gebhart/patrepeval huggingface dataset:
Chemoenzymatic Assembly of Bacterial Glycoconjugates for Site-Specific Orthogonal Labeling (2015)

The cell surfaces of bacteria are replete with diverse glycoconjugates that play pivotal roles in determining how bacteria interact with the environment and the hosts that they colonize. Studies to advance our understanding of these interactions rely on the availability of chemically defined glycoconjugates that can be selectively modified under orthogonal reaction conditions to serve as discrete ligands to probe biological interactions, in displayed arrays and as imaging agents. Herein, enzymes in the N-linked protein glycosylation (Pgl) pathway of Campylobacter jejuni are evaluated for their tolerance for azide-modified UDP-sugar substrates, including derivatives of 2,4-diacetamidobacillosamine and N-acetylgalactosamine. In vitro analyses reveal that chemoenzymatic approaches are useful for the preparation of undecaprenol diphosphate-linked glycans and glycopeptides with site-specific introduction of azide functionality for orthogonal labeling at three specific sites in the heptasaccharide glycan. The uniquely modified glycoconjugates represent valuable tools for investigating the roles of C. jejuni cell surface glycoconjugates in host pathogen interactions.
[Virtual colonoscopy in real life--is it that good?]. (2003)

The results presented herein, raise many questions and "red lights" as to the use of virtual colonoscopy in its present form for screening purposes in Israel unless it is in the setting of clinical research.
Magnetoencephalography in Pediatric Lesional Epilepsy Surgery (2012)

This study was performed to assess the usefulness of magnetoencephalography (MEG) as a presurgical evaluation modality in Korean pediatric patients with lesional localization-related epilepsy. The medical records and MEG findings of 13 pediatric patients (6 boys and 7 girls) with localization-related epilepsy, who underwent epilepsy surgery at Seoul National University Children's Hospital, were retrospectively reviewed. The hemispheric concordance rate was 100% (13/13 patients). The lobar or regional concordance rate was 77% (10/13 patients). In most cases, the MEG spike sources were clustered in the proximity of the lesion, either at one side of the margin (nine patients) or around the lesion (one patient); clustered spike sources were distant from the lesion in one patient. Among the patients with clustered spike sources near the lesion, further extensions (three patients) and distal scatters (three patients) were also observed. MEG spike sources were well lateralized and localized even in two patients without focal epileptiform discharges in the interictal scalp electroencephalography. Ten patients (77%) achieved Engel class I postsurgical seizure outcome. It is suggested that MEG is a safe and useful presurgical evaluation modality in pediatric patients with lesion localization-related epilepsy.
Needle Steering and Motion Planning in Soft Tissues (2005)

In this work, needle insertion into deformable tissue is formulated as a trajectory planning and control problem. A new concept of needle steering has been developed and a needle manipulation Jacobian defined using numerical needle insertion models that include needle deflection and soft tissue deformation. This concept is used in conjunction with a potential-field-based path planning technique to demonstrate needle tip placement and obstacle avoidance. Results from open loop insertion experiments are provided.
Investigating the Effect of Sensor Modalities in Multi-Sensor Detection-Prediction Models (2021)

Detection of surrounding objects and their motion prediction are critical components of a self-driving system. Recently proposed models that jointly address these tasks rely on a number of sensors to achieve state-of-the-art performance. However, this increases system complexity and may result in a brittle model that overfits to any single sensor modality while ignoring others, leading to reduced generalization. We focus on this important problem and analyze the contribution of sensor modalities towards the model performance. In addition, we investigate the use of sensor dropout to mitigate the above-mentioned issues, leading to a more robust, better-performing model on real-world driving data.
Tertiary-Amino-Functionalized Resin-Supported Palladium Catalyst for the Heterogeneous Suzuki–Miyaura Reaction of Aryl Chlorides (2015)

A palladium catalyst supported on a tertiary-amino-functionalized resin bearing <i>N</i>,<i>N</i>-dimethylamino substituents on the polystyrene-divinylbenzene-based resin was developed. The catalyst was effectively used for the ligand-free Suzuki–Miyaura reactions of less-reactive chloroarenes with arylboronic acids. No leached palladium species were detected in the reaction media after the reaction.
Multi-Mode Master-Slave Control Approach for More Modular and Reconfigurable Hybrid Microgrids (2023)

The increasing demand for energy and the high penetration of distributed energy resources require the evolution of current electrical systems toward smarter and more reliable electric grids. In this regard, microgrids (MG) play a vital role in integrating distributed energy resources (DER), loads, and storage systems. However, microgrid architectures lack versatility and flexibility in terms of control, limiting their expansion. This paper presents a multi-mode master-slave control approach to increase the flexibility of DC-coupled hybrid microgrids. The proposed control scheme allows optimal coordination of the power units connected to each bus. Coordination among buses is also achieved through interlinking and interfacing converters; thus, ensuring the reliable operation of the microgrid. Moreover, this approach considers the possible expansion of the capacity of the MG, providing more degrees of freedom for optimization and control. An MG with two DC distribution buses connected to the main grid is selected as a case study to develop dynamic modeling and establish a control architecture. The advantages of the proposed control are discussed via MATLAB simulation results considering the operation of the MG in several scenarios.
Exploiting the preferred domain of FDD massive MIMO systems with uniform planar arrays (2015)

Massive multiple-input multiple-output (MIMO) systems hold the potential to be an enabling technology for 5G cellular. Uniform planar array (UPA) antenna structures are a focus of much commercial discussion because of their ability to enable a large number of antennas in a relatively small area. With UPA antenna structures, the base station can control the beam direction in both the horizontal and vertical domains simultaneously. However, channel conditions may dictate that one dimension requires higher channel state information (CSI) accuracy than the other. We propose the use of an additional one bit of feedback information sent from the user to the base station to indicate the preferred domain on top of the feedback overhead of CSI quantization in frequency division duplexing (FDD) massive MIMO systems. Combined with variable-rate CSI quantization schemes, the numerical studies show that the additional one bit of feedback can increase the quality of CSI significantly for UPA antenna structures.
Identification of Essential Filovirion-associated Host Factors by Serial Proteomic Analysis and RNAi Screen (2010)

An assessment of the total protein composition of filovirus (ebolavirus and marburgvirus) virions is currently lacking. In this study, liquid chromatography-linked tandem mass spectrometry of purified ebola and marburg virions was performed to identify associated cellular proteins. Host proteins involved in cell adhesion, cytoskeleton, cell signaling, intracellular trafficking, membrane organization, and chaperones were identified. Significant overlap exists between this data set and proteomic studies of disparate viruses, including HIV-1 and influenza A, generated in multiple cell types. However, the great majority of proteins identified here have not been previously described to be incorporated within filovirus particles. Host proteins identified by liquid chromatography-linked tandem mass spectrometry could lack biological relevance because they represent protein contaminants in the virus preparation, or because they are incorporated within virions by chance. These issues were addressed using siRNA library-mediated gene knockdown (targeting each identified virion-associated host protein), followed by filovirus infection. Knockdown of several host proteins (e.g. HSPA5 and RPL18) significantly interfered with ebolavirus and marburgvirus infection, suggesting specific and relevant virion incorporation. Notably, select siRNAs inhibited ebolavirus, but enhanced marburgvirus infection, suggesting important differences between the two viruses. The proteomic analysis presented here contributes to a greater understanding of filovirus biology and potentially identifies host factors that can be targeted for antiviral drug development.
A Magic Bullet for Cancer — How Near and How Far? (2001)

The search for effective and specific antineoplastic therapy has led to considerable interest in antitumor antibodies. Attempts to treat cancer with antibodies date back to the early 1900s, but progress was stalled until discovery in 1975 of a way to produce mouse monoclonal antibodies in vitro.1 Early trials with these antibodies in patients with cancer found only short-lived responses.2 One exception is a class of mouse monoclonal antibodies against the unique antigen-binding structure (idiotype) of the surface immunoglobulin on a neoplastic B cell, which can be effective in low-grade non-Hodgkin's lymphoma.3 These early attempts drew attention to the potential benefits . . .
Innovative structures to test bonding alignment and characterize high density interconnects in 3D-IC (2017)

3D integration is a promising solution to meet the increased need for functionality, density and performance of future integrated circuits. But it is necessary to have a high interconnection density to reach a significant performance gain in 3D Integrated Circuits (3D-IC). The Cu-Cu hybrid bonding can offer higher interconnects density (Pitch around 2μm or less), but that generates new challenges for test and characterization. This paper focuses on test and characterization of Cu-Cu interconnects and propose smart test vehicles to measure several information after bonding: perfect alignment, misalignment (direction, value) and contact resistance. These test structures are implemented without active part for process development and also in an application circuit to assess performance of 3D-IC thanks to the DFT infrastructure. This paper describes simulation and logic synthesis results of both implementations.
High Resolution Optical Coherence Tomography using Deconvolution (1996)

Longitudinal resolution enhancement has been achieved in optical coherence tomography using digital deconvolution methods.
Interface studies of N2plasma-treated ZnSnO nanowire transistors using low-frequency noise measurements (2013)

Due to the large surface-to-volume ratio of nanowires, the quality of nanowire-insulator interfaces as well as the nanowire surface characteristics significantly influence the electrical characteristics of nanowire transistors (NWTs). To improve the electrical characteristics by doping or post-processing, it is important to evaluate the interface characteristics and stability of NWTs. In this study, we have synthesized ZnSnO (ZTO) nanowires using the chemical vapor deposition method, characterized the composition of ZTO nanowires using x-ray photoelectron spectroscopy, and fabricated ZTO NWTs. We have characterized the current-voltage characteristics and low-frequency noise of ZTO NWTs in order to investigate the effects of interface states on subthreshold slope (SS) and the noise before and after N2 plasma treatments. The as-fabricated device exhibited a SS of 0.29 V/dec and Hooge parameter of ~1.20 × 10(-2). Upon N2 plasma treatment with N2 gas flow rate of 40 sccm (20 sccm), the SS improved to 0.12 V/dec (0.21 V/dec) and the Hooge parameter decreased to ~4.99 × 10(-3) (8.14 × 10(-3)). The interface trap densities inferred from both SS and low-frequency noise decrease upon plasma treatment, with the highest flow rate yielding the smallest trap density. These results demonstrate that the N2 plasma treatment decreases the interface trap states and defects on ZTO nanowires, thereby enabling the fabrication of high-quality nanowire interfaces.
Computational X-ray Imaging using Document Scanners (2018)

We propose a computational imaging approach enabling document scanners to be used as frugal, high-resolution X-ray imagers. We modify the document scanner optics for X-ray sensitivity and design a post-processing algorithm to denoise images.
2D IR Line Shapes Probe Ovispirin Peptide Conformation and Depth in Lipid Bilayers (2010)

We report a structural study on the membrane binding of ovispirin using 2D IR line shape analysis, isotope labeling, and molecular dynamics simulations. Ovispirin is an antibiotic polypeptide that binds to the surfaces of membranes as an alpha-helix. By resolving individual backbone vibrational modes (amide I) using 1-(13)C=(18)O labeling, we measured the 2D IR line shapes for 15 of the 18 residues in this peptide. A comparison of the line shapes reveals an oscillation in the inhomogeneous line width that has a period equal to that of an alpha-helix (3.6 amino acids). The periodic trend is caused by the asymmetric environment of the membrane bilayer that exposes one face of the alpha-helix to much stronger environmental electrostatic forces than the other. We compare our experimental results to 2D IR line shapes calculated using the lowest free energy structure identified from molecular dynamics simulations. These simulations predict a periodic trend similar to the experiment and lead us to conclude that ovispirin lies in the membrane just below the headgroups, is tilted, and may be kinked. Besides providing insight into the antibiotic mechanism of ovispirin, our procedure provides an infrared method for studying peptide and protein structures that relies on the natural vibrational modes of the backbone. It is a complementary method to other techniques that utilize line shapes, such as fluorescence, NMR, and ESR spectroscopies, because it does not require mutations, the spectra can be quantitatively simulated using molecular dynamics, and the technique can be applied to difficult-to-study systems like ion channels, aggregated proteins, and kinetically evolving systems.
Supplementary Figure Legends from XPO1 (CRM1) Inhibition Represses STAT3 Activation to Drive a Survivin-Dependent Oncogenic Switch in Triple-Negative Breast Cancer (2023)

&lt;p&gt;PDF file - 84K&lt;/p&gt;
Image-Based, Fiber Guiding Scaffolds: A Platform for Regenerating Tissue Interfaces (2013)

In the oral and craniofacial complex, tooth loss is the most commonly acquired disfiguring injury. Among the most formidable challenges of reconstructing tooth-supporting osseous defects in the oral cavity is the regeneration of functional multi-tissue complexes involving bone, ligament, and tooth cementum. Furthermore, periodontal multi-tissue engineering with spatiotemporal orientation of the periodontal ligament (PDL) remains the most challenging obstacle for restoration of physiological loading and homeostasis. We report on the ability of a hybrid computer-designed scaffold--developed utilizing computed tomography--to predictably facilitate the regeneration and integration of dental supporting tissues. Here, we provide the protocol for rapid prototyping, manufacture, surgical implantation, and evaluation of dual-architecture scaffolds for controlling fiber orientation and facilitating morphogenesis of bone-ligament complexes. In contrast to conventional single-system methods of fibrous tissue formation, our protocol supports rigorous control of multi-compartmental scaffold architecture using computational scaffold design and manufacturing by 3D printing, as well as the evaluation of newly regenerated tissue physiology for clinical implementation.
Rapid and Reliable Identification of Food-Borne Yeasts by Fourier-Transform Infrared Spectroscopy (1998)

Computer-based Fourier-transform infrared spectroscopy (FT-IR) was used to identify food-borne, predominantly fermentative yeasts. Dried yeast suspensions provided the films suitable for FT-IR measurement. Informative windows in the spectrum were selected and combined to achieve optimal results. A reference spectrum library was assembled, based on 332 defined yeast strains from international yeast collections and our own isolates. All strains were identified with conventional methods using physiological and morphological characteristics. In order to assess identification quality, another 722 unknown yeast isolates not included in the reference spectrum library were identified both by classical methods and by comparison of their FT-IR spectra with those of the reference spectrum library. Ninety-seven and one-half percent of these isolates were identified correctly by FT-IR. Easy handling, rapid identification within 24 h when starting from a single colony, and a high differentiation capacity thus render FT-IR technology clearly superior to other routine methods for the identification of yeasts.
Context-Aware, adaptive information retrieval for investigative tasks (2007)

We are building an intelligent information system to aid users in their investigative tasks, such as detecting fraud. In such a task, users must progressively search and analyze relevant information before drawing a conclusion. In this paper, we address how to help users find relevant informa-tion during an investigation. Specifically, we present a novel approach that can improve information retrieval by exploiting a user's investigative context. Compared to existing retrieval systems, which are either context insensitive or leverage only limited user context, our work offers two unique contributions. First, our system works with users cooperatively to build an investigative context, which is otherwise very difficult to capture by machine or human alone. Second, we develop a context-aware method that can adaptively retrieve and evaluate information relevant to an ongoing investigation. Experiments show that our approach can improve the relevance of retrieved information significantly. As a result, users can fulfill their investigative tasks more efficiently and effectively.
Intramural esophageal cyst: the role of endoscopic ultrasonography. (1994)

We report a case of symptomatic congenital esophageal cyst. The diagnostic approach and the role of endoscopic ultrasonography in the preoperative diagnosis, especially when computed tomography demonstrates a high attenuation mass, are emphasized.
Mosaic Hemagglutinin-Based Whole Inactivated Virus Vaccines Induce Broad Protection Against Influenza B Virus Challenge in Mice (2021)

Influenza viruses undergo antigenic changes in the immuno-dominant hemagglutinin (HA) head domain, necessitating annual re-formulation of and re-vaccination with seasonal influenza virus vaccines for continuing protection. We previously synthesized mosaic HA (mHA) proteins of influenza B viruses which redirect the immune response towards the immuno-subdominant conserved epitopes of the HA <i>via</i> sequential immunization. As ~90% of current influenza virus vaccines are manufactured using the inactivated virus platform, we generated and sequentially vaccinated mice with inactivated influenza B viruses displaying either the homologous (same B HA backbones) or the heterologous (different B HA backbones) mosaic HAs. Both approaches induced long-lasting and cross-protective antibody responses showing strong antibody-dependent cellular cytotoxicity (ADCC) activity. We believe the B virus mHA vaccine candidates represent a major step towards a universal influenza B virus vaccine.
Hyperimmune bovine colostrum in the treatment of shigellosis in children: a double‐blind, randomized, controlled trial (2001)

Immunological approaches have been considered as an alternative therapeutic option for the treatment of enteric infections over the past few years. Hyperimmune bovine colostrum (HBC) is a potentially innovative immunological option in the management of shigellosis together with traditional antibiotic therapy. Children aged 1‐12 y with a history of bloody mucoid diarrhoea of less than 5 d duration were enrolled after their stool specimen was found to be positive for Shigella dysenteriae type 1 antigen by a rapid diagnostic fluorescent antibody staining test. They were randomized to receive either HBC containing very high titres of antibody against S. dysenteriae type 1 antigen or bovine colostrum (BC) without any antibody. The study group received 100ml of HBC three times a day orally for 3 d and control group received BC. Children also received pivmecillinam in a dose of 50mg kg −1 d −1 in four divided doses orally for 5 d. Admission characteristics of the 34 children in the HBC group and 35 in the BC group were comparable. No significant differences were observed in duration of diarrhoea, fever, anorexia, abdominal pain, tenesmus, stool frequency or visible blood in the stool between the groups. Two (6%) children in the study and five (14%) in the control group remained stool culture positive for S. dysenteriae type 1, even after 5 d of sensitive antimicrobial therapy. Conclusion : The results indicate that HBC as an adjuvant is unable to show any beneficial effect in reducing the stool frequency, duration or severity of childhood shigellosis due to S. dysenteriae type 1 infection.
The largest cognitive systems will be optoelectronic (2018)

Electrons and photons offer complementary strengths for information processing. Photons are excellent for communication, while electrons are superior for computation and memory. Cognition requires distributed computation to be communicated across the system for information integration. We present reasoning from neuroscience, network theory, and device physics supporting the conjecture that large-scale cognitive systems will benefit from electronic devices performing synaptic, dendritic, and neuronal information processing operating in conjunction with photonic communication. On the chip scale, integrated dielectric waveguides enable fan-out to thousands of connections. On the system scale, fiber and free-space optics can be employed. The largest cognitive systems will be limited by the distance light can travel during the period of a network oscillation. We calculate that optoelectronic networks the area of a large data center ($10^5$\,m$^2$) will be capable of system-wide information integration at $1$\,MHz. At frequencies of cortex-wide integration in the human brain ($4$\,Hz, theta band), optoelectronic systems could integrate information across the surface of the earth.
1024-Channel 3D ultrasound digital beamformer in a single 5W FPGA (2017)

3D ultrasound, an emerging medical imaging technique that is presently only used in hospitals, has the potential to enable breakthrough telemedicine applications, provided that its cost and power dissipation can be minimized. In this paper, we present an FPGA architecture suitable for a portable medical 3D ultrasound device. We show an optimized design for the digital part of the imager, including the delay calculation block, which is its most critical part. Our computationally efficient approach requires a single FPGA for 3D imaging, which is unprecedented. The design is scalable; a configuration supporting a 32×32-channel probe, which enables high-quality imaging, consumes only about 5W.