gebhart/patrepeval huggingface dataset:
SETDB1 Fuels the Lung Cancer Phenotype by Modulating Epigenome, 3D Genome Organization and Chromatin Mechanical Properties (2021)

Abstract Imbalance in the finely orchestrated system of chromatin-modifying enzymes is a hallmark of many pathologies such as cancers, since causing the affection of the epigenome and transcriptional reprogramming. Here, we demonstrate that a loss-of-function mutation (LOF) of the major histone lysine methyltransferase SETDB1 possessing oncogenic activity in lung cancer cells leads to broad changes in the overall architecture and mechanical properties of the nucleus through genome-wide redistribution of heterochromatin, which perturbs chromatin spatial compartmentalization. Together with the enforced activation of the epithelial expression program, cytoskeleton remodeling, reduced proliferation rate and restricted cellular migration, this leads to the reversed oncogenic potential of lung adenocarcinoma cells. These results emphasize an essential role of chromatin architecture in the determination of oncogenic programs and illustrate a relationship between gene expression, epigenome, 3D genome and nuclear mechanics.
CE‐ESI‐MS of biological anions in plastic capillaries at high pH (2007)

Abstract In this study, the potential of poly(methylmethacrylate) (PMMA, Plexiglas) and polyether ether ketone (PEEK) tubing for CE‐ESI‐MS separations of anions at high pH values was examined. A set of model compounds of biological interest was used to investigate the main operational parameters for CE‐ESI‐MS, such as the sheath‐flow interface design, the polarity of the ionization voltage, the use of ammonia‐based separation electrolytes, and the sheath liquid composition. Optimum separations and detection sensitivities in negative ESI mode were obtained using a running electrolyte of 75 mM of ammonia at pH 11 and a sheath liquid of 60:40 v/v or 75:25 v/v isopropanol/water with 0.5% v/v of ammonia. At these experimental conditions, PMMA and PEEK capillaries show good hydrolytic stabilities and lower EOF values than fused‐silica columns. Better separation resolutions were obtained with PMMA capillary, but this plastic rapidly swelled and bled because of its limited chemical resistance to the sheath liquid. PMMA columns equipped with a fused‐silica tip were used for a safer exposure to the sheath liquid, but the inner surface of the fused‐silica tips had limited stability at pH 11. On the other hand, good separations and reproducibility on migration times and peak areas were obtained using PEEK capillaries without capillary column deterioration.
Annex IV : public finance and the efficiency of urban development (1971)

This is a report on the economic status of Bombay and on the allocation of resources to the development of that city. Maps and statistical tables are provided.
Visualization of Light Propagation with Multifocal Intraocular Lenses Using the Ouzo Effect (2019)

The number of presbyopia correcting intraocular lenses (IOLs) is increasing and new technologies are constantly emerging with the aim of correcting the loss of accommodation after cataract surgery. Various optical designs have been proposed to implement multifocality or an extended depth of focus (EDOF). Depending on the optical principle of an implanted lens, the visual performance often is deteriorated by superposition of individual image planes and halos of varying intensity. This experimental study presents a concept to visualize the light fields and especially the halos of mono- and multifocal IOLs using the well known alcoholic beverage "ouzo" in order to obtain qualitative data on the imaging characteristics. We conclude that ouzo is a useful, cost effective, and nonpolluting medium for beam visualization and an alternative to fluorescein or milk, which could find an application for educational purposes.
An Effective Route to Highly Substituted Pyridines (1996)

A direct method is reported for synthesis of fused-ring 4-arylpyridines by condensation of cyclic ketones with β-arylenones and ammonium acetate in DMSO. The β-arylenones were prepared from corresponding ketones by condensation with aromatic aldehydes promoted by LiI (6 examples, 59-80 %) or by alumina (4 examples, 39-65 %). Several fused-ring terpyridyl derivatives were synthesized (6 examples, 41-66 %).
Wet anisotropic etching by TMAH with NCW-1002 surfactant on crystalline silicon surface (2008)

Paper reports the use of a new surfactant NCW-1002 as an addictive in TMAH wet anisotropic etching to improve the etching characteristic on three silicon principle planes (i.e. (100), (110), (111) planes). Concentrations of TMAH from 2.5% to 10% with addition of various concentration of NCW-1002 are studied to find an optimal combination for a improved smoothness and etch selectivity between (100) and (110) planes, which is necessary for the formation of 45&deg;mirror plane (110) in (100) silicon surface. Etch rate and roughness of silicon planes were measured by Dektak II and AFM respectively. Besides, this paper will explain the formation of 45&deg;slope. By improving the selectivity or extending the etching depth, we are able to enlarge the 45°portion on the mirror surface.
Electrostatic cylinder lenses II: Three element einzel lenses (1972)

For Pt. I see ibid., vol. 4, 625 of 1971 The potential distribution inside three equidiameter coaxial cylinders separated by finite distances has been used to calculate the focal lengths, mid focal lengths and spherical aberration coefficients of some triple cylinder einzel lenses. The lenses considered have the length of the middle cylinder equal to its diameter or to half its diameter. Data are presented for such lenses with the middle cylinder at either a higher or lower potential than the outer cylinders over a large range of voltage ratios.
Biomarkers for Monitoring Antiangiogenic Therapy (2007)

A variety of antiangiogenic agents are currently available for the treatment of renal cell carcinoma. With these exciting new therapeutic agents comes the challenge of elucidating useful biomarkers to monitor patients receiving these therapies. Although many patients benefit from antiangiogenic therapies, it is often by achieving stability of their disease. Thus, development of noninvasive biomarkers of disease response and relapse is a crucial objective to aid in the management of patients. The current technologies being explored in this field include circulating plasma proteins, cells, and nucleic acids and novel imaging techniques. Surrogate markers of angiogenesis could help with selecting patients for therapy, determining optimal dosing of therapy, deciding whether to change therapy, and assessing appropriate salvage therapy.
Supplementary Data from KRAS Inhibitor Resistance in <i>MET</i>-Amplified <i>KRAS</i><sup>G12C</sup> Non–Small Cell Lung Cancer Induced By RAS- and Non–RAS-Mediated Cell Signaling Mechanisms (2023)

Supplementary Data from KRAS Inhibitor Resistance in &lt;i&gt;MET&lt;/i&gt;-Amplified &lt;i&gt;KRAS&lt;/i&gt;&lt;sup&gt;G12C&lt;/sup&gt; Non–Small Cell Lung Cancer Induced By RAS- and Non–RAS-Mediated Cell Signaling Mechanisms
Nitric oxide induces hypoxia ischemic injury in the neonatal brain via the disruption of neuronal iron metabolism (2015)

We have recently shown that increased hydrogen peroxide (H2O2) generation is involved in hypoxia-ischemia (HI)-mediated neonatal brain injury. H2O2 can react with free iron to form the hydroxyl radical, through Fenton Chemistry. Thus, the objective of this study was to determine if there was a role for the hydroxyl radical in neonatal HI brain injury and to elucidate the underlying mechanisms. Our data demonstrate that HI increases the deposition of free iron and hydroxyl radical formation, in both P7 hippocampal slice cultures exposed to oxygen-glucose deprivation (OGD), and the neonatal rat exposed to HI. Both these processes were found to be nitric oxide (NO) dependent. Further analysis demonstrated that the NO-dependent increase in iron deposition was mediated through increased transferrin receptor expression and a decrease in ferritin expression. This was correlated with a reduction in aconitase activity. Both NO inhibition and iron scavenging, using deferoxamine administration, reduced hydroxyl radical levels and neuronal cell death. In conclusion, our results suggest that increased NO generation leads to neuronal cell death during neonatal HI, at least in part, by altering iron homeostasis and hydroxyl radical generation.
Thermodynamics of the denaturation of lysozyme by guanidine hydrochloride. I. Dependence on pH at 25° (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermodynamics of the denaturation of lysozyme by guanidine hydrochloride. I. Dependence on pH at 25°Kirk C. Aune and Charles TanfordCite this: Biochemistry 1969, 8, 11, 4579–4585Publication Date (Print):November 1, 1969Publication History Published online1 May 2002Published inissue 1 November 1969https://pubs.acs.org/doi/10.1021/bi00839a052https://doi.org/10.1021/bi00839a052research-articleACS PublicationsRequest reuse permissionsArticle Views1592Altmetric-Citations205LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Design of Location Information Management System in Positioning Systems (2007)

In ubiquitous environment, user devices are enabling to connect networks without any restrictions on accessible location. Moreover, ubiquitous environment provides a wide range of contents and services to users by the location throughout wire/wireless communication network. It is an essential technologies which can sense and track present location of users. As various positioning systems have a unique technology of sensing user location and characteristics, each produces location-data with a different type [1, 2]. Hence, it uses not only different standard technologies and classifications for expressing and categorizing the data, but also devices and applications dependent with the system. This paper proposes an integrated model to solve problems of different standards according to different location- data type from various positioning systems. The integrated model does not redefine metadata of location data expressed by different types, but is a classification model that includes metadata including all the types. This study shows an interoperability of integrated model between heterogeneous metadata, and a prototype of Location Information Management System to manage multimedia files created by positioning systems.
Cyclic Separation Processes (1974)

Abstract This review covers cyclic separation methods used for adsorption, ion exchange, and chromatographic separation processes where the cyclic parameter is a thermodynamic variable which changes the equilibrium distribution coefficients of the solutes. The cyclic methods reviewed include heatless or pressure-swing adsorption, parametric pumping, and cycling zone adsorption. These cyclic techniques have been studied as a possible preparative chromatographic separation method or for continuous production from adsorption or ion exchange columns.
Hypoplasia of Terminal Bile Ducts (1970)

The presence of an uncommon birth defect characterized by an absence of bile ducts from the portal areas in the more peripheral portions of the liver in two male infants of the same family could be mere coincidence, yet the possibility that this anomaly could be hereditary in this family cannot be excluded. Bile duct anomalies such as congenital obliteration of the common bile duct and congenital hepatic fibrosis have already been reported in two or more members of the same family.
(3R,4S,7S)-trans, trans-3,7-Dimethyl-1,8,8-tribromo-3,4,7-trichloro-1,5-octadiene, a novel monoterpene from the sea hare, Aplysia californica (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT(3R,4S,7S)-trans, trans-3,7-Dimethyl-1,8,8-tribromo-3,4,7-trichloro-1,5-octadiene, a novel monoterpene from the sea hare, Aplysia californicaD. John. Faulkner, Martha O. Stallard, Jose. Fayos, and Jon. ClardyCite this: J. Am. Chem. Soc. 1973, 95, 10, 3413–3414Publication Date (Print):May 1, 1973Publication History Published online1 May 2002Published inissue 1 May 1973https://pubs.acs.org/doi/10.1021/ja00791a073https://doi.org/10.1021/ja00791a073research-articleACS PublicationsRequest reuse permissionsArticle Views195Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Phenotypic characterization of hepatic proliferation. Antigenic expression by proliferating epithelial cells in fetal liver, massive hepatic necrosis, and nodular transformation of the liver. (1983)

Different forms of hepatocellular proliferation are seen in fetal livers, massive hepatic necrosis, and nodular transformation (nodular regenerative hyperplasia) of the liver. In an attempt to characterize the proliferating cells in these conditions, we studied the expression of several antigens by immunohistochemical methods. Alpha-fetoprotein (AFP), alpha 1-antitrypsin (AAT), a hepatocellular export protein, carcinoembryonic antigen (CEA), a marker of bile duct epithelial cells, and hepatitis B virus antigens (HBsAg, HBcAg), were localized by the peroxidase-antiperoxidase method in 11 fetal livers, 10 cases of nodular transformation, and 7 cases of massive hepatic necrosis. AFP was the most prevalent antigen in fetal hepatocytes. Many hyperplastic hepatocytes in nodular transformation contained AAT, but not oncofetal antigens, supporting the differentiated hepatocellular nature of these cells. A similar staining pattern was seen in two-cell-thick plates of hepatocytes in massive hepatic necrosis. In contrast, the ductlike structures at the periphery of necrotic lobules contained both AAT and CEA, suggesting that these cells exhibit features of hepatocytes and bile duct epithelial cells. Therefore, the appropriate term for these regenerating cells appears to be "ductular" or "biliary hepatocytes".
Design of Compact, Lightweight Power Transmission Devices for Specialized High Power Applications (2008)

&lt;div class="htmlview paragraph"&gt;The design of compact and lightweight power transmission devices was studied for specialized high power applications, including airborne with operating voltage fixed at 270 Volts and less than 30 meter length conductors. Only commercial-off-the-shelf components were considered for the design. It was found that by using superconducting wires operated at cryogenic temperatures instead of Cu conductors, a large increase of performance could be achieved; e.g. there is large reduction of heat loss; and for 5 MW-class or 20 kA power transmission there is a substantial reduction of weight of ∼ 80/kg per meter and an approximate 10x reduction of volume. A strong reduction of weight is achieved for &amp;gt; 1000 Amp power transmission.&lt;/div&gt;
Detecting stairs and pedestrian crosswalks for the blind by RGBD camera (2012)

A computer vision-based wayfinding and navigation aid can improve the mobility of blind and visually impaired people to travel independently. In this paper, we develop a new framework to detect and recognize stairs and pedestrian crosswalks using a RGBD camera. Since both stairs and pedestrian crosswalks are featured by a group of parallel lines, we first apply Hough transform to extract the concurrent parallel lines based on the RGB channels. Then, the Depth channel is employed to further recognize pedestrian crosswalks, upstairs, and downstairs using support vector machine (SVM) classifiers. Furthermore, we estimate the distance between the camera and stairs for the blind users. The detection and recognition results on our collected dataset demonstrate that the effectiveness and efficiency of our proposed framework.
Echocardiographic Assessment of the Right Heart in Mice (2013)

Transgenic and toxic models of pulmonary arterial hypertension (PAH) are widely used to study the pathophysiology of PAH and to investigate potential therapies. Given the expense and time involved in creating animal models of disease, it is critical that researchers have tools to accurately assess phenotypic expression of disease. Right ventricular dysfunction is the major manifestation of pulmonary hypertension. Echocardiography is the mainstay of the noninvasive assessment of right ventricular function in rodent models and has the advantage of clear translation to humans in whom the same tool is used. Published echocardiography protocols in murine models of PAH are lacking. In this article, we describe a protocol for assessing RV and pulmonary vascular function in a mouse model of PAH with a dominant negative BMPRII mutation; however, this protocol is applicable to any diseases affecting the pulmonary vasculature or right heart. We provide a detailed description of animal preparation, image acquisition and hemodynamic calculation of stroke volume, cardiac output and an estimate of pulmonary artery pressure.
FT-IR absorbance data for early detection of oil palm fungal disease infestation (2012)

Basal stem rot (BSR) is a serious fungal disease in oil palm plantations which potentially could reduce the market share of palm oil for Malaysia. Due to the preventing great losses in production and reducing the use of chemicals, early detection of Ganoderma fungal infection is critical for management of this disease. At present study, we propose to apply a mid-infrared spectroscopy technique for detection of infected oil palm trees at three stages of infection. Leaf samples of healthy, mild, moderate and sever-infected trees were measured using Fourier transform infrared (FTIR) spectrometers system to obtain absorbance data from the range of 2.55-25.05 μm. Single bounce ATR accessory with and without dilution with potassium bromide (KBr) were used in this study. Savitsky-Golay method was used for smoothing. The selected principal component (PC) scores were used as input features in quadratic discriminant analysis (QDA) as a pattern recognition algorithm. The results indicated that QDA-based algorithm can distinguish between healthy and infected leaves at three stages of infection with high classification accuracies (>80%) when leaves demonstrated that the proposed technique has the potential for early detection of the Ganoderma disease.
Exploration of jasmonate signalling via automated and standardized transient expression assays in tobacco cells (2005)

Although sequence information and genome annotation are improving at an impressive pace, functional ontology is still non-existent or rudimentary for most genes. In this regard, transient expression assays are very valuable for identification of short functional segments in particular pathways, because they can be performed rapidly and at a scale unattainable in stably transformed tissues. Vectors were constructed and protocols developed for systematic transient assays in plant protoplasts. To enhance throughput and reproducibility, protoplast treatments were performed entirely by a liquid-handling robot in multiwell plates, including polyethylene glycol/Ca2+ cell transfection with plasmid mixtures, washes and lysis. All transcriptional readouts were measured using a dual firefly/Renilla luciferase assay, in which the former was controlled by a reporter promoter and the latter by the 35S CaMV promoter, which served as internal normalization standard. The automated protocols were suitable for transient assays in protoplasts prepared from cell cultures of Nicotiana tabacum Bright Yellow-2 and Arabidopsis thaliana. They were implemented in a screen to discover potential regulators of genes coding for key enzymes in nicotine biosynthesis. Two novel tobacco transcription factors were found, NtORC1 and NtJAP1, that positively regulate the putrescine N-methyltransferase (PMT) promoter. In addition, combinatorial tests showed that these two factors act synergistically to induce PMT transcriptional activity. The development and use of high-throughput plant transient expression assays are discussed.
Irradiation-related ischemic heart disease. (1990)

An expectation for long-term survival has emerged among several groups of cancer patients treated with therapeutic irradiation (eg, Hodgkin's disease, early stage breast cancer). Therefore, the cardiovascular sequelae of thoracic irradiation have recently come under scrutiny. Animal models have demonstrated that cardiac irradiation can directly damage the myocardial microvasculature and can indirectly damage the coronary macrovasculature when coupled with cholesterol feeding. A clear association between thoracic radiotherapy and ischemic heart disease was observed among older clinical studies using radiotherapeutic techniques that are no longer optimal by today's standards. Such a relationship could not be confirmed in modern studies in which treatment factors (such as dose and volume of heart irradiated) were more carefully controlled.
Rendering of Constraints With Underactuated Haptic Devices (2020)

Several previous works have studied the application of proxy-based rendering algorithms to underactuated haptic devices. However, all these works make oversimplifying assumptions about the configuration of the haptic device, and they ignore the user's intent. In this article, we lift those assumptions, and we carry out a theoretical study that unveils the existence of unnatural ghost forces under typical proxy-based rendering. We characterize and quantify those ghost forces. In addition, we design a novel rendering strategy, with anisotropic coupling between the device and the proxy. With this strategy, the forces rendered by an underactuated device are a best match of the forces rendered by a fully actuated device. We have demonstrated our findings on synthetic experiments and a simple real-world experiment.