gebhart/patrepeval huggingface dataset:
Glycomic survey mapping of zebrafish identifies unique sialylation pattern (2005)

Functional genomics and proteomics studies of the developmental glycobiology of zebrafish are greatly hampered by the current lack of knowledge on its glycosylation profile. To furnish the requisite structural basis for a more insightful functional delineation and genetic manipulation, we have initiated a survey mapping of the possible expression of stage-specific glycoconjugates in zebrafish. High-sensitivity mass spectrometry (MS) analysis in conjunction with the usual array of enzymatic and chemical derivatization was employed as the principal method for rapid differential mapping of the glycolipids and sequentially liberated N- and O-glycans from the total extracts. We demonstrated that all developmental stages of the zebrafish under investigation, from fertilized eggs to hatched embryos, synthesize oligomannosyl types of N-glycans, as well as complex types with additionally beta4-galactosylated, Neu5Ac/Neu5Gc monosialylated Lewis x termini. A combination of collision-induced dissociation (CID)-MS/MS and nuclear magnetic resonance (NMR) analyses led to the identification of an abundant and unusual mucin-type O-glycosylation, based on a novel sequence Fucalpha1-3GalNAcbeta1-4(Neu5Ac/Neu5Gcalpha2-3)Galbeta1-3GalNAc. This core structure may be further oligosialylated, but exclusively in the earlier development stages. Similarly, MS and MS/MS analyses of the extracted glycolipid fraction revealed the presence of a heterogeneous family of oligosialylated lactosylceramide compounds. In contrast to the O-glycans, these glycolipids only appear in the later development stages, suggesting a complex pattern of regulation for sialyltransferase activities during zebrafish embryogenesis.
Pseudo Orthogonal Designs as Space-Time Block Codes (2002)

The idea of applying the theory of Orthogonal Designs in SpaceTime Coding was introduced in [1], [2]. The purpose was to create codes that provide full spatial diversity with maximal possible transmission rate R (preferably R = 1) while providing a linear decoding complexity. These designs have remarkably simple maximumlikelihood decoding algorithms via linear processing at the receiver. It was also shown that very few real orthogonal designs exist that provide full diversity and full rate. Assuming n to be the number of the transmit antennas, the 3 classical orthogonal designs for n = 2, 4 and 8 are the only existing square real orthogonal designs. The authors of [1] also introduce the concept of Complex Orthogonal Designs and prove that the case for complex orthogonal designs is even more stringent. The Alamouti design for n = 2 would turn out to be the only complex square orthogonal design [1]. Relaxing some of the conditions such as the rate would allow the authors to construct some new codes. The concept of generalized orthogonal designs was introduced that would provide codes for any possible value of n under the trade-off of having R ≤ 1/2. The estimation of R ≤ 1/2 would turn out not to be sharp and the authors were able to construct codes for sporadic values of n having higher rates. For instance, for n = 3 and n = 4 codes of rate R = 3/4 were constructed. Since the introduction of space-time block codes, there has been a lot of effort in designing higher rate codes, e.g. [3], [4]. The main conclusions are as follows. The maximum symbol transmission rate of a space-time block code from complex orthogonal designs is only 3/4 for three and four transmit antennas [3]. It means that it is impossible to improve the original orthogonal designs provided in [1] for three and four transmit antennas. Also, there are only few examples of codes with rate higher than 1/2 for more than four transmit antennas [4]. An orthogonal design is defined for any arbitrary indeterminate variables x1, x2, · · · , xn. The theory of orthogonal designs [5] and its generalization [1] provide designs that are orthogonal for any real or complex values of x1, x2, · · · , xn. However, in practice, in a communication system, x1, x2, · · · , xn are members of a constellation that has a finite number of signals instead of the real (or complex) numbers with infinite number of possibilities. For example, when the transmitter uses QPSK constellation x1, x2, · · · , xn can take one of the four possible QPSK symbols. From the results provided in [1] and the following studies in the literature, it is not clear if there exists designs that are orthogonal only for a finite set of constellation symbols. In this work, we study the possibility of such designs by defining Pseudo-Orthogonal Designs that are defined on a finite subset of real numbers. The case of complex pseudo-orthogonal designs will be handled in future. In the following we will shortly revisit the orthogonal designs and review their connection with space-time coding and will introduce the concept of Pseudo-Orthogonal Designs.
Backward-mode photoacoustic transducer for sensing optical scattering and ultrasonic attenuation: determining fraction consistencies in pulp suspensions (2010)

An innovative backward-mode photoacoustic transducer was developed, consisting of an optical fibre, a composite absorber, piezoelectric film and high impedance preamplifier. By receiving scattering light from a turbid suspension, the transducer produces a photoacoustic source in it. This source emits two photoacoustic waves travelling in opposite directions. The waves' amplitudes relate to the optical scattering properties of the suspension, and the echo of a wave returning from the suspension carries information of acoustic attenuation. By assessing the optical scattering and acoustic attenuation, fraction consistencies in a two-fractional suspension can be determined if one fraction dominantly scatters light and the other mainly attenuates ultrasound. This technique is used in this paper to investigate paper pulp suspensions. Pulp consists of wood celluloses and wood fines (or extra-added fillers in some cases), where cellulose lengths range from a few sub-millimetres to millimetres and fines/filler sizes are a few tens of micrometres or smaller. Due to their different size and shape, celluloses and fines (or fillers) have different optical scattering and acoustic attenuation properties. Experimental results showed that the transducer can measure pulp consistency with good linearity at least in the range from 0.5% to 3%, and that it can distinguish pulp cellulose from fines or fillers (TiO2 particles). Needless to say, this technique is also suitable for determining other suspensions in the food, pharmaceutical and mineral industries.
Treatment of mice bearing BCL1 lymphoma with bispecific antibodies (1991)

Bispecific antibodies with specificity for the CD3/TCR complex of CTL and a target cell Ag can bridge both cell types and trigger cellular cytoxicity. We have produced bispecific antibodies, directed against the surface-expressed Id of the mouse BCL1 lymphoma and the mouse CD3 complex, by hybrid-hybridoma fusion. Two recombination Ig were purified to homogeneity: B1 X 7D6F, which is univalent for Id and CD3 binding and B1 X 7D6M, which is univalent for Id binding but has lost the CD3 binding because of association of the anti-CD3 H chain with the inappropriate L chain. In vitro studies indicate that bridging the TCR/CD3 complex of resting T cells with tumor IgM Id and the appropriate bispecific antibody induced proliferation and secretion of IL-2. Furthermore, in cytotoxicity assays using 51Cr-labeled tumor cells, preactivated T cells could be targeted with the bispecific antibody to give complete lysis of the Ag+ tumor. Finally, the activity of the bispecific antibody was confirmed in vivo. Animals treated i.v. with 5 micrograms of bispecific antibody 9 days after receiving BCL1 cells were cured. Furthermore, when these animals were checked at 150 days for dormant or variant tumors, as have been reported after other forms of immunotherapy in this model, none could be found. Immunotherapy experiments comparing a mixture of control antibodies with the bispecific antibody demonstrate that tumor cell-T cell bridging is established in vivo and is required for therapeutic success. These results indicate the importance of bispecific antibodies as a novel form of treatment for cancer.
Hydroxylation of ansamitocin P-3. (1981)

Ansamitocin P-3 was converted into 15-hydroxyansamitocin P-3 (PHO-3), C32H43ClN2010, and 15-epi-15-hydroxyansamitocin P-3 (epi-PHO-3), C32H43ClN2010, by actinomycetes. PHO-3 was identical to deacetylmaytanbutacine and epi-PHO-3 was a new compound. The configuration at C15 was elucidated as R for PHO-3 and S for epi-PHO-3 on the basis of their physicochemical properties and X-ray analysis of epi-PHO-3.
Towards Effective Foraging by Data Scientists to Find Past Analysis Choices (2019)

Data scientists are responsible for the analysis decisions they make, but it is hard for them to track the process by which they achieved a result. Even when data scientists keep logs, it is onerous to make sense of the resulting large number of history records full of overlapping variants of code, output, plots, etc. We developed algorithmic and visualization techniques for notebook code environments to help data scientists forage for information in their history. To test these interventions, we conducted a think-aloud evaluation with 15 data scientists, where participants were asked to find specific information from the history of another person's data science project. The participants succeed on a median of 80% of the tasks they performed. The quantitative results suggest promising aspects of our design, while qualitative results motivated a number of design improvements. The resulting system, called Verdant, is released as an open-source extension for JupyterLab.
In vitro antitumor effect of hydroxyurea on hormone-refractory prostate cancer cells and its potentiation by phenylbutyrate (1994)

Previous clinical trials have suggested that hydroxyurea may possess some activity against prostate cancer. The in vitro antiproliferative activity of hydroxyurea was evaluated in three hormone-refractory prostate cancer cell lines, PC-3, DU-145 and PC-3M. Fifty-percent inhibition of growth in all three cell lines required prolonged (120 h) exposure to hydroxyurea at a concentration of approximately 100 microM. Using pharmacokinetic data obtained during the course of a clinical trial of hydroxyurea, we simulated a dosing regimen that would sustain plasma drug concentrations above 100 microM for 120 h (1 g loading dose, followed by 500 mg every 6 h for 5 days in a 70 kg man). Since this dosing regimen is likely to generate an unacceptable degree of myelosuppression, in vitro combination studies were conducted with hydroxyurea and phenylbutyrate, a new differentiating agent with no myelosuppressive effects. These studies resulted in a reduction of the hydroxyurea concentration necessary for 50% growth inhibition (50 microM of hydroxyurea plus 0.5 mM of phenylbutyrate). A regimen designed to achieve that hydroxyurea concentration (400 mg loading dose, followed by 200 mg every 6 h for 5 days) should be clinically achievable. Based on these results, this combination deserves further evaluation in patients with stage D prostate cancer.
TNT Testbed for Self-Organizing Tactical Networking and Collaboration Article and PowerPoint Presentation (2009)

Center for Network Innovation and Experimentation (CENETIX) Publication
Comparative genome mapping with mobile physical map landmarks (1994)

We describe a method for comparative macrorestriction mapping of the chromosomes of Escherichia coli strains. In this method, a series of physically tagged E. coli K-12 alleles serve as mobile landmarks for mapping DNAs from other strains. This technique revealed evidence of strain-specific chromosomal additions or deletions in a pathogenic isolate and can be applied to most strains, yielding information on genealogy as well as virulence. In theory, the same strategy can be used to map and compare genomic DNAs from a wide variety of species.
Affinity labeling of bovine carboxypeptidase A γLeu by N-bromoacetyl-N-methyl-L-phenylalanine. I. Kinetics of inactivation (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAffinity labeling of bovine carboxypeptidase A γLeu by N-bromoacetyl-N-methyl-L-phenylalanine. I. Kinetics of inactivationHans Neurath and G. Michael HassCite this: Biochemistry 1971, 10, 19, 3535–3540Publication Date (Print):September 14, 1971Publication History Published online1 May 2002Published inissue 14 September 1971https://pubs.acs.org/doi/10.1021/bi00795a007https://doi.org/10.1021/bi00795a007research-articleACS PublicationsRequest reuse permissionsArticle Views54Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
METEOR-S process design and development tool (2005)

The growing popularity of Service Oriented Computing based on Web services standards is creating a need for paradigms to represent and design business processes. Significant work has been done in the representation aspects with regards to WSBPEL. However, design and modeling of business processes is still an open issue. In this thesis, we present a novel designer which supports intuitive modeling of Web processes, using a template based approach for semiautomatically integrating partners either at design time or at deployment time. The process design and development tool described in this work helps process developers create complex business processes using an easy to use Graphical User Interface. The tool which provides a variety of features is developed as a plugin to Eclipse platform. This work has been done as part of
Ultra-wide bandwidth based tumor poles extraction in practical noise situation (2016)

In this paper, a method for evaluating the influence of noise on ultra-wide Bandwidth (UWB) based poles extraction is proposed. Three groups of tumors are chosen as the samples. Each group contains three tumor subcases with varying permittivities, conductivities or radii. White Gaussian noises with signal-to-noise ratios (SNRs) range from 25 dB to 50 dB are added with the tumor signals of each group. The Prony's method is used to extract tumor poles before and after noise additions. 1000 times Monte-Carlo experiment is conducted on each group. The results show that the Prony's poles extraction method has a good performance when SNR is higher than 25 dB in all three experiment groups.
Automatic segmentation and model identification in unordered 3D-point cloud (2002)

Segmentation and object recognition in point cloud are of topical interest for computer and machine vision. In this paper, we present a very robust and computationally efficient interactive procedure between segmentation, outlier detection, and model fitting in 3D-point cloud. For an accurate and reliable estimation of the model parameters, we apply the orthogonal distance fitting algorithms for implicit curves and surfaces, which minimize the square sum of the geometric (Euclidean) error distances. The model parameters are grouped and simultaneously estimated in terms of form, position, and rotation parameters, hence, providing a very advantageous algorithmic feature for applications, e.g., robot vision, motion analysis, and coordinate metrology. To achieve a high automation degree of the overall procedures of the segmentation and object recognition in point cloud, we utilize the properties of implicit features. We give an application example of the proposed procedure to a point cloud containing multiple objects taken by a laser radar.
Unicorn: Continual Learning with a Universal, Off-policy Agent (2018)

Some real-world domains are best characterized as a single task, but for others this perspective is limiting. Instead, some tasks continually grow in complexity, in tandem with the agent's competence. In continual learning, also referred to as lifelong learning, there are no explicit task boundaries or curricula. As learning agents have become more powerful, continual learning remains one of the frontiers that has resisted quick progress. To test continual learning capabilities we consider a challenging 3D domain with an implicit sequence of tasks and sparse rewards. We propose a novel agent architecture called Unicorn, which demonstrates strong continual learning and outperforms several baseline agents on the proposed domain. The agent achieves this by jointly representing and learning multiple policies efficiently, using a parallel off-policy learning setup.
Thin film integration of passives - single components, filters, integrated passive devices (2004)

The increasing demands on future electronic products require more efficient system integration technologies. Especially the package density gap at board level with the high integrated circuits (ICs) on the one hand and the discrete passive components on the other has to be closed by new packaging technologies which integrate the passive components into the substrate, an interposer or the IC itself. This paper presents investigations for the common integration of inductors, resistors, capacitors as well as passive filter structures in a thin film build up, based on copper and benzocyclobutene (BCB). Technologies from wafer level packaging were adapted for manufacturing of the integrated components. The examinations were carried out with special focus on integrated coils and passive filter structures. Build up, design, processing as well as results of the electrical characterization of the integrated components are described in detail. Furthermore, an integrated passive device (IPD) for application as a filter element in the Bluetooth band is presented.
Pyrido[2,3-d]pyrimidines. Latent 2-aminonicotinaldehydes (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPyrido[2,3-d]pyrimidines. Latent 2-aminonicotinaldehydesGeorges Evens and Paul CaluweCite this: J. Org. Chem. 1975, 40, 10, 1438–1439Publication Date (Print):May 1, 1975Publication History Published online1 May 2002Published inissue 1 May 1975https://pubs.acs.org/doi/10.1021/jo00898a012https://doi.org/10.1021/jo00898a012research-articleACS PublicationsRequest reuse permissionsArticle Views250Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Effects of once‐weekly dulaglutide on kidney function in patients with type 2 diabetes in phase <scp>II</scp> and <scp>III</scp> clinical trials (2016)

Dulaglutide is a once-weekly glucagon-like peptide-1 receptor agonist approved for the treatment of type 2 diabetes (T2D). Integrated data from 9 phase II and III trials in people with T2D (N = 6005) were used to evaluate the effects of dulaglutide on estimated glomerular filtration rate (eGFR [Chronic Kidney Disease Epidemiology Collaboration]), urine albumin-to-creatinine ratio (UACR) and kidney adverse events (AEs). No significant differences in eGFR were observed during treatment for dulaglutide vs placebo, active comparators or insulin glargine (mean ± standard deviation values: dulaglutide vs placebo: 87.8 ± 17.7 vs 88.2 ± 17.9 mL/min/1.73 m<sup>2</sup> , P = .075; dulaglutide vs active comparators: 89.9 ± 16.7 vs 88.8 ± 16.3 mL/min/1.73 m<sup>2</sup> , P = .223; and dulaglutide vs insulin glargine: 85.9 ± 18.2 vs 83.9 ± 18.6 mL/min/1.73 m<sup>2</sup> , P = .423). Lower UACR values were observed for dulaglutide vs placebo, active comparators and insulin glargine (at 26 weeks, median [Q1-Q3] values were: dulaglutide vs placebo: 8.0 [4.4-20.4] vs 8.0 [4.4-23.9] mg/g, P = .023; dulaglutide vs active comparators: 8.0 [4.4-21.2] vs 8.9 [4.4-27.4] mg/g, P = .013; and dulaglutide vs insulin glargine: 8.9 [4.4-29.2] vs 12.4 [5.3-50.5] mg/g, P = .029). AEs reflecting potential acute renal failure were 3.4, 1.7 and 7.0 events/1000 patient-years for dulaglutide, active comparators and placebo, respectively. In conclusion, dulaglutide treatment of clinical trial participants with T2D did not affect eGFR and slightly decreased albuminuria.
DNA Bending by Fos and Jun: The Flexible Hinge Model (1991)

DNA bending is essential for the assembly of multiprotein complexes that contact several DNA sequence elements. An approach based on phasing analysis was developed that allows determination of both the directed DNA bend angle and the orientation of DNA bending. This technique has been applied to the analysis of DNA bending by the transcription regulatory proteins Fos and Jun. Complexes that contained different combinations of full-length and truncated Fos and Jun induced DNA bends of different magnitudes and orientations. The DNA bends induced by the individual proteins were determined on the basis of a quantitative model for DNA bending by dimeric complexes. This information was used to visualize the consequences of DNA bending by Fos and Jun for the structures of Fos-Jun-DNA and Jun-DNA complexes.
InstaGAN: Instance-aware Image-to-Image Translation (2018)

Unsupervised image-to-image translation has gained considerable attention due to the recent impressive progress based on generative adversarial networks (GANs). However, previous methods often fail in challenging cases, in particular, when an image has multiple target instances and a translation task involves significant changes in shape, e.g., translating pants to skirts in fashion images. To tackle the issues, we propose a novel method, coined instance-aware GAN (InstaGAN), that incorporates the instance information (e.g., object segmentation masks) and improves multi-instance transfiguration. The proposed method translates both an image and the corresponding set of instance attributes while maintaining the permutation invariance property of the instances. To this end, we introduce a context preserving loss that encourages the network to learn the identity function outside of target instances. We also propose a sequential mini-batch inference/training technique that handles multiple instances with a limited GPU memory and enhances the network to generalize better for multiple instances. Our comparative evaluation demonstrates the effectiveness of the proposed method on different image datasets, in particular, in the aforementioned challenging cases. Code and results are available in https://github.com/sangwoomo/instagan