gebhart/patrepeval huggingface dataset:
Pore Filling of Spiro‐OMeTAD in Solid‐State Dye‐Sensitized Solar Cells Determined Via Optical Reflectometry (2012)

Abstract A simple strategy is presented to determine the pore‐filling fraction of the hole‐conductor 2,2‐7,7‐tetrakis‐ N , N ‐di‐pmethoxyphenylamine‐9,9‐spirobifluorene (spiro‐OMeTAD) into mesoporous photoanodes in solid‐state dye‐sensitized solar cells (ss‐DSCs). Based on refractive index determination by the film's reflectance spectra and using effective medium approximations the volume fractions of the constituent materials can be extracted, hence the pore‐filling fraction quantified. This non‐destructive method can be used with complete films and does not require detailed model assumptions. Pore‐filling fractions of up to 80% are estimated for optimized solid‐state DSC photoanodes, which is higher than that previously estimated by indirect methods. Additionally, transport and recombination lifetimes as a function of the pore‐filling fraction are determined using photovoltage and photocurrent decay measurements. While extended electron lifetimes are observed with increasing pore‐filling fractions, no trend is found in the transport kinetics. The data suggest that a pore‐filling fraction of greater than 60% is necessary to achieve optimized performance in ss‐DSCs. This degree of pore‐filling is even achieved in 5 μm thick mesoporous photoanodes. It is concluded that pore‐filling is not a limiting factor in the fabrication of “thick” ss‐DSCs with spiro‐OMeTAD as the hole‐conductor.
Nucleotide sequence of the HU-1 gene ofSalmonella typhimurium (1988)

Journal Article Nucleotide sequence of the HU-1 gene of Salmonella typhimurium Get access Maren Marsh, Maren Marsh The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar David R. Hillyard David R. Hillyard The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 14, 25 July 1988, Page 7196, https://doi.org/10.1093/nar/16.14.7196 Published: 25 July 1988 Article history Received: 25 May 1988 Published: 25 July 1988
Rapid Reversal of Cognitive Decline, Olfactory Dysfunction, and Quality of Life Using Multi-Modality Photobiomodulation Therapy: Case Report (2019)

<b><i>Objective:</i></b> We present a case report of reversal of cognitive impairment, olfactory dysfunction, and quality of life measures in a patient with cognitive decline after multi-modality photobiomodulation (PBM) therapy. <b><i>Background:</i></b> Transcranial and intranasal PBM has been introduced as a light-based therapeutic technique in which exposure to low levels of red to near-infrared (NIR) light stimulates neuronal function, leading to beneficial neurological effects. <b><i>Materials and methods:</i></b> Patient received twice-daily PBM therapy at home using three different wearable light-emitting diode (LED) devices. For the first week containing a mixture of continuous wave mode red (635 nm) and NIR (810 nm) LEDs, a prototype transcranial light helmet and a body pad were used. The body pad was placed on various areas on the lower back and the helmet was worn while seated. After the first week of treatment, an intranasal LED device, 10-Hz pulsed wave mode NIR (810 nm), was initiated in the left nostril twice daily. All three devices were applied simultaneously for an irradiation time of 25 min per session. <b><i>Results:</i></b> The patient showed a significant improvement in the Montreal Cognitive Assessment score from 18 to 24 and in the Working Memory Questionnaire score from 53 to 10. The cognitive enhancement was accompanied by reversal of olfactory dysfunction as measured by the Alberta Smell Test and peanut butter odor detection test. Quality-of-life measures improved and caregiver stress was reduced. No adverse effects were reported. <b><i>Conclusions:</i></b> PBM therapy may be a promising noninvasive approach for patients with neurodegenerative diseases.
High resolution parallel optical coherence tomography in scattering samples (2001)

Parallel optical coherence tomography in scattering samples is demonstrated using a 58 by 58 smart-pixel detector array. A femtosecond mode-locked Ti:Sapphire laser in combination with a free space Michelson interferometer was employed to achieve 4μm longitudinal resolution and 9μm transverse resolution on a 260×260 μm 2 field of view. We imaged a resolution target covered by an intralipid solution with different scattering coefficients as well as onion cells.
Burner Rig Evaluation of Ceramic Coatings With Vanadium-Contaminated Fuels (1989)

The performance of yttria stabilized zirconia (YSZ), ceria stabilized zirconia (CSZ), and magnesia stabilized zirconia (MSZ) coatings was evaluated using an atmospheric burner rig; the test environment contained compounds of vanadium, sodium and sulfur. The coatings were deposited by plasma spraying and electron beam physical vapor deposition (EB-PVD); sputtered sealant layers of hafnia, alumina and platinum were deposited on the yttria stabilized zirconia coating (YSZ). The tests were performed for up to 500 hours at 1650°F and 1300°F. The tests were designed to simulate the deposit chemistry and sulfur trioxide partial pressures expected in a marine gas turbine engine operating on contaminated fuel. YSZ, CSZ, and MSZ coatings all underwent reaction in the burner rig environment; the reaction products and their effects on spallation were varied. MSZ was by far the most reactive, readily forming MgSO4 in both 1650°F and 1300°F tests. The observed reaction products provided a measure of “protection” for the bond coat by preventing molten salt infiltration in the duration of the test. The mechanism of ceramic spallation is discussed. Sputtered overlayers of platinum, hafnia and alumina did not prevent salt infiltration and reaction with the underlying ceramic, although no reaction product between the overlayer and the salt was observed.
Improved Ponderomotive Guiding Center Algorithm (2007)

The original implementation of the ponderomotive guiding center algorithm is not suitable for modeling the propagation of short laser pulses over long distances. An improved algorithm is given, which improves the accuracy of the calculation, allowing much longer propagation distances to be modeled.
Epigenetic Changes and Functional Study of HOXA11 in Human Gastric Cancer (2015)

Aim: To examine epigenetic changes and the function of HOXA11 in human gastric cancer (GC). Materials & methods: Seven GC cell lines, five cases of normal gastric mucosa and 112 cases primary GC samples were used in this study. Results: Expression of HOXA11 and lack of promoter region methylation were found in NCI-N87, MKN45, BGC823 and HGC27 cells. Loss of expression and complete methylation were found in AGS gastric cancer cells. Reduced expression and partial methylation were found in MGC803 and SGC7901 cells. Restoration of HOXA11 expression was induced by 5-aza-2′-deoxycytidine. HOXA11 was methylated in 81.25% (91/112) of primary GCs. The presence of methylation was associated with male gender, tumor size, tumor differentiation and lymph node metastasis (all p < 0.05). Restoration of HOXA11 expression reduced cell proliferation, invasion, migration and induced apoptosis and G2/M phase arrest. HOXA11 was found to inhibit Wnt signaling by upregulating NKD1 expression. Conclusion: Epigenetic silencing of HOXA11 promotes GC proliferation, migration and invasion through activation of Wnt signaling.
“We are looking at the future right now”: community acceptability of a home-based viral load test device in the context of HIV cure-related research with analytical treatment interruptions in the United States (2022)

If proven effective, the home-based viral load test device will become a critical adjunct in HIV cure research and HIV care.
Relapse after bone marrow transplantation: evidence for distinct immunological mechanisms between adult and paediatric populations (2000)

Donor lymphocyte infusions are particularly effective for remission induction in malignant cells in patients who relapse after allogeneic progenitor cell transplantation (PCT) and who remain sensitive to the administration of unprimed donor T and/or natural killer (NK) cells present in donor lymphocyte infusions. To determine whether relapse after unmanipulated PCT could be ascribed to donor T and/or NK cell loss or tolerization, we evaluated the chimeric status of 81 patients with haematological malignancies who were receiving allogeneic unmanipulated PCT. The incidence of mixed chimaerism (MC) in unfractionated mononuclear leucocyte samples decreased rapidly after transplant, and was not detectable 4 months after PCT, even in patients who subsequently relapsed. The chimeric status of immune effector cell subsets was then evaluated in 15 patients at the time of relapse. All adults demonstrated complete donor haematopoiesis (CDH) for all cell lineages, whereas T- and NK-cell MC was only found in patients younger than age 13 years (P = 0.004). MC was not found in T nor NK cells of a control group consisting of age-matched paediatric patients in remission after allogeneic PCT. Thus, in adults, T and NK cell MC disappears early after unmanipulated allogeneic PCT and is absent at the time of relapse. However, the identification of donor T and NK cell loss in the paediatric relapsed but not remission patients suggests a distinct mechanism of relapse.
Data from Delineating the RAS Conformational Landscape (2023)

&lt;div&gt;Abstract&lt;p&gt;Mutations in RAS isoforms (KRAS, NRAS, and HRAS) are among the most frequent oncogenic alterations in many cancers, making these proteins high priority therapeutic targets. Effectively targeting RAS isoforms requires an exact understanding of their active, inactive, and druggable conformations. However, there is no structural catalog of RAS conformations to guide therapeutic targeting or examining the structural impact of RAS mutations. Here we present an expanded classification of RAS conformations based on analyses of the catalytic switch 1 (SW1) and switch 2 (SW2) loops. From 721 human KRAS, NRAS, and HRAS structures available in the Protein Data Bank (206 RAS–protein cocomplexes, 190 inhibitor-bound, and 325 unbound, including 204 WT and 517 mutated structures), we created a broad conformational classification based on the spatial positions of Y32 in SW1 and Y71 in SW2. Clustering all well-modeled SW1 and SW2 loops using a density-based machine learning algorithm defined additional conformational subsets, some previously undescribed. Three SW1 conformations and nine SW2 conformations were identified, each associated with different nucleotide states (GTP-bound, nucleotide-free, and GDP-bound) and specific bound proteins or inhibitor sites. The GTP-bound SW1 conformation could be further subdivided on the basis of the hydrogen bond type made between Y32 and the GTP γ-phosphate. Further analysis clarified the catalytic impact of G12D and G12V mutations and the inhibitor chemistries that bind to each druggable RAS conformation. Overall, this study has expanded our understanding of RAS structural biology, which could facilitate future RAS drug discovery.&lt;/p&gt;Significance:&lt;p&gt;Analysis of &gt;700 RAS structures helps define an expanded landscape of active, inactive, and druggable RAS conformations, the structural impact of common RAS mutations, and previously uncharacterized RAS inhibitor–binding modes.&lt;/p&gt;&lt;/div&gt;
Active repression by RARγ signaling is required for vertebrate axial elongation (2014)

Retinoic acid receptor gamma 2 (RARγ2) is the major RAR isoform expressed throughout the caudal axial progenitor domain in vertebrates. During a microarray screen to identify RAR targets, we identified a subset of genes that pattern caudal structures or promote axial elongation and are upregulated by increased RAR-mediated repression. Previous studies have suggested that RAR is present in the caudal domain, but is quiescent until its activation in late stage embryos terminates axial elongation. By contrast, we show here that RARγ2 is engaged in all stages of axial elongation, not solely as a terminator of axial growth. In the absence of RA, RARγ2 represses transcriptional activity in vivo and maintains the pool of caudal progenitor cells and presomitic mesoderm. In the presence of RA, RARγ2 serves as an activator, facilitating somite differentiation. Treatment with an RARγ-selective inverse agonist (NRX205099) or overexpression of dominant-negative RARγ increases the expression of posterior Hox genes and that of marker genes for presomitic mesoderm and the chordoneural hinge. Conversely, when RAR-mediated repression is reduced by overexpressing a dominant-negative co-repressor (c-SMRT), a constitutively active RAR (VP16-RARγ2), or by treatment with an RARγ-selective agonist (NRX204647), expression of caudal genes is diminished and extension of the body axis is prematurely terminated. Hence, gene repression mediated by the unliganded RARγ2-co-repressor complex constitutes a novel mechanism to regulate and facilitate the correct expression levels and spatial restriction of key genes that maintain the caudal progenitor pool during axial elongation in Xenopus embryos.
Sustained activation of ERK1/2 MAPK in Schwann cells causes corneal neurofibroma (2017)

Recent studies have shown that constitutive activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) in Schwann cells (SCs) increases myelin thickness in transgenic mice. In this secondary analysis, we report that these transgenic mice develop a postnatal corneal neurofibroma with the loss of corneal transparency by age six months. We show that expansion of non-myelinating SCs, under the control of activated ERK1/2, also drive myofibroblast differentiation that derives from both SC precursors and resident corneal keratocytes. Further, these mice also harbor activated mast cells in the central cornea, which contributes to pathological corneal neovascularization and fibrosis. This breach of corneal avascularity and immune status is associated with the growth of the tumor pannus, resulting in a corneal stroma that is nearly four times its normal size. In corneas with advanced disease, some axons became ectopically myelinated, and the disruption of Remak bundles is evident. To determine whether myofibroblast differentiation was linked to vimentin, we examined the levels and phosphorylation status of this fibrotic biomarker. Concomitant with the early upregulation of vimentin, a serine 38-phosphorylated isoform of vimentin (pSer38vim) increased in SCs, which was attributed primarily to the soluble fraction of protein-not the cytoskeletal portion. However, the overexpressed pSer38vim became predominantly cytoskeletal with the growth of the corneal tumor. Our findings demonstrate an unrecognized function of ERK1/2 in the maintenance of corneal homeostasis, wherein its over-activation in SCs promotes corneal neurofibromas. This study is also the first report of a genetically engineered mouse that spontaneously develops a corneal tumor.
Studies on glyoxalase inhibitor isolation of a new active agent, MS-3, from a nushroom culture. (1975)

Cultured broths were screened by measuring the inhibition of glyoxalse, using 105, 000g supernatant of rat liver homogenates as a crude enzyme. An active agent, MS-3 (C21H24O7), was isolated from a cultured mushroom. ID50 value of MS-3 against the crude glyoxalase was 12 mcg/ml. MS-3 has low toxicity and inhibited the growth of Yoshida rat sarcoma cells in cell culture. The production, isolation, and properties of MS-3 are described.
Simplified Transient Model of DFIG Wind Turbine for COI Frequency Dynamics and Frequency Spatial Variation Analysis (2023)

With the high penetration level of renewable power generation, their impacts on the power system frequency dynamics need to be considered, especially the doubly-fed induction generator (DFIG) based wind turbines. By analogy with the synchronous generator, this article proposes the simplified transient model of DFIG wind turbines, which consists of the equivalent circuit model and the equivalent rotor motion model. It provides a viable and tractable way to analytically quantify the contribution of DFIG wind turbines to the post-disturbance frequency, both in the center of inertia (COI) frequency and frequency spatial variation cases. The unique frequency-supporting features of the DFIG wind turbine are discussed. The model implementation at the wind farm level is provided. The correctness of the proposed model is verified by simulation results of a weak power system. The comparison with the existing models on frequency dynamics analysis is discussed.
Divide and Conquer: Sub-Grouping of ASD Improves ASD Detection Based on Brain Morphometry (2016)

Low success (<60%) in autism spectrum disorder (ASD) classification using brain morphometry from the large multi-site ABIDE dataset and inconsistent findings on brain morphometric abnormalities in ASD can be attributed to the ASD heterogeneity. In this study, we show that ASD brain morphometry is highly heterogeneous, and demonstrate that the heterogeneity can be mitigated and classification improved if autism severity (AS), verbal IQ (VIQ) and age are used with morphometric features. Morphometric features from structural MRIs (sMRIs) of 734 males (ASD: 361, controls: 373) of ABIDE were derived using FreeSurfer. Applying the Random Forest classifier, an AUC of 0.61 was achieved. Adding VIQ and age to morphometric features, AUC improved to 0.68. Sub-grouping the subjects by AS, VIQ and age improved the classification with the highest AUC of 0.8 in the moderate-AS sub-group (AS = 7-8). Matching subjects on age and/or VIQ in each sub-group further improved the classification with the highest AUC of 0.92 in the low AS sub-group (AS = 4-5). AUC decreased with AS and VIQ, and was the lowest in the mid-age sub-group (13-18 years). The important features were mainly from the frontal, temporal, ventricular, right hippocampal and left amygdala regions. However, they highly varied with AS, VIQ and age. The curvature and folding index features from frontal, temporal, lingual and insular regions were dominant in younger subjects suggesting their importance for early detection. When the experiments were repeated using the Gradient Boosting classifier similar results were obtained. Our findings suggest that identifying brain biomarkers in sub-groups of ASD can yield more robust and insightful results than searching across the whole spectrum. Further, it may allow identification of sub-group specific brain biomarkers that are optimized for early detection and monitoring, increasing the utility of sMRI as an important tool for early detection of ASD.
Using covariance matrices for unsupervised texture segmentation (2008)

In this paper we propose an efficient unsupervised texture segmentation method. We introduce a texture extension of a state-of-the-art color segmentation algorithm. We show how to use covariance matrices of low level features for texture description. These features are efficiently calculated using integral images. Furthermore, a multi-scale extension allows to provide accurate texture segmentation results. An experimental evaluation on a synthetic texture database and images of the Berkeley image database demonstrate the improved performance of the algorithm.
Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target (2013)

The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To study the transcriptional impact of NKX2-1 amplification, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma and analyzed DNA-binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation. Integration of these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1. Further cistromic and overexpression analyses indicated that NKX2-1 can cooperate with the forkhead box transcription factor FOXA1 to regulate LMO3 gene expression. RNAi analysis of NKX2-1-amplified cells compared with nonamplified cells demonstrated that LMO3 mediates cell survival downstream from NKX2-1. Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transcriptional signal transducer in NKX2-1-amplified lung adenocarcinomas.
Unsupervised Depth Completion from Inertial Odometry and Vision (2019)

We describe a method to infer dense depth from camera motion and sparse depth
as estimated using a visual-inertial odometry system. Unlike other scenarios
using point clouds from lidar or structured light sensors, we have few hundreds
to few thousand points, insufficient to inform the topology of the scene. Our
method first constructs a piecewise planar scaffolding of the scene, and then
uses it to infer dense depth using the image along with the sparse points. We
use a predictive cross-modal criterion, akin to `self-supervision,' measuring
photometric consistency across time, forward-backward pose consistency, and
geometric compatibility with the sparse point cloud. We also launch the first
visual-inertial + depth dataset, which we hope will foster additional
exploration into combining the complementary strengths of visual and inertial
sensors. To compare our method to prior work, we adopt the unsupervised KITTI
depth completion benchmark, and show state-of-the-art performance on it.
RAPID, MULTISTEP DNA HYBRIDISATION IN CONTINUOUS FLOW. (2010)

We present a microfluidic platform for performing fast, continuous flow DNA hybridisation on magnetic particles. Laminar flow streams containing sample oligonucleotides, washing buffer, fluorescently labelled oligonucleotides and washing buffer, were generated in the chamber of a microfluidic chip. Magnetic particles were then introduced into the chamber, and pulled through each of the streams by a permanent magnet placed opposite the particle inlet. DNA hybridisation was successfully performed, as determined by resulting increased fluorescence of the particles. A non-complementary sequence did not yield any signal, showing non-specific binding was minimal. The whole procedure required only several minutes, a significant reduction compared to conventional methods. A detection limit of 20 nM was achieved.
Grating-based X-ray phase contrast for biomedical imaging applications (2013)

In this review article we describe the development of grating-based X-ray phase-contrast imaging, with particular emphasis on potential biomedical applications of the technology. We review the basics of image formation in grating-based phase-contrast and dark-field radiography and present some exemplary multimodal radiography results obtained with laboratory X-ray sources. Furthermore, we discuss the theoretical concepts to extend grating-based multimodal radiography to quantitative transmission, phase-contrast, and dark-field scattering computed tomography.
ChemInform Abstract: Selective Palladium‐Catalyzed Arylation of Ammonia: Synthesis of Anilines as well as Symmetrical and Unsymmetrical Di‐ and Triarylamines. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.