gebhart/patrepeval huggingface dataset:
Regulation of fibronectin gene expression by cyclic AMP and phorbol myristate acetate in HT-1080 human fibrosarcoma cells (1998)

We studied the regulation of fibronectin (FN) gene expression by cAMP and phorbol-12-myristate-13-acetate (PMA) in HT-1080 human fibrosarcoma cells. Dibutyryl cAMP increased FN synthesis and mRNA levels, while PMA inhibited the cAMP-induced FN synthesis. In transient transfection assays, cAMP increased FN promoter activity, while PMA paradoxically enhanced the cAMP-induced promoter activity. Stable transfection experiments, however, showed that neither cAMP or PMA alone nor together affected FN promoter activity. These results suggest that PMA antagonizes the cAMP-induced FN gene expression and that both the action of cAMP and the inhibition of its action by PMA may occur at the posttranscriptional level in HT-1080 cells.
Robust speech recognition in Noisy Environments: The 2001 IBM spine evaluation system (2002)

We report on the system IBM fielded in the second SPeech In Noisy Environments (SPINE-2) evaluation, conducted by the Naval Research Laboratory in October 2001. The key components of the system include an HMM-based automatic segmentation module using a novel set of LDA-transformed voicing and energy features, a multiple-pass decoding strategy that uses several speaker-and environment-normalization operations to deal with the highly variable acoustics of the evaluation, the combination of hypotheses from decoders operating on three distinct acoustic feature sets, and a class-based language model that uses both the SPINE-1 and SPINE-2 training data to estimate reliable probabilities for the new SPINE-2 vocabulary.
Accurate Estimation of SRAM Dynamic Stability (2008)

In this paper, an accurate approach for estimating SRAM dynamic stability is proposed. The conventional methods of SRAM stability estimation suffer from two major drawbacks: 1) using static failure criteria, such as static noise margin (SNM), which does not capture the transient and dynamic behavior of SRAM operation and 2) using quasi-Monte Carlo simulation, which approximates the failure distribution, resulting in large errors at the tails where the desired failure probabilities exist. These drawbacks are eliminated by employing a new distribution-independent, most-probable-failure-point search technique for accurate probability calculation along with accurate simulation-based dynamic failure criteria. Compared to previously published techniques, the proposed technique offers orders of magnitude improvement in accuracy. Furthermore, the proposed technique enables the correct evaluation of stability in real operation conditions and for different dynamic circuit techniques, such as dynamic write-back, where the conventional methods are not applicable.
Study on partition of spontaneous combustion danger zone and prediction of self-ignition in coalmine based on numeric simulation (2006)

By solving steady model of air flow diffusion and chemical reaction in loose coal, distribution of oxygen concentration and flow velocity magnitude were obtained. Compared the simulating results with critic value as well as duration of spontaneous combustion from large-scale spontaneous combustion experiment, three zones of spontaneous combustion were partitioned and mining conditions to avoid spontaneous combustion were obtained. The above method was employed to partition three zones in gob of fully mechanized top-coal caving long wall face and got fairly good result. Calculation of the above method is much smaller than simulating the whole process of coal spontaneous combustion, but the prediction precision can satisfy the demand of predicting and extinguishing spontaneous combustion in mining.
Application of monoclonal antibodies to measure metabolism of an anti‐trypanosomal compound in vitro and in vivo (2010)

Human African trypanosomiasis (HAT), also called African sleeping sickness, is a neglected tropical parasitic disease indigenous to sub-Saharan Africa. Diamidine compounds, including pentamidine and CPD-0801, are potent anti-trypanosomal molecules. The latter is a potential drug in the development at the UNC based Consortium for Parasitic Drug Development. An orally bioavailable prodrug of CPD-0801, DB868, is metabolized primarily in the liver to the active form. A monoclonal antibody developed against a pentamidine derivative has shown significant reactivity with CPD-0801 (EC(50) 65.1 nM), but not with the prodrug (EC(50)>18,000 nM). An inhibitory enzyme-linked immunosorbent assay (IELISA) has been used to quantitatively monitor prodrug metabolism by detecting the production of the active compound over time in a sandwich culture rat hepatocyte system and in rats. These results were compared with the results of the standard LC/MS/MS assay. Spearman coefficients of 0.96 and 0.933 (in vitro and in vivo, respectively) indicate a high correlation between these two measurement methods. This novel IELISA provides a facile, inexpensive, and accurate method for drug detection that may aide in elucidating the mechanisms of action and toxicity of existing and future diamidine compounds.
Physical activity, physical fitness and cardiometabolic risk amongst adults with moderate and severe haemophilia (2022)

Low levels of PA and physical fitness, and significant rates of abdominal adiposity and hypertension may collectively influence the risk and severity of various cardiometabolic and/or musculoskeletal health issues amongst ageing PwMSH. Personalised multi-disciplinary health interventions involving PA, dietary and health psychology input for PwMSH warrant future investigation.
Effects of antioxidants on interleukin-1β, nitric oxide and prostaglandin E2 production by human chondrocytes (2000)

peer reviewed
Solvent as Catalyst: Computational Studies of Organic Reactions in Solution (1999)

Quantum and statistical mechanics are being used to study the origin of solvent effects on the rates of organic reactions. Typically, a reaction path is obtained from ab initio molecular orbital calculations in the gas phase. The effects of solvation are then determined for this pathway with free-energy perturbation calculations using Monte Carlo simulations in several solvents. The latter calculations feature a classical description of the intermolecular interactions with partial charges for the reacting system determined from the quantum mechanical wavefunctions. Application to a variety of reactions including substitutions, additions, and pericyclic reactions has revealed insightful details on variations in solvation along the reaction paths. Such information is valuable for the rational design of catalysts.
Ocular Anti-VEGF Therapy for Diabetic Retinopathy: Overview of Clinical Efficacy and Evolving Applications (2014)

Ocular anti-vascular endothelial growth factor (VEGF) therapy represents one of the most significant advances in modern medicine. The introduction and widespread use of ocular anti-VEGF therapy for age-related macular degeneration heralded a new era in the treatment of vascular and exudative diseases of the retina. Its expanding indications now include diabetic macular edema and proliferative diabetic retinopathy, two vision-threatening forms of diabetic retinopathy. It is widely anticipated that ocular anti-VEGF therapy could spark a dramatic shift in the treatment paradigm for diabetic retinopathy. However, despite its clear efficacy shown in clinical trials, the dynamic landscape of evolving medical, ethical, and economic issues related to this new treatment suggests significant challenges ahead. In this article, we provide a discussion of this topic as part of this two-part Bench to Clinic narrative. Here, our Clinic contribution provides an overview of the current evidence from clinical trials on anti-VEGF therapy for diabetic retinopathy, and highlights the hopes and fears of this new treatment from clinical and public health standpoints. In the Bench narrative that precedes this contribution, Simó et al. provide an overview of the role of VEGF in the pathogenesis of diabetic retinopathy.
Single-Cell RNAseq of Aging Lungs from Nlrp3 -/- Mice Reveals Genotype- and Cell Type-Specific Effects of Aging on the Transcriptomes of Several Myeloid-Derived Cells (2021)

Rationale: 'Inflammaging,' an age-related phenomenon characterized by increased basal levels of proinflammatory molecules in circulation, is thought to contribute to the age-related decline in lung function and increased susceptibility to infection and disease. Mice lacking NLRP3, a pattern recognition receptor of the NLRP3 inflammasome, show reduced signs of 'inflammaging', have increased life expectancy, overall live healthier, making these mice an especially suitable model for studies on healthy aging. Here we report the preliminary results of a pilot single-cell RNA sequencing experiment of aging lungs from Nlrp3 -/-mice. Methods: Single-cell dissociates were collected from four control (two young, age = 8 weeks; two old, age = 108 weeks) and four nlrp3 knockout (two young, age = 8 weeks; two old, age = 108 weeks) C57BL/6J-derived mice. The 10X Chromium 3' V2 technology was used for single-cell isolation, barcoding, and cDNA library preparation for sequencing on an Illumina sequencer. Raw sequencing data was run through a custom pipeline for filtering, read alignment and expression counts matrix construction. Processing and clustering of the matrix was performed in R using a modified version of the standard Seurat pipeline. Cell types were given to each cluster using known marker genes. Differential gene expression testing results were visualized using the ComplexHeatmap package in R. Results: 28 unique cellular types were identified by clustering 41,878 cells. Differential gene expression testing revealed Nlrp3 -/-genotype-specific differences in transcriptomic changes related to aging in the alveolar macrophages, interstitial macrophages, classical monocytes, and nonclassical monocytes. We observed a reduction with age in Nlrp3 -/-samples in the expression of several pro-inflammatory molecules related to the 'inflammaging' phenotype that include Tnf, Cxcl2, Chil3, Ccl3, and Ccl4. Interestingly, expression of Il1b was observed to increase noticeably with age in these cells in the Nlrp3 -/-samples. The most pronounced genotypespecific differences were observable in old Nlrp3 -/-interstitial macrophages which showed increases with age in expression of genes related to MHCII-mediated antigen presentation (Cd72, Cd74, various MHCII complex genes), proteasome subunits (Psma1, Psme1, Psme2, Psmb8), and anti-oxidation (Prdx5, Atox1). Conclusions:. Nlrp3 -/-knockout mice show distinct age-related transcriptomic changes in several myeloid-derived cell types of the lungs that are known to be primary producers of the NLRP3 inflammasome. Additionally, several inflammation-related results agree with the general finding of reduced 'inflammaging' in these mice. These results suggest NLRP3-specific differences in the aging innate immune cell transcriptomes that may contribute to both the lung aging and global aging phenotypes.
Antibacterial Characterization of Novel Synthetic Thiazole Compounds against Methicillin-Resistant Staphylococcus pseudintermedius (2015)

Staphylococcus pseudintermedius is a commensal organism of companion animals that is a significant source of opportunistic infections in dogs. With the emergence of clinical isolates of S. pseudintermedius (chiefly methicillin-resistant S. pseudintermedius (MRSP)) exhibiting increased resistance to nearly all antibiotic classes, new antimicrobials and therapeutic strategies are urgently needed. Thiazole compounds have been previously shown to possess potent antibacterial activity against multidrug-resistant strains of Staphylococcus aureus of human and animal concern. Given the genetic similarity between S. aureus and S. pseudintermedius, this study explores the potential use of thiazole compounds as novel antibacterial agents against methicillin-sensitive S. pseudintermedius (MSSP) and MRSP. A broth microdilution assay confirmed these compounds exhibit potent bactericidal activity (at sub-microgram/mL concentrations) against both MSSA and MRSP clinical isolates while the MTS assay confirmed three compounds (at 10 μg/mL) were not toxic to mammalian cells. A time-kill assay revealed two derivatives rapidly kill MRSP within two hours. However, this rapid bactericidal activity was not due to disruption of the bacterial cell membrane indicating an alternative mechanism of action for these compounds against MRSP. A multi-step resistance selection analysis revealed compounds 4 and 5 exhibited a modest (two-fold) shift in activity over ten passages. Furthermore, all six compounds (at a subinihibitory concentration) demonstrated the ability to re-sensitize MRSP to oxacillin, indicating these compounds have potential use for extending the therapeutic utility of β-lactam antibiotics against MRSP. Metabolic stability analysis with dog liver microsomes revealed compound 3 exhibited an improved physicochemical profile compared to the lead compound. In addition to this, all six thiazole compounds possessed a long post-antibiotic effect (at least 8 hours) against MRSP. Collectively the present study demonstrates these synthetic thiazole compounds possess potent antibacterial activity against both MSSP and MRSP and warrant further investigation into their use as novel antimicrobial agents.
A Case of Congenital Glycogen Storage Disease Type IV With a Novel GBE1 Mutation (2008)

Glycogen storage disease type IV (Andersen disease) is a rare metabolic disorder characterized by deficient glycogen branching enzyme activity resulting in abnormal, amylopectin-like glycogen deposition in multiple organs. This article reports on an infant with the congenital neuromuscular subtype of glycogen storage disease type IV who presented with polyhydramnios, hydrops fetalis, bilateral ankle contractures, biventricular cardiac dysfunction, and severe facial and extremity weakness. A muscle biopsy showed the presence of material with histochemical and ultrastructural characteristics consistent with amylopectin. Biochemical analysis demonstrated severely reduced branching enzyme activity in muscle tissue and fibroblasts. Genetic analysis demonstrated a novel deletion of exon 16 within GBE1, the gene associated with glycogen storage disease type IV. Continued genetic characterization of glycogen storage disease type IV patients may aid in predicting clinical outcomes in these patients and may also help in identifying treatment strategies for this potentially devastating metabolic disorder.
Inferring Caravaggio's studio lighting and praxis in The calling of St. Matthew by computer graphics modeling (2010)

We explored the working methods of the Italian Baroque master Caravaggio through computer graphics reconstruction of his studio, with special focus on his use of lighting and illumination in <i>The calling of St. Matthew</i>. Although he surely took artistic liberties while constructing this and other works and did not strive to provide a "photographic" rendering of the tableau before him, there are nevertheless numerous visual clues to the likely studio conditions and working methods within the painting: the falloff of brightness along the rear wall, the relative brightness of the faces of figures, and the variation in sharpness of cast shadows (i.e., umbrae and penumbrae). We explored two studio lighting hypotheses: that the primary illumination was local (and hence artificial) and that it was distant solar. We find that the visual evidence can be consistent with local (artificial) illumination if Caravaggio painted his figures separately, adjusting the brightness on each to compensate for the falloff in illumination. Alternatively, the evidence is consistent with solar illumination only if the rear wall had particular reflectance properties, as described by a bi-directional reflectance distribution function, BRDF. (Ours is the first research applying computer graphics to the understanding of artists' praxis that models subtle reflectance properties of surfaces through BRDFs, a technique that may find use in studies of other artists.) A somewhat puzzling visual feature-unnoted in the scholarly literature-is the upward-slanting cast shadow in the upper-right corner of the painting. We found this shadow is naturally consistent with a local illuminant passing through a small window perpendicular to the viewer's line of sight, but could also be consistent with solar illumination if the shadow was due to a slanted, overhanging section of a roof outside the artist's studio. Our results place likely conditions upon any hypotheses concerning Caravaggio's working methods and point to new sources of evidence that could be confirmed or disconfirmed by future art historical research.
ChemInform Abstract: MECHANISM OF ONE‐ELECTRON ELECTROCHEMICAL REDUCTIVE CLEAVAGE REACTIONS OF SULFONIUM SALTS (1984)

Abstract Für die irreversible Titelreaktion der Sulfoniumionen (I) ′ergeben sich Peak‐Potentiale, die einen ausgeprägten Gang mit der Elektronegativität der entstehenden Radikale zeigen, wobei die Abweichungen bis zu l.4V betragen.
Effect of Ar and N 2 plasma etching on adhesion between mold resin and sputtered Cu in semiconductor electromagnetic shielding (2023)

AbstractIn recent years, there has been growing demand for processes to form electromagnetic shielding films on the periphery of semiconductor packages, and shielding films are increasingly being formed by sputter deposition methods with stable processes. However, little consideration has been given to the adhesion mechanism between the mold resin and sputtered Cu film formed on the semiconductor devices. In this study, Cu films were sputtered on mold resin with different etching conditions, and X-ray photoelectron spectroscopy was used to analyze the state of the interface, which affects adhesion. The color difference of the mold resin surface under different Ar and N2 etching conditions was also evaluated. Excellent adhesion between the mold resin and sputtered Cu was achieved under a high flow rate for Ar + N2 etching. The amount of Si (SiO2) exposed on the mold resin surface was correlated with the color difference. We proposed a mechanism in which amino groups in particular were formed on the surface of the mold resin, the resin etching rate increased, and the amount of SiO2 exposed increased. Functional groups, especially amino groups, were also formed on the SiO2 surface by N2 plasma. Cuσ+ in the sputtered film and Nσ- formed on the SiO2 surface adhered to each other through polar interactions.Keywords: Sputteringmold resinCuAr + N2 etchingadhesionXPS analysis AcknowledgementsThe authors would like to thank Mr. Kiyokazu Okada, Mr. Hirohisa Iizuka, and Mr. Chiaki Takubo (Kioxia Corporation) for excellent advice and useful information.Disclosure statementThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.Data availability statementThe data that support the findings of this study are available from the corresponding author, S.H., upon reasonable request.Additional informationFundingThis work did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
CIDER: An Expressive, Nonlocal Feature Set for Machine Learning Density Functionals with Exact Constraints (2022)

Machine learning (ML) has recently gained attention as a means to develop more accurate exchange-correlation (XC) functionals for density functional theory, but functionals developed thus far need to be improved on several metrics, including accuracy, numerical stability, and transferability across chemical space. In this work, we introduce a set of nonlocal features of the density called the CIDER formalism, which we use to train a Gaussian process model for the exchange energy that obeys the critical uniform scaling rule for exchange. The resulting CIDER exchange functional is significantly more accurate than any semilocal functional tested here, and it has good transferability across main-group molecules. This work therefore serves as an initial step toward more accurate exchange functionals, and it also introduces useful techniques for developing robust, physics-informed XC models via ML.
Effects of Environmental Factors and Metallic Electrodes on AC Electrical Conduction Through DNA Molecule (2017)

This model explains clearly the mechanism of charge transfer mechanism in the DNA, and it sheds light on why the charge transfer through the DNA can lead to insulating, semiconducting, or metallic behavior on the same time. The model considers charges on DNA, in the extended bands, either could be free to move under electric field or localized in potential wells/hills. Localization of charges in DNA is an intrinsic structural-property of this solitaire molecule. At all temperatures, the expected increase in thermal-induced charge is attributed to the delocalization of holes (or/and electrons) in potential hills (or/and potential wells) which accurately accounts for the total electric and dielectric behavior through DNA molecule. We succeeded to fit the experimental data to the proposed model with reasonable magnitudes of potential hills/wells that are in the energy range from 0.068 eV.
Orientation Estimation for Multiple Large Fractures by Scattering Energy (2006)

We have done the numerical modeling of seismic response to multiple sets of vertical large fractures by using finite-difference method (FD), which can easily handle media with monoclinic anisotropy. We consider three types of fracture distributions: a set of parallel fractures, two sets of orthogonal fractures and two sets of non-orthogonal fractures intersecting at 45 degrees. We address the seismic scattering response to large fractures by using a 3-layer model and a 5-layer model, where a fractured reservoir is in the middle layer of these two models. Seismic scattered energy is analyzed by the Scattering Index (SI) method to estimate the orientation of these multiple fractures. In both models, SI indicates the correct orientation of the two orthogonal fracture sets but is ambiguous for non-orthogonal fracture sets. Information about the fracture spacing and compliance can also be extracted from the azimuthal SI in some situations. More compliant fracture sets result in higher SI values while the relationship between fracture spacing and SI depends on the source wavelength. Variations in the SI energy can be caused by fracture spacing and compliance variations, and these relationships need further investigation. 1.
Titanium Clip Ball Joint (2011)

The experimental data show that the new modified prosthesis headplate fulfills the requirements necessary for sound transmission. The joint allows the plate to follow movements of the tympanic membrane. This characteristic in conjunction with the proven clip design ensure for optimal prosthesis placement and effectiveness.
Threading a linear molecule through a macrocycle thanks to boron (2023)

A [2]pseudorotaxane was synthesized by threading a BoDiPy through a macrocycle bearing a 2,2’-biphenol unit, showing thus the ability of boron to act as a gathering atom. The new interlocked species was characterized by 1D and 2D NMR spectroscopy as well as by X-ray crystallography. It exhibited interesting fluorescence features with a high quantum yield of 93%.