gebhart/patrepeval huggingface dataset:
Functional diversification of hybridoma-produced antibodies by CRISPR/HDR genomic engineering (2019)

Hybridoma technology is instrumental for the development of novel antibody therapeutics and diagnostics. Recent preclinical and clinical studies highlight the importance of antibody isotype for therapeutic efficacy. However, since the sequence encoding the constant domains is fixed, tuning antibody function in hybridomas has been restricted. Here, we demonstrate a versatile CRISPR/HDR platform to rapidly engineer the constant immunoglobulin domains to obtain recombinant hybridomas, which secrete antibodies in the preferred format, species, and isotype. Using this platform, we obtained recombinant hybridomas secreting Fab' fragments, isotype-switched chimeric antibodies, and Fc-silent mutants. These antibody products are stable, retain their antigen specificity, and display their intrinsic Fc-effector functions in vitro and in vivo. Furthermore, we can site-specifically attach cargo to these antibody products via chemoenzymatic modification. We believe that this versatile platform facilitates antibody engineering for the entire scientific community, empowering preclinical antibody research.
3D harnessing of light with 2.5D photonic crystals (2009)

Abstract It is emphasized that two‐dimensional photonic crystals (2D PC) have not only a great potential for the development of 2D nanophotonics in the inplane waveguided configuration, but that they may also open the way to other brilliant developments, with an extension to out‐of‐plane operation, along a 2.5D nanophotonics approach. In this 2.5D approach, a 1D–2D high index contrast lateral structuration is combined with a 1D high index contrast vertical structuration, using multilayer membrane stacks including 1D–2D photonic crystal membranes, thus resulting in so‐called 2.5D PC. As a specific illustration of recent achievements along this approach, new families of VCSEL structures are presented.
ChemInform Abstract: Human β3 Adrenergic Receptor Agonists Containing Cyclic Ureidobenzenesulfonamides (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases (2019)

Abstract Summary DDAP is a tool for predicting the biosynthetic pathways of the products of type I modular polyketide synthase (PKS) with the focus on providing a more accurate prediction of the ordering of proteins and substrates in the pathway. In this study, the module docking domain (DD) affinity prediction performance on a hold-out testing data set reached AUC = 0.88; the MRR of pathway prediction reached 0.67. DDAP has advantages compared to previous informatics tools in several aspects: (i) it does not rely on large databases, making it a high efficiency tool, (ii) the predicted DD affinity is represented by a probability (0 to 1), which is more intuitive than raw scores, (iii) its performance is competitive compared to the current popular rule-based algorithm. To the best of our knowledge, DDAP is so far the first machine learning based algorithm for type I PKS pathway prediction. We also established the first database of type I modular PKSs, featuring a comprehensive annotation of available docking domains information in bacterial biosynthetic pathways. Availability and implementation The DDAP database is available at https://tylii.github.io/ddap . The prediction algorithm DDAP is freely available on GitHub ( https://github.com/tylii/ddap ) and released under the MIT license. Contact ukarvind@umich.edu
Architecture for Video Summarization Services Over Home Networks and the Internet (2006)

With increasing number of personal digital video recorders, the idea of having summarization functionality to view the recorded content has also been gaining importance. The summarization functionality can either be built into the video recording device or can reside in a computing device on the network. In this paper, we present a client-server architecture for the latter case. Then, we present two possible application scenarios that the proposed architecture can enable. The first application is to enable summarization services over a home network. The second application is to enable summarization services over the Internet.
Properties of a tetracyanopentacenequinone and its tetracyanoquinodimethane derivative (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProperties of a tetracyanopentacenequinone and its tetracyanoquinodimethane derivativeP. W. Kenny, T. H. Jozefiak, and L. L. MillerCite this: J. Org. Chem. 1988, 53, 21, 5007–5010Publication Date (Print):October 1, 1988Publication History Published online1 May 2002Published inissue 1 October 1988https://pubs.acs.org/doi/10.1021/jo00256a019https://doi.org/10.1021/jo00256a019research-articleACS PublicationsRequest reuse permissionsArticle Views357Altmetric-Citations16LEARN 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
Enhancing Technical Q&A Forums with CiteHistory (2021)

Software engineers often use Q&amp;A forums like Stack Overflow and MSDN to ask and answer technical questions. Through a survey study and web browser log analysis, we find that both askers and answerers of technical forum questions typically conduct extensive online research before composing their posts. The inclusion of links to these research materials is beneficial to the forum participants, though post authors do not always include such citations. Based on these findings, we developed CiteHistory, a browser plugin that simplifies the process of including relevant search queries and URLs as bibliographic supplements to forum posts, and supports information re-finding for post authors. We discuss the results of a two-week deployment of CiteHistory with professional software engineers, which demonstrated that CiteHistory increased reference inclusion in posts, and offered auxiliary benefits as a personal research tracker.
Analysis of Ion Behavior Affecting Voltage Holding Property of Liquid Crystal Displays (2011)

A mechanism for the decay of charged voltage, which leads to the lowering of the voltage holding ratio of liquid crystal displays (LCDs), was proposed using a model for the behavior of ions in an LC layer. The proposed model was verified by experimental results using two LC cells of different LC materials. The decay of the charged voltage occurs with two decay components; one originates from the ions arriving at the surface of an alignment layer due to the application of pulsed voltage diffusing toward the LC layer, and the other originates from the ions in the LC layer moving toward the opposite surface and canceling the dielectric polarization of LC molecules during an open-circuit period. We found that the decay of the charged voltage increases with increasing density of ions arriving at the surface before the open-circuit period.
Hyperspectral imaging for tumor segmentation on pigmented skin lesions (2022)

SignificanceMalignant skin tumors, which include melanoma and nonmelanoma skin cancers, are the most prevalent type of malignant tumor. Gross pathology of pigmented skin lesions (PSL) remains manual, time-consuming, and heavily dependent on the expertise of the medical personnel. Hyperspectral imaging (HSI) can assist in the detection of tumors and evaluate the status of tumor margins by their spectral signatures.AimTumor segmentation of medical HSI data is a research field. The goal of this study is to propose a framework for HSI-based tumor segmentation of PSL.ApproachAn HSI dataset of 28 PSL was prepared. Two frameworks for data preprocessing and tumor segmentation were proposed. Models based on machine learning and deep learning were used at the core of each framework.ResultsCross-validation performance showed that pixel-wise processing achieves higher segmentation performance, in terms of the Jaccard coefficient. Simultaneous use of spatio-spectral features produced more comprehensive tumor masks. A three-dimensional Xception-based network achieved performance similar to state-of-the-art networks while allowing for more detailed detection of the tumor border.ConclusionsGood performance was achieved for melanocytic lesions, but margins were difficult to detect in some cases of basal cell carcinoma. The frameworks proposed in this study could be further improved for robustness against different pathologies and detailed delineation of tissue margins to facilitate computer-assisted diagnosis during gross pathology.
Total Synthesis of the Antitumor Marine Sponge Alkaloid Agelastatin A (1999)

The first total synthesis of the cytotoxic marine metabolite agelastatin A (1) has been achieved in about 14 steps performed in 12 operations in approximately 7% overall yield starting from cyclopentadiene. Hetero Diels−Alder cycloaddition of cyclopentadiene with N-sulfinyl methyl carbamate (7) afforded cycloadduct 8, which without purification was converted to allylic sulfoxide 9 and then by a [2,3]-sigmatropic rearrangement into bicyclic oxazolidinone 11. The C-5a nitrogen was introduced into the oxazolidinone Boc derivative 16 by a Sharpless/Kresze allylic amination with SES sulfodiimide 12c. Palladium-promoted cyclization of 2-acyl pyrroles 20 and 21 via a π-allylpalladium intermediate 22 led to ABC-tricycles 23 and 24, respectively. A hydroxyl urea D-ring model system was constructed by hydroborating 24, leading eventually to keto amide 31 and then to tetracycle 33. A modified strategy was developed for synthesis of the pivotal tricyclic ketone 58, involving as key steps a chemoselective hydrolysis of N-Boc oxazolidinone 54 and an internal conjugate addition of pyrrolo cyclopentenone 57. A TMS group was used as a convenient substitute for the C-1 bromine substituent of agelastatin A, and thus silylpyrrole 58 could be converted to bromopyrrole 59. Finally, the D-ring could be annulated onto an α-amino ketone derived from 59 using methyl isocycanate, providing racemic agelastatin A (1).
Diffractive imaging for periodic samples: retrieving one-dimensional concentration profiles across microfluidic channels (2007)

A technique has been developed that allows determination of the concentration profiles of colloidal solutions or any kind of fluid under confinement. Currently, submicrometre-wide channels are sampled with a resolution in the 10 nm range. The method comprises regular arrays of microfluidic channels and one-dimensional X-ray phase-retrieval techniques for the analysis of small-angle X-ray diffraction from the array structures. Recording the X-ray diffraction data requires a low dose on each individual channel since the sum of the signals from all channels is detected. The determined concentration profiles represent the ensemble average rather than individual entities and are obtained in a model-independent way. As an example, amplitude and phase of the exit field and concentration profiles for a colloidal fluid within confining channels of different widths are shown.
Cavity Heat Transfer on a Transverse Grooved Wall in a Narrow Flow Channel (1989)

Measurements are presented of local convection heat transfer for the case of flow through a narrow slot-type channel where one of the bounding walls contains a transverse rectangular cavity. The experimental situation is a stationary modeling of some salient features of flow through the clearance gap at the grooved tips of axial turbine blades. Cavity depth-to-width ratios of 0.1, 0.2, and 0.5 are included for each of clearance-to-width ratios of 0.05, 0.10, and 0.15. Overall heat transfer on the cavity floor is in general reduced as cavity depth is increased, but reduction with the deepest cavity tested is essentially the same as that of the intermediate depth cavity. Resistance to flow through the gap is increased as cavity depth is increased, but again the change between the deepest and intermediate depth cavities is small. In addition to the stationary experiments, heat transfer in the cavity with a moving as well as stationary shroud is modeled with a finite-difference method. The numerical results indicate that, within the range of parameters considered, heat transfer characteristics in the cavity are virtually unaffected by the shroud movement. This is in agreement with a previous finding for heat transfer on ungrooved blade tips.
Publication 6 SelfOrganizing Map in Matlab: the SOM Toolbox (1999)

The Self-Organizing Map (SOM) is a vector quantization method which places the prototype vectors on a regular low-dimensional grid in an ordered fashion. This makes the SOM a powerful visualization tool. The SOM Toolbox is an implementation of the SOM and its visualization in the Matlab 5 computing environment. In this article, the SOM Toolbox and its usage are shortly presented. Also its performance in terms of computational load is evaluated and compared to a corresponding Cprogram.
Visual Attention in Deaf Children and Adults (2008)

This chapter focuses on visual attention — the ability to select and concentrate on information entering the brain via the visual pathway — and how significant hearing loss may affect how visual information is selected and attended. Deaf children have been reported to be inattentive and easily distracted. However, it is argued that this may be a reflection of how they allocate attentional resources, as well as other factors such as linguistic competence and teacher-parent attributions, as opposed to a state of inattentiveness and attentional pathology per se. Behavioral research suggests that deaf individuals cannot help but be distracted by visual information in their peripheral vision.
Computer-aided Discovery of Peptides that Specifically Attack Bacterial Biofilms (2018)

Biofilms represent a multicellular growth state of bacteria that are intrinsically resistant to conventional antibiotics. It was recently shown that a synthetic immunomodulatory cationic peptide, 1018 (VRLIVAVRIWRR-NH<sub>2</sub>), exhibits broad-spectrum antibiofilm activity but the sequence determinants of antibiofilm peptides have not been systematically studied. In the present work, a peptide library consisting of 96 single amino acid substituted variants of 1018 was SPOT-synthesized on cellulose arrays and evaluated against methicillin resistant Staphylococcus aureus (MRSA) biofilms. This dataset was used to establish quantitative structure-activity relationship (QSAR) models relating the antibiofilm activity of these peptides to hundreds of molecular descriptors derived from their sequences. The developed 3D QSAR models then predicted the probability that a peptide would possess antibiofilm activity from a library of 100,000 virtual peptide sequences in silico. A subset of these variants were SPOT-synthesized and their activity assessed, revealing that the QSAR models resulted in ~85% prediction accuracy. Notably, peptide 3002 (ILVRWIRWRIQW-NH<sub>2</sub>) was identified that exhibited an 8-fold increased antibiofilm potency in vitro compared to 1018 and proved effective in vivo, significantly reducing abscess size in a chronic MRSA mouse infection model. This study demonstrates that QSAR modeling can successfully be used to identify antibiofilm specific peptides with therapeutic potential.
The phosphorylation of serine55 in enamelin is essential for murine amelogenesis (2022)

Amelogenesis imperfecta (AI) is an inherited developmental enamel defect affecting tooth masticatory function, esthetic appearance, and the well-being of patients. As one of the major enamel matrix proteins (EMPs), enamelin (ENAM) has three serines located in Ser-x-Glu (S-x-E) motifs, which are potential phosphorylation sites for the Golgi casein kinase FAM20C. Defects in FAM20C have similarly been associated with AI. In our previous study of Enam<sup>Rgsc514</sup> mice, the Glu<sup>57</sup> in the S<sup>55</sup>-X<sup>56</sup>-E<sup>57</sup> motif was mutated into Gly, which was expected to cause a phosphorylation failure of Ser<sup>55</sup> because Ser<sup>55</sup> cannot be recognized by FAM20C. The severe enamel defects in ENAM<sup>Rgsc514</sup> mice reminiscent of Enam-knockout mouse enamel suggested a potentially important role of Ser<sup>55</sup> phosphorylation in ENAM function. However, the enamel defects and ENAM dysfunction may also be attributed to distinct physicochemical differences between Glu<sup>57</sup> and Gly<sup>57</sup>. To clarify the significance of Ser<sup>55</sup> phosphorylation to ENAM function, we generated two lines of Enam knock-in mice using CRISPR-Cas9 method to eliminate or mimic the phosphorylation state of Ser<sup>55</sup> by substituting it with Ala<sup>55</sup> or Asp<sup>55</sup> (designated as S55A or S55D), respectively. The teeth of 6-day or 4-week-old mice were subjected to histology, micro-CT, SEM, TEM, immunohistochemistry, and mass spectrometry analyses to characterize the morphological, microstructural and proteomic changes in ameloblasts, enamel matrix and enamel rods. Our results showed that the enamel formation and EMP expression in S55D heterozygotes (Het) were less disturbed than those in S55A heterozygotes, while both homozygotes (Homo) had no mature enamel formation. Proteomic analysis revealed alterations of enamel matrix biosynthetic and mineralization processes in S55A Hets. Our present findings indicate that Asp<sup>55</sup> substitution partially mimics the phosphorylation state of Ser<sup>55</sup> in ENAM. Ser<sup>55</sup> phosphorylation is essential for ENAM function during amelogenesis.
Dynamics of the reaction of N+ with H2. II. Reactive scattering at relative energies below 3 eV (1975)

The reaction N+ (H2,H) NH+ has been investigated in the range of initial relative energies from 0.79 to 2.8 eV. Despite the deep potential energy well (6 eV) associated with the symmetric NH2+ molecule ion, the reaction proceeds predominately by a direct interaction mechanism at relative energies as low as 2 eV. Only when the initial relative energy is near or below 1 eV does a long−lived complex mechanism appear to predominate. This behavior can be rationalized in terms of the qualitative features of potential energy surfaces deduced for the system from an electronic state correlation diagram.
Characterization of two human cell lines (TK-10, TK-164) of renal cell cancer. (1987)

Two previously unreported cell lines of human renal cell carcinoma are presented. TK-10 and TK-164 have each been in culture for over 4 years. The epithelial nature of both cell lines has been documented by light and electron microscopy. The cells in each line contain a Y chromosome, have specific marker chromosomes, and a distinct flow cytometric histogram. Both lines grow in agar, albeit not in athymic mice.
The Construction of New Proteins. II. Design, Synthesis and Conformational Studies of Folding Units with βαβ-Topology (1986)

The design, synthesis and preliminary conformational studies of two polypeptides exhibiting βαβ-type folding topologies are presented. In the design of the model peptides the general concept for the construction of new proteins developed in the preceeding paper was applied. According to this strategy, amphiphilic helices and β-sheets are linked together via hydrophilic loops to attain three-dimensional structures of higher order (‘supersecondary structures’). Com­puter-assisted molecular modelling served as a valuable tool for minimizing conformational con­straints within the molecules. The 38-residue peptide MI was synthesized using polyethylene glycol (PEG) as solubilizing polymeric support (‘Liquid-Phase synthesis'). Conformationally in­duced changes in the physico-chemical properties of the growing peptide chain stressed the significance of conformational effects in peptide synthesis reported earlier. Similar observations were made during the solid-phase synthesis of the 35-peptide MII. CD and IR spectroscopic studies revealed a high degree of secondary structure for both folding units. The present data strongly support the adoption of a three-dimensional structure for both models.
Catalytic Reductive Fractionation of Lignocellulose: A Lignin-first Bio-refinery Concept (2016)

status: Published
A SURVEY OF PASSENGER CAR NOISE LEVELS (1979)

&lt;div class="htmlview paragraph"&gt;Results from noise tests on 18 passenger cars are reported. The sample contains both diesel and gasoline engined vehicles and two (a SAAB 99 and Peugeot 504 GLD) are examined in detail over their normal operating range. The effects of vehicle operations are examined and differences between vehicles compared.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;For equivalent engines there is shown to be little difference between vehicle noise for diesel and gasoline engines for current legislative test procedures, although idle and low speed noise levels are increased significantly in the case of the diesel engine.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;At vehicle speeds above 80km/h in top gear, rolling noise dominates the total vehicle radiated noise.&lt;/div&gt;
Perspectives on interleukin-7 therapy in HIV infection (2007)

Numerous recent findings highlight the importance of interleukin-7 pathway impairment in the pathogenesis of HIV infection. Notably, interleukin-7 levels increased with advancing CD4 T-cell lymphopenia, whereas interleukin-7 receptor expression is downregulated mainly on CD8 T cells. Therapeutic trials conducted in monkeys and in humans (phase I) have provided evidence on the role of interleukin-7 in thymopoiesis and in restoration of T-cell functions. Interleukin-7 appeared to be well tolerated and to have no deleterious effects on viral load. These results should be confirmed in larger phase I/II studies.
Total Asymmetric Synthesis of Taxol by Dehydration Condensation between 7-TES Baccatin III and Protected N-Benzoylphenylisoserines Prepared by Enantioselective Aldol Reaction (1998)

Abstract Total asymmetric synthesis of Taxol was completed by dehydration condensation between a protected N-benzoylphenylisoserine 4 or 9 and 7-TES baccatin III which was prepared from 8-membered ring enone. Taxol side chains 4, 7, 9 and 11, optically active protected N-benzoylphenylisoserines, were successfully synthesized by enantioselective aldol reaction from two achiral starting materials, benzaldehyde and an enol silyl ether derived from S-ethyl benzyloxyethanethioate.