gebhart/patrepeval huggingface dataset:
Ultrafast 25-fs relaxation in highly excited states of methyl azide mediated by strong nonadiabatic coupling (2017)

Highly excited electronic states are challenging to explore experimentally and theoretically-due to the large density of states and the fact that small structural changes lead to large changes in electronic character with associated strong nonadiabatic dynamics. They can play a key role in astrophysical and ionospheric chemistry, as well as the detonation chemistry of high-energy density materials. Here, we implement ultrafast vacuum-UV (VUV)-driven electron-ion coincidence imaging spectroscopy to directly probe the reaction pathways of highly excited states of energetic molecules-in this case, methyl azide. Our data, combined with advanced theoretical simulations, show that photoexcitation of methyl azide by a 10-fs UV pulse at 8 eV drives fast structural changes and strong nonadiabatic coupling that leads to relaxation to other excited states on a surprisingly fast timescale of 25 fs. This ultrafast relaxation differs from dynamics occurring on lower excited states, where the timescale required for the wavepacket to reach a region of strong nonadiabatic coupling is typically much longer. Moreover, our theoretical calculations show that ultrafast relaxation of the wavepacket to a lower excited state occurs along one of the conical intersection seams before reaching the minimum energy conical intersection. These findings are important for understanding the unique strongly coupled non-Born-Oppenheimer molecular dynamics of VUV-excited energetic molecules. Although such observations have been predicted for many years, this study represents one of the few where such strongly coupled non-Born-Oppenheimer molecular dynamics of VUV-excited energetic molecules have been conclusively observed directly, making it possible to identify the ultrafast reaction pathways.
Impacts on a Test Setup for the Evaluation of Advanced Emergency Braking for Cyclists in Japan Using Event-Driver Recorder Data (2019)

The technical progess in the areas of driver assistance and active safety leads to valuable information to be used prior to, during and even after a crash event. Car makers and suppliers can make use of this situation and currently develop Advanced Emergency Braking (AEB) Systems for Vulnerable Road Users (VRUs) such as cyclists to either avoid a collision or in a crash event to reduce injury risks of the participants. Within Europe test scenarios were already defined aiming to cover the most common crash scenarios. Considering the advances of such AEB systems their impact towards Japan accident situation is of highly interest. This paper describes the impact to a possible test setup derived out from analysis of Event Driver Recorder data from Japan. Finally a comparison against Euro NCAP test protocol for car AEB-Cyclist is done.
Utilizing Fluorescent Probes for the Detection of TiO2 Nanoparticles of Known Characteristics and Their Photocatalytic Activity in Drinking Waters (2022)

To support the safe use of photocatalytic nanomaterials, it is essential to have portable and affordable methods to rapidly detect residual photocatalysts in water. Technologies with low detection limits are based upon mass quantification, which requires expensive analytical equipment and complex sample preparation. Therefore, we developed a portable method that utilizes the photocatalytic reactivity of titanium dioxide (TiO2) nanoparticles to detect and quantify TiO2 in treated drinking water. The method involves UV excitation of TiO2 nanoparticles in solution, which hydroxylates terephthalic acid, resulting in an increase in fluorescence emission, detected by a portable device. Within a 15 min analysis period, the detection limit for a NIST reference TiO2 in distilled water is 0.388 ppb with a quantitation limit of 1.30 ppb. However, these limits increased for soft (2.12 and 7.07 ppb) and hard (64.3 and 214 ppb) water, respectively. Interference from natural organics depended on the amount of TiO2 present. At 100 ppb of TiO2, the detection assay can operate in matrices containing up to 703 ppb of humic acid, within a 95% confidence interval. Overall, the presented assay is a reliable, sensitive, and accurate method for detecting TiO2 nanoparticles of known characteristics in drinking water, accomplished using affordable and portable instrumentation.
Evaluation of Endovascular Abdominal Aortic Aneurysm Repair: Anatomical Classification, Procedural Success, Clinical Assessment, and Data Collection (1997)

Purpose: To detail a methodology for evaluation of endovascular abdominal aortic aneurysm (AAA) repair that has been achieved through consensus of an international multidisciplinary team of investigators. Methods: This schema features an anatomical classification for AAAs, a definition of procedural success, and a procedure for clinical assessment, as well as the necessary data collection forms. Patient data include demographics, procedural and clinical success, complications, and follow-up. Procedural details can be related to anatomic situations, comorbid processes, devices, and effective aneurysmal exclusion. Results: These data would allow assessment of the procedures, physician learning curves, procedural indications, techniques, methodologies, the relationship of indications to success and complications, devices and subsequent graft patency, and aneurysmal exclusion. Conclusions: The use of this standardized data collection system could enable physicians and industry to better understand endovascular AAA repair and ultimately improve patient care.
Epidemiology of typical and atypical rotavirus infections in New Zealand pigs (1989)

Polyacrylamide gel electrophoresis (PAGE) and enzyme-linked immunosorbent assay (ELISA) were employed to investigate the epidemiology of typical and atypical rotavirus infections in five piggeries. Of 152 faecal samples examined, 46 (30 per cent) were positive by ELISA for group A rotavirus. Rotaviruses with electrophoretic patterns resembling groups A, B and C were detected. At least two and up to five different rotavirus electrophoretypes (typical and/or atypical) were detected in each of the five piggeries. Out of 152 faecal samples examined, 28 (18 per cent) contained rotaviruses with group A electrophoretypes, 9 (6 per cent) with group C but only 1 with Group B. Six samples contained both group A and group C rotaviruses. No common electrophoretypes of group A or C rotaviruses were detected in these five piggeries. The PAGE technique was also used to analyze group A rotavirus isolated sequentially from another piggery over a three year period. A single electrophoretype was found during the first two years, but in the third year a different electrophoretype was detected.
Direct‐Acting Antivirals for the Treatment of Chronic Hepatitis B Virus (HBV) Infection (2021)

More than 250 million people suffer from chronic HBV infection worldwide, causing more than 800,000 deaths annually due to resulting liver diseases. Nucleos(t)ide analog reverse transcriptase inhibitors are currently one of two standard-of-care (SOC) treatments against chronic HBV infection. Like interferon-α, the other SOC treatment, these inhibitors can suppress viral replication, but do not effectively eliminate covalently closed circular HBV DNA, the stable template for lifelong viral transcription, from the nucleus of infected cells. In this chapter two of the most promising classes of direct-acting antivirals under clinical development to overcome this problem are discussed: HBV entry inhibitors and capsid assembly modulators. The data from studies on these direct-acting antivirals give hope for a future combination therapy regimen for HBV cure.
A novel interference suppression receiver for LTE downlink systems (2018)

The intra-and/or inter-cell interference have been the major obstacle that constrain the performance of cellular systems. In this regard, there have been approaches to mitigate the inherent interference in the cellular systems, which support multiple user equipments (UEs) distributed in multiple adjacent cells. However, the previous approaches to cancel the interference at the receiver were mostly available at the cost of additional system information of the interference from the neighboring cells. In this paper, we propose an advanced receiver algorithm that efficiently suppresses interferences by utilizing statistical characteristics of interference signals, hence no need for additional information to detect the interference. It is shown that the proposed receiver suppresses inter-cell interference well and outperforms conventional receivers when applied to typical LTE systems.
Is the Algorithm Good in a Bad World, or Has It Learned to be Bad? The Ethical Challenges of “Locked” Versus “Continuously Learning” and “Autonomous” Versus “Assistive” AI Tools in Healthcare (2023)

Click to increase image sizeClick to decrease image sizeThis article refers to:Conversational Artificial Intelligence in Psychotherapy: A New Therapeutic Tool or Agent? Additional informationFundingFunding for this commentary was provided by Stanford Human-Centered Artificial Intelligence Seed Grant.
Quantification of morphology of bacterial colonies using laser scatter measurements and solid element optical modeling (2007)

Traditional biological and chemical methods for pathogen identification require complicated sample preparation for reliable results. Optical scattering technology has been used for identification of bacterial cells in suspension, but with only limited success. Our published reports have demonstrated that scattered light based identification of <i>Listeria</i> colonies growing on solid surfaces is feasible with proper pattern recognition tools. Recently we have extended this technique to classification of other bacterial genera including, <i>Salmonella</i>, <i>Bacillus</i>, and <i>Vibrio</i>. Our approach may be highly applicable to early detection and classification of pathogens in food-processing industry and in healthcare. The unique scattering patterns formed by colonies of different species are created through differences in colony microstructure (on the order of wavelength used), bulk optical properties, and the macroscopic morphology. While it is difficult to model the effect on scatter-signal patterns owing to the microstructural changes, the influence of bulk optical properties and overall shape of colonies can be modeled using geometrical optics. Our latest research shows that it is possible to model the scatter pattern of bacterial colonies using solid-element optical modeling software (TracePro), and theoretically assess changes in macro structure and bulk refractive indices. This study allows predicting the theoretical limits of resolution and sensitivity of our detection and classification methods. Moreover, quantification of changes in macro morphology and bulk refractive index provides an opportunity to study the response of colonies to various reagents and antibiotics.
Error-free 10-Gb/s, 11.4-km long transmission on 1.3-μm waveband photonic transport system with wavelength tunable quantum dot laser and holey fiber transmission line (2012)

A wavelength tunable quantum dot external-cavity laser and ultra-broadband holey fiber transmission line were developed using novel nano-structured materials for successful demonstration of error-free 10-Gb/s, 11.4-km long transmission on a 1.3-μm waveband photonic transport system.
Supplementary Table 2 from <i>BRAF/NRAS</i> Wild-Type Melanomas Have a High Mutation Load Correlating with Histologic and Molecular Signatures of UV Damage (2023)

&lt;p&gt;Supplementary Table 2 - PDF file 16632K, Single nucleotide variants identified for each sample&lt;/p&gt;
Combined in Silico and Experimental Approach for Drug Design: The Binding Mode of Peptidic and Non‐Peptidic Inhibitors to Hsp90 N‐Terminal Domain (2010)

Heat shock protein 90 (Hsp90) is a prime target for antitumor therapies. The information obtained by molecular dynamics (MD) simulations is combined with NMR data to provide a cross‐validated atomic resolution model of the complementary interactions of heat shock protein 90 with a peptidic (shepherdin) and a non‐peptidic (5‐aminoimidazole‐4‐carboxamide‐1‐β‐ d ‐ribofuranoside, AICAR) inhibitor, showing antiproliferative and proapoptotic activity in multiple tumor cell lines. This approach highlights the relevant role of imidazolic moiety in the interaction of both antagonist molecules. In 5‐aminoimidazole‐4‐carboxamide‐1‐β‐ d ‐ribofuranoside bound state, one conformation of those present in solution is selected, where imidazolic, H4 and H5 protons have a key role in defining a non‐polar region contacting heat shock protein 90 surface. The dynamic equilibrium between N‐type and S‐type puckered forms of 5‐aminoimidazole‐4‐carboxamide‐1‐β‐ d ‐ribofuranoside moiety is shown to be functional to inhibitor binding. The first experimental structural data on these inhibitors are presented and discussed as hints for future design of improved molecules.
Optimization methods for pattern recognition (1992)

Efficient signal processing is made possible by using hybrid electro-optical systems which can be trained to perform a specific task. Various architectures and procedures are implemented for optimization of pattern recognition and other signal processing systems.
Computational Fluid Dynamics for Brain Circulation and Aneurysm with Therapeutic Devices (2004)

We analysed fluid dynamics at brain arteries having multiple inflow and out flow like Willis ring based on clinical imaging modalities. In addition, we analysed fluid dynamics with therapeutic devices like coils and stents to simulate their influences to blood flow. 3D CTA and MRA obtained three-dimensional structures of the brain vessels. The centreline was obtained from the three dimensional structure. Diameter of the blood vessels was measured by 3D CTA/MRA then smooth surfaced blood vessel models were created. For the fluid analysis, we developed a home brew software which can display parameters such as streamline, etc. In addition, our CFD (computational fluid dynamics) software can work in collaboration with a CAD (computer aided design) software which we also developed (VCAD: Volume CAD). So, therapeutic devices such as coils, balloons and stents could be placed in the models and CFD analysis could be performed placing devices in the models. The flow pattern in the complicated vascular structure could be calculated such as Willis ring which has multiple inputs like ICA, VA and multiple outlets like MCA and PCA with communicating arteries. CFD with therapeutic devices could also analysed with our system. CFD including communicating arteries will assist the simulation of parent artery occlusion. CFD with therapeutic devices is helpful not only for simulation for embolization, but will help us to design therapeutic devices under computer simulation.
Enhancing Federated Learning in Fog-Aided IoT by CPU Frequency and Wireless Power Control (2020)

Machine learning models have been built in fog nodes in fog-aided Internet-of-Things (IoT) networks to provision future events prediction and image classification by training data collected from IoT devices. However, sending massive data from all devices to a fog node incurs huge network traffic in wireless links in between. Federated learning is proposed to address the challenge by training models locally in IoT devices and only sharing model parameters in the fog node. In this article, we investigate both the CPU frequency control and wireless transmission power control of all IoT devices to balance the tradeoff between the device energy consumption and federated learning time (consisting of both the computation and communication latencies) in fog-aided IoT networks. We formulate the joint optimization of CPU and power control as a nonlinear programming (NLP) problem with the objective to minimize the energy consumption of all IoT devices constrained by the federated learning time requirement. An alternative direction algorithm, which alternatively optimizes the CPU frequency and wireless transmission power until convergence, is hence designed to solve this problem and its performance is demonstrated via extensive simulations.
Design of Surface-Modified Electrodes for the Electrochemical Adsorption of Platinum-Based Anticancer Drugs (2019)

The design of a hemofiltration method that minimizes the side effects produced by the accumulation of Pt-based drugs such as cisplatin represents an important technology for cancer treatment. This work establishes the foundation for the development of an efficient platform for the electrochemical hemofiltration and simultaneous sensing of antitumor drugs, such as cisplatin and carboplatin, from physiological medium. The electrochemical filtration system is based on a gold surface-modified electrode using tris(carboxyethyl)phosphine ligands as scavengers of the Pt-based drug complexes. The platinum–phosphine interaction is shown to be more time efficient, as compared to the naturally occurring form of a glutathione–platinum adduct, and displayed a highly cooperative nature of binding. Altogether, we demonstrate that the presence of ligands capable of binding to Pt results in a differential spectroscopic and electrochemical response and the potential to adsorb and monitor the concentration of Pt salts in complex aqueous media.
Prognostic Impact of Peripelvic Fat Invasion in pT3 Renal Pelvic Transitional Cell Carcinoma (2008)

Renal pelvic transitional cell carcinoma (TCC), which invades beyond muscularis into peripelvic fat or the renal parenchyma, is diagnosed as stage pT3 despite its structural complexity. We evaluated the prognostic impact of peripelvic fat invasion in pT3 renal pelvic TCC. Between 1986 and 2004, the medical records on 128 patients who were surgically treated for renal pelvic TCC were retrospectively reviewed. Sixty patients with pT3 disease were eligible for the main analysis. The prognostic impact of various clinicopathological factors was analyzed using univariate and multivariate analyses. On univariate analysis, sex, age, concomitant bladder tumors, concomitant ureter tumors, lymphadenectomy, adjuvant chemotherapy, tumor grade, multiplicity, renal parenchymal invasion, and carcinoma in situ did not influence the disease-specific survival (p>0.05). By contrast, peripelvic fat invasion, lymph node invasion, and lymphovascular invasion were each significantly associated with disease-specific survival (p<0.05). Multivariate analysis showed that peripelvic fat invasion (p=0.012) and lymph node invasion (p=0.004) were independent prognostic factors. In conclusion, peripelvic fat invasion is a strong prognostic factor in pT3 renal pelvic TCC. Thus, systemic adjuvant therapy should be considered in the presence of peripelvic fat invasion, even if the lymph nodes are not involved.
Measurement of Neutralizing Serum Antibodies of Patients Vaccinated with Human Papillomavirus L1 or L2-Based Immunogens Using Furin-Cleaved HPV Pseudovirions (2014)

Antibodies specific for neutralizing epitopes in either Human papillomavirus (HPV) capsid protein L1 or L2 can mediate protection from viral challenge and thus their accurate and sensitive measurement at high throughput is likely informative for monitoring response to prophylactic vaccination. Here we compare measurement of L1 and L2-specific neutralizing antibodies in human sera using the standard Pseudovirion-Based Neutralization Assay (L1-PBNA) with the newer Furin-Cleaved Pseudovirion-Based Neutralization Assay (FC-PBNA), a modification of the L1-PBNA intended to improve sensitivity towards L2-specific neutralizing antibodies without compromising assay of L1-specific responses. For detection of L1-specific neutralizing antibodies in human sera, the FC- PBNA and L1-PBNA assays showed similar sensitivity and a high level of correlation using WHO standard sera (n = 2), and sera from patients vaccinated with Gardasil (n = 30) or an experimental human papillomavirus type 16 (HPV16) L1 VLP vaccine (n = 70). The detection of L1-specific cross-neutralizing antibodies in these sera using pseudovirions of types phylogenetically-related to those targeted by the L1 virus-like particle (VLP) vaccines was also consistent between the two assays. However, for sera from patients (n = 17) vaccinated with an L2-based immunogen (TA-CIN), the FC-PBNA was more sensitive than the L1-PBNA in detecting L2-specific neutralizing antibodies. Further, the neutralizing antibody titers measured with the FC-PBNA correlated with those determined with the L2-PBNA, another modification of the L1-PBNA that spacio-temporally separates primary and secondary receptor engagement, as well as the protective titers measured using passive transfer studies in the murine genital-challenge model. In sum, the FC-PBNA provided sensitive measurement for both L1 VLP and L2-specific neutralizing antibody in human sera. Vaccination with TA-CIN elicits weak cross-protective antibody in a subset of patients, suggesting the need for an adjuvant.
Differential Mobility Spectrometry-Hydrogen Deuterium Exchange (DMS-HDX) as a Probe of Protein Conformation in Solution (2016)

Differential mobility spectrometry (DMS) is an ion mobility technique that has been adopted chiefly as a pre-filter for small- to medium-sized analytes (<1 000 Da). With the exception of a handful of studies that employ an analogue of DMS-field asymmetric waveform ion mobility spectroscopy (FAIMS)-the application of DMS to intact biomacromolecules remains largely unexplored. In this work, we employ DMS combined with gas-phase hydrogen deuterium exchange (DMS-HDX) to probe the gas-phase conformations generated from proteins that were initially folded, partially-folded, and unfolded in solution. Our findings indicate that proteins with distinct structural features in solution exhibit unique deuterium uptake profiles as function of their optimal transmission through the DMS. Ultimately we propose that DMS-HDX can, if properly implemented, provide rapid measurements of liquid-phase protein structural stability that could be of use in biopharmaceuticals development. Graphical Abstract ᅟ.
Constitutive relation development through the FIRE test (2010)

The importance of well-developed constitutive models for predicting deformation behavior of materials at high strain rates cannot be overstated. The study and development of these constitutive models is pertinent to several fields, yet the test methods utilized to probe this high strain-rate realm are limited in both number and standardization. In an effort to augment current high rate tests, new technologies have been leveraged to revive an old, under-utilized test method - the axisymmetric expanding ring. The combination of Photon Doppler Velocimetry (PDV) and one of several ring launch techniques allows the successful testing and instrumentation of samples loaded in tension without wave effects at strain rates exceeding 10^4 s^-1. Design and construction of the embodiment of this test at OSU, dubbed the Fully Instrumented Ring Expansion (FIRE) system, will be discussed. The key difficulties to implementation of the test are examined, along with our efforts to overcome them and preliminary results.