gebhart/patrepeval huggingface dataset:
Plasminogen binding and activation at the breast cancer cell surface: the integral role of urokinase activity (2007)

We show that the majority of lysine-dependent plasminogen binding to breast cancer cells is ultimately regulated by plasmin activity and is dependent on the presence of significant levels of active uPA. The existence of a proteolytic positive feedback loop in plasminogen activation has profound implications for the ability of breast cancer cells expressing high amounts of uPA to accumulate a large proteolytic capacity at the cell surface, thereby conferring invasive potential.
A Small-Molecule Inhibitor Targeting the Mitotic Spindle Checkpoint Impairs the Growth of Uterine Leiomyosarcoma (2012)

Our results show that dysregulated centrosome function and spindle assembly are a robust feature of ULMS that can be targeted to slow its growth both in vitro and in vivo. These observations identify novel directions that can be potentially used to improve clinical outcomes for this disease.
Comparisons among the larger genome segments of six nodaviruses and their encoded RNA replicases (2001)

The Nodaviridae are a family of isometric RNA viruses that infect insects and fish. Their genomes, which are among the smallest known for animal viruses, consist of two co-encapsidated positive-sense RNA segments: RNA1 encodes the viral contribution to the RNA-dependent RNA polymerase (RdRp) which replicates the viral genome, whereas RNA2 encodes the capsid protein precursor. In this study, the RNA1 sequences of two insect nodaviruses - Nodamura virus (the prototype of the genus) and Boolarra virus - are reported as well as detailed comparisons of their encoded RdRps with those of three other nodaviruses of insects and one of fish. Although the 5' and 3' untranslated regions did not reveal common features of RNA sequence or secondary structure, these divergent viruses showed similar genome organizations and encoded RdRps that had from 26 to 99% amino acid sequence identity. All six RdRp amino acid sequences contained canonical RNA polymerase motifs in their C-terminal halves and conserved elements of predicted secondary structure throughout. A search for structural homologues in the protein structure database identified the poliovirus RdRp, 3D(pol), as the best template for homology modelling of the RNA polymerase domain of Pariacoto virus and allowed the construction of a congruent three-dimensional model. These results extend our understanding of the relationships among the RNA1 segments of nodaviruses and the predicted structures of their encoded RdRps.
Regenerative cell therapy for the treatment of hyperbilirubinemic Gunn rats with fresh and frozen human induced pluripotent stem cells‐derived hepatic stem cells (2019)

Pluripotent stem cells have been investigated as a renewable source of therapeutic hepatic cells, in order to overcome the lack of transplantable donor hepatocytes. Whereas different studies were able to correct hepatic defects in animal models, they focused on the most mature phenotype of hepatocyte-like cells (HLCs) derived from pluripotent stem cells and needed freshly prepared cells, which limits clinical applications of HLCs. Here, we report the production of hepatic stem cells (pHSCs) from human-induced pluripotent stem cells (hiPSCs) in xeno-free, feeder-free, and chemically defined conditions using as extracellular matrix a recombinant laminin instead of Matrigel, an undefined animal-derived matrix. Freshly prepared and frozen pHSCs were transplanted via splenic injection in Gunn rats, the animal model for Crigler-Najjar syndrome. Following cell transplantation and daily immunosuppression treatment, bilirubinemia was significantly decreased (around 30% decrease, P < .05) and remained stable throughout the 6-month study. The transplanted pHSCs underwent maturation in vivo to restore the deficient metabolic hepatic function (bilirubin glucuronidation by UGT1A1). In conclusion, we demonstrate for the first time the differentiation of hiPSCs into pHSCs that (a) are produced using a differentiation protocol compatible with Good Manufacturing Practices, (b) can be frozen, and (c) are sufficient to demonstrate in vivo therapeutic efficacy to significantly lower hyperbilirubinemia in a model of inherited liver disease, despite their immature phenotype. Thus, our approach provides major advances toward future clinical applications and would facilitate cell therapy manufacturing from human pluripotent stem cells.
Twenty years of progress in angiotensin converting enzyme 2 and its link to SARS-CoV-2 disease (2020)

The virulence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the aggressive nature of the disease has transformed the universal pace of research in the desperate attempt to seek effective therapies to halt the morbidity and mortality of this pandemic. The rapid sequencing of the SARS-CoV-2 virus facilitated identification of the receptor for angiotensin converting enzyme 2 (ACE2) as the high affinity binding site that allows virus endocytosis. Parallel evidence that coronavirus disease 2019 (COVID-19) disease evolution shows greater lethality in patients with antecedent cardiovascular disease, diabetes, or even obesity questioned the potential unfavorable contribution of angiotensin converting enzyme (ACE) inhibitors or angiotensin II (Ang II) receptor blockers as facilitators of adverse outcomes due to the ability of these therapies to augment the transcription of Ace2 with consequent increase in protein formation and enzymatic activity. We review, here, the specific studies that support a role of these agents in altering the expression and activity of ACE2 and underscore that the robustness of the experimental data is associated with weak clinical long-term studies of the existence of a similar regulation of tissue or plasma ACE2 in human subjects.
Health risk in agricultural villages practicing wastewater irrigation in central Mexico: perspectives for protection. (2000)

9,435 individuals participated in a cross-sectional survey in the irrigation districts of the Mezquital Valley (central Mexico). Exposure groups were: 848 households irrigating with untreated wastewater, 544 households irrigating with the effluent from a series of interconnected reservoirs, and 928 households farming with natural rainfall. The unit of analysis was the individual, and the health outcomes included diarrhoeal diseases and Ascaris lumbricoides infection. Water quality was assessed using faecal coliforms (FC) and nematode eggs, as suggested by (WHO, 1989) for the safe use of wastewater in agriculture. Children from households irrigating with untreated wastewater (10(8) FC/100 mL and 135 nematode eggs/L) had a 33% higher risk of diarrhoeal diseases and a fivefold increase in risk of A. lumbricoides infection (OR = 5.71) compared to children from the control group, farming with rainfall. The risk of A. lumbricoides infection in older individuals was even higher (OR = 13.18). The final analysis showed that drinking unboiled water and cultivating vegetables crops were both associated with a higher risk of diarrheal diseases (OR = 1.45 and 2.00); individuals infected with A. lumbricoides infection came mostly from landless households with poorer dwellings and low standards of sanitation (OR = 2.20, 2.23, 1.72 and 1.43, respectively). These results are discussed in the context of health protection measures and policy recommendations.
Diphtheria toxin‐mediated transposon‐driven poly (A)‐trapping efficiently disrupts transcriptionally silent genes in embryonic stem cells (2020)

Random gene trapping is the application of insertional mutagenesis techniques that are conventionally used to inactivate protein-coding genes in mouse embryonic stem (ES) cells. Transcriptionally silent genes are not effectively targeted by conventional random gene trapping techniques, thus we herein developed an unbiased poly (A) trap (UPATrap) method using a Tol2 transposon, which preferentially integrated into active genes rather than silent genes in ES cells. To achieve efficient trapping at transcriptionally silent genes using random insertional mutagenesis in ES cells, we generated a new diphtheria toxin (DT)-mediated trapping vector, DTrap that removed cells, through the expression of DT that was induced by the promoter activity of the trapped genes, and selected trapped clones using the neomycin-resistance gene of the vector. We found that a double-DT, the dDT vector, dominantly induced the disruption of silent genes, but not active genes, and showed more stable integration in ES cells than the UPATrap vector. The dDT vector disrupted differentiated cell lineage genes, which were silent in ES cells, and labeled trapped clone cells by the expression of EGFP upon differentiation. Thus, the dDT vector provides a systematic approach to disrupt silent genes and examine the cellular functions of trapped genes in the differentiation of target cells and development.
Little volume change in orbital ordering transition in manganite thin films (2010)

We have investigated the structural feature of orbital-ordering manganite thin films fabricated on the perovskite (011) substrates by means of synchrotron x-ray diffraction technique. Like bulk manganites, these films show large jumps in lattice parameters at the orbital ordering transition temperature, which clearly show the transitions are first order. However, the magnitude of the volume change at the transition temperature for the films is much smaller than that for the orbital ordering transition in bulk manganite. This difference is understood by taking into account the stress from the substrate.
Endothelin Receptor Blocker Reverses Breast Cancer–Induced Cardiac Remodeling (2023)

Although our findings should be further examined in other preclinical/clinical models, our data suggest that endothelin receptor blockers may play a role in cardiac health in individuals with breast cancer. (Understanding and Treating Heart Failure With Preserved Ejection Fraction: Novel Mechanisms, Diagnostics and Potential Therapeutics [Alberta HEART]; NCT02052804 and Multidisciplinary Team Intervention in Cardio-Oncology [TITAN]; NCT01621659).
Prologue (2006)

Abstract This chapter begins with the discussion of the low register (or plain English) and its history by looking closely at Shakespeare's King Lear. It draws up Lear's description of Edgar as an example of this low register. The chapter looks at the history of plain English by dividing it into two distinct periods that differ from one another greatly. The first period lasts roughly from 1500 to 1660, which includes Shakespeare. The second period begins with Wordsworth and continues on towards the present, presenting a gap of 140 years between the two periods. The chapter is also mostly devoted to the individual that lay the groundwork for Wordsworth: John Locke, and thus examines the earliest arguments for plain English.
Study of dynamic debris impact load on flexible debris-resisting barriers and the dynamic pressure coefficient (2022)

The use of steel flexible barriers to mitigate landslide risk on natural hillsides is becoming common in the past decade in Hong Kong. The current design approach for this kind of barrier structure involves the adoption of the hydrodynamic load model to predict dynamic impact forces, followed by non-linear structural analyses of flexible barriers using numerical programs based on the pseudo-static force method. From local design guidelines, the dynamic pressure coefficient, a critical input parameter in the hydrodynamic load model, is taken as 2.0. This empirically considers the effect of impacts from boulders up to 2.0 m in diameter. With a view to rationalising the design approach, a series of physical impact tests and numerical analyses was conducted to investigate the dynamic debris impact on flexible barriers and the resulting barrier response. The physical impact tests involved up to 9 m 3 of debris resisted by a 1.5 m high steel ring-net barrier. The tests were conducted in the 28 m long large-scale flume facility at the Kadoorie Centre in Hong Kong. Numerical modelling using computer programs LS-DYNA and NIDA-MNN was conducted to analyse the dynamic response of flexible barriers with different structural forms. The study aims to evaluate the dynamic pressure coefficient and to verify the current design approach based on the suggested dynamic pressure coefficient from this study. Results indicate that a dynamic pressure coefficient of 1.0 is, in general, appropriate for design purposes if the debris comprises primarily water and fine-grained particles.
Phase II study of weekly paclitaxel with trastuzumab and pertuzumab in patients with HER2-overexpressing metastatic breast cancer (MBC): Updated progression-free survival with overall survival result. (2015)

607 Background: We previously reported results of the phase II breast cancer (BC) trial of weekly paclitaxel (T), trastuzumab (H) and pertuzumab (P) with its primary endpoint of 6-month (mo) progression-free survival (PFS) of 86% (95% CI, 75% to 92%) in patients (pts) with HER2+ metastatic (M) BC treated in first- and second-line settings. At a median (med) follow-up (FU) of 21 mo, med PFS was 19.5 mo overall. Updated PFS and OS analysis from this fully accrued study is presented here. Methods: Pts with HER2+ MBC with 0-1 prior treatment (Rx) were eligible. Rx was weekly (w) T (80mg/m2), q3w H (loading dose 8mg/kg → 6mg/kg) and q3w P (loading dose 840mg → 420mg), all given intravenously. Primary endpoint was 6 mo-PFS. Secondary endpoints included 6-mo and median OS. Evaluable pts received at least one full dose of Rx. Results: From January 2011 to December 2013, 69 pts were enrolled: 51 (74%) and 18 (26%) treated in first- and second-line metastatic settings, respectively. 67 were evaluable for efficacy. As of 12-01-14, 26/67 pts (39%) remain progression-free (6 CR, 13 PR and 7 SD); 34 pts have progressed and there are 51 survivors. At a med FU of 23 mo (range, 3-40 mo), 6-mo PFS was 85% (95% CI, 74%-92%). Med PFS was 21.4 mo (95% CI, 13.8-NR) overall and 26.1 mo (95% CI, 17.0-NR) and 16.4 mo (95% CI, 8.5-NR) for pts with 0-1 prior Rx, respectively. 6-mo OS was 98% (95% CI, 90%-100%) and med OS was 37.5 mo (95% CI 31-NR). Median duration of ChemoRx was 30 weeks. Rx was well-tolerated; there were no febrile neutropenia and no symptomatic left ventricular systolic dysfunction. Conclusions: Updated analysis demonstrates that weekly paclitaxel, when added to H and P, is associated with prolonged PFS and OS and a favourable toxicity profile and should be considered as a therapeutic option in this patient population Clinical trial information: NCT01276041.
On the environmental competitiveness of sodium-ion batteries under a full life cycle perspective – a cell-chemistry specific modelling approach (2021)

Assessing different sodium-ion against current lithium-ion battery cells shows large difference between cell chemistries and a good environmental performance for manganese and Prussian blue-based cathodes under a full life cycle perspective.
Genetic variations on 31 and 450 residues of influenza A nucleoprotein affect viral replication and translation (2020)

These findings indicated variations identified in evolution have roles in modulating viral replication in vitro and in vivo. This study demonstrates that the interaction between variations of NP during virus evolution deserves future attention.
Polymer‐Supported Anisotropic Submicrometer‐Patterned Electrodes for Displays (2005)

An anisotropic electrode that exhibits one-dimensional conductivity is readily fabricated from self-organized metal deposition onto friction-transferred poly(tetrafluoroethylene) (PTFE) films. An organic electroluminescent device was constructed on the anisotropic electrode (see Figure), and the emitting area can be easily adjusted by varying the contact width of the silver paste applied subsequently on the electrode.
Controlled Synthesis of Cross-Linked Ultrathin Polymer Films by Using Surface-Initiated Atom Transfer Radical Polymerization (2001)

Oberflächeninitiierte Atom-Transfer-Radikal-Polymerisation von Ethylenglycoldimethacrylat bei Raumtemperatur führt zu homogenen quervernetzten Polymerfilmen (siehe Bild). Bei dieser „lebenden“ Reaktion findet keine Polymerisation in der Lösung statt, sodass Physisorption verhindert wird und einheitliche quervernetzte Filme mit kontrollierbaren Filmdicken zwischen 3 und 300 nm entstehen.
Emergence of Epidemic Dengue-1 Virus in the Southern Province of Sri Lanka (2016)

We describe the first epidemic of DENV-1 in the Southern Province of Sri Lanka in a population known to be susceptible to this serotype because of prior study. Dengue accounted for 40% of acute febrile illnesses in the current study. The emergence of DENV-1 as the foremost serotype in this densely populated but agrarian population highlights the changing epidemiology of dengue and the need for continued surveillance and prevention.
Bromoalkane-degrading Pseudomonas strains (1993)

Two Pseudomonas isolates, named ES-1 and ES-2, were shown to possess a wide degradative spectrum for haloalkanes in general and bromoalkanes in particular but did not degrade nonsubstituted alkanes. The utilization of water-insoluble haloalkanes, such as 1-bromooctane, appeared to consist of three phases: (i) extracellular emulsification by a constitutively excreted, broad-spectrum surface-active agent, (ii) dehalogenation by an inducible hydrolytic dehalogenase (possibly periplasmic), and (iii) intracellular degradation of the residual carbon skeleton. Several observations suggest the existence of more than one dehalogenase in strain ES-2.
4D AVO: Multi-Vintage Amplitude Versus Offset Analysis (2019)

Summary A seismic survey has up to five dimensions: the 3D cubes with inline, crossline and 2-way time (TWT) dimensions as well as offset and azimuth. With repeated measurements (4D seismic), there is an additional axis: the elapsed time. Time-lapse seismic data can then be seen as a six-dimensional volume or a 5D movie. In traditional pre-stack studies, amplitude is analyzed as a function of incidence angle (AVA) and/or azimuthal direction (AVAz). In this paper, we propose a tool to extend the analysis of the Amplitude Versus Offset (AVO) behavior in conjunction with the elapsed time dimension. The changes in AVO with elapsed time provides a data reduction, that can lead to a clean 4D response of the changes observed through the monitoring period. Its applications to various processing and interpretation processes are discussed in the paper.
Computation of the worst-case covariance for linear systems with uncertain parameters (2002)

For a class of linear systems with unknown parameters that lie in intervals, the authors present a branch and bound algorithm for computing the worst-case covariance of the state. An example is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Variance Reduced Stochastic Gradient Descent with Neighbors (2015)

Stochastic Gradient Descent (SGD) is a workhorse in machine learning, yet its slow convergence can be a computational bottleneck. Variance reduction techniques such as SAG, SVRG and SAGA have been proposed to overcome this weakness, achieving linear convergence. However, these methods are either based on computations of full gradients at pivot points, or on keeping per data point corrections in memory. Therefore speed-ups relative to SGD may need a minimal number of epochs in order to materialize. This paper investigates algorithms that can exploit neighborhood structure in the training data to share and re-use information about past stochastic gradients across data points, which offers advantages in the transient optimization phase. As a side-product we provide a unified convergence analysis for a family of variance reduction algorithms, which we call memorization algorithms. We provide experimental results supporting our theory.
CONTRIBUTION OF INTRAGENIC SEQUENCES TO CALCIUM REGULATION OF C-FOS TRANSCRIPTION (1999)

Conference Abstract| June 01 1999 CONTRIBUTION OF INTRAGENIC SEQUENCES TO CALCIUM REGULATION OF C-FOS TRANSCRIPTION Claudia Lange; Claudia Lange 1Medical Research Council, Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, England e-mail: cml@mrc-lmb.cam.ac.uk Search for other works by this author on: This Site PubMed Google Scholar Hilmar Bading Hilmar Bading 1Medical Research Council, Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, England e-mail: cml@mrc-lmb.cam.ac.uk Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1999) 27 (3): A99. https://doi.org/10.1042/bst027a099 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation Claudia Lange, Hilmar Bading; CONTRIBUTION OF INTRAGENIC SEQUENCES TO CALCIUM REGULATION OF C-FOS TRANSCRIPTION. Biochem Soc Trans 1 June 1999; 27 (3): A99. doi: https://doi.org/10.1042/bst027a099 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 ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1999 Biochemical Society1999 Article PDF first page preview Close Modal You do not currently have access to this content.
Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake (2011)

Lake Pavin is a meromictic crater lake located in the French Massif Central area. In this ecosystem, most methane (CH(4)) produced in high quantity in the anoxic bottom layers, and especially in sediments, is consumed in the water column, with only a small fraction of annual production reaching the atmosphere. This study assessed the diversity of methanogenic and methanotrophic populations along the water column and in sediments using PCR and reverse transcription-PCR-based approaches targeting functional genes, i.e. pmoA (α-subunit of the particulate methane monooxygenase) for methanotrophy and mcrA (α-subunit of the methyl-coenzyme M reductase) for methanogenesis as well as the phylogenetic 16S rRNA genes. Although methanogenesis rates were much higher in sediments, our results confirm that CH(4) production also occurs in the water column where methanogens were almost exclusively composed of hydrogenotrophic methanogens, whereas both hydrogenotrophs and acetotrophs were almost equivalent in the sediments. Sequence analysis of markers, pmoA and the 16S rRNA gene, suggested that Methylobacter may be an important group actively involved in CH(4) oxidation in the water column. Two main phylotypes were characterized, one of which could consume CH(4) under conditions where the oxygen amount is undetectable.
Gain saturation spectrum of backward-pumped broad-band Raman amplifiers (2005)

The gain saturation of optical amplifiers due to changes in wavelength-division-multiplexed channel loading is characterized using a technique that determines the saturation effect on each channel. This channel gain saturation (CGS) measurement is applied to a broad-band backward-pumped Raman amplifier and used to study how the CGS spectral tilt is controlled by the relative contributions of the pump-to-pump and channel-to-channel interactions. The CGS is also used to measure the gain dependence on the channel add-delete pattern.
Optic Nerve Degeneration in a Murine Model of Juvenile Ceroid Lipofuscinosis (2003)

The presence of apparent mast cells in cln3-/- optic nerve suggests compromise of the blood-brain barrier. The absence of Cln3 causes loss of axons, axonal hypertrophy, and a reduction in myelination of retinal ganglion cells. Furthermore, expression of CLN3 in mouse and primate optic nerve links degeneration to loss of Cln3.