gebhart/patrepeval huggingface dataset:
Role and Function of c-Jun Protein Complex in Cancer Cell Behavior (2009)

Transcription factors play a crucial role in the regulation of cell behavior by modulating gene expression profiles. Previous studies have described a dual role for the AP-1 family transcription factor c-Jun in the regulation of cellular fate. In various cell types weak and transient activations of c-Jun N-terminal kinase (JNK) and c-Jun appear to contribute to proliferation and survival, whereas strong and prolonged activation of JNK and c-Jun result in apoptosis. These opposite roles played by c-Jun are cell type specific and the molecular mechanisms defining these antonymous c-Jun-mediated responses remain incompletely understood.&#13;\n&#13;\nc-Jun activity in transformed cells is regulated by signalling cascades downstream of oncoproteins such as Ras and Raf. In addition, the pro-proliferative role and the survival promoting function for c-Jun has been described in various cancer models. Furthermore, c-Jun was described to be overexpressed in different cancer types. However, the molecular mechanisms by which c-Jun exerts these oncogenic functions are not all clearly established. Therefore it is of primary interest to further identify molecular mechanisms and functions for c-Jun in cancer. &#13;\n&#13;\nRegulation of gene expression is tightly dependent on accurate protein-protein interactions. Therefore, co-factors for c-Jun may define the functions for c-Jun in cancer. Identification of protein-protein interactions promoting cancer may provide novel possibilities for cancer treatment. In this study, we show that DNA topoisomerase I (TopoI) is a transcriptional co-factor for c-Jun. Moreover, c-Jun and TopoI together promote expression of epidermal growth factor receptor (EGFR) in cancer cells. We also show that the clinically used TopoI inhibitor topotecan reduces EGFR expression. Importantly, the effect of TopoI on EGFR transcription was shown to depend on c-Jun as Jun-/- cells or cells treated with JNK inhibitor SP600125 are resistant to topotecan treatment both in regulation of EGFR expression and cell proliferation. &#13;\n&#13;\nMoreover, c-Jun regulates the nucleolar localization and the function of the ribonucleic acid (RNA) helicase DDX21, a previously identified member of c-Jun protein complex. In addition, c-Jun stimulates rRNA processing by supporting DDX21 rRNA binding. Finally, this study characterizes a DDX21 dependent expression of cyclin dependent kinase (Cdk) 6, a correlation of DDX21 expression with prostate cancer progression and a substrate binding dependency of DDX21 nucleolar localization in prostate cancer cells. &#13;\n&#13;\nTaken together, the results of this study validate the c-Jun-TopoI interaction and precise the c-Jun-DDX21 interaction. Moreover, these results show the importance for protein-protein interaction in the regulation of their cellular functions in cancer cell behavior. Finally, the results presented here disclose new exciting therapeutic opportunities for cancer treatment.
An Algorithm for Determining the Endpoints of Isolated Utterances (1975)

An important problem in speech processing is to detect the presence of speech in a background of noise. This problem is often referred to as the endpoint location problem. By accurately detecting the beginning and end of an utterance, the amount of processing of speech data can be kept to a minimum. The algorithm proposed for locating the endpoints of an utterance is based on two measures of the signal, zero crossing rate and energy. The algorithm is inherently capable of performing correctly in any reasonable acoustic environment in which the signal-to-noise ratio is on the order of 30 dB or better. The algorithm has been tested over a variety of recording conditions and for a large number of speakers and has been found to perform well across all tested conditions.
Evaluating Human Operator Performance in a Fully Immersive Virtual Reality Environment (2002)

Abstract : The Virtual Reality Applications Center is a national leader in the increasingly important field of applications of virtual reality to the challenges of engineering and science. This DURIP contract provided peripheral equipment for VRAC's C6, a 360-degree immersion device used to display synthetic environments in real time. C6 includes six stereoscopic screens, a three-dimensional sound system, and wireless technologies. C6, which cost over $5 million to design and build, was made possible by support from the Air Force of Scientific Research, the National Science Foundation, Iowa State University and private industry. DURIP funds helped purchase a tracking system, networking hardware, and storage devices crucial to the operation of the system. We are now using the C6 on two major defense related projects applying virtual reality interfaces to improve operational readiness and situational awareness. The first of these projects, sponsored by the Air Force Research Lab's Human Effectiveness Directorate, is investigating the use of collaborative computer immersion to recreate a Joint Battlespace. The second is a multi-year collaboration between a VRAC research team, the Iowa National Guard, and the Iowa Technology Center. The objective of this effort is to investigate, create and evaluate the use of immersive interfaces as tools to improve the operational readiness of Iowa National Guard staff, both Army and Air.
Differential phosphorylation of IRS-1 and IRS-2 by insulin and IGF-I receptors (2006)

The specific contribution of insulin and IGF-I receptors to IRS-protein activation remains elusive. We studied the signalling properties of AspB10-insulin, an analog with enhanced affinity for the IGF-I receptor, in comparison to native insulin using primary human skeletal muscle cells. In myoblasts regular insulin and AspB10-insulin were equipotent in stimulating the IRS cascade, whereas this analog induced a significantly higher Shc phosphorylation. Phosphorylation of IRS-1 in response to insulin was inhibited equally by blocking either the insulin or the IGF-I receptor. IRS-1 activation by AspB10-insulin was only inhibited by blocking the IGF-I receptor. IRS-2 phosphorylation induced by both insulin and AspB10-insulin was nearly insensitive to blocking the insulin receptor, being predominantly mediated by the IGF-I receptor. We conclude that in myoblasts IRS-2, but not IRS-1, functions as preferred substrate for the IGF-I receptor. These data suggest a specific role for IRS-2 in growth and differentiation of human skeletal muscle.
LATE-PCR for LoC Molecular Diagnostics Devices and Its Application to the Sensitive Detection of SARS-CoV-2 (2021)

The emergence of the novel coronavirus, SARS-CoV-2, has highlighted the need for rapid, accurate, and point-of-care diagnostic testing. Lab-on-a-Chip (LoC) devices offer the possibility to run such tests at a low cost, while at the same time permitting the multiplexed detection of several viruses when coupled with microarray detection of the amplified products. Herein, we report the development of a protocol for the qualitative detection of SARS-CoV-2, through the design of appropriate primers that target the evolutionary conserved regions of the virus. The proposed protocol relies on an improved version of asymmetric RT-PCR, the linear-after-the-exponential (LATE)-PCR that uses primers that are deliberately designed for use at unequal concentrations. As a result, LATE-PCR exhibits similar efficiency to symmetric PCR, while promoting accumulation of single-stranded products that can subsequently hybridize to a single-strand DNA probe-spotted microarray. The performance of the developed LATE-PCR protocol was compared to that of symmetric RT-PCR, and validated with the use of artificial viral RNA and nasopharyngeal swab samples from real patients. Furthermore, and in order to illustrate its potential for integration into a biosensor platform, the amplicons were allowed to hybridize with probes that were covalently immobilized onto commercially available functionalized glass, without the need for heat denaturation.
Identification of an Extracellular Polysaccharide Network Essential for Cytochrome Anchoring and Biofilm Formation in Geobacter sulfurreducens (2010)

Transposon insertions in Geobacter sulfurreducens GSU1501, part of an ATP-dependent exporter within an operon of polysaccharide biosynthesis genes, were previously shown to eliminate insoluble Fe(III) reduction and use of an electrode as an electron acceptor. Replacement of GSU1501 with a kanamycin resistance cassette produced a similarly defective mutant, which could be partially complemented by expression of GSU1500 to GSU1505 in trans. The Δ1501 mutant demonstrated limited cell-cell agglutination, enhanced attachment to negatively charged surfaces, and poor attachment to positively charged poly-d-lysine- or Fe(III)-coated surfaces. Wild-type and mutant cells attached to graphite electrodes, but when electrodes were poised at an oxidizing potential inducing a positive surface charge (+0.24 V versus the standard hydrogen electrode [SHE]), Δ1501 mutant cells detached. Scanning electron microscopy revealed fibrils surrounding wild-type G. sulfurreducens which were absent from the Δ1501 mutant. Similar amounts of type IV pili and pilus-associated cytochromes were detected on both cell types, but shearing released a stable matrix of c-type cytochromes and other proteins bound to polysaccharides. The matrix from the mutant contained 60% less sugar and was nearly devoid of c-type cytochromes such as OmcZ. The addition of wild-type extracellular matrix to Δ1501 cultures restored agglutination and Fe(III) reduction. The polysaccharide binding dye Congo red preferentially bound wild-type cells and extracellular matrix material over mutant cells, and Congo red inhibited agglutination and Fe(III) reduction by wild-type cells. These results demonstrate a crucial role for the xap (extracellular anchoring polysaccharide) locus in metal oxide attachment, cell-cell agglutination, and localization of essential cytochromes beyond the Geobacter outer membrane.
Generation of New Enzymes via Covalent Modification of Existing Proteins (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneration of New Enzymes via Covalent Modification of Existing ProteinsDongfeng Qi, Cheng-Min Tann, Dietmar Haring, and Mark D. DistefanoView Author Information Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455 Cite this: Chem. Rev. 2001, 101, 10, 3081–3112Publication Date (Web):September 22, 2001Publication History Received20 February 2001Published online22 September 2001Published inissue 1 October 2001https://doi.org/10.1021/cr000059oCopyright © 2001 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2627Altmetric-Citations231LEARN 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 InReddit Read OnlinePDF (557 KB) Get e-AlertsSUBJECTS:Conjugate acid-base pairs,Crystal cleavage,Genetics,Monomers,Peptides and proteins Get e-Alerts
Time–Domain Propagation Measurements of the NASA Space-Power Facility (2010)

This report describes a recent measurement effort conducted by the Institute for Telecommunication Sciences at a chamber located at the NASA Space Power Facility (SPF) in Sandusky, Ohio. The report describes the chamber and the measurement system, and provides some selected time- and frequency-domain results. A detailed description of the measurement procedures and post-processing is provided. The results obtained indicate that the SPF chamber exhibits robust reverberant behavior. The flexibility and efficiency of time-domain measurements is also demonstrated.
Near real time information mining in multilingual news (2009)

This paper presents a near real-time multilingual news monitoring and analysis system that forms the backbone of our research work. The system integrates technologies to address the problems related to information extraction and analysis of open source intelligence on the World Wide Web. By chaining together different techniques in text mining, automated machine learning and statistical analysis, we can automatically determine who, where and, to a certain extent, what is being reported in news articles.
The Search for Peptidoleukotriene Antagonists (1991)

DOAJ is a unique and extensive index of diverse open access journals from around the world, driven by a growing community, committed to ensuring quality content is freely available online for everyone.
Palladium catalysed meta-C–H functionalization reactions (2016)

The directing group assisted site selective C-H functionalization approach is having a continuous impact in the field of natural product synthesis, drug discovery and material sciences. While ortho-selective C-H functionalization has been studied extensively, meta-selective C-H functionalization has been less explored. Recent studies have highlighted the efficacy of palladium as a catalyst in activating the meta-C-H bond of arenes. Notably, the introduction of a novel palladium catalysed directing template based approach to activate the remote meta-position has created a revolutionary impact towards seeking a solution to this long standing challenge. In this review we summarize recent advances in palladium catalysed meta-C-H functionalization that have helped in creating a new outlook towards modern organic synthesis.
Tn5Prime, a Tn5 based 5′ capture method for single cell RNA-seq (2018)

RNA-sequencing (RNA-seq) is a powerful technique to investigate and quantify entire transcriptomes. Recent advances in the field have made it possible to explore the transcriptomes of single cells. However, most widely used RNA-seq protocols fail to provide crucial information regarding transcription start sites. Here we present a protocol, Tn5Prime, that takes advantage of the Tn5 transposase-based Smart-seq2 protocol to create RNA-seq libraries that capture the 5' end of transcripts. The Tn5Prime method dramatically streamlines the 5' capture process and is both cost effective and reliable. By applying Tn5Prime to bulk RNA and single cell samples, we were able to define transcription start sites as well as quantify transcriptomes at high accuracy and reproducibility. Additionally, similar to 3' end-based high-throughput methods like Drop-seq and 10× Genomics Chromium, the 5' capture Tn5Prime method allows the introduction of cellular identifiers during reverse transcription, simplifying the analysis of large numbers of single cells. In contrast to 3' end-based methods, Tn5Prime also enables the assembly of the variable 5' ends of the antibody sequences present in single B-cell data. Therefore, Tn5Prime presents a robust tool for both basic and applied research into the adaptive immune system and beyond.
Treating Insomnia in Older Adult Patients: Limiting Benzodiazepine Use (2019)

As aging comes, an increased prevalence of medical maladies and chronic pain independently or interactively disrupt sleep, which in turn can exacerbate either one. Furthermore, anxiety about pain can further negatively impact sleep. Fortunately, good quality sleep can improve pain management. Because benzodiazepine receptor agonists (including the “Z” drugs) can reduce anxiety and improve sleep, they seem a convenient choice. However, their use in this population, particularly for more than short-term (guidelines range from 2 to 6 weeks max), is not recommended because of increased likelihood of falls, further disruption of sleep, dependence, and problems with discontinuation (withdrawal). Besides, this population is often likely to take concomitant medication for pain or other central nervous system depressants leading to potentially serious and even life-threatening interactions involving synergistic amplification of respiratory depression (opioids being a particularly dangerous interaction). Therefore, insomnia in older adults should ideally be treated with a non-benzodiazepine receptor agonist; if indicated, they may be used, but should be closely monitored and tapered to avoid long-term adverse problems (direct or from withdrawal). Older adult patients with insomnia may be more optimally treated with sleep aids that do not interact with the GABAA receptor.
Measuring the Failure of Planning and Its Impact on Sustainable Travel in Dublin, Ireland (2011)

With the end of the recent housing boom in Dublin, Ireland, it is perhaps a good time to analyze how the commuting and development patterns have been impacted by this unprecedented level of housing construction in recent years. In this research, the authors focus specifically on the commuting patterns of those individuals living in the newest housing stock to see how these patterns adhere to the Irish government’s stated transportation and sustainability goals. Data from the 2006 Census of Ireland is used to explore the commuting patterns of individuals living in the four counties that make up Dublin who lived in the most recently constructed housing stock (built between 2001 and 2006, constituting almost one fifth of all housing units in Dublin). The results demonstrate that the latter populations were more likely to have longer commute times and to depart earlier to get to work. The findings also suggest that, despite ambitious government level goals, housing built during the property boom was more likely to be in low-density areas.
Minimizing Energy and Computation in Long-Running Software (2021)

Long-running software may operate on hardware platforms with limited energy resources such as batteries or photovoltaic, or on high-performance platforms that consume a large amount of energy. Since such systems may be subject to hardware failures, checkpointing is often used to assure the reliability of the application. Since checkpointing introduces additional computation time and energy consumption, we study how checkpoint intervals need to be selected so as to minimize a cost function that includes the execution time and the energy. Expressions for both the program’s energy consumption and execution time are derived as a function of the failure probability per instruction. A first principle based analysis yields the checkpoint interval that minimizes a linear combination of the average energy consumption and execution time of the program, in terms of the classical “Lambert function”. The sensitivity of the checkpoint to the importance attributed to energy consumption is also derived. The results are illustrated with numerical examples regarding programs of various lengths and showing the relation between the checkpoint interval that minimizes energy consumption and execution time, and the one that minimizes a weighted sum of the two. In addition, our results are applied to a popular software benchmark, and posted on a publicly accessible web site, together with the optimization software that we have developed.
Trends in utilization of benzodiazepine and Z‐drugs in Israel (2017)

Conventional BZDs and Z-drugs remained the treatment of choice for sleeping disorders in Israel during the study period. These results are, in certain cases, in contrast to current practice recommendations and guidelines and point at a need in better dissemination of these guidelines among prescribers in Israel.
Peripheral Neuromodulation for the Treatment of Postamputation Neuroma Pain (2016)

Neuroma pain can be severe, persistent, and treatment resistant. We present a case of a 37-year-old female amputee who suffered from severe neuroma pain, which had proved resistant to pharmacologic treatment, glycerol injections, spinal cord stimulation, radiofrequency thermocoagulation, and repeated surgical removals. After treatment with peripheral nerve stimulation, using a St. Jude Medical Octrode lead implanted percutaneously under ultrasound guidance close to her painful neuroma, her ongoing pain dramatically decreased from 8 to 3 on a numeric rating scale (0-10). Peripheral neuromodulation is a promising relatively new treatment that can be used for neuroma pain.
Supplementary figure legends from Preclinical Anticancer Efficacy of BET Bromodomain Inhibitors Is Determined by the Apoptotic Response (2023)

&lt;p&gt;This file contains the legends for the six supplementary figures.&lt;/p&gt;
The oral secretion from Cotton Boll Weevil (Anthonomus grandis) induces defense responses in cotton (Gossypium spp) and Arabidopsis thaliana (2022)

Cotton Boll Weevil (CBW, Anthonomus grandis) is a devastating insect-pest affecting cotton (Gossypium spp), using cotton internal floral structures for larval development, making it difficult to control. Little is known about the mechanism underlying CBW-plant interactions leading to infestation or resistance. Here, we investigated the plant molecular responses triggered by CBW extracts from eggs, larvae, and oral secretions (OS) of larvae and adult. The MAPK pathway, one of the early signaling events in plant pattern-triggered immunity (PTI), was activated by CBW extracts in Arabidopsis thaliana. In cotton, CBW OS activated GhMPK3 and GhMPK6. Importantly, CBW OS activated the PTI marker gene FRK1 and the effector-triggered immunity (ETI) marker gene WRKY46 in Arabidopsis reporter lines, suggesting that Herbivore-Associated Molecular Patterns (HAMPs) present in OS from CBW can elicit plant defense responses in cotton and Arabidopsis. Interestingly, CBW OS-induced MAPK activation shows similar patterns in wild-type and Arabidopsis mutants, which bear mutations in already known receptor and co-receptors complex components, suggesting a distinct signaling cascade likely triggered by the putative HAMPs present in CBW OS. The work points to potentials in the identification and development of CBW extract-derived elicitors for effective pest control combating CBW infestation.
Confinement with Myosin-II suppression increases heritable loss of chromosomes, using live-cell ChReporters (2023)

ABSTRACT Matrix around cells exerts many effects, some of which depend on the putative tumor suppressor Myosin-II, but whether such factors affect DNA sequences in a cell remains unclear. Here, live-cell monitoring of changes to chromosome copy numbers is developed and studied under diverse perturbations, including Myosin-II inhibition in confined mitosis. Squeezing of mitotic cells is seen in vivo and kills in vitro , but stem cells and cancer cells that survive show heritable loss of mono-allelic GFP/RFP-tagged constitutive genes that function as novel Chromosome-reporters (ChReporters). Myosin-II suppression increases such loss in 3D &amp; 2D confinement but not in standard 2D, with “lethal” multipolar divisions proving myosin-dependent. Viable chromosome loss after confined mitosis associates more with mis-segregation than with multipolars or division number. Solid human tumors and teratomas in mice also show ChReporter loss and a confinement-signature of Myosin-II suppression, although losses are selected against in 2D culture. Heritable loss in rigid-confinement also appears independent of a spindle assembly checkpoint that functions in 2D. Confinement and myosin-II thus regulate pathways of heritable mechanogenetic change.