gebhart/patrepeval huggingface dataset:
Deeper Inside PageRank (2004)

This paper serves as a companion or extension to the "Inside PageRank" paper by Bianchini et al. [Bianchini et al. 03]. It is a comprehensive survey of all issues associated with PageRank, covering the basic PageRank model, available and recommended solution methods, storage issues, existence, uniqueness, and convergence properties, possible alterations to the basic model, suggested alternatives to the traditional solution methods, sensitivity and conditioning, and finally the updating problem. We introduce a few new results, provide an extensive reference list, and speculate about exciting areas of future research.
Benzo-ring diol epoxides of benzo[e]pyrene and triphenylene (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBenzo-ring diol epoxides of benzo[e]pyrene and triphenyleneHaruhiko Yagi, Dhiren R. Thakker, Roland E. Lehr, and Donald M. JerinaCite this: J. Org. Chem. 1979, 44, 19, 3439–3442Publication Date (Print):September 1, 1979Publication History Published online1 May 2002Published inissue 1 September 1979https://pubs.acs.org/doi/10.1021/jo01333a047https://doi.org/10.1021/jo01333a047research-articleACS PublicationsRequest reuse permissionsArticle Views152Altmetric-Citations29LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Design and Implementation of File Deduplication Framework on HDFS (2014)

File systems are designed to control how files are stored and retrieved. Without knowing the context and semantics of file contents, file systems often contain duplicate copies and result in redundant consumptions of storage space and network bandwidth. It has been a complex and challenging issue for enterprises to seek deduplication technologies to reduce cost and increase the storage efficiency. To solve such problem, researchers proposed in-line or offline solutions for primary storages or backup systems at the subfile or whole-file level. Some of the technologies are used for file servers and database systems. Fewer studies focus on the cloud file system deduplication technologies at the application level, especially for the Hadoop distributed file system. It is the goal of this paper to design a file deduplication framework on Hadoop distributed file system for cloud application developers. The architecture, interface, and implementation experiences are also shared in this paper.
Data from ASO-Based PKM Splice-Switching Therapy Inhibits Hepatocellular Carcinoma Growth (2023)

&lt;div&gt;Abstract&lt;p&gt;The M2 pyruvate kinase (PKM2) isoform is upregulated in most cancers and plays a crucial role in regulation of the Warburg effect, which is characterized by the preference for aerobic glycolysis over oxidative phosphorylation for energy metabolism. PKM2 is an alternative-splice isoform of the &lt;i&gt;PKM&lt;/i&gt; gene and is a potential therapeutic target. Antisense oligonucleotides (ASO) that switch &lt;i&gt;PKM&lt;/i&gt; splicing from the cancer-associated PKM2 to the PKM1 isoform have been shown to induce apoptosis in cultured glioblastoma cells when delivered by lipofection. Here, we explore the potential of ASO-based &lt;i&gt;PKM&lt;/i&gt; splice switching as a targeted therapy for liver cancer. A more potent lead constrained-ethyl (cEt)/DNA ASO induced &lt;i&gt;PKM&lt;/i&gt; splice switching and inhibited the growth of cultured hepatocellular carcinoma (HCC) cells. This &lt;i&gt;PKM&lt;/i&gt; isoform switch increased pyruvate-kinase activity and altered glucose metabolism. In an orthotopic HCC xenograft mouse model, the lead ASO and a second ASO targeting a nonoverlapping site inhibited tumor growth. Finally, in a genetic HCC mouse model, a surrogate mouse-specific ASO induced &lt;i&gt;Pkm&lt;/i&gt; splice switching and inhibited tumorigenesis, without observable toxicity. These results lay the groundwork for a potential ASO-based splicing therapy for HCC.&lt;/p&gt;Significance:&lt;p&gt;Antisense oligonucleotides are used to induce a change in &lt;i&gt;PKM&lt;/i&gt; isoform usage in hepatocellular carcinoma, reversing the Warburg effect and inhibiting tumorigenesis.&lt;/p&gt;&lt;/div&gt;
γδ T cells protect against lung fibrosis via IL-22 (2010)

Inflammation-induced pulmonary fibrosis (PF) leads to irreversible loss of lung function and is a predictor of mortality in numerous lung diseases. Why some subjects with lung inflammation but not others develop PF is unclear. In a mouse model of hypersensitivity pneumonitis that progresses to lung fibrosis upon repeated exposure to the ubiquitous microorganism Bacillus subtilis, γδ T cells expand in the lung and inhibit collagen deposition. We show that a subset of these γδ cells represents the predominant source of the Th17 cytokine IL-22 in this model. Preventing expression of IL-22, either by mutating the aryl hydrocarbon receptor (AhR) or inhibiting AhR signaling, accelerated lung fibrosis. Direct blockade of IL-22 also enhanced collagen deposition in the lung, whereas administration of recombinant IL-22 inhibited lung fibrosis. Moreover, the presence of protective γδ T cells and IL-22 diminished recruitment of CD4(+) T cells to lung. These data reveal a protective pathway that involves the inhibition of αβ T cells by regulatory IL-22-secreting γδ T cells.
TLX is an intrinsic regulator of the negative effects of IL‐1β on proliferating hippocampal neural progenitor cells (2017)

Hippocampal neurogenesis is a lifelong process whereby new neurons are produced and integrate into the host circuitry within the hippocampus. It is regulated by a multitude of extrinsic and intrinsic regulators and is believed to contribute to certain hippocampal-dependent cognitive tasks. Hippocampal neurogenesis and associated cognition have been demonstrated to be impaired after increases in the levels of proinflammatory cytokine IL-1β in the hippocampus, such as that which occurs in various neurodegenerative and psychiatric disorders. IL-1β also suppresses the expression of TLX (orphan nuclear receptor tailless homolog), which is an orphan nuclear receptor that functions to promote neural progenitor cell (NPC) proliferation and suppress neuronal differentiation; therefore, manipulation of TLX represents a potential strategy with which to prevent the antiproliferative effects of IL-1β. In this study, we assessed the mechanism that underlies IL-1β-induced changes in TLX expression and determined the protective capacity of TLX to mitigate the effects of IL-1β on embryonic rat hippocampal neurosphere expansion. We demonstrate that IL-1β activated the NF-κB pathway in proliferating NPCs and that this activation was responsible for IL-1β-induced changes in TLX expression. In addition, we report that enhancing TLX expression prevented the IL-1β-induced suppression of neurosphere expansion. Thus, we highlight TLX as a potential protective regulator of the antiproliferative effects of IL-1β on hippocampal neurogenesis.-Ó'Léime, C. S., Kozareva, D. A., Hoban, A. E., Long-Smith, C. M., Cryan, J. F., Nolan, Y. M. TLX is an intrinsic regulator of the negative effects of IL-1β on proliferating hippocampal neural progenitor cells.
Evolution strategy applied to global optimization of clusters in gene expression data of DNA microarrays (2002)

Cluster analysis is the most important method for analyzing large-scale gene expression patterns. The matrix representation of microarray data and its successive 'optimal' incisional hyperplanes that create top-down hierarchical tree are a useful platform for developing optimization algorithms to determine the 'optimal' clusters from a pairwise proximity matrix which represents completely connected and weighted graph. Evolution strategy is applied to determine the 'globally optimal' incisional hyperplanes to construct hierarchical tree structure and tested with Fisher's iris and Golub's leukemia data sets. The results were compared with those of bottom-up hierarchical clustering, K-means and SOMs (Self-Organizing Maps) algorithms with promising results.
Energy-efficient design of an always-on smart visual trigger (2016)

In this work, we present the design of an always-on smart visual trigger. To maximize the energy-efficiency, the whole system is kept in stand-by mode until a significant information is detected by the early-processing of the low-power imager. Within two considered scenarios of vehicle detection, the system runs at minimal power consumption for 84% and 39% of the time. When active, the generation of triggers due to relevant events is conducted by analyzing the trajectory of multiple tracked objects. A parallel event-driven implementation speeds-up the digital computation and leads to a duty cycle below 1% over the frame period. The optimized power management is enabled by defining an always-on camera interface for the System-on-Chip (SoC) processor, which is able to individually activate both the sensor and the processor while running at minimal power consumption. In the considered case-study of vehicle detection, an estimated power consumption of up to 23μW is accounted, depending on the context-activity, and the smart triggers fails one detection over 72 moving vehicles.
Imaging the response to DNA damage in heterochromatin domains reveals core principles of heterochromatin maintenance. Fortuny et al. (2021)

Original data used in our publication by Fortuny et al., 2021, including original microscopy images, western-blot scans, FACS data and results of image analyses. Folders are organized as Main Figures, Supplementary Figures and Supplementary videos with a subfolder for each figure panel. We dissect the mechanisms for pericentric heterochromatin maintenance following UV damage in mammalian cells.
JANUS-II-translation of spontaneous conversational speech (2002)

JANUS-II is a research system to design and test components of speech-to-speech translation systems as well as a research prototype for such a system. We focus on two aspects of the system: (1) the new features of the speech recognition component JANUS-SR, and (2) the end-to-end performance of JANUS-II, including a comparison of two machine translation strategies used for JANUS-MT (PHOENIX and GLR*).
Novel Chromosomal Abnormalities Identified by Comparative Genomic Hybridization in Parathyroid Adenomas1 (1998)

The molecular basis of parathyroid adenomatosis includes defects in the cyclin D1/PRAD1 and MEN1 genes but is, in large part, unknown. To identify new locations of parathyroid oncogenes or tumor suppressor genes, and to further establish the importance of DNA losses described by molecular allelotyping, we performed comparative genomic hybridization (CGH) on a panel of 53 typical sporadic (nonfamilial) parathyroid adenomas. CGH is a new molecular cytogenetic technique in which the entire tumor genome is screened for chromosomal gains and/or losses. Two abnormalities, not previously described, were found recurrently: gain of chromosome 16p (6 of 53 tumors, or 11%) and gain of chromosome 19p (5 of 53, or 9%). Losses were found frequently on 11p (14 of 53, or 26%), as well as 11q (18 of 53, or 34%). Recurrent losses were also seen on chromosomes 1p, 1q, 6q, 9p, 9q, 13q, and 15q, with frequencies ranging from 8-19%. Twenty-four of the 53 adenomas were also extensively analyzed with polymorphic microsatellite markers for allelic losses, either in this study (11 cases) or previously (13 cases). Molecular allelotyping results were highly concordant with CGH results in these tumors (concordance level of 97.5% for all informative markers/chromosome arms examined). In conclusion, CGH has identified the first two known chromosomal gain defects in parathyroid adenomas, suggesting the existence of direct-acting parathyroid oncogenes on chromosomes 16 and 19. CGH has confirmed the locations of putative parathyroid tumor suppressor genes, also defined by molecular allelotyping, on chromosomes 1p, 6q, 9p, 11q, 13q, and 15q. Finally, CGH has provided new evidence favoring the possibility that distinct parathyroid tumor suppressors exist on 1p and 1q, and has raised the possibility of a parathyroid tumor suppressor gene on 11p, distinct from the MEN1 gene on 11q. CGH can identify recurrent genetic abnormalities in hyperparathyroidism, especially chromosomal gains, that other methods to not detect.
Recalled maltreatment, migraine, and tension-type headache (2014)

ACEs are associated with a higher risk of migraine vs ETTH. Attenuation of the influence of ACEs by depression and anxiety suggests confounding or mediation, although results for emotional abuse were generally maintained.
Anomaly detection for a vibrating structure: A subspace identification/tracking approach (2017)

Mechanical devices operating in noisy environments lead to low signal-to-noise ratios creating a challenging signal processing problem to monitor the vibrational signature of the device in real-time. To detect/classify a particular type of device from noisy vibration data, it is necessary to identify signatures that make it unique. Resonant (modal) frequencies emitted offer a signature characterizing its operation. The monitoring of structural modes to determine the condition of a device under investigation is essential, especially if it is a critical entity of an operational system. The development of a model-based scheme capable of the on-line tracking of structural modal frequencies by applying both system identification methods to extract a modal model and state estimation methods to track their evolution is discussed along with the development of an on-line monitor capable of detecting anomalies in real-time. An application of this approach to an unknown structural device is discussed illustrating the approach and evaluating its performance.
Expression of the Antisense-to-Latency Transcript Long Noncoding RNA in Kaposi's Sarcoma-Associated Herpesvirus (2016)

Increasing data support the importance of noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and lncRNAs, which have been shown to exert critical regulatory functions without coding for recognizable proteins. Defining the sequences of these ncRNAs is essential for future studies aiming to functionally characterize a specific ncRNA. Most lncRNA studies are highly dependent on high-throughput sequencing and bioinformatic analyses, few studies follow up on the initial predictions, and analyses are at times discordant. The manuscript characterizes one key viral lncRNA, ALT, by physically isolating ALT and by a sequencing-independent assay. It provides for a simple assay to monitor lncRNA expression in experimental and clinical samples. ALT is expressed antisense to the major viral latency transcripts encoding LANA as well as the viral miRNAs and thus has the potential to regulate this key part of the viral life cycle.
Role of arbuscular mycorrhizal fungi on the accumulation of radiocaesium by plants (2007)

Numerous soils have been contaminated by radiocaesium (Cs) as a result of nuclear weapon testing and accidents at nuclear power-plant facilities. Management of the areas, which have been exposed to either intense or diffuse Cs pollution, has therefore become a major environmental concern. Strategies orientated toward the use of plants and microorganisms, or both in combination, have been proposed in the recent years as potential players in removing or stabilizing Cs in contaminated soils. Among these microorganisms, arbuscular mycorrhizal (AM) fungi are of particular interest due to their unique position at the soil/root interface and their recognized role in element transport and immobilization. In the recent years, contradictory results have been published on the impact of AM fungi on Cs accumulation by plants, failing to ascertain whether AM fungi could effectively transport this radionuclide to their host. Therefore, the objective of this work was to determine the role of AM fungi in plant Cs acquisition and accumulation. Using in vitro compartmented systems, we unambiguously demonstrated that AM fungi could transport Cs to their host, while its accumulation within the extraradical mycelium was rather limited. Our results also suggested that AM fungi could have an effect on Cs distribution within their host. Indeed, it appeared that AM fungi could potentially limit the translocation of Cs from roots to shoot. However, if the results obtained during this research project have shown that AM fungi could influence the acquisition and accumulation of Cs by plants, their capacity to take part in phytoremediation strategies remains questionable and would need additional investigations. In particular, attention should be focused on the mechanisms behind Cs transport by AM fungi, their influence on Cs root to shoot translocation and the subsequent validation of the findings obtained to in situ conditions.
ChemInform Abstract: A New Synthetic Methodology for Tiazofurin. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
DIESEL-PARTIKELFILTERSYSTEM MIT ADDITIVGESTUETZTER REGENERATION (1989)

Unter den Verfahren zur Reduzierung der Dieselpartikel mittels Abgasnachbehandlung erscheint die Filterung mit einem Keramikmonolithen und die Regeneration ueber ein dem Kraftstoff zugemischtes Additiv fuer die Praxis im Personenkraftwagen und leichten Nutzfahrzeug sehr erfolgversprechend. Einvon VW verfolgtes Konzept in Verbindung mit einer Abgasrueckfuehrung zur Stickoxyd-Absenkung wird vorgestellt. Das Additiv dazu entwickelt Chemische Betriebe Pluto/Vebaoel in Zusammenarbeit mit VW. Dargestellt werden der Aufbau des Gesamtsystems Abgasrueckfuehrung und Partikelfilter mit Einrichtung zur Additivzumischung, die Auswahl des Filtertyps und das Additiv.Physikalisch-chemische Untersuchungen an Partikelproben zeigen eine signifikante, verbrennungsfoerdernde und zuendtemperaturabsenkende Wirkung des Additivs. Pruefstandsversuche wie Fahrversuche bei unterschiedlichen klimatischen Verhaeltnissen lassen bisher auf eine hohe Funktionssicherheit schliessen. Mit einer Verbrauchserhoehung von rund 7 Prozent wirkt sich derPartikelfilter allerdings auf den Kraftstoffverbrauch nachteilig aus. Titel in Englisch: Diesel particulate filter system with additive supported regeneration.
Abstract 5336: Discovery of a novel activin receptor-like kinases (ALKs) inhibitor targeting TGF-β signaling pathways (2023)

Abstract Introduction: Transforming growth factor β (TGF-β) plays a key role in promoting tumor progression mainly through facilitating angiogenesis, epithelial-mesenchymal transition (EMT) and also inducing immunosuppression in tumor microenvironment, allowing cancer cells to escape immune surveillance. Activin receptor-like kinases (ALKs) consisting of seven type I receptor serine/threonine kinases are responsible for TGF-β family signal transduction by phosphorylating Smad proteins, which can activate target gene expression. Therefore, ALKs are attractive drug targets for intervention in TGF- β signaling pathways as cancer immunotherapy. Materials and methods: We have produced seven human recombinant ALK proteins (ALK1-7). The in vitro kinase assays for all ALKs have been developed using TR-FRET system. To evaluated cellular potency, TGF-β-dependent Smad3 phosphorylation assays in A549 (human lung adenocarcinoma cell line) and NMuMG (murine normal mammary gland cell line) cells were established. A TGF-β-mediated Treg differentiation assay was performed as an ex-vivo cellular assay using naive CD4+ T cell isolated from mouse spleen. In vivo anti-tumor efficacies of selected compounds, alone or in combination with anti-PD-1 antibody were assessed in a CT26.WT murine colon carcinoma syngeneic model. Results: We have implemented a high-throughput screening (HTS) against human ALK5 over our in-house compound library. Hit compound 1 was identified from the HTS, and the subsequent Hit-to-Lead study led to a novel thiazole analog 2 as the starting point of lead optimization. Our lead optimization efforts led to advanced lead compound AL1, which exhibited strong inhibitory potency for ALK5 with an IC50 value of single digit nanomolar. Unfortunately AL1 showed very low oral bioavailability in dogs, we continued the optimization study and identified compound AL2 having improved ADME property. In cellular assays, AL2 strongly suppressed the TGF-β-dependent Smad3 phosphorylation in A549 cells. In addition, treatment with AL2 decreased in the percentage of mouse CD4+/CD25+/Foxp3+ Treg cells dose-dependently in the ex vivo TGF-β-mediated Treg differentiation assay. As a monotherapy and combined with an anti-PD-1 antibody, oral administration of AL2 demonstrated robust in vivo antitumor efficacy in the CT26.WT murine colon carcinoma syngeneic model. Conclusions: On the basis of its in vitro potencies, PK profiles, and in vivo efficacies, AL2 is currently being further evaluated in preclinical studies. Citation Format: Mai Arai, Mitsuharu Hanada, Hideki Moriyama, Hiroshi Ohmoto, Kazuhito Naka, Masaaki Sawa. Discovery of a novel activin receptor-like kinases (ALKs) inhibitor targeting TGF-β signaling pathways. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5336.
Supplementary Figures 1-9 from Novel p21-Activated Kinase 4 (PAK4) Allosteric Modulators Overcome Drug Resistance and Stemness in Pancreatic Ductal Adenocarcinoma (2023)

&lt;p&gt;Supplementary Figure1. IC50 analysis for PAM activity across a panel of cell lines. MTT assay was performed at 72 hrs; Supplementary Figure 2. PDAC cell lines were grown at a density of 50,000 cells per well overnight and exposed to PAMs (at 5000 nM for 96 hrs). Apoptosis analysis was performed using Annexin V FITC assay; Supplementary Figure 3. Impact of PAK4 siRNA silencing on the activity of PAMs; Supplementary Figure 4. PAMs induce cancer cell selective cell cycle arrest; Supplementary Figure 5. PAMs suppress PDAC cellular migration; Supplementary Figure 6. DU145 prostate cancer cell line were grown in 100 mm petri dish overnight; Supplementary Figure 7: Flow sorted MiaPaCa-2 CSCs (CD44CD133EpCAM+++) as described in methods section were grown in six well plates at a density of 50,000 cells per well and exposed to 5 μM concentration of PAMs for 72 hrs; Supplementary Figure 8. PAMs molecularly synergize with gemcitabine and oxaliplatin; Supplementary Figure 9. Single agent and combination anti-tumor activity of PAM in sub-cutaneous PDAC tumor models.&lt;/p&gt;