gebhart/patrepeval huggingface dataset:
Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand (2022)

Summary We describe construction of the 660 kilobase synthetic yeast chromosome XI ( synXI ) and reveal how synthetic redesign of non-coding DNA elements impact the cell. To aid construction from synthesized 5 to 10 kilobase DNA fragments, we implemented CRISPR-based methods for synthetic crossovers in vivo and used these methods in an extensive process of bug discovery, redesign and chromosome repair, including for the precise removal of 200 kilobases of unexpected repeated sequence. In synXI , the underlying causes of several fitness defects were identified as modifications to non-coding DNA, including defects related to centromere function and mitochondrial activity that were subsequently corrected. As part of synthetic yeast chromosome design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI , we show here that targeted insertion of these sites can be used to create extrachromosomal circular DNA on demand, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI has uncovered effects of non-coding and extrachromosomal circular DNA, contributing to better understanding of these elements and informing future synthetic genome design.
V1394: Laped® Ureteroscopy Training Model (2007)

You have accessJournal of UrologyVideo Session 5, Tuesday, May 22, 2007, 10:00 am - 12:00 pm1 Apr 2007V1394: Laped® Ureteroscopy Training Model Hak J. Lee, Corollos S. Abdelshehid, Geoffrey N. Box, Jose B.A. Abraham, Elspeth M. McDougall, and Ralph V. Clayman Hak J. LeeHak J. Lee More articles by this author , Corollos S. AbdelshehidCorollos S. Abdelshehid More articles by this author , Geoffrey N. BoxGeoffrey N. Box More articles by this author , Jose B.A. AbrahamJose B.A. Abraham More articles by this author , Elspeth M. McDougallElspeth M. McDougall More articles by this author , and Ralph V. ClaymanRalph V. Clayman More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)32192-XAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "V1394: Laped® Ureteroscopy Training Model." The Journal of Urology, 177(4S), p. 459 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 459 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Hak J. Lee More articles by this author Corollos S. Abdelshehid More articles by this author Geoffrey N. Box More articles by this author Jose B.A. Abraham More articles by this author Elspeth M. McDougall More articles by this author Ralph V. Clayman More articles by this author Expand All Advertisement PDF DownloadLoading ...
3D coronary MR angiography in multiple breath‐holds using a respiratory feedback monitor (1995)

To reduce respiratory blur and ghosts in 3D coronary imaging, a data acquisition scheme using consistent multiple breath-holds was implemented. A navigator echo was acquired and processed in real time to dynamically measure diaphragm position. This information was provided as a visual prompt to the patient to maintain consistency in breath-hold levels such that the variation range of diastolic heart position was less than 2 mm. Preliminary results indicate that this multiple breath-hold acquisition scheme, compared with acquisition under respiration, can significantly reduce blur and ghost artifacts in 3D coronary imaging.
Introduction to network experiments using the GENI cyberinfrastructure (2012)

In this tutorial, we will introduce the SIGMETRICS/Performance community to the vast testbeds, tools and resources openly available through the GENI (Global Environment for Network Innovations) project. We will present details about the distributed computing resources available on GENI for researchers interested in simulation as well as measurement-based performance evaluation experiments. We will demonstrate simple experiments on GENI, and leave them with information on how to run experiments for research and education using GENI resources.
Mechanical Diagnostics System Engineering in IMD HUMS (2006)

The Goodrich Integrated Mechanical Diagnostics Health and Usage System (IMD-HUMS) mechanical diagnostics functionality is the integration of disparate subsystems. When the aircraft is in the appropriate capture window, the primary processing unit (PPU), commands the vibration processing unit (VPU) to capture vibration data and a tachometer reference. This time domain data is processed by standard and proprietary algorithms to generate component condition indicators (CI). These CI are statistics, which when used with a priori configuration data, are mapped into component health indicators (HI). The VPU passes the component HI data to both the PPU and the data transfer unit for ground station display. The PPU, taking the HI data for a component, can determine if the component has a degraded health state. If the component is degraded, the PPU can generate an exceedance message to be reviewed during maintenance debrief. After the flight, all CI and HI data are stored in a data base and is available for display against an aircraft, composite component (e.g. line replaceable unit) and the component itself. The acquisition process is complicated by noise from internal sources (non synchronous gears, shafts and bearing not under analysis) and external sources (changes in airspeed, torque, weight, etc). The HI becomes, in essence, a statistical indicator of the components health. As such, the best estimator of component health is calculated using a Kalman filter. This reduces variance in the data prior to display of the component HI to the aircraft operator. This filtered HI is called the DHI (display health indicator). The DHI uses a priori information and sampling theory to build the best available representation of health of the component. This paper addresses the system engineering required to integrate the vibration processing, decision algorithms, thresholding and filtering to give the operator the best representation of component health. The integration of the system allows IMD-HUMS to have a high degree of certainty in the information given to the operator. This information could potentially improve maintenance practices, lowering aircraft operating cost while improving aircraft safety. The system engineering insures that the recommendation for component maintenance has a low probability of false alarm while maintaining a high probability of component fault detection
Applications of Zeolites to C1 Chemistry: Recent Advances, Challenges, and Opportunities (2020)

C1 chemistry, which is the catalytic transformation of C1 molecules including CO, CO<sub>2</sub> , CH<sub>4</sub> , CH<sub>3</sub> OH, and HCOOH, plays an important role in providing energy and chemical supplies while meeting environmental requirements. Zeolites are highly efficient solid catalysts used in the chemical industry. The design and development of zeolite-based mono-, bi-, and multifunctional catalysts has led to a booming application of zeolite-based catalysts to C1 chemistry. Combining the advantages of zeolites and metallic catalytic species has promoted the catalytic production of various hydrocarbons (e.g., methane, light olefins, aromatics, and liquid fuels) and oxygenates (e.g., methanol, dimethyl ether, formic acid, and higher alcohols) from C1 molecules. The key zeolite descriptors that influence catalytic performance, such as framework topologies, nanoconfinement effects, Brønsted acidities, secondary-pore systems, particle sizes, extraframework cations and atoms, hydrophobicity and hydrophilicity, and proximity between acid and metallic sites are discussed to provide a deep understanding of the significance of zeolites to C1 chemistry. An outlook regarding challenges and opportunities for the conversion of C1 resources using zeolite-based catalysts to meet emerging energy and environmental demands is also presented.
The Google file system (2003)

Article Share on The Google file system Authors: Sanjay Ghemawat Google GoogleView Profile , Howard Gobioff Google GoogleView Profile , Shun-Tak Leung Google GoogleView Profile Authors Info & Claims SOSP '03: Proceedings of the nineteenth ACM symposium on Operating systems principlesOctober 2003Pages 29–43https://doi.org/10.1145/945445.945450Published:19 October 2003Publication History 3,240citation64,109DownloadsMetricsTotal Citations3,240Total Downloads64,109Last 12 Months2,787Last 6 weeks710 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Fibroblast growth factors 1 and 2 are distinct in oligomerization in the presence of heparin-like glycosaminoglycans (1999)

Fibroblast growth factor (FGF) 1 and FGF-2 are prototypic members of the FGF family, which to date comprises at least 18 members. Surprisingly, even though FGF-1 and FGF-2 share more than 80% sequence similarity and an identical structural fold, these two growth factors are biologically very different. FGF-1 and FGF-2 differ in their ability to bind isoforms of the FGF receptor family as well as the heparin-like glycosaminoglycan (HLGAG) component of proteoglycans on the cell surface to initiate signaling in different cell types. Herein, we provide evidence for one mechanism by which these two proteins could differ biologically. Previously, it has been noted that FGF-1 and FGF-2 can oligomerize in the presence of HLGAGs. Therefore, we investigated whether FGF-1 and FGF-2 oligomerize by the same mechanism or by a different one. Through a combination of matrix-assisted laser desorption ionization mass spectrometry and chemical crosslinking, we show here that, under identical conditions, FGF-1 and FGF-2 differ in the degree and kind of oligomerization. Furthermore, an extensive analysis of FGF-1 and FGF-2 uncomplexed and HLGAG complexed crystal structures enables us to readily explain why FGF-2 forms sequential oligomers whereas FGF-1 forms only dimers. FGF-2, which possesses an interface capable of protein association, forms a translationally related oligomer, whereas FGF-1, which does not have this interface, forms only a symmetrically related dimer. Taken together, these data show that FGF-1 and FGF-2, despite their sequence homology, differ in their mechanism of oligomerization.
Retrospective analysis of outpatient acupuncture treatments at MD Anderson Cancer Center. (2014)

e20681 Background: Cancer patients commonly use some form of complementary and alternative medicine, including acupuncture, during cancer treatment; however, there is limited available data about the impact of acupuncture treatment provided in the outpatient oncology clinical setting. Methods: Patients receiving acupuncture from June 2011 through December 2013 were asked to complete a modified Edmonton Symptom Assessment Scale (ESAS; 0-10 scale) before and after each visit. ESAS subscales analyzed included Physical Distress (PHS; range 0-70) and Psychological Distress (PSS; range 0-30). Data were analyzed examining the pre- and post-scores using paired t-tests. Results: A total of 3,915 (664 initial; 3,251 follow-up) acupuncture treatments were provided to 680 patients (average 5.8 visits/patient). The modified ESAS was completed for 2,836 visits (72.4%). The highest rated symptoms reported by all patients were fatigue 2.9 (±2.5), neuropathy 2.8 (±2.8), poor sleep 2.8 (±2.6), and pain 2.5 (±2.5). Symptoms with the greatest reduction in scores from before to after acupuncture included: fatigue (-1.0), pain (-0.8), neuropathy (-0.7), and poor sleep (-0.7), all with p-values <0.0001. There was a significant reduction from pre- to post-treatment in general well-being (-0.7) and in total symptom scores (mean [SD]: 19.4 [15.5] vs. 13 [12.9]; p<0.0001; N=1744). Both the PHS subscale (total of pain, fatigue, nausea, drowsiness, appetite, shortness of breath, and sleep) and the PSS subscale (total of anxiety, depression, and general well-being) demonstrated an improvement of 33% after acupuncture treatment. Conclusions: Patients receiving acupuncture treatment at a major cancer center commonly reported symptoms of fatigue, neuropathy, poor sleep and pain with some immediate improvement in symptoms after treatment. Acupuncture appears to have both physical and psychological benefits for patients. Further research is need to identify which patients are most likely to benefit from acupuncture as an adjunct to cancer treatment.
Abstract P435: Differential Responses of Cerebral Cortical and Renal Cortical Microvessels to Perfusion Pressure and Angiotensin II: Effect of Angiotensin II or DOCA/salt Hypertension (2017)

Background: The brain and kidney autoregulate their blood flow well yet both suffer from hypertensive damage. We found that a pressor infusion of angiotensin II (Ang II) reduced renal blood flow yet did not change cerebral blood flow. Therefore, we tested the hypothesis that their myogenic and Ang II responses differed. Methods: Cerebral cortical microvessels (cerebral) and renal afferent arterioles (afferent) were isolated and perfused from mice after 4 weeks of hypertension from Ang II infusion /high salt/uninephrectomy (Ang II hypertension) or DOCA/high salt/uninephrectomy (DOCA/salt hypertension) or normotensive controls without Ang II or DOCA (n=4-6 per group). Results: Normal cerebral and afferents had similar myogenic responses (Δ diameter: cerebral -21±3 versus afferent-19±2%, NS), but bath addition of Ang II or norepinephrine contracted afferents strongly (Ang II: -48±5%, P&lt;0.001, NE: -95±2%, P&lt;0.001), yet cerebrals were entirely unresponsive. Myogenic responses in Ang II hypertension were reduced selectively by 40% in cerebral microvessels compared to controls (-13±3 versus -21±3%, P&lt;0.001) yet maintained in afferents (-17±3 versus -19±2%, NS). However, myogenic responses in DOCA/salt hypertension were maintained in both groups. Contractions to Ang II in cerebral microvessels were increased in Ang II hypertension (-5±2 versus 0±1%, P&lt;0.01) and increased in DOCA/salt hypertension (-18±8 versus -2±2%, P&lt;0.01). In contrast, contractions to Ang II in afferent arterioles were reduced 50% in Ang II hypertension (-23±5 versus -48±5%, P&lt;0.001) and reduced 25% in DOCA/salt hypertension (-38±6 versus -50±10%, P=0.05). Conclusions: The kidney is well protected from hypertension and excessive Ang II vasoconstriction. However, the breakdown of myogenic responses in the cerebral microvessels during Ang II hypertension and the enhanced Ang II responses in the cerebral microvessels during Ang II and DOCA/salt hypertension make the brain especially vulnerable to hypertensive ischemia or damage.
Architectural considerations for next generation file systems (1999)

We evaluate two architectural alternatives—partitioned and integrated—for designing next generation file systems. Whereas a partitioned server employs a separate file system for each application class, an integrated file server multiplexes its resources among all application classes; we evaluate the performance of the two architectures with respect to sharing of disk bandwidth among the application classes. We show that although the problem of sharing disk bandwidth in integrated file systems is conceptually similar to that of sharing network link bandwidth in integrated services networks, the arguments that demonstrate the superiority of integrated services networks over separate networks are not applicable to file systems. Furthermore, we show that: (i) an integrated server outperforms the partitioned server in a large operating region and has slightly worse performance in the remaining region, (ii) the capacity of an integrated server is larger than that of the partitioned server, and (iii) an integrated server outperforms the partitioned server by up to a factor of 6 in the presence of bursty workloads.
Targeting STAT3 Signaling to Augment the Immunogenicity of B-Cell Lymphomas (2008)

Abstract STAT3 signaling has emerged as a negative regulator of inflammatory responses in immune cells. In bone-marrow derived antigen-presenting cells (APCs), genetic or pharmacologic disruption of STAT3 led to inflammatory cells that effectively prime antigen-specific T-cell responses and restore the responsiveness of tolerized T-cells. In contrast, enhanced Stat3 activity in APCs resulted in increased production of the immunosuppressive cytokine IL-10 and induction of T-cell tolerance1. B-cell lymphomas being tumors derived from B-lymphocytes display intrinsic antigen-presenting capabilities. Augmentation of this APC function has been shown to result in effective anti-lymphoma immunity2. In this study we determined whether targeting Stat3 signaling might influence the intrinsic APC function of malignant B-cells and the responsiveness –or not- of antigen-specific CD4+ T-cells. First, we specifically block STAT3 signaling in A20 lymphoma B-cells by using a dominant negative variant of STAT3, Stat3b. Inhibition of STAT3 resulted in tumor cells capable not only of fully priming naïve antigen-specific CD4+T-cells but also able of restoring the responsiveness of tolerant T-cells from lymphoma bearing mice. Conversely, transfection of A20 B-cells with Stat3c, a constitutively activated mutant form of STAT3, led to T-cell unresponsiveness. Of note, manipulation of STAT3 in B cell tumors was associated with changes in the mRNA expression and protein levels of IL-10. Second, we evaluated the effects of two novel Stat3 inhibitors, CPA-7 (a platinum-containing compound that disrupts STAT3 DNA binding activity) and S3I-201 (inhibitor of Stat3:Stat3 complex formation and Stat3 DNA binding and transcriptional activities) in a murine model of Mantle Cell Lymphoma (MCL). In vitro treatment of FC-muMCL1 cells - derived from a tumor elicited in Em-Cyclin D1 transgenic mice- with increasing concentrations of either CPA-7 or S3I-201 resulted in an enhanced presentation of OVA-peptide to naïve CD4+ T-cells specific for a MHC class II restricted epitope of ovalbumin (OT-II cells). Indeed, these T-cells produce higher levels of IL-2 and IFN-gamma compared to anti-OVA T cells that encountered cognate antigen in untreated FC-muMCL1 cells. More importantly, MCL cells treated with CPA-7 restored the responsiveness of tolerized anti-OVA CD4+ T-cells. Finally, in vivo treatment of MCL-bearing mice with CPA-7 (5 mg/kg/iv given on days +21, +24 and +27 after tumor challenge) resulted in significant inhibition of p-Stat3 in malignant B-cells and augmentation of their APC function. Taken together, STAT3 signaling is involved in the regulation of the antigen-presenting capabilities of B-cell lymphomas and as such represents a novel molecular target to augment the immunogenicity of these tumors.
‘Community cohesion’: Reflections on a flawed paradigm (2012)

This paper interrogates a concept at the core of a social policy agenda that has dominated thinking in the UK over the past decade. It argues that the notion of ‘community cohesion’ is based on a fundamentally flawed interpretation of the sources of tension and conflict in Britain’s towns and cities. It overly ethnicizes societal divisions and essentializes ethnicity. Examining the development of government policy since 2001 the paper shows that the result has been a predominantly culturalist agenda that obscures key sources of division, most notably those related to social class and material inequality. It is argued that the hegemonic status of this policy stream has also undermined the equalities agenda. The paper concludes with a reflection on the implications of the emergence of a Conservative-led coalition government in May 2010.
ChemInform Abstract: Stereoselective Chelate‐Controlled Addition of Grignard Reagents to Unsaturated Medium‐Ring Heterocycles. (1999)

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.
Pre bonding metrology solutions for 3D integration (2010)

This article reports the capability and the recent development of optical profilometry for monitoring 3D integrated circuits. In particular, the capability to profile transparent film stacks, which was quite challenging, is now accessible with the Unifire optical profilometer from Nanometrics. It is demonstrated that the obtained information in term of topography and edge roll off is paramount to improving the 3D integration process. In addition, the implementation of Nanometrics' Advanced Film Capability (AFC) and/or Index Corrected Topography (ICT) may enable more detailed mapping of local within die film thickness and topography respectively.
The transcription factor NAC102 confers cadmium tolerance by regulating WAKL11 expression and cell wall pectin metabolism in Arabidopsis (2023)

Cadmium (Cd) toxicity severely limits plant growth and development. Moreover, Cd accumulation in vegetables, fruits, and food crops poses health risks to animals and humans. Although the root cell wall has been implicated in Cd stress in plants, whether Cd binding by cell wall polysaccharides contributes to tolerance remains controversial, and the mechanism underlying transcriptional regulation of cell wall polysaccharide biosynthesis in response to Cd stress is unknown. Here, we functionally characterized an Arabidopsis thaliana NAC-type transcription factor, NAC102, revealing its role in Cd stress responses. Cd stress rapidly induced accumulation of NAC102.1, the major transcript encoding functional NAC102, especially in the root apex. Compared to wild type (WT) plants, a nac102 mutant exhibited enhanced Cd sensitivity, whereas NAC102.1-overexpressing plants displayed the opposite phenotype. Furthermore, NAC102 localizes to the nucleus, binds directly to the promoter of WALL-ASSOCIATED KINASE-LIKE PROTEIN11 (WAKL11), and induces transcription, thereby facilitating pectin degradation and decreasing Cd binding by pectin. Moreover, WAKL11 overexpression restored Cd tolerance in nac102 mutants to the WT levels, which was correlated with a lower pectin content and lower levels of pectin-bound Cd. Taken together, our work shows that the NAC102-WAKL11 module regulates cell wall pectin metabolism and Cd binding, thus conferring Cd tolerance in Arabidopsis.
Supplementary Fig S21-S24 from Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing (2023)

&lt;p&gt;Supplementary Figures S21-S24 and figure legends&lt;/p&gt;