gebhart/patrepeval huggingface dataset:
Dissecting Human Antibody Responses: Useful, Basic, and Surprising Findings (2017)

Abstract We use cell culture-based high-throughput methods to interrogate human memory B cell and plasma cell repertoires and to isolate antibodies selected on the basis of their neutralizing potency and breadth. Relevant examples are antibodies that neutralize all influenza A viruses or even four paramyxoviruses. By targeting conserved structures, these broadly neutralizing antibodies are less prone to select escape mutants and are promising candidates for prophylaxis and therapy of infections, as well as tools for vaccine design. The value of a target-agnostic approach to vaccine design is illustrated by our discovery of extremely potent antibodies that neutralize human cytomegalovirus, which led to the identification of their viral ligand, a pentameric complex that was then produced and tested as an effective vaccine. By reconstructing the genealogy trees of specific B cell clones, we investigate the role of somatic mutations in affinity maturation and in generation of antibody variants with broader or different specificity. Somatic mutations can also generate autoantibodies, as found in patients with pemphigus and autoimmune pulmonary alveolar proteinosis. Recently, while searching for antibodies that broadly react with malaria variant antigens, we discovered a new mechanism of antibody diversification, which relies on templated insertions of genomic DNA sequences into immunoglobulin genes, followed by somatic mutations. Disclosures Lanzavecchia: Humabs SA: Equity Ownership, Research Funding.
Use of in vivo -induced antigen technology (IVIAT) to identify genes uniquely expressed during human infection with Vibrio cholerae (2003)

In vivo-induced antigen technology is a method to identify proteins expressed by pathogenic bacteria during human infection. Sera from 10 patients convalescing from cholera infection in Bangladesh were pooled, adsorbed against in vitro-grown El Tor Vibrio cholerae O1, and used to probe a genomic expression library in Escherichia coli constructed from El Tor V. cholerae O1 strain N16961. We identified 38 positive clones in the screen, encoding pili (PilA and TcpA), cell membrane proteins (PilQ, MshO, MshP, and CapK), methyl-accepting chemotaxis proteins, chemotaxis and motility proteins (CheA and CheR), a quorum-sensing protein (LuxP), and four hypothetical proteins. Analysis of immune responses to purified PilA and TcpA in individual patients demonstrated that the majority seroconverted to these proteins, confirming results with pooled sera. These results suggest that PilA and its outer membrane secretin, PilQ, are expressed during human infection and may be involved in colonization of the gastrointestinal tract. These results also demonstrate substantial immune responses to TcpA in patients infected with El Tor V. cholerae O1. In vivo-induced antigen technology provides a simple method for identifying microbial proteins expressed during human infection, but not during in vitro growth.
Active defense against counterfeiting attacks through robust antifuse-based on-chip locks (2014)

The rapidly rising incidences of counterfeit Integrated Circuits (ICs) in the semiconductor supply chain pose a significant threat to the electronic industry. These ICs may suffer from functional, performance or reliability issues and can affect design houses, chip manufacturers, system designers as well as end users. The standard chip/package/system level tests are often inadequate in detecting various forms of counterfeit ICs. On the other hand, design approaches that enable IC authentication are often not attractive due to significant design effort, hardware overhead and test cost. In this paper, we propose a novel defense against counterfeiting attacks through a “chip locking approach”, where an IC is made non-operational by locking select pins through insertion of Antifuse (AF) devices in input/output circuitry. It can be unlocked through application of a hard-to-clone key. The key is internally stored in a onetime programmable non-volatile memory. The key storage and comparison circuit is protected against reverse engineering and side-channel analysis attacks. Through mathematical analysis and simulation results, we demonstrate that the proposed mechanism provides high level of protection against all major forms of counterfeiting attacks (reselling, remarking and cloning) at ultralow overhead (<; 0.01% area).
Learning shape writing by game playing (2007)

We present a computer game designed to efficiently and playfully teach users shape writing - a new text entry method for pen-based devices.
PepBio: predicting the bioactivity of host defense peptides (2017)

A large-scale QSAR study of host defense peptides sheds light on the origin of their bioactivities (antibacterial, anticancer, antiviral and antifungal).
A spoken dialogue system for conference/workshop services (2000)

This paper describes our progress towards building a telephony-based spoken dialogue system for workshop/conference services.A mixed-initiative dialogue system has been developed that is engineered to o er users natural interaction with the system, ease-of-use and robustness towards ambiguous requests and machine errors.A prototype system, known as W99, is described in this paper which w as deployed in the 1999 IEEE International Workshop on Automatic Speech Recognition and Understanding (ASRU'99), Keystone, Colorado.This system integrates advanced technologies in speech and dialogue design.An evaluation of the W99 system in terms of recognition performance, understanding accuracy and dialogue success rate during the live trial of the system are present e d i n t h i s p aper.
Resonant eddy current analysis: A selective screening method for electromagnetic shielding materials (2002)

The authors discuss both the principle and practice of resonant eddy current analysis (RECA) and its applicability as a screening agent for prospective electromagnetic shielding materials. The RECA methodology relies on the principle that a resonant RLC electrical circuit is detuned by inserting a sample into the coiled inductor. The change in capacitance needed to maintain the original resonant frequency and the change in impedance at resonance are measured. These measured changes define a constraint on an analytical relationship between the material's conductivity and permeability. In practice, however, measuring changes in frequency is more feasible than changing resonanting capacitors. The RECA methodology is contactless, timely, and efficient. It is inexpensive, requiring only an inductor, several capacitors, and an impedance meter. This method has been used to screen a variety of materials ranging from metals to composite materials.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Strong accountability for network storage (2007)

This article presents the design, implementation, and evaluation of CATS, a network storage service with strong accountability properties. CATS offers a simple web services interface that allows clients to read and write opaque objects of variable size. This interface is similar to the one offered by existing commercial Internet storage services. CATS extends the functionality of commercial Internet storage services by offering support for strong accountability. A CATS server annotates read and write responses with evidence of correct execution, and offers audit and challenge interfaces that enable clients to verify that the server is faithful. A faulty server cannot conceal its misbehavior, and evidence of misbehavior is independently verifiable by any participant. CATS clients are also accountable for their actions on the service. A client cannot deny its actions, and the server can prove the impact of those actions on the state views it presented to other clients. Experiments with a CATS prototype evaluate the cost of accountability under a range of conditions and expose the primary factors influencing the level of assurance and the performance of a strongly accountable storage server. The results show that strong accountability is practical for network storage systems in settings with strong identity and modest degrees of write-sharing. We discuss how the accountability concepts and techniques used in CATS generalize to other classes of network services.
A nanostructure thermal property measurement platform. (2010)

Measurements of the electrical and thermal transport properties of one-dimensional nanostructures (e.g., nanotubes and nanowires) typically are obtained without detailed knowledge of the specimen's atomic-scale structure or defects. To address this deficiency we have developed a microfabricated, chip-based characterization platform that enables both transmission electron microscopy (TEM) of atomic structure and defects as well as measurement of the thermal transport properties of individual nanostructures. The platform features a suspended heater line that contacts the center of a suspended nanostructure/nanowire that was placed using in-situ scanning electron microscope nanomanipulators. One key advantage of this platform is that it is possible to measure the thermal conductivity of both halves of the nanostructure (on each side of the central heater), and this feature permits identification of possible changes in thermal conductance along the wire and measurement of the thermal contact resistance. Suspension of the nanostructure across a through-hole enables TEM characterization of the atomic and defect structure (dislocations, stacking faults, etc.) of the test sample. As a model study, we report the use of this platform to measure the thermal conductivity and defect structure of GaN nanowires. The utilization of this platform for the measurements of other nanostructures will also be discussed.
Supplementary Table 14 from Somatic Mosaic Chromosomal Alterations and Death of Cardiovascular Disease Causes among Cancer Survivors (2023)

&lt;p&gt;Supplementary Table 14: Cox regression analyses of the effect of mosaic chromosomal alterations on the risk of death from cancer according to cancer type&lt;/p&gt;
ChemInform Abstract: From Chemical Solutions to Inorganic Nanostructured Materials: A Journey into Evaporation‐Driven Processes (2014)

Abstract Review: 170 refs.
Electromechanical Regenerative Actuator With Fault-Tolerance Capability for Automotive Chassis Applications (2013)

This paper investigates an electromechanical regenerative (EMR) actuator for automotive chassis applications. The actuator system comprises an electric machine, a ball screw, and a controller. The designs of these three components are examined first. Control algorithms are then developed for both converter and inverter topologies. A prototype actuator has been fabricated and tested in the laboratory. Test results indicate that the regenerative system achieves the required performance and has the capability to regenerate power to improve real-world fuel economy.
Impacts of Thermal Hydrolysis on Biosolids Quality Parameters: Dewaterability, Odors, Indicators and Pathogens (2010)

Impacts of Thermal Hydrolysis on Biosolids Quality Parameters: Dewaterability, Odors, Indicators and PathogensThe objectives of this research were to evaluate several different enhanced or advanced digestion processes for their ability to minimize the risk for a sustainable Class A biosolids program. The two key risks that were considered were odors and increases in indicator bacteria density after dewatering. The four processes evaluated included thermal hydrolysis pretreatment, dual digestion, enhanced...Author(s)Sudhir MurthyMatthew HigginsWalt BaileyPerry SchaferSteven BeightolYen-Chih ChenJohn NovakChris WilsonRumana RiffatSebnem AynurSourceProceedings of the Water Environment FederationSubjectSession 10: Anaerobic Digestion Pretreatment for Enhanced PerformanceDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2010ISSN1938-6478SICI1938-6478(20100101)2010:4L.687;1-DOI10.2175/193864710802767759Volume / Issue2010 / 4Content sourceResiduals and Biosolids ConferenceFirst / last page(s)687 - 697Copyright2010Word count228Subject keywordsBiosolidssustainabilityodorscoliformsthermal hydrolysis
Research Institutions’ Teaching Imperative: Rising to the Commitment of Service-Learning in Engineering Education (2020)

For over two decades, a number of engineering faculty members at a research institution of higher education in the United States have successfully integrated service-learning in their courses as an effective curricular strategy. While some faculty members have continued to integrate service-learning in their teaching, others have discontinued its use. This inquiry examines the reasons faculty discontinued the integration of service-learning in their courses. Specifically, it focuses on engineering faculty members at a public research university. Most studies on faculty involvement with service-learning have focused on factors that influence whether or not faculty adopt service-learning pedagogy, and no study has investigated factors for discontinuing the use of service-learning in engineering. A qualitative research approach is used to conduct in-depth interviews of engineering faculty using a semi structured protocol. The interviews were aimed at identifying the faculty experience, and at interpreting the reasons for discontinuation. The research findings indicate that faculty discontinued the use of servicelearning simply because they no longer teach the course. Even so, the common theme that emerged among the faculty was that most believed in service-learning's intended educational outcome.
A Simple Algorithm for Graph Reconstruction (2021)

How efficiently can we find an unknown graph using distance queries between its vertices? We assume that the unknown graph is connected, unweighted, and has bounded degree. The goal is to find every edge in the graph. This problem admits a reconstruction algorithm based on multi-phase Voronoi-cell decomposition and using Õ(n^{3/2}) distance queries [Kannan et al., 2018]. In our work, we analyze a simple reconstruction algorithm. We show that, on random Δ-regular graphs, our algorithm uses Õ(n) distance queries. As by-products, we can reconstruct those graphs using O(log² n) queries to an all-distances oracle or Õ(n) queries to a betweenness oracle, and we bound the metric dimension of those graphs by log² n. Our reconstruction algorithm has a very simple structure, and is highly parallelizable. On general graphs of bounded degree, our reconstruction algorithm has subquadratic query complexity.
Tailored anomalous group-velocity dispersion in silicon channel waveguides (2006)

We present the first experimental demonstration of anomalous group-velocity dispersion (GVD) in silicon waveguides across the telecommunication bands. We show that the GVD in such waveguides can be tuned from -2000 to 1000 ps/(nm*km) by tailoring the cross-sectional size and shape of the waveguide.
Abstract 1544: Early Statin Therapy Reduces Risk Of ICD Shocks In Patients With An Implantable Cardioverter-defibrillator Undergoing Ablation For Ventricular Tachycardia (2007)

Background : Lipid lowering therapy reduces mortality in patients with both ischemic and nonischemic cardiomyopathies and recently has been shown to decrease ICD shocks. Radiofrequency ablation (RFA) of recurrent VT in patients with an ICD also reduces shocks following intervention. It is unclear if statin therapy after VT RFA will further impact ICD shock rates. Methods : All patients from 1993–2005 who underwent a RFA procedure for recurrent VT at the Mayo Clinic with an ICD were included. Patient records were extracted for medical and procedural details and all ICD interrogations were reviewed for VT recurrence and therapies. Results: 63 patients (age 62±15 years) were followed over 3.9±3.6 years. Comorbid diseases included: coronary artery disease 37(58%, 34 prior myocardial infarction), ARVD/C 6(10%), nonischemic dilated cardiomyopathy 7(11%), moderate-severe valve disease 14(22%), hypertension 34(54%), and hyperlipidemia 35(56%). Ejection fraction was &lt;0.35 in 34(56%). VT was induced in all patients (LV 55 (LVOT 1), RV 8 (RVOT 3) with multiple inducible VTs in 21(33%). VT was noninducible after RFA in 39(62%) patients. Dismissal medications included: statins 19(30%), beta blockers 40(66%), ACE/ARB 37(61%), diuretics 34(55%), and digoxin 23(37%). 5-year overall survival was 63%(95% CI 55–71). Age, diabetes, and renal insufficiency were associated with increased post ablation mortality, with no medication improving survival. 5-year survival free of ICD shocks was 31%(95% CI 24–38). Only statin therapy at discharge was associated with a decreased risk of ICD shocks [5(26%) versus 26(59%), p=0.020]. 7 additional patients received statins during follow-up, but not at discharge, of these 5(71%) had shocks. Conclusion : Statin use at discharge in patients with an ICD undergoing RFA for refractory VT significantly reduced recurrent ventricular arrhythmias and ICD shocks. Although the mechanism underlying the effects of statins on arrhythmic recurrence early after RFA requires further study, these data support aggressive therapy of the underlying substrate responsible for the VT.
Non-invasive cardiac pacing with image-guided focused ultrasound (2016)

Currently, no non-invasive cardiac pacing device acceptable for prolonged use in conscious patients exists. High Intensity Focused Ultrasound (HIFU) can be used to perform remote pacing using reversibility of electromechanical coupling of cardiomyocytes. Here we described an extracorporeal cardiac stimulation device and study its efficacy and safety. We conducted experiments ex vivo and in vivo in a large animal model (pig) to evaluate clinical potential of such a technique. The stimulation threshold was determined in 10 different ex vivo hearts and different clinically relevant electrical effects such as consecutive stimulations of different heart chambers with a single ultrasonic probe, continuous pacing or the inducibility of ventricular tachycardia were shown. Using ultrasonic contrast agent, consistent cardiac stimulation was achievable in vivo for up to 1 hour sessions in 4 different animals. No damage was observed in inversion-recovery MR sequences performed in vivo in the 4 animals. Histological analysis revealed no differences between stimulated and control regions, for all ex vivo and in vivo cases.
The Effects of Resistance Training On Cardiac Muscle Function During Cancer Cachexia (2019)

THE EFFECTS OF RESISTANCE TRAINING ON CARDIAC MUSCLE FUNCTION DURING CANCER CACHEXIA Ashton A. Legenza1, Chase W. Reyes1, Matthew D. Dovgan1, Allison T. Tigner1, Wisam O. Najdawi1, Jacob A. Siedlik1, Joan M. Eckerson1, Kristen M. Drescher2, Eric C. Bredahl1 1Creighton University, Omaha, NE 2Creighton University School of Medicine, Omaha, NE It is estimated that half of all patients with cancer will eventually develop a condition called cachexia that is characterized by systemic inflammation, negative protein and energy balance, and an involuntary loss of cardiac and skeletal muscle. It is a dangerous syndrome that not only has a dramatic impact on patient quality of life but is also associated with poor responses to chemotherapy and decreased survival. PURPOSE: To investigate the effects of resistance training (RT) on cancer cachexia-induced cardiac muscle loss. METHODS: All procedures were done in accordance with an IACUC approved protocol. Male-Wistar rats (n=48) were randomly assigned to a sedentary (SED), RT, SED+cancer, and RT+cancer group. Animals assigned to RT groups trained for a total of 13 weeks using an elevated food model to simulate low intensity RT. SED animals were placed in standard animal housing for an equivalent amount of time. At week 10, animals were injected with Walker 256 mammarycarcinoma cells (106 cells) or an equivalent amount of 0.9% saline. Left ventricular morphology was measured using echocardiography prior to injection and at the end of the 13-week experiment. Animals were anesthetized with isoflurane during imaging. Differences in ventricular thickness and diameter between groups were analyzed using one-way ANOVA. Significance was set at α=0.05. RESULTS: There were no significant findings for ventricular morphology between or within groups. CONCLUSIONS: The findings suggest that RT had no effect on cancer-cachexia induced cardiac muscle loss. Since the Walker 256 mammarycarcinoma cells did not provide a significant cardiotoxic effect, future studies are warranted using different cancer cell lines or incubation periods to induce cardiotoxicity. This work was funded through a Haddix research grant.
Antisense Oligonucleotide Nanocapsules Efficiently Inhibit EWS-Fli1 Expression in a Ewing's Sarcoma Model (2006)

The cytogenetic abnormality of Ewing's sarcoma is related to the presence of a balanced t(11;22) translocation expressing the EWS-Fli1 chimeric fusion protein. Oligonucleotides (ODNs) are specific compounds that inhibit gene expression at the transcriptional level. They possess a poor bioavailability and are degraded by nucleases very rapidly. Therefore, there is a strong need for the development of ODN drug delivery systems. In the present study, polyisobutylcyanoacrylate nanocapsules entrapping ODNs in their aqueous core were prepared, with high encapsulation yield (99%). Previous studies have demonstrated that such complexes were able to inhibit tumor growth in mice. Nevertheless, no information was available about their mode of action at the cellular level. The aim of this study was to investigate the efficacy of these ODN nanocapsules on cultured tumor cells. We found that nanocapsules were capable of protecting ODN against degradation. Using confocal microscopy, we observed that cell uptake and nuclear accumulation of ODNs were importantly enhanced when ODNs were associated with these nanocapsules. Consequently, a specific cellular growth inhibition and suppression of EWSFli1 fusion gene expression was noticed. In conclusion, it was demonstrated that nanocapsules as nonviral vectors show great potential for the delivery of ODNs to cells.
Search for top squarks and dark matter particles in opposite-charge dilepton final states at s=13  TeV (2018)

A search for new physics is presented in final states with two oppositely charged leptons (electrons or muons), jets identified as originating from b quarks, and missing transverse momentum (p miss T ). The search uses proton-proton collision data at ffiffi ffi s p 13 TeV amounting to 35.9 fb -1 of integrated luminosity collected using the CMS detector in 2016. Hypothetical signal events are efficiently separated from the dominant t t background with requirements on p miss T and transverse-mass variables. No significant deviation is observed from the expected background. Exclusion limits are set in the context of simplified supersymmetric models with pair-produced top squarks. For top squarks, decaying exclusively to a top quark and a neutralino, exclusion limits are placed at 95% confidence level on the mass of the lightest top squark up to 800 GeV and on the lightest neutralino up to 360 GeV. These results, combined with searches in the single-lepton and all-jet final states, raise the exclusion limits up to 1050 GeV for the lightest top squark and up to 500 GeV for the lightest neutralino. For top squarks undergoing a cascade decay through charginos and sleptons, the mass limits reach up to 1300 GeV for top squarks and up to 800 GeV for the lightest neutralino. The results are also interpreted in a simplified model with a dark matter (DM) particle coupled to the top quark through a scalar or pseudoscalar mediator. For light DM, mediator masses up to 100 (50) GeV are excluded for scalar (pseudoscalar) mediators. The result for the scalar mediator achieves some of the most stringent limits to date in this model.