gebhart/patrepeval huggingface dataset:
Detection of Antisynthetic Mannoside Antibodies (AΣMA) Reveals Heterogeneity in the ASCA Response of Crohn's Disease Patients and Contributes to Differential Diagnosis, Stratification, and Prediction (2008)

ASigmaMA reveal the heterogeneity of the antioligomannose antibody response in CD patients and increase the sensitivity of CD diagnosis when combined with ASCA. The subset of ASCA-negative CD patients diagnosed by ASigmaMA had preferentially a colonic involvement, which confirms the high predictive value of ASigmaMA for determining IC evolution toward CD.
Efficient Numerical Methods for Secrecy Capacity of Gaussian MIMO\n Wiretap Channel (2021)

This paper presents two different low-complexity methods for obtaining the\nsecrecy capacity of multiple-input multiple-output (MIMO) wiretap channel\nsubject to a sum power constraint (SPC). The challenges in deriving\ncomputationally efficient solutions to the secrecy capacity problem are due to\nthe fact that the secrecy rate is a difference of convex functions (DC) of the\ntransmit covariance matrix, for which its convexity is only known for \\emph{the\ndegraded case}. In the first method, we capitalize on the accelerated DC\nalgorithm, which requires solving a sequence of convex subproblems. In\nparticular, we show that each subproblem indeed admits a water-filling\nsolution. In the second method, based on the equivalent convex-concave\nreformulation of the secrecy capacity problem, we develop a so-called partial\nbest response algorithm (PBRA). Each iteration of the PBRA is also done in\nclosed form. Simulation results are provided to demonstrate the superior\nperformance of the proposed methods.\n
Advancement of turfgrass biotechnology (2002)

Advances in genetic transformation of turfgrass, like other major crop species, have been made due to the development of plant regeneration from embryogenic tissue cultures. Three conventional methods of gene delivery, direct DNA uptake by protoplasts, biolistic transformation and Agrobacterium-mediated transformation have been used successfully to produce several species of transgenic turfgrass. In transformation, antibiotics (hygromycin or G418), and herbicides (bialaphos, or ppt) are used to select transformed cell lines. Gus gene and GFP gene are always used as reported genes. However, transgenic turfgrass may also have potential environmental risks.
Dislocation-Induced Local Modulation of the Surface States of Ag(111) Thin Films on Si(111)7×7Substrates (2010)

Local modulation of the Shockley-type surface state was studied around threading dislocations at the surfaces of ultrathin Ag(111) epitaxial films on Si(111) substrates. Scanning tunneling microscope (STM) observations indicated that the wavelength of the surface state electron was shortened around the dislocations in the electron standing wave pattern. Scanning tunneling spectroscopy (STS) revealed that the bottom of the local surface state (E0) shifts downward around the dislocation. The shift in E0 and the lattice displacement Delta u(z) have a linear relation, which indicates that the shift of the surface state is caused by local relaxation of the misfit strain around the dislocation.
A Switch for the Transfer of Substrate between Nonribosomal Peptide and Polyketide Modules of the Rifamycin Synthetase Assembly Line (2003)

A nonribosomal peptide synthetase (NRPS) loading module and a polyketide synthase (PKS) elongation module catalyze the preliminary steps in the biosynthesis of the rifamycin antibiotics. A benzoate molecule is covalently attached to the phosphopantetheine arm of the thiolation domain of the loading module when its reaction partner methylmalonyl-CoA is absent. Occupancy of the thiolation domain of the elongation module by a methylmalonyl moiety appears to trigger intermodular transfer of benzoate to the ketosynthase domain of the elongation module. This transthiolation event is fast relative to the initial loading of benzoate onto the loading module. It will be of interest to determine if these results are generally true for intermodular acyl transfer in other NRPS-PKS and PKS assembly lines.
Preface (2008)

Class-tested and coherent, this textbook teaches classical and web information retrieval, including web search and the related areas of text classification and text clustering from basic concepts. It gives an up-to-date treatment of all aspects of the design and implementation of systems for gathering, indexing, and searching documents; methods for evaluating systems; and an introduction to the use of machine learning methods on text collections. All the important ideas are explained using examples and figures, making it perfect for introductory courses in information retrieval for advanced undergraduates and graduate students in computer science. Based on feedback from extensive classroom experience, the book has been carefully structured in order to make teaching more natural and effective. Slides and additional exercises (with solutions for lecturers) are also available through the book's supporting website to help course instructors prepare their lectures.
Cell spreading controls endoplasmic and nuclear calcium: A physical gene regulation pathway from the cell surface to the nucleus (2003)

Cells attaching to an extracellular matrix through integrins flatten out (spread) on the matrix, eliciting cellular signals needed for survival. We show that the shape of the nucleus changes and the nuclear calcium level increases in spreading cells. Moreover, cell spreading and osmotic stretching of isolated nuclei cause release of perinuclear Ca(2+), and patch clamping of nuclei reveals stretch-activated Ca(2+) permeable channels. Gene expression assays with myocyte enhancer factor 2, which is activated by calmodulin-dependent kinase IV, indicate that the elevation in nuclear Ca(2+) is functionally significant. We propose a mechano-transduction pathway in which spreading-induced nuclear stretching releases Ca(2+) from the perinuclear space, and the resulting Ca(2+) elevation in the nucleus provokes changes in gene expression.
Rigorous coupled-wave analysis equivalent-index-slab method for analyzing 3D angular misalignment in interlayer grating couplers (2016)

The interlayer waveguide grating coupling efficiencies under angular (rotational) misalignments are simulated using the 3D rigorous coupled-wave analysis (3D-RCWA) together with the RCWA equivalent-index-slab (RCWA-EIS) method. As examples of conical diffraction, rotations about the two coordinate axes, x and z, defined by the vectors [1 0 0] and [0 0 1], respectively, as well as an arbitrary axis, defined by the vector [2 2 1], are simulated for binary rectangular-groove gratings. The interlayer grating coupling efficiency is approximated by the product of the top- and bottom-grating diffraction efficiencies (DEs). It is found that the bottom-grating DEs decrease about 25% when the bottom grating is rotated ±0.1 rad (5.73°) about the z-axis. DEs slightly increase (5% to 10% depending on the grating structures) when the bottom grating is rotated ±0.1 rad about the x-axis. This is consistent with the diffraction behavior of an over-modulated grating. When the bottom grating is rotated about the vector [2 2 1], the change in DEs is asymmetric with a 100% decrease at a rotation angle -0.1 rad and a 67% decrease at a rotation angle +0.1 rad. The method is shown to be computationally efficient and numerically stable for grating structures with optimized parameters, and the resulting bottom-grating diffraction efficiencies demonstrate similar trends as those calculated by the 3D finite-difference time-domain simulations. The procedure presented can be directly used in the analysis and design of interlayer waveguide grating coupling for optical interconnects in high-density integrated electronics.
ChemInform Abstract: Catalytic Enantioselective Synthesis of Halocyclopropanes. (2016)

Abstract Cyclopropanation of 2‐haloalkenes with α‐cyano‐diazoacetates in the presence of a chiral Rh‐catalyst provides a general synthesis of highly functionalized cyclopropanes such as (III) and (V).
Polymer-Based Protein Delivery Systems for Loco-Regional Administration (2021)

Extensive research and development work to promote preclinical and clinical use of the carrier has been documented in a decent number of literatures over the last decade. Proteins have the most dynamic and diverse role of any macromolecule in the body. They act as catalysts to biochemical reactions by forming receptors and channels in the membranes. Furthermore, proteins provide intracellular and extracellular scaffolding support and they transport molecules within the cells or from one organ to another. Proteins first emerged as a major class of pharmaceuticals in the 1980s, with a majority of them mainly developed for therapeutics and a small number for diagnostics and vaccines. Recombinant production of proteins is highly favoured over purification of proteins from their native source. Tremendous effort has been invested in cellular engineering to optimize various hosts for protein production and there are many examples in which proteins have been used in therapy successfully.
The effect of a lidocaine/prilocaine topical anesthetic on pain and discomfort associated with orthodontic elastomeric separator placement [Book Review] (2017)

Review(s) of: The effect of a lidocaine/prilocaine topical anesthetic on pain and discomfort associated with orthodontic elastomeric separator placement, by Abu Al-Melh M and Andersson L, Progress in Orthodontics 2017; 18: 1.
Electrosynthesis of phenyl-2-propanone derivatives from benzyl bromides and acetic anhydride in an unsupported micro-flow cell electrolysis process (2006)

A simple process for the synthesis of phenyl-2-propanone is described based on a one-step electrochemical acylation reaction, involving the direct electroreductive coupling of benzyl bromides and acetic anhydride in a micro-flow electrolysis cell, equipped with micro-gap Pt electrodes. The technique offered yields typically in excess of 80% with corresponding high levels of product selectivity. The electrochemical process was also scaled-up by connecting four identical micro electrochemical cells in parallel to increase product throughput.
Roadmap for Commercial Gigapixel Cameras (2014)

Multiscale array cameras allow 10–100× improvements in commercial camera resolution. This talk discussed the optical manufacturing, electronic processing and communications and cloud software ecosystem that enables economical multiscale cameras.
ChemInform Abstract: ATP‐Site Directed Inhibitors of Cyclin‐Dependent Kinases (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.
Compressed Sensing with Applications in Wireless Networks (2019)

Many natural signals possess only a few degrees of freedom. For instance, the occupied radio spectrum may be intermittently concentrated to only a few frequency bands of the system bandwidth. This special structural feature – signal sparsity – is conducive in designing efficient signal processing techniques for wireless networks. In particular, the signal sparsity can be leveraged by the recently emerged joint sampling and compression paradigm, compressed sensing (CS). This monograph reviews several recent CS advancements in wireless networks with an aim to improve the quality of signal reconstruction or detection while reducing the use of energy, radio, and computation resources. The monograph covers a diversity of compressive data reconstruction, gathering, and detection frameworks in cellular, cognitive, and wireless sensor networking systems. The monograph first gives an overview of the principles of CS for the readers unfamiliar with the topic. For the researchers knowledgeable in CS, the monograph provides in-depth reviews of several interesting CS advancements in designing tailored CS reconstruction techniques for wireless applications. The monograph can serve as a basis for the researchers intended to start working in the field, and altogether, lays a foundation for further research in the covered areas.
Highly Sensitive and Reliable Plasmonic Nanoparticle-based Microscopy Method for Quantification of Low Abundance Cell Surface Molecules (2017)

A microscopy-based method has been developed for the ultrasensitive quantification of low abundance cell surface molecules. This approach, where bound molecules are enumerated via the binding of plasmonic nanoparticles, enables near single molecule detection sensitivity.
Mid-infrared photothermal heterodyne spectroscopy in a liquid crystal using a quantum cascade laser (2012)

We report a technique to measure the mid-infrared photothermal response induced by a tunable quantum cascade laser in the neat liquid crystal 4-octyl-4'-cyanobiphenyl (8CB), without any intercalated dye. Heterodyne detection using a Ti:sapphire laser of the response in the solid, smectic, nematic and isotropic liquid crystal phases allows direct detection of a weak mid-infrared normal mode absorption using an inexpensive photodetector. At high pump power in the nematic phase, we observe an interesting peak splitting in the photothermal response. Tunable lasers that can access still stronger modes will facilitate photothermal heterodyne mid-infrared vibrational spectroscopy.
Noise and distortion characteristics of cryogenic vertical cavity lasers (2002)

Both the noise and distortion properties of a low power vertical cavity laser (VCL) have been studies under both room and cryogenic temperatures. The noise of the measurement link with high bias level is dominated by the photodiode shot noise.
Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody–antigen interaction (2018)

Growing numbers of therapeutic antibodies offer excellent treatment strategies for many diseases. Elucidation of the interaction between a potential therapeutic antibody and its target protein by structural analysis reveals the mechanism of action and offers useful information for developing rational antibody designs for improved affinity. Here, we developed a rapid, high-yield cell-free system using dialysis mode to synthesize antibody fragments for the structural analysis of antibody-antigen complexes. Optimal synthesis conditions of fragments (Fv and Fab) of the anti-EGFR antibody 059-152 were rapidly determined in a day by using a 30-μl-scale unit. The concentration of supplemented disulfide isomerase, DsbC, was critical to obtaining soluble antibody fragments. The optimal conditions were directly applicable to a 9-ml-scale reaction, with linear scalable yields of more than 1 mg/ml. Analyses of purified 059-152-Fv and Fab showed that the cell-free synthesized antibody fragments were disulfide-bridged, with antigen binding activity comparable to that of clinical antibodies. Examination of the crystal structure of cell-free synthesized 059-152-Fv in complex with the extracellular domain of human EGFR revealed that the epitope of 059-152-Fv broadly covers the EGF binding surface on domain III, including residues that formed critical hydrogen bonds with EGF (Asp355EGFR, Gln384EGFR, H409EGFR, and Lys465EGFR), so that the antibody inhibited EGFR activation. We further demonstrated the application of the cell-free system to site-specific integration of non-natural amino acids for antibody engineering, which would expand the availability of therapeutic antibodies based on structural information and rational design. This cell-free system could be an ideal antibody-fragment production platform for functional and structural analysis of potential therapeutic antibodies and for engineered antibody development.
Natural Orifice Translumenal Endoscopic Surgery Used for Perforated Viscus Repair Is Feasible Using Lower Peritoneal Pressures than Laparoscopy in a Porcine Model (2010)

Endoscopic ulcer repair appears technically feasible with similar clinical and infectious outcomes to laparoscopy. The lower required pneumoperitoneal pressures used in these NOTES techniques are recognizable different outcomes from laparoscopy and can be advantageous in critically ill patients.
A systematic review of the clinical application of data-driven population segmentation analysis (2018)

Data-driven population segmentation has been widely applied and holds great potential in managing population health. The evaluations of segmentation outcome require the interplay of data analytics and subject matter expertise. The optimal framework for segmentation requires further research.
A Calix[4]arenoporphyrin (1997)

All four porphyrin units on the same side—that is the surprising conformation adopted by calixarene 1. A “cogwheel” dimeric structure was identified for the compound in the solid state, in which π–π aggregation is the dominating structural feature.
An Enhanced Extract-Transform-Load System for Migrating Data in Telecom Billing (2008)

Data migration has become a priority in many industries, spawned by a variety of business needs. Most of the existing tools for Extract, Transform and Load (ETL) process of data migration are piece-meal and do not present a complete solution. Moreover, while research has focused on the problem of Schema Mapping, a key step in the ETL process, most of the current algorithms do not perform well on real-world data. Researchers have suggested the use of Domain Knowledge to enhance schema mapping. In this paper, we use domain knowledge in an innovative manner to improve schema mapping in an 'actual' industrial setting. Further, we take a comprehensive view of the data migration problem and present an end-to-end system for the ETL process, utilizing existing tools for each step and building connectors, wherever required. We focus on Data Migration for Telecom Billing and utilize domain knowledge captured in an ontology, a thesaurus and a set of rules to improve schema mapping. Experiments conducted on a real-life data demonstrate the effectiveness of our system and validate the utility of domain knowledge in data migration projects.
GraphTiles: Visualizing graphs on mobile devices (2013)

GraphTiles: Visualizing Graphs on Mobile DevicesFigure 1: Different explicit link representations for GraphTiles.(a) text: nodes with the same name are linked.(b) color: nodes with the same color are linked.(c) connectedness: nodes with lines between them are linked.(d) proximity: nodes at/containing the same vertical position are linked.(e) texture: nodes with/containing the same image are linked.
Mini‐synplastomes for plastid genetic engineering (2021)

In the age of synthetic biology, plastid engineering requires a nimble platform to introduce novel synthetic circuits in plants. While effective for integrating relatively small constructs into the plastome, plastid engineering via homologous recombination of transgenes is over 30 years old. Here we show the design-build-test of a novel synthetic genome structure that does not disturb the native plastome: the 'mini-synplastome'. The mini-synplastome was inspired by dinoflagellate plastome organization, which is comprised of numerous minicircles residing in the plastid instead of a single organellar genome molecule. The first mini-synplastome in plants was developed in vitro to meet the following criteria: (i) episomal replication in plastids; (ii) facile cloning; (iii) predictable transgene expression in plastids; (iv) non-integration of vector sequences into the endogenous plastome; and (v) autonomous persistence in the plant over generations in the absence of exogenous selection pressure. Mini-synplastomes are anticipated to revolutionize chloroplast biotechnology, enable facile marker-free plastid engineering, and provide an unparalleled platform for one-step metabolic engineering in plants.
Molecular Targeting of Lymphangiogenesis and Tumor Metastasis (2009)

Recent discoveries of essential factors regulating the development of the lymphatic system have resulted in the establishment of new biological models and the identification of lymphatic-specific markers, which have enabled further understanding of the lymphatic system and its associated diseases. Critical factors for development of the lymphatic system include vascular endothelial growth factor-C (VEGF-C) and its receptor VEGFR-3. In many cancers, expression of the VEGFR-3 ligands, VEGF-C and VEGF-D, is correlated with tumor metastasis. A number of additional molecules have since been identified to promote lymphangiogenesis as well as metastasis, including a number of receptor tyrosine kinases and downstream signaling molecules, chemokines and chemokine receptors, matrix and basement membrane proteins, and inflammatory mediators such as COX-2. The development of therapeutics interfering with lymphangiogenesis, particularly those inhibiting VEGFR-3 signaling, has therefore been of growing interest in oncology. Among these therapeutics are tyrosine kinase inhibitors, blocking antibodies, and ligand traps. As adjuvant therapy, these inhibitors offer great potential for impeding disease progression.
Automatic segmentation of closed-contour features in ophthalmic images using graph theory and dynamic programming (2012)

This paper presents a generalized framework for segmenting closed-contour anatomical and pathological features using graph theory and dynamic programming (GTDP). More specifically, the GTDP method previously developed for quantifying retinal and corneal layer thicknesses is extended to segment objects such as cells and cysts. The presented technique relies on a transform that maps closed-contour features in the Cartesian domain into lines in the quasi-polar domain. The features of interest are then segmented as layers via GTDP. Application of this method to segment closed-contour features in several ophthalmic image types is shown. Quantitative validation experiments for retinal pigmented epithelium cell segmentation in confocal fluorescence microscopy images attests to the accuracy of the presented technique.
Frequency and predictors of post-operative pericardial effusion requiring drainage following percutaneous epicardial access in the electrophysiology laboratory (2013)

Purpose: Percutaneous pericardial access is increasingly performed for mapping and ablation. Pericardial fat irritation, disruption of intrapericardial vessels, inadvertent right ventricular entry and periprocedural anticoagulation may predispose towards pericardial effusion but post-operative pericardial drains are associated with pain and pericarditis. While intra-procedural fluid accumulation is managed with existing epicardial access, post-procedural development of pericardial effusion following drain removal requires a separate invasive procedure with inherent risks. We sought to identify the frequency and predictors of pericardial effusion following epicardial sheath removal.