gebhart/patrepeval huggingface dataset:
Assessing airway repair capacity in very preterm infants (2019)

<b>Introduction:</b> Airway epithelial cells (AECs) line the airway to create a protective barrier between the lung and the external environment. Very preterm birth (&lt;32 weeks gestation) not only disrupts the normal development of the airway epithelium, but exposes it to potentially injurious treatments required for sustaining life. The current study aimed to assess the ability of the epithelium to recover from this trauma by characterising the repair mechanisms of AECs in preterm infants. <b>Methods:</b> Nasal brushings were used to collect AECs from infants born very preterm (n=35, 24-31.7wks gestation, 1.07-1.22yrs corrected at sampling). Control samples were provided by children born at term (n=6, &gt;37wks gestation, 2.4-6.5yrs at sampling). Cultured AECs were scratch wounded and repair tracked for 72 hours (IncuCyte ZOOM®, Essen Bioscience). Wound closure was then assessed for correlations with neonatal factors including gestation, birthweight, duration of respiratory support, and steroid exposure. <b>Results:</b> Term AECs achieved complete repair within 60 hours. Repair in successfully cultured preterm AECs (n=22) was significantly altered and fell into three categories; delayed but complete repair (&gt;80% n=5), significant but incomplete closure (50-80% n=6) and incomplete closure (20-50% n=10). Neonatal factors did not predict altered wound repair, though infants born to mothers completing a course of antenatal steroids (n=13) exhibited significantly worse repair (p=0.017, 47.30% vs 74.02%). <b>Conclusion:</b> Data confirm that preterm infants have an intrinsic functional defect in their airway reparative capacity. Exposure to antenatal steroids may further alter repair and raises questions about the long-term impact of antenatal steroid use.
Finite temperature effects on the structural stability of Si-doped HfO2 using first-principles calculations (2023)

The structural stabilities of the monoclinic and tetragonal phases of Si-doped HfO2 at finite temperatures were analyzed using a computational scheme to assess the effects of impurity doping. We proposed a method that the finite temperature effects, i.e., lattice vibration and impurity configuration effects, are considered. The results show that 6% Si doping stabilizes the tetragonal phase at room temperature, although a higher concentration of Si is required to stabilize the tetragonal phase at zero temperature. These data indicate that lattice vibration and impurity configuration effects are important factors determining structural stability at finite temperatures.
Cell Viability Assays in Three-Dimensional Hydrogels: A Comparative Study of Accuracy (2021)

Three-dimensional (3D) cell culture systems, such as tumor organoids and multicellular tumor spheroids, have been developed in part as a result of major advances in tissue engineering and biofabrication techniques. 3D cell culture offers great capabilities in drug development, screening, testing, and precision medicine owing to its physiological accuracy. However, since the inception of 3D systems, few methods have been reported to successfully analyze cell viability quantitatively within hydrogel constructs. In this study, we describe and compare commercially available viability assays developed for two-dimensional (2D) applications for use in 3D constructs composed of organic, synthetic, or hybrid hydrogel formulations. We utilized Promega's CellTiter-Glo<sup>®</sup>, CellTiter-Glo 3D, and CellTiter 96<sup>®</sup> MTS Assay along with Thermo Fisher's PrestoBlue<sup>™</sup> assay to determine if these assays can be used accurately in 3D systems. Compared with direct cell viability commonly used in 2D cell culture, our results show cellular health output inaccuracies among each assay in differing hydrogel formulations. Our results should inform researchers of potential errors when using cell viability measurements in 3D cultures and conclude that microscopic imaging should be used, in combination, for validation. Impact statement Three-dimensional (3D) tissue organoids models are a valuable tool not only for studying drug toxicity but also for understanding human embryonic development, intra-tissue morphogenesis, and mechanisms of disease. In cancer organoids, such 3D models may be used for preclinical chemotherapy screening and for understanding cell death and viability mechanisms under physiologically relevant conditions. Cell viability assays are necessary for assessing the effect of biological reagents on cellular health and have been used on <i>in vitro</i> cell cultures for many years. With the increase of 3D systems in cellular biology research to determine therapeutic efficacy, two-dimensional assays that measure cell viability are being used outside their intended use on 3D constructs. In this study, we assess the accuracy of using various commercially available cell viability assays on different 3D hydrogel constructs to help researchers understand expected variability in their experimentation along microscopic imaging validation.
Effect of Divalent Cations on Pore Formation and Degradation of Poly(D,L-lactide-co-glycolide) (2007)

Poly(D,L-lactide-co-glycolide) (PLG) is probably the biodegradable polymer most often used for polymeric controlled-release formulations. Different salts have been shown to affect the swelling and degradation of PLG, which, in turn, affect the release of encapsulated drugs. In this investigation the effect of divalent cations was especially investigated. Films of PLG were incubated in phosphate buffer saline (PBS), a buffer containing salts similar to plasma, Hepes buffer, and Hepes buffer with ZnCl2, CaCl2, MgCl2, or Na2CO3 added. Pore formation at the surface and inside the film was analyzed by scanning electron microscopy. The samples were also analyzed gravimetrically at predetermined intervals to determine the mass loss, and for some samples the pH within the PLG films was determined by confocal microscopy. Pores were formed faster in the presence of all divalent cations, and the results indicated a greater degradation rate in the presence of Zn2+. The catalyzing effect of the divalent cations on degradation was attributed to their ability to act as Lewis acids. Pores were formed more slowly in PBS than in a buffer containing salts similar to plasma, which should be considered when choosing the in vitro release medium.
Improving Real-Time Drilling Data Quality Using Artificial Intelligence and Machine Learning Techniques (2021)

Abstract Due to high demand for energy, oil and gas companies started to drill wells in remote areas and unconventional environments. This raised the complexity of drilling operations, which were already challenging and complex. To adapt, drilling companies expanded their use of the real-time operation center (RTOC) concept, in which real-time drilling data are transmitted from remote sites to companies’ headquarters. In RTOC, groups of subject matter experts monitor the drilling live and provide real-time advice to improve operations. With the increase of drilling operations, processing the volume of generated data is beyond a human's capability, limiting the RTOC impact on certain components of drilling operations. To overcome this limitation, artificial intelligence and machine learning (AI/ML) technologies were introduced to monitor and analyze the real-time drilling data, discover hidden patterns, and provide fast decision-support responses. AI/ML technologies are data-driven technologies, and their quality relies on the quality of the input data: if the quality of the input data is good, the generated output will be good; if not, the generated output will be bad. Unfortunately, due to the harsh environments of drilling sites and the transmission setups, not all of the drilling data is good, which negatively affects the AI/ML results. The objective of this paper is to utilize AI/ML technologies to improve the quality of real-time drilling data. The paper fed a large real-time drilling dataset, consisting of over 150,000 raw data points, into Artificial Neural Network (ANN), Support Vector Machine (SVM) and Decision Tree (DT) models. The models were trained on the valid and not-valid datapoints. The confusion matrix was used to evaluate the different AI/ML models including different internal architectures. Despite the slowness of ANN, it achieved the best result with an accuracy of 78%, compared to 73% and 41% for DT and SVM, respectively. The paper concludes by presenting a process for using AI technology to improve real-time drilling data quality. To the author's knowledge based on literature in the public domain, this paper is one of the first to compare the use of multiple AI/ML techniques for quality improvement of real-time drilling data. The paper provides a guide for improving the quality of real-time drilling data.
Detection of early-stage pancreatic ductal adenocarcinoma (PDAC): Sensitivity, specificity, and discriminatory properties of the serum-based PAM4-immunoassay. (2012)

151 Background: We recently reported that a serum-based enzyme immunoassay employing the PAM4 antibody was able to correctly identify 82% of patients with known PDAC and, importantly, that this assay had promising sensitivity for detecting early-stage disease. We now extend these findings in a much larger patient population that includes over 600 sera from both malignant and benign diseases of the pancreas and surrounding tissues. Methods: In a blinded analysis, sera from patients with confirmed PDAC (N=298), other cancers (N=99), benign disease of the pancreas (N=126), and healthy adults (N=79) were evaluated by enzyme immunoassay for concentration of PAM4-antigen levels. Results: Overall sensitivity for detection of PDAC was 76%, with 64% of stage-1 patients testing positive and a higher sensitivity (85%) for advanced disease. For the most part, sera from patients with neuroendocrine tumors of the pancreas or cancers of other origin (squamous, GIST, etc.) did not have elevated levels of the PAM4-antigen. Approximately half of the patients with ampullary (48%) and extrahepatic biliary (50%) adenocarcinomas had positive levels of circulating PAM4-antigen. Of 126 patients diagnosed with benign conditions of the pancreas, only 24 (19%) were positive and, in particular, 18 of 80 (23%) patients with chronic pancreatitis (CP) were positive. ROC curve analysis demonstrated a statistically significant difference between the PDAC and CP groups (P &lt; 0.0001), with an area under the curve of 0.84 ± 0.02 (95% CI: 0.79 – 0.89). The positive- and negative-likelihood ratios for differentiating PDAC from benign conditions of the pancreas were 4.00 and 0.30, respectively. Conclusions: The PAM4-immunoassay detects nearly two-thirds of stage-1 PDAC patients, and does so with high discriminatory power with respect to benign pancreatic disease. Our results provide a rationale for longitudinal surveillance of patients considered at high-risk for PDAC (e.g., familial pancreatic cancer, new-onset diabetes, etc.) with the PAM4 assay. (Supported in part by NIH grants CA096924, CA120432 and CA62924, and the Turpin Foundation.)
Tunnel Magnetoresistance in MgO-Based Magnetic Tunnel Junctions (2019)

The spin polarization of a ferromagnet at low temperature can be directly measured using ferromagnet/Al-O/superconductor tunnel junctions. Spin injection into semiconductors is the key to developing semiconductor spintronic devices such as Datta-Das-type spin-dependent field-effect transistors and spin-dependent metal-oxide-semiconductor field-effect transistors. An inverse of the spin-torque diode effect is the microwave emissions that occur when a DC current flows through a 100-nm-scale magnetoresistive device. Spin-transfer torque acting on the free-layer magnetic moment can induce steady precession of the free-layer moment at an ferromagnetic resonance frequency. Spin Dice can theoretically generate enormous amounts of random numbers using large parallel data processing. Random numbers are essential building blocks in modern cryptographic systems to keep information communication technologies highly secure and confidential. The giant tunneling magnetoresistance effect in magnetic tunnel junctions is therefore expected not only to extend the applications of existing devices but also to help achieve novel spintronic applications.
Supplementary Figure 5 from Transformation-Dependent Silencing of Tumor-Selective Apoptosis-Inducing TRAIL by DNA Hypermethylation Is Antagonized by Decitabine (2023)

Supplementary Figure 5 from Transformation-Dependent Silencing of Tumor-Selective Apoptosis-Inducing TRAIL by DNA Hypermethylation Is Antagonized by Decitabine
Generation of induced pluripotent stem cell line, CSSi004-A (2962), from a patient diagnosed with Huntington's disease at the presymptomatic stage (2018)

Huntington's disease (HD) is an incurable, autosomal dominant, hereditary neurodegenerative disorder that typically manifests itself in midlife. This pathology is linked to the deregulation of multiple, as yet unknown, cellular processes starting before HD onset. A human iPS cell line was generated from skin fibroblasts of a subject at the presymptomatic life stage, carrying a polyglutamine expansion in HTT gene codifying Huntingtin protein. The iPSC line contained the expected CAG expansion, expressed the expected pluripotency markers, displayed in vivo differentiation potential to the three germ layers and had a normal karyotype.
Excited state and charge dynamics of hybrid organic/inorganic heterojunctions. I. Theory (2014)

The different cohesive forces that bond organic (i.e. excitonic) and inorganic semiconductors lead to widely disparate dielectric constants, charge mobilities, and other fundamental optoelectronic properties that make junctions between these materials interesting for numerous practical applications. Yet, there are no detailed theories addressing charge and energy transport across interfaces between these hybrid systems. Here, we develop a comprehensive physical model describing charge transport and photocurrent generation based on first-principles charge and excited state dynamics at the organic/inorganic heterojunction. We consider interfaces that are trap-free, as well as those with an exponential distribution of trap states. We find that the hybrid charge-transfer state resulting from photon absorption near the junction that subsequently migrates to the heterointerface is often unstable at room temperature, leading to its rapid dissociation into free charges that are collected at the device contacts. In the companion Paper II [A. Panda et al., Phys. Rev. B 90, 045303 (2014)], we apply our theories to understanding the optical and electronic properties of archetype organic/inorganic heterojunction diodes. Our analysis provides insights for developing high performance optoelectronic devices whose properties are otherwise inaccessible to either conventional excitonic or inorganic semiconductor junctions.
Olfactory Receptors Reduce Inflammation of Lung Epithelial Cells (2022)

<b>Background:</b> COPD is associated with chronic inflammation but anti-inflammatory therapy is largely lacking. Lung epithelial cells are central in disease development. Extra nasally expressed olfactory receptors (ORs) regulate various cellular processes. <b>Hypothesis:</b> ORs are able to regulate immune responses and thereby are promising therapeutic targets for COPD patients. <b>Methods:</b> Screening by calcium imaging was used to identify ORs in the lung epithelial cell line A549. RT-PCR and immunocytochemical staining validated OR expression in A549 or primary air-exposed lung epithelial cells. Effects of receptor activation were investigated in A549 by measuring 1) intracellular cAMP concentrations, 2) cellular vitality by annexin/propidium iodide staining, 3) the secretion of the proinflammatory and COPD key cytokine IL-8 in the absence and presence of bacterial PAMPs by ELISA. <b>Results:</b> A screening with 100 substances in A549 cells revealed dose-dependently an increase of intracellular calcium by brahmanol and cinnamaldehyde. The corresponding receptors OR2AT4 and OR2J3 were detected on mRNA- and protein level. Stimulation of OR2J3 but not of OR2AT4 increased the cAMP concentration and inhibited the secretion of IL-8 both in the absence and presence of bacterial PAMPs. Cell viability was not affected. mRNA expression of the receptors was also verified in primary air-exposed lung epithelial cells. <b>Conclusion:</b> Our experiments showed that A549 and primary lung epithelial cells express OR2AT4 and OR2J3. Stimulation of OR2J3 reduced IL8 probably via cAMP. ORs in lung epithelial cells are potential drug targets for COPD. More details of the regulatory mechanism should be acquired in primary cells of healthy and COPD donors.
Quantification of the collagen fibre architecture of human cranial dura mater (1998)

The purpose of this study was to quantify and map the gross fibre architecture of the cranial dura mater (CDM) using small angle light scattering (SALS). In SALS, HeNe laser light is passed through the tissue, and the resultant scattering pattern is analysed to determine the preferred fibre direction and degree of orientation. The dura mater was found to be a complex structure with fibre orientations ranging from highly aligned to nearly random. In the temporal region, 80% of the samples (n = 20) were found to have regions composed of highly oriented fibres with a mean fibre direction of 6.3 degrees +/- 0.8 degree with respect to the sagittal plane (i.e. almost parallel to the superior sagittal sinus). These highly aligned regions were found in symmetric anatomical locations about the median sagittal sinus and had similar fibre orientations over both hemispheres. Although our sample size was small, we found that the size of the symmetric regions, which covered 14.4 +/- 1.6% of the total CDM area, was not influenced by subject's age or sex. The presence of these highly oriented fibre regions in CDM may be due to mechanical forces exerted on dura mater during its development. These forces may have induced realignment of the collagen fibres in the direction of tensile pull, although the exact basis for the unique gross fibre architecture of CDM remains unknown.
Non-invasive determination by cardiovascular magnetic resonance of right ventricular-vascular coupling in children and adolescents with pulmonary hypertension (2015)

Measurement of VVCRm in pediatrics is feasible. Pulmonary vascular non-reactivity may be contribute to ventricular-vascular decoupling in severe PH. Therapeutic intervention to maintain a low vascular afterload in reactive patients may preserve right ventricular functional reserve and delay the onset of RV-PA decoupling. Use of VVCRm may have significant prognostic implication.
Poled, chromophore-functionalized polymeric nonlinear optical materials. Probing second harmonic generation temporal characteristics via site-selective crosslinking/hydrogen bonding (1992)

Appending high-β chromophores to glassy macromolecules represents an advance in NLO materials design in that chromophore number densities are greatly enhanced and structural disorientation/physical aging processes subsequent to cessation of electric field poling are impeded. Further enhancements in the SHG (second harmonic generation) temporal stability of such materials can be achieved by effecting thermal cross-linking/vitrification of the matrix in concert with the poling process. Nevertheless, optimum architectural strategies for such cross-linking processes, either chemical or hydrogen hydrogen-bonding, have not been systematically addressed. We report here modifications of our previously investigated poly(p-hydroxystyrene)-N-(4-nitrophenyl)-(S)-prolinol (NPP-PHS) chromophore-functionalized polymer system, which afford the first opportunity to probe SHG temporal stability as a function of cross-link/hydrogenbond location (I)
A MEMS microphone with repulsive sensing (2017)

The most common types of MEMS microphones are based on the capacitive sensing principle because of their ease of integration and their ability to detect low pressure fluctuations. One bottleneck in the design of conventional electrostatic MEMS microphones is that the sensitivity is impaired by the pull-in effect in parallel-plate capacitors. The electrical sensitivity of the microphone is a linear function of the bias voltage applied on the microphone. To increase the sensitivity and signal to noise ratio, the bias voltage should be increased, but the bias voltage is severely limited to the pull-in voltage, where the diaphragm will collapse into the backplate. To address the sensitivity issue in MEMS microphones, we devised a new type of capacitive sensor that creates a repulsive force rather than an attractive force, thereby completely avoiding the pull-in effect. The pull-in voltage has constrained the performance of capacitive microphones since their invention by Edward C. Wente in 1916. The ability to avoid pull-in will enable microphone designs with more compliant diaphragms and will result in significantly higher sensitivity, higher resolution, less noise and flatter frequency response. We will demonstrate our simulation results on the dynamic and acoustic responses of the MEMS microphone and present our experimental results for validation.
Beryllium-copper diffusion bonding for an ITER first wall application (2002)

Several different joint assemblies were evaluated in support of a manufacturing technology for diffusion bonding a beryllium armor tile to a copper alloy heat sink for fusion reactor applications. Because beryllium reacts with all but a few elements to form intermetallic compounds, this study considered several different surface treatments as a means of both inhibiting these reactions and promoting a good diffusion bond between the two substrates. All diffusion bonded assemblies used aluminum or an aluminum-beryllium composite (AlBeMet-150) as the interfacial material in contact with beryllium. In most cases, explosive bonding was utilized as a technique for joining the copper alloy heat sink to an aluminum or AlBeMet-150 substrate, which was subsequently diffusion bonded to an aluminum coated beryllium tile. In this approach, a 250 /spl mu/m thick titanium foil is used as a diffusion barrier between the copper and aluminum to prevent the formation of Cu-Al intermetallic phases. In all cases, a hot isostatic pressing (HIP) furnace was used in conjunction with canned assemblies in order to minimize oxidation and apply sufficient pressure on the assembly for excellent metal-to-metal contact and subsequent bonding. Several different processing schedules were evaluated during the course of this study; bonded assemblies were produced with up to 100% joint efficiency. At this writing, a beryllium-copper divertor mock-up has survived 1000 thermal cycles at 10 MW/m/sup 2/ without damage during testing at the electron beam test system (EBTS) facility at Sandia National Laboratory in New Mexico.
Post-processing of compressed images with side information (1998)

This paper investigates the usage of side information for linear post-processing in subband image compression systems. In particular, side information is used to determine a custom synthesis filter bank for each image. It has been shown that perfect reconstruction filters are not optimal in the presence of quantization noise. However, most of the previous related work concentrated on optimizing analysis-synthesis pairs jointly, which requires very strong conditions. Limiting our attention to the decoder, we find optimal synthesis filters by solving a system of regression equations. Neither high-rate quantization, whiteness of the quantization noise, nor optimality of the quantizer is assumed. By allowing transmission of side information, we take a deterministic approach, thus finding the best reconstruction without any constraints such as stationarity. Optimal coefficients are independent of the internal machinery of the quantizers, and can therefore be used with "canned" software packages for post-processing purposes.