gebhart/patrepeval huggingface dataset:
Hepatic lipase overexpression lowers remnant and LDL levels by a noncatalytic mechanism in LDL receptor-deficient mice (2001)

To address the role of the noncatalytic ligand function of hepatic lipase (HL) in low density lipoprotein (LDL) receptor-mediated lipoprotein metabolism, we characterized transgenic mice lacking the LDL receptor (LDLR) that express either catalytically active ( Ldlr / HL ) or inactive ( Ldlr / HL S145G ) human HL on both chow and high fat diets and compared them with nontransgenic Ldlr / mice. In mice fed a chow diet, apolipoprotein (apo)B-containing lipoprotein levels were 40-60% lower in Ldlr / HL and Ldlr / HL S145G mice than in Ldlr / mice. This decrease was mainly reflected by decreased apoB-48 levels in the Ldlr / HL mice and by decreased apoB-100 levels in Ldlr / HL S145G mice. These findings indicate that HL can reduce apoB-100-containing lipoproteins through a noncatalytic ligand activity that is independent of the LDLR. Cholesterol enrichment of the apoB-containing lipoproteins induced by feeding Ldlr / HL and Ldlr / HL S145G mice a cholesterolenriched high fat (Western) diet resulted in parallel decreases in both apoB-100 and apoB-48 levels, indicating that HL is particularly efficient at reducing cholesterol-enriched apoB-containing lipoproteins through both catalytic and noncatalytic mechanisms.
Parkinson’s disease biomarker: a patent evaluation of WO2013153386 (2014)

This patent describes a much needed methodology that can easily be adapted in the clinical setting by which a biological sample, such as serum or cerebrospinal fluid, is collected and analyzed for the phosphorylation markers. Here, the phosphorylation activity seen in PINK1 and PARKIN can differentiate between age-matched controls and PD patients. This patent presents a novel diagnostic measure in early PD, as well as determines which medications would have a beneficial effect on a patient's disease progression.
"m=1" coatings for neutron guides (2014)

A substantial fraction of the price for a supermirror neutron guide system is the shielding, which is needed because of the gamma radiation produced as a result of neutron absorption in the supermirror layers. Traditional coatings have been made of nickel-titanium heterostructures, but Ni and Ti also have a fairly high absorption cross section for cold and thermal neutrons. We examine a number of alternatives to Ni as part of a study to reduce the gamma radiation from neutron guides. Materials such as diamond and Be have higher neutron scattering density than Ni, smaller absorption cross section, and when a neutron is absorbed they emit gamma photons with lower energies. We present reflectivity data comparing Ni with Be and preliminary results from diamond coatings showing there use as neutron guide coatings. Calculations show that Be and diamond coatings emit two orders of magnitude fewer gamma photons compared to Ni, mainly because of the lower absorption cross section.
A Combined TLR7/TLR9/GATA3 Score Can Predict Prognosis in Biliary Tract Cancer (2021)

Biliary tract cancer (BTC) refers to a heterogenous group of epithelial malignancies arising along the biliary tree. The highly aggressive nature combined with its silent presentation contribute to the dismal prognosis of this tumor. Tumor-infiltrating immune cells (TIICs) are frequently present in BTC and there is growing evidence regarding their role as therapeutic targets. In this study, we analyzed the immune cell infiltration in BTC and developed a promising immune signature score to predict prognosis in BTC. Immunohistochemistry (IHC) was carried out on tissue microarray sections from 45 patients with resectable cholangiocarcinoma for the detection of 6-sulfoLacNAc+ monocytes (slanMo), BDCA-2+ plasmacytoid dendritic cells (pDC), CD8+ or CD4+T-lymphocytes, CD103+ cells, GATA3+ cells, Toll-like receptor (TLR) 3, 7 and 9-expressing cells as well as programmed cell death protein 1 and programmed cell death ligand 1 positive cells. Data from the IHC staining were analyzed and correlated with clinicopathological and survival data. High expression of TLR7, TLR9, and GATA3 was associated with improved overall survival (OS, Log-rank <i>p</i> < 0.05). In addition, TLR9 was associated with better disease-free survival (Log-rank <i>p</i> < 0.05). In the multivariate Cox proportional-hazards model for OS, the TLR/TLR9/GATA3 score was found to be an independent prognostic factor for OS ("Score 2" vs. "Score 0": HR 11.17 95% CI 2.27-54.95, <i>p</i> < 0.01).
Effects of intestinal spirochaete infection on egg production in meat breeders (2000)

This trial examined whether infection with intestinal spirochaetes affected egg production in female Cobb meat breeders. Infection with Serpulina pilosicoli led to delayed onset of laying and reduced egg production when compared with the control group. Egg production by birds infected with S. innocens, however, was not significantly different from that of the control group. These results suggest that infection with S. pilosicoli may be a significant cause of egg production loss in commercial birds.
R-HTDetector: Robust Hardware-Trojan Detection Based on Adversarial Training (2022)

Hardware Trojans (HTs) have become a serious problem, and extermination of them is strongly required for enhancing the security and safety of integrated circuits. An effective solution is to identify HTs at the gate level via machine learning techniques. However, machine learning has specific vulnerabilities, such as adversarial examples. In reality, it has been reported that adversarial modified HTs greatly degrade the performance of a machine learning-based HT detection method. Therefore, we propose a robust HT detection method using adversarial training (R-HTDetector). We formally describe the robustness of R-HTDetector in modifying HTs. Our work gives the world-first adversarial training for HT detection with theoretical backgrounds. We show through experiments with Trust-HUB benchmarks that R-HTDetector overcomes adversarial examples while maintaining its original accuracy.
Chasing the Paradigm: Clinical Translation of 25 Years of Tissue Engineering (2019)

In this Perspective, we discuss the impact of the past 25 years of tissue engineering on the development of clinical therapies. Based on their success and other significant research accomplishments, platforms of innovation were identified. Their discoveries will enable tissue engineering inspired therapies to meet the requirements necessary for large-scale manufacturing and Food and Drug Administration (FDA) approval for a diverse range of indications.
Reconstruction of three-dimensional biventricular activation based on the 12-lead electrocardiogram via patient-specific modelling (2020)

Non-invasive assessment of biventricular 3D activation using the 12-lead ECG and MR imaging is feasible. Potential applications include patient-specific modelling and pre-/per-procedural evaluation of ventricular activation.
Table S2 from Genetic Disruption of the Multifunctional CD98/LAT1 Complex Demonstrates the Key Role of Essential Amino Acid Transport in the Control of mTORC1 and Tumor Growth (2023)

&lt;p&gt;Table S2: Analysis of the mutations generated by ZFN in each LS174T-derived cell line used.&lt;/p&gt;
T Cell Epitope-Containing Domains of Ragweed Amb a 1 and Mugwort Art v 6 Modulate Immunologic Responses in Humans and Mice (2017)

Accumulation of T cell epitopes and deletion of IgE reactive areas of Amb a 1 and Art v 6, modulated the immunologic properties of the allergen immuno-domains, leading to promising novel candidates for therapeutic approach.
Usability of an At-Home Anterior Nares SARS-CoV-2 RT-PCR Sample Collection Kit: Human Factors Feasibility Study (Preprint) (2021)

<sec> <title>BACKGROUND</title> Readily available testing for SARS-CoV-2 is necessary to mitigate COVID-19 disease outbreaks. At-home collection kits, in which samples are self-collected without requiring a laboratory or clinic visit and sent to an external laboratory for testing, can provide convenient testing to those with barriers to access. They can prevent unnecessary exposure between patient and clinical staff, increase access for patients with disabilities or remote workers, and decrease burdens on health care resources, such as provider time and personal protective equipment. Exact Sciences developed an at-home collection kit for samples to be tested to detect SARS-CoV-2 that includes an Instructions for Use (IFU) document, which guides people without prior experience on collecting a nasal swab sample. Demonstrating successful sample collection and usability is critical to ensure that these samples meet the same high-quality sample collection standards as samples collected in clinics. </sec> <sec> <title>OBJECTIVE</title> The aim of this study was to determine the usability of a SARS-CoV-2 at-home nasal swab sample collection kit. </sec> <sec> <title>METHODS</title> A human factors usability study was conducted with 30 subjects without prior medical, laboratory, or health care training and without COVID-19 sample self-collection experience. Subjects were observed while they followed the IFU for the at-home sample collection portion of the SARS-CoV-2 test in a setting that simulated a home environment. IFU usability was further evaluated by requiring the subjects to complete a survey, answer comprehension questions, provide written feedback, and respond to questions from the observer about problems during use. </sec> <sec> <title>RESULTS</title> All 30 subjects successfully completed the sample collection process, and all 30 samples were determined by reverse transcription–polymerase chain reaction (RT-PCR) testing to meet quality standards for SARS-CoV-2 testing. The subjects’ written feedback and comments revealed several recommendations to improve the IFU. </sec> <sec> <title>CONCLUSIONS</title> The study demonstrated the overall usability of an at-home SARS-CoV-2 collection kit. Various feedback mechanisms provided opportunities to improve the wording and graphics for some critical tasks, including placing the label correctly on the tube. A modified IFU was prepared based on study outcomes. </sec>
Three-Electron SN2 Reactions of Arylcyclopropane Cation Radicals. 1. Mechanism1 (1997)

The mechanism of photosensitized nucleophilic substitution reactions on arylcyclopropanes was investigated. Stereochemical experiments with methanol, water, and cyanide as nucleophiles showed that the reactions occurred stereospecifically with complete inversion of configuration at the carbon atom undergoing substitution. Independent generation of the arylcyclopropane cation radicals by nanosecond transient methods showed that they reacted rapidly with nucleophiles with kinetics that were first-order in both the cation radical and the nucleophiles. Through a combination of transient kinetics and steady-state Stern−Volmer quenching experiments, the reaction of the phenylcyclopropane cation radical with methanol was kinetically correlated with the formation of the substitution product. The reaction of phenylcyclopropane cation radical with a series of alcohols as nucleophiles showed small steric effects.
Music Recognition in Frontotemporal Lobar Degeneration and Alzheimer Disease (2011)

The results support a view that the anterior temporal lobes play a role in familiar melody recognition, and that musical functions are affected differentially across forms of dementia.
Contour integration and scale combination processes in visual edge detection (1999)

Contours in the natural visual environment consist mainly of edges which are spatially broad-band and whose (cosinusoidal) components have arrival phases close to +/-90 deg. Because early visual processing is thought to be based on a local Fourier description, the representation of edges requires two forms of filter combination: scale integration (filter combination across spatial frequency) and contour integration (filter combination across space). In order to determine how these two types of combination fit together, we determined spatial-frequency tuning for the detection of contours composed of broadband edge elements, alternating with narrow-band Gabor elements. A contour integration system operating independently at a number of spatial scales should be able to ignore the distracting influence of edge structure in such patterns. However, subjects cannot ignore edge structure indicating that local phase-alignment across spatial scale is coded prior to, or concurrent with, contour integration. Moreover, unlike contours composed of Gabors, the bandwidth of local elements is important for edge integration; the coding of element bandwidth seems to be dependent on the phase alignment of features across spatial frequency.
Enantioselective synthesis of (S)‐(+)‐2‐tridecanol acetate, an aggregation pheromone component of Drosophila mulleri (1991)

Abstract The enantioselective synthesis of ( S )‐(+)‐2‐tridecanol acetate [( S )‐ 6 ] (ee = 93.5%), an aggregation pheromone of Drosophila mulleri , is described. Key steps are the α‐alkylation of the propiophenone SAMP‐hydrazone ( S )‐ 2 (de ≥ 96%) and the Baeyer‐Villiger reaction of the ketone ( S )‐ 4 .
115 DNA and Protein Vaccination via Electroporation Confers Protection Upon Mucosal Challenge With Heterologous SIVsmE660 (2012)

We have previously shown that macaques vaccinated by DNA intramuscular electroporation with optimized plasmid DNAs expressing SIVmac239 antigens develop potent immune responses able to reduce viremia of the high dose SIVmac251 challenge. To further improve immune responses and protection, different protocols combining DNA with protein immunization (coimmunization, prime-boost) were tested. Co-delivery of SIV DNA and protein increased the magnitude, longevity, and avidity of humoral responses and the ability to cross-neutralize heterologous Envs. SIV-specific cellular responses were readily measured in blood and mucosal sites after the first immunization and remained high during the entire follow-up. Vaccinated macaques resisted infection by SIVsmE660 compared to naïve controls (P = 0.05; stratified for Trim5a genotype). Two of 8 DNA-protein coimmunized animals did not get infected after 14 exposures, while all controls were infected by 6 exposures. Vaccinees had significantly lower peak VL (1.7 log, P = 0.03). A majority (75%) of vaccinees suppressed virus replication rapidly to undetectable levels, maintaining normal CD4 counts (40 weeks of follow-up). Virus acquisition correlated with antibody avidity to SIVsmE660 at day of challenge; acquisition and control of viremia also correlated with the presence of vaccine-induced cellular immune responses (CD4+ Effector Memory T-cells and IFNgamma+ GranzymeB+ cytotoxic T-cells).The vaccine combining DNA and protein in a single administration is a novel concept to achieve rapid, high, persistent, broad and effective immune responses, and captures the best properties of both procedures: high and broad range of cellular immune responses produced by DNA and strong antibody responses.
Invisible Interfaces: From pen & paper to shared table interaction (2004)

Here we present our interface model and research demonstrators based on our context-aware virtual personal server space system, called “Nightingale”. Based on digital paper and collaborative interface technologies, we focus on reminiscence activities for their use in promoting social and intellectual fitness in the elderly. The Nightingale middleware consists of three planes of service (data, context and activity). The context plane mediates access to various services (depending on the current user activity) while optimising data access (data plane) around simple activity models tied to user defined contextual states. Our research efforts have led to the development of a “Physical/Digital Scrapbook” based on the Anoto Pen system in conjunction with a “Gesture based sharing interface” based on the MERL DiamondTouch system. (Less)
An Interfacial Label-Free Electrochemical Approach to in-Situ Soil pH Monitoring (2022)

Soil is a critical entity of Earth’s ecosystem. Healthy soil supports a landscape that is more resilient to the impacts of drought, flood, or fire. It also helps regulate the Earth’s climate. Real time assessment of soil health is imperative to improving crop yield as well to sustain an ever growing human population. Soil health encompasses moisture content, phosphorus, pH, nitrate, and other parameters. One of the most important parameters is soil pH which affects nutrients availability to plants and nutrients leaching in the soil. Current soil pH assessment techniques require destructive sampling of the soil where a core of soil is collected then treated at a lab before measuring the pH. This method measures pH at time points and doesn’t provide a continuous real time monitoring of pH. This work utilizes commercial screen printed electrodes with a pH sensitive coating for low cost continuous in-situ soil pH measurement. The coating is made up from alizarin an anthraquinone compound that undergoes a redox reaction in the presence of hydrogen ions and nafion an ion permeable membrane. Square wave voltammetry (SWV) is utilized since the output current signal shows the redox of alizarin while rejecting the capacitive current that’s inherent in soil. This redox peak current potential is dependent on the concentration of hydrogen ions which is gives a direct measure of pH. Due to the sensitivity of SWV, it is possible to measure unbuffered soil ph (without CaCl 2 and KCl to improve the electrolyte ionic strength) accurately. The nafion layer protects the alizarin from dissolving in water present in soil as well as promoting the diffusion of hydrogen ions into the coating thus improving sensitivity. The alizarin has been used previously in screen printed electrodes however, this is the first work to our knowledge to utilize it to measure soil pH in-situ over a period of time. The sensor output was first calibrated in different unbuffered soil textures against the gold standard glass electrode. The calibrated response of the sensor in unbuffered sandy loam soil slurry is shown in Fig. 1. Then the sensor accuracy was validated by testing different soil samples using the sensor and later mixing it with deionized water and measuring the pH using the glass electrode. The sensor’s stability was evaluated by taking a measurement every hour for 48 hours without removing it from the soil sample. The temporal study showed a coefficient of variation less than 1% and an average reading of within 0.3 pH of the actual pH of the soil sample. Fig. 1 Calibrated response of proposed sensor in sandy loam soil slurries with 40% water Figure 1
Full-Scale Impact Test of Four Traffic Barriers on Top of an Instrumented MSE Wall (2009)

This paper presents the results of four full-scale impact tests against barriers placed on top of an instrumented mechanically stabilized earth (MSE) wall. The impact was created by a head-on collision of a 2,268-kg bogie going at about 32.2 km/h. The barriers were New Jersey and vertical wall barriers with a 1.37-m-wide moment slab in 9.14-m-long sections. The wall was 1.52 m high with one panel and two layers of reinforcement. The reinforcement was 2.44-m-long strips, 4.88-m-long strips, and 2.44-m-long bar mats. The backfill was crushed rock. The instrumentation consisted of accelerometers, strain gauges, contact switch, displacement targets, string lines, and high-speed cameras. The test was designed to represent a commonly used installation in current practice including an impact load on the barrier at least equal to 240 kN. Most of the barriers sustained significant damage but overall the behavior of the wall was satisfactory since the displacements of the panels were minimal (less than 25 mm) and the panel damage was acceptable except possibly in the case of the 4.88-m-long strips. The loads measured in the reinforcement indicate that the reinforcement was brought to its ultimate capacity for the duration of the impact but since the impact duration was so short and since the displacements of the panels were within tolerable limits of 25 mm, this is considered acceptable. The use of the longer strips (4.88-m-long strips) leads to slightly smaller panel displacements and higher panel stresses as evidenced by a bending crack in the panel. The 2.44-m-long strips permitted more displacement of the wall panels, but the magnitude of the displacement was considered to be tolerable. The measured maximum dynamic loads in the strips were found to be 3–5 times higher than the calculated maximum static loads by AASHTO guidelines.
Monocular Localization of a moving person onboard a Quadrotor MAV (2015)

In this paper, we propose a novel method to recover the 3D trajectory of a moving person from a monocular camera mounted on a quadrotor micro aerial vehicle (MAV). The key contribution is an integrated approach that simultaneously performs visual odometry (VO) and persistent tracking of a person automatically detected in the scene. All computation pertaining to VO, detection and tracking runs onboard the MAV from a front-facing monocular RGB camera. Given the gravity direction from an inertial sensor and the knowledge of the individual's height, a complete 3D trajectory of the person within the reconstructed scene can be estimated. When the ground plane is detected from the triangulated 3D points, the absolute metric scale of the trajectory and the 3D map is also recovered. Our extensive indoor and outdoor experiments show that the system can localize a person moving naturally within a large area. The system runs at 17 frames per second on the onboard computer. A walking person was successfully tracked for two minutes and an accurate trajectory was recovered over a distance of 140 meters with our system running onboard.
Recruitment of Brd4 to the Human Papillomavirus Type 16 DNA Replication Complex Is Essential for Replication of Viral DNA (2013)

Replication of the human papillomavirus (HPV) DNA genome relies on viral factors E1 and E2 and the cellular replication machinery. Bromodomain-containing protein 4 (Brd4) interacts with viral E2 protein to mediate papillomavirus (PV) genome maintenance and viral transcription. However, the functional role of Brd4 in the HPV life cycle remains to be clearly defined. In this study, we provide the first look into the E2-Brd4 interaction in the presence of other important viral factors, such as the HPV16 E1 protein and the viral genome. We show that Brd4 is recruited to actively replicating HPV16 origin foci together with HPV16 E1, E2, and a number of the cellular replication factors: replication protein A70 (RPA70), replication factor C1 (RFC1), and DNA polymerase δ. Mutagenesis disrupting the E2-Brd4 interaction abolishes the formation of the HPV16 replication complex and impairs HPV16 DNA replication in cells. Brd4 was further demonstrated to be necessary for HPV16 viral DNA replication using a cell-free replication system in which depletion of Brd4 by small interfering RNA (siRNA) silencing leads to impaired HPV16 viral DNA replication and recombinant Brd4 protein is able to rescue viral DNA replication. In addition, releasing endogenous Brd4 from cellular chromatin by using the bromodomain inhibitor JQ1(+) enhances HPV16 DNA replication, demonstrating that the role of Brd4 in HPV DNA replication could be uncoupled from its function in chromatin-associated transcriptional regulation and cell cycle control. Our study reveals a new role for Brd4 in HPV genome replication, providing novel insights into understanding the life cycle of this oncogenic DNA virus.