured in CSF did not correlate with levels in serum. Using cluster analysis we found expression pattern in serum that, in part, reflects the genomic organization and affiliation to a specific miRNA family and that were specifically altered in bvFTD, AD, and control groups. Applying factor analysis we identified a 3-factor model characterized by a miRNA signature that explained 80% of the variance classifying healthy controls with 97%, bvFTD with 77% and AD with 72% accuracy. MANOVA confirmed signals like miR-320a and miR-26b-5p at BH corrected significance that contributed most to discriminate bvFTD cases with 96% sensitivity and 90% specificity and AD cases with 89% sensitivity and specificity compared to healthy controls, respectively. Correlation analysis revealed that miRNAs from the 3-factor model also correlated with levels of protein biomarker amyloid-beta1-42 and phosphorylated neurofilament heavy chain, indicating their potential role in the monitoring of progressive neuronal degeneration. Our data show that miRNAs can be reproducibly measured in serum and CSF without pre-amplification and that serum includes higher expressed signals that demonstrate an overall better ability to classify bvFTD, AD and healthy controls compared to signals detected in CSF.
A Low-Cost Snap-Through-Buckling Inkjet-Printed Device for Vibrational Energy Harvesting (2014)

This paper covers a novel methodology for the realization of devices that are able to harvest energy from background mechanical vibrations. The novelties reside in the nonlinear mechanism ruling the harvester behavior and the printed technology used to realize the lab-scale prototype. The nonlinearity of the harvester is desirable, because vibrational energy is usually distributed in a band at low frequency and does not, therefore, lend itself to harvesting through a (linear) resonant device. Printed technology has the advantage of being ultracheap and, hence, suitable for proof-of-concept and rapid laboratory prototyping. In particular, inkjet printing technology affords the realization of low-cost electrodes with high resolution and multiple functional layers. This paper covers the mechanical properties of a snap-through buckling beam and details the results of experiments aimed at investigating the (nonlinear) mechanical properties as well as a theoretical fit to the experimental observations. Moreover, the electrical response of the device and, hence, its suitability for energy-harvesting applications are addressed. Powers on the order of 100 nW have been experimentally estimated by a lab-scale prototype with the aim of demonstrating the proof-of-concept of the snap-through buckling mechanism for energy harvesting.
Dissociation between plasma and monocyte‐associated cytokines during sepsis (1991)

We report our investigations of circulating interleukin (IL) 1 beta, IL 6 and tumor necrosis factor (TNF)-alpha, as well as cell-associated IL 1 alpha, IL 1 beta and TNF-alpha in plasma and monocytes of 21 patients with sepsis syndrome and 6 patients with non-septic shock. Longitudinal studies reveal that (a) the most frequent detectable plasma cytokines were TNF-alpha and IL 6, (b) the presence and the kinetics of circulating cytokines were independent of one other, (c) detectable levels of cytokines could be found for a long period of time, and (d) significantly higher levels of IL 6 were found for non-surviving patients. Because of the in vivo half-life of cytokines and of the existence of numerous specific high-affinity receptors, it is quite probable that detectable plasma cytokines represent the excess of produced mediators which have not been trapped by the target cells. TNF-alpha (410 +/- 65 pg/10(6) monocytes) and IL 1 beta (153 +/- 60 pg/10(6) monocytes) were frequently found associated to monocyte lysates (88% and 50%, respectively). Despite the fact that IL 1 alpha is the most abundant cytokine found associated to monocytes following in vitro activation, IL 1 alpha was rarely found in monocytes of intensive care unit patients (29%). No correlation was found to exist between the levels of plasma cytokines and cell-associated cytokines. Some patients had plasma TNF-alpha or IL 1 beta in the absence of the corresponding monocyte-associated cytokine. This observation suggests that cells other than monocytes can participate in the production of circulating cytokines. At the end of the longitudinal study (day 14 +/- 2), only 2/12 surviving patients still had plasma TNF-alpha, whereas 8/12 had monocyte-associated TNF-alpha. These results indicate that activation of monocytes still occurs in patients for whom no plasma cytokines can be detected. Thus, in addition to the measurement of plasma cytokine, measurement of cell-associated cytokine appears useful to assess cytokine production and monocyte activation in vivo.
Mutation of cysteine 46 in IKK-beta increases inflammatory responses (2015)

Activation of IκB kinase β (IKK-β) and nuclear factor (NF)-κB signaling contributes to cancer pathogenesis and inflammatory disease; therefore, the IKK-β-NF-κB signaling pathway is a potential therapeutic target. Current drug design strategies focus on blocking NF-κB signaling by binding to specific cysteine residues on IKK-β. However, mutations in IKK-β have been found in patients who may eventually develop drug resistance. For these patients, a new generation of IKK-β inhibitors are required to provide novel treatment options. We demonstrate in vitro that cysteine-46 (Cys-46) is an essential residue for IKK-β kinase activity. We then validate the role of Cys-46 in the pathogenesis of inflammation using delayed-type hypersensitivity (DTH) and an IKK-β C46A transgenic mouse model. We show that a novel IKK-β inhibitor, dihydromyricetin (DMY), has anti-inflammatory effects on WT DTH mice but not IKK-β C46A transgenic mice. These findings reveal the role of Cys-46 in the promotion of inflammatory responses, and suggest that Cys-46 is a novel drug-binding site for the inhibition of IKK-β.
Synthesis of g‐C<sub>3</sub>N<sub>4</sub> Nanoparticles in Mesoporous Silica Host Matrices (2005)

Highly crystalline g-C3N4 nanoparticles have been synthesized from molecular precursors via polycondensation, using mesoporous silica with different pore sizes as host matrices. The particles isolated after removal of the host matrix (see Figure) are characterized using electron microscopy and various spectroscopic techniques. Structural and electronic size effects are identified by comparing nanoparticles that are 5, 13, and 60 nm in diameter. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2005/c1756_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Reduction strategies for the Cardinality Constrained Knapsack problem (2017)

In the paper the Cardinality Constrained Knapsack Problem is considered. It is a variant of the Continuous Knapsack Problem in which no more than a specified number of variables are allowed to have positive values. This problem arises when a limited resource is allocated among competing activities, and an upper bound is imposed on the number of activities that can be selected in a solution. The Cardinality Constrained Knapsack Problem is NP-hard. We analyze the structural properties of its optimal solutions and propose procedure allowing to reduce the size of the original problem.
Recent Advances in Scaffold Hopping (2016)

Scaffold hopping refers to the computer-aided search for active compounds containing different core structures, which is a topic of high interest in medicinal chemistry. Herein foundations and caveats of scaffold hopping approaches are discussed and recent methodological developments analyzed. Despite the conceptual prevalence of pharmacophore methods for scaffold hopping, a variety of computational approaches have been successfully applied. In recent years, scaffold hopping calculations are increasingly carried out at the level of scaffolds rather than compounds, and scaffold queries increasingly abstract from chemical structures. In addition, relationships between compounds, scaffolds, and biological activities are beginning to be globally explored, beyond individual applications. Going forward, computational scaffold hopping is thought to benefit from the consideration of new scaffold concepts and the development of methods capable of guiding search calculations toward scaffolds that are likely to represent potent compounds.
Calcium–nickel–lithium oxide: a high selectivity catalyst for the oxidative dehydrogenation of ethane to ethylene (1993)

Novel calcium–nickel oxides promoted by alkali metal are shown to be highly selective for the oxidative dehydrogenation of ethane to ethylene; 93.6% selectivity for ethylene with 25% ethane conversion over Ca1Ni0.4Li0.35 oxide catalyst is attained at 600 °C.
Pulsed amperometric detection based on direct and indirect anodic reactions: A review (1989)

Abstract Pulsed amperometric detection (PAD) is applicable for the quantitative detection of numerous organic compounds that adsorb at noble metal electrodes but cannot be detected satisfactorily by conventional amperometry at constant (dc) applied potential. A multistep waveform is applied in PAD with chrono‐amperometric detection based on faradaic signals, which frequently are produced by surface‐controlled reactions. We briefly review applications of PAD for liquid chromatography and present a unified explanation of the various modes of anodic response.
Nicotinamide, a missing link in the early stress response in eukaryotic cells: A hypothesis with special reference to oxidative stress in plants (1994)

A hypothesis is presented suggesting that nicotinamide (NIC) is an initial signal substance in the response of eukaryotic cells to conditions which cause DNA-strand breakage, especially in connection with oxidative stress. In the stressed cell, NIC is released as a result of the activity of poly(ADP-ribose)polymerase (PADPRP). PADPRP is known to be activated by DNA-strand breakage, caused by e.g. oxidative stress or mutagens. NIC and its metabolite trigonelline (N-methylnicotinic acid) can induce defensive metabolism at the gene level. Connections between NIC and DNA-methylation are also considered. This hypothesis is discussed in the light of own observations and literature reports.
Chromosome alterations in human hepatocellular carcinomas correlate with aetiology and histological grade – results of an explorative CGH meta-analysis (2005)

All available comparative genomic hybridisation (CGH) analyses (n=31, until 12/2003) of human hepatocellular carcinomas (HCCs; n=785) and premalignant dysplastic nodules (DNs; n=30) were compiled and correlated with clinical and histological parameters. The most prominent amplifications of genomic material were present in 1q (57.1%), 8q (46.6%), 6p (22.3%), and 17q (22.2%), while losses were most prevalent in 8p (38%), 16q (35.9%), 4q (34.3%), 17p (32.1%), and 13q (26.2%). Deletions of 4q, 16q, 13q, and 8p positively correlated with hepatitis B virus aetiology, while losses of 8p were more frequently found in hepatitis C virus-negative cases. In poorly differentiated HCCs, 13q and 4q were significantly under-represented. Moreover, gains of 1q were positively correlated with the occurrence of all other high-frequency alterations in HCCs. In DNs, amplifications were most frequently present in 1q and 8q, while deletions occurred in 8p, 17p, 5p, 13q, 14q, and 16q. In conclusion, aetiology and dedifferentiation correlate with specific genomic alterations in human HCCs. Gains of 1q appear to be rather early events that may predispose to further chromosomal abnormalities. Thus, explorative CGH meta-analysis generates novel and testable hypotheses regarding the cause and functional significance of genomic alterations in human HCCs.