gebhart/patrepeval huggingface dataset:
Increased cell motility and invasion upon siRNA knockdown of LSR in bladder cancer (2007)

2013 Bladder cancer is the ninth most common cancer world wide with an incidence of 357,000 and 145,000 deaths annually. The disease presents in two different forms: a superficial form, which often recur and in some cases progress to an invasive stage, and an invasive form with a poor survival rate despite radical cystectomy and systemic therapy. The molecular mechanisms involved in disease progression are still poorly understood. Identification of target molecules involved in the disease development and progression would have great impact on the future understanding and treatment of the disease. Using HG-U133A oligonucleotide microarray analyses on tumor specimens from 90 patients (55 Ta, 3 T1, 23 T2-T4, 9 normal samples) we identified an elevated expression of LSR in all stages of bladder cancer compared to normal samples. IHC on tumor specimens showed that the LSR expression was found in the malignant urothelial cells. In an effort to identify the function and effect of this cancer specific overexpression we knocked down the expression of LSR in a bladder cancer cell line (SW780). Cells were transfected using five different constructs: mock-siRNA, two LSR-siRNA variants, TP53-siRNA and LSR+TP53 siRNAs. Cells were harvested at three different time points; 18h (one replicate), 48h (four replicates) and 72h (two replicates). siRNA knock down was QPCR verified and global gene expression consequences of the knockdown were analysed using 35 HG-U133 Plus 2.0 microarrays. The microarray gene expression levels of three genes (EMP3, AGR2, CTGF) were verified by QPCR. Microarray data was analysed with the novel bioinformatic software application, Ingenuity Pathway Analysis. Using this approach we found that cellular movement, including cell motility and invasion, were the main cellular functions affected by the knockdown of LSR using both siRNAs against LSR. This result was experimentally verified in a matrigel based assay demonstrating that the cell’s invasive capacity was elevated 3-fold in cells transfected with LSR-siRNAs compared to mock transfected cells. The molecular changes and affected molecular pathways identified from the cell line experiments will be correlated to the the gene expression data from clinical samples and the results will be presented at the meeting. Consequently, our results indicate that LSR is involved in disease progression in bladder cancer. Future studies will be needed to further delineate the role of LSR in bladder cancer progression.
Targeting the Bromodomain of BRG-1/BRM Subunit of the SWI/SNF Complex Increases the Anticancer Activity of Temozolomide in Glioblastoma (2021)

Glioblastoma (GBM) is a deadly and incurable brain cancer with limited therapeutic options. PFI-3 is a small-molecule bromodomain (BRD) inhibitor of the BRM/BRG1 subunits of the SWI/SNF chromatin remodeling complex. The objective of this study is to determine the efficacy of PFI-3 as a potential GBM therapy. We report that PFI-3 binds to these BRDs when expressed in GBM cells. PFI-3 markedly enhanced the antiproliferative and cell death-inducing effects of temozolomide (TMZ) in TMZ-sensitive GBM cells as well as overcame the chemoresistance of highly TMZ-resistant GBM cells. PFI-3 also altered gene expression in GBM and enhanced the basal and interferon-induced expression of a subset of interferon-responsive genes. Besides the effects of PFI-3 on GBM cells in vitro, we found that PFI-3 markedly potentiated the anticancer effect of TMZ in an intracranial GBM animal model, resulting in a marked increase in survival of animals bearing GBM tumors. Taken together, we identified the BRG1 and BRM subunits of SWI/SNF as novel targets in GBM and revealed the therapeutic potential of applying small molecule inhibitors of SWI/SNF to improve the clinical outcome in GBM using standard-of-care chemotherapy.
First Signature of Islet β-Cell-Derived Naturally Processed Peptides Selected by Diabetogenic Class II MHC Molecules (2008)

The diversity of Ags targeted by T cells in autoimmune diabetes is unknown. In this study, we identify and characterize a limited number of naturally processed peptides from pancreatic islet beta-cells selected by diabetogenic I-A(g7) molecules of NOD mice. We used insulinomas transfected with the CIITA transactivator, which resulted in their expression of class II histocompatibility molecules and activation of diabetogenic CD4 T cells. Peptides bound to I-A(g7) were isolated and examined by mass spectrometry: some peptides derived from proteins present in secretory granules of endocrine cells, and a number were shared with cells of neuronal lineage. All proteins to which peptides were identified were expressed in beta cells from normal islets. Peptides bound to I-A(g7) molecules contained the favorable binding motif characterized by acidic amino acids at the P9 position. The draining pancreatic lymph nodes of prediabetic NOD mice contained CD4 T cells that recognized three different natural peptides. Furthermore, four different peptides elicited CD4 T cells, substantiating the presence of such self-reactive T cells. The overall strategy of identifying natural peptides from islet beta-cells opens up new avenues to evaluate the repertoire of self-reactive T cells and its role in onset of diabetes.
Mutations in the gene 5 DNA polymerase of bacteriophage T7 suppress the dominant lethal phenotype of gene 2.5 ssDNA binding protein lacking the C‐terminal phenylalanine (2009)

In the article by Marintcheva et al. (2009), the last author's name has been amended to Charles C. Richardson.
Cloud-Enabled High-Altitude Platform Systems: Challenges and\n Opportunities (2021)

Augmenting ground-level communications with flying networks, such as the\nhigh-altitude platform system (HAPS), is among the major innovative initiatives\nof the next generation of wireless systems (6G). Given HAPS quasi-static\npositioning at the stratosphere, HAPS-to-ground and HAPS-to-air connectivity\nframeworks are expected to be prolific in terms of data acquisition and\ncomputing, especially given the mild weather and quasi-constant wind speed\ncharacteristics of the stratospheric layer. This paper explores the\nopportunities stemming from the realization of cloud-enabled HAPS in the\ncontext of telecommunications applications and services. The paper first\nadvocates for the potential physical advantages of deploying HAPS as flying\ndata-centers, also known as super-macro base stations. The paper then describes\nvarious cloud services that can be offered from the HAPS and the merits that\ncan be achieved by this integration, such as enhancing the quality, speed, and\nrange of the offered services. The proposed services span a wide range of\nfields, including satellites, Internet of Things (IoT), ad hoc networks (such\nas sensor; vehicular; and aerial networks), gaming, and social networks. For\neach service, the paper illustrates the methods that would be used by cloud\nproviders to offload the service data to the HAPS and enable the cloud\ncustomers to consume the service. The paper further sheds light on the\nchallenges that need to be addressed for realizing practical cloud-enabled\nHAPS, mainly, those related to high energy, processing power, quality of\nservice (QoS), and security considerations. Finally, the paper discusses some\nopen issues on the topic, namely, HAPS mobility and message routing, HAPS\nsecurity via blockchain and machine learning, artificial intelligence-based\nresource allocation in cloud-enabled HAPS, and integration with vertical\nheterogeneous networks.\n
Repeated roll-to-roll transfer of two-dimensional materials by electrochemical delamination (2018)

Two-dimensional (2D) materials such as graphene (Gr), molybdenum disulfide and hexagonal boron nitride (hBN) hold great promise for low-cost and ubiquitous electronics for flexible displays, solar cells or smart sensors. To implement this vision, scalable production, transfer and patterning technologies of 2D materials are needed. Recently, roll-to-roll (R2R) processing, a technique that is widely used in industry and known to be cost-effective and scalable, was applied to continuously grow and transfer graphene. However, more work is needed to understand the possibilities and limitations of this technology to make R2R processing of 2D materials feasible. In this work, we fabricated a custom R2R transferring system that allows the accurate control of the process parameters. We employ continuous electrochemical delamination, known as "bubble transfer", to eliminate chemical etchant waste and enable the continuous transfer of 2D materials from metal foils. This also makes our transfer method a renewable and environmentally friendly process. We investigate the surface topology as well as the electrical parameters of roll-to-roll transferred graphene on polyethylene terephthalate (PET) coated with ethylene-vinyl acetate (EVA). Furthermore, we demonstrate for the first time the stacking of two layers of graphene or graphene on hBN by repeated lamination and delamination onto EVA/PET. These results are an important contribution to creating low-cost, large scale and flexible electronics based on 2D materials.
New patented histone deacetylase inhibitors (2009)

Although competition in this field is intense, the future application of HDACis to treat human disease either as single agents or in combination with existing drugs holds real promise.
Prevalence and Characteristics of Choroidal Nevi in an Asian vs White Population (2009)

Choroidal nevi were detected in 1.4% of Malay persons. There were no significant racial or ethnic differences in nevi characteristics between Malay and white persons.
A novel, selective free-radical carbamoylation of heteroaromatic bases by Ce(iv) oxidation of formamide, catalysed by N-hydroxyphthalimide (2002)

The Ce(IV)-NHPI system was used to generate a carbamoyl radical by oxidation of formamide; this nucleophilic radical has been successfully used in the carbamoylation of heteroaromatic bases.
The genetic requirements for UmuDC-mediated cold sensitivity are distinct from those for SOS mutagenesis (1996)

The umuDC operon of Escherichia coli, a member of the SOS regulon, is required for SOS mutagenesis. Following the posttranslational processing of UmuD to UmuD' by RecA-mediated cleavage, UmuD' acts in concert with UmuC, RecA, and DNA polymerase III to facilitate the process of translesion synthesis, which results in the introduction of mutations. Constitutive expression of the umuDC operon causes an inhibition of growth at 30 degrees C (cold sensitivity). The umuDC-dependent physiological phenomenon manifested as cold-sensitive growth is shown to differ from SOS mutagenesis in two respects. Intact UmuD, the form inactive in SOS mutagenesis, confers a significantly higher degree of cold sensitivity in combination with UmUC than does UmuD'. In addition, umuDC-mediated cold sensitivity, unlike SOS mutagenesis, does not require recA function. Since the RecA protein mediates the autodigestion of UnmD to UmuD', this finding supports the conclusion that intact UmuD is capable of conferring cold sensitivity in the presence of UmuC. The degree of inhibition of growth at 30 degrees C correlates with the levels of UmuD and UmuC, which are the only two SOS-regulated proteins required to observe cold sensitivity. Analysis of the cellular morphology of strains that exhibit cold sensitivity for growth led to the finding that constitutive expression of the umuDC operon causes a novel form of sulA- and sfiC-independent filamentation at 30 degrees C. This filamentation is observed in a strain constitutively expressing the single, chromosomal copy of umuDC and can be suppressed by overexpression of the ftsQAZ operon.
EXAFS studies of Bi2Sr2CaCu2O8 glass and glass-ceramic (1991)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation S. S. Bayya, R. Kudesia, R. L. Snyder; EXAFS studies of Bi2Sr2CaCu2O8 glass and glass‐ceramic. AIP Conf. Proc. 1 April 1991; 219 (1): 306–316. https://doi.org/10.1063/1.40276 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Modeling and simulation of IEF in 2‐D microgeometries (2007)

A 2-D finite-volume model is developed to simulate nonlinear IEF in complex microgeometries. This mathematical model is formulated based on the mass conservation and ionic dissociation relations of amphoteric macromolecules, charge conservation, and the electroneutrality condition. Based on the 2-D model, three different separation cases are studied: an IPG in a planar channel, an ampholyte-based pH gradient in a planar channel, and an ampholyte-based pH gradient in a contraction-expansion channel. In the IPG case, cacodylic acid (pK(1) = 6.21) and Tris (pK(1) = 8.3) are used as the acid and base, respectively, to validate the 2-D IEF model. In the ampholyte-based pH gradient cases, IEF is performed in the pH range, 6.21-8.3 using 10 ampholytes in the planar channel and 20 ampholytes in the contraction-expansion channel. The numerical results reveal different focusing efficiencies and resolution in the narrow and wide sections of the contraction-expansion channel. To explain this, the expressions for separation resolution and peak concentrations of separands in the contraction-expansion channel are presented in terms of the channel shape factor. In a 2-D planar channel, a focused band remains straight all the time. However, in a contraction-expansion channel, initially straight bands take on a crescent profile as they pass through the trapezoidal sections joining the contraction and expansion sections.
Understanding the Early Major Transitions in Evolutionary History Part 1: Stages in the Emergence of Complex Life (2021)

Whitepaper #247 submitted to the Planetary Science and Astrobiology Decadal Survey 2023-2032. Topics: life and prebiotic organics; other science themes: Early Evolution; theory, computation, and modeling
Contributions of Professor Tayur N. Guru Row to Research in Small-Molecule Crystallography (2023)

ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTContributions of Professor Tayur N. Guru Row to Research in Small-Molecule CrystallographyDeepak Chopra*Deepak Chopra*Email: [email protected]More by Deepak Choprahttps://orcid.org/0000-0002-0018-6007, Sajesh P. Thomas*Sajesh P. Thomas*Email: [email protected]More by Sajesh P. Thomas, and Giuseppe Resnati*Giuseppe Resnati*Email: [email protected]More by Giuseppe Resnatihttps://orcid.org/0000-0002-0797-9296Cite this: Cryst. Growth Des. 2023, 23, 6, 3931–3934Publication Date (Web):April 28, 2023Publication History Received25 November 2022Published online28 April 2023Published inissue 7 June 2023https://pubs.acs.org/doi/10.1021/acs.cgd.2c01383https://doi.org/10.1021/acs.cgd.2c01383editorialACS PublicationsCopyright © Published 2023 by American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1361Altmetric-Citations-LEARN 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 PDF (1 MB) Get e-AlertscloseSUBJECTS:Crystal structure,Crystallography,Crystals,Diffraction,Electrical properties Get e-Alerts
Dysregulated T-Helper Type 1 (Th1):Th2 Cytokine Profile and Poor Immune Response in Pregnant Ferrets Infected With 2009 Pandemic Influenza A(H1N1) Virus (2017)

Pregnancy has been associated with severe influenza, an association highlighted during the 2009 pandemic of influenza A(H1N1) virus (A[H1N1]pdm09) infection. To assess the underlying mechanism, we infected pregnant and non-pregnant ferrets with A(H1N1) pdm09 virus. A(H1N1)pdm09-infected pregnant ferrets also had higher levels of inflammatory cytokines in their pulmonary tracts. Systemically, total CD8+ T cell counts and A(H1N1)pdm09-specific B-cell responses in blood were significantly lower in pregnant ferrets. This model predicts that the poorer outcome for pregnant women during the A(H1N1)pdm09 pandemic was due to an elevated level of viral replication and to a cytokine imbalance that led to a less effective immune response.
Optimized Overlay Metrology Marks: Theory and Experiment (2004)

In this paper, we provide a detailed analysis of overlay metrology mark and find the mapping between various properties of mark patterns and the expected dynamic precision and fidelity of measurements. We formulate the optimality criteria and suggest an optimal overlay mark design in the sense of minimizing the Cramer-Rao lower bound on the estimation error. Based on the developed theoretical results, a new overlay mark family is proposed-the grating marks. A thorough testing performed on the new grating marks shows a strong correlation with the underlying theory and demonstrate the superior quality of the new design over the overlay patterns used today.
Asphyxial cardiac arrest (2007)

There is no malice in this burning coal;The breath of heaven has blown his spirit out …But with my breath I can revive it, …William Shakespeare
Genetic analysis in young patients with sporadic pituitary macroadenomas: besides AIP don't forget MEN1 genetic analysis (2013)

Mutations in MEN1 can be of significance in young patients with sporadic isolated pituitary macroadenomas, particularly PRL, and together with AIP, we suggest genetic analysis of MEN1 in such a population.
Performance of an Impulse Radio Communication System in the Presence of Gaussian Jitter (2007)

In this paper, the bit error rate (BER) performance for an ultra-wide bandwidth (UWB) impulse radio in an additive white Gaussian noise (AWGN) transmission channel and with Gaussian jitter is estimated. The assumed receiver combines the received pulses to increase the signal to noise ratio (SNR) and correlates the received signal with a locally generated template. The resulting performances are discussed separately for a large number and a small number of combined pulses. In the former case, the BER is derived analytically and verified using numerical simulations, and in the latter case, lower bounds for the BER are provided for low and large SNRs. Simulation results are shown to approach asymptotically the provided bounds.
Microwave-Assisted Synthesis of Potent Antimicrobial Agents of Flavanone Derivatives (2014)

Oriental Journal of Chemistry is a peer reviewed quarterly research journal of pure and applied chemistry. It publishes standard research papers in almost all thrust areas of current chemistry of academic and commercial importance. It provides a platform for rapid publication of quality research papers, reviews and chemistry letters. Oriental Journal of Chemistry is abstracted and indexed in almost all reputed National and International agencies.
Window-based error recovery and flow control with a slow acknowledgement channel: a study of TCP/IP performance (2002)

With the envisaged growth in Internet access services over networks with asymmetric links such as asymmetric digital subscriber line (ADSL) and hybrid fiber coax (HFC), it becomes crucial to evaluate the performance of window-based protocols over systems in which the reverse link is considerably slower than the forward link. Even if the actual bandwidth asymmetry is moderate, high effective asymmetries can result because of bidirectional traffic. Our objective is to determine, whether TCP/IP performs reasonably in a setting in which the reverse link is the primary bottleneck. Our main results are as follows. (1) For both the prevalent Tahoe version with Fast Retransmit and the Reno version of TCP we determine the throughput as a function of buffering, round-trip times and normalized asymmetry (taken to be the ratio of the transmission time of ACKs in the reverse path to that of data packets in the forward path). We identify three modes of operation which are dependent on the forward buffer sizes and the normalized asymmetry. (2) Asymmetry increases the TCP's already high sensitivity to random packet losses that might be caused by transient bursts in real-time traffic. Specifically, random loss leads to significant throughput deterioration when the product of the loss probability, the asymmetry and the square of the bandwidth delay product is large. (3) Congestion in the reverse path adds considerably to the TCP's unfairness when multiple connections share the reverse link. Link bandwidth sharing is unfair even for connections with identical round-trip times and hence use of per connection buffer allocation on the reverse path appears essential.
Supplementary Figure 4 from Global Evaluation of Eph Receptors and Ephrins in Lung Adenocarcinomas Identifies EphA4 as an Inhibitor of Cell Migration and Invasion (2023)

&lt;p&gt;PDF file, 48K, EFNA1, EFNB2, EPHB2 mRNA levels.&lt;/p&gt;
Humanized Gene Replacement in Mice Reveals the Contribution of Cancer Stroma-Derived HB-EGF to Tumor Growth (2010)

Tumor progression is a complex process that involves the interaction of cancer cells with the cancer-surrounding stromal cells. The cancer stroma influences the cancer cell growth and metastatic potential. The EGF family growth factor HB-EGF is synthesized in cancer cells and plays pivotal roles in oncogenic transformation and tumor progression, but the contribution of HB-EGF expressed in tumor stromal cells to tumor growth remains unclear. In the present study, we found that HB-EGF was expressed in host-derived cancer stromal cells in xenograft and allograft mouse tumor models. CRM197 is a specific inhibitor of human HB-EGF that has no effect on mouse HB-EGF. To elucidate whether host-derived stromal HB-EGF contributes to tumor growth, we generated knock-in mice expressing a CRM197-inhibitable humanized mutant form of HB-EGF. Administration of CRM197 to humanized knock-in mice that were bearing tumors derived from human or mouse cancer cells revealed that inhibition of host-derived stromal HB-EGF by CRM197 significantly reduced tumor growth. These results suggest that HB-EGF in the cancer-associated stroma plays a significant role for tumor growth, and that the HB-EGF derived from the stroma, as well as that expressed by cancer cells, is a potential target for cancer therapy. The present results also suggest that the humanized HB-EGF knock-in mice could be utilized for pathophysiological studies of HB-EGF as well as the development of therapeutic strategies targeting HB-EGF.