gebhart/patrepeval huggingface dataset:
Chemical Properties of Human Dentin Blocks and Vertical Augmentation by Ultrasonically Demineralized Dentin Matrix Blocks on Scratched Skull without Periosteum of Adult-Aged Rats (2021)

Vertical augmentation is one of the most challenging techniques in bone engineering. Several parameters, such mechano-chemical characteristics, are important to optimize vertical bone regeneration using biomaterials. The aims of this study were to chemically characterize human dentin blocks (calcified demineralized dentin matrix: CDM, partially demineralized dentin matrix: PDDM and completely demineralized dentin matrix: CDDM) (2 × 2 × 1 mm<sup>3</sup>) chemically and evaluate the behavior of PDDM blocks on non-scratched or scratched skulls without periosteum of adult rats (10-12 months old, female) as a vertical augmentation model. The dissolved efficiency of CDM showed 32.3% after ultrasonic demineralization in 1.0 L of 2% HNO<sub>3</sub> for 30 min. The 30 min-demineralized dentin was named PDDM. The SEM images of PDDM showed the opening of dentinal tubes, nano-microcracks and the smooth surface. In the collagenase digestion test, the weight-decreasing rates of CDM, PDDM and CDDM were 9.2%, 25.5% and 78.3% at 12 weeks, respectively. CDM inhibited the collagenase digestion, compared with PDDM and CDDM. In the PDDM onlay graft on an ultrasonically scratched skull, the bone marrow-space opening from original bone was found in the bony bridge formation between the human PDDM block and dense skull of adult senior rats at 4 and 8 weeks. On the other hand, in the cases of the marrow-space closing in both non-scratched skulls and scratched skulls, the bony bridge was not formed. The results indicated that the ultrasonic scratching into the compact parietal bone might contribute greatly to the marrow-space opening from skull and the supply of marrow cells, and then bony bridge formation could occur in the vertical augmentation model without a periosteum.
Isolation, Detection, and Quantification of Cancer Biomarkers in HPV-Associated Malignancies (2017)

Human Papillomavirus (HPV) infection has been recognized as the main etiologic factor in the development of various cancers including penile, vulva, oropharyngeal and cervical cancers. In the development of cancer, persistent HPV infections induce E6 and E7 oncoproteins, which promote cell proliferation and carcinogenesis resulting elevated levels of host antibodies (e.g., anti-HPV16 E7 antibody). Currently, these cancers are clinically diagnosed using invasive biopsy-based tests, which are performed only in centralized labs by experienced clinical staff using time-consuming and expensive tools and technologies. Therefore, these obstacles constrain their utilization at primary care clinics and in remote settings, where resources are limited. Here, we present a rapid, inexpensive, reliable, easy-to-use, customized immunoassay platform following a microfluidic filter device to detect and quantify anti-HPV16 E7 antibodies from whole blood as a non-invasive assisting technology for diagnosis of HPV-associated malignancies, especially, at primary healthcare and remote settings. The platform can detect and quantify anti-HPV16 E7 antibody down to 2.87 ng/mL. We further validated our immunoassay in clinical patient samples and it provided significantly high responses as compared to control samples. Thus, it can be potentially implemented as a pretesting tool to identify high-risk groups for broad monitoring of HPV-associated cancers in resource-constrained settings.
Targeting the Mevalonate Pathway to Overcome Acquired Anti-HER2 Treatment Resistance in Breast Cancer (2019)

Despite effective strategies, resistance in HER2<sup>+</sup> breast cancer remains a challenge. While the mevalonate pathway (MVA) is suggested to promote cell growth and survival, including in HER2<sup>+</sup> models, its potential role in resistance to HER2-targeted therapy is unknown. Parental HER2<sup>+</sup> breast cancer cells and their lapatinib-resistant and lapatinib + trastuzumab-resistant derivatives were used for this study. MVA activity was found to be increased in lapatinib-resistant and lapatinib + trastuzumab-resistant cells. Specific blockade of this pathway with lipophilic but not hydrophilic statins and with the N-bisphosphonate zoledronic acid led to apoptosis and substantial growth inhibition of R cells. Inhibition was rescued by mevalonate or the intermediate metabolites farnesyl pyrophosphate or geranylgeranyl pyrophosphate, but not cholesterol. Activated Yes-associated protein (YAP)/transcriptional coactivator with PDZ-binding motif (TAZ) and mTORC1 signaling, and their downstream target gene product Survivin, were inhibited by MVA blockade, especially in the lapatinib-resistant/lapatinib + trastuzumab-resistant models. Overexpression of constitutively active YAP rescued Survivin and phosphorylated-S6 levels, despite blockade of the MVA. These results suggest that the MVA provides alternative signaling leading to cell survival and resistance by activating YAP/TAZ-mTORC1-Survivin signaling when HER2 is blocked, suggesting novel therapeutic targets. MVA inhibitors including lipophilic statins and N-bisphosphonates may circumvent resistance to anti-HER2 therapy warranting further clinical investigation. IMPLICATIONS: The MVA was found to constitute an escape mechanism of survival and growth in HER2<sup>+</sup> breast cancer models resistant to anti-HER2 therapies. MVA inhibitors such as simvastatin and zoledronic acid are potential therapeutic agents to resensitize the tumors that depend on the MVA to progress on anti-HER2 therapies.
Machine learning used for simulation of MitraClip intervention: A proof-of-concept study (2023)

<b>Introduction:</b> Severe mitral regurgitation (MR) is a mitral valve disease that can lead to lifethreatening complications. MitraClip (MC) therapy is a percutaneous solution for patients who cannot tolerate surgical solutions. In MC therapy, a clip is implanted in the heart to reduce MR. To achieve optimal MC therapy, the cardiologist needs to foresee the outcomes of different scenarios for MC implantation, including the location of the MC. Although finite element (FE) modeling can simulate the outcomes of different MC scenarios, it is not suitable for clinical usage because it requires several hours to complete. <b>Methods:</b> In this paper, we used machine learning (ML) to predict the outcomes of MC therapy in less than 1 s. Two ML algorithms were used: XGBoost, which is a decision tree model, and a feed-forward deep learning (DL) model. The MC location, the geometrical attributes of the models and baseline stress and MR were the features of the ML models, and the predictions were performed for MR and maximum von Mises stress in the leaflets. The parameters of the ML models were determined to achieve the minimum errors obtained by applying the ML models on the validation set. <b>Results:</b> The results for the test set (not used during training) showed relative agreement between ML predictions and ground truth FE predictions. The accuracy of the XGBoost models were better than DL models. Mean absolute percentage error (MAPE) for the XGBoost predictions were 0.115 and 0.231, and the MAPE for DL predictions were 0.154 and 0.310, for MR and stress, respectively. <b>Discussion:</b> The ML models reduced the FE runtime from 6 hours (on average) to less than 1 s. The accuracy of ML models can be increased by increasing the dataset size. The results of this study have important implications for improving the outcomes of MC therapy by providing information about the outcomes of MC implantation in real-time.
Plasmonic Core–Satellite Assemblies as Highly Sensitive Refractive Index Sensors (2015)

Highly sensitive and spectrally tunable plasmonic nanostructures are of great demand for applications such as SERS and parallel biosensing. However, there is a lack of such nanostructures for the midvisible spectral regions as most available chemically stable nanostructures offer high sensitivity in the red to far red spectrum. In this work, we report the assembly of highly sensitive nanoparticle structures using a hydroxylamine mediated core–satellite assembly of 20 nm gold nanoparticle satellites onto 60 nm spherical gold cores. The average number of satellites allows tuning the plasmon resonance wavelength from 543 to 575 nm. The core–satellite nanostructures are stable in pH ranges from 5 to 9 and show about 2-fold higher plasmonic sensitivity than similar sized gold nanospheres.
Nitrospira‐dominated biofilm within a thermal artesian spring: a case for nitrification‐driven primary production in a geothermal setting (2012)

Water chemistry, energetic modeling, and molecular analyses were combined to investigate the microbial ecology of a biofilm growing in a thermal artesian spring within Hot Springs National Park, AR. This unique fresh water spring has a low dissolved chemical load and is isolated from both light and direct terrestrial carbon input - resulting in an oligotrophic ecosystem limited for fixed carbon and electron donors. Evaluation of energy yields of lithotrophic reactions putatively linked to autotrophy identified the aerobic oxidation of methane, hydrogen, sulfide, ammonia, and nitrite as the most exergonic. Small subunit (SSU) rRNA gene libraries from biofilm revealed a low-diversity microbial assemblage populated by bacteria and archaea at a gene copy ratio of 45:1. Members of the bacterial family 'Nitrospiraceae', known for their autotrophic nitrite oxidation, dominated the bacterial SSU rRNA gene library (approximately 45%). Members of the Thaumarchaeota ThAOA/HWCGIII (>96%) and Thaumarchaeota Group I.1b (2.5%), which both contain confirmed autotrophic ammonia oxidizers, dominated the archaeal SSU rRNA library. Archaea appear to dominate among the ammonia oxidizers, as only ammonia monooxygenase subunit A (amoA) genes belonging to members of the Thaumarchaeota were detected. The geochemical, phylogenetic, and genetic data support a model that describes a novel thermophilic biofilm built largely by an autotrophic nitrifying microbial assemblage. This is also the first observation of 'Nitrospiraceae' as the dominant organisms within a geothermal environment.
Field dependent negative capacitance in small-molecule organic light-emitting diodes (2006)

Frequency dependent charge transport in organic light-emitting diodes, including marked negative capacitance (NC), is reproduced through an equivalent circuit model. The robustness of the model is tested through impedance spectroscopy characterization as a function of bias changes and layer thickness modifications. Correlations with current-voltage measurements reveal that the NC occurs once trap assisted space charge limited transport is reached. Through variation of the organic layer thicknesses, the magnitude of the NC response can be precisely tuned. In particular, increasing the thickness of the electron transport layer increases the NC magnitude, whereas hole transport layer thickness modifications have little effect on the magnitude of NC. Subsequent modeling indicates that alterations in the distribution of the electric field across the individual organic layers account for the observed variations in NC. In addition, it is found that the time constants for the inductive elements of the model increase with applied bias, unlike their capacitive counterparts, suggesting that an accumulation of charge at the organic/organic interface is responsible for both the increasing NC and redistribution of the applied field.
An Experiment-Based Methodology for Evaluating the Impacts of Full Bandwidth Load on the Hybrid Energy Storage System for Electrified Vehicles (2018)

In Electrified Vehicles, the cost, efficiency, and durability of electrified vehicles are dependent on the energy storage system (ESS) components, configuration and its performance. This paper, pursuing a minimal size tactic, describes a methodology for quantitatively and qualitatively investigating the impacts of a full bandwidth load on the ESS in the HEV. However, the methodology can be extended to other electrified vehicles. The full bandwidth load, up to the operating frequency of the electric motor drive (20 kHz), is empirically measured which includes a frequency range beyond the usually covered frequency range by published standard drive cycles (up to 0.5 Hz). The higher frequency band is shown to be more efficiently covered by a Hybrid Energy Storage System (HESS) which in this paper is defined as combination of a high energy density battery, an Ultra-Capacitor (UC), an electrolytic capacitor, and a film capacitor. In this paper, the harmonic and dc currents and voltages are measured through two precision methods and then the results are used to discuss about overall HEV efficiency and durability. More importantly, the impact of the addition of high-band energy storage devices in reduction of power loss during transient events is disclosed through precision measurement based methodology.
Development of a data acquisition system for electrical conductivity images of biological tissues via contactless measurements (2005)

The data acquisition system of a new medical imaging system is developed and system performance is presented. The ultimate aim of the system is to image electrical conductivity of biological tissues via contactless measurements. Two different measurement systems are designed based upon measurement of impedance change of an eddy current type sensor. The first design (based upon excitation of a single coil probe) gives 100 Hz output frequency change for a conductivity change of 1.9 mS/cm and is tested at high frequency (1.4 MHz). Second design (based on one excitation and one receiving coil) operates at low frequency (15 KHz) and gives 18 /spl mu/V change in output voltage for similar conductivity variation. Field images of 30 mm diameter cylindrical objects were obtained while scanning a region of 225 cm/sup 2/. The sensitivities of the two systems show a possible wide scale use of these systems for measurement, monitoring and imaging of local conductivity variations in biological tissues.
Backscattering X-ray imaging using Fresnel zone aperture (2021)

We demonstrate backscattering X-ray imaging using a Fresnel zone aperture (FZA), where the line width of the outermost circle is 100 μm. The method is a lensless imaging technique employing an optical aperture instead of a lens. We successfully reconstructed test objects from four images observed using a series of FZAs without an iterative procedure during the reconstruction process. We also confirmed the successful reconstruction of a series of images by changing the focal plane in a short computer calculation time, indicating that 3D information can be obtained by measuring a single set of four images.
INHERITANCE OF PHOTOPERIODIC HEADING RESPONSE IN WINTER AND SPRING CULTIVARS OF BREAD WHEAT (1973)

Populations from crosses between two winter wheat (Triticum aestivum L. em. Thell.) parents, Lancer and Warrior, which were sensitive to photoperiod, and Sonora 64, a photoperiod-insensitive spring wheat, were studied under a 10-h photoperiod. F 2 distributions supported by F 3 data demonstrated a two-gene inheritance system with dominant epistasis for insensitivity. The F 2 distributions fit the hypothesis of a 12 early:3 late:1 very late ratio, where early heading in short days was associated with photoperiod insensitivity. Minor factors also appeared to affect the earliness of heading.
Differentiable Hybrid Traffic Simulation (2022)

We introduce a novel differentiable hybrid traffic simulator, which simulates traffic using a hybrid model of both macroscopic and microscopic models and can be directly integrated into a neural network for traffic control and flow optimization. This is the first differentiable traffic simulator for macroscopic and hybrid models that can compute gradients for traffic states across time steps and inhomogeneous lanes. To compute the gradient flow between two types of traffic models in a hybrid framework, we present a novel intermediate conversion component that bridges the lanes in a differentiable manner as well. We also show that we can use analytical gradients to accelerate the overall process and enhance scalability. Thanks to these gradients, our simulator can provide more efficient and scalable solutions for complex learning and control problems posed in traffic engineering than other existing algorithms. Refer to https://sites.google.com/umd.edu/diff-hybrid-traffic-sim for our project.
High-speed carrier-depletion silicon Mach-Zehnder optical modulators with lateral PN junctions (2014)

This paper presents new experimental data from a lateral PN junction silicon Mach-Zehnder optical modulator. Efficiencies in the 1.4V.cm to 1.9V.cm range are demonstrated for drive voltages between 0V and 6V. High speed operation up to 52Gbit/s is also presented. The performance of the device which has its PN junction positioned in the centre of the waveguide is then compared to previously reported data from a lateral PN junction device with the junction self-aligned to the edge of the waveguide rib. An improvement in modulation efficiency is demonstrated when the junction is positioned in the centre of the waveguide. Finally we propose schemes for achieving high modulation efficiency whilst retaining self-aligned formation of the PN junction.
Suzuki Coupling Reactions (2005)

This chapter contains sections titled: Palladium-catalysed borylation and Suzuki coupling (BSC) to obtain β-benzo[b]thienyldehydroamino acid derivatives Palladium-catalysed cross-coupling reactions of 4-tosylcoumarins and arylboronic acids: synthesis of 4-arylcoumarin compounds Cyclopropyl arenes, alkynes and alkenes from the in situ generation of B-cyclopropyl-9-BBN and the Suzuki-Miyaura coupling of aryl, alkynyl and alkenyl bromides One-pot synthesis of unsymmetrical 1,3-dienes through palladium-catalysed sequential borylation of a vinyl electrophile by a diboron and cross-coupling with a distinct vinyl electrophile Pd(OAc)2/2-Aryl oxazoline catalysed Suzuki coupling reactions of aryl bromides and boronic acids Palladium-catalysed reactions of haloaryl phosphine oxides: modular routes to functionalised ligands Bulky electron rich phosphino-amines as ligands for the Suzuki coupling reaction of aryl chlorides Arylation of ketones, aryl amination and Suzuki-Miyaura cross coupling using a well-defined palladium catalyst bearing an N-heterocyclic carbene ligand
Frontispiece: Modular Bi‐Directional One‐Pot Strategies for the Diastereoselective Synthesis of Structurally Diverse Collections of Constrained β‐Carboline‐Benzoxazepines (2017)

Modular access to a range of tailored heterocyclic scaffolds with diverse 3D-complexity is provided by a novel cascade one-pot methodology based on Pictet–Spengler/aza-Michael addition and Schiff base/aza-Michael addition/reduction protocols. The versatile approach is highly diastereoselectivity and provides direct access to drug-like molecules in good yields. The large substrate scope will enable broad coverage of chemical space and allow for rapid SAR exploration. For more information see the Full Paper by R. Mazitschek, T. H. Al-Tel, et al. on page 14182 ff.
High Prevalence of Pituitary Adenomas: A Cross-Sectional Study in the Province of Liege, Belgium (2006)

The prevalence of pituitary adenomas in the study population (one case in 1064 individuals) was more than 3.5-5 times that previously reported. This increased prevalence may have important implications when prioritizing funding for research and treatment of pituitary adenomas.
Corticotroph tumor progression after bilateral adrenalectomy (Nelson’s syndrome): systematic review and expert consensus recommendations (2021)

We endorse the definition of CTP-BADX/NS as radiological progression or new detection of a pituitary tumor on thin-section MRI. We recommend surveillance by MRI after 3 months and every 12 months for the first 3 years after BADX. Subsequently, we suggest clinical evaluation every 12 months and MRI at increasing intervals every 2-4 years (depending on ACTH and clinical parameters). We recommend pituitary surgery as first-line therapy in patients with CTP-BADX/NS. Surgery should be performed before extrasellar expansion of the tumor to obtain complete and long-term remission. Conventional radiotherapy or stereotactic radiosurgery should be utilized as second-line treatment for remnant tumor tissue showing extrasellar extension.
Can Social Media Help Analyze Public Opinion? A Case Study of Iranian Public Opinion After the 2009 Election (2012)

Describes a methodology for analyzing public opinion and mood in closed societies, focusing on a case study that analyzed Iranian public opinion and mood as expressed over Twitter in the nine months following Iran's 2009 presidential election.
The EPS of Acidithiobacillus ferrooxidans - a model for structure-function relationships of attached bacteria and their physiology (2001)

To dissolve pyrite or sulphur, leaching bacteria like Acidithiobacillus ferrooxidans attach to these substrata by extracellular polymeric substances (specifically, lipopolysaccharides). The primary attachment to pyrite at pH 2 is mediated by exopolymer-complexed iron(III) ions in an electrostatic interaction with the negatively charged pyrite surface. Cells grown on sulphur exhibit a different composition of the extracellular lipopolysaccharides, namely with increased hydrophobic properties, and do not attach to pyrite. Thus, the cells adapt the chemical composition of their exopolymers to the substrate/substratum. It is concluded that the mechanism of bacterial pyrite oxidation is basically indirect. The actual corrosive agents are iron(III) ions. Preliminary data indicate that active strains complex more iron(III) ions in their EPS than less active ones. Obviously, the exopolymeric layer comprises a reaction space for the regeneration of these ions by the activity of the iron oxidising bacteria.
Common Variants Show Predicted Polygenic Effects on Height in the Tails of the Distribution, Except in Extremely Short Individuals (2011)

Common genetic variants have been shown to explain a fraction of the inherited variation for many common diseases and quantitative traits, including height, a classic polygenic trait. The extent to which common variation determines the phenotype of highly heritable traits such as height is uncertain, as is the extent to which common variation is relevant to individuals with more extreme phenotypes. To address these questions, we studied 1,214 individuals from the top and bottom extremes of the height distribution (tallest and shortest ∼1.5%), drawn from ∼78,000 individuals from the HUNT and FINRISK cohorts. We found that common variants still influence height at the extremes of the distribution: common variants (49/141) were nominally associated with height in the expected direction more often than is expected by chance (p<5×10⁻²⁸), and the odds ratios in the extreme samples were consistent with the effects estimated previously in population-based data. To examine more closely whether the common variants have the expected effects, we calculated a weighted allele score (WAS), which is a weighted prediction of height for each individual based on the previously estimated effect sizes of the common variants in the overall population. The average WAS is consistent with expectation in the tall individuals, but was not as extreme as expected in the shortest individuals (p<0.006), indicating that some of the short stature is explained by factors other than common genetic variation. The discrepancy was more pronounced (p<10⁻⁶) in the most extreme individuals (height<0.25 percentile). The results at the extreme short tails are consistent with a large number of models incorporating either rare genetic non-additive or rare non-genetic factors that decrease height. We conclude that common genetic variants are associated with height at the extremes as well as across the population, but that additional factors become more prominent at the shorter extreme.