gebhart/patrepeval huggingface dataset:
Footprint removal from seismic data with residual dictionary learning (2020)

Dictionary learning (DL) is a machine learning technique that can be used to find a sparse representation of a given data set by means of a relatively small set of atoms, which are learned from the input data. DL allows for the removal of random noise from seismic data very effectively. However, when seismic data are contaminated with footprint noise, the atoms of the learned dictionary are often a mixture of data and coherent noise patterns. In this scenario, DL requires carrying out a morphological attribute classification of the atoms to separate the noisy atoms from the dictionary. Instead, we have developed a novel DL strategy for the removal of footprint patterns in 3D seismic data that is based on an augmented dictionary built upon appropriately filtering the learned atoms. The resulting augmented dictionary, which contains the filtered atoms and their residuals, has a high discriminative power in separating signal and footprint atoms, thus precluding the use of any statistical classification strategy to segregate the atoms of the learned dictionary. We filter the atoms using a domain transform filtering approach, a very efficient edge-preserving smoothing algorithm. As in the so-called coherence-constrained DL method, the proposed DL strategy does not require the user to know or adjust the noise level or the sparsity of the solution for each data set. Furthermore, it only requires one pass of DL and is shown to produce successful transfer learning. This increases the speed of the denoising processing because the augmented dictionary does not need to be calculated for each time slice of the input data volume. Results on synthetic and 3D public-domain poststack field data demonstrate effective footprint removal with accurate edge preservation.
Characterization of refractive index change induced by electron irradiation in amorphous thin As2S3 films (1997)

Binary diffraction gratings in As2S3 films were prepared with the aid of an electron beam. The dose of the electrons was varied. The gratings were read with a HeNe laser, and the zero-order and first-order diffraction efficiencies were noted. Rigorous diffraction theory was used to give a homogeneous approximation for the refractive index change. Reactive ion etching was applied to reduce the thickness of the film, and a new value for the refractive index change was evaluated. The refractive index change versus film thickness dependence was found to be linear at low electron doses and Gaussian shaped at higher doses. Through a simple mathematical analysis, the absolute value of the refractive index was determined as a function of the position inside the film. At higher doses, the refractive index change was found to have a maximum value of 3%, approximately 1.2 μm from the film surface.
Amplify-and-Forward Cooperative Transmission with Multiple Relays Using Phase Feedback (2006)

Cooperative transmission obtains the spatial diversity gains created by sharing antennas of terminals in wireless networks. Although the amplify-and-forward (AF) cooperative transmission has the advantages of low implementation complexity and simplicity compared to the decode-and- forward (DF) cooperative transmission, studies on the AF cooperative transmission with multiple relays have not been sufficiently investigated. In this paper, we introduce the AF cooperative transmission with multiple relays using phase feedback. Simulation results show that the proposed schemes obtain the diversity gain according to the number of the cooperating terminals. The performance of proposed scheme using tolerable quantized feedback is close to that of proposed scheme using full feedback.
Omega‐Carboxypyridyl Substituted Ureas as Raf Kinase Inhibitors: SAR of the Amide Substituent. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Transgenic mice aberrantly expressing human ornithine decarboxylase gene. (1991)

We have generated transgenic mice carrying human ornithine decarboxylase gene. Two different transgene constructs were used: (i) a 5'-truncated human ornithine decarboxylase gene and (ii) an intact human ornithine decarboxylase gene. Transgenic mice carrying the 5'-truncated gene did not express human ornithine decarboxylase-specific mRNA. Transgenic mice carrying the intact human ornithine decarboxylase gene expressed human-specific ornithine decarboxylase mRNA in all tissues studied. However, as indicated by actual enzyme assays, the expression pattern was highly unusual. In comparison with their wild-type littermates, the transgenic mice exhibited greatly elevated enzyme activity in almost every tissue studied. Ornithine decarboxylase activity was moderately elevated in parenchymal organs such as liver, kidney, and spleen. Tissues like heart, muscle, lung, thymus, testis, and brain displayed an enzyme activity that was 20 to 80 times higher than that in the respective tissues of nontransgenic animals. The offspring of the first transgenic male founder animal did not show any overt abnormalities, yet their reproductive performance was reduced. The second transgenic founder animal, showing similar aberrant expression of ornithine decarboxylase in all tissues studied, including an extremely high activity in testis, was found to be infertile. Histological examination of the tissues of the latter animal revealed marked changes in testicular morphology. The germinal epithelium was hypoplastic, and the spermatogenesis was virtually totally shut off. Similar examination of male members of the first transgenic mouse line revealed comparable, yet less severe, histological changes in testis.
Impact of Myocardial Infarct Proteins and Oscillating Pressure on the Differentiation of Mesenchymal Stem Cells: Effect of Acute Myocardial Infarction on Stem Cell Differentiation (2008)

Stem cell transplantation in acute myocardial infarction (AMI) has emerged as a promising therapeutic option. We evaluated the impact of AMI on mesenchymal stem cell (MSC) differentiation into cardiomyocyte lineage. Cord blood-derived human MSCs were exposed to in vitro conditions simulating in vivo environments of the beating heart with acute ischemia, as follows: (a) myocardial proteins or serum obtained from sham-operated rats, and (b) myocardial proteins or serum from AMI rats, with or without application of oscillating pressure. Expression of cardiac-specific markers on MSCs was greatly induced by the infarcted myocardial proteins, compared with the normal proteins. It was also induced by application of oscillating pressure to MSCs. Treatment of MSCs with infarcted myocardial proteins and oscillating pressure greatly augmented expression of cardiac-specific genes. Such expression was blocked by inhibitor of transforming growth factor beta(1) (TGF-beta(1)) or bone morphogenetic protein-2 (BMP-2). In vitro cellular and electrophysiologic experiments showed that these differentiated MSCs expressing cardiomyocyte-specific markers were able to make a coupling with cardiomyocytes but not to selfbeat. The pathophysiologic significance of in vitro results was confirmed using the rat AMI model. The protein amount of TGF-beta(1) and BMP-2 in myocardium of AMI was significantly higher than that in normal myocardium. When MSCs were transplanted to the heart and analyzed 8 weeks later, they expressed cardiomyocyte-specific markers, leading to improved cardiac function. These in vitro and in vivo results suggest that infarct-related biological and physical factors in AMI induce commitment of MSCs to cardiomyocyte-like cells through TGF-beta/BMP-2 pathways.
Diene-modified nucleotides for the Diels–Alder-mediated functional tagging of DNA (2009)

We explore the potential of the Diels-Alder cycloaddition for the functional tagging of DNA strands. A deoxyuridine triphosphate derivative carrying a diene at position 5 of the pyrimidine base was synthesized using a two-step procedure. The derivative was efficiently accepted as substrate in enzymatic polymerization assays. Diene carrying strands underwent successful cycloaddition with maleimide-terminated fluorescence dyes and a polymeric reagent. Furthermore, a nucleotide carrying a peptide via a Diels-Alder cyclohexene linkage was prepared and sequence-specifically incorporated into DNA. The Diels-Alder reaction presents a number of positive attributes such as good chemoselectivity, water compatibility, high-yield under mild conditions and no additional reagents apart from a diene and a dienophile. Furthermore, suitable dienophiles are commercially available in the form of maleimide-derivatives of fluorescent dyes and bioaffinity tags. Based on these advantages, diene- and cyclohexene-based nucleotide triphosphates are expected to find wider use in the area of nucleic acid chemistry.
Game Analysis and Countermeasures Discussion on Green Marketing (2011)

On the basis of making certain assumption on the game situation of carrying our green marketing, this paper conducts game analysis on the green marketing choice among enterprises, the green marketing choice between enterprises and consumers, and the green marketing choice of consumers. Then this paper expounds the necessity of implementing green marketing as follows: the green marketing is the inevitable requirements of sustainable development of economy; the green marketing is the inevitable choice of green consumption mode; the green marketing is the inevitable results of legalization of environmental problems. The problems faced by the implementation of green marketing are analyzed as follows, first, the concept of green marketing has not yet been established; second, the sociality of green demand has not yet taken shape; third, production characteristic of green products has not yet formed. The countermeasures of implementing green marketing as follows: pay attention to the propaganda and education of modern marketing concept; regulate the competition in the market of green products; strengthen transparency of green market information; reinforce the legislation work of food safety.
Correctness of query execution strategies in distributed databases (1983)

A major requirement of a Distributed DataBase Management System (DDBMS) is to enable users to write queries as though the database were not distributed (distribution transparency). The DDBMS transforms the user's queries into execution strategies, that is, sequences of operations on the various nodes of the network and of transmissions between them. An execution strategy on a distributed database is correct if it returns the same result as if the query were applied to a nondistributed database. This paper analyzes the correctness problem for query execution strategies. A formal model, called Multirelational Algebra, is used as a unifying framework for this purpose. The problem of proving the correctness of execution strategies is reduced to the problem of proving the equivalence of two expressions of Multirelational Algebra. A set of theorems on equivalence is given in order to facilitate this task. The proposed approach can be used also for the generation of correct execution strategies, because it defines the rules which allow the transformation of a correct strategy into an equivalent one. This paper does not deal with the problem of evaluating equivalent strategies, and therefore is not in itself a proposal for a query optimizer for distributed databases. However, it constitutes a theoretical foundation for the design of such optimizers.
Adiabatic and nonadiabatic nanofocusing of plasmons by tapered gap plasmon waveguides (2006)

Adiabatic and nonadiabatic nanofocusing of plasmons in tapered gap plasmon waveguides is analyzed using the finite-difference time-domain algorithm. Optimal adaptors between two different subwavelength waveguides and conditions for maximal local field enhancement are determined, investigated, and explained on the basis of dissipative and reflective losses in the taper. Nanofocusing of plasmons into a gap of ∼1nm width with more than 20 times increase in the plasmon energy density is demonstrated in a silver-vacuum taper of ∼1μm long. Comparison with the approximate theory based on the geometrical optics approximation is conducted.
STRUCTURE BASED DRUG DESIGN OF HIGH AFFINITY KRAS INHIBITORS (2018)

RAS, one of the most well characterized membrane-associated small GTPases, is a notorious oncogene with >15% of all tumors harboring RAS mutations. When RAS is mutated it becomes constitutively active sending cell growth, survival and proliferation into overdrive, which subsequently leads to cancer. Although, RAS has been aggressively targeted with drug design efforts for more than 30 years an FDA approved direct inhibitor has not yet been developed. There are three isoforms of RAS in cells; HRAS, NRAS and KRAS. We focused on KRAS since it is the most frequently mutated isoform in cancer. To identify novel non-covalent small molecules that bind to mutant KRAS, we conducted a high-throughput virtual screen of drug-like compounds against a previously characterized allosteric pocket on a molecular dynamics simulation-derived KRASG12D structure. The in silico predicted hits were then validated with a battery of cell-based and biophysical assays. Specifically, the hits effects on KRAS signaling, binding affinities for KRAS and mechanisms of activity were evaluated. We found two key hit compounds (i) a pyrazolopyrimidine based molecule compound 11 and (ii) a indazole based molecule compound M1. Compound 11 exhibited a monotonous dose-dependent inhibition of KRAS signaling, however compound M1 demonstrated a biphasic dose-depended effect. With the potential to elucidate the structure-activity relationships between these molecules and their unique structures we tested both in cell-based and vi biophysical assays. We found that compound 11 binds to KRAS with nanomolar affinity and completely abolishes CRaf binding in vitro, subsequently leading to a significant reduction in RAS dependent CRaf/ERK activation and son of sevenless (SOS) mediated nucleotide exchange. Moreover, treatment at low micromolar concentrations of compound 11 reduced cell proliferation in six cancer cell lines. Further, compound M1, binds to KRAS in NMR-based studies and both reduced and enhanced signaling in cell-based assays as indicated by western blotting. We attributed this to M1 enhancing and disrupting nucleotide exchange through different mechanisms. Additionally, we noted that M1 showed remarkable selectivity towards inhibiting proliferation of MiaPaCa-2 cells. We then screened a second small-molecule library based on M1 and generated additional hits which decreased mutant KRAS signaling. Likewise, we generated two derivatives of compound 11 which were tested and gave insights to critical functional groups. Combining our results with detailed structural analysis, we are able to describe key ligand-receptor interactions that correlate with activity. Thus, showing that our screening techniques were very successful at generating KRAS binders that have effects on signaling in cells. To our knowledge compound 11 is the first known nanomolar binder of KRAS that disrupts interaction with CRaf resulting in decreased p-ERK levels and cell proliferation. Therefore, compound 11 is a promising hit for the development of novel non-covalent KRAS inhibitors.
A generic tool-set for SoC multiprocessor debugging and synchronization (2004)

Current and future SoC designs will contain an increasing number of programmable units. To be able to tailor and debug these processors in their system context at the highest possible overall simulation speed, we propose a methodology and the necessary tooling for a multiprocessor debugging environment which allows a flexible runtime tradeoff between observability and simulation speed. This approach has been applied on a complex SoC case study.
Comparing the Accuracy of RDD Telephone Surveys and Internet Surveys Conducted with Probability and Non-Probability Samples (2011)

This study assessed the accuracy of telephone and Internet surveys of probability samples and Internet surveys of non-probability samples of American adults by comparing aggregate survey results against benchmarks. The probability sample surveys were consistently more accurate than the non-probability sample surveys, even after post-stratification with demographics. The non-probability sample survey measurements were much more variable in their accuracy, both across measures within a single survey and across surveys with a single measure. Post-stratification improved the overall accuracy of some of the non-probability sample surveys but decreased the overall accuracy of others. Higher completion and response rates of the surveys were associated with less accuracy. Accuracy did not appear to change from 2004/2005 to 2009 for any of the methods, and these conclusions are reinforced by data collected in 2008 as well. These results are consistent with the conclusion that non-probability samples yield data that are neither as accurate as nor more accurate than data obtained from probability samples.
Novel radiotherapy approaches for lung cancer: combining radiation therapy with targeted and immunotherapies. (2015)

Targeted therapies and immunotherapies have quickly become fixtures in the treatment armamentarium for metastatic non-small cell lung cancer (NSCLC). Targeted therapies directed against epidermal growth factor receptor (EGFR) mutations, anaplastic lymphoma kinase (ALK) translocations, and ROS-1 rearrangements have demonstrated improved progression free survival (PFS) and, in selected populations, improved overall survival (OS) compared with cytotoxic chemotherapy. Immunotherapies, including checkpoint inhibitor monoclonal antibodies against programmed death receptor 1 (PD-1) and programmed death ligand 1 (PD-L1), have now also demonstrated improved survival compared with chemotherapy. The use of these novel systemic agents in non-metastatic patient populations and in combination with radiation therapy is not well defined. As radiation therapy has become more effective and more conformal with fewer toxicities, it has increasingly been used in the oligometastatic or oligoprogression setting. This has allowed improvement in PFS and potentially OS, and in the oligoprogressive setting may overcome acquired drug resistance of a specific lesion(s) to allow patients to remain on their targeted therapies. Molecularly targeted therapies and immunotherapies for patients with metastatic NSCLC have demonstrated much success. Advances in radiation therapy and stereotactic body radiotherapy, radiation therapy have led to combination strategies with targeted therapies among patients with lung cancer. Radiation therapy has also been combined with immunotherapies predominantly in the metastatic setting. In the metastatic population, radiation therapy has the ability to provide durable local control and also augment the immune response of systemic agents, which may lead to an abscopal effect of immune-mediated tumor response in disease sites outside of the radiation field in select patients.
Narrowband Internet of Things: Implementations and Applications (2017)

Recently, narrowband Internet of Things (NB-IoT), one of the most promising low power wide area (LPWA) technologies, has attracted much attention from both academia and industry. It has great potential to meet the huge demand for machine-type communications in the era of IoT. To facilitate research on and application of NB-IoT, in this paper, we design a system that includes NB devices, an IoT cloud platform, an application server, and a user app. The core component of the system is to build a development board that integrates an NB-IoT communication module and a subscriber identification module, a micro-controller unit and power management modules. We also provide a firmware design for NB device wake-up, data sensing, computing and communication, and the IoT cloud configuration for data storage and analysis. We further introduce a framework on how to apply the proposed system to specific applications. The proposed system provides an easy approach to academic research as well as commercial applications.
Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer (2010)

Shotgun proteomics has been used extensively for characterization of a number of proteomes. High-resolution Fourier transform mass spectrometry (FTMS) has emerged as a powerful tool owing to its high mass accuracy and resolving power. One of its major limitations, however, is that the confidence level of peptide identification and sensitivity cannot be maximized simultaneously. Although it is generally assumed that higher resolution is better for peptide identifications, the precise effect of varying resolution as a parameter on peptide identification has not yet been systematically evaluated. We used the Escherichia coli proteome and a standard 48 protein mix to study the effect of different resolution parameters on peptide identifications in the setting of a shotgun proteomics experiment on an LTQ-Orbitrap mass spectrometer. We observed a higher number of peptide-spectrum matches (PSMs) whenever the MS scan was carried out by FT and the MS/MS in the ion-trap (IT) with the maximum PSMs obtained at an MS resolution of 30,000. In contrast, when samples were analyzed by FT for both MS and MS/MS, the number of PSMs was significantly lower (approximately 40% compared with FT-IT experiments) with the maximum PSMs obtained when both the MS and MS/MS resolution were set to 15,000. Thus, a 15K-15K resolution setting may provide the best compromise for studies where both speed and accuracy such as high-throughput post-translational analysis and de novo sequencing are important. We hope that our study will allow researchers to choose between different resolution parameters to achieve their desired results from proteomic analyses.
Politik der Schönheit: Zur Konstruktion einer ›wissenschaftlichen‹ Bildästhetik schöner weiblicher Körper um 1900 am Beispiel des Gynäkologen Carl Heinrich Stratz (2018)

In diesem Beitrag wird am Beispiel ausgewählter Schriften des Gynäkologen Carl Heinrich Stratz analysiert, wie dieser anhand von Fotografien politische, kulturelle und gesellschaftliche Grenzen in Darstellungen des Schönen respek-tive des Nicht-Schönen übersetzt. Zunächst wird ein Einblick in die Verflech-tung des Stratz’schen Schönheitsideals mit Werten des deutschen Bildungs-bürgertums um 1900 gegeben. Im Anschluss daran werden verschiedene Merkmale betrachtet, die Stratz beschreibt, um äußere Anzeichen des Nicht-Schönen mit Wertigkeiten zu versehen, die bildungsbürgerlichen Werten wi-dersprechen. Abschließend wird seine Vorgehensweise, die ein anthropomet-risches Verfahren mit dem Evidenz versprechenden Medium der Fotografie kombiniert, genauer untersucht. Dabei soll deutlich werden, dass Stratz unter Rückgriff auf Bilder von normierten Vorstellungen weiblicher Schönheit Alteri-täten konstruiert, bei denen es keineswegs schlichtweg um oberflächlich schöne vs. nicht-schöne Körper geht. Vielmehr ist diese ›Veranderung‹ von als nicht-schön bezeichneten Körpern in politisiertem Sinne als Stärkung eines he-teronormativen, bürgerlichen, eurozentrischen und deutsch-nationalen Welt-bildes zu verstehen.