gebhart/patrepeval huggingface dataset:
Data from Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features of Ductal Carcinoma <i>In Situ</i> (2023)

&lt;div&gt;Abstract&lt;p&gt;Ductal carcinoma &lt;i&gt;in situ&lt;/i&gt; (DCIS) is a precursor to invasive breast cancer. The frequency of DCIS is increasing because of routine mammography; however, the biological features and intratumoral heterogeneity of DCIS remain obscure. To address this deficiency, we performed single-cell transcriptomic profiling of DCIS and invasive ductal carcinoma (IDC). DCIS was found to be composed of several transcriptionally distinct subpopulations of cancer cells with specific functions. Several transcripts, including long noncoding RNAs, were highly expressed in IDC compared with DCIS and might be related to the invasive phenotype. Closeness centrality analysis revealed extensive heterogeneity in DCIS, and the prediction model for cell-to-cell interactions implied that the interaction network among luminal cells and immune cells in DCIS was comparable with that in IDC. In addition, transcriptomic profiling of HER2&lt;sup&gt;+&lt;/sup&gt; luminal DCIS indicated HER2 genomic amplification at the DCIS stage. These data provide novel insight into the intratumoral heterogeneity and molecular features of DCIS, which exhibit properties similar to IDC.&lt;/p&gt;Significance:&lt;p&gt;Investigation of the molecular features of ductal carcinoma &lt;i&gt;in situ&lt;/i&gt; at single cell resolution provides new insights into breast cancer biology and identifies candidate therapeutic targets and diagnostic biomarkers.&lt;/p&gt;&lt;/div&gt;
The anti‐ageing potential of a new jasmonic acid derivative (LR2412): in vitro evaluation using reconstructed epidermis episkin™ (2012)

Jasmonic acid is involved in plant wound repair and tissue regeneration, but no study has been reported in human skin. The effect of a jasmonic acid derivative, tetra-hydro-jasmonic acid (LR2412, 1 and 10 μm) was investigated on an in vitro reconstructed skin model, Episkin™. Using real time RTQPCR studies, results showed an increase in hyaluronan synthase 2 (HAS2) and hyaluronase synthase 3 (HAS3) expression. Furthermore, an increase in hyaluronic acid (HA) deposits in basal and suprabasal layers of the epidermis was observed. The percentage of positive Ki67 keratinocytes in the basal layer as well as the epidermis thickness were seen to increase. Immunohistochemistry studies showed that the synthesis of late differentiation proteins filaggrin and transglutaminase 1 was not modified. The human epidermis is known to thin with age while HA content has been reported to decrease. These results illustrate the potential of LR2412 in counteracting signs of skin ageing.
Experimental determination and calculations of redox potential descriptors of compounds directed against retroviral zinc fingers: Implications for rational drug design (2001)

A diverse set of electrophilic compounds that react with cysteine thiolates in retroviral nucleocapsid (NC) proteins and abolish virus infectivity has been identified. Although different in chemical composition, these compounds are all oxidizing agents that lead to the ejection of Zn(II) ions bound to conserved structural motifs (zinc fingers) present in retroviral NC proteins. The reactivity of a congeneric series of aromatic disulfides toward the NC protein of the human immunodeficiency virus type 1 (HIV-1), NCp7, has been characterized by HPLC separation of starting reagents from reaction products. We calculated the absolute redox potentials of these compounds in the gas phase and in aqueous solvent, using a density functional theory method and a continuum solvation model. Pulsed polarography experiments were performed and showed a direct correlation between calculated and experimentally determined redox propensities. A dependence between protein reactivity and redox potential for a specific compound was shown: Reaction with NCp7 did not take place below a threshold value of redox potential. This relationship permits the distinction between active and nonactive compounds targeted against NCp7, and provides a theoretical basis for a scale of reactivity with retroviral zinc fingers. Our results indicate that electrophilic agents with adequate thiophilicity to react with retroviral NC fingers can now be designed using known or calculated electrochemical properties. This may assist in the design of antiretroviral compounds with greater specificity for NC protein. Such electrophilic agents can be used in retrovirus inactivation with the intent of preparing a whole-killed virus vaccine formulation that exhibits unaffected surface antigenic properties.
Functional analysis of new transporters involved in stress tolerance in Pseudomonas putida DOT‐T1E (2009)

Pseudomonas putida DOT-T1E is a highly solvent-tolerant strain. Although the main mechanism that confers solvent tolerance to the strain is the TtgGHI efflux pump, a number of other proteins are also involved in the response to toluene. Previous proteomic and transcriptomic analysis carried out in our lab with P. putida DOT-T1E, and the solvent-sensitive strain, P. putida KT2440, revealed several transporters that were induced in the presence of toluene. We prepared five mutants of the corresponding genes in P. putida DOT-T1E and analysed their phenotypes with respect to solvent tolerance, stress endurance and growth with different carbon, nitrogen and sulfur sources. The data clearly demonstrated that two transporters (Ttg2ABC and TtgK) are involved in multidrug resistance and toluene tolerance, whereas another (homologous to PP0219 of P. putida KT2440) is a sulfate/sulfite transporter. No clear function could be assigned to the other two transporters. Of the transporters shown to be involved in toluene tolerance, one (ttg2ABC) belongs to the ATP-Binding Cassette (ABC) family, and is involved in multidrug resistance in P. putida DOT-T1E, while the other belongs to the Major Facilitator Superfamily and exhibits homology to a putative transporter of the Bcr/CflA family that has not previously been reported to be involved in toluene tolerance.
Semipolar {2021} GaN Edge-Emitting Laser Diode on Epitaxial Lateral Overgrown Wing (2021)

Edge-emitting laser diodes (LDs) were fabricated on a reduced dislocation density epitaxial lateral overgrown (ELO) wing of a semipolar {202 1} GaN substrate, termed an ELO wing LD. Two types of facet feasibility studies were conducted: (1) "handmade" facets, wherein lifted-off ELO wing LDs were cleaved manually, and (2) facets formed on wafers through reactive ion etching (RIE). Pulsed operation electrical and optical measurements confirmed the laser action in the RIE facet LDs with a threshold current of ~19 kAcm -2 and maximum light output power of 20 mW from a single uncoated facet. Handmade facet devices showed spontaneous, LED-like emission, confirming device layers remain intact after mechanical liftoff.
B cell development (PP-030) (2010)

Mammalian TOR is a key component of a signaling pathway that integrates inputs from nutrients and growth factors to regulate cell growth and metabolism.Because disruption of the mouse mTOR gene leads to early postimplantation lethality, we generated a mouse knockdown model, which recapitulates mTOR inhibition by drugs.Neo insertion interrupts transcription, leading to a 70% reduction in mTOR expression.The homozygous knockdown mice exhibit reductions in body, organ and cell size.Spleens are disproportionately smaller relative to overall body weight than other organs.Cell proliferation was decreased in splenic B cells.LPS-induced proliferation in B cells was reduced.Splenic B cell populations had more mature cells (IgDhi CD21+ IgM-), with fewer transitional cells (IgDhiIgMhi), and markedly reduced marginal zone B cells (IgDlowCD21hiIgMhi). Phosphorylation of AKT was increased in B cells after LPS stimulation, similar to what has been reported in PBMCs receiving long-term rapamycin treatment.B220+ B cells were decreased in bone marrow and alterations were seen in pre-B cell maturation.Antibody production, germinal center formation and class switch recombination were compromised in the mTOR knockdown mice.These data suggest that mTOR plays a role in the maturation and differentiation of B cell lineages, as well as in the regulation of immune responses.
Small nuclei identification with a hemispherical brain PET (2022)

This was the first time that the raphe nuclei, anterior nuclei, and dorsomedial nuclei were successfully visualised using the first hemispherical brain PET. TRIAL REGISTRATION : Japan Registry of Clinical Trials, jRCTs032210086, Registered 13 May 2021, https://jrct.niph.go.jp/latest-detail/jRCTs032210086 .
Alcohol Oxidase and Catalase in Peroxisomes of Methanol-Grown Candida boidinii (1975)

Microbodies, designated as peroxisomes because of their enzyme complement, have been isolated from methanol-grown cells of Candida boidinii. Spheroplast lysates were separated on non-continuous Ficoll density gradients, resulting in a mitochondrial fraction and a peroxisome fraction. Estimates of purity using the mitochondrial enzyme markers suggested that the contamination of mitochondria in the peroxisome fraction was about 2-3%. As shown by electron microscopy the peroxisomes were 0.4-0.6 mum in diameter and contained crystalloid inclusions. Alcohol oxidase and catalase, which catalyse the oxidation of methanol to formaldehyde in Candida boidinii, could be localized within the peroxisomes. Gel-electrophoretic studies of the peroxisome fraction demonstrated that it contained only two predominant protein bands consistent with alcohol oxidase and catalase. No alcohol oxidase and catalase activity was found in mitochondria.
[The medical gastroenterology department]. (2002)

The present paper summarizes the various themes of research which have been developed in the department of medical gastroenterology since it was created in 1977. These include: in pancreatology, the study of chronic pancreatitis pathogenesis, acute pancreatitis pathogenesis and immunomodulation, endoscopic treatment of chronic pancreatitis, the development of new imaging techniques of the bile ducts and the pancreas, as well as the treatment of pancreatic cancer and benign or malignant biliary diseases. in hepatology, the immunomodulation of liver cirrhosis, especially alcoholic liver disease, the modulation of experimental acute and chronic hepatitis, the study of liver ischemia-reperfusion. Clinical hepatology has focused on liver transplantation, prognosis factors of chronic liver disease and treatment of portal hypertension and viral hepatitis. in gut diseases, the treatment of gastro-oesophageal reflux and its complications, the therapeutic endoscopy of the upper and lower GI and the prevention, as well as the treatment, of colon cancer, the pathogenesis and the immunopharmacology of inflammatory bowel diseases and the clinical enteral and parenteral nutrition.
A Case Study for Augmented Reality Based Geography Learning Contents (2011)

최근 정보통신기술의 발전과 더불어 geographic information system(GIS)의 사용이 점차 일반화되고 그 응용분야와 활용범위가 확대되고 있다. 특히, 지리정보 관찰과 학습에서도 GIS의 활용은 긍정적인 효과가 기대되며, 2차원 시각 교보재인 사진이나 영상물에 비해 보다 사실적으로 지리적 특성을 파악하는데 도움이 될 것이다. 다소 복잡한 지형정보의 효과적인 시각화는 학습자로 하여금 지리정보 이해를 도울 뿐만 아니라, 지리적 정보를 파악하고 분석하는 능력을 키울 수 있다. 본 논문에서는 지리 학습에서 활용할 수 있는 학습보조자료 개발을 목표로 증강현실기술을 이용한 다양한 지형정보 가시화 기법과 사례를 연구하였다. 더불어 증강현실기반의 지리 학습을 위해, 기존에 구축된 GIS 데이터의 가공과정과 가공사례를 소개함으로써 3차원 지리정보의 효과적 가시화를 위해 증강현실 기술을 적용할 가치가 있음을 나타내었다. Recently, the geographic information system(GIS) is generally used in various fields with the development of information and communication technology, with expansion of its applications and utilization scope. Especially, utilizing GIS is expected to have positive effects on the geography learning and more helpful for the geographic information observation compared to the picture or 2D based media. The effective visualization of complex geographic data does not only take realization of its visual information but also increases the human ability in analysis and understanding to use the geographic information. In this paper, we examine a method to develop the geography learning contents based on the technology with augmented reality and GIS, and then we have a case study for various kinds of visualization techniques and examples to use in geography learning situation. Moreover, we introduce an example of the manufacturing process from the existing GIS data to augmented reality based geography learning system. From the above, we show that the usefulness of our method is applicable for effective visualization of the three-dimensional geographic information in the geography learning environment.
Zinc ion interactions in a two-dimensional covalent organic framework based aqueous zinc ion battery (2019)

The two-dimensional structural features of covalent organic frameworks (COFs) can promote the electrochemical storage of cations like H<sup>+</sup>, Li<sup>+</sup>, and Na<sup>+</sup> through both faradaic and non-faradaic processes. However, the electrochemical storage of cations like Zn<sup>2+</sup> ion is still unexplored although it bears a promising divalent charge. Herein, for the first time, we have utilized hydroquinone linked β-ketoenamine COF acting as a Zn<sup>2+</sup> anchor in an aqueous rechargeable zinc ion battery. The charge-storage mechanism comprises of an efficient reversible interlayer interaction of Zn<sup>2+</sup> ions with the functional moieties in the adjacent layers of COF (-182.0 kcal mol<sup>-1</sup>). Notably, due to the well-defined nanopores and structural organization, a constructed full cell, displays a discharge capacity as high as 276 mA h g<sup>-1</sup> at a current rate of 125 mA g<sup>-1</sup>.
Supplementary Table 1 from <i>PRKAR1A</i> Inactivation Leads to Increased Proliferation and Decreased Apoptosis in Human B Lymphocytes (2023)

Supplementary Table 1 from &lt;i&gt;PRKAR1A&lt;/i&gt; Inactivation Leads to Increased Proliferation and Decreased Apoptosis in Human B Lymphocytes
Development of High Affinity Camptothecin-Bombesin Conjugates That Have Targeted Cytotoxicity for Bombesin Receptor-containing Tumor Cells (2004)

Mammalian bombesin (BN) receptors are among those most frequently overexpressed by a number of common tumors including prostate, breast, lung, and colon cancers. The aim of this study was to develop a camptothecin-bombesin (CPT-BN) conjugate that interacts with all classes of BN receptors and possibly functions as a prodrug via a labile linker with site-specific cytotoxicity for cancer cells bearing these receptors. CPT was coupled to analogs of [D-Tyr6,beta-Ala11,Phe13,Nle14]BN-(6-14) (BA0) using carbamate linkers (L1 and L2) with built-in nucleophile-assisted releasing groups for intracellular cleavage of free cytotoxic agents. One conjugate, CPT-L2-BA3, bound to all three BN receptor classes with high affinity and functioned as a full agonist at each. 125I-CPT-L2-BA3 was rapidly internalized by cells expressing each BN receptor class and, using fluorescent imaging, was found to co-localize with BN receptors initially and later to be internalized in cytoplasmic compartments. HPLC analysis of internalized ligand showed that 40% was intact, 25% was metabolized by releasing free CPT, and 35% was metabolized to other breakdown products. CPT-L2-BA3 inhibited the growth of NCI-H1299 non-small cell lung cancer cells in 3-(4,5-dimethylthiazol-2-yl)-2.5-diphenyl-2H-tetrazolium bromide (MTT) and clonal growth assays. CPT-L2-BA3 was cytotoxic in an MTT assay for cells transfected with each class of BN receptor; however, it had significantly less effect in cells lacking BN receptors. These results indicate that CTP-L2-BA3 is a potent agonist that is cytotoxic for cells overexpressing any of the three BN receptor classes and functions as a prodrug for receptor-mediated cytoxicity. It therefore should be a useful prototype to explore the effectiveness of tumor-specific cytotoxicity delivery using a receptor-mediated mechanism.
Failover time evaluation between checkpoint services in multi-tier stateful applications (2017)

Cloud applications are offered to users with high availability and minimal data loss. Any (hardware or software) failure must be detected and recovered quickly, in order to maintain customer trust and avoid financial losses. When we are dealing with multi-tier and stateful applications, the failure recovery process is a big challenge because the whole state of the failed application must be retrieved and restored in a new instance. This process is named as failover; it can be performed by a checkpoint service at application-level or at system-level. Depending on the location of the checkpoint data storage, it can be classified as non-collocated, collocated warm, or collocated hot. This work presents an evaluation between these two checkpoint services in both virtualized and physical environments, considering a multi-tier and stateful application.
Efficient Simulation of Tree-Structured, Free-Floating Multibody Systems Using Momentum Integrals* (1996)

ABSTRACT The kinematic simulation of a free-floating multibody system, with joint motion commands as inputs and inertial description of the motion as outputs, can be performed by the following methods: (1) joint commands are treated as rheonomic inputs to a multibody dynamics code and the motion of the free-floating base is computed by integrating the resulting dynamic differential equations of motion; (2) the kinematics is coupled with momentum integrals of equations of motion of the system to result in a map between the inertial velocities and joint velocities, which on integration results in inertial description of the system. The first method requires the full simulation tools of multibody dynamics, while the second method constructs the same information starting at the velocity level. The second viewpoint results in a compact mapping between the joint velocities and inertial velocities of the system, which is useful for motion planning. The objective of this paper is to develop the equations for kinematic simulation of a general tree-structured, free-floating system using the second method. Some important contributions are (1) explicit description of the momentum integrals, (2) explicit mapping between inertial velocities and the joint velocities of the system, and (3) an efficient computational procedure for formulation of the necessary equations. Notes *communicated by E. J. Haug
Intrazeolite metal carbonyl phototopotaxy: from tungsten(VI) oxide quantum dots to a zero-dimensional semiconductor quantum supralattice (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntrazeolite metal carbonyl phototopotaxy: from tungsten(VI) oxide quantum dots to a zero-dimensional semiconductor quantum supralatticeGeoffrey A. Ozin and Saim. OzkarCite this: J. Phys. Chem. 1990, 94, 19, 7556–7561Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/j100382a046https://doi.org/10.1021/j100382a046research-articleACS PublicationsRequest reuse permissionsArticle Views239Altmetric-Citations31LEARN 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 options Get e-Alerts
Transient Pressure Response of a Well With Partial Completion in a Two-Layer Crossflowing Reservoir (1992)

ABSTRACT Although the technical literature contains several transient pressure response models for reservoirs producing multiple crossflowing layers, none of these models is adequate for the applications where they are most needed. None of these models accounts for partial completion. Further, all but one of these models approximate the crossflow through a steady-state assumption and ignore the variation of the pressure within each layer in the vertical direction. Layered models with crossflow are often used to interpret tests in thick carbonate reservoirs or in wells with bot-tomwater drive or gas caps. Partial completion, often in the extreme form, is invariably employed in such systems. Ignoring it in test interpretation may lead to incorrect estimation of some key parameters and unidentifiability of others. An analytic model is presented for the transient pressure response of such systems. This model rigorously accounts for both partial completion and the dynamics of vertical flow. The Laplace domain solution includes a different skin factor in each layer and can account for the effects of wellbore storage and dual porosities. The solution is obtained by applying the finite Hankel transforms and employing the pressure averaging technique. Computer-based symbolic manipulation was necessary to render the solution into a form suitable for practical evaluation. The new model enables improved interpretation of well tests in several types of reservoirs to yield parameters that cannot be estimated with the existing models (e.g., the vertical permeabilities in two communicating layers, and. the horizontal mobility in the gas cap or in the water zone communicating with an oil reservoir). This model can also be used for interpretation of the single well vertical interference test.
Gating Design (2016)

No AccessInjection Mold Design EngineeringApr 2016Gating DesignDavid O. KazmerDavid O. Kazmerhttps://doi.org/10.3139/9781569905715.007SectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF key 'share (en)' returned an object instead of string.FacebookTwitterEmailLinkedIn previous chapternext chapter FiguresReferencesRelatedDetails 2016Pages: 197-226Print ISBN: 978-1-56990-570-8eISBN: 978-1-56990-571-5 Copyright & Permissions© 2016 Carl Hanser Verlag GmbH & Co. KGPDF downloadLoading ...